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PubMed2005

Probiotics and prebiotics in human health.

Probiotic bacteria are found in the intestines of humans and other mammals where they provide health benefits to the host. They do so by (1) providing nutrients and cofactors, (2) successfully competing with pathogens, and (3) stimulating host immune responses by producing specific polysaccharides. These bacteria can also alleviate the symptoms of disease-related metabolic disorders. Prebiotics are substances, usually poorly metabolized polysaccharides and oligosaccharides, that cannot be ingested effectively by the animal. They stimulate the growth of intestinal probiotic bacteria, which can utilize these carbohydrates, thereby promoting health of the organism. Genetic engineering has proven useful for the design of probiotic bacteria that counteract the symptoms of genetic and age-related diseases. Can these bacteria be engineered, through human-promoted accelerative evolution, so that they stimulate their own growth and that of other probiotic bacteria so as to crowd pathogens out of the intestine?

Animals↗

PubMed2005

Applying science to conservation and restoration of the world's wetlands.

The world has an estimated 7 to 9 million km2 of wetlands which can be defined through their hydrology, physiochemical environment, and biota. Many human cultures have lived in harmony with wetland environments for centuries. Many others have not, resulting in drainage or severe impact of wetlands throughout the world. Conservation of wetlands needs to be a priority for the cultural and ecological values they provide. But a more optimistic note is that large-scale restoration and re-creation of wetlands and riverine systems is beginning to happen throughout the world through ecological engineering. Examples of large-scale wetland restoration projects are presented for Delaware Bay, the Skjern River (Denmark), Florida Everglades, Louisiana Delta, the Mississippi River Basin, and the Mesopotamian Marshlands of Iraq.

Conservation of Natural Resources↗

PubMed2003

Impact of biocontrol agents Pseudomonas fluorescens CHA0 and its genetically modified derivatives on the diversity of culturable fungi in the rhizosphere of mungbean.

AIMS: To assess whether Pseudomonas fluorescens strain CHA0 and its genetically modified derivatives, CHA0/pME3424 (antibiotic over-producer) and CHA89 (antibiotic-deficient) could have an impact on the fungal community structure and composition in the rhizosphere of mungbean. METHODS AND RESULTS: Under glasshouse conditions, mungbean was grown repeatedly in the same soil, which was inoculated with CHA0, CHA0/pME3424, CHA89 or was left untreated. Treatments were applied to soil at the start of each 36-day mungbean growth cycle, and their effects on the diversity of the rhizosphere populations of culturable fungi were assessed at the end of the first, second and third cycles. The effects of CHA0 and CHA0/pME3424 did differ from the controls while CHA89 did not. Whereas all major fungal species were frequently isolated from both bacterized and nonbacterized rhizospheres, certain fungal species were exclusively promoted or specifically suppressed from Pseudomonas-treated soils. In general, fungal diversity and equitability tended to decrease with time while species richness slightly increased. Whilst a total of 29 fungal species were isolated from the mungbean rhizosphere, only eight species colonized the root tissues. CONCLUSIONS: Soil inoculation with Ps. fluorescens CHA0 or CHA0/pME3424 altered fungal community structure in mungbean rhizosphere but strain CHA89 failed to produce such effect. SIGNIFICANCE AND IMPACT OF THE STUDY: Pseudomonas fluorescens-mediated alteration in the composition and structure of fungal communities might have acute or lasting effects on ecosystem functioning. Furthermore, the study provides useful data pertinent to characterization of the fate of genetically modified inoculants (e.g. antibiotic-overproducing Pseudomonas strains) released into the environment.

Antibiosis↗

PubMed1999

Developments in terrestrial bacterial remediation of metals.

Recent advances in understanding the role and application of bacteria to the remediation of toxic metal and radionuclide contaminated terrestrial environments have come from several avenues. Novel species capable of mobilization and immobilization of metal ions have been discovered. Remediation of toxicity has been accelerated by nutrient amendment, the use of chelating agents and novel methods for phosphate amendment. Major advances in the use of natural and genetically engineered species for bioprotection and remediation of organic co-contaminants have been reported. Construction of wetland function continues to be developed for containment and decontamination of wastewaters.

Bacteria↗

PubMed1988

Fate of genetically-engineered bacteria in activated sludge microcosms.

