Woody vegetation structure of xeric forest stands under different edaphic site conditions and disturbance histories in the Biosphere Reserve 'Parque Costero del Sur', Argentina

We studied stand structures and soil properties in an old-growth forest and two 30-yr-old second-growth stands. In the old-growth forest, the total density and basal area average 1566 trees > 1.25 m height ha^-1 and 46.73 m² ha^-1. The dominant trees are Scutia buxifolia and Celtis tala. Using multivariate techniques we distinguished three stands: PS1, dominated by S. buxifolia, is 1000 m far from the river. Its soil is shallow and loamy. PS2 and PS3, co-dominated by S. buxifolia and C. tala, are over 1200 m distant from the river. There the soil is deeper and has thicker texture and higher phosphorus and calcium concentrations than the near-the-river forest soil. Scutia buxifolia shows reverse J-shaped size-distributions and has morphological features of stress-tolerant species. Celtis tala shows oscillating decay size-curves that suggest recruitment pulses related to small gaps and it has morphological features of competitive species. Celtis tala was selectively cut in the past in the second-growth stands SNRD and SRD. The stand SNRD, 1000 m far from the river, is dominated by S. buxifolia. The second species is Schinus polygamus which presents the bell-shaped size-structure of the pioneer species. SNRD does not differ from its old-growth counterpart PS1 in total tree density, basal area and tree branching. The stand SRD, over 1200 m distant from the river, is co-dominated by S. buxifolia and by C. tala trees regenerated from stumps. SRD does not differ from its old-growth counterparts PS2 and PS3 in total tree density and basal area. As to tree branching, it does not differ from PS3, but differs from PS2. All the stands are being invaded by the exotic tree Ligustrum lucidum.The differences between the old-growth stands seem to be related to the gradients of soil texture and nutrient concentrations raising edaphic stress towards the river. In SNRD, the stress, the stress-tolerance of S. buxifolia, and the aptitude of S. polygamus to recruit in disturbed habitats seem to have prevented the post-logging recruitment of C. tala. In SRD, C. tala regenerated possibly due to a better competitive performance in a more favorable site. Under protection the second-growth stands recovered the old-growth quantitative features. We recommend the restoration of the qualitative features and the control of L. lucidum.     

Blastocladiella emersonii expresses a centrin similar to Chlamydomonas reinhardtii isoform not found in late-diverging fungi

Centrins are members of the calcium-binding EF-hand protein superfamily which can be divided into two subfamilies, probably associated with different functions: one related to Chlamydomonas reinhardtii centrin, CrCenp, and the other, represented by Saccharomyces cerevisiae isoform, ScCdc31p. ESTs encoding the two isoforms (BeCen1 and BeCen3) from the chytridiomycete Blastocladiella emersonii were isolated, and expression of the CrCenp-type centrin, BeCen1, was analyzed throughout the fungus life cycle. Becen1 mRNA levels increase transiently during sporulation and protein levels present a similar pattern. Immunolocalization studies seem to localize BeCen1 at the basal body zone and in the cytoplasm surrounding the nuclear cap, a zoospore organelle.     

Comparative EST analysis provides insights into the basal aquatic fungus Blastocladiella emersonii

Background

Whole genome amplification is an increasingly common technique through which minute amounts of DNA can be multiplied to generate quantities suitable for genetic testing and analysis. Questions of amplification-induced error and template bias generated by these methods have previously been addressed through either small scale (SNPs) or large scale (CGH array, FISH) methodologies. Here we utilized whole genome sequencing to assess amplification-induced bias in both coding and non-coding regions of two bacterial genomes. Halobacterium species NRC-1 DNA and Campylobacter jejuni were amplified by several common, commercially available protocols: multiple displacement amplification, primer extension pre-amplification and degenerate oligonucleotide primed PCR. The amplification-induced bias of each method was assessed by sequencing both genomes in their entirety using the 454 Sequencing System technology and comparing the results with those obtained from unamplified controls.

