Technical considerations for the implementation of subsurface microbial barriers for restoration of groundwater at UMTRA sites

International Nuclear Information System (INIS)

Tucker, M.D.

1996-01-01

The Uranium Mill Tailings Remediation Action (UMTRA) Program is responsible for the assessment and remedial action at the 24 former uranium mill tailings sites located in the United States. The surface remediation phase, which has primarily focused on containment and stabilization of the abandoned uranium mill tailings piles, is nearing completion. Attention has now turned to the groundwater restoration phase. One alternative under consideration for groundwater restoration at UMTRA sites is the use of in-situ permeable reactive subsurface barriers. In this type of a system, contaminated groundwater will be allowed to flow naturally through a barrier filled with material which will remove hazardous constituents from the water by physical, chemical or microbial processes while allowing passage of the pore water. The subject of this report is a reactive barrier which would remove uranium and other contaminants of concern from groundwater by microbial action (i.e., a microbial barrier). The purpose of this report is to assess the current state of this technology and to determine issues that must be addressed in order to use this technology at UMTRA sites. The report focuses on six contaminants of concern at UMTRA sites including uranium, arsenic, selenium, molybdenum, cadmium and chromium. In the first section of this report, the fundamental chemical and biological processes that must occur in a microbial barrier to control the migration of contaminants are described. The second section contains a literature review of research which has been conducted on the use of microorganisms to immobilize heavy metals. The third section addresses areas which need further development before a microbial barrier can be implemented at an UMTRA site

Effects of post-processing handling and packaging on microbial populations

International Nuclear Information System (INIS)

Zagory, D.

1999-01-01

The type of produce, process conditions, and prior temperature management will all affect the mix of microorganisms found on fresh produce. Normally, fresh produce will be covered by a complex mix of bacteria, fungi and yeasts that are characteristic of that fruit or vegetable. For example, carrots typically have large numbers of Lactobacillus and other lactic acid bacteria while apples may have relatively large numbers of yeasts. Which of these microorganisms will come to dominate the population will be a function of the make-up of the original population on the product in the field, distribution time, distribution temperature and the atmosphere within the package. Another chief determinant of microbial populations will be the physiological condition of the product. Factors that injure or weaken the plant tissues may be expected to encourage microbial growth while conditions that maintain the physiological integrity of the tissues may be expected to discourage microbial growth. Each of these factors can be expected to affect the make-up of the microbial population in characteristic ways but always constrained by the initial condition of original population makeup. This paper describes which microorganisms are favored by given conditions in order to develop a concept of microbial management designed to favor desirable microbes at the expense of undesirable ones. Particular emphasis will be placed on the effects of modified atmospheres on microorganisms, especially human pathogens

Septic tank additive impacts on microbial populations.

Science.gov (United States)

Pradhan, S; Hoover, M T; Clark, G H; Gumpertz, M; Wollum, A G; Cobb, C; Strock, J

2008-01-01

Environmental health specialists, other onsite wastewater professionals, scientists, and homeowners have questioned the effectiveness of septic tank additives. This paper describes an independent, third-party, field scale, research study of the effects of three liquid bacterial septic tank additives and a control (no additive) on septic tank microbial populations. Microbial populations were measured quarterly in a field study for 12 months in 48 full-size, functioning septic tanks. Bacterial populations in the 48 septic tanks were statistically analyzed with a mixed linear model. Additive effects were assessed for three septic tank maintenance levels (low, intermediate, and high). Dunnett's t-test for tank bacteria (alpha = .05) indicated that none of the treatments were significantly different, overall, from the control at the statistical level tested. In addition, the additives had no significant effects on septic tank bacterial populations at any of the septic tank maintenance levels. Additional controlled, field-based research iswarranted, however, to address additional additives and experimental conditions.

A cat's tale: the impact of genetic restoration on Florida panther population dynamics and persistence.

Science.gov (United States)

Hostetler, Jeffrey A; Onorato, David P; Jansen, Deborah; Oli, Madan K

2013-05-01

1. Genetic restoration has been suggested as a management tool for mitigating detrimental effects of inbreeding depression in small, inbred populations, but the demographic mechanisms underlying population-level responses to genetic restoration remain poorly understood. 2. We studied the dynamics and persistence of the endangered Florida panther Puma concolor coryi population and evaluated the potential influence of genetic restoration on population growth and persistence parameters. As part of the genetic restoration programme, eight female Texas pumas P. c. stanleyana were released into Florida panther habitat in southern Florida in 1995. 3. The overall asymptotic population growth rate (λ) was 1.04 (5th and 95th percentiles: 0.95-1.14), suggesting an increase in the panther population of approximately 4% per year. Considering the effects of environmental and demographic stochasticities and density-dependence, the probability that the population will fall below 10 panthers within 100 years was 0.072 (0-0.606). 4. Our results suggest that the population would have declined at 5% per year (λ = 0.95; 0.83-1.08) in the absence of genetic restoration. Retrospective life table response experiment analysis revealed that the positive effect of genetic restoration on survival of kittens was primarily responsible for the substantial growth of the panther population that would otherwise have been declining. 5. For comparative purposes, we also estimated probability of quasi-extinction under two scenarios - implementation of genetic restoration and no genetic restoration initiative - using the estimated abundance of panthers in 1995, the year genetic restoration was initiated. Assuming no density-dependence, the probability that the panther population would fall below 10 panthers by 2010 was 0.098 (0.002-0.332) for the restoration scenario and 0.445 (0.032-0.944) for the no restoration scenario, providing further evidence that the panther population would have faced a

Physiological heterogeneities in microbial populations and implications for physical stress tolerance

DEFF Research Database (Denmark)

Carlquist, Magnus; Fernandes, Rita Lencastre; Helmark, Søren

2012-01-01

Background: Traditionally average values of the whole population are considered when analysing microbial cell cultivations. However, a typical microbial population in a bioreactor is heterogeneous in most phenotypes measurable at a single-cell level. There are indications that such heterogeneity...

The effects of boron management on soil microbial population and ...

African Journals Online (AJOL)

Soil microorganisms directly influence boron content of soil as maximum boron release corresponds with the highest microbial activity. The objective of this study is to determine the effects of different levels of boron fertilizer on microbial population, microbial respiration and soil enzyme activities in different soil depths in ...

2007 Microbial Population Biology (July 22-26, 2007)

Energy Technology Data Exchange (ETDEWEB)

Anthony M. Dean

2008-04-01

Microbial Population Biology covers 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 meetings have covered topics ranging from the dynamics and genetics of adaptation to the evolution of mutation rate, community ecology, evolutionary genomics, altruism, and epidemiology. This meeting is never dull: some of the most significant and contentious issues in biology have been thrashed out here. We anticipate the 2007 meeting being no exception. The final form of the 2007 meeting is yet to be decided, but the following topics are likely to be included: evolutionary emergence of infectious disease and antibiotic resistance, genetic architecture and implications for the evolution of microbial populations, ageing in bacteria, biogeography, evolution of symbioses, the role of microbes in ecosystem function, and ecological genomics.

Shifts in microbial populations in Rusitec fermenters as affected by the type of diet and impact of the method for estimating microbial growth (15N v. microbial DNA).

Science.gov (United States)

Mateos, I; Ranilla, M J; Saro, C; Carro, M D

2017-11-01

Rusitec fermenters are in vitro systems widely used to study ruminal fermentation, but little is known about the microbial populations establishing in them. This study was designed to assess the time evolution of microbial populations in fermenters fed medium- (MC; 50% alfalfa hay : concentrate) and high-concentrate diets (HC; 15 : 85 barley straw : concentrate). Samples from solid (SOL) and liquid (LIQ) content of fermenters were taken immediately before feeding on days 3, 8 and 14 of incubation for quantitative polymerase chain reaction and automated ribosomal intergenic spacer analysis analyses. In SOL, total bacterial DNA concentration and relative abundance of Ruminococcus flavefaciens remained unchanged over the incubation period, but protozoal DNA concentration and abundance of Fibrobacter succinogenes, Ruminococcus albus and fungi decreased and abundance of methanogenic archaea increased. In LIQ, total bacterial DNA concentration increased with time, whereas concentration of protozoal DNA and abundance of methanogens and fungi decreased. Diet×time interactions were observed for bacterial and protozoal DNA and relative abundance of F. succinogenes and R. albus in SOL, as well as for protozoal DNA in LIQ. Bacterial diversity in SOL increased with time, but no changes were observed in LIQ. The incubated diet influenced all microbial populations, with the exception of total bacteria and fungi abundance in LIQ. Bacterial diversity was higher in MC-fed than in HC-fed fermenters in SOL, but no differences were detected in LIQ. Values of pH, daily production of volatile fatty acids and CH4 and isobutyrate proportions remained stable over the incubation period, but other fermentation parameters varied with time. The relationships among microbial populations and fermentation parameters were in well agreement with those previously reported in in vivo studies. Using 15N as a microbial marker or quantifying total microbial DNA for estimating microbial protein synthesis

Dynamics of buckbrush populations under simulated forest restoration alternatives

Science.gov (United States)

David W. Huffman; Margaret M. Moore

2008-01-01

Plant population models are valuable tools for assessing ecological tradeoffs between forest management approaches. In addition, these models can provide insight on plant life history patterns and processes important for persistence and recovery of populations in changing environments. In this study, we evaluated a set of ecological restoration alternatives for their...

Impact of Peat Mining and Restoration on Methane Turnover Potential and Methane-Cycling Microorganisms in a Northern Bog.

Science.gov (United States)

Reumer, Max; Harnisz, Monika; Lee, Hyo Jung; Reim, Andreas; Grunert, Oliver; Putkinen, Anuliina; Fritze, Hannu; Bodelier, Paul L E; Ho, Adrian

2018-02-01

Ombrotrophic peatlands are a recognized global carbon reservoir. Without restoration and peat regrowth, harvested peatlands are dramatically altered, impairing their carbon sink function, with consequences for methane turnover. Previous studies determined the impact of commercial mining on the physicochemical properties of peat and the effects on methane turnover. However, the response of the underlying microbial communities catalyzing methane production and oxidation have so far received little attention. We hypothesize that with the return of Sphagnum spp. postharvest, methane turnover potential and the corresponding microbial communities will converge in a natural and restored peatland. To address our hypothesis, we determined the potential methane production and oxidation rates in natural (as a reference), actively mined, abandoned, and restored peatlands over two consecutive years. In all sites, the methanogenic and methanotrophic population sizes were enumerated using quantitative PCR (qPCR) assays targeting the mcrA and pmoA genes, respectively. Shifts in the community composition were determined using Illumina MiSeq sequencing of the mcrA gene and a pmoA -based terminal restriction fragment length polymorphism (t-RFLP) analysis, complemented by cloning and sequence analysis of the mmoX gene. Peat mining adversely affected methane turnover potential, but the rates recovered in the restored site. The recovery in potential activity was reflected in the methanogenic and methanotrophic abundances. However, the microbial community composition was altered, being more pronounced for the methanotrophs. Overall, we observed a lag between the recovery of the methanogenic/methanotrophic activity and the return of the corresponding microbial communities, suggesting that a longer duration (>15 years) is needed to reverse mining-induced effects on the methane-cycling microbial communities. IMPORTANCE Ombrotrophic peatlands are a crucial carbon sink, but this environment

Effect of Gamma radiation on microbial population of natural casings

International Nuclear Information System (INIS)

Trigo, M.J.; Fraqueza, M.J.

1998-01-01

The high microbial load of fresh and dry natural casings increases the risk of meat product contamination with pathogenic microorganims, agents of foodborn diseases. The aim of this work is to evaluate the killing effect of gamma radiation on the resident microbial population of pork and beef casings, to improve their hygiene and safety. Portions of fresh pork (small intestine and colon) and dry beef casings were irradiated in a Cobalt 60 source with absorbed doses of 1, 2, 5 and 10 kGy. The D 10 values of total aerobic microorganisms in the pork casings were 1.65 kGy for colon and 1.54 kGy for small intestine. The D 10 value found in beef dry casings (small intestine) was 10.17 kGy. Radurization with 5 kGy was able to reduce, at least, 6 logs the coliform bacteria in pork casings. The killing effect over faecal Streptococci was 4 logs for pork fresh casings and 2 logs for beef dry casings. Gamma radiation with 5 kGy proved to be a convenient method to reduce substantially the microbial population of pork fresh casings. Otherwise, the microbial population of beef dry casings still resisted to 10 kGy

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

The role of bifidobacteria in newborn health and the intestinal microbial balance

OpenAIRE

Mazzola, Giuseppe

2015-01-01

Gut microbial acquisition during the early stage of life is an extremely important event since it affects the health status of the host. In this contest the healthy properties of the genus Bifidobacterium have a central function in newborns. The aim of this thesis was to explore the dynamics of the gut microbial colonization in newborns and to suggest possible strategies to maintain or restore a correct balance of gut bacterial population in inf...

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).

Gear and survey efficiency of patent tongs for oyster populations on restoration reefs.

Science.gov (United States)

Schulte, David M; Lipcius, Romuald N; Burke, Russell P

2018-01-01

Surveys of restored oyster reefs need to produce accurate population estimates to assess the efficacy of restoration. Due to the complex structure of subtidal oyster reefs, one effective and efficient means to sample is by patent tongs, rather than SCUBA, dredges, or bottom cores. Restored reefs vary in relief and oyster density, either of which could affect survey efficiency. This study is the first to evaluate gear (the first full grab) and survey (which includes selecting a specific half portion of the first grab for further processing) efficiencies of hand-operated patent tongs as a function of reef height and oyster density on subtidal restoration reefs. In the Great Wicomico River, a tributary of lower Chesapeake Bay, restored reefs of high- and low-relief (25-45 cm, and 8-12 cm, respectively) were constructed throughout the river as the first large-scale oyster sanctuary reef restoration effort (sanctuary acreage > 20 ha at one site) in Chesapeake Bay. We designed a metal frame to guide a non-hydraulic mechanical patent tong repeatedly into the same plot on a restored reef until all oysters within the grab area were captured. Full capture was verified by an underwater remotely-operated vehicle. Samples (n = 19) were taken on nine different reefs, including five low- (n = 8) and four high-relief reefs (n = 11), over a two-year period. The gear efficiency of the patent tong was estimated to be 76% (± 5% standard error), whereas survey efficiency increased to 81% (± 10%) due to processing. Neither efficiency differed significantly between young-of-the-year oysters (spat) and adults, high- and low-relief reefs, or years. As this type of patent tong is a common and cost-effective tool to evaluate oyster restoration projects as well as population density on fished habitat, knowing the gear and survey efficiencies allows for accurate and precise population estimates.

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

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.

Dynamics of buckbrush populations under simulated forest restoration alternatives (P-53)

Science.gov (United States)

David W. Huffman; Margaret M. Moore

2008-01-01

Plant population models are valuable tools for assessing ecological tradeoffs between forest management approaches. In addition, these models can provide insight on plant life history patterns and processes important for persistence and recovery of populations in changing environments. In this study, we evaluated a set of ecological restoration alternatives for their...

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

Effect of inclusion of different levels of silage on rumen microbial population and microbial protein synthesis in dairy steers fed on rice straw

Directory of Open Access Journals (Sweden)

Thien Truong Giang Nguyen

2017-02-01

Full Text Available Objective Leucaena leucocephala (Leucaena is a perennial tropical legume that can be directly grazed or harvested and offered to ruminants as hay, silage, or fresh. However, Leucaena contain phenolic compounds, which are considered anti-nutritional factors as these may reduce intake, digestibility and thus animal performance. Therefore, the objective of this experiment was to determine effects of Leucaena silage (LS feeding levels on rumen microbial populations, N-balance and microbial protein synthesis in dairy steers. Methods Four, rumen fistulated dairy steers with initial weight of 167±12 kg were randomly assigned to receive dietary treatments according to a 4×4 Latin square design. Treatments were as followings: T1 = untreated rice straw (RS; Control, T2 = 70% RS+30% LS, T3 = 40% RS+60% LS, and T4 = 100% LS. Dairy steers were fed rice straw and LS ad libitum and supplemented with concentrate at 0.2% of body weight/d. Results Results revealed that the rumen microbial population, especially cellulolytic, proteolytic bacteria and fungal zoospores were enhanced in steers that received 60% of LS (p0.05. Protozoal population was linearly decreased with increasing level of LS (p<0.05. Moreover, N-balance and microbial protein synthesis were enhanced by LS feeding (p<0.05 and were the highest in 60% LS group. Conclusion Based on this study, it could be concluded that replacement of RS with 60% LS significantly improved microbial population and microbial protein synthesis in diary steers.

Gear and survey efficiency of patent tongs for oyster populations on restoration reefs.

Directory of Open Access Journals (Sweden)

David M Schulte

Full Text Available Surveys of restored oyster reefs need to produce accurate population estimates to assess the efficacy of restoration. Due to the complex structure of subtidal oyster reefs, one effective and efficient means to sample is by patent tongs, rather than SCUBA, dredges, or bottom cores. Restored reefs vary in relief and oyster density, either of which could affect survey efficiency. This study is the first to evaluate gear (the first full grab and survey (which includes selecting a specific half portion of the first grab for further processing efficiencies of hand-operated patent tongs as a function of reef height and oyster density on subtidal restoration reefs. In the Great Wicomico River, a tributary of lower Chesapeake Bay, restored reefs of high- and low-relief (25-45 cm, and 8-12 cm, respectively were constructed throughout the river as the first large-scale oyster sanctuary reef restoration effort (sanctuary acreage > 20 ha at one site in Chesapeake Bay. We designed a metal frame to guide a non-hydraulic mechanical patent tong repeatedly into the same plot on a restored reef until all oysters within the grab area were captured. Full capture was verified by an underwater remotely-operated vehicle. Samples (n = 19 were taken on nine different reefs, including five low- (n = 8 and four high-relief reefs (n = 11, over a two-year period. The gear efficiency of the patent tong was estimated to be 76% (± 5% standard error, whereas survey efficiency increased to 81% (± 10% due to processing. Neither efficiency differed significantly between young-of-the-year oysters (spat and adults, high- and low-relief reefs, or years. As this type of patent tong is a common and cost-effective tool to evaluate oyster restoration projects as well as population density on fished habitat, knowing the gear and survey efficiencies allows for accurate and precise population estimates.

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 ...

A theoretical analysis of population genetics of plants on restored habitats

Energy Technology Data Exchange (ETDEWEB)

Bogoliubov, A.G. [Botanical Institute, Russian Academy of Science, St. Petersburg (Russian Federation); Loehle, C. [Argonne National Lab., IL (United States)

1995-02-01

Seed and propagules used for habitat restoration are not likely to be closely adapted to local site conditions. Rapid changes of genotypes frequencies on local microsites and/or microevolution would allow plants to become better adapted to a site. These same factors would help to maintain genetic diversity and ensure the survival of small endangered populations. We used population genetics models to examine the selection of genotypes during establishment on restored sites. Vegetative spread was shown to affect selection and significantly reduce genetic diversity. To study general microevolution, we linked a model of resource usage with a genetics model and analyzed competition between genotypes. A complex suite of feasible ecogenetic states was shown to result. The state actually resulting would depend strongly on initial conditions. This analysis indicated that genetic structure can vary locally and can produce overall genetic variability that is not simply the result of microsite adaptations. For restoration activities, the implication is that small differences in seed source could lead to large differences in local genetic structure after selection.

A theoretical analysis of population genetics of plants on restored habitats

Energy Technology Data Exchange (ETDEWEB)

Bogoliubov, A.G. [Russian Academy of Science, St. Petersburg (Russian Federation). Botanical Inst.; Loehle, C. [Argonne National Lab., IL (United States). Environmental Research Div.

1997-07-01

Seed and propagules used for habitat restoration are not likely to be closely adapted to local site conditions. Rapid changes of genotypes frequencies on local microsites and/or microevolution would allow plants to become better adapted to a site. These same factors would help to maintain genetic diversity and ensure the survival of small endangered populations. The authors used population genetics models to examine the selection of genotypes during establishment on restored sites. Vegetative spread was shown to affect selection and significantly reduce genetic diversity. To study general microevolution, the authors linked a model of resource usage with a genetics model and analyzed competition between genotypes. A complex suite of feasible ecogenetic states was shown to result. The state actually resulting would depend strongly on initial conditions. This analysis indicated that genetic structure can vary locally and can produce overall genetic variability that is not simply the result of microsite adaptations. For restoration activities, the implication is that small differences in seed source could lead to large differences in local genetic structure after selection.

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.

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...

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.

Restoration of oyster reefs in an estuarine lake: population dynamics and shell accretion

Science.gov (United States)

Casas, Sandra M.; La Peyre, Jerome F.; La Peyre, Megan K.

2015-01-01

Restoration activities inherently depend on understanding the spatial and temporal variation in basic demographic rates of the species of interest. For species that modify and maintain their own habitat such as the eastern oyster Crassostrea virginica, understanding demographic rates and their impacts on population and habitat success are crucial to ensuring restoration success. We measured oyster recruitment, density, size distribution, biomass, mortality and Perkinsus marinus infection intensity quarterly for 3 yr on shallow intertidal reefs created with shell cultch in March 2009. All reefs were located within Sister Lake, LA. Reefs were placed in pairs at 3 different locations within the lake; pairs were placed in low and medium energy sites within each location. Restored reefs placed within close proximity (biomass (>14.6 kg m-2) at the end of 3 yr. Shell accretion, on average, exceeded estimated rates required to keep pace with local subsidence and shell loss. Variation in recruitment, growth and survival drives local site-specific population success, which highlights the need to understand local water quality, hydrodynamics, and metapopulation dynamics when planning restoration.

Microbial control of pollution

Energy Technology Data Exchange (ETDEWEB)

Fry, J C; Gadd, G M; Herbert, R A; Jones, C W; Watson-Craik, I A [eds.

1992-01-01

12 papers are presented on the microbial control of pollution. Topics covered include: bioremediation of oil spills; microbial control of heavy metal pollution; pollution control using microorganisms and magnetic separation; degradation of cyanide and nitriles; nitrogen removal from water and waste; and land reclamation and restoration.

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...

Microbial Character Related Sulfur Cycle under Dynamic Environmental Factors Based on the Microbial Population Analysis in Sewerage System.

Science.gov (United States)

Dong, Qian; Shi, Hanchang; Liu, Yanchen

2017-01-01

The undesired sulfur cycle derived by microbial population can ultimately causes the serious problems of sewerage systems. However, the microbial community characters under dynamic environment factors in actual sewerage system is still not enough. This current study aimed to character the distributions and compositions of microbial communities that participate in the sulfur cycle under the dynamic environmental conditions in a local sewerage system. To accomplish this, microbial community compositions were assessed using 454 high-throughput sequencing (16S rDNA) combined with dsrB gene-based denaturing gradient gel electrophoresis. The results indicated that a higher diversity of microbial species was present at locations in sewers with high concentrations of H 2 S. Actinobacteria and Proteobacteria were dominant in the sewerage system, while Actinobacteria alone were dominant in regions with high concentrations of H 2 S. Specifically, the unique operational taxonomic units could aid to characterize the distinct microbial communities within a sewerage manhole. The proportion of sulfate-reducing bacteria, each sulfur-oxidizing bacteria (SOB) were strongly correlated with the liquid parameters (DO, ORP, COD, Sulfide, NH 3 -N), while the Mycobacterium and Acidophilic SOB (M&A) was strongly correlated with gaseous factors within the sewer, such as H 2 S, CH 4 , and CO. Identifying the distributions and proportions of critical microbial communities within sewerage systems could provide insights into how the microbial sulfur cycle is affected by the dynamic environmental conditions that exist in sewers and might be useful for explaining the potential sewerage problems.

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

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

Directory of Open Access Journals (Sweden)

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 ...

Soil amendments improve microbial ecology parameters of "topsoil inoculum" used in post-mining restoration

Science.gov (United States)

Kumaresan, Deepak; Munoz-Rojas, Miriam; Moreira-Grez, Benjamin; Kariman, Khalil; Whiteley, Andrew

2017-04-01

Mine operations generate substantial volumes of waste substrates, which are crushed and/or chemically treated waste rock from which ores are extracted. Establishment of rehabilitated landforms using post-mining substrates (i.e. waste rocks, tailings) that typically exhibit extreme conditions (such as high pH, nutrient deficiency, excessive salinity and metal toxicity) can be a major environmental problem and a critical issue during mine closure operations. More importantly, mine sites are located predominantly in arid or semi-arid lands where our understanding of basic ecosystem processes and microbial interactions with native plants (e.g. Eucalyptus spp., Acacia spp., Grevillea spp. in Western Australia) are limited. Despite the wide acknowledgement on the impact of microbial functional diversity on overall soil and plant health, no detailed attention has been paid to understand the role of belowground microbial functional diversity in the context of mine rehabilitation strategies. In this research, we investigated the role of nitrogen-based and microbial consortia amendments on improving the microbial ecology parameters of "topsoil inoculum" and subsequently its cascading effect on seedling establishment and plant morphology of Acacia ancistrocarpa, a legume native to the Pilbara and other regions of Western Australia and commonly used in arid zone restoration. The study was conducted under controlled environmental conditions in potted plants using topsoil retrieved from previously stockpiled material as growth media. A morphological assessment was undertaken to measure shoot length, shoot weight, root length, root area and root weight. Soil chemical properties, e.g. carbon, nitrogen and trace metals concentrations were determined Microbial activity was measured with the 1-day CO2 test, which determines soil microbial respiration rate based on the measurement of the CO2 burst produced after moistening dry soil (Muñoz-Rojas et al., 2016). Bacterial and archaeal

Effects of Alachlor and Metolachlor on Microbial Populations in the Soil

Directory of Open Access Journals (Sweden)

Ismail, B. S.

2005-01-01

Full Text Available A study of the impact of two acetanilide herbicides, viz. alachlor and metolachlor on bacterial and fungal populations and biomass in the Sungai Buluh soil series samples was carried out under laboratory conditions. The effects of the two herbicides were monitored for 70 days under ambient conditions. Metolachlor caused greater reduction in bacterial counts than on fungal populations. There was approximately 75% reduction in bacterial counts 14 days after treatment (DAT with 2 µg/g metolachlor. Alachlor however was less toxic to bacterial and fungal populations. Alachlor caused a reduction in bacterial counts at 7 and 14 DAT with 2µg/g or above. Fungal population decreased significantly in the presence of 20 µg/g alachlor at 7 DAT but no further effects were observed as the incubation period was prolonged. The study showed that the microbial biomass immediately decreased significantly in the presence of 2 µg/g or more of metolachlor at 0 and 28 DAT. Alachlor, on the other hands, at the lowest experimental dose of 2 µg/g reduced the microbial biomass almost immediately upon incubation, but had no further effects when the incubation period was prolonged.

The biological model of postradiation restoration of plants on the organismic and population levels of organization

International Nuclear Information System (INIS)

Ivanishvili, N.I.; Gogebashvili, M.E.

2012-01-01

Full text : When studying postradiating restoration of plants, the question of working out of biological models for testing of biosystems' reliability has become rather urgent. It is known that each organization level of a live organism is characterized by certain mechanisms of postradiating restoration at the formation of various radiobiological reactions. For example, the basic processes at cellular, tissue and organism levels are reparation and regeneration whereas at cenosis level the leading processes are often the forms of population restoration. Besides, in spite of the fact that the population restoration at cenosis level is continuously inked with restoration at the lower organization levels, at this level the specific forms of restoration characterized for only this level are seen. It is natural that studying of the mechanisms of response to the influence of damaging factors needs new methodological approaches on various forms of population restoration with the use of adequate test systems. For this purpose the species of duckweed was used. It was seen that this test-system is characterized by the two levels of response to radiation influence. The first one - at a rather low level of radiation influence (up to 50Gy) when decrease in intensity of leaf growth as well as in colony formation was observed and the second one - at a high level of radiation influence (up to 200Gy) when a crushing of colonies took place and an increase in quantity of undeveloped plant leaves was seen. Thus, thanks to the step character of response of culture duckweed it becomes possible to definite quantity indicators for the investigated populations, not only at the influence of concrete physical and chemical factors but also at multifactorial influences that is often difficult to be calculated. It can be concluded that at the first level of damage an increase of plant resistance to unfavorable factors takes place that is due to the inhibition of growth processes

Molecular Characterization of Swine Manure Lagoon Microbial and Antibiotic Resistant Populations

Science.gov (United States)

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...

Soil bacterial diversity in degraded and restored lands of Northeast Brazil.

Science.gov (United States)

Araújo, Ademir Sérgio Ferreira; Borges, Clovis Daniel; Tsai, Siu Mui; Cesarz, Simone; Eisenhauer, Nico

2014-11-01

Land degradation deteriorates biological productivity and affects environmental, social, and economic sustainability, particularly so in the semi-arid region of Northeast Brazil. Although some studies exist reporting gross measures of soil microbial parameters and processes, limited information is available on how land degradation and restoration strategies influence the diversity and composition of soil microbial communities. In this study we compare the structure and diversity of bacterial communities in degraded and restored lands in Northeast Brazil and determine the soil biological and chemical properties influencing bacterial communities. We found that land degradation decreased the diversity of soil bacteria as indicated by both reduced operational taxonomic unit (OTU) richness and Shannon index. Soils under native vegetation and restoration had significantly higher bacterial richness and diversity than degraded soils. Redundancy analysis revealed that low soil bacterial diversity correlated with a high respiratory quotient, indicating stressed microbial communities. By contrast, soil bacterial communities in restored land positively correlated with high soil P levels. Importantly, however, we found significant differences in the soil bacterial community composition under native vegetation and in restored land, which may indicate differences in their functioning despite equal levels of bacterial diversity.

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

Directory of Open Access Journals (Sweden)

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.

Environmental restoration issues relevant to lands that support native populations

International Nuclear Information System (INIS)

Simon, S.L.

1999-01-01

Islands and other remote locations that support indigenous (native) populations require special considerations in the setting of criteria for maximum allowable radioactivity contamination of the environment. The criteria can differ from those applicable to Western continental urban settings because of particular attributes related to lifestyle or environment. Conventionally, guidelines for land cleanup are derived by using a pathway model and descriptions of conventional intake patterns to calculate backwards from an acceptable dose or risk. However, pathways of possible exposure differ in characteristics and relative importance for indigenous populations, and conventional exposure-assessment models need considerable revision for them. More primitive lifestyles usually imply a need for stricter standards. In contrast, somewhat higher risk might not produce any excess cancer incidence if the population is small enough, as is often the case for islanders or other indigenous populations. This paper discusses various factors peculiar to indigenous populations that require consideration when criteria for restoration of contaminated environments are being determined. (author)

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

Science.gov (United States)

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

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.

Science.gov (United States)

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.

Recolonization after habitat restoration leads to decreased genetic variation in populations of a terrestrial orchid.

Science.gov (United States)

Vandepitte, K; Gristina, A S; De Hert, K; Meekers, T; Roldán-Ruiz, I; Honnay, O

2012-09-01

Colonization is crucial to habitat restoration projects that rely on the spontaneous regeneration of the original vegetation. However, as a previously declining plant species spreads again, the likelihood of founder effects increases through recurrent population founding and associated serial bottlenecks. We related Amplified Fragment Length Polymorphism markers genetic variation and fitness to colonization history for all extant populations of the outcrossing terrestrial orchid Dactylorhiza incarnata in an isolated coastal dune complex. Around 1970, D. incarnata suffered a severe bottleneck yet ultimately persisted and gradually spread throughout the spatially segregated dune slacks, aided by the restoration of an open vegetation. Genetic assignment demonstrated dispersal to vacant sites from few nearby extant populations and very limited inflow from outside the spatially isolated reserve. Results further indicated that recurrent founding from few local sources resulted in the loss of genetic diversity and promoted genetic divergence (F(ST) = 0.35) among populations, but did not influence population fitness. The few source populations initially available and the limited inflow of genes from outside the study reserve, as a consequence of habitat degradation and spatial isolation, may have magnified the genetic effects of recurrent population founding. © 2012 Blackwell Publishing Ltd.

Genetic diversity of Dyera polyphylla (Miq.) Steenis populations used in tropical peatland restoration in Indonesia

NARCIS (Netherlands)

Tata, Hesti Lestari; Muchugi, A.; Kariba, R.; Noordwijk, van M.

2018-01-01

Dyera polyphylla is a native tree species of peat swamp forests in Southeast Asia. Where it has been used in peatland restoration, the trees are of uncertain genetic origin. We analysed the genetic diversity of seven populations of D. polyphylla (9–20 individual trees per population) from both

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.

Microbial diversity and carbon cycling in San Francisco Bay wetlands

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.

2014-03-21

Wetland restoration efforts in San Francisco Bay aim to rebuild habitat for endangered species and provide an effective carbon storage solution, reversing land subsidence caused by a century of industrial and agricultural development. However, the benefits of carbon sequestration may be negated by increased methane production in newly constructed wetlands, making these wetlands net greenhouse gas (GHG) sources to the atmosphere. We investigated the effects of wetland restoration on below-ground microbial communities responsible for GHG cycling in a suite of historic and restored wetlands in SF Bay. Using DNA and RNA sequencing, coupled with real-time GHG monitoring, we profiled the diversity and metabolic potential of wetland soil microbial communities. The wetland soils harbor diverse communities of bacteria and archaea whose membership varies with sampling location, proximity to plant roots and sampling depth. Our results also highlight the dramatic differences in GHG production between historic and restored wetlands and allow us to link microbial community composition and GHG cycling with key environmental variables including salinity, soil carbon and plant species.

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

Directory of Open Access Journals (Sweden)

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.

High methane emissions from restored Norway spruce swamps in southern Finland over one growing season

Directory of Open Access Journals (Sweden)

M. Koskinen

2016-02-01

Full Text Available Forestry-drained peatlands in the boreal region are currently undergoing restoration in order to bring these ecosystems closer to their natural (undrained state. Drainage affects the methane (CH4 dynamics of a peatland, often changing sites from CH4 sources to sinks. Successful restoration of a peatland would include restoration of not only the surface vegetation and hydrology, but also the microbial populations and thus CH4 dynamics. As a pilot study, CH4 emissions were measured on two pristine, two drained and three restored boreal spruce swamps in southern Finland for one growing season. Restoration was successful in the sense that the water table level in the restored sites was significantly higher than in the drained sites, but it was also slightly higher than in the pristine sites. The restored sites were surprisingly large sources of CH4 (mean emissions of 52.84 mg CH4 m-2 d-1, contrasting with both the pristine (1.51 mg CH4 m-2 d-1 and the drained sites (2.09 mg CH4 m-2 d-1. More research is needed to assess whether the high CH4 emissions observed in this study are representative of restored spruce mires in general.

