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Bacillus cereus sensu lato (Bcsl) strains are widely explored due to their capacity to antagonize a broad range of plant pathogens. These include B. cereus sp. UW85, whose antagonistic capacity is attributed to the secondary metabolite Zwittermicin A (ZwA). We recently isolated four soil and root-associated Bcsl strains (MO2, S−10, S-25, LSTW-24) that displayed different growth profiles and in-vitro antagonistic effects against three soilborne plant pathogens models: Pythium aphanidermatum (oomycete) Rhizoctonia solani (basidiomycete), and Fusarium oxysporum (ascomycete). To identify genetic mechanisms potentially responsible for the differences in growth and antagonistic phenotypes of these Bcsl strains, we sequenced and compared their genomes, and that of strain UW85 using a hybrid sequencing pipeline. Despite similarities, specific Bcsl strains had unique secondary metabolite and chitinase-encoding genes that could potentially explain observed differences in in-vitro chitinolytic potential and anti-fungal activity. Strains UW85, S-10 and S-25 contained a (~500 Kbp) mega-plasmid that harbored the ZwA biosynthetic gene cluster. The UW85 mega-plasmid contained more ABC transporters than the other two strains, whereas the S-25 mega-plasmid carried a unique cluster containing cellulose and chitin degrading genes. Collectively, comparative genomics revealed several mechanisms that can potentially explain differences in in-vitro antagonism of Bcsl strains toward fungal plant pathogens.

Freshwater bodies are critical components of terrestrial ecosystems. The microbial communities of freshwater ecosystems are intimately linked water quality. These microbes interact with, utilize and recycle inorganic elements and organic matter. Here, we present three metagenomic sequence datasets (total of 182.9 Gbp) from different freshwater environments in Israel. The first dataset is from diverse freshwater bodies intended for different usages – a nature reserve, irrigation and aquaculture facilities, a tertiary wastewater treatment plant and a desert rainfall reservoir. The second represents a two-year time-series, collected during 2013–2014 at roughly monthly intervals, from a water reservoir connected to an aquaculture facility. The third is from several time-points during the winter and spring of 2015 in Lake Kinneret, including a bloom of the cyanobacterium Microcystis sp. These datasets are accompanied by physical, chemical, and biological measurements at each sampling point. We expect that these metagenomes will facilitate a wide range of comparative studies that seek to illuminate new aspects of freshwater microbial ecosystems and inform future water quality management approaches.

Bacteria produce a large number of volatile organic compounds (VOCs) into the environment. VOCs are species-specific and their emission depends on environmental conditions, such as growth medium, pH, temperature, incubation time and interaction with other microorganisms. These VOCs can enhance plant growth, suppress pathogens and act as signaling molecules during plant-microorganism interactions. Bacterial VOCs have been reported to show strong antimicrobial, nematicidal, pesticidal, plant defense, induced tolerance and plant-growth-promoting activities under controlled conditions. Commonly produced antifungal VOCs include dimethyl trisulfide, dimethyl disulfide, benzothiazole, nonane, decanone and 1-butanol. Species of Bacillus, Pseudomonas, Arthrobacter, Enterobacter and Burkholderia produce plant growth promoting VOCs, such as acetoin and 2,3-butenediol. These VOCs affect genes involved in defense and development in plant species (i.e., Arabidopsis, tobacco, tomato, potato, millet and maize). VOCs are also implicated in altering pathogenesis-related genes, inducing systemic resistance, modulating plant metabolic pathways and acquiring nutrients. However, detailed mechanisms of action of VOCs need to be explored. This review summarizes the bioactive VOCs produced by diverse bacterial species as an alternative to agrochemicals, their mechanism of action and challenges for employment of bacterial VOCs for sustainable agricultural practices. Future studies on technological improvements for bacterial VOC application under greenhouse and open field conditions are warranted.

Elevated CO2 stimulates plant growth and affects quantity and composition of root exudates, followed by response of its microbiome. Three scenarios representing nitrate fertilization regimes: limited (30 ppm), moderate (70 ppm) and excess nitrate (100 ppm) were compared under ambient and elevated CO2 (eCO2, 850 ppm) to elucidate their combined effects on root-surface-associated bacterial community abundance, structure and function. Wheat root-surface-associated microbiome structure and function, as well as soil and plant properties, were highly influenced by interactions between CO2 and nitrate levels. Relative abundance of total bacteria per plant increased at eCO2 under excess nitrate. Elevated CO2 significantly influenced the abundance of genes encoding enzymes, transporters and secretion systems. Proteobacteria, the largest taxonomic group in wheat roots (~ 75%), is the most influenced group by eCO2 under all nitrate levels. Rhizobiales, Burkholderiales and Pseudomonadales are responsible for most of these functional changes. A correlation was observed among the five gene-groups whose abundance was significantly changed (secretion systems, particularly type VI secretion system, biofilm formation, pyruvate, fructose and mannose metabolism). These changes in bacterial abundance and gene functions may be the result of alteration in root exudation at eCO2, leading to changes in bacteria colonization patterns and influencing their fitness and proliferation.

Bacteria are social organisms that interact extensively within and between species while responding to external stimuli from their environments. Designing synthetic microbial communities can enable efficient and beneficial microbiome implementation in many areas. However, in order to design an efficient community, one must consider the interactions between their members. Using a reductionist approach, we examined pairwise interactions of three related Pseudomonas species in various microenvironments including plant roots and inert surfaces. Our results show that the step between monoculture and co-culture is already very complex. Monoculture root colonization patterns demonstrate that each isolate occupied a particular location on wheat roots, such as root tip, distance from the tip, or scattered along the root. However, pairwise colonization outcomes on the root did not follow the bacterial behavior in monoculture, suggesting various interaction patterns. In addition, we show that interspecies interactions on a microscale on inert surface take part in co-culture colonization and that the interactions are affected by the presence of root extracts and depend on its source. The understanding of interrelationships on the root may contribute to future attempts to manipulate and improve bacterial colonization and to intervene with root microbiomes to construct and design effective synthetic microbial consortia.

With increasing fresh water (FW) scarcity, the use of treated wastewater (TWW) for crop irrigation is expanding globally. Besides clear benefits, some undesired long-term effects of irrigation with this low quality water on plant performance have been reported. As the rhizosphere microbiome can mediate plant-soil interactions, an examination of the response of these organisms to TWW is necessary to understand the full effects of water quality. In the current study, the effects of irrigation water quality on the microbial community structure of soil and roots as well as edaphic properties and plant performance were evaluated. We compared soil and roots microbiomes of two different plant species (tomato and lettuce), each grown in two distinct soils, and irrigated with either FW or TWW. Irrigation with TWW significantly increase soil pH, EC, K, Na and DOC, and decrease plant fruit and shoot weight, relatively to samples irrigated with FW. We calculated the effect size of plant species, soil type, and irrigation water quality on microbial community structure in soil and root. In the roots, plant species and irrigation water were the dominant factors in shaping both total (DNA based) and active (RNA based) microbial communities, with both factors contributing similarly to the observed microbial population. Soil type and irrigation water were the dominant factors shaping the total microbial community in the soil and were of similar magnitude. Irrigation water quality is demonstrated to be a major force in shaping root-associated microbiome, leading to altered microbial community structure in the critical juncture between plant and soil.

