Computational modeling of factors that modulate the unique FeNO bonding in {FeNO}6 heme–thiolate model complexes

A density functional theory account of the changes in FeNO bonding that occur in response to both bonded and nonbonded structural perturbations is reported for a series of {FeNO}(6) heme-thiolate model complexes. Using [Fe(porphine)(SCH(3))NO] as the reference complex, we constructed models to mimic equatorial (cis), distal, and proximal influences of protein environments. Overall, the results from these calculations reveal that the Fe-NO and N-O bond strengths change in the same direction upon variations in structure and environment. These bonding changes are manifested in unique direct correlations between the Fe-NO and N-O vibrational frequencies and bond lengths, as evidenced by their positive slopes (slopes of the familiar inverse or backbonding correlations are negative). The electronic origin of the direct correlations appears to derive from the electron density distribution in high-energy molecular orbitals. This variability modulates the FeNO antibonding character throughout the triatomic FeNO moiety. The results of this study suggest that the stabilities and reactivities of {FeNO}(6) centers in heme-thiolate enzymes can be modulated over a significant range through a variety of bonded and nonbonded means.     

Structure and development of ‘witches' broom’ galls in reproductive organs of Byrsonima sericea (Malpighiaceae) and their effects on host plants

Galls are anomalies in plant development of parasitic origin that affect the cellular differentiation or growth and represent a remarkable plant–parasite interaction. Byrsonima sericea DC. (Malpighiaceae) is a super host of several different types of gall in both vegetative and reproductive organs. The existence of galls in reproductive organs and their effects on the host plant are seldom described in the literature. In this paper, we present a novel study of galls in plants of the Neotropical region: the ‘witches' broom’ galls developed in floral structures of B. sericea. The unaffected inflorescences are characterised by a single indeterminate main axis with spirally arranged flower buds. The flower buds developed five unaffected brownish hairy sepals and five pairs of elliptical yellow elaiophores, five yellow fringed petals, 10 stamens and a pistil with superior tricarpellar and trilocular ovary. The affected inflorescences showed changes in architecture, with branches arising from the main axis and flower buds. The flower buds exhibited several morphological and anatomical changes. The sepals, petals and carpels converted into leaf‐like structures after differentiation. Stamens exhibited degeneration of the sporogenous tissue and structures containing hyphae and spores. The gynoecium did not develop, forming a central meristematic region, from which emerges the new inflorescence. In this work, we discuss the several changes in development of reproductive structures caused by witches' broom galls and their effects on reproductive success of the host plants.     

Open resource metagenomics: a model for sharing metagenomic libraries

Both sequence-based and activity-based exploitation of environmental DNA have provided unprecedented access to the genomic content of cultivated and uncultivated microorganisms. Although researchers deposit microbial strains in culture collections and DNA sequences in databases, activity-based metagenomic studies typically only publish sequences from the hits retrieved from specific screens. Physical metagenomic libraries, conceptually similar to entire sequence datasets, are usually not straightforward to obtain by interested parties subsequent to publication. In order to facilitate unrestricted distribution of metagenomic libraries, we propose the adoption of open resource metagenomics, in line with the trend towards open access publishing, and similar to culture- and mutant-strain collections that have been the backbone of traditional microbiology and microbial genetics. The concept of open resource metagenomics includes preparation of physical DNA libraries, preferably in versatile vectors that facilitate screening in a diversity of host organisms, and pooling of clones so that single aliquots containing complete libraries can be easily distributed upon request. Database deposition of associated metadata and sequence data for each library provides researchers with information to select the most appropriate libraries for further research projects. As a starting point, we have established the Canadian MetaMicroBiome Library (CM²BL [1]). The CM²BL is a publicly accessible collection of cosmid libraries containing environmental DNA from soils collected from across Canada, spanning multiple biomes. The libraries were constructed such that the cloned DNA can be easily transferred to Gateway® compliant vectors, facilitating functional screening in virtually any surrogate microbial host for which there are available plasmid vectors. The libraries, which we are placing in the public domain, will be distributed upon request without restriction to members of both the academic research community and industry. This article invites the scientific community to adopt this philosophy of open resource metagenomics to extend the utility of functional metagenomics beyond initial publication, circumventing the need to start from scratch with each new research project.     

Aquarium nitrification revisited: Thaumarchaeota are the dominant ammonia oxidizers in freshwater aquarium biofilters

Ammonia-oxidizing archaea (AOA) outnumber ammonia-oxidizing bacteria (AOB) in many terrestrial and aquatic environments. Although nitrification is the primary function of aquarium biofilters, very few studies have investigated the microorganisms responsible for this process in aquaria. This study used quantitative real-time PCR (qPCR) to quantify the ammonia monooxygenase (amoA) and 16S rRNA genes of Bacteria and Thaumarchaeota in freshwater aquarium biofilters, in addition to assessing the diversity of AOA amoA genes by denaturing gradient gel electrophoresis (DGGE) and clone libraries. AOA were numerically dominant in 23 of 27 freshwater biofilters, and in 12 of these biofilters AOA contributed all detectable amoA genes. Eight saltwater aquaria and two commercial aquarium nitrifier supplements were included for comparison. Both thaumarchaeal and bacterial amoA genes were detected in all saltwater samples, with AOA genes outnumbering AOB genes in five of eight biofilters. Bacterial amoA genes were abundant in both supplements, but thaumarchaeal amoA and 16S rRNA genes could not be detected. For freshwater aquaria, the proportion of amoA genes from AOA relative to AOB was inversely correlated with ammonium concentration. DGGE of AOA amoA genes revealed variable diversity across samples, with nonmetric multidimensional scaling (NMDS) indicating separation of freshwater and saltwater fingerprints. Composite clone libraries of AOA amoA genes revealed distinct freshwater and saltwater clusters, as well as mixed clusters containing both freshwater and saltwater amoA gene sequences. These results reveal insight into commonplace residential biofilters and suggest that aquarium biofilters may represent valuable biofilm microcosms for future studies of AOA ecology.     

Rock-scissors-paper game in a chaotic flow: the effect of dispersion on the cyclic competition of microorganisms

Laboratory experiments and numerical simulations have shown that the outcome of cyclic competition is significantly affected by the spatial distribution of the competitors. Short-range interaction and limited dispersion allows for coexistence of competing species that cannot coexist in a well-mixed environment. In order to elucidate the mechanisms that destroy species diversity we study the intermediate situation of imperfect mixing, typical in aquatic media, in a model of cyclic competition between toxin producing, sensitive and resistant phenotypes. It is found, that chaotic mixing, by changing the character of the spatial distribution, induces coherent oscillations in the populations. The magnitude of the oscillations increases with the strength of mixing, leading to the extinction of some species beyond a critical mixing rate. When mixing is non-uniform in space, coexistence can be sustained at much stronger mixing by the formation of partially isolated regions, that prevent global extinction. The heterogeneity of mixing may enable toxin producing and sensitive strains to coexist for very long time at strong mixing.