Astrid Vivas

Assessing the impact of composting and vermicomposting on bacterial community size and structure, and microbial functional diversity of an olive-mill waste

The aim of this study was to couple biochemical and molecular methodologies for evaluating the impact of two recycling technologies (composting and vermicomposting) on a toxic organic waste. To do this, six enzyme activities controlling the key metabolic pathways of the breakdown of organic matter, real-time PCR assays targeting 16S rRNA genes, and denaturing gradient gel electrophoresis (DGGE) profiling-sequence analysis of PCR-amplified 16S rRNA fragments have been used to determine the functional diversity, bacterial number, and bacterial community structure, respectively, in a mixture of olive waste and sheep manure, and in the derived compost and vermicompost. Both the recycling technologies were effective in activating the microbial parameters of the toxic waste, the vermicomposting being the best process to produce greater bacterial diversity, greater bacterial numbers and greater functional diversity. Although several identical populations were detected in the processed and non-processed materials, each technology modified the original microbial communities of the waste in a diverse way, indicating the different roles of each one in the bacterial selection.

Influence of a Bacillus sp. on physiological activities of two arbuscular mycorrhizal fungi and on plant responses to PEG-induced drought stress

The effects of bacterial inoculation (Bacillus sp.) on the development and physiology of the symbiosis between lettuce and the arbuscular mycorrhizal (AM) fungi Glomus mosseae (Nicol. and Gerd.) Gerd. and Trappe and Glomus intraradices (Schenck and Smith) were investigated. Plant growth, mineral nutrition and gas–exchange values in response to bacterial inoculation after PEG–induced drought stress were also evaluated. In AM plants, inoculation with Bacillus sp. enhanced fungal development and metabolism, measured as succinate dehydrogenase (SDH) and alkaline phosphatase (ALP) activities, more than plant growth. Under non-stressed conditions, G. intraradices colonization increased all plant physiological values to a higher extent when in dual inoculation with the bacterium. Under stress conditions, the bacterium had an important stimulatory effect on G. intraradices development. Under such conditions, the effects of the bacterium on photosynthetic rate, water use efficiency (WUE) and stomatal conductance of lettuce plants differed with the fungus species. Plant-gas exchange was enhanced in G. intraradices- and reduced in G. mosseae-colonized plants when co-inoculated with Bacillus sp. Thus, the effects of each fungus on plant physiology were modulated by the bacterium. Stress was detrimental, particularly in G. intraradices-colonized plants without the bacterium, reducing intra and extraradical mycelium growth and vitality (SDH), as well as plant-gas exchange. Nevertheless, Bacillus sp. inoculation improved all these plant and fungal parameters to the same level as in non-stressed plants. The highest amount of alive and active AM mycelium for both fungi was obtained after co-inoculation with Bacillus sp. These results suggest that selected free-living bacteria and AM fungi should be co-inoculated to optimize the formation and functioning of the AM symbiosis in both normal and adverse environments.

Symbiotic efficiency of autochthonous arbuscular mycorrhizal fungus (G. mosseae) and Brevibacillus sp. isolated from cadmium polluted soil under increasing cadmium levels

The effect of inoculation with indigenous naturally occurring microorganisms (an arbuscular mycorrhizal (AM) fungus and rhizosphere bacteria) isolated from a Cd polluted soil was assayed on Trifolium repens growing in soil contaminated with a range of Cd. One of the bacterial isolate showed a marked PGPR effect and was identified as a Brevibacillus sp. Mycorrhizal colonization also enhanced Trifolium growth and N, P, Zn and Ni content and the dually inoculated (AM fungus plus Brevibacillus sp.) plants achieved further growth and nutrition and less Cd concentration, particularly at the highest Cd level. Increasing Cd level in the soil decreased Zn and Pb shoot accumulation. Coinoculation of Brevibacillus sp. and AM fungus increased shoot biomass over single mycorrhizal plants by 18% (at 13.6 mg Cd kg(-1)), 26% (at 33.0 mg Cd kg(-1)) and 35% (at 85.1 mg Cd (kg(1)). In contrast, Cd transfer from soil to plants was substantially reduced and at the highest Cd level Brevibacillus sp. lowered this value by 37.5% in AM plants. Increasing Cd level highly reduced plant mycorrhization and nodulation. Strong positive effect of the bacterium on inocula, are important in plant Cd tolerance and development in Cd polluted soils.