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.

Contaminant immobilization via microbial activity

International Nuclear Information System (INIS)

1991-11-01

The aim of this study was to search the literature to identify biological techniques that could be applied to the restoration of contaminated groundwaters near uranium milling sites. Through bioremediation it was hypothesized that the hazardous heavy metals could be immobilized in a stable, low-solubility form, thereby halting their progress in the migrating groundwater. Three basic mechanisms were examined: reduction of heavy metals by microbially produced hydrogen sulfide; direct microbial mediated reduction; and biosorption

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.

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

Legacy effects overwhelm the short-term effects of exotic plant invasion and restoration on soil microbial community structure, enzyme activities, and nitrogen cycling.

Science.gov (United States)

Elgersma, Kenneth J; Ehrenfeld, Joan G; Yu, Shen; Vor, Torsten

2011-11-01

Plant invasions can have substantial consequences for the soil ecosystem, altering microbial community structure and nutrient cycling. However, relatively little is known about what drives these changes, making it difficult to predict the effects of future invasions. In addition, because most studies compare soils from uninvaded areas to long-established dense invasions, little is known about the temporal dependence of invasion impacts. We experimentally manipulated forest understory vegetation in replicated sites dominated either by exotic Japanese barberry (Berberis thunbergii), native Viburnums, or native Vacciniums, so that each vegetation type was present in each site-type. We compared the short-term effect of vegetation changes to the lingering legacy effects of the previous vegetation type by measuring soil microbial community structure (phospholipid fatty acids) and function (extracellular enzymes and nitrogen mineralization). We also replaced the aboveground litter in half of each plot with an inert substitute to determine if changes in the soil microbial community were driven by aboveground or belowground plant inputs. We found that after 2 years, the microbial community structure and function was largely determined by the legacy effect of the previous vegetation type, and was not affected by the current vegetation. Aboveground litter removal had only weak effects, suggesting that changes in the soil microbial community and nutrient cycling were driven largely by belowground processes. These results suggest that changes in the soil following either invasion or restoration do not occur quickly, but rather exhibit long-lasting legacy effects from previous belowground plant inputs.

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.

Public support for river restoration funding in relation to local river ecomorphology, population density, and mean income

Science.gov (United States)

SchläPfer, Felix; Witzig, Pieter-Jan

2006-12-01

In 1997, about 140,000 citizens in 388 voting districts in the Swiss canton of Bern passed a ballot initiative to allocate about 3 million Swiss Francs annually to a canton-wide river restoration program. Using the municipal voting returns and a detailed georeferenced data set on the ecomorphological status of the rivers, we estimate models of voter support in relation to local river ecomorphology, population density, mean income, cultural background, and recent flood damage. Support of the initiative increased with increasing population density and tended to increase with increasing mean income, in spite of progressive taxation. Furthermore, we found evidence that public support increased with decreasing "naturalness" of local rivers. The model estimates may be cautiously used to predict the public acceptance of similar restoration programs in comparable regions. Moreover, the voting-based insights into the distribution of river restoration benefits provide a useful starting point for debates about appropriate financing schemes.

Occurrence, composition and ecological restoration of organic pollutants in water environment of South Canal, China

Science.gov (United States)

Wang, Y. Z.; Lin, C.; Zhou, X. S.; Zhang, Y.; Han, C. G.

2017-08-01

Ecological restoration of polluted river water was carried out in South Canal by adding microbial water purifying agents and biological compound enzymes. The objective of present study was to investigate the ecological restoration effect of organic pollutants by this efficient immobilized microbial technologies, analysis the occurrence and composition of organic pollutants including fifteen persistent organochlorine pesticides (OCPs), seventeen polycyclic aromatic hydrocarbons (PAHs) and eighteen organophosphorus pesticides (OPPs) both in natural water environment and ecological restoration area of South Canal, China. Results showed that the total concentrations of OCPs ranged from 1.11 to 1.78 ng·L-1, PAHs from 52.76 to 60.28 ng·L-1, and OPPs from 6.51 to 17.50 ng·L-1. Microbial water purifying agents and biological compound enzymes essentially had no effects on biological degradation of OCPs and PAHs in the river, but could remove OPPs with degradation rates ranging from 19.6% to 62.8% (35.2% in average). Degradation mechanisms of microbial water purifying agents and biological compound enzymes on OCPs, PAHs and OPPs remained to be further studied. This technology has a certain value in practical ecological restoration of organic pollutants in rivers and lakes.

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

Synbiotic approach restores intestinal homeostasis and prolongs survival in leukaemic mice with cachexia.

Science.gov (United States)

Bindels, Laure B; Neyrinck, Audrey M; Claus, Sandrine P; Le Roy, Caroline I; Grangette, Corinne; Pot, Bruno; Martinez, Inés; Walter, Jens; Cani, Patrice D; Delzenne, Nathalie M

2016-06-01

Cancer cachexia is a multifactorial syndrome that includes muscle wasting and inflammation. As gut microbes influence host immunity and metabolism, we investigated the role of the gut microbiota in the therapeutic management of cancer and associated cachexia. A community-wide analysis of the caecal microbiome in two mouse models of cancer cachexia (acute leukaemia or subcutaneous transplantation of colon cancer cells) identified common microbial signatures, including decreased Lactobacillus spp. and increased Enterobacteriaceae and Parabacteroides goldsteinii/ASF 519. Building on this information, we administered a synbiotic containing inulin-type fructans and live Lactobacillus reuteri 100-23 to leukaemic mice. This treatment restored the Lactobacillus population and reduced the Enterobacteriaceae levels. It also reduced hepatic cancer cell proliferation, muscle wasting and morbidity, and prolonged survival. Administration of the synbiotic was associated with restoration of the expression of antimicrobial proteins controlling intestinal barrier function and gut immunity markers, but did not impact the portal metabolomics imprinting of energy demand. In summary, this study provided evidence that the development of cancer outside the gut can impact intestinal homeostasis and the gut microbial ecosystem and that a synbiotic intervention, by targeting some alterations of the gut microbiota, confers benefits to the host, prolonging survival and reducing cancer proliferation and cachexia.

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 ...

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

Filling the interspace—restoring arid land mosses: source populations, organic matter, and overwintering govern success

Science.gov (United States)

Condon, Lea; Pyke, David A.

2016-01-01

Biological soil crusts contribute to ecosystem functions and occupy space that could be available to invasive annual grasses. Given disturbances in the semiarid shrub steppe communities, we embarked on a set of studies to investigate restoration potential of mosses in sagebrush steppe ecosystems. We examined establishment and growth of two moss species common to the Great Basin, USA: Bryum argenteum and Syntrichia ruralis from two environmental settings (warm dry vs. cool moist). Moss fragments were inoculated into a third warm dry setting, on bare soil in spring and fall, both with and without a jute net and with and without spring irrigation. Moss cover was monitored in spring seasons of three consecutive years. Both moss species increased in cover over the winter. When Bryum received spring irrigation that was out of sync with natural precipitation patterns, moss cover increased and then crashed, taking two seasons to recover. Syntrichia did not respond to the irrigation treatment. The addition of jute net increased moss cover under all conditions, except Syntrichia following fall inoculation, which required a second winter to increase in cover. The warm dry population of Bryum combined with jute achieved on average 60% cover compared to the cool moist population that achieved only 28% cover by the end of the study. Differences were less pronounced for Syntrichia where moss from the warm dry population with jute achieved on average 51% cover compared to the cool moist population that achieved 43% cover by the end of the study. Restoration of arid land mosses may quickly protect soils from erosion while occupying sites before invasive plants. We show that higher moss cover will be achieved quickly with the addition of organic matter and when moss fragments originate from sites with a climate that is similar to that of the restoration site.

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

Flood management: prediction of microbial contamination in large-scale floods in urban environments.

Science.gov (United States)

Taylor, Jonathon; Lai, Ka Man; Davies, Mike; Clifton, David; Ridley, Ian; Biddulph, Phillip

2011-07-01

With a changing climate and increased urbanisation, the occurrence and the impact of flooding is expected to increase significantly. Floods can bring pathogens into homes and cause lingering damp and microbial growth in buildings, with the level of growth and persistence dependent on the volume and chemical and biological content of the flood water, the properties of the contaminating microbes, and the surrounding environmental conditions, including the restoration time and methods, the heat and moisture transport properties of the envelope design, and the ability of the construction material to sustain the microbial growth. The public health risk will depend on the interaction of these complex processes and the vulnerability and susceptibility of occupants in the affected areas. After the 2007 floods in the UK, the Pitt review noted that there is lack of relevant scientific evidence and consistency with regard to the management and treatment of flooded homes, which not only put the local population at risk but also caused unnecessary delays in the restoration effort. Understanding the drying behaviour of flooded buildings in the UK building stock under different scenarios, and the ability of microbial contaminants to grow, persist, and produce toxins within these buildings can help inform recovery efforts. To contribute to future flood management, this paper proposes the use of building simulations and biological models to predict the risk of microbial contamination in typical UK buildings. We review the state of the art with regard to biological contamination following flooding, relevant building simulation, simulation-linked microbial modelling, and current practical considerations in flood remediation. Using the city of London as an example, a methodology is proposed that uses GIS as a platform to integrate drying models and microbial risk models with the local building stock and flood models. The integrated tool will help local governments, health authorities

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.

Evaluation of chemical immersion treatments to reduce microbial populations in fresh beef.

Science.gov (United States)

Kassem, Ahmed; Meade, Joseph; Gibbons, James; McGill, Kevina; Walsh, Ciara; Lyng, James; Whyte, Paul

2017-11-16

The aim of the current study was to assess the ability of a number of chemicals (acetic Acid (AA), citric acid (CA) lactic acid (LA), sodium decanoate (SD) and trisodium phosphate (TSP)) to reduce microbial populations (total viable count, Campylobacter jejuni, Escherichia coli, Salmonella typhimurium and Listeria monocytogenes) on raw beef using an immersion system. The following concentrations of each chemical were used: 3 & 5% for AA, CA, LA, SD and 10 &12% for TSP. Possible synergistic effects of using combinations of two chemicals sequentially (LA+CA and LA+AA) were also investigated. L*, a* and b* values were measured before and after treatments and ΔE* values were calculated in order to determine any changes in the color of meat due to the use of these chemicals. In general, all chemical treatments resulted in significantly (p0.05). The application of combinations of chemical immersion treatments (LA3%+AA3% and LA3%+CA3%) did not result in further significant reductions in microbial populations when compared to single chemical treatments (P3 immediately after treatment and after 24h storage. The remaining treatments did not result in significant changes to the color of raw beef. Copyright © 2017 Elsevier B.V. All rights reserved.

Genetic restoration of a stocked brown trout Salmo trutta population using microsatellite DNA analysis of historical and contemporary samples

DEFF Research Database (Denmark)

Hansen, Michael Møller; Bekkevold, Dorte; Jensen, L.F.

2006-01-01

1. Gene flow from domesticated to wild populations is a major threat to wild salmonid fish. However, few studies have addressed how populations could be restored after admixture has occurred. We analysed the prospects for restoring the previously intensively stocked brown trout population...... of the Skjern River, Denmark, by identifying remaining non-admixed individuals to be used for supportive breeding. 2. We analysed microsatellite DNA markers in historical (1940-50s) and contemporary (1992-2004) samples from the Skjern River system, from the strain of domesticated trout previously used...... for stocking, and from the neighbouring Stora River. We analysed admixture proportions to estimate the genetic contribution by domesticated trout. We identified non-admixed trout using assignment tests, and further analysed the possible sources of indigenous trout by estimating contemporary migration among...

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

Technologies for lake restoration

Directory of Open Access Journals (Sweden)

Helmut KLAPPER

2003-09-01

Full Text Available Lakes are suffering from different stress factors and need to be restored using different approaches. The eutrophication remains as the main water quality management problem for inland waters: both lakes and reservoirs. The way to curb the degradation is to stop the nutrient sources and to accelerate the restoration with help of in-lake technologies. Especially lakes with a long retention time need (eco- technological help to decrease the nutrient content in the free water. The microbial and other organic matter from sewage and other autochthonous biomasses, causes oxygen depletion, which has many adverse effects. In less developed countries big reservoirs function as sewage treatment plants. Natural aeration solves problems only partly and many pollutants tend to accumulate in the sediments. The acidification by acid rain and by pyrite oxidation has to be controlled by acid neutralizing technologies. Addition of alkaline chemicals is useful only for soft waters, and technologies for (microbial alkalinization of very acidic hardwater mining lakes are in development. The corrective measures differ from those in use for eutrophication control. The salinization and water shortage mostly occurs if more water is used than available. L. Aral, L. Tschad, the Dead Sea or L. Nasser belong to waters with most severe environmental problems on a global scale. Their hydrologic regime needs to be evaluated. The inflow of salt water at the bottom of some mining lakes adds to stability of stratification, and thus accumulation of hydrogen sulphide in the monimolimnion of the meromictic lakes. Destratification, which is the most used technology, is only restricted applicable because of the dangerous concentrations of the byproducts of biological degradation. The contamination of lakes with hazardous substances from industry and agriculture require different restoration technologies, including subhydric isolation and storage, addition of nutrients for better self

Bacterial Community Structure in a Mollisol Under Long-Term Natural Restoration, Cropping, and Bare Fallow History Estimated by PCR-DGGE

Institute of Scientific and Technical Information of China (English)

WANG Guang-Hua; JIN Jian; LIU Jun-Jie; CHEN Xue-Li; LIU Ju-Dong; LIU Xiao-Bing

2009-01-01

Soil microbial biomass and community structures are commonly used as indicators for soil quality and fertility.A investigation was performed to study the effects of long-term natural restoration,cropping,and bare fallow managements on the soil microbial biomass and bacterial community structures in depths of 0-10,20-30,and 40-50 cm in a black soil (Mollisol).Microbial biomass was estimated from chloroform fumigation-extraction,and bacterial community structures were determined by analysis of 16S rDNA using polymerase chain reaction-denaturing gradient gel electrophoresis (PCRDGGE).Experimental results showed that microbial biomass significantly declined with soil depth in the managements of restoration and cropping,but not in the bare fallow.DGGE profiles indicated that the band number in top 0-10 cm soils was less than that in depth of 20-30 or 40-50 cm.These suggested that the microbial population was high but the bacterial community structure was simple in the topsoil.Cluster and principle component analysis based on DGGE banding patterns showed that the bacterial community structure was affected by soil depth more primarily than by managements,and the succession of bacterial community as increase of soil depth has a similar tendency in the three managements.Fourteen predominating DGGE bands were excised and sequenced,in which 6 bands were identified as the taxa of Verrucomicrobia,2 bands as Actinobacteria,2 bands as α-Proteobacteria,and the other 4 bands as δ-Proteobacteria,Acidobacteria,Nitrospira,and unclassified bacteria.In addition,the sequences of 11 DGGE bands were closely related to uncultured bacteria.Thus,the bacterial community structure in black soil was stable,and the predominating bacterial groups were uncultured.

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.

Effects of organic amendments and mulches on soil microbial communities in quarry restoration under semiarid climate

Science.gov (United States)

Luna Ramos, Lourdes; Pastorelli, Roberta; Miralles Mellado, Isabel; Fabiani, Arturo; Bastida López, Felipe; Hernández Fernández, María Teresa; García Izquierdo, Carlos; Solé Benet, Albert

2015-04-01

Mining activities generate loss of the quality of the environment and landscape specially in arid and semiarid Mediterranean regions. A precondition for ecosystem reclamation in such highly disturbed mining areas is the development of functional soils with appropriate levels of organic matter. In an experimental soil restoration in limestone quarries from Sierra de Gádor (Almería), SE Spain, 9 plots 15 x 5 m were prepared to test organic amendments (compost from solid urban residues-DOW-, sludge from urban water treatment-SS-, control-NA-) and different mulches (fine gravel-GM-, wood chips-WM-, control-NM-) with the aim to improve soil/substrate properties and to reduce evaporation and erosion. In each experimental plot, 75 native plants (Macrochloa tenacissima, Anthyllis terniflora and Anthyllis cytisoides) were planted. After 5 years from the start of the experiment, we evaluated how microbial community composition responded to the organic amendments and mulches. Microbial community composition of both bacteria and fungi was determined by phospholipid fatty acid (PLFA) and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) fingerprinting. The results of the two-way ANOVA showed that PLFAs were significantly affected by organic amendments but not by the mulches or interaction of both factors. Experimental plots with DOW showed significantly higher level of fungal PLFAs than those with SS and NA, even higher than the reference undisturbed soil. However, any plot with organic amendments did not reach the content of bacterial PLFAs of the reference soils. The bacterial diversity (evaluated by diversity indices calculated from DGGE profiles) was greater in soil samples taken under NA and GM. Comparing these indices in fungal DGGE, we found greater values for soil samples taken under DOW and without mulches. Results from UPGMA analysis showed significant differences in the structure of soil bacterial communities from the different treatments

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

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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.

Spatial and stage-structured population model of the American crocodile for comparison of comprehensive Everglades Restoration Plan (CERP) alternatives

Science.gov (United States)

Green, Timothy W.; Slone, Daniel H.; Swain, Eric D.; Cherkiss, Michael S.; Lohmann, Melinda; Mazzotti, Frank J.; Rice, Kenneth G.

2010-01-01

As part of the U.S. Geological Survey Priority Ecosystems Science (PES) initiative to provide the ecological science required during Everglades restoration, we have integrated current regional hydrologic models with American crocodile (Crocodylus acutus) research and monitoring data to create a model that assesses the potential impact of Comprehensive Everglades Restoration Plan (CERP) efforts on the American crocodile. A list of indicators was created by the Restoration Coordination and Verification (RECOVER) component of CERP to help determine the success of interim restoration goals. The American crocodile was established as an indicator of the ecological condition of mangrove estuaries due to its reliance upon estuarine environments characterized by low salinity and adequate freshwater inflow. To gain a better understanding of the potential impact of CERP restoration efforts on the American crocodile, a spatially explicit crocodile population model has been created that has the ability to simulate the response of crocodiles to various management strategies for the South Florida ecosystem. The crocodile model uses output from the Tides and Inflows in the Mangroves of the Everglades (TIME) model, an application of the Flow and Transport in a Linked Overland/Aquifer Density Dependent System (FTLOADDS) simulator. TIME has the capability to link to the South Florida Water Management Model (SFWMM), which is the primary regional tool used to assess CERP restoration scenarios. A crocodile habitat suitability index and spatial parameter maps that reflect salinity, water depth, habitat, and nesting locations are used as driving functions to construct crocodile finite rate of increase maps under different management scenarios. Local stage-structured models are integrated with a spatial landscape grid to display crocodile movement behavior in response to changing environmental conditions. Restoration efforts are expected to affect salinity levels throughout the habitat of

Habitat Restoration as a Key Conservation Lever for Woodland Caribou: A review of restoration programs and key learnings from Alberta

Directory of Open Access Journals (Sweden)

Paula Bentham

2015-12-01

Full Text Available The Recovery Strategy for the Woodland Caribou (Rangifer tarandus caribou, Boreal Population in Canada (EC, 2012, identifies coordinated actions to reclaim woodland caribou habitat as a key step to meeting current and future caribou population objectives. Actions include restoring industrial landscape features such as roads, seismic lines, pipelines, cut-lines, and cleared areas in an effort to reduce landscape fragmentation and the changes in caribou population dynamics associated with changing predator-prey dynamics in highly fragmented landscapes. Reliance on habitat restoration as a recovery action within the federal recovery strategy is high, considering all Alberta populations have less than 65% undisturbed habitat, which is identified in the recovery strategy as a threshold providing a 60% chance that a local population will be self-sustaining. Alberta’s Provincial Woodland Caribou Policy also identifies habitat restoration as a critical component of long-term caribou habitat management. We review and discuss the history of caribou habitat restoration programs in Alberta and present outcomes and highlights of a caribou habitat restoration workshop attended by over 80 representatives from oil and gas, forestry, provincial and federal regulators, academia and consulting who have worked on restoration programs. Restoration initiatives in Alberta began in 2001 and have generally focused on construction methods, revegetation treatments, access control programs, and limiting plant species favourable to alternate prey. Specific treatments include tree planting initiatives, coarse woody debris management along linear features, and efforts for multi-company and multi-stakeholder coordinated habitat restoration on caribou range. Lessons learned from these programs have been incorporated into large scale habitat restoration projects near Grande Prairie, Cold Lake, and Fort McMurray. A key outcome of our review is the opportunity to provide a

The contribution of microbial biotechnology to mitigating coral reef degradation.

Science.gov (United States)

Damjanovic, Katarina; Blackall, Linda L; Webster, Nicole S; van Oppen, Madeleine J H

2017-09-01

The decline of coral reefs due to anthropogenic disturbances is having devastating impacts on biodiversity and ecosystem services. Here we highlight the potential and challenges of microbial manipulation strategies to enhance coral tolerance to stress and contribute to coral reef restoration and protection. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

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.

The use of soil quality indicators to assess soil functionality in restored semi-arid ecosystems

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Muñoz-Rojas, Miriam; Erickson, Todd E.; Dixon, Kingsley W.; Merritt, David J.

2016-04-01

Keywords: Pilbara, 1-day CO2 test, microbial activity, mine restoration, soil health, ecosystem services. Introduction Semi-arid and arid environments are highly vulnerable to land degradation and their restoration has commonly showed low rates of success (James et al., 2013). A systematic knowledge of soil functionality is critical to successful restoration of degraded ecosystems since approximately 80% of ecosystem services can be connected to soil functions. The assessment of soil functionality generally involves the evaluation of soil properties and processes as they relate to the ability of soil to function effectively as a component of a healthy ecosystem (Costantini et al., 2015) Using soil quality indicators may be a valuable approach to assess functionality of topsoil and novel substrates used in restoration (Muñoz-Rojas et al., 2014; 2015). A key soil chemical indicator is soil organic C, that has been widely used as an attribute of soil quality because of the many functions that it provides and supports (Willaarts et al., 2015). However, microbial indicators can be more sensitive to disturbances and could be a valuable addition in soil assessment studies in restoration programs. Here, we propose a set of soil quality indicators to assess the soil status in restored soils (topsoil and waste material) of semi-arid environments. The study was conducted during March 2015 in the Pilbara biogeographical region (northwestern Australia) at an iron ore mine site rehabilitated in 2011. Methods Soil samples were collected from two sub-areas with different soil materials used as growth media: topsoil retrieved from nearby stockpiles and a lateritic waste material utilised for its erosive stability and physical competence. An undisturbed natural shrub-grassland ecosystem dominated by Triodia spp. and Acacia spp. representative of the restored area was selected as the analogue reference site. Soil physicochemical analysis were undertaken according to standard methods

A resilience approach can improve anadromous fish restoration

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Waldman, John R.; Wilson, Karen A.; Mather, Martha E.; Snyder, Noah P.

2016-01-01

Most anadromous fish populations remain at low levels or are in decline despite substantial investments in restoration. We explore whether a resilience perspective (i.e., a different paradigm for understanding populations, communities, and ecosystems) is a viable alternative framework for anadromous fish restoration. Many life history traits have allowed anadromous fish to thrive in unimpacted ecosystems but have become contemporary curses as anthropogenic effects increase. This contradiction creates a significant conservation challenge but also makes these fish excellent candidates for a resilience approach. A resilience approach recognizes the need to maintain life history, population, and habitat characteristics that increase the ability of a population to withstand and recover from multiple disturbances. To evaluate whether a resilience approach represents a viable strategy for anadromous fish restoration, we review four issues: (1) how resilience theory can inform anadromous fish restoration, (2) how a resilience-based approach is fundamentally different than extant anadromous fish restoration strategies, (3) ecological characteristics that historically benefited anadromous fish persistence, and (4) examples of how human impacts harm anadromous fish and how a resilience approach might produce more successful outcomes. We close by suggesting new research and restoration directions for implementation of a resilience-based approach.

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

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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.

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

Science.gov (United States)

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.

Microbial degradation of trichloroethylene in the rhizosphere: Potential application to biological remediation of waste sites

International Nuclear Information System (INIS)

Walton, B.T.; Anderson, T.A.

1990-01-01

The possibility that vegetation may be used to actively promote microbial restoration of chemically contaminated soils was tested by using rhizosphere and nonvegetated soils collected from a trichloroethylene (TCE)-contaminated field site. Biomass determinations, disappearance of TCE from the headspace of spiked soil slurries, and mineralization of [14C]TCE to 14CO2 all showed that microbial activity is greater in rhizosphere soils and that TCE degradation occurs faster in the rhizosphere than in the edaphosphere. Thus, vegetation may be an important variable in the biological restoration of surface and near-surface soils

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.

Durability and regeneration of activated carbon air-cathodes in long-term operated microbial fuel cells

Science.gov (United States)

Zhang, Enren; Wang, Feng; Yu, Qingling; Scott, Keith; Wang, Xu; Diao, Guowang

2017-08-01

The performance of activated carbon catalyst in air-cathodes in microbial fuel cells was investigated over one year. A maximum power of 1722 mW m-2 was produced within the initial one-month microbial fuel cell operation. The air-cathodes produced a maximum power >1200 mW m-2 within six months, but gradually became a limiting factor for the power output in prolonged microbial fuel cell operation. The maximum power decreased by 55% when microbial fuel cells were operated over one year due to deterioration in activated carbon air-cathodes. While salt/biofilm removal from cathodes experiencing one-year operation increased a limiting performance enhancement in cathodes, a washing-drying-pressing procedure could restore the cathode performance to its original levels, although the performance restoration was temporary. Durable cathodes could be regenerated by re-pressing activated carbon catalyst, recovered from one year deteriorated air-cathodes, with new gas diffusion layer, resulting in ∼1800 mW m-2 of maximum power production. The present study indicated that activated carbon was an effective catalyst in microbial fuel cell cathodes, and could be recovered for reuse in long-term operated microbial fuel cells by simple methods.

Identifying Societal Preferences for River Restoration in a Densely Populated Urban Environment: Evidence from a Discrete Choice Experiment in Central Brussels

Science.gov (United States)

Chen, Wendy Y.; Liekens, Inge; Broekx, Steven

2017-08-01

One of the major challenges facing river restoration in densely populated urban areas has been the disparity between the expectations of policy-makers and societal preferences. This study aimed to elicit public preferences and elucidate underlying sources of preference heterogeneity, using the Zenne River in central Brussels, Belgium, as a case study. A discrete choice experiment was administered to a representative sample of the Brussels population. Five attributes were specified, including water quality, ecological status, hydromorphological features of channels, recreational opportunities, and monetary cost. Our econometric analysis based on mixed logit models revealed that overall public would like to have a more natural river (open and naturalized channel, good water quality, and with rich species diversity), while achieving good water quality was the most preferred attribute. Respondents categorized as male, non-Belgian citizen, or not being a member of an environmental organization constituted an inclination to prefer the status quo. Belgian citizens showed a pronounced preference for good biodiversity, and being a member of an environmental organization could moderate the strong preference for good water quality. This study provided insights into the relative attractiveness of key attributes pertaining to river restoration, in general, and served as a useful input to the ongoing discussion concerning the future plan for the Zenne River in Brussels, specifically. Possible implications also exist for other urban river restorations in the rest of Europe, where the Water Framework Directive has become a major impetus for the expansion of freshwater ecosystem restoration from rural and peri-urban areas to densely populated urban areas. Particularly, the cultural heterogeneity of societal preferences should be tested and accounted for to compare the welfare impacts of river restoration and to facilitate benefit transfer, within and between river basins, in the

Identifying Societal Preferences for River Restoration in a Densely Populated Urban Environment: Evidence from a Discrete Choice Experiment in Central Brussels.

Science.gov (United States)

Chen, Wendy Y; Liekens, Inge; Broekx, Steven

2017-08-01

One of the major challenges facing river restoration in densely populated urban areas has been the disparity between the expectations of policy-makers and societal preferences. This study aimed to elicit public preferences and elucidate underlying sources of preference heterogeneity, using the Zenne River in central Brussels, Belgium, as a case study. A discrete choice experiment was administered to a representative sample of the Brussels population. Five attributes were specified, including water quality, ecological status, hydromorphological features of channels, recreational opportunities, and monetary cost. Our econometric analysis based on mixed logit models revealed that overall public would like to have a more natural river (open and naturalized channel, good water quality, and with rich species diversity), while achieving good water quality was the most preferred attribute. Respondents categorized as male, non-Belgian citizen, or not being a member of an environmental organization constituted an inclination to prefer the status quo. Belgian citizens showed a pronounced preference for good biodiversity, and being a member of an environmental organization could moderate the strong preference for good water quality. This study provided insights into the relative attractiveness of key attributes pertaining to river restoration, in general, and served as a useful input to the ongoing discussion concerning the future plan for the Zenne River in Brussels, specifically. Possible implications also exist for other urban river restorations in the rest of Europe, where the Water Framework Directive has become a major impetus for the expansion of freshwater ecosystem restoration from rural and peri-urban areas to densely populated urban areas. Particularly, the cultural heterogeneity of societal preferences should be tested and accounted for to compare the welfare impacts of river restoration and to facilitate benefit transfer, within and between river basins, in the

Overcoming restoration paradigms: value of the historical record and metapopulation dynamics in native oyster restoration

Directory of Open Access Journals (Sweden)

Romuald N. Lipcius

2015-09-01

Full Text Available Restoration strategies for native oyster populations rely on multiple sources of information, which often conflict due to time- and space-varying patterns in abundance and distribution. For instance, strategies based on population connectivity and disease resistance can differ, and extant and historical records of abundance and distribution are often at odds, such that the optimal strategy is unclear and valuable restoration sites may be excluded from consideration. This was the case for the Lynnhaven River subestuary of lower Chesapeake Bay, which was deemed unsuitable for Eastern Oyster restoration based on physical conditions, disease challenge, and extant oyster abundance. Consequently, we (i evaluated previously unknown historical data from the 1800s, (ii quantified extant oyster recruitment and abundance, physical conditions, and disease presence on constructed restoration reefs and alternative substrates, and (iii assessed simulations from biophysical models to identify potential restoration sites in the metapopulation. The collective data distinguished numerous restoration sites (i in the polyhaline zone (salinity 18.4-22.2 where disease resistance is evolving, (ii where oysters were abundant in the late 1800s-early 1900s, (iii of recent high recruitment, abundance and survival, despite consistent and elevated disease challenge, and (iv interconnected as a metapopulation via larval dispersal. Moreover, a network of constructed restoration reefs met size structure, abundance and biomass standards of restoration success. These findings demonstrate that assumptions about the suitability of sites for oyster restoration based on individual processes can be severely flawed, and that in-depth examination of multiple processes and sources of information are required for oyster reef restoration plans to maximize success. We use these findings and previous information to recommend a strategy for successful restoration of subtidal oyster reefs

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

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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.

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.

Selection of culturable environmental microbial strains for cellular ...

African Journals Online (AJOL)

Environmental pollution by organic compounds is a global problem. Biological treatment methods are used to restore polluted environments. Microbial immobilization on abiotic surfaces is a recent strategy to improve the efficiency of these processes. In this technique, cell adhesion is a fundamental step for subsequent ...

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

A Multiple Watershed Approach to Assessing the Effects of Habitat Restoration Actions on Anadromous and Resident Fish Populations, Technical Report 2003-2004.

Energy Technology Data Exchange (ETDEWEB)

Marmorek, David

2004-03-01

Habitat protection and restoration is a cornerstone of current strategies to restore ecosystems, recover endangered fish species, and rebuild fish stocks within the Columbia River Basin. Strategies featuring habitat restoration include the 2000 Biological Opinion on operation of the Federal Columbia River Power System (FCRPS BiOp) developed by the National Marine Fisheries Service (NMFS), the 2000 Biological Opinion on Bull Trout developed by the US Fish and Wildlife Service (USFWS), and Sub-Basin Plans developed under the Fish and Wildlife Program of the Northwest Power and Conservation Council (NWPCC). There is however little quantitative information about the effectiveness of different habitat restoration techniques. Such information is crucial for helping scientists and program managers allocate limited funds towards the greatest benefits for fish populations. Therefore, it is critical to systematically test the hypotheses underlying habitat restoration actions for both anadromous and resident fish populations. This pilot project was developed through a proposal to the Innovative Projects fund of the NWPCC (ESSA 2002). It was funded by the Bonneville Power Administration (BPA) following reviews by the Independent Scientific Review Panel (ISRP 2002), the Columbia Basin Fish and Wildlife Authority (CBFWA 2002), the NWPCC and BPA. The study was designed to respond directly to the above described needs for information on the effectiveness of habitat restoration actions, including legal measures specified in the 2000 FCRPS BiOp (RPA 183, pg. 9-133, NMFS 2000). Due to the urgency of addressing these measures, the timeline of the project was accelerated from a duration of 18 months to 14 months. The purpose of this pilot project was to explore methods for evaluating past habitat restoration actions and their effects on fish populations. By doing so, the project will provide a foundation of retrospective analyses, on which to build prospective, multi-watershed designs

Mercury behaviour and C, N, and P biogeochemical cycles during ecological restoration processes of old mining sites in French Guiana.

Science.gov (United States)

Couic, Ewan; Grimaldi, Michel; Alphonse, Vanessa; Balland-Bolou-Bi, Clarisse; Livet, Alexandre; Giusti-Miller, Stéphanie; Sarrazin, Max; Bousserrhine, Noureddine

2018-04-25

Several decades of gold mining extraction activities in the Amazonian rainforest have caused deforestation and pollution. While ecological rehabilitation is essential for restoring biodiversity and decreasing erosion on deforested lands, few studies note the behaviour or toxicity of trace elements during the rehabilitation process. Our original study focused on the potential use of microbial activity and Hg speciation and compared them with As, Cu, Zn and Cr speciation in assessing the chemical and biological quality of ecological restoration efforts. We sampled two sites in French Guyana 17 years after rehabilitation efforts began. The former site was actively regenerated (R) with the leguminous species Clitoria racemosa and Acacia mangium, and the second site was passively regenerated with spontaneous vegetation (Sv). We also sampled soil from a control site without a history of gold mining (F). We performed microcosm soil experiments for 30 days, where trace element speciation and enzyme activities (i.e., FDA, dehydrogenase, β-glucosidase, urease, alkaline and acid phosphatase) were estimated to characterise the behaviour of trace elements and the soil microbial activity. As bioindicators, the use of soil microbial carbon biomass and soil enzyme activities related to the carbon and phosphorus cycles seems to be relevant for assessing soil quality in rehabilitated and regenerated old mining sites. Our results showed that restoration with leguminous species had a positive effect on soil chemical quality and on soil microbial bioindicators, with activities that tended toward natural non-degraded soil (F). Active restoration processes also had a positive effect on Hg speciation by reducing its mobility. While in Sv we found more exchangeable and soluble mercury, in regenerated sites, Hg was mostly bound to organic matter. These results also suggested that enzyme activities and mercury cycles are sensitive to land restoration and must be considered when evaluating

Increased resiliency and activity of microbial mediated carbon cycling enzymes in diversified bioenergy cropping systems

Science.gov (United States)

Upton, R.; Bach, E.; Hofmockel, K. S.

