Isabelle George

Fecal coliform removal in wastewater treatment plants studied by plate counts and enzymatic methods.

Twelve wastewater treatment plants (WWTPs) were sampled in France and Belgium in 1999 and 2000 in order to estimate the fecal coliform (FC) removal efficiency of various types of treatment. Only one of these WWTPs was equipped with a specific step to eliminate microorganisms (UV disinfection preceded by sand filtration). FC abundance was measured in raw and treated sewage by plate counts on selective medium and rapid beta-D-glucuronidase (GLUase)-based assays. Removal of culturable FC was the most efficient in treatments with high retention time (activated sludge process with nitrification and denitrification, lagooning), in biofiltration and in the treatment with a tertiary disinfection step. GLUase activity measurements showed the same removal pattern as plate counts except for UV disinfection, where no reduction of GLUase activity was measured. Specific loads of culturable FC and GLUase activity, i.e. daily amounts of culturable FC or GLUase activity in sewage per inhabitant-equivalent, were calculated in raw and treated wastewater for the different WWTPs.

Use of enzymatic methods for rapid enumeration of coliforms in freshwaters

Rapid enumeration methods based on the enzymatic hydrolysis of 4‐methylumbelliferyl‐β‐ d‐galactoside and 4‐methylumbelliferyl‐β‐ d‐glucuronide were optimized for freshwaters. The enzymes β‐ d‐galactosidase (GALase) and β‐ d‐glucuronidase (GLUase) were shown to be already induced in freshwaters when tested, respectively, with the inducers isopropyl‐β‐ d‐thiogalactopyranoside and methyl‐β‐ d‐glucuronide. Both enzymatic activities were compared, respectively, with plate counts of total and faecal coliforms in freshwaters. Enzymatic methods and reference plate counts were significantly correlated in log–log plots. Moreover, the GLUase method allowed the detection of viable (presenting a detectable GLUase activity) but nonculturable Escherichia coli.

Environmental genomics: exploring the unmined richness of microbes to degrade xenobiotics.

Increasing pollution of water and soils by xenobiotic compounds has led in the last few decades to an acute need for understanding the impact of toxic compounds on microbial populations, the catabolic degradation pathways of xenobiotics and the set-up and improvement of bioremediation processes. Recent advances in molecular techniques, including high-throughput approaches such as microarrays and metagenomics, have opened up new perspectives and pointed towards new opportunities in pollution abatement and environmental management. Compared with traditional molecular techniques dependent on the isolation of pure cultures in the laboratory, microarrays and metagenomics allow specific environmental questions to be answered by exploring and using the phenomenal resources of uncultivable and uncharacterized micro-organisms. This paper reviews the current potential of microarrays and metagenomics to investigate the genetic diversity of environmentally relevant micro-organisms and identify new functional genes involved in the catabolism of xenobiotics.

Emerging high-throughput approaches to analyze bioremediation of sites contaminated with hazardous and/or recalcitrant wastes.

Sustainable development requires the promotion of environmental management and a constant search for new technologies to treat a wide range of aquatic and terrestrial habitats contaminated by increasing anthropogenic activities. Bioremediation, i.e. the elimination of natural or xenobiotic pollutants by living organisms, is an environmentally friendly and cost-effective alternative to physico-chemical cleanup options. However, the strategy and outcome of bioremediation in open systems or confined environments depend on a variety of physico-chemical and biological factors that need to be assessed and monitored. In particular, microorganisms are key players in bioremediation applications, yet their catabolic potential and their dynamics in situ remain poorly characterized. To perform a comprehensive assessment of the biodegradative potential of a contaminated site and efficiently monitor changes in the structure and activities of microbial communities involved in bioremediation processes, sensitive, fast and large-scale methods are needed. Over the last few years, the scientific literature has revealed the progressive emergence of genomic high-throughput technologies in environmental microbiology and biotechnology. In this review, we discuss various high--throughput techniques and their possible--or already demonstrated-application to assess biotreatment of contaminated environments.

Recovery of As-Yet-Uncultured Soil Acidobacteria on Dilute Solid Media

ABSTRACT A growing number of Acidobacteria strains have been isolated from environments worldwide, with most isolates derived from acidic samples and affiliated with subdivision 1. We recovered 18 Acidobacteria strains from an alkaline soil, among which 11 belonged to the previously uncultured subdivision 6. Various medium formulations were tested for their effects on Acidobacteria growth.

Distribution of Coliforms in the Seine River and Estuary (France) Studied by Rapid Enzymatic Methods and Plate Counts

Fecal contamination in the Seine River and its estuary was studied for the first time by rapid enzymatic methods in parallel with traditional enumerations on selective culture media. The study consisted of four sampling campaigns focused on a 450-km stretch including the Parisian area and presenting highly variable levels of fecal pollution. Enzymatic assays (based on the activity of the β-D-galactosidase and β-D-glucuronidase enzymes in total [TC] and fecal [FC] coliforms, respectively) were in good agreement with classical plate counts of TC and FC. Both methods reflected the strong impact of the wastewater discharge from the Parisian area and of the presence of a maximum turbidity zone (at the mouth of the estuary) on the abundance of fecal bacteria in the river. Downstream from the Parisian outfalls, enzymatic measurements probably detected enzymatically active but nonculturable bacteria disregarded by plate counts. Enzymatic measurements in the Seine River downstream from the Parisian area were used to estimate net disappearance rates of coliforms in the river, which were close to total mortality rates measured with a method based on bacterial DNA labeling with tritiated thymidine. The part of total mortality due to grazing by protozoa was also investigated by the thymidine method. Grazing activity was responsible for 47% to 99% of the mortality of coliforms in the river. Attachment of coliforms to suspended matter (SM) was another factor which could be important in controlling the dynamics of coliforms in the Seine River and particularly in its estuary. Results of filtration and decantation experiments suggested that a significant part of the coliforms can be linked to SM depending on the nature and concentration of the SM.

