Cellulose digestion in primitive hexapods: Effect of ingested antibiotics on gut microbial populations and gut cellulase levels in the firebrat,Thermobia domestica (Zygentoma, Lepismatidae).

Science.gov (United States)

Treves, D S; Martin, M M

1994-08-01

Antibiotic feeding studies were conducted on the firebrat,Thermobia domestica (Zygentoma, Lepismatidae) to determine if the insect's gut cellulases were of insect or microbial origin. Firebrats were fed diets containing either nystatin, metronidazole, streptomycin, tetracycline, or an antibiotic cocktail consisting of all four antibiotics, and then their gut microbial populations and gut cellulase levels were monitored and compared with the gut microbial populations and gut cellulase levels in firebrats feeding on antibiotic-free diets. Each antibiotic significantly reduced the firebrat's gut micro-flora. Nystatin reduced the firebrat's viable gut fungi by 89%. Tetracycline and the antibiotic cocktail reduced the firebrat's viable gut bacteria by 81% and 67%, respectively, and metronidazole, streptomycin, tetracycline, and the antibiotic cocktail reduced the firebrat's total gut flora by 35%, 32%, 55%, and 64%, respectively. Although antibiotics significantly reduced the firebrat's viable and total gut flora, gut cellulase levels in firebrats fed antibiotics were not significantly different from those in firebrats on an antibiotic-free diet. Furthermore, microbial populations in the firebrat's gut decreased significantly over time, even in firebrats feeding on the antibiotic-free diet, without corresponding decreases in gut cellulase levels. Based on this evidence, we conclude that the gut cellulases of firebrats are of insect origin. This conclusion implies that symbiont-independent cellulose digestion is a primitive trait in insects and that symbiont-mediated cellulose digestion is a derived condition.

Microbial community analysis of perchlorate-reducing cultures growing on zero-valent iron

International Nuclear Information System (INIS)

Son, Ahjeong; Schmidt, Carl J.; Shin, Hyejin; Cha, Daniel K.

2011-01-01

Anaerobic microbial mixed cultures demonstrated its ability to completely remove perchlorate in the presence of zero-valent iron. In order to understand the major microbial reaction in the iron-supported culture, community analysis comprising of microbial fatty acids and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) techniques was performed for perchlorate reducing cultures. Analysis of fatty acid methyl esters (FAMEs) and subsequent principal component analysis (PCA) showed clear distinctions not only between iron-supported perchlorate reducing culture and seed bacteria, but also among perchlorate-reducing cultures receiving different electron donors. The DGGE pattern targeting the chlorite dismutase (cld) gene showed that iron-supported perchlorate reducing culture is similar to hydrogen-fed cultures as compared to acetate-fed culture. The phylogenetic tree suggested that the dominant microbial reaction may be a combination of the autotrophic and heterotrophic reduction of perchlorate. Both molecular and chemotaxonomic experimental results support further understanding in the function of zero-valent iron as an adequate electron source for enhancing the microbial perchlorate reduction in natural and engineered systems.

Microbial community analysis of perchlorate-reducing cultures growing on zero-valent iron

Energy Technology Data Exchange (ETDEWEB)

Son, Ahjeong, E-mail: ason@auburn.edu [Department of Civil Engineering, Auburn University, Auburn, AL 36849 (United States); Schmidt, Carl J. [Department of Animal and Food Sciences, University of Delaware, Newark, DE 19716 (United States); Shin, Hyejin [Department of Mathematics and Statistics, Auburn University, Auburn, AL 36849 (United States); Cha, Daniel K. [Department of Civil and Environmental Engineering, University of Delaware, Newark, DE 19716 (United States)

2011-01-30

Anaerobic microbial mixed cultures demonstrated its ability to completely remove perchlorate in the presence of zero-valent iron. In order to understand the major microbial reaction in the iron-supported culture, community analysis comprising of microbial fatty acids and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) techniques was performed for perchlorate reducing cultures. Analysis of fatty acid methyl esters (FAMEs) and subsequent principal component analysis (PCA) showed clear distinctions not only between iron-supported perchlorate reducing culture and seed bacteria, but also among perchlorate-reducing cultures receiving different electron donors. The DGGE pattern targeting the chlorite dismutase (cld) gene showed that iron-supported perchlorate reducing culture is similar to hydrogen-fed cultures as compared to acetate-fed culture. The phylogenetic tree suggested that the dominant microbial reaction may be a combination of the autotrophic and heterotrophic reduction of perchlorate. Both molecular and chemotaxonomic experimental results support further understanding in the function of zero-valent iron as an adequate electron source for enhancing the microbial perchlorate reduction in natural and engineered systems.

Microbial population changes in tropical agricultural soil ...

African Journals Online (AJOL)

Impacts of crude petroleum pollution on the soil environment and microbial population dynamics as well as recovery rates of an abandoned farmland was monitored for seven months spanning the two major seasons in Nigeria with a ... The physico-chemistry of the control and contaminated soils differed just significantly (P ...

Experimental demonstration of an Allee effect in microbial populations.

Science.gov (United States)

Kaul, RajReni B; Kramer, Andrew M; Dobbs, Fred C; Drake, John M

2016-04-01

Microbial populations can be dispersal limited. However, microorganisms that successfully disperse into physiologically ideal environments are not guaranteed to establish. This observation contradicts the Baas-Becking tenet: 'Everything is everywhere, but the environment selects'. Allee effects, which manifest in the relationship between initial population density and probability of establishment, could explain this observation. Here, we experimentally demonstrate that small populations of Vibrio fischeri are subject to an intrinsic demographic Allee effect. Populations subjected to predation by the bacterivore Cafeteria roenbergensis display both intrinsic and extrinsic demographic Allee effects. The estimated critical threshold required to escape positive density-dependence is around 5, 20 or 90 cells ml(-1)under conditions of high carbon resources, low carbon resources or low carbon resources with predation, respectively. This work builds on the foundations of modern microbial ecology, demonstrating that mechanisms controlling macroorganisms apply to microorganisms, and provides a statistical method to detect Allee effects in data. © 2016 The Author(s).

Experimental demonstration of an Allee effect in microbial populations

OpenAIRE

Kaul, RajReni B.; Kramer, Andrew M.; Dobbs, Fred C.; Drake, John M.

2016-01-01

Microbial populations can be dispersal limited. However, microorganisms that successfully disperse into physiologically ideal environments are not guaranteed to establish. This observation contradicts the Baas-Becking tenet: ?Everything is everywhere, but the environment selects?. Allee effects, which manifest in the relationship between initial population density and probability of establishment, could explain this observation. Here, we experimentally demonstrate that small populations of Vi...

Molecular characterization of microbial population dynamics during sildenafil citrate degradation.

Science.gov (United States)

De Felice, Bruna; Argenziano, Carolina; Guida, Marco; Trifuoggi, Marco; Russo, Francesca; Condorelli, Valerio; Inglese, Mafalda

2009-02-01

Little is known about pharmaceutical and personal care products pollutants (PPCPs), but there is a growing interest in how they might impact the environment and microbial communities. The widespread use of Viagra (sildenafil citrate) has attracted great attention because of the high usage rate, the unpredictable disposal and the unknown potential effects on wildlife and the environment. Until now information regarding the impact of Viagra on microbial community in water environment has not been reported. In this research, for the first time, the genetic profile of the microbial community, developing in a Viagra polluted water environment, was evaluated by means of the 16S and 18S rRNA genes, for bacteria and fungi, respectively, amplified by polymerase chain reaction (PCR) and separated using the denaturing gradient gel electrophoresis (DGGE) technique. The DGGE results revealed a complex microbial community structure with most of the population persisting throughout the experimental period. DNA sequences from bands observed in the different denaturing gradient gel electrophoresis profiles exhibited the highest degree of identity to uncultured bacteria and fungi found previously mainly in polluted environmental and treating bioreactors. Biotransformation ability of sildenafil citrate by the microbial pool was studied and the capability of these microorganisms to detoxify a polluted water ecosystem was assessed. The bacterial and fungal population was able to degrade sildenafil citrate entirely. Additionally, assays conducted on Daphnia magna, algal growth inhibition assay and cell viability determination on HepG2 human cells showed that biotransformation products obtained from the bacterial growth was not toxic. The higher removal efficiency for sildenafil citrate and the lack of toxicity by the biotransformation products obtained showed that the microbial community identified here represented a composite population that might have biotechnological relevance to

Feedback between Population and Evolutionary Dynamics Determines the Fate of Social Microbial Populations

Science.gov (United States)

Sanchez, Alvaro; Gore, Jeff

2013-01-01

The evolutionary spread of cheater strategies can destabilize populations engaging in social cooperative behaviors, thus demonstrating that evolutionary changes can have profound implications for population dynamics. At the same time, the relative fitness of cooperative traits often depends upon population density, thus leading to the potential for bi-directional coupling between population density and the evolution of a cooperative trait. Despite the potential importance of these eco-evolutionary feedback loops in social species, they have not yet been demonstrated experimentally and their ecological implications are poorly understood. Here, we demonstrate the presence of a strong feedback loop between population dynamics and the evolutionary dynamics of a social microbial gene, SUC2, in laboratory yeast populations whose cooperative growth is mediated by the SUC2 gene. We directly visualize eco-evolutionary trajectories of hundreds of populations over 50–100 generations, allowing us to characterize the phase space describing the interplay of evolution and ecology in this system. Small populations collapse despite continual evolution towards increased cooperative allele frequencies; large populations with a sufficient number of cooperators “spiral” to a stable state of coexistence between cooperator and cheater strategies. The presence of cheaters does not significantly affect the equilibrium population density, but it does reduce the resilience of the population as well as its ability to adapt to a rapidly deteriorating environment. Our results demonstrate the potential ecological importance of coupling between evolutionary dynamics and the population dynamics of cooperatively growing organisms, particularly in microbes. Our study suggests that this interaction may need to be considered in order to explain intraspecific variability in cooperative behaviors, and also that this feedback between evolution and ecology can critically affect the demographic fate

feedback between population and evolutionary dynamics determines the fate of social microbial populations.

Directory of Open Access Journals (Sweden)

Alvaro Sanchez

Full Text Available The evolutionary spread of cheater strategies can destabilize populations engaging in social cooperative behaviors, thus demonstrating that evolutionary changes can have profound implications for population dynamics. At the same time, the relative fitness of cooperative traits often depends upon population density, thus leading to the potential for bi-directional coupling between population density and the evolution of a cooperative trait. Despite the potential importance of these eco-evolutionary feedback loops in social species, they have not yet been demonstrated experimentally and their ecological implications are poorly understood. Here, we demonstrate the presence of a strong feedback loop between population dynamics and the evolutionary dynamics of a social microbial gene, SUC2, in laboratory yeast populations whose cooperative growth is mediated by the SUC2 gene. We directly visualize eco-evolutionary trajectories of hundreds of populations over 50-100 generations, allowing us to characterize the phase space describing the interplay of evolution and ecology in this system. Small populations collapse despite continual evolution towards increased cooperative allele frequencies; large populations with a sufficient number of cooperators "spiral" to a stable state of coexistence between cooperator and cheater strategies. The presence of cheaters does not significantly affect the equilibrium population density, but it does reduce the resilience of the population as well as its ability to adapt to a rapidly deteriorating environment. Our results demonstrate the potential ecological importance of coupling between evolutionary dynamics and the population dynamics of cooperatively growing organisms, particularly in microbes. Our study suggests that this interaction may need to be considered in order to explain intraspecific variability in cooperative behaviors, and also that this feedback between evolution and ecology can critically affect the

Soil biochar amendment shapes the composition of N_2O-reducing microbial communities

International Nuclear Information System (INIS)

Harter, Johannes; Weigold, Pascal; El-Hadidi, Mohamed; Huson, Daniel H.; Kappler, Andreas; Behrens, Sebastian

2016-01-01

Soil biochar amendment has been described as a promising tool to improve soil quality, sequester carbon, and mitigate nitrous oxide (N_2O) emissions. N_2O is a potent greenhouse gas. The main sources of N_2O in soils are microbially-mediated nitrogen transformation processes such as nitrification and denitrification. While previous studies have focused on the link between N_2O emission mitigation and the abundance and activity of N_2O-reducing microorganisms in biochar-amended soils, the impact of biochar on the taxonomic composition of the nosZ gene carrying soil microbial community has not been subject of systematic study to date. We used 454 pyrosequencing in order to study the microbial diversity in biochar-amended and biochar-free soil microcosms. We sequenced bacterial 16S rRNA gene amplicons as well as fragments of common (typical) nosZ genes and the recently described ‘atypical’ nosZ genes. The aim was to describe biochar-induced shifts in general bacterial community diversity and taxonomic variations among the nosZ gene containing N_2O-reducing microbial communities. While soil biochar amendment significantly altered the 16S rRNA gene-based community composition and structure, it also led to the development of distinct functional traits capable of N_2O reduction containing typical and atypical nosZ genes related to nosZ genes found in Pseudomonas stutzeri and Pedobacter saltans, respectively. Our results showed that biochar amendment can affect the relative abundance and taxonomic composition of N_2O-reducing functional microbial traits in soil. Thus these findings broaden our knowledge on the impact of biochar on soil microbial community composition and nitrogen cycling. - Highlights: • Biochar promoted anaerobic, alkalinity-adapted, and polymer-degrading microbial taxa. • Biochar fostered the development of distinct N_2O-reducing microbial taxa. • Taxonomic shifts among N_2O-reducing microbes might explain lower N_2O emissions.

Interval scanning photomicrography of microbial cell populations.

Science.gov (United States)

Casida, L. E., Jr.

1972-01-01

A single reproducible area of the preparation in a fixed focal plane is photographically scanned at intervals during incubation. The procedure can be used for evaluating the aerobic or anaerobic growth of many microbial cells simultaneously within a population. In addition, the microscope is not restricted to the viewing of any one microculture preparation, since the slide cultures are incubated separately from the microscope.

On the use of antibiotics to reduce rhizoplane microbial populations in root physiology and ecology investigations

Science.gov (United States)

Smart, D. R.; Ferro, A.; Ritchie, K.; Bugbee, B. G.

1995-01-01

No straightforward method exists for separating the proportion of ion exchange and respiration due to rhizoplane microbial organisms from that of root ion exchange and respiration. We examined several antibiotics that might be used for the temporary elimination of rhizoplane bacteria from hydroponically grown wheat roots (Triticum aestivum cv. Veery 10). Each antibiotic was tested for herbicidal activity and plate counts were used to enumerate bacteria and evaluate antibiotic kinetics. Only lactam antibiotics (penicillins and cephalosporins) did not reduce wheat growth rates. Aminoglycosides, the pyrimidine trimethoprim, colistin and rifampicin reduced growth rates substantially. Antibiotics acted slowly, with maximum reductions in rhizoplane bacteria occurring after more than 48 h of exposure. Combinations of nonphytotoxic antibiotics reduced platable rhizoplane bacteria by as much as 98%; however, this was generally a reduction from about 10(9) to 10(6) colony forming units per gram of dry root mass, so that many viable bacteria remained on root surfaces. We present evidence which suggests that insufficient bacterial biomass exists on root surfaces of nonstressed plants grown under well-aerated conditions to quantitatively interfere with root nitrogen absorption measurements.

Cutaneous Microbial Community Variation across Populations of Eastern Hellbenders (Cryptobranchus alleganiensis alleganiensis

Directory of Open Access Journals (Sweden)

Obed Hernández-Gómez

2017-07-01

Full Text Available Multicellular hosts maintain complex associations with microbial communities. While microbial communities often serve important functional roles for their hosts, our understanding of the local and regional processes that structure these communities remains limited. Metacommunity analyses provide a promising tool for investigating mechanisms shaping microbiome heterogeneity, which is essential for predicting functional variation between hosts. Using a metacommunity framework, we examined heterogeneity in the skin microbiome of the eastern hellbender (Cryptobranchus alleganiensis alleganiensis. Hellbenders are broadly distributed throughout river systems in the eastern United States, but are present in specific environmental locations throughout their range. The large range of the species and history of population fragmentation suggest that local and regional processes contribute to the distribution of cutaneous symbiont diversity. Therefore, we characterized the skin and environmental bacterial communities at eight rivers throughout the range of the species. We observed variation among hellbender populations in skin microbial community diversity and proportion of shared operational taxonomic units (OTUs between animal and river water communities. Among populations sampled, we noted significant clumped OTU turnover (i.e., Clementsian structure resulting in unique cutaneous communities. In addition, we observed a significant positive correlation between skin community divergence and hellbender population genetic divergence. Host-population skin community dissimilarity did not correlate strongly with distance between sampling locations, indicating a weak spatial effect on the distribution of symbionts. These results suggest that species sorting mechanisms (i.e., local processes structure local skin microbial communities in hellbenders. The variation in skin community composition observed among host populations foreshadows a similar pattern in

Microbial control of caged population of Zonocerus variegatus using ...

African Journals Online (AJOL)

Microbial control of caged populations of Zonocerus variegatus was carried out using indigenous fungal entomopathogens isolated from the grasshopper's cadaver. Bioassay response indicated a dose-dependent mortality coupled with drastic reduction in food consumption among spores infected grasshoppers. Lethal time ...

The effects of different uranium concentrations on soil microbial populations and enzymatic activities

International Nuclear Information System (INIS)

Bagherifam, S.; Lakziyan, A.; Ahmadi, S. J.; Fotovvat, A.; Rahimi, M. F.

2010-01-01

Uranium is an ubiquitous constituent of natural environment with an average concentration of 4 mg/kg in earth crust. However, in local areas it may exceed the normal concentration due to human activities resulting in radionuclide contamination in groundwater and surface soil. The effect of six levels of uranium concentration (0, 50, 100,250. 500 and 1000 mg kg -1 ) on soil phosphatase activities and microbial populations were studied in a completely randomized design as a factorial experiment with three replications. The results showed a significant decrease in phosphatase activity. The result of the experiment suggests that soil microbial populations (bacteria, funji and actinomycetes) decrease by increasing the uranium levels in the soil. Therefore, assessment of soil enzymatic activities and microbial populations can be helpful as a useful index for a better management of uranium and radioactive contaminated soils.

Microbial population analysis improves the evidential value of faecal traces in forensic investigations.

Science.gov (United States)

Quaak, Frederike C A; de Graaf, Mei-Lan M; Weterings, Rob; Kuiper, Irene

2017-01-01

The forensic science community has a growing interest in microbial population analysis, especially the microbial populations found inside and on the human body. Both their high abundance, microbes outnumber human cells by a factor 10, and their diversity, different sites of the human body harbour different microbial communities, make them an interesting tool for forensics. Faecal material is a type of trace evidence which can be found in a variety of criminal cases, but is often being ignored in forensic investigations. Deriving a human short tandem repeat (STR) profile from a faecal sample can be challenging. However, the microbial communities within faecal material can be of additional criminalistic value in linking a faecal trace to the possible donor. We present a microarray technique in which the faecal microbial community is used to differentiate between faecal samples and developed a decision model to predict the possible common origin of questioned samples. The results show that this technique may be a useful additional tool when no or only partial human STR profiles can be generated.

Anomalous electrical signals associated with microbial activity: Results from Iron and Nitrate-Reducing Columns

Science.gov (United States)

Aaron, R. B.; Zheng, Q.; Flynn, P.; Singha, K.; Brantley, S.

2008-12-01

Three flow-through columns outfitted with Ag/AgCl electrodes were constructed to test the effects of different microbial processes on the geophysical measurements of self potential (SP), bulk electrical conductivity (σ b), and induced polarization (IP). The columns were filled with sieved, Fe-bearing subsurface sediment from the Delmarva Peninsula near Oyster, VA, inoculated (9:1 ratio) with a freshly-collected, shallow subsurface sediment from a wetland floodplain (Dorn Creek) near Madison, WI. Each of the columns was fed anoxic and sterile PIPES buffered artificial groundwater (PBAGW) containing different concentrations of acetate and nitrate. The medium fed to Column 1 (nitrate-reducing) was amended with 100 μM acetate and 2 mM nitrate. Column 2 (iron-reducing) was run with PBAGW containing 1.0 mM acetate and 0 mM nitrate. Column 3 (alternating redox state) was operated under conditions designed to alternately stimulate nitrate-reducing and iron-reducing populations to provide conditions, i.e., the presence of both nitrate and microbially-produced Fe(II), that would allow growth of nitrate-dependent Fe(II)-oxidizing populations. We operated Column 3 with a cycling strategy of 14-18 days of high C medium (1 mM acetate and 100 μ M nitrate) followed by 14-18 days of low C medium (100 μ M acetate and 2 mM nitrate). Effluent chemistry (NO3-, NO2-, NH4+, acetate, and Fe2+) was sampled daily for four months so as to be concurrent with the electrical measurements. We observed chemical evidence of iron reduction (dissolved [Fe(II)] = 0.2mM) in the effluent from the iron reduction and alternating redox columns. Chemical depletion of NO3- ([NO3-] ranged from 1 to 0.02mM), the production of NO2-, and possible production of NH4+ (0.2 mM) was observed in the nitrate reducing column as well as the alternating redox column. All three columns displayed loss of acetate as microbial activity progressed. σ b remained constant in the alternating redox column (~0.15 S

Meta-Transcriptomic Analysis of a Chromate-Reducing Aquifer Microbial Community

Science.gov (United States)

Beller, H. R.; Brodie, E. L.; Han, R.; Karaoz, U.

2010-12-01

A major challenge for microbial ecology that has become more tractable in the advent of new molecular techniques is characterizing gene expression in complex microbial communities. We are using meta-transcriptomic analysis to characterize functional changes in an aquifer-derived, chromate-reducing microbial community as it transitions through various electron-accepting conditions. We inoculated anaerobic microcosms with groundwater from the Cr-contaminated Hanford 100H site and supplemented them with lactate and electron acceptors present at the site, namely, nitrate, sulfate, and Fe(III). The microcosms progressed successively through various electron-accepting conditions (e.g., denitrifying, sulfate-reducing, and ferric iron-reducing conditions, as well as nitrate-dependent, chemolithotrophic Fe(II)-oxidizing conditions). Cr(VI) was rapidly reduced initially and again upon further Cr(VI) amendments. Extensive geochemical sampling and analysis (e.g., lactate, acetate, chloride, nitrate, nitrite, sulfate, dissolved Cr(VI), total Fe(II)), RNA/DNA harvesting, and PhyloChip analyses were conducted. Methods were developed for removal of rRNA from total RNA in preparation for meta-transcriptome sequencing. To date, samples representing denitrifying and fermentative/sulfate-reducing conditions have been sequenced using 454 Titanium technology. Of the non-rRNA related reads for the denitrifying sample (which was also actively reducing chromate), ca. 8% were associated with denitrification and ca. 0.9% were associated with chromate resistance/transport, in contrast to the fermentative/sulfate-reducing sample (in which chromate had already been reduced), which had zero reads associated with either of these categories but many predicted proteins associated with sulfate-reducing bacteria. We observed sequences for key functional transcripts that were unique at the nucleotide level compared to the GenBank non-redundant database [such as L-lactate dehydrogenase (iron

Microbial Population Dynamics Associated with Crude-Oil Biodegradation in Diverse Soils

OpenAIRE

Hamamura, Natsuko; Olson, Sarah H.; Ward, David M.; Inskeep, William P.

2006-01-01

Soil bacterial population dynamics were examined in several crude-oil-contaminated soils to identify those organisms associated with alkane degradation and to assess patterns in microbial response across disparate soils. Seven soil types obtained from six geographically distinct areas of the United States (Arizona, Oregon, Indiana, Virginia, Oklahoma, and Montana) were used in controlled contamination experiments containing 2% (wt/wt) crude oil spiked with [1-14C]hexadecane. Microbial populat...

Soil biochar amendment shapes the composition of N{sub 2}O-reducing microbial communities

Energy Technology Data Exchange (ETDEWEB)

Harter, Johannes; Weigold, Pascal [Geomicrobiology & Microbial Ecology, Center for Applied Geosciences, University of Tuebingen, Sigwartstr. 10, 72076 Tuebingen (Germany); El-Hadidi, Mohamed; Huson, Daniel H. [Algorithms in Bioinformatics, Center for Bioinformatics, University of Tuebingen, Sand 14, 72076 Tuebingen (Germany); Kappler, Andreas [Geomicrobiology & Microbial Ecology, Center for Applied Geosciences, University of Tuebingen, Sigwartstr. 10, 72076 Tuebingen (Germany); Behrens, Sebastian, E-mail: sbehrens@umn.edu [Geomicrobiology & Microbial Ecology, Center for Applied Geosciences, University of Tuebingen, Sigwartstr. 10, 72076 Tuebingen (Germany); Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, 500 Pillsbury Drive S.E., Minneapolis, MN 55455-0116 (United States); BioTechnology Institute, 140 Gortner Labs, 1479 Gortner Avenue, St. Paul, MN 55108-6106 (United States)

2016-08-15

Soil biochar amendment has been described as a promising tool to improve soil quality, sequester carbon, and mitigate nitrous oxide (N{sub 2}O) emissions. N{sub 2}O is a potent greenhouse gas. The main sources of N{sub 2}O in soils are microbially-mediated nitrogen transformation processes such as nitrification and denitrification. While previous studies have focused on the link between N{sub 2}O emission mitigation and the abundance and activity of N{sub 2}O-reducing microorganisms in biochar-amended soils, the impact of biochar on the taxonomic composition of the nosZ gene carrying soil microbial community has not been subject of systematic study to date. We used 454 pyrosequencing in order to study the microbial diversity in biochar-amended and biochar-free soil microcosms. We sequenced bacterial 16S rRNA gene amplicons as well as fragments of common (typical) nosZ genes and the recently described ‘atypical’ nosZ genes. The aim was to describe biochar-induced shifts in general bacterial community diversity and taxonomic variations among the nosZ gene containing N{sub 2}O-reducing microbial communities. While soil biochar amendment significantly altered the 16S rRNA gene-based community composition and structure, it also led to the development of distinct functional traits capable of N{sub 2}O reduction containing typical and atypical nosZ genes related to nosZ genes found in Pseudomonas stutzeri and Pedobacter saltans, respectively. Our results showed that biochar amendment can affect the relative abundance and taxonomic composition of N{sub 2}O-reducing functional microbial traits in soil. Thus these findings broaden our knowledge on the impact of biochar on soil microbial community composition and nitrogen cycling. - Highlights: • Biochar promoted anaerobic, alkalinity-adapted, and polymer-degrading microbial taxa. • Biochar fostered the development of distinct N{sub 2}O-reducing microbial taxa. • Taxonomic shifts among N{sub 2}O-reducing microbes

Development of a microbial population within a hot-drinks vending machine and the microbial load of vended hot chocolate drink.

Science.gov (United States)

Hall, A; Short, K; Saltmarsh, M; Fielding, L; Peters, A

2007-09-01

In order to understand the development of the microbial population within a hot-drinks vending machine a new machine was placed in a staff area of a university campus vending only hot chocolate. The machine was cleaned weekly using a detergent based protocol. Samples from the mixing bowl, dispense area, and drink were taken over a 19-wk period and enumerated using plate count agar. Bacillus cereus was identified using biochemical methods. Vended drinks were sampled at 0, 3, 6, and 9 min after vending; the hot chocolate powder was also sampled. Over the 1st 8 wk, a significant increase in the microbial load of the machine components was observed. By the end of the study, levels within the vended drink had also increased significantly. Inactivation of the automatic flush over a subsequent 5-wk period led to a statistically but not operationally significant increase in the microbial load of the dispense area and vended drink. The simple weekly clean had a significant impact on the microbial load of the machine components and the vended drink. This study demonstrated that a weekly, detergent-based cleaning protocol was sufficient to maintain the microbial population of the mixing bowl and dispense point in a quasi-steady state below 3.5 log CFU/cm2 ensuring that the microbial load of the vended drinks was maintained below 3.4 log CFU/mL. The microbial load of the drinks showed no significant changes over 9 min after vending, suggesting only spores are present in the final product.

Allee effect: the story behind the stabilization or extinction of microbial ecosystem.

Science.gov (United States)

Goswami, Madhurankhi; Bhattacharyya, Purnita; Tribedi, Prosun

2017-03-01

A population exhibiting Allee effect shows a positive correlation between population fitness and population size or density. Allee effect decides the extinction or conservation of a microbial population and thus appears to be an important criterion in population ecology. The underlying factor of Allee effect that decides the stabilization and extinction of a particular population density is the threshold or the critical density of their abundance. According to Allee, microbial populations exhibit a definite, critical or threshold density, beyond which the population fitness of a particular population increases with the rise in population density and below it, the population fitness goes down with the decrease in population density. In particular, microbial population displays advantageous traits such as biofilm formation, expression of virulence genes, spore formation and many more only at a high population density. It has also been observed that microorganisms exhibiting a lower population density undergo complete extinction from the residual microbial ecosystem. In reference to Allee effect, decrease in population density or size introduces deleterious mutations among the population density through genetic drift. Mutations are carried forward to successive generations resulting in its accumulation among the population density thus reducing its microbial fitness and thereby increasing the risk of extinction of a particular microbial population. However, when the microbial load is high, the chance of genetic drift is less, and through the process of biofilm formation, the cooperation existing among the microbial population increases that increases the microbial fitness. Thus, the high microbial population through the formation of microbial biofilm stabilizes the ecosystem by increasing fitness. Taken together, microbial fitness shows positive correlation with the ecosystem conservation and negative correlation with ecosystem extinction.

Milankovitch-scale correlations between deeply buried microbial populations and biogenic ooze lithology

Science.gov (United States)

Aiello, I.W.; Bekins, B.A.

2010-01-01

The recent discoveries of large, active populations of microbes in the subseafloor of the world's oceans supports the impact of the deep biosphere biota on global biogeochemical cycles and raises important questions concerning the functioning of these extreme environments for life. These investigations demonstrated that subseafloor microbes are unevenly distributed and that cell abundances and metabolic activities are often independent from sediment depths, with increased prokaryotic activity at geochemical and/or sedimentary interfaces. In this study we demonstrate that microbial populations vary at the scale of individual beds in the biogenic oozes of a drill site in the eastern equatorial Pacific (Ocean Drilling Program Leg 201, Site 1226). We relate bedding-scale changes in biogenic ooze sediment composition to organic carbon (OC) and microbial cell concentrations using high-resolution color reflectance data as proxy for lithology. Our analyses demonstrate that microbial concentrations are an order of magnitude higher in the more organic-rich diatom oozes than in the nannofossil oozes. The variations mimic small-scale variations in diatom abundance and OC, indicating that the modern distribution of microbial biomass is ultimately controlled by Milankovitch-frequency variations in past oceanographic conditions. ?? 2010 Geological Society of America.

Effect of oil spill on the microbial population in Andaman Sea around Nicobar Island

Digital Repository Service at National Institute of Oceanography (India)

Gupta, R.

The microbial studiees of the follow up cruise by FORV Sagar Sampada (cruise No. 113), 9 months after the oil spill in the Andaman Sea due to accident of VLCC Maersk Navigator revealed disturbance in the natural microbial population. Higher...

Sequential enrichment of microbial population exhibiting enhanced biodegradation of crude oil

International Nuclear Information System (INIS)

Venkateswaran, Kasthuri; Harayama, Shigeaki.

1995-01-01

The distribution of oil-degrading bacteria in the coastal waters and sediments of Hokkaido, Japan, was surveyed. It was found that the potential of mixed microbial populations to degrade weathered crude oil was not confined to any ecological components (water or sediment) nor to the sampling stations. One microbial culture that was stable during repeated subculturing degraded 45% of the saturates and 20% of the aromatics present in crude oil in 10 days during the initial screening. The residual hydrocarbons in this culture were extracted by chloroform and dispersed in a fresh seawater-based medium and subsequently inoculated with microorganisms from the first culture. After full growth of the second culture, the residual hydrocarbons were extracted and dispersed in a fresh medium in which microorganisms from the second culture had been inoculated. This sequential process was carried out six times to enrich those microorganisms that grew on the recalcitrant components of crude oil. After repeated exposure of the residual crude oil to the enriched microorganisms, about 80% of the initially added crude oil was degraded. The cultures obtained after each enrichment cycle were kept, and the degradation of fresh crude oil by the enriched microorganisms was monitored. The degrading activity of the enriched cultures increased as the number of enrichment cycles increased. A microbial population that had been selected six times on the residual crude oil could degrade 70% of the saturates and 30% of the aromatics of crude oil, indicating that growth of a microbial population on residual crude oil improved its ability to biodegrade crude oil. 21 refs., 2 tabs., 7 figs

Exogenous Nitrogen Addition Reduced the Temperature Sensitivity of Microbial Respiration without Altering the Microbial Community Composition

Directory of Open Access Journals (Sweden)

Hui Wei

2017-12-01

Full Text Available Atmospheric nitrogen (N deposition is changing in both load quantity and chemical composition. The load effects have been studied extensively, whereas the composition effects remain poorly understood. We conducted a microcosm experiment to study how N chemistry affected the soil microbial community composition characterized by phospholipid fatty acids (PLFAs and activity indicated by microbial CO2 release. Surface and subsurface soils collected from an old-growth subtropical forest were supplemented with three N-containing materials (ammonium, nitrate, and urea at the current regional deposition load (50 kg ha-1 yr-1 and incubated at three temperatures (10, 20, and 30°C to detect the interactive effects of N deposition and temperature. The results showed that the additions of N, regardless of form, did not alter the microbial PLFAs at any of the three temperatures. However, the addition of urea significantly stimulated soil CO2 release in the early incubation stage. Compared with the control, N addition consistently reduced the temperature dependency of microbial respiration, implying that N deposition could potentially weaken the positive feedback of the warming-stimulated soil CO2 release to the atmosphere. The consistent N effects for the surface and subsurface soils suggest that the effects of N on soil microbial communities may be independent of soil chemical contents and stoichiometry.

Among-Population Variation in Microbial Community Structure in the Floral Nectar of the Bee-Pollinated Forest Herb Pulmonaria officinalis L

Science.gov (United States)

Jacquemyn, Hans; Lenaerts, Marijke; Brys, Rein; Willems, Kris; Honnay, Olivier; Lievens, Bart

2013-01-01

Background Microbial communities in floral nectar have been shown to be characterized by low levels of species diversity, yet little is known about among-plant population variation in microbial community composition. Methodology/Principal Findings We investigated the microbial community structure (yeasts and bacteria) in floral nectar of ten fragmented populations of the bee-pollinated forest herb Pulmonaria officinalis. We also explored possible relationships between plant population size and microbial diversity in nectar, and related microbial community composition to the distance separating plant populations. Culturable bacteria and yeasts occurring in the floral nectar of a total of 100 plant individuals were isolated and identified by partially sequencing the 16S rRNA gene and D1/D2 domains of the 26S rRNA gene, respectively. A total of 9 and 11 yeast and 28 and 39 bacterial OTUs was found, taking into account a 3% (OTU0.03) and 1% sequence dissimilarity cut-off (OTU0.01). OTU richness at the plant population level (i.e. the number of OTUs per population) was low for yeasts (mean: 1.7, range: 0–4 OTUs0.01/0.03 per population), whereas on average 6.9 (range: 2–13) OTUs0.03 and 7.9 (range 2–16) OTUs0.01 per population were found for bacteria. Both for yeasts and bacteria, OTU richness was not significantly related to plant population size. Similarity in community composition among populations was low (average Jaccard index: 0.14), and did not decline with increasing distance between populations. Conclusions/Significance We found low similarity in microbial community structure among populations, suggesting that the assembly of nectar microbiota is to a large extent context-dependent. Although the precise factors that affect variation in microbial community structure in floral nectar require further study, our results indicate that both local and regional processes may contribute to among-population variation in microbial community structure in nectar. PMID

BSocial: Deciphering Social Behaviors within Mixed Microbial Populations

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Jessica Purswani

2017-05-01

Full Text Available Ecosystem functionality depends on interactions among populations, of the same or different taxa, and these are not just the sum of pairwise interactions. Thus, know-how of the social interactions occurring in mixed-populations are of high interest, however they are commonly unknown due to the limitations posed in tagging each population. The limitations include costs/time in tediously fluorescent tagging, and the number of different fluorescent tags. Tag-free strategies exist, such as high-throughput sequencing, but ultimately both strategies require the use of expensive machinery. Our work appoints social behaviors on individual strains in mixed-populations, offering a web-tool (BSocialhttp://m4m.ugr.es/BSocial.html for analyzing the community framework. Our quick and cheap approach includes the periodic monitoring of optical density (OD from a full combinatorial testing of individual strains, where number of generations and growth rate are determined. The BSocial analyses then enable us to determine how the addition/absence of a particular species affects the net productivity of a microbial community and use this to select productive combinations, i.e., designate their social effect on a general community. Positive, neutral, or negative assignations are applied to describe the social behavior within the community by comparing fitness effects of the community against the individual strain. The usefulness of this tool for selection of optimal inoculum in biofilm-based methyl tert-butyl ether (MTBE bioremediation was demonstrated. The studied model uses seven bacterial strains with diverse MTBE degradation/growth capacities. Full combinatorial testing of seven individual strains (triplicate tests of 127 combinations were implemented, along with MTBE degradation as the desired function. Sole observation of highest species fitness did not render the best functional outcome, and only when strains with positive and neutral social assignations were

Effect of four herbicides on microbial population, soil organic matter ...

African Journals Online (AJOL)

The effect of four herbicides (atrazine, primeextra, paraquat and glyphosate) on soil microbial population, soil organic matter and dehydrogenase activity was assessed over a period of six weeks. Soil samples from cassava farms were treated with herbicides at company recommended rates. Soil dehydrogenase activity was ...

Determining the specific microbial populations and their spatial distribution within the stromatolite ecosystem of Shark Bay.

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Goh, Falicia; Allen, Michelle A; Leuko, Stefan; Kawaguchi, Tomohiro; Decho, Alan W; Burns, Brendan P; Neilan, Brett A

2009-04-01

The stromatolites at Shark Bay, Western Australia, are analogues of some of the oldest evidence of life on Earth. The aim of this study was to identify and spatially characterize the specific microbial communities associated with Shark Bay intertidal columnar stromatolites. Conventional culturing methods and construction of 16S rDNA clone libraries from community genomic DNA with both universal and specific PCR primers were employed. The estimated coverage, richness and diversity of stromatolite microbial populations were compared with earlier studies on these ecosystems. The estimated coverage for all clone libraries indicated that population coverage was comprehensive. Phylogenetic analyses of stromatolite and surrounding seawater sequences were performed in ARB with the Greengenes database of full-length non-chimaeric 16S rRNA genes. The communities identified exhibited extensive diversity. The most abundant sequences from the stromatolites were alpha- and gamma-proteobacteria (58%), whereas the cyanobacterial community was characterized by sequences related to the genera Euhalothece, Gloeocapsa, Gloeothece, Chroococcidiopsis, Dermocarpella, Acaryochloris, Geitlerinema and Schizothrix. All clones from the archaeal-specific clone libraries were related to the halophilic archaea; however, no archaeal sequence was identified from the surrounding seawater. Fluorescence in situ hybridization also revealed stromatolite surfaces to be dominated by unicellular cyanobacteria, in contrast to the sub-surface archaea and sulphate-reducing bacteria. This study is the first to compare the microbial composition of morphologically similar stromatolites over time and examine the spatial distribution of specific microorganismic groups in these intertidal structures and the surrounding seawater at Shark Bay. The results provide a platform for identifying the key microbial physiology groups and their potential roles in modern stromatolite morphogenesis and ecology.

ECONOMIC RETURNS FROM REDUCING POULTRY LITTER PHOSPHORUS WITH MICROBIAL PHYTASE

OpenAIRE

Bosch, Darrell J.; Zhu, Minkang; Kornegay, Ervin T.

1997-01-01

Requiring that crop applications of manure be based on phosphorus content (P-standard) could increase poultry litter disposal costs. Microbial phytase reduces litter P content and could reduce litter disposal costs under a P-standard. For a representative Virginia turkey farm, phytase costs $2,500 and could increase value of litter used for fertilizer on the turkey farm by $390 and reduce supplemental P feed costs by $1,431. Based on assumed litter demand and supply, estimated litter export p...

Soil biochar amendment shapes the composition of N2O-reducing microbial communities.

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Harter, Johannes; Weigold, Pascal; El-Hadidi, Mohamed; Huson, Daniel H; Kappler, Andreas; Behrens, Sebastian

2016-08-15

Soil biochar amendment has been described as a promising tool to improve soil quality, sequester carbon, and mitigate nitrous oxide (N2O) emissions. N2O is a potent greenhouse gas. The main sources of N2O in soils are microbially-mediated nitrogen transformation processes such as nitrification and denitrification. While previous studies have focused on the link between N2O emission mitigation and the abundance and activity of N2O-reducing microorganisms in biochar-amended soils, the impact of biochar on the taxonomic composition of the nosZ gene carrying soil microbial community has not been subject of systematic study to date. We used 454 pyrosequencing in order to study the microbial diversity in biochar-amended and biochar-free soil microcosms. We sequenced bacterial 16S rRNA gene amplicons as well as fragments of common (typical) nosZ genes and the recently described 'atypical' nosZ genes. The aim was to describe biochar-induced shifts in general bacterial community diversity and taxonomic variations among the nosZ gene containing N2O-reducing microbial communities. While soil biochar amendment significantly altered the 16S rRNA gene-based community composition and structure, it also led to the development of distinct functional traits capable of N2O reduction containing typical and atypical nosZ genes related to nosZ genes found in Pseudomonas stutzeri and Pedobacter saltans, respectively. Our results showed that biochar amendment can affect the relative abundance and taxonomic composition of N2O-reducing functional microbial traits in soil. Thus these findings broaden our knowledge on the impact of biochar on soil microbial community composition and nitrogen cycling. Copyright © 2016 Elsevier B.V. All rights reserved.

Molecular Characterization of Swine Manure Lagoon Microbial and Antibiotic Resistant Populations

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Background: The differences in swine manure lagoon effluent based on differing management styles or approaches such as different stages of swine rearing determines the presence of variable antibiotic resistance determinants and functional microbial populations. These concerns determine the suitabil...

Mineralogic control on abundance and diversity of surface-adherent microbial communities

Science.gov (United States)

Mauck, Brena S.; Roberts, Jennifer A.

2007-01-01

In this study, we investigated the role of mineral-bound P and Fe in defining microbial abundance and diversity in a carbon-rich groundwater. Field colonization experiments of initially sterile mineral surfaces were combined with community structure characterization of the attached microbial population. Silicate minerals containing varying concentrations of P (∼1000 ppm P) and Fe (∼4 wt % Fe 2 O3), goethite (FeOOH), and apatite [Ca5(PO4)3(OH)] were incubated for 14 months in three biogeochemically distinct zones within a petroleum-contaminated aquifer. Phospholipid fatty acid analysis of incubated mineral surfaces and groundwater was used as a measure of microbial community structure and biomass. Microbial biomass on minerals exhibited distinct trends as a function of mineralogy depending on the environment of incubation. In the carbon-rich, aerobic groundwater attached biomass did not correlate to the P- or Fe- content of the mineral. In the methanogenic groundwater, however, biomass was most abundant on P-containing minerals. Similarly, in the Fe-reducing groundwater a correlation between Fe-content and biomass was observed. The community structure of the mineral-adherent microbial population was compared to the native groundwater community. These two populations were significantly different regardless of mineralogy, suggesting differentiation of the planktonic community through attachment, growth, and death of colonizing cells. Biomarkers specific for dissimilatory Fe-reducing bacteria native to the aquifer were identified only on Fe-containing minerals in the Fe-reducing groundwater. These results demonstrate that the trace nutrient content of minerals affects both the abundance and diversity of surface-adherent microbial communities. This behavior may be a means to access limiting nutrients from the mineral, creating a niche for a particular microbial population. These results suggest that heterogeneity of microbial populations and their associated

The effects of water potential on some microbial populations and ...

African Journals Online (AJOL)

The effects of water potential on some microbial populations and decrease kinetic of organic carbon in soil treated with cow manure under laboratory conditions. ... Fourth irrigation treatment was drying-rewetting cycle (D-W) between -0.3 to -15 bars. After 0, 10, 20, 40, 60 and 90 days of incubation, soils were sampled for ...

Effect of Plants Containing Secondary Compounds with Palm Oil on Feed Intake, Digestibility, Microbial Protein Synthesis and Microbial Population in Dairy Cows

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N. Anantasook

2013-06-01

Full Text Available The objective of this study was to determine the effect of rain tree pod meal with palm oil supplementation on feed intake, digestibility, microbial protein synthesis and microbial populations in dairy cows. Four, multiparous early-lactation Holstein-Friesian crossbred (75% lactating dairy cows with an initial body weight (BW of 405±40 kg and 36±8 DIM were randomly assigned to receive dietary treatments according to a 4×4 Latin square design. The four dietary treatments were un-supplementation (control, supplementation with rain tree pod meal (RPM at 60 g/kg, supplementation with palm oil (PO at 20 g/kg, and supplementation with RPM at 60 g/kg and PO at 20 g/kg (RPO, of total dry matter intake. The cows were offered concentrates, at a ratio of concentrate to milk production of 1:2, and chopped 30 g/kg of urea treated rice straw was fed ad libitum. The RPM contained condensed tannins and crude saponins at 88 and 141 g/kg of DM, respectively. It was found that supplementation with RPM and/or PO to dairy cows diets did not show negative effects on feed intake and ruminal pH and BUN at any times of sampling (p>0.05. However, RPM supplementation resulted in lower crude protein digestibility, NH3-N concentration and number of proteolytic bacteria. It resulted in greater allantoin absorption and microbial crude protein (p<0.05. In addition, dairy cows showed a higher efficiency of microbial N supply (EMNS in both RPM and RPO treatments. Moreover, NDF digestibility and cellulolytic bacteria numbers were highest in RPO supplementation (p<0.05 while, supplementation with RPM and/or PO decreased the protozoa population in dairy cows. Based on this study, supplementation with RPM and/or PO in diets could improve fiber digestibility, microbial protein synthesis in terms of quantity and efficiency and microbial populations in dairy cows.

Genome-centric metatranscriptomes and ecological roles of the active microbial populations during cellulosic biomass anaerobic digestion.

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Jia, Yangyang; Ng, Siu-Kin; Lu, Hongyuan; Cai, Mingwei; Lee, Patrick K H

2018-01-01

Although anaerobic digestion for biogas production is used worldwide in treatment processes to recover energy from carbon-rich waste such as cellulosic biomass, the activities and interactions among the microbial populations that perform anaerobic digestion deserve further investigations, especially at the population genome level. To understand the cellulosic biomass-degrading potentials in two full-scale digesters, this study examined five methanogenic enrichment cultures derived from the digesters that anaerobically digested cellulose or xylan for more than 2 years under 35 or 55 °C conditions. Metagenomics and metatranscriptomics were used to capture the active microbial populations in each enrichment culture and reconstruct their meta-metabolic network and ecological roles. 107 population genomes were reconstructed from the five enrichment cultures using a differential coverage binning approach, of which only a subset was highly transcribed in the metatranscriptomes. Phylogenetic and functional convergence of communities by enrichment condition and phase of fermentation was observed for the highly transcribed populations in the metatranscriptomes. In the 35 °C cultures grown on cellulose, Clostridium cellulolyticum -related and Ruminococcus -related bacteria were identified as major hydrolyzers and primary fermenters in the early growth phase, while Clostridium leptum -related bacteria were major secondary fermenters and potential fatty acid scavengers in the late growth phase. While the meta-metabolism and trophic roles of the cultures were similar, the bacterial populations performing each function were distinct between the enrichment conditions. Overall, a population genome-centric view of the meta-metabolism and functional roles of key active players in anaerobic digestion of cellulosic biomass was obtained. This study represents a major step forward towards understanding the microbial functions and interactions at population genome level during the

Microbial fuel cell based on electroactive sulfate-reducing biofilm

International Nuclear Information System (INIS)

Angelov, Anatoliy; Bratkova, Svetlana; Loukanov, Alexandre

2013-01-01

Highlights: ► Regulation and management of electricity generation by variation of residence time. ► Design of microbial fuel cell based on electroactive biofilm on zeolite. ► Engineering solution for removing of the obtained elemental sulfur. - abstract: A two chambered laboratory scale microbial fuel cell (MFC) has been developed, based on natural sulfate-reducing bacterium consortium in electroactive biofilm on zeolite. The MFC utilizes potassium ferricyanide in the cathode chamber as an electron acceptor that derives electrons from the obtained in anode chamber H 2 S. The molecular oxygen is finally used as a terminal electron acceptor at cathode compartment. The generated power density was 0.68 W m −2 with current density of 3.2 A m −2 at 150 Ω electrode resistivity. The hydrogen sulfide itself is produced by microbial dissimilative sulfate reduction process by utilizing various organic substrates. Finally, elemental sulfur was identified as the predominant final oxidation product in the anode chamber. It was removed from MFC through medium circulation and gathering in an external tank. This report reveals dependence relationship between the progress of general electrochemical parameters and bacterial sulfate-reduction rate. The presented MFC design can be used for simultaneous sulfate purification of mining drainage wastewater and generation of renewable electricity

Microcomputer package for statistical analysis of microbial populations.

Science.gov (United States)

Lacroix, J M; Lavoie, M C

1987-11-01

We have developed a Pascal system to compare microbial populations from different ecological sites using microcomputers. The values calculated are: the coverage value and its standard error, the minimum similarity and the geometric similarity between two biological samples, and the Lambda test consisting of calculating the ratio of the mean similarity between two subsets by the mean similarity within subsets. This system is written for Apple II, IBM or compatible computers, but it can work for any computer which can use CP/M, if the programs are recompiled for such a system.

Experimental evolution and the dynamics of adaptation and genome evolution in microbial populations.

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Lenski, Richard E

2017-10-01

Evolution is an on-going process, and it can be studied experimentally in organisms with rapid generations. My team has maintained 12 populations of Escherichia coli in a simple laboratory environment for >25 years and 60 000 generations. We have quantified the dynamics of adaptation by natural selection, seen some of the populations diverge into stably coexisting ecotypes, described changes in the bacteria's mutation rate, observed the new ability to exploit a previously untapped carbon source, characterized the dynamics of genome evolution and used parallel evolution to identify the genetic targets of selection. I discuss what the future might hold for this particular experiment, briefly highlight some other microbial evolution experiments and suggest how the fields of experimental evolution and microbial ecology might intersect going forward.

Multitaxon activity profiling reveals differential microbial response to reduced seawater pH and oil pollution.

Science.gov (United States)

Coelho, Francisco J R C; Cleary, Daniel F R; Costa, Rodrigo; Ferreira, Marina; Polónia, Ana R M; Silva, Artur M S; Simões, Mário M Q; Oliveira, Vanessa; Gomes, Newton C M

2016-09-01

There is growing concern that predicted changes to global ocean chemistry will interact with anthropogenic pollution to significantly alter marine microbial composition and function. However, knowledge of the compounding effects of climate change stressors and anthropogenic pollution is limited. Here, we used 16S and 18S rRNA (cDNA)-based activity profiling to investigate the differential responses of selected microbial taxa to ocean acidification and oil hydrocarbon contamination under controlled laboratory conditions. Our results revealed that a lower relative abundance of sulphate-reducing bacteria (Desulfosarcina/Desulfococcus clade) due to an adverse effect of seawater acidification and oil hydrocarbon contamination (reduced pH-oil treatment) may be coupled to changes in sediment archaeal communities. In particular, we observed a pronounced compositional shift and marked reduction in the prevalence of otherwise abundant operational taxonomic units (OTUs) belonging to the archaeal Marine Benthic Group B and Marine Hydrothermal Vent Group (MHVG) in the reduced pH-oil treatment. Conversely, the abundance of several putative hydrocarbonoclastic fungal OTUs was higher in the reduced pH-oil treatment. Sediment hydrocarbon profiling, furthermore, revealed higher concentrations of several alkanes in the reduced pH-oil treatment, corroborating the functional implications of the structural changes to microbial community composition. Collectively, our results advance the understanding of the response of a complex microbial community to the interaction between reduced pH and anthropogenic pollution. In future acidified marine environments, oil hydrocarbon contamination may alter the typical mixotrophic and k-/r-strategist composition of surface sediment microbiomes towards a more heterotrophic state with lower doubling rates, thereby impairing the ability of the ecosystem to recover from acute oil contamination events. © 2016 John Wiley & Sons Ltd.

Microbial ecology of a crude oil contaminated aquifer

Science.gov (United States)

Bekins, B.A.; Cozzarelli, I.M.; Warren, E.; Godsy, E.M.

2002-01-01

Detailed microbial analyses of a glacial outwash aquifer contaminated by crude oil provide insights into the pattern of microbial succession from iron reducing to methanogenic in the anaerobic portion of the contaminant plume. We analysed sediments from this area for populations of aerobes, iron reducers, fermenters and methanogens, using the most probable number method. On the basis of the microbial data the anaerobic area can be divided into distinct physiological zones dominated by either iron-reducers or a consortium of fermenters and methanogens. Chemistry and permeability data show that methanogenic conditions develop first in areas of high hydrocarbon flux. Thus, we find methanogens both in high permeability horizons and also where separate-phase crude oil is present in either the saturated or unsaturated zone. Microbial numbers peak at the top of the separate-phase oil suggesting that growth is most rapid in locations with access to both hydrocarbons and nutrients infiltrating from the surface.

Methodological flaws introduce strong bias into molecular analysis of microbial populations.

Science.gov (United States)

Krakat, N; Anjum, R; Demirel, B; Schröder, P

2017-02-01

In this study, we report how different cell disruption methods, PCR primers and in silico analyses can seriously bias results from microbial population studies, with consequences for the credibility and reproducibility of the findings. Our results emphasize the pitfalls of commonly used experimental methods that can seriously weaken the interpretation of results. Four different cell lysis methods, three commonly used primer pairs and various computer-based analyses were applied to investigate the microbial diversity of a fermentation sample composed of chicken dung. The fault-prone, but still frequently used, amplified rRNA gene restriction analysis was chosen to identify common weaknesses. In contrast to other studies, we focused on the complete analytical process, from cell disruption to in silico analysis, and identified potential error rates. This identified a wide disagreement of results between applied experimental approaches leading to very different community structures depending on the chosen approach. The interpretation of microbial diversity data remains a challenge. In order to accurately investigate the taxonomic diversity and structure of prokaryotic communities, we suggest a multi-level approach combining DNA-based and DNA-independent techniques. The identified weaknesses of commonly used methods to study microbial diversity can be overcome by a multi-level approach, which produces more reliable data about the fate and behaviour of microbial communities of engineered habitats such as biogas plants, so that the best performance can be ensured. © 2016 The Society for Applied Microbiology.

Phosphatase Activity of Microbial Populations in Different Milk Samples in Relation to Protein and Carbohydrate Content

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Sosanka Protim SANDILYA

2014-12-01

Full Text Available Cattle milk is a rich source of protein, carbohydrate, vitamins, minerals and all other major and micro nutrients. At a moderate pH, milk is an excellent media for the growth of microbes and thus, intake of raw milk is precarious. In this study, attempt was made for a qualitative study of eight raw milk samples of different varieties of cow and goat milk, collected from Jorhat district of Assam, India, on the basis of nutritional value and microbial population. The highest microbial population was found in the milk collected from cross hybrid variety of cow, whereas microbial contamination was the least in Jersey cow milk. Samples of C1 (Jersey cow variety showed presence of the highest amount of protein and carbohydrate content as compared to the others. Almost all the milk samples showed positive acid and alkaline phosphatase activity. Maximum acid phosphatase activity was observed in cross hybrid cow milk, whereas local cow milk exhibited the highest alkaline phosphatase activity. Phosphatase activity did not show any co-relationship with microbial population of the milk samples. Similarly, the protein and carbohydrate content of the samples did not have any significant impact on both acid and alkaline phosphatase activity.

Physicochemical and sensory analyses on egg powder irradiated to inactivate Salmonella and reduce microbial load

International Nuclear Information System (INIS)

Narvaiz, P.; Lescano, G.; Kairiyama, E.

1992-01-01

Egg powder was treated with 0, 2, 5 and 10 kGy of gamma radiation at 20 C to inactivate Salmonella and to stabilize its microbial load. Microbial, physicochemical and sensory determinations were performed during 4 months of storage to select the optimal radiation dose to attain the objective without significantly reducing egg quality. Microbial results show that 2.0 kGy inactivated Salmonella and reduced microbial load to levels below those stipulated by the Argentine regulations. Physicochemical determinations of egg powder extracts for peroxide number, spectrophotometric measurements in the visible and ultraviolet regions, functional properties on sponge cakes made with egg powder (height, compression-relaxation cycle parameters), foam stability and viscosity showed that gamma radiation at the dose of 2 kGy, did not cause significant changes in these parameters. Higher radiation doses (5 and 10 kGy) did increase rancidity, pigment loss and protein chain scission. Sensory determinations performed on egg powder, and on cakes manufactured with it, agreed with the physicochemical results. After 110 storage days, 2 kGy was the most suitable of the tested doses

Microbial biotechnology and circular economy in wastewater treatment.

Science.gov (United States)

Nielsen, Per Halkjaer

2017-09-01

Microbial biotechnology is essential for the development of circular economy in wastewater treatment by integrating energy production and resource recovery into the production of clean water. A comprehensive knowledge about identity, physiology, ecology, and population dynamics of process-critical microorganisms will improve process stability, reduce CO2 footprints, optimize recovery and bioenergy production, and help finding new approaches and solutions. Examples of research needs and perspectives are provided, demonstrating the great importance of microbial biotechnology. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Diets of differentially processed wheat alter ruminal fermentation parameters and microbial populations in beef cattle.

Science.gov (United States)

Jiang, S Z; Yang, Z B; Yang, W R; Li, Z; Zhang, C Y; Liu, X M; Wan, F C

2015-11-01

The influences of differently processed wheat products on rumen fermentation, microbial populations, and serum biochemistry profiles in beef cattle were studied. Four ruminally cannulated Limousin × Luxi beef cattle (400 ± 10 kg) were used in the experiment with a 4 × 4 Latin square design. The experimental diets contained (on a DM basis) 60% corn silage as a forage source and 40% concentrate with 4 differently processed wheat products (extruded, pulverized, crushed, and rolled wheat). Concentrations of ruminal NH-N and microbial protein (MCP) in cattle fed crushed and rolled wheat were greater ( Ruminal concentrations of total VFA and acetate and the ratio of acetate to propionate decreased ( 0.05). Our findings suggest that the method of wheat processing could have a significant effect on ruminal fermentation parameters and microbial populations in beef cattle and that crushed and rolled processing is better in terms of ruminal NH-N and MCP content, acetate-to-propionate ratio, and relative abundance of rumen microorganisms.

Effects of Variety and Postharvest Handling Practices on Microbial Population at Different Stages of the Value Chain of Fresh Tomato (Solanum lycopersicum) in Western Terai of Nepal.

Science.gov (United States)

Khadka, Ram B; Marasini, Madan; Rawal, Ranjana; Gautam, Durga M; Acedo, Antonio L

2017-01-01

Background . Fresh vegetables such as tomato should have low microbial population for safe consumption and long storage life. The aerobic bacterial count (ABC) and coliform bacterial count (CBC), yeast, and mold population are the most widely used microbial indicators in fresh vegetables which should be lower than 4 log CFU g -1 for safe consumption. The stages of the supply chain, postharvest handling methods, and crop varieties had significant effects on microbial population. ABC, CBC, yeast, and mold population were significantly highest ( P < 0.05) at retail market (5.59, 4.38, 2.60, and 3.14 log CFU g -1 , resp.), followed by wholesale market (4.72, 4.71, 2.43, and 2.44 log CFU g -1 , resp.), and were least at farm gate (3.89, 3.63, 2.38, and 2.03 log CFU g -1 , resp.). Improved postharvest practices (washing in clean water and grading and packaging in clean plastic crate) helped to reduce ABC, CBC, and mold population by 2.51, 32.70, and 29.86 percentage as compared to the conventional method (no washing and no grading and packaging in mud plastered bamboo baskets). Among varieties, Pusa ruby had the lowest microbial load of 2.58, 4.53, 0.96, and 1.77 log CFU g -1 for ABC, CBC, yeast, and mold count, respectively. Significantly negative correlation ( P < 0.05) was observed between fruit pH & ABC and pH & mold count. Although the microbial quality of fresh tomato is safe in the local market of western Terai of Nepal both in conventional and in improved practices however still it is essential to follow improved postharvest handling practices in production and marketing of newly introduced tomato cultivars (high-pH cultivars) for ensuring the safe availability of fresh tomato in the market.

Are Microbial Nanowires Responsible for Geoelectrical Changes at Hydrocarbon Contaminated Sites?

Science.gov (United States)

Hager, C.; Atekwana, E. A.; Gorby, Y. A.; Duris, J. W.; Allen, J. P.; Atekwana, E. A.; Ownby, C.; Rossbach, S.

2007-05-01

Significant advances in near-surface geophysics and biogeophysics in particular, have clearly established a link between geoelectrical response and the growth and enzymatic activities of microbes in geologic media. Recent studies from hydrocarbon contaminated sites suggest that the activities of distinct microbial populations, specifically syntrophic, sulfate reducing, and dissimilatory iron reducing microbial populations are a contributing factor to elevated sediment conductivity. However, a fundamental mechanistic understanding of the processes and sources resulting in the measured electrical response remains uncertain. The recent discovery of bacterial nanowires and their electron transport capabilities suggest that if bacterial nanowires permeate the subsurface, they may in part be responsible for the anomalous conductivity response. In this study we investigated the microbial population structure, the presence of nanowires, and microbial-induced alterations of a hydrocarbon contaminated environment and relate them to the sediments' geoelectrical response. Our results show that microbial communities varied substantially along the vertical gradient and at depths where hydrocarbons saturated the sediments, ribosomal intergenic spacer analysis (RISA) revealed signatures of microbial communities adapted to hydrocarbon impact. In contrast, RISA profiles from a background location showed little community variations with depth. While all sites showed evidence of microbial activity, a scanning electron microscope (SEM) study of sediment from the contaminated location showed pervasive development of "nanowire-like structures" with morphologies consistent with nanowires from laboratory experiments. SEM analysis suggests extensive alteration of the sediments by microbial Activity. We conclude that, excess organic carbon (electron donor) but limited electron acceptors in these environments cause microorganisms to produce nanowires to shuttle the electrons as they seek for

Microbial Populations of Stony Meteorites: Substrate Controls on First Colonizers

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Alastair W. Tait

2017-06-01

Full Text Available Finding fresh, sterilized rocks provides ecologists with a clean slate to test ideas about first colonization and the evolution of soils de novo. Lava has been used previously in first colonizer studies due to the sterilizing heat required for its formation. However, fresh lava typically falls upon older volcanic successions of similar chemistry and modal mineral abundance. Given enough time, this results in the development of similar microbial communities in the newly erupted lava due to a lack of contrast between the new and old substrates. Meteorites, which are sterile when they fall to Earth, provide such contrast because their reduced and mafic chemistry commonly differs to the surfaces on which they land; thus allowing investigation of how community membership and structure respond to this new substrate over time. We conducted 16S rRNA gene analysis on meteorites and soil from the Nullarbor Plain, Australia. We found that the meteorites have low species richness and evenness compared to soil sampled from directly beneath each meteorite. Despite the meteorites being found kilometers apart, the community structure of each meteorite bore more similarity to those of other meteorites (of similar composition than to the community structure of the soil on which it resided. Meteorites were dominated by sequences that affiliated with the Actinobacteria with the major Operational Taxonomic Unit (OTU classified as Rubrobacter radiotolerans. Proteobacteria and Bacteroidetes were the next most abundant phyla. The soils were also dominated by Actinobacteria but to a lesser extent than the meteorites. We also found OTUs affiliated with iron/sulfur cycling organisms Geobacter spp. and Desulfovibrio spp. This is an important finding as meteorites contain abundant metal and sulfur for use as energy sources. These ecological findings demonstrate that the structure of the microbial community in these meteorites is controlled by the substrate, and will not

Microbial quality of food available to populations of differing socioeconomic status.

Science.gov (United States)

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.

Increasing atmospheric deposition nitrogen and ammonium reduced microbial activity and changed the bacterial community composition of red paddy soil.

Science.gov (United States)

Zhou, Fengwu; Cui, Jian; Zhou, Jing; Yang, John; Li, Yong; Leng, Qiangmei; Wang, Yangqing; He, Dongyi; Song, Liyan; Gao, Min; Zeng, Jun; Chan, Andy

2018-03-27

Atmospheric deposition nitrogen (ADN) increases the N content in soil and subsequently impacts microbial activity of soil. However, the effects of ADN on paddy soil microbial activity have not been well characterized. In this study, we studied how red paddy soil microbial activity responses to different contents of ADN through a 10-months ADN simulation on well managed pot experiments. Results showed that all tested contents of ADN fluxes (27, 55, and 82kgNha -1 when its ratio of NH 4 + /NO 3 - -N (R N ) was 2:1) enhanced the soil enzyme activity and microbial biomass carbon and nitrogen and 27kgNha -1 ADN had maximum effects while comparing with the fertilizer treatment. Generally, increasing of both ADN flux and R N (1:2, 1:1 and 2:1 with the ADN flux of 55kgNha -1 ) had similar reduced effects on microbial activity. Furthermore, both ADN flux and R N significantly reduced soil bacterial alpha diversity (pADN flux and R N were the main drivers in shaping paddy soil bacteria community. Overall, the results have indicated that increasing ADN flux and ammonium reduced soil microbial activity and changed the soil bacterial community. The finding highlights how paddy soil microbial community response to ADN and provides information for N management in paddy soil. Copyright © 2018 Elsevier B.V. All rights reserved.

Variation in microbial population during composting of agro-industrial waste.

