Species-specific Partition Research Articles

Manufacturing triple-isotopically labeled microbial necromass to track C, N and P cycles in terrestrial ecosystems

The functional relevance of microbial necromass in terrestrial biogeochemical cycles remains one of the unresolved mysteries of element cycling in ecosystems, especially considering the high microbial abundance and turnover in soil. We therefore established a protocol to manufacture multi-isotope (14C, 15N and 33P) labeled microbial necromass to comprehensively track the turnover of microbial necromass elements within element cycles. This protocol encompasses the i) microbial cultivation of Pseudomonas kilonensis ACN4 (Gram-negative) and Bacillus licheniformis DSM13 (Gram-positive) on labeled minimal medium as well as fungal cultivation of Hypsizygus tessulatus on a complex yeast medium, ii) quantification of radio- (14C, 33P) and stable (15N) isotope incorporation as well their cellular pool partitioning, and iii) determination of element and tracer isotope uptake efficiency. We achieved 1 g of bacterial biomass per liter minimum medium within 24 h and 2.9 g l−1 fungal biomass in complex medium within 18 d. This production rate enabled us to produce more than 100 g of necromass within only one half-life time of 33P, including post-harvest processing. Isotope uptake and incorporation for 33P ranged from 10 to 73%, for 15N from 24 to 52%, and for 14C from 12 to 23%. Each of the cultivated species showed individual patterns of tracer element uptake. The nutritional value of the carbon- (C), nitrogen- (N) and phosphorus- (P) labeled microbial necromass was characterized by a water-based, necromass species-specific partitioning scheme with subsequent elemental analysis of the pools. We separated Gram-negative, Gram-positive and fungi’s cellular pools to characterize element and tracer partitioning among dissolved versus particulate fractions. That is essential because these properties subsequently affect the respective pool's availability for ecosystem nutrition. Our procedure allows a defined production of microorganism-based necromass, enabling versatile use to determine necromass-related nutrient fluxes in terrestrial ecosystem studies.

Life table invasion models: spatial progression and species-specific partitioning.

Biological invasions are increasingly being considered important spatial processes that drive global changes, threatening biodiversity, regional economies, and ecosystem functions. A unifying conceptual model of the invasion dynamics could serve as a useful tool for comparison and classification of invasion processes involving different species across large geographic ranges. By dividing these geographic ranges that are subject to invasions into discrete spatial units, we here conceptualize the invasion process as the transition from pristine to invaded spatial units. We use California cities as the spatial units and a long-term database of invasive tropical tephritids to characterize the invasion patterns. A new life-table method based on insect demography, including the progression model of invasion stage transition and the species-specific partitioning model of multispecies invasions, was developed to analyze the invasion patterns. The progression model allows us to estimate the probability and rate of transition for individual cities from pristine to infested stages and subsequently differentiate the first year of detection from detection recurrences. Importantly, we show that the interval of invasive tephritid recurrence in a city declines with increasing invasion stages of the city. The species-specific partitioning model revealed profound differences in invasion outcome depending on which tephritid species was first detected (and then locally eradicated) in the early stage of invasion. Taken together, we discuss how these two life-table invasion models can cast new light on existing invasion concepts; in particular, on formulating invasion dynamics as the state transition of cities and partitioning species-specific roles during multispecies invasions. These models provide a new set of tools for predicting the spatiotemporal progression of invasion and providing early warnings of recurrent invasions for efficient management.

Passive Membrane Penetration of the Serotonin Precursor 5-Hydroxytryptophan is Controlled by Its Zwitterion.