2017-12-01

Microbes are mediators of soil carbon (C) and are influenced in membership and activity by nitrogen (N) fertilization and inter-annual abiotic factors. Microbial communities and their extracellular enzyme activities (EEA) are important parameters that influence ecosystem C cycling properties and are often included in microbial explicit C cycling models. In an effort to generate model relevant, empirical findings, we investigated how both microbial community structure and C degrading enzyme activity are influenced by inter-annual variability and N inputs in bioenergy crops. Our study was performed at the Comparison of Biofuel Systems field-site from 2011 to 2014, in three bioenergy cropping systems, continuous corn (CC) and two restored prairies, both fertilized (FP) and unfertilized (P). We hypothesized microbial community structure would diverge during the prairie restoration, leading to changes in C cycling enzymes over time. Using a sequencing approach (16S and ITS) we determined the bacterial and fungal community structure response to the cropping system, fertilization, and inter-annual variability. Additionally, we used EEA of β-glucosidase, cellobiohydrolase, and β-xylosidase to determine inter-annual and ecosystem impacts on microbial activity. Our results show cropping system was a main effect for microbial community structure, with corn diverging from both prairies to be less diverse. Inter-annual changes showed that a drought occurring in 2012 significantly impacted microbial community structure in both the P and CC, decreasing microbial richness. However, FP increased in microbial richness, suggesting the application of N increased resiliency to drought. Similarly, the only year in which C cycling enzymes were impacted by ecosystem was 2012, with FP supporting higher potential enzymatic activity then CC and P. The highest EEA across all ecosystems occurred in 2014, suggesting the continued root biomass and litter build-up in this no till system

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.

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...

Mucosal immunity in HIV infection: what can be done to restore gastrointestinal-associated lymphoid tissue function?

Science.gov (United States)

George, Michael D; Asmuth, David M

2014-06-01

This review describes the impact of HIV infection on gut-associated lymphoid tissue, the mechanisms for persistent gut-associated lymphoid tissue dysfunction despite effective antiretroviral therapy, and potential strategies to restore gut-associated lymphoid tissue function and promote immune reconstitution. Recent studies indicate that unresolved microbial translocation and intestinal dysbiosis may continue to promote enteropathy as well as HIV-associated and non-HIV-associated conditions in many HIV patients who otherwise maintain therapeutic control of systemic viral replication. Several novel therapeutic approaches to reduce intestinal inflammation and mitigate microbial translocation may hold promise for restoring gastrointestinal health and thereby increasing the efficacy of immune reconstitution in HIV-infected patients undergoing antiretroviral therapy.

Sediment denitrification and nitrification is enhanced by the presence of macrophytes in a restored agricultural stream, Black Earth Creek, WI USA

Science.gov (United States)

Restoration of habitats that support microbial processing can enhance nitrate removal in agricultural streams. Macrophytes are common both in-stream and in the wetted fringe of agricultural stream systems, but are often removed in restoration to increase stream velocity or stabil...

The importance of hydrology in restoration of bottomland hardwood wetland functions

Science.gov (United States)

Hunter, R.G.; Faulkner, S.P.; Gibson, K.A.

2008-01-01

Bottomland hardwood (BLH) forests have important biogeochemical functions and it is well known that certain structural components, including pulsed hydrology, hydric soils, and hydrophytic vegetation, enhance these functions. It is unclear, however, how functions of restored BLH wetlands compare to mature, undisturbed wetlands. We measured a suite of structural and functional attributes in replicated natural BLH wetlands (NAT), restored BLH wetlands with hydrology re-established (RWH), and restored BLH wetlands without hydrology re-established (RWOH) in this study. Trees were replanted in all restored wetlands at least four years prior to the study and those wetlands with hydrology re-established had flashboard risers placed in drainage ditches to allow seasonal surface flooding. Vegetation, soils, and selected biogeochemical functions were characterized at each site. There was a marked difference in woody vegetation among the wetlands that was due primarily to site age. There was also a difference in herbaceous vegetation among the restored sites that may have been related to differences in age or hydrology. Water table fluctuations of the RWH wetlands were comparable to those of the NAT wetlands. Thus, placing flashboard risers in existing drainage ditches, along with proper management, can produce a hydroperiod that is similar to that of a relatively undisturbed BLH. Average length of saturation within the upper 15 cm of soils was 37, 104, and 97 days for RWOH, RWH, and NAT, respectively. Soil moisture, denitrification potential, and soluble organic carbon concentrations differed among wetland sites, but soil carbon and nitrogen concentrations, heterotrophic microbial activity, and readily mineralizable carbon concentrations did not. Significant linear relationships were also found between soil moisture and heterotrophic microbial activity, readily mineralizable carbon, and soluble organic carbon. In addition, sedimentation rates were higher in NAT and RWH

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

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.

A restoration genetics guide for coral reef conservation.

Science.gov (United States)

Baums, Iliana B

2008-06-01

Worldwide degradation of coral reef communities has prompted a surge in restoration efforts. They proceed largely without considering genetic factors because traditionally, coral populations have been regarded as open over large areas with little potential for local adaptation. Since, biophysical and molecular studies indicated that most populations are closed over shorter time and smaller spatial scales. Thus, it is justified to re-examine the potential for site adaptation in corals. There is ample evidence for differentiated populations, inbreeding, asexual reproduction and the occurrence of ecotypes, factors that may facilitate local adaptation. Discovery of widespread local adaptation would influence coral restoration projects mainly with regard to the physical and evolutionary distance from the source wild and/or captive bred propagules may be moved without causing a loss of fitness in the restored population. Proposed causes for loss of fitness as a result of (plant) restoration efforts include founder effects, genetic swamping, inbreeding and/or outbreeding depression. Direct evidence for any of these processes is scarce in reef corals due to a lack of model species that allow for testing over multiple generations and the separation of the relative contributions of algal symbionts and their coral hosts to the overall performance of the coral colony. This gap in our knowledge may be closed by employing novel population genetic and genomics approaches. The use of molecular tools may aid managers in the selection of appropriate propagule sources, guide spatial arrangement of transplants, and help in assessing the success of coral restoration projects by tracking the performance of transplants, thereby generating important data for future coral reef conservation and restoration projects.

Microbial Biomass and Activity in Geomorphic Features in Forested and Urban Restored and Degraded Streams

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Geomorphic spatial heterogeneity affects sediment denitrification, an anaerobic microbial process that results in the loss of nitrogen (N), and other anaerobic microbial processes such as methanogenesis in urban streams. We measured sediment denitrification potential (DEA), metha...

Microbial Populations of Stony Meteorites: Substrate Controls on First Colonizers

Directory of Open Access Journals (Sweden)

Alastair W. Tait

2017-06-01

reach homeostasis with the Nullarbor community, even after ca. 35,000 years. Our findings show that meteorites provide a unique, sterile substrate with which to test ideas relating to first-colonizers. Although meteorites are colonized by microorganisms, the microbial population is unlikely to match the community of the surrounding soil on which they fall.

Differential Effects of Legume Species on the Recovery of Soil Microbial Communities, and Carbon and Nitrogen Contents, in Abandoned Fields of the Loess Plateau, China

Science.gov (United States)

Li, Jin Hua; Jiao, Shu Mei; Gao, Rong Qing; Bardgett, Richard D.

2012-12-01

Plant-soil interactions are known to influence a wide range of ecosystem-level functions. Moreover, the recovery of these functions is of importance for the successful restoration of soils that have been degraded through intensive and/or inappropriate land use. Here, we assessed the effect of planting treatments commonly used to accelerate rates of grassland restoration, namely introduction of different legume species Medicago sativa, Astragalus adsurgens, Melilotus suaveolens, on the recovery of soil microbial communities and carbon and nitrogen contents in abandoned fields of the Loess Plateau, China. The results showed effects were species-specific, and either positive, neutral or negative depending on the measure and time-scale. All legumes increased basal respiration and metabolic quotient and had a positive effect on activity and functional diversity of the soil microbial community, measured using Biolog EcoPlate. However, soil under Astragalus adsurgens had the highest activity and functional diversity relative to the other treatments. Soil carbon and nitrogen content and microbial biomass were effectively restored in 3-5 years by introducing Medicago sativa and Astragalus adsurgens into early abandoned fields. Soil carbon and nitrogen content were retarded in 3-5 years and microbial biomass was retarded in the fifth year by introducing Melilotus suaveolens. Overall, the restoration practices of planting legumes can significantly affect soil carbon and nitrogen contents, and the biomass, activity, and functional diversity of soil microbial community. Therefore, we propose certain legume species could be used to accelerate ecological restoration of degraded soils, hence assist in the protection and preservation of the environment.

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...

Skjern River Restoration Counterfactual

DEFF Research Database (Denmark)

Clemmensen, Thomas Juel

2014-01-01

In 2003 the Skjern River Restoration Project in Denmark was awarded the prestigious Europa Nostra Prize for ‘conserving the European cultural heritage’ (Danish Nature Agency 2005). In this case, however, it seems that the conservation of one cultural heritage came at the expense of another cultural...... this massive reconstruction work, which involved moving more than 2,7 million cubic meters of earth, cause a lot of ‘dissonance’ among the local population, the resulting ‘nature’ and its dynamic processes are also constantly compromising the preferred image of the restored landscape (Clemmensen 2014......). The presentation offers insight into an on-going research and development project - Skjern River Restoration Counterfactual, which question existing trends and logics within nature restoration. The project explores how the Skjern River Delta could have been ‘restored’ with a greater sensibility for its cultural...

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.

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

The Abundance and Activity of Nitrate-Reducing Microbial Populations in Estuarine Sediments

Science.gov (United States)

Cardarelli, E.; Francis, C. A.

2014-12-01

Estuaries are productive ecosystems that ameliorate nutrient and metal contaminants from surficial water supplies. At the intersection of terrestrial and aquatic environments, estuarine sediments host major microbially-mediated geochemical transformations. These include denitrification (the conversion of nitrate to nitrous oxide and/or dinitrogen) and dissimilatory nitrate reduction to ammonium (DNRA). Denitrification has historically been seen as the predominant nitrate attenuation process and functions as an effective sink for nitrate. DNRA has previously been believed to be a minor nitrate reduction process and transforms nitrate within the ecosystem to ammonium, a more biologically available N species. Recent studies have compared the two processes in coastal environments and determined fluctuating environmental conditions may suppress denitrification, supporting an increased role for DNRA in the N cycle. Nitrate availability and salinity are factors thought to influence the membership of the microbial communities present, and the nitrate reduction process that predominates. The aim of this study is to investigate how nitrate concentration and salinity alter the transcript abundances of N cycling functional gene markers for denitrification (nirK, nirS) and DNRA (nrfA) in estuarine sediments at the mouth of the hypernutrified Old Salinas River, CA. Short-term whole core incubations amended with artificial freshwater/artificial seawater (2 psu, 35 psu) and with varying NO3- concentrations (200mM, 2000mM) were conducted to assess the activity as well as the abundance of the nitrate-reducing microbial populations present. Gene expression of nirK, nirS, and nrfA at the conclusion of the incubations was quantified using reverse transcription quantitative polymerase chain reaction (RT-qPCR). High abundances of nirK, nirS, and nrfA under particular conditions coupled with the resulting geochemical data ultimately provides insight onto how the aforementioned factors

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...

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.

Controls on bacterial and archaeal community structure and greenhouse gas production in natural, mined, and restored Canadian peatlands

Directory of Open Access Journals (Sweden)

Nathan eBasiliko

2013-07-01

Full Text Available Northern peatlands are important global C reservoirs, largely because of their slow rates of microbial C mineralization. Particularly in sites that are heavily influenced by anthropogenic disturbances, there is scant information about microbial ecology and whether or not microbial community structure influences greenhouse gas production. This work characterized communities of bacteria and archaea using terminal restriction fragment length polymorphism and sequence analysis of 16S rRNA and functional genes across eight natural, mined, or restored peatlands in two locations in eastern Canada. Correlations were explored among chemical properties of peat, bacterial and archaeal community structure, and carbon dioxide and methane production rates under oxic and anoxic conditions. Bacteria and archaea similar to those found in other peat soil environments were detected. In contrast to other reports, methanogen diversity was low in our study, with only 2 groups of known or suspected methanogens. Although mining and restoration affected substrate availability and microbial activity, these land-uses did not consistently affect bacterial or archaeal community composition. In fact, larger differences were observed between the two locations and between oxic and anoxic peat samples than between mined and restored sites, with anoxic samples characterized by less detectable bacterial diversity and stronger dominance by members of the phylum Acidobacteria. There were also no apparent strong linkages between prokaryote community structure and methane or carbon dioxide production, suggesting that different organisms exhibit functional redundancy and/or that the same taxa function at very different rates when exposed to different peat substrates. In contrast to other earlier work focusing on fungal communities across similar mined and restored peatlands, bacterial and archaeal communities appeared to be more resistant or resilient to peat substrate changes brought

Restoration of a Mediterranean forest after a fire: bioremediation and rhizoremediation field-scale trial.

Science.gov (United States)

Pizarro-Tobías, Paloma; Fernández, Matilde; Niqui, José Luis; Solano, Jennifer; Duque, Estrella; Ramos, Juan-Luis; Roca, Amalia

2015-01-01

Forest fires pose a serious threat to countries in the Mediterranean basin, often razing large areas of land each year. After fires, soils are more likely to erode and resilience is inhibited in part by the toxic aromatic hydrocarbons produced during the combustion of cellulose and lignins. In this study, we explored the use of bioremediation and rhizoremediation techniques for soil restoration in a field-scale trial in a protected Mediterranean ecosystem after a controlled fire. Our bioremediation strategy combined the use of Pseudomonas putida strains, indigenous culturable microbes and annual grasses. After 8 months of monitoring soil quality parameters, including the removal of monoaromatic and polycyclic aromatic hydrocarbons as well as vegetation cover, we found that the site had returned to pre-fire status. Microbial population analysis revealed that fires induced changes in the indigenous microbiota and that rhizoremediation favours the recovery of soil microbiota in time. The results obtained in this study indicate that the rhizoremediation strategy could be presented as a viable and cost-effective alternative for the treatment of ecosystems affected by fires. © 2014 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

Restoration ecology: two-sex dynamics and cost minimization.

Directory of Open Access Journals (Sweden)

Ferenc Molnár

Full Text Available We model a spatially detailed, two-sex population dynamics, to study the cost of ecological restoration. We assume that cost is proportional to the number of individuals introduced into a large habitat. We treat dispersal as homogeneous diffusion in a one-dimensional reaction-diffusion system. The local population dynamics depends on sex ratio at birth, and allows mortality rates to differ between sexes. Furthermore, local density dependence induces a strong Allee effect, implying that the initial population must be sufficiently large to avert rapid extinction. We address three different initial spatial distributions for the introduced individuals; for each we minimize the associated cost, constrained by the requirement that the species must be restored throughout the habitat. First, we consider spatially inhomogeneous, unstable stationary solutions of the model's equations as plausible candidates for small restoration cost. Second, we use numerical simulations to find the smallest rectangular cluster, enclosing a spatially homogeneous population density, that minimizes the cost of assured restoration. Finally, by employing simulated annealing, we minimize restoration cost among all possible initial spatial distributions of females and males. For biased sex ratios, or for a significant between-sex difference in mortality, we find that sex-specific spatial distributions minimize the cost. But as long as the sex ratio maximizes the local equilibrium density for given mortality rates, a common homogeneous distribution for both sexes that spans a critical distance yields a similarly low cost.

Restoration ecology: two-sex dynamics and cost minimization.

Science.gov (United States)

Molnár, Ferenc; Caragine, Christina; Caraco, Thomas; Korniss, Gyorgy

2013-01-01

We model a spatially detailed, two-sex population dynamics, to study the cost of ecological restoration. We assume that cost is proportional to the number of individuals introduced into a large habitat. We treat dispersal as homogeneous diffusion in a one-dimensional reaction-diffusion system. The local population dynamics depends on sex ratio at birth, and allows mortality rates to differ between sexes. Furthermore, local density dependence induces a strong Allee effect, implying that the initial population must be sufficiently large to avert rapid extinction. We address three different initial spatial distributions for the introduced individuals; for each we minimize the associated cost, constrained by the requirement that the species must be restored throughout the habitat. First, we consider spatially inhomogeneous, unstable stationary solutions of the model's equations as plausible candidates for small restoration cost. Second, we use numerical simulations to find the smallest rectangular cluster, enclosing a spatially homogeneous population density, that minimizes the cost of assured restoration. Finally, by employing simulated annealing, we minimize restoration cost among all possible initial spatial distributions of females and males. For biased sex ratios, or for a significant between-sex difference in mortality, we find that sex-specific spatial distributions minimize the cost. But as long as the sex ratio maximizes the local equilibrium density for given mortality rates, a common homogeneous distribution for both sexes that spans a critical distance yields a similarly low cost.

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.

Genetic diversity, kinship analysis, and broodstock management of captive Atlantic sturgeon for population restoration

Science.gov (United States)

Henderson, A.P.; Spidle, A.P.; King, T.L.

2005-01-01

Captive Atlantic sturgeon Acipenser oxyrinchus considered for use as broodstock in a restoration program were genotyped using nuclear DNA microsatellites and compared to wild collections from the Hudson River, New York (source of parents of the captive sturgeon) and from Albemarle Sound, North Carolina. Because the potential broodfish were the progeny of a small number of parents, maintaining genetic diversity and minimizing inbreeding is essential to a successful breeding and supplementation program. The microsatellite loci used in this analysis generated unique multilocus genotypes for each of 136 Atlantic sturgeon. Analyses indicated significant genetic separation between the New York and North Carolina collections and correctly identified the potential broodstock as a subset of the Hudson River population. Pairwise genetic distance (-In proportion of shared alleles) between half and full siblings in the potential broodfish was as great as 1.386, a value exceeded by only 36% of the sampled broodfish pairs available for mating. Because the current broodstock population does not seem to have deviated far from their ancestral population in the Hudson River, progeny from that broodstock, or the parents themselves, would seem to be genetically suitable for release back into the Hudson River.

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...

Methanogenesis limitations in degraded peatlands after their hydrological restoration

Science.gov (United States)

Urbanová, Zuzana

2017-04-01

Peatlands are ecosystems that can have a high degree of carbon sequestration due to CO2 fixation and low decomposition rates, but on the other hand, they are a source of CH4. Past drainage or mining can disturb these natural functions with rewetting being the main method used to bring back their original ecosystem properties. Methanogenic community composition and its activity seems to be very sensitive to environmental changes and therefore its limited activity after restoration can reflect the not fully restored functioning of the microbial community and its processes in the rewetted peatlands. To find the cause for this methanogenesis limitation we determined the abundance and composition of the methanogenic community and methane potential production in pristine, long-term drained and rewetted bogs and spruce swamp forests (SSF) in the Šumava Mountains (Czech Republic), using high-throughput barcoded sequencing, qPCR and anaerobic incubation of peat samples in relation to peat biochemical properties. Long-term drainage led to a strongly reduced diversity, abundance and activity of the methanogenic community in both peatland types. In restored sites, methanogenic abundance and community composition reached a pristine like state, however their activity measured as CH4 production remained as low as in drained sites. Substrate limitation was expected; therefore we further added different substrates during anaerobic incubation of the peat samples. In addition to glucose and ethanol, we added natural complex substrates from peatland plants (sedges, Sphagnum) to simulate the effect of the spreading of peatland species and their litter on methanogenic activity. The results unambiguously confirmed the limitation of methanogens by substrate availability due to the previous long-term drainage and strongly decomposed peat. The addition of natural substrates led to an increase in CH4 production, which was close to values in pristine sites. The limited CH4 production

Restoration of rare earth mine areas: organic amendments and phytoremediation.

Science.gov (United States)

Zhou, Lingyan; Li, Zhaolong; Liu, Wen; Liu, Shenghong; Zhang, Limin; Zhong, Liyan; Luo, Ximei; Liang, Hong

2015-11-01

Overexploitation of rare earth mine has caused serious desertification and various environmental issues, and ecological restoration of a mining area is an important concern in China. In this study, experiments involving dry grass landfilling, chicken manure broadcasting, and plant cultivation were carried out to reclaim a rare earth mine area located in Heping County, Guangdong Province, China. The prime focus was to improve soil quality in terms of nutrients, microbial community, enzyme activity, and physicochemical properties so as to reclaim the land. After 2 years of restoration, an increase of organic matter (OM), available potassium (K), available phosphorus (P) levels, and acid phosphatase (ACP) activity and a reduction of the available nitrogen (N) level and urease (URE) activity in soil were achieved compared to the original mined land. The nutrients and enzyme activities in soil with 5 years of restoration were close to or surpass those in the unexploited land as control. The bulk density, total porosity, water holding capacity, pH, and electrical conductivity (EC) of soil were improved, and the number of cultivable microorganisms and the bacterial diversity in soil were greatly increased with time during ecological restoration, especially for surface soil. Furthermore, the artificial vegetation stably grew at the restored mining sites. The results indicated that organic amendments and phytoremediation could ecologically restore the rare earth mining sites and the mined land could finally be planted as farmland.

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.

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.

Microbial healing of cracks in concrete: a review.

Science.gov (United States)

Joshi, Sumit; Goyal, Shweta; Mukherjee, Abhijit; Reddy, M Sudhakara

2017-11-01

Concrete is the most widely used construction material of the world and maintaining concrete structures from premature deterioration is proving to be a great challenge. Early age formation of micro-cracking in concrete structure severely affects the serviceability leading to high cost of maintenance. Apart from conventional methods of repairing cracks with sealants or treating the concrete with adhesive chemicals to prevent the cracks from widening, a microbial crack-healing approach has shown promising results. The unique feature of the microbial system is that it enables self-healing of concrete. The effectiveness of microbially induced calcium carbonate precipitation (MICCP) in improving durability of cementitious building materials, restoration of stone monuments and soil bioclogging is discussed. Main emphasis has been laid on the potential of bacteria-based crack repair in concrete structure and the applications of different bacterial treatments to self-healing cracks. Furthermore, recommendations to employ the MICCP technology at commercial scale and reduction in the cost of application are provided in this review.

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.

Conservation of eelgrass (Zostera marina) genetic diversity in a mesocosm-based restoration experiment.

Science.gov (United States)

Ort, Brian S; Cohen, C Sarah; Boyer, Katharyn E; Reynolds, Laura K; Tam, Sheh May; Wyllie-Echeverria, Sandy

2014-01-01

Eelgrass (Zostera marina) forms the foundation of an important shallow coastal community in protected estuaries and bays. Widespread population declines have stimulated restoration efforts, but these have often overlooked the importance of maintaining the evolutionary potential of restored populations by minimizing the reduction in genetic diversity that typically accompanies restoration. In an experiment simulating a small-scale restoration, we tested the effectiveness of a buoy-deployed seeding technique to maintain genetic diversity comparable to the seed source populations. Seeds from three extant source populations in San Francisco Bay were introduced into eighteen flow-through baywater mesocosms. Following seedling establishment, we used seven polymorphic microsatellite loci to compare genetic diversity indices from 128 shoots to those found in the source populations. Importantly, allelic richness and expected heterozygosity were not significantly reduced in the mesocosms, which also preserved the strong population differentiation present among source populations. However, the inbreeding coefficient F IS was elevated in two of the three sets of mesocosms when they were grouped according to their source population. This is probably a Wahlund effect from confining all half-siblings within each spathe to a single mesocosm, elevating F IS when the mesocosms were considered together. The conservation of most alleles and preservation of expected heterozygosity suggests that this seeding technique is an improvement over whole-shoot transplantation in the conservation of genetic diversity in eelgrass restoration efforts.

Conservation of eelgrass (Zostera marina genetic diversity in a mesocosm-based restoration experiment.

Directory of Open Access Journals (Sweden)

Brian S Ort

Full Text Available Eelgrass (Zostera marina forms the foundation of an important shallow coastal community in protected estuaries and bays. Widespread population declines have stimulated restoration efforts, but these have often overlooked the importance of maintaining the evolutionary potential of restored populations by minimizing the reduction in genetic diversity that typically accompanies restoration. In an experiment simulating a small-scale restoration, we tested the effectiveness of a buoy-deployed seeding technique to maintain genetic diversity comparable to the seed source populations. Seeds from three extant source populations in San Francisco Bay were introduced into eighteen flow-through baywater mesocosms. Following seedling establishment, we used seven polymorphic microsatellite loci to compare genetic diversity indices from 128 shoots to those found in the source populations. Importantly, allelic richness and expected heterozygosity were not significantly reduced in the mesocosms, which also preserved the strong population differentiation present among source populations. However, the inbreeding coefficient F IS was elevated in two of the three sets of mesocosms when they were grouped according to their source population. This is probably a Wahlund effect from confining all half-siblings within each spathe to a single mesocosm, elevating F IS when the mesocosms were considered together. The conservation of most alleles and preservation of expected heterozygosity suggests that this seeding technique is an improvement over whole-shoot transplantation in the conservation of genetic diversity in eelgrass restoration efforts.

Adaptive Management of Urban Ecosystem Restoration: Learning From Restoration Managers in Rhode Island, USA

Science.gov (United States)

Urban aquatic restoration can be difficult to accomplish because of complications like industrial pollutants, population density, infrastructure, and expense; however, unique opportunities in urban settings, including the potential to provide benefits to many diverse people, can ...

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

Contrasting the roles of section length and instream habitat enhancement for river restoration success: a field study on 20 European restoration projects

NARCIS (Netherlands)

Hering, D.; Aroviita, J.; Baattrup-Pedersen, A.; Brabec, K.; Buijse, T.; Ecke, F.; Friberg, N.; Gielczewski, Marek; Januschke, K.; Köhler, J.; Kupilas, Benjamin; Lorenz, A.W.; Muhar, S.; Paillex, Amael; Poppe, Michaela; Schmidt, T.; Schmutz, S.; Vermaat, J.; Verdonschot, R.C.M.; Verdonschot, P.F.M.; Wolter, Christian; Kail, J.

2015-01-01

1. Restoration of river hydromorphology often has limited detected effects on river biota. One frequently discussed reason is that the restored river length is insufficient to allow populations to develop and give the room for geomorphologic processes to occur. 2. We investigated ten pairs of

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.

Estimating temporal trend in the presence of spatial complexity: a Bayesian hierarchical model for a wetland plant population undergoing restoration.

Directory of Open Access Journals (Sweden)

Thomas J Rodhouse

Full Text Available Monitoring programs that evaluate restoration and inform adaptive management are important for addressing environmental degradation. These efforts may be well served by spatially explicit hierarchical approaches to modeling because of unavoidable spatial structure inherited from past land use patterns and other factors. We developed bayesian hierarchical models to estimate trends from annual density counts observed in a spatially structured wetland forb (Camassia quamash [camas] population following the cessation of grazing and mowing on the study area, and in a separate reference population of camas. The restoration site was bisected by roads and drainage ditches, resulting in distinct subpopulations ("zones" with different land use histories. We modeled this spatial structure by fitting zone-specific intercepts and slopes. We allowed spatial covariance parameters in the model to vary by zone, as in stratified kriging, accommodating anisotropy and improving computation and biological interpretation. Trend estimates provided evidence of a positive effect of passive restoration, and the strength of evidence was influenced by the amount of spatial structure in the model. Allowing trends to vary among zones and accounting for topographic heterogeneity increased precision of trend estimates. Accounting for spatial autocorrelation shifted parameter coefficients in ways that varied among zones depending on strength of statistical shrinkage, autocorrelation and topographic heterogeneity--a phenomenon not widely described. Spatially explicit estimates of trend from hierarchical models will generally be more useful to land managers than pooled regional estimates and provide more realistic assessments of uncertainty. The ability to grapple with historical contingency is an appealing benefit of this approach.

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.

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

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

Microbial and molecular techniques to evaluate and to implement in-situ biodegradation potential and activity at sites contaminated with aromatic and chlorinated hydrocarbons

International Nuclear Information System (INIS)

Karg, F.; Henkler, Ch.

2005-01-01

Intrinsic bio-remediation harnesses the ability of indigenous microorganisms to degrade contaminants that are present in soil and groundwater. Over the past decade many environmental regulatory agencies especially in Europe have come to recognize the importance of these natural processes in contaminant attenuation. In order to use in-situ bio-remediation to clean up a site successfully it is necessary to investigate the indigenous microbial population and its potential activity to degrade the contaminants of concern (COCs). The evaluation of naturally-occurring degradative activity in initial screening of soil and groundwater samples using recently developed molecular and microbial methods may allow for the implementation of a contaminant reduction and management program without the need for fully engineered remediation intervention. Limited engineering approaches (nutrient delivery etc.) can be implemented to support naturally-occurring bio-restoration processes to achieve a controlled, dynamic attenuation of COCs. Techniques for monitoring pollutant-degrading microorganisms were previously limited to standard culturing techniques. More recently, techniques based upon detection of genetic elements and metabolic activities have been developed in collaboration with university partners Europe, especially in France. The modern techniques are more sensitive for monitoring microbial populations, metabolic activity and the genetic potential to degrade the COCs, and avoid the need for cultivation of microbes under artificial conditions in the laboratory. Especially the application of PCR-Tests (Polymerase Chain Reaction) are able to quantify the Genetic Potential of Pollutant Microbiological Degradation on a contaminated site. This enables to use very economic in-situ site rehabilitation strategies as for example (Dynamic Natural Attenuation). For this modern application of these new strategies PLANREAL created with HPC Envirotec and together with a French University

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

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

growth only in a few clades directly involved in methanogenesis, rather than in the whole microbial community. IMPORTANCE Many microbes cannot be isolated in pure culture to determine their preferential growth conditions and predict their response to changing environmental conditions. We created a microcosm of marine sediments that allowed us to simulate a diagenetic profile using a temporal analog for depth. This allowed for the observation of the microbial community population dynamics caused by the natural shift from sulfate reduction to methanogenesis. Our research provides evidence for the population dynamics of uncultured microbes as well as the application of a novel method of turnover rate analysis for individual taxa within a mixed incubation, FRAxC, which stands for "fraction of read abundance times cells," which was verified by quantitative PCR. This allows for the calculation of population turnover times for microbes in a natural setting and the identification of uncultured clades involved in geochemical processes. Copyright © 2017 American Society for Microbiology.

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

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.

Mastering events of the past. Restoration strategies for radioactive contaminated ecosystems (RESTORE)

International Nuclear Information System (INIS)

Voigt, G.; Burrough, P.; Crout, N.; Desmet, G.; Howard, B.J.; Rauret, G.; Sansone, U.; Strand, P.

1996-01-01

In this paper a short presentation of the results of the European Commission funded ECP is given, and how the programme RESTORE will contribute to solving some of these deficiencies of existing models paying little attention to factors such as spatial and temporal variation in radioecological operative parameters which influence transfer to foodstuffs and man. Data obtained after the Chernobyl accident are mainly based on information of collective systems and do inadequately consider private farming, different consumption behaviours or socio-economic factors of special groups within the population. However, the effect of countermeasures will depend very much on these factors. The work programme of RESTORE is designed to improve these models and to provide a model which is suitably constructed so that different sources and subsets of population are appropriately considered. It will make maximum use of data and information available from studies carried out in the CIS countries in recent years, and will include a radioecological evaluation of the Semipalatinsk test site and provide detailed, scientifically based recommendations for restoration techniques based on spatial analysis of selected regions. The overall aim is to produce an environmental management package integrating over areas contaminated by radioactive fallout based on an understanding of the nature of contamination, the processes and routes by which radioactivity is transferred in a variety of ecosystems, and the importance and potential of appropriate countermeasures to reduce radiation doses to humans and to minimize adverse socio-economic effects. (J.P.N.)

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 ...

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.

Transplanting a Microbial Organ: the Good, the Bad, and the Unknown

Directory of Open Access Journals (Sweden)

Dionysios A. Antonopoulos

2016-05-01

Full Text Available Fecal microbiota transplantation (FMT has received increased attention as a therapy for correcting intestinal dysbiosis and restoring a state of health in patients suffering from either recalcitrant infection by Clostridium difficile or more complex disease states, such as inflammatory bowel disease (IBD. The “gut microbial organ” from the donor that is used in these transplants may serve to transfer genetic material between donor and recipient via virus-like particles, specifically bacteriophages, that infect the bacterial component of the microbiota. The recently published study by Chehoud et al. provides evidence for not only the transfer of bacteriophages during FMT but also the transfer of multiple populations of bacteriophages to recipients from the donor microbiota used (C. Chehoud et al., mBio 7:e00322-16, 2016, http://dx.doi.org/10.1128/mBio.00322-16. While the clinical significance of these findings remains unclear, nothing short of a diligent and persistent effort is needed to define the intended and unintended consequences of FMT.

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.

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

Endangered species management and ecosystem restoration: Finding the common ground

Science.gov (United States)

Casazza, Michael L.; Overton, Cory T.; Bui, Thuy-Vy D.; Hull, Joshua M.; Albertson, Joy D.; Bloom, Valary K.; Bobzien, Steven; McBroom, Jennifer; Latta, Marilyn; Olofson, Peggy; Rohmer, Tobias M.; Schwarzbach, Steven E.; Strong, Donald R.; Grijalva, Erik; Wood, Julian K.; Skalos, Shannon; Takekawa, John Y.