Science.gov (United States)

Coelho, Luísa; Reis, Mário; Dionísio, Lídia

2013-05-01

Two compost piles were prepared, using two ventilation systems: forced ventilation and ventilation through mechanical turning. The material to compost was a mixture of orange waste, olive pomace, and grass clippings (2:1:1 v/v). During the composting period (375 days), samples were periodically taken from both piles, and the enumeration of fungi, actinomycetes, and heterotrophic bacteria was carried out. All studied microorganisms were incubated at 25 and 55 °C after inoculation in appropriate growth media. Fungi were dominant in the early stages of both composting processes; heterotrophic bacteria proliferated mainly during the thermophilic stage, and actinomycetes were more abundant in the final stage of the composting process. Our results showed that the physical and chemical parameters: temperature, pH, moisture, and aeration influenced the variation of the microbial population along the composting process. This study demonstrated that composting of these types of wastes, despite the prolonged mesophilic stage, provided an expected microbial variation.

Estimating Population Turnover Rates by Relative Quantification Methods Reveals Microbial Dynamics in Marine Sediment.

Science.gov (United States)

Kevorkian, Richard; Bird, Jordan T; Shumaker, Alexander; Lloyd, Karen G

2018-01-01

The difficulty involved in quantifying biogeochemically significant microbes in marine sediments limits our ability to assess interspecific interactions, population turnover times, and niches of uncultured taxa. We incubated surface sediments from Cape Lookout Bight, North Carolina, USA, anoxically at 21°C for 122 days. Sulfate decreased until day 68, after which methane increased, with hydrogen concentrations consistent with the predicted values of an electron donor exerting thermodynamic control. We measured turnover times using two relative quantification methods, quantitative PCR (qPCR) and the product of 16S gene read abundance and total cell abundance (FRAxC, which stands for "fraction of read abundance times cells"), to estimate the population turnover rates of uncultured clades. Most 16S rRNA reads were from deeply branching uncultured groups, and ∼98% of 16S rRNA genes did not abruptly shift in relative abundance when sulfate reduction gave way to methanogenesis. Uncultured Methanomicrobiales and Methanosarcinales increased at the onset of methanogenesis with population turnover times estimated from qPCR at 9.7 ± 3.9 and 12.6 ± 4.1 days, respectively. These were consistent with FRAxC turnover times of 9.4 ± 5.8 and 9.2 ± 3.5 days, respectively. Uncultured Syntrophaceae , which are possibly fermentative syntrophs of methanogens, and uncultured Kazan-3A-21 archaea also increased at the onset of methanogenesis, with FRAxC turnover times of 14.7 ± 6.9 and 10.6 ± 3.6 days. Kazan-3A-21 may therefore either perform methanogenesis or form a fermentative syntrophy with methanogens. Three genera of sulfate-reducing bacteria, Desulfovibrio , Desulfobacter , and Desulfobacterium , increased in the first 19 days before declining rapidly during sulfate reduction. We conclude that population turnover times on the order of days can be measured robustly in organic-rich marine sediment, and the transition from sulfate-reducing to methanogenic conditions stimulates

Microbial electrosynthetic cells

Energy Technology Data Exchange (ETDEWEB)

May, Harold D.; Marshall, Christopher W.; Labelle, Edward V.

2018-01-30

Methods are provided for microbial electrosynthesis of H.sub.2 and organic compounds such as methane and acetate. Method of producing mature electrosynthetic microbial populations by continuous culture is also provided. Microbial populations produced in accordance with the embodiments as shown to efficiently synthesize H.sub.2, methane and acetate in the presence of CO.sub.2 and a voltage potential. The production of biodegradable and renewable plastics from electricity and carbon dioxide is also disclosed.

Monomethylhydrazine degradation and its effect on carbon dioxide evolution and microbial populations in soil

International Nuclear Information System (INIS)

Ou, L.T.; Street, J.J.

1988-01-01

Monomethylhydrazine (MMH), along with hydrazine and 1,1-dimethylhydrazine are the main components of hydrazine fuels. Information on the fate of MMH in soil and its overall effect on soil microbial activity is not known, though MMH is known to be toxic to a number of soil bacteria. Despite the fact that axenic bacterial cultures are inhibited by the three hydrazines, Ou and Street reported that soil respiration, and total bacterial and fungal populations in soil, were not inhibited by hydrazine at concentrations of 100 μg/g and lower. Even at 500 μg/g, only total bacterial populations in soil were inhibited by the presence of hydrazine. They also reported that hydrazine rapidly disappeared in soil. The authors initiated this study to investigate the effect of MMH on soil microbial activity and on degradation of the chemical in soil

The Effect of Long Term Mercury Pollution on the Soil Microbial Community

DEFF Research Database (Denmark)

Müller, A.K.; Westergaard, K.; Christensen, Søren

2001-01-01

The effect of long-term exposure to mercury on the soil microbial community was investigated in soil from three different sites along a pollution gradient. The amount of total and bioavailable mercury was negatively correlated to the distance from the center of contamination. The size...... of the bacterial and protozoan populations was reduced in the most contaminated soil, whereas there was no significant difference in fungal biomass measured as chitinase activity. Based on the number of colony morphotypes, moreover, the culturable bacterial population was structurally less diverse and contained...... of the number and abundance of bands. The functional potential of the microbial population measured as sole carbon source utilization by Ecoplates® differed between the soils, but there was no change in the number of substrates utilized. The observed changes in the different soil microbial populations...

Effects of replacing dietary starch with neutral detergent-soluble fibre on ruminal fermentation, microbial synthesis and populations of ruminal cellulolytic bacteria using the rumen simulation technique (RUSITEC).

Science.gov (United States)

Zhao, X H; Liu, C J; Liu, Y; Li, C Y; Yao, J H

2013-12-01

A rumen simulation technique (RUSITEC) apparatus with eight 800 ml fermenters was used to investigate the effects of replacing dietary starch with neutral detergent-soluble fibre (NDSF) by inclusion of sugar beet pulp in diets on ruminal fermentation, microbial synthesis and populations of ruminal cellulolytic bacteria. Experimental diets contained 12.7, 16.4, 20.1 or 23.8% NDSF substituted for starch on a dry matter basis. The experiment was conducted over two independent 15-day incubation periods with the last 8 days used for data collection. There was a tendency that 16.4% NDSF in the diet increased the apparent disappearance of organic matter (OM) and neutral detergent fibre (NDF). Increasing dietary NDSF level increased carboxymethylcellulase and xylanase activity in the solid fraction and apparent disappearance of acid detergent fibre (ADF) but reduced the 16S rDNA copy numbers of Ruminococcus albus in both liquid and solid fractions and R. flavefaciens in the solid fraction. The apparent disappearance of dietary nitrogen (N) was reduced by 29.6% with increased dietary NDSF. Substituting NDSF for starch appeared to increase the ratios of acetate/propionate and methane/volatile fatty acids (VFA) (mol/mol). Replacing dietary starch with NDSF reduced the daily production of ammonia-N and increased the growth of the solid-associated microbial pellets (SAM). Total microbial N flow and efficiency of microbial synthesis (EMS), expressed as g microbial N/kg OM fermented, tended to increase with increased dietary NDSF, but the numerical increase did not continue as dietary NDSF exceeded 20.1% of diet DM. Results suggested that substituting NDSF for starch up to 16.4% of diet DM increased digestion of nutrients (except for N) and microbial synthesis, and further increases (from 16.4% to 23.8%) in dietary NDSF did not repress microbial synthesis but did significantly reduce digestion of dietary N. © 2012 Blackwell Verlag GmbH.

[Formation of microbial populations on the surface of protective coatings].

Science.gov (United States)

Kopteva, Zh P; Zanina, V V; Piliashenko-Novokhatnyĭ, A I; Kopteva, A E; Kozlova, I A

2001-01-01

Formation of microbial cenosis on the surface of polyethylene-, polyurethane- and oil-bitumen-based protective coatings was studied in dynamics during 1, 3, 7, 14 and 21 days. It has been shown that the biofilm was formed on the protective materials during 14 days and consisted of ammonifying, denitrifying, hydrocarbon-oxidizing and sulphate-reducing bacteria referred to Pseudomonas, Arthrobacter, Bacillus and Kesulfovibrio genera. The bacteria which form the biofilm on coatings possess high denitrifying and sulphate-reducing activities. Corrosion inhibitors-biocydes, introduced in composition of oil-bitumen coatings suppressed growth and metabolic activity of corrosion-active bacteria.

Microbial population changes in tropical agricultural soil ...

African Journals Online (AJOL)

STORAGESEVER

2008-12-17

Dec 17, 2008 ... Microbial degradation is known to be an efficient process in the in ..... exhibited a great impact on the ecology of the soil by causing drastic ... city of the soil (Dibble and Bartha, 1979). Hydrocarbon .... Atlas RM (1991). Microbial ...

Diversity and function of the microbial community on anodes of sediment microbial fuel cells fueled by root exudates

Energy Technology Data Exchange (ETDEWEB)

Cabezas da Rosa, Angela

2010-11-26

Anode microbial communities are essential for current production in microbial fuel cells. Anode reducing bacteria are capable of using the anode as final electron acceptor in their respiratory chain. The electrons delivered to the anode travel through a circuit to the cathode where they reduce oxygen to water generating an electric current. A novel type of sediment microbial fuel cell (SMFC) harvest energy from photosynthetically derived compounds released through the roots. Nothing is known about anode microbial communities of this type of microbial fuel cell. This work consists of three parts. The first part focuses on the study of bacterial and archaeal community compositions on anodes of SMFCs fueled by rice root exudates. By using terminal restriction fragment length polymorphism (T-RFLP), a profiling technique, and cloning / sequencing of 16S rRNA, we determined that the support type used for the plant (vermiculite, potting soil or rice field soil) is an important factor determining the composition of the microbial community. Finally, by comparing microbial communities of current producing anodes and non-current producing controls we determined that Desulfobulbus- and Geobacter-related populations were probably most important for current production in potting soil and rice field soil SMFCs, respectively. However, {delta}-proteobacterial Anaeromyxobacter spp., unclassified {delta}-proteobacteria and Anaerolineae were also part of the anode biofilm in rice field soil SMFCs and these populations might also play a role in current production. Moreover, distinct clusters of Geobacter and Anaeromyxobacter populations were stimulated by rice root exudates. Regarding Archaea, uncultured Euryarchaea were abundant on anodes of potting soil SMFCs indicating a potential role in current production. In both, rice field soil and potting soil SMFCs, a decrease of Methanosaeta, an acetotrophic methanogen, was detected on current producing anodes. In the second part we focused

Effects of nitrate addition to a diet on fermentation and microbial populations in the rumen of goats, with special reference to Selenomonas ruminantium having the ability to reduce nitrate and nitrite.

Science.gov (United States)

Asanuma, Narito; Yokoyama, Shota; Hino, Tsuneo

2015-04-01

This study investigated the effects of dietary nitrate addition on ruminal fermentation characteristics and microbial populations in goats. The involvement of Selenomonas ruminantium in nitrate and nitrite reduction in the rumen was also examined. As the result of nitrate feeding, the total concentration of ruminal volatile fatty acids decreased, whereas the acetate : propionate ratio and the concentrations of ammonia and lactate increased. Populations of methanogens, protozoa and fungi, as estimated by real-time PCR, were greatly decreased as a result of nitrate inclusion in the diet. There was modest or little impact of nitrate on the populations of prevailing species or genus of bacteria in the rumen, whereas Streptococcus bovis and S. ruminantium significantly increased. Both the activities of nitrate reductase (NaR) and nitrite reductase (NiR) per total mass of ruminal bacteria were increased by nitrate feeding. Quantification of the genes encoding NaR and NiR by real-time PCR with primers specific for S. ruminantium showed that these genes were increased by feeding nitrate, suggesting that the growth of nitrate- and nitrite-reducing S. ruminantium is stimulated by nitrate addition. Thus, S. ruminantium is likely to play a major role in nitrate and nitrite reduction in the rumen. © 2014 Japanese Society of Animal Science.

Microbial population analysis of the salivary glands of ticks; a possible strategy for the surveillance of bacterial pathogens.

Directory of Open Access Journals (Sweden)

Yongjin Qiu

Full Text Available Ticks are one of the most important blood-sucking vectors for infectious microorganisms in humans and animals. When feeding they inject saliva, containing microbes, into the host to facilitate the uptake of blood. An understanding of the microbial populations within their salivary glands would provide a valuable insight when evaluating the vectorial capacity of ticks. Three tick species (Ixodes ovatus, I. persulcatus and Haemaphysalis flava were collected in Shizuoka Prefecture of Japan between 2008 and 2011. Each tick was dissected and the salivary glands removed. Bacterial communities in each salivary gland were characterized by 16S amplicon pyrosequencing using a 454 GS-Junior Next Generation Sequencer. The Ribosomal Database Project (RDP Classifier was used to classify sequence reads at the genus level. The composition of the microbial populations of each tick species were assessed by principal component analysis (PCA using the Metagenomics RAST (MG-RAST metagenomic analysis tool. Rickettsia-specific PCR was used for the characterization of rickettsial species. Almost full length of 16S rDNA was amplified in order to characterize unclassified bacterial sequences obtained in I. persulcatus female samples. The numbers of bacterial genera identified for the tick species were 71 (I. ovatus, 127 (I. persulcatus and 59 (H. flava. Eighteen bacterial genera were commonly detected in all tick species. The predominant bacterial genus observed in all tick species was Coxiella. Spiroplasma was detected in Ixodes, and not in H. flava. PCA revealed that microbial populations in tick salivary glands were different between tick species, indicating that host specificities may play an important role in determining the microbial complement. Four female I. persulcatus samples contained a high abundance of several sequences belonging to Alphaproteobacteria symbionts. This study revealed the microbial populations within the salivary glands of three species of

Dehydrochlorination of 1,1,1-trichloroethane and pentachloroethane by microbially reduced ferruginous smectite.

Science.gov (United States)

Cervini-Silva, Javiera; Kostka, Joel E; Larson, Richard A; Stucki, Joseph W; Wu, Jun

2003-05-01

Reduction of structural Fe(III) in smectite clay minerals has been identified as a means to promote dechlorination of polychlorinated ethanes, but its environmental significance has yet to be fully assessed because Fe reduction has normally been achieved by agents uncommon in the environment (e.g., dithionite). This study reports the dehydrochlorination of pentachloroethane and 1,1,1-trichloroethane in the presence of ferruginous smectite reduced by two cultures of microorganisms, Shewanella oneidensis strain MR-1 (MR-R) and an enrichment culture from rice paddy soils (PS-R), in aqueous suspension under anoxic conditions. Microbially reduced ferruginous smectite facilitated dehydrochlorination of 1,1,1-trichloroethane to 1,1-dichloroethene with up to 60% conversion within 3 h of incubation time. In contrast, no formation of 1,1-dichloroethene was observed after incubation of 1,1,1-trichloroethane with chemically reduced ferruginous smectite for 24 h. Microbially reduced ferruginous smectite by MR-R and PS-R promoted the dehydrochlorination of pentachloroethane to tetrachloroethene by 80 and 15%, respectively, after 3 h of incubation time. The conversion of pentachloroethane to tetrachloroethene in the presence of chemically reduced ferruginous smectite after 24 h was 65%. These results indicate that structural Fe(II) in clay minerals has the potential to be an important reductant controlling the fate of organic chemicals in contaminated sediments.

In situ Microbial Community Control of the Stability of Bio-Reduced Uranium

International Nuclear Information System (INIS)

Long, Phillip E.; McKinley, James P.; White, David C.

2006-01-01

In aerobic aquifers typical of many Department of Energy (DOE) legacy waste sites, uranium is present in the oxidized U(VI) form which is soluble and thus mobile compared to U(IV). Previous work at the Old Rifle Uranium Mill Tailings Remedial Action (UMTRA) site demonstrated that biostimulation by acetate injection promoted growth of Geobacteraceae and stimulated the microbial reduction of U(VI) to less soluble U(IV) (1, 4). Despite the potential for oxidative dissolution of bio-reduced U(IV), field experiments at the Old Rifle site show that although the rate of U(VI) reduction decreases following the on-set of sulfate reduction, U(VI) reduction continues even following the cessation of acetate injection (1, 4). However, U(VI) reduction is reversible and the basis for the observed maintenance of U(VI) reduction post-stimulation is a critical but as yet unresolved issue for the application of biostimulation as a treatment technology. The continued U(VI) reduction and the maintenance of reduced U(IV) may result from many factors including U(VI) reduction by sulfate reducing bacteria (SRB), generation of H2S or FeS0.9 which serves as an oxygen sink, or the preferential sorption of U(VI) by microbial cells or biopolymers. The overall goal of the project is to develop an understanding of the mechanisms for the maintenance of bio-reduced uranium in an aerobic aquifer under field conditions following the cessation of electron donor addition

Bioremediation of hydrocarbon degradation in a petroleum-contaminated soil and microbial population and activity determination.

Science.gov (United States)

Wu, Manli; Li, Wei; Dick, Warren A; Ye, Xiqiong; Chen, Kaili; Kost, David; Chen, Liming

2017-02-01

Bioremediation of hydrocarbon degradation in petroleum-polluted soil is carried out by various microorganisms. However, little information is available for the relationships between hydrocarbon degradation rates in petroleum-contaminated soil and microbial population and activity in laboratory assay. In a microcosm study, degradation rate and efficiency of total petroleum hydrocarbons (TPH), alkanes, and polycyclic aromatic hydrocarbons (PAH) in a petroleum-contaminated soil were determined using an infrared photometer oil content analyzer and a gas chromatography mass spectrometry (GC-MS). Also, the populations of TPH, alkane, and PAH degraders were enumerated by a modified most probable number (MPN) procedure, and the hydrocarbon degrading activities of these degraders were determined by the Biolog (MT2) MicroPlates assay. Results showed linear correlations between the TPH and alkane degradation rates and the population and activity increases of TPH and alkane degraders, but no correlation was observed between the PAH degradation rates and the PAH population and activity increases. Petroleum hydrocarbon degrading microbial population measured by MPN was significantly correlated with metabolic activity in the Biolog assay. The results suggest that the MPN procedure and the Biolog assay are efficient methods for assessing the rates of TPH and alkane, but not PAH, bioremediation in oil-contaminated soil in laboratory. Copyright © 2016 Elsevier Ltd. All rights reserved.

Population density of Beauveria bassiana in soil under the action of fungicides and native microbial populations

Directory of Open Access Journals (Sweden)

Flávia Barbosa Soares

2017-08-01

Full Text Available This study investigated whether populations of naturally-occurring soil bacteria, fungi and actinomycetes influence the effect of fungicides on the survival and growth of Beauveria bassiana. The toxicity of methyl thiophanate, pyraclostrobin, mancozeb and copper oxychloride at the recommended doses was analyzed in culture medium and in soil inoculated with fungus at various time points after addition of fungicides. All fungicides completely inhibited the growth and sporulation of B. bassiana in the culture medium. The fungicides were less toxic in soil, emphasizing the action of the microbial populations, which interfered with the toxic effects of these products to the fungus. Actinomycetes had the greatest influence on the entomopathogen, inhibiting it or degrading the fungicides to contribute to the survival and growth of B. bassiana in soil. Native populations of fungi and bacteria had a smaller influence on the population density of B. bassiana and the action of fungicides towards entomopathogen. The toxic effect of the fungicides was greater when added to the soil one hour before or after inoculation than at 48h after inoculation.

Population cycles and species diversity in dynamic Kill-the-Winner model of microbial ecosystems

Science.gov (United States)

Maslov, Sergei; Sneppen, Kim

2017-01-01

Determinants of species diversity in microbial ecosystems remain poorly understood. Bacteriophages are believed to increase the diversity by the virtue of Kill-the-Winner infection bias preventing the fastest growing organism from taking over the community. Phage-bacterial ecosystems are traditionally described in terms of the static equilibrium state of Lotka-Volterra equations in which bacterial growth is exactly balanced by losses due to phage predation. Here we consider a more dynamic scenario in which phage infections give rise to abrupt and severe collapses of bacterial populations whenever they become sufficiently large. As a consequence, each bacterial population in our model follows cyclic dynamics of exponential growth interrupted by sudden declines. The total population of all species fluctuates around the carrying capacity of the environment, making these cycles cryptic. While a subset of the slowest growing species in our model is always driven towards extinction, in general the overall ecosystem diversity remains high. The number of surviving species is inversely proportional to the variation in their growth rates but increases with the frequency and severity of phage-induced collapses. Thus counter-intuitively we predict that microbial communities exposed to more violent perturbations should have higher diversity. PMID:28051127

Ecological distribution and population physiology defined by proteomics in a natural microbial community

Science.gov (United States)

Mueller, Ryan S.; Denef, Vincent J.; Kalnejais, Linda H.; Suttle, K. Blake; Thomas, Brian C.; Wilmes, Paul; Smith, Richard L.; Nordstrom, D. Kirk; McCleskey, R. Blaine; Shah, Menesh B.; VerBekmoes, Nathan C.; Hettich, Robert L.; Banfield, Jillian F.

2010-01-01

An important challenge in microbial ecology is developing methods that simultaneously examine the physiology of organisms at the molecular level and their ecosystem level interactions in complex natural systems. We integrated extensive proteomic, geochemical, and biological information from 28 microbial communities collected from an acid mine drainage environment and representing a range of biofilm development stages and geochemical conditions to evaluate how the physiologies of the dominant and less abundant organisms change along environmental gradients. The initial colonist dominates across all environments, but its proteome changes between two stable states as communities diversify, implying that interspecies interactions affect this organism's metabolism. Its overall physiology is robust to abiotic environmental factors, but strong correlations exist between these factors and certain subsets of proteins, possibly accounting for its wide environmental distribution. Lower abundance populations are patchier in their distribution, and proteomic data indicate that their environmental niches may be constrained by specific sets of abiotic environmental factors. This research establishes an effective strategy to investigate ecological relationships between microbial physiology and the environment for whole communities in situ.

An approach to mitigating soil CO2 emission by biochemically inhibiting cellulolytic microbial populations through mediation via the medicinal herb Isatis indigotica

Science.gov (United States)

Wu, Hong-Sheng; Chen, Su-Yun; Li, Ji; Liu, Dong-Yang; Zhou, Ji; Xu, Ya; Shang, Xiao-Xia; Wei, Dong-yang; Yu, Lu-ji; Fang, Xiao-hang; Li, Shun-yi; Wang, Ke-ke

2017-06-01

Greenhouse gases (GHGs, particularly carbon dioxide (CO2)) emissions from soil under wheat production are a significant source of agricultural carbon emissions that have not been mitigated effectively. A field experiment and a static incubation study in a lab were conducted to stimulate wheat growth and investigate its potential to reduce CO2 emissions from soil through intercropping with a traditional Chinese medicinal herb called Isatis indigotica. This work was conducted by adding I. indigotica root exudates based on the quantitative real-time PCR (qPCR) analysis of the DNA copy number of the rhizosphere or bulk soil microbial populations. This addition was performed in relation to the CO2 formation by cellulolytic microorganisms (Penicillium oxalicum, fungi and Ruminococcus albus) to elucidate the microbial ecological basis for the molecular mechanism that decreases CO2 emissions from wheat fields using I. indigotica. The results showed that the panicle weight and full grains per panicle measured through intercropping with I. indigotica (NPKWR) increased by 39% and 28.6%, respectively, compared to that of the CK (NPKW). Intercropping with I. indigotica significantly decreased the CO2 emissions from soil under wheat cultivation. Compared with CK, the total CO2 emission flux during the wheat growth period in the I. indigotica (NPKWR) intercropping treatment decreased by 29.26%. The intensity of CO2 emissions per kg of harvested wheat grain declined from 7.53 kg CO2/kg grain in the NPKW (CK) treatment to 5.55 kg CO2/kg grain in the NPKWR treatment. The qPCR analysis showed that the DNA copy number of the microbial populations of cellulolytic microorganisms (P. oxalicum, fungi and R. albus) in the field rhizosphere around I. indigotica or in the bulk soil under laboratory incubation was significantly lower than that of CK. This finding indicated that root exudates from I. indigotica inhibited the activity and number of cellulolytic microbial populations, which led

Effect of common pesticides used in the Niger Delta basin of southern Nigeria on soil microbial populations.

Science.gov (United States)

Ekundayo, E O

2003-11-01

The effects of eleven pesticides on the populations of bacteria, actinomycetes, fungi and protozoa was investigated by treating a garden soil with their recommended rates. The microbial populations were estimated using the standard plate-count technique. Of the 11 pesticides investigated, phenylmercuric acetate (agrosan) at 50 microg g(-1) inhibited bacterial density the most, i.e. from 4,600,000 to 220 cells g(-1). The pesticides were Pentachloronitrobenzene (PCNB), tetramethylmethylthiuram disulphide (thiram), 1-naphthylmethylcarbamate (Vetox 85), 1,2,3,4,5,6-hexachlorocyclohexane (Gammalin 20), phenylmercuric acetate (Agrosan), tetrachloroterephthalic acid (Dacthal), 4-nitrophenyl-2-nitro-4-trifluoromethylphenyl ether (Preforan), 2-ethyl-6-methyl-N-2-methoxy-1-methyl ethyl-chloroacetanide (Dual), Benlate, Brestan and Gramoxone. Pentachloronitrobenzene (PCNB) at 240,000 microg g(-1) reduced bacterial population from 4,600,000 to 2,100 cells g(-1), whereas tetramethylthiuram disulphide (thiram) at 100 microg g(-1) suppressed it by 2 log orders of magnitude. Soil application of 1-naphthylmethylcarbamate (Vetox 85) at 100 microg g(-1) and 1,2,3,4,5,6,-hexachlorocyclohexane (Gamalin 20) at 1,300 microg g(-1) repressed the bacterial numbers by 2 log orders of magnitude each. Pentachloronitrobenzene reduced the actinomycetes density from 340,000 to 320 cells g(-1) and completely eliminated all fungal and protozoan propagules from the soil. The Gammalin 20 completely wiped out all the fungi, whereas phenylmercuric acetate totally eliminated all the protozoa and reduced the fungal population from 34,000 to 60 cells g(-1). In general, protozoa and fungi were more susceptible to fungicides than bacteria and actinomycetes. Pentachloronitrobenzene, 1,2,3,4,5,6,-hexachlorocyclohexane and phenylmercuric acetate were toxic particularly to soil microorganisms, whereas the herbicides dacthal, Preforan and Dual were quite harmless in soil at application rates of 0.1, 0.06 and 0

Dynamics of organic matter and microbial populations in amended soil: a multidisciplinary approach

Science.gov (United States)

Gigliotti, Giovanni; Pezzolla, Daniela; Zadra, Claudia; Albertini, Emidio; Marconi, Gianpiero; Turchetti, Benedetta; Buzzini, Pietro

2013-04-01

The application of organic amendments to soils, such as pig slurry, sewage sludge and compost is considered a tool for improving soil fertility and enhancing C stock. The addition of these different organic materials allows a good supply of nutrients for plants but also contributes to C sequestration, affects the microbial activity and the transformation of soil organic matter (SOM). Moreover, the addition of organic amendment has gained importance as a source of greenhouse gas (GHG) emissions and then as a cause of the "Global Warming". Therefore, it is important to investigate the factors controlling the SOM mineralization in order to improve soil C sequestration and decreasing at the same time the GHG emissions. The quality of organic matter added to the soil will play an important role in these dynamics, affecting the microbial activity and the changes in microbial community structure. A laboratory, multidisciplinary experiment was carried out to test the effect of the amendment by anaerobic digested livestock-derived organic materials on labile organic matter evolution and on dynamics of microbial population, this latter both in terms of consistence of microbial biomass, as well as in terms of microbial biodiversity. Different approaches were used to study the microbial community structure: chemical (CO2 fluxes, WEOC, C-biomass, PLFA), microbiological (microbial enumeration) and molecular (DNA extraction and Roche 454, Next Generation Sequencing, NGS). The application of fresh digestate, derived from the anaerobic treatment of animal wastes, affected the short-term dynamics of microbial community, as reflected by the increase of CO2 emissions immediately after the amendment compared to the control soil. This is probably due to the addition of easily available C added with the digestate, demonstrating that this organic material was only partially stabilized by the anaerobic process. In fact, the digestate contained a high amounts of available C, which led to

Microbial deposition of gold nanoparticles by the metal-reducing bacterium Shewanella algae

International Nuclear Information System (INIS)

Konishi, Y.; Tsukiyama, T.; Tachimi, T.; Saitoh, N.; Nomura, T.; Nagamine, S.

2007-01-01

Microbial reduction and deposition of gold nanoparticles was achieved at 25 deg. C over the pH range 2.0-7.0 using the mesophilic bacterium Shewanella algae in the presence of H 2 as the electron donor. The reductive deposition of gold by the resting cells of S. algae was a fast process: 1 mM AuCl 4 - ions were completely reduced to elemental gold within 30 min. At a solution pH of 7, gold nanoparticles 10-20 nm in size were deposited in the periplasmic space of S. algae cells. At pH 2.8, gold nanoparticles 15-200 nm in size were deposited on the bacterial cells, and the biogenic nanoparticles exhibited a variety of shapes that included nanotriangles: in particular, single crystalline gold nanotriangles 100-200 nm in size were microbially deposited. At a solution pH of 2.0, gold nanoparticles about 20 nm in size were deposited intracellularly, and larger gold particles approximately 350 nm in size were deposited extracellularly. The solution pH was an important factor in controlling the morphology of the biogenic gold particles and the location of gold deposition. Microbial deposition of gold nanoparticles is potentially attractive as an environmentally friendly alternative to conventional methods

Long-term application of winery wastewater - Effect on soil microbial populations and soil chemistry

Science.gov (United States)

Mosse, Kim; Patti, Antonio; Smernik, Ron; Cavagnaro, Timothy

2010-05-01

The ability to reuse winery wastewater (WWW) has potential benefits both with respect to treatment of a waste stream, as well as providing a beneficial water resource in water limited regions such as south-eastern Australia, California and South Africa. Over an extended time period, this practice leads to changes in soil chemistry, and potentially, also to soil microbial populations. In this study, we compared the short term effects of WWW (both treated and untreated) application on soil biology and chemistry in two adjacent paired sites with the same soil type, one of which had received WWW for approximately 30 years, and the other which had not. The paired sites were treated with an industrially relevant quantity of WWW, and the soil microbial activity (measured as soil CO2 efflux) and common soil physicochemical properties were monitored over a 16-day period. In addition, Solid State 13C NMR was employed on whole soil samples from the two sites, to measure and compare the chemical nature of the soil organic matter at the paired sites. The acclimatised soil showed a high level of organic matter and a greater spike in microbial activity following WWW addition, in comparison with the non-acclimatised soil, suggesting differences in soil chemistry and soil microbial communities between the two sites. Soil nitrate and phosphorus levels showed significant differences between WWW treatments; these differences likely to be microbially mediated.

Epigeic earthworms exert a bottleneck effect on microbial communities through gut associated processes.

Science.gov (United States)

Gómez-Brandón, María; Aira, Manuel; Lores, Marta; Domínguez, Jorge

2011-01-01

Earthworms play a critical role in organic matter decomposition because of the interactions they establish with microorganisms. The ingestion, digestion, assimilation of organic material in the gut and then casting is the first step in earthworm-microorganism interactions. The current knowledge of these direct effects is still limited for epigeic earthworm species, mainly those living in man-made environments. Here we tested whether and to what extent the earthworm Eisenia andrei is capable of altering the microbiological properties of fresh organic matter through gut associated processes; and if these direct effects are related to the earthworm diet. To address these questions we determined the microbial community structure (phospholipid fatty acid profiles) and microbial activity (fluorescein diacetate hydrolysis) in the earthworm casts derived from three types of animal manure (cow, horse and pig manure), which differed in microbial composition. The passage of the organic material through the gut of E. andrei reduced the total microbial biomass irrespective of the type of manure, and resulted in a decrease in bacterial biomass in all the manures; whilst leaving the fungi unaffected in the egested materials. However, unlike the microbial biomass, no such reduction was detected in the total microbial activity of cast samples derived from the pig manure. Moreover, no differences were found between cast samples derived from the different types of manure with regards to microbial community structure, which provides strong evidence for a bottleneck effect of worm digestion on microbial populations of the original material consumed. Our data reveal that earthworm gut is a major shaper of microbial communities, thereby favouring the existence of a reduced but more active microbial population in the egested materials, which is of great importance to understand how biotic interactions within the decomposer food web influence on nutrient cycling.

Epigeic earthworms exert a bottleneck effect on microbial communities through gut associated processes.

Directory of Open Access Journals (Sweden)

María Gómez-Brandón

Full Text Available BACKGROUND: Earthworms play a critical role in organic matter decomposition because of the interactions they establish with microorganisms. The ingestion, digestion, assimilation of organic material in the gut and then casting is the first step in earthworm-microorganism interactions. The current knowledge of these direct effects is still limited for epigeic earthworm species, mainly those living in man-made environments. Here we tested whether and to what extent the earthworm Eisenia andrei is capable of altering the microbiological properties of fresh organic matter through gut associated processes; and if these direct effects are related to the earthworm diet. METHODOLOGY: To address these questions we determined the microbial community structure (phospholipid fatty acid profiles and microbial activity (fluorescein diacetate hydrolysis in the earthworm casts derived from three types of animal manure (cow, horse and pig manure, which differed in microbial composition. PRINCIPAL FINDINGS: The passage of the organic material through the gut of E. andrei reduced the total microbial biomass irrespective of the type of manure, and resulted in a decrease in bacterial biomass in all the manures; whilst leaving the fungi unaffected in the egested materials. However, unlike the microbial biomass, no such reduction was detected in the total microbial activity of cast samples derived from the pig manure. Moreover, no differences were found between cast samples derived from the different types of manure with regards to microbial community structure, which provides strong evidence for a bottleneck effect of worm digestion on microbial populations of the original material consumed. CONCLUSIONS/SIGNIFICANCE: Our data reveal that earthworm gut is a major shaper of microbial communities, thereby favouring the existence of a reduced but more active microbial population in the egested materials, which is of great importance to understand how biotic interactions

Effect of buctril super (Bromoxynil herbicide on soil microbial biomass and bacterial population

Directory of Open Access Journals (Sweden)

Zafar Abbas

2014-02-01

Full Text Available The present study aimed to evaluate the effect of bromoxynil herbicide on soil microorganisms, with the hypothesis that this herbicide caused suppression in microbial activity and biomass by exerting toxic effect on them. Nine sites of Punjab province (Pakistan those had been exposed to bromoxynil herbicide for about last ten years designated as soil 'A' were surveyed in 2011 and samples were collected and analyzed for Microbial Biomass Carbon (MBC, Biomass Nitrogen (MBN, Biomass Phosphorus (MBP and bacterial population. Simultaneously, soil samples from the same areas those were not exposed to herbicide designated as soil 'B' were taken. At all the sites MBC, MBN and MBP ranged from 131 to 457, 1.22 to 13.1 and 0.59 to 3.70 µg g-1 in the contaminated soils (Soil A, which was 187 to 573, 1.70 to 14.4 and 0.72 to 4.12 µg g-1 in the soils without contamination (soil B. Bacterial population ranged from 0.67 to 1.84x10(8 and 0.87 to 2.37x10(8 cfu g-1 soil in the soils A and B, respectively. Bromoxynil residues ranged from 0.09 to 0.24 mg kg-1 at all the sites in soil A. But no residues were detected in the soil B. Due to lethal effect of bromoxynil residues on the above parameters, considerable decline in these parameters was observed in the contaminated soils. Results depicted that the herbicide had left toxic effects on soil microbial parameters, thus confirmed that continuous use of this herbicide affected the quality of soil and sustainable crop production.

Decline in Performance of Biochemical Reactors for Sulphate Removal from Mine-Influenced Water is Accompanied by Changes in Organic Matter Characteristics and Microbial Population Composition

Directory of Open Access Journals (Sweden)

Parissa Mirjafari

2016-03-01

Full Text Available Successful long-term bioremediation of mining-influenced water using complex organic matter and naturally-occurring microorganisms in sub-surface flow constructed wetlands requires a balance between easily and more slowly degrading material. This can be achieved by combining different types of organic materials. To provide guidance on what mixture combinations to use, information is needed on how the ratio of labile to recalcitrant components affects the degradation rate and the types of microbial populations supported. To investigate this, different ratios of wood and hay were used in up-flow column bioreactors treating selenium- and sulphate-containing synthetic mine-influenced water. The degradation rates of crude fibre components appeared to be similar regardless of the relative amounts of wood and hay. However, the nature of the degradation products might have differed in that those produced in the hay-rich bioreactors were more biodegradable and supported high sulphate-reduction rates. Microorganisms in the sulphate-reducing and cellulose-degrading inocula persisted in the bioreactors indicating that bio-augmentation was effective. There was a shift in microbial community composition over time suggesting that different microbial groups were involved in decomposition of more recalcitrant material. When dissolved organic carbon (DOC was over-supplied, the relative abundance of sulphate-reducers was low even through high sulphate-reduction rates were achieved. As DOC diminished, sulphate-reducers become more prevalent and their relative abundance correlated with sulphate concentrations rather than sulphate-reduction rate.

The nanostructure of microbially-reduced graphene oxide fosters thick and highly-performing electrochemically-active biofilms

Science.gov (United States)

Virdis, Bernardino; Dennis, Paul G.

2017-07-01

Biofilms of electrochemically-active organisms are used in microbial electrochemical technologies (METs) to catalyze bioreactions otherwise not possible at bare electrodes. At present, however, achievable current outputs are still below levels considered sufficient for economic viability of large-scale METs implementations. Here, we report three-dimensional, self-aggregating biofilm composites comprising of microbial cells embedded with microbially-reduced graphene oxide (rGO) nanoparticles to form a thick macro-porous network with superior electrochemical properties. In the presence of metabolic substrate, these hybrid biofilms are capable of producing up to five times more catalytic current than the control biofilms. Cyclic voltammetry, linear sweep voltammetry, and electrochemical impedance spectroscopy, show that in spite of the increased thickness, the biofilms amended with GO display lower polarization/charge transfer resistance compared to the controls, which we ascribe to the incorporation of rGO into the biofilms, which (1) promotes fast electron transfer, yet conserving a macroporous structure that allows free diffusion of reactants and products, and (2) enhances the interfacial dynamics by allowing a higher load of microbial cells per electrode surface area. These results suggest an easy-to-apply and cost-effective method to produce high-performing electrochemically-active biofilms in situ.

Microbial O2 consumption in the Aespoe tunnel

International Nuclear Information System (INIS)

Kotelnikova, S.; Pedersen, Karsten

1998-04-01

The report presents data on microbial O 2 reduction activities by microorganisms obtained with different techniques: Winkler method, gas chromatography, most probable numbering, enrichment technique, inhibitor analysis and radiotracer measurements. The samples were collected from boreholes and open funnel ponds at Aespoe in 1996-1998. The evaluation of the microbial activities in open ponds predicts the future microbial activities after the O 2 intrusion around the future repository. The metabolic potential of the microbial population inhabiting groundwater was evaluated on the basis of electron donors available and microbial 16S rRNA gene diversity. The contribution of different microbial groups to the O 2 reduction was elucidated using specific inhibitors selectively affecting different microbial groups. Our experiments show that microbial O 2 reduction occurs in deep groundwater. Carbon dioxide was produced concurrently with O 2 reduction confirming the biogenic nature of the reduction. The populations developed O 2 reduction rates and capacity depending on the initial concentration of dissolved O 2 reduction. Rates of O 2 reduction ranged from 0.32 to 4.5 μM/day. Depending on temperature and the type of groundwater the approximate time needed for consumption of 500 μM of dissolved O 2 ranged from 0.31 to 3.99 years. After approximately a 2 weeks period the microbial population in vitro was able to consume O 2 both at 30 deg C and 60 deg C. At 16 deg C no delay in O 2 consumption was observed. Our results demonstrated that methanotrophs survive in deep groundwater and that they were induced by O 2 . Some bacteria use Hg or CH 4 as electron donor instead of organic matter, which means that microbial O 2 reduction will occur also in deep groundwaters where the availability of organic carbon is limited. Specific CH 4 oxidation rates ranged between 3.00 and 220 nM CH 4 per litre per day. Comparison of the total O 2 reducing activities by gas chromatography and

Effects of extracts on ruminal fermentation characteristics, methanogenesis, and microbial populations

Directory of Open Access Journals (Sweden)

Shin Ja Lee

2018-01-01

Full Text Available Objective Gelidium amansii (Lamouroux is a red alga belonging to the family Gelidaceae and is commonly found in the shallow coasts of many East Asian countries, including Korea, China, and Japan. G. amansii has traditionally been utilized as an edible alga, and has various biological activities. The objective of this study was to determine whether dietary supplementation of G. amansii could be useful for improving ruminal fermentation. Methods As assessed by in vitro fermentation parameters such as pH, total gas, volatile fatty acid (VFA production, gas profile (methane, carbon dioxide, hydrogen, and ammonia, and microbial growth rate was compared to a basal diet with timothy hay. Cannulated Holstein cows were used as rumen fluid donors and 15 mL rumen fluid: buffer (1:2 was incubated for up to 72 h with four treatments with three replicates. The treatments were: control (timothy only, basal diet with 1% G. amansii extract, basal diet with 3% G. amansii extract, and basal diet with 5% G. amansii extract. Results Overall, the results of our study indicate that G. amansii supplementation is potentially useful for improving ruminant growth performance, via increased total gas and VFA production, but does come with some undesirable effects, such as increasing pH, ammonia concentration, and methane production. In particular, real-time polymerase chain reaction indicated that the methanogenic archaea and Fibrobacter succinogenes populations were significantly reduced, while the Ruminococcus flavefaciens populations were significantly increased at 24 h, when supplemented with G. amansii extracts as compared with controls. Conclusion More research is required to elucidate what G. amansii supplementation can do to improve growth performance, and its effect on methane production in ruminants.

Ambient ultraviolet radiation in the Arctic reduces root biomass and alters microbial community composition but has no effects on microbial biomass

DEFF Research Database (Denmark)

Rinnan, R.; Keinänen, M.M.; Kasurinen, A.

2005-01-01

We assessed the effects of ambient solar ultraviolet (UV) radiation on below-ground parameters in an arctic heath in north-eastern Greenland. We hypothesized that the current UV fluxes would reduce root biomass and mycorrhizal colonization and that these changes would lead to lower soil microbial...... biomass and altered microbial community composition. These hypotheses were tested on cored soil samples from a UV reduction experiment with three filter treatments (Mylar, 60% UV-B reduction; Lexan, up to 90% UV-B reduction+UV-A reduction; UV transparent Teflon, filter control) and an open control...... treatment in two study sites after 3 years' manipulation. Reduction of both UV-A and UV-B radiation caused over 30% increase in the root biomass of Vaccinium uliginosum, which was the dominant plant species. UV reduction had contrasting effects on ericoid mycorrhizal colonization of V. uliginosum roots...

Porosity and Organic Carbon Controls on Naturally Reduced Zone (NRZ) Formation Creating Microbial ';Hotspots' for Fe, S, and U Cycling in Subsurface Sediments

Science.gov (United States)

Jones, M. E.; Janot, N.; Bargar, J.; Fendorf, S. E.

2013-12-01

Previous studies have illustrated the importance of Naturally Reduced Zones (NRZs) within saturated sediments for the cycling of metals and redox sensitive contaminants. NRZs can provide a source of reducing equivalents such as reduced organic compounds or hydrogen to stimulate subsurface microbial communities. These NRZ's are typically characterized by low permeability and elevated concentrations of organic carbon and trace metals. However, both the formation of NRZs and their importance to the overall aquifer carbon remineralization is not fully understood. Within NRZs the hydrolysis of particulate organic carbon (POC) and subsequent fermentation of dissolved organic carbon (DOC) to form low molecular weight dissolved organic carbon (LMW-DOC) provides electron donors necessary for the respiration of Fe, S, and in the case of the Rifle aquifer, U. Rates of POC hydrolysis and subsequent fermentation have been poorly constrained and rates in excess and deficit to the rates of subsurface anaerobic respiratory processes have been suggested. In this study, we simulate the development of NRZ sediments in diffusion-limited aggregates to investigate the physical and chemical conditions required for NRZ formation. Effects of sediment porosity and POC loading on Fe, S, and U cycling on molecular and nanoscale are investigated with synchrotron-based Near Edge X-ray Absorption Fine Structure Spectroscopy (NEXAFS). Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR-MS) and Fourier Transform Infrared spectroscopy (FTIR) are used to characterize the transformations in POC and DOC. Sediment aggregates are inoculated with the natural microbial biota from the Rifle aquifer and population dynamics are monitored by 16S RNA analysis. Overall, establishment of low permeability NRZs within the aquifer stimulate microbial respiration beyond the diffusion-limited zones and can limit the transport of U through a contaminated aquifer. However, the long-term stability of

2009 MICROBIAL POPULATION BIOLOGY GORDON RESEARCH CONFERENCES JULY 19-24,2009

Energy Technology Data Exchange (ETDEWEB)

ANTHONY DEAN

2009-07-24

The 2009 Gordon Conference on Microbial Population Biology will cover a diverse range of cutting edge issues in the microbial sciences and beyond. Firmly founded in evolutionary biology and with a strongly integrative approach, past Conferences have covered a range of topics from the dynamics and genetics of adaptation to the evolution of mutation rate, community ecology, evolutionary genomics, altruism, and epidemiology. The 2009 Conference is no exception, and will include sessions on the evolution of infectious diseases, social evolution, the evolution of symbioses, experimental evolution, adaptive landscapes, community dynamics, and the evolution of protein structure and function. While genomic approaches continue to make inroads, broadening our knowledge and encompassing new questions, the conference will also emphasize the use of experimental approaches to test hypotheses decisively. As in the past, this Conference provides young scientists and graduate students opportunities to present their work in poster format and exchange ideas with leading investigators from a broad spectrum of disciplines. This meeting is never dull: some of the most significant and contentious issues in biology have been thrashed out here. The 2009 meeting will be no exception.

Reduced Nutrient Excretion and Environmental Microbial Load with the Addition of a Combination of Enzymes and Direct-Fed Microbials to the Diet of Broiler Chickens

Directory of Open Access Journals (Sweden)

MFFM Praes

2016-03-01

Full Text Available Abstract This study evaluated the effects of the dietary inclusion of an enzyme blend and a direct-fed microbials in broiler diets on litter production and quality. In total, 900 Cobb 500(r broiler chicks were distributed according to a completely randomized design into 4 treatments and 9 replicates of 25 birds each. Broilers were reared from 1 to 42 days of age. The treatments consisted of the following diets: NC: negative control; DFM: NC + 500 ppm of direct-fed microbials product (DFM, containing Bacillus subtilis and Bacillus licheniformis; ENZ: diet formulated with an enzyme blend (20 ppm phytase, 200 ppm protease and 200 ppm of xylanase; DFM+E: ENZ + DFM. Birds and litter were weighed at the start and end of the rearing period, for litter production and waste ratio (Rw determination. Litter samples were analyzed for dry matter (DM content, total and thermotolerant coliform counts, nutrient composition (nitrogen (N, phosphorous (P and potassium (K, and fiber fraction (neutral detergent fiber (NDF, acid detergent fiber (ADF and lignin. The dietary inclusion of the evaluated additivesdid not influence litter production or Rw; however, ADF (%, NDF (kg and kg/kg DM litter, and total and thermotolerant coliform counts were reduced, and N content increased in the litter. The diets containing enzymes (ENZ and DFM+E reduced litter P content. The addition of exogenous enzymes and their combination with a DFM based on Bacillus spp .Did not affect waste production, and reduced litter microbial load, and the contents of P and insoluble fiber in the litter.

Development of dielectric barrier discharge for reducing microbial contamination in pepper (Piper nigrum) and sesame (Sesamum indicum Linn.) powder

Science.gov (United States)

Promping, J.; Prakongsil, P.; Picha, R.; Traikool, T.

2017-09-01

This research is designed to determine the efficacy of DBD plasma to reduce the microbial contamination of pepper and sesame powder. The AC high voltage power supply was used with voltages of up to 20 kV and the frequency of 5.5 kHz was applied to the DBD. The gap of DBD electrodes was set at 5 mm. In raw initial samples, the total aerobic count of pepper (Piper nigrum) was found at quite a high level at 5.40 × 105 CFU/g. Coliform bacteria was also found in both the sesame (Sesamum indicum Linn.) powder and pepper (Piper nigrum) powder. Both kinds of samples were treated with plasma for 2, 4, 6 and 10 minutes. Results indicated that plasma treatment at 2-10 minutes reduced the total aerobic count of pepper allowed to achieve the acceptable microbial level for spices. The plasma treatment times in this experiment were also effective in reducing faecal coliform bacteria in both pepper and sesame powders (MPN/g <3) as indicated in the standard. Plasma from dielectric barrier charge can reduce Staphylococcus epidermidis in sesame powder which was artificially contaminated with 3.50 × 102 CFU/g resulting in 0.15-0.5 log cycle reductions of microbial load.

MICROBIAL DEGRADATION OF SEVEN AMIDES BY SUSPENDED BACTERIAL POPULATIONS

Science.gov (United States)

Microbial transformation rate constants were determined for seven amides in natural pond water. A second-order mathematical rate expression served as the model for describing the microbial transformation. Also investigated was the relationship between the infrared spectra and the...

Changes in microbial populations and enzyme activities during the bioremediation of oil-contaminated soil.

Science.gov (United States)

Lin, Xin; Li, Xiaojun; Sun, Tieheng; Li, Peijun; Zhou, Qixing; Sun, Lina; Hu, Xiaojun

2009-10-01

In the process of bioremediation in the soil contaminated by different oil concentrations, the changes in the microbial numbers (bacteria and fungi) and the enzyme (catalase (CAT), polyphenol oxidase (PPO) and lipase) activities were evaluated over a 2-year period. The results showed that the microbial numbers after 2-year bioremediation were one to ten times higher than those in the initial. The changes in the bacterial and the fungal populations were different during the bioremediation, and the highest microbial numbers for bacteria and fungi were 5.51 x 10(9) CFU g(-1) dry soil in treatment 3 (10,000 mg kg(-1)) in the initial and 5.54 x 10(5) CFU g(-1) dry soil in treatment 5 (50,000 mg kg(-1)) after the 2-year bioremediation period, respectively. The CAT and PPO activities in the contaminated soil decreased with increasing oil concentration, while the lipase activity increased. The activities of CAT and PPO improved after the bioremediation, but lipase activity was on the contrary. The CAT activity was more sensible to the oil than others, and could be alternative to monitor the bioremediation process.

Microbial O{sub 2} consumption in the Aespoe tunnel

Energy Technology Data Exchange (ETDEWEB)

Kotelnikova, S.; Pedersen, Karsten [Goeteborg Univ. (Sweden). Dept. of Cell and Molecular Biology, Microbiology

1998-04-01

day. Comparison of the total O{sub 2} reducing activities by gas chromatography and radiotracer tests showed that CH{sub 4} oxidation was responsible for 6.7% of the total O{sub 2} reduction in the groundwater, for 9.1 % of the total O{sub 2} reduction on stones and 57% of total O{sub 2} reduction in pond water. Most probable numbering showed that CH{sub 4} oxidation organisms constituted 0.15% and 35% of the total cell population in the groundwater and pond water, respectively. Methane oxidation is proposed as one of the dominating microbial mechanisms for O{sub 2} reduction. The contribution of hydrogen and organic carbon depending organisms remains to be studied. A kinetic model for microbial O{sub 2} has been developed, and it may be applied to performance assessment calculations of nuclear waste repositories.

Significant association between sulfate-reducing bacteria and uranium-reducing microbial communities as revealed by a combined massively parallel sequencing-indicator species approach.

Science.gov (United States)

Cardenas, Erick; Wu, Wei-Min; Leigh, Mary Beth; Carley, Jack; Carroll, Sue; Gentry, Terry; Luo, Jian; Watson, David; Gu, Baohua; Ginder-Vogel, Matthew; Kitanidis, Peter K; Jardine, Philip M; Zhou, Jizhong; Criddle, Craig S; Marsh, Terence L; Tiedje, James M

2010-10-01

Massively parallel sequencing has provided a more affordable and high-throughput method to study microbial communities, although it has mostly been used in an exploratory fashion. We combined pyrosequencing with a strict indicator species statistical analysis to test if bacteria specifically responded to ethanol injection that successfully promoted dissimilatory uranium(VI) reduction in the subsurface of a uranium contamination plume at the Oak Ridge Field Research Center in Tennessee. Remediation was achieved with a hydraulic flow control consisting of an inner loop, where ethanol was injected, and an outer loop for flow-field protection. This strategy reduced uranium concentrations in groundwater to levels below 0.126 μM and created geochemical gradients in electron donors from the inner-loop injection well toward the outer loop and downgradient flow path. Our analysis with 15 sediment samples from the entire test area found significant indicator species that showed a high degree of adaptation to the three different hydrochemical-created conditions. Castellaniella and Rhodanobacter characterized areas with low pH, heavy metals, and low bioactivity, while sulfate-, Fe(III)-, and U(VI)-reducing bacteria (Desulfovibrio, Anaeromyxobacter, and Desulfosporosinus) were indicators of areas where U(VI) reduction occurred. The abundance of these bacteria, as well as the Fe(III) and U(VI) reducer Geobacter, correlated with the hydraulic connectivity to the substrate injection site, suggesting that the selected populations were a direct response to electron donor addition by the groundwater flow path. A false-discovery-rate approach was implemented to discard false-positive results by chance, given the large amount of data compared.

Strategies for Reducing the Start-up Operation of Microbial Electrochemical Treatments of Urban Wastewater

Directory of Open Access Journals (Sweden)

Zulema Borjas

2015-12-01

Full Text Available Microbial electrochemical technologies (METs constitute the core of a number of emerging technologies with a high potential for treating urban wastewater due to a fascinating reaction mechanism—the electron transfer between bacteria and electrodes to transform metabolism into electrical current. In the current work, we focus on the model electroactive microorganism Geobacter sulfurreducens to explore both the design of new start-up procedures and electrochemical operations. Our chemostat-grown plug and play cells, were able to reduce the start-up period by 20-fold while enhancing chemical oxygen demand (COD removal by more than 6-fold during this period. Moreover, a filter-press based bioreactor was successfully tested for both acetate-supplemented synthetic wastewater and real urban wastewater. This proof-of-concept pre-pilot treatment included a microbial electrolysis cell (MEC followed in time by a microbial fuel cell (MFC to finally generate electrical current of ca. 20 A·m−2 with a power of 10 W·m−2 while removing 42 g COD day−1·m−2. The effective removal of acetate suggests a potential use of this modular technology for treating acetogenic wastewater where Geobacter sulfurreducens outcompetes other organisms.

Dynamics of microbial communities in an integrated ultrafiltration–reverse osmosis desalination pilot plant located at the Arabian Gulf

KAUST Repository

Hong, Pei-Ying

2015-08-27

This study demonstrated the use of high-throughput sequencing to assess the efficacy of an integrated ultrafiltration (UF)–reverse osmosis (RO) desalination pilot plant located at the Arabian Gulf, and to identify potential microbial-associated problems that may arise in this plant. When integrated into the desalination treatment system, the UF membranes were able to serve as a good pretreatment strategy to delay RO fouling by achieving up to 1.96-log removal of cells from the seawater. Consequently, the differential pressure of the RO membrane remained around 1 bar for the entire six-month study, suggesting no significant biofouling performance issue identified for this RO system. Examples of microbial populations effectively removed by the UF membranes from the feed waters included Nitrosoarchaeum limnia and phototrophic eukaryotes. Microbial-associated problems observed in this pilot plant included the presence of Pseudomonas spp. in coexistence with Desulfovibrio spp. These two bacterial populations can reduce sulfate and produce hydrogen sulfide, which would in turn cause corrosion problems or compromise membrane integrities. Chemical-enhanced backwashing (CEB) can be used as an effective strategy to minimize the associated microbial problems by removing bacterial populations including sulfate reducers from the UF membranes.

Dynamics of microbial communities in an integrated ultrafiltration–reverse osmosis desalination pilot plant located at the Arabian Gulf

KAUST Repository

Hong, Pei-Ying; Moosa, Nasir; Mink, Justine

2015-01-01

This study demonstrated the use of high-throughput sequencing to assess the efficacy of an integrated ultrafiltration (UF)–reverse osmosis (RO) desalination pilot plant located at the Arabian Gulf, and to identify potential microbial-associated problems that may arise in this plant. When integrated into the desalination treatment system, the UF membranes were able to serve as a good pretreatment strategy to delay RO fouling by achieving up to 1.96-log removal of cells from the seawater. Consequently, the differential pressure of the RO membrane remained around 1 bar for the entire six-month study, suggesting no significant biofouling performance issue identified for this RO system. Examples of microbial populations effectively removed by the UF membranes from the feed waters included Nitrosoarchaeum limnia and phototrophic eukaryotes. Microbial-associated problems observed in this pilot plant included the presence of Pseudomonas spp. in coexistence with Desulfovibrio spp. These two bacterial populations can reduce sulfate and produce hydrogen sulfide, which would in turn cause corrosion problems or compromise membrane integrities. Chemical-enhanced backwashing (CEB) can be used as an effective strategy to minimize the associated microbial problems by removing bacterial populations including sulfate reducers from the UF membranes.

Artificial soil microcosms: a tool for studying microbial autecology under controlled conditions.

Science.gov (United States)

Ellis, Richard J

2004-02-01

A novel artificial microcosm containing all the essential chemical components of soil, but with reduced heterogeneity and biological complexity, has been developed. Its utility for supporting realistic microbial populations was demonstrated and an example of how competing bacteria can be studied is illustrated.

Dynamics in population heterogeneity during batch and continuous fermentation of Saccharomyces cerevisiae

DEFF Research Database (Denmark)

Heins, Anna-Lena; Lencastre Fernandes, Rita; Lundin, L.

2012-01-01

Traditionally, microbial populations in optimization studies of fermentation processes have been considered homogeneous. However, research has shown that a typical microbial population in fermentation is heterogeneous. There are indications that this heterogeneity may be both beneficial...... (facilitates quick adaptation to new conditions) and harmful (reduces yields and productivities)[1,2]. Typically, gradients of e.g. dissolved oxygen, substrates, and pH are observed in industrial scale fermentation processes. Consequently, microbial cells circulating throughout a bioreactor experience rapid...... distribution during different growth stages. To further simulate which effect gradients have on population heterogeneity, glucose and ethanol perturbations during continuous cultivation were performed. Physiological changes were analyzed on single cell level by using flow cytometry followed by cell sorting...

Impact of an indigenous microbial enhanced oil recovery field trial on microbial community structure in a high pour-point oil reservoir

Energy Technology Data Exchange (ETDEWEB)

Zhang, Fan; Zhang, Xiao-Tao; Hou, Du-Jie [China Univ. of Geosciences, Beijing (China). The Key Lab. of Marine Reservoir Evolution and Hydrocarbon Accumulation Mechanism; She, Yue-Hui [Yangtze Univ., Jingzhou, Hubei (China). College of Chemistry and Environmental Engineering; Huazhong Univ. of Science and Technology, Wuhan (China). College of Life Science and Technology; Li, Hua-Min [Beijing Bioscience Research Center (China); Shu, Fu-Chang; Wang, Zheng-Liang [Yangtze Univ., Jingzhou, Hubei (China). College of Chemistry and Environmental Engineering; Yu, Long-Jiang [Huazhong Univ. of Science and Technology, Wuhan (China). College of Life Science and Technology

2012-08-15

Based on preliminary investigation of microbial populations in a high pour-point oil reservoir, an indigenous microbial enhanced oil recovery (MEOR) field trial was carried out. The purpose of the study is to reveal the impact of the indigenous MEOR process on microbial community structure in the oil reservoir using 16Sr DNA clone library technique. The detailed monitoring results showed significant response of microbial communities during the field trial and large discrepancies of stimulated microorganisms in the laboratory and in the natural oil reservoir. More specifically, after nutrients injection, the original dominant populations of Petrobacter and Alishewanella in the production wells almost disappeared. The expected desirable population of Pseudomonas aeruginosa, determined by enrichment experiments in laboratory, was stimulated successfully in two wells of the five monitored wells. Unexpectedly, another potential population of Pseudomonas pseudoalcaligenes which were not detected in the enrichment culture in laboratory was stimulated in the other three monitored production wells. In this study, monitoring of microbial community displayed a comprehensive alteration of microbial populations during the field trial to remedy the deficiency of culture-dependent monitoring methods. The results would help to develop and apply more MEOR processes. (orig.)

Impact of an indigenous microbial enhanced oil recovery field trial on microbial community structure in a high pour-point oil reservoir.

Science.gov (United States)

Zhang, Fan; She, Yue-Hui; Li, Hua-Min; Zhang, Xiao-Tao; Shu, Fu-Chang; Wang, Zheng-Liang; Yu, Long-Jiang; Hou, Du-Jie

2012-08-01

Based on preliminary investigation of microbial populations in a high pour-point oil reservoir, an indigenous microbial enhanced oil recovery (MEOR) field trial was carried out. The purpose of the study is to reveal the impact of the indigenous MEOR process on microbial community structure in the oil reservoir using 16Sr DNA clone library technique. The detailed monitoring results showed significant response of microbial communities during the field trial and large discrepancies of stimulated microorganisms in the laboratory and in the natural oil reservoir. More specifically, after nutrients injection, the original dominant populations of Petrobacter and Alishewanella in the production wells almost disappeared. The expected desirable population of Pseudomonas aeruginosa, determined by enrichment experiments in laboratory, was stimulated successfully in two wells of the five monitored wells. Unexpectedly, another potential population of Pseudomonas pseudoalcaligenes which were not detected in the enrichment culture in laboratory was stimulated in the other three monitored production wells. In this study, monitoring of microbial community displayed a comprehensive alteration of microbial populations during the field trial to remedy the deficiency of culture-dependent monitoring methods. The results would help to develop and apply more MEOR processes.

Biostimulation of Iron Reduction and Uranium Immobilization: Microbial and Mineralogical Controls

International Nuclear Information System (INIS)

Joel E. Kostka; Lainie Petrie; Nadia North; David L. Balkwill; Joseph W. Stucki; Lee Kerkhof

2004-01-01

The overall objective of our project is to understand the microbial and geochemical mechanisms controlling the reduction and immobilization of U(VI) during biostimulation in subsurface sediments of the Field Research Center (FRC) which are cocontaminated with uranium and nitrate. The focus will be on activity of microbial populations (metal- and nitrate-reducing bacteria) and iron minerals which are likely to make strong contributions to the fate of uranium during in situ bioremediation. The project will: (1) quantify the relationships between active members of the microbial communities, iron mineralogy, and nitrogen transformations in the field and in laboratory incubations under a variety of biostimulation conditions, (2) purify and physiologically characterize new model metal-reducing bacteria isolated from moderately acidophilic FRC subsurface sediments, and (3) elucidate the biotic and abiotic mechanisms by which FRC aluminosilicate clay minerals are reduced and dissolved under environmental conditions resembling those during biostimulation. Active microbial communities will be assessed using quantitative molecular techniques along with geochemical measurements to determine the different terminal-electron-accepting pathways. Iron minerals will be characterized using a suite of physical, spectroscopic, and wet chemical methods. Monitoring the activity and composition of the denitrifier community in parallel with denitrification intermediates during nitrate removal will provide a better understanding of the indirect effects of nitrate reduction on uranium speciation. Through quantification of the activity of specific microbial populations and an in-depth characterization of Fe minerals likely to catalyze U sorption/precipitation, we will provide important inputs for reaction-based biogeochemical models which will provide the basis for development of in situ U bioremediation strategies. In collaboration with Jack Istok and Lee Krumholz, we have begun to study the

Extreme CO2 disturbance and the resilience of soil microbial communities

Science.gov (United States)

McFarland, Jack W.; Waldrop, Mark P.; Haw, Monica

2013-01-01

Carbon capture and storage (CSS) technology has the potential to inadvertently release large quantities of CO2 through geologic substrates and into surrounding soils and ecosystems. Such a disturbance has the potential to not only alter the structure and function of plant and animal communities, but also soils, soil microbial communities, and the biogeochemical processes they mediate. At Mammoth Mountain, we assessed the soil microbial community response to CO2 disturbance (derived from volcanic ‘cold’ CO2) that resulted in localized tree kill; soil CO2 concentrations in our study area ranged from 0.6% to 60%. Our objectives were to examine how microbial communities and their activities are restructured by extreme CO2 disturbance, and assess the response of major microbial taxa to the reintroduction of limited plant communities following an extensive period (15–20 years) with no plants. We found that CO2-induced tree kill reduced soil carbon (C) availability along our sampling transect. In response, soil microbial biomass decreased by an order of magnitude from healthy forest to impacted areas. Soil microorganisms were most sensitive to changes in soil organic C, which explained almost 60% of the variation for microbial biomass C (MBC) along the CO2gradient. We employed phospholipid fatty acid analysis and quantitative PCR (qPCR) to determine compositional changes among microbial communities in affected areas and found substantial reductions in microbial biomass linked to the loss of soil fungi. In contrast, archaeal populations responded positively to the CO2 disturbance, presumably due to reduced competition of bacteria and fungi, and perhaps unique adaptations to energy stress. Enzyme activities important in the cycling of soil C, nitrogen (N), and phosphorus (P) declined with increasing CO2, though specific activities (per unit MBC) remained stable or increased suggesting functional redundancy among restructured communities. We conclude that both the

Analysis of rumen microbial populations in lactating dairy cattle fed diets varying in carbohydrate profiles and Saccharomyces cerevisiae fermentation product.

