Explaining the inhibition of cyclin-dependent kinase 5 by peptides derived from p25 with molecular dynamics simulations and MM-PBSA

10.1007/s00894-009-0514-1Journal of Molecular Modeling1611-8JMMO

The role of iron in the bacterial degradation of organic matter derived from Phaeocystis antarctica

In high-nutrient low-chlorophyll areas, bacterial degradation of organic matter may be iron-limited. The response of heterotrophic bacteria to Fe addition may be directly controlled by Fe availability and/or indirectly controlled through the effect of enhanced phytoplankton productivity and the subsequent supply of organic matter suitable for bacteria. In the present study, the role of Fe on bacterial carbon degradation was investigated through regrowth experiments by monitoring bacterial response to organic substrates derived from Phaeocystis antarctica cultures set up in <1 nM Fe (LFe) and in Fe-amended (HFe) Antarctic seawater. Results showed an impact of Fe addition on the morphotype dominance (colonies vs. single cells) of P. antarctica and on the quality of Phaeocystis-derived organic matter. Fe addition leaded to a decrease of C/N ratio of Phaeocystis material. The bacterial community composition was modified as observed from denaturing gradient gel electrophoresis (DGGE) profiles in LFe as compared to HFe bioassays. The percentage of active bacteria as well as their specific metabolic activities (ectoenzymatic hydrolysis, growth rates and bacterial growth efficiency) were enhanced in HFe bioassays. As a consequence, the lability of Phaeocystis-derived organic matter was altered, i.e. after seven days more than 90% was degraded in HFe and only 9% (dissolved) and 55% (total) organic carbon were degraded in LFe bioassays. By inducing increased bacterial degradation and preventing the accumulation of dissolved organic carbon, the positive effect of Fe supply on the carbon biological pump may partly be counteracted.info:eu-repo/semantics/publishe

The role of iron in the bacterial degradation of organic matter derived from Phaeocystis antarctica

In high-nutrient low-chlorophyll areas, bacterial degradation of organic matter may be iron-limited. The response of heterotrophic bacteria to Fe addition may be directly controlled by Fe availability and/or indirectly controlled through the effect of enhanced phytoplankton productivity and the subsequent supply of organic matter suitable for bacteria. In the present study, the role of Fe on bacterial carbon degradation was investigated through regrowth experiments by monitoring bacterial response to organic substrates derived from Phaeocystis antarctica cultures set up in <1 nM Fe (LFe) and in Fe-amended (HFe) Antarctic seawater. Results showed an impact of Fe addition on the morphotype dominance (colonies vs. single cells) of P. antarctica and on the quality of Phaeocystis-derived organic matter. Fe addition leaded to a decrease of C/N ratio of Phaeocystis material. The bacterial community composition was modified as observed from denaturing gradient gel electrophoresis (DGGE) profiles in LFe as compared to HFe bioassays. The percentage of active bacteria as well as their specific metabolic activities (ectoenzymatic hydrolysis, growth rates and bacterial growth efficiency) were enhanced in HFe bioassays. As a consequence, the lability of Phaeocystis-derived organic matter was altered, i.e. after seven days more than 90% was degraded in HFe and only 9% (dissolved) and 55% (total) organic carbon were degraded in LFe bioassays. By inducing increased bacterial degradation and preventing the accumulation of dissolved organic carbon, the positive effect of Fe supply on the carbon biological pump may partly be counteracted. © 2007 Springer Science+Business Media B.V.SCOPUS: ch.binfo:eu-repo/semantics/publishe

The carbohydrates of Phaeocystis and their degradation in the microbial food web

The ubiquity and high productivity associated with blooms of colonial Phaeocystis makes it an important contributor to the global carbon cycle. During blooms organic matter that is rich in carbohydrates is produced. We distinguish five different pools of carbohydrates produced by Phaeocystis. Like all plants and algal cells, both solitary and colonial cells produce (1) structural carbohydrates, (hetero) polysaccharides that are mainly part of the cell wall, (2) mono- and oligosaccharides, which are present as intermediates in the synthesis and catabolism of cell components, and (3) intracellular storage glucan. Colonial cells of Phaeocystis excrete (4) mucopolysaccharides, heteropolysaccharides that are the main constituent of the mucous colony matrix and (5) dissolved organic matter (DOM) rich in carbohydrates, which is mainly excreted by colonial cells. In this review the characteristics of these pools are discussed and quantitative data are summarized. During the exponential growth phase, the ratio of carbohydrate-carbon (C) to particulate organic carbon (POC) is approximately 0.1. When nutrients are limited, Phaeocystis blooms reach a stationary growth phase, during which excess energy is stored as carbohydrates. This so-called overflow metabolism increases the ratio of carbohydrate-C to POC to 0.4–0.6 during the stationary phase, leading to an increase in the C/N and C/P ratios of Phaeocystis organic matter. Overflow metabolism can be channeled towards both glucan and mucopolysaccharides. Summarizing the available data reveals that during the stationary phase of a bloom glucan contributes 0–51% to POC, whereas mucopolysaccharides contribute 5–60%. At the end of a bloom, lysis of Phaeocystis cells and deterioration of colonies leads to a massive release of DOM rich in glucan and mucopolysaccharides. Laboratory studies have revealed that this organic matter is potentially readily degradable by heterotrophic bacteria. However, observations in the field of accumulation of DOM and foam indicate that microbial degradation is hampered. The high C/N and C/P ratios of Phaeocystis organic matter may lead to nutrient limitation of microbial degradation, thereby prolonging degradation times. Over time polysaccharides tend to self-assemble into hydrogels. This may have a profound effect on carbon cycling, since hydrogels provide a vehicle to move DOM up the size spectrum to sizes subject to sedimentation. In addition, it changes the physical nature and microscale structure of the organic matter encountered by bacteria which may affect the degradation potential of the Phaeocystis organic matter.