Microbial transformations in phosphonate biosynthesis and catabolism, and their importance in nutrient cycling

Phosphorus cycling in the biosphere has traditionally been thought to involve almost exclusively transformations of the element in its pentavalent oxidation state. Recent evidence, however, suggests that a significant fraction of environmental phosphorus may exist in a more reduced form. Most abundant of these reduced phosphorus compounds are the phosphonates, with their direct carbon–phosphorus bonds, and striking progress has recently been made in elucidating the biochemistry of microbial phosphonate transformations. These advances are now presented in the context of their contribution to our understanding of phosphorus biogeochemistry and of such diverse fields as the productivity of the oceans, marine methanogenesis and the discovery of novel microbial antimetabolites.

Organophosphonates revealed: new insights into the microbial metabolism of ancient molecules.

Organophosphonates are ancient molecules that contain the chemically stable C–P bond, which is considered a relic of the reducing atmosphere on primitive earth. Synthetic phosphonates now have a wide range of applications in the agricultural, chemical and pharmaceutical industries. However, the existence of C–P compounds as contemporary biogenic molecules was not discovered until 1959, with the identification of 2-aminoethylphosphonic acid in rumen protozoa. Here, we review advances in our understanding of the biochemistry and genetics of microbial phosphonate metabolism, and discuss the role of these compounds and of the organisms engaged in their turnover within the P cycle.

Coordination chemistry for information acquisition and processing

In the 21st century, information has become the most valuable resource that is available to modern societies. Thus, great efforts have been made to develop new information processing and storage techniques. Chemistry can offer a wide variety of computing paradigms that are closely related to the natural processes found in living organisms (e.g., in the nervous systems of animals). Moreover, these phenomena cannot be reproduced easily by solely using silicon-based technology. Other great advantages of molecular-scale systems include their simplicity and the diversity of interactions that occur among them. Thus, devices constructed using chemical entities may be programmed to deal with different information carriers (photons, electrons, ions, and molecules), possibly surpassing the capabilities of classic electronic circuits.

Effect of water chemistry on the physiology and toxicity assessment in Daphnia

Todos os sistemas aquáticos estão potencialmente expostos a alterações nos parâmetros da água em consequência de fenómenos ambientais tais como deposição ácida, lixiviação de iões dos solos e alterações climáticas. Dado que os parâmetros químicos da água estão geralmente correlacionados, é pertinente estudar os seus efeitos combinados para o biota aquático. Assim, o principal objetivo desta tese é avaliar a importância ecológica da variação simultânea dos principais parâmetros fisico-químicos da água nos parâmetros de história de vida dos crustáceos tanto na ausência como na presença de metais. Foram estudados os seguintes parâmetros: dureza (0.5 - 3.5 mM), alcalinidade (0.3 - 2.3 mM), pH (5.7 - 9.0) e temperatura (13 - 30ºC). A Daphnia magna foi usada como espécie modelo representando os crustáceos aquáticos. A variação simultânea da dureza e alcalinidade afetou significativamente o crescimento, reprodução e crescimento populacional de Daphnia; no entanto, os efeitos da dureza excederam os efeitos da alcalinidade. Pareceu haver interação entre a dureza e alcalinidade na reprodução dos dafnídeos, o que sugere que os efeitos da variação da dureza para Daphnia e provavelmente outros crustáceos poderão depender do nível de alcalinidade. O pH e dureza da água exerceram efeitos combinados para Daphnia, sendo os efeitos do pH mais pronunciados do que os efeitos da dureza. A diminuição do pH reduziu a sobrevivência, crescimento, reprodução, taxa de ingestão e crescimento populacional dos dafnídeos. No entanto, os efeitos do pH baixo foram mais adversos a baixa dureza, o que sugere uma interação entre estes parâmetros. Assim, a diminuição do pH em lagos de água mole pode ser um estressor determinante para os crustáceos sensíveis à acidez, ameaçando a sua sobrevivência e, consequentemente, afetando a estrutura das cadeias alimentares aquáticas. A temperatura e a química da água (dureza e alcalinidade) interagiram entre si nos parâmetros de história de vida de Daphnia; no entanto, os efeitos da temperatura excederam os efeitos da química da água. De um modo geral, temperaturas extremas reduziram o crescimento, reprodução e, consequentemente, o crescimento populacional de Daphnia. Os efeitos do aumento da temperatura foram mais adversos a baixa dureza e alcalinidade, aumentando a preocupação com os efeitos ecológicos do aquecimento global em águas moles. A dureza e alcalinidade da água também desempenharam um papel importante na toxicidade aguda e subletal (inibição da ingestão) dos metais para Daphnia. A diminuição da dureza aumentou a toxicidade aguda do zinco. Por outro lado, a diminuição da alcalinidade aumentou a toxicidade aguda e subletal do cobre, mas reduziu a toxicidade subletal do zinco, tornando evidente o importante papel da alcalinidade na toxicidade subletal dos metais para Daphnia. Globalmente, os parâmetros fisico-químicos da água parecem interagir entre si, afetando os parâmetros de história de vida e o crescimento populacional de Daphnia e também afetam a toxicidade dos metais. Em particular, a baixa dureza agrava os efeitos adversos da diminuição do pH, aumento da temperatura e toxicidade dos metais, o que aumenta a preocupação com os efeitos ecológicos da sua variação simultânea sobre os crustáceos e, portanto, sobre as cadeias alimentares aquáticas.