Bacteria are social organisms that interact extensively within and between species while responding to external stimuli from their environments. Designing synthetic microbial communities can enable efficient and beneficial microbiome implementation in many areas. However, in order to design an efficient community, one must consider the interactions between their members. Using a reductionist approach, we examined pairwise interactions of three related Pseudomonas species in various microenvironments including plant roots and inert surfaces. Our results show that the step between monoculture and co-culture is already very complex. Monoculture root colonization patterns demonstrate that each isolate occupied a particular location on wheat roots, such as root tip, distance from the tip, or scattered along the root. However, pairwise colonization outcomes on the root did not follow the bacterial behavior in monoculture, suggesting various interaction patterns. In addition, we show that interspecies interactions on a microscale on inert surface take part in co-culture colonization and that the interactions are affected by the presence of root extracts and depend on its source. The understanding of interrelationships on the root may contribute to future attempts to manipulate and improve bacterial colonization and to intervene with root microbiomes to construct and design effective synthetic microbial consortia.

Background Roots select their associated microbiome and affect its composition and activities through exudates that provide a nutrient-rich environment based on distance from the root. Root-exudation patterns depend on the plant's developmental stage. We followed field-grown wheat from emergence to spike maturation and compared the structure and functions of the microbiomes in two niches: adjacent, root-associated bacteria and the rhizosphere. The effects of growth stage on root-associated and rhizospheric communities structure and functions were investigated to enhance our understanding of plant–microbe interactions. Results A significant impact of wheat developmental stage during the transition from vegetative growth to spike formation was observed on structure and functions of both root-associated and rhizosphere microbiomes. On the root surface, abundance of the well-known wheat colonizers Proteobacteria and Actinobacteria decreased and increased, respectively, during spike formation, whereas abundance of Bacteroidetes was independent of spike formation. Three microbiome functional clusters were specifically associated with root proximity: (1) biofilm and sensorial movement; (2) antibiotic production and resistance; and (3) carbon biosynthesis, degradation and transporters, and amino acid biosynthesis and transporters. Interestingly, in the root-associated microbiome, genes related to all of these functions were influenced by spike formation. Abundance of genes related to nine other functions (lipopolysaccharide transporter and biosynthesis, beta-lactam resistance, metabolism of methane, alanine-aspartate-glutamate and arginine-proline, and biosynthesis of peptidoglycan, lysine and enediyne antibiotics) was significantly influenced by spike formation in both roots and rhizosphere. All of these genes were abundant in the rhizosphere, more so before spike formation when root exudation is high, supporting the notion that some of the root exudates are not fully utilized by the root-associated bacteria and subsequently diffuse into the surrounding soil, creating the rhizosphere. Conclusions We demonstrated functional division in the microbiome of the wheat root zone in both time and space: pre- and post-spike formation and root-associated vs. rhizospheric niches. The responses of the root microbiome were driven by both the plant and the microbial physiology and activities, both of which respond to environmental cues. These findings shed light on the dynamics of plant–microbe and microbe–microbe interactions in the root zone.

Ultraviolet (UV) irradiation is an emerging strategy for controlling the formation of undesired biofilms in water desalination facilities using reverse osmosis (RO). However, most studies examining these pretreatments are limited as they have been conducted on single-species cultures, while biofilms are composed of multiple-species communities. The goal of this study was to investigate the effect of UV-C irradiation on a model community composed of six environmental isolates from a marine biofilm formed in RO seawater desalination plant. There was a high variance in the susceptibility of the single-isolate cultures to UV-C, from no response (isolate Eryth23) to complete inactivation (isolate Vib3). The most active wavelength was around 260 nm, resulting in a loss of viability of single-isolate cultures and loss of vitality of the mixed-isolate cultures. With respect to biofilm formation, the activity of this wavelength was completely different compared to its activity on planktonic suspension. Irradiation with 260 nm did not inhibit the total biofilm formation by the six-isolate culture; moreover, isolates such as the resistant Eryth23 or the susceptible Pseudoalt17, even gained abundance in the mixed isolate biofilm. The only decrease in total biofilm was obtained from irradiation at 280 nm, which was less active against the planktonic culture. These results indicate that the complexity of the biofilm-forming microbial community may contribute to its resistance to UV-C irradiation. Significance and impact of the study This study examined the resistance of a multiple-isolate native marine culture to UV-C irradiation, in terms of viability, vitality and the ability to form biofilm. Results of this study showed that even though most of the cells were inactivated both in single-isolate and in multiple-isolate cultures, still the multiple-isolate cultures manages to form biofilms, surprisingly with higher biomass than without irradiation. The significance of the study is in its conclusion that studies on UV-C irradiation of biofilm-forming model micro-organisms are not always applicable to natural multiple-species communities.

Soil solarization, a method of chemical-free pest treatment, is a practical and cost-effective way to treat organic farming soil. This method uses polyethylene sheets to capture solar irradiation that heats the soil. Together with heat generated during composting of fresh organic matter, this method can effectively treat many soil-borne pathogens. In this study we examined the effects of solarization with the addition of compost at three maturation levels, on soil microbial community structure and function along with plant performance. Similar hydrolytic activity among the treatments (as measured by FDA hydrolysis) was measured in the first year of solarization. High level of activity was obtained in soil amended with immature compost at the beginning of the second year, suggesting residual (carry-over) effects of previous-year treatments. Amplicon sequencing of 16S rRNA encoding genes was used to study soil bacterial community structure. Diversity and richness of bacterial communities were found to be negatively affected by solarization in all treatments. Interestingly, bacterial communities of solarized soils clustered together, regardless of compost amended and type, separated from the cluster of communities from non-solarized soils of all amendments. Specifically, long and short terms negative effects of solarization on the relative abundance of Alphaproteobacteria, Acidobacteria and Actinobacteria were noticed. In contrast, solarization positively affected Bacilli and Gammaproteobacteria abundance in both long and short term. Furthermore, solarization had long and short term positive effects on productivity of eggplant and wheat plants. This study is the first to describe in high details the combined effects of solarization and amendment of composts of different maturation levels.

Plant hosts recruit and maintain a distinct root-associated microbiota based on host and bacterium traits. However, past studies disregarded microbial strain-host specificity and spatial micro-heterogeneity of the root compartment. Using genetic manipulation, confocal laser scanning microscopy, real-time quantitative PCR, and genome sequencing we characterized the colonization patterns of three Pseudomonas spp. isolates native to wheat roots, on the micro-scale. Namely, isolates P. fluorescens NT0133, P. stutzeri NT124, and P. stutzeri NT128. All three isolates preferentially colonized wheat over cucumber roots that served as control for host specificity. Furthermore, not only had the isolates strong host specificity but each isolate had a distinct spatial distribution on the root, all within a few millimeters. Isolate P. stutzeri-NT0124 preferentially colonized root tips, whereas P. fluorescens-NT0133 showed a preference for zones distant from the tip. In contrast, isolate P. stutzeri-NT0128 had no preference for a specific niche on the root. While all isolates maintained genetic potential for motility and biofilm formation their phenotype varied significantly and corresponded to their niche preference. These results demonstrate the importance of spatial colonization patterns, governed by both niche and bacterial characteristics which will have great importance in future attempts to manipulate the plant microbiome by constructing synthetic microbial consortia.