Significance of treated agrowaste residue and autochthonous inoculates (Arbuscular mycorrhizal fungi and Bacillus cereus) on bacterial community structure and phytoextraction to remediate soils contaminated with heavy metals

In this study, we analyzed the impact of treatments such as Aspergillus niger-treated sugar beet waste (SB), PO4(3-) fertilization and autochthonous inoculants [arbuscular mycorrhizal (AM) fungi and Bacillus cereus], on the bacterial community structure in a soils contaminated with heavy metals as well as, the effectiveness on plant growth (Trifolium repens). The inoculation with AM fungi in SB amended soil, increased plant growth similarly to PO4(3-) addition, and both treatments matched in P acquisition but bacterial biodiversity estimated by denaturing gradient gel electrophoresis of amplified 16S rDNA sequences, was more stimulated by the presence of the AM fungus than by PO4(3-) fertilization. The SB amendment plus AM inoculation increased the microbial diversity by 233% and also changed (by 215%) the structure of the bacterial community. The microbial inoculants and amendment used favoured plant growth and the phytoextraction process and concomitantly modified bacterial community in the rhizosphere; thus they can be used for remediation. Therefore, the understanding of such microbial ecological aspects is important for phytoremediation and the recovery of contaminated soils.

Effectiveness of autochthonous bacterium and mycorrhizal fungus on Trifolium growth, symbiotic development and soil enzymatic activities in Zn contaminated soil

Aims:  This study investigates how autochthonous micro‐organisms [bacterium and/or arbuscular mycorrhizal (AM) fungi] affected plant tolerance to Zn contamination.

Physiological characteristics (SDH and ALP activities) of arbuscular mycorrhizal colonization as affected by Bacillus thuringiensis inoculation under two phosphorus levels

The effect of Bacillus thuringiensis (B.t.) inoculation on plant growth and on the intra- and extraradical mycorrhizal development of lettuce roots colonized by Glomus mosseae or Glomus intraradices was examined in an inert, soil-less substrate. Histochemical determination of succinate dehydrogenase (SDH) and alkaline phosphatase (ALP) activities which indicate active fungal metabolism was carried out at two phosphorus (P) levels. The presence of B.t. increased extra- and intraradical colonization [measured as frequency ð%FÞ; intensity ð%IÞ and percentage of arbuscules (%A)] for both arbuscular mycorrhizal fungi (AMF) rather than plant growth or nutrition regardless P level. Under the lowest level of P fertilization, B.t. enhanced to a similar extent the extra- and intraradical development of both endophytes, but the proportion of fungal tissue showing SDH or ALP was increased in G. intraradices-colonized plants. [SDH: 458% (M) and 512% (A); ALP: 358% (M) and 300% (A)]. P supply decreased G. intraradices colonization to a higher extent than G. mosseae. Nevertheless, the totality of G. intraradices structures developed in P-amended medium showed intraradical o extraradical activity, while in G. mosseae-colonized roots, SDH and ALP activities highly decreased relative to fungal tissue determined by TB staining as affected by P. Our results show that bacterial inoculation compensates the negative effect of P on the intraradical fungal growth and vitality. P amendment reduced in a higher extent G. intraradices infection intensity (non-vital and vital staining) and G. mosseae activity (ALP staining). Thus, big differences in the proportion of SDH-active infection showing ALP activity in mycelium developed by each endophyte were noted at the highest P level. Physiological plant parameters such as photosynthetic activity did not explain specific changes on each arbuscular-mycorrhizal fungus as affected by P or B.t. inoculation. The increased extraradical mycelium development and metabolic fungal activity as a result of B.t. inoculation positively affected N and P plant content and photosynthetic rate in G. intraradices-colonized plants under the lowest P conditions. In general, the increased metabolically active fungal biomass in co-inoculated plants was irrespective of P level and was not related to the P plant uptake from the inert soil-less substrate. These results show the bacterial effect increasing the physiological and metabolic status of AM endophytes, which not only confirms but also extends previous findings on arbuscular mycorrhizae-bacteria interactions. The present study emphasizes the ecological and practical importance of rhizosphere free-living bacteria as mycorrhizae-helper microorganisms. q 2003 Elsevier Science Ltd. All rights reserved.

Brevibacillus brevis isolated from cadmium- or zinc-contaminated soils improves in vitro spore germination and growth of Glomus mosseae under high Cd or Zn concentrations.