The conclusions that can be derived from this study regarding the fate of the GEMs and their ability to degrade added pollutants are as follows: 1. Both GEMs were able to survive in the microcoms. Because Pseudomonas sp. B13 has been cultured for a long time in the laboratory, it was not expected to survive well in the microcosm. Surprisingly, it and the derivative GEMs persisted at a high population level of approximately 10(5) bacteria/ml. Pure culture studies had demonstrated an ability of FR1(pFRC20P) to readily degrade simultaneous mixtures of 3CB and 4MB. In the microcosms, however, the GEM did not perform as well as expected, particularly when confronted with a shock load of a 3CB and 4MB mixture. Thus, the microcosm studies may be of potential help for making predictions concerning environmental applications of GEMs. 2. Pseudomonas sp. B13 derivative strains FR1 and FR1(pFRC20P) were able to degrade low concentrations of substituted benzoates within the complex ecosystem of the activated sludge microcosm. A good deal of information concerning the degradation pathway for aromatics by Pseudomonas sp. B13 was already known. This allowed for the construction of the stable, regulated pathways for the degradation of substituted aromatic compounds in both GEMs and indicates that the construction of similar GEMs for the degradation of environmental pollutants is a promising experimental strategy. 3. There was not any demonstrable, adverse effect of GEM addition to the microbial population level in the microcosm. The GEMs were even able to function in a protective manner for the indigenous populations by buffering them against the adverse effects of addition of substituted benzoates. In contrast, for microcosms lacking GEM addition, a wash-out of the bacterial population in the microcosm occurred (data not shown). 4. Lateral transfer of new genetic information (xylXYZLS) from the GEM chromosome to indigenous microorganisms was not detected, whereas transfer of the hybrid, mobilizable pFRC20P carrying the gene for lactone isomerase did apparently occur. In this particular case, transfer may have been beneficial for the community as a whole if it increased the ecosystem's ability to cope with the presence of toxic pollutants. As more GEMs are constructed for specific biotechnological applications the diversity and complexity of microcosms used to study their fate and function will increase. The ability of such studies to predict a priori the fate of these microorganisms will help to develop strategies both to decrease the risks associated with introducing GEMs into the environment and to increase and regulate the capacity of GEMs to degrade toxic pollutants.(ABSTRACT TRUNCATED AT 400 WORDS)

Bacteria↗

PubMed2006

Genomics for environmental microbiology.

The utilization of natural microbial diversity in biotechnology is hindered by our inability to culture the vast majority of microorganisms and the observation that laboratory engineered bacteria rarely function in the wild. It is now clear that an understanding of the community structure, function and evolution of bacteria in their natural environments is required to meet the promise of microbial biotechnology. To meet these new challenges, microbiologists are applying the tools of genomics and related high-throughput technologies to both cultured microbes and environmental samples. This work will lead to new views on ecosystems and biological function together with the biotechnology enabled by this science.

Environmental Microbiology↗

PubMed2002

Fulfilling the promise of biotechnology.

Genetic engineering has produced pharmaceuticals, disease-resistant plants, cloned animals and research and industrial products. While the comparably mature field of medical biotechnology now reveals its true potential, marine biotechnology is still in the realm of the future. As we explore the earth for new sources of natural chemicals, we now search the waters. Myriad organisms, most unknown to us, live there. Many produce compounds that can be commercialized, or the organisms themselves may be commercialized, through genetic engineering methods. For decades, scientists studied the ocean depths searching for unique molecules and organisms. But not until the early 1980s was there a synthesis uniting marine natural products, ecology, aquaculture and bioremediation research under the heading of marine biotechnology. As harvesting enough products from marine sources to produce sufficient amounts, even for study, is nearly impossible, we need to use genomics techniques to identify biologically active compounds. As we damage our oceanic ecosystems through pollution, overfishing and destructive fishing methods, opportunities to learn more about marine organisms and their commercial potential may be limited. Although governments and intergovernmental agencies are committed to funding and expanding oceanic research, more funding is needed to discover and study the ocean's vast, unplumbed resources.

Journal Article↗

PubMed2006

Nanomedicine: An unresolved regulatory issue.