Changes in soil Acidobacteria communities after 2,4,6-trinitrotoluene contamination

Despite their widespread occurrence in soils, the ecology of Acidobacteria and their response to environmental perturbations due to human activities remain very poorly documented. This study was aimed at assessing changes in the diversity and abundance of Acidobacteria in soils contaminated with 2,4,6-trinitrotoluene (TNT) compared with nonpolluted soils. The analysis of Acidobacteria communities at two sites with long-term and short-term contamination revealed that TNT has a drastic impact on the relative abundance of Acidobacteria in soil bacterial 16S rRNA gene libraries. The disappearance of most Acidobacteria from these soils was concomitant with a shift in Acidobacteria community composition and a loss of diversity, although the extent of diversity erosion depended on the sampling site.

The Rhizosphere Selects for Particular Groups of Acidobacteria and Verrucomicrobia

There is a lack in our current understanding on the putative interactions of species of the phyla of Acidobacteria and Verrucomicrobia with plants. Moreover, progress in this area is seriously hampered by the recalcitrance of members of these phyla to grow as pure cultures. The purpose of this study was to investigate whether particular members of Acidobacteria and Verrucomicrobia are avid colonizers of the rhizosphere. Based on previous work, rhizosphere competence was demonstrated for the Verrucomicrobia subdivision 1 groups of Luteolibacter and Candidatus genus Rhizospheria and it was hypothesized that the rhizosphere is a common habitat for Acidobacteria subdivision 8 (class Holophagae). We assessed the population densities of Bacteria, Verrucomicrobia subdivision 1 groups Luteolibacter and Candidatus genus Rhizospheria and Acidobacteria subdivisions 1, 3, 4, 6 and Holophagae in bulk soil and in the rhizospheres of grass, potato and leek in the same field at different points in time using real-time quantitative PCR. Primers of all seven verrucomicrobial, acidobacterial and holophagal PCR systems were based on 16S rRNA gene sequences of cultivable representatives of the different groups. Luteolibacter, Candidatus genus Rhizospheria, subdivision 6 acidobacteria and Holophaga showed preferences for one or more rhizospheres. In particular, the Holophaga 16S rRNA gene number were more abundant in the leek rhizosphere than in bulk soil and the rhizospheres of grass and potato. Attraction to, and colonization of, leek roots by Holophagae strain CHC25 was further shown in an experimental microcosm set-up. In the light of this remarkable capacity, we propose to coin strain CHC25 Candidatus Porrumbacterium oxyphilus (class Holophagae, Phylum Acidobacteria), the first cultured representative with rhizosphere competence.

Polyketide synthase pathways identified from a metagenomic library are derived from soil Acidobacteria

Polyketides are structurally diverse secondary metabolites, many of which have antibiotic or anticancer activity. Type I modular polyketide synthase (PKS) genes are typically large and encode repeating enzymatic domains that elongate and modify the nascent polyketide chain. A fosmid metagenomic library constructed from an agricultural soil was arrayed and the macroarray was screened for the presence of conserved ketosynthase [β-ketoacyl synthase (KS)] domains, enzymatic domains present in PKSs. Thirty-four clones containing KS domains were identified by Southern hybridization. Many of the KS domains contained within metagenomic clones shared significant similarity to PKS or nonribosomal peptide synthesis genes from members of the Cyanobacteria or the Proteobacteria phyla. However, analysis of complete clone insert sequences indicated that the blast analysis for KS domains did not reflect the true phylogenetic origin of many of these metagenomic clones that had a %G+C content and significant sequence similarity to genes from members of the phylum Acidobacteria. This conclusion of an Acidobacteria origin for several clones was further supported by evidence that cultured soil Acidobacteria from different subdivisions have genetic loci closely related to PKS domains contained within metagenomic clones, suggesting that Acidobacteria may be a source of novel polyketides. This study also demonstrates the utility of combining data from culture-dependent and -independent investigations in expanding our collective knowledge of microbial genomic diversity.

Antagonistic Interactions among Bacteria Isolated from either the Same or from Different Sponges Native to the Brazilian Coast

Marine sponges are sessile and filter-feeding organisms that harbor dense and diverse microbial communities of considerable ecological and biotechnological importance. They represent an important target for the study of bacterial interactions in marine ecosystems. The purpose of this study was to examine the frequency of antagonistic interactions among the culturable microbial communities associated with sponges from the Brazilian coast. The specimens were collected over six years at Cagarras Archipelago, Praia Vermelha Beach and Urca square, Rio de Janeiro State, SE Brazil. Fifty-six bacterial isolates representing four classes of cultivable sponge-associated bacteria were studied for their ability to produce inhibitory substances. Antagonistic interactions occurred among isolates from both, the same and different sponge species. Most isolates (98.2%) were able to inhibit growth of at least one indicator bacterium. In contrast, there were few antagonistic interactions among bacteria obtained from the same sponge specimen. Our results suggest that chemical antagonism could play a significant role in shaping the bacterial communities within sponge tissues.