Species-specific partition coefficients in the octanol/water system were determined for the neurotransmitter serotonin (5-HT) and its precursor 5-hydroxytryptophan (5-HTP). The pH-independent partition coefficients (p) of the individual microspecies were determined by combination of experimentally measured distribution constants and a custom-tailored evaluation method, using highly similar auxiliary compounds. Experimental microscopic partition coefficients for triprotic molecules have only been reported before for thyroxine and its derivatives. The parabolic pH-distribution profile of 5-HT shows the dominance of the lipophilic non-charged microspecies, with a log p of 0.66. However, the most lipophilic non-charged form of 5-HTP, with a log p of 0.31, has no significant contribution to the distribution coefficient at any pH value. Instead, the less lipophilic zwitterionic protonation isomer dominates the distribution in the pH range 2.10-11.11. Although the non-charged microspecies of 5-HTP is 151 times more lipophilic than its zwitterionic protonation isomer, the overwhelming dominance of the zwitterionic form ensures that its contribution to the overall lipophilicity exceeds 1320 times that of the non-charged one. This fact is another counter-example of the widespread belief that passive diffusion into lipophilic media is predominated by the non-charged species. The lipophilicity profile of 5-HT and 5-HTP is depicted in terms of species-specific lipophilicities.

OMDY: a new model of organic matter decomposition based on biomolecular content as assessed by 13C-CPMAS-NMR

Modelling organic matter decomposition is fundamental to understand biogeochemical cycling in terrestrial ecosystems. Current models use C/N or Lignin/N ratios to describe susceptibility to decomposition, or implement separate C pools decaying with different rates, disregarding biomolecular transformations and interactions and their effect on decomposition dynamics. We present a new process-based model of decomposition including a description of biomolecular dynamics obtained by 13C-CPMAS NMR spectroscopy. Baseline decay rates for relevant molecular classes and intermolecular protection were calibrated by best fitting of experimental data from leaves of 20 plant species decomposing for 180 days in controlled optimal conditions. The model was validated against field data from leaves of 32 plant species decomposing for 1-year at four sites in Mediterranean ecosystems. Simulations correctly reproduced mass loss data and variations of selected molecular classes both in controlled conditions and in the field, for a wide range of plant molecular composition and environmental conditions. Our innovative approach accurately predicted decomposition of a wide range of litters across different climates. Prediction accuracy emerged from the species-specific partitioning of molecular types and from the representation of intermolecular interactions. Further application should be planned in other ecosystems based on long-term decomposition datasets.

Advances in microspeciation of drugs and biomolecules: Species-specific concentrations, acid-base properties and related parameters

The pharmacokinetic and pharmacodynamic behaviour of drugs and the interacting biomolecules are highly influenced by their species-specific physico-chemical properties. The first of such bio-relevant, structure-dependent properties were the species-specific acid-base constants and the co-dependent concentrations, but the past decade brought significant advances to previously uncharted territories, including the experimental determination of species-specific partition coefficients, solubilities and redox equilibrium constants.This review gives an overview of the types and definitions of species-specific physico-chemical and analytical properties. We survey the pertinent literature, the fundamental relationships, and summarize some of our recent work that enabled the determination of species-specific partition coefficients for coexisting, inseparable protonation isomers and pH-independent, microscopic redox equilibrium constants.The thorough insight provided by these species-specific properties improves our understanding of the submolecular mechanism of pharmacokinetic processes. As a result, there are some pieces of clear-cut evidence of practical significance. A few of them are as follows:– passive diffusion into lipophilic media is not necessarily predominated by the non-charged species, contrary to the widespread misbelief.– the reactive microspecies in structure-controlled, highly specific biochemical reactions is not necessarily the major one.– a preventive defence system against oxidative stress can be based upon thiol-disulfide equilibria of custom-tailored redox potentials.