Nanomedicine is a science that uses nanotechnology to maintain and improve human health at the molecular scale. Current and potential applications of nanotechnology in medicine range from research involving diagnostic devices, drug delivery vehicles to enhanced gene therapy and tissue engineering procedures. Its advantage over conventional medicine lies on its size. Particle size has effect on serum lifetime and pattern of deposition. This allows drugs of nanosize be used in lower concentration and has an earlier onset of therapeutic action. It also provides materials for controlled drug delivery by directing carriers to a specific location. Major efforts are underway, however, very little attention is devoted to assessment of health risks to human or to the ecosystem. Inhaled nanoparticles have already been related to lung injury. It is recognized that physico-chemical properties in conjunction with environmental factors and stability of the nanomaterial all contribute to the overall toxicological responses. Nanotoxicological information, currently insufficient, will be vital in aiding academia, industry and regulatory bodies in elucidating the mechanisms of action, balancing its risk and benefit, thus maximizing the utility of these materials in medicine without compromising public health and environmental integrity.

Animals↗

PubMed2002

The anammox case-a new experimental manifesto for microbiological eco-physiology.

The anaerobic ammonium oxidation process is a new process for ammonia removal from wastewater. It is also a new microbial physiology that was previously believed to be impossible. The identification of Candidatus Brocadia anammoxidans and its relatives as the responsible bacteria was only possible with the development of a new experimental approach. That approach is the focus of this paper. The approach is a modernisation of the Winogradsky/Beyerinck strategy of selective enrichment and is based on the introduction of the molecular toolbox and modern bioreactor engineering to microbial ecology. It consists of five steps: (1) postulation of an ecological niche based on thermodynamic considerations and macro-ecological field data; (2) engineering of this niche into a laboratory bioreactor for enrichment culture; (3) black-box physiological characterisation of the enrichment culture as a whole; (4) phylogenetic characterisation of the enriched community using molecular tools; (5) physical separation of the dominant members of the enrichment culture using gradient centrifugation and the identification of the species of interest in accordance with Koch's postulates; (6) verification of the in situ importance of these species in the actual ecosystems. The power of this approach is illustrated with a case study: the identification of the planctomycetes responsible for anaerobic ammonium oxidation. We argue that this was impossible using molecular ecology or conventional 'cultivation based techniques' alone. We suggest that the approach might also be used for the microbiological study of many interesting microbes such as anaerobic methane oxidisers.

Bacteria, Anaerobic↗

PubMed2006

Gradual soil water depletion results in reversible changes of gene expression, protein profiles, ecophysiology, and growth performance in Populus euphratica, a poplar growing in arid regions.

The responses of Populus euphratica Oliv. plants to soil water deficit were assessed by analyzing gene expression, protein profiles, and several plant performance criteria to understand the acclimation of plants to soil water deficit. Young, vegetatively propagated plants originating from an arid, saline field site were submitted to a gradually increasing water deficit for 4 weeks in a greenhouse and were allowed to recover for 10 d after full reirrigation. Time-dependent changes and intensity of the perturbations induced in shoot and root growth, xylem anatomy, gas exchange, and water status were recorded. The expression profiles of approximately 6,340 genes and of proteins and metabolites (pigments, soluble carbohydrates, and oxidative compounds) were also recorded in mature leaves and in roots (gene expression only) at four stress levels and after recovery. Drought successively induced shoot growth cessation, stomatal closure, moderate increases in oxidative stress-related compounds, loss of CO2 assimilation, and root growth reduction. These effects were almost fully reversible, indicating that acclimation was dominant over injury. The physiological responses were paralleled by fully reversible transcriptional changes, including only 1.5% of the genes on the array. Protein profiles displayed greater changes than transcript levels. Among the identified proteins for which expressed sequence tags were present on the array, no correlation was found between transcript and protein abundance. Acclimation to water deficit involves the regulation of different networks of genes in roots and shoots. Such diverse requirements for protecting and maintaining the function of different plant organs may render plant engineering or breeding toward improved drought tolerance more complex than previously anticipated.

Climate↗

PubMed2002

Microbial contamination in Lake Pontchartrain Basin and best management practices on microbial contamination reduction.

The Lake Pontchartrain Basin is a complex system of physical and biological elements. Due to the actions of man, the Basin's ecosystem has changed significantly over the past half century. These changes have impaired water quality and habitats throughout the Pontchartrain Basin. Recreational activities including swimming have been banned in areas of the lake. This paper discusses sources of microbial contamination impacting designated use criteria and the need of disinfection for water quality enhancement. Quantification of microbial loadings and identification of organisms of particular concern are made. Alternative Best Management Practices (BMPs) are suggested with emphasis on disinfection and engineered microbial reduction technologies.

Conservation of Natural Resources↗

PubMed2024

Tapping the treasure trove of atypical phages.