Effect of temperature on the survival of Macrophomina phaseolina s.l. (Mp) was tested under laboratory conditions using an incubation system programmed for a cyclic temperature regime, simulating soil solarization. Mp culture and soil with and without Mp were incubated under two cyclic temperature regimes, with maximum temperatures of 50 °C or 52 °C, simulating solarization processes, and at a constant temperature of 25 °C, as a control. Total fungal community and Mp levels were not affected negatively by constant temperature of 25 °C. However, total soil fungal community was significantly decreased at temperature regime of 50 °C, whereas Mp did not change significantly whether in soil mixture or as pure propagules culture. In Mp-amended soil treated by temperature regime of 50 °C, total fungal community decreased while Mp CFU number did not change significantly. However, temperature regime of 52 °C almost completely eradicated total fungal community, as well as that of Mp. When Mp was amended to soils after being treated at 50 °C and 52 °C temperature regimes and incubated for two additional weeks at 25 °C, an indirect temperature effects on Mp survival were apparent. The 50 °C pre-treatment did affect significantly neither the total fungal nor Mp levels. In soil previously treated by 52 °C, total fungal growth was somewhat decreased while Mp growth was promoted. The results suggest that Mp survival may be affected by temperature directly as well as indirectly via effects on total fungal population. Studying these biological factors may contribute to the control of Mp pathogen using environment-friendly methods.

The combined effects of soil solarization and application of compost of various maturity levels upon soil microbial activity were studied under field conditions during 2010–2012. Eight treatments were divided into solarized and non-solarized treatments, and each was either non-amended or annually amended with compost at 6 kg (DW) m-2. The composts were mature, partially mature, or immature. In all three tested parameters of microbial activity (respiration rate, heat output, and dehydrogenase activity) the immature compost showed higher activity than the other compost types. Soil samples were collected weekly in order to assess microbial activity, which was evaluated from measurements of soil respiration rate, heat output, and dehydrogenase activity. Significant and year-to-year reproducible differences in all three parameters were observed between soils amended with the three compost types. Some residual (carry-over) effects of previous-year treatments were obtained. Microbial activity decreased in both solarized and non-solarized treatments during the experimental period, probably because of increasing summer temperatures, but the decline was sharper in the solarized treatments probably due to oxygen deficiency under the tarp. Significantly higher activity was found in the treatments amended with the immature compost, both in the solarized and non-solarized treatments. This could be a result of the high level of dissolved organic matter in the immature compost, which enhanced microbial activity.

Elevated CO2 (eCO2) stimulates plant growth and photosynthesis, which affect root deposition, leading to altered structure and function of the root microbiome. We studied the effect of eCO2 on wheat-root microbiome composition and plant development, with an emphasis on denitrifying communities. Wheat plants were grown in a greenhouse with continuous fertigation for 6 weeks under ambient CO2 (400 ppm) or eCO2 (850 ppm). The total bacterial community was quantified using qPCR with universal 16S rRNA gene primers, and denitrifying genes (nirK, nirS, nosZ) were measured. In addition, total (16S-based) and N2O-reducing (nosZ-based) bacterial community compositions in the soil and roots were analyzed by amplicon sequencing during plant growth. eCO2 had a significant impact on abundance of the studied denitrifying genes, particularly during the late stages of wheat growth before spike formation. Moreover, eCO2 had a significant impact on N2O-reducing community structure in roots. This effect was more pronounced on Burkholderiales and Rhizobiales, with a minor effect on Pseudomonadales. In addition, as expected, bacterial community structure (total and N2O-reducing bacteria), and denitrifying gene abundance, were primary influenced by habitat (soil vs. roots), and secondarily by plant developmental stage. In summary, it is suggested that eCO2 may change root microbiome, enhance wheat development and N demand without an increase in N2O emission.

No-tillage (NT) is a common soil-conservation management practice with known agricultural advantages and drawbacks. However, its short- and long-term effects on the soil microbiome have not been well established. Here, we compared conventional (CT), minimal (MT) and NT practices in two agricultural fields in the north of Israel over a period of 3 years. Edaphic properties, plant-associated pests, weed species abundance and soil microbial community structure were assessed to examine the effects of tillage. Tillage significantly altered physical and chemical soil properties, and a significant increase in hydrolytic and redox microbial activities was observed in NT soils from both sites. Consistent with this, the microbial community structure of NT samples diverged significantly over time from those of CT samples. Repetitive tillage and even a single tillage event caused significant changes in the relative abundance of microorganisms at taxonomic levels ranging from phylum to OTU. However, no significant difference between treatments was found in microbial community alpha-diversity or crop yield. Conversely, higher levels of weed diversity and some pests number were found in NT samples. Overall, we demonstrate that tillage plays a major role in shaping microbial community structure, and in influencing additional environmental, ecological and agricultural soil parameters.

Plant hosts recruit and maintain a distinct root-associated microbiota based on host and bacterium traits. However, past studies disregarded microbial strain-host specificity and spatial micro-heterogeneity of the root compartment. Using genetic manipulation, confocal laser scanning microscopy, real-time quantitative PCR, and genome sequencing we characterized the colonization patterns of three Pseudomonas spp. isolates native to wheat roots, on the micro-scale. Namely, isolates P. fluorescens NT0133, P. stutzeri NT124, and P. stutzeri NT128. All three isolates preferentially colonized wheat over cucumber roots that served as control for host specificity. Furthermore, not only had the isolates strong host specificity but each isolate had a distinct spatial distribution on the root, all within a few millimeters. Isolate P. stutzeri-NT0124 preferentially colonized root tips, whereas P. fluorescens-NT0133 showed a preference for zones distant from the tip. In contrast, isolate P. stutzeri-NT0128 had no preference for a specific niche on the root. While all isolates maintained genetic potential for motility and biofilm formation their phenotype varied significantly and corresponded to their niche preference. These results demonstrate the importance of spatial colonization patterns, governed by both niche and bacterial characteristics which will have great importance in future attempts to manipulate the plant microbiome by constructing synthetic microbial consortia.

Plant roots create specific microbial habitat in the soil - the rhizosphere. In this study, we characterized the rhizosphere microbiome of four host plant species to get insight into the impact of the host (host signature effect) on resident vs. active communities. Results show a distinct plant host specific signature found among wheat, maize, tomato and cucumber, based on the following three parameters: (i) each plant promoted the activity of a unique suite of soil bacterial populations; (ii) significant variations were observed in the number and the degree of dominance of active populations; and (iii) the level of contribution of active (rRNA-based) populations to the resident (DNA-based) community profiles. In the rhizoplane of all four plants, a significant reduction of diversity was observed, relative to the bulk soil. Moreover, an increase in DNA-RNA correspondence indicated higher representation of active bacterial populations in the residing rhizoplane community. This study demonstrates that the host plant determines the bacterial community composition in its immediate vicinity, especially with respect to the active populations.

Summary Limited freshwater (FW) availability due to climate change and increasing global populations is driving agriculture in arid and semi-arid regions to recycle vast quantities of water for irrigation. However, irrigation with treated wastewater (TWW), which contains dissolved organic matter, salts and microorganisms might alter soil microbial populations, and thus affect soil fertility. We characterized the effects of irrigation with TWW and FW on soil bacterial community composition for three consecutive years. Orchard samples were collected at the end of each of the rainy (winter) and irrigation (summer) season. Community composition, determined by 16S ribosomal DNA amplicon pyrosequencing, was highly similar in soil samples obtained at the end of three consecutive rainy seasons, regardless of irrigation season water quality. However, whereas composition in soil shifted slightly during irrigation seasons by FW irrigation, it was greatly influenced by TWW irrigation. During the irrigation season, a decrease in the relative abundance of Actinobacteria was observed; along with an increase in the relative abundance Gammaproteobacteria within TWW-irrigated soils. The return to the ‘baseline state’ during the rainy season demonstrates that the soil community is not resistant to anthropogenic impact imposed by irrigation water quality, yet is resilient in long term.