Evolution of Koch's postulates: towards a twenty-first century understanding of microbial infection

This editorial discusses strengths and limitations of Koch's postulates reviews modifications that have been used over time, and provides a brief introductory comment to the four papers that comprise the themed section herein.

Chemical and microbial changes during the natural fermentation of strawberry tree (Arbutus unedo L.) fruits

Aguardente de medronho is the name given in Portugal to a spirit made from the fermented fruit of Arbutus unedo (strawberry tree), a plant grown in the Mediterranean region. In order to gain a better understanding of the fermentation process, as it is performed in the farms, a natural fermentation with wild microbiota was carried out during 36 days, and some physicochemical and microbiological parameters were studied. The microbial parameters analyzed were total viable, lactic and acetic acids bacteria, and yeast counts. The physicochemical parameters monitored were sugars, minerals, ethanol, organic acids and pH. Yeasts were the main responsible for the fermentation of the fruits, as the lactic and acetic acids bacteria are absent. As the fermentation progressed, the sugars increased during the first 2 days and gradually decreased along the fermentation period. Maintaining the good quality of the product could contribute to the preservation and valorization of traditional resources that are of great importance to prevent their disappearance.

Phytoplankton and microbial plankton of the Bay of Biscay and Western Iberian Shelf

The region of the Northeast Atlantic represents a gradient between two oceanographic regimes: (i) the subtropical waters of southern Portugal and southwestern Spain, and (ii) the temperate waters characterizing the northwestern and northern Iberian coasts (Cantabrian Sea) and the rest of the Bay of Biscay along the French coast.

Effect of oxygen carriers in microbial and plant cell cultures.

Dissolved oxygen concentration is one of the most limiting factors in aerobic cultures, due to the poor solubility of oxygen in aqueous media. In many processes, the microorganisms growth and production can be affected as a result of insufficient oxygen supply to the broths [1, 2]. To increase oxygen solubility, some methods can be used, such as the increment of aeration or agitation rates or decrease of the solution temperature.

Microbial community composition and mercury cycling in sediments of tagus estuary

Tese de doutoramento, Farmácia (Toxicologia), Universidade de Lisboa, Faculdade de Farmácia, 2016

Medicinal chemistry approaches to malaria drug discovery

Tese de doutoramento, Farmácia (Química Farmacêutica e Terapêutica), Universidade de Lisboa, Faculdade de Farmácia, 2016

High field chemistry with scanning probes

Fabricating Ge and Si integrated structures with nanoscale accuracy is a challenging pursuit essential for novel advances in electronics and photonics. While several scanning probe-based techniques have been proposed, no current technique offers control of nanostructure size, shape, placement, and chemical composition. To this end, atomic force microscope direct write uses a high electric field (> 109 V m-1) to create nanoscale features as fast as 1 cm s-1 by reacting a liquid precursor with a biased AFM tip. In this work, I present the first results on fabricating inorganic nanostructures via AFM direct write. Using diphenylgermane (DPG) and diphenylsilane (DPS), carbon-free germanium and silicon nanostructures (SIMS, x-ray PEEM) are fabricated. For this chemistry, I propose a model that involves electron capture and precursor fragmentation under the high electric field. To verify this model, experimental data and simulations are presented. High field chemistry for DPG and DPS has also been demonstrated for both sequential deposition and the creation of nanoscale heterostuctures, in addition to microscale deposition using a flexible stamp approach. This high field chemistry approach to the deposition of organometallic precursors could offer a low-cost, high throughput alternative for future optical, electronic, and photovoltaic applications.