Results

All amplification methodologies induced statistically significant bias relative to the unamplified control. For the Halobacterium species NRC-1 genome, assessed at 100 base resolution, the D-statistics from GenomiPhi-amplified material were 119 times greater than those from unamplified material, 164.0 times greater for Repli-G, 165.0 times greater for PEP-PCR and 252.0 times greater than the unamplified controls for DOP-PCR. For Campylobacter jejuni, also analyzed at 100 base resolution, the D-statistics from GenomiPhi-amplified material were 15 times greater than those from unamplified material, 19.8 times greater for Repli-G, 61.8 times greater for PEP-PCR and 220.5 times greater than the unamplified controls for DOP-PCR.

Conclusion

Of the amplification methodologies examined in this paper, the multiple displacement amplification products generated the least bias, and produced significantly higher yields of amplified DNA.     

From null community to non-randomly structured actual plant assemblages: parsimony analysis of species co-occurrences

Null community is a spatio‐temporal abstraction of an initial regional species pool from which local species pools and actual community assemblages are organized. Any process that causes joint responses of species with similar susceptibilities affects community assembly. Through time, sequential assembly processes change the composition of a species pool in a way analogous to the one in which evolutionary processes promote character changes from an ancestor to current species. The segregation of species occurrences in an actual community suggests that assembly processes non‐randomly structured the observed community assemblages. However, going backwards to imply the causes of a particular arrangement of species is a non‐trivial challenge. I merge these premises with the philosophical and methodological foundations of cladistics. I propound parsimony analysis of species co‐occurrences as an outstanding means of devising operational hypotheses about the assembly of any non‐randomly structured set of actual community assemblages related to a common species pool. To explore this approach, I used field data gathered in a suite of 10 wetland assemblages. First, I tested independence of 101 plant species occurrences by a null model. As significant non‐random species co‐occurrence was detected, I applied a parsimony analysis taking the species occurrences as attributes, the assemblages as terminal units, and a putative null community constituted by all the present local species as the root of the assembly suite. The analysis produced four most parsimonious trees of assembly relationships. These trees maximize the number of similarities among community assemblages that can be explained by the sole fact of sharing a common regional species pool. One most parsimonious spatio‐temporal arrangement of species occurrence changes was reconstructed on one of the trees. I interpret this reconstruction in terms of assembly events, species exclusions and recruitments, showing the potentialities of this analysis to formulate operational hypotheses about community organization.     

Structural and thermodynamic studies of two centrin isoforms from Blastocladiella emersonii upon calcium binding

Centrins are calcium-binding proteins associated with microtubules organizing centers. Members of two divergent subfamilies of centrins were found in the aquatic fungus Blastocladiella emersonii, contrasting with the occurrence of only one member known for the better explored terrestrial fungi. BeCen1 shows greatest identity with human centrins HsCen1, HsCen2 and green algae centrin CrCenp, while BeCen3 records largest identity with human centrin HsCen3 and yeast centrin Cdc31p. Following the discovery of this unique feature, BeCen1 and BeCen3 centrins were produced to study whether these proteins had distinct features upon calcium binding. Circular dichroism showed opposite calcium binding effects on the α-helix arrangement of the secondary structure. The spectra indicated a decrease in α-helix signal for holo-BeCen1 contrasting with an increase for holo-BeCen3. In addition, only BeCen1 refolds after being de-natured. The fluorescence emission of the hydrophobic probe ANS increases for both proteins likely due to hydrophobic exposure, however, only BeCen1 presents a clear blue shift when calcium is added. ITC experiments identified four calcium binding sites for both proteins. In contrast to calcium binding to BeCen1, which is mainly endothermic, binding to BeCen3 is mainly exothermic. Light-scattering evidenced the formation of large particles in solution for BeCen1 and BeCen3 at temperatures above 30 °C and 40 °C, respectively. Atomic force microscopy confirmed the presence of supramolecular structures, which differ in the compactness and branching degree. Binding of calcium leads to different structural changes in BeCen1 and BeCen3 and the thermodynamic characteristics of the interaction also differ.