The formation of biofilms and biofouling is a common feature in aquatic environments. The aim of this study was to identify the primary colonizers of biofilm formed in Eastern Mediterranean Coastal water at different seasons and follow early dynamics of biofilm community development. Pre-treated coastal seawater and biofilm samples were collected from six different sampling events of 2 weeks' duration each during 1 year. The microbial community composition and specific abundance were estimated by 16S rRNA gene clone libraries and fluorescence in situ hybridization-confocal laser scanning microscopy (FISH-CLSM), respectively. The biofilm formed over the course of the year was fairly consistent in terms of community composition and overall abundance with the exception of spring season. Alphaproteobacteria (30-70% of total bacteria), in particular Rhodobacteraceae, were the dominant bacteria in the biofilm, regardless of season, followed by Bacteroidetes (5-35%) and Gammaproteobacteria (6-35%). There was a decrease in relative abundance of Alphaproteobacteria and an increase in the abundance of Bacteroidetes between the initial and 2-week-old biofilm. This observation may aid man-made facilities that have to deal with biofilm formation and help the development of appropriate strategies to control those biofilms.

Colletotrichum and its teleomorph Glomerella are considered major fungal plant pathogens worldwide. They cause significant economic damage to fruit crops in tropical, subtropical and temperate regions. Several Colletotrichum species or biotypes are known to cause disease in a single host such as C. acutatum and C. gloeosporioides on apple, avocado, mango, papaya, passiflora, strawberry and tamarillo. It is also common to find a single species infecting multiple hosts such as C. gloeosporioides on apple, avocado, mango, papaya, peach, strawberry, and other hosts. Cross-infection potential was shown for two species, C. gloeosporioides from limonium and C. acutatum from strawberry, when inoculating peach, pear, mango, nectarine and strawberry. Molecular analyses including species-specific PCR amplification and ITS sequencing was reliable for identification of Colletotrichum isolates infecting apple, avocado, mango, papaya, passiflora, peach, strawberry and tamarillo fruits. Sub-populations within C. acutatum, C. gloeosporioides and C. boninense were characterized using ITS sequence analysis, while the latter appears to be a diverse and emerging new species infecting multiple fruit crops.

In recent years the behavior and properties of nanoparticles released to the environment have been studied extensively to better assess the potential consequences of their broad use in commercial products. The fate, transport and mobility of nanoparticles in soil were shown to be strongly dependent on environmental conditions. However, little is known about the possible effects of nanoparticles on soil chemical, physical and biological properties. In this study, two types of metal oxide nanoparticles, CuO and Fe3O4 were mixed into two types of soil and the effects of the nanoparticles on various soil properties were assessed. Metal oxide nanoparticles were shown previously to catalyze the oxidation of organic pollutants in aqueous suspensions, and they were therefore expected to induce changes in the organic material in the soil, especially upon addition of an oxidant. It was found that the nanoparticles did not change the total amount of organic materials in the soil or the total organic carbon in the soil extract; however, three-dimensional fluorescence spectroscopy demonstrated changes in humic substances. The nanoparticles also affected the soil bacterial community composition, based on denaturing gradient gel electrophoresis (DGGE) fingerprinting, but had little impact on the macroscopic properties of the soil.

The genus Aeromonas is ubiquitous in aquatic environments encompassing a broad range of fish and human pathogens. Aeromonas strains are known for their enhanced capacity to acquire and exchange antibiotic resistance genes and therefore, are frequently targeted as indicator bacteria for monitoring antimicrobial resistance in aquatic environments. This study evaluated temporal trends in Aeromonas diversity and antibiotic resistance in two adjacent semi-intensive aquaculture facilities to ascertain the effects of antibiotic treatment on antimicrobial resistance. In the first facility, sulfadiazine-trimethoprim was added prophylactically to fingerling stocks and water column-associated Aeromonas were monitored periodically over an 11-month fish fattening cycle to assess temporal dynamics in taxonomy and antibiotic resistance. In the second facility, Aeromonas were isolated from fish skin ulcers sampled over a 3-year period and from pond water samples to assess associations between pathogenic strains to those in the water column. A total of 1200 Aeromonas isolates were initially screened for sulfadiazine resistance and further screened against five additional antimicrobials. In both facilities, strong correlations were observed between sulfadiazine resistance and trimethoprim and tetracycline resistances, whereas correlations between sulfadiazine resistance and ceftriaxone, gentamicin, and chloramphenicol resistances were low. Multidrug resistant strains as well as sul1, tetA, and intI1 gene-harboring strains were significantly higher in profiles sampled during the fish cycle than those isolated prior to stocking and these genes were extremely abundant in the pathogenic strains. Five phylogenetically distinct Aeromonas clusters were identified using partial rpoD gene sequence analysis. Interestingly, prior to fingerling stocking the diversity of water column strains was high, and representatives from all five clusters were identified, including an A. salmonicida cluster that harbored all characterized fish skin ulcer samples. Subsequent to stocking, diversity was much lower and most water column isolates in both facilities segregated into an A. veronii-associated cluster. This study demonstrated a strong correlation between aquaculture, Aeromonas diversity and antibiotic resistance. It provides strong evidence for linkage between prophylactic and systemic use of antibiotics in aquaculture and the propagation of antibiotic resistance.

Russeting of smooth-skinned potato varieties affect the protective characteristics of the skin against water loss and pathogens invasion. A distinctive russeting disorder, differs from previously reported tuber blemishes, has been observed in the Negev area of Israel and was named ‘Magen russeting’ after one of the repeatedly affected plots. The russeted skin appears as protruding dark-brown patches on the surface of the tubers. Histological studies identified the russet as old skin cells that remain adhered to the newly formed skin layers below them. Phytopathological tests and rDNA pyrosequencing analysis for whole bacterial community suggested that ‘Magen russeting’ is a physiological disorder. Mineral analysis of isolated pure skin samples indicated that russeted skin areas have higher concentrations of Ca and lower concentrations of K than the smooth skin of normal tubers, irrespective of CaCl2 or KCl fertilization of the soil prior to sowing, or of the irrigation regime during the growing season. Nevertheless, application of CaCl2 prior to tuber-seed sowing reduces the rate of affected mature tubers and the severity of the russeting.

Summary Detailed analysis revealed fundamental differences between bacterial association with cucumber (Cucumis sativus) seeds and seedlings roots. Seed colonization by bacteria seems to result from passive encounter between bacteria, conveyed by imbibed soil solution, and the germinating seed. In accordance, the seed-associated bacterial community composition directly reflected that of the germination medium and was characterized by low dominance. Transition from seed to root was marked by a shift in bacterial community composition and in an increase in dominance values. Furthermore, settlement of bacteria on roots was tightly controlled by the specific properties of each root segment. Size and richness of the seed-associated bacterial community were clearly determinate by the community in the germination medium. In contrast, for fully developed and active roots, the medium effect on these parameters was negligible. Perturbation of the seed environment by a pathogen (Pythium aphanidermatum) had major consequences on the seed bacterial community. However, those were mostly related to direct pathogen–bacteria rather than seed–bacteria interactions. In conclusion, simple, even passive processes may determine the initial stage of plant–microbe association during seed germination, prior to extension of the primary root. Therefore, seed germination is a unique phase in the plant life cycle, with respect to its interaction with the below-ground microbiome.

