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PubMed2001

Bifidobacteria: genetic modification and the study of their role in the colon.

Bifidobacteria are among the most common bacteria in the human intestine and are thought to have a positive effect on human health. Therefore, there is an increasing interest in using these microorganisms as probiotics, either in fermented dairy products or formulated as tablets. However, convincing scientific data supporting their health claims are scarce. The study of the role of bifidobacteria in the colon is complicated by the fact that they are part of a complex ecosystem also interacting with the human host and by the fact that their in vivo study encounters many ethical constraints. Several tools have been developed at TNO with which the role of bifidobacteria can be studied. These include (i) an efficient transformation protocol for the introduction of foreign DNA into Bifidobacterium strains and (ii) in vitro models of the stomach/small intestine (TIM-1) and large intestine (TIM-2), creating an environment closely resembling that of the in vivo situation. With these tools, biomarkers from bifidobacteria quantifying their positive effect on gut health can be identified.

Bifidobacterium↗

PubMed1986

UK issues field testing guidelines.

The planned release of genetically manipulated organisms may over the coming decades bring considerable benefits in agriculture and the environment. The foreseeable applications are generating justifiable excitement and as biological knowledge and expertise in genetic manipulation increase, so without doubt will the range of these applications. Nevertheless this novel use of genetic manipulation does pose questions of potential hazard to human, animal and plant health and of environmental impact in general. While there is some accumulated experience of risk assessment based on the evolution of novel traits in existing populations and the introduction of organisms to ecosystems, there is no experience as yet involving the introduction of genetically manipulated organisms. The risk assessment of such projects may involve many factors, reflecting the complexity of environmental interactions. It is not yet possible to devise a single, broadly applicable risk assessment scheme. However, a number of factors relevant to the majority of foreseeable release applications can be identified and these should be used to develop a consistent approach to risk assessment. As evidence accumulates, these guidelines will be subject to review by ACGM. Meanwhile, all proposals to release genetically manipulated organisms must be considered by ACGM on a case by case basis.

Genetic Engineering↗

PubMed2000

Use of bioassays for assessment of water-extractable ecotoxic potential of soils.

The characterization of contaminated soils is based on heterogeneous strategies considering chemical analyses or bioassays. In the report Bioassays for soils, test methods which are at an advanced state of development and standardization are recommended by the German DECHEMA (German Society for Chemical Apparatus, Chemical Engineering and Biotechnology e.V.). Following this report six soil samples contaminated with different organic and inorganic substances are applied to bioassays using the following organisms: Scenedesmus subspicatus, Daphnia magna, Vibrio fischeri, and Pseudomonas putida. Additionally, they are chemically analyzed. The test results demonstrate that toxic contaminants are present and bioavailable in water elutriates from two soils, indicating the necessity of bioassays and chemical analyses to predict potential risks from contaminated soils. Furthermore it is demonstrated that the described qualitative approach for the assessment of test results is not sufficient to quantify the risk potential of contaminated soils.

Animals↗

PubMedDate not supplied

The fate of estrogenic hormones in an engineered treatment wetland with dense macrophytes.

Recently, the estrogenic hormones 17beta-estradiol (E2) and 17alpha-ethinyl estradiol (EE2) have been detected in municipal wastewater effluent and surface waters at concentrations sufficient to cause feminization of male fish. To evaluate the fate of steroid hormones in an engineered treatment wetland, lithium chloride, E2, and EE2 were added to a treatment wetland test cell. Comparison of hormone and tracer data indicated that 36% of the E2 and 41% of the EE2 were removed during the cell's 84-h hydraulic retention time (HRT). The observed attenuation was most likely the result of sorption to hydrophobic surfaces in the wetland coupled with biotransformation. Sorption was indicated by the retardation of the hormones relative to the conservative tracer. Biotransformation was indicated by elevated concentrations of the E2 metabolite, estrone. It may be possible to improve the removal efficiency by increasing the HRT or the density of plant materials.

Biodegradation, Environmental↗

PubMed1998

Biosafety of E. coli beta-glucuronidase (GUS) in plants.