Science.gov (United States)

Mullins, C R; Mamedova, L K; Carpenter, A J; Ying, Y; Allen, M S; Yoon, I; Bradford, B J

2013-09-01

The rumen microbial ecosystem is a critical factor that links diets to bovine physiology and productivity; however, information about dietary effects on microbial populations has generally been limited to small numbers of samples and qualitative assessment. To assess whether consistent shifts in microbial populations occur in response to common dietary manipulations in dairy cattle, samples of rumen contents were collected from 2 studies for analysis by quantitative real-time PCR (qPCR). In one study, lactating Holstein cows (n=8) were fed diets in which a nonforage fiber source replaced an increasing proportion of forages and concentrates in a 4×4 Latin square design, and samples of ruminal digesta were collected at 9-h intervals over 3 d at the end of each period. In the second study, lactating Holstein cows (n=15) were fed diets with or without the inclusion of a Saccharomyces cerevisiae fermentation product (SCFP) in a crossover design. In this study, rumen liquid and solid samples were collected during total rumen evacuations before and after feeding in a 42-h period. In total, 146 samples of ruminal digesta were used for microbial DNA isolation and analysis by qPCR. Validated primer sets were used to quantify total bacterial and anaerobic fungal populations as well as 12 well-studied bacterial taxa. The relative abundance of the target populations was similar to those previously reported. No significant treatment effects were observed for any target population. A significant interaction of treatment and dry matter intake was observed, however, for the abundance of Eubacterium ruminantium. Increasing dry matter intake was associated with a quadratic decrease in E. ruminantium populations in control animals but with a quadratic increase in E.ruminantium populations in cows fed SCFP. Analysis of sample time effects revealed that Fibrobacter succinogenes and fungal populations were more abundant postfeeding, whereas Ruminococcus albus tended to be more abundant

In Situ Microbial Community Control of the Stability of Bio-reduced Uranium

International Nuclear Information System (INIS)

Baldwin, Brett R.; Peacock, Aaron D.; Resch, Charles T.; Arntzen, Evan; Smithgall, Amanda N.; Pfiffner, Susan; Gan, M.; McKinley, James P.; Long, Philip E.; White, David C.

2008-01-01

In aerobic aquifers typical of many Department of Energy (DOE) legacy waste sites, uranium is present in the oxidized U(VI) form which is more soluble and thus more mobile. Field experiments at the Old Rifle UMTRA site have demonstrated that biostimulation by electron donor addition (acetate) promotes biological U(VI) reduction (2). However, U(VI) reduction is reversible and oxidative dissolution of precipitated U(IV) after the cessation of electron donor addition remains a critical issue for the application of biostimulation as a treatment technology. Despite the potential for oxidative dissolution, field experiments at the Old Rifle site have shown that rapid reoxidation of bio-reduced uranium does not occur and U(VI) concentrations can remain at approximately 20% of background levels for more than one year. The extent of post-amendment U(VI) removal and the maintenance of bioreduced uranium may result from many factors including U(VI) sorption to iron-containing mineral phases, generation of H2S or FeS0.9, or the preferential sorption of U(VI) by microbial cells or biopolymers, but the processes controlling the reduction and in situ reoxidation rates are not known. To investigate the role of microbial community composition in the maintenance of bioreduced uranium, in-well sediment incubators (ISIs) were developed allowing field deployment of amended and native sediments during on-going experiments at the site. Field deployment of the ISIs allows expedient interrogation of microbial community response to field environmental perturbations and varying geochemical conditions.

In Situ Microbial Community Control of the Stability of Bio-reduced Uranium

Energy Technology Data Exchange (ETDEWEB)

Baldwin, Brett, R.; Peacock, Aaron, D.; Resch, Charles, T.; Arntzen, Evan; Smithgall, Amanda, N.; Pfiffner, Susan; Gan, M.; McKinley, James, P.; Long, Philip, E.; White, David, C.

2008-03-28

In aerobic aquifers typical of many Department of Energy (DOE) legacy waste sites, uranium is present in the oxidized U(VI) form which is more soluble and thus more mobile. Field experiments at the Old Rifle UMTRA site have demonstrated that biostimulation by electron donor addition (acetate) promotes biological U(VI) reduction (2). However, U(VI) reduction is reversible and oxidative dissolution of precipitated U(IV) after the cessation of electron donor addition remains a critical issue for the application of biostimulation as a treatment technology. Despite the potential for oxidative dissolution, field experiments at the Old Rifle site have shown that rapid reoxidation of bio-reduced uranium does not occur and U(VI) concentrations can remain at approximately 20% of background levels for more than one year. The extent of post-amendment U(VI) removal and the maintenance of bioreduced uranium may result from many factors including U(VI) sorption to iron-containing mineral phases, generation of H2S or FeS0.9, or the preferential sorption of U(VI) by microbial cells or biopolymers, but the processes controlling the reduction and in situ reoxidation rates are not known. To investigate the role of microbial community composition in the maintenance of bioreduced uranium, in-well sediment incubators (ISIs) were developed allowing field deployment of amended and native sediments during on-going experiments at the site. Field deployment of the ISIs allows expedient interrogation of microbial community response to field environmental perturbations and varying geochemical conditions.

Microbial biotechnology and circular economy in wastewater treatment

OpenAIRE

Nielsen, Per Halkjær

2017-01-01

Summary Microbial biotechnology is essential for the development of circular economy in wastewater treatment by integrating energy production and resource recovery into the production of clean water. A comprehensive knowledge about identity, physiology, ecology, and population dynamics of process‐critical microorganisms will improve process stability, reduce CO2 footprints, optimize recovery and bioenergy production, and help finding new approaches and solutions. Examples of research needs an...

Significant Association between Sulfate-Reducing Bacteria and Uranium-Reducing Microbial Communities as Revealed by a Combined Massively Parallel Sequencing-Indicator Species Approach▿ †

Science.gov (United States)

Cardenas, Erick; Wu, Wei-Min; Leigh, Mary Beth; Carley, Jack; Carroll, Sue; Gentry, Terry; Luo, Jian; Watson, David; Gu, Baohua; Ginder-Vogel, Matthew; Kitanidis, Peter K.; Jardine, Philip M.; Zhou, Jizhong; Criddle, Craig S.; Marsh, Terence L.; Tiedje, James M.

2010-01-01

Massively parallel sequencing has provided a more affordable and high-throughput method to study microbial communities, although it has mostly been used in an exploratory fashion. We combined pyrosequencing with a strict indicator species statistical analysis to test if bacteria specifically responded to ethanol injection that successfully promoted dissimilatory uranium(VI) reduction in the subsurface of a uranium contamination plume at the Oak Ridge Field Research Center in Tennessee. Remediation was achieved with a hydraulic flow control consisting of an inner loop, where ethanol was injected, and an outer loop for flow-field protection. This strategy reduced uranium concentrations in groundwater to levels below 0.126 μM and created geochemical gradients in electron donors from the inner-loop injection well toward the outer loop and downgradient flow path. Our analysis with 15 sediment samples from the entire test area found significant indicator species that showed a high degree of adaptation to the three different hydrochemical-created conditions. Castellaniella and Rhodanobacter characterized areas with low pH, heavy metals, and low bioactivity, while sulfate-, Fe(III)-, and U(VI)-reducing bacteria (Desulfovibrio, Anaeromyxobacter, and Desulfosporosinus) were indicators of areas where U(VI) reduction occurred. The abundance of these bacteria, as well as the Fe(III) and U(VI) reducer Geobacter, correlated with the hydraulic connectivity to the substrate injection site, suggesting that the selected populations were a direct response to electron donor addition by the groundwater flow path. A false-discovery-rate approach was implemented to discard false-positive results by chance, given the large amount of data compared. PMID:20729318

Treatment and electricity harvesting from sulfate/sulfide-containing wastewaters using microbial fuel cell with enriched sulfate-reducing mixed culture

International Nuclear Information System (INIS)

Lee, Duu-Jong; Lee, Chin-Yu; Chang, Jo-Shu

2012-01-01

Highlights: ► We started up microbial fuel cell (MFC) using enriched sulfate-reducing mixed culture. ► Sulfate-reducing bacteria and anode-respiring bacteria were enriched in anodic biofilms. ► The MFC effectively remove sulfate to elementary sulfur in the presence of lactate. ► The present device can treat sulfate laden wastewaters with electricity harvesting. - Abstract: Anaerobic treatment of sulfate-laden wastewaters can produce excess sulfide, which is corrosive to pipelines and is toxic to incorporated microorganisms. This work started up microbial fuel cell (MFC) using enriched sulfate-reducing mixed culture as anodic biofilms and applied the so yielded MFC for treating sulfate or sulfide-laden wastewaters. The sulfate-reducing bacteria in anodic biofilm effectively reduced sulfate to sulfide, which was then used by neighboring anode respiring bacteria (ARB) as electron donor for electricity production. The presence of organic carbons enhanced MFC performance since the biofilm ARB were mixotrophs that need organic carbon to grow. The present device introduces a route for treating sulfate laden wastewaters with electricity harvesting.

Treatment and electricity harvesting from sulfate/sulfide-containing wastewaters using microbial fuel cell with enriched sulfate-reducing mixed culture

Energy Technology Data Exchange (ETDEWEB)

Lee, Duu-Jong, E-mail: cedean@mail.ntust.edu.tw [Department of Chemical Engineering, National Taiwan University, Taipei, Taiwan (China); Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei, Taiwan (China); Lee, Chin-Yu [Department of Chemical Engineering, National Taiwan University, Taipei, Taiwan (China); Chang, Jo-Shu [Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan (China); Center for Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan (China); Research Center for Energy Technology and Strategy, National Cheng Kung University, Tainan, Taiwan (China)

2012-12-15

Highlights: Black-Right-Pointing-Pointer We started up microbial fuel cell (MFC) using enriched sulfate-reducing mixed culture. Black-Right-Pointing-Pointer Sulfate-reducing bacteria and anode-respiring bacteria were enriched in anodic biofilms. Black-Right-Pointing-Pointer The MFC effectively remove sulfate to elementary sulfur in the presence of lactate. Black-Right-Pointing-Pointer The present device can treat sulfate laden wastewaters with electricity harvesting. - Abstract: Anaerobic treatment of sulfate-laden wastewaters can produce excess sulfide, which is corrosive to pipelines and is toxic to incorporated microorganisms. This work started up microbial fuel cell (MFC) using enriched sulfate-reducing mixed culture as anodic biofilms and applied the so yielded MFC for treating sulfate or sulfide-laden wastewaters. The sulfate-reducing bacteria in anodic biofilm effectively reduced sulfate to sulfide, which was then used by neighboring anode respiring bacteria (ARB) as electron donor for electricity production. The presence of organic carbons enhanced MFC performance since the biofilm ARB were mixotrophs that need organic carbon to grow. The present device introduces a route for treating sulfate laden wastewaters with electricity harvesting.

Gradient simulation experiments for targeting population heterogeneity in continuous Saccharomyces cerevisiae fermentation

DEFF Research Database (Denmark)

Heins, Anna-Lena; Lencastre Fernandes, Rita; Lundin, L.

Traditionally, a microbial population has been considered homogeneous in optimization studies of fermentation processes. However, research has shown that a typical microbial population in a fermenter is heterogeneous. There are indications that such heterogeneity may be both beneficial (facilitates...... quick adaptation to new conditions) and harmful (reduces yields and productivities) (Bylund et al. (1998); Enfors et al. (2001)). Significant gradients of e.g. dissolved oxygen, substrates, and pH are typically observed in many industrial scale fermentation processes. Consequently, the microbial cells...... reporter strain demonstrated a highly dynamic behaviour with regards to subpopulation distribution during the different growth stages. To simulate which effect glucose gradients, often seen in large scale cultivations, have on population heterogeneity, glucose perturbations during continuous cultivation...

Effective photodynamic therapy against microbial populations in human deep tissue abscess aspirates.

Science.gov (United States)

Haidaris, Constantine G; Foster, Thomas H; Waldman, David L; Mathes, Edward J; McNamara, Joanne; Curran, Timothy

2013-10-01

The primary therapy for deep tissue abscesses is drainage accompanied by systemic antimicrobial treatment. However, the long antibiotic course required increases the probability of acquired resistance, and the high incidence of polymicrobial infections in abscesses complicates treatment choices. Photodynamic therapy (PDT) is effective against multiple classes of organisms, including those displaying drug resistance, and may serve as a useful adjunct to the standard of care by reduction of abscess microbial burden following drainage. Aspirates were obtained from 32 patients who underwent image-guided percutaneous drainage of the abscess cavity. The majority of the specimens (24/32) were abdominal, with the remainder from liver and lung. Conventional microbiological techniques and nucleotide sequence analysis of rRNA gene fragments were used to characterize microbial populations from abscess aspirates. We evaluated the sensitivity of microorganisms to methylene blue-sensitized PDT in vitro both within the context of an abscess aspirate and as individual isolates. Most isolates were bacterial, with the fungus Candida tropicalis also isolated from two specimens. We examined the sensitivity of these microorganisms to methylene blue-PDT. Complete elimination of culturable microorganisms was achieved in three different aspirates, and significant killing (P abscess treatment. © 2013 Wiley Periodicals, Inc.

Microbial activities and communities in oil sands tailings ponds

Energy Technology Data Exchange (ETDEWEB)

Gieg, Lisa; Ramos, Esther; Clothier, Lindsay; Bordenave, Sylvain; Lin, Shiping; Voordouw, Gerrit; Dong, Xiaoli; Sensen, Christoph [University of Calgary (Canada)

2011-07-01

This paper discusses how the microbial communities and their activity play a vital role in tailings ponds. The ponds contain microorganisms along with metals, hydrocarbon diluent, naphthenic acid and others. The ponds play an important role in mining operations because they store bitumen extraction waste and also allow water to be re-used in the bitumen extraction process. Pond management presents a few challenges that include, among others, gas emissions and the presence of toxic and corrosive acids. Microbial activities and communities help in managing these ponds. Microbial activity measurement in active and inactive ponds is described and analyzed and the results are presented. The conditions for reducing sulfate, nitrate and iron are also presented. From the results it can be concluded that naphthenic acids can potentially serve as substrates for anaerobic populations in tailings ponds.

Process optimization by decoupled control of key microbial populations: distribution of activity and abundance of polyphosphate-accumulating organisms and nitrifying populations in a full-scale IFAS-EBPR plant

DEFF Research Database (Denmark)

Onnis-Hayden, Annalisa; Majed, Nehreen; Schramm, Andreas

2011-01-01

This study investigated the abundance and distribution of key functional microbial populations and their activities in a full-scale integrated fixed film activated sludgeeenhanced biological phosphorus removal (IFAS-EBPR) process. Polyphosphate accumulating organisms (PAOs) including Accumulibacter...

Effect of Saccharomyces cerevisiae on alfalfa nutrient degradation characteristics and rumen microbial populations of steers fed diets with different concentrate-to-forage ratios.

Science.gov (United States)

Ding, Gengzhi; Chang, Ying; Zhao, Liping; Zhou, Zhenming; Ren, Liping; Meng, Qingxiang

2014-01-01

Live yeast (Saccharomyces cerevisiae) constitutes an effective additive for animal production; its probiotic effect may be related to the concentrate-to-forage ratio (CTFR). The objective of this study was to assess the effects of S. cerevisiae (SC) on fiber degradation and rumen microbial populations in steers fed diets with different levels of dietary concentrate. Ten Simmental × Local crossbred steers (450 ± 50 kg BW) were assigned to a control group or an SC group. Both groups were fed the same basal diet but the SC group received SC supplementation (8 × 10(9) cfu/h/d through the ruminal fistula) following a two-period crossover design. Each period consisted of four phases, each of which lasted 17 d: 10 d for dietary adaptation, 6 d for degradation study, and 1 d for rumen sample collection. From the 1(st) to the 4(th) phase, steers were fed in a stepwise fashion with increasing CTFRs, i.e., 30:70, 50:50, 70:30, and 90:10. The kinetics of dry matter and fiber degradation of alfalfa pellets were evaluated; the rumen microbial populations were detected using real-time PCR. The results revealed no significant (P > 0.05) interactions between dietary CTFR and SC for most parameters. Dietary CTFR had a significant effect (P trend for these parameters. SC supplementation significantly (P trend of rumen fungi and protozoa in SC group (P < 0.1); copies of total bacteria in SC group were significantly higher (P < 0.05). Additionally, percentage of Ruminobacter amylophilus was significantly lower (P < 0.05) but percentage of Selenomonas ruminantium was significantly higher (P < 0.05) in the SC group. In a word, dietary CTFR had a significant effect on degradation characteristics of forage and rumen microbial population. S. cerevisiae had positive effects on DM and NDF degradation rate or effective degradability of forage; S. cerevisiae increased rumen total bacteria, fungi, protozoa, and lactate-utilizing bacteria but reduced

Influence of diet and microbial activity in the digestive tract on digestibility, and nitrogen and energy metabolism in rats and pigs

DEFF Research Database (Denmark)

Eggum, B O; Thorbek, G; Beames, R M

1982-01-01

-55 kg. Measurements were made on the influence of microbial activity in the digestive tract on digestibility and nitrogen and energy metabolism. Dietary inclusion of the antibiotic Nebacitin was the method used to reduce the microbial population. 2. The microbial activity in the hind-gut (mumol ATP....../g air-dry contents) of antibiotic-treated rats was reduced to approximately one-tenth of that of untreated rats. 3. Live-weight gain was not significantly affected in either species by a reduction in the microbial activity, in spite of a reduction in dry matter digestibility in animals with reduced...... microflora. 4. For rats on low-crude-fibre diets, a reduction in microflora reduced digestibility of all nutrients and energy and metabolizability of digestible energy by approximately 5.4%. All differences were highly significant. On high-crude-fibre diets the decrease was approximately 5.9%. In pigs...

Metagenomics reveals pervasive bacterial populations and reduced community diversity across the Alaska tundra ecosystem

Directory of Open Access Journals (Sweden)

Eric Robert Johnston

2016-04-01

Full Text Available How soil microbial communities contrast with respect to taxonomic and functional composition within and between ecosystems remains an unresolved question that is central to predicting how global anthropogenic change will affect soil functioning and services. In particular, it remains unclear how small-scale observations of soil communities based on the typical volume sampled (1-2 grams are generalizable to ecosystem-scale responses and processes. This is especially relevant for remote, northern latitude soils, which are challenging to sample and are also thought to be more vulnerable to climate change compared to temperate soils. Here, we employed well-replicated shotgun metagenome and 16S rRNA gene amplicon sequencing to characterize community composition and metabolic potential in Alaskan tundra soils, combining our own datasets with those publically available from distant tundra and temperate grassland and agriculture habitats. We found that the abundance of many taxa and metabolic functions differed substantially between tundra soil metagenomes relative to those from temperate soils, and that a high degree of OTU-sharing exists between tundra locations. Tundra soils were an order of magnitude less complex than their temperate counterparts, allowing for near-complete coverage of microbial community richness (~92% breadth by sequencing, and the recovery of twenty-seven high-quality, almost complete (>80% completeness population bins. These population bins, collectively, made up to ~10% of the metagenomic datasets, and represented diverse taxonomic groups and metabolic lifestyles tuned toward sulfur cycling, hydrogen metabolism, methanotrophy, and organic matter oxidation. Several population bins, including members of Acidobacteria, Actinobacteria, and Proteobacteria, were also present in geographically distant (~100-530 km apart tundra habitats (full genome representation and up to 99.6% genome-derived average nucleotide identity. Collectively

Reducing methane emissions and the methanogen population in the rumen of Tibetan sheep by dietary supplementation with coconut oil.

Science.gov (United States)

Ding, Xuezhi; Long, Ruijun; Zhang, Qian; Huang, Xiaodan; Guo, Xusheng; Mi, Jiandui

2012-10-01

The objective was to evaluate the effect of dietary coconut oil on methane (CH(4)) emissions and the microbial community in Tibetan sheep. Twelve animals were assigned to receive either a control diet (oaten hay) or a mixture diet containing concentrate (maize meal), in which coconut oil was supplemented at 12 g/day or not for a period of 4 weeks. CH(4) emissions were measured by using the 'tunnel' technique, and microbial communities were examined using quantitative real-time PCR. Daily CH(4) production for the control and forage-to-concentrate ratio of 6:4 was 17.8 and 15.3 g, respectively. Coconut oil was particularly effective at reducing CH(4) emissions from Tibetan sheep. The inclusion of coconut oil for the control decreased CH(4) production (in grams per day) by 61.2%. In addition, there was a positive correlation between the number of methanogens and the daily CH(4) production (R = 0.95, P coconut oil supplemented at 12 g/day decreases the number of methanogens by 77% and a decreases in the ruminal fungal population (85-95%) and Fibrobacter succinogenes (50-98%) but an increase in Ruminococcus flavefaciens (25-70%). The results from our experiment suggest that adding coconut oil to the diet can reduce CH(4) emissions in Tibetan sheep and that these reductions persist for at least the 4-week feeding period.

Soil microbial population and nitrogen fixation in peanut under fly ash and sewage sludge

International Nuclear Information System (INIS)

Sarkar, S.; Khan, A.R.

2002-06-01

Surface disposal of municipal sludge and industrial wastes is an old practice that recently has been attracting concerns due to associated soil, air and water pollution. Wise utilization and recycling of these wastes in agricultural land brings in the much-needed organic and mineral matter to the soil. However, the assimilative capacity of the soil with respect to its physical, chemical and biological properties and the performance of crop grown, needs thorough investigation. Industrial wastes like fly ash (FA) from Thermal Power Plant and Sewage Sludge from municipal and city activities (untreated and treated CW) are some such important organic based waste resources having a potentiality for recycling in the agricultural land. The characteristics of these wastes with respect to their pH, plant nutrient and heavy metals content differs. Fly ash, being a burnt residue of coal, is rich in essential mineral elements and also has capacity in neutralizing soil acidity and supplying the nutrients to the plants (Molliner and Street, 1982). Sewage sludge application also has a significant influence on the physical, chemical and biological properties of soil. The soil biological systems can be altered by new energy input for the organisms, which is reflected by changes in the micro and macrobiological populations, in turn influencing the synthesis and decomposition of soil organic substances, nutrient availability, interactions with soil inorganic components and other exchanges with physical and chemical properties (Clapp et al, 1986). So far, much information is known regarding changes in physico-chemical properties of soil and performance of crop due to applications of such wastes. However, long term studies are needed to improve our understanding of the effects of land application of such wastes on soil biological systems (McGrath et al. 1995). It is known that native soil microbial population is responsible for decomposition of organic matter and recycling of nutrients

Microbial populations in an agronomically managed mollisol treated with simulated acid rain

International Nuclear Information System (INIS)

Miller, K.W.; Cole, M.A.; Banwart, W.L.

1991-01-01

A fertile well-buffered mollisol (Flanagan silt loam, fine montmorillonitic mesic Aquic Arguidoll) under cultivation with corn (Zea mays L.) and soybean [Glycine max (L.) Merr.] was subjected to simulated rain of pH 5.6, 4.2, and 3.0, while moisture-activated rain exclusion shelters provided protection from ambient rain. Soil was sampled to a depth of 3 cm on four dates throughout the 1985 growing season. The following microorganisms were enumerated by plate counts or most probable number: general heterotrophic bacteria, general soil fungi, free-living N-fixing bacteria, fluorescent pseudomonads, autotrophic ammonium-oxidizing, nitrite-oxidizing, and thio-sulfate-oxidizing bacteria. The ANOVA was used to determine the combined and individual effects of rain treatments, crop field, and sampling date. Crop field and sampling date affected microbial numbers more than rain treatments. Overall, rain treatment effects were limited to nitrite-oxidizing bacteria; lower numbers occurred in the corn field in subplots treated with rain of pH 4.2 and 3.0, and in the soybean field treated with rain of pH 3.0. The trend was strongest in June and July. In the corn field in subplots treated with rain of pH 3.0, numbers of thiosulfate-oxidizing bacteria were higher an numbers of general heterotrophic bacteria were lower; however, these trends were comparatively weak. Rain treatments caused essentially no decrease in soil pH, suggesting that acid rain constituents affect certain microbial populations without causing overt changes in pH. Because they appear to be unusually sensitive, nitrite-oxidizing bacteria could be used as experimental indicators of changes in soil microbial communities subjected to acid rain

Assessing the effects of iron enrichment across holobiont compartments reveals reduced microbial nitrogen fixation in the Red Sea coral Pocillopora verrucosa

KAUST Repository

Radecker, Nils; Pogoreutz, Claudia; Ziegler, Maren; Ashok, Ananya; Barreto, Marcelle M.; Chaidez, Veronica; Grupstra, Carsten G. B.; Ng, Yi Mei; Perna, Gabriela; Aranda, Manuel; Voolstra, Christian R.

2017-01-01

The productivity of coral reefs in oligotrophic tropical waters is sustained by an efficient uptake and recycling of nutrients. In reef-building corals, the engineers of these ecosystems, this nutrient recycling is facilitated by a constant exchange of nutrients between the animal host and endosymbiotic photosynthetic dinoflagellates (zooxanthellae), bacteria, and other microbes. Due to the complex interactions in this so-called coral holobiont, it has proven difficult to understand the environmental limitations of productivity in corals. Among others, the micronutrient iron has been proposed to limit primary productivity due to its essential role in photosynthesis and bacterial processes. Here, we tested the effect of iron enrichment on the physiology of the coral Pocillopora verrucosa from the central Red Sea during a 12-day experiment. Contrary to previous reports, we did not see an increase in zooxanthellae population density or gross photosynthesis. Conversely, respiration rates were significantly increased, and microbial nitrogen fixation was significantly decreased. Taken together, our data suggest that iron is not a limiting factor of primary productivity in Red Sea corals. Rather, increased metabolic demands in response to iron enrichment, as evidenced by increased respiration rates, may reduce carbon (i.e., energy) availability in the coral holobiont, resulting in reduced microbial nitrogen fixation. This decrease in nitrogen supply in turn may exacerbate the limitation of other nutrients, creating a negative feedback loop. Thereby, our results highlight that the effects of iron enrichment appear to be strongly dependent on local environmental conditions and ultimately may depend on the availability of other nutrients.

Assessing the effects of iron enrichment across holobiont compartments reveals reduced microbial nitrogen fixation in the Red Sea coral Pocillopora verrucosa

KAUST Repository

Radecker, Nils

2017-07-31

The productivity of coral reefs in oligotrophic tropical waters is sustained by an efficient uptake and recycling of nutrients. In reef-building corals, the engineers of these ecosystems, this nutrient recycling is facilitated by a constant exchange of nutrients between the animal host and endosymbiotic photosynthetic dinoflagellates (zooxanthellae), bacteria, and other microbes. Due to the complex interactions in this so-called coral holobiont, it has proven difficult to understand the environmental limitations of productivity in corals. Among others, the micronutrient iron has been proposed to limit primary productivity due to its essential role in photosynthesis and bacterial processes. Here, we tested the effect of iron enrichment on the physiology of the coral Pocillopora verrucosa from the central Red Sea during a 12-day experiment. Contrary to previous reports, we did not see an increase in zooxanthellae population density or gross photosynthesis. Conversely, respiration rates were significantly increased, and microbial nitrogen fixation was significantly decreased. Taken together, our data suggest that iron is not a limiting factor of primary productivity in Red Sea corals. Rather, increased metabolic demands in response to iron enrichment, as evidenced by increased respiration rates, may reduce carbon (i.e., energy) availability in the coral holobiont, resulting in reduced microbial nitrogen fixation. This decrease in nitrogen supply in turn may exacerbate the limitation of other nutrients, creating a negative feedback loop. Thereby, our results highlight that the effects of iron enrichment appear to be strongly dependent on local environmental conditions and ultimately may depend on the availability of other nutrients.

What is microbial community ecology?

Science.gov (United States)

Konopka, Allan

2009-11-01

The activities of complex communities of microbes affect biogeochemical transformations in natural, managed and engineered ecosystems. Meaningfully defining what constitutes a community of interacting microbial populations is not trivial, but is important for rigorous progress in the field. Important elements of research in microbial community ecology include the analysis of functional pathways for nutrient resource and energy flows, mechanistic understanding of interactions between microbial populations and their environment, and the emergent properties of the complex community. Some emergent properties mirror those analyzed by community ecologists who study plants and animals: biological diversity, functional redundancy and system stability. However, because microbes possess mechanisms for the horizontal transfer of genetic information, the metagenome may also be considered as a community property.

Performance and microbial community dynamics of a sulfate-reducing bioreactor treating coal generated acid mine drainage.

Science.gov (United States)

Burns, Andrew S; Pugh, Charles W; Segid, Yosief T; Behum, Paul T; Lefticariu, Liliana; Bender, Kelly S

2012-06-01

The effectiveness of a passive flow sulfate-reducing bioreactor processing acid mine drainage (AMD) generated from an abandoned coal mine in Southern Illinois was evaluated using geochemical and microbial community analysis 10 months post bioreactor construction. The results indicated that the treatment system was successful in both raising the pH of the AMD from 3.09 to 6.56 and in lowering the total iron level by 95.9%. While sulfate levels did decrease by 67.4%, the level post treatment (1153 mg/l) remained above recommended drinking water levels. Stimulation of biological sulfate reduction was indicated by a +2.60‰ increase in δ(34)S content of the remaining sulfate in the water post-treatment. Bacterial community analysis targeting 16S rRNA and dsrAB genes indicated that the pre-treated samples were dominated by bacteria related to iron-oxidizing Betaproteobacteria, while the post-treated water directly from the reactor outflow was dominated by sequences related to sulfur-oxidizing Epsilonproteobacteria and complex carbon degrading Bacteroidetes and Firmicutes phylums. Analysis of the post-treated water, prior to environmental release, revealed that the community shifted back to predominantly iron-oxidizing Betaproteobacteria. DsrA analysis implied limited diversity in the sulfate-reducing population present in both the bioreactor outflow and oxidation pond samples. These results support the use of passive flow bioreactors to lower the acidity, metal, and sulfate levels present in the AMD at the Tab-Simco mine, but suggest modifications of the system are necessary to both stimulate sulfate-reducing bacteria and inhibit sulfur-oxidizing bacteria.

Microbial removal of Fe(III) impurities from clay using dissimilatory iron reducers.

Science.gov (United States)

Lee, E Y; Cho, K S; Ryu, H W; Chang, Y K

1999-01-01

Fe(III) impurities, which detract refractoriness and whiteness from porcelain and pottery, could be biologically removed from low-quality clay by indigenous dissimilatory Fe(III)-reducing microorganisms. Insoluble Fe(III) in clay particles was leached out as soluble Fe(II), and the Fe(III) reduction reaction was coupled to the oxidation of sugars such as glucose, maltose and sucrose. A maximum removal of 44-45% was obtained when the relative amount of sugar was 5% (w/w; sugar/clay). By the microbial treatment, the whiteness of the clay was increased from 63.20 to 79.64, whereas the redness was clearly decreased from 13.47 to 3.55.

Advanced Microscopy of Microbial Cells

DEFF Research Database (Denmark)

Haagensen, Janus Anders Juul; Regenberg, Birgitte; Sternberg, Claus

2011-01-01

Growing awareness of heterogeneity in cells of microbial populations has emphasized the importance of advanced microscopy for visualization and understanding of the molecular mechanisms underlying cell-to-cell variation. In this review, we highlight some of the recent advances in confocal...... microscopy, super-resolution optical microscopy (STED, SIM, PALM) as well as atomic force microscopy and Raman spectroscopy. Using examples of bistability in microbial populations as well as biofilm development and differentiation in bacterial and yeast consortia, we demonstrate the importance of microscopy...

Effects of Flavonoid-rich Plant Extracts on Ruminal Methanogenesis, Microbial Populations and Fermentation Characteristics

Directory of Open Access Journals (Sweden)

Eun T. Kim

2015-04-01

Full Text Available The objective of this study was to evaluate the in vitro effects of flavonoid-rich plant extracts (PE on ruminal fermentation characteristics and methane emission by studying their effectiveness for methanogenesis in the rumen. A fistulated Holstein cow was used as a donor of rumen fluid. The PE (Punica granatum, Betula schmidtii, Ginkgo biloba, Camellia japonica, and Cudrania tricuspidata known to have high concentrations of flavonoid were added to an in vitro fermentation incubated with rumen fluid. Total gas production and microbial growth with all PE was higher than that of the control at 24 h incubation, while the methane emission was significantly lower (p<0.05 than that of the control. The decrease in methane accumulation relative to the control was 47.6%, 39.6%, 46.7%, 47.9%, and 48.8% for Punica, Betula, Ginkgo, Camellia, and Cudrania treatments, respectively. Ciliate populations were reduced by more than 60% in flavonoid-rich PE treatments. The Fibrobacter succinogenes diversity in all added flavonoid-rich PE was shown to increase, while the Ruminoccocus albus and R. flavefaciens populations in all PE decreased as compared with the control. In particular, the F. succinogenes community with the addition of Birch extract increased to a greater extent than that of others. In conclusion, the results of this study showed that flavonoid-rich PE decreased ruminal methane emission without adversely affecting ruminal fermentation characteristics in vitro in 24 h incubation time, suggesting that the flavonoid-rich PE have potential possibility as bio-active regulator for ruminants.

Microbial conversion technologies

Energy Technology Data Exchange (ETDEWEB)

Lau, P. [National Research Council of Canada, Ottawa, ON (Canada). Bioconversion and Sustainable Development

2006-07-01

Microbes are a biomass and an valuable resource. This presentation discussed microbial conversion technologies along with background information on microbial cells, their characteristics and microbial diversity. Untapped opportunities for microbial conversion were identified. Metagenomic and genome mining approaches were also discussed, as they can provide access to uncultivated or unculturable microorganisms in communal populations and are an unlimited resource for biocatalysts, novel genes and metabolites. Genome mining was seen as an economical approach. The presentation also emphasized that the development of microbial biorefineries would require significant insights into the relevant microorganisms and that biocatalysts were the ultimate in sustainability. In addition, the presentation discussed the natural fibres initiative for biochemicals and biomaterials. Anticipated outputs were identified and work in progress of a new enzyme-retting cocktail to provide diversity and/or consistency in fibre characteristics for various applications were also presented. It was concluded that it is necessary to leverage understanding of biological processes to produce bioproducts in a clean and sustainable manner. tabs., figs.

Effect of sucrose and potassium metabisulphite on the physicochemical and microbial analysis of apricot pulp

International Nuclear Information System (INIS)

Ayub, M.; Durrani, T.; Zeb, A.

2007-01-01

Effect of different concentration of sucrose and potassium metabisulphite on the apricot pulp was studied fortnightly for 90 days through physicochemical and microbial analysis. No significant change in total soluble solids (TSS) of apricot pulp was observed during the storage. Acidity and non-reducing sugar significantly (p<0.05) decreased, while pH and reducing sugars significantly (p<0.05) increased during the storage. Samples with added 20% sucrose and 0.2% potassium metabisulphite, packed in plastic and glass containers, had negligible microbial population maintained maximum nutrients and the best sensory characteristics during the storage. Storage duration and treatments had significant (p<0.05) effect on pH, acidity, non reducing sugars and total fungal count, while on TSS (total soluble solids) and reducing sugar, the effect of treatments was nonsignificant (p<0.05). (author)

Analysis of the structural diversity of the microbial community in a ...

African Journals Online (AJOL)

drinie

2002-10-04

Oct 4, 2002 ... Microbial populations in paper-mill water systems are usually enumerated using microbiological techniques such as plate counts and the most probable number technique. These conventional methods can only quantify a limited percentage of the microbial populations and the microbial numbers are, ...

VAMPS: a website for visualization and analysis of microbial population structures.

Science.gov (United States)

Huse, Susan M; Mark Welch, David B; Voorhis, Andy; Shipunova, Anna; Morrison, Hilary G; Eren, A Murat; Sogin, Mitchell L

2014-02-05

The advent of next-generation DNA sequencing platforms has revolutionized molecular microbial ecology by making the detailed analysis of complex communities over time and space a tractable research pursuit for small research groups. However, the ability to generate 10⁵-10⁸ reads with relative ease brings with it many downstream complications. Beyond the computational resources and skills needed to process and analyze data, it is difficult to compare datasets in an intuitive and interactive manner that leads to hypothesis generation and testing. We developed the free web service VAMPS (Visualization and Analysis of Microbial Population Structures, http://vamps.mbl.edu) to address these challenges and to facilitate research by individuals or collaborating groups working on projects with large-scale sequencing data. Users can upload marker gene sequences and associated metadata; reads are quality filtered and assigned to both taxonomic structures and to taxonomy-independent clusters. A simple point-and-click interface allows users to select for analysis any combination of their own or their collaborators' private data and data from public projects, filter these by their choice of taxonomic and/or abundance criteria, and then explore these data using a wide range of analytic methods and visualizations. Each result is extensively hyperlinked to other analysis and visualization options, promoting data exploration and leading to a greater understanding of data relationships. VAMPS allows researchers using marker gene sequence data to analyze the diversity of microbial communities and the relationships between communities, to explore these analyses in an intuitive visual context, and to download data, results, and images for publication. VAMPS obviates the need for individual research groups to make the considerable investment in computational infrastructure and bioinformatic support otherwise necessary to process, analyze, and interpret massive amounts of next

In situ exposure to low herbicide concentrations affects microbial population composition and catabolic gene frequency in an aerobic shallow aquifer

DEFF Research Database (Denmark)

de Lipthay, J.R.; Tuxen, Nina; Johnsen, Kaare

2003-01-01

and were analyzed for the presence of general microbial populations, Pseudomonas bacteria, and specific phenoxy acid degraders. Both culture-dependent and culture-independent methods were applied. The abundance of microbial phenoxy acid degraders (10(0) to 10(4) g(-1) sediment) was determined by most...... measured by either PCR or plating on selective agar media was higher in sediments subjected to high levels of phenoxy acid. Furthermore, high numbers of CFU compared to direct counting of 4',6-diamidino-2-phenylindole-stained cells in the microscope suggested an increased culturability of the indigenous...

Microbial Biotechnology 2020; microbiology of fossil fuel resources.

Science.gov (United States)

Head, Ian M; Gray, Neil D

2016-09-01

This roadmap examines the future of microbiology research and technology in fossil fuel energy recovery. Globally, the human population will be reliant on fossil fuels for energy and chemical feedstocks for at least the medium term. Microbiology is already important in many areas relevant to both upstream and downstream activities in the oil industry. However, the discipline has struggled for recognition in a world dominated by geophysicists and engineers despite widely known but still poorly understood microbially mediated processes e.g. reservoir biodegradation, reservoir souring and control, microbial enhanced oil recovery. The role of microbiology is even less understood in developing industries such as shale gas recovery by fracking or carbon capture by geological storage. In the future, innovative biotechnologies may offer new routes to reduced emissions pathways especially when applied to the vast unconventional heavy oil resources formed, paradoxically, from microbial activities in the geological past. However, despite this potential, recent low oil prices may make industry funding hard to come by and recruitment of microbiologists by the oil and gas industry may not be a high priority. With regards to public funded research and the imperative for cheap secure energy for economic growth in a growing world population, there are signs of inherent conflicts between policies aimed at a low carbon future using renewable technologies and policies which encourage technologies which maximize recovery from our conventional and unconventional fossil fuel assets. © 2016 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Microbial population changes during bioremediation of an experimental oil spill

International Nuclear Information System (INIS)

MacNaughton, S.J.; Stephen, J.R.; Chang, Y.J.; Davis, G.A.; White, D.C.; Oak Ridge National Lab., TN

1999-01-01

Three crude oil bioremediation techniques were applied in a randomized block field experiment simulating a coastal oil spill. Four treatments (no oil control, oil alone, oil plus nutrients, and oil plus nutrients plus an indigenous inoculum) were applied. In situ microbial community structures were monitored by phospholipid fatty acid (PLFA) analysis and 16S rDNA PCR-denaturing gradient gel electrophoresis (DGGE) to (i) identify the bacterial community members responsible for the decontamination of the site and (ii) define an end point for the removal of the hydrocarbon substrate. The results of PLFA analysis demonstrated a community shift in all plots from primarily eukaryotic biomass to gram-negative bacterial biomass with time. PLFA profiles from the oiled plots suggested increased gram-negative biomass and adaptation to metabolic stress compared to unoiled controls. DGGE analysis of untreated control plots revealed a simple, dynamic dominant population structure throughout the experiment. This banding pattern disappeared in all oiled plots, indicating that the structure and diversity of the dominant bacterial community changed substantially. No consistent differences were detected between nutrient-amended and indigenous inoculum-treated plots, but both differed from the oil-only plots. Prominent bands were excised for sequence analysis and indicated that oil treatment encouraged the growth of gram-negative microorganisms within the α-proteobacteria and Flexibacter-Cytophaga-Bacteroides phylum. α-Proteobacteria were never detected in unoiled controls. PLFA analysis indicated that by week 14 the microbial community structures of the oiled plots were becoming similar to those of the unoiled controls from the same time point, but DGGE analysis suggested that major differences in the bacterial communities remained

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

Science.gov (United States)

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.

Reducing nitrogen crossover in microbial reverse-electrodialysis cells by using adjacent anion exchange membranes and anion exchange resin

KAUST Repository

Wallack, Maxwell J.; Geise, Geoffrey M.; Hatzell, Marta C.; Hickner, Michael A.; Logan, Bruce E.

2015-01-01

Microbial reverse electrodialysis cells (MRECs) combine power generation from salinity gradient energy using reverse electrodialysis (RED), with power generation from organic matter using a microbial fuel cell. Waste heat can be used to distill ammonium bicarbonate into high (HC) and low salt concentration (LC) solutions for use in the RED stack, but nitrogen crossover into the anode chamber must be minimized to avoid ammonia loses, and foster a healthy microbial community. To reduce nitrogen crossover, an additional low concentration (LC) chamber was inserted before the anode using an additional anion exchange membrane (AEM) next to another AEM, and filled with different amounts of anion or cation ion exchange resins. Addition of the extra AEM increased the ohmic resistance of the test RED stack from 103 Ω cm2 (1 AEM) to 295 Ω cm2 (2 AEMs). However, the use of the anion exchange resin decreased the solution resistance of the LC chamber by 74% (637 Ω cm2, no resin; 166 Ω cm2 with resin). Nitrogen crossover into the anode chamber was reduced by up to 97% using 50% of the chamber filled with an anion exchange resin compared to the control (no additional chamber). The added resistance contributed by the use of the additional LC chamber could be compensated for by using additional LC and HC membrane pairs in the RED stack.

Fermentation couples Chloroflexi and sulfate-reducing bacteria to Cyanobacteria in hypersaline microbial mats

Directory of Open Access Journals (Sweden)

Jackson Z Lee

2014-02-01

Full Text Available Past studies of hydrogen cycling in hypersaline microbial mats have shown an active nighttime cycle, with production largely from Cyanobacteria and consumption from sulfate-reducing bacteria (SRB. However, the mechanisms and magnitude of hydrogen cycling have not been extensively studied. Two mats types near Guerrero Negro, Mexico -- permanently submerged Microcoleus microbial mats (GN-S, and intertidal Lyngbya microbial mats (GN-I -- were used in microcosm diel manipulation experiments with 3-(3,4-dichlorophenyl-1,1-dimethylurea (DCMU, molybdate, ammonium addition, and physical disruption to understand the processes responsible for hydrogen cycling between mat microbes. Across microcosms, H2 production occurred under dark anoxic conditions with simultaneous production of a suite of organic acids. H2 production was not significantly affected by inhibition of nitrogen fixation, but rather appears to result from constitutive fermentation of photosynthetic storage products by oxygenic phototrophs. Comparison to accumulated glycogen and to CO2 flux indicated that, in the GN-I mat, fermentation released almost all of the carbon fixed via photosynthesis during the preceding day, primarily as organic acids. Across mats, although oxygenic and anoxygenic phototrophs were detected, cyanobacterial [NiFe]-hydrogenase transcripts predominated. Molybdate inhibition experiments indicated that SRBs from a wide distribution of dsrA phylotypes were responsible for H2 consumption. Incubation with 13C-acetate and nanoSIMS (secondary ion mass-spectrometry indicated higher uptake in both Chloroflexi and SRBs relative to other filamentous bacteria. These manipulations and diel incubations confirm that Cyanobacteria were the main fermenters in Guerrero Negro mats and that the net flux of nighttime fermentation byproducts (not only hydrogen was largely regulated by the interplay between Cyanobacteria, SRBs, and Chloroflexi.

Patterns in wetland microbial community composition and functional gene repertoire associated with methane emissions.

Science.gov (United States)

He, Shaomei; Malfatti, Stephanie A; McFarland, Jack W; Anderson, Frank E; Pati, Amrita; Huntemann, Marcel; Tremblay, Julien; Glavina del Rio, Tijana; Waldrop, Mark P; Windham-Myers, Lisamarie; Tringe, Susannah G

2015-05-19

Wetland restoration on peat islands previously drained for agriculture has potential to reverse land subsidence and sequester atmospheric carbon dioxide as peat accretes. However, the emission of methane could potentially offset the greenhouse gas benefits of captured carbon. As microbial communities play a key role in governing wetland greenhouse gas fluxes, we are interested in how microbial community composition and functions are associated with wetland hydrology, biogeochemistry, and methane emission, which is critical to modeling the microbial component in wetland methane fluxes and to managing restoration projects for maximal carbon sequestration. Here, we couple sequence-based methods with biogeochemical and greenhouse gas measurements to interrogate microbial communities from a pilot-scale restored wetland in the Sacramento-San Joaquin Delta of California, revealing considerable spatial heterogeneity even within this relatively small site. A number of microbial populations and functions showed strong correlations with electron acceptor availability and methane production; some also showed a preference for association with plant roots. Marker gene phylogenies revealed a diversity of major methane-producing and -consuming populations and suggested novel diversity within methanotrophs. Methanogenic archaea were observed in all samples, as were nitrate-, sulfate-, and metal-reducing bacteria, indicating that no single terminal electron acceptor was preferred despite differences in energetic favorability and suggesting spatial microheterogeneity and microniches. Notably, methanogens were negatively correlated with nitrate-, sulfate-, and metal-reducing bacteria and were most abundant at sampling sites with high peat accretion and low electron acceptor availability, where methane production was highest. Wetlands are the largest nonanthropogenic source of atmospheric methane but also a key global carbon reservoir. Characterizing belowground microbial communities

Use of and microbial resistance to antibiotics in China: a path to reducing antimicrobial resistance.

Science.gov (United States)

Cui, Dan; Liu, Xinliang; Hawkey, Peter; Li, Hao; Wang, Quan; Mao, Zongfu; Sun, Jing

2017-12-01

We analyzed China's current use of and microbial resistance to antibiotics, and possible means of reducing antimicrobial resistance. Interventions like executive orders within clinical settings and educational approach with vertical approaches rather than an integrated strategy to curb the use of antimicrobials remain limited. An underlying problem is the system of incentives that has resulted in the intensification of inappropriate use by health professionals and patients. There is an urgent need to explore the relationship between financial and non-financial incentives for providers and patients, to eliminate inappropriate incentives. China's national health reforms have created an opportunity to contain inappropriate use of antibiotics through more comprehensive and integrated strategies. Containment of microbial resistance may be achieved by strengthening surveillance at national, regional and hospital levels; eliminating detrimental incentives within the health system; and changing prescribing behaviors to a wider health systems approach, to achieve long-term, equitable and sustainable results and coordinate stakeholders' actions through transparent sharing of information.

Effect of pesticides on soil microbial community.

Science.gov (United States)

Lo, Chi-Chu

2010-07-01

According to guidelines for the approval of pesticides, information about effects of pesticides on soil microorganisms and soil fertility are required, but the relationships of different structures of pesticides on the growth of various groups of soil microorganisms are not easily predicted. Some pesticides stimulate the growth of microorganisms, but other pesticides have depressive effects or no effects on microorganisms. For examples, carbofuran stimulated the population of Azospirillum and other anaerobic nitrogen fixers in flooded and non-flooded soil, but butachlor reduced the population of Azospirillum and aerobic nitrogen fixers in non-flooded soil. Diuron and chlorotoluron showed no difference between treated and nontreated soil, and linuron showed a strong difference. Phosphorus(P)-contains herbicides glyphosate and insecticide methamidophos stimulated soil microbial growth, but other P-containing insecticide fenamiphos was detrimental to nitrification bacteria. Therefore, the following review presents some data of research carried out during the last 20 years. The effects of twenty-one pesticides on the soil microorganisms associated with nutrient and cycling processes are presented in section 1, and the applications of denaturing gradient gel electrophoresis (DGGE) for studying microbial diversity are discussed in section 2.

Modeling of Nonlinear Dynamics and Synchronized Oscillations of Microbial Populations, Carbon and Oxygen Concentrations, Induced by Root Exudation in the Rhizosphere

Science.gov (United States)

Molz, F. J.; Faybishenko, B.; Jenkins, E. W.

2012-12-01

Mass and energy fluxes within the soil-plant-atmosphere continuum are highly coupled and inherently nonlinear. The main focus of this presentation is to demonstrate the results of numerical modeling of a system of 4 coupled, nonlinear ordinary differential equations (ODEs), which are used to describe the long-term, rhizosphere processes of soil microbial dynamics, including the competition between nitrogen-fixing bacteria and those unable to fix nitrogen, along with substrate concentration (nutrient supply) and oxygen concentration. Modeling results demonstrate the synchronized patterns of temporal oscillations of competing microbial populations, which are affected by carbon and oxygen concentrations. The temporal dynamics and amplitude of the root exudation process serve as a driving force for microbial and geochemical phenomena, and lead to the development of the Gompetzian dynamics, synchronized oscillations, and phase-space attractors of microbial populations and carbon and oxygen concentrations. The nonlinear dynamic analysis of time series concentrations from the solution of the ODEs was used to identify several types of phase-space attractors, which appear to be dependent on the parameters of the exudation function and Monod kinetic parameters. This phase space analysis was conducted by means of assessing the global and local embedding dimensions, correlation time, capacity and correlation dimensions, and Lyapunov exponents of the calculated model variables defining the phase space. Such results can be used for planning experimental and theoretical studies of biogeochemical processes in the fields of plant nutrition, phyto- and bio-remediation, and other ecological areas.

In situ examination of microbial populations in a model drinking water distribution system

DEFF Research Database (Denmark)

Martiny, Adam Camillo; Nielsen, Alex Toftgaard; Arvin, Erik

2002-01-01

A flow cell set-up was used as a model drinking water distribution system to analyze the in situ microbial population. Biofilm growth was followed by transmission light microscopy for 81 days and showed a biofilm consisting of microcolonies separated by a monolayer of cells. Protozoans (ciliates...... of a mixed population of α- and β-Proteobacteria. 65 strains from the inlet water and 20 from the biofilm were isolated on R2A agar plates and sorted into groups with amplified rDNA restriction analysis. The 16S rDNA gene was sequenced for representatives of the abundant groups. A phylogenetic analysis...... revealed that the majority of the isolated strains from the bulk water and biofilm were affiliated to the family of Comamonadaceae in the β-lineage of Proteobacteria. The majority of the strains from the α-lineage were affiliated to the family of Sphingomonadaceae. We were unable to detect any strains from...

Microbial community of high arsenic groundwater in agricultural irrigation area of Hetao Plain, Inner Mongolia

Directory of Open Access Journals (Sweden)

Yanhong Wang

2016-12-01

Full Text Available Microbial communities can play important role in arsenic release in groundwater aquifers. To investigate the microbial communities in high arsenic groundwater aquifers in agricultural irrigation area, 17 groundwater samples with different arsenic concentrations were collected along the agricultural drainage channels of Hangjinhouqi County, Inner Mongolia and examined by illumina Miseq sequencing approach targeting the V4 region of the 16S rRNA gene. Both principal component analysis and hierarchical clustering results indicated that these samples were divided into two groups (high and low arsenic groups according to the variation of geochemical characteristics. Arsenic concentrations showed strongly positive correlations with NH4+ and TOC. Sequencing results revealed that a total of 329-2823 OTUs were observed at the 97% OTU level. Microbial richness and diversity of high arsenic groundwater samples along the drainage channels were lower than those of low arsenic groundwater samples but higher than those of high arsenic groundwaters from strongly reducing areas. The microbial community structure in groundwater along the drainage channels was different from those in strongly reducing As-rich aquifers of Hetao Plain and other high As groundwater aquifers including Bangladesh, West Bengal and Vietnam. Acinetobacter and Pseudomonas dominated with high percentages in both high and low arsenic groundwaters. Alishewanella, Psychrobacter, Methylotenera and Crenothrix showed relatively high abundances in high arsenic groundwater, while Rheinheimera and the unidentified OP3 were predominant populations in low arsenic groundwater. Archaeal populations displayed a low occurrence and mainly dominated by methanogens such as Methanocorpusculum and Methanospirillum. Microbial community compositions were different between high and low arsenic groundwater samples based on the results of principal coordinate analysis and co-inertia analysis. Other geochemical

Microbial Community Response to Carbon Substrate Amendment in Mercury Impacted Sediments: Implications on Microbial Methylation of Mercury.

Science.gov (United States)

Elias, D. A.; Somenahally, A. C.; Moberly, J. G.; Hurt, R. A., Jr.; Brown, S. D.; Podar, M.; Palumbo, A. V.; Gilmour, C. C.

2015-12-01

Methylmercury (MeHg) is a neurotoxic and bio-accumulative product of the microbial methylation of inorganic mercury (Hg(II)). Methylating organisms are now known to exist in almost all anaerobic niches including fermentation, Fe(III)- and sulfate- reduction as well as methanogenesis. The study objective was to determine the effect of different carbon sources on the microbial community and methylating populations in particular along a Hg contaminated creek. Sediment cores from upstream and downstream at the Hg contaminated East Fork Poplar Creek (EFPC), Oak Ridge TN, and a background site were sectioned by depth, and Hg-methylation potential (HgMP) assays were performed using stable isotope spikes. Sediments from the lowest depth possessed the highest in-situ activity. Replicate samples were amended with different carbon substrates (cellulose, acetate, propionate, lactate, ethanol and methanol), spiked with stable isotopes for HgMP assays and incubated for 24hrs. Sequencing of the 16S rRNA gene was performed to determine alterations in Bacterial and Archaeal population dynamics. Additionally, bioinformatics and our new qualitative and quantitative hgcAB primers were utilized to determine microbial community structure alterations and correlate organism and gene abundance with altered MeHg generation. HgMP was significantly reduced in cellulose amended sediments while acetate and propionate slightly decreased HgMP in both sites. Methanol, ethanol and lactate increased the HgMP in EFPC downstream while cellulose amendment significantly decreased the Proteobacteria, and the Firmicutes increased but none are currently known to produce MeHg. Geobacter bemidjiensis in particular significantly decreased in cellulose amended sediments in all three sites from being predominant in-situ. This suggests that in EFPC downstream and background sites, the prevalent Hg-methyaltors might be Deltaprotebacteria, since upstream, cellulose amendment did not reduce HgMP even though

Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments

Directory of Open Access Journals (Sweden)

Elizabeth Trembath-Reichert

2016-04-01

Full Text Available Methane seep systems along continental margins host diverse and dynamic microbial assemblages, sustained in large part through the microbially mediated process of sulfate-coupled Anaerobic Oxidation of Methane (AOM. This methanotrophic metabolism has been linked to consortia of anaerobic methane-oxidizing archaea (ANME and sulfate-reducing bacteria (SRB. These two groups are the focus of numerous studies; however, less is known about the wide diversity of other seep associated microorganisms. We selected a hierarchical set of FISH probes targeting a range of Deltaproteobacteria diversity. Using the Magneto-FISH enrichment technique, we then magnetically captured CARD-FISH hybridized cells and their physically associated microorganisms from a methane seep sediment incubation. DNA from nested Magneto-FISH experiments was analyzed using Illumina tag 16S rRNA gene sequencing (iTag. Enrichment success and potential bias with iTag was evaluated in the context of full-length 16S rRNA gene clone libraries, CARD-FISH, functional gene clone libraries, and iTag mock communities. We determined commonly used Earth Microbiome Project (EMP iTAG primers introduced bias in some common methane seep microbial taxa that reduced the ability to directly compare OTU relative abundances within a sample, but comparison of relative abundances between samples (in nearly all cases and whole community-based analyses were robust. The iTag dataset was subjected to statistical co-occurrence measures of the most abundant OTUs to determine which taxa in this dataset were most correlated across all samples. Many non-canonical microbial partnerships were statistically significant in our co-occurrence network analysis, most of which were not recovered with conventional clone library sequencing, demonstrating the utility of combining Magneto-FISH and iTag sequencing methods for hypothesis generation of associations within complex microbial communities. Network analysis pointed to

Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments.

Science.gov (United States)

Trembath-Reichert, Elizabeth; Case, David H; Orphan, Victoria J

2016-01-01

Methane seep systems along continental margins host diverse and dynamic microbial assemblages, sustained in large part through the microbially mediated process of sulfate-coupled Anaerobic Oxidation of Methane (AOM). This methanotrophic metabolism has been linked to consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). These two groups are the focus of numerous studies; however, less is known about the wide diversity of other seep associated microorganisms. We selected a hierarchical set of FISH probes targeting a range of Deltaproteobacteria diversity. Using the Magneto-FISH enrichment technique, we then magnetically captured CARD-FISH hybridized cells and their physically associated microorganisms from a methane seep sediment incubation. DNA from nested Magneto-FISH experiments was analyzed using Illumina tag 16S rRNA gene sequencing (iTag). Enrichment success and potential bias with iTag was evaluated in the context of full-length 16S rRNA gene clone libraries, CARD-FISH, functional gene clone libraries, and iTag mock communities. We determined commonly used Earth Microbiome Project (EMP) iTAG primers introduced bias in some common methane seep microbial taxa that reduced the ability to directly compare OTU relative abundances within a sample, but comparison of relative abundances between samples (in nearly all cases) and whole community-based analyses were robust. The iTag dataset was subjected to statistical co-occurrence measures of the most abundant OTUs to determine which taxa in this dataset were most correlated across all samples. Many non-canonical microbial partnerships were statistically significant in our co-occurrence network analysis, most of which were not recovered with conventional clone library sequencing, demonstrating the utility of combining Magneto-FISH and iTag sequencing methods for hypothesis generation of associations within complex microbial communities. Network analysis pointed to many co

Invited review: Essential oils as modifiers of rumen microbial fermentation.

Science.gov (United States)

Calsamiglia, S; Busquet, M; Cardozo, P W; Castillejos, L; Ferret, A

2007-06-01

Microorganisms in the rumen degrade nutrients to produce volatile fatty acids and synthesize microbial protein as an energy and protein supply for the ruminant, respectively. However, this fermentation process has energy (losses of methane) and protein (losses of ammonia N) inefficiencies that may limit production performance and contribute to the release of pollutants to the environment. Antibiotic ionophores have been very successful in reducing these energy and protein losses in the rumen, but the use of antibiotics in animal feeds is facing reduced social acceptance, and their use has been banned in the European Union since January 2006. For this reason, scientists have become interested in evaluating other alternatives to control specific microbial populations to modulate rumen fermentation. Essential oils can interact with microbial cell membranes and inhibit the growth of some gram-positive and gram-negative bacteria. As a result of such inhibition, the addition of some plant extracts to the rumen results in an inhibition of deamination and methanogenesis, resulting in lower ammonia N, methane, and acetate, and in higher propionate and butyrate concentrations. Results have indicated that garlic oil, cinnamaldehyde (the main active component of cinnamon oil), eugenol (the main active component of the clove bud), capsaicin (the active component of hot peppers), and anise oil, among others, may increase propionate production, reduce acetate or methane production, and modify proteolysis, peptidolysis, or deamination in the rumen. However, the effects of some of these essential oils are pH and diet dependent, and their use may be beneficial only under specific conditions and production systems. For example, capsaicin appears to have small effects in high-forage diets, whereas the changes observed in high-concentrate diets (increases in dry matter intake and total VFA, and reduction in the acetateto-propionate ratio and ammonia N concentration) may be beneficial

Electricity Recovery from Municipal Sewage Wastewater Using a Hydrogel Complex Composed of Microbially Reduced Graphene Oxide and Sludge

Directory of Open Access Journals (Sweden)

Naoko Yoshida

2016-08-01

Full Text Available Graphene oxide (GO has recently been shown to be an excellent anode substrate for exoelectrogens. This study demonstrates the applicability of GO in recovering electricity from sewage wastewater. Anaerobic incubation of sludge with GO formed a hydrogel complex that embeds microbial cells via π-π stacking of microbially reduced GO. The rGO complex was electrically conductive (23 mS·cm−1 and immediately produced electricity in sewage wastewater under polarization at +200 mV vs. Ag/AgCl. Higher and more stable production of electricity was observed with rGO complexes (179–310 μA·cm−3 than with graphite felt (GF; 79–95 μA·cm−3. Electrochemical analyses revealed that this finding was attributable to the greater capacitance and smaller internal resistance of the rGO complex. Microbial community analysis showed abundances of Geobacter species in both rGO and GF complexes, whereas more diverse candidate exoelectrogens in the Desulfarculaceae family and Geothrix genus were particularly prominent in the rGO complex.

Microbial Inoculants and Their Impact on Soil Microbial Communities: A Review

Directory of Open Access Journals (Sweden)

Darine Trabelsi

2013-01-01

Full Text Available The knowledge of the survival of inoculated fungal and bacterial strains in field and the effects of their release on the indigenous microbial communities has been of great interest since the practical use of selected natural or genetically modified microorganisms has been developed. Soil inoculation or seed bacterization may lead to changes in the structure of the indigenous microbial communities, which is important with regard to the safety of introduction of microbes into the environment. Many reports indicate that application of microbial inoculants can influence, at least temporarily, the resident microbial communities. However, the major concern remains regarding how the impact on taxonomic groups can be related to effects on functional capabilities of the soil microbial communities. These changes could be the result of direct effects resulting from trophic competitions and antagonistic/synergic interactions with the resident microbial populations, or indirect effects mediated by enhanced root growth and exudation. Combination of inoculants will not necessarily produce an additive or synergic effect, but rather a competitive process. The extent of the inoculation impact on the subsequent crops in relation to the buffering capacity of the plant-soil-biota is still not well documented and should be the focus of future research.

Microbial Diversity in Sulfate-Reducing Marine Sediment Enrichment Cultures Associated with Anaerobic Biotransformation of Coastal Stockpiled Phosphogypsum (Sfax, Tunisia

Directory of Open Access Journals (Sweden)

Hana Zouch

2017-08-01

Full Text Available Anaerobic biotechnology using sulfate-reducing bacteria (SRB is a promising alternative for reducing long-term stockpiling of phosphogypsum (PG, an acidic (pH ~3 by-product of the phosphate fertilizer industries containing high amounts of sulfate. The main objective of this study was to evaluate, for the first time, the diversity and ability of anaerobic marine microorganisms to convert sulfate from PG into sulfide, in order to look for marine SRB of biotechnological interest. A series of sulfate-reducing enrichment cultures were performed using different electron donors (i.e., acetate, formate, or lactate and sulfate sources (i.e., sodium sulfate or PG as electron acceptors. Significant sulfide production was observed from enrichment cultures inoculated with marine sediments, collected near the effluent discharge point of a Tunisian fertilizer industry (Sfax, Tunisia. Sulfate sources impacted sulfide production rates from marine sediments as well as the diversity of SRB species belonging to Deltaproteobacteria. When PG was used as sulfate source, Desulfovibrio species dominated microbial communities of marine sediments, while Desulfobacter species were mainly detected using sodium sulfate. Sulfide production was also affected depending on the electron donor used, with the highest production obtained using formate. In contrast, low sulfide production (acetate-containing cultures was associated with an increase in the population of Firmicutes. These results suggested that marine Desulfovibrio species, to be further isolated, are potential candidates for bioremediation of PG by immobilizing metals and metalloids thanks to sulfide production by these SRB.

Influence of cereal non-starch polysaccharides on ileo-caecal and rectal microbial populations in growing pigs

DEFF Research Database (Denmark)

Høgberg, Ann; Lindberg, Jan; Leser, Thomas

2004-01-01

The effect of cereal non-starch polysaccharides (NSP) on the gut microbial populations was studied in 5 growing pigs between 39-116 kg body weight according to a Latin square design. The diets were composed to contain different NSP levels. The control diet had a normal NSP content (139 g/kg dry...... matter (DM)), 2 diets had a low total amount of NSP (95 and 107 g/kg DM) and 2 diets had a high amount of total NSP (191 and 199 g/kg DM). Furthermore, one of the diets within each category had a content of insoluble NSP similar to the control diet and one had a high content of insoluble NSP. Samples...... were collected from the ileum, via intestinal post valve T-caecum (PVTC) cannulas surgically inserted at the ileo-caecal ostium, and from the rectum. The total microbial flora of the ileal samples were analysed for by defining base pair length with terminal restriction fraction length polymorphism (T...

Microbial populations and activities of mangrove, restinga and Atlantic forest soils from Cardoso Island, Brazil.

Science.gov (United States)

Pupin, B; Nahas, E

2014-04-01

Mangroves provide a distinctive ecological environment that differentiates them from other ecosystems. This study deal to evaluate the frequency of microbial groups and the metabolic activities of bacteria and fungi isolated from mangrove, restinga and Atlantic forest soils. Soil samples were collected during the summer and winter at depths of 0-2, 2-5 and 5-10 cm. Except for fungi, the counts of the total, sporulating, Gram-negative, actinomycetes, nitrifying and denitrifying bacteria decreased significantly in the following order: Atlantic forest >mangrove > restinga. The counts of micro-organisms decreased by 11 and 21% from the surface to the 2-5 and 5-10 cm layers, but denitrifying bacteria increased by 44 and 166%, respectively. A larger growth of micro-organisms was verified in the summer compared with the winter, except for actinomycetes and fungi. The average frequency of bacteria isolated from mangrove, restinga and Atlantic forest soils was 95, 77 and 78%, and 93, 90 and 95% for fungi, respectively. Bacteria were amylolytic (33%), producers of acid phosphatase (79%) and solubilizers (18%) of inorganic phosphate. The proportions of fungi were 19, 90 and 27%. The mangrove soil studied had higher chemical characteristics than the Atlantic forest, but the high salinity may have restricted the growth of microbial populations. Estimates of the microbial counts and activities were important to elucidate the differences of mangrove ecosystem from restinga and Atlantic forest. © 2013 The Society for Applied Microbiology.