The use of biocides, particularly chlorine, in reverse osmosis (RO) desalination is widely practiced despite documented evidence that although biocides may be advantageous in controlling microbial counts in the water, in some cases they can actually exacerbate biofouling of the membranes. The adverse effects, associated with widespread biocide use, have spurred the need for finding alternative RO pre-treatment disinfection methods. Ultraviolet (UV) disinfection, and specifically medium pressure ultraviolet (MP-UV) disinfection has been considered a possible alternative and is now gaining recognition as a viable disinfection method applicable to RO desalination; however documentation on the effects of UV pre-treatment on RO membrane biofouling is scarce. This paper reports the findings from a four month field study conducted at a brackish water reverse osmosis (BWRO) desalination plant, treating groundwater, in the north of Israel, in which MP-UV was applied as a pre-treatment disinfection step prior to RO...

Amendment of organic wastes and composts to soil is a common agricultural practice. The soil microbiota is responsible for the recycling and mineralization of these organic amendments and their activity affects soil structure and agricultural viability. In this study we assessed the short-term effects of compost amendment on bacterial community composition and activity in agricultural soil. Changes in biomass, respiration and enzymatic activity were correlated with bacterial community profiles, as determined by Denaturing Gradient Gel Electrophoresis (DGGE) of PCR-amplified 16S ribosomal RNA (rRNA) gene fragments and sequencing of relevant bands. Prior to wetting, the community profile of the compost amended soils was almost identical to that of the original compost, implying that the compost bacterial content was much higher than that of the soil. Nonetheless, wetting of compost-amended soils caused an immediate shift in the bacterial community profile resulting in a pattern similar to that of the original soil profile. Initially, in the first three days following wetting, the bacterial community profiles of the control and compost-amended soils were highly similar to each other. However, from day five to day 13, significant differences in the bacterial profiles developed between the control and compost-amended soils, indicating that the compost-related effect on the bacterial community is somewhat delayed. Compost-amended soils showed enhanced rates of nitrification, respiration, hydrolytic and metabolic activities relative to the control soils without compost. They were also characterized by proliferation of communities associated with the Bacteroidetes phylum, which may be explained by the involvement of this clade in the degradation of compost-derived complex organic substrates in the soil microcosms.

Preplant soil fumigation with metam sodium is used worldwide to control soilborne diseases. The development of accelerated degradation of pesticides in soil, including metam sodium, results in reduced pesticide efficacy. Therefore, we studied microbial involvement in accelerated degradation of methyl isothiocyanate (MITC) following repeated soil applications of the parent compound, metam sodium. MITC degradation was reduced in soil with a history of metam sodium applications following sterilization, indicating the key role of microorganisms in accelerated degradation. Accelerated degradation of MITC was induced by inoculation of soil with no previous application of metam sodium with soil with a history of metam sodium applications. We developed a method to extract the active microbial fraction responsible for MITC degradation from soil with a history of metam sodium applications. This concentrated soil extract induced accelerated degradation of MITC when added to two different soils with no previous application of metam sodium. An extensive shift in total bacterial community composition in concentrated soil extracts occurred after a single metam sodium application. Two Oxalobacteraceae strains, MDB3 and MDB10, isolated from Rehovot soil following triple application of metam sodium rapidly degraded MITC in soil with no previous application of metam sodium. Polymerase chain reaction–denaturing gradient gel electrophoresis analysis of bacterial community composition showed relative enrichment of MDB3 following metam sodium application, suggesting its potential in situ involvement in accelerated degradation development in Rehovot soil. Responses of resident Oxalobacteraceae community members to metam sodium applications differed between Rehovot and En Tamar soils. Isolate MDB10 did not induce accelerated degradation of MITC in En Tamar soil and, with the slow dissipation of MITC, soil suppressiveness of accelerated degradation is suggested. The isolation and identification of MITC-degrading bacteria might be helpful in developing tools for managing accelerated degradation.

The idea of using constructed wetlands for the treatment and improving of wastewater emerged in the second half of the last century. Despite relatively wide use of this environmentally friendly technology, relatively little is known about the microbial populations involved in biotransformation and removal of contaminants in this system. The aim of the current study was to investigate the assembly and function of microbial populations in vertical-flow constructed wetland microcosms designed to improve the quality of wastewater after activated sludge treatment. Also, the performance of 3-year-old wetland ponds was investigated. Even though the quality of the influent water was relatively high, improvement in water parameters such as coliform level, ammonia concentration, BOD, and TSS was observed. The performance of the wetland ponds was comparable to that of the microcosms. The microbial community composition of the biofilm formed on the surface of gravel particles in vegetated and plant-free microcosms was studied by denaturing gradient gel electrophoresis (DGGE) and sequencing of 16S rRNA gene fragments. Highly complex bacterial diversity was observed in the biofilm. Cluster analysis of DGGE patterns demonstrated that depth within the wetland microcosm has a stronger effect on microbial community composition of the biofilm formed on wetland matrix than vegetation. Measurements of fluorescein diacetate hydrolysis activity and nitrification potential revealed that hydrolytic activity was affected by both microcosm depth and vegetation presence, whereas nitrification potential was mostly influenced by depth. Resolving the bacterial assemblage of wetland biofilm, which often is considered a black box, will help to understand the interactions involved in the development of diverse and mature biofilm and its function.

Almond anthracnose was reported for the first time in Australia in 1998 and has since been observed in all of the major almond-growing regions. The organism causing anthracnose was confirmed as Colletotrichum acutatum using taxon-specific polymerase chain reaction (PCR). Three main morphotypes of C. acutatum from almond in Australia were identified (namely, pink, orange, and cream colony color) and the optimum temperature for mycelial growth of representative isolates was 25°C. Australian isolates of C. acutatum were more similar morphologically to the pink subpopulation of C. acutatum from California than to the gray Californian subpopulation and the isolates of Colletotrichum from Israel. Inter-simple-sequence-repeat (ISSR) PCR analysis revealed that the majority of Australian isolates shared an identical banding pattern whereas Australian isolates of C. acutatum from almond were distinct from isolates of the pink and gray subpopulations of C. acutatum from almond in California and of Colletotrichum spp. from almond in Israel. Sequence analysis of the internally transcribed spacer (ITS1-2) ribosomal DNA region of representative isolates differed from the results of ISSR-PCR in that polymorphisms were revealed among isolates, indicating that some genetic variation may be present. Pathogenicity experiments on detached leaves and fruit revealed pathogenic variation among representative isolates of C. acutatum from almond in Australia, California, and Israel; however, all isolates tested caused disease. Distinct subgroups among Australian isolates of C. acutatum from almond were not supported on the basis of morphology, mycelial growth rates, ISSR-PCR, and pathogenicity.