The beta-glucuronidase (GUS) gene is to date the most frequently used reporter gene in plants. Marketing of crops containing this gene requires prior evaluation of their biosafety. To aid such evaluations of the GUS gene, irrespective of the plant into which the gene has been introduced, the ecological and toxicological aspects of the gene and gene product have been examined. GUS activity is found in many bacterial species, is common in all tissues of vertebrates and is also present in organisms of various invertebrate taxa. The transgenic GUS originates from the enterobacterial species Escherichia coli that is widespread in the vertebrate intestine, and in soil and water ecosystems. Any GUS activity added to the ecosystem through genetically modified plants will be of no or minor influence. Selective advantages to genetically modified plants that posses and express the E. coli GUS transgene are unlikely. No increase of weediness of E. coli GUS expressing crop plants, or wild relatives that might have received the transgene through outcrossing, is expected. Since E. coli GUS naturally occurs ubiquitously in the digestive tract of consumers, its presence in food and feed from genetically modified plants is unlikely to cause any harm. E. coli GUS in genetically modified plants and their products can be regarded as safe for the environment and consumers.

Ecology↗

PubMed2026

Exploring biohydrogen producing potential of Arctic ice and water through metagenomics and dark fermentation kinetics.

Cryospheric ecosystems in the high Arctic harbor largely unexplored microbiomes with significant biotechnological potential. The present study evaluates the biohydrogen production capabilities of the indigenous microbiome of Ny-Ålesund, Svalbard, using glacial ice and surface water samples. Dark fermentation batch assays were performed at 4 °C and 20 °C with 2-bromoethanesulfonate (BES), a methanogenic inhibitor, to track the succession of metabolic and taxonomic diversity. Metagenomic and functional analyses revealed that under 20 °C and BES conditions, psychrotolerant microbial communities maximize biohydrogen production to 85% of the total biogas produced, with an acetate-dominant fermentation pathway, as inferred from volatile fatty acid (VFA) analysis. This evolves into a highly coordinated system utilizing a coupled Rnf-nitrogenase route alongside Formate Hydrogenlyase and [FeFe]-hydrogenase pathways. Kinetic modelling using the Modified Gompertz equation, along with Q10 temperature-sensitivity indices, demonstrated a very high latent catalytic potential in these cold-adapted microbiomes. This study indicates that Arctic microbiomes are highly elastic thermodynamically and could serve as highly efficient, manipulatable biocatalysts for the environmental recovery of bioenergy through engineered low-temperature systems.

Fermentation↗

PubMed2003

The impact of parietal cells on Helicobacter pylori tropism and host pathology: an analysis using gnotobiotic normal and transgenic mice.

Helicobacter pylori infection of the human stomach is common and typically benign, although a subset of hosts develops severe pathology. Infection occurs in an organ with distinct microenvironments characterized by pronounced differences in the composition of acid-producing parietal cells. In this study, we examine determinants of bacterial tropism to various gastric niches by using germ-free normal and transgenic mice with an engineered parietal cell ablation. Mice were colonized for 8 weeks with a clinical isolate (Hp1) that expresses adhesins recognized by epithelial NeuAcalpha2,3Galbeta1,4 glycan receptors. In normal mice, Hp1 has tropism for a parietal cell-deficient niche where sialylated glycans are expressed by a narrow band of pit cells positioned at the boundary between the squamous epithelium (forestomach) and the proximal glandular epithelium. Lymphoid aggregates that develop in this niche, but not elsewhere in the stomach, were analyzed by GeneChip and quantitative RT-PCR studies of laser capture microdissected mucosa and yielded a series of biomarkers indicative of immune cell activation and maturation. Genetic ablation of parietal cells produced a new source of NeuAcalpha2,3Galbeta1,4 glycans in amplified gastric epithelial lineage progenitors, with accompanying expansion of Hp1 within the glandular epithelium. Lymphoid aggregates that develop in this formerly acid-protected epithelium have molecular features similar to those observed at the forestomach/glandular junction. These findings demonstrate the important roles played by parietal cells and glycan receptors in determining the positioning of H. pylori within the gastric ecosystem, and emphasize the need to consider the evolution of pathology within a given host in a niche-specific context.