With advancements in genomics technologies, a vast diversity of 'atypical' phages, that is, with single-stranded DNA or RNA genomes, are being uncovered from different ecosystems. Though these efforts have revealed the existence and prevalence of these nonmodel phages, computational approaches often fail to associate these phages with their specific bacterial host(s), while the lack of methods to isolate these phages has limited our ability to characterize infectivity pathways and new gene function. In this review, we call for the development of generalizable experimental methods to better capture this understudied viral diversity via isolation and study them through gene-level characterization and engineering. Establishing a diverse set of new 'atypical' phage model systems has the potential to provide many new biotechnologies, including potential uses of these atypical phages in halting the spread of antibiotic resistance and engineering of microbial communities for beneficial outcomes.

Bacteriophages↗

PubMed2001

[Ecotoxicology, human ecology, laser biotechnology in primary prevention of environmental health hazards].

Interdisciplinary studies in ecotoxicology (including the influence of complex physical, chemical and biological factors on ecosystems and human food chain), human ecology (related to estimation of individuals exposition to different pollutants both in the natural environment and in-door environment, as well as by food) and environmental biotechnology (based on application of high sensitive biological, especially embryological criteria in biotests for water quality, including image computisation and biosensors)--are scientific base for primary prevention of disturbances of the ecological balance as well as environmental risk factors for human health. Large scale applications of laser biostimulation in environmental engineering is a new chance for system approach in primary prevention by more efficient nutritional prevention, protection of proper water quality (including biotests) and protection of the human environment in working and living places.

Biotechnology↗

PubMedDate not supplied

Diversity of alternative hosts of maize stemborers in Trans-Nzoia district of Kenya.

Genetically-engineered (GE) crops such as those expressing insecticidal Bacillus thuringiensis (Bt) toxin genes have the potential to greatly reduce the use of broad spectrum insecticides and increase crop productivity. However, development of resistance by the target insect species is an important consideration in the deployment of this strategy. In areas where GE crops are deployed on a large scale, current resistance management strategies rely on a 'refuge strategy', comprising the incorporation of a certain proportion of non-GE plants in the agro-ecosystems, to conserve susceptible individuals of the target pests. In the USA, simulation models indicate that at least 20% of the crop should be non-Bt plants. In Africa, the target lepidopteran stemborers attack a wide range of wild grass species as well as cultivated cereal crops. Wild grasses generally occur in the vicinity of maize and other cereal fields, and may provide a refuge if GE crops are in the farming systems. To assess the quality of these grasses as refuges, it is critical to obtain information about their size and spatial distribution. In this study, we have assessed the abundance and diversity of alternative refuge of stemborers, mainly wild grasses occurring in the proximity of maize fields, in Trans-Nzoia district, one of the most important maize growing areas in Kenya. The proportion of wild host plants relative to maize was found to decline from 100% during the non-cropping season to <8% during the maize-growing season. The Shannon-Weaver diversity index indicated high variation in the diversity of wild hosts of stemborers between agro-ecological zones in the district. The results of this study are discussed in light of the possible role that wild host plant species might play in stemborer resistance management following the introduction of Bt maize.

Adaptation, Physiological↗

PubMed2006

An overview of challenges in modeling heat and mass transfer for living on Mars.

Engineering a life-support system for living on Mars requires the modeling of heat and mass transfer. This report describes the analysis of heat and mass transfer phenomena in a greenhouse dome, which is being designed as a pressurized life-support system for agricultural production on Mars. In this Martian greenhouse, solar energy will be converted into chemical energy in plant biomass. Agricultural products will be harvested for food and plant cultivation, and waste materials will be processed in a composting microbial ecosystem. Transpired water from plants will be condensed and recycled. In our thermal design and analysis for the Martian greenhouse, we addressed the question of whether temperature and pressure would be maintained in the appropriate range for humans as well as plants. Energy flow and material circulation should be controlled to provide an artificial ecological system on Mars. In our analysis, we assumed that the greenhouse would be maintained at a subatmospheric pressure under 1/3-G gravitational force with 1/2 solar light intensity on Earth. Convection of atmospheric gases will be induced inside the greenhouse, primarily by heating from sunlight. Microclimate (thermal and gas species structure) could be generated locally around plant bodies, which would affect gas transport. Potential effects of those environmental factors are discussed on the phenomena including plant growth and plant physiology and focusing on transport processes. Fire safety is a crucial issue and we evaluate its impact on the total gas pressure in the greenhouse dome.