Species-specific lipophilicity of thyroid hormones and their precursors in view of their membrane transport properties

A total of 30 species-specific partition coefficients of three thyroid hormones (thyroxine, liothyronine, reverse liothyronine) and their two biological precursors (monoiodotyrosine, diiodotyrosine) are presented. The molecules were studied using combined methods of microspeciation and lipophilicity. Microspeciation was carried out by 1H NMR-pH and UV-pH titration techniques on the title compounds and their auxiliary derivatives of reduced complexity. Partition of some of the individual microspecies was mimicked by model compounds of the closest possible similarity, then correction factors were determined and introduced. Our data show that the iodinated aromatic ring system is the definitive structural element that fundamentally determines the lipophilicity of thyroid hormones, whereas the protonation state of the aliphatic part plays a role of secondary importance. On the other hand, the lipophilicity of the precursors is highly influenced by the protonation state due to the relative lack of overwhelmingly lipophilic moieties. The different logp values of the positional isomers liothyronine and reverse liothyronine represent the importance of steric and electronic factors in lipophilicity. Our investigations provided clear indication that overall partition, the best membrane transport – predicting physico-chemical parameter depends collectively on the site-specific basicity and species-specific partition coefficient. At physiological pH these biomolecules are strongly amphipathic due to the lipophilic aromatic rings and hydrophilic amino acid side chains which can well be the reason why thyroid hormones cannot cross membranes by passive diffusion and they are constituents of biological membranes.The lipophilicity profile of thyroid hormones and their precursors are calculated and depicted in terms of species-specific lipophilicities over the entire pH range.

Thyroxine lipophilicity is dominated by its zwitterionic microspecies

Species-specific partition coefficients were determined for a triprotic molecule for the first time. Thyroxine, the vitally important thyroid hormone which exists in solution in the forms of eight microspecies due to its phenolate, amino and carboxylate basic sites, was studied by combined methods of microspeciation and lipophilicity. Partition of the individual microspecies was mimicked by model compounds of the closest possible similarity, then correction factors were determined and introduced. The non-charged microspecies is only 2.40 times as lipophilic as its zwitterionic protonation isomer, showing that for thyroxine the iodinated aromatic rings are the structural elements that determine the lipophilicity of this molecule, and the protonation state of the other substituents plays only a minor role. The overwhelming dominance of the zwitterionic form, however, ensures that its contribution to the overall lipophilicity exceeds 14,500 times that of the non-charged one. This fact is so far the sharpest counter-example of the widespread belief that passive diffusion into lipophilic media is predominated by the non-charged species. The lipophilicity profile of thyroxine is expressed, calculated and depicted in terms of species-specific lipophilicities over the entire pH range.

Zwitterions Can Be Predominant in Membrane Penetration of Drugs: Experimental Proof

The complete set of species-specific partition coefficients was determined, and the predominant contribution of zwitterionic species to the overall lipophilicity was experimentally proven for the first time. The compounds studied were the amphoteric eburnane alkaloid cis- and trans-apovincaminic acids of therapeutic interest. Partition of the individual microspecies was mimicked by model compounds of the closest possible similarity, and then correction factors were determined and introduced. The noncharged microspecies of the cis-epimer is 30 900 times as lipophilic as its zwitterionic protonation isomer, while the analogous ratio for the trans-epimer is around 15 800. Due to the overwhelming dominance of the zwitterionic form, however, its contribution to the overall lipophilicity exceeds 8 and 5 times that of the noncharged form for the two epimers, respectively. The lipophilicity profile of these zwitterionic compounds is expressed, calculated, and depicted in terms of species-specific lipophilicities over the entire pH range.

Substituent effects on the ionization and partitioning of p-(aminoethyl)phenols and structurally related compounds: Electrostatic effects dependent on conformation

Computational methods to predict pKa values and partition coefficients of drug molecules based on linear free energy relationships (LFERs) rely largely on the principles of independence and additivity of the functional group contributions in each molecule to the overall free energy. Nonadditivities in functional group contributions are often seen when multiple polar functional groups are in close proximity and in cases where conformational flexibility allows widely separated polar functional groups to interact. The degree to which long-range interactions may alter group contributions in more conformationally constrained molecules such as p-(aminoethyl)phenol and structurally similar analogs is more difficult to predict. In this study, both macroscopic and microscopic ionization constants and decadiene/water partition coefficients as a function of pH at 25°C were obtained for p-(aminoethyl)phenol and six structurally related compounds to explore the reliability of the independence and additivity assumptions necessary in using the LFERs for predictions. A long-range interaction between the phenol and amine groups in the series has been found to affect the pKa values of both groups and to alter species-specific partition coefficients. Pronounced shifts in microscopic ionization constants involving zwitterion forms are clearly indicative of amplified long-range interactions between ionized substituents. © 2009 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 98:4534–4544, 2009