Animals↗

PubMed2004

[Emergy analysis on an added loop in Spartina alterniflora ecological engineering].

Based on the principle of multi-grade utilization of resources to get ecological, economic and social benefits of ecological engineering, this paper designed an added loop, following the Spartina alterniflora Ecological Engineering (SAEE). All the added loop design included SAEE, and the capsule was named SAEEC. In the added loop design, the Biological Mineral Liquid (BML) was made into antihyperlipidemia capsules, of which, the total flavonoids added up to 9.58 mg x g(-1). Emergy analysis method was applied to evaluate the SAEEC project. Compared with SAEE, the added loop design increased emergy investment ratio (EIR) by 1.37 fold, net economic benefit of the SAEEC by 2.13 fold, economic yield/input ratio by 1.46 fold, net emergy yield (NEY) by 3.18 fold, and net emergy yield ratio (EYR) by 2.20 fold, showing its more efficiency.

Agriculture↗

PubMed2026

Metabolic niche differentiation and napA evolution stabilize partial denitrification in wastewater ecosystems.

Although partial denitrification (PD) is increasingly applied as a nitrite-supplying strategy for anammox-based nitrogen removal, the ecological distribution, metabolic specialization, and genomic determinants of stable nitrite accumulation remain poorly understood at the ecosystem scale. Here, we reconstructed 516 high-quality metagenome-assembled genomes (MAGs) using high-depth metagenomic sequencing of 107 wastewater treatment plants and classified denitrifiers according to their nitrite production or consumption capacities. Of these genomes, 23% (120 MAGs) were classified as partial denitrifiers, 41% (211 MAGs) as complete denitrifiers, and 36% (185 MAGs) as nitrite-reducing denitrifiers, revealing pronounced functional partitioning rather than dominance by complete denitrification pathways. Comparative genomics showed that partial denitrifiers possess metabolic architectures favoring rapid carbon oxidation and NADH generation while exhibiting constrained NADPH production and biosynthetic investment, thereby promoting nitrate-to-nitrite conversion but limiting subsequent nitrite reduction. Nitrite accumulation does not result from incomplete denitrification pathways but from metabolic niche differentiation. These metabolic trade-offs were further associated with the evolutionary divergence of the periplasmic nitrate reductase gene, napA, which displayed distinct sequence characteristics and genomic contexts between partial and complete denitrifiers. Integration of carbohydrate-active enzyme repertoires further revealed metabolic complementarity between partial denitrifiers and anammox bacteria, supporting efficient carbon handoff without direct substrate competition. From an engineering perspective, operating conditions that impose moderate electron limitation, such as low or fluctuating C/N ratios and intermittent carbon feeding, may selectively enrich partial denitrifiers and enhance a stable nitrite supply for PD-anammox systems. Together, these findings identify PD as a predictable ecological state shaped by genome-encoded metabolic specialization and provide a mechanistic basis for designing robust, low-carbon nitrogen-removal processes.

Anammox↗

PubMed2004

Establishment risks for invasive species.

This article presents a quantitative methodology for evaluating the probability of invasive pest species establishing persistent populations. The estimation of pest establishment relies on data and information describing the biology and ecology of the pest and its interactions with potential host species and the regional environment. This information is developed using a model construct borrowed from theoretical population ecology. The methodology for estimating the probability of pest establishment is part of an overall framework that explores the implications of reductions in pest invasions on subsequent establishment. The risk reduction framework integrates the engineering aspects of different technologies for reducing pest entry, the biology and ecology of pest species, the suitability of potentially susceptible hosts, and the quality of available habitats. The methodology for estimating the risk of establishment is presented using an example pest, the Asian longhorned beetle (Anoplophora glabripennis), which has been introduced into the United States via solid wood packing materials (SWPM) used in international commerce. Uncertainties inherent to the estimation of model parameters that determine the risk of establishment are defined, quantified, and propagated through the population model. Advantages and limitations of the proposed methodology are discussed along with recommendations to make the approach more useful in the management of risks posed by the establishment of pest populations.

Algorithms↗

PubMed2006

Revegetation strategies for bauxite refinery residue: a case study of Alcan Gove in Northern Territory, Australia.