2016-01-01

Management actions to protect endangered species and conserve ecosystem function may not always be in precise alignment. Efforts to recover the California Ridgway’s Rail (Rallus obsoletus obsoletus; hereafter, California rail), a federally and state-listed species, and restoration of tidal marsh ecosystems in the San Francisco Bay estuary provide a prime example of habitat restoration that has conflicted with species conservation. On the brink of extinction from habitat loss and degradation, and non-native predators in the 1990s, California rail populations responded positively to introduction of a non-native plant, Atlantic cordgrass (Spartina alterniflora). California rail populations were in substantial decline when the non-native Spartina was initially introduced as part of efforts to recover tidal marshes. Subsequent hybridization with the native Pacific cordgrass (Spartina foliosa) boosted California rail populations by providing greater cover and increased habitat area. The hybrid cordgrass (S. alterniflora × S. foliosa) readily invaded tidal mudflats and channels, and both crowded out native tidal marsh plants and increased sediment accretion in the marsh plain. This resulted in modification of tidal marsh geomorphology, hydrology, productivity, and species composition. Our results show that denser California rail populations occur in invasive Spartina than in native Spartina in San Francisco Bay. Herbicide treatment between 2005 and 2012 removed invasive Spartina from open intertidal mud and preserved foraging habitat for shorebirds. However, removal of invasive Spartina caused substantial decreases in California rail populations. Unknown facets of California rail ecology, undesirable interim stages of tidal marsh restoration, and competing management objectives among stakeholders resulted in management planning for endangered species or ecosystem restoration that favored one goal over the other. We have examined this perceived conflict and propose

Endangered species management and ecosystem restoration: finding the common ground

Directory of Open Access Journals (Sweden)

Michael L. Casazza

2016-03-01

Full Text Available Management actions to protect endangered species and conserve ecosystem function may not always be in precise alignment. Efforts to recover the California Ridgway's Rail (Rallus obsoletus obsoletus; hereafter, California rail, a federally and state-listed species, and restoration of tidal marsh ecosystems in the San Francisco Bay estuary provide a prime example of habitat restoration that has conflicted with species conservation. On the brink of extinction from habitat loss and degradation, and non-native predators in the 1990s, California rail populations responded positively to introduction of a non-native plant, Atlantic cordgrass (Spartina alterniflora. California rail populations were in substantial decline when the non-native Spartina was initially introduced as part of efforts to recover tidal marshes. Subsequent hybridization with the native Pacific cordgrass (Spartina foliosa boosted California rail populations by providing greater cover and increased habitat area. The hybrid cordgrass (S. alterniflora à - S. foliosa readily invaded tidal mudflats and channels, and both crowded out native tidal marsh plants and increased sediment accretion in the marsh plain. This resulted in modification of tidal marsh geomorphology, hydrology, productivity, and species composition. Our results show that denser California rail populations occur in invasive Spartina than in native Spartina in San Francisco Bay. Herbicide treatment between 2005 and 2012 removed invasive Spartina from open intertidal mud and preserved foraging habitat for shorebirds. However, removal of invasive Spartina caused substantial decreases in California rail populations. Unknown facets of California rail ecology, undesirable interim stages of tidal marsh restoration, and competing management objectives among stakeholders resulted in management planning for endangered species or ecosystem restoration that favored one goal over the other. We have examined this perceived conflict

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.

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.

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....

Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer.

Science.gov (United States)

Dominguez-Bello, Maria G; De Jesus-Laboy, Kassandra M; Shen, Nan; Cox, Laura M; Amir, Amnon; Gonzalez, Antonio; Bokulich, Nicholas A; Song, Se Jin; Hoashi, Marina; Rivera-Vinas, Juana I; Mendez, Keimari; Knight, Rob; Clemente, Jose C

2016-03-01

Exposure of newborns to the maternal vaginal microbiota is interrupted with cesarean birthing. Babies delivered by cesarean section (C-section) acquire a microbiota that differs from that of vaginally delivered infants, and C-section delivery has been associated with increased risk for immune and metabolic disorders. Here we conducted a pilot study in which infants delivered by C-section were exposed to maternal vaginal fluids at birth. Similarly to vaginally delivered babies, the gut, oral and skin bacterial communities of these newborns during the first 30 d of life was enriched in vaginal bacteria--which were underrepresented in unexposed C-section-delivered infants--and the microbiome similarity to those of vaginally delivered infants was greater in oral and skin samples than in anal samples. Although the long-term health consequences of restoring the microbiota of C-section-delivered infants remain unclear, our results demonstrate that vaginal microbes can be partially restored at birth in C-section-delivered babies.

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

The report presents data on microbial O{sub 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{sub 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{sub 2} reduction was elucidated using specific inhibitors selectively affecting different microbial groups. Our experiments show that microbial O{sub 2} reduction occurs in deep groundwater. Carbon dioxide was produced concurrently with O{sub 2} reduction confirming the biogenic nature of the reduction. The populations developed O{sub 2} reduction rates and capacity depending on the initial concentration of dissolved O{sub 2} reduction. Rates of O{sub 2} reduction ranged from 0.32 to 4.5 {mu}M/day. Depending on temperature and the type of groundwater the approximate time needed for consumption of 500 {mu}M of dissolved O{sub 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{sub 2} both at 30 deg C and 60 deg C. At 16 deg C no delay in O{sub 2} consumption was observed. Our results demonstrated that methanotrophs survive in deep groundwater and that they were induced by O{sub 2}. Some bacteria use Hg or CH{sub 4} as electron donor instead of organic matter, which means that microbial O{sub 2} reduction will occur also in deep groundwaters where the availability of organic carbon is limited. Specific CH{sub 4} oxidation rates ranged between 3.00 and 220 nM CH{sub 4} per litre per

Restored agricultural wetlands in Central Iowa: habitat quality and amphibian response

Science.gov (United States)

Reeves, Rebecca A.; Pierce, Clay; Smalling, Kelly L.; Klaver, Robert W.; Vandever, Mark W.; Battaglin, William A.; Muths, Erin L.

2016-01-01

Amphibians are declining throughout the United States and worldwide due, partly, to habitat loss. Conservation practices on the landscape restore wetlands to denitrify tile drainage effluent and restore ecosystem services. Understanding how water quality, hydroperiod, predation, and disease affect amphibians in restored wetlands is central to maintaining healthy amphibian populations in the region. We examined the quality of amphibian habitat in restored wetlands relative to reference wetlands by comparing species richness, developmental stress, and adult leopard frog (Lithobates pipiens) survival probabilities to a suite of environmental metrics. Although measured habitat variables differed between restored and reference wetlands, differences appeared to have sub-lethal rather than lethal effects on resident amphibian populations. There were few differences in amphibian species richness and no difference in estimated survival probabilities between wetland types. Restored wetlands had more nitrate and alkaline pH, longer hydroperiods, and were deeper, whereas reference wetlands had more amphibian chytrid fungus zoospores in water samples and resident amphibians exhibited increased developmental stress. Restored and reference wetlands are both important components of the landscape in central Iowa and maintaining a complex of fish-free wetlands with a variety of hydroperiods will likely contribute to the persistence of amphibians in this landscape.

Microbial and geochemical assessment of bauxitic un-mined and post-mined chronosequence soils from Mocho Mountains, Jamaica.

Science.gov (United States)

Lewis, Dawn E; Chauhan, Ashvini; White, John R; Overholt, Will; Green, Stefan J; Jasrotia, Puja; Wafula, Denis; Jagoe, Charles

2012-10-01

Microorganisms are very sensitive to environmental change and can be used to gauge anthropogenic impacts and even predict restoration success of degraded environments. Here, we report assessment of bauxite mining activities on soil biogeochemistry and microbial community structure using un-mined and three post-mined sites in Jamaica. The post-mined soils represent a chronosequence, undergoing restoration since 1987, 1997, and 2007. Soils were collected during dry and wet seasons and analyzed for pH, organic matter (OM), total carbon (TC), nitrogen (TN), and phosphorus. The microbial community structure was assessed through quantitative PCR and massively parallel bacterial ribosomal RNA (rRNA) gene sequencing. Edaphic factors and microbial community composition were analyzed using multivariate statistical approaches and revealed a significant, negative impact of mining on soil that persisted even after greater than 20 years of restoration. Seasonal fluctuations contributed to variation in measured soil properties and community composition, but they were minor in comparison to long-term effects of mining. In both seasons, post-mined soils were higher in pH but OM, TC, and TN decreased. Bacterial rRNA gene analyses demonstrated a general decrease in diversity in post-mined soils and up to a 3-log decrease in rRNA gene abundance. Community composition analyses demonstrated that bacteria from the Proteobacteria (α, β, γ, δ), Acidobacteria, and Firmicutes were abundant in all soils. The abundance of Firmicutes was elevated in newer post-mined soils relative to the un-mined soil, and this contrasted a decrease, relative to un-mined soils, in proteobacterial and acidobacterial rRNA gene abundances. Our study indicates long-lasting impacts of mining activities to soil biogeochemical and microbial properties with impending loss in soil productivity.

Restoring rocky intertidal communities: Lessons from a benthic macroalgal ecosystem engineer

International Nuclear Information System (INIS)

Bellgrove, Alecia; McKenzie, Prudence F.; Cameron, Hayley; Pocklington, Jacqueline B.

2017-01-01

As coastal population growth increases globally, effective waste management practices are required to protect biodiversity. Water authorities are under increasing pressure to reduce the impact of sewage effluent discharged into the coastal environment and restore disturbed ecosystems. We review the role of benthic macroalgae as ecosystem engineers and focus particularly on the temperate Australasian fucoid Hormosira banksii as a case study for rocky intertidal restoration efforts. Research focussing on the roles of ecosystem engineers is lagging behind restoration research of ecosystem engineers. As such, management decisions are being made without a sound understanding of the ecology of ecosystem engineers. For successful restoration of rocky intertidal shores it is important that we assess the thresholds of engineering traits (discussed herein) and the environmental conditions under which they are important. - Highlights: • Fucoid algae can be important ecosystem engineers in rocky reef ecosystems • Sewage-effluent disposal negatively affects fucoids and associated communities • Restoring fucoid populations can improve biodiversity of degraded systems • Clarifying the roles of fucoids in ecosystem function can improve restoration efforts • Thresholds of engineering traits and associated environmental conditions important

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.

Urban wetlands: restoration or designed rehabilitation?

Directory of Open Access Journals (Sweden)

Beth Ravit

2017-05-01

Full Text Available The continuing loss of urban wetlands due to an expanding human population and urban development pressures makes restoration or creation of urban wetlands a high priority. However, urban wetland restorations are particularly challenging due to altered hydrologic patterns, a high proportion of impervious surface and stormwater runoff, degraded urban soils, historic contamination, and competitive pressure from non-native species. Urban wetland projects must also consider human-desired socio-economic benefits. We argue that using current wetland restoration approaches and existing regulatory “success” criteria, such as meeting restoration targets for vegetation structure based on reference sites in non-urban locations, will result in “failed” urban restorations. Using three wetland Case Studies in highly urbanized locations, we describe geophysical tools, stormwater management methods, and design approaches useful in addressing urban challenges and in supporting “successful” urban rehabilitation outcomes. We suggest that in human-dominated landscapes, the current paradigm of “restoration” to a previous state must shift to a paradigm of “rehabilitation”, which prioritizes wetland functions and values rather than vegetation structure in order to provide increased ecological benefits and much needed urban open space amenities.

Carbonate Precipitation through Microbial Activities in Natural Environment, and Their Potential in Biotechnology: A Review

Science.gov (United States)

Zhu, Tingting; Dittrich, Maria

2016-01-01

Calcium carbonate represents a large portion of carbon reservoir and is used commercially for a variety of applications. Microbial carbonate precipitation, a by-product of microbial activities, plays an important metal coprecipitation and cementation role in natural systems. This natural process occurring in various geological settings can be mimicked and used for a number of biotechnologies, such as metal remediation, carbon sequestration, enhanced oil recovery, and construction restoration. In this study, different metabolic activities leading to calcium carbonate precipitation, their native environment, and potential applications and challenges are reviewed. PMID:26835451

Carbonate precipitation through microbial activities in natural environment, and their potential in biotechnology: a review

Directory of Open Access Journals (Sweden)

Tingting eZhu

2016-01-01

Full Text Available Calcium carbonate represents a large portion of carbon reservoir and is used commercially for a variety of applications. Microbial carbonate precipitation (MCP, a by-product of microbial activities, plays an important metal coprecipitation and cementation role in natural systems. This natural process occurring in various geological settings can be mimicked and used for a number of biotechnology such as metal remediation, carbon sequestration, enhanced oil recovery and construction restoration. In this study, different metabolic activities leading to calcium carbonate precipitation, their native environment, and potential applications and challenges are reviewed.

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

Sediment nitrogen cycling rates and microbial abundance along a submerged vegetation gradient in a eutrophic lake.

Science.gov (United States)

Yao, Lu; Chen, Chengrong; Liu, Guihua; Liu, Wenzhi

2018-03-01

Decline of submerged vegetation is one of the most serious ecological problems in eutrophic lakes worldwide. Although restoration of submerged vegetation is widely assumed to enhance ecological functions (e.g., nitrogen removal) and aquatic biodiversity, the evidence for this assumption is very limited. Here, we investigated the spatio-temporal patterns of sediment potential nitrification, unamended denitrification and N 2 O production rates along a vegetation gradient in the Lake Honghu, where submerged vegetation was largely restored by prohibiting net-pen aquaculture. We also used five functional genes as markers to quantify the abundance of sediment nitrifying and denitrifying microorganisms. Results showed that unvegetated sediments supported greater nitrification rates than rhizosphere sediments of perennial or seasonal vegetation. However, the absence of submerged vegetation had no significant effect on denitrification and N 2 O production rates. Additionally, the abundance of functional microorganisms in sediments was not significantly different among vegetation types. Season had a strong effect on both nitrogen cycling processes and microbial abundances. The highest nitrification rates were observed in September, while the highest denitrification rates occurred in December. The temporal variation of sediment nitrification, denitrification and N 2 O production rates could be due to changes in water quality and sediment properties rather than submerged vegetation and microbial abundances. Our findings highlight that vegetation restoration in eutrophic lakes improves water quality but does not enhance sediment nitrogen removal rates and microbial abundances. Therefore, for reducing the N level in eutrophic lakes, major efforts should be made to control nutrients export from terrestrial ecosystems. Copyright © 2017 Elsevier B.V. All rights reserved.

Preventing Advanced Carious Lesions with Caries Atraumatic Restorative Technique.

Science.gov (United States)

Byrd, Tammi O

2016-06-01

An alternative approach to controlling dental caries and preventing the associated pain, called atraumatic restorative technique (ART), is described for populations in need, where dental hygienists restore decayed teeth with glass ionomer restorations without prior removal of all decayed tooth structure. There are populations whose decay needs are not adequately being met within the current oral health care delivery system. These include those in poverty conditions, vulnerable children, and the elderly who are often in long-term care facilities without adequate resources or opportunities for traditional dentistry. ART provides a viable option for controlling caries and relieving the pain of untreated decay. The purpose of this article is to suggest that the evidence surrounding ART be viewed objectively and that dental hygienists, with additional education in this approach, can contribute to relieving the pain of untreated dental decay. Evidence suggests that teeth can be effectively restored with ART. Dental hygienists represent an appropriate workforce to provide ART with their current background and education combined plus a brief training program; it is suggested that dental hygiene educational programs include ART within the curriculum. Along with dental sealants and fluoride varnish application, ART can be an important component of a comprehensive preventive program to address the unmet needs of vulnerable populations. Copyright © 2016 Elsevier Inc. All rights reserved.

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 community evolution of black and stinking rivers during in situ remediation through micro-nano bubble and submerged resin floating bed technology.

Science.gov (United States)

Sun, Yanmei; Wang, Shiwei; Niu, Junfeng

2018-06-01

Microbes play important roles during river remediation and the interaction mechanism illustration between microorganisms and sewage is of great significance to improve restoration technology. In this study, micro-nano bubble and submerged resin floating bed composite technology (MBSR) was firstly used to restore two black and stinking urban rivers. After restoration, the water pollution indices such as dissolved oxygen (DO), ammonia nitrogen (NH 4 + -N), total phosphorous (TP), chemical oxygen demand (COD Cr ), water clarity, and the number of facial coliform were significantly improved. Microbial community composition and relative abundance both varied and more aerobic microbes emerged after remediation. The microbial changes showed correlation with DO, NH 4 + -N, TP and COD Cr of the rivers. In summary, the MBSR treatment improved the physiochemical properties of the two black and stinking urban rivers probably through oxygen enrichment of micro-nano bubble and adsorption of submerged resin floating bed, which thereby stimulated functional microbes to degrade pollutants. Copyright © 2018 Elsevier Ltd. All rights reserved.

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

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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.

Directory of Open Access Journals (Sweden)

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.

Soil-covered strategy for ecological restoration alters the bacterial community structure and predictive energy metabolic functions in mine tailings profiles.

Science.gov (United States)

Li, Yang; Sun, Qingye; Zhan, Jing; Yang, Yang; Wang, Dan

2017-03-01

Native soil amendment has been widely used to stabilize mine tailings and speed up the development of soil biogeochemical functions before revegetation; however, it remains poorly understood about the response of microbial communities to ecological restoration of mine tailings with soil-covered strategy. In this study, microbial communities along a 60-cm profile were investigated in mine tailings during ecological restoration of two revegetation strategies (directly revegetation and native soil covered) with different plant species. The mine tailings were covered by native soils as thick as 40 cm for more than 10 years, and the total nitrogen, total organic carbon, water content, and heavy metal (Fe, Cu, and Zn) contents in the 0-40 cm intervals of profiles were changed. In addition, increased microbial diversity and changed microbial community structure were also found in the 10-40 cm intervals of profiles in soil-covered area. Soil-covered strategy rather than plant species and soil depth was the main factor influencing the bacterial community, which explained the largest portion (29.96%) of the observed variation. Compared directly to revegetation, soil-covered strategy exhibited the higher relative abundance of Acidobacteria and Deltaproteobacteria and the lower relative abundance of Bacteroidetes, Gemmatimonadetes, Betaproteobacteria, and Gammaproteobacteria. PICRUSt analysis further demonstrated that soil-covered caused energy metabolic functional changes in carbon, nitrogen, and sulfur metabolism. Given all these, the soil-covered strategy may be used to fast-track the establishment of native microbial communities and is conducive to the rehabilitation of biogeochemical processes for establishing native plant species.

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.

Salt Marsh Ecosystem Responses to Restored Tidal Connectivity across a 14y Chronosequence

Science.gov (United States)

Capooci, M.; Spivak, A. C.; Gosselin, K.

2016-02-01

Salt marshes support valuable ecosystem services. Yet, human activities negatively impact salt marsh function and contribute to their loss at a global scale. On Cape Cod, MA, culverts and impoundments under roads and railways restricted tidal exchange and resulted in salt marsh conversion to freshwater wetlands. Over the past 14 y, these structures have been removed or replaced, restoring tidal connectivity between marshes and a saltwater bay. We evaluated differences in plant community composition, sediment properties, and pore water chemistry in marshes where tidal connectivity was restored using a space-for-time, or chronosequence approach. Each restored marsh was paired with a nearby, natural salt marsh to control for variability between marshes. In each restored and natural salt marsh we evaluated the plant community by measuring species-specific percent cover and biomass and collected sediment cores for bulk density and pore water analyses. Plant communities responded rapidly: salt-tolerant species, such as Spartina alterniflora, became established while freshwater species, including Phragmites australis, were less abundant within 3 y of restoration. The number of plant species was generally greater in marshes restored within 10 y, compared to older and natural marshes. Sediment bulk density varied with depth and across sites. This likely reflects differences in site history and local conditions. Deeper horizons (24-30cm) generally had higher values in restored sites while surface values (0-3cm) were similar in restored and natural marshes. Porewater pH and sulfide were similar in restored and natural marshes, suggesting rapid microbial responses to seawater reintroduction. Overall, marsh properties and processes reflecting biological communities responded rapidly to tidal restoration. However, variability between study locations underscores the potential importance of site history, local hydrology, and geomorphology in shaping marsh biogeochemistry.

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

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

Portfolio theory as a management tool to guide conservation and restoration of multi-stock fish populations

Science.gov (United States)

DuFour, Mark R.; May, Cassandra J.; Roseman, Edward F.; Ludsin, Stuart A.; Vandergoot, Christopher S.; Pritt, Jeremy J.; Fraker, Michael E.; Davis, Jeremiah J.; Tyson, Jeffery T.; Miner, Jeffery G.; Marschall, Elizabeth A.; Mayer, Christine M.

2015-01-01

Habitat degradation and harvest have upset the natural buffering mechanism (i.e., portfolio effects) of many large-scale multi-stock fisheries by reducing spawning stock diversity that is vital for generating population stability and resilience. The application of portfolio theory offers a means to guide management activities by quantifying the importance of multi-stock dynamics and suggesting conservation and restoration strategies to improve naturally occurring portfolio effects. Our application of portfolio theory to Lake Erie Sander vitreus (walleye), a large population that is supported by riverine and open-lake reef spawning stocks, has shown that portfolio effects generated by annual inter-stock larval fish production are currently suboptimal when compared to potential buffering capacity. Reduced production from riverine stocks has resulted in a single open-lake reef stock dominating larval production, and in turn, high inter-annual recruitment variability during recent years. Our analyses have shown (1) a weak average correlation between annual river and reef larval production (ρ̄ = 0.24), suggesting that a natural buffering capacity exists in the population, and (2) expanded annual production of larvae (potential recruits) from riverine stocks could stabilize the fishery by dampening inter-annual recruitment variation. Ultimately, our results demonstrate how portfolio theory can be used to quantify the importance of spawning stock diversity and guide management on ecologically relevant scales (i.e., spawning stocks) leading to greater stability and resilience of multi-stock populations and fisheries.

Estimation of the Ideal Lumbar Lordosis to Be Restored From Spinal Fusion Surgery: A Predictive Formula for Chinese Population.

Science.gov (United States)

Xu, Leilei; Qin, Xiaodong; Zhang, Wen; Qiao, Jun; Liu, Zhen; Zhu, Zezhang; Qiu, Yong; Qian, Bang-ping

2015-07-01

A prospective, cross-sectional study. To determine the independent variables associated with lumbar lordosis (LL) and to establish the predictive formula of ideal LL in Chinese population. Several formulas have been established in Caucasians to estimate the ideal LL to be restored for lumbar fusion surgery. However, there is still a lack of knowledge concerning the establishment of such predictive formula in Chinese population. A total of 296 asymptomatic Chinese adults were prospectively recruited. The relationships between LL and variables including pelvic incidence (PI), age, sex, and body mass index were investigated to determine the independent factors that could be used to establish the predictive formula. For the validation of the current formula, other 4 reported predictive formulas were included. The absolute value of the gap between the actual LL and the ideal LL yielded by these formulas was calculated and then compared between the 4 reported formulas and the current one to determine its reliability in predicting the ideal LL. The logistic regression analysis showed that there were significant associations of LL with PI and age (R = 0.508, P < 0.001 for PI; R = 0.088, P = 0.03 for age). The formula was, therefore, established as follows: LL = 0.508 × PI - 0.088 × Age + 28.6. When applying our formula to these subjects, the gap between the predicted ideal LL and the actual LL was averaged 3.9 ± 2.1°, which was significantly lower than that of the other 4 formulas. The calculation formula derived in this study can provide a more accurate prediction of the LL for the Chinese population, which could be used as a tool for decision making to restore the LL in lumbar corrective surgery. 3.

Restoring proximal caries lesions conservatively with tunnel restorations.

Science.gov (United States)

Chu, Chun-Hung; Mei, May L; Cheung, Chloe; Nalliah, Romesh P

2013-07-30

The tunnel restoration has been suggested as a conservative alternative to the conventional box preparation for treating proximal caries. The main advantage of tunnel restoration over the conventional box or slot preparation includes being more conservative and increasing tooth integrity and strength by preserving the marginal ridge. However, tunnel restoration is technique-sensitive and can be particularly challenging for inexperienced restorative dentists. Recent advances in technology, such as the contemporary design of dental handpieces with advanced light-emitting diode (LED) and handheld comfort, offer operative dentists better vision, illumination, and maneuverability. The use of magnifying loupes also enhances the visibility of the preparation. The advent of digital radiographic imaging has improved dental imaging and reduced radiation. The new generation of restorative materials has improved mechanical properties. Tunnel restoration can be an option to restore proximal caries if the dentist performs proper case selection and pays attention to the details of the restorative procedures. This paper describes the clinical technique of tunnel restoration and reviews the studies of tunnel restorations.

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.

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.

Responses of soil microbial biomass and bacterial community structure to closed-off management (an ecological natural restoration measures): A case study of Dongting Lake wetland, middle China.

Science.gov (United States)

Dai, Juan; Wu, Haipeng; Zhang, Chang; Zeng, Guangming; Liang, Jie; Guo, Shenglian; Li, Xiaodong; Huang, Lu; Lu, Lunhui; Yuan, Yujie

2016-09-01

Soil microbial biomass (SMB) and bacterial community structure, which are critical to global ecosystem and fundamental ecological processes, are sensitive to anthropogenic activities and environmental conditions. In this study, we examined the possible effects of closed-off management (an ecological natural restoration measures, ban on anthropogenic activity, widely employed for many important wetlands) on SMB, soil bacterial community structure and functional marker genes of nitrogen cycling in Dongting Lake wetland. Soil samples were collected from management area (MA) and contrast area (CA: human activities, such as hunting, fishing and draining, are permitted) in November 2013 and April 2014. Soil properties, microbial biomass carbon (MBC), and bacterial community structure were investigated. Comparison of the values of MA and CA showed that SMB and bacterial community diversity of the MA had a significant increase after 7 years closed-off management. The mean value of Shannon-Weiner diversity index of MA and CA respectively were 2.85 and 2.07. The gene copy numbers of 16S rRNA and nosZ of MA were significant higher than those of CA. the gene copy numbers of ammonia-oxidizing archaea (AOA) and nirK of MA were significant lower than those of CA. However, there was no significant change in the gene copy numbers of ammonia-oxidizing bacteria (AOB) and nirS. Copyright © 2016 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Optimise the microbial flora with milk and yoghurt to prevent disease.

Science.gov (United States)

Morris, James A

2018-05-01

Pathogenic bacteria, which are temporary or permanent members of our microbial flora, cause or contribute to a wide range of human disease at all ages. Conditions include Alzheimer's disease, atherosclerosis, diabetes mellitus, obesity, cancer, autoimmunity and psychosis, amongst others. The mechanism of damage is inflammation which can be chronic or acute. An optimal microbial flora includes a wide range of pathogenic bacteria in low dose. This allows specific immunity to be developed and maintained with minimal inflammatory damage. Human milk has evolved to deliver an optimal microbial flora to the infant. Cow's milk has the potential, following appropriate fortification, to maintain an optimal human microbial flora throughout life. Yoghurt is a fermented milk product in which bacteria normally present in milk convert sugars to lactic acid. The acid suppresses the growth of pathogens in the oral cavity, oropharynx and oesophagus. Thus yoghurt can restore an optimal flora in these regions in the short term. Since bacteria are transported between epithelial surfaces, yoghurt will also optimise the flora elsewhere. The judicious use of milk and yogurt could prevent a high proportion of human disease. Copyright © 2018 The Author. Published by Elsevier Ltd.. All rights reserved.

Sorption of radioiodide in an acidic, nutrient-poor boreal bog: insights into the microbial impact

International Nuclear Information System (INIS)

Lusa, M.; Bomberg, M.; Aromaa, H.; Knuutinen, J.; Lehto, J.

2015-01-01

Batch sorption experiments were conducted to evaluate the sorption behaviour of iodide and the microbial impact on iodide sorption in the surface moss, subsurface peat, gyttja, and clay layers of a nutrient-poor boreal bog. The batch distribution coefficient (K d ) values of iodide decreased as a function of sampling depth. The highest K d values, 4800 L/Kg dry weight (DW) (geometric mean), were observed in the fresh surface moss and the lowest in the bottom clay (geometric mean 90 mL/g DW). In the surface moss, peat and gyttja layers, which have a high organic matter content (on average 97%), maximum sorption was observed at a pH between ∼4 and 5 and in the clay layer at pH 2. The K d values were significantly lower in sterilized samples, being 20-fold lower than the values found for the unsterilized samples. In addition, the recolonization of sterilized samples with a microbial population from the fresh samples restored the sorption capacity of surface moss, peat and gyttja samples, indicating that the decrease in the sorption was due to the destruction of microbes and supporting the hypothesis that microbes are necessary for the incorporation of iodide into the organic matter. Anoxic conditions reduced the sorption of iodide in fresh, untreated samples, similarly to the effect of sterilization, which supports the hypothesis that iodide is oxidized into I 2 /HIO before incorporation into the organic matter. Furthermore, the K d values positively correlated with peroxidase activity in surface moss, subsurface peat and gyttja layers at +20 °C, and with the bacterial cell counts obtained from plate count agar at +4 °C. Our results demonstrate the importance of viable microbes for the sorption of iodide in the bog environment, having a high organic matter content and a low pH. - Highlights: • Sorption of iodide is highest on the surface Sphagnum layer of the bog. • Sterilization of peat decreases the sorption of iodide. • Anoxic conditions decrease

Structure, Variation, and Co-occurrence of Soil Microbial Communities in Abandoned Sites of a Rare Earth Elements Mine.

Science.gov (United States)

Chao, Yuanqing; Liu, Wenshen; Chen, Yanmei; Chen, Wenhui; Zhao, Lihua; Ding, Qiaobei; Wang, Shizhong; Tang, Ye-Tao; Zhang, Tong; Qiu, Rong-Liang

2016-11-01

Mining activity for rare earth elements (REEs) has caused serious environmental pollution, particularly for soil ecosystems. However, the effects of REEs on soil microbiota are still poorly understood. In this study, soils were collected from abandoned sites of a REEs mine, and the structure, diversity, and co-occurrence patterns of soil microbiota were evaluated by Illumina high-throughput sequencing targeting 16S rRNA genes. Although microbiota developed significantly along with the natural restoration, the microbial structure on the site abandoned for 10 years still significantly differed from that on the unmined site. Potential plant growth promoting bacteria (PGPB) were identified by comparing 16S sequences against a self-constructed PGPB database via BLAST, and it was found that siderophore-producing and phosphorus-solubilizing bacteria were more abundant in the studied soils than in reference soils. Canonical correspondence analysis indicated that species richness of plant community was the prime factor affecting microbial structure, followed by limiting nutrients (total carbon and total nitrogen) and REEs content. Further co-occurring network analysis revealed nonrandom assembly patterns of microbiota in the studied soils. These results increase our understanding of microbial variation and assembly pattern during natural restoration in REE contaminated soils.

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...

Use of compost for the restoration of mine wastes and mine soils; Utilizacion de materiales compostados en la rehabilitacion potencial de espacios afectados por residuos mineros y suelos de mina

Energy Technology Data Exchange (ETDEWEB)

Paradelo, R.

2013-09-01

One of the main limitations for the successful restoration of the environmental damages produced by quarrying and mining activities is that mine waste and mine soils are largely devoid of organic matter. For this reason, amelioration with organic materials such as sewage sludge, manure or compost is gaining attention as a desirable strategy that may render good results in restoration. In this paper, recent experiences on the use of composted materials for the amelioration of mine wastes and mine soils are reviewed. The benefits obtained from the use of compost in restoration studies include improvement of the unfavourable physical, chemical and biological properties of mine waste and mine soils. The increase in the organic matter concentrations produces an improvement of the structure which leads to reduced bulk density and increased porosity, thus decreasing the risks of compaction, sealing and erosion. Correction of extreme pH is usually observed. N and P, two elements that are usually lacking in mine waste, are also added with compost in plant-available forms. The introduction of microbial populations leads to the reactivation of biogeochemical cycles which are essential for the long-term fertility and sustainability of new ecosystems. (Author)

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.

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

Science.gov (United States)

Saad, Sainab; Bhatnagar, Srijak; Tegetmeyer, Halina E.; Geelhoed, Jeanine S.; Strous, Marc

2017-01-01

Summary For the anaerobic remineralization of organic matter in marine sediments, sulfate reduction coupled to fermentation plays a key role. Here, we enriched sulfate‐reducing/fermentative communities from intertidal sediments under defined conditions in continuous culture. We transiently exposed the cultures to oxygen or nitrate twice daily and investigated the community response. Chemical measurements, provisional genomes and transcriptomic profiles revealed trophic networks of microbial populations. Sulfate reducers coexisted with facultative nitrate reducers or aerobes enabling the community to adjust to nitrate or oxygen pulses. Exposure to oxygen and nitrate impacted the community structure, but did not suppress fermentation or sulfate reduction as community functions, highlighting their stability under dynamic conditions. The most abundant sulfate reducer in all cultures, related to Desulfotignum balticum, appeared to have coupled both acetate‐ and hydrogen oxidation to sulfate reduction. We describe a novel representative of the widespread uncultured candidate phylum Fermentibacteria (formerly candidate division Hyd24‐12). For this strictly anaerobic, obligate fermentative bacterium, we propose the name ‘USabulitectum silens’ and identify it as a partner of sulfate reducers in marine sediments. Overall, we provide insights into the function of fermentative, as well as sulfate‐reducing microbial communities and their adaptation to a dynamic environment. PMID:28836729

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.

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...

Restoring monarch butterfly habitat in the Midwestern US: 'All hands on deck'

Science.gov (United States)

Thogmartin, Wayne E.; Lopez-Hoffman, Laura; Rohweder, Jason; Diffendorfer, James E.; Drum, Ryan G.; Semmens, Darius J.; Black, Scott; Caldwell, Iris; Cotter, Donita; Drobney, Pauline; Jackson, Laura L.; Gale, Michael; Helmers, Doug; Hilburger, Steven B.; Howard, Elizabeth; Oberhauser, Karen S.; Pleasants, John M.; Semmens, Brice X.; Taylor, Orley R.; Ward, Patrick; Weltzin, Jake F.; Wiederholt, Ruscena

2017-01-01

The eastern migratory population of monarch butterflies (Danaus plexippus plexippus) has declined by >80% within the last two decades. One possible cause of this decline is the loss of ≥1.3 billion stems of milkweed (Asclepias spp.), which monarchs require for reproduction. In an effort to restore monarchs to a population goal established by the US Fish and Wildlife Service and adopted by Mexico, Canada, and the US, we developed scenarios for amending the Midwestern US landscape with milkweed. Scenarios for milkweed restoration were developed for protected area grasslands, Conservation Reserve Program land, powerline, rail and roadside rights of way, urban/suburban lands, and land in agricultural production. Agricultural land was further divided into productive and marginal cropland. We elicited expert opinion as to the biological potential (in stems per acre) for lands in these individual sectors to support milkweed restoration and the likely adoption (probability) of management practices necessary for affecting restoration. Sixteen of 218 scenarios we developed for restoring milkweed to the Midwestern US were at levels (>1.3 billion new stems) necessary to reach the monarch population goal. One of these scenarios would convert all marginal agriculture to conserved status. The other 15 scenarios converted half of marginal agriculture (730 million stems), with remaining stems contributed by other societal sectors. Scenarios without substantive agricultural participation were insufficient for attaining the population goal. Agricultural lands are essential to reaching restoration targets because they occupy 77% of all potential monarch habitat. Barring fundamental changes to policy, innovative application of economic tools such as habitat exchanges may provide sufficient resources to tip the balance of the agro-ecological landscape toward a setting conducive to both robust agricultural production and reduced imperilment of the migratory monarch butterfly.