Enhancement of the sweep efficiency of waterflooding operations by the in-situ microbial population of petroleum reservoirs

Energy Technology Data Exchange (ETDEWEB)

Brown, L.R.; Vadie, A.A.; Stephens, J.O.; Azadpour, A.

1995-12-31

Live cores were obtained from five reservoirs using special precautions to prevent contamination by exogenous microorganisms and minimize exposure to oxygen. The depths from which the cores were obtained ranged from 2,705 ft to 6,568 ft. Core plugs were cut radially from live cores, encased in heat-shrink plastic tubes, placed in core holders, and fitted with inlets and outlets. Nutrient additions stimulated the in-situ microbial population to increase, dissolve stratal material, produce gases, and release oil. Reduction in flow through the core plugs was observed in some cases, while in other cases flow was increased, probably due to the dissolution of carbonates in the formation. A field demonstration of the ability of the in-situ microbial population to increase oil recovery by blocking the more permeable zones of the reservoir is currently underway. This demonstration is being conducted in the North Blowhorn Creek Unit situated in Lamar County, Alabama. Live cores were obtained from a newly drilled well in the field and tested as described above. The field project involves four test patterns each including one injector, four to five producers, and a comparable control injector with its four to five producers. Nutrient injection in the field began November 1994.

Phylogenetic & Physiological Profiling of Microbial Communities of Contaminated Soils/Sediments: Identifying Microbial consortia...

Energy Technology Data Exchange (ETDEWEB)

Terence L. Marsh

2004-05-26

The goals of this study were: (1) survey the microbial community in soil samples from a site contaminated with heavy metals using new rapid molecular techniques that are culture-independent; (2) identify phylogenetic signatures of microbial populations that correlate with metal ion contamination; and (3) cultivate these diagnostic strains using traditional as well as novel cultivation techniques in order to identify organisms that may be of value in site evaluation/management or bioremediation.

Using microbial desalination cells to reduce water salinity prior to reverse osmosis

KAUST Repository

Mehanna, Maha

2010-01-01

A microbial desalination cell (MDC) is a new method to reduce the salinity of one solution while generating electrical power from organic matter and bacteria in another (anode) solution. Substantial reductions in the salinity can require much larger volumes of the anode solution than the saline water, but any reduction of salinity will benefit the energy efficiency of a downstream reverse osmosis (RO) desalination system. We investigated here the use of an MDC as an RO pre-treatment method using a new type of air-cathode MDC containing three equally sized chambers. A single cycle of operation using a 1 g L -1 acetate solution reduced the conductivity of salt water (5 g L-1 NaCl) by 43 ± 6%, and produced a maximum power density of 480 mW m-2 with a coulombic efficiency of 68 ± 11%. A higher concentration of acetate (2 g L-1) reduced solution conductivity by 60 ± 7%, and a higher salt concentration (20 g L-1 NaCl) reduced solution conductivity by 50 ± 7%. The use of membranes with increased ion exchange capacities further decreased the solution conductivity by 63 ± 2% (20 g L-1 NaCl). These results demonstrate substantial (43-67%) desalination of water is possible using equal volumes of anode solution and salt water. These results show that MDC treatment could be used to substantially reduce salt concentrations and thus energy demands for downstream RO processing, while at the same time producing electrical power. © 2010 The Royal Society of Chemistry.

Reduced neonatal regulatory T cell response to microbial stimuli associates with subsequent eczema in high-risk infants.

Science.gov (United States)

Ismail, Intan H; Boyle, Robert J; Mah, Li-Jeen; Licciardi, Paul V; Tang, Mimi L K

2014-11-01

Regulatory T cells (Treg) play an essential role in early immune programming and shaping the immune response towards a pro-allergic or tolerant state. We evaluated cord blood Treg and cytokine responses to microbial and non-microbial stimuli in infants at high risk of allergic disease and their associations with development of allergic disease in the first year. Cord blood mononuclear cells from 72 neonates were cultured with toll-like receptors (TLR2) ligands: lipoteichoic acid (LTA) and heat-killed Lactobacillus rhamnosus GG (HKL); TLR4 ligand: lipopolysaccharide (LPS); ovalbumin (OVA); anti-CD3; or media for 48 h. Treg numbers and Treg cytokines were assessed in relation to allergic disease outcomes during the first year of life (eczema and atopic sensitization). Infants with eczema (n = 24) had reduced percentages of FoxP3(hi)CD25(hi) Treg in LTA (p = 0.01, adj p = 0.005) and HKL (p = 0.04, adj p = 0.02) stimulated cultures as well as reduced IL-10 (p = 0.01) production following HKL stimulation compared to those without eczema (n = 48). No differences in Treg or cytokine responses to LPS, OVA or anti-CD3 were seen. Infants who developed sensitization had lower percentages of Treg following TLR2 stimulation (but not other stimuli) compared to non-sensitized infants. High-risk children who develop allergic disease in the first year of life have deficient Treg responses to microbial stimuli but not allergen from the time of birth, which may contribute to failure of immune tolerance development in infancy. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Microbially produced phytotoxins and plant disease management ...

African Journals Online (AJOL)

Nowadays, these evaluation techniques are becoming an important complement to classical breeding methods. The knowledge of the inactivation of microbial toxins has led to the use of microbial enzymes to inactivate phytotoxins thereby reducing incidence and severity of disease induced by microbial toxins. Considering ...

Effects of operational shocks on key microbial populations for biogas production in UASB (Upflow Anaerobic Sludge Blanket) reactors

International Nuclear Information System (INIS)

Couras, C.S.; Louros, V.L.; Grilo, A.M.; Leitão, J.H.; Capela, M.I.; Arroja, L.M.; Nadais, M.H.

2014-01-01

This work compares the overall performance and biogas production of continuous and intermittent UASB (Upflow Anaerobic Sludge Blanket) reactors treating dairy wastewater and subjected to fat, hydraulic and temperature shocks. The systems were monitored for methane production, effluent concentration, volatile fatty acids, and microbial populations of the Eubacteria, Archaea and Syntrophomonadaceae groups. This last microbial group has been reported in literature as being determinant for the degradation of fatty substrates present in the wastewater and subsequent biogas production. Results show that both continuous and intermittent systems supported the applied shocks. However, the intermittent systems exhibited better performance than the continuous systems in biogas production and physical-chemical parameters. Syntrophomonadaceae microbial group was present in the intermittent systems, but was not detected in the biomass from the continuous systems. Hydraulic and temperature shocks, but not the fat shock, caused severe losses in the relative abundance of the Syntrophomonadaceae group in intermittent systems, leading to undetectable levels during the temperature shock. The severity of the effects of the applied shocks on the key microbial group Syntrophomonadaceae, were classified as: fats < hydraulic < temperature. Results from a full-scale anaerobic reactor confirm the effect of intermittent operation on the presence of Syntrophomonadaceae and the effect on reactor performance. - Highlights: • We compared intermittent and continuous UASB reactors upon operational shocks. • Syntrophomonadaceae key microbial group for maximizing biogas was quantified by FISH. • Syntrophomonadaceae is present in intermittent but not in continuous UASB reactors. • Syntrophomonadaceae abundance increases with fat shock in intermittent UASB reactor. • Syntrophomonadaceae abundance decreases with hydraulic or temperature shock

Effect of sulfur supplements on cellulolytic rumen micro-organisms and microbial protein synthesis in cattle fed a high fibre diet.

Science.gov (United States)

McSweeney, C S; Denman, S E

2007-11-01

To examine the effect of sulfur-containing compounds on the growth of anaerobic rumen fungi and the fibrolytic rumen bacteria Ruminococcus albus, Ruminococcus flavefaciens and Fibrobacter succinogenes in pure culture and within the cattle rumen. The effect of two reduced sulfur compounds, 3-mercaptopropionic acid (MPA) or 3-mercapto-1-propanesulfonic acid as the sole S source on growth of pure fibroyltic fungal and bacterial cultures showed that these compounds were capable of sustaining growth. An in vivo trial was then conducted to determine the effect of sulfur supplements (MPA and sodium sulfate) on microbial population dynamics in cattle fed the roughage Dichanthium aristatum. Real-time PCR showed significant increases in fibrolytic bacterial and fungal populations when cattle were supplemented with these compounds. Sulfate supplementation leads to an increase in dry matter intake without a change in whole tract dry matter digestibility. Supplementation of low S-containing diets with either sodium sulfate or MPA stimulates microbial growth with an increase in rumen microbial protein supply to the animal. Through the use of real-time PCR monitoring, a better understanding of the effect of S supplementation on discrete microbial populations within the rumen is provided.

Taking Exception. Reduced mortality leads to population growth: an inconvenient truth.

Science.gov (United States)

Shelton, James D

2014-05-01

Reduced mortality has been the predominant cause of the marked global population growth over the last 3/4 of a century. While improved child survival increases motivation to reduce fertility, it comes too little and too late to forestall substantial population growth. And, beyond motivation, couples need effective means to control their fertility. It is an inconvenient truth that reducing child mortality contributes considerably to the population growth destined to compromise the quality of life of many, particularly in sub-Saharan Africa. Vigorous child survival programming is of course imperative. Wide access to voluntary family planning can help mitigate that growth and provide many other benefits.

Effects of Gelidium amansii extracts on in vitro ruminal fermentation characteristics, methanogenesis, and microbial populations.

Science.gov (United States)

Lee, Shin Ja; Shin, Nyeon Hak; Jeong, Jin Suk; Kim, Eun Tae; Lee, Su Kyoung; Lee, Il Dong; Lee, Sung Sill

2018-01-01

Gelidium amansii (Lamouroux) is a red alga belonging to the family Gelidaceae and is commonly found in the shallow coasts of many East Asian countries, including Korea, China, and Japan. G. amansii has traditionally been utilized as an edible alga, and has various biological activities. The objective of this study was to determine whether dietary supplementation of G. amansii could be useful for improving ruminal fermentation. As assessed by in vitro fermentation parameters such as pH, total gas, volatile fatty acid (VFA) production, gas profile (methane, carbon dioxide, hydrogen, and ammonia), and microbial growth rate was compared to a basal diet with timothy hay. Cannulated Holstein cows were used as rumen fluid donors and 15 mL rumen fluid: buffer (1:2) was incubated for up to 72 h with four treatments with three replicates. The treatments were: control (timothy only), basal diet with 1% G. amansii extract, basal diet with 3% G. amansii extract, and basal diet with 5% G. amansii extract. Overall, the results of our study indicate that G. amansii supplementation is potentially useful for improving ruminant growth performance, via increased total gas and VFA production, but does come with some undesirable effects, such as increasing pH, ammonia concentration, and methane production. In particular, real-time polymerase chain reaction indicated that the methanogenic archaea and Fibrobacter succinogenes populations were significantly reduced, while the Ruminococcus flavefaciens populations were significantly increased at 24 h, when supplemented with G. amansii extracts as compared with controls. More research is required to elucidate what G. amansii supplementation can do to improve growth performance, and its effect on methane production in ruminants.

An Exogenous Surfactant-Producing Bacillus subtilis Facilitates Indigenous Microbial Enhanced Oil Recovery.

Science.gov (United States)

Gao, Peike; Li, Guoqiang; Li, Yanshu; Li, Yan; Tian, Huimei; Wang, Yansen; Zhou, Jiefang; Ma, Ting

2016-01-01

This study used an exogenous lipopeptide-producing Bacillus subtilis to strengthen the indigenous microbial enhanced oil recovery (IMEOR) process in a water-flooded reservoir in the laboratory. The microbial processes and driving mechanisms were investigated in terms of the changes in oil properties and the interplay between the exogenous B. subtilis and indigenous microbial populations. The exogenous B. subtilis is a lipopeptide producer, with a short growth cycle and no oil-degrading ability. The B. subtilis facilitates the IMEOR process through improving oil emulsification and accelerating microbial growth with oil as the carbon source. Microbial community studies using quantitative PCR and high-throughput sequencing revealed that the exogenous B. subtilis could live together with reservoir microbial populations, and did not exert an observable inhibitory effect on the indigenous microbial populations during nutrient stimulation. Core-flooding tests showed that the combined exogenous and indigenous microbial flooding increased oil displacement efficiency by 16.71%, compared with 7.59% in the control where only nutrients were added, demonstrating the application potential in enhanced oil recovery in water-flooded reservoirs, in particular, for reservoirs where IMEOR treatment cannot effectively improve oil recovery.

Effects of intermittent and continuous aeration on accelerative stabilization and microbial population dynamics in landfill bioreactors.

Science.gov (United States)

Sang, Nguyen Nhu; Soda, Satoshi; Inoue, Daisuke; Sei, Kazunari; Ike, Michihiko

2009-10-01

Performance and microbial population dynamics in landfill bioreactors were investigated in laboratory experiments. Three reactors were operated without aeration (control reactor, CR), with cyclic 6-h aeration and 6-h non-aeration (intermittently aerated reactor, IAR), and with continuous aeration (continuously aerated reactor, CAR). Each reactor was loaded with high-organic solid waste. The performance of IAR was highest among the reactors up to day 90. The respective solid weight, organic matter content, and waste volume on day 90 in the CR, IAR, and CAR were 50.9, 39.1, and 47.5%; 46.5, 29.3 and 35.0%; and 69, 38, and 53% of the initial values. Organic carbon and nitrogen compounds in leachate in the IAR and the CAR showed significant decreases in comparison to those in the CR. The most probable number (MPN) values of fungal 18S rDNA in the CAR and the IAR were higher than those in the CR. Terminal restriction fragment length polymorphism analysis showed that unique and diverse eubacterial and archaeal communities were formed in the IAR. The intermittent aeration strategy was favorable for initiation of solubilization of organic matter by the aerobic fungal populations and the reduction of the acid formation phase. Then the anaerobic H(2)-producing bacteria Clostridium became dominant in the IAR. Sulfate-reducing bacteria, which cannot use acetate/sulfate but which instead use various organics/sulfate as the electron donor/acceptor were also dominant in the IAR. Consequently, Methanosarcinales, which are acetate-utilizing methanogens, became the dominant archaea in the IAR, where high methane production was observed.

Energy, ecology and the distribution of microbial life.

Science.gov (United States)

Macalady, Jennifer L; Hamilton, Trinity L; Grettenberger, Christen L; Jones, Daniel S; Tsao, Leah E; Burgos, William D

2013-07-19

Mechanisms that govern the coexistence of multiple biological species have been studied intensively by ecologists since the turn of the nineteenth century. Microbial ecologists in the meantime have faced many fundamental challenges, such as the lack of an ecologically coherent species definition, lack of adequate methods for evaluating population sizes and community composition in nature, and enormous taxonomic and functional diversity. The accessibility of powerful, culture-independent molecular microbiology methods offers an opportunity to close the gap between microbial science and the main stream of ecological theory, with the promise of new insights and tools needed to meet the grand challenges humans face as planetary engineers and galactic explorers. We focus specifically on resources related to energy metabolism because of their direct links to elemental cycling in the Earth's history, engineering applications and astrobiology. To what extent does the availability of energy resources structure microbial communities in nature? Our recent work on sulfur- and iron-oxidizing autotrophs suggests that apparently subtle variations in the concentration ratios of external electron donors and acceptors select for different microbial populations. We show that quantitative knowledge of microbial energy niches (population-specific patterns of energy resource use) can be used to predict variations in the abundance of specific taxa in microbial communities. Furthermore, we propose that resource ratio theory applied to micro-organisms will provide a useful framework for identifying how environmental communities are organized in space and time.

Microbial biosensors for environmental monitoring

Directory of Open Access Journals (Sweden)

David VOGRINC

2015-12-01

Full Text Available Microbial biosensors are analytical devices capable of sensing substances in the environment due to the specific biological reaction of the microorganism or its parts. Construction of a microbial biosensor requires knowledge of microbial response to the specific analyte. Linking this response with the quantitative data, using a transducer, is the crucial step in the construction of a biosensor. Regarding the transducer type, biosensors are divided into electrochemical, optical biosensors and microbial fuel cells. The use of the proper configuration depends on the selection of the biosensing element. With the use of transgenic E. coli strains, bioluminescence or fluorescence based biosensors were developed. Microbial fuel cells enable the use of the heterogeneous microbial populations, isolated from wastewater. Different microorganisms are used for different pollutants – pesticides, heavy metals, phenolic compounds, organic waste, etc. Biosensing enables measurement of their concentration and their toxic or genotoxic effects on the microbes. Increasing environmental awareness has contributed to the increase of interest for biomonitoring. Although technologies, such as bioinformatics and genetic engineering, allow us to design complex and efficient microbial biosensors for environmental pollutants, the transfer of the laboratory work to the field still remains a problem to solve.

Soil microbial community response to land use and various soil ...

African Journals Online (AJOL)

Soil microbial community response to land use and various soil elements in a city landscape of north China. ... African Journal of Biotechnology ... Legumes played an important role in stimulating the growth and reproduction of various soil microbial populations, accordingly promoting the microbial catabolic activity.

Effects of simulated acid rain on microbial characteristics in a lateritic red soil.

Science.gov (United States)

Xu, Hua-qin; Zhang, Jia-en; Ouyang, Ying; Lin, Ling; Quan, Guo-ming; Zhao, Ben-liang; Yu, Jia-yu

2015-11-01

A laboratory experiment was performed to examine the impact of simulated acid rain (SAR) on nutrient leaching, microbial biomass, and microbial activities in a lateritic red soil in South China. The soil column leaching experiment was conducted over a 60-day period with the following six SAR pH treatments (levels): 2.5, 3.0, 3.5, 4.0, 4.5, and 5.0 and one control treatment (pH = 7). Compared with the control treatment, the concentrations of soil organic matter, total nitrogen, total phosphorus, total potassium, soil microbial biomass carbon (MBC), soil microbial biomass nitrogen (MBN), and average well color density (AWCD) in the Ecoplates were all significantly decreased by leaching with SAR at different pH levels. The decrease in MBC and MBN indicated that acid rain reduced the soil microbial population, while the decrease in AWCD revealed that acid rain had a negative effect on soil bacterial metabolic function. Soil basal respiration increased gradually from pH 4.0 to 7.0 but decreased dramatically from pH 2.5 to 3.0. The decrease in soil nutrient was the major reason for the change of soil microbial functions. A principal component analysis showed that the major carbon sources used by the bacteria were carbohydrates and carboxylic acids.

Effects of Subsurface Microbial Ecology on Geochemical Evolution of a Crude-Oil Contaminated Aquifer

Science.gov (United States)

Bekins, B. A.; Cozzarelli, I. M.; Godsy, E. M.; Warren, E.; Hostettler, F. D.

2001-12-01

We have identified several subsurface habitats for microorganisms in a crude oil contaminated located near Bemidji, Minnesota. These aquifer habitats include: 1) the unsaturated zone contaminated by hydrocarbon vapors, 2) the zones containing separate-phase crude oil, and 3) the aqueous-phase contaminant plume. The surficial glacial outwash aquifer was contaminated when a crude oil pipeline burst in 1979. We analyzed sediment samples from the contaminated aquifer for the most probable numbers of aerobes, iron reducers, fermenters, and three types of methanogens. The microbial data were then related to gas, water, and oil chemistry, sediment extractable iron, and permeability. The microbial populations in the various contaminated subsurface habitats each have special characteristics and these affect the aquifer and contaminant chemistry. In the eight-meter-thick, vapor-contaminated vadose zone, a substantial aerobic population has developed that is supported by hydrocarbon vapors and methane. Microbial numbers peak in locations where access to both hydrocarbons and nutrients infiltrating from the surface is maximized. The activity of this population prevents hydrocarbon vapors from reaching the land surface. In the zone where separate-phase crude oil is present, a consortium of methanogens and fermenters dominates the populations both above and below the water table. Moreover, gas concentration data indicate that methane production has been active in the oily zone since at least 1986. Analyses of the extracted separate-phase oil show that substantial degradation of C15 -C35 n-alkanes has occurred since 1983, raising the possibility that significant degradation of C15 and higher n-alkanes has occurred under methanogenic conditions. However, lab and field data suggest that toxic inhibition by crude oil results in fewer acetate-utilizing methanogens within and adjacent to the separate-phase oil. Data from this and other sites indicate that toxic inhibition of

Enumeration of microbial populations in radioactive environments by epifluorescence microscopy

International Nuclear Information System (INIS)

Pansoy-Hjelvik, M.E.; Strietelmeier, B.A.; Paffett, M.T.

1997-01-01

Epifluorescence microscopy was utilized to enumerate halophilic bacterial populations in two studies involving inoculated, actual waste/brine mixtures and pure brine solutions. The studies include an initial set of experiments designed to elucidate potential transformations of actinide-containing wastes under salt-repository conditions, including microbially mediated changes. The first study included periodic enumeration of bacterial populations of a mixed inoculum initially added to a collection of test containers. The contents of the test containers are the different types of actual radioactive waste that could potentially be stored in nuclear waste repositories in a salt environment. The transuranic waste was generated from materials used in actinide laboratory research. The results show that cell numbers decreased with time. Sorption of the bacteria to solid surfaces in the test system is discussed as a possible mechanism for the decrease in cell numbers. The second study was designed to determine radiological and/or chemical effects of 239 Pu, 243 Am, 237 Np, 232 Th and 238 U on the growth of pure and mixed anaerobic, denitrifying bacterial cultures in brine media. Pu, Am, and Np isotopes at concentrations of ≤1x10 -6 M , ≤5x10 -6 M and ≤5x10 -4 M respectively, and Th and U isotopes ≤4x10 -3 M were tested in these media. The results indicate that high concentrations of certain actinides affected both the bacterial growth rate and morphology. However, relatively minor effects from Am were observed at all tested concentrations with the pure culture

Microbial Community Structure of an Alluvial Aquifer Treated to Encourage Microbial Induced Calcite Precipitation

Science.gov (United States)

Ohan, J.; Saneiyan, S.; Lee, J.; Ntarlagiannis, D.; Burns, S.; Colwell, F. S.

2017-12-01

An oligotrophic aquifer in the Colorado River floodplain (Rifle, CO) was treated with molasses and urea to encourage microbial induced calcite precipitation (MICP). This would stabilize the soil mass by reducing porosity and strengthening the mineral fabric. Over the course of a 15-day treatment period, microbial biomass was collected from monitoring well groundwater for DNA extraction and sequencing. Bromide, a conservative tracer, was co-injected and subsequently detected in downgradient wells, confirming effective nutrient delivery. Conductivity increased during the injection regime and an overall decrease in pH was observed. Groundwater chemistry showed a marked increase in ammonia, suggesting urea hydrolysis - a process catalyzed by the enzyme urease - the primary enzyme implicated in MICP. Additionally, soluble iron was detected, suggesting a general increase in microbial activity; possibly as iron-reducing bacteria changed insoluble ferric oxide to soluble ferrous hydroxide in the anoxic aquifer. DNA sequencing of the 16S rRNA gene confirmed the presence of iron reducing bacteria, including Shewanella and Desulfuromonadales. Generally, a decrease in microbial community diversity was observed when pre-injection community taxa were compared with post-injection community taxa. Phyla indicative of anoxic aquifers were represented in accordance with previous literature at the Rifle site. Linear discriminant analysis showed significant differences in representative phyla over the course of the injection series. Geophysical monitoring of the site further suggested changes that could be due to MICP. Induced polarization increased the phase shift in the primary treated area, in agreement with laboratory experiments. Cross-hole seismic testing confirmed that the shear wave velocities increased in the treated soil mass, implying the soil matrix became more stable. Future investigations will help elucidate the viability and efficacy of MICP treatment in changing

A bacterial population analysis of granular sludge from an anaerobic digester treating a maize-processing waste

Energy Technology Data Exchange (ETDEWEB)

Howgrave-Graham, A.R.; Wallis, F.M. (Natal Univ., Pietermaritzburg (ZA). Dept. of Microbiology and Plant Pathology); Steyn, P.L. (Pretoria Univ. (South Africa))

1991-01-01

Microbial population studies were conducted on a dense granular sludge, with excellent settling, thickening and nutrient removal properties, from a South African clarigester treating effluent from a factory producing glucose and other carbohydrates from maize. The bacterial population comprised a heterogeneous group including acetogens, enterobacteria, sulphate-reducers, spirochaetes, heterofermentative lactobacilli and methanogens. The presence of these bacteria and lack of propionic acid and butyric acid bacteria suggests that the microbial activity of this anaerobic digester involved acetate and lactate metabolism rather than propionate or butyrate catabolism as a source of precursors for methane production. (author).

Effects of feeding whole linseed on ruminal fatty acid composition and microbial population in goats

Directory of Open Access Journals (Sweden)

Kamaleldin Abuelfatah

2016-12-01

Full Text Available The objective of the present study was to evaluate the effect of feeding different levels of whole linseed, as a source of n-3 polyunsaturated fatty acids (PUFA, on ruminal fatty acid composition and microbial population in the goat. Twenty-four crossbred Boer goats were assigned to 3 dietary treatments: L0 (control, L10 and L20 containing 0, 10%, or 20% whole linseed, respectively. The ruminal pH and concentration of total volatile fatty acids (VFA were not affected by dietary treatments. The feeding of L10 and L20 diets produced higher (P < 0.05 molar proportions of acetate and lower (P < 0.05 molar proportions of butyrate and valerate than the L0 diet. Molar proportions of myristic acid (C14:0 and palmitic acid (C16:0 were lower (P < 0.05 in the rumen of goats offered L10 and L20 diets than the control diet. However, stearic acid (C18:0, vaccenic acid (C18:1 trans-11, conjugated linoleic acid (CLA, C18:2 trans-10, cis-12 and α-lenolenic acid (C18:3 n-3 were higher (P < 0.05 in the rumen of goats fed L10 and L20 than L0. Both inclusion levels of linseed in the diet (L10 and L20 reduced the ruminal total bacteria, methanogens, and protozoa compared with L0 (P < 0.05. The effect of the dietary treatments on cellulolytic bacteria, varied between the individual species. Both inclusion levels of linseed resulted in a significant decrease (P < 0.05 in the population of Fibrobacter succinogenes, and Rumunococus flavefaciens compared with L0, with no significant difference between the groups fed linseed diets. The population of Rumunococus albus was not affected by the different dietary treatments. It was concluded that inclusion of whole linseed in the diet of goats could increase the concentration of PUFA in the rumen, and decrease the population of F. succinogenes, R. flavefaciens, methanogens and protozoa in rumen liquid of goats.

The electric picnic: synergistic requirements for exoelectrogenic microbial communities

KAUST Repository

Kiely, Patrick D; Regan, John M; Logan, Bruce E

2011-01-01

(BESs). Analysis of the community profiles of exoelectrogenic microbial consortia in BESs fed different substrates gives a clearer picture of the different microbial populations present in these exoelectrogenic biofilms. Rapid utilization of fermentation

Biotic interactions reduce microbial carbon use efficiency

Science.gov (United States)

Bradford, M.; Maynard, D. S.

2017-12-01

The efficiency by which microbes decompose organic matter governs the amount of carbon that is retained in microbial biomass versus lost to the atmosphere as respiration. This carbon use efficiency (CUE) is affected by various abiotic conditions, such as temperature and nutrient availability. In biogeochemical model simulations, CUE is a key variable regulating how much soil carbon is stored or lost from ecosystems under simulated global changes, such as climate warming. Theoretically, the physiological costs of biotic interactions such as competition should likewise alter CUE, yet the direction and magnitude of these costs are untested. Here we conduct a microcosm experiment to quantify how competitive interactions among saprotrophic fungi alter growth, respiration, and CUE. Free-living decomposer fungi representing a broad range of traits and phylogenies were grown alone, in pairwise competition, and in multi-species (up to 15) communities. By combing culturing and stable carbon isotope approaches, we could resolve the amount of carbon substrate allocated to fungal biomass versus respiration, and so estimate CUE. By then comparing individual performance to community-level outcomes, we show that species interactions induce consistent declines in CUE, regardless of abiotic conditions. Pairwise competition lowers CUE by as much as 25%, with the magnitude of these costs equal to or greater than the observed variation across abiotic conditions. However, depending on the competitive network structure, increasing species richness led to consistent gains or declines in CUE. Our results suggest that the extent to which microbial-mediated carbon fluxes respond to environmental change may be influenced strongly by competitive interactions. As such, knowledge of abiotic conditions and community composition is necessary to confidently project CUE and hence ecosystem carbon dynamics.

Localized electron transfer rates and microelectrode-based enrichment of microbial communities within a phototrophic microbial mat

Directory of Open Access Journals (Sweden)

Jerome eBabauta

2014-01-01

Full Text Available Phototrophic microbial mats frequently exhibit sharp, light-dependent redox gradients that regulate microbial respiration on specific electron acceptors as a function of depth. In this work, a benthic phototrophic microbial mat from Hot Lake, a hypersaline, epsomitic lake located near Oroville in north-central Washington, was used to develop a microscale electrochemical method to study local electron transfer processes within the mat. To characterize the physicochemical variables influencing electron transfer, we initially quantified redox potential, pH and dissolved oxygen gradients by depth in the mat under photic and aphotic conditions. We further demonstrated that power output of a mat fuel cell was light-dependent. To study local electron transfer processes, we deployed a microscale electrode (microelectrode with tip size ~20 µm. To enrich a subset of microorganisms capable of interacting with the microelectrode, we anodically polarized the microelectrode in the mat. Subsequently, to characterize the microelectrode-associated community and compare it to the neighboring mat community, we performed amplicon sequencing of the V1-V3 region of the 16S gene. Differences in Bray-Curtis beta diversity, illustrated by large changes in relative abundance at the phylum level, suggested successful enrichment of specific mat community members on the microelectrode surface. The microelectrode-associated community exhibited substantially reduced alpha diversity and elevated relative abundances of Prosthecochloris, Loktanella, Catellibacterium, other unclassified members of Rhodobacteraceae, Thiomicrospira, and Limnobacter, compared with the community at an equivalent depth in the mat. Our results suggest that local electron transfer to an anodically polarized microelectrode selected for a specific microbial population, with substantially more abundance and diversity of sulfur-oxidizing phylotypes compared with the neighboring mat community.

Localized electron transfer rates and microelectrode-based enrichment of microbial communities within a phototrophic microbial mat.

Science.gov (United States)

Babauta, Jerome T; Atci, Erhan; Ha, Phuc T; Lindemann, Stephen R; Ewing, Timothy; Call, Douglas R; Fredrickson, James K; Beyenal, Haluk

2014-01-01

Phototrophic microbial mats frequently exhibit sharp, light-dependent redox gradients that regulate microbial respiration on specific electron acceptors as a function of depth. In this work, a benthic phototrophic microbial mat from Hot Lake, a hypersaline, epsomitic lake located near Oroville in north-central Washington, was used to develop a microscale electrochemical method to study local electron transfer processes within the mat. To characterize the physicochemical variables influencing electron transfer, we initially quantified redox potential, pH, and dissolved oxygen gradients by depth in the mat under photic and aphotic conditions. We further demonstrated that power output of a mat fuel cell was light-dependent. To study local electron transfer processes, we deployed a microscale electrode (microelectrode) with tip size ~20 μm. To enrich a subset of microorganisms capable of interacting with the microelectrode, we anodically polarized the microelectrode at depth in the mat. Subsequently, to characterize the microelectrode-associated community and compare it to the neighboring mat community, we performed amplicon sequencing of the V1-V3 region of the 16S gene. Differences in Bray-Curtis beta diversity, illustrated by large changes in relative abundance at the phylum level, suggested successful enrichment of specific mat community members on the microelectrode surface. The microelectrode-associated community exhibited substantially reduced alpha diversity and elevated relative abundances of Prosthecochloris, Loktanella, Catellibacterium, other unclassified members of Rhodobacteraceae, Thiomicrospira, and Limnobacter, compared with the community at an equivalent depth in the mat. Our results suggest that local electron transfer to an anodically polarized microelectrode selected for a specific microbial population, with substantially more abundance and diversity of sulfur-oxidizing phylotypes compared with the neighboring mat community.

Microbial Anaerobic Ammonium Oxidation Under Iron Reducing Conditions, Alternative Electron Acceptors

Science.gov (United States)

Ruiz-Urigüen, M.; Jaffe, P. R.

2015-12-01

Autotrophic Acidimicrobiaceae-bacterium named A6 (A6), part of the Actinobacteria phylum have been linked to anaerobic ammonium (NH4+) oxidation under iron reducing conditions. These organisms obtain their energy by oxidizing NH4+ and transferring the electrons to a terminal electron acceptor (TEA). Under environmental conditions, the TEAs are iron oxides [Fe(III)], which are reduced to Fe(II), this process is known as Feammox. Our studies indicate that alternative forms of TEAs can be used by A6, e.g. iron rich clays (i.e. nontronite) and electrodes in bioelectrochemical systems such as Microbial Electrolysis Cells (MECs), which can sustain NH4+removal and A6 biomass production. Our results show that nontronite can support Feammox and promote bacterial cell production. A6 biomass increased from 4.7 x 104 to 3.9 x 105 cells/ml in 10 days. Incubations of A6 in nontronite resulted in up to 10 times more NH4+ removal and 3 times more biomass production than when ferrihydrite is used as the Fe(III) source. Additionally, Fe in nontronite can be reoxidized by aeration and A6 can reutilize it; however, Fe is still finite in the clay. In contrast, in MECs, A6 harvest electrons from NH4+ and use an anode as an unlimited TEA, as a result current is produced. We operated multiple MECs in parallel using a single external power source, as described by Call & Logan (2011). MECs were run with an applied voltage of 0.7V and different growing mediums always containing initial 5mM NH4+. Results show that current production is favored when anthraquinone-2,6-disulfonate (AQDS), an electron shuttled, is present in the medium as it facilitates the transfer of electrons from the bacterial cell to the anode. Additionally, A6 biomass increased from 1 x 104 to 9.77 x 105cells/ml in 14 days of operation. Due to Acidimicrobiaceae-bacterium A6's ability to use various TEAs, MECs represent an alternative, iron-free form, for optimized biomass production of A6 and its application in NH4

Microbial metagenomes from three aquifers in the Fennoscandian shield terrestrial deep biosphere reveal metabolic partitioning among populations.

Science.gov (United States)

Wu, Xiaofen; Holmfeldt, Karin; Hubalek, Valerie; Lundin, Daniel; Åström, Mats; Bertilsson, Stefan; Dopson, Mark

2016-05-01

Microorganisms in the terrestrial deep biosphere host up to 20% of the earth's biomass and are suggested to be sustained by the gases hydrogen and carbon dioxide. A metagenome analysis of three deep subsurface water types of contrasting age (from 86% coverage. The populations were dominated by Proteobacteria, Candidate divisions, unclassified archaea and unclassified bacteria. The estimated genome sizes of the biosphere. The data were finally used to create a combined metabolic model of the deep terrestrial biosphere microbial community.

Stability of U(VI) and Tc(VII) Reducing Microbial Communities to Environmental Perturbation: Development and Testing of a Thermodynamic Network Model

International Nuclear Information System (INIS)

McKinley, James P.; Istok, Jonathan

2005-01-01

Previously published research from in situ field experiments at the NABIR Field Research Center have shown that cooperative metabolism of denitrifiers and Fe(III)/sulfate reducers is essential for creating subsurface conditions favorable for U(VI) and Tc(VII) bioreduction (Istok et al., 2004). The overall goal of this project is to develop and test a thermodynamic network model for predicting the effects of substrate additions and environmental perturbations on the composition and functional stability of subsurface microbial communities. The overall scientific hypothesis is that a thermodynamic analysis of the energy-yielding reactions performed by broadly defined groups of microorganisms can be used to make quantitative and testable predictions of the change in microbial community composition that will occur when a substrate is added to the subsurface or when environmental conditions change. An interactive computer program was developed to calculate the overall growth equation and free energy yield for microorganisms that grow by coupling selected combinations of electron acceptor and electron donor half-reactions. Each group performs a specific function (e.g. oxidation of acetate coupled to reduction of nitrate); collectively the groups provide a theoretical description of the entire natural microbial community. The microbial growth data are combined with an existing thermodynamic data base for associated geochemical reactions and used to simulate the coupled microbial-geochemical response of a complex natural system to substrate addition or any other environmental perturbations

Triclosan affects the microbial community in simulated sewage-drain-field soil and slows down xenobiotic degradation

Energy Technology Data Exchange (ETDEWEB)

Svenningsen, Hanne [Department of Geochemistry, Geological Survey of Denmark and Greenland (GEUS), Oster Voldgade 10, DK-1350 Copenhagen K (Denmark); Department of Biology, University of Copenhagen, Solvgade 83H, DK-1307 Copenhagen K (Denmark); Henriksen, Trine [Department of Geochemistry, Geological Survey of Denmark and Greenland (GEUS), Oster Voldgade 10, DK-1350 Copenhagen K (Denmark); Prieme, Anders [Department of Biology, University of Copenhagen, Solvgade 83H, DK-1307 Copenhagen K (Denmark); Johnsen, Anders R., E-mail: arj@geus.dk [Department of Geochemistry, Geological Survey of Denmark and Greenland (GEUS), Oster Voldgade 10, DK-1350 Copenhagen K (Denmark)

2011-06-15

Effects of the common antibacterial agent triclosan on microbial communities and degradation of domestic xenobiotics were studied in simulated sewage-drain-field soil. Cultivable microbial populations decreased 22-fold in the presence of 4 mg kg{sup -1} of triclosan, and triclosan-resistant Pseudomonas strains were strongly enriched. Exposure to triclosan also changed the general metabolic profile (Ecoplate substrate profiling) and the general profile (T-RFLP) of the microbial community. Triclosan degradation was slow at all concentrations tested (0.33-81 mg kg{sup -1}) during 50-days of incubation. Mineralization experiments ({sup 14}C-tracers) and chemical analyses (LC-MS/MS) showed that the persistence of a linear alkylbenzene sulfonate (LAS) and a common analgesic (ibuprofen) increased with increasing triclosan concentrations (0.16-100 mg kg{sup -1}). The largest effect was seen for LAS mineralization which was severely reduced by 0.16 mg kg{sup -1} of triclosan. Our findings indicate that environmentally realistic concentrations of triclosan may affect the efficiency of biodegradation in percolation systems. - Highlights: > Triclosan may enter the soil environment through sewage. > Triclosan impacts the microbial community in sewage-drain-field soil. > Triclosan-resistant pseudomonads are strongly enriched. > Degradation of co-occurring LAS and ibuprofen is reduced. - Environmentally realistic triclosan concentrations in percolation systems may reduce the biodegradation of other xenobiotics and select for triclosan-resistant bacteria.

Triclosan affects the microbial community in simulated sewage-drain-field soil and slows down xenobiotic degradation

International Nuclear Information System (INIS)

Svenningsen, Hanne; Henriksen, Trine; Prieme, Anders; Johnsen, Anders R.

2011-01-01

Effects of the common antibacterial agent triclosan on microbial communities and degradation of domestic xenobiotics were studied in simulated sewage-drain-field soil. Cultivable microbial populations decreased 22-fold in the presence of 4 mg kg -1 of triclosan, and triclosan-resistant Pseudomonas strains were strongly enriched. Exposure to triclosan also changed the general metabolic profile (Ecoplate substrate profiling) and the general profile (T-RFLP) of the microbial community. Triclosan degradation was slow at all concentrations tested (0.33-81 mg kg -1 ) during 50-days of incubation. Mineralization experiments ( 14 C-tracers) and chemical analyses (LC-MS/MS) showed that the persistence of a linear alkylbenzene sulfonate (LAS) and a common analgesic (ibuprofen) increased with increasing triclosan concentrations (0.16-100 mg kg -1 ). The largest effect was seen for LAS mineralization which was severely reduced by 0.16 mg kg -1 of triclosan. Our findings indicate that environmentally realistic concentrations of triclosan may affect the efficiency of biodegradation in percolation systems. - Highlights: → Triclosan may enter the soil environment through sewage. → Triclosan impacts the microbial community in sewage-drain-field soil. → Triclosan-resistant pseudomonads are strongly enriched. → Degradation of co-occurring LAS and ibuprofen is reduced. - Environmentally realistic triclosan concentrations in percolation systems may reduce the biodegradation of other xenobiotics and select for triclosan-resistant bacteria.

Microbial growth and sensory quality of dried potato slices irradiated by electrons

International Nuclear Information System (INIS)

Kim, Hyun-Jin; Song, Hyeon-Jeong; Song, Kyung-Bin

2011-01-01

Electron beam irradiation was applied to secure the microbial safety of dried purple sweet potato. After purple sweet potato slices had been dehydrated with 20% (w/w) maltodextrin solution, the samples were irradiated at doses 2, 4, 6, 8, and 10 kGy and then stored at 20 o C for 60 days. Microbiological data indicated that the populations of total aerobic bacteria and of yeast and molds significantly decreased with increase in irradiation dosage. Specifically, microbial load was reduced by about three log cycles at 6 kGy compared to those of the control. Based on the color measurement of the potato slices, electron beam irradiation treatment did not affect the color quality. Sensory evaluation results also showed that electron beam irradiation did not affect overall sensory scores during storage. These results suggest that electron beam irradiation could be useful for improving microbial safety without impairing the quality of the potato slices during storage.

Bioremediation of soil heavily contaminated with crude oil and its products: composition of the microbial consortium

Directory of Open Access Journals (Sweden)

JELENA S. MILIĆ

2009-04-01

Full Text Available Bioremediation, a process that utilizes the capability of microorganism to degrade toxic waste, is emerging as a promising technology for the treatment of soil and groundwater contamination. The technology is very effective in dealing with petroleum hydrocarbon contamination. The aim of this study was to examine the composition of the microbial consortium during the ex situ experiment of bioremediation of soil heavily contaminated with crude oil and its products from the Oil Refinery Pančevo, Serbia. After a 5.5-month experiment with biostimulation and bioventilation, the concentration of the total petroleum hydrocarbons (TPH had been reduced from 29.80 to 3.29 g/kg (89 %. In soil, the dominant microorganism population comprised Gram-positive bacteria from actinomycete-Nocardia group. The microorganisms which decompose hydrocarbons were the dominant microbial population at the end of the process, with a share of more than 80 % (range 107 CFU/g. On the basis of the results, it was concluded that a stable microbial community had been formed after initial fluctuations.

Microbial content of abattoir wastewater and its contaminated soil in ...

African Journals Online (AJOL)

Microbial content of wastewater in two abattoirs and the impact on microbial population of receiving soil was studied in Agege and Ojo Local Government Areas in Lagos State, Nigeria. Wastewater samples were collected from each of the abattoirs over three months period and examined for microbial content. Soil samples ...

Efficacy of Denture Cleansers in Reducing Microbial Counts from Removable Partial Dentures: A Short-Term Clinical Evaluation

OpenAIRE

Lucena-Ferreira,Silvia Carneiro de; Cavalcanti,Indira Moraes Gomes; Cury,Altair Antoninha Del Bel

2013-01-01

This clinical study investigated if daily immersion in denture cleansers reduces microbial counts on removable partial denture's (RPD) biofilm. Twenty-five RPD wearer volunteers were selected and instructed to complement the hygiene of their dentures by immersing them in an enzymatic peroxide-based denture cleanser (Polident® 3 minute) once a day for 3 min for a period of 15 days. The biofilm was collected from RPD surfaces with a swab immediately before (baseline) and after the experimental ...

The electric picnic: synergistic requirements for exoelectrogenic microbial communities

KAUST Repository

Kiely, Patrick D

2011-06-01

Characterization of the various microbial populations present in exoelectrogenic biofilms provides insight into the processes required to convert complex organic matter in wastewater streams into electrical current in bioelectrochemical systems (BESs). Analysis of the community profiles of exoelectrogenic microbial consortia in BESs fed different substrates gives a clearer picture of the different microbial populations present in these exoelectrogenic biofilms. Rapid utilization of fermentation end products by exoelectrogens (typically Geobacter species) relieves feedback inhibition for the fermentative consortia, allowing for rapid metabolism of organics. Identification of specific syntrophic processes and the communities characteristic of these anodic biofilms will be a valuable aid in improving the performance of BESs. © 2011 Elsevier Ltd.

Population-Sequencing as a Biomarker of Burkholderia mallei and Burkholderia pseudomallei Evolution through Microbial Forensic Analysis

Directory of Open Access Journals (Sweden)

John P. Jakupciak

2013-01-01

Full Text Available Large-scale genomics projects are identifying biomarkers to detect human disease. B. pseudomallei and B. mallei are two closely related select agents that cause melioidosis and glanders. Accurate characterization of metagenomic samples is dependent on accurate measurements of genetic variation between isolates with resolution down to strain level. Often single biomarker sensitivity is augmented by use of multiple or panels of biomarkers. In parallel with single biomarker validation, advances in DNA sequencing enable analysis of entire genomes in a single run: population-sequencing. Potentially, direct sequencing could be used to analyze an entire genome to serve as the biomarker for genome identification. However, genome variation and population diversity complicate use of direct sequencing, as well as differences caused by sample preparation protocols including sequencing artifacts and mistakes. As part of a Department of Homeland Security program in bacterial forensics, we examined how to implement whole genome sequencing (WGS analysis as a judicially defensible forensic method for attributing microbial sample relatedness; and also to determine the strengths and limitations of whole genome sequence analysis in a forensics context. Herein, we demonstrate use of sequencing to provide genetic characterization of populations: direct sequencing of populations.

Molecular analysis of the metabolic rates of discrete subsurface populations of sulfate reducers

Energy Technology Data Exchange (ETDEWEB)

Miletto, M.; Williams, K.H.; N' Guessan, A.L.; Lovley, D.R.

2011-04-01

Elucidating the in situ metabolic activity of phylogenetically diverse populations of sulfate-reducing microorganisms that populate anoxic sedimentary environments is key to understanding subsurface ecology. Previous pure culture studies have demonstrated that transcript abundance of dissimilatory (bi)sulfite reductase genes is correlated with the sulfate reducing activity of individual cells. To evaluate whether expression of these genes was diagnostic for subsurface communities, dissimilatory (bi)sulfite reductase gene transcript abundance in phylogenetically distinct sulfate-reducing populations was quantified during a field experiment in which acetate was added to uranium-contaminated groundwater. Analysis of dsrAB sequences prior to the addition of acetate indicated that Desulfobacteraceae, Desulfobulbaceae, and Syntrophaceae-related sulfate reducers were the most abundant. Quantifying dsrB transcripts of the individual populations suggested that Desulfobacteraceae initially had higher dsrB transcripts per cell than Desulfobulbaceae or Syntrophaceae populations, and that the activity of Desulfobacteraceae increased further when the metabolism of dissimilatory metal reducers competing for the added acetate declined. In contrast, dsrB transcript abundance in Desulfobulbaceae and Syntrophaceae remained relatively constant, suggesting a lack of stimulation by added acetate. The indication of higher sulfate-reducing activity in the Desulfobacteraceae was consistent with the finding that Desulfobacteraceae became the predominant component of the sulfate-reducing community. Discontinuing acetate additions resulted in a decline in dsrB transcript abundance in the Desulfobacteraceae. These results suggest that monitoring transcripts of dissimilatory (bi)sulfite reductase genes in distinct populations of sulfate reducers can provide insight into the relative rates of metabolism of different components of the sulfate-reducing community and their ability to respond to

Reduced fine-scale spatial genetic structure in grazed populations of Dianthus carthusianorum.

Science.gov (United States)

Rico, Y; Wagner, H H

2016-11-01

Strong spatial genetic structure in plant populations can increase homozygosity, reducing genetic diversity and adaptive potential. The strength of spatial genetic structure largely depends on rates of seed dispersal and pollen flow. Seeds without dispersal adaptations are likely to be dispersed over short distances within the vicinity of the mother plant, resulting in spatial clustering of related genotypes (fine-scale spatial genetic structure, hereafter spatial genetic structure (SGS)). However, primary seed dispersal by zoochory can promote effective dispersal, increasing the mixing of seeds and influencing SGS within plant populations. In this study, we investigated the effects of seed dispersal by rotational sheep grazing on the strength of SGS and genetic diversity using 11 nuclear microsatellites for 49 populations of the calcareous grassland forb Dianthus carthusianorum. Populations connected by rotational sheep grazing showed significantly weaker SGS and higher genetic diversity than populations in ungrazed grasslands. Independent of grazing treatment, small populations showed significantly stronger SGS and lower genetic diversity than larger populations, likely due to genetic drift. A lack of significant differences in the strength of SGS and genetic diversity between populations that were recently colonized and pre-existing populations suggested that populations colonized after the reintroduction of rotational sheep grazing were likely founded by colonists from diverse source populations. We conclude that dispersal by rotational sheep grazing has the potential to considerably reduce SGS within D. carthusianorum populations. Our study highlights the effectiveness of landscape management by rotational sheep grazing to importantly reduce genetic structure at local scales within restored plant populations.

Chemical and microbial quality of irradiated ground ginger

International Nuclear Information System (INIS)

Andrews, L.S.

1995-01-01

Fresh ground ginger was irradiated with a 10-kGy ionizing radiation dose from a Cobalt-60 source. Gamma radiation decreased most of the extractable volatile flavor components. Those known to contribute to typical ginger flavor, e.g., zingiberene, beta-sesquiphellandrene, beta-bisabolene, farnesene isomers, arcurcumene, and alpha-cubebene, decreased 27-59% following irradiation. Most odors recognized through gas chromatography/olfactometry produced similar patterns from irradiated and nonirradiated samples. The radiation treatment reduced the aerobic microbial population from 10(8) to 10(1) CFU/g. Sensory qualities of flavor, color and odor of ginger powder were similar for treated and untreated ginger

On reducibility and ergodicity of population projection matrix models

DEFF Research Database (Denmark)

Stott, Iain; Townley, Stuart; Carslake, David

2010-01-01

from all stages to all other stages) and therefore ergodic (whatever initial stage structure is used in the population projection, it will always exhibit the same stable asymptotic growth rate). 2. Evaluation of 652 PPM models for 171 species from the literature suggests that 24·7% of PPM models...... structure used in the population projection). In our sample of published PPMs, 15·6% are non-ergodic. 3. This presents a problem: reducible–ergodic models often defy biological rationale in their description of the life cycle but may or may not prove problematic for analysis as they often behave similarly...... of reducibility in published PPMs, with significant implications for the predictive power of such models in many cases. We suggest that as a general rule, reducibility of PPM models should be avoided. However, we provide a guide to the pertinent analysis of reducible matrix models, largely based upon whether...

Microbial processes in coastal pollution

International Nuclear Information System (INIS)

Capone, D.G.; Bauer, J.E.

1992-01-01

In this chapter, the authors describe the nature and range of some of the interactions that can occur between the microbiota and environmental contaminants in coastal areas. The implications of such interactions are also discussed. Pollutant types include inorganic nutrients, heavy metals, bulk organics, organic contaminants, pathogenic microorganisms and microbial pollutants. Both the effects of pollutants such as petroleum hydrocarbons on natural microbial populations and the mitigation of contaminant effects by complexation and biodegradation are considered. Finally, several areas of emerging concerns are presented that involve a confluence of biogeochemistry, microbial ecology and applied and public health microbiology. These concerns range in relevance from local/regional to oceanic/global scales. 308 ref

Theory of microbial genome evolution

Science.gov (United States)

Koonin, Eugene

Bacteria and archaea have small genomes tightly packed with protein-coding genes. This compactness is commonly perceived as evidence of adaptive genome streamlining caused by strong purifying selection in large microbial populations. In such populations, even the small cost incurred by nonfunctional DNA because of extra energy and time expenditure is thought to be sufficient for this extra genetic material to be eliminated by selection. However, contrary to the predictions of this model, there exists a consistent, positive correlation between the strength of selection at the protein sequence level, measured as the ratio of nonsynonymous to synonymous substitution rates, and microbial genome size. By fitting the genome size distributions in multiple groups of prokaryotes to predictions of mathematical models of population evolution, we show that only models in which acquisition of additional genes is, on average, slightly beneficial yield a good fit to genomic data. Thus, the number of genes in prokaryotic genomes seems to reflect the equilibrium between the benefit of additional genes that diminishes as the genome grows and deletion bias. New genes acquired by microbial genomes, on average, appear to be adaptive. Evolution of bacterial and archaeal genomes involves extensive horizontal gene transfer and gene loss. Many microbes have open pangenomes, where each newly sequenced genome contains more than 10% `ORFans', genes without detectable homologues in other species. A simple, steady-state evolutionary model reveals two sharply distinct classes of microbial genes, one of which (ORFans) is characterized by effectively instantaneous gene replacement, whereas the other consists of genes with finite, distributed replacement rates. These findings imply a conservative estimate of at least a billion distinct genes in the prokaryotic genomic universe.

The microbial fate of carbon in high-latitude seas: Impact of the microbial loop on oceanic uptake of CO{sub 2}

Energy Technology Data Exchange (ETDEWEB)

Yager, P.L.

1996-12-31

This dissertation examines pelagic microbial processes in high-latitude seas, how they affect regional and global carbon cycling, and how they might respond to hypothesized changes in climate. Critical to these interests is the effect of cold temperature on bacterial activity. Also important is the extent to which marine biological processes in general impact the inorganic carbon cycle. The study area is the Northeast Water (NEW) Polynya, a seasonally-recurrent opening in the permanent ice situated over the northeastern Greenland continental shelf. This work was part of an international, multi-disciplinary research project studying carbon cycling in the coastal Arctic. The first chapter describes a simple model which links a complex marine food web to a simplified ocean and atmosphere. The second chapter investigates the inorganic carbon inventory of the summertime NEW Polynya surface waters to establish the effect of biological processes on the air-sea pCO{sub 2} gradient. The third and fourth chapters use a kinetic approach to examine microbial activities in the NEW Polynya as a function of temperature and dissolved organic substrate concentration, testing the so-called Pomeroy hypothesis that microbial activity is disproportionately reduced at low environmental temperatures owing to increased organic substrate requirements. Together, the suite of data collected on microbial activities, cell size, and grazing pressure suggest how unique survival strategies adopted by an active population of high-latitude bacteria may contribute to, rather than detract from, an efficient biological carbon pump.

Reducing assembly complexity of microbial genomes with single-molecule sequencing

Science.gov (United States)

Genome assembly algorithms cannot fully reconstruct microbial chromosomes from the DNA reads output by first or second-generation sequencing instruments. Therefore, most genomes are left unfinished due to the significant resources required to manually close gaps left in the draft assemblies. Single-...

Microbial ecology of terrestrial Antarctica: Are microbial systems at risk from human activities?

Energy Technology Data Exchange (ETDEWEB)

White, G.J.

1996-08-01

Many of the ecological systems found in continental Antarctica are comprised entirely of microbial species. Concerns have arisen that these microbial systems might be at risk either directly through the actions of humans or indirectly through increased competition from introduced species. Although protection of native biota is covered by the Protocol on Environmental Protection to the Antarctic Treaty, strict measures for preventing the introduction on non-native species or for protecting microbial habitats may be impractical. This report summarizes the research conducted to date on microbial ecosystems in continental Antarctica and discusses the need for protecting these ecosystems. The focus is on communities inhabiting soil and rock surfaces in non-coastal areas of continental Antarctica. Although current polices regarding waste management and other operations in Antarctic research stations serve to reduce the introduction on non- native microbial species, importation cannot be eliminated entirely. Increased awareness of microbial habitats by field personnel and protection of certain unique habitats from physical destruction by humans may be necessary. At present, small-scale impacts from human activities are occurring in certain areas both in terms of introduced species and destruction of habitat. On a large scale, however, it is questionable whether the introduction of non-native microbial species to terrestrial Antarctica merits concern.

Distribution of microbial populations and their relationship with environmental variables in the North Yellow Sea, China

Science.gov (United States)

Bai, Xiaoge; Wang, Min; Liang, Yantao; Zhang, Zhifeng; Wang, Fang; Jiang, Xuejiao

2012-03-01

In order to understand the large-scale spatial distribution characteristics of picoplankton, nanophytoplankton and virioplankton and their relationship with environmental variables in coastal and offshore waters, flow cytometry (FCM) was used to analyze microbial abundance of samples collected in summer from four depths at 36 stations in the North Yellow Sea (NYS). The data revealed spatial heterogeneity in microbial populations in the offshore and near-shore waters of the NYS during the summer. For the surface layer, picoeukaryotes were abundant in the near-shore waters, Synechococcus was abundant in the offshore areas, and bacterial and viral abundances were high in the near-shore waters around the Liaodong peninsula. In the near-shore waters, no significant vertical variation of picophytoplankton (0.2-2μm) abundance was found. However, the nanophytoplankton abundance was higher in the upper layers (from the surface to 10 m depth) than in the bottom layer. For the offshore waters, both pico- and nanophytoplankton (2-20μm) abundance decreased sharply with depth in the North Yellow Sea Cold Water Mass (NYSCWM). But, for the vertical distribution of virus and bacteria abundance, no significant variation was observed in both near-shore and offshore waters. Autotrophic microbes were more sensitive to environmental change than heterotrophic microbes and viruses. Viruses showed a positive correlation with bacterial abundance, suggesting that the bacteriophage might be prominent for virioplankton (about 0.45μm) in summer in the NYS and that viral abundance might play an important role in microbial loop functions.

Reduced Oral Microbial Diversity in Individuals Harbor Periodontal Diseases

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Jinghua Sun

2012-02-01

Full Text Available Introduction: Bacteria colonize a variety of surfaces of the hu-man body. The bacterial diversity in the oral cavity is estimated to be more than 700 different species. The oral cavity is home to microbial communities, with important implications for human health and disease. Oral microbial flora is responsible for two major human infectious diseases of the oral cavity, dental caries and periodontal diseases. From the clinical samples, previously, using polymerase chain reaction-based denaturing gradient gel electrophoresis (PCR-DGGE technique, we found a significantly greater diversity of oral microbes in caries-free individuals compared with caries-active individuals. The hypothesis: We hypothesize that a greater diversity of indigenous bacteria inhabits a healthy oral environment, and that a sig-nificant proportion of oral biota may be absent, suppressed, or replaced in a periodontal diseases environment. Evaluation of the hypothesis: The microbiota undergoes a transition from a commensal to a pathogenic relationship with the host due to factors that trigger a shift in the proportions of resident microorganisms. If our hypothesis is true, many techniques which were used to detect the oral bacterial diversity can be used in diagnosis and prognosis of periodontal diseases.

Microbial and plant ecology of a long-term TNT-contaminated site

International Nuclear Information System (INIS)

Travis, Emma R.; Bruce, Neil C.; Rosser, Susan J.

2008-01-01

The contamination of the environment with explosive residues presents a serious ecological problem at sites across the world, with the highly toxic compound trinitrotoluene (TNT) the most widespread contaminant. This study examines the soil microbial community composition across a long-term TNT-contaminated site. It also investigates the extent of nitroaromatic contamination and its effect on vegetation. Concentrations of TNT and its metabolites varied across the site and this was observed to dramatically impact on the extent and diversity of the vegetation, with the most heavily contaminated area completely devoid of vegetation. Bryophytes were seen to be particularly sensitive to TNT contamination. The microbial population experienced both a reduction in culturable bacterial numbers and a shift in composition at the high concentrations of TNT. DGGE and community-level physiological profiling (CLPP) revealed a clear change in both the genetic and functional diversity of the soil when soil was contaminated with TNT. - Long-term contamination of soil with TNT reduces the extent and diversity of vegetation, decreases culturable bacterial numbers and shifts the microbial community composition

Neonatal microbial colonization in mice promotes prolonged dominance of CD11b+Gr-1+cells and accelerated establishment of the CD4+T cell population in the spleen

DEFF Research Database (Denmark)

Kristensen, Matilde Bylov; Metzdorff, Stine Broeng; Bergström, Anders

2015-01-01

To assess the microbial influence on postnatal hematopoiesis, we examined the role of early life microbial colonization on the composition of leukocyte subsets in the neonatal spleen. A high number of CD11b+Gr-1+ splenocytes present perinatally was sustained for a longer period in conventionally...... event, which we suggest impacts the subsequent development of the T cell population in the murine spleen....

Microbial activity and community composition during bioremediation of diesel-oil-contaminated soil: effects of hydrocarbon concentration, fertilizers, and incubation time.

Science.gov (United States)

Margesin, Rosa; Hämmerle, Marion; Tscherko, Dagmar

2007-02-01

We investigated the influence of three factors-diesel oil concentration [2500, 5000, 10,000, 20,000 mg total petroleum hydrocarbons (TPH) kg(-1) soil], biostimulation (unfertilized, inorganic fertilization with NPK nutrients, or oleophilic fertilization with Inipol EAP22), and incubation time-on hydrocarbon removal, enzyme activity (lipase), and microbial community structure [phospholipid fatty acids (PLFA)] in a laboratory soil bioremediation treatment. Fertilization enhanced TPH removal and lipase activity significantly (P 0.05). Microbial communities, as assessed by PLFA patterns, were primarily influenced by the TPH content, followed by fertilization, and the interaction of these two factors, whereas incubation time was of minor importance. This was demonstrated by three-factorial analysis of variance and multidimensional scaling analysis. Low TPH content had no significant effect on soil microbial community, independent of the treatment. High TPH content generally resulted in increased PLFA concentrations, whereby a significant increase in microbial biomass with time was only observed with inorganic fertilization, whereas oleophilic fertilization (Inipol EAP22) tended to inhibit microbial activity and to reduce PLFA contents with time. Among bacteria, PLFA indicative of the Gram-negative population were significantly (P diesel oil and fertilized with NPK after 21-38 days of incubation at 20 degrees C. The Gram-positive population was not significantly influenced by TPH content or biostimulation treatment.

Functional and Structural Succession of Soil Microbial Communities below Decomposing Human Cadavers

Science.gov (United States)

Cobaugh, Kelly L.; Schaeffer, Sean M.; DeBruyn, Jennifer M.

2015-01-01

The ecological succession of microbes during cadaver decomposition has garnered interest in both basic and applied research contexts (e.g. community assembly and dynamics; forensic indicator of time since death). Yet current understanding of microbial ecology during decomposition is almost entirely based on plant litter. We know very little about microbes recycling carcass-derived organic matter despite the unique decomposition processes. Our objective was to quantify the taxonomic and functional succession of microbial populations in soils below decomposing cadavers, testing the hypotheses that a) periods of increased activity during decomposition are associated with particular taxa; and b) human-associated taxa are introduced to soils, but do not persist outside their host. We collected soils from beneath four cadavers throughout decomposition, and analyzed soil chemistry, microbial activity and bacterial community structure. As expected, decomposition resulted in pulses of soil C and nutrients (particularly ammonia) and stimulated microbial activity. There was no change in total bacterial abundances, however we observed distinct changes in both function and community composition. During active decay (7 - 12 days postmortem), respiration and biomass production rates were high: the community was dominated by Proteobacteria (increased from 15.0 to 26.1% relative abundance) and Firmicutes (increased from 1.0 to 29.0%), with reduced Acidobacteria abundances (decreased from 30.4 to 9.8%). Once decay rates slowed (10 - 23 d postmortem), respiration was elevated, but biomass production rates dropped dramatically; this community with low growth efficiency was dominated by Firmicutes (increased to 50.9%) and other anaerobic taxa. Human-associated bacteria, including the obligately anaerobic Bacteroides, were detected at high concentrations in soil throughout decomposition, up to 198 d postmortem. Our results revealed the pattern of functional and compositional succession

Effect of electrokinetic remediation on indigenous microbial activity and community within diesel contaminated soil.

Science.gov (United States)

Kim, Seong-Hye; Han, Hyo-Yeol; Lee, You-Jin; Kim, Chul Woong; Yang, Ji-Won

2010-07-15

Electrokinetic remediation has been successfully used to remove organic contaminants and heavy metals within soil. The electrokinetic process changes basic soil properties, but little is known about the impact of this remediation technology on indigenous soil microbial activities. This study reports on the effects of electrokinetic remediation on indigenous microbial activity and community within diesel contaminated soil. The main removal mechanism of diesel was electroosmosis and most of the bacteria were transported by electroosmosis. After 25 days of electrokinetic remediation (0.63 mA cm(-2)), soil pH developed from pH 3.5 near the anode to pH 10.8 near the cathode. The soil pH change by electrokinetics reduced microbial cell number and microbial diversity. Especially the number of culturable bacteria decreased significantly and only Bacillus and strains in Bacillales were found as culturable bacteria. The use of EDTA as an electrolyte seemed to have detrimental effects on the soil microbial activity, particularly in the soil near the cathode. On the other hand, the soil dehydrogenase activity was enhanced close to the anode and the analysis of microbial community structure showed the increase of several microbial populations after electrokinetics. It is thought that the main causes of changes in microbial activities were soil pH and direct electric current. The results described here suggest that the application of electrokinetics can be a promising soil remediation technology if soil parameters, electric current, and electrolyte are suitably controlled based on the understanding of interaction between electrokinetics, contaminants, and indigenous microbial community. Copyright 2010 Elsevier B.V. All rights reserved.

Linking specific heterotrophic bacterial populations to bioreduction of uranium and nitrate using stable isotope probing in contaminated subsurface sediments

International Nuclear Information System (INIS)

Akob, Denise M.; Kerkhof, Lee; Kusel, Kirsten; Watson, David B.; Palumbo, Anthony Vito; Kostka, Joel

2011-01-01

Shifts in terminal electron-accepting processes during biostimulation of uranium-contaminated sediments were linked to the composition of stimulated microbial populations using DNA-based stable isotope probing. Nitrate reduction preceded U(VI) and Fe(III) reduction in [ 13 C]ethanol-amended microcosms. The predominant, active denitrifying microbial groups were identified as members of the Betaproteobacteria, whereas Actinobacteria dominated under metal-reducing conditions.