Agriculture↗

PubMed2002

Field and pulping performances of transgenic trees with altered lignification.

The agronomic and pulping performance of transgenic trees with altered lignin has been evaluated in duplicated, long-term field trials. Poplars expressing cinnamyl alcohol dehydrogenase (CAD) or caffeate/5-hydroxy-ferulate O-methyltransferase (COMT) antisense transgenes were grown for four years at two sites, in France and England. The trees remained healthy throughout the trial. Growth indicators and interactions with insects were normal. No changes in soil microbial communities were detected beneath the transgenic trees. The expected modifications to lignin were maintained in the transgenics over four years, at both sites. Kraft pulping of tree trunks showed that the reduced-CAD lines had improved characteristics, allowing easier delignification, using smaller amounts of chemicals, while yielding more high-quality pulp. This work highlights the potential of engineering wood quality for more environmentally benign papermaking without interfering with tree growth or fitness.

Alcohol Oxidoreductases↗

PubMed1988

Plasmids in the environment.

Bacterial plasmids existed in bacteria before the antibiotic era but their presence was brought into prominence by the use of antibiotics which selected for antibiotic resistant strains. Subsequently, the range of genes carried on plasmids was shown to extend far beyond those coding for antibiotic resistance. Any consideration of plasmids in the environment, therefore, must include all plasmids whether or not they are genetically linked with antibiotic resistance. Antibiotic resistant bacteria may be found in the environment either by contamination with excreta from man and animals in which the strains were selected, or by their selection within the environment by antibiotics synthesized in situ or reaching the environment in an undegraded form in sewage from man and animals, or from industry. Other agents, also contaminating the environment, exert a selective pressure such as heavy metals in industrial effluents which select for metal resistance. This paper reviews the incidences and role of plasmids in various habitats including natural waters, soil, pastures, farm wastes, and human sewage from both hospitalised and other populations. Aspects of plasmid ecology, their biological role, and the transmissibility of genetic material between bacteria within the environment are considered. Two recent studies in Bristol, UK, are reported. The first was a genetic study on Escherichia coli isolates from calf slurry. Various DNA probes were used to determine the extent of gene exchange between the various serotypes within the natural environment. The second was a preliminary study to determine the stability of a recombinant plasmid, in a wild strain of Escherichia coli of pig origin, after its release into a semi-contained farm situation. It is now recognized that plasmids are widely distributed in bacterial populations in terrestrial and aquatic environments. Many have been detected by their carriage of genes coding for antibiotic or heavy metal resistance. Others, mainly cryptic in nature, have been demonstrated by plasmid profile studies on isolates from various habitats. Plasmids were shown to be present in a relatively few bacteria deposited in culture collections prior to the antibiotic era. Subsequently, the increased prevalence of R plasmids in bacteria in most ecosystems were due mainly to the selective pressure imposed by the use of antibiotics. This pressure may have been exerted either in the environment in which the strains were found or elsewhere, the environment subsequently being contaminated by antibiotic resistant bacteria.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗

PubMed2003

Decision support for road system analysis and modification on the Tahoe National Forest.

The United States Forest Service is required to analyze road systems on each of the national forests for potential environmental impacts. We have developed a novel and inexpensive way to do this using the Ecosystem Management Decision Support program (EMDS). We used EMDS to integrate a user-developed fuzzy logic knowledge base with a grid-based geographic information system to evaluate the degree of truth for assertions about a road's environmental impact. Using spatial data for natural and human processes in the Tahoe National Forest (TNF, California, USA), we evaluated the assertion "the road has a high potential for impacting the environment." We found a high level of agreement between the products of this evaluation and ground observations of a TNF transportation engineer, as well as occurrences of road failures. We used the modeled potential environmental impact to negatively weight roads for a least-cost path network analysis to 1573 points of interest in the forest. The network analysis showed that out of 8233 km of road analyzed in the forest, 3483 km (42%) must be kept in a modified road network to ensure access to these points. We found that the modified network had improved patch characteristics, such as significantly fewer "cherry stem" roads intruding into patches, an improved area-weighted mean shape index, and larger mean patch sizes, as compared to the original network. This analysis system could be used by any public agency to analyze infrastructure for environmental or other risk and included in other mandated analyses such as risks to watersheds.

Conservation of Natural Resources↗