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.

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

Restoring proximal caries lesions conservatively with tunnel restorations

Directory of Open Access Journals (Sweden)

Chu CH

2013-07-01

Full Text Available Chun-Hung Chu1, May L Mei,1 Chloe Cheung,1 Romesh P Nalliah2 1Faculty of Dentistry, The University of Hong Kong, Hong Kong, People's Republic of China; 2Department of Restorative Dentistry and Biomaterials Sciences, Harvard School of Dental Medicine, Boston, MA, USA Abstract: The tunnel restoration has been suggested as a conservative alternative to the conventional box preparation for treating proximal caries. The main advantage of tunnel restoration over the conventional box or slot preparation includes being more conservative and increasing tooth integrity and strength by preserving the marginal ridge. However, tunnel restoration is technique-sensitive and can be particularly challenging for inexperienced restorative dentists. Recent advances in technology, such as the contemporary design of dental handpieces with advanced light-emitting diode (LED and handheld comfort, offer operative dentists better vision, illumination, and maneuverability. The use of magnifying loupes also enhances the visibility of the preparation. The advent of digital radiographic imaging has improved dental imaging and reduced radiation. The new generation of restorative materials has improved mechanical properties. Tunnel restoration can be an option to restore proximal caries if the dentist performs proper case selection and pays attention to the details of the restorative procedures. This paper describes the clinical technique of tunnel restoration and reviews the studies of tunnel restorations. Keywords: operative, practice, tunnel preparation, composite, amalgam, glass ionomer

Barriers, Opportunities, and Strategies for Urban Ecosystem Restoration: Lessons Learned from Restoration Managers in Rhode Island, U.S.A.

Science.gov (United States)

Urban ecosystem restoration can be especially difficult to accomplish because of complications like industrial pollutants, population density, infrastructure, and expense, however, the unique opportunities in urban settings, including the potential to provide benefits to many peo...

Global analysis of seagrass restoration: the importance of large-scale planting

KAUST Repository

van Katwijk, Marieke M.; Thorhaug, Anitra; Marbà , Nú ria; Orth, Robert J.; Duarte, Carlos M.; Kendrick, Gary A.; Althuizen, Inge H. J.; Balestri, Elena; Bernard, Guillaume; Cambridge, Marion L.; Cunha, Alexandra; Durance, Cynthia; Giesen, Wim; Han, Qiuying; Hosokawa, Shinya; Kiswara, Wawan; Komatsu, Teruhisa; Lardicci, Claudio; Lee, Kun-Seop; Meinesz, Alexandre; Nakaoka, Masahiro; O'Brien, Katherine R.; Paling, Erik I.; Pickerell, Chris; Ransijn, Aryan M. A.; Verduin, Jennifer J.

2015-01-01

In coastal and estuarine systems, foundation species like seagrasses, mangroves, saltmarshes or corals provide important ecosystem services. Seagrasses are globally declining and their reintroduction has been shown to restore ecosystem functions. However, seagrass restoration is often challenging, given the dynamic and stressful environment that seagrasses often grow in. From our world-wide meta-analysis of seagrass restoration trials (1786 trials), we describe general features and best practice for seagrass restoration. We confirm that removal of threats is important prior to replanting. Reduced water quality (mainly eutrophication), and construction activities led to poorer restoration success than, for instance, dredging, local direct impact and natural causes. Proximity to and recovery of donor beds were positively correlated with trial performance. Planting techniques can influence restoration success. The meta-analysis shows that both trial survival and seagrass population growth rate in trials that survived are positively affected by the number of plants or seeds initially transplanted. This relationship between restoration scale and restoration success was not related to trial characteristics of the initial restoration. The majority of the seagrass restoration trials have been very small, which may explain the low overall trial survival rate (i.e. estimated 37%). Successful regrowth of the foundation seagrass species appears to require crossing a minimum threshold of reintroduced individuals. Our study provides the first global field evidence for the requirement of a critical mass for recovery, which may also hold for other foundation species showing strong positive feedback to a dynamic environment. Synthesis and applications. For effective restoration of seagrass foundation species in its typically dynamic, stressful environment, introduction of large numbers is seen to be beneficial and probably serves two purposes. First, a large-scale planting

Global analysis of seagrass restoration: the importance of large-scale planting

KAUST Repository

van Katwijk, Marieke M.

2015-10-28

In coastal and estuarine systems, foundation species like seagrasses, mangroves, saltmarshes or corals provide important ecosystem services. Seagrasses are globally declining and their reintroduction has been shown to restore ecosystem functions. However, seagrass restoration is often challenging, given the dynamic and stressful environment that seagrasses often grow in. From our world-wide meta-analysis of seagrass restoration trials (1786 trials), we describe general features and best practice for seagrass restoration. We confirm that removal of threats is important prior to replanting. Reduced water quality (mainly eutrophication), and construction activities led to poorer restoration success than, for instance, dredging, local direct impact and natural causes. Proximity to and recovery of donor beds were positively correlated with trial performance. Planting techniques can influence restoration success. The meta-analysis shows that both trial survival and seagrass population growth rate in trials that survived are positively affected by the number of plants or seeds initially transplanted. This relationship between restoration scale and restoration success was not related to trial characteristics of the initial restoration. The majority of the seagrass restoration trials have been very small, which may explain the low overall trial survival rate (i.e. estimated 37%). Successful regrowth of the foundation seagrass species appears to require crossing a minimum threshold of reintroduced individuals. Our study provides the first global field evidence for the requirement of a critical mass for recovery, which may also hold for other foundation species showing strong positive feedback to a dynamic environment. Synthesis and applications. For effective restoration of seagrass foundation species in its typically dynamic, stressful environment, introduction of large numbers is seen to be beneficial and probably serves two purposes. First, a large-scale planting

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.

Information to support to monitoring and habitat restoration on Ash Meadows National Wildlife Refuge

Science.gov (United States)

Scoppettone, G. Gary

2013-01-01

for monitoring native fish populations in relation to restoration efforts on the Ash Meadows National Wildlife Refuge. There are no precise records on conditions of each of the spring systems prior to anthropogenic alteration; however, fostering conditions that favor native over non-natives will be key to habitat restoration. Information regarding native species carbon source is needed to create habitat that favors native species, thus habitat restoration fostering food stuff consumed by native species should be considered in restoration efforts. In compiling data for the first part of this report, we tracked carbon source for native and non-native species at four stations along the Jackrabbit Spring system. Thus, we were able to contrast carbon source in warm- and cool-water habitats. Habitat in Jackrabbit Spring was improved for native fishes in 2007. The second paper in this report focuses on native fish populations in Jackrabbit Spring system pre- and post-restoration. Much of the Ash Meadows Oases is marsh habitat where non-native red swamp crayfish and western mosquitofish are often abundant, to the detriment of non-natives. Because marsh habitat is broadly represented in the Ash Meadows landscape, establishing marsh habitat most conducive to the native fishes is important to the restoration effort, and the third paper addresses marsh habitat type with the relative abundance of fishes and crayfish. There are previous years of monitoring Ash Meadows’ native fish populations, but not all monitoring occurred at the same time of year. Desert-fish populations sometimes undergo seasonal fluctuation, so it might not be valid to compare population trends using difference seasons. For report four, we tracked a closed population of Amargosa pupfish (Cyprinodon nevadensis) year round to track seasonal trends. Knowledge of seasonal trends is important in tracking changes of populations pre- and post-restoration.

Restoration of Tidal Flow to Impounded Salt Marsh Exerts Mixed Effect on Leaf Litter Decomposition

Science.gov (United States)

Henry, B. A.; Schade, J. D.; Foreman, K.

2015-12-01

Salt marsh impoundments (e.g. roads, levees) disconnect marshes from ocean tides, which impairs ecosystem services and often promotes invasive species. Numerous restoration projects now focus on removing impoundments. Leaf litter decomposition is a central process in salt marsh carbon and nutrient cycles, and this study investigated the extent to which marsh restoration alters litter decomposition rates. We considered three environmental factors that can potentially change during restoration: salinity, tidal regime, and dominant plant species. A one-month field experiment (Cape Cod, MA) measured decay of litter bags in impounded, restored, and natural marshes under ambient conditions. A two-week lab experiment measured litter decay in controlled incubations under experimental treatments for salinity (1ppt and 30 ppt), tidal regime (inundated and 12 hr wet-dry cycles), and plant species (native Spartina alterniflora and invasive Phragmites australis). S. alterniflora decomposed faster in situ than P. australis (14±1.0% mass loss versus 0.74±0.69%). Corroborating this difference in decomposition, S. alterniflora supported greater microbial respiration during lab incubation, measured as CO2 flux from leaf litter and biological oxygen demand of water containing leached organic matter (OM). However, nutrient analysis of plant tissue and leached OM show P. australis released more nitrogen than S. alterniflora. Low salinity treatments in both lab and field experiments decayed more rapidly than high salinity treatments, suggesting that salinity inhibited microbial activity. Manipulation of inundation regime did not affect decomposition. These findings suggest the reintroduction of tidal flow to an impounded salt marsh can have mixed effects; recolonization by the native cordgrass could supply labile OM to sediment and slow carbon sequestration, while an increase in salinity might inhibit decomposition and accelerate sequestration.

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...

Genetic diversity of wild and hatchery lake trout populations: Relevance for management and restoration in the Great Lakes

Science.gov (United States)

Page, K.S.; Scribner, K.T.; Burnham-Curtis, M.

2004-01-01

emphasize that the management of wild remnant lake trout populations and the restoration of extirpated populations should recognize and make greater use of the genetic diversity that still exists.

A systematic review of ecological attributes that confer resilience to climate change in environmental restoration.

Directory of Open Access Journals (Sweden)

Britta L Timpane-Padgham

Full Text Available Ecological restoration is widely practiced as a means of rehabilitating ecosystems and habitats that have been degraded or impaired through human use or other causes. Restoration practices now are confronted by climate change, which has the potential to influence long-term restoration outcomes. Concepts and attributes from the resilience literature can help improve restoration and monitoring efforts under changing climate conditions. We systematically examined the published literature on ecological resilience to identify biological, chemical, and physical attributes that confer resilience to climate change. We identified 45 attributes explicitly related to climate change and classified them as individual- (9, population- (6, community- (7, ecosystem- (7, or process-level attributes (16. Individual studies defined resilience as resistance to change or recovery from disturbance, and only a few studies explicitly included both concepts in their definition of resilience. We found that individual and population attributes generally are suited to species- or habitat-specific restoration actions and applicable at the population scale. Community attributes are better suited to habitat-specific restoration at the site scale, or system-wide restoration at the ecosystem scale. Ecosystem and process attributes vary considerably in their type and applicability. We summarize these relationships in a decision support table and provide three example applications to illustrate how these classifications can be used to prioritize climate change resilience attributes for specific restoration actions. We suggest that (1 including resilience as an explicit planning objective could increase the success of restoration projects, (2 considering the ecological context and focal scale of a restoration action is essential in choosing appropriate resilience attributes, and (3 certain ecological attributes, such as diversity and connectivity, are more commonly considered to

A systematic review of ecological attributes that confer resilience to climate change in environmental restoration.

Science.gov (United States)

Timpane-Padgham, Britta L; Beechie, Tim; Klinger, Terrie

2017-01-01

Ecological restoration is widely practiced as a means of rehabilitating ecosystems and habitats that have been degraded or impaired through human use or other causes. Restoration practices now are confronted by climate change, which has the potential to influence long-term restoration outcomes. Concepts and attributes from the resilience literature can help improve restoration and monitoring efforts under changing climate conditions. We systematically examined the published literature on ecological resilience to identify biological, chemical, and physical attributes that confer resilience to climate change. We identified 45 attributes explicitly related to climate change and classified them as individual- (9), population- (6), community- (7), ecosystem- (7), or process-level attributes (16). Individual studies defined resilience as resistance to change or recovery from disturbance, and only a few studies explicitly included both concepts in their definition of resilience. We found that individual and population attributes generally are suited to species- or habitat-specific restoration actions and applicable at the population scale. Community attributes are better suited to habitat-specific restoration at the site scale, or system-wide restoration at the ecosystem scale. Ecosystem and process attributes vary considerably in their type and applicability. We summarize these relationships in a decision support table and provide three example applications to illustrate how these classifications can be used to prioritize climate change resilience attributes for specific restoration actions. We suggest that (1) including resilience as an explicit planning objective could increase the success of restoration projects, (2) considering the ecological context and focal scale of a restoration action is essential in choosing appropriate resilience attributes, and (3) certain ecological attributes, such as diversity and connectivity, are more commonly considered to confer

Modeling the impacts of wetland restoration in former cranberry farms on nitrogen removal

Science.gov (United States)

In population-dense Massachusetts (USA) acquiring historical wetlands for ecological restoration efforts can be difficult and expensive. Retiring cranberry bogs create a rare opportunity to restore historical wetlands. Environmental managers face important decisions about how to ...

Landscape and vegetation effects on avian reproduction on bottomland forest restorations

Science.gov (United States)

Twedt, Daniel J.; Somershoe, Scott G.; Hazler, Kirsten R.; Cooper, Robert J.

2010-01-01

Forest restoration has been undertaken on >200,000 ha of agricultural land in the Mississippi Alluvial Valley, USA, during the past few decades. Decisions on where and how to restore bottomland forests are complex and dependent upon landowner objectives, but for conservation of silvicolous (forest-dwelling) birds, ecologists have espoused restoration through planting a diverse mix of densely spaced seedlings that includes fast-growing species. Application of this planting strategy on agricultural tracts that are adjacent to extant forest or within landscapes that are predominately forested has been advocated to increase forest area and enhance forested landscapes, thereby benefiting area-sensitive, silvicolous birds. We measured support for these hypothesized benefits through assessments of densities of breeding birds and reproductive success of 9 species on 36 bottomland forest restoration sites. Densities of thamnic (shrub-scrub dwelling) and silvicolous birds, such as yellow-breasted chat (Icteria virens), indigo bunting (Passerina cyanea), and white-eyed vireo (Vireo griseus) were positively associated with 1) taller trees, 2) greater stem densities, and 3) a greater proportion of forest within the landscape, whereas densities of birds associated with grasslands, such as dickcissel (Spiza americana) and red-winged blackbird (Agelaius phoeniceus), were negatively associated with these variables. Vegetation structure, habitat edge, and temporal effects had greater influence on nest success than did landscape effects. Taller trees, increased density of woody stems, greater vegetation density, and more forest within the landscape were often associated with greater nest success. Nest success of grassland birds was positively related to distance from forest edge but, for thamnic birds, success was greater near edges. Moreover, nest success and estimated fecundity of thamnic species suggested their populations are self-sustaining on forest restoration sites, whereas

Forest restoration, biodiversity and ecosystem functioning

Science.gov (United States)

2011-01-01

Globally, forests cover nearly one third of the land area and they contain over 80% of terrestrial biodiversity. Both the extent and quality of forest habitat continue to decrease and the associated loss of biodiversity jeopardizes forest ecosystem functioning and the ability of forests to provide ecosystem services. In the light of the increasing population pressure, it is of major importance not only to conserve, but also to restore forest ecosystems. Ecological restoration has recently started to adopt insights from the biodiversity-ecosystem functioning (BEF) perspective. Central is the focus on restoring the relation between biodiversity and ecosystem functioning. Here we provide an overview of important considerations related to forest restoration that can be inferred from this BEF-perspective. Restoring multiple forest functions requires multiple species. It is highly unlikely that species-poor plantations, which may be optimal for above-ground biomass production, will outperform species diverse assemblages for a combination of functions, including overall carbon storage and control over water and nutrient flows. Restoring stable forest functions also requires multiple species. In particular in the light of global climatic change scenarios, which predict more frequent extreme disturbances and climatic events, it is important to incorporate insights from the relation between biodiversity and stability of ecosystem functioning into forest restoration projects. Rather than focussing on species per se, focussing on functional diversity of tree species assemblages seems appropriate when selecting tree species for restoration. Finally, also plant genetic diversity and above - below-ground linkages should be considered during the restoration process, as these likely have prominent but until now poorly understood effects at the level of the ecosystem. The BEF-approach provides a useful framework to evaluate forest restoration in an ecosystem functioning context, but

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.

Restoration of areas degraded by alluvial sand mining: use of soil microbiological activity and plant biomass growth to assess evolution of restored riparian vegetation.

Science.gov (United States)

Venson, Graziela R; Marenzi, Rosemeri C; Almeida, Tito César M; Deschamps-Schmidt, Alexandre; Testolin, Renan C; Rörig, Leonardo R; Radetski, Claudemir M

2017-03-01

River or alluvial sand mining is causing a variety of environmental problems in the Itajaí-açú river basin in Santa Catarina State (south of Brazil). When this type of commercial activity degrades areas around rivers, environmental restoration programs need to be executed. In this context, the aim of this study was to assess the evolution of a restored riparian forest based on data on the soil microbial activity and plant biomass growth. A reference site and three sites with soil degradation were studied over a 3-year period. Five campaigns were performed to determine the hydrolysis of the soil enzyme fluorescein diacetate (FDA), and the biomass productivity was determined at the end of the studied period. The variation in the enzyme activity for the different campaigns at each site was low, but this parameter did differ significantly according to the site. Well-managed sites showed the highest biomass productivity, and this, in turn, showed a strong positive correlation with soil enzyme activity. In conclusion, soil enzyme activity could form the basis for monitoring and the early prediction of the success of vegetal restoration programs, since responses at the higher level of biological organization take longer, inhibiting the assessment of the project within an acceptable time frame.

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.

Science.gov (United States)

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

Microbial Genetic Memory to Study Heterogeneous Soil Processes

Science.gov (United States)

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.

Science.gov (United States)

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.

Microfluidics expanding the frontiers of microbial ecology.

Science.gov (United States)

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.

MARKET ANALYSIS AND MICROBIAL BIOPREPARATIONS CREATION FOR CROP GROWING IN UKRAINE

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MARKET ANALYSIS AND MICROBIAL BIOPREPARATIONS CREATION FOR CROP GROWING IN UKRAINE

2014-08-01

Full Text Available А microbial biopreparations, particularly for the leguminous, grains, industrial and other agricultural crops of Ukrainian as well as foreign production are analyzed. All biopreparations on the market of Ukraine may be divided into basic groups — growth-activating preparations, phytoprotective preparations, preparations for the accelerated decomposition of plant wastes, preparations for restoration and preservation of soil fertility (depending on the functional activity of a biological agent as well as info mono- and complex biopreparations (depending on the number of components within them. Approaches to the creation of complex biopreparations and compositions based on biological agents — microorganisms with agronomically valuable properties, fungi, algae, biologically active metabolites of plants and microorganisms as well as microelements in chelated forms are considered to solve the following key environmental goals: getting organic crop production, restoration and preservation of soil fertility. The results of original research on the complex compositions based on nodule bacteria, rhizobacteria, microorganisms — destructors of xenobiotics, microbial (exopolysaccharides, exometabolites and plant (phytolectins, extract of blue-green algae metabolites for growth of legumes and grain cultures are presented. It is established that the complex biopreparations and compositions have more effective and stable action as compared to monoculture. The examples of biopreparations of a new generation which are created using the innovative technologies such as IGET Technology (Induced Gene Expression Triggers, LHO-promoter (lipohitooligosaccharides-promoter technology, TOP-technology (technology osmoprotector involving achievements of molecular and cell biology, nanotechnology as well as the modern solid carriers, adhesives, lipkogenes, formularies that provide high titer of microbial cells in biopreparations, close contact the bacterial cells with

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

Science.gov (United States)

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.

Restoring habitat connectivity across roads: where to begin?

NARCIS (Netherlands)

Grift, van der E.A.; Reijnen, R.; Veen, van der M.; Pelk, M.

2002-01-01

A study of the potential effect of migration measures on the viability of wildlife populations to prioritize the construction of wildlife passages and the restoration of habitat connectivity across roads in The Netherlands.

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

Science.gov (United States)

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.

PCB126 modulates fecal microbial fermentation of the dietary fiber inulin

Science.gov (United States)

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...

Pacific Lamprey Research and Restoration Project : Annual Report 2001.

Energy Technology Data Exchange (ETDEWEB)

Close, David A.

2002-11-01

Pacific lamprey (Lampetra tridentata) has significantly declined along the Oregon coast and in the Columbia River Basin (Downey et al. 1993; Close and Jackson 2001). Declines in adults can be partially attributed to hydroelectric dams, which have impeded passage of adult Pacific lamprey in the Columbia and Snake rivers, thus effecting larval recruitment in the basin. Adult pacific lamprey also declined in numbers in the Umatilla River, a tributary of the Columbia River. In addition to hydro power dams in the Columbia River, habitat alterations and chemical treatments have been involved in the collapse of Pacific lamprey populations in the Umatilla River. To initiate the restoration effort, CTUIR began developing a restoration plan in 1998. The goal of the lamprey research and restoration project is to restore natural production of Pacific lampreys in the Umatilla River to self-sustaining and harvestable level. This report is summarizing the studies and restoration efforts concluded in 2001.

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

Directory of Open Access Journals (Sweden)

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.

Restoring monarch butterfly habitat in the Midwestern US: ‘all hands on deck’

Science.gov (United States)

Thogmartin, Wayne E.; López-Hoffman, Laura; Rohweder, Jason; Diffendorfer, Jay; Drum, Ryan; Semmens, Darius; Black, Scott; Caldwell, Iris; Cotter, Donita; Drobney, Pauline; Jackson, Laura L.; Gale, Michael; Helmers, Doug; Hilburger, Steve; Howard, Elizabeth; Oberhauser, Karen; Pleasants, John; Semmens, Brice; Taylor, Orley; Ward, Patrick; Weltzin, Jake F.; Wiederholt, Ruscena

2017-07-01

The eastern migratory population of monarch butterflies (Danaus plexippus plexippus) has declined by >80% within the last two decades. One possible cause of this decline is the loss of ≥1.3 billion stems of milkweed (Asclepias spp.), which monarchs require for reproduction. In an effort to restore monarchs to a population goal established by the US Fish and Wildlife Service and adopted by Mexico, Canada, and the US, we developed scenarios for amending the Midwestern US landscape with milkweed. Scenarios for milkweed restoration were developed for protected area grasslands, Conservation Reserve Program land, powerline, rail and roadside rights of way, urban/suburban lands, and land in agricultural production. Agricultural land was further divided into productive and marginal cropland. We elicited expert opinion as to the biological potential (in stems per acre) for lands in these individual sectors to support milkweed restoration and the likely adoption (probability) of management practices necessary for affecting restoration. Sixteen of 218 scenarios we developed for restoring milkweed to the Midwestern US were at levels (>1.3 billion new stems) necessary to reach the monarch population goal. One of these scenarios would convert all marginal agriculture to conserved status. The other 15 scenarios converted half of marginal agriculture (730 million stems), with remaining stems contributed by other societal sectors. Scenarios without substantive agricultural participation were insufficient for attaining the population goal. Agricultural lands are essential to reaching restoration targets because they occupy 77% of all potential monarch habitat. Barring fundamental changes to policy, innovative application of economic tools such as habitat exchanges may provide sufficient resources to tip the balance of the agro-ecological landscape toward a setting conducive to both robust agricultural production and reduced imperilment of the migratory monarch butterfly.

Mathematical modeling of microbial growth in milk

Directory of Open Access Journals (Sweden)

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

Digital collection of aerial photographs from the Common Murre Restoration Project, 1996 (NODC Accession 0015544)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — The Common Murre Restoration Project is a comprehensive seabird restoration effort aimed at enhancing depleted seabird populations in central California,...

Digital collection of aerial photographs from the Common Murre Restoration Project, 1997 (NODC Accession 0037159)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — The Common Murre Restoration Project is a comprehensive seabird restoration effort aimed at enhancing depleted seabird populations in central California,...

Digital collection of aerial photographs from the Common Murre Restoration Project, 2005 (NODC Accession 0057025)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — The Common Murre Restoration Project is a comprehensive seabird restoration effort aimed at enhancing depleted seabird populations in central California,...

Digital collection of aerial photographs from the Common Murre Restoration Project, 1998 (NODC Accession 0037160)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — The Common Murre Restoration Project is a comprehensive seabird restoration effort aimed at enhancing depleted seabird populations in central California,...

Digital collection of aerial photographs from the Common Murre Restoration Project, 2006 (NODC Accession 0058096)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — The Common Murre Restoration Project is a comprehensive seabird restoration effort aimed at enhancing depleted seabird populations in central California,...

The conservation and restoration of wild bees.

Science.gov (United States)

Winfree, Rachael

2010-05-01

Bees pollinate most of the world's wild plant species and provide economically valuable pollination services to crops; yet knowledge of bee conservation biology lags far behind other taxa such as vertebrates and plants. There are few long-term data on bee populations, which makes their conservation status difficult to assess. The best-studied groups are the genus Bombus (the bumble bees), and bees in the EU generally; both of these are clearly declining. However, it is not known to what extent these groups represent the approximately 20,000 species of bees globally. As is the case for insects in general, bees are underrepresented in conservation planning and protection efforts. For example, only two bee species are on the global IUCN Red List, and no bee is listed under the U.S. Endangered Species Act, even though many bee species are known to be in steep decline or possibly extinct. At present, bee restoration occurs mainly in agricultural contexts, funded by government programs such as agri-environment schemes (EU) and the Farm Bill (USA). This is a promising approach given that many bee species can use human-disturbed habitats, and bees provide valuable pollination services to crops. However, agricultural restorations only benefit species that persist in agricultural landscapes, and they are more expensive than preserving natural habitat elsewhere. Furthermore, such restorations benefit bees in only about half of studied cases. More research is greatly needed in many areas of bee conservation, including basic population biology, bee restoration in nonagricultural contexts, and the identification of disturbance-sensitive bee species.

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

Science.gov (United States)

Saad, Sainab; Bhatnagar, Srijak; Tegetmeyer, Halina E; Geelhoed, Jeanine S; Strous, Marc; Ruff, S Emil

2017-12-01

For the anaerobic remineralization of organic matter in marine sediments, sulfate reduction coupled to fermentation plays a key role. Here, we enriched sulfate-reducing/fermentative communities from intertidal sediments under defined conditions in continuous culture. We transiently exposed the cultures to oxygen or nitrate twice daily and investigated the community response. Chemical measurements, provisional genomes and transcriptomic profiles revealed trophic networks of microbial populations. Sulfate reducers coexisted with facultative nitrate reducers or aerobes enabling the community to adjust to nitrate or oxygen pulses. Exposure to oxygen and nitrate impacted the community structure, but did not suppress fermentation or sulfate reduction as community functions, highlighting their stability under dynamic conditions. The most abundant sulfate reducer in all cultures, related to Desulfotignum balticum, appeared to have coupled both acetate- and hydrogen oxidation to sulfate reduction. We describe a novel representative of the widespread uncultured candidate phylum Fermentibacteria (formerly candidate division Hyd24-12). For this strictly anaerobic, obligate fermentative bacterium, we propose the name ' U Sabulitectum silens' and identify it as a partner of sulfate reducers in marine sediments. Overall, we provide insights into the function of fermentative, as well as sulfate-reducing microbial communities and their adaptation to a dynamic environment. © 2017 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

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

A preliminary identification of Rf*-A619, a novel restorer gene for CMS-C in maize (Zea mays L.).

Science.gov (United States)

Yongming, Liu; Zhuofan, Zhao; Yanli, Lu; Chuan, Li; Jing, Wang; Boxiao, Dong; Bing, Liang; Tao, Qiu; Wenbing, Zeng; Moju, Cao

2016-01-01

C-type cytoplasmic male sterility (CMS-C) is widely utilized for hybrid maize seed production. However, genetic mechanisms underlying the fertility restoration are very complicated. At present, there is a divergence on the number of fertility restorer genes in maize inbred line A619 for CMS-C. To further elucidate the restoring mechanism of A619, we used genetic analysis and molecular markers to confirm the restorer genes of maize inbred line A619 for C-type male sterile line C48-2 in this study. Firstly, the fertility segregations of (C48-2 × A619)F 2 populations were investigated under three environments during 2013-2015. The segregation ratio of fertile and sterile plants in the F 2 population fit to 15:1 via chi-square test and this result suggested that there are two dominant restorer genes in A619 for CMS-C, i.e., Rf4 and a novel gene named Rf*-A619 . Next, based on the sequence differences between Rf4 and its recessive allelic rf4 , a novel dominant marker F2/R2 was developed and validated to genotyping Rf4 in the F 2 population. Through genotypic analysis, we found that there were a certain amount of fertile individuals without Rf4 which accounted for 3/16 in the F 2 population via chi-square test at the 0.05 level. These results provided another proof to sustain that the inbred line A619 contains one additional restorer gene for CMS-C fertility restoration except Rf4 . At last, we used one SSR marker which is tightly linked with the dominant restorer gene Rf5 to analyze those fertile plants without Rf4 in the F 2 population. The PCR amplification results showed that Rf*-A619 is not allelic to Rf5 but a novel restorer gene for CMS-C. These results not only provide a basis for the mapping and characterization of a novel restorer gene but also give a new insight into the mechanism of CMS-C fertility restoration.

[Genetics of fertility restoration in the isocytoplasm allonuclear C-group of cytoplasmic male sterility in maize].

Science.gov (United States)

Zhao, Zhuo Fan; Huang, Ling; Liu, Yong Ming; Zhang, Peng; Wei, Gui; Cao, Mo Ju

2018-05-20

Maize is one of the first crops to produce hybrids using cytoplasmic male sterile lines. The C-type cytoplasmic male sterile (CMS-C) line is vital for hybrid seed production, and the fertility-restoration reaction along with its stability has a direct bearing on its applications. However, fertility restoration mechanism of CMS-C is complex and is still not clear so far. To further explore the factors affecting the fertility restoration of maize CMS, a series of test crosses were carried out by pollinating the isocytoplasm allonuclear CMS-C lines C48-2, Chuangzaosi and C478 with the test lines 18 bai, zi 330, 5022 and the restorer line A619, respectively. Four F 2 populations and six double-cross combinations were obtained from the self-cross of fertility restored F 1 and pollinating male-sterility-maintained F 1 with the male-fertility-restored F 1 , respectively. Meanwhile, we developed the incomplete diallel-cross combinations using the isocytoplasm allonuclear male sterile lines as maternal parents and their respective maintainer lines 48-2, huangzaosi and 478 as paternal parents. All the F 1 , F 2 and double-cross populations were planted at distinct locations in different years, and the fertility-restoration reaction was scored by field investigation and pollen staining with I 2 -IK. The results were as follows: 1) The same test line could restore the CMS-C line at a certain genetic background, but failed to restore the CMS-C line at the other genetic backgrounds, suggesting that the genetic background of CMS-C lines plays an important role in the fertility restoration. 2) The fertile-to-sterile segregation ratio of (C48-2×A619) F 2 population planted in both Sichuan and Yunnan fited well to 15:1 by the χ 2 test. However, the fertility level of individuals in Yunnan mainly belonged to the 3 and 4grades, but which in Sichuan mainly belonged to the 5 grade, indicating the environmental factors had effect on the fertility-restoration reaction of (C48-2×A619) F

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.

Linking restoration ecology with coastal dune restoration

Science.gov (United States)

Lithgow, D.; Martínez, M. L.; Gallego-Fernández, J. B.; Hesp, P. A.; Flores, P.; Gachuz, S.; Rodríguez-Revelo, N.; Jiménez-Orocio, O.; Mendoza-González, G.; Álvarez-Molina, L. L.

2013-10-01

Restoration and preservation of coastal dunes is urgently needed because of the increasingly rapid loss and degradation of these ecosystems because of many human activities. These activities alter natural processes and coastal dynamics, eliminate topographic variability, fragment, degrade or eliminate habitats, reduce diversity and threaten endemic species. The actions of coastal dune restoration that are already taking place span contrasting activities that range from revegetating and stabilizing the mobile substrate, to removing plant cover and increasing substrate mobility. Our goal was to review how the relative progress of the actions of coastal dune restoration has been assessed, according to the ecosystem attributes outlined by the Society of Ecological Restoration: namely, integrity, health and sustainability and that are derived from the ecological theory of succession. We reviewed the peer reviewed literature published since 1988 that is listed in the ISI Web of Science journals as well as additional references, such as key books. We exclusively focused on large coastal dune systems (such as transgressive and parabolic dunefields) located on natural or seminatural coasts. We found 150 articles that included "coastal dune", "restoration" and "revegetation" in areas such as title, keywords and abstract. From these, 67 dealt specifically with coastal dune restoration. Most of the studies were performed in the USA, The Netherlands and South Africa, during the last two decades. Restoration success has been assessed directly and indirectly by measuring one or a few ecosystem variables. Some ecosystem attributes have been monitored more frequently (ecosystem integrity) than others (ecosystem health and sustainability). Finally, it is important to consider that ecological succession is a desirable approach in restoration actions. Natural dynamics and disturbances should be considered as part of the restored system, to improve ecosystem integrity, health and

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

Where to restore ecological connectivity? Detecting barriers and quantifying restoration benefits.

Directory of Open Access Journals (Sweden)

Brad H McRae

Full Text Available Landscape connectivity is crucial for many ecological processes, including dispersal, gene flow, demographic rescue, and movement in response to climate change. As a result, governmental and non-governmental organizations are focusing efforts to map and conserve areas that facilitate movement to maintain population connectivity and promote climate adaptation. In contrast, little focus has been placed on identifying barriers-landscape features which impede movement between ecologically important areas-where restoration could most improve connectivity. Yet knowing where barriers most strongly reduce connectivity can complement traditional analyses aimed at mapping best movement routes. We introduce a novel method to detect important barriers and provide example applications. Our method uses GIS neighborhood analyses in conjunction with effective distance analyses to detect barriers that, if removed, would significantly improve connectivity. Applicable in least-cost, circuit-theoretic, and simulation modeling frameworks, the method detects both complete (impermeable barriers and those that impede but do not completely block movement. Barrier mapping complements corridor mapping by broadening the range of connectivity conservation alternatives available to practitioners. The method can help practitioners move beyond maintaining currently important areas to restoring and enhancing connectivity through active barrier removal. It can inform decisions on trade-offs between restoration and protection; for example, purchasing an intact corridor may be substantially more costly than restoring a barrier that blocks an alternative corridor. And it extends the concept of centrality to barriers, highlighting areas that most diminish connectivity across broad networks. Identifying which modeled barriers have the greatest impact can also help prioritize error checking of land cover data and collection of field data to improve connectivity maps. Barrier detection

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...

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.

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.

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

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.