Alumina extraction from bauxite ore with strong alkali produces waste bauxite refinery residue consisting of residue sand and red mud. The amount and composition of refinery residue depend on the purity of the bauxite ore and extraction conditions, and differs between refineries. The refinery residue is usually stored in engineered disposal areas that eventually have to be revegetated. This is challenging because of the alkaline and sodic nature of the residue. At Alcan Gove's bauxite refinery in Gove, Northern Territory, Australia, research into revegetation of bauxite residue has been conducted since the mid-1970s. In this review, we discuss approaches taken by Alcan Gove to achieve revegetation outcomes (soil capping of refinery residue) on wet-slurry disposal areas. Problems encountered in the past include poor drainage and water logging during the wet season, and salt scalding and capillary rise during the dry season. The amount of available water in the soil capping is the most important determinant of vegetation survival in the seasonally dry climate. Vegetation cover was found to prevent deterioration of the soil cover by minimising capillary rise of alkalinity from the refinery residue. The sodicity and alkalinity of the residue in old impoundments has diminished slightly over the 25 years since it was deposited. However, development of a blocky structure in red mud, presumably due to desiccation, allows root penetration, thereby supplying additional water to salt and alkali-tolerant plant species. This has led to the establishment of an ecosystem that approaches a native woodland.

Aluminum↗

PubMed2001

The costing of carbon credits from ocean nourishment plants.

Ocean nourishment is a process for stimulating the sequestration of atmospheric carbon dioxide in the deep ocean by providing the nutrients needed to enhance the production of phytoplankton. The carbon dioxide sink thus created, can be used to generate tradeable carbon credits. The costs of sequestering carbon by the process of ocean nourishment have been estimated using as a basis, the previous experience in nitrogen fixing of Toyo Engineering Corporation. While there are uncertainties about the biological uptake efficiency, these introduce only a moderate uncertainty in our overall estimates of costs. The major determinants of the costs are the interest that must be paid on capital and the cost of the feedstock, natural gas. We have used for discussion purposes, an interest rate of 4-8% per annum and natural gas costs of US$0.5-$2 per GJ. The costs of carbon credits lie in the range US$6.70-$12.40 per tonne of carbon dioxide emissions sequestered. It should be noted that we have adopted the measure of carbon avoided by non-emission, because of the complex partitioning of anthropogenic carbon between the atmosphere, land and ocean.

Animals↗

PubMed2003

Bacterial community structure and function in a metal-working fluid.

The diversity of bacterial populations colonizing spatially and temporally separated samples of the same metal-working fluid (MWF) formulation was investigated. Analyses were performed with a view to improve strategies for bioaugmentation of waste MWF in bioreactor systems and prevention of in-use MWF biodeterioration in engineering workshops. Significantly, complementary phenotypic, genotypic and in situ methods revealed that the bacterial communities in operationally exhausted MWFs had low diversity and were similar in species composition from different locations and uses. Of the 179 bacterial isolates studied, only 11 genera and 15 species were identified using fatty acid methyl ester (FAME) analysis, with culture independent analyses by 16S rDNA denaturing gradient gel electrophoresis (DGGE) and fluorescent in situ hybridization being congruent with these FAME data. In order to gain some insight into functional role of detected populations, we correlated the MWF chemical composition and potential pollution load with bacterial abundance and community composition detected within samples.

Bacteria↗

PubMed2006

Sediment management in sustainable urban drainage system ponds.

Since removal and disposal of sustainable urban drainage system (SUDS) sediment can incur high maintenance costs, assessments of sediment volumes, quality and frequency of removal are required. Sediment depth and quality were surveyed annually from 1999-2003 in three ponds and one wetland in Dunfermline, Scotland, UK. Highest sediment accumulation occurred in Halbeath Pond, in the most developed watershed and with no surface water management train. From comparison of measured potentially toxic metal concentrations (Cd, Cr, Cu, Fe, Ni, Pb, Zn) with standards, the average sediment quality should not impair aquatic ecosystems. 72-84% of the metal flux into the SUDS was estimated to be associated with coarse sediment (> 500 microm diameter) suggesting that management of coarse sediment is particularly important at this site. The timing of sediment removal for these SUDS is expected to be determined by loss of storage volume, rather than by accumulation of contaminants. If sediment removal occurs when 25% of the SUDS storage volume has infilled, it would be required after 17 years in Halbeath Pond, but only after 98 years in Linburn Pond (which has upstream detention basins). From the quality measurements, sediment disposal should be acceptable on adjacent land within the boundaries of the SUDS studied.

