M. Ines M. Soares

Biogeography of soil archaea and bacteria along a steep precipitation gradient

For centuries, biodiversity has spellbound biologists focusing mainly on macroorganisms diversity and almost neglecting the geographic mediated dynamics of microbial communities. We surveyed the diversity of soil bacteria and archaea along a steep precipitation gradient ranging from the Negev Desert in the south of Israel (<100 mm annual rain) to the Mediterranean forests in the north (>900 mm annual rain). Soil samples were retrieved from triplicate plots at five long-term ecological research stations, collected from two types of patches: plant interspaces and underneath the predominant perennial at each site. The molecular fingerprint of each soil sample was taken using terminal restriction length polymorphism of the 16S rRNA gene to evaluate the bacterial and archaeal community composition and diversity within and across sites. The difference in community compositions was not statistically significant within sites (P=0.33 and 0.77 for bacteria and archaea, respectively), but it differed profoundly by ecosystem type. These differences could largely be explained by the precipitation gradient combined with the vegetation cover: the archaeal and bacterial operational taxonomic units were unique to each climatic region, that is, arid, semiarid and Mediterranean (P=0.0001, for both domains), as well as patch type (P=0.009 and 0.02 for bacteria and archaea, respectively). Our results suggest that unlike macroorganisms that are more diverse in the Mediterranean ecosystems compared with the desert sites, archaeal and bacterial diversities are not constrained by precipitation. However, the community composition is unique to the climate and vegetation cover that delineates each ecosystem.

Biological denitrification of drinking water using newspaper

Microbial denitrification of drinking water was studied in laboratory columns packed with shredded newspapers. Newspaper served as the sole carbon and energy substrate as well as the only physical support for the microbial population. Complete removal of nitrate (100 mg 1−1) was readily achieved, without accumulation of nitrite. The treated water contained low dissolved organic carbon (4–10 mg 1−1). The cellulose-dependent denitrification process was sensitive to changes in temperature: nitrate removal rates at 14°C were approximately one third of the rates observed at 32°C. Pretreatment of newspaper with diluted NaOH or diluted HCl, or by autoclave did not improve the efficiency of the process. A time-dependent decay in denitrification rate was noticeable after several months of operation. The reasons for this phenomenon, which may be due to weakened adhesion of the bacteria to the substrate, are under investigation.

Hydrogen-dependent denitrification in a two-reactor bio-electrochemical system.

An autotrophic biological process was developed for the treatment of nitrate-contaminated drinking water. The system comprised of two steps: the water to be treated was first enriched with hydrogen (energy source) in the cathodic chamber of an electrochemical cell, and then denitrified in the bioreactor. The bioreactor was a packed bed of granulated activated carbon, and the water flow was directed in an upward continuous mode. The system was operated for one year, at various water velocities and current intensities. Denitrification rates up to 0.25 kg N m-3 d-1 were obtained at the hydraulic residence time of 1 h. The system was stable. When detected in the effluent, the concentration of nitrite was low, even under conditions that resulted in the elution of very high concentrations of nitrate.

Microbial population in a hydrogen-dependent denitrification reactor.

The bacterial population in an H2-dependent denitrification system was studied. The laboratory set-up was designed for the treatment of potable water and consisted of an electrochemical cell, where the water to be treated was enriched with H2 prior to entering a bioreactor. Bioreactors (columns packed with granulated active carbon) were inoculated with denitrifying bacterial strains isolated from a previous reactor, then sampled immediately after inoculation, or after 1 or 3 months of continuous operation. Total number of the bacteria and numbers of each different strain were determined at various levels of the bioreactor. The strains present in the inoculum were identified as Ochrobactrum anthropi, Pseudomonas stutzeri, Paracoccus panthotrophus and Paracoccus denitrificans. Numbers of the latter declined markedly with time with the other three strains being responsible for nitrate removal. A correlation was found between the relative abundance of each strain and its specific denitrification activity.

The Effect of Resource Islands on Abundance and Diversity of Bacteria in Arid Soils

Bacteria and nutrients were determined in upper soil samples collected underneath and between canopies of the dominant perennial in each of three sites along a steep precipitation gradient ranging from the Negev desert in the south of Israel to a Mediterranean forest in the north. Bacterial abundance, monitored by phospholipid fatty acid analysis, was significantly higher under the shrub canopy (compared to barren soils) in the arid and semi-arid sites but not in the Mediterranean soils. Bacterial community composition, determined using terminal restriction fragment length polymorphism and clone libraries, differed according to the sample’s origin. Closer examination revealed that in the arid and semi-arid sites, α-Proteobacteria are more abundant under the shrub canopy, while barren soils are characterized by a higher abundance of Actinobacteria. The bacterial communities in the Mediterranean soils were similar in both patch types. These results correspond to the hypothesis of “resource islands”, suggesting that shrub canopies provide a resource haven in low-resource landscapes. Yet, a survey of the physicochemical parameters of inter- and under-shrub soils could not attribute the changes in bacterial diversity to soil moisture, organic matter, or essential macronutrients. We suggest that in the nutrient-poor soils of the arid and semi-arid sites, bacteria occupying the soil under the shrub canopy may have longer growth periods under favorable conditions, resulting in their increased biomass and altered community composition.

