CASE: Complex Adaptive Systems Ecology

Trichloroethylene inhibits nitrogen transformation and microbial community structure in Mollisol

Trichloroethylene (TCE) is the most ubiquitous halogenated organic pollutant in the environment, it is one of the 129 priority control pollutants. In order to clarify the influence of TCE on microorganisms and nitrogen transformation in Mollisol is the core purpose of this study. Results showed that 10 mg kg^-1 TCE is the concentration limit of ammonification in Mollisol. When the concentration of TCE reached 10 mg kg^-1 and the effect lasted for over 7 days, the process of ammonia oxidation to nitric acid in Mollisol will be affected. TCE affected the process of nitrate (NO₃^-) transformation into nitrite (NO₂^-) by affecting the activity of nitrate reductase, thereby affected the denitrification process in soil. When the concentration of TCE is more than 10 mg kg^-1 it reduced the ability of soil microorganisms to obtain nitrogen, thereby affecting soil nitrogen transformation. RDA (Redundancy analysis) showed that the activity of nitrate reductase and the number of nitrifying bacteria and denitrifying bacteria in soil was negatively correlated with the incubation of TCE. In addition, soil nitrate reductase, nitrite reductase, peroxidase activity, ammonifying bacteria, nitrifying bacteria and denitrifying bacteria were negatively correlated with TCE concentration. Beyond that PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) of functional gene structure depend on KEGG (Kyoto Encyclopedia of Genes and Genomes) showed that 20 mg kg^-1 TCE significantly inhibited the metabolism of energy and other substances in Mollisol. Based on the above, it is found that TCE significantly affected nitrification and denitrification in Mollisol, thus the nitrogen transformation in Mollisol was affected by TCE contamination.

Bio-deposition of a calcium carbonate layer on degraded limestone by Bacillus species

To obtain a restoring and protective calcite layer on degraded limestone, five different strains of the Bacillus sphaericus group and one strain of Bacillus lentus were tested for their ureolytic driven calcium carbonate precipitation. Although all the Bacillus strains were capable of depositing calcium carbonate, differences occurred in the amount of precipitated calcium carbonate on agar plate colonies. Seven parameters involved in the process were examined: calcite deposition on limestone cubes, pH increase, urea degrading capacity, extracellular polymeric substances (EPS)-production, biofilm formation, zeta-potential and deposition of dense crystal layers. The strain selection for optimal deposition of a dense CaCO(3) layer on limestone, was based on decrease in water absorption rate by treated limestone. Not all of the bacterial strains were effective in the restoration of deteriorated Euville limestone. The best calcite precipitating strains were characterised by high ureolytic efficiency, homogeneous calcite deposition on limestone cubes and a very negative zeta-potential.

Search and Discovery Strategies for Biotechnology: the Paradigm Shift

SUMMARY

Profound changes are occurring in the strategies that biotechnology-based industries are deploying in the search for exploitable biology and to discover new products and develop new or improved processes. The advances that have been made in the past decade in areas such as combinatorial chemistry, combinatorial biosynthesis, metabolic pathway engineering, gene shuffling, and directed evolution of proteins have caused some companies to consider withdrawing from natural product screening. In this review we examine the paradigm shift from traditional biology to bioinformatics that is revolutionizing exploitable biology. We conclude that the reinvigorated means of detecting novel organisms, novel chemical structures, and novel biocatalytic activities will ensure that natural products will continue to be a primary resource for biotechnology. The paradigm shift has been driven by a convergence of complementary technologies, exemplified by DNA sequencing and amplification, genome sequencing and annotation, proteome analysis, and phenotypic inventorying, resulting in the establishment of huge databases that can be mined in order to generate useful knowledge such as the identity and characterization of organisms and the identity of biotechnology targets. Concurrently there have been major advances in understanding the extent of microbial diversity, how uncultured organisms might be grown, and how expression of the metabolic potential of microorganisms can be maximized. The integration of information from complementary databases presents a significant challenge. Such integration should facilitate answers to complex questions involving sequence, biochemical, physiological, taxonomic, and ecological information of the sort posed in exploitable biology. The paradigm shift which we discuss is not absolute in the sense that it will replace established microbiology; rather, it reinforces our view that innovative microbiology is essential for releasing the potential of microbial diversity for biotechnology penetration throughout industry. Various of these issues are considered with reference to deep-sea microbiology and biotechnology.