Effects of Culture and 2-Hydroxy-4-(Methylthio-Butanoic Acid on Rumen Fermentation and Microbial Populations between Different Roughage Sources

Directory of Open Access Journals (Sweden)

H. Sun

2014-09-01

Full Text Available An in vitro experiment was conducted to evaluate the effects of Aspergillus oryzae culture (AOC and 2-hydroxy-4-(methylthio-butanoic acid (HMB on rumen fermentation and microbial populations between different roughage sources. Two roughage sources (Chinese wild rye [CWR] vs corn silage [CS] were assigned in a 2×3 factorial arrangement with HMB (0 or 15 mg and AOC (0, 3, or 6 mg. Gas production (GP, microbial protein (MCP and total volatile fatty acid (VFA were increased in response to addition of HMB and AOC (p<0.01 for the two roughages. The HMB and AOC showed inconsistent effects on ammonia-N with different substrates. For CWR, neither HMB nor AOC had significant effect on molar proportion of individual VFA. For CS, acetate was increased (p = 0.02 and butyrate was decreased (p<0.01 by adding HMB and AOC. Increase of propionate was only occurred with AOC (p<0.01. Populations of protozoa (p≤0.03 and fungi (p≤0.02 of CWR were differently influenced by HMB and AOC. Percentages of F. succinogenes, R. albus, and R. flavefaciens (p<0.01 increased when AOC was added to CWR. For CS, HMB decreased the protozoa population (p = 0.01 and increased the populations of F. succinogenes and R. albus (p≤0.03. Populations of fungi, F. succinogenes (p = 0.02 and R. flavefacien (p = 0.03 were increased by adding AOC. The HMB×AOC interactions were noted in MCP, fungi and R. flavefacien for CWR and GP, ammonia-N, MCP, total VFA, propionate, acetate/propionate (A/P and R. albus for CS. It is inferred that addition of HMB and AOC could influence rumen fermentation of forages by increasing the number of rumen microbes.

Evaluation of Sanitizing Methods for Reducing Microbial Contamination on Fresh Strawberry, Cherry Tomato, and Red Bayberry

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Wei Wei

2017-12-01

Full Text Available Strawberries, cherry tomatoes, and red bayberries, which are the most popular types of fresh produce in China, are vulnerable to microbial contamination. In this study, different sanitizing methods [treatment with 2% organic acids, 0.02% sodium hypochlorite (SH, 0.1% sodium chlorite (SC, and 0.1% acidified sodium chlorite (ASC] were applied to fresh strawberry, cherry tomato, and red bayberry, and their abilities to reduce aerobic bacteria, Escherichia coli O157:H7, mold, yeast, and Salmonella Typhimurium were evaluated. The commercially used SH method reduced the background microbiota on strawberry, cherry tomato, and red bayberry by 0.20–2.07 log cfu/g. The ASC method reduced background microbiota (except for mold on strawberry and cherry tomato by more than 3.0 log cfu/g. ASC was the only sanitizer that significantly reduced mold on red bayberry, and lactic acid was the only organic acid sanitizer that effectively reduced yeast on red bayberry. The ASC method had the best sterilizing effect on the three fresh fruits and also required the shortest sanitizing time and low chlorite content. The application of ASC method significantly reduced the microbiota on retail grocery samples, and the effect was similar to that achieved by sanitizing methods comparison.

Identification of active dehalorespiring microbial populations in anoxic river sediment by RNA-based stable isotope probing

Science.gov (United States)

Kittelmann, S.; Friedrich, M. W.

2005-12-01

Tetrachloroethene (perchloroethylene, PCE), a persistent contaminant in aquifers, soils and sediments, can be reductively dechlorinated by anaerobic microorganisms in a process referred to as dehalorespiration. However, the biodiversity of dehalorespiring microorganisms and their distribution especially in pristine environments is largely unexplored. Therefore, the aim of this study was to detect potentially novel PCE-dehalorespiring microorganisms by using stable isotope probing (SIP), a technique that allows to directly identify the function of uncultivated microbial populations. We simulated a PCE contamination by incubating pristine river sediment in the presence of PCE at a steady, low aqueous concentration (20 μM). Dehalogenation activity in microcosms (20 nmol cis-dichloroethene per ml slurry per day formed) was detected already after 4 weeks at 20°C with sediment indigenous electron donors. The microbial community in sediment incubations was probed with 13C-labelled acetate (0.5 mM) as electron donor and carbon source at 15°C for 3 days. After RNA extraction, "heavy" 13C-rRNA and light 12C-rRNA were separated by isopycnic centrifugation, and Bacteria-related populations in gradient fractions were characterised by terminal restriction fragment length polymorphism analysis and cloning. In heavy gradient fractions from the microcosm with PCE, we detected a prominent 506-bp terminal restriction fragment (T-RF) and a few minor T-RFs only. In contrast, in the control without PCE, Bacteria-specific rRNA was restricted to light gradient fractions, and the prominent T-RFs found in the PCE-dechlorinating microcosm were of minor importance. Apparently, 13C-acetate was incorporated into bacterial rRNA more effectively in PCE-respiring microcosms. Thus, rRNA-SIP provides strong evidence for the presence of PCE-dehalorespiring, 13C-acetate-utilising populations in river sediment microcosms. Cloning/sequencing analysis identified the prominent members of the heavy

Understanding the performance of sulfate reducing bacteria based packed bed reactor by growth kinetics study and microbial profiling.

Science.gov (United States)

Dev, Subhabrata; Roy, Shantonu; Bhattacharya, Jayanta

2016-07-15

A novel marine waste extract (MWE) as alternative nitrogen source was explored for the growth of sulfate reducing bacteria (SRB). Variation of sulfate and nitrogen (MWE) showed that SRB growth follows an uncompetitive inhibition model. The maximum specific growth rates (μmax) of 0.085 and 0.124 h(-1) and inhibition constants (Ki) of 56 and 4.6 g/L were observed under optimized sulfate and MWE concentrations, respectively. The kinetic data shows that MWE improves the microbial growth by 27%. The packed bed bioreactor (PBR) under optimized sulfate and MWE regime showed sulfate removal efficiency of 62-66% and metals removal efficiency of 66-75% on using mine wastewater. The microbial community analysis using DGGE showed dominance of SRB (87-89%). The study indicated the optimum dosing of sulfate and cheap organic nitrogen to promote the growth of SRB over other bacteria. Copyright © 2016 Elsevier Ltd. All rights reserved.

Natural disturbance reduces disease risk in endangered rainforest frog populations.

Science.gov (United States)

Roznik, Elizabeth A; Sapsford, Sarah J; Pike, David A; Schwarzkopf, Lin; Alford, Ross A

2015-08-21

Natural disturbances can drive disease dynamics in animal populations by altering the microclimates experienced by hosts and their pathogens. Many pathogens are highly sensitive to temperature and moisture, and therefore small changes in habitat structure can alter the microclimate in ways that increase or decrease infection prevalence and intensity in host populations. Here we show that a reduction of rainforest canopy cover caused by a severe tropical cyclone decreased the risk of endangered rainforest frogs (Litoria rheocola) becoming infected by a fungal pathogen (Batrachochytrium dendrobatidis). Reductions in canopy cover increased the temperatures and rates of evaporative water loss in frog microhabitats, which reduced B. dendrobatidis infection risk in frogs by an average of 11-28% in cyclone-damaged areas, relative to unaffected areas. Natural disturbances to the rainforest canopy can therefore provide an immediate benefit to frogs by altering the microclimate in ways that reduce infection risk. This could increase host survival and reduce the probability of epidemic disease outbreaks. For amphibian populations under immediate threat from this pathogen, targeted manipulation of canopy cover could increase the availability of warmer, drier microclimates and therefore tip the balance from host extinction to coexistence.

Effects of Elevated Carbon Dioxide and Salinity on the Microbial Diversity in Lithifying Microbial Mats

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Steven R. Ahrendt

2014-03-01

Full Text Available Atmospheric levels of carbon dioxide (CO2 are rising at an accelerated rate resulting in changes in the pH and carbonate chemistry of the world’s oceans. However, there is uncertainty regarding the impact these changing environmental conditions have on carbonate-depositing microbial communities. Here, we examine the effects of elevated CO2, three times that of current atmospheric levels, on the microbial diversity associated with lithifying microbial mats. Lithifying microbial mats are complex ecosystems that facilitate the trapping and binding of sediments, and/or the precipitation of calcium carbonate into organosedimentary structures known as microbialites. To examine the impact of rising CO2 and resulting shifts in pH on lithifying microbial mats, we constructed growth chambers that could continually manipulate and monitor the mat environment. The microbial diversity of the various treatments was compared using 16S rRNA gene pyrosequencing. The results indicated that elevated CO2 levels during the six month exposure did not profoundly alter the microbial diversity, community structure, or carbonate precipitation in the microbial mats; however some key taxa, such as the sulfate-reducing bacteria Deltasulfobacterales, were enriched. These results suggest that some carbonate depositing ecosystems, such as the microbialites, may be more resilient to anthropogenic-induced environmental change than previously thought.

Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances.

Science.gov (United States)

Xu, Jianping

2006-06-01

Microbial ecology examines the diversity and activity of micro-organisms in Earth's biosphere. In the last 20 years, the application of genomics tools have revolutionized microbial ecological studies and drastically expanded our view on the previously underappreciated microbial world. This review first introduces the basic concepts in microbial ecology and the main genomics methods that have been used to examine natural microbial populations and communities. In the ensuing three specific sections, the applications of the genomics in microbial ecological research are highlighted. The first describes the widespread application of multilocus sequence typing and representational difference analysis in studying genetic variation within microbial species. Such investigations have identified that migration, horizontal gene transfer and recombination are common in natural microbial populations and that microbial strains can be highly variable in genome size and gene content. The second section highlights and summarizes the use of four specific genomics methods (phylogenetic analysis of ribosomal RNA, DNA-DNA re-association kinetics, metagenomics, and micro-arrays) in analysing the diversity and potential activity of microbial populations and communities from a variety of terrestrial and aquatic environments. Such analyses have identified many unexpected phylogenetic lineages in viruses, bacteria, archaea, and microbial eukaryotes. Functional analyses of environmental DNA also revealed highly prevalent, but previously unknown, metabolic processes in natural microbial communities. In the third section, the ecological implications of sequenced microbial genomes are briefly discussed. Comparative analyses of prokaryotic genomic sequences suggest the importance of ecology in determining microbial genome size and gene content. The significant variability in genome size and gene content among strains and species of prokaryotes indicate the highly fluid nature of prokaryotic

Microbial activity in bentonite buffers. Literature study

Energy Technology Data Exchange (ETDEWEB)

Ratto, M.; Itavaara, M.

2012-07-01

The proposed disposal concept for high-level radioactive wastes involves storing the wastes underground in copper-iron containers embedded in buffer material of compacted bentonite. Hydrogen sulphide production by sulphate-reducing prokaryotes is a potential mechanism that could cause corrosion of waste containers in repository conditions. The prevailing conditions in compacted bentonite buffer will be harsh. The swelling pressure is 7-8 MPa, the amount of free water is low and the average pore and pore throat diameters are small. This literature study aims to assess the potential of microbial activity in bentonite buffers. Literature on the environmental limits of microbial life in extreme conditions and the occurrence of sulphatereducing prokaryotes in extreme environments is reviewed briefly and the results of published studies characterizing microbes and microbial processes in repository conditions or in relevant subsurface environments are presented. The presence of bacteria, including SRBs, has been confirmed in deep groundwater and bentonite-based materials. Sulphate reducers have been detected in various high-pressure environments, and sulphate-reduction based on hydrogen as an energy source is considered a major microbial process in deep subsurface environments. In bentonite, microbial activity is strongly suppressed, mainly due to the low amount of free water and small pores, which limit the transport of microbes and nutrients. Spore-forming bacteria have been shown to survive in compacted bentonite as dormant spores, and they are able to resume a metabolically active state after decompaction. Thus, microbial sulphide production may increase in repository conditions if the dry density of the bentonite buffer is locally reduced. (orig.)

Differences in microbial community composition between injection and production water samples of water flooding petroleum reservoirs

Directory of Open Access Journals (Sweden)

P. K. Gao

2015-06-01

Full Text Available Microbial communities in injected water are expected to have significant influence on those of reservoir strata in long-term water flooding petroleum reservoirs. To investigate the similarities and differences in microbial communities in injected water and reservoir strata, high-throughput sequencing of microbial partial 16S rRNA of the water samples collected from the wellhead and downhole of injection wells, and from production wells in a homogeneous sandstone reservoir and a heterogeneous conglomerate reservoir were performed. The results indicate that a small number of microbial populations are shared between the water samples from the injection and production wells in the sandstone reservoir, whereas a large number of microbial populations are shared in the conglomerate reservoir. The bacterial and archaeal communities in the reservoir strata have high concentrations, which are similar to those in the injected water. However, microbial population abundance exhibited large differences between the water samples from the injection and production wells. The number of shared populations reflects the influence of microbial communities in injected water on those in reservoir strata to some extent, and show strong association with the unique variation of reservoir environments.

The Influence of Age and Gender on Skin-Associated Microbial Communities in Urban and Rural Human Populations.

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Shi Ying

Full Text Available Differences in the bacterial community structure associated with 7 skin sites in 71 healthy people over five days showed significant correlations with age, gender, physical skin parameters, and whether participants lived in urban or rural locations in the same city. While body site explained the majority of the variance in bacterial community structure, the composition of the skin-associated bacterial communities were predominantly influenced by whether the participants were living in an urban or rural environment, with a significantly greater relative abundance of Trabulsiella in urban populations. Adults maintained greater overall microbial diversity than adolescents or the elderly, while the intragroup variation among the elderly and rural populations was significantly greater. Skin-associated bacterial community structure and composition could predict whether a sample came from an urban or a rural resident ~5x greater than random.

Influence of Bicarbonate, Sulfate, and Electron Donors on Biological reduction of Uranium and Microbial Community Composition

Energy Technology Data Exchange (ETDEWEB)

Luo, Wensui [ORNL; Zhou, Jizhong [ORNL; Wu, Weimin [ORNL; Yan, Tingfen [ORNL; Criddle, Craig [ORNL; Jardine, Philip M [ORNL; Gu, Baohua [ORNL

2007-01-01

A microcosm study was performed to investigate the effect of ethanol and acetate on uranium(VI) biological reduction and microbial community changes under various geochemical conditions. Each microcosm contained an uranium-contaminated sediment (up to 2.8 g U/kg) suspended in buffer with bicarbonate at concentrations of either 1 mM or 40 mM and sulfate at either 1.1 or 3.2 mM. Ethanol or acetate was used as an electron donor. Results indicate that ethanol yielded in significantly higher U(VI) reduction rates than acetate. A low bicarbonate concentration (1 mM) was favored for U(VI) bioreduction to occur in sediments, but high concentrations of bicarbonate (40 mM) and sulfate (3.2 mM) decreased the reduction rates of U(VI). Microbial communities were dominated by species from the Geothrix genus and Proteobacteria phylum in all microcosms. However, species in the Geobacteraceae family capable of reducing U(VI) were significantly enriched by ethanol and acetate in low bicarbonate buffer. Ethanol increased the population of unclassified Desulfuromonales, while acetate increased the population of Desulfovibrio. Additionally, species in the Geobacteraceae family were not enriched in high bicarbonate buffer, but the Geothrix and the unclassified Betaproteobacteria species were enriched. This study concludes that ethanol could be a better electron donor than acetate for reducing U(VI) under given experimental conditions, and electron donor and geoundwater geochemistry alter microbial communities responsible for U(VI) reduction.

Influence of bicarbonate, sulfate, and electron donors on biological reduction of uranium and microbial community composition

Energy Technology Data Exchange (ETDEWEB)

Luo Wensui [Oak Ridge Inst. for Science and Education, TN (United States); Oak Ridge National Lab., TN (United States). Environmental Sciences Div.; Wu Wei-Min; Criddle, C.S. [Stanford Univ., CA (United States). Dept. of Civil and Environmental Engineering; Yan Tingfen [Oak Ridge Inst. for Science and Education, TN (United States); Jardine, P.M.; Gu Baohua [Oak Ridge National Lab., TN (United States). Environmental Sciences Div.; Zhou Jizhong [Oklahoma Univ., Norman, OK (United States). Dept. of Botany and Microbiology

2007-12-15

A microcosm study was performed to investigate the effect of ethanol and acetate on uranium(VI) biological reduction and microbial community changes under various geochemical conditions. Each microcosm contained an uranium-contaminated sediment (up to 2.8 g U/kg) suspended in buffer with bicarbonate at concentrations of either 1 or 40 mM and sulfate at either 1.1 or 3.2 mM. Ethanol or acetate was used as an electron donor. Results indicate that ethanol yielded in significantly higher U(VI) reduction rates than acetate. A low bicarbonate concentration (1 mM) was favored for U(VI) bioreduction to occur in sediments, but high concentrations of bicarbonate (40 mM) and sulfate (3.2 mM) decreased the reduction rates of U(VI). Microbial communities were dominated by species from the Geothrix genus and Proteobacteria phylum in all microcosms. However, species in the Geobacteraceae family capable of reducing U(VI) were significantly enriched by ethanol and acetate in low-bicarbonate buffer. Ethanol increased the population of unclassified Desulfuromonales, while acetate increased the population of Desulfovibrio. Additionally, species in the Geobacteraceae family were not enriched in high-bicarbonate buffer, but the Geothrix and the unclassified Betaproteobacteria species were enriched. This study concludes that ethanol could be a better electron donor than acetate for reducing U(VI) under given experimental conditions, and electron donor and groundwater geochemistry alter microbial communities responsible for U(VI) reduction. (orig.)

Effect of biostimulation on the microbial community in PCB-contaminated sediments through periodic amendment of sediment with iron.

Science.gov (United States)

Srinivasa Varadhan, A; Khodadoust, Amid P; Brenner, Richard C

2011-10-01

Reductive dehalogenation of polychlorinated biphenyls (PCBs) by indigenous dehalorespiring microorganisms in contaminated sediments may be enhanced via biostimulation by supplying hydrogen generated through the anaerobic corrosion of elemental iron added to the sediment. In this study, the effect of periodic amendment of sediment with various dosages of iron on the microbial community present in sediment was investigated using phospholipid fatty acid analysis (PLFA) over a period of 18 months. Three PCB-contaminated sediments (two freshwater lake sediments and one marine sediment) were used. Signature biomarker analysis of the microbial community present in all three sediments revealed the enrichment of Dehalococcoides species, the population of which was sustained for a longer period of time when the sediment microcosms were amended with the lower dosage of iron (0.01 g iron per g dry sediment) every 6 months as compared to the blank system (without iron). Lower microbial stress levels were reported for the system periodically amended with 0.01 g of iron per g dry sediment every 6 months, thus reducing the competition from other hydrogen-utilizing microorganisms like methanogens, iron reducers, and sulfate reducers. The concentration of hydrogen in the system was found to be an important factor influencing the shift in microbial communities in all sediments with time. Periodic amendment of sediment with larger dosages of iron every 3 months resulted in the early prevalence of Geobacteraceae and sulfate-reducing bacteria followed by methanogens. An average pH of 8.4 (range of 8.2-8.6) and an average hydrogen concentration of 0.75% (range of 0.3-1.2%) observed between 6 and 15 months of the study were found to be conducive to sustaining the population of Dehalococcoides species in the three sediments amended with 0.01 g iron per g dry sediment. Biostimulation of indigenous PCB dechlorinators by the periodic amendment of contaminated sediments with low dosages of

Social interaction in synthetic and natural microbial communities.

Science.gov (United States)

Xavier, Joao B

2011-04-12

Social interaction among cells is essential for multicellular complexity. But how do molecular networks within individual cells confer the ability to interact? And how do those same networks evolve from the evolutionary conflict between individual- and population-level interests? Recent studies have dissected social interaction at the molecular level by analyzing both synthetic and natural microbial populations. These studies shed new light on the role of population structure for the evolution of cooperative interactions and revealed novel molecular mechanisms that stabilize cooperation among cells. New understanding of populations is changing our view of microbial processes, such as pathogenesis and antibiotic resistance, and suggests new ways to fight infection by exploiting social interaction. The study of social interaction is also challenging established paradigms in cancer evolution and immune system dynamics. Finding similar patterns in such diverse systems suggests that the same 'social interaction motifs' may be general to many cell populations.

Microbial Reduction of Fe(III) and SO42- and Associated Microbial Communities in the Alluvial Aquifer Groundwater and Sediments.

Science.gov (United States)

Lee, Ji-Hoon; Lee, Bong-Joo

2017-11-25

Agricultural demands continuously increased use of groundwater, causing drawdown of water table and need of artificial recharge using adjacent stream waters. River water intrusion into groundwater can alter the geochemical and microbiological characteristics in the aquifer and subsurface. In an effort to investigate the subsurface biogeochemical activities before operation of artificial recharge at the test site, established at the bank of Nakdong River, Changwon, South Korea, organic carbon transported from river water to groundwater was mimicked and the effect on the indigenous microbial communities was investigated with the microcosm incubations of the groundwater and subsurface sediments. Laboratory incubations indicated microbial reduction of Fe(III) and sulfate. Next-generation Illumina MiSeq sequences of V4 region of 16S rRNA gene provided that the shifts of microbial taxa to Fe(III)-reducing and/or sulfate-reducing microorganisms such as Geobacter, Albidiferax, Desulfocapsa, Desulfuromonas, and Desulfovibrio were in good correlation with the sequential flourishment of microbial reduction of Fe(III) and sulfate as the incubations progressed. This suggests the potential role of dissolved organic carbons migrated with the river water into groundwater in the managed aquifer recharge system on the indigenous microbial community composition and following alterations of subsurface biogeochemistry and microbial metabolic activities.

Microbial conversion of food wastes for biofertilizer production with thermophilic lipolytic microbes

Energy Technology Data Exchange (ETDEWEB)

Tsai, Shu-Hsien; Yang, Shang-Shyng [Institute of Microbiology and Biochemistry, National Taiwan University, Taipei 10617, (Taiwan); Liu, Ching-Piao [Department of Biological Science and Technology, Meiho Institute of Technology, Pingtung 91201, (Taiwan)

2007-05-15

Food waste is approximately one quarter of the total garbage in Taiwan. To investigate the feasibility of microbial conversion of food waste to multiple functional biofertilizer, food waste was mixed with bulking materials, inoculated with thermophilic and lipolytic microbes and incubated at 50{sup o}C in a mechanical composter. Microbial inoculation enhanced the degradation of food wastes, increased the total nitrogen and the germination rate of alfalfa seed, shortened the maturity period and improved the quality of biofertilizer. In food waste inoculated with thermophilic and lipolytic Brevibacillus borstelensis SH168 for 28 days, total nitrogen increased from 2.01% to 2.10%, ash increased from 24.94% to 29.21%, crude fat decreased from 4.88% to 1.34% and the C/N ratio decreased from 18.02 to 17.65. Each gram of final product had a higher population of thermophilic microbes than mesophilic microbes. Microbial conversion of food waste to biofertilizer is a feasible and potential technology in the future to maintain the natural resources and to reduce the impact on environmental quality. (author)

Assessment of the microbial populations in field and test pit experiments at Elliot Lake, Ontario, Canada

International Nuclear Information System (INIS)

Silver, M.; Taylor, J.B.

1981-01-01

Enumeration of aerobic and anaerobic heterotrophic (organic carbon-using) bacteria shows the establishment of a microbial population on vegetated tailings. The development of a population of heterotrophic bacteria, 90% of which are obligate aerobes, in the top 5 cm of the tailings is indicative of normal soil formation. The cell concentration decrease is greater than that found in older, well-developed soils. Iron-oxidizing thiobacilli are rarely present in the revegetated tailings, and then only at depths below 40 cm and at cell concentrations less than 100 cells/g. On an adjacent unvegetated portion of the tailings, fewer heterotrophic bacteria are found in the top 5 cm of the tailings. Iron-oxidizing thiobacilli are present uniformly in the top 47 cm. Enumeration of iron-oxidizing bacteria in the effluents of four test pit experiments indicate blockage of the drainage tiles in two experiments. Chemical conditions of the effluents are suitable for the formation of basic ferric precipitates that could cause this blockage

Use of Fe-Impregnated Biochar To Efficiently Sorb Chlorpyrifos, Reduce Uptake by Allium fistulosum L., and Enhance Microbial Community Diversity.

Science.gov (United States)

Tang, Xiao-Yan; Huang, Wen-Da; Guo, Jing-Jing; Yang, Yang; Tao, Ran; Feng, Xu

2017-07-05

Fe-impregnated biochar was assessed as a method to remove the pesticide pollutant chlorpyrifos, utilizing biochar/FeO x composite synthesized via chemical coprecipitation of Fe 3+ /Fe 2+ onto Cyperus alternifolius biochar. Fe-impregnated biochar exhibited a higher sorption capacity than pristine biochar, resulting in more efficient removal of chlorpyrifos from water. Soil was dosed with pristine or Fe-impregnated biochar at 0.1 or 1.0% w/w, to evaluate chlorpyrifos uptake in Allium fistulosum L. (Welsh onion). The results showed that the average concentration of chlorpyrifos and its degradation product, 3,5,6-trichloro-2-pyridinol (TCP), decreased in A. fistulosum L. with increased levels of pristine biochar and Fe-biochar. Fe-biochar was found to be more effective in reducing the uptake of chlorpyrifos by improving the sorption ability and increasing plant root iron plaque. Bioavailability of chlorpyrifos is reduced with both biochar and Fe-biochar soil dosing; however, the greatest persistence of chlorpyrifos residues was observed with 1.0% pristine biochar. Microbial community analysis showed Fe-biochar to have a positive impact on the efficiency of chlorpyrifos degradation in soils, possibly by altering microbial communities.

Final Report: Stability of U (VII) and Tc (VII) Reducing Microbial Communities To Environmental Perturbation

Energy Technology Data Exchange (ETDEWEB)

Istok, Jonathan D

2008-07-07

'Bioimmobilization' of redox-sensitive metals and radionuclides is being investigated as a way to remediate contaminated groundwater and sediments. In this approach, growth-limiting substrates are added to stimulate the activity of targeted groups of indigenous microorganisms and create conditions favorable for the microbially-mediated precipitation ('bioimmobilization') of targeted contaminants. This project investigated a fundamentally new approach for modeling this process that couples thermodynamic descriptions for microbial growth with associated geochemical reactions. In this approach, a synthetic microbial community is defined as a collection of defined microbial groups; each with a growth equation derived from bioenergetic principles. The growth equations and standard-state free energy yields are appended to a thermodynamic database for geochemical reactions and the combined equations are solved simultaneously to predict the effect of added substrates on microbial biomass, community composition, and system geochemistry. This approach, with a single set of thermodynamic parameters (one for each growth equation), was used to predict the results of laboratory and field bioimmobilization experiments at two geochemically diverse research sites. Predicted effects of ethanol or acetate addition on uranium and technetium solubility, major ion geochemistry, mineralogy, microbial biomass and community composition were in general agreement with experimental observations although the available experimental data precluded rigorous model testing. Model simulations provide insight into the long-standing difficulty in transferring experimental results from the laboratory to the field and from one field site to the next, especially if the form, concentration, or delivery of growth substrate is varied from one experiment to the next. Although originally developed for use in better understanding bioimmobilization of uranium and technetium via reductive

Reducing microbial contamination on wastewater-irrigated lettuce by cessation of irrigation before harvesting

DEFF Research Database (Denmark)

Keraita, Bernard; Konradsen, Flemming; Drechsel, Pay

2007-01-01

OBJECTIVE: To assess the effectiveness of cessation of irrigation before harvesting in reducing microbial contamination of lettuce irrigated with wastewater in urban vegetable farming in Ghana. METHODS: Assessment was done under actual field conditions with urban vegetable farmers in Ghana. Trials...... were arranged in completely randomized block design and done both in the dry and wet seasons. Seven hundred and twenty-six lettuce samples and 36 water samples were analysed for thermotolerant coliforms and helminth eggs. RESULTS: On average, 0.65 log units for indicator thermotolerant coliforms and 0.......4 helminth eggs per 100 g of lettuce were removed on each non-irrigated day from lettuce in the dry season. This corresponded to a daily loss of 1.4 tonnes/ha of fresh weight of lettuce. As an input for exposure analysis to make risk estimates, the decay coefficient, k, for thermotolerant coliforms was 0...

The pig gut microbial diversity: Understanding the pig gut microbial ecology through the next generation high throughput sequencing.

Science.gov (United States)

Kim, Hyeun Bum; Isaacson, Richard E

2015-06-12

The importance of the gut microbiota of animals is widely acknowledged because of its pivotal roles in the health and well being of animals. The genetic diversity of the gut microbiota contributes to the overall development and metabolic needs of the animal, and provides the host with many beneficial functions including production of volatile fatty acids, re-cycling of bile salts, production of vitamin K, cellulose digestion, and development of immune system. Thus the intestinal microbiota of animals has been the subject of study for many decades. Although most of the older studies have used culture dependent methods, the recent advent of high throughput sequencing of 16S rRNA genes has facilitated in depth studies exploring microbial populations and their dynamics in the animal gut. These culture independent DNA based studies generate large amounts of data and as a result contribute to a more detailed understanding of the microbiota dynamics in the gut and the ecology of the microbial populations. Of equal importance, is being able to identify and quantify microbes that are difficult to grow or that have not been grown in the laboratory. Interpreting the data obtained from this type of study requires using basic principles of microbial diversity to understand importance of the composition of microbial populations. In this review, we summarize the literature on culture independent studies of the pig gut microbiota with an emphasis on its succession and alterations caused by diverse factors. Copyright © 2015 Elsevier B.V. All rights reserved.

Screen-Printed Electrodes: New Tools for Developing Microbial Electrochemistry at Microscale Level

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Marta Estevez-Canales

2015-11-01

Full Text Available Microbial electrochemical technologies (METs have a number of potential technological applications. In this work, we report the use of screen-printed electrodes (SPEs as a tool to analyze the microbial electroactivity by using Geobacter sulfurreducens as a model microorganism. We took advantage of the small volume required for the assays (75 μL and the disposable nature of the manufactured strips to explore short-term responses of microbial extracellular electron transfer to conductive materials under different scenarios. The system proved to be robust for identifying the bioelectrochemical response, while avoiding complex electrochemical setups, not available in standard biotechnology laboratories. We successfully validated the system for characterizing the response of Geobacter sulfurreducens in different physiological states (exponential phase, stationary phase, and steady state under continuous culture conditions revealing different electron transfer responses. Moreover, a combination of SPE and G. sulfurreducens resulted to be a promising biosensor for quantifying the levels of acetate, as well as for performing studies in real wastewater. In addition, the potential of the technology for identifying electroactive consortia was tested, as an example, with a mixed population with nitrate-reducing capacity. We therefore present SPEs as a novel low-cost platform for assessing microbial electrochemical activity at the microscale level.

Marine snow microbial communities: scaling of abundances with aggregate size

DEFF Research Database (Denmark)

Kiørboe, Thomas

2003-01-01

Marine aggregates are inhabited by diverse microbial communities, and the concentration of attached microbes typically exceeds concentrations in the ambient water by orders of magnitude. An extension of the classical Lotka-Volterra model, which includes 3 trophic levels (bacteria, flagellates...... are controlled by flagellate grazing, while flagellate and ciliate populations are governed by colonization and detachment. The model also suggests that microbial populations are turned over rapidly (1 to 20 times d-1) due to continued colonization and detachment. The model overpredicts somewhat the scaling...... of microbial abundances with aggregate size observed in field-collected aggregates. This may be because it disregards the aggregation/disaggregation dynamics of aggregates, as well as interspecific interactions between bacteria....

Improvement in shelf life of minimally processed cilantro leaves through integration of kinetin pretreatment and packaging interventions: Studies on microbial population dynamics, biochemical characteristics and flavour retention.

Science.gov (United States)

Ranjitha, K; Shivashankara, K S; Sudhakar Rao, D V; Oberoi, Harinder Singh; Roy, T K; Bharathamma, H

2017-04-15

Effect of integrating optimized combination of pretreatment with packaging on shelf life of minimally processed cilantro leaves (MPCL) was appraised through analysis of their sensory attributes, biochemical characteristics, microbial population and flavour profile during storage. Minimally pretreated cilantro leaves pretreated with 50ppm kinetin and packed in 25μ polypropylene bags showed a shelf life of 21days. Optimized combination helped in efficiently maintaining sensory parameters, flavour profile, and retention of antioxidants in MPCL until 21days. Studies conducted on the effect of optimized combination on microbial population and flavour profile revealed that among different microorganisms, pectinolysers had a significant effect on spoilage of MPCL and their population of ⩽3.59logcfu/g was found to be acceptable. Principal component analysis of headspace volatiles revealed that (E)-2-undecenal, (E)-2-hexadecenal, (E)-2-tetradecenal & (E)-2-tetradecen-1-ol in stored samples clustered with fresh samples and therefore, could be considered as freshness indicators for MPCL. Copyright © 2016 Elsevier Ltd. All rights reserved.

Selection dramatically reduces effective population size in HIV-1 infection

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Mittler John E

2008-05-01

Full Text Available Abstract Background In HIV-1 evolution, a 100–100,000 fold discrepancy between census size and effective population size (Ne has been noted. Although it is well known that selection can reduce Ne, high in vivo mutation and recombination rates complicate attempts to quantify the effects of selection on HIV-1 effective size. Results We use the inbreeding coefficient and the variance in allele frequency at a linked neutral locus to estimate the reduction in Ne due to selection in the presence of mutation and recombination. With biologically realistic mutation rates, the reduction in Ne due to selection is determined by the strength of selection, i.e., the stronger the selection, the greater the reduction. However, the dependence of Ne on selection can break down if recombination rates are very high (e.g., r ≥ 0.1. With biologically likely recombination rates, our model suggests that recurrent selective sweeps similar to those observed in vivo can reduce within-host HIV-1 effective population sizes by a factor of 300 or more. Conclusion Although other factors, such as unequal viral reproduction rates and limited migration between tissue compartments contribute to reductions in Ne, our model suggests that recurrent selection plays a significant role in reducing HIV-1 effective population sizes in vivo.

Melimine-Coated Antimicrobial Contact Lenses Reduce Microbial Keratitis in an Animal Model.

Science.gov (United States)

Dutta, Debarun; Vijay, Ajay K; Kumar, Naresh; Willcox, Mark D P

2016-10-01

To determine the ability of antimicrobial peptide melimine-coated contact lenses to reduce the incidence of microbial keratitis (MK) in a rabbit model of contact lens wear. In vitro antimicrobial activity of melimine-coated contact lenses was determined against Pseudomonas aeruginosa by viable count and a radiolabeled assay. The amount of lipopolysaccharide (LPS) associated with bacteria bound to melimine-coated and control lenses was determined. Ocular swabs from rabbit eyes were collected for assessment of ocular microflora. A rabbit model for MK was developed that used overnight wear of contact lenses colonized by P. aeruginosa in the absence of a corneal scratch. During lens wear, detailed ocular examinations were performed, and the incidence of MK was investigated. Bacteria associated with worn lenses and infected corneas were determined by viable plate count. Inhibition in viable and total P. aeruginosa adhesion by melimine-coated contact lenses was 3.1 log10 and 0.4 log10, respectively. After colonization, the amount of LPS on lenses was approximately the same with or without melimine. Gram-positive bacteria were found in all the ocular swabs followed by fungus (42%). Melimine-coated lens wear was protective and significantly (odds ratio 10.12; P = 0.012) reduced the incidence of P. aeruginosa-driven MK in the rabbit model. The antimicrobial lenses were associated with significantly (P lenses can produce MK without corneal epithelial defect in an animal model. Melimine-coated contact lenses reduced the incidence of MK associated with P. aeruginosa in vivo. Development of MK requires viable bacteria adherent to contact lenses, and bacterial debris adherent at the lens surface did not cause keratitis.

The ecological effects of different loading rates of metalaxyl on microbial biomass in unplanted and planted soils under field conditions

Directory of Open Access Journals (Sweden)

M. Mansourzadeh

2016-05-01

Full Text Available Fungicides are most widely used pesticides in Iran and the world. Application of fungicides may affect the populations and activity of soil microorganisms, particularly fungi, with a consequence for soil fertility and crop growth. In the current study, the effects of different levels of metalaxyl on soil microbial biomass carbon (C and nitrogen (N, microbial biomass C/N ratio and metabolic quotient under field conditions were assessed. Two levels of metalaxyl (30 and 60 kg.ha-1 were applied in planted soils with corn and unplanted calcareous soils, using a split-plots experiment in a completely randomized design with three replications. The C and N contents in soil microbial biomass as well as metabolic quotient were measured at 30 and 90 days after the onset of the experiment. Results showed that in cultivated soils metalaxyl application at 30 kg.ha-1 increased (15-80% significantly (p≤0.01 the amounts of microbial biomass C and N at both intervals (except microbial biomass C at 90 days compared to the control soil (0 kg.ha-1, while in uncultivated soils both microbial biomass C and N reduced by almost 1-34%. Microbial biomass C/N ratios in unplanted soils decreased (15 and 53% with increasing loading rates of metalaxyl, without a clear effect in cultivated soils. On the other hand, metabolic quotient values reduced (48% at 30 and 60 kg.ha-1 metalaxyl in corn-cultivated soils when compared to untreated soils while in uncultivated soils metalaxyl rate at 30 kg.a-1 had the greatest values at 30 days, and increased with increasing the levels of metalaxyl at 90 days. In summary, application of metalaxyl can either reduce or increase soil biological indices, and the direction and changes are depended upon the application rate of metalaxyl, time elapsed since metalaxyl application and the presence or absence of plant.

Response of African marigold (Tagetes erecta L. to different concentrations of chlorpyrifos and microbial diversity in root rhizosphere

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Mani Santhoshkumar

2017-04-01

Full Text Available Objective: To assess the response of African marigold (Tagetes erecta L. to exposed different concentration of chlorpyrifos by evaluating morphology (root and shoot length, biomass (fresh weight and dry weight, photosynthetic pigments (chlorophyll a and b, protein and microbial diversity in root rhizosphere. Methods: The study was carried out in pot culture and treated with various concentrations (0.5%, 1.0%, 2.0%, and 2.5% as well as control treatments. The morphological, biomass, photosynthetic pigments, protein, and microbial diversity were analyzed on 30, 60, and 90 days. Results: The obtained results revealed that the tested pesticide reduced the growth, biomass and photosynthetic pigment of African marigold when applied at higher concentration than the optimum dosage. But the lower dose the pesticide had some stimulatory effect of analyzed parameters. A similar effect of pesticide was observed on the microbial population of root rhizosphere that is decreased in microbial population was caused at higher doses. But it was increased at lower doses. Conclusions: It can be concluded that pesticide above the certain dosage level adversely affect all the analyzed parameters at higher doses. The application of recommended doses should be discouraged. Further study is needed for the effect of pesticide use on microbial diversity, since these studies are carried out in a controlled pot experiment, including the current study. Thus, future study directed towards by studying the phyoremediation of theses contaminted site with intraction of microbes.

Microbial diversity arising from thermodynamic constraints

Science.gov (United States)

Großkopf, Tobias; Soyer, Orkun S

2016-01-01

The microbial world displays an immense taxonomic diversity. This diversity is manifested also in a multitude of metabolic pathways that can utilise different substrates and produce different products. Here, we propose that these observations directly link to thermodynamic constraints that inherently arise from the metabolic basis of microbial growth. We show that thermodynamic constraints can enable coexistence of microbes that utilise the same substrate but produce different end products. We find that this thermodynamics-driven emergence of diversity is most relevant for metabolic conversions with low free energy as seen for example under anaerobic conditions, where population dynamics is governed by thermodynamic effects rather than kinetic factors such as substrate uptake rates. These findings provide a general understanding of the microbial diversity based on the first principles of thermodynamics. As such they provide a thermodynamics-based framework for explaining the observed microbial diversity in different natural and synthetic environments. PMID:27035705

Microbial diversity arising from thermodynamic constraints.

Science.gov (United States)

Großkopf, Tobias; Soyer, Orkun S

2016-11-01

The microbial world displays an immense taxonomic diversity. This diversity is manifested also in a multitude of metabolic pathways that can utilise different substrates and produce different products. Here, we propose that these observations directly link to thermodynamic constraints that inherently arise from the metabolic basis of microbial growth. We show that thermodynamic constraints can enable coexistence of microbes that utilise the same substrate but produce different end products. We find that this thermodynamics-driven emergence of diversity is most relevant for metabolic conversions with low free energy as seen for example under anaerobic conditions, where population dynamics is governed by thermodynamic effects rather than kinetic factors such as substrate uptake rates. These findings provide a general understanding of the microbial diversity based on the first principles of thermodynamics. As such they provide a thermodynamics-based framework for explaining the observed microbial diversity in different natural and synthetic environments.

Comparative metagenomic analysis of PAH degradation in soil by a mixed microbial consortium.

Science.gov (United States)

Zafra, German; Taylor, Todd D; Absalón, Angel E; Cortés-Espinosa, Diana V

2016-11-15

In this study, we used a taxonomic and functional metagenomic approach to analyze some of the effects (e.g. displacement, permanence, disappearance) produced between native microbiota and a previously constructed Polycyclic Aromatic Hydrocarbon (PAH)-degrading microbial consortium during the bioremediation process of a soil polluted with PAHs. Bioaugmentation with a fungal-bacterial consortium and biostimulation of native microbiota using corn stover as texturizer produced appreciable changes in the microbial diversity of polluted soils, shifting native microbial communities in favor of degrading specific populations. Functional metagenomics showed changes in gene abundance suggesting a bias towards aromatic hydrocarbon and intermediary degradation pathways, which greatly favored PAH mineralization. In contrast, pathways favoring the formation of toxic intermediates such as cytochrome P450-mediated reactions were found to be significantly reduced in bioaugmented soils. PAH biodegradation in soil using the microbial consortium was faster and reached higher degradation values (84% after 30 d) as a result of an increased co-metabolic degradation when compared with other mixed microbial consortia. The main differences between inoculated and non-inoculated soils were observed in aromatic ring-hydroxylating dioxygenases, laccase, protocatechuate, salicylate and benzoate-degrading enzyme genes. Based on our results, we propose that several concurrent metabolic pathways are taking place in soils during PAH degradation. Copyright © 2016 Elsevier B.V. All rights reserved.

The effect of alum addition on microbial communities in poultry litter.

Science.gov (United States)

Rothrock, M J; Cook, K L; Warren, J G; Sistani, K

2008-08-01

Alum [Al(2)(SO(4))(3).14H(2)O] is a common poultry litter amendment used to decrease water-soluble phosphorus or reduce ammonia volatilization, or both. Although the physiochemical effects of alum addition have been well researched, little attention has been given to the poultry litter microbial communities. The goal of this study was to use molecular biological methods [denaturing gradient gel electrophoresis (DGGE), community cloning, and quantitative real-time PCR] to characterize general, group-specific and pathogenic microbial communities in alum (10% wt/wt) and non-alum-treated litter. According to quantitative real-time PCR analyses, alum addition to the poultry litter resulted in significant reductions in both Campylobacter jejuni and Escherichia coli concentrations by the end of the first month of the experiment (3 log and 2 log, respectively). The concentrations of Salmonella spp. were below detection (Eubacterium and low %GC gram-positive groups in the alum-treated litters by the end of the first month, with no bands detectable for either group after 8 wk of incubation. Conversely, minimal effects of alum addition were observed in the Actinomycetes community. The most significant shift in the microbial community (based on DGGE analyses) occurred in the fungal population, with a large increase in diversity and abundance within 1 mo of alum addition (1 dominant band on d 0 to 9 dominant bands at 4 wk). Specifically, the incidence of Aspergillus spp. increased from 0 to 50% of the sequences in fungal clone libraries (n = 80) over the course of the experiment. This suggests that the addition of alum to poultry litter potentially shifts the microbial populations from bacterially dominated to dominated by fungi. The ramifications of this shift in dominance are still unknown, and future work will be aimed at characterizing these fungi and elucidating their role in the acidified litter environment.

Influence of cotton crop development and level of irrigation of microbial community structure

Science.gov (United States)

Soil microbial population densities can easily reach one billion cells per gram of soil;and soil microbial diversity has been shown to exceed fifty thousand individual species per gram of soil. Soil type and underlying soil structure are considered primary determinants of microbial community structu...

Coastal microbial mats: the physiology of a small-scale ecosystem

NARCIS (Netherlands)

Stal, L.J.

2001-01-01

Coastal inter-tidal sandy sediments, salt marshes and mangrove forests often support the development of microbial mats. Microbial mats are complex associations of one or several functional groups of microorganisms and their formation usually starts with the growth of a cyanobacterial population on a

Status of microbial diversity in agroforestry systems in Tamil Nadu, India.

Science.gov (United States)

Radhakrishnan, Srinivasan; Varadharajan, Mohan

2016-06-01

Soil is a complex and dynamic biological system. Agroforestry systems are considered to be an alternative land use option to help and prevent soil degradation, improve soil fertility, microbial diversity, and organic matter status. An increasing interest has emerged with respect to the importance of microbial diversity in soil habitats. The present study deals with the status of microbial diversity in agroforestry systems in Tamil Nadu. Eight soil samples were collected from different fields in agroforestry systems in Cuddalore, Villupuram, Tiruvanamalai, and Erode districts, Tamil Nadu. The number of microorganisms and physico-chemical parameters of soils were quantified. Among different microbial population, the bacterial population was recorded maximum (64%), followed by actinomycetes (23%) and fungi (13%) in different samples screened. It is interesting to note that the microbial population was positively correlated with the physico-chemical properties of different soil samples screened. Total bacterial count had positive correlation with soil organic carbon (C), moisture content, pH, nitrogen (N), and micronutrients such as Iron (Fe), copper (Cu), and zinc (Zn). Similarly, the total actinomycete count also showed positive correlations with bulk density, moisture content, pH, C, N, phosphorus (P), potassium (K), calcium (Ca), copper (Cu), magnesium (Mg), manganese (Mn), and zinc (Zn). It was also noticed that the soil organic matter, vegetation, and soil nutrients altered the microbial community under agroforestry systems. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Microbial diversity and metabolic networks in acid mine drainage habitats

Directory of Open Access Journals (Sweden)

Celia eMendez-Garcia

2015-05-01

Full Text Available Acid mine drainage (AMD emplacements are low-complexity natural systems. Low-pH conditions appear to be the main factor underlying the limited diversity of the microbial populations thriving in these environments, although temperature, ionic composition, total organic carbon and dissolved oxygen are also considered to significantly influence their microbial life. This natural reduction in diversity driven by extreme conditions was reflected in several studies on the microbial populations inhabiting the various micro-environments present in such ecosystems. Early studies based on the physiology of the autochthonous microbiota and the growing success of omics technologies have enabled a better understanding of microbial ecology and function in low-pH mine outflows; however, complementary omics-derived data should be included to completely describe their microbial ecology. Furthermore, recent updates on the distribution of eukaryotes and ultra-micro-archaea demand their inclusion in the microbial characterisation of AMD systems. In this review, we present a complete overview of the bacterial, archaeal (including ultra-micro-archaeal and eukaryotic diversity in these ecosystems and include a thorough depiction of the metabolism and element cycling in AMD habitats. We also review different metabolic network structures at the organismal level, which is necessary to disentangle the role of each member of the AMD communities described thus far.

Advanced Microscopy of Microbial Cells

DEFF Research Database (Denmark)

Haagensen, Janus Anders Juul; Regenberg, Birgitte; Sternberg, Claus

2011-01-01

microscopy, super-resolution optical microscopy (STED, SIM, PALM) as well as atomic force microscopy and Raman spectroscopy. Using examples of bistability in microbial populations as well as biofilm development and differentiation in bacterial and yeast consortia, we demonstrate the importance of microscopy...

Evaluation of methyl bromide alternatives efficacy against soil-borne pathogens, nematodes and soil microbial community.

Directory of Open Access Journals (Sweden)

Hongwei Xie

Full Text Available Methyl bromide (MB and other alternatives were evaluated for suppression of Fusarium spp., Phytophthora spp., and Meloidogyne spp. and their influence on soil microbial communities. Both Fusarium spp. and Phytophthora spp. were significantly reduced by the MB (30.74 mg kg-1, methyl iodide (MI: 45.58 mg kg-1, metham sodium (MS: 53.92 mg kg-1 treatments. MS exhibited comparable effectiveness to MB in controlling Meloidogyne spp. and total nematodes, followed by MI at the tested rate. By contrast, sulfuryl fluoride (SF: 33.04 mg kg-1 and chloroform (CF: 23.68 mg kg-1 showed low efficacy in controlling Fusarium spp., Phytophthora spp., and Meloidogyne spp. MB, MI and MS significantly lowered the abundance of different microbial populations and microbial biomass in soil, whereas SF and CF had limited influence on them compared with the control. Diversity indices in Biolog studies decreased in response to fumigation, but no significant difference was found among treatments in PLFA studies. Principal component and cluster analyses of Biolog and PLFA data sets revealed that MB and MI treatments greatly influenced the soil microbial community functional and structural diversity compared with SF treatment. These results suggest that fumigants with high effectiveness in suppressing soil-borne disease could significantly influence soil microbial community.

MICROBIAL SURFACTANTS IN ENVIRONMENTAL TECHNOLOGIES

Directory of Open Access Journals (Sweden)

T. P. Pirog

2015-08-01

Full Text Available It was shown literature and own experimental data concerning the use of microbial surface active glycolipids (rhamno-, sophoro- and trehalose lipids and lipopeptides for water and soil purification from oil and other hydrocarbons, removing toxic heavy metals (Cu2+, Cd2+, Ni2+, Pb2+, degradation of complex pollution (oil and other hydrocarbons with heavy metals, and the role of microbial surfactants in phytoremediation processes. The factors that limit the use of microbial surfactants in environmental technologies are discussed. Thus, at certain concentrations biosurfactant can exhibit antimicrobial properties and inhibit microorganisms destructing xenobiotics. Microbial biodegradability of surfactants may also reduce the effectiveness of bioremediation. Development of effective technologies using microbial surfactants should include the following steps: monitoring of contaminated sites to determine the nature of pollution and analysis of the autochthonous microbiota; determining the mode of surfactant introduction (exogenous addition of stimulation of surfactant synthesis by autochthonous microbiota; establishing an optimal concentration of surfactant to prevent exhibition of antimicrobial properties and rapid biodegradation; research both in laboratory and field conditions.

Effects of mannan oligosaccharide and virginiamycin on the cecal microbial community and intestinal morphology of chickens raised under suboptimal conditions.

Science.gov (United States)

Pourabedin, Mohsen; Xu, Zhengxin; Baurhoo, Bushansingh; Chevaux, Eric; Zhao, Xin

2014-05-01

There is an increasing movement against use of antibiotic growth promoters in animal feed. Prebiotic supplementation is a potential alternative to enhance the host's natural defense through modulation of gut microbiota. In the present study, the effect of mannan oligosaccharide (MOS) and virginiamycin (VIRG) on cecal microbial ecology and intestinal morphology of broiler chickens raised under suboptimal conditions was evaluated. MOS and VIRG induced different bacterial community structures, as revealed by denaturing gradient gel electrophoresis of 16S rDNA. The antibiotic treatment reduced cecal microbial diversity while the community equitability increased. A higher bacterial diversity was observed in the cecum of MOS-supplemented birds. Quantitative polymerase chain reaction results indicated that MOS changed the cecal microbiota in favor of the Firmicutes population but not the Bacteroidetes population. No difference was observed in total bacterial counts among treatments. MOS promoted the growth of Lactobacillus spp. and Bifidobacterium spp. in the cecum and increased villus height and goblet cell numbers in the ileum and jejunum. These results provide a deeper insight into the microbial ecological changes after supplementation of MOS prebiotic in poultry diets.

Systems biology of Microbial Communities

Energy Technology Data Exchange (ETDEWEB)

Navid, A; Ghim, C; Fenley, A; Yoon, S; Lee, S; Almaas, E

2008-04-11

Microbes exist naturally in a wide range of environments, spanning the extremes of high acidity and high temperature to soil and the ocean, in communities where their interactions are significant. We present a practical discussion of three different approaches for modeling microbial communities: rate equations, individual-based modeling, and population dynamics. We illustrate the approaches with detailed examples. Each approach is best fit to different levels of system representation, and they have different needs for detailed biological input. Thus, this set of approaches is able to address the operation and function of microbial communities on a wide range of organizational levels.

Feedbacks Between Soil Structure and Microbial Activities in Soil

Science.gov (United States)

Bailey, V. L.; Smith, A. P.; Fansler, S.; Varga, T.; Kemner, K. M.; McCue, L. A.

2017-12-01

Soil structure provides the physical framework for soil microbial habitats. The connectivity and size distribution of soil pores controls the microbial access to nutrient resources for growth and metabolism. Thus, a crucial component of soil research is how a soil's three-dimensional structure and organization influences its biological potential on a multitude of spatial and temporal scales. In an effort to understand microbial processes at scale more consistent with a microbial community, we have used soil aggregates as discrete units of soil microbial habitats. Our research has shown that mean pore diameter (x-ray computed tomography) of soil aggregates varies with the aggregate diameter itself. Analyzing both the bacterial composition (16S) and enzyme activities of individual aggregates showed significant differences in the relative abundances of key members the microbial communities associated with high enzyme activities compared to those with low activities, even though we observed no differences in the size of the biomass, nor in the overall richness or diversity of these communities. We hypothesize that resources and substrates have stimulated key populations in the aggregates identified as highly active, and as such, we conducted further research that explored how such key populations (i.e. fungal or bacterial dominated populations) alter pathways of C accumulation in aggregate size domains and microbial C utilization. Fungi support and stabilize soil structure through both physical and chemical effects of their hyphal networks. In contrast, bacterial-dominated communities are purported to facilitate micro- and fine aggregate stabilization. Here we quantify the direct effects fungal versus bacterial dominated communities on aggregate formation (both the rate of aggregation and the quality, quantity and distribution of SOC contained within aggregates). A quantitative understanding of the different mechanisms through which fungi or bacteria shape aggregate

Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning.

Science.gov (United States)

He, Zhili; Zhang, Ping; Wu, Linwei; Rocha, Andrea M; Tu, Qichao; Shi, Zhou; Wu, Bo; Qin, Yujia; Wang, Jianjun; Yan, Qingyun; Curtis, Daniel; Ning, Daliang; Van Nostrand, Joy D; Wu, Liyou; Yang, Yunfeng; Elias, Dwayne A; Watson, David B; Adams, Michael W W; Fields, Matthew W; Alm, Eric J; Hazen, Terry C; Adams, Paul D; Arkin, Adam P; Zhou, Jizhong

2018-02-20

Contamination from anthropogenic activities has significantly impacted Earth's biosphere. However, knowledge about how environmental contamination affects the biodiversity of groundwater microbiomes and ecosystem functioning remains very limited. Here, we used a comprehensive functional gene array to analyze groundwater microbiomes from 69 wells at the Oak Ridge Field Research Center (Oak Ridge, TN), representing a wide pH range and uranium, nitrate, and other contaminants. We hypothesized that the functional diversity of groundwater microbiomes would decrease as environmental contamination (e.g., uranium or nitrate) increased or at low or high pH, while some specific populations capable of utilizing or resistant to those contaminants would increase, and thus, such key microbial functional genes and/or populations could be used to predict groundwater contamination and ecosystem functioning. Our results indicated that functional richness/diversity decreased as uranium (but not nitrate) increased in groundwater. In addition, about 5.9% of specific key functional populations targeted by a comprehensive functional gene array (GeoChip 5) increased significantly ( P contamination and ecosystem functioning. This study indicates great potential for using microbial functional genes to predict environmental contamination and ecosystem functioning. IMPORTANCE Disentangling the relationships between biodiversity and ecosystem functioning is an important but poorly understood topic in ecology. Predicting ecosystem functioning on the basis of biodiversity is even more difficult, particularly with microbial biomarkers. As an exploratory effort, this study used key microbial functional genes as biomarkers to provide predictive understanding of environmental contamination and ecosystem functioning. The results indicated that the overall functional gene richness/diversity decreased as uranium increased in groundwater, while specific key microbial guilds increased significantly as

Microbial growth associated with granular activated carbon in a pilot water treatment facility.

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Wilcox, D P; Chang, E; Dickson, K L; Johansson, K R

1983-01-01

The microbial dynamics associated with granular activated carbon (GAC) in a pilot water treatment plant were investigated over a period of 16 months. Microbial populations were monitored in the influent and effluent waters and on the GAC particles by means of total plate counts and ATP assays. Microbial populations between the influent and effluent waters of the GAC columns generally increased, indicating microbial growth. The dominant genera of microorganisms isolated from interstitial waters and GAC particles were Achromobacter, Acinetobacter, Aeromonas, Alcaligenes, Bacillus, Chromobacterium, Corynebacterium, Micrococcus, Microcyclus, Paracoccus, and Pseudomonas. Coliform bacteria were found in small numbers in the effluents from some of the GAC columns in the later months of the study. Oxidation of influent waters with ozone and maintenance of aerobic conditions on the GAC columns failed to appreciably enhance the microbial growth on GAC. PMID:6625567

Density-dependent microbial turnover improves soil carbon model predictions of long-term litter manipulations

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Georgiou, Katerina; Abramoff, Rose; Harte, John; Riley, William; Torn, Margaret

2017-04-01

Climatic, atmospheric, and land-use changes all have the potential to alter soil microbial activity via abiotic effects on soil or mediated by changes in plant inputs. Recently, many promising microbial models of soil organic carbon (SOC) decomposition have been proposed to advance understanding and prediction of climate and carbon (C) feedbacks. Most of these models, however, exhibit unrealistic oscillatory behavior and SOC insensitivity to long-term changes in C inputs. Here we diagnose the sources of instability in four models that span the range of complexity of these recent microbial models, by sequentially adding complexity to a simple model to include microbial physiology, a mineral sorption isotherm, and enzyme dynamics. We propose a formulation that introduces density-dependence of microbial turnover, which acts to limit population sizes and reduce oscillations. We compare these models to results from 24 long-term C-input field manipulations, including the Detritus Input and Removal Treatment (DIRT) experiments, to show that there are clear metrics that can be used to distinguish and validate the inherent dynamics of each model structure. We find that widely used first-order models and microbial models without density-dependence cannot readily capture the range of long-term responses observed across the DIRT experiments as a direct consequence of their model structures. The proposed formulation improves predictions of long-term C-input changes, and implies greater SOC storage associated with CO2-fertilization-driven increases in C inputs over the coming century compared to common microbial models. Finally, we discuss our findings in the context of improving microbial model behavior for inclusion in Earth System Models.

Microbial Genetic Memory to Study Heterogeneous Soil Processes

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Fulk, E. M.; Silberg, J. J.; Masiello, C. A.

2017-12-01

Microbes can be engineered to sense environmental conditions and produce a detectable output. These microbial biosensors have traditionally used visual outputs that are difficult to detect in soil. However, recently developed gas-producing biosensors can be used to noninvasively monitor complex soil processes such as horizontal gene transfer or cell-cell signaling. While these biosensors report on the fraction of a microbial population exposed to a process or chemical signal at the time of measurement, they do not record a "memory" of past exposure. Synthetic biologists have recently developed a suite of genetically encoded memory circuits capable of reporting on historical exposure to the signal rather than just the current state. We will provide an overview of the microbial memory systems that may prove useful to studying microbial decision-making in response to environmental conditions. Simple memory circuits can give a yes/no report of any past exposure to the signal (for example anaerobic conditions, osmotic stress, or high nitrate concentrations). More complicated systems can report on the order of exposure of a population to multiple signals or the experiences of spatially distinct populations, such as those in root vs. bulk soil. We will report on proof-of-concept experiments showing the function of a simple permanent memory system in soil-cultured microbes, and we will highlight additional applications. Finally, we will discuss challenges still to be addressed in applying these memory circuits for biogeochemical studies.

Microbial community dynamics of an urban drinking water distribution system subjected to phases of chloramination and chlorination treatments.

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Hwang, Chiachi; Ling, Fangqiong; Andersen, Gary L; LeChevallier, Mark W; Liu, Wen-Tso

2012-11-01

Water utilities in parts of the U.S. control microbial regrowth in drinking water distribution systems (DWDS) by alternating postdisinfection methods between chlorination and chloramination. To examine how this strategy influences drinking water microbial communities, an urban DWDS (population ≅ 40,000) with groundwater as the source water was studied for approximately 2 years. Water samples were collected at five locations in the network at different seasons and analyzed for their chemical and physical characteristics and for their microbial community composition and structure by examining the 16S rRNA gene via terminal restriction fragment length polymorphism and DNA pyrosequencing technology. Nonmetric multidimension scaling and canonical correspondence analysis of microbial community profiles could explain >57% of the variation. Clustering of samples based on disinfection types (free chlorine versus combined chlorine) and sampling time was observed to correlate to the shifts in microbial communities. Sampling location and water age (chlorinated water, and Methylophilaceae, Methylococcaceae, and Pseudomonadaceae were more abundant in chloraminated water. No correlation was observed with minor populations that were detected frequently (water and survived through the treatment process. Transient microbial populations including Flavobacteriaceae and Clostridiaceae were also observed. Overall, reversible shifts in microbial communities were especially pronounced with chloramination, suggesting stronger selection of microbial populations from chloramines than chlorine.

Yeast population dynamics reveal a potential 'collaboration' between Metschnikowia pulcherrima and Saccharomyces uvarum for the production of reduced alcohol wines during Shiraz fermentation.

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Contreras, A; Curtin, C; Varela, C

2015-02-01

The wine sector is actively seeking strategies and technologies that facilitate the production of wines with lower alcohol content. One of the simplest approaches to achieve this aim would be the use of wine yeast strains which are less efficient at transforming grape sugars into ethanol; however, commercial wine yeasts have very similar ethanol yields. We recently demonstrated that Metschnikowia pulcherrima AWRI1149 was able to produce wine with reduced alcohol concentration when used in sequential inoculation with a wine strain of Saccharomyces cerevisiae. Here, different inoculation regimes were explored to study the effect of yeast population dynamics and potential yeast interactions on the metabolism of M. pulcherrima AWRI1149 during fermentation of non-sterile Shiraz must. Of all inoculation regimes tested, only ferments inoculated with M. pulcherrima AWRI1149 showed reduced ethanol concentration. Population dynamics revealed the presence of several indigenous yeast species and one of these, Saccharomyces uvarum (AWRI 2846), was able to produce wine with reduced ethanol concentration in sterile conditions. Both strains however, were inhibited when a combination of three non-Saccharomyces strains, Hanseniaspora uvarum AWRI863, Pichia kluyveri AWRI1896 and Torulaspora delbrueckii AWRI2845 were inoculated into must, indicating that the microbial community composition might impact on the growth of M. pulcherrima AWRI1149 and S. uvarum AWRI 2846. Our results indicate that mixed cultures of M. pulcherrima AWRI1149 and S. uvarum AWRI2846 enable an additional reduction of wine ethanol concentration compared to the same must fermented with either strain alone. This work thus provides a foundation to develop inoculation regimes for the successful application of non-cerevisiae yeast to the production of wines with reduced alcohol.

Selenite reduction by anaerobic microbial aggregates: Microbial community structure, and proteins associated to the produced selenium spheres.

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Graciela eGonzalez-Gil

2016-04-01

Full Text Available Certain types of anaerobic granular sludge, which consists of microbial aggregates, can reduce selenium oxyanions. To envisage strategies for removing those oxyanions from wastewater and recovering the produced elemental selenium (Se0, insights into the microbial community structure and synthesis of Se0 within these microbial aggregates are required. High-throughput sequencing showed that Veillonellaceae (c.a. 20 % and Pseudomonadaceae (c.a.10 % were the most abundant microbial phylotypes in selenite reducing microbial aggregates. The majority of the Pseudomonadaceae sequences were affiliated to the genus Pseudomonas. A distinct outer layer (~200 m of selenium deposits indicated that bioreduction occurred in the outer zone of the microbial aggregates. In that outer layer, SEM analysis showed abundant intracellular and extracellular Se0 (nano spheres, with some cells having high numbers of intracellular Se0 spheres. Electron tomography showed that microbial cells can harbor a single large intracellular sphere that stretches the cell body. The Se0 spheres produced by the microorganisms were capped with organic material. X-ray photoelectron spectroscopy (XPS analysis of extracted Se0 spheres, combined with a mathematical approach to analyzing XPS spectra from biological origin, indicated that proteins and lipids were components of the capping material associated to the Se0 spheres. The most abundant proteins associated to the spheres were identified by proteomic analysis. Most of the proteins or peptide sequences capping the Se0 spheres were identified as periplasmic outer membrane porins and as the cytoplasmic elongation factor Tu protein, suggesting an intracellular formation of the Se0 spheres. In view of these and previous findings, a schematic model for the synthesis of Se0 spheres by the microorganisms inhabiting the granular sludge is proposed.

Selenite Reduction by Anaerobic Microbial Aggregates: Microbial Community Structure, and Proteins Associated to the Produced Selenium Spheres

KAUST Repository

Gonzalez-Gil, Graciela

2016-04-26

Certain types of anaerobic granular sludge, which consists of microbial aggregates, can reduce selenium oxyanions. To envisage strategies for removing those oxyanions from wastewater and recovering the produced elemental selenium (Se0), insights into the microbial community structure and synthesis of Se0 within these microbial aggregates are required. High-throughput sequencing showed that Veillonellaceae (c.a. 20%) and Pseudomonadaceae (c.a.10%) were the most abundant microbial phylotypes in selenite reducing microbial aggregates. The majority of the Pseudomonadaceae sequences were affiliated to the genus Pseudomonas. A distinct outer layer (∼200 μm) of selenium deposits indicated that bioreduction occurred in the outer zone of the microbial aggregates. In that outer layer, SEM analysis showed abundant intracellular and extracellular Se0 (nano)spheres, with some cells having high numbers of intracellular Se0 spheres. Electron tomography showed that microbial cells can harbor a single large intracellular sphere that stretches the cell body. The Se0 spheres produced by the microorganisms were capped with organic material. X-ray photoelectron spectroscopy (XPS) analysis of extracted Se0 spheres, combined with a mathematical approach to analyzing XPS spectra from biological origin, indicated that proteins and lipids were components of the capping material associated to the Se0 spheres. The most abundant proteins associated to the spheres were identified by proteomic analysis. Most of the proteins or peptide sequences capping the Se0 spheres were identified as periplasmic outer membrane porins and as the cytoplasmic elongation factor Tu protein, suggesting an intracellular formation of the Se0 spheres. In view of these and previous findings, a schematic model for the synthesis of Se0 spheres by the microorganisms inhabiting the granular sludge is proposed.