Isolation and Characterization of a Novel Leaf-Inhabiting Osmo-, Salt-, and Alkali-Tolerant Yarrowia lipolytica Yeast Strain

Salt‐excreting leaves of Atriplex halimus plants harvested in the central Negev Highlands of Israel were screened for yeasts inhabiting their surfaces. Several aerobic, moderately salt‐ and alkalitolerant yeasts were isolated. One of the isolates (tentatively designated S‐8) was identified as Yarrowia lipolytica (Wick.) van der Walt and Arx, on the basis of its morphological, biochemical/physiological characteristics, and of quantitative chemotaxonomic and molecular marker analyses. However, the strain is distinguished from the known members of the type Y. lipolytica strain by its pronounced osmo‐, salt‐, and pH tolerance. Cells displayed a unique capacity to grow over a wide pH range (from 3.5 to 11.5) with a pH optimum at 4.5 to 7.5. It is proposed that the S‐8 strain be assigned to a single Y. lipolytica species as its anamorpha, or as a new variety, Y. lipolytica var. alkalitolerance. The ecophysiological properties and biotechnological potentials of the new strain are discussed.

Mathematical model for analysis of recirculating vertical flow constructed wetlands.

The recirculating vertical flow constructed wetland (RVFCW) was developed for the treatment of domestic wastewater (DWW). In this system, DWW is applied to a vertical flow bed through which it trickles into a reservoir located beneath the bed. It is then recirculated back to the root zone of the bed. In this study, a compartmental model was developed to simulate the RVFCW. The model, which addresses transport and removal kinetics of total suspended solids, 5-day biological oxygen demand and nitrogen, was fitted to kinetical results obtained from pilot field setups and a local sensitivity analysis was performed on the model parameters and operational conditions. This analysis showed that after 5h of treatment water quality is affected more by stochastic events than by the model parameter values, emphasizing the stability of the RVFCW system to large variations in operational conditions. Effluent quality after 1h of treatment, when the sensitivity analysis showed the parameter impacts to be largest, was compared to model predictions. The removal rate was found to be dependent on the recirculation rate. The predictions correlated well with experimental observations, leading to the conclusion that the proposed model is a satisfactory tool for studying RVFCWs.

Evaluating amplified rDNA restriction analysis assay for identification of bacterial communities

Amplified ribosomal DNA restriction analysis (ARDRA) and restriction fragment length polymorphism were originally used for strain typing and for screening clone libraries to identify phylogenetic clusters within a microbial community. Here we used ARDRA as a model to examine the capacity of restriction-based techniques for clone identification, and the possibility of deriving phylogenetic information from ARDRA-based dendrograms. ARDRA was performed in silico on 48,759 sequences from the Ribosomal Database Project, and it was found that the fragmentation profiles were not necessarily unique for each sequence in the database, resulting in different species sharing fragmentation profiles. Although ARDRA-based clusters separated clones into different genera, these phylogenetic clusters did not overlap with trees constructed according to sequence alignment, calling into question the intra-genus ARDRA-based phylogeny. It is thus suggested that the prediction power of ARDRA clusters in identifying clone phylogeny be regarded with caution.

The role of stress in colicin regulation

Bacteriocins produced by Enterobacteriaceae are high molecular weight toxic proteins that kill target cells through a variety of mechanisms, including pore formation and nucleic acid degradation. What is remarkable about these toxins is that their expression results in death to the producing cells and therefore bacteriocin induction have to be tightly regulated, often confined to times of stress. Information on the regulation of bacteriocins produced by enteric bacteria is sketchy as their expression has only been elucidated in a handful of bacteria. Here, we review the known regulatory mechanisms of enteric bacteriocins and explore the expression of 12 of them in response to various triggers: DNA-damaging agents, stringent response, catabolite repression, oxidative stress, growth phase, osmolarity, cold shock, nutrient deprivation, anaerobiosis and pH stress. Our results indicate that the expression of bacteriocins is mostly confined to mutagenic triggers, while all other triggers tested are limited inducers.

Auto-regulation of DNA degrading bacteriocins: molecular and ecological aspects.

Colicins, proteinaceous antibiotics produced by Escherichia coli, specifically target competing strains killing them through one of a variety of mechanisms, including pore formation and nucleic acid degradation. The genes encoding colicins display a unique form of expression, which is tightly regulated, involving the DNA damage response regulatory system (the SOS response system), confined to stressful conditions and released by degradation of the producing cell. Given their lethal nature, colicin production has evolved a sophisticated system for repression and expression. While exploring the expression of 13 colicins we identified a novel means of induction unique to strains that kill by DNA degradation: these colicinogenic strains mildly poison themselves inflicting DNA damage that induces their DNA repair system (the SOS system), and their own expression. We established that among the four known DNase colicins (E2, E7, E8 and E9), three act to induce their own production. Using different stresses we show that this form of self-regulation entails high cost when growth conditions are not optimal, and is not carried out by individual cells but is a population-mediated trait. We discuss this novel form of colicins’ regulation and expression, and its possible molecular mechanism and evolutionary implications.