Cities↗

PubMed2000

[Medium selection and compounding of environmental eco-engineering through making use of life rubbish to produce carpet turf].

Through making use of life rubbish as medium and choosing several materials with high feasibility as compound materials to produce carpet turf, the medium selection and compounding were carried out, and the growth effect of several kinds of turfgrass on each compound medium, its pH value and water stress function were also studied. Sawdust could raise the drought-resistant capacity of turfgrass by strengthening the water-retaining capacity of medium, and promote turfgrass growth. Plant ash showed a strong basicity, and when it made up 25% of medium, the pH value of the medium could be over 9. Fine river sand could improve the ventilating capacity of medium, but if mixed too much, it would decrease its nutritional level. It is suggested that the performance of compound mediums differed greatly with compound materials. Synthesizing each index studied showed that among all compounding mediums sawdust had a significantly positive effect, and had a broad application value.

Ecosystem↗

PubMed2005

Monitoring the development of intertidal habitats on former agricultural land after the managed realignment of coastal defences at Tollesbury, Essex, UK.

The managed realignment of coastal defences and subsequent creation of intertidal habitats is one of several 'soft' engineering options that could reduce the costs of maintaining embankments and at the same time deliver environmental benefits. The managed realignment at Tollesbury was one of the first in the UK, undertaken as an experimental test case to improve understanding of the practical techniques and processes involved. Independent studies were undertaken on the development of soils, benthic invertebrates and vegetation within the site in addition to methods of enhancing the process of natural colonisation of saltmarsh plants. Bathymetric and vegetation monitoring were undertaken on the adjacent estuary to determine any breach effect that may be attributed to the realignment. This paper summarises the results from the vegetation, sedimentation and invertebrate monitoring and discusses the implications for other managed realignment schemes in the UK.

Agriculture↗

PubMed2006

Transgenic approaches to manipulate the environmental responses of the C3 carbon fixation cycle.

The limitation to photosynthetic CO2 assimilation in C3 plants in hot, dry environments is dominated by ribulose 1.5-bisphosphate carboxylase/oxygenase (Rubisco) because CO2 availability is restricted and photorespiration is stimulated. Using a combination of genetic engineering and transgenic technology, three approaches to reduce photorespiration have been taken; two of these focused on increasing the carboxylation efficiency of Rubisco either by reducing the oxygenase reaction directly or by manipulating the Rubisco enzyme by concentrating CO2 in the region of Rubisco through the introduction of enzymes of the C4 pathway. The third approach attempted to reduce photorespiration directly by manipulation of enzymes in this pathway. The progress in each of these areas is discussed, and the most promising approaches are highlighted. Under saturating CO2 conditions, Rubisco did not limit photosynthesis, and limitation shifted to ribulose bisphosphate (RuBP) regeneration capacity of the C3 cycle. Transgenic analysis was used to identify the specific enzymes that may be targets for improving carbon fixation, and the way this may be exploited in the high CO2 future is considered.

Carbon↗

PubMed2006

Quantifying the roles of immigration and chance in shaping prokaryote community structure.

Naturally occurring populations of bacteria and archaea are vital to life on the earth and are of enormous practical significance in medicine, engineering and agriculture. However, the rules governing the formation of such communities are still poorly understood, and there is a need for a usable mathematical description of this process. Typically, microbial community structure is thought to be shaped mainly by deterministic factors such as competition and niche differentiation. Here we show, for a wide range of prokaryotic communities, that the relative abundance and frequency with which different taxa are observed in samples can be explained by a neutral community model (NCM). The NCM, which is a stochastic, birth-death immigration process, does not explicitly represent the deterministic factors and therefore cannot be a complete or literal description of community assembly. However, its success suggests that chance and immigration are important forces in shaping the patterns seen in prokaryotic communities.

Archaea↗