Strawberry anthracnose was first reported in Bulgaria in 2002. Since then, the disease has reached epidemic levels in production fields. More than one-hundred Colletotrichum cultures were isolated from different strawberry cultivars, pepper and tomato fruits, and the weed species Cirsium arveuse that were cultivated in close proximity with infected strawberry field crops. The Colletotrichum isolates were identified and characterized by classical morphological criteria and by various molecular methods. Morphological characterization identified all the tested isolates as C. acutatum, which was further confirmed by species-specific polymerase chain reaction (PCR) amplification using the universal ITS4 and CaInt2 primers. No PCR products were amplified using C. gloeosporoides specific primers. Arbitrarily-primed PCR determined that all the studied isolates were uniform, regardless of origin of plant species, indicating that they belong to an asexually reproducing population. Sequence analysis of the complete internal transcribed spacer (ITS) region confirmed that the populations belonged to the species C. acutatum. Pathogenicity tests using representative isolates caused cross infections on the respective alternative hosts. These findings emphasize that various crops including weeds may serve as a potential inoculum source for C. acutatum.

(2009). Proceedings of the Thirty-Seventh Meeting of the Israel Society of Ecology and Environmental Science (Isees) Israel Journal of Ecology & Evolution: Vol. 55, No. 3, pp. 281-304.

Strawberry anthracnose was first reported in Bulgaria in 2002, subsequently reaching disease epidemic proportions in production fields from 2004. Isolates of Colletotrichum species from different strawberry cultivars (112), pepper (2), tomato (1), and the weed species Cirsium arvense (1), Abuthilon theophrasti (1) and Rumex obtusifolius (1) growing adjacent to cultivated strawberry fields, were characterized by morphological criteria and by various molecular methods. Morphological characterization defined all the isolates as Colletotrichum acutatum, which was ultimately confirmed by species-specific polymerase chain reaction (PCR) analysis. No PCR products were amplified using Colletotrichum gloeosporioides specific primers. Arbitrarily primed PCR determined that all the studied isolates, regardless of which plant species they originated from, were uniform indicating that they belong to an asexually reproducing population. Sequence analysis of the complete ITS (ITS 1 – 5.8S – ITS 2) region further identified the pathogen populations as C. acutatum and grouped them within the previously defined subgroup II, ‘Ca-clonal’, which is uniform. Pathogenicity tests and alternate host infections imply that cross-inoculation of C. acutatum between strawberry and other susceptible hosts is occurring under field conditions.

The general objectives of this study were (i) to determine the kinetics and mechanisms of Mn(II) removal from solution by a representative plant-growth substrate; (ii) to assess the role of biotic components on Mn(II) cycling in this system; and (iii) to assess the roles of pH and temperature in determining Mn(II) partitioning between the solution and the solid phases. The Mn(II) solubility in typical growth medium (perlite) was predominantly controlled by pH-dependent reactions, i.e., adsorption and oxidation. The role of precipitation, including formation of new solid phases of Mn-P or Mn-carbonates, as possible contributing factors to Mn(II) removal from perlite suspensions was assessed and ruled out. Under acidic pH (below pH 6), Mn(II) was elevated above concentrations expected in an inert medium; it was attributed to releases from indigenous sources, on one hand, and both low adsorptive capacity and Mn-bacteria activity, on the other hand. The Mn(II) concentration declined sharply above pH 6, and at pH 7.7 dropped almost to zero, 48 h after application. On a time scale of seconds to a few hours after application to perlite media the Mn(II) solubility was controlled by adsorption reactions, mainly onto the organic constituents accumulated from root excretions or decomposition and rhizosphere biota. With advancing time, biotic oxidation became important and it became the predominant mechanism of Mn(II) removal.

Declining yields from farmland in the Bet She'an Valley, Israel, irrigated with Jordan River water, raised concerns about resource management and long term sustainability. An experiment was conducted in a commercial cotton field of the Bet She'an region, to assess the impact of irrigation water quality on soil quality. A randomized block design compared four irrigation sources: Jordan River Water, Spring Water, Treated Waste Water, and Salty Spring Water, applied via drip irrigation to a calcareous silty clay soil for 3 years. Soil samples were collected and analyzed for 20 different physical, chemical and biological attributes. Samples from an adjacent uncultivated area were used as a reference. Principal component analysis (PCA) identified electrical conductivity (EC), fluorescein diacetate enzymatic activity (FDA), exchangeable Na (Ex-Na), apparent steady state saturated hydraulic conductivity (Ksat), and available P as the most important indicators for inclusion in a minimum data set (MDS) used to evaluate soil quality. Multiple regression tested these indicators against each of 4 specified management goals, reflecting soil quality attributes, i.e., sodium adsorption ratio (SAR) of soil solution, infiltration rate, soil loss, and cotton yield. There was a significant relationship between the indicators and 3 of the goals but not with cotton yield. Soil quality indices (SQI) were calculated using a PCA weighting factor and each MDS indicator scored using linear transformation. The SQI was highest for uncultivated soil (2.945), followed by Treated Waste Water (1.471), Spring Water (0.923), Salty Spring Water (0.823) and Jordan River Water (0.582) irrigated soils. The order of relative contribution of the indicators to the SQI was FDA (35.2%), Ksat (25.0%), Ex-Na (19.2%), EC (13.4%), and available P (7.2%). The method successfully identified Jordan River Water as the most deleterious, and Treated Waste Water as the best, irrigation treatment when considering soil quality.

The structure and microbial communities of biofilms developing on cross-flow nanofiltration (NF) membranes at different temperatures (20, 25 or 34 degrees C) and operation lengths (8h-24days) were studied. Feedwater comprised tertiary quality wastewater effluent or synthetic media mimicking effluents of intermediate quality. After each run, the membranes were autopsied for bacterial enumeration, bacterial community composition and microscopy visualization (SEM, CLSM and AFM/NSOM). Community composition was analyzed by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) coupled with sequence analysis of 16S rRNA gene fragments from dominant bands. Deposition of polysaccharides and initial bacterial colonization were observed within 8h, whereas developed biofilms markedly affecting membrane permeability were evident from days 2-3 onwards. Regardless of applied conditions, the heterotrophic plate counts in the biofilm were 3-4x10(6)CFU/cm(2) and the thickness of the biofouling layer was 20-30microm. From a total of 22 sequences obtained from 14 independent experiments, most species identified were Gram negative (19 of 22 sequences). Proteobacteria were found to be a prevalent group in all cases (16 of 22 sequences) and among it, the beta-subclass was the most predominant (8 sequences), followed by the gamma-subclass (5 sequences). Pseudomonas/Burkholderia, Ralstonia, Bacteroidetes and Sphingomonas were the dominant groups found in most cases. Even though the microbial population might be important with respect to biofouling patterns, membrane permeability decline seems to be more substantially influenced by the formation and accumulation of exopolymeric substances (EPS).