In this study we investigated the saprophyte growth of two arbuscular–mycorrhizal fungi (Glomus mosseae isolate) under increasing Cd or Zn levels and the influence of a selected bacterial strain of Brevibacillus brevis. Microorganisms here assayed were isolated from Cd or Zn polluted soils. B. brevis increased the presymbiotic growth (germination rate growth and mycelial development) of Glomus mosseae. Spore germination and mycelial development of both G. mosseae isolate were reduced as much as the amount of Cd or Zn increased in the growth medium. In medium supplemented with 20 μg Cd mL−1, the spore germination was only 12% after 20 days of incubation, but the coinoculation with B. brevis increased this value to 40% after only 15 days. The addition of 20 μg Cd mL−1 to the growth medium drastically inhibited hyphal development, but the presence of the bacterium increased hyphal growth of G. mosseae from 195% (without Cd) until 254% (with 20 μg Cd mL−1). The corresponding bacterial effect increasing micelial growth ranged from 125% (without Zn) to 232% (200 μg Zn mL−1) in the case of G. mosseae isolated from Zn-polluted soil. Mycelial growth under 5 μg Cd mL−1 (without bacterium) was similarly reduced from that produced at 15 μg Cd mL−1 in the presence of the bacteria. As well, 50 μg Zn mL−1 (without bacterium) reduced hyphal growth as much as 200 μg Zn mL−1 did in the presence of B. brevis. The bacterial effect on the saprophytic growth of G. mosseae in absence of metal may be due to the involvement of indole acetic acid (IAA) produced by these bacteria. The Cd bioaccumulation ability exhibited (76%) by Cd-adapted B. brevis reduced the Cd damage on G. mosseae in Cd-contaminated medium. These capabilities of B. brevis isolates partially alleviate the inhibitory effects of Cd or Zn on the axenic growth of G. mosseae.

Restoring biochemical activity and bacterial diversity in a trichloroethylene-contaminated soil: the reclamation effect of vermicomposted olive wastes.

Background, aim, and scopeIn this work, the potential for using olive-mill solid waste as an organic amendment for biochemical and biological restoration of a trichloroethylene-contaminated soil, which has previously been stabilized through vermicomposting processes, has been explored.Materials and methodsTrichloroethylene-contaminated water was pumped into soil columns with a layer of vermicompost at 10-cm depth (biobarrier system). The impacts of the trichloroethylene on the microbial community were evaluated by determining: (1) the overall microbial activity (estimated as dehydrogenase activity) and enzyme activities related to the main nutrient cycles (β-glucosidase, o-diphenoloxidase, phosphatase, urease, and arylsulphatase activities). In addition, isoelectric focusing of the soil extracellular humic-β-glucosidase complexes was performed to study the enzymatically active humic matter related to the soil carbon cycle. (2) The soil bacterial diversity and the molecular mechanisms for the bacterial resistance to organic solvents were also determined. For this, polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) was used to detect changes in bacterial community structure and PCR-single-strand conformational polymorphism (SSCP) was developed and optimised for detection and discrimination of the resistance-nodulation-division (RND) genes amplified from the contaminated soils.ResultsVermicompost reduced, with respect to the unamended soil, about 30% of the trichloroethylene leaching during the first month of the experiment. Trichloroethylene had a marked negative effect on soil dehydrogenase, β-glucosidase, urease, phosphatase, and arylsulphatase activities. Nevertheless, the vermicompost tended to avoid this toxic effect. Vermicompost also displays stable humic-β-glucosidase complexes that increased the extracellular activity related to C-cycle in the contaminated soils. The isoelectric focusing technique showed a more biochemically active humic matter in the soil sampled under the vermicompost. The behaviour of the three main phyla of bacteria isolated from the DGGE bands was quite different. Bands corresponding to Actinobacteria disappeared, whereas those affiliated with Proteobacteria remained after the trichloroethylene contamination. The disappeared Actinobacteria became visible in the soil amended with the vermicompost. Bands corresponding to Bacteriodetes appeared only in columns of contaminated soils. In this study, six types of RND proteins were detected by PCR-SSCP in the natural soil, three in the trichloroethylene-contaminated soil and 7/5 in trichloroethylene-contaminated soil above/below the vermicompost in the biobarrier columns. Trichloroethylene tended to reduce or eliminate all the clones detected in the uncontaminated soil, whereas new efflux pumps appeared in the biobarrier columns.DiscussionAlthough enzymes incorporated into the humic substances of vermicomposted olive wastes are quite stable, trichloroethylene also inhibited the background levels of the soil extracellular β-glucosidase activity in the amended soils. The decrease was less severe in the biobarrier system, but in any case, no relation was found between the levels of trichloroethylene in soil and extracellular β-glucosidase activity, or between the latter and the quantity of humic carbon in soils. The isoelectric focusing technique was carried out in the humic fraction to determine whether the loss of activity occurred in overall extracellular β-glucosidase or in that linked to stable humic substances (humic–enzyme complexes). The contaminated soils showed the lower enzyme activities, whereas contaminated and amended soils presented greater quantity of focalised (and therefore stable) humic carbon and spectra heterogeneity: very different bands with higher enzyme activities. No clear relationship between trichloroethylene concentration in soil and diversity of the bacterial population was noted. Similar patterns could be found when the community structures of bacteria and microbial activity were considered. Since the use of the dehydrogenase assay has been recognised as a useful indicator of the overall measure of the intensity of microbial metabolism, these results could be attributed to PCR-DGGE methodology, since the method reveals the presence of dominant populations regardless of their metabolic state. Trichloroethylene maintained or even increased the number of clones with the DNA encoding for RND proteins, except for the contaminated soil located above the vermicompost. However, the main effect of trichloroethylene was to modify the structure of the community in contaminated soils, considering the type of efflux pumps encoded by the DNA extracted from soil bacteria.ConclusionsTrichloroethylene inhibited specific functions in soil and had a clear influence on the structure of the autochthonous bacterial community. The organic matter released by the vermicomposted olive waste tended to avoid the toxic effect of the contaminant. Trichloroethylene also inhibited the background levels of the soil extracellular β-glucosidase activity, even when vermicompost was present. In this case, the effect of the vermicompost was to provide and/or to stimulate the humic-β-glucosidase complexes located in the soil humic fraction >104, increasing the resistance of the enzyme to the inhibition. The bacterial community from the soil presented significantly different mechanisms to resistance to solvents (RND proteins) under trichloroethylene conditions. The effect of the vermicompost was to induce these mechanisms in the autochthonous bacterial community and/or incorporated new bacterial species, able to grow in a trichloroethylene-contaminated ambient. Coupled biochemical and molecular methodologies are therefore helpful approaches in assessing the effect of an organic amendment on the biochemical and biological restoration of a trichloroethylene-contaminated soil.Recommendations and perspectivesSince the main biochemical and biological effects of the organic amendment on the contaminated soil seem to be the incorporation of biochemically active humic matter, as well as new bacterial species able to grow in a trichloroethylene-contaminated ambient, isoelectric focusing and PCR-SSCP methodologies should be considered as parts of an integrated approach to determine the success of a restoration scheme.