Search and discovery strategies for biotechnology: the paradigm shift

Profound changes are occurring in the strategies that biotechnology-based industries are deploying in the search for exploitable biology and to discover new products and develop new or improved processes. The advances that have been made in the past decade in areas such as combinatorial chemistry, combinatorial biosynthesis, metabolic pathway engineering, gene shuffling, and directed evolution of proteins have caused some companies to consider withdrawing from natural product screening. In this review we examine the paradigm shift from traditional biology to bioinformatics that is revolutionizing exploitable biology. We conclude that the reinvigorated means of detecting novel organisms, novel chemical structures, and novel biocatalytic activities will ensure that natural products will continue to be a primary resource for biotechnology. The paradigm shift has been driven by a convergence of complementary technologies, exemplified by DNA sequencing and amplification, genome sequencing and annotation, proteome analysis, and phenotypic inventorying, resulting in the establishment of huge databases that can be mined in order to generate useful knowledge such as the identity and characterization of organisms and the identity of biotechnology targets. Concurrently there have been major advances in understanding the extent of microbial diversity, how uncultured organisms might be grown, and how expression of the metabolic potential of microorganisms can be maximized. The integration of information from complementary databases presents a significant challenge. Such integration should facilitate answers to complex questions involving sequence, biochemical, physiological, taxonomic, and ecological information of the sort posed in exploitable biology. The paradigm shift which we discuss is not absolute in the sense that it will replace established microbiology; rather, it reinforces our view that innovative microbiology is essential for releasing the potential of microbial diversity for biotechnology penetration throughout industry. Various of these issues are considered with reference to deep-sea microbiology and biotechnology.

Perspectives in agrobiotechnology

This review surveys the most important and promising contributions of agricultural biotechnology to the development of sustainable, environment-friendly agriculture. It deals with the recent achievements of genetic technology for the development of new transgenic microbial, plant and animal products. It also deals with the newest developments and perspectives of microbial intervention in agricultural practices, such as biofertilizers, biocontrol agents, and various microbiological products used in modern agriculture. The review surveys the outlook for a waste-free, environment-friendly sustainable agricultural practice, including waste management, recycling and bioremediation technologies. The review lists the most important marketable agrobiotechnological products, and their present and projected sales volume.

In situ gene expression in mixed-culture biofilms: evidence of metabolic interactions between community members

Microbial communities growing in laboratory-based flow chambers were investigated in order to study compartmentalization of specific gene expression. Among the community members studied, the focus was in particular on Pseudomonas putida and a strain of an Acinetobacter sp., and the genes studied are involved in the biodegradation of toluene and related aromatic compounds. The upper-pathway promoter (Pu) and the meta-pathway promoter (Pm) from the TOL plasmid were fused independently to the gene coding for the green fluorescent protein (GFP), and expression from these promoters was studied in P. putida, which was a dominant community member. Biofilms were cultured in flow chambers, which in combination with scanning confocal laser microscopy allowed direct monitoring of promoter activity with single-cell spatial resolution. Expression from the Pu promoter was homogeneously induced by benzyl alcohol in both community and pure-culture biofilms, while the Pm promoter was induced in the mixed community but not in a pure-culture biofilm. By sequentially adding community members, induction of Pm was shown to be a consequence of direct metabolic interactions between an Acinetobacter species and P. putida. Furthermore, in fixed biofilm samples organism identity was determined and gene expression was visualized at the same time by combining GFP expression with in situ hybridization with fluorescence-labeled 16S rRNA targeting probes. This combination of techniques is a powerful approach for investigating structure-function relationships in microbial communities.