Fertilizer use in modern agriculture is highly inefficient; much of the applied fertilizer is released into the environment, causing environmental degradation. One way in which fertilizer use can be reduced without damaging plant nutrition is to enhance crop uptake of nutrients through the use of biostimulants. A broad definition of plant biostimulants, including substances sometimes categorized as biofertilizers or biopesticides, is used throughout this review: “Plant biostimulants are substances or materials, with the exception of nutrients and pesticides, which, when applied to plants, seeds, or growing substrates in specific formulations, have the capacity to modify physiological processes in plants in a way that provides potential benefits to growth, development, or stress response.” This definition includes a variety of substances, four of which will be reviewed in this article: seaweed extract, humic substances, amino acids, and plant-growth-promoting bacteria. We will concentrate on the positive effects of biostimulant application on plant nutrient uptake, and the underlying mechanisms, which include positive changes in soil structure or nutrient solubility, root morphology, plant physiology, and symbiotic relationships, will be discussed. Recommendations for future research directions include finding the most promising substances, isolating the active ingredients and clearly demonstrating the mechanisms by which they affect nutrient uptake. The beneficial effects and mechanisms must be consistently demonstrated in greenhouse and field experiments.

Compost amendments to soils and potting mixes are routinely applied to improve soil fertility and plant growth and health. These amendments, which contain high levels of organic matter and microbial cells, can influence microbial communities associated with plants grown in such soils. The purpose of this study was to follow the bacterial community compositions of seed and subsequent root surfaces in the presence and absence of compost in the potting mix. The bacterial community compositions of potting mixes, seed, and root surfaces sampled at three stages of plant growth were analyzed via general and newly developed Bacteroidetes -specific, PCR-denaturing gradient gel electrophoresis methodologies. These analyses revealed that seed surfaces were colonized primarily by populations detected in the initial potting mixes, many of which were not detected in subsequent root analyses. The most persistent bacterial populations detected in this study belonged to the genus Chryseobacterium ( Bacteroidetes ) and the family Oxalobacteraceae ( Betaproteobacteria ). The patterns of colonization by populations within these taxa differed significantly and may reflect differences in the physiology of these organisms. Overall, analyses of bacterial community composition revealed a surprising prevalence and diversity of Bacteroidetes in all treatments.

Sixty-four isolates of Colletotrichum gloeosporioides were isolated from infected Limonium spp. cultivated in 12 different locations in Israel. All isolates were identified as belonging to the C. gloeosporioides complex by species-specific primers. Of these isolates, 46 were resistant to benomyl at 10 μg/ml and 18 were sensitive to this concentration of fungicide. Based on arbitrarily primed polymerase chain reaction of all isolates and internal transcribed spacer-1 sequence analyses of 12 selected isolates, the benomyl-resistant and -sensitive populations belong to two distinct genotypes. Sequence analyses of the β-tubulin genes, TUB1 and TUB2, of five sensitive and five resistant representative isolates of C. gloeosporioides from Limonium spp. revealed that the benomyl-resistant isolates had an alanine substitute instead of a glutamic acid at position 198 in TUB2. All data suggest that the resistant and sensitive genotypes are two independent and separate populations. Because all Limonium plant propagation material is imported from various geographic regions worldwide, and benomyl is not applied to this crop or for the control of Colletotrichum spp. in Israel, it is presumed that plants are bearing quiescent infections from the points of origin prior to arrival.

In the present work we describe a comprehensive analysis of sulfide oxidation in a fluidized bed reactor (FBR) from an environmentally sustainable, zero-discharge mariculture system. The FBR received oxygen-depleted effluent from a digestion basin (DB) that is responsible for gasification of organic matter and nitrogen. The FBR is a crucial component in this recirculating system because it safeguards the fish from the toxic sulfide produced in the DB. Microscale sulfide oxidation potential and bacterial community composition within FBR biofilms were correlated to biofilter performance by integrating bulk chemical, microsensor (O2, pH, and H2S), and molecular microbial community analyses. The FBR consistently oxidized sulfide during two years of continuous operation, with an estimated average sulfide removal rate of 1.3 g of sulfide-S L(FBR)(-1) d(-1). Maximum sulfide oxidation rates within the FBR biofilms were 0.36 and 0.21 mg of sulfide-S cm(-3) h(-1) in the oxic and anoxic layers, respectively, indicating that both oxygen and nitrate serve as electron acceptors for sulfide oxidation. The estimated anoxic sulfide removal rate, as extrapolated from bench scale, autotrophic, nitrate-amended experiments, was 0.7 g of sulfide-S L(FBR)(-1) d(-1), which is approximately 50% of the total estimated sulfide removal in the FBR. Community composition analyses using denaturing gradient gel electrophoresis (DGGE) of bacterial 16S rRNA gene fragments from FBR samples taken at six-month intervals revealed several sequences that were closely affiliated with sulfide-oxidizing bacteria. These included the denitrifying, sulfide-oxidizing bacteria Thiomicrospira denitrificans, members of the filamentous Thiothrix genus, and sulfide-oxidizing symbionts from the Gammaproteobacteria. In addition, marine Alphaproteobacteria and Bacteroidetes species were present in all of the DGGE profiles examined. DGGE analyses showed significant shifts in the bacterial community composition between profiles over two years of sampling, indicating the presence of a diverse and dynamic microbial community within the functionally stable FBR. The FBR's combined capacity for both oxic and anoxic sulfide oxidation, as indicated by bulk chemical, microsensor, and molecular microbial analyses, gives it significant functional elasticity, which is crucial for proper performance in the dynamic environment of this mariculture system.

A collection ofTrichoderma isolates, with different biocontrol capabilities, were identified by molecular methods. Arbitrarily-primed PCR (ap-PCR) using repeat motif primers was performed on DNA from aTrichoderma spp. collection of 76 isolates, and representative isolates were further characterized into three main clades by internal transcribed spacer (ITS) sequence analysis. Consequently, a reliable phylogenetic tree was constructed containing isolates belonging to theT. harzianum clade (comprisingT. aureoviride, T. inhamatum, andT. virens), theT. longibrachiatum andT. saturnisporum cluster, and that including the speciesT. asperellum, T. atroviride, T. koningii andT. viride.

Trichoderma isolates are known for their ability to control plant pathogens. It has been shown that various isolates of Trichoderma, including T. harzianum isolate T-39 from the commercial biological control product TRICHODEX, were effective in controlling anthracnose (Colletotrichum acutatum) and grey mould (Botrytis cinerea) in strawberry, under controlled and greenhouse conditions. Three selected Trichoderma strains, namely T-39, T-161 and T-166, were evaluated in large-scale experiments using different timing application and dosage rates for reduction of strawberry anthracnose and grey mould. All possible combinations of single, double or triple mixtures of Trichoderma strains, applied at 0.4% and 0.8% concentrations, and at 7 or 10 day intervals, resulted in reduction of anthracnose severity; the higher concentration (0.8%) was superior in control whether used with single isolates or as a result of combined application of two isolates, each at 0.4%. Only a few treatments resulted in significant control of grey mould. Isolates T-39 applied at 0.4% at 2 day intervals, T-166 at 0.4%, or T-161 combined with T-39 at 0.4% were as effective as the chemical fungicide fenhexamide. The survival dynamics of populations of the Trichoderma isolates (T-39, T-105, T-161 and T-166) applied separately was determined by dilution plating and isolates in the mixtures calculated according to the polymerase chain reaction (PCR) using repeat motif primers. The biocontrol isolates were identified to the respective species T. harzianum (T-39), T. hamatum (T-105), T. atroviride (T-161) and T. longibrachiatum (T-166), according to internal transcribed spacer sequence analysis.