A Valuation of the Restoration of Hwangnyongsa Temple in South Korea

Directory of Open Access Journals (Sweden)

Ju-Hee Kim

2018-01-01

Full Text Available Hwangnyongsa Temple (HT in South Korea belongs to the Gyeongju Historic Areas, designated as a UNESCO World Heritage Site in 2000. The temple was destroyed by fire in AD 1238 and today there are few traces left, however the government is seeking to restore HT. This paper aims to evaluate the economic benefits of the restoration using contingent valuation (CV, and to then perform a cost-benefit analysis of the restoration. For this purpose, people’s willingness to pay (WTP for the restoration is elicited from a survey of 1000 households. The average household’s WTP is estimated as KRW 2341 (USD 2.07 per annum. The current values of the benefits and costs of the restoration computed for the relevant period and population are KRW 415.3 billion (USD 366.9 million and KRW 232.2 billion (USD 205.1 million, respectively. As the former is more than the latter, the restoration is socially profitable.

Lower Red River Meadow Stream Restoration Project

International Nuclear Information System (INIS)

1996-05-01

As part of a continuing effort to restore anadromous fish populations in the South Fork Clearwater River basin of Idaho, Bonneville Power Administration (BPA) proposes to fund the Lower Red River Meadow Restoration Project (Project). The Project is a cooperative effort with the Idaho Soil and Water Conservation District, Nez Perce National Forest, Idaho Department of Fish and Game (IDFG), and the Nez Perce Tribe of Idaho. The proposed action would allow the sponsors to perform stream bank stabilization, aquatic and riparian habitat improvement activities on IDFG's Red River Management Area and to secure long-term conservation contracts or agreements for conducting streambank and habitat improvement activities with participating private landowners located in the Idaho County, Idaho, study area. This preliminary Environmental Assessment (EA) examines the potential environmental effects of stabilizing the stream channel, restoring juvenile fish rearing habitat and reestablishing a riparian shrub community along the stream

Pacific Lamprey Research and Restoration Project, Annual Report 2002.

Energy Technology Data Exchange (ETDEWEB)

Close, David; Aronsuu, Kimmo; Jackson, Aaron

2003-07-01

Pacific lamprey (Lampetra tridentata) has significantly declined along the Oregon coast and in the Columbia River Basin (Downey et al. 1993, Close and Jackson 2001). Declines in adults can be partially attributed to hydroelectric dams, which have impeded passage of adult Pacific lamprey in the Columbia and Snake rivers (Moser et al. 2002), thus effecting larval recruitment in the basin (Moser and Close in press). Adult Pacific lamprey also declined in numbers in the Umatilla River, a tributary of the Columbia River (Close and Jackson 2001). In addition to hydro power dams in the Columbia River, habitat alterations and chemical treatments have been involved in the collapse of Pacific lamprey populations in the Umatilla River (Close 1999). To initiate the restoration effort, CTUIR began developing a restoration plan in 1998. The goal of the lamprey research and restoration project is to restore natural production of Pacific lampreys in the Umatilla River to self-sustaining and harvestable level. This report is summarizing the studies and restoration efforts concluded in 2002.

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

Clinical outcome of root caries restorations using ART and rotary techniques in institutionalized elders

Directory of Open Access Journals (Sweden)

Alberto Carlos CRUZ GONZALEZ

2016-01-01

Full Text Available Abstract The aim of this study was to compare the clinical performance of root caries restorations after a six-month period using two methods, a conventional technique with rotary instruments and an atraumatic restorative technique (ART, in an institutionalized elderly population in the city of Bogotá, Colombia. Root caries represents a multifactorial, progressive, chronic lesion with softened, irregular and darkened tissue involving the radicular surface; it is highly prevalent in the elderly, especially in those who are physically or cognitively impaired. A quasi-experimental, double-blind, longitudinal study was carried out after cluster randomization of the sample. Two different experienced dentists, previously trained, performed the restorations using each technique. After six months, two new investigators performed a blind evaluation of the condition of the restorations. The results showed a significantly higher rate of success (92.9% using the conventional technique (p < 0.03. However, we concluded that ART may have been the preferred technique in the study population because 81% of those restorations survived or were successful during the observation period.

Use of microorganisms to improve the cementation of granular structures. Applications in the restoration of monuments

Science.gov (United States)

González, Isabel; Mayoral, Eduardo; Ortiz, Pilar; Segura, Dolores; Vazquez, Auxiliadora; Barba, Cinta; Ortiz, Rocio; Romero, Antonio

2015-04-01

This researching work focuses on the development of new procedures to be applied in heritage rehabilitation, through the implementation of low-cost biotechnological processes in the realm of engineering and architecture. In doing so, it explores the possibilities of MICP (Microbially Induced Calcite Precipitation), which is a biomineralization process applied to improve the engineering properties of granular structures. This is a novelty approach at present, as there are few researches putting together knowledge in biotechnology and mineralogy to by applied in architecture and engineer. Some authors propose the bacteria use to generate habitable structures that reduce desertification (Magnus Larsson 2008). Innovative research teams led by De Jong and the University of California UC Davis (XXXX) study how cement or stabilize soils to prevent landslides, improving the foundation injecting populations of Bacillus pasteurii in the field. Bacterially induced mineralization has emerged as a method for protecting and consolidating decayed ornamental stone, which offers noticeable advantages compared to traditional restoration procedures (Tiano et al., 1999). Castanier et al. (2000) found that Bacillus cereus was able to induce extracellular precipitation of calcium carbonate on decayed limestones. Rodriguez-Navarro et al. (2003) tested the ability of Myxococcus xanthus to induce calcium carbonate precipitation. Current studies are evaluating the potential of bacteria as self-healing agents for the autonomous decrease of permeability of concrete upon crack formation (De Muynck, et al 2010) In the urban area of Seville, most historical buildings are constructed with calcarenites, limestones, sandstones and bricks, the weathering forms associated to this building materials often are granular disintegration, so the proposed technology has a huge potential to be applied to these materials for possible restoration. This research is mainly grounded on laboratory work, which

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.

A preliminary identification of Rf*-A619, a novel restorer gene for CMS-C in maize (Zea mays L.

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Liu Yongming

2016-11-01

Full Text Available C-type cytoplasmic male sterility (CMS-C is widely utilized for hybrid maize seed production. However, genetic mechanisms underlying the fertility restoration are very complicated. At present, there is a divergence on the number of fertility restorer genes in maize inbred line A619 for CMS-C. To further elucidate the restoring mechanism of A619, we used genetic analysis and molecular markers to confirm the restorer genes of maize inbred line A619 for C-type male sterile line C48-2 in this study. Firstly, the fertility segregations of (C48-2 × A619F2 populations were investigated under three environments during 2013–2015. The segregation ratio of fertile and sterile plants in the F2 population fit to 15:1 via chi-square test and this result suggested that there are two dominant restorer genes in A619 for CMS-C, i.e., Rf4 and a novel gene named Rf*-A619. Next, based on the sequence differences between Rf4 and its recessive allelic rf4, a novel dominant marker F2/R2 was developed and validated to genotyping Rf4 in the F2 population. Through genotypic analysis, we found that there were a certain amount of fertile individuals without Rf4 which accounted for 3/16 in the F2 population via chi-square test at the 0.05 level. These results provided another proof to sustain that the inbred line A619 contains one additional restorer gene for CMS-C fertility restoration except Rf4. At last, we used one SSR marker which is tightly linked with the dominant restorer gene Rf5 to analyze those fertile plants without Rf4 in the F2 population. The PCR amplification results showed that Rf*-A619 is not allelic to Rf5 but a novel restorer gene for CMS-C. These results not only provide a basis for the mapping and characterization of a novel restorer gene but also give a new insight into the mechanism of CMS-C fertility restoration.

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

Exposures to thoracic particulate matter, endotoxin, and glucan during post-Hurricane Katrina restoration work, New Orleans 2005-2012.

Science.gov (United States)

Rando, Roy J; Kwon, Cheol-Woong; Lefante, John J

2014-01-01

In the aftermath of Hurricane Katrina, which devastated the city of New Orleans in August 2005, restoration workers were at risk for respiratory illness from exposure to airborne particles and microbial agents. In support of an epidemiologic investigation of this risk, an exposure assessment for restoration work activities (demolition, trash & debris management, landscape restoration, sewer/waterline repair, and mold remediation) was performed from 2005 to 2012. For 2005 and 2006, Occupational Safety and Health Administration (OSHA) data (n = 730) for personal and area monitoring of total and respirable dust exposures of restoration workers were accessed and analyzed. The most significant exposures were for demolition work, with average respirable dust exposures in 2005 above the action level of 2.5 mg/m(3) and 17.6% of exposures exceeding the permissible exposure limit (PEL) (5 mg/m(3)). Additional personal and area monitoring for thoracic particulate matter was performed from 2007 to 2012 (n = 774) and samples were assayed for endotoxin and (1→3, 1→6)-β-D-glucan (n = 202). In order to integrate the OSHA data with the later monitoring data, three independent predictive models were developed to convert total and respirable dust measures into the equivalent thoracic dust. The three models were not statistically different and the modeling results were in good agreement with an overall coefficient of variation of 16% for the thoracic dust means across work activities estimated by each of the three models. Overall, thoracic dust exposure levels decreased by about an order of magnitude within the first year after Katrina and then more gradually declined and stabilized through 2012. Estimated average exposures to endotoxin and microbial glucan in 2005 were as high as 256 EU/m(3) and 118 μg/m(3), respectively, and likewise were seen to decrease dramatically and stabilize after 2005. The results of this exposure assessment support previously published reports of

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.

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

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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.

Assessing Genetic Diversity after Mangrove Restoration in Brazil: Why Is It So Important?

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Renan Granado

2018-04-01

Full Text Available Vital for many marine and terrestrial species, and several other environmental services, such as carbon sink areas, the mangrove ecosystem is highly threatened due to the proximity of large urban centers and climate change. The forced fragmentation of this ecosystem affects the genetic diversity distribution among natural populations. Moreover, while restoration efforts have increased, few studies have analyzed how recently-planted areas impact the original mangrove genetic diversity. We analyzed the genetic diversity of two mangroves species (Laguncularia racemosa and Avicennia schaueriana in three areas in Brazil, using inter-simple sequence repeat (ISSR markers. Using the local approach, we identified the genetic diversity pool of a restored area compared to nearby areas, including the remnant plants inside the restored area, one well-conserved population at the shore of Guanabara Bay, and one impacted population in Araçá Bay. The results for L. racemosa showed that the introduced population has lost genetic diversity by drift, but remnant plants with high genetic diversity or incoming propagules could help improve overall genetic diversity. Avicennia schaueriana showed similar genetic diversity, indicating an efficient gene flow. The principal component analysis showing different connections between both species indicate differences in gene flow and dispersal efficiencies, highlighting the needed for further studies. Our results emphasize that genetic diversity knowledge and monitoring associated with restoration actions can help avoid bottlenecks and other pitfalls, especially for the mangrove ecosystem.

Contrasting the roles of section length and instream habitat enhancement for river restoration success

NARCIS (Netherlands)

Hering, Daniel; Aroviita, Jukka; Baattrup-Pedersen, Annette; Brabec, Karel; Buijse, Tom; Ecke, Frauke; Friberg, Nikolai; Gielczewski, Marek; Januschke, Kathrin; Köhler, Jan; Kupilas, Benjamin; Lorenz, Armin W.; Muhar, Susanne; Paillex, Amael; Poppe, Michaela; Schmidt, Torsten; Schmutz, Stefan; Vermaat, Jan; Verdonschot, Piet F.M.; Verdonschot, Ralf C.M.; Wolter, Christian; Kail, Jochem

2015-01-01

Restoration of river hydromorphology often has limited detected effects on river biota. One frequently discussed reason is that the restored river length is insufficient to allow populations to develop and give the room for geomorphological processes to occur. We investigated ten pairs of

Clinical decisions for anterior restorations: the concept of restorative volume.

Science.gov (United States)

Cardoso, Jorge André; Almeida, Paulo Júlio; Fischer, Alex; Phaxay, Somano Luang

2012-12-01

The choice of the most appropriate restoration for anterior teeth is often a difficult decision. Numerous clinical and technical factors play an important role in selecting the treatment option that best suits the patient and the restorative team. Experienced clinicians have developed decision processes that are often more complex than may seem. Less experienced professionals may find difficulties making treatment decisions because of the widely varied restorative materials available and often numerous similar products offered by different manufacturers. The authors reviewed available evidence and integrated their clinical experience to select relevant factors that could provide a logical and practical guideline for restorative decisions in anterior teeth. The presented concept of restorative volume is based on structural, optical, and periodontal factors. Each of these factors will influence the short- and long-term behavior of restorations in terms of esthetics, biology, and function. Despite the marked evolution of esthetic restorative techniques and materials, significant limitations still exist, which should be addressed by researchers. The presented guidelines must be regarded as a mere orientation for risk analysis. A comprehensive individual approach should always be the core of restorative esthetic treatments. The complex decision process for anterior esthetic restorations can be clarified by a systematized examination of structural, optical, and periodontal factors. The basis for the proposed thought process is the concept of restorative volume that is a contemporary interpretation of restoration categories and their application. © 2012 Wiley Periodicals, Inc.

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

Directory of Open Access Journals (Sweden)

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.

Soil microbial activity in Aleppo pine stands naturally regenerated after fire: silvicultural management and induced drought

Directory of Open Access Journals (Sweden)

D. Moya

2013-01-01

Full Text Available In post-fire restoration, early monitoring is mandatory to check impacts and ecosystem responses to apply proper management according to social standards and ecological conditions. In areas where the natural regeneration was successful, excessive tree density can be found which induces to high intraspecific competence and assisted restoration management could be adequate. In addition, climatic changes will have large impacts on vegetation productivity and resilience since the regional models for south-eastern Spain predicts a rainfall decrease of about 20% and temperature increase of 4.5 ºC. The microbial biomass could be used as indicator of ecosystem recovery, since it is negatively affected by wildfires and depends on fire characteristics, vegetation and soil properties. Our aim is to determine how forest management may affect the ecosystem recovery in different climatic scenarios, included drought scenarios with and without forest management (thinning.We compared soil physicochemical properties and microbial activity in four scenarios: unmanaged and thinned stands in two rainfall scenarios (under induced drought. The study areas were set close to Yeste (Albacete where Aleppo pine forest were burned in summer 1994 (nearly 14000 ha. We set sixteen rectangular plots (150 m2; 15 m ×10 m implementing experimental silvicultural treatments: thinning eight plots in 2004, reducing the naturally recovered tree density from about 12000 to 1600 pine trees ha-1. In addition, in half the plots, we induced drought conditions from about 500 to 400 mm (20% from March 2009. In every plot, we monitored temperature at ground level (Ts, 10 cm depth (T10d and soil relative humidity (RH. Taking into account season of the year and canopy coverage, we collected soil samples in mid-winter (ending January 2011 and mid-spring (ending May 2011 under pine trees and in bare soil. The soil samples were used to evaluate soil physicochemical properties and soil microbial

Soil Organic Carbon Fractions and Stocks Respond to Restoration Measures in Degraded Lands by Water Erosion

Science.gov (United States)

Nie, Xiaodong; Li, Zhongwu; Huang, Jinquan; Huang, Bin; Xiao, Haibing; Zeng, Guangming

2017-05-01

Assessing the degree to which degraded soils can be recovered is essential for evaluating the effects of adopted restoration measures. The objective of this study was to determine the restoration of soil organic carbon under the impact of terracing and reforestation. A small watershed with four typical restored plots (terracing and reforestation (four different local plants)) and two reference plots (slope land with natural forest (carbon-depleted) and abandoned depositional land (carbon-enriched)) in subtropical China was studied. The results showed that soil organic carbon, dissolved organic carbon and microbial biomass carbon concentrations in the surface soil (10 cm) of restored lands were close to that in abandoned depositional land and higher than that in natural forest land. There was no significant difference in soil organic carbon content among different topographic positions of the restored lands. Furthermore, the soil organic carbon stocks in the upper 60 cm soils of restored lands, which were varied between 50.08 and 62.21 Mg C ha-1, were higher than 45.90 Mg C ha-1 in natural forest land. Our results indicated that the terracing and reforestation could greatly increase carbon sequestration and accumulation and decrease carbon loss induced by water erosion. And the combination measures can accelerate the restoration of degraded soils when compared to natural forest only. Forest species almost have no impact on the total amount of soil organic carbon during restoration processes, but can significantly influence the activity and stability of soil organic carbon. Combination measures which can provide suitable topography and continuous soil organic carbon supply could be considered in treating degraded soils caused by water erosion.

Soil Organic Carbon Fractions and Stocks Respond to Restoration Measures in Degraded Lands by Water Erosion.

Science.gov (United States)

Nie, Xiaodong; Li, Zhongwu; Huang, Jinquan; Huang, Bin; Xiao, Haibing; Zeng, Guangming

2017-05-01

Assessing the degree to which degraded soils can be recovered is essential for evaluating the effects of adopted restoration measures. The objective of this study was to determine the restoration of soil organic carbon under the impact of terracing and reforestation. A small watershed with four typical restored plots (terracing and reforestation (four different local plants)) and two reference plots (slope land with natural forest (carbon-depleted) and abandoned depositional land (carbon-enriched)) in subtropical China was studied. The results showed that soil organic carbon, dissolved organic carbon and microbial biomass carbon concentrations in the surface soil (10 cm) of restored lands were close to that in abandoned depositional land and higher than that in natural forest land. There was no significant difference in soil organic carbon content among different topographic positions of the restored lands. Furthermore, the soil organic carbon stocks in the upper 60 cm soils of restored lands, which were varied between 50.08 and 62.21 Mg C ha -1 , were higher than 45.90 Mg C ha -1 in natural forest land. Our results indicated that the terracing and reforestation could greatly increase carbon sequestration and accumulation and decrease carbon loss induced by water erosion. And the combination measures can accelerate the restoration of degraded soils when compared to natural forest only. Forest species almost have no impact on the total amount of soil organic carbon during restoration processes, but can significantly influence the activity and stability of soil organic carbon. Combination measures which can provide suitable topography and continuous soil organic carbon supply could be considered in treating degraded soils caused by water erosion.

Assessment of manual restorative treatment (MRT) with amalgam in high-caries Filipino children: results after 2 years.

Science.gov (United States)

Monse-Schneider, B; Heinrich-Weltzien, R; Schug, D; Sheiham, A; Borutta, A

2003-04-01

The atraumatic restorative treatment (ART), using only hand instruments and glass-ionomer cement as adhesive material is recommended for restorative dental treatment in disadvantaged communities lacking electricity and sophisticated dental equipment. Research is required on more durable restorative materials appropriate for populations with high-caries experience. The aim of the study was to evaluate, under field conditions, the applicability and effectiveness of an encapsulated amalgam as restorative material in ART prepared cavities in permanent teeth of children with high-caries rates. As the definition of ART restricts the manual treatment to adhesive materials the approach used is called the manual restorative treatment (MRT). Two dentists and two trained healthcare workers, using hand instruments and an encapsulated amalgam that was mixed with a manually driven triturator, placed a total of 934 restorations in the permanent dentition in 466 children. Due to irregular school attendance of Filipino children only 611 restorations could be evaluated by one independent dentist. The average age at reassessment of restorations was 27 +/- 4.5 months. 93.3% of the restorations were acceptable. The failure rate of occlusal surface restorations was 5.6% compared with 13.6% of buccal surface fillings. The survival rate of large occlusal restorations was 95.1% compared with 93.7% for small restorations. The survival of MRT restorations was not influenced by the experience and professional level of the operator. Amalgam is a suitable MRT material, especially for extensive occlusal lesions in high-caries populations. Studies of longer duration are needed to confirm this finding.

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.

Potential ?Ecological Traps? of Restored Landscapes: Koalas Phascolarctos cinereus Re-Occupy a Rehabilitated Mine Site

OpenAIRE

Cristescu, Romane H.; Banks, Peter B.; Carrick, Frank N.; Fr?re, C?line

2013-01-01

With progressively increasing anthropogenic habitat disturbances, restoration of impacted landscapes is becoming a critical element of biodiversity conservation. Evaluation of success in restoration ecology rarely includes faunal components, usually only encompassing abiotic and floral components of the ecosystems. Even when fauna is explicitly included, it is usually only species presence/absence criteria that are considered. If restoration is to have a positive outcome, however, populations...

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.

Effect of calcium cyanamide, ammonium bicarbonate and lime mixture, and ammonia water on survival of Ralstonia solanacearum and microbial community

Science.gov (United States)

Liu, Lijuan; Sun, Chengliang; Liu, Xingxing; He, Xiaolin; Liu, Miao; Wu, Hao; Tang, Caixian; Jin, Chongwei; Zhang, Yongsong

2016-01-01

The inorganic nitrogenous amendments calcium cyanamide (CC), ammonia water (AW), and a mixture of ammonium bicarbonate with lime (A+L) are popularly used as fumigants to control soil-borne disease in China. However, it is unclear which of these fumigants is more effective in controlling R. solanacearum. This present study compared the efficiencies of the three nitrogenous amendments listed above at four nitrogen levels in suppressing the survival of R. solanacearum in soil. The CC showed the best ability to suppress R. solanacearum due to its highest capacity to increase soil and NO2− contents and pH. However, AW was more suitable to controlling bacterial wilt caused by R. solanacearum because it had a lower cost and its application rate of 0.25 g N kg−1 soil could effectively suppress the survival of R. solanacearum. Additionally, soil microbial activity and community populations were restored to their initial state four weeks after the application of each fumigant, indicating that the three fumigants had few detrimental impacts on soil microbial activity and community structure with an exception of the suppression of R. solanacearum. The present study provides guidance for the selection of a suitable alkaline nitrogenous amendment and its application rate in controlling bacterial wilt. PMID:26738601

Effect of calcium cyanamide, ammonium bicarbonate and lime mixture, and ammonia water on survival of Ralstonia solanacearum and microbial community

Science.gov (United States)

Liu, Lijuan; Sun, Chengliang; Liu, Xingxing; He, Xiaolin; Liu, Miao; Wu, Hao; Tang, Caixian; Jin, Chongwei; Zhang, Yongsong

2016-01-01

The inorganic nitrogenous amendments calcium cyanamide (CC), ammonia water (AW), and a mixture of ammonium bicarbonate with lime (A+L) are popularly used as fumigants to control soil-borne disease in China. However, it is unclear which of these fumigants is more effective in controlling R. solanacearum. This present study compared the efficiencies of the three nitrogenous amendments listed above at four nitrogen levels in suppressing the survival of R. solanacearum in soil. The CC showed the best ability to suppress R. solanacearum due to its highest capacity to increase soil and NO2- contents and pH. However, AW was more suitable to controlling bacterial wilt caused by R. solanacearum because it had a lower cost and its application rate of 0.25 g N kg-1 soil could effectively suppress the survival of R. solanacearum. Additionally, soil microbial activity and community populations were restored to their initial state four weeks after the application of each fumigant, indicating that the three fumigants had few detrimental impacts on soil microbial activity and community structure with an exception of the suppression of R. solanacearum. The present study provides guidance for the selection of a suitable alkaline nitrogenous amendment and its application rate in controlling bacterial wilt.

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.

15 CFR 990.53 - Restoration selection-developing restoration alternatives.

Science.gov (United States)

2010-01-01

... OIL POLLUTION ACT REGULATIONS NATURAL RESOURCE DAMAGE ASSESSMENTS Restoration Planning Phase § 990.53... justify restoration, trustees may proceed with the Restoration Planning Phase. Otherwise, trustees may not... discount all service quantities and/or values to the date the demand is presented to the responsible...

Adaptively Addressing Uncertainty in Estuarine and Near Coastal Restoration Projects

Energy Technology Data Exchange (ETDEWEB)

Thom, Ronald M.; Williams, Greg D.; Borde, Amy B.; Southard, John A.; Sargeant, Susan L.; Woodruff, Dana L.; Laufle, Jeffrey C.; Glasoe, Stuart

2005-03-01

Act; CWPPRA) have incorporated very specific and detailed elements in a more active adaptive management effort. In Puget Sound, the Puget Sound Action Team uses site-specific case studies, monitoring, and public involvement to direct actions to reduce microbial contamination of harvestable shellfish. Small-scale projects can also be improved through application of adaptive management. For example, directed research and site assessments resulted in successful restoration of seagrasses near a ferry terminal in Puget Sound. It is recommended that all restoration programs be conducted in an adaptive management framework, and where appropriate, a more active adaptive management approach be applied. The net effect should be less uncertainty, improved project success, advancement of the science of restoration, and cost savings.

The precision problem in conservation and restoration

Science.gov (United States)

Hiers, J. Kevin; Jackson, Stephen T.; Hobbs, Richard J.; Bernhardt, Emily S.; Valentine, Leonie E.

2016-01-01

Within the varied contexts of environmental policy, conservation of imperilled species populations, and restoration of damaged habitats, an emphasis on idealized optimal conditions has led to increasingly specific targets for management. Overly-precise conservation targets can reduce habitat variability at multiple scales, with unintended consequences for future ecological resilience. We describe this dilemma in the context of endangered species management, stream restoration, and climate-change adaptation. Inappropriate application of conservation targets can be expensive, with marginal conservation benefit. Reduced habitat variability can limit options for managers trying to balance competing objectives with limited resources. Conservation policies should embrace habitat variability, expand decision-space appropriately, and support adaptation to local circumstances to increase ecological resilience in a rapidly changing world.

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.

Small mammal populations in a restored stream corridor

International Nuclear Information System (INIS)

Wike, L.D.

2000-01-01

An opportunity to study the response of a small mammal community to restoration of a riparian wetland was provided by the Pen Branch project at the Savannah River Site (SRS). Live trapping of small mammals was conducted on six transects at Pen Branch in 1996 and 1998 and at three transects at Meyer's Branch, an unimpacted stream at SRS, in 1997 and 1998. Distributions of rates of capture of the four most common species were both spatially and temporally uneven. Kruskal-Wallis one-way analysis of variance found no significant differences in the relationship of capture rates between species and between treatment and both the within-stream control and Meyers Branch. Habitat use and movement within stream corridors appears to be dependent primarily on species, with age and sex perhaps contributing to preference and distance moved. The lack of differences in capture rates related to transect or treatment may be due to the close proximity of sample transects relative to the movement potential of the species sampled

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.

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%).

Wildlife Response to Riparian Restoration on the Sacramento River

Directory of Open Access Journals (Sweden)

Gregory H Golet

2008-06-01

Full Text Available Studies that assess the success of riparian restoration projects seldom focus on wildlife. More generally, vegetation characteristics are studied, with the assumption that animal populations will recover once adequate habitats are established. On the Sacramento River, millions of dollars have been spent on habitat restoration, yet few studies of wildlife response have been published. Here we present the major findings of a suite of studies that assessed responses of four taxonomic groups (insects, birds, bats, and rodents. Study designs fell primarily into two broad categories: comparisons of restoration sites of different ages, and comparisons of restoration sites with agricultural and remnant riparian sites. Older restoration sites showed increased abundances of many species of landbirds and bats relative to younger sites, and the same trend was observed for the Valley elderberry longhorn beetle (Desmocerus californicus dimorphus, a federally threatened species. Species richness of landbirds and ground-dwelling beetles appeared to increase as restoration sites matured. Young restoration sites provided benefits to species that utilize early successional riparian habitats, and after about 10 years, the sites appeared to provide many of the complex structural habitat elements that are characteristic of remnant forest patches. Eleven-year old sites were occupied by both cavity-nesting birds and special-status crevice-roosting bats. Restored sites also supported a wide diversity of bee species, and had richness similar to remnant sites. Remnant sites had species compositions of beetles and rodents more similar to older sites than to younger sites. Because study durations were short for all but landbirds, results should be viewed as preliminary. Nonetheless, in aggregate, they provide convincing evidence that restoration along the Sacramento River has been successful in restoring riparian habitats for a broad suite of faunal species. Not only did

Habitat Re-Creation (Ecological Restoration) as a Strategy for Conserving Insect Communities in Highly Fragmented Landscapes.

Science.gov (United States)

Shuey, John A

2013-12-05

Because of their vast diversity, measured by both numbers of species as well as life history traits, insects defy comprehensive conservation planning. Thus, almost all insect conservation efforts target individual species. However, serious insect conservation requires goals that are set at the faunal level and conservation success requires strategies that conserve intact communities. This task is complicated in agricultural landscapes by high levels of habitat fragmentation and isolation. In many regions, once widespread insect communities are now functionally trapped on islands of ecosystem remnants and subject to a variety of stressors associated with isolation, small population sizes and artificial population fragmentation. In fragmented landscapes ecological restoration can be an effective strategy for reducing localized insect extinction rates, but insects are seldom included in restoration design criteria. It is possible to incorporate a few simple conservation criteria into restoration designs that enhance impacts to entire insect communities. Restoration can be used as a strategy to address fragmentation threats to isolated insect communities if insect communities are incorporated at the onset of restoration planning. Fully incorporating insect communities into restoration designs may increase the cost of restoration two- to three-fold, but the benefits to biodiversity conservation and the ecological services provided by intact insect communities justify the cost.

Fernald restoration: ecologists and engineers integrate restoration and cleanup

Energy Technology Data Exchange (ETDEWEB)

Woods, Eric; Homer, John

2002-07-15

As cleanup workers excavate pits and tear down buildings at the Fernald site in southwest Ohio, site ecologists are working side-by-side to create thriving wetlands and develop the early stages of forest, prairie, and savanna ecosystems to restore natural resources that were impacted by years of site operations. In 1998, the U.S. Department of Energy-Fernald Office (DOE-FN) and its cleanup contractor, Fluor Fernald, Inc., initiated several ecological restoration projects in perimeter areas of the site (e.g., areas not used for or impacted by uranium processing or waste management). The projects are part of Fernald's final land use plan to restore natural resources over 904 acres of the 1,050-acre site. Pete Yerace, the DOE-FN Natural Resource Trustee representative is working with the Fernald Natural Resource Trustees in an oversight role to resolve the state of Ohio's 1986 claim against DOE for injuries to natural resources. Fluor Fernald, Inc., and DOE-FN developed the ''Natural Resource Restoration Plan'', which outlines 15 major restoration projects for the site and will restore injured natural resources at the site. In general, Fernald's plan includes grading to maximize the formation of wetlands or expanded floodplain, amending soil where topsoil has been removed during excavation, and establishing native vegetation throughout the site. Today, with cleanup over 35 percent complete and site closure targeted for 2006, Fernald is entering a new phase of restoration that involves heavily remediated areas. By working closely with engineers and cleanup crews, site ecologists can take advantage of remediation fieldwork (e.g., convert an excavated depression into a wetland) and avoid unnecessary costs and duplication. This collaboration has also created opportunities for relatively simple and inexpensive restoration of areas that were discovered during ongoing remediation. To ensure the survival of the plant material in heavily

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...

Formulation of an organic carbon trajectory over a 10-year period on a restored spoil island in south-central Florida

Science.gov (United States)

Schafer, T.; Ellis, R.; Osborne, T.; Hicks Pries, C.

2015-12-01

Long-term monitoring of restoration projects aims to determine long-term sustainability and stability of restored systems. In coastal wetlands, one indicator of restoration of ecosystem function can be seen with organic matter (specifically carbon) accretion. SL-15, a spoil island in Fort Pierce, Fl was restored in 2005, and has been monitored for return to natural condition over the last 10 years.. To assess sediment carbon accretion, sediment cores were collected in a set of eight plots, located on the SL-15 mangrove island and the surrounding seagrass recruitment area. These were analyzed for organic carbon, microbial biomass carbon, extractable carbon, and total nitrogen. The biogeochemical data collected in the previous year was compared to data collected in 2005-2007. Vegetation surveys were also completed to show the build-up of organic material in accordance with vegetation shift over the 9-year period. From this information, a trajectory has been formulated on organic carbon accretion and vegetation shift from the time of orginal restoration activities. By comparison to control sites nearby, realistic estimates of time required to reach natural levels of carbon and vegetation community structure can be calculated..

Bridge Creek IMW database - Bridge Creek Restoration and Monitoring Project

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — The incised and degraded habitat of Bridge Creek is thought to be limiting a population of ESA-listed steelhead (Oncorhynchus mykiss). A logical restoration approach...

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

Potential 'ecological traps' of restored landscapes: koalas Phascolarctos cinereus re-occupy a rehabilitated mine site.

Science.gov (United States)

Cristescu, Romane H; Banks, Peter B; Carrick, Frank N; Frère, Céline

2013-01-01

With progressively increasing anthropogenic habitat disturbances, restoration of impacted landscapes is becoming a critical element of biodiversity conservation. Evaluation of success in restoration ecology rarely includes faunal components, usually only encompassing abiotic and floral components of the ecosystems. Even when fauna is explicitly included, it is usually only species presence/absence criteria that are considered. If restoration is to have a positive outcome, however, populations in restored habitats should exhibit comparable survival and reproductive rates to populations found in undisturbed surroundings. If a species recolonises restored areas but later experiences decreased fitness, restored areas could become ecological sinks or traps. We investigated this possibility in a case study of koalas Phascolarctos cinereus occupying rehabilitated mining areas on North Stradbroke Island, Australia. Our holistic approach compared rehabilitated and undisturbed areas on the basis of their vegetation characteristics, of koalas' body condition, roosting trees, diet, as well as predator index. Koalas using rehabilitated areas appeared to be able to access an adequate supply of roosting and fodder trees, were in good condition and had high reproductive output. We did not find any significant differences in predator density between rehabilitated areas and undisturbed surroundings. The results presented in this study showed there was no evidence that the post-mining rehabilitated areas constitute ecological sinks or traps. However, to reach a definitive conclusion as to whether areas rehabilitated post-mining provide at least equivalent habitat to undisturbed locations, additional research could be undertaken to assess foliar nutrient/water/toxin differences and predation risk in rehabilitated areas compared with undisturbed areas. More generally, the evaluation of whether restoration successfully produces a functional ecological community should include criteria

Potential 'ecological traps' of restored landscapes: koalas Phascolarctos cinereus re-occupy a rehabilitated mine site.

