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Microbial characterisation before and after the treatment in the well A

Microbial characterisation before and after the treatment in the well A

Annalisa Balloi, Massimo Marzorati1, Francesca de Ferra2, Sara Borin1, Elena Allifranchini2 ,Giovanna Carpani2, Luca Serbolisca2 ,Willy Verstraete3 and Daniele Daffonchio1.

Catabolic gene redundancy in Contaminated GroundwaterCatabolic gene redundancy in Contaminated Groundwater

Laboratory for Microbial Ecology and Technology

(LabMET),Ghent University

San Donato Milanese

Università degli Studi di Milano

DISTAM Dipartimento di Scienze e Tecnologie

Alimentari e Microbiologiche

A BPump&Treat

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FormiateAcetate Cheese whey Control

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Dichloro-elimination

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Desulfitobacterium dichloroeliminans

Dehalobacter sp. E1

Desulfitobacterium hafniense

D.restrictus Uncult. Clostridium

Microbial characterisation before and after the treatment in the well B

Microbial characterisation before and after the treatment in the well B

Characterisation of the RD from 6vs culture (DcA RD-54) Characterisation of the RD from 6vs culture (DcA RD-54) DNA RNA DNase RNA cDNA nc MM

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dcaA dcaBtnpA

Expression of dcaA geneExpression of dcaA gene

Southern blot hybridization analysis performed to survey the RD genes in the genome of strain DCA1

Southern blot hybridization analysis performed to survey the RD genes in the genome of strain DCA1

In well A lactate addition stimulates the increase of well known degraders of chlorinated alkanes such as D. restrictus, D.

dichloeliminans, D. hafniense and many others. No Archaea can be identified.

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In well B lactate addition stimulates the enrichment of a

clostridium clone. The interaction between Archaea and Bacteria

can play a major role in the DCA degradation.

Transciption of dcaA and dcaB in culture 6VS during dechlorination of 1,2-DCA. PCR experiment using:A) specific primers for the dcaA gene (DHL F1, DHL F2 and DHL R1) to assess the transcription of dcaA; PCR on genomic DNA (lanes 1, 2), total RNA before the treatment with DNAse (lanes 3, 4), total extracted RNA following the treatment with DNAse (lanes 5, 6) and on the cDNA synthesized from the pure RNA (lanes 7, 8). Negative control (lane 9). B) Primer DcaB Rev (specific for dcaB) coupled with DHL F1; PCR on genomic DNA (lane 1), total extracted RNA following the treatment with RNAse (lane 2) and on the cDNA synthesized from the pure RNA (lane 3). M = marker (band size is given in bp)

The phylogentic and functional gene diversity of the bacterial communities of a double layer aquifer contaminated with 1,2-dichloroethane (1,2-DCA) was examined in anaerobic water microcosms. Biotransformation of 1,2-dichloroethane to ethene in a single step via reductive dihaloelimination was enhanced by 5 mM lactate addition as electron donor. Bacterial and archaeal diversity were analysed by sequencing 16S rRNA gene clone libraries prepared prior and after a biostimulation treatment. Upper aquifer was characterized by microrganisms belonging to low G + C gram positive bacteria, e and b Proteobacteria. The clone library following the treatment was dominated by Clostridiaceae such as Desulfitobacterium or Dehalobacter, all phylotypes known to be active dechlorinators. A rather different microbial community characterized lower aquifer. Archaeal nested PCR allowed to obtain 16S rRNA amplicons and the clone libraries of bacterial 16S rRNA gene showed a population characterized by a wide bacterial diversity (b-, d-, e-Proteobacteria and a phylotype referred to Trichlorobacter thiogenes) that was substituted by a less diverse microflora predominated by a distinct phylotype most similar to an uncultured Clostridiaceae. Hence, it appeared that very different microbial populations could lead to the same complete degradation of DCA. Functional redundancy was evaluated through gene libraries of the catabolic genes associated with the key steps of the detoxification process using primers previously developed for reductive dehalogenases. Two major groups of RD genes have been identified: one with a high sequence homology to the RD identified in Desulfitobacterium dichloroeliminans strain DCA1, a microorganism that can couple 1,2-DCA dechlorination to ethene with energy production; a second group with sequences that differed in two small regions both from the previous one and from the PCE specific RDs. Catabolic gene redundancy in a contaminated site is a key aspect, index of the ability of different metabioses to adapt to environmental changes and potentially, of their ability in degrading different xenobiotic compounds.

Aminoacidic alignment of DcaA RD-54 Vs Other A subunits of well known RDs proteins

No changes in N-terminal sequence, restriction site and signal peptide

Rectangles 1 and 2 = a double Arg and Pro is typical of consensus of TAT System

Rectangles 3 and 4 = two iron-sulfur cluster binding motifs:

•FeS cluster I is totally conserved

•Some changes in FeS cluster II

•Cys conserved in both FeS clusters, in the fixed position typical of RDases

About 53% of the diversity between the RD-54 from 6VS culture and the other RDs was localized in two regions (A and B ) that represented only the 19% of the total Dca residues.

1,2 DCA dechlorinating culture

named 6Vs

tpnA = Transposase; dcaA = Catalytic subunit ; dcaB = Anchor protein; dcaC = Membrane bound regulatory protein dcaT = Trigger factor; Orf1 = Unknown function

Alignment of the complete gene cluster sequence, named RD-54, with known gene clusters encoding emzyme complexes active in reductive dechlorination of clorinated aliphatics, showed that all of the genes except dcaA were >98% identical, at the nucleotide level, to the corresponding genes of Dehalobecter restictus strain DSMZ 9455t and of Desulfobacteium dihloroeliminans DCA1.

Enterococcus faecium

Trichlorobacter thiogenes

Trichlorobacter thiogenes

Uncult. Epsilon Proteo

Dechloromonas sp.

Uncult. Crenarchaeota

Phylogenetic relationship between DcaA of the 6VS culture (DcaA RD-54) and D.dichloroeliminans strain DCA1 with other A subunits of genetically characterized RDases.The numbers at each branch point represent bootstrap percentage calculated from 1000 replicate trees. The scale bar represents the sequence divergence.

The two DcaA proteins (RD-54 and RD-DCA1) clustered in a phylogenetic brnch divergent from the other corresponding RD proteins active on chlorinated ethens and chlorophenol

A) Southern blot analyses of gel in panel A using Probe A specific for dcaA gene of strain DCA1.

B) Southern blot analyses of gel in panel A using Probe B universal for gene B known up to date (dcaB, pceB).

The Ds. Dichloroeliminans strain DCA1 harbors two identical or highly similar copies of the same RD cluster

CONCLUSIONS

• The two aquifers are characterized by different microbial communities

• The levels of known degraders of halogenated alkanes increased during the biostimulation treatment

•Following the lactate treatment a new dehalogenase gene cluster composed of 6 genes is enriched

•The dehalogenase (gene dcaA) is expressed during the incubation with lactate

• Gene dcaA can be used as a molecular tool during the bioremediation treatment Strain DCA1 has the same unique gene cluster

Light gray areas A and B indicate the two amino acid stretches were resides about 53% of the diversity between the RD-54 from 6VS culture and the other RDs.

Black areas indicate the different positions between PcaA and DcaA, but conserved between DcaA of RD-54 and RD-DCA1.

The genes dcaA and dcaB are co-transcipted

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B