Microfluidics expanding the frontiers of microbial ecology.

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Rusconi, Roberto; Garren, Melissa; Stocker, Roman

2014-01-01

Microfluidics has significantly contributed to the expansion of the frontiers of microbial ecology over the past decade by allowing researchers to observe the behaviors of microbes in highly controlled microenvironments, across scales from a single cell to mixed communities. Spatially and temporally varying distributions of organisms and chemical cues that mimic natural microbial habitats can now be established by exploiting physics at the micrometer scale and by incorporating structures with specific geometries and materials. In this article, we review applications of microfluidics that have resulted in insightful discoveries on fundamental aspects of microbial life, ranging from growth and sensing to cell-cell interactions and population dynamics. We anticipate that this flexible multidisciplinary technology will continue to facilitate discoveries regarding the ecology of microorganisms and help uncover strategies to control microbial processes such as biofilm formation and antibiotic resistance.

Influence of pulsed magnetic field on soybean (Glycine max L.) seed germination, seedling growth and soil microbial population.

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Radhakrishnan, Ramalingam; Kumari, Bollipo Dyana Ranjitha

2013-08-01

The effects of pulsed magnetic field (PMF) treatment of soybean (Glycine max L. cv CO3) seeds were investigated on rate of seed germination, seedling growth, physico-chemical properties of seed leachates and soil microbial population under laboratory conditions. Seeds were exposed to PMF of 1500 nT at 0.1, 1.0 10.0 and 100.0 Hz for 5 h per day for 20 days, induced by enclosure coil systems. Non-treated seeds were considered as controls. All PMF treatments significantly increased the rate of seed germination, while 10 and 100 Hz PMFs showed the most effective response. The 1.0 and 10 Hz PMFs remarkably improved the fresh weight of shoots and roots, leaf area and plant height from seedlings from magnetically-exposed seeds compared to the control, while 10 Hz PMF increased the total soluble sugar, total protein and phenol contents. The leaf chlorophyll a, b and total chlorophyll were higher in PMF (10 and 100 Hz) pretreated plants, as compared to other treatments. In addition, activities of alpha-amylase, acid phosphatase, alkaline phosphatase, nitrate reductase, peroxidase and polyphenoloxidase were increased, while beta-amylase and protease activities were declined in PMF (10 Hz)-exposed soybean plants. Similarly, the capacity of absorbance of water by seeds and electrical conductivity of seed leachates were significantly enhanced by 10 Hz PMF exposure, whereas PMF (10 Hz) pretreated plants did not affect the microbial population in rhizosphere soil. The results suggested the potential of 10 Hz PMF treatment to enhance the germination and seedling growth of soybean.

Population structure of microbial communities associated with two deep, anaerobic, alkaline aquifers.

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Fry, N K; Fredrickson, J K; Fishbain, S; Wagner, M; Stahl, D A

1997-04-01

Microbial communities of two deep (1,270 and 316 m) alkaline (pH 9.94 and 8.05), anaerobic (Eh, -137 and -27 mV) aquifers were characterized by rRNA-based analyses. Both aquifers, the Grande Ronde (GR) and Priest rapids (PR) formations, are located within the Columbia River Basalt Group in south-central Washington, and sulfidogenesis and methanogenesis characterize the GR and PR formations, respectively. RNA was extracted from microorganisms collected from groundwater by ultrafiltration through hollow-fiber membranes and hybridized to taxon-specific oligonucleotide probes. Of the three domains, Bacteria dominated both communities, making up to 92.0 and 64.4% of the total rRNA from the GR and PR formations, respectively. Eucarya comprised 5.7 and 14.4%, and Archaea comprised 1.8% and 2.5%, respectively. The gram-positive target group was found in both aquifers, 11.7% in GR and 7.6% in PR. Two probes were used to target sulfate- and/or metal-reducing bacteria within the delta subclass of Proteobacteria. The Desulfobacter groups was present (0.3%) only in the high-sulfate groundwater (GR). However, comparable hybridization to a probe selective for the desulfovibrios and some metal-reducing bacteria was found in both aquifers, 2.5 and 2.9% from the GR and PR formations, respectively. Selective PCR amplification and sequencing of the desulfovibrio/metal-reducing group revealed a predominance of desulfovibrios in both systems (17 of 20 clones), suggesting that their environmental distribution is not restricted by sulfate availability.

Microbial Community Structure of a Leachfield Soil: Response to Intermittent Aeration and Tetracycline Addition

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David A. Potts

2013-04-01

Full Text Available Soil-based wastewater treatment systems, or leachfields, rely on microbial processes for improving the quality of wastewater before it reaches the groundwater. These processes are affected by physicochemical system properties, such as O2 availability, and disturbances, such as the presence of antimicrobial compounds in wastewater. We examined the microbial community structure of leachfield mesocosms containing native soil and receiving domestic wastewater under intermittently-aerated (AIR and unaerated (LEACH conditions before and after dosing with tetracycline (TET. Community structure was assessed using phospholipid fatty acid analysis (PLFA, analysis of dominant phylotypes using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR–DGGE, and cloning and sequencing of 16S rRNA genes. Prior to dosing, the same PLFA biomarkers were found in soil from AIR and LEACH treatments, although AIR soil had a larger active microbial population and higher concentrations for nine of 32 PLFA markers found. AIR soil also had a larger number of dominant phylotypes, most of them unique to this treatment. Dosing of mesocosms with TET had a more marked effect on AIR than LEACH soil, reducing the size of the microbial population and the number and concentration of PLFA markers. Dominant phylotypes decreased by ~15% in response to TET in both treatments, although the AIR treatment retained a higher number of phylotypes than the LEACH treatment. Fewer than 10% of clones were common to both OPEN ACCESS Water 2013, 5 506 AIR and LEACH soil, and fewer than 25% of the clones from either treatment were homologous with isolates of known genus and species. These included human pathogens, as well as bacteria involved in biogeochemical transformations of C, N, S and metals, and biodegradation of various organic contaminants. Our results show that intermittent aeration has a marked effect on the size and structure of the microbial community that develops in

Range expansions transition from pulled to pushed waves with increasing cooperativity in an experimental microbial population

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Gandhi, Saurabh; Yurtsev, Eugene; Korolev, Kirill; Gore, Jeff

Range expansions are becoming more frequent due to environmental changes and rare long distance dispersal, often facilitated by anthropogenic activities. Simple models in theoretical ecology explain many emergent properties of range expansions, such as a constant expansion velocity, in terms of organism-level properties such as growth and dispersal rates. Testing these quantitative predictions in natural populations is difficult because of large environmental variability. Here, we used a controlled microbial model system to study range expansions of populations with and without intra-specific cooperativity. For non-cooperative growth, the expansion dynamics were dominated by population growth at the low-density front, which pulled the expansion forward. We found these expansions to be in close quantitative agreement with the classical theory of pulled waves by Fisher and Skellam, suitably adapted to our experimental system. However, as cooperativity increased, the expansions transitioned to being pushed, i.e. controlled by growth in the bulk as well as in the front. Although both pulled and pushed waves expand at a constant velocity and appear otherwise similar, their distinct dynamics leads to very different evolutionary consequences. Given the prevalence of cooperative growth in nature, understanding the effects of cooperativity is essential to managing invading species and understanding their evolution.

Reply to 'Comment on kinetic modeling of microbially-driven redox chemistry of subsurface environments: coupling transport, microbial metabolism and geochemistry' by J. Griffioen

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Hunter, K. S.; Van Cappellen, P.

2000-01-01

Our paper, 'Kinetic modeling of microbially-driven redox chemistry of subsurface environments: coupling transport, microbial metabolism and geochemistry' (Hunter et al., 1998), presents a theoretical exploration of biogeochemical reaction networks and their importance to the biogeochemistry of groundwater systems. As with any other model, the kinetic reaction-transport model developed in our paper includes only a subset of all physically, biologically and chemically relevant processes in subsurface environments. It considers aquifer systems where the primary energy source driving microbial activity is the degradation of organic matter. In addition to the primary biodegradation pathways of organic matter (i.e. respiration and fermentation), the redox chemistry of groundwaters is also affected by reactions not directly involving organic matter oxidation. We refer to the latter as secondary reactions. By including secondary redox reactions which consume reduced reaction products (e.g., Mn2+, FeS, H2S), and in the process compete with microbial heterotrophic populations for available oxidants (i.e. O2, NO3-, Mn(IV), Fe(III), SO42-), we predict spatio-temporal distributions of microbial activity which differ significantly from those of models which consider only the biodegradation reactions. That is, the secondary reactions have a significant impact on the distributions of the rates of heterotrophic and chemolithotrophic metabolic pathways. We further show that secondary redox reactions, as well as non-redox reactions, significantly influence the acid-base chemistry of groundwaters. The distributions of dissolved inorganic redox species along flowpaths, however, are similar in simulations with and without secondary reactions (see Figs. 3(b) and 7(b) in Hunter et al., 1998), indicating that very different biogeochemical reaction dynamics may lead to essentially the same chemical redox zonation of a groundwater system.

PCB126 modulates fecal microbial fermentation of the dietary fiber inulin

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Exposure to environmental pollutants can alter gut microbial populations. Short-chain fatty acids (SCFAs), produced from gut microbial fermentation of dietary fibers such as inulin, exert numerous effects on host energy metabolism. SCFAs are also linked to health promoting effects, including a red...

Effect of adding herbs (Ziziphora clinopodioides, Mentha spicata and Mentha pulegium in milk on performance, blood metabolites and fecal microbial population on Holstein calves

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narges ghahhari

2016-08-01

Full Text Available Introduction Many herbal products (herbs and essential oils are currently used as feed additives by the feed industry in the European Union and elsewhere. These phytogenic substances which increase feed aroma or palatability of feeds are classified as sensory additives by European Council. However, several publications show that some essential oils may have beneficial effects on animal performance and health status because of other properties except their sensory characteristics. These claimed properties are stimulation of digestive secretions; antimicrobial, coccidiostat, anthelmintic, and anti-inflammatory activities; and antioxidant properties. Most research revealed that supplementing herbal essential oils to diets resulted in reducing blood cholesterol, increasing palatability of feed and stimulating the immune system in poultry, while different results obtained by ruminants because of rumen microbial population and ruminal fermentation conditions. The use of large and repeated quantities of antibiotics in animal feed may cause to eliminate beneficial intestinal microflora and innate immune system and subsequently cause to antibiotic resistance and remains antibiotics in animal products. Recently, many herbal products because having flavoring and antimicrobial properties as introduced as good alternatives for antibiotics. The aim of the present investigation was to study of effect of Ziziphora clinopodioies, Mentha spicata and Mentha pulegium on the performance of suckling calves, dry matter digestibility, blood parameters and the immune system, the effect on the incidence of diarrhea and fecal microbial population (Escherichia coli, lactobacillus and total aerobic bacteria. Materials and Methods In the present study, extraction of essential oils from three plant species (Ziziphora clinopodioies, Mentha spicata and Mentha pulegium by means of gas chromatography coupled to mass spectrometry (GC–MS were analyzed. In order to determine the

The effect of D123 wheat as a companion crop on soil enzyme activities, microbial biomass and microbial communities in the rhizosphere of watermelon

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Wei Hui Xu

2015-09-01

Full Text Available The growth of watermelon is often threatened by Fusarium oxysporum f. sp. niveum (Fon in successively monocultured soil, which results in economic loss. The objective of this study was to investigate the effect of D123 wheat as a companion crop on soil enzyme activities, microbial biomass and microbial communities in the rhizosphere of watermelon and to explore the relationship between the effect and the incidence of wilt caused by Fon. The results showed that the activities of soil polyphenol oxidase, urease and invertase were increased, the microbial biomass nitrogen (MBN and microbial biomass phosphorus (MBP were significantly increased, and the ratio of MBC/MBN was decreased (P<0.05. Real-time PCR analysis showed that the Fon population declined significantly in the watermelon/wheat companion system compared with the monoculture system (P<0.05. The analysis of microbial communities showed that the relative abundance of microbial communities was changed in the rhizosphere of watermelon. Compared with the monoculture system, the relative abundances of Alphaproteobacteria, Actinobacteria, Gemmatimonadetes and Sordariomycetes were increased, and the relative abundances of Gammaproteobacteria, Sphingobacteria, Cytophagia, Pezizomycetes, and Eurotiomycetes were decreased in the rhizosphere of watermelon in the watermelon/wheat companion system; importantly, the incidence of Fusarium wilt was also decreased in the watermelon/wheat companion system. In conclusion, this study indicated that D123 wheat as a companion crop increased soil enzyme activities and microbial biomass, decreased the Fon population, and changed the relative abundance of microbial communities in the rhizosphere of watermelon, which may be related to the reduction of Fusarium wilt in the watermelon/wheat companion system.

Mathematical modeling of microbial growth in milk

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Jhony Tiago Teleken

2011-12-01

Full Text Available A mathematical model to predict microbial growth in milk was developed and analyzed. The model consists of a system of two differential equations of first order. The equations are based on physical hypotheses of population growth. The model was applied to five different sets of data of microbial growth in dairy products selected from Combase, which is the most important database in the area with thousands of datasets from around the world, and the results showed a good fit. In addition, the model provides equations for the evaluation of the maximum specific growth rate and the duration of the lag phase which may provide useful information about microbial growth.

Microbial characterization of a radionuclide- and metal-contaminated waste site

International Nuclear Information System (INIS)

Bolton, H. Jr.; Lumppio, H.L.; Ainsworth, C.C.; Plymale, A.E.

1993-04-01

The operation of nuclear processing facilities and defense-related nuclear activities has resulted in contamination of near-surface and deep-subsurface sediments with both radionuclides and metals. The presence of mixed inorganic contaminants may result in undetectable microbial populations or microbial populations that are different from those present in uncontaminated sediments. To determine the impact of mixed radionuclide and metal contaminants on sediment microbial communities, we sampled a processing pond that was used from 1948 to 1975 for the disposal of radioactive and metal-contaminated wastewaters from laboratories and nuclear fuel fabrication facilities on the Hanford Site in Washington State. Because the Hanford Site is located in a semiarid environment with average rainfall of 159 mm/year, the pond dried and a settling basin remained after wastewater input into the pond ceased in 1975. This processing pond basin offered a unique opportunity to obtain near-surface sediments that had been contaminated with both radionuclides and metals for several decades. Our objectives were to determine the viable populations of microorganisms in the sediments and to test several hypotheses about how the addition of both radionuclides and metals influenced the microbial ecology of the sediments. Our first hypothesis was that viable populations of microorganisms would be lower in the more contaminated sediments. Second, we expected that long-term metal exposure would result in enhanced metal resistance. Finally, we hypothesized that microorganisms from the most radioactive sediments should have had enhanced radiation resistance

Enhancement of electricity production by graphene oxide in soil microbial fuel cells and plant microbial fuel cells

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Yuko eGoto

2015-04-01

Full Text Available The effects of graphene oxide (GO on electricity generation in soil microbial fuel cells (SMFCs and plant microbial fuel cell (PMFCs were investigated. GO at concentrations ranging from 0 to 1.9 g•kg-1 was added to soil and reduced for 10 days under anaerobic incubation. All SMFCs (GO-SMFCs utilizing the soils incubated with GO produced electricity at a greater rate and in higher quantities than the SMFCs which did not contain GO. In fed-batch operations, the overall average electricity generation in GO-SMFCs containing 1.0 g•kg-1 of GO was 40 ± 19 mW•m-2, which was significantly higher than the value of 6.6 ± 8.9 mW•m-2 generated from GO-free SMFCs (p -2 of electricity after 27 days of operation. Collectively, this study demonstrates that GO added to soil can be microbially reduced in soil, and facilitates electron transfer to the anode in both SMFCs and PMFCs.

Synbiotic preparation with Lactic acid bacteria and inulin as a functional food: In vivo evaluation of microbial activities, and preneoplastic aberrant crypt foci

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Chaiyavat CHAIYASUT

Full Text Available Abstract Host microbiome and metabolome are associated with the incidence of colorectal cancer (CC, one of the major health problems in developed countries. The pro and prebiotic supplementation helps to improve the host health. Inulin is one such prebiotic used for the enhancement of naïve probiotic bacterial population. This paper explains the impact of inulin (PRE extracted from Jerusalem artichoke (JA, Lactobacillus plantarum HII11 (PRO, and synbiotic (SYN; inulin + L. plantarum HII11 preparation on Azoxymethane mediated CC induced rat model with respect to changes in microbial load, microbial enzymes, and preneoplastic aberrant crypt foci. The results suggested that the PRE and SYN supplementation effectively reduced the selected pathogenic bacteria (Salmonella spp., and Escherichia coli, microbial enzymes and increased the probiotic load. The intervention of SYN significantly reduced the colonic ACF in CC model. The study results revealed that the supplementation of SYN diet (inulin and L. plantarum HII11 protects the AOM-mediated colon cancer induced host.

Surveillance study of bacterial contamination of the parent's cell phone in the NICU and the effectiveness of an anti-microbial gel in reducing transmission to the hands.

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Beckstrom, A C; Cleman, P E; Cassis-Ghavami, F L; Kamitsuka, M D

2013-12-01

To determine the bacterial contamination rate of the parent's cell phone and the effectiveness of anti-microbial gel in reducing transmission of bacteria from cell phone to hands. Cross-sectional study of cultures from the cell phone and hands before and after applying anti-microbial gel (n=50). All cell phones demonstrated bacterial contamination. Ninety percent had the same bacteria on the cell phone and their cleaned hands. Twenty two percent had no growth on their hands after applying anti-microbial gel after they had the same bacteria on the cell phone and hands. Ninety-two percent of parents were aware that cell phones carried bacteria, but only 38% cleaned their cell phones at least weekly. Bacterial contamination of cell phones may serve as vectors for nosocomial infection in the neonatal intensive care unit. Bacteria transmitted from cell phone to hands may not be eliminated using anti-microbial gel. Development of hand hygiene and cell phone cleaning guidelines are needed regarding bedside cell phone use.

Microbial-meiofaunal interrelationships in coastal sediments of the Red Sea.

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El-Serehy, Hamed A; Al-Rasheid, Khaled A; Al-Misned, Fahad A; Al-Talasat, Abdul Allah R; Gewik, Mohamed M

2016-05-01

Population density and biomass of bacteria and meiofauna were investigated seasonally in the sediments of the north-western bank of Red Sea. Samples of sediments were collected seasonally from three different stations to determine microphytobenthic biomass (chlorophyll a), protein, lipid, carbohydrate, and total organic matter concentrations. These investigations revealed that microbial components tended to increase their dominancy, whereas sensitive meiofauna were extremely reduced during the entire study period. Thus a very low density of the total meiofauna (with an annual average of 109 ± 26 ind./10 cm(2)) was recorded whilst the benthic microbial population densities exhibited higher values (ranging from 0.31 ± 0.02 × 10(8) to 43.67 ± 18.62 × 10(8)/g dry sediment). These changes in the relative importance analysis of benthic microbial components versus meiofaunal ones seem to be based on the impact of organic matter accumulation on the function and structure of these benthic communities. Proteins, lipids and carbohydrates showed very low concentration values, and the organic matter mostly consisted of carbohydrates, reflecting lower nutritional values for benthic fauna in general and meiofauna in particular. The distribution of microbial and meiofaunal communities seems to be dependent on the quality of the organic matter rather than on its quantity. Total organic matter concentrations varied between 5.8 and 7.6 mg/g, with organic carbon accounting for only 32% of the total organic matter. Chlorophyll a attained very low values, fluctuating between 0.11 and 0.56 μg/g, indicating the oligotrophy of the studied area. The very low concentration of chlorophyll a in the Red Sea sediment suggests that the sedimentary organic matter, heterotrophic bacteria and/or protozoa constitute an alternative resource that is consumed by meiofauna when algae are less abundant. Protozoa, therefore, represent the "missing link in bacteria-meiofauna interaction

Microbial Diversity of a Heavily Polluted Microbial Mat and Its Community Changes following Degradation of Petroleum Compounds

Science.gov (United States)

Abed, Raeid M. M.; Safi, Nimer M. D.; Köster, Jürgen; de Beer, Dirk; El-Nahhal, Yasser; Rullkötter, Jürgen; Garcia-Pichel, Ferran

2002-01-01

We studied the microbial diversity of benthic cyanobacterial mats inhabiting a heavily polluted site in a coastal stream (Wadi Gaza) and monitored the microbial community response induced by exposure to and degradation of four model petroleum compounds in the laboratory. Phormidium- and Oscillatoria-like cyanobacterial morphotypes were dominant in the field. Bacteria belonging to different groups, mainly the Cytophaga-Flavobacterium-Bacteriodes group, the γ and β subclasses of the class Proteobacteria, and the green nonsulfur bacteria, were also detected. In slurry experiments, these communities efficiently degraded phenanthrene and dibenzothiophene completely in 7 days both in the light and in the dark. n-Octadecane and pristane were degraded to 25 and 34% of their original levels, respectively, within 7 days, but there was no further degradation until 40 days. Both cyanobacterial and bacterial communities exhibited noticeable changes concomitant with degradation of the compounds. The populations enriched by exposure to petroleum compounds included a cyanobacterium affiliated phylogenetically with Halomicronema. Bacteria enriched both in the light and in the dark, but not bacteria enriched in any of the controls, belonged to the newly described Holophaga-Geothrix-Acidobacterium phylum. In addition, another bacterial population, found to be a member of green nonsulfur bacteria, was detected only in the bacteria treated in the light. All or some of the populations may play a significant role in metabolizing the petroleum compounds. We concluded that the microbial mats from Wadi Gaza are rich in microorganisms with high biodegradative potential. PMID:11916684

Genome-scale biological models for industrial microbial systems.

Science.gov (United States)

Xu, Nan; Ye, Chao; Liu, Liming

2018-04-01

The primary aims and challenges associated with microbial fermentation include achieving faster cell growth, higher productivity, and more robust production processes. Genome-scale biological models, predicting the formation of an interaction among genetic materials, enzymes, and metabolites, constitute a systematic and comprehensive platform to analyze and optimize the microbial growth and production of biological products. Genome-scale biological models can help optimize microbial growth-associated traits by simulating biomass formation, predicting growth rates, and identifying the requirements for cell growth. With regard to microbial product biosynthesis, genome-scale biological models can be used to design product biosynthetic pathways, accelerate production efficiency, and reduce metabolic side effects, leading to improved production performance. The present review discusses the development of microbial genome-scale biological models since their emergence and emphasizes their pertinent application in improving industrial microbial fermentation of biological products.

Effect of postharvest practices including degreening on citrus carpoplane microbial biomes.

Science.gov (United States)

Gomba, A; Chidamba, L; Korsten, L

2017-04-01

To investigate the effect of commercial citrus packhouse processing steps on the fruit surface microbiome of Clementines and Palmer navel oranges. Viable bacteria, yeast and fungi counts, and the pyrosequencing analysis of the 16S rRNA and ITS were used to evaluate the community structure and population dynamics of phylloepiphytic bacteria and fungi associated with commercial postharvest processing. Drenching significantly reduced microbial counts in all cases except for yeasts on navels, while the extent of degreening effects varied between the citrus varieties. Pyrosequencing analysis showed a total of 4409 bacteria and 5792 fungi nonchimeric unique sequences with an average of 1102 bacteria and 1448 fungi reads per sample. Dominant phyla on the citrus carpoplane were Proteobacteria (53·5%), Actinobacteria (19·9%), Bacteroidetes (5·6%) and Deinococcus-Thermus (5·4%) for bacteria and Ascomycota (80·5%) and Basidiomycota (9·8%) for fungi. Beginning with freshly harvested fruit fungal diversity declined significantly after drenching, but had little effect on bacteria and populations recovered during degreening treatments, including those for Penicillium sp. Packhouse processing greatly influences microbial communities on the citrus carpoplane. A broad orange biome was described with pyrosequencing and gave insight into the likely survival and persistence of pathogens, especially as they may affect the quality and safety of the packed product. A close examination of the microbiota of fruit and the impact of intervention strategies on the ecological balance may provide a more durable approach to reduce losses and spoilage. © 2017 The Society for Applied Microbiology.

Microbial reprogramming inhibits Western diet-associated obesity.

Directory of Open Access Journals (Sweden)

Theofilos Poutahidis

Full Text Available A recent epidemiological study showed that eating 'fast food' items such as potato chips increased likelihood of obesity, whereas eating yogurt prevented age-associated weight gain in humans. It was demonstrated previously in animal models of obesity that the immune system plays a critical role in this process. Here we examined human subjects and mouse models consuming Westernized 'fast food' diet, and found CD4(+ T helper (Th17-biased immunity and changes in microbial communities and abdominal fat with obesity after eating the Western chow. In striking contrast, eating probiotic yogurt together with Western chow inhibited age-associated weight gain. We went on to test whether a bacteria found in yogurt may serve to lessen fat pathology by using purified Lactobacillus reuteri ATCC 6475 in drinking water. Surprisingly, we discovered that oral L. reuteri therapy alone was sufficient to change the pro-inflammatory immune cell profile and prevent abdominal fat pathology and age-associated weight gain in mice regardless of their baseline diet. These beneficial microbe effects were transferable into naïve recipient animals by purified CD4(+ T cells alone. Specifically, bacterial effects depended upon active immune tolerance by induction of Foxp3(+ regulatory T cells (Treg and interleukin (Il-10, without significantly changing the gut microbial ecology or reducing ad libitum caloric intake. Our finding that microbial targeting restored CD4(+ T cell balance and yielded significantly leaner animals regardless of their dietary 'fast food' indiscretions suggests population-based approaches for weight management and enhancing public health in industrialized societies.

Effects of Plant Extracts on Microbial Population, Methane Emission and Ruminal Fermentation Characteristics in

Directory of Open Access Journals (Sweden)

E. T. Kim

2012-06-01

Full Text Available This study was conducted to evaluate effects of plant extracts on methanogenesis and rumen microbial diversity in in vitro. Plant extracts (Artemisia princeps var. Orientalis; Wormwood, Allium sativum for. Pekinense; Garlic, Allium cepa; Onion, Zingiber officinale; Ginger, Citrus unshiu; Mandarin orange, Lonicera japonica; Honeysuckle were obtained from the Plant Extract Bank at Korea Research Institute of Bioscience and Biotechnology. The rumen fluid was collected before morning feeding from a fistulated Holstein cow fed timothy and commercial concentrate (TDN; 73.5%, crude protein; 19%, crude fat; 3%, crude fiber; 12%, crude ash; 10%, Ca; 0.8%, P; 1.2% in the ratio of 3 to 2. The 30 ml of mixture, comprising McDougall buffer and rumen liquor in the ratio of 4 to 1, was dispensed anaerobically into serum bottles containing 0.3 g of timothy substrate and plant extracts (1% of total volume, respectively filled with O2-free N2 gas and capped with a rubber stopper. The serum bottles were held in a shaking incubator at 39°C for 24 h. Total gas production in all plant extracts was higher (p<0.05 than that of the control, and total gas production of ginger extract was highest (p<0.05. The methane emission was highest (p<0.05 at control, but lowest (p<0.05 at garlic extract which was reduced to about 20% of methane emission (40.2 vs 32.5 ml/g DM. Other plant extracts also resulted in a decrease in methane emissions (wormwood; 8%, onion; 16%, ginger; 16.7%, mandarin orange; 12%, honeysuckle; 12.2%. Total VFAs concentration and pH were not influenced by the addition of plant extracts. Acetate to propionate ratios from garlic and ginger extracts addition samples were lower (p<0.05, 3.36 and 3.38 vs 3.53 than that of the control. Real-time PCR indicted that the ciliate-associated methanogen population in all added plant extracts decreased more than that of the control, while the fibrolytic bacteria population increased. In particular, the F. succinogens

Elucidating Microbial Adaptation Dynamics via Autonomous Exposure and Sampling

Science.gov (United States)

Grace, Joseph M.; Verseux, Cyprien; Gentry, Diana; Moffet, Amy; Thayabaran, Ramanen; Wong, Nathan; Rothschild, Lynn

2013-01-01

The adaptation of micro-organisms to their environments is a complex process of interaction between the pressures of the environment and of competition. Reducing this multifactorial process to environmental exposure in the laboratory is a common tool for elucidating individual mechanisms of evolution, such as mutation rates. Although such studies inform fundamental questions about the way adaptation and even speciation occur, they are often limited by labor-intensive manual techniques. Current methods for controlled study of microbial adaptation limit the length of time, the depth of collected data, and the breadth of applied environmental conditions. Small idiosyncrasies in manual techniques can have large effects on outcomes; for example, there are significant variations in induced radiation resistances following similar repeated exposure protocols. We describe here a project under development to allow rapid cycling of multiple types of microbial environmental exposure. The system allows continuous autonomous monitoring and data collection of both single species and sampled communities, independently and concurrently providing multiple types of controlled environmental pressure (temperature, radiation, chemical presence or absence, and so on) to a microbial community in dynamic response to the ecosystem's current status. When combined with DNA sequencing and extraction, such a controlled environment can cast light on microbial functional development, population dynamics, inter- and intra-species competition, and microbe-environment interaction. The project's goal is to allow rapid, repeatable iteration of studies of both natural and artificial microbial adaptation. As an example, the same system can be used both to increase the pH of a wet soil aliquot over time while periodically sampling it for genetic activity analysis, or to repeatedly expose a culture of bacteria to the presence of a toxic metal, automatically adjusting the level of toxicity based on the

Microbial hydrocarbon degradation - bioremediation of oil spills

Energy Technology Data Exchange (ETDEWEB)

Atlas, R M [Louisville Univ., KY (United States). Dept. of Biology

1991-01-01

Bioremediation has become a major method employed in restoration of oil-polluted environments that makes use of natural microbial biodegradative activities. Bioremediation of petroleum pollutants overcomes the factors limiting rates of microbial hydrocarbon biodegradation. Often this involves using the enzymatic capabilities of the indigenous hydrocarbon-degrading microbial populations and modifying environmental factors, particularly concentrations of molecular oxygen, fixed forms of nitrogen and phosphate to achieve enhanced rates of hydrocarbon biodegradation. Biodegradation of oily sludges and bioremediation of oil-contaminated sites has been achieved by oxygen addition-e.g. by tilling soils in landfarming and by adding hydrogen peroxide or pumping oxygen into oiled aquifers along with addition of nitrogen- and phosphorous-containing fertilizers. The success of seeding oil spills with microbial preparations is ambiguous. Successful bioremediation of a major marine oil spill has been achieved based upon addition of nitrogen and phosphorus fertilizers. (author).

Mapping the ecological networks of microbial communities.

Science.gov (United States)

Xiao, Yandong; Angulo, Marco Tulio; Friedman, Jonathan; Waldor, Matthew K; Weiss, Scott T; Liu, Yang-Yu

2017-12-11

Mapping the ecological networks of microbial communities is a necessary step toward understanding their assembly rules and predicting their temporal behavior. However, existing methods require assuming a particular population dynamics model, which is not known a priori. Moreover, those methods require fitting longitudinal abundance data, which are often not informative enough for reliable inference. To overcome these limitations, here we develop a new method based on steady-state abundance data. Our method can infer the network topology and inter-taxa interaction types without assuming any particular population dynamics model. Additionally, when the population dynamics is assumed to follow the classic Generalized Lotka-Volterra model, our method can infer the inter-taxa interaction strengths and intrinsic growth rates. We systematically validate our method using simulated data, and then apply it to four experimental data sets. Our method represents a key step towards reliable modeling of complex, real-world microbial communities, such as the human gut microbiota.

[Immunomodulators of microbial origin enhance cytotoxicity of human mononuclear leukocytes and reduce metastatic progression of Lewis lung carcinoma in mice].

Science.gov (United States)

Akhmatova, N K; Semenova, I B; Donenko, F V; Kiselevskiĭ, M V; Kurbatova, E A; Egorova, N B

2006-01-01

Effect of immunomodulators for microbial origin on innate immunity and antitumor system was continued to study. Immunomodificator Immunovac VP-4, purified staphylococcal toxoid and glucosaminyl muramyl dipeptide (GMDP) equally enhanced cytotoxicity of mononuclear leukocytes of peripheral blood of healthy donors. Index of cytotoxicity was 2.78, 2.77 and 2.70 respectively. Reduced metastatic progression of Lewis lung carcinoma in mice was observed after Immunovac VP-4 and GMDP administration. Effectiveness was seen when preparations administered according to schedules including their administration before implantation of the tumor. If preparations were administered number of metastases reduced in 4.4-5.6 times and size of metastases reduced in 7-10 times. Interplay between antitumor activity of studied immunomodulators and cytotoxic activity of NK-cells, which are base effectors of antitumor immune response, are discussed.

Assessment of the impact of textile effluents on microbial diversity in Tirupur district, Tamil Nadu

Science.gov (United States)

Prabha, Shashi; Gogoi, Anindita; Mazumder, Payal; Ramanathan, AL.; Kumar, Manish

2017-09-01

The expedited advent of urbanization and industrialization for economic growth has adversely affected the biological diversity, which is one of the major concerns of the developing countries. Microbes play a crucial role in decontaminating polluted sites and degrades pollution load of textile effluent. The present study was based on identification of microbial diversity along the Noyaal river of Tirupur area. River water samples from industrial and non-industrial sites and effluent samples of before and after treatment were tested and it was found that microbial diversity was higher in the river water at the industrial site (Kasipalayam) as compared to the non-industrial site (Perur). Similarly, the microbial populations were found to be high in the untreated effluent as compared to the treated one by conventional treatment systems. Similar trends were observed for MBR treatment systems as well. Pseudomonas sp ., Achromobacter sp. (bacterial species) and Aspergillus fumigates (fungal species), found exclusively at the industrial site have been reported to possess decolorization potential of dye effluent, thus can be used for treatment of dye effluent. The comparison of different microbial communities from different dye wastewater sources and textile effluents was done, which showed that the microbes degrade dyestuffs, reduce toxicity of wastewaters, etc. From the study, it can be concluded that the microbial community helps to check on the pollutants and minimize their affect. Therefore, there is a need to understand the systematic variation in microbial diversity with the accumulation of pollution load through monitoring.

Microbial ecology of denitrification in biological wastewater treatment.

Science.gov (United States)

Lu, Huijie; Chandran, Kartik; Stensel, David

2014-11-01

Globally, denitrification is commonly employed in biological nitrogen removal processes to enhance water quality. However, substantial knowledge gaps remain concerning the overall community structure, population dynamics and metabolism of different organic carbon sources. This systematic review provides a summary of current findings pertaining to the microbial ecology of denitrification in biological wastewater treatment processes. DNA fingerprinting-based analysis has revealed a high level of microbial diversity in denitrification reactors and highlighted the impacts of carbon sources in determining overall denitrifying community composition. Stable isotope probing, fluorescence in situ hybridization, microarrays and meta-omics further link community structure with function by identifying the functional populations and their gene regulatory patterns at the transcriptional and translational levels. This review stresses the need to integrate microbial ecology information into conventional denitrification design and operation at full-scale. Some emerging questions, from physiological mechanisms to practical solutions, for example, eliminating nitrous oxide emissions and supplementing more sustainable carbon sources than methanol, are also discussed. A combination of high-throughput approaches is next in line for thorough assessment of wastewater denitrifying community structure and function. Though denitrification is used as an example here, this synergy between microbial ecology and process engineering is applicable to other biological wastewater treatment processes. Copyright © 2014 Elsevier Ltd. All rights reserved.

Microbial ecology of two hot springs of Sikkim: Predominate population and geochemistry.

Science.gov (United States)

Najar, Ishfaq Nabi; Sherpa, Mingma Thundu; Das, Sayak; Das, Saurav; Thakur, Nagendra

2018-10-01

Northeastern regions of India are known for their floral and faunal biodiversity. Especially the state of Sikkim lies in the eastern Himalayan ecological hotspot region. The state harbors many sulfur rich hot springs which have therapeutic and spiritual values. However, these hot springs are yet to be explored for their microbial ecology. The development of neo generation techniques such as metagenomics has provided an opportunity for inclusive study of microbial community of different environment. The present study describes the microbial diversity in two hot springs of Sikkim that is Polok and Borong with the assist of culture dependent and culture independent approaches. The culture independent techniques used in this study were next generation sequencing (NGS) and Phospholipid Fatty Acid Analysis (PLFA). Having relatively distinct geochemistry both the hot springs are thermophilic environments with the temperature range of 50-77 °C and pH range of 5-8. Metagenomic data revealed the dominance of bacteria over archaea. The most abundant phyla were Proteobacteria and Bacteroidetes although other phyla were also present such as Acidobacteria, Nitrospirae, Firmicutes, Proteobacteria, Parcubacteria and Spirochaetes. The PLFA studies have shown the abundance of Gram Positive bacteria followed by Gram negative bacteria. The culture dependent technique was correlative with PLFA studies. Most abundant bacteria as isolated and identified were Gram-positive genus Geobacillus and Anoxybacillus. The genus Geobacillus has been reported for the first time in North-Eastern states of India. The Geobacillus species obtained from the concerned hot springs were Geobacillus toebii, Geobacillus lituanicus, Geobacillus Kaustophillus and the Anoxybacillus species includes Anoxybacillus gonensis and Anoxybacillus Caldiproteolyticus. The distribution of major genera and their statistical correlation analyses with the geochemistry of the springs predicted that the temperature, p

Corn silage in dairy cow diets to reduce ruminal methanogenesis: effects on the rumen metabolically active microbial communities.

Science.gov (United States)

Lettat, A; Hassanat, F; Benchaar, C

2013-08-01

Methane produced by the methanogenic Archaea that inhabit the rumen is a potent greenhouse gas and represents an energy loss for the animal. Although several strategies have been proposed to mitigate enteric CH4 production, little is known about the effects of dietary changes on the microbial consortia involved in ruminal methanogenesis. Thus, the current study aimed to examine how the metabolically active microbes are affected when dairy cows were fed diets with increasing proportions of corn silage (CS). For this purpose, 9 ruminally cannulated lactating dairy cows were used in a replicated 3 × 3 Latin square design and fed a total mixed ration (60:40 forage:concentrate ratio on a dry matter basis) with the forage portion being either alfalfa silage (0% CS), corn silage (100% CS), or a 50:50 mixture (50% CS). Enteric CH4 production was determined using respiration chambers and total rumen content was sampled for the determination of fermentation characteristics and molecular biology analyses (cDNA-based length heterogeneity PCR, quantitative PCR). The cDNA-based length heterogeneity PCR targeting active microbes revealed similar bacterial communities in cows fed 0% CS and 50% CS diets, whereas important differences were observed between 0% CS and 100% CS diets, including a reduction in the bacterial richness and diversity in cows fed 100% CS diet. As revealed by quantitative PCR, feeding the 100% CS diet increased the number of total bacteria, Prevotella spp., Archaea, and methanogenic activity, though it reduced protozoal number. Meanwhile, increasing the CS proportion in the diet increased propionate concentration but decreased ruminal pH, CH4 production (L/kg of dry matter intake), and concentrations of acetate and butyrate. Based on these microbial and fermentation changes, and because CH4 production was reduced by feeding 100% CS diet, this study shows that the use of cDNA-based quantitative PCR to estimate archaeal growth and activity is not reliable

Microbial contamination and effects of combination treatments and gamma irradiation on reducing microbial contamination of dried cuttle fish

International Nuclear Information System (INIS)

Yen, B.T.

1989-01-01

Dried cuttle fish is one of the most valuable sea products but it rapidly becomes mouldy and spoiled. To solve this problem, the studies on microbial contamination and effects of combination treatments and gamma irradiation for dried cuttle fish have been caried out base on IAEA Research Contracts No 4397/AG and 4397/R1/AG

Microbial population responses in three stratified Antarctic meltwater ponds during the autumn freeze

DEFF Research Database (Denmark)

Safi, Karl; Hawes, Ian; Sorrell, Brian Keith

2012-01-01

The planktonic microbial communities of three meltwater ponds, located on the McMurdo Ice Shelf, were investigated from the end of January 2008 to early April, during which almost the entire pond volumes froze. The ponds were comprised of an upper mixed layer overlying a salt-stabilized density g...... for increasing heterotrophy within the remaining microbial communities, although all components of the food web eventually decline as the final freeze approaches....... role of autotrophic and heterotrophic microplankton within the ponds. The results showed that microbial groups responded to the onset of winter by declining in abundance, though an exception was the appearance of filamentous cyanobacteria in the water column in March. As freezing progressed, autotrophs...... declined more rapidly than heterotrophs and grazing rates and abundances of mixotrophic and heterotrophic organisms increased. Grazing pressure on bacteria and picophytoplankton also increased, in part explaining their decline over time. The results indicate that stressors imposed during freezing select...

D:L-Amino Acid Modeling Reveals Fast Microbial Turnover of Days to Months in the Subsurface Hydrothermal Sediment of Guaymas Basin.

Science.gov (United States)

Møller, Mikkel H; Glombitza, Clemens; Lever, Mark A; Deng, Longhui; Morono, Yuki; Inagaki, Fumio; Doll, Mechthild; Su, Chin-Chia; Lomstein, Bente A

2018-01-01

We investigated the impact of temperature on the microbial turnover of organic matter (OM) in a hydrothermal vent system in Guaymas Basin, by calculating microbial bio- and necromass turnover times based on the culture-independent D:L-amino acid model. Sediments were recovered from two stations near hydrothermal mounds (community of microorganisms in the hydrothermal sediment demonstrated short turnover times. The modeled turnover times of microbial bio- and necromass in the hydrothermal sediments were notably faster (biomass: days to months; necromass: up to a few hundred years) than in the cold sediments (biomass: tens of years; necromass: thousands of years), suggesting that temperature has a significant influence on the microbial turnover rates. We suggest that short biomass turnover times are necessary for maintance of essential cell funtions and to overcome potential damage caused by the increased temperature.The reduced OM quality at the hyrothemal sites might thus only allow for a small population size of microorganisms.

Microbial flora of oil-spilled sites in Egbema, Imo State, Nigeria ...

African Journals Online (AJOL)

The microbial flora of areas with and without oil spillage within the Egbema oil field in Ohaji/Egbema of Imo State was determined by standard microbiological methods. Preliminary results show moderate biological activities in both environments studied. The average microbial population of the area with oil spillage was ...

Microbial flora of oil-spilled sites in Egbema, Imo State, Nigeria

African Journals Online (AJOL)

GREGO

2007-04-16

Apr 16, 2007 ... The microbial flora of areas with and without oil spillage within the Egbema oil field in Ohaji/Egbema of. Imo State was determined by standard microbiological methods. Preliminary results show moderate biological activities in both environments studied. The average microbial population of the area with oil.

The shift of microbial communities and their roles in sulfur and iron cycling in a copper ore bioleaching system

Science.gov (United States)

Niu, Jiaojiao; Deng, Jie; Xiao, Yunhua; He, Zhili; Zhang, Xian; van Nostrand, J. D.; Liang, Yili; Deng, Ye; Liu, Xueduan; Yin, Huaqun

2016-10-01

Bioleaching has been employed commercially to recover metals from low grade ores, but the production efficiency remains to be improved due to limited understanding of the system. This study examined the shift of microbial communities and S&Fe cycling in three subsystems within a copper ore bioleaching system: leaching heap (LH), leaching solution (LS) and sediment under LS. Results showed that both LH and LS had higher relative abundance of S and Fe oxidizing bacteria, while S and Fe reducing bacteria were more abundant in the Sediment. GeoChip analysis showed a stronger functional potential for S0 oxidation in LH microbial communities. These findings were consistent with measured oxidation activities to S0 and Fe2+, which were highest by microbial communities from LH, lower by those from LS and lowest form Sediment. Moreover, phylogenetic molecular ecological network analysis indicated that these differences might be related to interactions among microbial taxa. Last but not the least, a conceptual model was proposed, linking the S&Fe cycling with responsible microbial populations in the bioleaching systems. Collectively, this study revealed the microbial community and functional structures in all three subsystems of the copper ore, and advanced a holistic understanding of the whole bioleaching system.

Subsurface microbial habitats on Mars

Science.gov (United States)

Boston, P. J.; Mckay, C. P.

1991-01-01

We developed scenarios for shallow and deep subsurface cryptic niches for microbial life on Mars. Such habitats could have considerably prolonged the persistence of life on Mars as surface conditions became increasingly inhospitable. The scenarios rely on geothermal hot spots existing below the near or deep subsurface of Mars. Recent advances in the comparatively new field of deep subsurface microbiology have revealed previously unsuspected rich aerobic and anaerobic microbal communities far below the surface of the Earth. Such habitats, protected from the grim surface conditions on Mars, could receive warmth from below and maintain water in its liquid state. In addition, geothermally or volcanically reduced gases percolating from below through a microbiologically active zone could provide the reducing power needed for a closed or semi-closed microbial ecosystem to thrive.

Looking for Darwin's footprints in the microbial world

Energy Technology Data Exchange (ETDEWEB)

Shapiro, B. Jesse; David, Lawrence A.; Friedman, Jonathan; Alm, Eric J.

2009-03-30

As we observe the 200th anniversary of Charles Darwin's birthday, microbiologists interested in the application of Darwin's ideas to the microscopic world have a lot to celebrate: an emerging picture of the (mostly microbial) Tree of Life at ever-increasing resolution, an understanding of horizontal gene transfer as a driving force in the evolution of microbes, and thousands of complete genome sequences to help formulate and refine our theories. At the same time, quantitative models of the microevolutionary processes shaping microbial populations remain just out of reach, a point that is perhaps most dramatically illustrated by the lack of consensus on how (or even whether) to define bacterial species. We summarize progress and prospects in bacterial population genetics, with an emphasis on detecting the footprint of positive Darwinian selection in microbial genomes.

Do roads reduce painted turtle (Chrysemys picta populations?

Directory of Open Access Journals (Sweden)

Alexandra Dorland

Full Text Available Road mortality is thought to be a leading cause of turtle population decline. However, empirical evidence of the direct negative effects of road mortality on turtle population abundance is lacking. The purpose of this study was to provide a strong test of the prediction that roads reduce turtle population abundance. While controlling for potentially confounding variables, we compared relative abundance of painted turtles (Chrysemys picta in 20 ponds in Eastern Ontario, 10 as close as possible to high traffic roads (Road sites and 10 as far as possible from any major roads (No Road sites. There was no significant effect of roads on painted turtle relative abundance. Furthermore, our data do not support other predictions of the road mortality hypothesis; we observed neither a higher relative frequency of males to females at Road sites than at No Road sites, nor a lower average body size of turtles at Road than at No Road sites. We speculate that, although roads can cause substantial adult mortality in turtles, other factors, such as release from predation on adults and/or nests close to roads counter the negative effect of road mortality in some populations. We suggest that road mitigation for painted turtles can be limited to locations where turtles are forced to migrate across high traffic roads due, for example, to destruction of local nesting habitat or seasonal drying of ponds. This conclusion should not be extrapolated to other species of turtles, where road mortality could have a larger population-level effect than on painted turtles.

Do roads reduce painted turtle (Chrysemys picta) populations?

Science.gov (United States)

Dorland, Alexandra; Rytwinski, Trina; Fahrig, Lenore

2014-01-01

Road mortality is thought to be a leading cause of turtle population decline. However, empirical evidence of the direct negative effects of road mortality on turtle population abundance is lacking. The purpose of this study was to provide a strong test of the prediction that roads reduce turtle population abundance. While controlling for potentially confounding variables, we compared relative abundance of painted turtles (Chrysemys picta) in 20 ponds in Eastern Ontario, 10 as close as possible to high traffic roads (Road sites) and 10 as far as possible from any major roads (No Road sites). There was no significant effect of roads on painted turtle relative abundance. Furthermore, our data do not support other predictions of the road mortality hypothesis; we observed neither a higher relative frequency of males to females at Road sites than at No Road sites, nor a lower average body size of turtles at Road than at No Road sites. We speculate that, although roads can cause substantial adult mortality in turtles, other factors, such as release from predation on adults and/or nests close to roads counter the negative effect of road mortality in some populations. We suggest that road mitigation for painted turtles can be limited to locations where turtles are forced to migrate across high traffic roads due, for example, to destruction of local nesting habitat or seasonal drying of ponds. This conclusion should not be extrapolated to other species of turtles, where road mortality could have a larger population-level effect than on painted turtles.

Effects of microbial inhibitors on anaerobic degradation of DDT

Energy Technology Data Exchange (ETDEWEB)

Wang, Y.S.; Chiu, T.C.; Yen, J.H. [National Taiwan Univ., Taipei (Taiwan)

2004-09-15

Chlorinated insecticide DDT [1,1,1-trichloro-2,2-bis(p-chlorophenyl)ethane] was extensively used for controlling pests in the agricultural field and human-being living environments in the past several decades. Due to the chemical stability, DDT was extremely persistent and recalcitrant in soils and sediments and it was banned by nations. Microorganisms usually play important roles in reducing organochlorine compounds in the environments. Under low-oxygen conditions, microbial dechlorination is thought as the onset of highly chlorinated compounds. Methanogenic and sulfate-reducing bacteria participate in microbial dechlorination under anaerobic condition has been reported. In this study, a mixed anaerobic culture enabling to dechlorinate DDT was obtained from river sediment in Taiwan. In order to understand the effect of these microorganisms on DDT dechlorination, microbial inhibitors BESA (2-bromoethanesulfonate) and molybdate, for inhibiting methanogenic and sulfate-reducing bacteria, respectively, were chosen to investigate the interaction between specific microbial communities and their degradation activities. Besides, a molecular technique, denaturing gradient gel electrophoresis (DGGE), based on analyzing the 16S rDNA of bacteria, was used for monitoring the bacterial community structure in this study.

Cooperation, cheating, and collapse in microbial populations

Science.gov (United States)

Gore, Jeff

2012-02-01

Natural populations can suffer catastrophic collapse in response to small changes in environmental conditions, and recovery after such a collapse can be exceedingly difficult. We have used laboratory yeast populations to study proposed early warning signals of impending extinction. Yeast cooperatively breakdown the sugar sucrose, meaning that there is a minimum number of cells required to sustain the population. We have demonstrated experimentally that the fluctuations in the population size increase in magnitude and become slower as the population approaches collapse. The cooperative nature of yeast growth on sucrose suggests that the population may be susceptible to cheater cells, which do not contribute to the public good and instead merely take advantage of the cooperative cells. We have confirmed this possibility experimentally by using a cheater yeast strain that lacks the gene encoding the cooperative behavior [1]. However, recent results in the lab demonstrate that the presence of a bacterial competitor may drive cooperation within the yeast population.[4pt] [1] Gore et al, Nature 459, 253 -- 256 (2009)

Effect of levels of urea and cassava chip on feed intake, rumen fermentation, blood metabolites and microbial populations in growing goats

Directory of Open Access Journals (Sweden)

Metha Wanapat

2007-01-01

Full Text Available The study was conducted to assess effect of levels of urea and cassava chip (CC on feed intake, rumen ecology, blood metabolites and microbial populations. Four, Thai Native X Anglo Nubian crossbred growing male goats with an average liveweight 19.0+1 kg were randomly assigned according to a 4x4 Latin square design to receive one of four diets: T1=urea at 0 % (CC=30%, T2=urea at 1% (CC=40%, T3=urea at 2% (CC = 50% and T4=urea at 3%(CC=60%, of DM basis, respectively. Elephant grass (Pennisetum purpureum was offered on an ad lib basis. The results revealed that total DM intake (%BW and g/kg W0.75 and BW change were similar among treatments (p>0.05. Likewise, rumen pH, BUN, blood glucose, PCV and microbial populations were similar among treatments (p>0.05, while NH3-N increased as the urea level increased and were found highest (p<0.05 in T4 at 12.8 mg/dL. Based on this experiment, it can be concluded that a higher level of urea (3% could be used with a high level of CC in concentrate and it was good approach in exploiting the use of local feed resources for goat production.

Evaluation of treatments with hot water, chemicals and ventilated containers to reduce microbial spoilage in irradiated potatoes

International Nuclear Information System (INIS)

Shirsat, S.G.; Thomas, P.; Nair, P.M.

1991-01-01

Potatoes irradiated to control sprouting were dipped in: hot water (56°C, 5 min; 52°C, 10, 15 and 20 min); cold (25°C, 5 min) or hot (56°C, 5 min) salicylic acid (1000 and 2000 ppm); or sodium hypochlorite (0.1 and 0.2%, 5 min); or dusted with salicylic acid (1 and 2%), to try to reduce the incidence of bacterial soft rot (Erwinia sp.) during controlled temperature (10°C, 15°C) and ambient temperature (20–34°C) storage. All treatments, particularly hot water and hot salicylic acid dip, increased microbial spoilage, possibly as a result of handling damage during the treatments combined with the inhibition of wound periderm formation as a result of irradiation. Storing irradiated tubers in well ventilated containers reduced soft rot compared to storing them in sacks and after 6 months storage at 10, 15 and 20–34°C, 95, 90 and 77% respectively were healthy and marketable. (author)

MICROBIAL MATS - A JOINT VENTURE

NARCIS (Netherlands)

VANGEMERDEN, H

Microbial mats characteristically are dominated by a few functional groups of microbes: cyanobacteria, colorless sulfur bacteria, purple sulfur bacteria, and sulfate-reducing bacteria. Their combined metabolic activities result in steep environmental microgradients, particularly of oxygen and

Abundance, production and stabilization of microbial biomass under conventional and reduced tillage

NARCIS (Netherlands)

Groenigen, van K.J.; Bloem, J.; Baath, E.; Boeckx, P.; Rousk, J.; Bodé, S.; Forristal, P.D.; Jones, M.B.

2010-01-01

Soil tillage practices affect the soil microbial community in various ways, with possible consequences for nitrogen (N) losses, plant growth and soil organic carbon (C) sequestration. As microbes affect soil organic matter (SOM) dynamics largely through their activity, their impact may not be

Effects of different soil management practices on soil properties and microbial diversity

Science.gov (United States)

Gajda, Anna M.; Czyż, Ewa A.; Dexter, Anthony R.; Furtak, Karolina M.; Grządziel, Jarosław; Stanek-Tarkowska, Jadwiga

2018-01-01

The effects of different tillage systems on the properties and microbial diversity of an agricultural soil was investigated. In doing so, soil physical, chemical and biological properties were analysed in 2013-2015, on a long-term field experiment on a loamy sand at the IUNG-PIB Experimental Station in Grabów, Poland. Winter wheat was grown under two tillage treatments: conventional tillage using a mouldboard plough and traditional soil tillage equipment, and reduced tillage based on soil crushing-loosening equipment and a rigid-tine cultivator. Chopped wheat straw was used as a mulch on both treatments. Reduced tillage resulted in increased water content throughout the whole soil profile, in comparison with conventional tillage. Under reduced tillage, the content of readily dispersible clay was also reduced, and, therefore, soil stability was increased in the toplayers, compared with conventional tillage. In addition, the beneficial effects of reduced tillage were reflected in higher soil microbial activity as measured with dehydrogenases and hydrolysis of fluorescein diacetate, compared with conventional tillage. Moreover, the polimerase chain reaction - denaturing gradient gel electrophoresis analysis showed that soil under reduced till-age had greater diversity of microbial communities, compared with conventionally-tilled soil. Finally, reduced tillage increased organic matter content, stability in water and microbial diversity in the top layer of the soil.

Microbial inactivation and MLF performances of Tempranillo Rioja wines treated with PEF after alcoholic fermentation.

Science.gov (United States)

González-Arenzana, Lucía; López-Alfaro, Isabel; Garde-Cerdán, Teresa; Portu, Javier; López, Rosa; Santamaría, Pilar

2018-03-23

This study was performed with the aim of reducing the microbial communities of wines after alcoholic fermentation to improve the establishment of commercial Oenococcus oeni inoculum for developing the malolactic fermentation. Microbial community reduction was accomplished by applying Pulsed Electric Field (PEF) technology to four different wines. Overall, significant reductions in yeast population were observed. To a lesser extent, lactic acid bacteria were reduced while acetic acid bacteria were completely eliminated after the PEF treatment. In three out of the four tested wines, a decrease in the competitive pressure between microorganisms due to the detected reduction led to a general but slight shortening of the malolactic fermentation duration. In the wine with the most adverse conditions to commercial starter establishment, the shortest malolactic fermentation was reached after PEF treatment. Finally, the sensorial quality of three out of the four treated wines was considered better after the PEF treatment. Therefore, PEF technology meant an important tool for improving the malolactic fermentation performance. Copyright © 2018 Elsevier B.V. All rights reserved.

Developing Model Benchtop Systems for Microbial Experimental Evolution

Science.gov (United States)

Gentry, D.; Wang, J.; Arismendi, D.; Alvarez, J.; Ouandji, C.; Blaich, J.

2017-12-01

Understanding how microbes impact an ecosystem has improved through advances of molecular and genetic tools, but creating complex systems that emulate natural biology goes beyond current technology. In fact, many chemical, biological, and metabolic pathways of even model organisms are still poorly characterized. Even then, standard laboratory techniques for testing microbial impact on environmental change can have many drawbacks; they are time-consuming, labor intensive, and are at risk of contamination. By having an automated process, many of these problems can be reduced or even eliminated. We are developing a benchtop system that can run for long periods of time without the need for human intervention, involve multiple environmental stressors at once, perform real-time adjustments of stressor exposure based on current state of the population, and minimize contamination risks. Our prototype device allows operators to generate an analogue of real world micro-scale ecosystems that can be used to model the effects of disruptive environmental change on microbial ecosystems. It comprises of electronics, mechatronics, and fluidics based systems to control, measure, and evaluate the before and after state of microbial cultures from exposure to environmental stressors. Currently, it uses four parallel growth chambers to perform tests on liquid cultures. To measure the population state, optical sensors (LED/photodiode) are used. Its primary selection pressure is UV-C radiation, a well-studied stressor known for its cell- and DNA- damaging effects and as a mutagen. Future work will involve improving the current growth chambers, as well as implementing additional sensors and environmental stressors into the system. Full integration of multiple culture testing will allow inter-culture comparisons. Besides the temperature and OD sensors, other types of sensors can be integrated such as conductivity, biomass, pH, and dissolved gasses such as CO2 and O2. Additional

Non-tuberculous mycobacteria and microbial populations in drinking water distribution systems

Directory of Open Access Journals (Sweden)

Rossella Briancesco

2010-01-01

Full Text Available Data on the occurrence of non-tuberculous mycobacteria (NTM, in parallel with those obtained for bacterial indicators and amoebae, are presented with the aim to collect information on the spread of NTM in drinking water distribution systems in Italy. Samples were collected from taps of hospitals and households in Central and Southern Italy. The concentration values obtained for the more traditional microbial parameters complied with the mandatory requirements for drinking water. Conversely, moderate-to-high microbial loads (till 300 CFU/L were observed for the NTM. Positive samples were obtained from 62% of the investigated water samples. Analogous results were observed for amoebae showing a higher percentage of positive samples (76%. In terms of public health, the presence of mycobacteria in water distribution systems may represent a potential risk especially for vulnerable people such as children, the elderly or immunocompromised individuals.

Mineralization of PAHs in coal-tar impacted aquifer sediments and associated microbial community structure investigated with FISH

Energy Technology Data Exchange (ETDEWEB)

Rogers, S W; Ong, S K; Moorman, T B [Iowa State University, Ames, IA (USA)

2007-11-15

The microbial community structure and mineralization of polycyclic aromatic hydrocarbons (PAHs) in a coal-tar contaminated aquifer were investigated spatially using fluorescence in situ hybridization (FISH) and in laboratory-scale incubations of the aquifer sediments. DAPI-detected microbial populations in the contaminated sediments were three orders of magnitude greater than nearby uncontaminated sediments, suggesting growth on coal-tar constituents in situ. Actinobacteria, {beta}- and {gamma}-Proteobacteria, and Flavobacteria dominated the in situ aerobic (> 1 mg l{sup -1} dissolved oxygen) microbial community, whereas sulfate-reducing bacteria comprised 37% of the microbial community in the sulfidogenic region of the aquifer. Rapid mineralization of naphthalene and phenanthrene were observed in aerobic laboratory microcosms and resulted in significant enrichment of {beta}- and {gamma}-Proteobacteria potentially explaining their elevated presence in situ. Nitrate- and sulfate-limited mineralization of naphthalene in laboratory microcosms occurred to a small degree in aquifer sediments from locations where groundwater chemistry indicated nitrate- and sulfate-reduction, respectively. The results of this study suggest that FISH may be a useful tool for providing a link between laboratory microcosms and groundwater measurements made in situ necessary to better demonstrate the potential for natural attenuation at complex PAH contaminated sites.

Microbial diversity in soil : Selection of microbial populations by plant and soil type and implications for disease suppressiveness

NARCIS (Netherlands)

Garbeva, P; van Veen, JA; van Elsas, JD

2004-01-01

An increasing interest has emerged with respect to the importance of microbial diversity in soil habitats. The extent of the diversity of microorganisms in soil is seen to be critical to the maintenance of soil health and quality, as a wide range of microorganisms is involved in important soil

Reduced inflammation in expanding populations of a neotropical bird species.

Science.gov (United States)

Bailly, Juliette; Garnier, Stéphane; Khimoun, Aurélie; Arnoux, Emilie; Eraud, Cyril; Goret, Jean-Yves; Luglia, Thomas; Gaucher, Philippe; Faivre, Bruno

2016-10-01

The loss of regulating agents such as parasites is among the most important changes in biotic interactions experienced by populations established in newly colonized areas. Under a relaxed parasite pressure, individuals investing less in costly immune mechanisms might experience a selective advantage and become successful colonizers as they re-allocate resources to other fitness-related traits. Accordingly, a refinement of the evolution of increased competitive ability (EICA) hypothesis proposed that immunity of invasive populations has evolved toward a reduced investment in innate immunity, the most costly component of immunity, and an increased humoral immunity that is less costly. Biogeographical approaches comparing populations between native and expansion ranges are particularly relevant in exploring this issue, but remain very scarce. We conducted a biogeographical comparison between populations of Spectacled Thrush ( Turdus nudigenis ) from the native area (South America) and from the expansion range (Caribbean islands). First, we compared haemosporidian prevalence and circulating haptoglobin (an acute-phase protein produced during inflammation). Second, we challenged captive birds from both ranges with Escherichia coli lipopolysaccharides ( LPS ) and measured postchallenge haptoglobin production and body mass change. Birds from the expansion range showed lower haemosporidian prevalence and lower levels of haptoglobin than birds from the native range. In addition, the inflammation elicited by LPS injection and its associated cost in terms of body mass loss were lower in birds from the expansion range than in birds from the native range. In accordance with the enemy release hypothesis, our results suggest that range expansion is associated with a reduced infection risk. Our study also supports the hypothesis that individuals from newly established populations have evolved mechanisms to dampen the inflammatory response and are in accordance with one prediction

Flow cytometric fingerprinting for microbial strain discrimination and physiological characterization.

Science.gov (United States)

Buysschaert, Benjamin; Kerckhof, Frederiek-Maarten; Vandamme, Peter; De Baets, Bernard; Boon, Nico

2018-02-01

The analysis of microbial populations is fundamental, not only for developing a deeper understanding of microbial communities but also for their engineering in biotechnological applications. Many methods have been developed to study their characteristics and over the last few decades, molecular analysis tools, such as DNA sequencing, have been used with considerable success to identify the composition of microbial populations. Recently, flow cytometric fingerprinting is emerging as a promising and powerful method to analyze bacterial populations. So far, these methods have primarily been used to observe shifts in the composition of microbial communities of natural samples. In this article, we apply a flow cytometric fingerprinting method to discriminate among 29 Lactobacillus strains. Our results indicate that it is possible to discriminate among 27 Lactobacillus strains by staining with SYBR green I and that the discriminatory power can be increased by combined SYBR green I and propidium iodide staining. Furthermore, we illustrate the impact of physiological changes on the fingerprinting method by demonstrating how flow cytometric fingerprinting is able to discriminate the different growth phases of a microbial culture. The sensitivity of the method is assessed by its ability to detect changes in the relative abundance of a mix of polystyrene beads down to 1.2%. When a mix of bacteria was used, the sensitivity was as between 1.2% and 5%. The presented data demonstrate that flow cytometric fingerprinting is a sensitive and reproducible technique with the potential to be applied as a method for the dereplication of bacterial isolates. © 2017 International Society for Advancement of Cytometry. © 2017 International Society for Advancement of Cytometry.

Changes of Microbial Population in the Rumen of Dairy Steers as Influenced by Plant Containing Tannins and Saponins and Roughage to Concentrate Ratio

Directory of Open Access Journals (Sweden)

N. Anantasook

2013-11-01

Full Text Available The objective of this study was to investigate microbial population in the rumen of dairy steers as influenced by supplementing with dietary condensed tannins and saponins and different roughage to concentrate ratios. Four, rumen fistulated dairy steers (Bos indicus were used in a 2×2 factorial arrangement in a 4×4 Latin square design. The main factors were two roughage to concentrate ratios (R:C, 60:40 and 40:60 and two supplementations of rain tree pod meal (RPM (0 and 60 g/kg of total DM intake. Chopped 30 g/kg urea treated rice straw was used as a roughage source. All animals received feed according to respective R:C ratios at 25 g/kg body weight. The RPM contained crude tannins and saponins at 84 and 143 g/kg of DM, respectively. It was found that ruminal pH decreased while ruminal temperature increased by a higher concentrate ratio (R:C 40:60 (p<0.05. In contrast, total bacterial, Ruminococus albus and viable proteolytic bacteria were not affected by dietary supplementation. Numbers of fungi, cellulolytic bacteria, Fibrobactor succinogenes and Ruminococus flavefaciens were higher while amylolytic bacteria was lower when steers were fed at 400 g/kg of concentrate. The population of Fibrobactor succinogenes, was found to be higher with RPM supplementation. In addition, the use of real-time PCR technique indicated that the population of protozoa and methanogens were decreased (p<0.05 with supplementation of RPM and with an increasing concentrate ratio. Supplementation of RPM and feeding different concentrate ratios resulted in changing the rumen microbes especially, when the animals were fed at 600 g/kg of concentrate and supplemented with RPM which significantly reduced the protozoa and methanogens population.