This study was conducted to identify the species of Colletotrichum infecting tamarillo, mango, and passiflora in Colombia and to assess whether cross-infection between host species is occurring. Isolates of Colletotrichum spp. from tamarillo (n = 54), passiflora (n = 26), and mango (n = 15) were characterized by various molecular methods and by morphological criteria. Morphological characterization grouped the tamarillo isolates as C. acutatum and the passiflora and mango isolates as C. gloeosporioides. Species-specific primer analysis was reliable and confirmed grouping of the tamarillo isolates (besides Tom-6) as C. acutatum and the mango isolates (besides Man-76) as C. gloeosporioides. However, DNA of the passiflora isolates was not amplified by either C. acutatum- or C. gloeosporioides-specific primers, but reacted with a new primer, Col1, designed according to the internal transcribed spacer (ITS) 1 region of these isolates. Isolates Tom-6 and Man-76 also reacted positively with the Col1 primer. All the isolates reacting with the C. acutatum- and C. gloeosporioides-specific primers failed to react with primer Col1. Isolate Pass-35 from passiflora did not react with any of the taxon-specific primers. Arbitrarily primed polymerase chain reaction (ap-PCR), random amplified polymerase DNA (RAPD)-PCR, and A+T-rich DNA analyses delineated representative isolates into subgroups within the designated species. Molecular analyses indicated that the C. acutatum tamarillo isolates were uniform or clonal, whereas the C. gloeosporioides mango isolates and Colletotrichum passiflora isolates were heterogeneous. Likewise, sequence analysis of the complete ITS (ITS1-5.8S-ITS2) region identified certain isolates to their respective species: tamarillo isolates as C. acutatum; mango isolates as C. gloeosporioides; passiflora, Tom-6, and Man-76 isolates as a Colletotrichum sp. as yet undefined; and the Pass-35 isolate as an additional undefined Colletot-richum sp. Molecular analyses of the population of Colletotrichum isolates from passiflora, Tom-6 from tamarillo, and Man-76 from mango indicate that this population may not be host specific.

Ninety-five isolates of Colletotrichum including 81 isolates of C. acutatum (62 from strawberry) and 14 isolates of C. gloeosporioides (13 from strawberry) were characterized by various molecular methods and pathogenicity tests. Results based on random amplified polymorphic DNA (RAPD) polymorphism and internal transcribed spacer (ITS) 2 sequence data provided clear genetic evidence of two subgroups in C. acutatum. The first subgroup, characterized as CA-clonal, included only isolates from strawberry and exhibited identical RAPD patterns and nearly identical ITS2 sequence analysis. A larger genetic group, CA-variable, included isolates from various hosts and exhibited variable RAPD patterns and divergent ITS2 sequence analysis. Within the C. acutatum population isolated from strawberry, the CA-clonal group is prevalent in Europe (54 isolates of 62). A subset of European C. acutatum isolates isolated from strawberry and representing the CA-clonal and CA-variable groups was assigned to two pathogenicity groups. No correlation could be drawn between genetic and pathogenicity groups. On the basis of molecular data, it is proposed that the CA-clonal subgroup contains closely related, highly virulent C. acutatum isolates that may have developed host specialization to strawberry. C. gloeosporioides isolates from Europe, which were rarely observed were either slightly or nonpathogenic on strawberry. The absence of correlation between genetic polymorphism and geographical origin in Colletotrichum spp. suggests a worldwide dissemination of isolates, probably through international plant exchanges.

Bacterial community structure and physiochemical parameters were examined in a sedimentation basin of a zero-discharge mariculture system. The system consisted of an intensively stocked fish basin from which water was recirculated through two separate treatment loops. Surface water from the basin was pumped over a trickling filter in one loop while bottom-water was recirculated through a sedimentation basin followed by a fluidized bed reactor in the other. Ammonia oxidation to nitrate in the trickling filter and organic matter digestion together with nitrate reduction in the sedimentation basin and fluidized bed reactor, allowed zero-discharge operation of the system. Relatively high concentrations of oxygen, nitrate, sulphate and organic matter detected simultaneously in the digestion basin suggested the potential for a wide range of microbially-mediated transformation processes. In this study, physiochemical parameters were correlated to bacterial diversity and distribution in horizontal and vertical profiles within this basin in an effort to obtain a basic understanding of the chemical and microbial processes in this system. Chemical activity and microbial diversity, the latter measured by denaturing gradient gel electrophoresis (DGGE) analysis of polymerase chain reaction (PCR) amplified 16S rDNA fragments, were higher in the sludge layer than in the overlying aqueous layer of the basin. Chemical parameters in sludge samples close to the basin inlet suggested enhanced microbial activity relative to other sampling areas with evidence of both nitrate and sulphate reduction. Four of the nine DGGE bands identified in this zone were affiliated with the Bacteroidetes phylum. Detected sequences closely related to sequences of organisms involved in the sulphur cycle included Desulfovibrio, Dethiosulfovibrio and apparent sulphur oxidizers from the gamma-proteobacteria. In addition, a number of sequences from the beta and alpha-proteobacteria were identified.

Plant microbiomes are critical to host adaptation and impact plant productivity and health. Root-associated microbiomes vary by soil and host genotype, but the contribution of these factors to community structure and metabolic potential has not been fully addressed. Here we characterize root microbial communities of two disparate agricultural crops grown in the same natural soil in a controlled and replicated experimental system. Metagenomic (genetic potential) analysis identifies a core set of functional genes associated with root colonization in both plant hosts, and metatranscriptomic (functional expression) analysis revealed that most genes enriched in the root zones are expressed. Root colonization requires multiple functional capabilities, and these capabilities are enriched at the community level. Differences between the root-associated microbial communities from different plants are observed at the genus or species level, and are related to root-zone environmental factors.

The effect of effluent irrigation on community composition and function of ammonia-oxidizing bacteria (AOB) in soil was evaluated, using techniques of molecular biology and analytical soil chemistry. Analyses were conducted on soil sampled from lysimeters and from a grapefruit orchard which had been irrigated with wastewater effluent or fertilizer-amended water (FAW). Specifically, comparisons of AOB community composition were conducted using denaturing gradient gel electrophoresis (DGGE) of PCR-amplified fragments of the gene encoding the a-subunit of the ammonia monooxygenase gene (amoA) recovered from soil samples and subsequent sequencing of relevant bands. A significant and consistent shift in the population composition of AOB was detected in soil irrigated with effluent. This shift was absent in soils irrigated with FAW, despite the fact that the ammonium concentration in the FAW was similar. At the end of the irrigation period, Nitrosospiralike populations were dominant in soils irrigated with FAW, while Nitrosomonas-like populations were dominant in effluent-irrigated soils. Furthermore, DGGE analysis of the amoA gene proved to be a powerful tool in evaluating the soil AOB community population and population shifts therein. Agricultural irrigation with wastewater effluent is a common practice in arid and semiarid regions, and it is used as a readily available and inexpensive option to fresh water. However, irrigation with effluent has possible public health and environmental side effects, as effluents may contain pathogens and high levels of sodium, dissolved organic carbon, detergents, and toxic metals (22). Furthermore, the addition of such a “mixed bag” of compounds may cause significant shifts in structure and function of a microbial community, which in turn may influence the viability of the soil for agriculture. One important group of organisms that may be affected is the chemolithotrophic ammonia-oxidizing bacteria (AOB). The AOB, which are responsible for the first, rate-limiting step in nitrification in which ammonia (NH3) is transformed to nitrate (NO3 2 ) via nitrite (NO2 2 ), play a critical role in natural ni