Vertical Distribution of Microbial Community Functionality under the Canopies of <Emphasis Type="Italic">Zygophyllum dumosum</Emphasis> and <Emphasis Type="Italic">Hammada scoparia</Emphasis> in the Negev Desert,Israel

Patchy desert shrubs magnify the horizontal heterogeneities of carbon source and nutrient availability in an arid ecosystem, significantly affecting the abundance and activity of the soil microbial community. Since each shrub species develops special ecophysiological adaptations to the extreme harsh desert environments, previous studies elucidated that the effects of perennial shrubs on microbial diversity are unequal. The aim of the present study, conducted in the Negev Desert, Israel, was to illustrate the vertical changes of soil microbial community functionality in the root zone of perennial shrubs. Soil samples were collected from the 0–50 cm depth at 10-cm intervals under the canopy of Zygophyllum dumosum, Hammada scoparia, and from the open spaces between them, in the wet and dry seasons. Soil moisture and organic matter exhibited a significant (P < 0.001) plant and depth dependence. The mean basal respiration rates and microbial biomass in soils collected beneath perennial shrubs were relatively higher than the control during the wet season, however, a contrasting trend was observed at some soil depths during the dry season. Relatively high abundance and activity of aromatic and carboxylic acid utilizers were observed in the vicinity of perennial shrubs, and the values recorded during the dry season were generally higher than the corresponding values during the wet season. In addition, a “mirror effect” in vertical changes of the community-level physiological profile was observed between Z. dumosum and H. scoparia. This study demonstrated the stratification of the functional aspects in soils under the canopy of perennial shrubs, thus indicating that the scattered distribution of vegetation not only causes horizontal heterogeneities of the microbial community in an arid system, but also that the ecophysiological adaptations developed by xerophytes regulate the abundance and saprotrophic functionality of microorganisms in the root zone.     

Epigenetic information can reveal phylogenetic relationships within Zygophyllales

The desert plant Zygophyllum dumosum displays unique epigenetic constraints, not found in other perennial desert plants, namely, it possesses mono- but not di- and tri-methylated histone H3 at lysine 9 (H3K9). We investigated the proposal that lack of dimethylated H3K9 (H3K9me2) is not restricted to Z. dumosum, but a feature uniquely evolved in the Zygophyllaceae. To this end, we analyzed the state of H3K9me2 in various species including Z. simplex (annual), Peganum harmala (hemicryptophyte), Nitraria retusa (shrub) and Balanites aegyptiaca (tree) from the Negev Desert (Israel) and Larrea tridentata (creosote bush), a prominent species in the Mojave, Sonoran, and Chihuahuan Deserts of western North America. All but one of these plants showed dimethylation of H3 at lysine 4 (H3K4me2), but no detectable levels of H3K9me2. The exception was Nitraria retusa, recently separated from the Zygophyllaceae family, which possesses H3K9me2, further supporting its partition into a distinct family (Nitrariaceae). Interestingly, the analysis of Krameria cistoidea (Krameriaceae), which is listed under the Zygophyllales, showed the presence of H3K9me2. It appears that lack of H3K9me2 has uniquely evolved in the Zygophyllaceae (sensu stricto), suggesting that this phenomenon has a strong genetic background. Thus, epigenetic information revealed for Zygophyllaceae can be useful to phylogenetic approaches.     

Trimethylation of Histone H3 Lysine 36 by Human Methyltransferase PRDM9 Protein

PRDM9 (PR domain-containing protein 9) is a meiosis-specific protein that trimethylates H3K4 and controls the activation of recombination hot spots. It is an essential enzyme in the progression of early meiotic prophase. Disruption of the PRDM9 gene results in sterility in mice. In human, several PRDM9 SNPs have been implicated in sterility as well. Here we report on kinetic studies of H3K4 methylation by PRDM9 in vitro indicating that PRDM9 is a highly active histone methyltransferase catalyzing mono-, di-, and trimethylation of the H3K4 mark. Screening for other potential histone marks, we identified H3K36 as a second histone residue that could also be mono-, di-, and trimethylated by PRDM9 as efficiently as H3K4. Overexpression of PRDM9 in HEK293 cells also resulted in a significant increase in trimethylated H3K36 and H3K4 further confirming our in vitro observations. Our findings indicate that PRDM9 may play critical roles through H3K36 trimethylation in cells.     

Seasonal Changes in Free-Living Amoeba Species in the Root Canopy of Zygophyllum dumosum in the Negev Desert, Israel

The influence of seasonality and Zygophyllum dumosum root canopy on the species diversity of free-living amoebae at two soil depths (0–10 and 10–20 cm) was studied in a Negev Desert ecosystem in Israel. Free-living amoebae were extracted and identified after cultivation in non-nutritive agar plates. A total of 90 amoeba species were identified in the soil during the study period, with the most common genera present being Hartmannella, Platyamoeba, Vahlkampfia, Acanthamoeba, and Echinamoeba. Differences between the control soil and the soil under Z. dumosum were found mainly during the dry seasons, when 97% similarity was found between the two soil layers, which could be due to the effect of the shrub on the soil microenvironment. The amoeba community exhibited more species diversity in spring (reaching a value of 34 species) than in the winter (18 species) or summer and autumn (20 species), since the community has a time lag for becoming stabilized after the dry summer and autumn. This is one of the first studies on the amoeba population in the Negev Desert and elucidates the importance and the need for taking trophic and functional groups into consideration in order to understand biomineralization processes.     