Enhanced bio-decolourisation of acid orange 7 by Shewanella oneidensis through co-metabolism in a microbial fuel cell

The decolourisation of acid orange 7 (AO7) (C.I.15510) through co-metabolism in a microbial fuel cell by Shewanella oneidensis strain 14063 was investigated with respect to the kinetics of decolourisation, extent of degradation and toxicity of biotransformation products. Rapid decolourisation of AO7 (>98% within 30 h) was achieved at all tested dye concentrations with concomitant power production. The aromatic amine degradation products were recalcitrant under tested conditions. The first-order kinetic constant of decolourisation (k) decreased from 0.709 ± 0.05 h−1 to 0.05 ± 0.01 h−1 (co-substrate – pyruvate) when the dye concentration was raised from 35 mg l−1 to 350 mg l−1. The use of unrefined co-substrates such as rapeseed cake, corn-steep liquor and molasses also indicated comparable or better AO7 decolourisation kinetic constant values. The fully decolourised solutions indicated increased toxicity as the initial AO7 concentration was increased. This work highlights the possibility of using microbial fuel cells to achieve high kinetic rates of AO7 decolourisation through co-metabolism with concomitant electricity production and could potentially be utilised as the initial step of a two stage anaerobic/aerobic process for azo dye biotreatment.

Laccase bio-grafting a versatile modification tool from green chemistry technologies

Today more than 99% of plastics are petroleum-based because of availability and cost of the raw material. The durability of these disposed plastics contributes to the environmental problems as waste and their persistence in the environment causes deleterious effects on the ecosystem. Environmental pollution awareness and the demand for green technology have drawn considerable attention of both academia and industry into biodegradable polymers. In this regard green chemistry technology has the potential to provide solution to this problematic issue. Laccase bio-grafting has recently been the focus of green chemistry technologies due to the growing environmental concerns, legal restrictions and increasing availability of scientific knowledge. In the last several years, research covering various applications of laccases has been increased rapidly particularly in the field of grafting. In principle, laccase-assisted graft co-polymerization may impart a variety of new functionalities to a polymer. The modified polymers through grafting have a bright future and their development is practically boundless. In present work, novel biodegradable graft copolymers combining the advantages of bacterial cellulose backbone and PHB side chains will be prepared by introducing enzymatic grafting technique. The present research will be a first step in the biopolymer modification. To date no report has been found in literature explaining the enzymatic grafting of PHAs. The technique would also provide an efficient modulation approach to improve the biodegradability and biocompatibility of the graft copolymer. The newly grafted copolymers will exhibit unique functionalities with wider range of potential applications mainly in tissue engineering, biosensors, pharmaceutical industry (drug delivery systems) and bio-plastics.

Contribution of direct electron transfer mechanisms to overall electron transfer in microbial fuel cells utilising Shewanella oneidensis as biocatalyst

Objectives To investigate the contribution of direct electron transfer mechanisms to electricity production in microbial fuel cells by physically retaining Shewanella oneidensis cells close to or away from the anode electrode. Results A maximum power output of 114 ± 6 mWm−2 was obtained when cells were retained close to the anode using a dialysis membrane. This was 3.5 times more than when the cells were separated away from the anode. Without the membrane the maximum power output was 129 ± 6 mWm−2. The direct mechanisms of electron transfer contributed significantly to overall electron transfer from S. oneidensis to electrodes, a result that was corroborated by another experiment where S. oneidensis cells were entrapped in alginate gels. Conclusion S. oneidensis transfers electrons primarily by direct electron transfer as opposed to mediated electron transfer.

Development of paper-based color test-strip for drug detection in aquatic environment: Application to oxytetracycline

The wide use of antibiotics in aquaculture has led to the emergence of resistant microbial species. It should be avoided/minimized by controlling the amount of drug employed in fish farming. For this purpose, the present work proposes test-strip papers aiming at the detection/semi-quantitative determination of organic drugs by visual comparison of color changes, in a similar analytical procedure to that of pH monitoring by universal pH paper. This is done by establishing suitable chemical changes upon cellulose, attributing the paper the ability to react with the organic drug and to produce a color change. Quantitative data is also enabled by taking a picture and applying a suitable mathematical treatment to the color coordinates given by the HSL system used by windows. As proof of concept, this approach was applied to oxytetracycline (OXY), one of the antibiotics frequently used in aquaculture. A bottom-up modification of paper was established, starting by the reaction of the glucose moieties on the paper with 3-triethoxysilylpropylamine (APTES). The so-formed amine layer allowed binding to a metal ion by coordination chemistry, while the metal ion reacted after with the drug to produce a colored compound. The most suitable metals to carry out such modification were selected by bulk studies, and the several stages of the paper modification were optimized to produce an intense color change against the concentration of the drug. The paper strips were applied to the analysis of spiked environmental water, allowing a quantitative determination for OXY concentrations as low as 30 ng/mL. In general, this work provided a simple, method to screen and discriminate tetracycline drugs, in aquaculture, being a promising tool for local, quick and cheap monitoring of drugs.