Directory of Open Access Journals (Sweden)

Romane H Cristescu

Full Text Available With progressively increasing anthropogenic habitat disturbances, restoration of impacted landscapes is becoming a critical element of biodiversity conservation. Evaluation of success in restoration ecology rarely includes faunal components, usually only encompassing abiotic and floral components of the ecosystems. Even when fauna is explicitly included, it is usually only species presence/absence criteria that are considered. If restoration is to have a positive outcome, however, populations in restored habitats should exhibit comparable survival and reproductive rates to populations found in undisturbed surroundings. If a species recolonises restored areas but later experiences decreased fitness, restored areas could become ecological sinks or traps. We investigated this possibility in a case study of koalas Phascolarctos cinereus occupying rehabilitated mining areas on North Stradbroke Island, Australia. Our holistic approach compared rehabilitated and undisturbed areas on the basis of their vegetation characteristics, of koalas' body condition, roosting trees, diet, as well as predator index. Koalas using rehabilitated areas appeared to be able to access an adequate supply of roosting and fodder trees, were in good condition and had high reproductive output. We did not find any significant differences in predator density between rehabilitated areas and undisturbed surroundings. The results presented in this study showed there was no evidence that the post-mining rehabilitated areas constitute ecological sinks or traps. However, to reach a definitive conclusion as to whether areas rehabilitated post-mining provide at least equivalent habitat to undisturbed locations, additional research could be undertaken to assess foliar nutrient/water/toxin differences and predation risk in rehabilitated areas compared with undisturbed areas. More generally, the evaluation of whether restoration successfully produces a functional ecological community

Factors mediating the restoration of structurally degraded soils

DEFF Research Database (Denmark)

Arthur, Emmanuel; Moldrup, Per; Schjønning, Per

with the ability of soils to perform these functions. The present study examines the roles of clay mineralogy, native organic matter, and exogenous organic material on the restoration of structurally degraded soils. Totally seven soils from Denmark and Ghana - five soils dominated by illites, one kaolinitic soil...... the incubation period, structural stability estimated as the amount of water-dispersible clay decreased with prevailing moisture content, and native organic matter. Also, microbial activity significantly increased with addition of exogenous organic matter. At the end of incubation, there was significant...... macroaggregation, decreased bulk density, and increased equivalent pore diameter and tortuosity (derived from measurements of soil-gas diffusivity and soil-air permeability) for all soils. Although aggregate friability was not affected by clay type, aggregate workability was highest for the kaolinitic soil...

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

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.

Changes in Microbial Community Structure and Soil Biological Properties in Mined Dune Areas During Re-vegetation.

Science.gov (United States)

Escobar, Indra Elena C; Santos, Vilma M; da Silva, Danielle Karla A; Fernandes, Marcelo F; Cavalcante, Uided Maaze T; Maia, Leonor C

2015-06-01

The aim of this study was to describe the impact of re-vegetation on the restoration of microbial community structure and soil microbiological properties in sand dunes that had been affected by mining activity. Soil samples were collected during the dry and rainy seasons from a chronosequence (1, 9, 21 years) of re-vegetated dunes using a single preserved dune as a reference. The composition of the fatty acid methyl esters and soil microbial properties were evaluated. The results showed that the changes in microbial community structure were related to seasonal variations: biomarkers of Gram-positive bacteria were higher than Gram-negative bacteria during the dry season, showing that this group of organisms is more tolerant to these stressful conditions. The microbial community structure in the natural dune was less affected by seasonal variation compared to the re-vegetated areas, whereas the opposite was observed for microbiological properties. Thus, in general, the proportion of saprobic fungi was higher in the natural dune, whereas Gram-negative bacteria were proportionally more common in the younger areas. Although over time the re-vegetation allows the recovery of the microbial community and the soil functions, these communities and functions are different from those found in the undisturbed areas.

Anterior provisional restorations used to determine form, function, and esthetics for complex restorative situations, using all-ceramic restorative systems.

Science.gov (United States)

Reshad, Mamaly; Cascione, Domenico; Kim, Tae

2010-02-01

A technique is proposed for the restoration of a large and visible maxillary anterior defect. The importance of proper diagnosis, treatment planning, and communication is emphasized. Irreversible treatment should only be rendered once patient approval has been obtained through objective evaluation with provisional restorations. The techniques presented in this article use a combination of ceramic systems currently available to satisfy functional demands while achieving acceptable esthetics. A controlled series of steps, where the provisional restorative components are being replaced by the definitive ones is planned. The only difference between the provisional and definitive restorative components is the material used. The definitive restorations consisted of an implant-supported zirconium oxide framework. Individual pressed porcelain restorations were luted to the framework and a natural tooth. CLINICAL SIGNIFICANCE Provisional restorations allow an objective form of communication. Vertical and horizontal transitional lines can be effectively masked with appropriate treatment planning and a skilled ceramist. Many traditional dental laboratory steps may be eliminated or simplified without compromising the definitive restorations.

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.

Endangered river fish: factors hindering conservation and restoration

Science.gov (United States)

Cooke, Steven J.; Paukert, Craig P.; Hogan, Zeb

2012-01-01

Globally, riverine fish face many anthropogenic threats including riparian and flood plain habitat degradation, altered hydrology, migration barriers, fisheries exploitation, environmental (climate) change, and introduction of invasive species. Collectively, these threats have made riverine fishes some of the most threatened taxa on the planet. Although much effort has been devoted to identifying the threats faced by river fish, there has been less effort devoted to identifying the factors that may hinder our ability to conserve and restore river fish populations and their watersheds. Therefore, we focus our efforts on identifying and discussing 10 general factors (can also be viewed as research and implementation needs) that constrain or hinder effective conservation action for endangered river fish: (1) limited basic natural history information; (2) limited appreciation for the scale/extent of migrations and the level of connectivity needed to sustain populations; (3) limited understanding of fish/river-flow relationships; (4) limited understanding of the seasonal aspects of river fish biology, particularly during winter and/or wet seasons; (5) challenges in predicting the response of river fish and river ecosystems to both environmental change and various restoration or management actions; (6) limited understanding of the ecosystem services provided by river fish; (7) the inherent difficulty in studying river fish; (8) limited understanding of the human dimension of river fish conservation and management; (9) limitations of single species approaches that often fail to address the broader-scale problems; and (10) limited effectiveness of governance structures that address endangered river fish populations and rivers that cross multiple jurisdictions. We suggest that these issues may need to be addressed to help protect, restore, or conserve river fish globally, particularly those that are endangered.

Restoring rocky intertidal communities: Lessons from a benthic macroalgal ecosystem engineer.

Science.gov (United States)

Bellgrove, Alecia; McKenzie, Prudence F; Cameron, Hayley; Pocklington, Jacqueline B

2017-04-15

As coastal population growth increases globally, effective waste management practices are required to protect biodiversity. Water authorities are under increasing pressure to reduce the impact of sewage effluent discharged into the coastal environment and restore disturbed ecosystems. We review the role of benthic macroalgae as ecosystem engineers and focus particularly on the temperate Australasian fucoid Hormosira banksii as a case study for rocky intertidal restoration efforts. Research focussing on the roles of ecosystem engineers is lagging behind restoration research of ecosystem engineers. As such, management decisions are being made without a sound understanding of the ecology of ecosystem engineers. For successful restoration of rocky intertidal shores it is important that we assess the thresholds of engineering traits (discussed herein) and the environmental conditions under which they are important. Copyright © 2017 Elsevier Ltd. All rights reserved.

Restoring proximal caries lesions conservatively with tunnel restorations

OpenAIRE

Chu, Chun-Hung; Cheung,; Nalliah,Romesh; Mei,May L

2013-01-01

Chun-Hung Chu1, May L Mei,1 Chloe Cheung,1 Romesh P Nalliah2 1Faculty of Dentistry, The University of Hong Kong, Hong Kong, People's Republic of China; 2Department of Restorative Dentistry and Biomaterials Sciences, Harvard School of Dental Medicine, Boston, MA, USA Abstract: The tunnel restoration has been suggested as a conservative alternative to the conventional box preparation for treating proximal caries. The main advantage of tunnel restoration over the conventional box or slo...

Long-term competence restoration.

Science.gov (United States)

Morris, Douglas R; DeYoung, Nathaniel J

2014-01-01

While the United States Supreme Court's Jackson v. Indiana decision and most state statutes mandate determinations of incompetent defendants' restoration probabilities, courts and forensic clinicians continue to lack empirical evidence to guide these determinations and do not yet have a consensus regarding whether and under what circumstances incompetent defendants are restorable. The evidence base concerning the restoration likelihood of those defendants who fail initial restoration efforts is even further diminished and has largely gone unstudied. In this study, we examined the disposition of a cohort of defendants who underwent long-term competence restoration efforts (greater than six months) and identified factors related to whether these defendants were able to attain restoration and adjudicative success. Approximately two-thirds (n = 52) of the 81 individuals undergoing extended restoration efforts were eventually deemed restored to competence. Lengths of hospitalization until successful restoration are presented with implications for the reasonable length of time that restoration efforts should persist. Older individuals were less likely to be restored and successfully adjudicated, and individuals with more severe charges and greater factual legal understanding were more likely to be restored and adjudicated. The significance of these findings for courts and forensic clinicians is discussed.

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.

Disease dynamics and potential mitigation among restored and wild staghorn coral, Acropora cervicornis

Science.gov (United States)

Lohr, Kathryn E.; Cameron, Caitlin M.; Williams, Dana E.; Peters, Esther C.

2014-01-01

The threatened status (both ecologically and legally) of Caribbean staghorn coral, Acropora cervicornis, has prompted rapidly expanding efforts in culture and restocking, although tissue loss diseases continue to affect populations. In this study, disease surveillance and histopathological characterization were used to compare disease dynamics and conditions in both restored and extant wild populations. Disease had devastating effects on both wild and restored populations, but dynamics were highly variable and appeared to be site-specific with no significant differences in disease prevalence between wild versus restored sites. A subset of 20 haphazardly selected colonies at each site observed over a four-month period revealed widely varying disease incidence, although not between restored and wild sites, and a case fatality rate of 8%. A tropical storm was the only discernable environmental trigger associated with a consistent spike in incidence across all sites. Lastly, two field mitigation techniques, (1) excision of apparently healthy branch tips from a diseased colony, and (2) placement of a band of epoxy fully enclosing the diseased margin, gave equivocal results with no significant benefit detected for either treatment compared to controls. Tissue condition of associated samples was fair to very poor; unsuccessful mitigation treatment samples had severe degeneration of mesenterial filament cnidoglandular bands. Polyp mucocytes in all samples were infected with suspect rickettsia-like organisms; however, no bacterial aggregates were found. No histological differences were found between disease lesions with gross signs fitting literature descriptions of white-band disease (WBD) and rapid tissue loss (RTL). Overall, our results do not support differing disease quality, quantity, dynamics, nor health management strategies between restored and wild colonies of A. cervicornis in the Florida Keys. PMID:25210660

Effects of reforestation on ammonia-oxidizing microbial community composition and abundance in subtropical acidic forest soils.

Science.gov (United States)

Wu, Ruo-Nan; Meng, Han; Wang, Yong-Feng; Gu, Ji-Dong

2018-06-01

Forest ecosystems have great ecological values in mitigation of climate change and protection of biodiversity of flora and fauna; re-forestry is commonly used to enhance the sequestration of atmospheric CO 2 into forest storage biomass. Therefore, seasonal and spatial dynamics of the major microbial players in nitrification, ammonia-oxidizing archaea (AOA) and bacteria (AOB), in acidic soils of young and matured revegetated forests were investigated to elucidate the changes of microbial communities during forest restoration, and compared to delineate the patterns of community shifts under the influences of environmental factors. AOA were more abundant than AOB in both young and matured revegetated forest soils in both summer and winter seasons. In summer, however, the abundance of amoA-AOA decreased remarkably (p < 0.01), ranging from 1.90 (± 0.07) × 10 8 copies per gram dry soil in matured forest to 5.04 (± 0.43) × 10 8 copies per gram dry soil in young forest, and amoA-AOB was below detection limits to obtain any meaningful values. Moreover, exchangeable Al 3+ and organic matter were found to regulate the physiologically functional nitrifiers, especially AOA abundance in acidic forest soils. AOB community in winter showed stronger correlation with the restoration status of revegetated forests and AOA community dominated by Nitrosotalea devanaterra, in contrast, was more sensitive to the seasonal and spatial variations of environmental factors. These results enrich the current knowledge of nitrification during re-forestry and provide valuable information to developmental status of revegetated forests for management through microbial analysis.

The Precision Problem in Conservation and Restoration.

Science.gov (United States)

Hiers, J Kevin; Jackson, Stephen T; Hobbs, Richard J; Bernhardt, Emily S; Valentine, Leonie E

2016-11-01

Within the varied contexts of environmental policy, conservation of imperilled species populations, and restoration of damaged habitats, an emphasis on idealized optimal conditions has led to increasingly specific targets for management. Overly-precise conservation targets can reduce habitat variability at multiple scales, with unintended consequences for future ecological resilience. We describe this dilemma in the context of endangered species management, stream restoration, and climate-change adaptation. Inappropriate application of conservation targets can be expensive, with marginal conservation benefit. Reduced habitat variability can limit options for managers trying to balance competing objectives with limited resources. Conservation policies should embrace habitat variability, expand decision-space appropriately, and support adaptation to local circumstances to increase ecological resilience in a rapidly changing world. Copyright © 2016 Elsevier Ltd. All rights reserved.

Risk assessment and restoration possibilities of some abandoned mining ponds in Murcia Region, SE Spain

Science.gov (United States)

Faz, Angel; Acosta, Jose A.; Martinez-Martinez, Silvia; Carmona, Dora M.; Zornoza, Raul; Kabas, Sebla; Bech, Jaume

2010-05-01

In Murcia Region, SE Spain, there are 85 tailing ponds due to intensive mining activities that occurred during last century, especially in Sierra Minera de Cartagena-La Union. Although mining activity was abandoned several decades ago, those tailing ponds with high amounts of heavy metals still remain in the area. The ponds, due to their composition and location, may create environmental risks of geochemical pollution, negatively affecting soil, water, and plant, animal, and human populations, as well as infrastructures. The main objective of this research is to evaluate the restoration possibilities of two representative mining ponds in order to minimize the risk for human and ecosystems. To achieve this objective, two tailing ponds generated by mining activities were selected, El Lirio and El Gorguel. These ponds are representative of the rest of existent ponds in Sierra Minera de Cartagena-La Unión, with similar problems and characteristics. Several techniques and studies were applied to the tailing ponds for their characterization, including: geophysics, geotechnics, geochemical, geological, hydrological, and vegetation studies. In addition, effects of particulate size in the distribution of heavy metals will be used to assess the risk of dispersion of these metals in finest particles. Once the ponds were characterized, they were divided in several sectors in order to apply different amendments (pig slurry and marble waste) to reduce the risk of metal mobility and improve soil quality for a future phytostabilization. It is known that organic amendments promote soil development processes, microbial diversity, and finally, soil ecosystem restoration to a state of self-sustainability. By comparing the results before and after applications we will be able to evaluate the effect of the different amendments on soil quality and their effectively on risk reduction. Finally, plant metal-tolerant species are used to restore vegetation in the ponds, thereby decreasing

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.

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

Hangman Restoration Project Year-End Report FY2008.

Energy Technology Data Exchange (ETDEWEB)

Coeur d' Alene Tribe Department of Natural Resources.

2008-11-12

This report covers the main goals of FY2008 from which the Work Elements were derived. The goals and products are listed by heading and the associated work elements are referenced in the text. A list of the FY2008 Work Elements is included as Appendix A. FY2008 witnessed the completion of the hntkwipn Management Plan and the first substantive efforts to restore the important habitats encompassed by the mitigation properties in the Upper Hangman Watershed. Native grasses were planted and germination was evaluated. Also, drain tiles that greatly altered the hydrologic function of the Sheep and Hangman Creek Flood Plains were removed and/or disrupted. Preparation for future restoration efforts were also made in FY2008. Designs were produced for the realignment of Sheep Creek and the decommissioning of seven drainage ditches within hntkwipn. A prioritization plan was drafted that greatly expands the area of focus for restoring native fish population in Hangman Creek.

Regional restoration benchmarks for Acropora cervicornis

Science.gov (United States)

Schopmeyer, Stephanie A.; Lirman, Diego; Bartels, Erich; Gilliam, David S.; Goergen, Elizabeth A.; Griffin, Sean P.; Johnson, Meaghan E.; Lustic, Caitlin; Maxwell, Kerry; Walter, Cory S.

2017-12-01

Coral gardening plays an important role in the recovery of depleted populations of threatened Acropora cervicornis in the Caribbean. Over the past decade, high survival coupled with fast growth of in situ nursery corals have allowed practitioners to create healthy and genotypically diverse nursery stocks. Currently, thousands of corals are propagated and outplanted onto degraded reefs on a yearly basis, representing a substantial increase in the abundance, biomass, and overall footprint of A. cervicornis. Here, we combined an extensive dataset collected by restoration practitioners to document early (1-2 yr) restoration success metrics in Florida and Puerto Rico, USA. By reporting region-specific data on the impacts of fragment collection on donor colonies, survivorship and productivity of nursery corals, and survivorship and productivity of outplanted corals during normal conditions, we provide the basis for a stop-light indicator framework for new or existing restoration programs to evaluate their performance. We show that current restoration methods are very effective, that no excess damage is caused to donor colonies, and that once outplanted, corals behave just as wild colonies. We also provide science-based benchmarks that can be used by programs to evaluate successes and challenges of their efforts, and to make modifications where needed. We propose that up to 10% of the biomass can be collected from healthy, large A. cervicornis donor colonies for nursery propagation. We also propose the following benchmarks for the first year of activities for A. cervicornis restoration: (1) >75% live tissue cover on donor colonies; (2) >80% survivorship of nursery corals; and (3) >70% survivorship of outplanted corals. Finally, we report productivity means of 4.4 cm yr-1 for nursery corals and 4.8 cm yr-1 for outplants as a frame of reference for ranking performance within programs. Such benchmarks, and potential subsequent adaptive actions, are needed to fully assess the

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.

Multiple CMS-restorer gene polymorphism in gynodioecious Plantago coronopus

NARCIS (Netherlands)

Damme, van J.M.M.; Hundscheid, M.P.J.; Ivanovic, S.; Koelewijn, H.P.

2004-01-01

The mode of inheritance of the male sterility trait is crucial for understanding the evolutionary dynamics of the sexual system gynodioecy, which is the co-occurrence of female and hermaphrodite plants in natural populations. Both cytoplasmic (CMS) and nuclear (restorer) genes are known to be

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 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

"I Was Dead Restorative Today": From Restorative Justice to Restorative Approaches in School

Science.gov (United States)

McCluskey, G.; Lloyd, G.; Stead, J.; Kane, J.; Riddell, S.; Weedon, E.

2008-01-01

This paper explores definitions and understandings of restorative practices in education. It offers a critique of current theoretical models of restorative justice originally derived from the criminal justice system and now becoming popular in educational settings. It questions the appropriateness of these concepts as they are being introduced to…

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.

GSD Update: Ushering in a new age of genetics to restore lands and conserve species

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Deborah M. Finch

2013-01-01

Plant genetic information provides critical knowledge necessary to mitigate the impacts of climate change through ecological restoration. The first step in restoration is recognizing and delineating genetic boundaries at different taxonomic and spatial hierarchies (e.g., species, subspecies and populations). The second step is an assessment of the genetic diversity...

Restoration of critically endangered elkhorn coral (Acropora palmata populations using larvae reared from wild-caught gametes

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Valérie F. Chamberland

2015-07-01

Full Text Available Elkhorn coral (Acropora palmata populations provide important ecological functions on shallow Caribbean reefs, many of which were lost when a disease reduced their abundance by more than 95% beginning in the mid-1970s. Since then, a lack of significant recovery has prompted rehabilitation initiatives throughout the Caribbean. Here, we report the first successful outplanting and long-term survival of A. palmata settlers reared from gametes collected in the field. A. palmata larvae were settled on clay substrates (substrate units and either outplanted on the reef two weeks after settlement or kept in a land-based nursery. After 2.5 years, the survival rate of A. palmata settlers outplanted two weeks after settlement was 6.8 times higher (3.4% than that of settlers kept in a land-based nursery (0.5%. Furthermore, 32% of the substrate units on the reef still harbored one or more well-developed recruit compared to 3% for substrate units kept in the nursery. In addition to increasing survival, outplanting A. palmata settlers shortly after settlement reduced the costs to produce at least one 2.5-year-old A. palmata individual from $325 to $13 USD. Thus, this study not only highlights the first successful long-term rearing of this critically endangered coral species, but also shows that early outplanting of sexually reared coral settlers can be more cost-effective than the traditional approach of nursery rearing for restoration efforts aimed at rehabilitating coral populations.

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 ...

Potential ‘Ecological Traps’ of Restored Landscapes: Koalas Phascolarctos cinereus Re-Occupy a Rehabilitated Mine Site

Science.gov (United States)

Cristescu, Romane H.; Banks, Peter B.; Carrick, Frank N.; Frère, Céline

2013-01-01

With progressively increasing anthropogenic habitat disturbances, restoration of impacted landscapes is becoming a critical element of biodiversity conservation. Evaluation of success in restoration ecology rarely includes faunal components, usually only encompassing abiotic and floral components of the ecosystems. Even when fauna is explicitly included, it is usually only species presence/absence criteria that are considered. If restoration is to have a positive outcome, however, populations in restored habitats should exhibit comparable survival and reproductive rates to populations found in undisturbed surroundings. If a species recolonises restored areas but later experiences decreased fitness, restored areas could become ecological sinks or traps. We investigated this possibility in a case study of koalas Phascolarctos cinereus occupying rehabilitated mining areas on North Stradbroke Island, Australia. Our holistic approach compared rehabilitated and undisturbed areas on the basis of their vegetation characteristics, of koalas' body condition, roosting trees, diet, as well as predator index. Koalas using rehabilitated areas appeared to be able to access an adequate supply of roosting and fodder trees, were in good condition and had high reproductive output. We did not find any significant differences in predator density between rehabilitated areas and undisturbed surroundings. The results presented in this study showed there was no evidence that the post-mining rehabilitated areas constitute ecological sinks or traps. However, to reach a definitive conclusion as to whether areas rehabilitated post-mining provide at least equivalent habitat to undisturbed locations, additional research could be undertaken to assess foliar nutrient/water/toxin differences and predation risk in rehabilitated areas compared with undisturbed areas. More generally, the evaluation of whether restoration successfully produces a functional ecological community should include criteria

Bridges to life: evaluation of an in-prison restorative justice intervention.

Science.gov (United States)

Armour, Marilyn Peterson; Sage, John; Rubin, Allen; Windsor, Liliane C

2005-12-01

Restorative justice initiatives have been identified as primarily, if not exclusively, useful as a "front-end" diversionary option reserved for non violent property crimes and minor assaults. In-prison restorative justice programs are rare and have not been examined for their impact on recidivism. Bridges to Life (BTL) is a voluntary, manualized, ecumenical faith-based restorative justice program offered to incarcerated offenders who are within nine months of their release. A survey of BTL graduates (n=1021) found an appreciatively lower recidivism rate than the general population of released inmates. Quantitative and qualitative analyses suggest that BTL helps break through offenders' denial and self-centeredness, exposing them to the impact of their actions and helping them feel the pain their crimes created. Possible reasons for the positive nature of participants' responses are advanced. The use of in-prison restorative justice programs to facilitate offender re-entry is also discussed.

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...

Progress report: baseline monitoring of indicator species (butterflies) at tallgrass prairie restorations

Science.gov (United States)

Allain, Larry; Vidrine, Malcolm

2014-01-01

This project provides baseline data of butterfly populations at two coastal prairie restoration sites in Louisiana, the Duralde Unit of Lacassine National Wildlife Refuge (hereafter, the Duralde site) and the Cajun Prairie Restoration Project in Eunice (hereafter, the Eunice site). In all, four distinct habitat types representing different planting methods were sampled. These data will be used to assess biodiversity and health of native grasslands and also provide a basis for adaptive management.

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.

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.

Sex in an uncertain world: environmental stochasticity helps restore competitive balance between sexually and asexually reproducing populations.

Science.gov (United States)

Park, A W; Vandekerkhove, J; Michalakis, Y

2014-08-01

Like many organisms, individuals of the freshwater ostracod species Eucypris virens exhibit either obligate sexual or asexual reproductive modes. Both types of individual routinely co-occur, including in the same temporary freshwater pond (their natural habitat in which they undergo seasonal diapause). Given the well-known two-fold cost of sex, this begs the question of how sexually reproducing individuals are able to coexist with their asexual counterparts in spite of such overwhelming costs. Environmental stochasticity in the form of 'false dawn' inundations (where the first hydration is ephemeral and causes loss of early hatching individuals) may provide an advantage to the sexual subpopulation, which shows greater variation in hatching times following inundation. We explore the potential role of environmental stochasticity in this system using life-history data analysis, climate data, and matrix projection models. In the absence of environmental stochasticity, the population growth rate is significantly lower in sexual subpopulations. Climate data reveal that 'false dawn' inundations are common. Using matrix projection modelling with and without environmental stochasticity, we demonstrate that this phenomenon can restore appreciable balance to the system, in terms of population growth rates. This provides support for the role of environmental stochasticity in helping to explain the maintenance of sex and the occurrence of geographical parthenogenesis. © 2014 The Authors. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

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.

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.

Application of Science-Based Restoration Planning to a Desert River System

Science.gov (United States)

Laub, Brian G.; Jimenez, Justin; Budy, Phaedra

2015-06-01

Persistence of many desert river species is threatened by a suite of impacts linked to water infrastructure projects that provide human water security where water is scarce. Many desert rivers have undergone regime shifts from spatially and temporally dynamic ecosystems to more stable systems dominated by homogenous physical habitat. Restoration of desert river systems could aid in biodiversity conservation, but poses formidable challenges due to multiple threats and the infeasibility of recovery to pre-development conditions. The challenges faced in restoring desert rivers can be addressed by incorporating scientific recommendations into restoration planning efforts at multiple stages, as demonstrated here through an example restoration project. In particular, use of a watershed-scale planning process can identify data gaps and irreversible constraints, which aid in developing achievable restoration goals and objectives. Site-prioritization focuses limited the resources for restoration on areas with the greatest potential to improve populations of target organisms. Investment in research to understand causes of degradation, coupled with adoption of a guiding vision is critical for identifying feasible restoration actions that can enhance river processes. Setting monitoring as a project goal, developing hypotheses for expected outcomes, and implementing restoration as an experimental design will facilitate adaptive management and learning from project implementation. Involvement of scientists and managers during all planning stages is critical for developing process-based restoration actions and an implementation plan to maximize learning. The planning process developed here provides a roadmap for use of scientific recommendations in future efforts to recover dynamic processes in imperiled riverine ecosystems.

Application of science-based restoration planning to a desert river system

Science.gov (United States)

Laub, Brian G.; Jimenez, Justin; Budy, Phaedra

2015-01-01

Persistence of many desert river species is threatened by a suite of impacts linked to water infrastructure projects that provide human water security where water is scarce. Many desert rivers have undergone regime shifts from spatially and temporally dynamic ecosystems to more stable systems dominated by homogenous physical habitat. Restoration of desert river systems could aid in biodiversity conservation, but poses formidable challenges due to multiple threats and the infeasibility of recovery to pre-development conditions. The challenges faced in restoring desert rivers can be addressed by incorporating scientific recommendations into restoration planning efforts at multiple stages, as demonstrated here through an example restoration project. In particular, use of a watershed-scale planning process can identify data gaps and irreversible constraints, which aid in developing achievable restoration goals and objectives. Site-prioritization focuses limited the resources for restoration on areas with the greatest potential to improve populations of target organisms. Investment in research to understand causes of degradation, coupled with adoption of a guiding vision is critical for identifying feasible restoration actions that can enhance river processes. Setting monitoring as a project goal, developing hypotheses for expected outcomes, and implementing restoration as an experimental design will facilitate adaptive management and learning from project implementation. Involvement of scientists and managers during all planning stages is critical for developing process-based restoration actions and an implementation plan to maximize learning. The planning process developed here provides a roadmap for use of scientific recommendations in future efforts to recover dynamic processes in imperiled riverine ecosystems.

Health-Related Quality of Life after Restorative Proctocolectomy: A Cross-Sectional Study.

Science.gov (United States)

Helavirta, I; Hyöty, M; Oksanen, P; Huhtala, H; Haapamäki, J; Aitola, P

2018-05-01

Patients undergoing restorative proctocolectomy have often suffered from active ulcerative colitis which should be remembered when assessing quality of life after operation. The aim of this study was to explore health-related quality of life after restorative proctocolectomy in those with poor or good pouch function and to compare that to patients with active or inactive ulcerative colitis and to the general population. Altogether, 282 restorative proctocolectomy patients were investigated. The control group comprised 408 ulcerative colitis patients from the local register. Generic 15D and disease-specific inflammatory bowel disease questionnaire health-related quality of life instruments were used. Population-based data were available for 15D. Pouch function was evaluated with Öresland score and colitis activity with simple clinical colitis activity index. 15D results showed that patients with good pouch function had health-related quality of life similar to that of the general population. Health-related quality of life with inflammatory bowel disease questionnaire was equally good in patients with good pouch function (n = 131; 70%) and inactive colitis (n = 95; 63%), and equally impaired in patients with poor pouch function (n = 56; 30%) and active colitis (n = 18; 12%). The majority of patients had health-related quality of life comparable to that in general population. Most patients with active ulcerative colitis are likely to improve their health-related quality of life after successful surgery. These findings are important when informing colitis patients about life after surgery.

American social work, corrections and restorative justice: an appraisal.

Science.gov (United States)

Gumz, Edward J

2004-08-01

Social work played an active role in American corrections until the 1980s when the ethic of rehabilitation began to give way to a more conservative doctrine of retribution. Changes in the field of social work, characterized by preference of social workers to work only with certain populations, contributed to social work's diminishment in corrections. Although efforts at rehabilitation continue in corrections, the concept of restorative justice that emphasizes assisting victims, communities, and offenders in dealing with the consequences of crime is gaining acceptance in the field of corrections in the United States and in other countries. This study explored social work's presence in corrections, the decline of that presence, and how the concept of restorative justice can invigorate social work within the field of corrections. Several examples of social work's contemporary efforts to use the concept of restorative justice in the United Kingdom are presented.

TO THE ISSUE OF PRESERVATION AND RESTORATION OF STURGEON STOCKS IN THE VOLGA-CASPIAN BASIN

Directory of Open Access Journals (Sweden)

L. M. Vasilieva

2012-01-01

Full Text Available It is shown that for the preservation and restoration of natural sturgeon populations it is necessary to increase the eff iciency of reproduction, both natural and artificial Article determines the crucial role of artificial reproduction of sturgeon at the present stage to keep the gene pool of these valuable fish species and restoration of biological resources for commercial fishing.The article contains a set of measures for the conservation, restoration and rational use of natural resources of sturgeon.

Guidelines for seagrass restoration : Importance of habitat selection and donor population, spreading of risks, and ecosystem engineering effects

NARCIS (Netherlands)

van Katwijk, M. M.; Bos, A. R.; de Jonge, V. N.; Hanssen, L. S. A. M.; Hermus, D. C. R.; de Jong, D. J.

Large-scale losses of seagrass beds have been reported for decades and lead to numerous restoration programs. From worldwide scientific literature and 20 years of seagrass restoration research in the Wadden Sea, we review and evaluate the traditional guidelines and propose new guidelines for

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.

Heavy Metal Phytoremediation: Microbial Indicators of Soil Health for the Assessment of Remediation Efficiency

Science.gov (United States)

Epelde, Lur; Ma Becerril, José; Alkorta, Itziar; Garbisu, Carlos

Phytoremediation is an effective, non-intrusive, inexpensive, aesthetically pleasing, socially accepted, promising phytotechnology for the remediation of polluted soils. The objective of any soil remediation process must be not only to remove the contaminant(s) from the soil but, most importantly, to restore the continued capacity of the soil to perform or function according to its potential (i.e., to recover soil health). Hence, indicators of soil health are needed to properly assess the efficiency of a phytoremediation process. Biological indicators of soil health, especially those related to the size, activity and diversity of the soil microbial communities, are becoming increasingly used, due to their sensitivity and capacity to provide information that integrates many environmental factors. In particular, microbial indicators of soil health are valid tools to evaluate the success of metal phytoremediation procedures such as phytoextraction and phytostabilization processes.

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.

Vegetation development following stream/river restoration: more natural fluvial dynamics and morphology, return of aquatic and riparian plant species?

Science.gov (United States)

Soons, M. B.

2012-04-01

After centuries of human interventions in stream/river dynamics and morphology aimed at optimizing landscapes for agricultural and industrial purposes, new insights have inspired water managers to try and combine stream and river ecosystem functions with the conservation of biodiversity. Around the world, aquatic and riparian species have declined strongly due to pollution, destruction and fragmentation of their habitat, so that biodiversity conservation initiatives primarily focus on habitat restoration. In the past decades many stream and river restoration projects have been carried out and often hydrological dynamics and morphology have been restored to a more natural state. However, the successful restoration of aquatic and riparian habitats very often failed to result in restoration of their biodiversity. This lack of success from a biodiversity conservation perspective is usually attributed to 'dispersal limitation', meaning that the habitat may be restored, but species fail to reach the site and re-colonize it. Especially re-colonization by aquatic and riparian plant species is important, as such species function as ecosystem engineers: their presence alters fluvial dynamics and morphology, generates additional habitat heterogeneity and provides habitat and food for animal species. Following minor disturbances, re-colonization is often possible through locally remaining populations, by seeds in the seed bank or by surviving plant fragments. However, following major disturbances, colonization and establishment from other source populations are necessary. This usually occurs through dispersal of seeds (and in more aquatic species also by dispersal of vegetative fragments) into the restored wetland area. As dispersal occurs predominantly over short distances and source populations of aquatic and riparian species may be lacking in the surroundings, dispersal may be a limiting factor in the development of aquatic and riparian vegetation at a restored site. But

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

Interim restorations.

Science.gov (United States)

Gratton, David G; Aquilino, Steven A

2004-04-01

Interim restorations are a critical component of fixed prosthodontic treatment, biologically and biomechanically. Interim restoration serves an important diagnostic role as a functional and esthetic try-in and as a blueprint for the design of the definitive prosthesis. When selecting materials for any interim restoration, clinicians must consider physical properties, handling properties, patient acceptance, and material cost. Although no single material meets all the requirements and material classification alone of a given product is not a predictor of clinical performance, bis-acryl materials are typically best suited to single-unit restorations, and poly(methylmethacrylate) interim materials are generally ideal for multi-unit, complex, long-term, interim fixed prostheses. As with most dental procedures, the technique used for fabrication has a greater effect on the final result than the specific material chosen.

Restoring forests

DEFF Research Database (Denmark)

Jacobs, Douglass F.; Oliet, Juan A.; Aronson, James

2015-01-01

of land requiring restoration implies the need for spatial prioritization of restoration efforts according to cost-benefit analyses that include ecological risks. To design resistant and resilient ecosystems that can adapt to emerging circumstances, an adaptive management approach is needed. Global change......, in particular, imparts a high degree of uncertainty about the future ecological and societal conditions of forest ecosystems to be restored, as well as their desired goods and services. We must also reconsider the suite of species incorporated into restoration with the aim of moving toward more stress resistant...... and competitive combinations in the longer term. Non-native species may serve an important role under some circumstances, e.g., to facilitate reintroduction of native species. Propagation and field establishment techniques must promote survival through seedling stress resistance and site preparation. An improved...