An Evaluation of Subsurface Microbial Activity Conditional to Subsurface Temperature, Porosity, and Permeability at North American Carbon Sequestration Sites

Energy Technology Data Exchange (ETDEWEB)

Wilson, B. [Oak Ridge Inst. for Science and Education (ORISE), Oak Ridge, TN (United States); National Energy Technology Lab. (NETL), Albany, OR (United States); Mordensky, S. [Oak Ridge Inst. for Science and Education (ORISE), Oak Ridge, TN (United States); National Energy Technology Lab. (NETL), Albany, OR (United States); Verba, Circe [National Energy Technology Lab. (NETL), Albany, OR (United States); Rabjohns, K. [Oak Ridge Inst. for Science and Education (ORISE), Oak Ridge, TN (United States); National Energy Technology Lab. (NETL), Albany, OR (United States); Colwell, F. [National Energy Technology Lab. (NETL), Albany, OR (United States); Oregon State Univ., Corvallis, OR (United States). College of Earth, Ocean, and Atmospheric Sciences

2016-06-21

Several nations, including the United States, recognize global climate change as a force transforming the global ecosphere. Carbon dioxide (CO₂) is a greenhouse gas that contributes to the evolving climate. Reduction of atmospheric CO₂ levels is a goal for many nations and carbon sequestration which traps CO₂ in the Earth’s subsurface is one method to reduce atmospheric CO₂ levels. Among the variables that must be considered in developing this technology to a national scale is microbial activity. Microbial activity or biomass can change rock permeability, alter artificial seals around boreholes, and play a key role in biogeochemistry and accordingly may determine how CO₂ is sequestered underground. Certain physical parameters of a reservoir found in literature (e.g., temperature, porosity, and permeability) may indicate whether a reservoir can host microbial communities. In order to estimate which subsurface formations may host microbes, this report examines the subsurface temperature, porosity, and permeability of underground rock formations that have high potential to be targeted for CO₂ sequestration. Of the 268 North American wellbore locations from the National Carbon Sequestration Database (NATCARB; National Energy and Technology Laboratory, 2015) and 35 sites from Nelson and Kibler (2003), 96 sequestration sites contain temperature data. Of these 96 sites, 36 sites have temperatures that would be favorable for microbial survival, 48 sites have mixed conditions for supporting microbial populations, and 11 sites would appear to be unfavorable to support microbial populations. Future studies of microbe viability would benefit from a larger database with more formation parameters (e.g. mineralogy, structure, and groundwater chemistry), which would help to increase understanding of where CO₂ sequestration could be most efficiently implemented.

Evolution with a seed bank: The population genetic consequences of microbial dormancy.

Science.gov (United States)

Shoemaker, William R; Lennon, Jay T

2018-01-01

Dormancy is a bet-hedging strategy that allows organisms to persist through conditions that are suboptimal for growth and reproduction by entering a reversible state of reduced metabolic activity. Dormancy allows a population to maintain a reservoir of genetic and phenotypic diversity (i.e., a seed bank) that can contribute to the long-term survival of a population. This strategy can be potentially adaptive and has long been of interest to ecologists and evolutionary biologists. However, comparatively little is known about how dormancy influences the fundamental evolutionary forces of genetic drift, mutation, selection, recombination, and gene flow. Here, we investigate how seed banks affect the processes underpinning evolution by reviewing existing theory, implementing novel simulations, and determining how and when dormancy can influence evolution as a population genetic process. We extend our analysis to examine how seed banks can alter macroevolutionary processes, including rates of speciation and extinction. Through the lens of population genetic theory, we can understand the extent that seed banks influence the evolutionary dynamics of microorganisms as well as other taxa.

Mapping the Centimeter-Scale Spatial Variability of PAHs and Microbial Populations in the Rhizosphere of Two Plants.

Directory of Open Access Journals (Sweden)

Amélia Bourceret

Full Text Available Rhizoremediation uses root development and exudation to favor microbial activity. Thus it can enhance polycyclic aromatic hydrocarbon (PAH biodegradation in contaminated soils. Spatial heterogeneity of rhizosphere processes, mainly linked to the root development stage and to the plant species, could explain the contrasted rhizoremediation efficiency levels reported in the literature. Aim of the present study was to test if spatial variability in the whole plant rhizosphere, explored at the centimetre-scale, would influence the abundance of microorganisms (bacteria and fungi, and the abundance and activity of PAH-degrading bacteria, leading to spatial variability in PAH concentrations. Two contrasted rhizospheres were compared after 37 days of alfalfa or ryegrass growth in independent rhizotron devices. Almost all spiked PAHs were degraded, and the density of the PAH-degrading bacterial populations increased in both rhizospheres during the incubation period. Mapping of multiparametric data through geostatistical estimation (kriging revealed that although root biomass was spatially structured, PAH distribution was not. However a greater variability of the PAH content was observed in the rhizosphere of alfalfa. Yet, in the ryegrass-planted rhizotron, the Gram-positive PAH-degraders followed a reverse depth gradient to root biomass, but were positively correlated to the soil pH and carbohydrate concentrations. The two rhizospheres structured the microbial community differently: a fungus-to-bacterium depth gradient similar to the root biomass gradient only formed in the alfalfa rhizotron.

Microbial analysis of the buffer/container experiment at AECL's Underground Research Laboratory

International Nuclear Information System (INIS)

Stroes-Gascoyne, S.; Hamon, C.J.; Haveman, S.A.; Delaney, T.L.

1996-05-01

The Buffer/Container experiment was carried out for 2.5 years to examine the in-situ performance of compacted buffer material in a single emplacement borehole under vault-relevant conditions. During decommissioning of this experiment, numerous samples were taken for microbial analysis to determine if the naturally present microbial population in buffer material survived to conditions and to determine which groups of microorganisms would be dominant in such a simulated vault environment. Microbial analyses were initiated within 24 hour of sampling for all types of samples taken. The culture results showed an almost universal disappearance of viable microorganisms in the samples taken from near the heater surface. The microbial activity measurements confirmed the lack of viable organisms with very weak or no activity measured in most of these samples. Generally, aerobic heterotrophic culture conditions gave the highest mean colony-forming units (CFU) values at both 25 and 50 C. Under anaerobic conditions, and especially at 50 C, lower mean CFU values were obtained. In all samples analyzed, numbers of sulfate reducing bacteria were less than 1000 CFU/g dry material. Methanogens were either not present or were found in very low numbers. Anaerobic sulfur oxidizing bacteria were found in higher numbers in most sample types with sufficient moisture. The statistical evaluation of the culture data demonstrated clearly that the water content was the variable limiting the viability of the bacteria present, and not the temperature. 68 refs, 35 figs, 37 tabs

Microbial phylogeny determines transcriptional response of resistome to dynamic composting processes.

Science.gov (United States)

Wang, Cheng; Dong, Da; Strong, P J; Zhu, Weijing; Ma, Zhuang; Qin, Yong; Wu, Weixiang

2017-08-16

Animal manure is a reservoir of antibiotic resistance genes (ARGs) that pose a potential health risk globally, especially for resistance to the antibiotics commonly used in livestock production (such as tetracycline, sulfonamide, and fluoroquinolone). Currently, the effects of biological treatment (composting) on the transcriptional response of manure ARGs and their microbial hosts are not well characterized. Composting is a dynamic process that consists of four distinct phases that are distinguished by the temperature resulting from microbial activity, namely the mesophilic, thermophilic, cooling, and maturing phases. In this study, changes of resistome expression were determined and related to active microbiome profiles during the dynamic composting process. This was achieved by integrating metagenomic and time series metatranscriptomic data for the evolving microbial community during composting. Composting noticeably reduced the aggregated expression level of the manure resistome, which primarily consisted of genes encoding for tetracycline, vancomycin, fluoroquinolone, beta-lactam, and aminoglycoside resistance, as well as efflux pumps. Furthermore, a varied transcriptional response of resistome to composting at the ARG levels was highlighted. The expression of tetracycline resistance genes (tetM-tetW-tetO-tetS) decreased during composting, where distinctive shifts in the four phases of composting were related to variations in antibiotic concentration. Composting had no effect on the expression of sulfonamide and fluoroquinolone resistance genes, which increased slightly during the thermophilic phase and then decreased to initial levels. As indigenous populations switched greatly throughout the dynamic composting, the core resistome persisted and their reservoir hosts' composition was significantly correlated with dynamic active microbial phylogenetic structure. Hosts for sulfonamide and fuoroquinolone resistance genes changed notably in phylognetic structure

Detailed analysis of the microbial population in Malaysian spontaneous cocoa pulp fermentations reveals a core and variable microbiota.

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Esther Meersman

Full Text Available The fermentation of cocoa pulp is one of the few remaining large-scale spontaneous microbial processes in today's food industry. The microbiota involved in cocoa pulp fermentations is complex and variable, which leads to inconsistent production efficiency and cocoa quality. Despite intensive research in the field, a detailed and comprehensive analysis of the microbiota is still lacking, especially for the expanding Asian production region. Here, we report a large-scale, comprehensive analysis of four spontaneous Malaysian cocoa pulp fermentations across two time points in the harvest season and two fermentation methods. Our results show that the cocoa microbiota consists of a "core" and a "variable" part. The bacterial populations show a remarkable consistency, with only two dominant species, Lactobacillus fermentum and Acetobacter pasteurianus. The fungal diversity is much larger, with four dominant species occurring in all fermentations ("core" yeasts, and a large number of yeasts that only occur in lower numbers and specific fermentations ("variable" yeasts. Despite this diversity, a clear pattern emerges, with early dominance of apiculate yeasts and late dominance of Saccharomyces cerevisiae. Our results provide new insights into the microbial diversity in Malaysian cocoa pulp fermentations and pave the way for the selection of starter cultures to increase efficiency and consistency.

Detailed analysis of the microbial population in Malaysian spontaneous cocoa pulp fermentations reveals a core and variable microbiota.

Science.gov (United States)

Meersman, Esther; Steensels, Jan; Mathawan, Melissa; Wittocx, Pieter-Jan; Saels, Veerle; Struyf, Nore; Bernaert, Herwig; Vrancken, Gino; Verstrepen, Kevin J

2013-01-01

The fermentation of cocoa pulp is one of the few remaining large-scale spontaneous microbial processes in today's food industry. The microbiota involved in cocoa pulp fermentations is complex and variable, which leads to inconsistent production efficiency and cocoa quality. Despite intensive research in the field, a detailed and comprehensive analysis of the microbiota is still lacking, especially for the expanding Asian production region. Here, we report a large-scale, comprehensive analysis of four spontaneous Malaysian cocoa pulp fermentations across two time points in the harvest season and two fermentation methods. Our results show that the cocoa microbiota consists of a "core" and a "variable" part. The bacterial populations show a remarkable consistency, with only two dominant species, Lactobacillus fermentum and Acetobacter pasteurianus. The fungal diversity is much larger, with four dominant species occurring in all fermentations ("core" yeasts), and a large number of yeasts that only occur in lower numbers and specific fermentations ("variable" yeasts). Despite this diversity, a clear pattern emerges, with early dominance of apiculate yeasts and late dominance of Saccharomyces cerevisiae. Our results provide new insights into the microbial diversity in Malaysian cocoa pulp fermentations and pave the way for the selection of starter cultures to increase efficiency and consistency.

A novel aromatic oil compound inhibits microbial overgrowth on feet: a case study

Directory of Open Access Journals (Sweden)

Misner Bill D

2007-07-01

Full Text Available Abstract Background Athlete's Foot (Tinea pedis is a form of ringworm associated with highly contagious yeast-fungi colonies, although they look like bacteria. Foot bacteria overgrowth produces a harmless pungent odor, however, uncontrolled proliferation of yeast-fungi produces small vesicles, fissures, scaling, and maceration with eroded areas between the toes and the plantar surface of the foot, resulting in intense itching, blisters, and cracking. Painful microbial foot infection may prevent athletic participation. Keeping the feet clean and dry with the toenails trimmed reduces the incidence of skin disease of the feet. Wearing sandals in locker and shower rooms prevents intimate contact with the infecting organisms and alleviates most foot-sensitive infections. Enclosing feet in socks and shoes generates a moisture-rich environment that stimulates overgrowth of pungent both aerobic bacteria and infectious yeast-fungi. Suppression of microbial growth may be accomplished by exposing the feet to air to enhance evaporation to reduce moistures' growth-stimulating effect and is often neglected. There is an association between yeast-fungi overgrowths and disabling foot infections. Potent agents virtually exterminate some microbial growth, but the inevitable presence of infection under the nails predicts future infection. Topical antibiotics present a potent approach with the ideal agent being one that removes moisture producing antibacterial-antifungal activity. Severe infection may require costly prescription drugs, salves, and repeated treatment. Methods A 63-y female volunteered to enclose feet in shoes and socks for 48 hours. Aerobic bacteria and yeast-fungi counts were determined by swab sample incubation technique (1 after 48-hours feet enclosure, (2 after washing feet, and (3 after 8-hours socks-shoes exposure to a aromatic oil powder-compound consisting of arrowroot, baking soda, basil oil, tea tree oil, sage oil, and clove oil. Conclusion

A wooded riparian strip set up for nitrogen removal can affect the water flux microbial composition

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Mizanur Md. Rahman

2014-02-01

Full Text Available This research is part of a project aimed at verifying the potential of a specifically assessed wooded riparian zone in removing excess of combined nitrogen from the Zero river flow for the reduction of nutrient input into Venice Lagoon. Specific objectives were pursued to determine seasonal fluctuations of the microbial populations from the input water to a drainage ditch, conveying back the flux into the river after passing through the soil of the wooded riparian strip. The bacterial communities were determined by combined approaches involving cultivation, microscopic methods and DNA based techniques to determine both culturable and total microbial community in water. The results indicate that the size of the bacterial population, including the culturable fraction, increases from the river to the drainage ditch especially on the warm season. The multiple approach here adopted enabled also to demonstrate that the special condition created in the buffer strip supports the development and the metabolism of the microbial community. The nature of the bacterial population, in terms of phylotypes distribution, was investigated by 16S rDNA analysis indicating that the most represented genera belong to Gamma-proteobacteria, which is known to include an exceeding number of important pathogens. In spring, the effect of the buffer strip seems to significantly reduce such a sub-population. The changes observed for the total bacterial community composition become much evident in summer, as revealed by both denaturing gradient gel electrophoresis cluster analysis and by the diversity index calculation. The hydraulic management coupled to the suspension of farming practices and the development of the woody and herbaceous vegetation resulted in a condition suitable for the containment of undesired microbiota (mainly during the spring season while continuing to support denitrification activity (especially throughout the summer as verified by the total nitrogen

Kinetic modeling of microbially-driven redox chemistry of radionuclides in subsurface environments: Coupling transport, microbial metabolism and geochemistry

International Nuclear Information System (INIS)

Wang, Yifeng; Papenguth, Hans W.

2000-01-01

Microbial degradation of organic matter is a driving force in many subsurface geochemical systems, and therefore may have significant impacts on the fate of radionuclides released into subsurface environments. In this paper, the authors present a general reaction-transport model for microbial metabolism, redox chemistry, and radionuclide migration in subsurface systems. The model explicitly accounts for biomass accumulation and the coupling of radionuclide redox reactions with major biogeochemical processes. Based on the consideration that the biomass accumulation in subsurface environments is likely to achieve a quasi-steady state, they have accordingly modified the traditional microbial growth kinetic equation. They justified the use of the biogeochemical models without the explicit representation of biomass accumulation, if the interest of modeling is in the net impact of microbial reactions on geochemical processes. They then applied their model to a scenario in which an oxic water flow containing both uranium and completing organic ligands is recharged into an oxic aquifer in a carbonate formation. The model simulation shows that uranium can be reduced and therefore immobilized in the anoxic zone created by microbial degradation

Kinetic modeling of microbially-driven redox chemistry of radionuclides in subsurface environments: Coupling transport, microbial metabolism and geochemistry

Energy Technology Data Exchange (ETDEWEB)

WANG,YIFENG; PAPENGUTH,HANS W.

2000-05-04

Microbial degradation of organic matter is a driving force in many subsurface geochemical systems, and therefore may have significant impacts on the fate of radionuclides released into subsurface environments. In this paper, the authors present a general reaction-transport model for microbial metabolism, redox chemistry, and radionuclide migration in subsurface systems. The model explicitly accounts for biomass accumulation and the coupling of radionuclide redox reactions with major biogeochemical processes. Based on the consideration that the biomass accumulation in subsurface environments is likely to achieve a quasi-steady state, they have accordingly modified the traditional microbial growth kinetic equation. They justified the use of the biogeochemical models without the explicit representation of biomass accumulation, if the interest of modeling is in the net impact of microbial reactions on geochemical processes. They then applied their model to a scenario in which an oxic water flow containing both uranium and completing organic ligands is recharged into an oxic aquifer in a carbonate formation. The model simulation shows that uranium can be reduced and therefore immobilized in the anoxic zone created by microbial degradation.

Bioaugmentation of anaerobic sludge digestion with iron-reducing bacteria: process and microbial responses to variations in hydraulic retention time.

Science.gov (United States)

Baek, Gahyun; Kim, Jaai; Shin, Seung Gu; Lee, Changsoo

2016-01-01

Although anaerobic digestion (AD) is a widely used option to manage waste activated sludge (WAS), there are some drawbacks related to its slow reaction rate and low energy productivity. This study examined an anaerobic WAS digester, augmented with an iron-reducing microbial consortium, relative to changes in microbial community structure and process performance at decreasing hydraulic retention times (HRTs) of 20 to 10 days. The enhanced methanation performance (approximately 40 % increase in methane yield) by the bioaugmentation was sustained until the HRT was decreased to 12.5 days, under Fe(3+)-rich conditions (ferric oxyhydroxide, 20 mM Fe). Enhanced iron-reducing activity was evidenced by the increased Fe(2+) to total Fe ratio maintained above 50 % during the stable operational phases. A further decrease in HRT to 10 days resulted in a significant performance deterioration, along with a drop in the Fe(2+) to total Fe ratio to bacteria (IRBs) was identified by denaturing gradient gel electrophoresis (DGGE), with Spirochaetaceae- and Thauera-related organisms being dominant members, and clear dominance shifts among them with respect to decrease in HRT were observed. Lowering HRT led to evident shifts in bacterial community structure likely associated with washout of IRBs, leading to decreases in iron respiration activity and AD performance at a lower HRT. The bacterial community structure shifted dynamically over phases, and the community transitions correlated well with the changes in process performance. Overall, the combined biostimulation and bioaugmentation investigated in this study proved effective for enhanced methane recovery from anaerobic WAS digestion, which suggests an interesting potential for high-rate AD.

Effects of Aspergillus Oryzae Culture and 2-Hydroxy-4-(Methylthio)-Butanoic Acid on In vitro Rumen Fermentation and Microbial Populations between Different Roughage Sources.

Science.gov (United States)

Sun, H; Wu, Y M; Wang, Y M; Liu, J X; Myung, K H

2014-09-01

An in vitro experiment was conducted to evaluate the effects of Aspergillus oryzae culture (AOC) and 2-hydroxy-4-(methylthio)-butanoic acid (HMB) on rumen fermentation and microbial populations between different roughage sources. Two roughage sources (Chinese wild rye [CWR] vs corn silage [CS]) were assigned in a 2×3 factorial arrangement with HMB (0 or 15 mg) and AOC (0, 3, or 6 mg). Gas production (GP), microbial protein (MCP) and total volatile fatty acid (VFA) were increased in response to addition of HMB and AOC (p<0.01) for the two roughages. The HMB and AOC showed inconsistent effects on ammonia-N with different substrates. For CWR, neither HMB nor AOC had significant effect on molar proportion of individual VFA. For CS, acetate was increased (p = 0.02) and butyrate was decreased (p<0.01) by adding HMB and AOC. Increase of propionate was only occurred with AOC (p<0.01). Populations of protozoa (p≤0.03) and fungi (p≤0.02) of CWR were differently influenced by HMB and AOC. Percentages of F. succinogenes, R. albus, and R. flavefaciens (p<0.01) increased when AOC was added to CWR. For CS, HMB decreased the protozoa population (p = 0.01) and increased the populations of F. succinogenes and R. albus (p≤0.03). Populations of fungi, F. succinogenes (p = 0.02) and R. flavefacien (p = 0.03) were increased by adding AOC. The HMB×AOC interactions were noted in MCP, fungi and R. flavefacien for CWR and GP, ammonia-N, MCP, total VFA, propionate, acetate/propionate (A/P) and R. albus for CS. It is inferred that addition of HMB and AOC could influence rumen fermentation of forages by increasing the number of rumen microbes.

The benzoquinone-mediated electrochemical microbial biosensor for water biotoxicity assay

International Nuclear Information System (INIS)

Li, Jiuming; Yu, Yuan; Wang, Yuning; Qian, Jun; Zhi, Jinfang

2013-01-01

Graphical abstract: The mediator can participate in microorganism respiration, accept the electrons from respiratory chains, and therefore be reduced by microorganism. The re-oxidization currents of mediators on electrode can reflect the microbial activity, and when respiration is suppressed by toxicants, it can be detected by the resulting change of currents. Unlike other biotoxicity tests, which record the toxic effect after a fixed time for incubation of biocomponents and toxicants, this mediated whole cell biosensor can provide a real-time monitor of the microbial activity during the measurement. -- Abstract: A simple mediated microbial biosensor providing real-time monitoring of water quality and evaluation of biotoxicity was fabricated by entrapping Escherichia coli (E. coli) cells in gelatin on glassy carbon electrode with benzoquinone as the redox mediator. The biotoxicity assay was based on the respiratory activity of E. coli cells estimated by the oxidation current of microbially reduced benzoquinone. The neutrality and lipophilicity rendered benzoquinone better efficiency than ferricyanide in mediated microbial reactions. After the optimization of preparation conditions, the prepared microbial biosensors have measured several common toxicants with different concentrations. In addition, the biotoxicity of binary mixtures of heavy metals and wastewater were investigated. The fabricated biosensor exhibited good repeatability and stability in the biotoxicity measurements

Toxicity of zero-valent iron nanoparticles to a trichloroethylene-degrading groundwater microbial community.

Science.gov (United States)

Zabetakis, Kara M; Niño de Guzmán, Gabriela T; Torrents, Alba; Yarwood, Stephanie

2015-01-01

The microbiological impact of zero-valent iron used in the remediation of groundwater was investigated by exposing a trichloroethylene-degrading anaerobic microbial community to two types of iron nanoparticles. Changes in total bacterial and archaeal population numbers were analyzed using qPCR and were compared to results from a blank and negative control to assess for microbial toxicity. Additionally, the results were compared to those of samples exposed to silver nanoparticles and iron filings in an attempt to discern the source of toxicity. Statistical analysis revealed that the three different iron treatments were equally toxic to the total bacteria and archaea populations, as compared with the controls. Conversely, the silver nanoparticles had a limited statistical impact when compared to the controls and increased the microbial populations in some instances. Therefore, the findings suggest that zero-valent iron toxicity does not result from a unique nanoparticle-based effect.

Microbial contaminants in Pakistan: a review

Directory of Open Access Journals (Sweden)

Maida Kanwal

2016-04-01

Full Text Available Worldwide contamination of surface waters with microbial pathogens is of substantial health concern. These contaminants are usually transmitted by improper sanitation measures, unsafe waste disposal, excretions from patients, and physical contacts, i.e., sexual and nonsexual. Majority of these microbial pathogens have been categorized into three classes, i.e., bacteria, viruses and protozoa. Pakistan, being a developing country, is facing a noteworthy threat due to microbial contamination. In Pakistan, bacterial contaminants are reported extensively followed by viral and protozoa contaminants. The health issues associated with bacterial population includes dysentery, abdominal pain, headache, diarrhea etc.; and usually includes faecal and total coliforms, E. coli, Salmonella, Shigella and Campylobacter. The cases related to viral contamination are lesser but chronic and evidenced the presence of HCV, HAV, HEV viruses causing hepatitis, and other hepatic disorders. Lastly, the health impacts associated with protozoans are least reported; and a number of diseases such as giardia, cryptosporidium and toxoplasma have been linked with this class of contaminants. The current review compiles information of these biological contaminants along with their health issues in Pakistan. Moreover, potential sources and fate of microbial contaminants are also discussed.

Transient exposure to oxygen or nitrate reveals ecophysiology of fermentative and sulfate-reducing benthic microbial populations

NARCIS (Netherlands)

Saad, S.; Bhatnagar, S.; Tegetmeyer, H.E.; Geelhoed, J.S.; Strous, M.; Ruff, S.E.

2017-01-01

SummaryFor the anaerobic remineralization of organic matter inmarine sediments, sulfate reduction coupled to fer-mentation plays a key role. Here, we enriched sulfate-reducing/fermentative communities from intertidalsediments under defined conditions in continuousculture. We transiently exposed

Environmental Impact of Tributyltin-Resistant Marine Bacteria in the Indigenous Microbial Population of Tributyltin-Polluted Surface Sediments.

Science.gov (United States)

Mimura, Haruo; Yagi, Masahiro; Yoshida, Kazutoshi

2017-01-01

　We compared the TBT-resistant ability of resting cells prepared from isolates that formed colonies on nutrient agar plates containing 100 µM tributyltin (TBT) chloride, such as Photobacterium sp. TKY1, Halomonas sp. TKY2, and Photobacterium sp. NGY1, with those from taxonomically similar type strains. Photobacterium sp. TKY1 showed the highest ability among those three isolates. The number of surviving Photobacterium sp. TKY1 cells was hardly decreased after 1 h of exposure to 100 µM TBTCl, regardless of the number of resting cells in the range from 10 9.4 to 10 4.2 CFU mL -1 . In such an experimental condition, the maximum number of TBT molecules available to associate with a single cell was estimated to be approximately 6.0 x 10 11.8 . Resting cells prepared from type strains Photobacterium ganghwense JCM 12487 T and P. halotolerans LMG 22194 T , which have 16S rDNA sequences highly homologous with those of Photobacterium sp. TKY1, showed sensitivity to TBT, indicating that TBT-resistant marine bacterial species are not closely related in spite of their taxonomic similarity. We also estimated the impact of TBT-resistant bacterial species to indigenous microbial populations of TBT-polluted surface sediments. The number of surviving TBT-sensitive Vibrio natriegens ATCC 14048 T cells, 10 6.2±0.3 CFU mL -1 , was reduced to 10 4.4±0.4 CFU mL -1 when TBT-resistant Photobacterium sp. TKY1 cells, 10 9.1±0.2 CFU mL -1 , coexisted with 10 9.4±0.2 CFU mL -1 of V. natriegens ATCC 14048 T cells in the presence of 100 µM TBTCl. These results indicate that the toxicity of TBT to TBT-sensitive marine bacterial populations might be enhanced when a TBT-resistant marine bacterial species inhabits TBT-polluted surface sediments.

Ability of Hand Hygiene Interventions Using Alcohol-Based Hand Sanitizers and Soap To Reduce Microbial Load on Farmworker Hands Soiled during Harvest.

Science.gov (United States)

de Aceituno, Anna Fabiszewski; Bartz, Faith E; Hodge, Domonique Watson; Shumaker, David J; Grubb, James E; Arbogast, James W; Dávila-Aviña, Jorgé; Venegas, Fabiola; Heredia, Norma; García, Santos; Leon, Juan S

2015-11-01

Effective hand hygiene is essential to prevent the spread of pathogens on produce farms and reduce foodborne illness. The U.S. Food and Drug Administration Food Safety Modernization Act Proposed Rule for Produce Safety recommends the use of soap and running water for hand hygiene of produce handlers. The use of alcohol-based hand sanitizer (ABHS) may be an effective alternative hygiene intervention where access to water is limited. There are no published data on the efficacy of either soap or ABHS-based interventions to reduce microbial contamination in agricultural settings. The goal of this study was to assess the ability of two soap-based (traditional or pumice) and two ABHS-based (label-use or two-step) hygiene interventions to reduce microbes (coliforms, Escherichia coli, and Enterococcus spp.) and soil (absorbance of hand rinsate at 600 nm [A600]) on farmworker hands after harvesting produce, compared with the results for a no-hand-hygiene control. With no hand hygiene, farmworker hands were soiled (median A600, 0.48) and had high concentrations of coliforms (geometric mean, 3.4 log CFU per hand) and Enterococcus spp. (geometric mean, 5.3 log CFU per hand) after 1 to 2 h of harvesting tomatoes. Differences in microbial loads in comparison to the loads in the control group varied by indicator organism and hygiene intervention (0 to 2.3 log CFU per hand). All interventions yielded lower concentrations of Enterococcus spp. and E. coli (P hands (P hand washing with soap at reducing indicator organisms on farmworker hands. Based on these results, ABHS is an efficacious hand hygiene solution for produce handlers, even on soiled hands.

Species-specific effects of epigeic earthworms on microbial community structure during first stages of decomposition of organic matter.

Science.gov (United States)

Gómez-Brandón, María; Lores, Marta; Domínguez, Jorge

2012-01-01

Epigeic earthworms are key organisms in organic matter decomposition because of the interactions they establish with microorganisms. The earthworm species and the quality and/or substrate availability are expected to be major factors influencing the outcome of these interactions. Here we tested whether and to what extent the epigeic earthworms Eisenia andrei, Eisenia fetida and Perionyx excavatus, widely used in vermicomposting, are capable of altering the microbiological properties of fresh organic matter in the short-term. We also questioned if the earthworm-induced modifications to the microbial communities are dependent on the type of substrate ingested. To address these questions we determined the microbial community structure (phospholipid fatty acid profiles) and microbial activity (basal respiration and microbial growth rates) of three types of animal manure (cow, horse and rabbit) that differed in microbial composition, after being processed by each species of earthworm for one month. No differences were found between earthworm-worked samples with regards to microbial community structure, irrespective of type of manure, which suggests the existence of a bottleneck effect of worm digestion on microbial populations of the original material consumed. Moreover, in mesocosms containing cow manure the presence of E. andrei resulted not only in a decrease in bacterial and fungal biomass, but also in a reduced bacterial growth rate and total microbial activity, while no such reduction was found with E. fetida and P. excavatus. Our results point to the species of earthworm with its associated gut microbiota as a strong determinant of the process shaping the structure of microbial communities in the short-term. This must nonetheless be weighed against the fact that further knowledge is necessary to evaluate whether the changes in the composition of microbiota in response to the earthworm species is accompanied by a change in the microbial community diversity and

Species-specific effects of epigeic earthworms on microbial community structure during first stages of decomposition of organic matter.

Directory of Open Access Journals (Sweden)

María Gómez-Brandón

Full Text Available Epigeic earthworms are key organisms in organic matter decomposition because of the interactions they establish with microorganisms. The earthworm species and the quality and/or substrate availability are expected to be major factors influencing the outcome of these interactions. Here we tested whether and to what extent the epigeic earthworms Eisenia andrei, Eisenia fetida and Perionyx excavatus, widely used in vermicomposting, are capable of altering the microbiological properties of fresh organic matter in the short-term. We also questioned if the earthworm-induced modifications to the microbial communities are dependent on the type of substrate ingested.To address these questions we determined the microbial community structure (phospholipid fatty acid profiles and microbial activity (basal respiration and microbial growth rates of three types of animal manure (cow, horse and rabbit that differed in microbial composition, after being processed by each species of earthworm for one month. No differences were found between earthworm-worked samples with regards to microbial community structure, irrespective of type of manure, which suggests the existence of a bottleneck effect of worm digestion on microbial populations of the original material consumed. Moreover, in mesocosms containing cow manure the presence of E. andrei resulted not only in a decrease in bacterial and fungal biomass, but also in a reduced bacterial growth rate and total microbial activity, while no such reduction was found with E. fetida and P. excavatus.Our results point to the species of earthworm with its associated gut microbiota as a strong determinant of the process shaping the structure of microbial communities in the short-term. This must nonetheless be weighed against the fact that further knowledge is necessary to evaluate whether the changes in the composition of microbiota in response to the earthworm species is accompanied by a change in the microbial community

Evolution of increased phenotypic diversity enhances population performance by reducing sexual harassment in damselflies.

Science.gov (United States)

Takahashi, Yuma; Kagawa, Kotaro; Svensson, Erik I; Kawata, Masakado

2014-07-18

The effect of evolutionary changes in traits and phenotypic/genetic diversity on ecological dynamics has received much theoretical attention; however, the mechanisms and ecological consequences are usually unknown. Female-limited colour polymorphism in damselflies is a counter-adaptation to male mating harassment, and thus, is expected to alter population dynamics through relaxing sexual conflict. Here we show the side effect of the evolution of female morph diversity on population performance (for example, population productivity and sustainability) in damselflies. Our theoretical model incorporating key features of the sexual interaction predicts that the evolution of increased phenotypic diversity will reduce overall fitness costs to females from sexual conflict, which in turn will increase productivity, density and stability of a population. Field data and mesocosm experiments support these model predictions. Our study suggests that increased phenotypic diversity can enhance population performance that can potentially reduce extinction rates and thereby influence macroevolutionary processes.

Optimisation of the two-phase dry-thermophilic anaerobic digestion process of sulphate-containing municipal solid waste: population dynamics.

Science.gov (United States)

Zahedi, S; Sales, D; Romero, L I; Solera, R

2013-11-01

Microbial population dynamics and anaerobic digestion (AD) process to eight different hydraulic retention times (HRTs) (from 25d to 3.5d) in two-phase dry-thermophilic AD from sulphate-containing solid waste were investigated. Maximum values of gas production (1.9 ± 0.2 l H2/l/d; 5.4 ± 0.3 l CH4/l/d and 82 ± 9 ml H2S/l/d) and microbial activities were obtained at 4.5d HRT; where basically comprised hydrolysis step in the first phase (HRT=1.5d) and acidogenic step finished in the second phase as well as acetogenic-methanogenic steps (HRT=3d). In the first phase, hydrolytic-acidogenic bacteria (HABs) was the main group (44-77%) and Archaea, acetogens and sulphate-reducing bacteria (SRBs) contents were not significant; in the second phase (except to 2d HRT), microbial population was able to adapt to change in substrate and HRTs to ensure the proper functioning of the system and both acetogens and Archaea were dominated over SRBs. Decreasing HRT resulted in an increase in microbial activities. Copyright © 2013 Elsevier Ltd. All rights reserved.

Control of Pecan Weevil With Microbial Biopesticides.

Science.gov (United States)

Shapiro-Ilan, David I; Cottrell, Ted E; Bock, Clive; Mai, Kim; Boykin, Debbie; Wells, Lenny; Hudson, William G; Mizell, Russell F

2017-12-08

The pecan weevil, Curculio caryae (Horn) (Coleoptera: Curculionidae), is a key pest of pecans Carya illinoinensis ([Wangenh.] K. Koch) (Fagales: Juglandaceae). Control recommendations rely on broad spectrum chemical insecticides. Due to regulatory and environmental concerns, effective alternatives for C. caryae control must be sought for pecan production in conventional and organic systems. We explored the use of microbial biopesticides for control of C. caryae in Georgia pecan orchards. Three experiments were conducted. The first investigated an integrated microbial control approach in an organic system at two locations. Three microbial agents, Grandevo (based on byproducts of the bacterium Chromobacterium subtsugae Martin, Gundersen-Rindal, Blackburn & Buyer), the entomopathogenic nematode Steinernema carpocapsae (Weiser), and entomopathogenic fungus Beauveria bassiana (Balsamo) Vuillemin, were applied to each treatment plot (0.6 ha) at different times during the season. A second experiment compared the effects of S. carpocapsae and B. bassiana applied as single treatments relative to application of both agents (at different times); survival of C. caryae was assessed approximately 11 mo after larvae were added to pots sunk in an organic pecan orchard. In a conventional orchard (with 1.0 ha plots), the third experiment compared Grandevo applications to a commonly used regime of chemical insecticides (carbaryl alternated with a pyrethroid). All experiments were repeated in consecutive years. The combined pest management tactic (experiment 1) reduced C. caryae infestation relative to non-treated control plots in both locations in 2014 and one of the two locations in 2015 (the other location had less than 1% infestation). In experiment 2, no differences among combined microbial treatments, single-applied microbial treatments or different numbers of application were observed, yet all microbial treatments reduced C. caryae survival relative to the control. In the third

A Modeling Comparison of Methanogenesis from Noncompetitive vs Competitive Substrates in a Simulated Hypersaline Microbial Mat

Science.gov (United States)

Decker, K. L.; Potter, C.; Hoehler, T.

2005-12-01

The well-documented assumption about methanogens that co-occur in hypersaline mat communities with sulfate-reducing bacteria (SRB) is that they rely entirely on non-competitive substrates for methanogenesis. The reason for this is that during sulfate reduction, sulfur-reducing bacteria efficiently utilize H2, leaving a concentration too low for methanogenesis. Early results from recent work on a hypersaline microbial mat from salt evaporation ponds of Guerrero Negro, Baja, Mexico cast doubt that methanogenesis only occurs via non-competitive substrates, because it shows an excess of H2 in the mat rather than a paucity. We explore the use of our simulation model of the microbial biogeochemistry of a hypersaline mat (named MBGC) to compare methane production rates in a 1 cm thick mat when the methanogens use competitive substrates versus noncompetitive substrates. In the `non-competitive substrate' version of the model, methanogens rely exclusively on methylated amines that are accumulated as compatible solutes in cyanobacteria and released after lysis. In contrast, the `competitive substrate' models examine methanogen use of substrates (such as H2 + acetate) with different SRB population sizes (from absent to low). The comparison of these models of methane and sulfide biogeochemistry of a hypersaline mat has both ecological and geobiological significance, as one hypothesis of Archean microbial mats is that they existed in a low sulfate environment.

Connecting the dots: could microbial translocation explain commonly reported symptoms in HIV disease?

Science.gov (United States)

Wilson, Natalie L; Vance, David E; Moneyham, Linda D; Raper, James L; Mugavero, Michael J; Heath, Sonya L; Kempf, Mirjam-Colette

2014-01-01

Microbial translocation within the context of HIV disease has been described as one of the contributing causes of inflammation and disease progression in HIV infection. HIV-associated symptoms have been related to inflammatory markers and sCD14, a surrogate marker for microbial translocation, suggesting a plausible link between microbial translocation and symptom burden in HIV disease. Similar pathophysiological responses and symptoms have been reported in inflammatory bowel disease. We provide a comprehensive review of microbial translocation, HIV-associated symptoms, and symptoms connected with inflammation. We identify studies showing a relationship among inflammatory markers, sCD14, and symptoms reported in HIV disease. A conceptual framework and rationale to investigate the link between microbial translocation and symptoms is presented. The impact of inflammation on symptoms supports recommendations to reduce inflammation as part of HIV symptom management. Research in reducing microbial translocation-induced inflammation is limited, but needed, to further promote positive health outcomes among HIV-infected patients. Published by Elsevier Inc.

The effect of D123 wheat as a companion crop on soil enzyme activities, microbial biomass and microbial communities in the rhizosphere of watermelon.

Science.gov (United States)

Xu, Weihui; Wang, Zhigang; Wu, Fengzhi

2015-01-01

The growth of watermelon is often threatened by Fusarium oxysporum f. sp. niveum (Fon) in successively monocultured soil, which results in economic loss. The objective of this study was to investigate the effect of D123 wheat as a companion crop on soil enzyme activities, microbial biomass and microbial communities in the rhizosphere of watermelon and to explore the relationship between the effect and the incidence of wilt caused by Fon. The results showed that the activities of soil polyphenol oxidase, urease and invertase were increased, the microbial biomass nitrogen (MBN) and microbial biomass phosphorus (MBP) were significantly increased, and the ratio of MBC/MBN was decreased (P Fusarium wilt was also decreased in the watermelon/wheat companion system. In conclusion, this study indicated that D123 wheat as a companion crop increased soil enzyme activities and microbial biomass, decreased the Fon population, and changed the relative abundance of microbial communities in the rhizosphere of watermelon, which may be related to the reduction of Fusarium wilt in the watermelon/wheat companion system.

Distinct Trajectories of Massive Recent Gene Gains and Losses in Populations of a Microbial Eukaryotic Pathogen.

Science.gov (United States)

Hartmann, Fanny E; Croll, Daniel

2017-11-01

Differences in gene content are a significant source of variability within species and have an impact on phenotypic traits. However, little is known about the mechanisms responsible for the most recent gene gains and losses. We screened the genomes of 123 worldwide isolates of the major pathogen of wheat Zymoseptoria tritici for robust evidence of gene copy number variation. Based on orthology relationships in three closely related fungi, we identified 599 gene gains and 1,024 gene losses that have not yet reached fixation within the focal species. Our analyses of gene gains and losses segregating in populations showed that gene copy number variation arose preferentially in subtelomeres and in proximity to transposable elements. Recently lost genes were enriched in virulence factors and secondary metabolite gene clusters. In contrast, recently gained genes encoded mostly secreted protein lacking a conserved domain. We analyzed the frequency spectrum at loci segregating a gene presence-absence polymorphism in four worldwide populations. Recent gene losses showed a significant excess in low-frequency variants compared with genome-wide single nucleotide polymorphism, which is indicative of strong negative selection against gene losses. Recent gene gains were either under weak negative selection or neutral. We found evidence for strong divergent selection among populations at individual loci segregating a gene presence-absence polymorphism. Hence, gene gains and losses likely contributed to local adaptation. Our study shows that microbial eukaryotes harbor extensive copy number variation within populations and that functional differences among recently gained and lost genes led to distinct evolutionary trajectories. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Microbial pattern of pressure ulcer in pediatric patients

Science.gov (United States)

Paramita, D. A.; Khairina; Lubis, N. Z.

2018-03-01

Pressure ulcer (PU) is a localized trauma to the skin and or tissue beneath which lies in bony prominence due to pressure or pressure that combines with a sharp surface. Several studies have found that PU is a common problem in pediatrics population. Infection at the site of a PU is the most common complication in which the PU may host a resistant microorganism and may turn into a local infection that will be the source of bacteremia in hospitalized patients. To reveal which is the most common microbial species that underlie in pressure ulcer of pediatrics patients.A cross-sectional study was conducted in July-September 2017, involving 18 PU pediatric patients in Haji Adam Malik Hospital. To each subject, swab culture from the ulcer was madein microbial laboratory in Haji Adam Malik Hospital to determine the microbial pattern. This study found that the most common microbial pattern in pressure ulcers of pediatrics patient in Haji Adam Malik Hospital is Acinetobacter baumannii (22.2%).

Enhanced microbial reduction of vanadium (V) in groundwater with bioelectricity from microbial fuel cells

Science.gov (United States)

Hao, Liting; Zhang, Baogang; Tian, Caixing; Liu, Ye; Shi, Chunhong; Cheng, Ming; Feng, Chuanping

2015-08-01

Bioelectricity generated from the microbial fuel cell (MFC) is applied to the bioelectrical reactor (BER) directly to enhance microbial reduction of vanadium (V) (V(V)) in groundwater. With the maximum power density of 543.4 mW m-2 from the MFC, V(V) removal is accelerated with efficiency of 93.6% during 12 h operation. Higher applied voltage can facilitate this process. V(V) removals decrease with the increase of initial V(V) concentration, while extra addition of chemical oxygen demand (COD) has little effect on performance improvement. Microbial V(V) reduction is enhanced and then suppressed with the increase of conductivity. High-throughput 16S rRNA gene pyrosequencing analysis implies the accumulated Enterobacter and Lactococcus reduce V(V) with products from fermentative microorganisms such as Macellibacteroides. The presentation of electrochemically active bacteria as Enterobacter promotes electron transfers. This study indicates that application of bioelectricity from MFCs is a promising strategy to improve the efficiency of in-situ bioremediation of V(V) polluted groundwater.

Enhancing microbial production of biofuels by expanding microbial metabolic pathways.

Science.gov (United States)

Yu, Ping; Chen, Xingge; Li, Peng

2017-09-01

Fatty acid, isoprenoid, and alcohol pathways have been successfully engineered to produce biofuels. By introducing three genes, atfA, adhE, and pdc, into Escherichia coli to expand fatty acid pathway, up to 1.28 g/L of fatty acid ethyl esters can be achieved. The isoprenoid pathway can be expanded to produce bisabolene with a high titer of 900 mg/L in Saccharomyces cerevisiae. Short- and long-chain alcohols can also be effectively biosynthesized by extending the carbon chain of ketoacids with an engineered "+1" alcohol pathway. Thus, it can be concluded that expanding microbial metabolic pathways has enormous potential for enhancing microbial production of biofuels for future industrial applications. However, some major challenges for microbial production of biofuels should be overcome to compete with traditional fossil fuels: lowering production costs, reducing the time required to construct genetic elements and to increase their predictability and reliability, and creating reusable parts with useful and predictable behavior. To address these challenges, several aspects should be further considered in future: mining and transformation of genetic elements related to metabolic pathways, assembling biofuel elements and coordinating their functions, enhancing the tolerance of host cells to biofuels, and creating modular subpathways that can be easily interconnected. © 2016 International Union of Biochemistry and Molecular Biology, Inc.

Reducing the extinction risk of stochastic populations via nondemographic noise

Science.gov (United States)

Be'er, Shay; Assaf, Michael

2018-02-01

We consider nondemographic noise in the form of uncertainty in the reaction step size and reveal a dramatic effect this noise may have on the stability of self-regulating populations. Employing the reaction scheme m A →k A but allowing, e.g., the product number k to be a priori unknown and sampled from a given distribution, we show that such nondemographic noise can greatly reduce the population's extinction risk compared to the fixed k case. Our analysis is tested against numerical simulations, and by using empirical data of different species, we argue that certain distributions may be more evolutionary beneficial than others.

Microbial reduction of uranium using cellulosic substrates

International Nuclear Information System (INIS)

Thombre, M.S.; Thomson, B.M.; Barton, L.L.

1996-01-01

Previous work at the University of New Mexico and elsewhere has shown that sulfate-reducing bacteria are capable of reducing uranium from the soluble +6 oxidation state to the insoluble +4 oxidation state. This chemistry forms the basis of a proposed ground water remediation strategy in which microbial reduction would be used to immobilize soluble uranium. One such system would consist of a subsurface permeable barrier which would stimulate microbial growth resulting in the reduction of sulfate and nitrate and immobilization of metals while permitting the unhindered flow of ground water through it. This research investigated some of the engineering considerations associated with a microbial reducing barrier such as identifying an appropriate biological substrate, estimating the rate of substrate utilization, and identifying the final fate of the contaminants concentrated in the barrier matrix. The performance of batch reactors and column systems that treated simulated plume water was evaluated using cellulose, wheat straw, alfalfa hay, sawdust, and soluble starch as substrates. The concentrations of sulfate, nitrate, and U(VI) were monitored over time. Precipitates from each system were collected, and the precipitated U(IV) was determined to be crystalline UO 2(s) by x-ray diffraction. The results of this study support the proposed use of cellulosic substrates as candidate barrier materials

Microbial diversity in restored wetlands of San Francisco Bay

Energy Technology Data Exchange (ETDEWEB)

Theroux, Susanna [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.; Hartman, Wyatt [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.; He, Shaomei [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.; Univ. of Wisconsin, Madison, WI (United States); Tringe, Susannah [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.

2013-12-09

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, 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.

Microbial analysis of the buffer/container experiment at AECL`s Underground Research Laboratory

Energy Technology Data Exchange (ETDEWEB)

Stroes-Gascoyne, S; Hamon, C J; Haveman, S A; Delaney, T L [Atomic Energy of Canada Ltd., Pinawa, MB (Canada). Whiteshell Labs; Pedersen, K; Ekendahl, S; Jahromi, N; Arlinger, J; Hallbeck, L [Univ. of Goeteborg, (Sweden). Dept. of General and Marine Microbiology; Daumas, S; Dekeyser, K [Guiges Recherche Appliquee en Microbiologie, Aix-en-Provence, (France)

1996-05-01

The Buffer/Container experiment was carried out for 2.5 years to examine the in-situ performance of compacted buffer material in a single emplacement borehole under vault-relevant conditions. During decommissioning of this experiment, numerous samples were taken for microbial analysis to determine if the naturally present microbial population in buffer material survived to conditions and to determine which groups of microorganisms would be dominant in such a simulated vault environment. Microbial analyses were initiated within 24 hour of sampling for all types of samples taken. The culture results showed an almost universal disappearance of viable microorganisms in the samples taken from near the heater surface. The microbial activity measurements confirmed the lack of viable organisms with very weak or no activity measured in most of these samples. Generally, aerobic heterotrophic culture conditions gave the highest mean colony-forming units (CFU) values at both 25 and 50 C. Under anaerobic conditions, and especially at 50 C, lower mean CFU values were obtained. In all samples analyzed, numbers of sulfate reducing bacteria were less than 1000 CFU/g dry material. Methanogens were either not present or were found in very low numbers. Anaerobic sulfur oxidizing bacteria were found in higher numbers in most sample types with sufficient moisture. The statistical evaluation of the culture data demonstrated clearly that the water content was the variable limiting the viability of the bacteria present, and not the temperature. 68 refs, 35 figs, 37 tabs.

Role of Genomic Typing in Taxonomy, Evolutionary Genetics, and Microbial Epidemiology

OpenAIRE

van Belkum, Alex; Struelens, Marc; de Visser, Arjan; Verbrugh, Henri; Tibayrenc, Michel

2001-01-01

Currently, genetic typing of microorganisms is widely used in several major fields of microbiological research. Taxonomy, research aimed at elucidation of evolutionary dynamics or phylogenetic relationships, population genetics of microorganisms, and microbial epidemiology all rely on genetic typing data for discrimination between genotypes. Apart from being an essential component of these fundamental sciences, microbial typing clearly affects several areas of applied microbiogical research. ...

Role of genomic typing in taxonomy, evolutionary genetics, and microbial epidemiology.

OpenAIRE

Belkum, Alex; Struelens, M.; Visser, Arjan; Verbrugh, Henri; Tibayrench, M.

2001-01-01

textabstractCurrently, genetic typing of microorganisms is widely used in several major fields of microbiological research. Taxonomy, research aimed at elucidation of evolutionary dynamics or phylogenetic relationships, population genetics of microorganisms, and microbial epidemiology all rely on genetic typing data for discrimination between genotypes. Apart from being an essential component of these fundamental sciences, microbial typing clearly affects several areas of applied microbiologi...

Effects of two diamine biocides on the microbial community from an oil field

International Nuclear Information System (INIS)

Telang, A.; Voordouw, G.; Ebert, S.; Foght, J. M.; Westlake, D. W. S.

1998-01-01

Oil production facilities are routinely treated with biocides to control or eliminate microbes responsible for souring odor, or microbially influenced corrosion. In this study the effects of diamine biocides A and B on the microbial population from an oil field were investigated using reverse sample genome probing (RSGP), a technique designed to track multiple oil field bacteria in a single assay. RSGP studies of sessile microbial populations scraped from corrosion coupons obtained from biocide-treated oil field installations indicate dominance of Desulfovibrio species Lac6 and Eth3. Laboratory studies suggest that batchwise application of high doses (400 ppm) of biocide A is capable of killing planktonic populations of Desulfovibrio spp. Lac6 and Eth3. Batchwise application of similar doses of biocide B did not have this effect. Overall results indicate that the application of 400 ppm biocide B and 40 ppm biocide A may actually promote survival of selected Desulfovibrio spp., which may then effectively colonize available metal surfaces. 15 refs., 3 figs

Microbial Energy Conversion

Energy Technology Data Exchange (ETDEWEB)

Buckley, Merry [American Society for Microbiology (ASM), Washington, DC (United States); Wall, Judy D. [Univ. of Missouri, Columbia, MO (United States)

2006-10-01

The American Academy of Microbiology convened a colloquium March 10-12, 2006, in San Francisco, California, to discuss the production of energy fuels by microbial conversions. The status of research into various microbial energy technologies, the advantages and disadvantages of each of these approaches, research needs in the field, and education and training issues were examined, with the goal of identifying routes for producing biofuels that would both decrease the need for fossil fuels and reduce greenhouse gas emissions. Currently, the choices for providing energy are limited. Policy makers and the research community must begin to pursue a broader array of potential energy technologies. A diverse energy portfolio that includes an assortment of microbial energy choices will allow communities and consumers to select the best energy solution for their own particular needs. Funding agencies and governments alike need to prepare for future energy needs by investing both in the microbial energy technologies that work today and in the untested technologies that will serve the world’s needs tomorrow. More mature bioprocesses, such as ethanol production from starchy materials and methane from waste digestors, will find applications in the short term. However, innovative techniques for liquid fuel or biohydrogen production are among the longer term possibilities that should also be vigorously explored, starting now. Microorganisms can help meet human energy needs in any of a number of ways. In their most obvious role in energy conversion, microorganisms can generate fuels, including ethanol, hydrogen, methane, lipids, and butanol, which can be burned to produce energy. Alternatively, bacteria can be put to use in microbial fuel cells, where they carry out the direct conversion of biomass into electricity. Microorganisms may also be used some day to make oil and natural gas technologies more efficient by sequestering carbon or by assisting in the recovery of oil and

Microbial community structure characteristics associated membrane fouling in A/O-MBR system.

Science.gov (United States)

Gao, Da-Wen; Wen, Zhi-Dan; Li, Bao; Liang, Hong

2014-02-01

The study demonstrated the potential relationship between microbial community structure and membrane fouling in an anoxic-oxic membrane bioreactor (A/O-MBR). The results showed that the microbial community structure in biocake was different with aerobic mixture, and the dominant populations were out of sync during the fouling process. Based on microbial community structure and metabolites analysis, the results showed that the succession of microbial community might be the leading factor to the variation of metabolites, and it might be the primary cause of membrane fouling. The rise of Shannon diversity index (H) of the microbial community in A/O-MBR went with the gradually serious membrane fouling. Pareto-Lorenz curve was used to describe the evenness of microbial distribution in A/O-MBR, and the result indicated when community evenness was low, the membrane fouling took place smoothly or slightly, otherwise, high evenness of microbial community would lead to more seriously membrane fouling. Copyright © 2013 Elsevier Ltd. All rights reserved.

Microbial Response to UV Exposure and Nitrogen Limitation in Desert Soil Crusts

Science.gov (United States)

Fulton, J. M.; Van Mooy, B. A.

2016-12-01

Microbiotic soil crusts have diverse biomarker distributions and C and N stable isotopic compositions that covary with soil type. Sparse plant cover and the relative lack of soil disturbance in arid/semi-arid landscapes allows populations of soil cyanobacteria to develop along with fungi and heterotrophic bacteria. Microbial communities in this extreme environment depend in part on the production of scytonemin, a UV protective pigment, by cyanobacteria near the top of the crust. N limitation of microbial growth also affects soil crust population dynamics, increasing the requirement of N2fixation by diazotrophic cyanobacteria. We collected 56 soil crust samples from 27 locations throughout the Great Salt Lake Desert, including four transects spanning high-elevation, erosion-dominated soils to lower elevation soils dominated by silt-accumulation. Erosion-dominated soil surfaces included rounded gravel and cobbles; in the interstices there were poorly-developed microbiotic crusts on sandy loam with low δ15N values near 0‰ that point toward microbial growth dependent on cyanobacterial N2 fixation. Nutrients regenerated by heterotrophic bacteria may have been eroded from the system, providing a positive feedback for N2 fixation. High scytonemin:chlorophyll a ratios suggest that cyanobacteria required enhanced protection from UV damage in these crusts. A similar increase in scytonemin:chlorophyll a ratio during soil crust rehydration experiments also points toward the importance of UV protection. Glycolipid:phospholipid ratios were lowest where N2 fixation was favored, however, suggesting that the cyanobacterial population was relatively small, possibly because of the metabolic cost of N2fixation. Microbiotic crusts on silt loam soils, on the other hand, had higher δ15N values between 3.5 and 7.8‰, consistent with heterotrophic growth and nutrient recycling. Lower scytonemin:chlorophyll a ratios suggest that relatively high photosynthetic activity was supported in

Microbial populations in Antarctic permafrost: biodiversity, state, age, and implication for astrobiology.

Science.gov (United States)

Gilichinsky, D A; Wilson, G S; Friedmann, E I; McKay, C P; Sletten, R S; Rivkina, E M; Vishnivetskaya, T A; Erokhina, L G; Ivanushkina, N E; Kochkina, G A; Shcherbakova, V A; Soina, V S; Spirina, E V; Vorobyova, E A; Fyodorov-Davydov, D G; Hallet, B; Ozerskaya, S M; Sorokovikov, V A; Laurinavichyus, K S; Shatilovich, A V; Chanton, J P; Ostroumov, V E; Tiedje, J M

2007-04-01

Antarctic permafrost soils have not received as much geocryological and biological study as has been devoted to the ice sheet, though the permafrost is more stable and older and inhabited by more microbes. This makes these soils potentially more informative and a more significant microbial repository than ice sheets. Due to the stability of the subsurface physicochemical regime, Antarctic permafrost is not an extreme environment but a balanced natural one. Up to 10(4) viable cells/g, whose age presumably corresponds to the longevity of the permanently frozen state of the sediments, have been isolated from Antarctic permafrost. Along with the microbes, metabolic by-products are preserved. This presumed natural cryopreservation makes it possible to observe what may be the oldest microbial communities on Earth. Here, we describe the Antarctic permafrost habitat and biodiversity and provide a model for martian ecosystems.

Investigations of potential microbial methanogenic and carbon monoxide utilization pathways in ultra-basic reducing springs associated with present-day continental serpentinization: the Tablelands, NL, CAN.

Science.gov (United States)

Morrill, Penny L; Brazelton, William J; Kohl, Lukas; Rietze, Amanda; Miles, Sarah M; Kavanagh, Heidi; Schrenk, Matthew O; Ziegler, Susan E; Lang, Susan Q

2014-01-01

Ultra-basic reducing springs at continental sites of serpentinization act as portals into the biogeochemistry of a subsurface environment with H2 and CH4 present. Very little, however, is known about the carbon substrate utilization, energy sources, and metabolic pathways of the microorganisms that live in this ultra-basic environment. The potential for microbial methanogenesis with bicarbonate, formate, acetate, and propionate precursors and carbon monoxide (CO) utilization pathways were tested in laboratory experiments by adding substrates to water and sediment from the Tablelands, NL, CAD, a site of present-day continental serpentinization. Microbial methanogenesis was not observed after bicarbonate, formate, acetate, or propionate addition. CO was consumed in the live experiments but not in the killed controls and the residual CO in the live experiments became enriched in (13)C. The average isotopic enrichment factor resulting from this microbial utilization of CO was estimated to be 11.2 ± 0.2‰. Phospholipid fatty acid concentrations and δ(13)C values suggest limited incorporation of carbon from CO into microbial lipids. This indicates that in our experiments, CO was used primarily as an energy source, but not for biomass growth. Environmental DNA sequencing of spring fluids collected at the same time as the addition experiments yielded a large proportion of Hydrogenophaga-related sequences, which is consistent with previous metagenomic data indicating the potential for these taxa to utilize CO.

Tropical forest soil microbial communities couple iron and carbon biogeochemistry

Energy Technology Data Exchange (ETDEWEB)

Dubinsky, E.A.; Silver, W.L.; Firestone, M.K.

2009-10-15

We report that iron-reducing bacteria are primary mediators of anaerobic carbon oxidation in upland tropical soils spanning a rainfall gradient (3500 - 5000 mm yr-1) in northeast Puerto Rico. The abundant rainfall and high net primary productivity of these tropical forests provide optimal soil habitat for iron-reducing and iron-oxidizing bacteria. Spatially and temporally dynamic redox conditions make iron-transforming microbial communities central to the belowground carbon cycle in these wet tropical forests. The exceedingly high abundance of iron-reducing bacteria (up to 1.2 x 10{sup 9} cells per gram soil) indicated that they possess extensive metabolic capacity to catalyze the reduction of iron minerals. In soils from the higher rainfall sites, measured rates of ferric iron reduction could account for up to 44 % of organic carbon oxidation. Iron reducers appeared to compete with methanogens when labile carbon availability was limited. We found large numbers of bacteria that oxidize reduced iron at sites with high rates of iron reduction and large numbers of iron-reducers. the coexistence of large populations of ironreducing and iron-oxidizing bacteria is evidence for rapid iron cycling between its reduced and oxidized states, and suggests that mutualistic interactions among these bacteria ultimately fuel organic carbon oxidation and inhibit CH4 production in these upland tropical forests.

Testing nickel tolerance of Sorghastrum nutans and its associated soil microbial community from serpentine and prairie soils

International Nuclear Information System (INIS)

Doherty, Jennifer H.; Ji Baoming; Casper, Brenda B.

2008-01-01

Ecotypes of Sorghastrum nutans from a naturally metalliferous serpentine grassland and the tallgrass prairie were assessed for Ni tolerance and their utility in remediation of Ni-polluted soils. Plants were inoculated with serpentine arbuscular mycorrhizal (AM) root inoculum or whole soil microbial communities, originating from either prairie or serpentine, to test their effects on plant performance in the presence of Ni. Serpentine plants had marginally higher Ni tolerance as indicated by higher survival. Ni reduced plant biomass and AM root colonization for both ecotypes. The serpentine AM fungi and whole microbial community treatments decreased plant biomass relative to uninoculated plants, while the prairie microbial community had no effect. Differences in how the soil communities affect plant performance were not reflected in patterns of root colonization by AM fungi. Thus, serpentine plants may be suited for reclamation of Ni-polluted soils, but AM fungi that occur on serpentine do not improve Ni tolerance. - Ni tolerance of Sorghastrum nutans differs slightly between serpentine and prairie populations and is negatively affected by serpentine soil and root inoculation

Microbial-Host Co-metabolites Are Prodromal Markers Predicting Phenotypic Heterogeneity in Behavior, Obesity, and Impaired Glucose Tolerance

Directory of Open Access Journals (Sweden)

Marc-Emmanuel Dumas

2017-07-01

Full Text Available The influence of the gut microbiome on metabolic and behavioral traits is widely accepted, though the microbiome-derived metabolites involved remain unclear. We carried out untargeted urine 1H-NMR spectroscopy-based metabolic phenotyping in an isogenic C57BL/6J mouse population (n = 50 and show that microbial-host co-metabolites are prodromal (i.e., early markers predicting future divergence in metabolic (obesity and glucose homeostasis and behavioral (anxiety and activity outcomes with 94%–100% accuracy. Some of these metabolites also modulate disease phenotypes, best illustrated by trimethylamine-N-oxide (TMAO, a product of microbial-host co-metabolism predicting future obesity, impaired glucose tolerance (IGT, and behavior while reducing endoplasmic reticulum stress and lipogenesis in 3T3-L1 adipocytes. Chronic in vivo TMAO treatment limits IGT in HFD-fed mice and isolated pancreatic islets by increasing insulin secretion. We highlight the prodromal potential of microbial metabolites to predict disease outcomes and their potential in shaping mammalian phenotypic heterogeneity.

Enriching acid rock drainage related microbial communities from surface-deposited oil sands tailings.

Science.gov (United States)

Dean, Courtney; Xiao, Yeyuan; Roberts, Deborah J

2016-10-01

Little is known about the microbial communities native to surface-deposited pyritic oil sands tailings, an environment where acid rock drainage (ARD) could occur. The goal of this study was to enrich sulfur-oxidizing organisms from these tailings and determine whether different populations exist at pH levels 7, 4.5, and 2.5. Using growth-based methods provides model organisms for use in the future to predict potential activities and limitations of these organisms and to develop possible control methods. Thiosulfate-fed enrichment cultures were monitored for approximately 1 year. The results showed that the enrichments at pH 4.5 and 7 were established quicker than at pH 2.5. Different microbial community structures were found among the 3 pH environments. The sulfur-oxidizing microorganisms identified were most closely related to Halothiobacillus neapolitanus, Achromobacter spp., and Curtobacterium spp. While microorganisms related to Chitinophagaceae and Acidocella spp. were identified as the only possible iron-oxidizing and -reducing microbes. These results contribute to the general knowledge of the relatively understudied microbial communities that exist in pyritic oil sands tailings and indicate these communities may have a potential role in ARD generation, which may have implications for future tailings management.

Effect of phenotypic residual feed intake and dietary forage content on the rumen microbial community of beef cattle.

Science.gov (United States)

Carberry, Ciara A; Kenny, David A; Han, Sukkyan; McCabe, Matthew S; Waters, Sinead M

2012-07-01

Feed-efficient animals have lower production costs and reduced environmental impact. Given that rumen microbial fermentation plays a pivotal role in host nutrition, the premise that rumen microbiota may contribute to host feed efficiency is gaining momentum. Since diet is a major factor in determining rumen community structure and fermentation patterns, we investigated the effect of divergence in phenotypic residual feed intake (RFI) on ruminal community structure of beef cattle across two contrasting diets. PCR-denaturing gradient gel electrophoresis (DGGE) and quantitative PCR (qPCR) were performed to profile the rumen bacterial population and to quantify the ruminal populations of Entodinium spp., protozoa, Fibrobacter succinogenes, Ruminococcus flavefaciens, Ruminococcus albus, Prevotella brevis, the genus Prevotella, and fungi in 14 low (efficient)- and 14 high (inefficient)-RFI animals offered a low-energy, high-forage diet, followed by a high-energy, low-forage diet. Canonical correspondence and Spearman correlation analyses were used to investigate associations between physiological variables and rumen microbial structure and specific microbial populations, respectively. The effect of RFI on bacterial profiles was influenced by diet, with the association between RFI group and PCR-DGGE profiles stronger for the higher forage diet. qPCR showed that Prevotella abundance was higher (P < 0.0001) in inefficient animals. A higher (P < 0.0001) abundance of Entodinium and Prevotella spp. and a lower (P < 0.0001) abundance of Fibrobacter succinogenes were observed when animals were offered the low-forage diet. Thus, differences in the ruminal microflora may contribute to host feed efficiency, although this effect may also be modulated by the diet offered.