Influence of soil pH on the sorption of ionizable chemicals: Modeling advances

The soil-water distribution coefficient of ionizable chemicals (K(d)) depends on the soil acidity, mainly because the pH governs speciation. Using pH-specific K(d) values normalized to organic carbon (K(OC)) from the literature, a method was developed to estimate the K(OC) of monovalent organic acids and bases. The regression considers pH-dependent speciation and species-specific partition coefficients, calculated from the dissociation constant (pK(a)) and the octanol-water partition coefficient of the neutral molecule (log P(n)). Probably because of the lower pH near the organic colloid-water interface, the optimal pH to model dissociation was lower than the bulk soil pH. The knowledge of the soil pH allows calculation of the fractions of neutral and ionic molecules in the system, thus improving the existing regression for acids. The same approach was not successful with bases, for which the impact of pH on the total sorption is contrasting. In fact, the shortcomings of the model assumptions affect the predictive power for acids and for bases differently. We evaluated accuracy and limitations of the regressions for their use in the environmental fate assessment of ionizable chemicals.

Species-specific partitioning of soil water resources in an old-growth Douglas-fir-western hemlock forest

Although tree- and stand-level estimates of forest water use are increasingly common, relatively little is known about partitioning of soil water resources among co-occurring tree species. We studied seasonal courses of soil water utilization in a 450-year-old Pseudotsuga menziesii (Mirb.) Franco-Tsuga heterophylla (Raf.) Sarg. forest in southwestern Washington State. Soil volumetric water content (theta) was continuously monitored with frequency domain capacitance sensors installed at eight depths from 0.2 to 2 m at four locations in the vicinity of each species. Vertical profiles of root distribution and seasonal and daily courses of hydraulic redistribution (HR), sap flow and tree water status were also measured. Mean root area in the upper 60 cm of soil was significantly greater in the vicinity of T. heterophylla trees. However, seasonal water extraction on a root area basis was significantly greater near P. menziesii trees at all depths between 15 and 65 cm, leading to significantly lower water storage in the upper 65 cm of soil near P. menziesii trees at the end of the summer dry season. Greater apparent efficiency of P. menziesii roots at extracting soil water was attributable to a greater driving force for water uptake rather than to differences in root hydraulic properties between the species. The dependence of HR on theta was similar in soil near individuals of both species, but seasonal maximum rates of HR were greater in soil near P. menziesii because minimum values of theta were lower, implying a steeper water potential gradient between the upper and lower soil that acted as a driving force for water efflux from shallow roots. The results provide information on functional traits relevant for understanding the ecological distributions of these species and have implications for spatial variability of processes such as soil respiration and nutrient cycling.

Determination of conformer-specific partition coefficients in octanol/water systems.

The first conformer-specific experimental partition coefficients are presented for octanol/water, the most widespread solvent system to predict lipophilicity of drugs. Rotamer populations in octanol and water were elucidated from 1H NMR vicinal coupling constants and were combined with classical partition coefficients to obtain the conformer-specific ones. Feasibility of the determination of conformer-specific partition coefficients is exemplified on amphetamine and clenbuterol, two flexible drug molecules. Partition capacities of the amphetamine rotamers have been proven to be essentially equal. The conformers of clenbuterol, however, have been found to be greatly different in partition properties, which could be interpreted in terms of intramolecular interactions between the vicinal polar sites and the solvent-accessibility of the groups. The conformers could be put into order of their membrane-influx and -outflow propensities. Deviations between experimental and calculated log P values could also be interpreted in view of the species-specific partition coefficients.