Forward-looking farmers owning multiple potential wetland restoration sites: implications for efficient restoration

Science.gov (United States)

Schroder (Kushch), Svetlana; Lang, Zhengxin; Rabotyagov, Sergey

2018-04-01

Wetland restoration can increase the provision of multiple non-market ecosystem services. Environmental and socio-economic factors need to be accounted for when land is withdrawn from agriculture and wetlands are restored. We build multi-objective optimization models to provide decision support for wetland restoration in the Le Sueur river watershed in Southern Minnesota. We integrate environmental objectives of sediment reduction and habitat protection with socio-economic factors associated with the overlap of private land with potential wetland restoration sites in the watershed and the costs representing forward-looking farmers voluntarily taking land out of agricultural production in favor of wetland restoration. Our results demonstrate that the inclusion of these factors early on in the restoration planning process affects both the total costs of the restoration project and the spatial distribution of optimally selected wetland restoration sites.

Applying soil science for restoration of post mining degraded landscapes in semi-arid Australia: challenges and opportunities

Science.gov (United States)

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

2015-04-01

Introduction Current challenges in ecological restoration of post mining environments include the deficit of original topsoil which is frequently lost or damaged, and the lack of soil forming materials. A comprehensive knowledge of soil properties and processes and an adequate management of soil resources are critical to improve the restoration success of these degraded areas. In particular, understanding soil physical, chemical and biological parameters is decisive in environments where water is a limiting factor for seedling establishment and plant survival. To improve the restoration success of biodiverse semi-arid areas disturbed by mining activities (Pilbara region, Western Australia), we conducted experiments to (i) analyse changes in soil physico-chemical properties and soil microbial activity of topsoil stockpiles to optimise its handling and minimise deterioration of nutrients and soil biota, (ii) test climate effects on seedling emergence of native plant species and (iii) assess the potential of mine waste materials as a suitable growth medium for seedling emergence of native plant species under various water regimes. Methods The experimental studies were conducted in controlled environment facilities where air temperature, relative humidity and soil moisture were monitored routinely. Watering regimes were selected to represent rainfall patterns of the area. As a growth media we used material obtained from topsoil stockpiles and waste materials from an active mine site, which were mixed at different ratios. Samples were collected from different parts of the topsoil stockpiles and analysed to determine physical, chemical and biological properties. Results No large discrepancies in physical and chemical values were detected at different positions of the stockpiles. However, microbial activity was highly variable, particularly inside the stockpiles. Seedling emergence on topsoil growth media was highly dependent on climate factors with emergence rates

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...

New UK graduates' knowledge of training and service provision within restorative dentistry - a survey.

Science.gov (United States)

Kalsi, A S; Kochhar, S; Lewis, N J; Hemmings, K W

2017-06-09

Objective To assess new UK graduates' knowledge of training and service provision within restorative dentistry.Design A national descriptive cross-sectional survey.Subjects and methods An online survey assessing clinicians' knowledge of restorative dentistry, who had graduated within the last four years in the UK, was distributed across the UK via postgraduate dental deaneries. One-hundred responses were accepted as a sample of a potential population of 4,000.Main outcome measure How well respondents understood the service provision and training aspects of the specialty of restorative dentistry.Results The responses were received from graduates from a variety of dental schools across the UK. Of those respondents, 41 reported receiving career guidance within restorative dentistry. 45 new graduates were confident in their understanding of the specialty, while 53 were confident in the differences between restorative dentistry and monospecialty training. The respondents appeared unaware regarding treatment priorities within restorative dentistry departments. Most respondents felt that receiving teaching on restorative dentistry as a specialty and career pathway would be beneficial.Conclusion The results suggest that new graduates may benefit from clarification regarding the specialty of restorative dentistry, however, caution must be taken due to the limitations of the study.

Silage review: Using molecular approaches to define the microbial ecology of silage.

Science.gov (United States)

McAllister, T A; Dunière, L; Drouin, P; Xu, S; Wang, Y; Munns, K; Zaheer, R

2018-05-01

Ensiling of forages was recognized as a microbial-driven process as early as the late 1800s, when it was associated with the production of "sweet" or "sour" silage. Classical microbiological plating techniques defined the epiphytic microbial populations associated with fresh forage, the pivotal role of lactic acid-producing bacteria in the ensiling process, and the contribution of clostridia, bacilli, yeast, and molds to the spoilage of silage. Many of these classical studies focused on the enumeration and characterization of a limited number of microbial species that could be readily isolated on selective media. Evidence suggested that many of the members of these microbial populations were viable but unculturable, resulting in classical studies underestimating the true microbial diversity associated with ensiling. Polymerase chain reaction-based techniques, including length heterogeneity PCR, terminal RFLP, denaturing gradient gel electrophoresis, and automated ribosomal intergenic spacer analysis, were the first molecular methods used to study silage microbial communities. Further advancements in whole comparative genomic, metagenomic, and metatranscriptomic sequencing have or are in the process of superseding these methods, enabling microbial communities during ensiling to be defined with a degree of detail that is impossible using classical microbiology. These methods have identified new microbial species in silage, as well as characterized shifts in microbial communities with forage type and composition, ensiling method, and in response to aerobic exposure. Strain- and species-specific primers have been used to track the persistence and contribution of silage inoculants to the ensiling process and the role of specific species of yeast and fungi in silage spoilage. Sampling and the methods used to isolate genetic materials for further molecular analysis can have a profound effect on results. Primer selection for PCR amplification and the presence of inhibitors

Organic nitrogen rearranges both structure and activity of the soil-borne microbial seedbank.

Science.gov (United States)

Leite, Márcio F A; Pan, Yao; Bloem, Jaap; Berge, Hein Ten; Kuramae, Eiko E

2017-02-15

Use of organic amendments is a valuable strategy for crop production. However, it remains unclear how organic amendments shape both soil microbial community structure and activity, and how these changes impact nutrient mineralization rates. We evaluated the effect of various organic amendments, which range in Carbon/Nitrogen (C/N) ratio and degradability, on the soil microbiome in a mesocosm study at 32, 69 and 132 days. Soil samples were collected to determine community structure (assessed by 16S and 18S rRNA gene sequences), microbial biomass (fungi and bacteria), microbial activity (leucine incorporation and active hyphal length), and carbon and nitrogen mineralization rates. We considered the microbial soil DNA as the microbial seedbank. High C/N ratio favored fungal presence, while low C/N favored dominance of bacterial populations. Our results suggest that organic amendments shape the soil microbial community structure through a feedback mechanism by which microbial activity responds to changing organic inputs and rearranges composition of the microbial seedbank. We hypothesize that the microbial seedbank composition responds to changing organic inputs according to the resistance and resilience of individual species, while changes in microbial activity may result in increases or decreases in availability of various soil nutrients that affect plant nutrient uptake.

Evolution in an Afternoon: Rapid Natural Selection and Adaptation of Bacterial Populations

Science.gov (United States)

Delpech, Roger

2009-01-01

This paper describes a simple, rapid and low-cost technique for growing bacteria (or other microbes) in an environmental gradient, in order to determine the tolerance of the microbial population to varying concentrations of sodium chloride ions, and suggests how the evolutionary response of a microbial population to the selection pressure of the…

Models of microbiome evolution incorporating host and microbial selection.

Science.gov (United States)

Zeng, Qinglong; Wu, Steven; Sukumaran, Jeet; Rodrigo, Allen

2017-09-25

Numerous empirical studies suggest that hosts and microbes exert reciprocal selective effects on their ecological partners. Nonetheless, we still lack an explicit framework to model the dynamics of both hosts and microbes under selection. In a previous study, we developed an agent-based forward-time computational framework to simulate the neutral evolution of host-associated microbial communities in a constant-sized, unstructured population of hosts. These neutral models allowed offspring to sample microbes randomly from parents and/or from the environment. Additionally, the environmental pool of available microbes was constituted by fixed and persistent microbial OTUs and by contributions from host individuals in the preceding generation. In this paper, we extend our neutral models to allow selection to operate on both hosts and microbes. We do this by constructing a phenome for each microbial OTU consisting of a sample of traits that influence host and microbial fitnesses independently. Microbial traits can influence the fitness of hosts ("host selection") and the fitness of microbes ("trait-mediated microbial selection"). Additionally, the fitness effects of traits on microbes can be modified by their hosts ("host-mediated microbial selection"). We simulate the effects of these three types of selection, individually or in combination, on microbiome diversities and the fitnesses of hosts and microbes over several thousand generations of hosts. We show that microbiome diversity is strongly influenced by selection acting on microbes. Selection acting on hosts only influences microbiome diversity when there is near-complete direct or indirect parental contribution to the microbiomes of offspring. Unsurprisingly, microbial fitness increases under microbial selection. Interestingly, when host selection operates, host fitness only increases under two conditions: (1) when there is a strong parental contribution to microbial communities or (2) in the absence of a strong

Environmental drivers of differences in microbial community structure in crude oil reservoirs across a methanogenic gradient

Directory of Open Access Journals (Sweden)

Jenna L Shelton

2016-09-01

Full Text Available 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, and formation water chemistry. Twenty-two oil production wells from north central Louisiana, USA, were sampled for analysis of microbial community structure and fluid geochemistry. Archaea were the dominant microbial community in the majority of the wells sampled. Methanogens, including hydrogenotrophic and methylotrophic organisms, were numerically dominant in every well, accounting for, on average, over 98% of the total archaea present. The dominant Bacteria groups were Pseudomonas, Acinetobacter, Enterobacteriaceae, and Clostridiales, which have also been identified in other microbially-altered oil reservoirs. Comparing microbial community structure to fluid (gas, water, and oil geochemistry revealed that the relative extent of biodegradation, salinity, and spatial location were the major drivers of microbial diversity. Archaeal relative abundance was independent of the extent of methanogenesis, but closely correlated to the extent of crude oil biodegradation; therefore, microbial community structure is likely not a good sole predictor of methanogenic activity, but may predict the extent of crude oil biodegradation. However, when the shallow, highly biodegraded, low salinity wells were excluded from the statistical analysis, no environmental parameters could explain the differences in microbial community structure. This suggests that the microbial community structure of the 5 shallow up-dip wells was different than the 17 deeper, down-dip wells, and that

Ecological Restoration: Guidance from Theory

Directory of Open Access Journals (Sweden)

Joy Zedler

2005-09-01

Full Text Available A review of the science and practice of ecosystem restoration led me to identify key ecological theories and concepts that are relevant to planning, implementing, and sustaining restoration efforts. From experience with actual restoration projects, I provide guidance for improving the restoration process. Despite an abundance of theory and guidance, restoration goals are not always achieved, and pathways toward targets are not highly predictable. This is understandable, since each restoration project has many constraints and unique challenges. To improve restoration progress, I advise that sites be designed as experiments to allow learning while doing. At least the larger projects can be restored in phases, each designed as experimental treatments to test alternative restoration approaches. Subsequent phases can then adopt one or more of the treatments that best achieved goals in earlier phases while applying new tests of other restoration measures. Both science and restoration can progress simultaneously. This phased, experimental approach (called “adaptive restoration” is an effective tool for improving restoration when monitoring, assessment, interpretation and research are integrated into the process.

Methodology for ranking restoration options

International Nuclear Information System (INIS)

Hedemann Jensen, Per

1999-04-01

The work described in this report has been performed as a part of the RESTRAT Project FI4P-CT95-0021a (PL 950128) co-funded by the Nuclear Fission Safety Programme of the European Commission. The RESTRAT project has the overall objective of developing generic methodologies for ranking restoration techniques as a function of contamination and site characteristics. The project includes analyses of existing remediation methodologies and contaminated sites, and is structured in the following steps: characterisation of relevant contaminated sites; identification and characterisation of relevant restoration techniques; assessment of the radiological impact; development and application of a selection methodology for restoration options; formulation of generic conclusions and development of a manual. The project is intended to apply to situations in which sites with nuclear installations have been contaminated with radioactive materials as a result of the operation of these installations. The areas considered for remedial measures include contaminated land areas, rivers and sediments in rivers, lakes, and sea areas. Five contaminated European sites have been studied. Various remedial measures have been envisaged with respect to the optimisation of the protection of the populations being exposed to the radionuclides at the sites. Cost-benefit analysis and multi-attribute utility analysis have been applied for optimisation. Health, economic and social attributes have been included and weighting factors for the different attributes have been determined by the use of scaling constants. (au)

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

In Silico Gene-Level Evolution Explains Microbial Population Diversity through Differential Gene Mobility

NARCIS (Netherlands)

van Dijk, Bram; Hogeweg, P.

2016-01-01

Microbial communities can show astonishing ecological and phylogenetic diversity. What is the role of pervasive horizontal gene transfer (HGT) in shaping this diversity in the presence of clonally expanding "killer strains"? Does HGT of antibiotic production and resistance genes erase phylogenetic

[Comparison of color reappearance between metal-ceram restoration and foundry-ceram restoration using crystaleye spectrophotometer].

Science.gov (United States)

Shi, Tao; Zhang, Ning; Kong, Fan-wen; Zhan, De-song

2010-10-01

To study the color reappearance effect of metal-ceram restoration and foundry-ceram restoration using Crystaleye spectrophotometer. 58 metal-ceram restorations and 58 foundry-ceram restorations according to the result of the Crystaleye spectrophotometer were made respectively. The deltaE between restorations and natural teeth as referenced were analyzed. And satisfaction of dentists and patients were evaluated. The deltaE between metal-ceram restorations and natural teeth was 7.13 +/- 0.74. The deltaE between foundry-ceram restorations and teeth was 1.47 +/- 0.84. There were statistical differences between the deltaE (P spectrophotometer can provide accurate reference for foundry-ceram restoration, but for metal-ceram restoration it is not accurate.

Variable responses of fish assemblages, habitat, and stability to natural-channel-design restoration in Catskill Mountain streams

Science.gov (United States)

Baldigo, Barry P.; Ernst, Anne G.; Warren, Dana R.; Miller, Sarah J.

2010-01-01

Natural-channel-design (NCD) restorations were recently implemented within large segments of five first- and second-order streams in the Catskill Mountains of New York in an attempt to increase channel stability, reduce bed and bank erosion, and sustain water quality. In conjunction with these efforts, 54 fish and habitat surveys were done from 1999 to 2007 at six restored reaches and five stable control reaches to evaluate the effects of NCD restoration on fish assemblages, habitat, and bank stability. A before–after–control–impact study design and two-factor analysis of variance were used to quantify the net changes in habitat and fish population and community indices at treatment reaches relative to those at unaltered control reaches. The density and biomass of fish communities were often dominated by one or two small prey species and no or few predator species before restoration and by one or more trout (Salmonidae) species after restoration. Significant increases in community richness (30%), diversity (40%), species or biomass equitability (32%), and total biomass (up to 52%) in at least four of the six restored reaches demonstrate that NCD restorations can improve the health and sustainability of fish communities in geomorphically unstable Catskill Mountain streams over the short to marginally long term. Bank stability, stream habitat, and trout habitat suitability indices (HSIs) generally improved significantly at the restored reaches, but key habitat features and trout HSIs did not change or decreased at two of them. Fish communities and trout populations at these two reaches were not positively affected by NCD restorations. Though NCD restorations often had a positive effect on habitat and fish communities, our results show that the initial habitat conditions limit the relative improvements than can be achieved, habitat quality and stability do not necessarily respond in unison, and biotic and abiotic responses cannot always be generalized.

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...

[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.

Drivers of Ecological Restoration: Lessons from a Century of Restoration in Iceland

Directory of Open Access Journals (Sweden)

Ása L. Aradóttir

2013-12-01

Full Text Available We analyzed the main drivers for ecological restoration in Iceland from 1907 to 2010 and assessed whether the drivers have changed over time and what factors might explain the changes, if any. Our study was based on a catalogue of 100 restoration projects, programs, and areas, representing 75% to 85% of all restoration activities in Iceland. Catastrophic erosion was an early driver for soil conservation and restoration efforts that still ranked high in the 2000s, reflecting the immense scale of soil erosion and desertification in Iceland. Socioeconomic drivers such as farming and the provision of wood products were strong motivators of ecological restoration over most of the 20th century, although their relative importance decreased with time as the number and diversity of drivers increased. In the 1960s and 1970s, the construction of hard infrastructure, and moral values such as improving the aesthetics of the countryside and "repaying the debt to the land" emerged as motivations for restoration actions. In the late 1990s, the United Nations Climate Change Convention became a driver for restoration, and the importance of nature conservation and recreation increased. Technological development and financial incentives did not show up as drivers of ecological restoration in our study, although there are some indications of their influence. Furthermore, policy was a minor driver, which might reflect weak policy instruments for ecological restoration and some counteractive policies.

Microbial examination of anaerobic sludge adaptation to animal slurry.

Science.gov (United States)

Moset, V; Cerisuelo, A; Ferrer, P; Jimenez, A; Bertolini, E; Cambra-López, M

2014-01-01

The objective of this study was to evaluate changes in the microbial population of anaerobic sludge digesters during the adaptation to pig slurry (PS) using quantitative real-time polymerase chain reaction (qPCR) and qualitative scanning electron microscopy (SEM). Additionally, the relationship between microbial parameters and sludge physicochemical composition and methane yield was examined. Results showed that the addition of PS to an unadapted thermophilic anaerobic digester caused an increase in volatile fatty acids (VFA) concentration, a decrease in removal efficiency and CH4 yield. Additionally, increases in total bacteria and total archaea were observed using qPCR. Scanning electron micrographs provided a general overview of the sludge's cell morphology, morphological diversity and degree of organic matter degradation. A change in microbial morphotypes from homogeneous cell morphologies to a higher morphological diversity, similar to that observed in PS, was observed with the addition of PS by SEM. Therefore, the combination of qPCR and SEM allowed expanding the knowledge about the microbial adaptation to animal slurry in thermophilic anaerobic digesters.

Microbial ecology-based engineering of Microbial Electrochemical Technologies.

Science.gov (United States)

Koch, Christin; Korth, Benjamin; Harnisch, Falk

2018-01-01

Microbial ecology is devoted to the understanding of dynamics, activity and interaction of microorganisms in natural and technical ecosystems. Bioelectrochemical systems represent important technical ecosystems, where microbial ecology is of highest importance for their function. However, whereas aspects of, for example, materials and reactor engineering are commonly perceived as highly relevant, the study and engineering of microbial ecology are significantly underrepresented in bioelectrochemical systems. This shortfall may be assigned to a deficit on knowledge and power of these methods as well as the prerequisites for their thorough application. This article discusses not only the importance of microbial ecology for microbial electrochemical technologies but also shows which information can be derived for a knowledge-driven engineering. Instead of providing a comprehensive list of techniques from which it is hard to judge the applicability and value of information for a respective one, this review illustrates the suitability of selected techniques on a case study. Thereby, best practice for different research questions is provided and a set of key questions for experimental design, data acquisition and analysis is suggested. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Effects of probiotic supplement ( and on feed efficiency, growth performance, and microbial population of weaning rabbits

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Thanh Lam Phuoc

2017-02-01

Full Text Available Objective This study aimed to investigate the effects of single or/and double strains of probiotic supplement on feed efficiency, growth performance, and microbial population in distal gastrointestinal tract (GIT of weaning rabbits. Methods Sixty-four weaning (28 days old New Zealand White rabbits were randomly distributed into four groups with treatments including: basal diet without probiotic supplement (control or supplemented as follows: 1×106 cfu/g B. subtilis (BS group, 1×107 cfu/g L. acidophilus (LA group, or 0.5×106 cfu/g B. subtilis plus 0.5×107 cfu/g L. acidophilus (BL group. During the research, the male and female rabbits were fed separately. Body weight of the rabbits was recorded at 28, 42, and 70 d of age. Results There was an increase (p<0.05 in body weight gain for the LA group at 42 d. Rabbits fed BL responsed with a greater growth (p<0.05 and better feed conversion ratio (p<0.05 than those fed with no probiotic. Digestibility coefficients of dry matter, organic matter, crude protein, neutral detergent fiber, and gross energy were higher (p<0.05 in LA and BL groups than those in the control group. Male rabbits had higher (p<0.05 Bacilli spp. and Coliformis spp. in the ileum than female rabbits. Rabbits supplemented with BS had greater (p<0.05 numbers of bacilli in all intestinal segments than those receiving no probiotic, whereas intestinal Lactobacilli populations were greater (p<0.001 in the LA and BL diets compared to control. Average intestinal coliform populations were lowest (p<0.05 in the rabbits supplemented with LA as compared to those fed the control and BS. Conclusion Supplementation of L. acidophilus alone or in combination with B. subtilis at a half of dose could enhance number of gut beneficial bacteria populations, nutrient digestibility, cecal fermentation, feed efficiency, and growth performance, but rabbits receiving only B. subtilis alone were not different from the controls without probiotic.

Microbial bebop: creating music from complex dynamics in microbial ecology.

Science.gov (United States)

Larsen, Peter; Gilbert, Jack

2013-01-01

In order for society to make effective policy decisions on complex and far-reaching subjects, such as appropriate responses to global climate change, scientists must effectively communicate complex results to the non-scientifically specialized public. However, there are few ways however to transform highly complicated scientific data into formats that are engaging to the general community. Taking inspiration from patterns observed in nature and from some of the principles of jazz bebop improvisation, we have generated Microbial Bebop, a method by which microbial environmental data are transformed into music. Microbial Bebop uses meter, pitch, duration, and harmony to highlight the relationships between multiple data types in complex biological datasets. We use a comprehensive microbial ecology, time course dataset collected at the L4 marine monitoring station in the Western English Channel as an example of microbial ecological data that can be transformed into music. Four compositions were generated (www.bio.anl.gov/MicrobialBebop.htm.) from L4 Station data using Microbial Bebop. Each composition, though deriving from the same dataset, is created to highlight different relationships between environmental conditions and microbial community structure. The approach presented here can be applied to a wide variety of complex biological datasets.

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.

Impact of fermentation and addition of non-starch polysaccharide-degrading enzymes on microbial population and on digestibility of dried distillers grains with solubles in pigs

DEFF Research Database (Denmark)

Venås Jakobsen, Grethe; Jensen, Bent Borg; Knudsen, Knud Erik Bach

2015-01-01

Fluctuating prices on feedstock has led to a growing interest in alternative feed ingredients. Co-products from the biofuel industry are hence interesting to include in pig feeds, primarily due to the high protein content. Low nutritional value due to a high content of dietary fibre, however...... of cellulase and xylanase (CelXyl). Microbial population during fermentation of the treatments was determined and apparent ileal and total tract digestibility were measured on eight barrows surgically fitted with a simple T-shaped cannula at the distal ileum and fed the four treatments according to a double......-Latin square design. Microbial activity of the three fermented DDGS treatments was relatively low with lactic acid bacteria counts between 8.8 and 8.9 log cfu/g and lactic acid concentrations between 60.2 and 70.5 mmol/kg. The addition of CelXyl to DDGS resulted in a significant decrease in the amount of non...

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

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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.

Bioremediation of diesel contamination at an underground storage tank site: a spatial analysis of the microbial community.

Science.gov (United States)

Andreolli, Marco; Albertarelli, Nicola; Lampis, Silvia; Brignoli, Pierlorenzo; Khoei, Nazaninalsadat Seyed; Vallini, Giovanni

2016-01-01

The present study reports on a real case of contamination due to the chronic leakage of diesel fuel from an underground tank at a dismissed service station. Speciation of the microbial community according to both lateral and vertical gradients from the origin of the contaminant release was analyzed by means of the PCR-DGGE technique. Moreover, the effects of a landfarming treatment on both the microbial community structure and the abatement of contamination were analyzed. The concentration of total petrol hydrocarbons (TPHs) decreased along the horizontal gradient (from 7042.2 ± 521.9 to 112.2 ± 24.3 mg kg(-1)), while increased downwards from the position of the tank (from 502.6 ± 43.7 to 4972.5 ± 275.3 mg kg(-1)). PCR-DGGE analyses and further statistical treatment of the data indicated a correlation between structure of the bacterial communities and amount of diesel fuel contamination. On the other hand, level of contamination, soil texture and depth were shown to affect the fungal community. Chloroflexi and Ascomycota were the most abundant microbes ascertained through culture-independent procedures. Landfarming promoted 91.6 % reduction of TPHs in 75 days. Furthermore, PCR-DGGE analyses evidenced that both bacterial and fungal communities of the treated soil were restored to the pristine conditions of uncontaminated topsoil. The present study demonstrated that bacterial and fungal communities were affected differently by soil factors such as level of hydrocarbon contamination as well as soil depth and texture. This report shows that a well-planned landfarming treatment can drive the restoration of the soil in terms of both abatement of the contaminants and resilience of the microbial community structure.

Intestinal intraepithelial lymphocyte-enterocyte crosstalk regulates production of bactericidal angiogenin 4 by Paneth cells upon microbial challenge.

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Catherine R Walker

Full Text Available Antimicrobial proteins influence intestinal microbial ecology and limit proliferation of pathogens, yet the regulation of their expression has only been partially elucidated. Here, we have identified a putative pathway involving epithelial cells and intestinal intraepithelial lymphocytes (iIELs that leads to antimicrobial protein (AMP production by Paneth cells. Mice lacking γδ iIELs (TCRδ(-/- express significantly reduced levels of the AMP angiogenin 4 (Ang4. These mice were also unable to up-regulate Ang4 production following oral challenge by Salmonella, leading to higher levels of mucosal invasion compared to their wild type counterparts during the first 2 hours post-challenge. The transfer of γδ iIELs from wild type (WT mice to TCRδ(-/- mice restored Ang4 production and Salmonella invasion levels were reduced to those obtained in WT mice. The ability to restore Ang4 production in TCRδ(-/- mice was shown to be restricted to γδ iIELs expressing Vγ7-encoded TCRs. Using a novel intestinal crypt co-culture system we identified a putative pathway of Ang4 production initiated by exposure to Salmonella, intestinal commensals or microbial antigens that induced intestinal epithelial cells to produce cytokines including IL‑23 in a TLR-mediated manner. Exposure of TCR-Vγ7(+ γδ iIELs to IL-23 promoted IL‑22 production, which triggered Paneth cells to secrete Ang4. These findings identify a novel role for γδ iIELs in mucosal defence through sensing immediate epithelial cell cytokine responses and influencing AMP production. This in turn can contribute to the maintenance of intestinal microbial homeostasis and epithelial barrier function, and limit pathogen invasion.

Stimulation of biological N2-fixation to accelerate the microbial remediation of soil contaminated by petroleum hydrocarbons

International Nuclear Information System (INIS)

Tereshenko, N.N.; Lushnikov, S.V.

2005-01-01

All remediation projects are comprised at least in accelerating the processes of the self-cleaning and self-restoration of biocenose which is led to increasing the functional activity of hydrocarbon-oxidizing microflora (HOM). Some of experts are carefully relate to introducing the commercial cultures of active hydrocarbon-consuming microbes into soils. They are afraid of unpredictable behavior of the cultures in soils. That why the stimulation of metabolic activity of indigenous soil microflora seems to be most preferable. In fact, contamination of soil with low nitrogen capacity by oil spills leads to significant deficient of nitrogen for HOM. Nitrogen content limits the soil self-restoration. Inorganic nitrogen fertilizers are supplied to recover the balance. The study of the microbial destruction of petroleum-hydrocarbons in association with biochemical transformation of nitrogen was carried out in lab and field experiments during 2000-2004. Study showed the activity of HOM correlates with rate of microbial fixing atmospheric nitrogen. Activity of biological N 2 -fixation significantly depends on supplying fertilizers (dose, date and kind). General practice of remediation of hydrocarbon-contaminated soils applies high initial doses of nitrogen-fertilizers (0.5-1 t per ha). Such practice leads to inhibition of N 2 -fixation processes, decreasing rate of oil destruction and loosing nitrogen due to activation of microbial denitrification. In opposition to that, the fractioned and advanced supplying mineral nitrogen fertilizers with aluminosilicate is the cost-effective approach to remediation of hydrocarbon-contaminated soils. Field experiments showed that the approach allows to increase efficiency of treatment up to 70-75% and to decrease operational expenses 2-3 times at least. (authors)

Ecological restoration success is higher for natural regeneration than for active restoration in tropical forests.

Science.gov (United States)

Crouzeilles, Renato; Ferreira, Mariana S; Chazdon, Robin L; Lindenmayer, David B; Sansevero, Jerônimo B B; Monteiro, Lara; Iribarrem, Alvaro; Latawiec, Agnieszka E; Strassburg, Bernardo B N

2017-11-01

Is active restoration the best approach to achieve ecological restoration success (the return to a reference condition, that is, old-growth forest) when compared to natural regeneration in tropical forests? Our meta-analysis of 133 studies demonstrated that natural regeneration surpasses active restoration in achieving tropical forest restoration success for all three biodiversity groups (plants, birds, and invertebrates) and five measures of vegetation structure (cover, density, litter, biomass, and height) tested. Restoration success for biodiversity and vegetation structure was 34 to 56% and 19 to 56% higher in natural regeneration than in active restoration systems, respectively, after controlling for key biotic and abiotic factors (forest cover, precipitation, time elapsed since restoration started, and past disturbance). Biodiversity responses were based primarily on ecological metrics of abundance and species richness (74%), both of which take far less time to achieve restoration success than similarity and composition. This finding challenges the widely held notion that natural forest regeneration has limited conservation value and that active restoration should be the default ecological restoration strategy. The proposition that active restoration achieves greater restoration success than natural regeneration may have arisen because previous comparisons lacked controls for biotic and abiotic factors; we also did not find any difference between active restoration and natural regeneration outcomes for vegetation structure when we did not control for these factors. Future policy priorities should align the identified patterns of biophysical and ecological conditions where each or both restoration approaches are more successful, cost-effective, and compatible with socioeconomic incentives for tropical forest restoration.

Environmental restoration by natural effects - Advantages and limits

International Nuclear Information System (INIS)

Mueck, K.

2002-01-01

After a major contamination of a territory due to fallout from a reactor accident, a reprocessing plant accident or a weapon's detonation one of the important questions to be addressed is the time period required for the countermeasures to be applied. This is particularly important for countermeasures with high costs and consequences to the involved population such as relocation. Therefore, the time period required for a contamination with long-lived fission products to decrease below established intervention levels by natural processes of decay and removal from the soil layer relevant to the exposure is investigated. Natural processes which result in a decrease in activity concentrations in foodstuffs and external exposure, are the least detrimental to a territory as compared to other long-term countermeasures and therefore, the most favorable in that respect. The influence of the contribution of different foodstuffs on the time-span required until a resettlement of a dislocated population is feasible, is assessed and the advantages and limits of natural restoration effects on the required intervention periods are discussed. It is shown that natural restoration effects may contribute substantially to an environmentally safe and sustainable resettlement of an area substantially contaminated with fission products. (author)

Soil functional diversity analysis of a bauxite-mined restoration chronosequence.

Science.gov (United States)

Lewis, Dawn E; White, John R; Wafula, Denis; Athar, Rana; Dickerson, Tamar; Williams, Henry N; Chauhan, Ashvini

2010-05-01

Soil microorganisms are sensitive to environmental perturbations such that changes in microbial community structure and function can provide early signs of anthropogenic disturbances and even predict restoration success. We evaluated the bacterial functional diversity of un-mined and three chronosequence sites at various stages of rehabilitation (0, 10, and 20 years old) located in the Mocho Mountains of Jamaica. Samples were collected during the dry and wet seasons and analyzed for metal concentrations, microbial biomass carbon, bacterial numbers, and functional responses of soil microbiota using community-level physiological profile (CLPP) assays. Regardless of the season, un-mined soils consisted of higher microbial biomass and numbers than any of the rehabilitated sites. Additionally, the number and rate of substrates utilized and substrate evenness (the distribution of color development between the substrates) were significantly greater in the un-mined soils with carbohydrates being preferentially utilized than amino acids, polymers, carboxylic acids, and esters. To some extent, functional responses varied with the seasons but the least physiological activity was shown by the site rehabilitated in 1987 indicating long-term perturbation to this ecosystem. Small subunit ribosomal DNA (SSUrDNA)-denaturing gradient-gel electrophoresis analyses on the microbiota collected from the most preferred CLPP substrates followed by taxonomic analyses showed Proteobacteria, specifically the gamma-proteobacteria, as the most functionally active phyla, indicating a propensity of this phyla to out-compete other groups under the prevailing conditions. Additionally, multivariate statistical analyses, Shannon's diversity, and evenness indices, principal component analysis, biplot and un-weighted-pair-group method with arithmetic averages dendrograms further confirmed that un-mined sites were distinctly different from the rehabilitated soils.

An Introduction to the San Francisco Estuary Tidal Wetlands Restoration Series

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Larry R. Brown

2003-10-01

Full Text Available Restoration of tidal wetlands may provide an important tool for improving ecological health and water management for beneficial uses of the San Francisco Estuary (hereafter “Estuary”. Given the large losses of tidal wetlands from San Francisco Bay and the Sacramento-San Joaquin Delta in the last 150 years, it seems logical to assume that restoring tidal wetlands will have benefits for a variety of aquatic and terrestrial native species that have declined during the same time period. However, many other changes have also occurred in the Estuary concurrent with the declines of native species. Other factors that might be important in species declines include the effects of construction of upstream dams, large and small water diversions within the Sacramento-San Joaquin Delta, agricultural pesticides, trace elements from industrial and agricultural activities, and invasions of alien species. Discussions among researchers, managers, and stakeholders have identified a number of uncertainties regarding the potential benefits of tidal wetland restoration. The articles of the Tidal Wetlands Restoration Series address four major issues of concern. Stated as questions, these are: 1. Will tidal wetland restoration enhance populations of native fishes? 2. Will wetland restoration increase rates of methylation of mercury? 3. Will primary production and other ecological processes in restored tidal wetlands result in net export of organic carbon to adjacent habitats, resulting in enhancement of the food web? Will the carbon produced contribute to the formation of disinfection byproducts when disinfected for use as drinking water? 4. Will restored tidal wetlands provide long-term ecosystem benefits that can be sustained in response to ongoing physical processes, including sedimentation and hydrodynamics? Reducing the uncertainty surrounding these issues is of critical importance because tidal wetland restoration is assumed to be a critical tool for

Recent Updates on Treatment of Ocular Microbial Infections by Stem Cell Therapy: A Review