Decomposition process in Negev ecosystems

Summary The effects of supplemental water and natural rainfall on decomposition were studied in the Negev Highland desert, Israel. There was a mass loss of approximately 40% in Hammada scoparia leaves and Salsola inermis litter placed on the soil surface and buried in fine mesh bags. There was an annual mass loss of 80% in S. inermis litter buried in large fiberglass mesh bags. Supplemental water provided during the wet season (January to March) did not result in more rapid decomposition of litter of the annual grass Stipa capensis but irrigation during the dry season (August to September) produced a marked increase in the decomposition rate of S. capensis. These data suggest that rain events, not water quantity, are the most important regulators of decomposition in the Negev. Annual rates of decomposition were higher than predicted by models utilizing actual evapotranspiration and lignin content as regulating variables. Rates of decomposition were equal to those reported for tropical wet forests.     

Extreme water stress and photosynthetic activity of the desert plant Artemisia herba-alba asso

Summary During the dry season in the Negev desert (Israel) Artemisia herbaalba in its natural habitat has a very low water content. It shows values of negative hydrostatic pressure in the xylem down to -163 bars and an extreme of osmotic potential in the leaves of -92 bars. The diurnal water stress does not decrease strongly in the night. Under these conditions Artemisia is still photosynthetically active for a few hours of the day during the whole dry period.     

Are Biological Effects of Desert Shrubs More Important than Physical Effects on Soil Microorganisms?

Vegetation cover plays a major role in providing organic matter and in acting as a physical barrier, with both together contributing to the formation of “fertile islands,” which play an active role in prolonging biological activity in desert ecosystems. By undertaking this study, a long-term research, we designed an experiment to separate the two components—the physical and biotic parts of the perennial plants—and to identify the factor that contributes the most to the ecosystem. The study site was located in the northern Negev Desert, Israel, where 50 Hammada scoparia shrubs and 50 artificial plants were randomly marked. Soil samples were collected monthly over 3 years of research at three locations: under the canopy of H. scoparia shrubs, in the vicinity of the artificial plants, and between the shrubs (control). The contribution to microbial activity was measured by evaluation of the microbial community functions in soil. The functional aspects of the microbial community that were measured were CO₂ evolution, microbial biomass, microbial functional diversity, and the physiological profile of the community. The results of this study are presented in two ways: (1) according to the three locations/treatments; and (2) according to the phenological situation of the vegetation (annual and perennial plants) in the research field: the growing phase, the drying process, and the absence of annual plants. The only parameters that were found to affect microbial activity were the contribution of the organic matter of perennial shrubs and the growth of vegetation (annual and perennial) during the growing seasons. The physical component was found to have no effect on soil microbial functional diversity, which elucidates the important contribution of the desert shrub in enhancing biological multiplicity and activity.     

Catalytic and Functional Roles of Conserved Amino Acids in the SET Domain of the S. cerevisiae Lysine Methyltransferase Set1

In S. cerevisiae, the lysine methyltransferase Set1 is a member of the multiprotein complex COMPASS. Set1 catalyzes mono-, di- and trimethylation of the fourth residue, lysine 4, of histone H3 using methyl groups from S-adenosylmethionine, and requires a subset of COMPASS proteins for this activity. The methylation activity of COMPASS regulates gene expression and chromosome segregation in vivo. To improve understanding of the catalytic mechanism of Set1, single amino acid substitutions were made within the SET domain. These Set1 mutants were evaluated in vivo by determining the levels of K4-methylated H3, assaying the strength of gene silencing at the rDNA and using a genetic assessment of kinetochore function as a proxy for defects in Dam1 methylation. The findings indicate that no single conserved active site base is required for H3K4 methylation by Set1. Instead, our data suggest that a number of aromatic residues in the SET domain contribute to the formation of an active site that facilitates substrate binding and dictates product specificity. Further, the results suggest that the attributes of Set1 required for trimethylation of histone H3 are those required for Pol II gene silencing at the rDNA and kinetochore function.     

Partitioning of the maize epigenome by the number of methyl groups on histone H3 lysines 9 and 27

We report a detailed analysis of maize chromosome structure with respect to seven histone H3 methylation states (dimethylation at lysine 4 and mono-, di-, and trimethylation at lysines 9 and 27). Three-dimensional light microscopy and the fine cytological resolution of maize pachytene chromosomes made it possible to compare the distribution of individual histone methylation events to each other and to DNA staining intensity. Major conclusions are that (1) H3K27me2 marks classical heterochromatin; (2) H3K4me2 is limited to areas between and around H3K27me2-marked chromomeres, clearly demarcating the euchromatic gene space; (3) H3K9me2 is restricted to the euchromatic gene space; (4) H3K27me3 occurs in a few (roughly seven) focused euchromatic domains; (5) centromeres and CENP-C are closely associated with H3K9me2 and H3K9me3; and (6) histone H4K20 di- and trimethylation are nearly or completely absent in maize. Each methylation state identifies different regions of the epigenome. We discuss the evolutionary lability of histone methylation profiles and draw a distinction between H3K9me2-mediated gene silencing and heterochromatin formation.