Solvent tolerance acquired by Brevibacillus brevis during an olive-waste vermicomposting process

In this work, a cultivable, Gram-positive, solvent-resistant bacterium was isolated from vermicomposted olive wastes (VOW). The highest 16S rRNA sequence similarity (99%) was found in Brevibacillus brevis. The genome of the isolate, selected for trichloroethylene (TCE)-tolerance, contained a nucleotide sequence encoding a conserved protein domain (ACR_tran) ascribable to the HAE1-RND family. Members of this family are hydrophobic/amphiphilic efflux pumps largely restricted to Gram-negative bacteria. No DNA sequences of HAE1 transporters were detected in the genome of a reference B. brevis strain isolated from natural soil. Since no cultivable solvent-tolerant bacterium was detected in the unvermicomposted olive waste, a transfer of solvent-resistance genes from Gram-negative bacteria during the vermicomposting process could explain the presence of HAE1 transporters in B. brevis isolated from the vermicompost. Under TCE stress conditions, the acquired nucleotide sequence could be translated into proteins, and the tolerance to solvents is conferred to the bacterium. The isolate was designated as strain BEA1 (EF079071).

Effect of Natural Vegetation Strips and Herbicides on Enzyme Activities and Bacterial Diversity in Olive-Orchard Systems

The use of vegetation strips in mountainous olive-orchards is of major importance in reducing soil erosion and minimizing the adverse effects of the herbicides transfer to surface waters. This study was carried out to evaluate the effects of natural vegetation strips and herbicides on soil enzyme activities and changes in bacterial community structures. Thus, four enzyme activities were determined in soil samples from different zones in an integrated olive-orchard system on slopes. Changes in microbial population were analysed by using PCR assays to target 16S rDNA genes and denaturing gradient gel electrophoresis. Soil samples were collected at a depth of 0–5 cm from the experimental plot upslope and downslope: (1) under the vegetation strips before and after application of glyphosate, (2) from bare soil between the strips and under the olive trees treated with oxyfluorfen and glyphosate, (3) native soil from a non-cultivated area. Enzyme activities and bacterial diversity were lower in soils from the olive-orchard system than in the native soil. In the olive-orchard system, the enzyme activities in soils from the strips were higher than in bare soils and soils under trees. In the soils under strips, the level of β-glucosidase and phosphatase activities increased after the application of glyphosate while dehydrogenase and urease activities decreased. The presence of natural vegetation in the strips as well as herbicide application modified the bacterial community structure and the biodiversity indices. Soil sampled in the downslope strip and after glyphosate addition showed the highest biodiversity values and dominance indices.