Membrane biofouling in a wastewater nitrification reactor: microbial succession from autotrophic colonization to heterotrophic domination

KAUST Repository

Lu, Huijie

2015-10-22

Membrane biofouling is a complex process that involves bacterial adhesion, extracellular polymeric substances (EPS) excretion and utilization, and species interactions. To obtain a better understanding of the microbial ecology of biofouling process, this study conducted rigorous, time-course analyses on the structure, EPS and microbial composition of the fouling layer developed on ultrafiltration membranes in a nitrification bioreactor. During a 14-day fouling event, three phases were determined according to the flux decline and microbial succession patterns. In Phase I (0-2 days), small sludge flocs in the bulk liquid were selectively attached on membrane surfaces, leading to the formation of similar EPS and microbial community composition as the early biofilms. Dominant populations in small flocs, e.g., Nitrosomonas, Nitrobacter, and Acinetobacter spp., were also the major initial colonizers on membranes. In Phase II (2-4 d), fouling layer structure, EPS composition, and bacterial community went through significant changes. Initial colonizers were replaced by fast-growing and metabolically versatile heterotrophs (e.g., unclassified Sphingobacteria). The declining EPS polysaccharide to protein (PS:PN) ratios could be correlated well with the increase in microbial community diversity. In Phase III (5-14 d), heterotrophs comprised over 90% of the community, whereas biofilm structure and EPS composition remained relatively stable. In all phases, AOB and NOB were constantly found within the top 40% of the fouling layer, with the maximum concentrations around 15% from the top. The overall microbial succession pattern from autotrophic colonization to heterotrophic domination implied that MBR biofouling could be alleviated by forming larger bacterial flocs in bioreactor suspension (reducing autotrophic colonization), and by designing more specific cleaning procedures targeting dominant heterotrophs during typical filtration cycles.

High rates of sulfate reduction in a low-sulfate hot spring microbial mat are driven by a low level of diversity of sulfate-respiring microorganisms

DEFF Research Database (Denmark)

Dillon, Jesse G; Fishbain, Susan; Miller, Scott R

2007-01-01

The importance of sulfate respiration in the microbial mat found in the low-sulfate thermal outflow of Mushroom Spring in Yellowstone National Park was evaluated using a combination of molecular, microelectrode, and radiotracer studies. Despite very low sulfate concentrations, this mat community...... was shown to sustain a highly active sulfur cycle. The highest rates of sulfate respiration were measured close to the surface of the mat late in the day when photosynthetic oxygen production ceased and were associated with a Thermodesulfovibrio-like population. Reduced activity at greater depths...... was correlated with novel populations of sulfate-reducing microorganisms, unrelated to characterized species, and most likely due to both sulfate and carbon limitation....

Population characteristics may reduce the levels of individual call identity.

Directory of Open Access Journals (Sweden)

María del Mar Delgado

Full Text Available Individual variability influences the demographic and evolutionary dynamics of spatially structured populations, and conversely ecological and evolutionary dynamics provide the context under which variations at the individual level occur. Therefore, it is essential to identify and characterize the importance of the different factors that may promote or hinder individual variability. Animal signaling is a prime example of a type of behavior that is largely dependent on both the features of individuals and the characteristics of the population to which they belong. After 10 years studying the dynamics of a population of a long-lived species, the eagle owl (Bubo bubo, we investigated the emergence and maintenance of traits that reveal individual identity by focusing on vocal features. We found that individuals inhabiting a high density population characterized by a relative lack of heterogeneity (in terms of prey availability and breeding success among breeding sites might be selected for reducing the levels of identity. Two non-mutually exclusive hypotheses may explain the structural call patterns we detected: (1 similarity in calls may be principally a consequence of the particular characteristics of the population; and (2 high density may encourage individuals to mimic each other's vocalizations in a cascade effect, leading to a widespread and unique communication network.

The Arsenite Oxidation Potential of Native Microbial Communities from Arsenic-Rich Freshwaters.

Science.gov (United States)

Fazi, Stefano; Crognale, Simona; Casentini, Barbara; Amalfitano, Stefano; Lotti, Francesca; Rossetti, Simona

2016-07-01

Microorganisms play an important role in speciation and mobility of arsenic in the environment, by mediating redox transformations of both inorganic and organic species. Since arsenite [As(III)] is more toxic than arsenate [As(V)] to the biota, the microbial driven processes of As(V) reduction and As(III) oxidation may play a prominent role in mediating the environmental impact of arsenic contamination. However, little is known about the ecology and dynamics of As(III)-oxidizing populations within native microbial communities exposed to natural high levels of As. In this study, two techniques for single cell quantification (i.e., flow cytometry, CARD-FISH) were used to analyze the structure of aquatic microbial communities across a gradient of arsenic (As) contamination in different freshwater environments (i.e., groundwaters, surface and thermal waters). Moreover, we followed the structural evolution of these communities and their capacity to oxidize arsenite, when experimentally exposed to high As(III) concentrations in experimental microcosms. Betaproteobacteria and Deltaproteobacteria were the main groups retrieved in groundwaters and surface waters, while Beta and Gammaproteobacteria dominated the bacteria community in thermal waters. At the end of microcosm incubations, the communities were able to oxidize up to 95 % of arsenite, with an increase of Alphaproteobacteria in most of the experimental conditions. Finally, heterotrophic As(III)-oxidizing strains (one Alphaproteobacteria and two Gammaproteobacteria) were isolated from As rich waters. Our findings underlined that native microbial communities from different arsenic-contaminated freshwaters can efficiently perform arsenite oxidation, thus contributing to reduce the overall As toxicity to the aquatic biota.

Microbial Transformations of Actinides and Fission Products in Radioactive Waste

Energy Technology Data Exchange (ETDEWEB)

Francis, A. J. [Pohang Univ. Science and Technology, Pohang (Korea, Republic of)

2011-07-01

The environmental factors that can affect microbial growth and activity include moisture, temperature, ph, Eh, availability of organic and inorganic nutrients, and radiation. The microbial activity in a specific repository is influenced by the ambient environment of the repository, and the materials to be emplaced. For example, a repository in unsaturated igneous rock formations such as volcanic tuff rocks at Yucca Mountain is generally expected to be oxidizing; a repository in a hydrologically expected to be oxidizing; a repository in a hydrologically saturated zone, especially in sedimentary rocks, could be reducing. Sedimentary rocks contain a certain amount of organic matter, which may stimulate microbial activities and, thus maintain the repository and its surrounding areas at reducing conditions. Although the impacts of microbial activity on high-level nuclear waste and the long-term performance of the repository have not fully investigated, little microbial activity is expected in the near-field because of the radiation, lack of nutrients and the harsh conditions. However in the far-field microbial effects could be significant. Much of our understanding of the microbial effects on radionuclides stems from studies conducted with selected transuranic elements and fission products and limited studies with low-level radioactive wastes. Significant aerobic- and anaerobic-microbial activity is expected to occur in the waste because of the presence of electron donors and acceptors. The actinides initially may be present as soluble- or insoluble-forms but, after disposal, may be converted from one to the other by microorganisms. The direct enzymatic or indirect non-enzymatic actions of microbes could alter the speciation, solubility, and sorption properties of the actinides, thereby increasing or decreasing their concentrations in solution.

Central role of the cell in microbial ecology.

Science.gov (United States)

Zengler, Karsten

2009-12-01

Over the last few decades, advances in cultivation-independent methods have significantly contributed to our understanding of microbial diversity and community composition in the environment. At the same time, cultivation-dependent methods have thrived, and the growing number of organisms obtained thereby have allowed for detailed studies of their physiology and genetics. Still, most microorganisms are recalcitrant to cultivation. This review not only conveys current knowledge about different isolation and cultivation strategies but also discusses what implications can be drawn from pure culture work for studies in microbial ecology. Specifically, in the light of single-cell individuality and genome heterogeneity, it becomes important to evaluate population-wide measurements carefully. An overview of various approaches in microbial ecology is given, and the cell as a central unit for understanding processes on a community level is discussed.

Effect of moisture, organic matter, microbial population and fortification level on dissipation of pyraclostrobin in soils.

Science.gov (United States)

Reddy, S Navakishore; Gupta, Suman; Gajbhiye, Vijay T

2013-09-01

The dissipation of pyraclostrobin, a strobilurin fungicide, in soil was found to be influenced by soil moisture, organic matter content and microbial population. Among the different moisture regimes, dissipation was faster under submerged condition (T1/2 10 days) followed by field capacity (T1/2 28.7 days) and in dry soil (T1/2 41.8 days). Use of sludge at 5 % level to Inceptisol favoured a faster dissipation of pyraclostrobin, whereas a slower rate of dissipation was observed in partial organic matter removed soil as compared to normal soil. Slower rate of dissipation was also observed in sterile soil (T1/2 47 days) compared to normal soil. Pyraclostrobin dissipated faster in Vertisol (T1/2 21.8 days) than in Inceptisol (T1/2 28.7 days). No significant difference in the dissipation rate was observed at 1 and 10 μg g(-1) fortification levels.

Molecular microbial ecology of lignocellulose mobilisation as a ...

African Journals Online (AJOL)

The community structure of complex microbial consortia which develop in lignocellulose packed passive treatment systems for acid mine drainage remediation were investigated. An understanding of interactions between these populations is important in determining mechanisms by which such systems operate.

Microbial enhancement of non-Darcy flow: Theoretical consideration

Energy Technology Data Exchange (ETDEWEB)

Shi, Jianxin; Schneider, D.R.

1995-12-31

In the near well-bore region and perforations, petroleum fluids usually flow at high velocities and may exhibit non-Darcy-flow behavior. Microorganisms can increase permeability and porosity by removing paraffin or asphaltene accumulations. They can also reduce interfacial tension by producing biosurfactants. These changes can significantly affect non-Darcy flow behavior. Theoretical analysis shows that microbial activities can enhance production by decreasing the turbulence pressure drop and in some cases increasing the drag force exerted to the oil phase. This implies that the effects of microbial activities on non-Darcy flow are important and should be considered in the evaluation of microbial well stimulation and enhanced oil recovery.

Microbial diversity and biomarker analysis of modern freshwater microbialites from Laguna Bacalar, Mexico.

Science.gov (United States)

Johnson, D B; Beddows, P A; Flynn, T M; Osburn, M R

2018-05-01

Laguna Bacalar is a sulfate-rich freshwater lake on the Yucatan Peninsula that hosts large microbialites. High sulfate concentrations distinguish Laguna Bacalar from other freshwater microbialite sites such as Pavilion Lake and Alchichica, Mexico, as well as from other aqueous features on the Yucatan Peninsula. While cyanobacterial populations have been described here previously, this study offers a more complete characterization of the microbial populations and corresponding biogeochemical cycling using a three-pronged geobiological approach of microscopy, high-throughput DNA sequencing, and lipid biomarker analyses. We identify and compare diverse microbial communities of Alphaproteobacteria, Deltaproteobacteria, and Gammaproteobacteria that vary with location along a bank-to-bank transect across the lake, within microbialites, and within a neighboring mangrove root agglomeration. In particular, sulfate-reducing bacteria are extremely common and diverse, constituting 7%-19% of phylogenetic diversity within the microbialites, and are hypothesized to significantly influence carbonate precipitation. In contrast, Cyanobacteria account for less than 1% of phylogenetic diversity. The distribution of lipid biomarkers reflects these changes in microbial ecology, providing meaningful biosignatures for the microbes in this system. Polysaturated short-chain fatty acids characteristic of cyanobacteria account for Bacalar microbialites. By contrast, even short-chain and monounsaturated short-chain fatty acids attributable to both Cyanobacteria and many other organisms including types of Alphaproteobacteria and Gammaproteobacteria constitute 43%-69% and 17%-25%, respectively, of total abundance in microbialites. While cyanobacteria are the largest and most visible microbes within these microbialites and dominate the mangrove root agglomeration, it is clear that their smaller, metabolically diverse associates are responsible for significant biogeochemical cycling in this

Subseafloor Microbial Life in Venting Fluids from the Mid Cayman Rise Hydrothermal System

Science.gov (United States)

Huber, J. A.; Reveillaud, J.; Reddington, E.; McDermott, J. M.; Sylva, S. P.; Breier, J. A.; German, C. R.; Seewald, J.

2012-12-01

In hard rock seafloor environments, fluids emanating from hydrothermal vents are one of the best windows into the subseafloor and its resident microbial community. The functional consequences of an extensive population of microbes living in the subseafloor remains unknown, as does our understanding of how these organisms interact with one another and influence the biogeochemistry of the oceans. Here we report the abundance, activity, and diversity of microbes in venting fluids collected from two newly discovered deep-sea hydrothermal vents along the ultra-slow spreading Mid-Cayman Rise (MCR). Fluids for geochemical and microbial analysis were collected from the Von Damm and Piccard vent fields, which are located within 20 km of one another, yet have extremely different thermal, geological, and depth regimes. Geochemical data indicates that both fields are highly enriched in volatiles, in particular hydrogen and methane, important energy sources for and by-products of microbial metabolism. At both sites, total microbial cell counts in the fluids ranged in concentration from 5 x 10 4 to 3 x 10 5 cells ml-1 , with background seawater concentrations of 1-2 x 10 4 cells ml-1 . In addition, distinct cell morphologies and clusters of cells not visible in background seawater were seen, including large filaments and mineral particles colonized by microbial cells. These results indicate local enrichments of microbial communities in the venting fluids, distinct from background populations, and are consistent with previous enumerations of microbial cells in venting fluids. Stable isotope tracing experiments were used to detect utilization of acetate, formate, and dissolve inorganic carbon and generation of methane at 70 °C under anaerobic conditions. At Von Damm, a putatively ultra-mafic hosted site located at ~2200 m with a maximum temperature of 226 °C, stable isotope tracing experiments indicate methanogenesis is occurring in most fluid samples. No activity was detected

Microbial mechanisms of using enhanced ecological floating beds for eutrophic water improvement.

Science.gov (United States)

Wu, Qing; Hu, Yue; Li, Shuqun; Peng, Sen; Zhao, Huabing

2016-07-01

Enhanced ecological floating beds were implemented to reduce nutrient quantity and improve the water quality of a eutrophic lake. The results showed that average removal efficiencies of CODCr, total nitrogen, NH3-N and total phosphorus for Canna indica L. set-up were 23.1%, 15.3%, 18.1% and 19.4% higher, respectively, than that of the setup with only substrate, and 14.2%, 12.8%, 7.9% and 11.9% higher than Iris pseudacorus L. ecological floating bed. The microbial community structure had obvious differences between devices and low similarity; bacteria were mainly attached on the fiber filling. The microbial population was abundant at the start and end of the experiment. Shannon index of samples selected ranged from 0.85 to 1.05. The sequencing results showed that fiber filling collected most uncultured bacteria species and the majority of bacteria on the plant roots were β-Proteobacteria and α-Proteobacteria. The co-dominant species attaching to the filling and plant was Nitrosomonadaceae. Copyright © 2016 Elsevier Ltd. All rights reserved.

Resistance to post-harvest microbial rot in yam: Integration of ...

African Journals Online (AJOL)

Post-harvest microbial rot is an important disease that causes severe losses in yam (Dioscorea spp.) storage. Rot from microbial infection of healthy yam tubers reduces their table quality and renders them unappealing to consumers. A study was carried out at Bimbilla in the Nanumba North District of Ghana to evaluate ...

Microbial Ecology and Evolution in the Acid Mine Drainage Model System.

Science.gov (United States)

Huang, Li-Nan; Kuang, Jia-Liang; Shu, Wen-Sheng

2016-07-01

Acid mine drainage (AMD) is a unique ecological niche for acid- and toxic-metals-adapted microorganisms. These low-complexity systems offer a special opportunity for the ecological and evolutionary analyses of natural microbial assemblages. The last decade has witnessed an unprecedented interest in the study of AMD communities using 16S rRNA high-throughput sequencing and community genomic and postgenomic methodologies, significantly advancing our understanding of microbial diversity, community function, and evolution in acidic environments. This review describes new data on AMD microbial ecology and evolution, especially dynamics of microbial diversity, community functions, and population genomes, and further identifies gaps in our current knowledge that future research, with integrated applications of meta-omics technologies, will fill. Copyright © 2016 Elsevier Ltd. All rights reserved.

Application of molecular microbial ecology tools to facilitate the development of feeding systems for ruminant livestock that reduce greenhouse gas emissions

International Nuclear Information System (INIS)

McCrabb, G.J.; Fernandez-Rivera, S.; McSweeney, C.S.; Denman, S.; Mitsumori, M.; Makkar, H.P.S.

2005-01-01

Ruminant livestock populations in developing countries are increasing in response to increasing demand for meat and milk. These animals are a major global source of methane, a greenhouse gas produced during the degradation of organic matter by micro-organisms in the foregut of ruminant livestock. Chemical inhibition of methanogenic micro-organisms has been reported; however, associated improvements in feed digestion and livestock productivity have not been consistently demonstrated. Gene-based technologies have the potential to contribute new knowledge of the rumen microbial populations involved in these processes, which will assist in identifying feeding practices that lead to methane abatement and improved livestock productivity. For small-scale farmers, feeding interventions that achieve greenhouse gas abatement need also to be associated with improved feed conversion efficiency and enterprise profitability. During the adoption of methane abatement technologies, other regionally important issues such as poverty, food security, sustainable agriculture production systems and environmental management must also be addressed. (author)

COMPOSITION AND METHOD FOR CONTROLLING MICROBIAL ADHESION AND BIOFILM FORMATION OF SURFACES

DEFF Research Database (Denmark)

2003-01-01

The present invention describes how coating of surfaces with an extract, particularly a fish extract, can significantly reduce microbial adhesion, attachment, colonization and biofilm formation on surfaces. Such reduction of microbial adherence, attachment and colonization will be applicable...

Microbial Surface Colonization and Biofilm Development in Marine Environments

Science.gov (United States)

2015-01-01

SUMMARY Biotic and abiotic surfaces in marine waters are rapidly colonized by microorganisms. Surface colonization and subsequent biofilm formation and development provide numerous advantages to these organisms and support critical ecological and biogeochemical functions in the changing marine environment. Microbial surface association also contributes to deleterious effects such as biofouling, biocorrosion, and the persistence and transmission of harmful or pathogenic microorganisms and their genetic determinants. The processes and mechanisms of colonization as well as key players among the surface-associated microbiota have been studied for several decades. Accumulating evidence indicates that specific cell-surface, cell-cell, and interpopulation interactions shape the composition, structure, spatiotemporal dynamics, and functions of surface-associated microbial communities. Several key microbial processes and mechanisms, including (i) surface, population, and community sensing and signaling, (ii) intraspecies and interspecies communication and interaction, and (iii) the regulatory balance between cooperation and competition, have been identified as critical for the microbial surface association lifestyle. In this review, recent progress in the study of marine microbial surface colonization and biofilm development is synthesized and discussed. Major gaps in our knowledge remain. We pose questions for targeted investigation of surface-specific community-level microbial features, answers to which would advance our understanding of surface-associated microbial community ecology and the biogeochemical functions of these communities at levels from molecular mechanistic details through systems biological integration. PMID:26700108

Characterization of sulfate-reducing granular sludge in the SANI(®) process.

Science.gov (United States)

Hao, Tianwei; Wei, Li; Lu, Hui; Chui, Hokwong; Mackey, Hamish R; van Loosdrecht, Mark C M; Chen, Guanghao

2013-12-01

Hong Kong practices seawater toilet flushing covering 80% of the population. A sulfur cycle-based biological nitrogen removal process, the Sulfate reduction, Autotrophic denitrification and Nitrification Integrated (SANI(®)) process, had been developed to close the loop between the hybrid water supply and saline sewage treatment. To enhance this novel process, granulation of a Sulfate-Reducing Up-flow Sludge Bed (SRUSB) reactor has recently been conducted for organic removal and provision of electron donors (sulfide) for subsequent autotrophic denitrification, with a view to minimizing footprint and maximizing operation resilience. This further study was focused on the biological and physicochemical characteristics of the granular sulfate-reducing sludge. A lab-scale SRUSB reactor seeded with anaerobic digester sludge was operated with synthetic saline sewage for 368 days. At 1 h nominal hydraulic retention time (HRT) and 6.4 kg COD/m(3)-d organic loading rate, the SRUSB reactor achieved 90% COD and 75% sulfate removal efficiencies. Granular sludge was observed within 30 days, and became stable after 4 months of operation with diameters of 400-500 μm, SVI5 of 30 ml/g, and extracellular polymeric substances of 23 mg carbohydrate/g VSS. Fluorescence in situ hybridization (FISH) analysis revealed that the granules were enriched with abundant sulfate-reducing bacteria (SRB) as compared with the seeding sludge. Pyrosequencing analysis of the 16S rRNA gene in the sulfate-reducing granules on day 90 indicated that the microbial community consisted of a diverse SRB genera, namely Desulfobulbus (18.1%), Desulfobacter (13.6%), Desulfomicrobium (5.6%), Desulfosarcina (0.73%) and Desulfovibrio (0.6%), accounting for 38.6% of total operational taxonomic units at genera level, with no methanogens detected. The microbial population and physicochemical properties of the granules well explained the excellent performance of the granular SRUSB reactor. Copyright © 2013 Elsevier

Relationships between Microbial Activities and Subduction-related Outgassing and Volatile Flux at Aleutian Arc Volcanoes

Science.gov (United States)

Miller, H.; Lopez, T. M.; Fischer, T. P.; Schrenk, M. O.

2016-12-01

Subduction-related processes, including the movement and alteration of carbon compounds, are an important component of global geochemical cycles. Actively degassing volcanoes of the Aleutian Island arc offer interesting opportunities to not only characterize the composition and abundance of volatiles, but also to identify the origin of the discharging gases (e.g. mantle, organic matter, or carbonates). Taking this approach a step further, microbial activities in and around volcanic fumarole areas may impact the composition and flux of reduced volcanic gases, either through their modification or their assimilation into fixed biomass. Microbiological studies of these systems can be used to develop predictive models to complement those based upon geochemical data while providing greater understanding of the causal relationships between microbial populations and their environment, and ultimately refine estimates of volcanic outgassing. Coupled fumarole soil and gas samples were collected from several Aleutian Island volcanoes in 2015 (Gareloi, Kanaga, Kiska, Little Sitkin) and 2016 (Okmok, Resheschnoi). DNA was extracted from the soil and used to describe microbial community composition, while gas samples were analyzed through chromatography and mass spectrometry. Preliminary data suggests a relationship between the abundance of specific groups of prokaryotes known to metabolize reduced gases, such as sulfur-oxidizers and methanotrophs, and the abundances of the degassing volatiles, including sulfur dioxide and methane. Ongoing studies aimed at investigating the relationship between the genomic composition of the fumarolic microbial community and the physical and chemical properties of the soil (i.e. mineralogy, bulk geochemistry, nutrient concentration, gas flux, and environmental measurements) are underway. These data will be used to evaluate the potential for microbial communities to remove volcanic carbon and store it as biomass, or to modify the volatile carbon

Shifts in the Microbial Population in Relation to in situ Caries Progression

NARCIS (Netherlands)

Thomas, R. Z.; Zijnge, V.; Cicek, A.; de Soet, J. J.; Harmsen, H. J. M.; Huysmans, M. C. D. N. J. M.

2012-01-01

The shift in microbial diversity from young to mature plaque, related to caries activity on sound and restored surfaces, was studied using denaturing gradient gel electrophoresis. During a 20-week in situ study on caries progression 8 subjects wearing restored and unrestored dentin and enamel

Shifts in the microbial population in relation to in situ caries progression

NARCIS (Netherlands)

Thomas, R.Z.; Zijnge, V.; Ciçek, A.; de Soet, J.J.; Harmsen, H.J.M.; Huysmans, M.C.D.N.J.M.

2012-01-01

The shift in microbial diversity from young to mature plaque, related to caries activity on sound and restored surfaces, was studied using denaturing gradient gel electrophoresis. During a 20-week in situ study on caries progression 8 subjects wearing restored and unrestored dentin and enamel

Effect of Rhodophyta extracts on ruminal fermentation characteristics, methanogenesis and microbial populations

Directory of Open Access Journals (Sweden)

Shin Ja Lee

2018-01-01

Full Text Available Objective Due to the threat of global warming, the livestock industry is increasingly interested in exploring how feed additives may reduce anthropogenic greenhouse gas emissions, especially from ruminants. This study investigated the effect of Rhodophyta supplemented bovine diets on in vitro rumen fermentation and rumen microbial diversity. Methods Cannulated Holstein cows were used as rumen fluid donors. Rumen fluid:buffer (1:2; 15 mL solution was incubated for up to 72 h in six treatments: a control (timothy hay only, along with substrates containing 5% extracts from five Rhodophyta species (Grateloupia lanceolata [Okamura] Kawaguchi, Hypnea japonica Tanaka, Pterocladia capillacea [Gmelin] Bornet, Chondria crassicaulis Harvey, or Gelidium amansii [Lam.] Lamouroux. Results Compared with control, Rhodophyta extracts increased cumulative gas production after 24 and 72 h (p = 0.0297 and p = 0.0047. The extracts reduced methane emission at 12 and 24 h (p<0.05. In particular, real-time polymerase chain reaction analysis indicated that at 24 h, ciliate-associated methanogens, Ruminococcus albus and Ruminococcus flavefaciens decreased at 24 h (p = 0.0002, p<0.0001, and p<0.0001, while Fibrobacter succinogenes (F. succinogenes increased (p = 0.0004. Additionally, Rhodophyta extracts improved acetate concentration at 12 and 24 h (p = 0.0766 and p = 0.0132, as well as acetate/propionate (A/P ratio at 6 and 12 h (p = 0.0106 and p = 0.0278. Conclusion Rhodophyta extracts are a viable additive that can improve ruminant growth performance (higher total gas production, lower A/P ratio and methane abatement (less ciliate-associated methanogens, Ruminococcus albus and Ruminococcus flavefaciens and more F. succinogenes.

Genome-centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion.

Science.gov (United States)

Vanwonterghem, Inka; Jensen, Paul D; Rabaey, Korneel; Tyson, Gene W

2016-09-01

Our understanding of the complex interconnected processes performed by microbial communities is hindered by our inability to culture the vast majority of microorganisms. Metagenomics provides a way to bypass this cultivation bottleneck and recent advances in this field now allow us to recover a growing number of genomes representing previously uncultured populations from increasingly complex environments. In this study, a temporal genome-centric metagenomic analysis was performed of lab-scale anaerobic digesters that host complex microbial communities fulfilling a series of interlinked metabolic processes to enable the conversion of cellulose to methane. In total, 101 population genomes that were moderate to near-complete were recovered based primarily on differential coverage binning. These populations span 19 phyla, represent mostly novel species and expand the genomic coverage of several rare phyla. Classification into functional guilds based on their metabolic potential revealed metabolic networks with a high level of functional redundancy as well as niche specialization, and allowed us to identify potential roles such as hydrolytic specialists for several rare, uncultured populations. Genome-centric analyses of complex microbial communities across diverse environments provide the key to understanding the phylogenetic and metabolic diversity of these interactive communities. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Long-term effects of aided phytostabilisation of trace elements on microbial biomass and activity, enzyme activities, and composition of microbial community in the Jales contaminated mine spoils

Energy Technology Data Exchange (ETDEWEB)

Renella, Giancarlo [Department of Soil Science and Plant Nutrition, University of Florence, Piazzale delle Cascine 28, I-50144 Florence (Italy)], E-mail: giancarlo.renella@unifi.it; Landi, Loretta; Ascher, Judith; Ceccherini, Maria Teresa; Pietramellara, Giacomo; Mench, Michel; Nannipieri, Paolo [Department of Soil Science and Plant Nutrition, University of Florence, Piazzale delle Cascine 28, I-50144 Florence (Italy)

2008-04-15

We studied the effectiveness of remediation on microbial endpoints, namely microbial biomass and activity, microbial and plant species richness, of an As-contaminated mine spoil, amended with compost (C) alone and in combination with beringite (B) or zerovalent iron grit (Z), to increase organic matter content and reduce trace elements mobility, and to allow Holcus lanatus and Pinus pinaster growth. Untreated spoil showed the lowest microbial biomass and activity and hydrolase activities, and H. lanatus as sole plant species, whereas the presented aided phytostabilisation option, especially CBZ treatment, significantly increased microbial biomass and activity and allowed colonisation by several plant species, comparable to those of an uncontaminated sandy soil. Microbial species richness was only increased in spoils amended with C alone. No clear correlation occurred between trace element mobility and microbial parameters and plant species richness. Our results indicate that the choice of indicators of soil remediation practices is a bottleneck. - Organo-mineral amendment and revegetation of a gold mine spoil increased microbial activity but did not increase microbial species richness.

Long-term effects of aided phytostabilisation of trace elements on microbial biomass and activity, enzyme activities, and composition of microbial community in the Jales contaminated mine spoils

International Nuclear Information System (INIS)

Renella, Giancarlo; Landi, Loretta; Ascher, Judith; Ceccherini, Maria Teresa; Pietramellara, Giacomo; Mench, Michel; Nannipieri, Paolo

2008-01-01

We studied the effectiveness of remediation on microbial endpoints, namely microbial biomass and activity, microbial and plant species richness, of an As-contaminated mine spoil, amended with compost (C) alone and in combination with beringite (B) or zerovalent iron grit (Z), to increase organic matter content and reduce trace elements mobility, and to allow Holcus lanatus and Pinus pinaster growth. Untreated spoil showed the lowest microbial biomass and activity and hydrolase activities, and H. lanatus as sole plant species, whereas the presented aided phytostabilisation option, especially CBZ treatment, significantly increased microbial biomass and activity and allowed colonisation by several plant species, comparable to those of an uncontaminated sandy soil. Microbial species richness was only increased in spoils amended with C alone. No clear correlation occurred between trace element mobility and microbial parameters and plant species richness. Our results indicate that the choice of indicators of soil remediation practices is a bottleneck. - Organo-mineral amendment and revegetation of a gold mine spoil increased microbial activity but did not increase microbial species richness

The effect of glyphosate application on soil microbial activities in ...

African Journals Online (AJOL)

In this study, glyphosate effects as N, P and C nutrient sources on microbial population and the effect of different concentration of it on dehydrogenease activity and soil respiration were investigated. The results show that in a soil with a long historical use of glyphosate (soil 1), the hetrotrophic bacterial population was ...

Halitosis: An oral microbial faction

Directory of Open Access Journals (Sweden)

Rajiv Saini

2010-01-01

Full Text Available Halitosis is a widespread condition and believed to affect one-quarter of the population around the world; also, most people have this condition from time to time. Breath malodour may be an important factor in social communication, and therefore may be the origin of concern not only for a possible health condition but also for frequent psychological alterations, leading to social and personal isolation. The most conspicuous malodorous compounds are termed volatile sulphur compounds (VSCs, with hydrogen sulphide, methyl mercaptan, and dimethyl sulphide accounting for roughly 90% of the VSCs. A number of oral bacteria, especially Gram-negative anaerobic species found in the subgingival plaque, produce a diverse array of malodorous compounds as byproducts of their metabolism, including VSCs and short-chain organic acids. Assessment and management of halitosis is of paramount importance in enhancing the overall health; moreover, dentists play a significant role in combating halitosis by reducing the oral microbial stack. Thus, the aim of the present review was to describe the aetiological factors, assessment tools, and therapeutic approaches related to halitosis.

Effects of diets containing different concentrations of mannanoligosaccharide or antibiotics on growth performance, intestinal development, cecal and litter microbial populations, and carcass parameters of broilers.

Science.gov (United States)

Baurhoo, B; Ferket, P R; Zhao, X

2009-11-01

The effects of 2 levels of mannanoligosaccharide (MOS) in feed were compared with antibiotic growth promoters on growth performance, intestinal morphology, cecal and litter microbial populations, and carcass parameters in broilers raised in a sanitary environment. Dietary treatments included: 1) antibiotic growth promoter-free diet (control), 2) VIRG (diet 1 + 16.5 mg/kg of virginiamycin), 3) BACT (diet 1 + 55 mg/kg of bacitracin), 4) LMOS (diet 1 + 0.2% MOS), and 5) HMOS (diet 1 + 0.5% MOS). Birds were randomly assigned to 3 replicate pens/treatment (n = 55/pen). Body weight and feed intake were recorded weekly throughout 38 d. At d 14, 24, and 34, a 1-cm segment of duodenum, jejunum, and ileum was used in morphological analysis (n = 9 birds/d per treatment). At the same bird ages, cecal contents were assayed for lactobacilli, bifidobacteria, Salmonella, Campylobacter, and Escherichia coli, whereas litter was analyzed for Salmonella, Campylobacter, and E. coli. Carcass yields (breast fillet and tenders, thigh, drumstick, and wing) were determined at d 38. Body weight, feed conversion, and carcass yields did not differ among treatments. In contrast to birds fed VIRG or BACT, LMOS and HMOS consistently increased (P litter from all treatments were free of Salmonella. At d 14 and 24, cecal E. coli and Campylobacter counts were not different among treatments. In comparison to birds fed control, at d 34, BACT, LMOS, and HMOS significantly reduced (P Litter bacterial counts were not altered by dietary treatments. In conclusion, under conditions of this study, MOS conferred intestinal health benefits to chickens by improving its morphological development and microbial ecology. But, there were no additional benefits of the higher MOS dosage.

Simultaneous inhibition of sulfate-reducing bacteria, removal of H2S and production of rhamnolipid by recombinant Pseudomonas stutzeri Rhl: Applications for microbial enhanced oil recovery.

Science.gov (United States)

Zhao, Feng; Zhou, Ji-Dong; Ma, Fang; Shi, Rong-Jiu; Han, Si-Qin; Zhang, Jie; Zhang, Ying

2016-05-01

Sulfate-reducing bacteria (SRB) are widely existed in oil production system, and its H2S product inhibits rhamnolipid producing bacteria. In-situ production of rhamnolipid is promising for microbial enhanced oil recovery. Inhibition of SRB, removal of H2S and production of rhamnolipid by recombinant Pseudomonas stutzeri Rhl were investigated. Strain Rhl can simultaneously remove S(2-) (>92%) and produce rhamnolipid (>136mg/l) under S(2-) stress below 33.3mg/l. Rhl reduced the SRB numbers from 10(9) to 10(5)cells/ml, and the production of H2S was delayed and decreased to below 2mg/l. Rhl also produced rhamnolipid and removed S(2-) under laboratory simulated oil reservoir conditions. High-throughput sequencing data demonstrated that addition of strain Rhl significantly changed the original microbial communities of oilfield production water and decreased the species and abundance of SRB. Bioaugmentation of strain Rhl in oilfield is promising for simultaneous control of SRB, removal of S(2-) and enhance oil recovery. Copyright © 2016 Elsevier Ltd. All rights reserved.

Study on Dynamic Characteristics of Microbial Enhanced Oil Recovery

Science.gov (United States)

Zhao, Yang; Shi, Fang; Qin, Wuying; Yan, Jing

2018-01-01

With the rapid development of economy, the demand for oil is increasing day by day. MEOR has the advantages of low cost and no pollution to the environment, attracted widespread attention. In this paper, the dynamic characteristics of microbial enhanced oil recovery were studied by laboratory experiments. The result showed that all the microbial flooding recovery rate could reach more than 5%, and the total recovery could reach more than 35% and if the injection period of microbial composite system was advanced, the whole oil displacement process could be shortened and the workload would be reduced.

Microbial genome-wide association studies: lessons from human GWAS.

Science.gov (United States)

Power, Robert A; Parkhill, Julian; de Oliveira, Tulio

2017-01-01

The reduced costs of sequencing have led to whole-genome sequences for a large number of microorganisms, enabling the application of microbial genome-wide association studies (GWAS). Given the successes of human GWAS in understanding disease aetiology and identifying potential drug targets, microbial GWAS are likely to further advance our understanding of infectious diseases. These advances include insights into pressing global health problems, such as antibiotic resistance and disease transmission. In this Review, we outline the methodologies of GWAS, the current state of the field of microbial GWAS, and how lessons from human GWAS can direct the future of the field.

Targeting population heterogeneity for optimal cell factories

DEFF Research Database (Denmark)

Heins, Anna-Lena; Carlqvist, Magnus; Helmark, S.

the heterogeneity level of the population. To further investigate these phenomena and gain a deeper understanding of population heterogeneity, Saccharomyces cerevisiae growth reporter strains based on the expression of green fluorescent protein (GFP) were constructed which enabled us to perform single cell level...... analysis, and thereby created the possibility to map population heterogeneity. A factorial design with pH, glucose concentration and oxygen level was performed in batch cultivations using the growth reporter strains to evaluate the effect of those environmental factors on heterogeneity level and amount......To achieve an efficient production process, it is essential to optimize both the strain and the cultivation conditions. Traditionally, a microbial population has been considered homogeneous in optimization studies of fermentation processes. However, research has shown that a typical microbial...

Soil Microbes and soil microbial proteins: interactions with clay minerals

International Nuclear Information System (INIS)

Spence, A.; Kelleher, B. P.

2009-01-01

Bacterial enumeration in soil environments estimates that the population may reach approximately 10 1 0 g - 1 of soil and comprise up to 90% of the total soil microbial biomass. Bacteria are present in soils as single cells or multicell colonies and often strongly adsorb onto mineral surfaces such as sand and clay. The interactions of microbes and microbial biomolecules with these minerals have profound impacts on the physical, chemical and biological properties of soils. (Author)

Microbial changes during pregnancy, birth and infancy

Directory of Open Access Journals (Sweden)

Meital Nuriel-Ohayon

2016-07-01

Full Text Available Several healthy developmental processes such as pregnancy, fetal development and infant development include a multitude of physiological changes: weight gain, hormonal and metabolic changes, as well as immune changes. In this review we present an additional important factor which both influences and is affected by these physiological processes- the microbiome. We summarize the known changes in microbiota composition at a variety of body sites including gut, vagina, oral cavity and placenta, throughout pregnancy, fetal development and early childhood. There is still a lot to be discovered; yet several pieces of research point to the healthy desired microbial changes. Future research is likely to unravel precise roles and mechanisms of the microbiota in gestation; perhaps linking the metabolic, hormonal and immune changes together. Although some research has started to link microbial dysbiosis and specific microbial populations with unhealthy pregnancy complications, it is important to first understand the context of the natural healthy microbial changes occurring. Until recently the placenta and developing fetus were considered to be germ free, containing no apparent microbiome. We present multiple study results showing distinct microbiota compositions in the placenta and meconium, alluding to early microbial colonization. These results may change dogmas and our overall understanding of the importance and roles of microbiota from the beginning of life. We further review the main factors shaping the infant microbiome- modes of delivery, feeding, weaning, and exposure to antibiotics. Taken together, we are starting to build a broader understanding of healthy vs. abnormal microbial alterations throughout major developmental time-points.

Investigations of potential microbial methanogenic and carbon monoxide utilization pathways in ultra-basic reducing springs associated with present-day continental serpentinization: the Tablelands, NL, CAN

Directory of Open Access Journals (Sweden)

Penny Lea Morrill

2014-11-01

Full Text Available Ultra-basic reducing springs at continental sites of serpentinization act as portals into the biogeochemistry of a subsurface environment with H2 and CH4 present. Very little, however, is known about the carbon substrate utilization, energy sources, and metabolic pathways of the microorganisms that live in this ultra-basic environment. The potential for microbial methanogenesis with bicarbonate, formate, acetate, and propionate precursors and carbon monoxide (CO utilization pathways were tested in laboratory experiments by adding substrates to water and sediment from the Tablelands, NL, CAD, a site of present-day continental serpentinization. Microbial methanogenesis was not observed after bicarbonate, formate, acetate, or propionate addition. CO was consumed in the live experiments but not in the killed controls and the residual CO in the live experiments became enriched in 13 C. The average isotopic enrichment factor resulting from this microbial utilization of CO was estimated to be 11.2 ± 0.2‰. Phospholipid fatty acid concentrations and δ13C values suggest limited incorporation of carbon from CO into microbial lipids. This indicates that in our experiments, CO was used primarily as an energy source, but not for biomass growth. Environmental DNA sequencing of spring fluids collected at the same time as the addition experiments yielded a large proportion of Hydrogenophaga-related sequences, which is consistent with previous metagenomic data indicating the potential for these taxa to utilize CO.

Effect of Portulaca oleracea extracts on growth performance and microbial populations in ceca of broilers.

Science.gov (United States)

Zhao, X H; He, X; Yang, X F; Zhong, X H

2013-05-01

The aim of this study was to investigate the effects of Portulaca oleracea extracts on growth performance and microbial populations in the ceca of broilers. A total of 120 one-day-old broilers were randomly divided into 3 groups. Portulaca oleracea extracts were added to diets at 0.2 and 0.4% (wt/wt; POL-0.2, POL-0.4), respectively. The control (CON) group was administered with no P. oleracea extract supplementation. Body weight gain and feed conversion ratio were recorded every 2 wk. On d 28 and 42, the cecal contents were collected and assayed for Escherichia coli, Lactobacillus, and Bifidobacterium populations. Additionally, the pH of the ileum and cecum was measured. The results showed that both on d 28 and 42 BW gain of P. oleracea extract supplementation groups was significantly higher, whereas the feed conversion ratio was lower (P < 0.05) compared with CON. On d 28 and 42, significantly (P < 0.05) fewer E. coli were recovered from ceca of broilers provided with the POL-0.2 diet than from broilers provided with the control diet. The quantities of Lactobacillus and Bifidobacterium of POL-0.2 were significantly (P < 0.05) higher than CON. Results showed P. oleracea extracts have no distinct influence on intestinal pH. These data suggest that P. oleracea extract supplementation significantly altered the cecal bacterial community without affecting the intestinal pH.

CRISPR associated diversity within a population of Sulfolobus islandicus.

Directory of Open Access Journals (Sweden)

Nicole L Held

2010-09-01

Full Text Available Predator-prey models for virus-host interactions predict that viruses will cause oscillations of microbial host densities due to an arms race between resistance and virulence. A new form of microbial resistance, CRISPRs (clustered regularly interspaced short palindromic repeats are a rapidly evolving, sequence-specific immunity mechanism in which a short piece of invading viral DNA is inserted into the host's chromosome, thereby rendering the host resistant to further infection. Few studies have linked this form of resistance to population dynamics in natural microbial populations.We examined sequence diversity in 39 strains of the archeaon Sulfolobus islandicus from a single, isolated hot spring from Kamchatka, Russia to determine the effects of CRISPR immunity on microbial population dynamics. First, multiple housekeeping genetic markers identify a large clonal group of identical genotypes coexisting with a diverse set of rare genotypes. Second, the sequence-specific CRISPR spacer arrays split the large group of isolates into two very different groups and reveal extensive diversity and no evidence for dominance of a single clone within the population.The evenness of resistance genotypes found within this population of S. islandicus is indicative of a lack of strain dominance, in contrast to the prediction for a resistant strain in a simple predator-prey interaction. Based on evidence for the independent acquisition of resistant sequences, we hypothesize that CRISPR mediated clonal interference between resistant strains promotes and maintains diversity in this natural population.

Microwave-Assisted Synthesis of Reduced Graphene Oxide/SnO2 Nanocomposite for Oxygen Reduction Reaction in Microbial Fuel Cells.

Science.gov (United States)

Garino, Nadia; Sacco, Adriano; Castellino, Micaela; Muñoz-Tabares, José Alejandro; Chiodoni, Angelica; Agostino, Valeria; Margaria, Valentina; Gerosa, Matteo; Massaglia, Giulia; Quaglio, Marzia

2016-02-01

We report on an easy, fast, eco-friendly, and reliable method for the synthesis of reduced graphene oxide/SnO2 nanocomposite as cathode material for application in microbial fuel cells (MFCs). The material was prepared starting from graphene oxide that has been reduced to graphene during the hydrothermal synthesis of the nanocomposite, carried out in a microwave system. Structural and morphological characterizations evidenced the formation of nanocomposite sheets, with SnO2 crystals of few nanometers integrated in the graphene matrix. Physico-chemical analysis revealed the formation of SnO2 nanoparticles, as well as the functionalization of the graphene by the presence of nitrogen atoms. Electrochemical characterizations put in evidence the ability of such composite to exploit a cocatalysis mechanism for the oxygen reduction reaction, provided by the presence of both SnO2 and nitrogen. In addition, the novel composite catalyst was successfully employed as cathode in seawater-based MFCs, giving electrical performances comparable to those of reference devices employing Pt as catalyst.

Reduced flight-to-light behaviour of moth populations exposed to long-term urban light pollution.

Science.gov (United States)

Altermatt, Florian; Ebert, Dieter

2016-04-01

The globally increasing light pollution is a well-recognized threat to ecosystems, with negative effects on human, animal and plant wellbeing. The most well-known and widely documented consequence of light pollution is the generally fatal attraction of nocturnal insects to artificial light sources. However, the evolutionary consequences are unknown. Here we report that moth populations from urban areas with high, globally relevant levels of light pollution over several decades show a significantly reduced flight-to-light behaviour compared with populations of the same species from pristine dark-sky habitats. Using a common garden setting, we reared moths from 10 different populations from early-instar larvae and experimentally compared their flight-to-light behaviour under standardized conditions. Moths from urban populations had a significant reduction in the flight-to-light behaviour compared with pristine populations. The reduced attraction to light sources of 'city moths' may directly increase these individuals' survival and reproduction. We anticipate that it comes with a reduced mobility, which negatively affects foraging as well as colonization ability. As nocturnal insects are of eminent significance as pollinators and the primary food source of many vertebrates, an evolutionary change of the flight-to-light behaviour thereby potentially cascades across species interaction networks. © 2016 The Author(s).

Solar energy system reduces time taken to inhibit microbial growth in soil

Energy Technology Data Exchange (ETDEWEB)

Phitthayarachasak, Thanathep; Thepa, Sirichai; Kongkiattikajorn, Jirasak [Energy Technology Division, School of Energy Environment and Materials, King Mongkut' s University of Technology Thonburi, 126 Prachauthid Road, Tungkru, Bangkok 10140 (Thailand)

2009-11-15

This research studied how to reduce the time consumption and to increase and improve the efficiency of the solarization process. The asymmetry compound parabolic concentrator (ACPC) was developed to produce boiling water to be utilized while the solarization process was in operation. This could decrease the time consumed in the solarization process from 4 to 6 weeks to 4 h, with a temperature of approximately 41.25 C at the various depth levels, not exceeding 50 cm. The test to inhibit the growth of Ralstonia solanacearum, the causative agent of wilt in crops leaves, indicated that R. solanacearum was reduced from the total bacterial population of 10.9 x 10{sup 8} colony forming unit/g soil (cfu g{sup -1}) at soil surface to 9.0 x 10{sup 7}, 7.5 x 10{sup 4} and 4.1 x 10{sup 3} cfu g{sup -1} within 1, 2 and 4 h, respectively. (author)

Ecological feedbacks can reduce population-level efficacy of wildlife fertility control

Science.gov (United States)

Ransom, Jason I.; Powers, Jenny G.; Hobbs, N. Thompson; Baker, Dan L.

2014-01-01

1. Anthropogenic stress on natural systems, particularly the fragmentation of landscapes and the extirpation of predators from food webs, has intensified the need to regulate abundance of wildlife populations with management. Controlling population growth using fertility control has been considered for almost four decades, but nearly all research has focused on understanding effects of fertility control agents on individual animals. Questions about the efficacy of fertility control as a way to control populations remain largely unanswered. 2. Collateral consequences of contraception can produce unexpected changes in birth rates, survival, immigration and emigration that may reduce the effectiveness of regulating animal abundance. The magnitude and frequency of such effects vary with species-specific social and reproductive systems, as well as connectivity of populations. Developing models that incorporate static demographic parameters from populations not controlled by contraception may bias predictions of fertility control efficacy. 3. Many population-level studies demonstrate that changes in survival and immigration induced by fertility control can compensate for the reduction in births caused by contraception. The most successful cases of regulating populations using fertility control come from applications of contraceptives to small, closed populations of gregarious and easily accessed species. 4. Fertility control can result in artificial selection pressures on the population and may lead to long-term unintentional genetic consequences. The magnitude of such selection is dependent on individual heritability and behavioural traits, as well as environmental variation. 5. Synthesis and applications. Understanding species' life-history strategies, biology, behavioural ecology and ecological context is critical to developing realistic expectations of regulating populations using fertility control. Before time, effort and funding are invested in wildlife

Synthetic microbial ecology and the dynamic interplay between microbial genotypes.

Science.gov (United States)

Dolinšek, Jan; Goldschmidt, Felix; Johnson, David R

2016-11-01

Assemblages of microbial genotypes growing together can display surprisingly complex and unexpected dynamics and result in community-level functions and behaviors that are not readily expected from analyzing each genotype in isolation. This complexity has, at least in part, inspired a discipline of synthetic microbial ecology. Synthetic microbial ecology focuses on designing, building and analyzing the dynamic behavior of ‘ecological circuits’ (i.e. a set of interacting microbial genotypes) and understanding how community-level properties emerge as a consequence of those interactions. In this review, we discuss typical objectives of synthetic microbial ecology and the main advantages and rationales of using synthetic microbial assemblages. We then summarize recent findings of current synthetic microbial ecology investigations. In particular, we focus on the causes and consequences of the interplay between different microbial genotypes and illustrate how simple interactions can create complex dynamics and promote unexpected community-level properties. We finally propose that distinguishing between active and passive interactions and accounting for the pervasiveness of competition can improve existing frameworks for designing and predicting the dynamics of microbial assemblages.

Turnover of microbial lipids in the deep biosphere and growth of benthic archaeal populations.

Science.gov (United States)

Xie, Sitan; Lipp, Julius S; Wegener, Gunter; Ferdelman, Timothy G; Hinrichs, Kai-Uwe

2013-04-09

Deep subseafloor sediments host a microbial biosphere with unknown impact on global biogeochemical cycles. This study tests previous evidence based on microbial intact polar lipids (IPLs) as proxies of live biomass, suggesting that Archaea dominate the marine sedimentary biosphere. We devised a sensitive radiotracer assay to measure the decay rate of ([(14)C]glucosyl)-diphytanylglyceroldiether (GlcDGD) as an analog of archaeal IPLs in continental margin sediments. The degradation kinetics were incorporated in model simulations that constrained the fossil fraction of subseafloor IPLs and rates of archaeal turnover. Simulating the top 1 km in a generic continental margin sediment column, we estimated degradation rate constants of GlcDGD being one to two orders of magnitude lower than those of bacterial IPLs, with half-lives of GlcDGD increasing with depth to 310 ky. Given estimated microbial community turnover times of 1.6-73 ky in sediments deeper than 1 m, 50-96% of archaeal IPLs represent fossil signals. Consequently, previous lipid-based estimates of global subseafloor biomass probably are too high, and the widely observed dominance of archaeal IPLs does not rule out a deep biosphere dominated by Bacteria. Reverse modeling of existing concentration profiles suggest that archaeal IPL synthesis rates decline from around 1,000 pg⋅mL(-1) sediment⋅y(-1) at the surface to 0.2 pg⋅mL(-1)⋅y(-1) at 1 km depth, equivalent to production of 7 × 10(5) to 140 archaeal cells⋅mL(-1) sediment⋅y(-1), respectively. These constraints on microbial growth are an important step toward understanding the relationship between the deep biosphere and the carbon cycle.

Membrane biofouling in a wastewater nitrification reactor: Microbial succession from autotrophic colonization to heterotrophic domination.

Science.gov (United States)

Lu, Huijie; Xue, Zheng; Saikaly, Pascal; Nunes, Suzana P; Bluver, Ted R; Liu, Wen-Tso

2016-01-01

Membrane biofouling is a complex process that involves bacterial adhesion, extracellular polymeric substances (EPS) excretion and utilization, and species interactions. To obtain a better understanding of the microbial ecology of biofouling process, this study conducted rigorous, time-course analyses on the structure, EPS and microbial composition of the fouling layer developed on ultrafiltration membranes in a nitrification bioreactor. During a 14-day fouling event, three phases were determined according to the flux decline and microbial succession patterns. In Phase I (0-2 days), small sludge flocs in the bulk liquid were selectively attached on membrane surfaces, leading to the formation of similar EPS and microbial community composition as the early biofilms. Dominant populations in small flocs, e.g., Nitrosomonas, Nitrobacter, and Acinetobacter spp., were also the major initial colonizers on membranes. In Phase II (2-4 d), fouling layer structure, EPS composition, and bacterial community went through significant changes. Initial colonizers were replaced by fast-growing and metabolically versatile heterotrophs (e.g., unclassified Sphingobacteria). The declining EPS polysaccharide to protein (PS:PN) ratios could be correlated well with the increase in microbial community diversity. In Phase III (5-14 d), heterotrophs comprised over 90% of the community, whereas biofilm structure and EPS composition remained relatively stable. In all phases, AOB and NOB were constantly found within the top 40% of the fouling layer, with the maximum concentrations around 15% from the top. The overall microbial succession pattern from autotrophic colonization to heterotrophic domination implied that MBR biofouling could be alleviated by forming larger bacterial flocs in bioreactor suspension (reducing autotrophic colonization), and by designing more specific cleaning procedures targeting dominant heterotrophs during typical filtration cycles. Copyright © 2015 Elsevier Ltd. All

The effect of microbial starter composition on cassava chips fermentation for the production of fermented cassava flour

Science.gov (United States)

Kresnowati, M. T. A. P.; Listianingrum, Zaenudin, Ahmad; Trihatmoko, Kharisrama

2015-12-01

The processing of cassava into fermented cassava flour (fercaf) or the widely known as modified cassava flour (mocaf) presents an alternative solution to improve the competitiveness of local foods and to support national food security. However, the mass production of fercaf is being limited by several problems, among which is the availability of starter cultures. This paper presents the mapping of the effect of microbial starter compositions on the nutritional content of fercaf in order to obtain the suitable nutritional composition. Based on their enzymatic activities, the combination of Lactobacillus plantarum, Bacillus subtilis, and Aspergillus oryzae were tested during the study. In addition, commercial starter was also tested. During the fermentation, the dynamics in microbial population were measured as well as changes in cyanogenic glucoside content. The microbial starter composition was observed to affect the dynamics in microbial populationcynaogenic glucoside content of the produced fercaf. In general, steady state microbial population was reached within 12 hours of fermentation. Cyanogenic glucoside was observed to decrease along the fermentation.

Biochar application to hardrock mine tailings: Soil quality, microbial activity, and toxic element sorption

Science.gov (United States)

Kelly, Charlene N.; Peltz, Christopher D.; Stanton, Mark R.; Rutherford, David W.; Rostad, Colleen E.

2014-01-01

Waste rock piles from historic mining activities remain unvegetated as a result of metal toxicity and high acidity. Biochar has been proposed as a low-cost remediation strategy to increase soil pH and reduce leaching of toxic elements, and improve plant establishment. In this laboratory column study, biochar made from beetle-killed pine wood was assessed for utility as a soil amendment by mixing soil material from two mine sites collected near Silverton, Colorado, USA with four application rates of biochar (0%, 10%, 20%, 30% vol:vol). Columns were leached seven times over 65 days and leachate pH and concentration of toxic elements and base cations were measured at each leaching. Nutrient availability and soil physical and biological parameters were determined following the incubation period. We investigated the hypotheses that biochar incorporation into acidic mine materials will (1) reduce toxic element concentrations in leaching solution, (2) improve soil parameters (i.e. increase nutrient and water holding capacity and pH, and decrease compaction), and (3) increase microbial populations and activity. Biochar directly increased soil pH (from 3.33 to 3.63 and from 4.07 to 4.77 in the two materials) and organic matter content, and decreased bulk density and extractable salt content in both mine materials, and increased nitrate availability in one material. No changes in microbial population or activity were detected in either mine material upon biochar application. In leachate solution, biochar increased base cations from both materials and reduced the concentrations of Al, Cd, Cu, Pb, and Zn in leachate solution from one material. However, in the material with greater toxic element content, biochar did not reduce concentrations of any measured dissolved toxic elements in leachate and resulted in a potentially detrimental release of Cd and Zn into solution at concentrations above that of the pure mine material. The length of time of effectiveness and specific

Mammalian engineers drive soil microbial communities and ecosystem functions across a disturbance gradient.

Science.gov (United States)

Eldridge, David J; Delgado-Baquerizo, Manuel; Woodhouse, Jason N; Neilan, Brett A

2016-11-01

The effects of mammalian ecosystem engineers on soil microbial communities and ecosystem functions in terrestrial ecosystems are poorly known. Disturbance from livestock has been widely reported to reduce soil function, but disturbance by animals that forage in the soil may partially offset these negative effects of livestock, directly and/or indirectly by shifting the composition and diversity of soil microbial communities. Understanding the role of disturbance from livestock and ecosystem engineers in driving soil microbes and functions is essential for formulating sustainable ecosystem management and conservation policies. We compared soil bacterial community composition and enzyme concentrations within four microsites: foraging pits of two vertebrates, the indigenous short-beaked echidna (Tachyglossus aculeatus) and the exotic European rabbit (Oryctolagus cuniculus), and surface and subsurface soils along a gradient in grazing-induced disturbance in an arid woodland. Microbial community composition varied little across the disturbance gradient, but there were substantial differences among the four microsites. Echidna pits supported a lower relative abundance of Acidobacteria and Cyanobacteria, but a higher relative abundance of Proteobacteria than rabbit pits and surface microsites. Moreover, these microsite differences varied with disturbance. Rabbit pits had a similar profile to the subsoil or the surface soils under moderate and high, but not low disturbance. Overall, echidna foraging pits had the greatest positive effect on function, assessed as mean enzyme concentrations, but rabbits had the least. The positive effects of echidna foraging on function were indirectly driven via microbial community composition. In particular, increasing activity was positively associated with increasing relative abundance of Proteobacteria, but decreasing Acidobacteria. Our study suggests that soil disturbance by animals may offset, to some degree, the oft-reported negative

Effects of Biochar Amendment on Tomato Bacterial Wilt Resistance and Soil Microbial Amount and Activity

Directory of Open Access Journals (Sweden)

Yang Lu

2016-01-01

Full Text Available Bacterial wilt is a serious soilborne disease of Solanaceae crops which is caused by Ralstonia solanacearum. The important role of biochar in enhancing disease resistance in plants has been verified; however, the underlying mechanism remains not fully understood. In this study, two different biochars, made from peanut shell (BC1 and wheat straw (BC2, were added to Ralstonia solanacearum-infected soil to explore the interrelation among biochar, tomato bacterial wilt, and soil microbial properties. The results showed that both BC1 and BC2 treatments significantly reduced the disease index of bacterial wilt by 28.6% and 65.7%, respectively. The populations of R. solanacearum in soil were also significantly decreased by biochar application. Ralstonia solanacearum infection significantly reduced the densities of soil bacteria and actinomycetes and increased the ratio of soil fungi/bacteria in the soil. By contrast, BC1 and BC2 addition to pathogen-infected soil significantly increased the densities of soil bacteria and actinomycetes but decreased the density of fungi and the ratios of soil fungi/bacteria and fungi/actinomycetes. Biochar treatments also increased soil neutral phosphatase and urease activity. Furthermore, higher metabolic capabilities of microorganisms by biochar application were found at 96 and 144 h in Biolog EcoPlates. These results suggest that both peanut and wheat biochar amendments were effective in inhibiting tomato bacterial wilt caused by R. solanacearum. The results suggest a relationship between the disease resistance of the plants and the changes in soil microbial population densities and activity.

Oxygen-Reducing Biocathodes Operating with Passive Oxygen Transfer in Microbial Fuel Cells

KAUST Repository

Xia, Xue

2013-02-19

Oxygen-reducing biocathodes previously developed for microbial fuel cells (MFCs) have required energy-intensive aeration of the catholyte. To avoid the need for aeration, the ability of biocathodes to function with passive oxygen transfer was examined here using air cathode MFCs. Two-chamber, air cathode MFCs with biocathodes produced a maximum power density of 554 ± 0 mW/m 2, which was comparable to that obtained with a Pt cathode (576 ± 16 mW/m2), and 38 times higher than that produced without a catalyst (14 ± 3 mW/m2). The maximum current density with biocathodes in this air-cathode MFC was 1.0 A/m2, compared to 0.49 A/m2 originally produced in a two-chamber MFC with an aqueous cathode (with cathode chamber aeration). Single-chamber, air-cathode MFCs with the same biocathodes initially produced higher voltages than those with Pt cathodes, but after several cycles the catalytic activity of the biocathodes was lost. This change in cathode performance resulted from direct exposure of the cathodes to solutions containing high concentrations of organic matter in the single-chamber configuration. Biocathode performance was not impaired in two-chamber designs where the cathode was kept separated from the anode solution. These results demonstrate that direct-air biocathodes can work very well, but only under conditions that minimize heterotrophic growth of microorganisms on the cathodes. © 2013 American Chemical Society.

Effects of uranium on soil microbial biomass carbon, enzymes, plant biomass and microbial diversity in yellow soils

International Nuclear Information System (INIS)

Yan, X.; Zhang, Y.; Luo, X.; Yu, L.

2016-01-01

We conducted an experiment to investigate the effects of uranium (U) on soil microbial biomass carbon (MBC), enzymes, plant biomass and microbial diversity in yellow soils under three concentrations: 0 mg kg"-"1 (T1, control), 30 mg kg"-"1 (T2) and 60 mg kg"-"1 (T3). Under each treatment, elevated U did not reduce soil MBC or plant biomass, but inhibited the activity of the soil enzymes urease (UR), dehydrogenase (DH) and phosphatase (PHO). The microbial diversity was different, with eight dominant phyla in T1 and six in T2 and T3. Furthermore, Proteobacteria and material X were both detected in each treatment site (T1, T2 and T3). Pseudomonas sp. was the dominant strain, followed by Acidiphilium sp. This initial study provided valuable data for further research toward a better understanding of U contamination in yellow soils in China. (authors)

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

OpenAIRE

BoonFei eTan; Charmaine Marie Ng; Jean Pierre Nshimyimana; Jean Pierre Nshimyimana; Lay-Leng eLoh; Lay-Leng eLoh; Karina Yew-Hoong Gin; Janelle Renee Thompson; Janelle Renee Thompson

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 reg...

Environmental Drivers of Differences in Microbial Community Structure in Crude Oil Reservoirs across a Methanogenic Gradient

OpenAIRE

Shelton, Jenna L.; Akob, Denise M.; McIntosh, Jennifer C.; Fierer, Noah; Spear, John R.; Warwick, Peter D.; McCray, John E.

2016-01-01

Stimulating in situ microbial communities in oil reservoirs to produce natural gas is a potentially viable strategy for recovering additional fossil fuel resources following traditional recovery operations. Little is known about what geochemical parameters drive microbial population dynamics in biodegraded, methanogenic oil reservoirs. We investigated if microbial community structure was significantly impacted by the extent of crude oil biodegradation, extent of biogenic methane production, a...

Effects of experimental drought on microbial processes in two temperate heathlands at contrasting water conditions

DEFF Research Database (Denmark)

Jensen, K.D.; Beier, C.; Michelsen, A.

2003-01-01

by a 27% reduced below ground CO(2) emission, and reduced microbial and soil solution carbon (C) and nitrogen (N) levels. In contrast, microbial activity at the wetter UK site seemed to benefit from the drought as indicated by a 22% increase in below ground CO(2) emission caused by the drought treatment...

Effect of composts on microbial dynamics and activity, dry root rot severity and seed yield of cowpea in the Indian arid region

Directory of Open Access Journals (Sweden)

Meenu BAREJA

2011-01-01

Full Text Available Nutrient-deficient sandy soil, having poor moisture retention, favors  Macrophomina phaseolina, a soil-borne plant pathogen, occurring in severe form on many important crops grown in the Indian arid region. In a 2-year field experiment, five composts (4 ton/ha prepared from residues of Calotropis procera, Prosopis juliflora, Azadirachta indica, Acacia nilotica, and on-farm weeds were tested on cowpea (Vigna unguiculata to determine their effectiveness in limiting the  severity of charcoal rot caused by M. phaseolina in relation to the microbial population dynamics, microbial activity and the seed yield of cowpea.  In general, compost-amended plots retained 8.9% higher moisture than unamended plots. The microbial population increased in amended plots during the crop season. Populations of total fungi and actinomycetes were heighest in Calotropis compost-amended soil, while total bacteria were maximum in weed- compost amended soil. Microbial activity in amended plots was  26.3% higher than in unamended plots. Among trace elements,  uptake of Zn, Mn, Fe and Cu was  heighest  in plants grown in weed-compost amended soil followed by A. nilotica compost-amended soil. Soil amendment with the composts significantly reduced  plant mortality due to charcoal rot. The lowest mortality was recorded in plants amended with A. nilotica compost (5.5% followed by P. juliflora compost (5.8, while the  highest plant mortality (11.5% from charcoal rot occurred in the unamended control on the basis of the pooled average of two years. There was a significant inverse correlation between microbial activity and charcoal rot incidence in cowpea at 20 days after planting. Composts also had a beneficial effect on yield, with a 28.3% increase in seed yield in P. juliflora compost-amended plots. These results suggest that in resource-deficient farming , certain on-farm wastes can be effectively utilized for managing soil-borne pathogens, as well as  for �

Viable cold-tolerant iron-reducing microorganisms in geographically diverse subglacial environments

Science.gov (United States)

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.