Unveiling Ecological and Genetic Novelty within Lytic and Lysogenic Viral Communities of Hot Spring Phototrophic Microbial Mats

Viruses exert diverse ecosystem impacts by controlling their host community through lytic predator-prey dynamics. However, the mechanisms by which lysogenic viruses influence their host-microbial community are less clear. In hot springs, lysogeny is considered an active lifestyle, yet it has not been systematically studied in all habitats, with phototrophic microbial mats (PMMs) being particularly not studied. We carried out viral metagenomics following in situ mitomycin C induction experiments in PMMs from Porcelana hot spring (Northern Patagonia, Chile). The compositional changes of viral communities at two different sites were analyzed at the genomic and gene levels. Furthermore, the presence of integrated prophage sequences in environmental metagenome-assembled genomes from published Porcelana PMM metagenomes was analyzed. Our results suggest that virus-specific replicative cycles (lytic and lysogenic) were associated with specific host taxa with different metabolic capacities. One of the most abundant lytic viral groups corresponded to cyanophages, which would infect the cyanobacteria Fischerella, the most active and dominant primary producer in thermophilic PMMs. Likewise, lysogenic viruses were related exclusively to chemoheterotrophic bacteria from the phyla Proteobacteria, Firmicutes, and Actinobacteria. These temperate viruses possess accessory genes to sense or control stress-related processes in their hosts, such as sporulation and biofilm formation. Taken together, these observations suggest a nexus between the ecological role of the host (metabolism) and the type of viral lifestyle in thermophilic PMMs. This has direct implications in viral ecology, where the lysogenic-lytic switch is determined by nutrient abundance and microbial density but also by the metabolism type that prevails in the host community.This work was financially supported by Ph.D. scholarships ANID N°21130667 and N°21172022, ANID-FONDECYT grants N°1150171 and N°1190998, ANID-ECOS160025, and Iniciativa de Investigación UnACh 2020-132-Unach

Reductive dechlorination of tetrachloroethene by a stepwise catalysis of different organohalide respiring bacteria and reductive dehalogenases

The enrichment culture SL2 dechlorinating tetrachloroethene (PCE) to ethene with strong trichloroethene (TCE) accumulation prior to cis-1,2-dichloroethene (cis-DCE) formation was analyzed for the presence of organohalide respiring bacteria and reductive dehalogenase genes (rdhA). Sulfurospirillum-affiliated bacteria were identified to be involved in PCE dechlorination to cis-DCE whereas "Dehalococcoides”-affiliated bacteria mainly dechlorinated cis-DCE to ethene. Two rdhA genes highly similar to tetrachloroethene reductive dehalogenase genes (pceA) of S. multivorans and S. halorespirans were present as well as an rdhA gene very similar to the trichloroethene reductive dehalogenase gene (tceA) of "Dehalococcoides ethenogenes” strain 195. A single strand conformation polymorphism (SSCP) method was developed allowing the simultaneous detection of the three rdhA genes and the estimation of their abundance. SSCP analysis of different SL2 cultures showed that one pceA gene was expressed during PCE dechlorination whereas the second was expressed during TCE dechlorination. The tceA gene was involved in cis-DCE dechlorination to ethene. Analysis of the internal transcribed spacer region between the 16S and 23S rRNA genes revealed two distinct sequences originating from Sulfurospirillum suggesting that two Sulfurospirillum populations were present in SL2. Whether each Sulfurospirillum population was catalyzing a different dechlorination step could however not be elucidate

Reductive dechlorination of tetrachloroethene by a stepwise catalysis of different organohalide respiring bacteria and reductive dehalogenases

The enrichment culture SL2 dechlorinating tetrachloroethene (PCE) to ethene with strong trichloroethene (TCE) accumulation prior to cis-1,2-dichloroethene (cis-DCE) formation was analyzed for the presence of organohalide respiring bacteria and reductive dehalogenase genes (rdhA). Sulfurospirillum-affiliated bacteria were identified to be involved in PCE dechlorination to cis-DCE whereas "Dehalococcoides"-affiliated bacteria mainly dechlorinated cis-DCE to ethene. Two rdhA genes highly similar to tetrachloroethene reductive dehalogenase genes (pceA) of S. multivorans and S. halorespirans were present as well as an rdhA gene very similar to the trichloroethene reductive dehalogenase gene (tceA) of "Dehalococcoides ethenogenes" strain 195. A single strand conformation polymorphism (SSCP) method was developed allowing the simultaneous detection of the three rdhA genes and the estimation of their abundance. SSCP analysis of different SL2 cultures showed that one pceA gene was expressed during PCE dechlorination whereas the second was expressed during TCE dechlorination. The tceA gene was involved in cis-DCE dechlorination to ethene. Analysis of the internal transcribed spacer region between the 16S and 23S rRNA genes revealed two distinct sequences originating from Sulfurospirillum suggesting that two Sulfurospirillum populations were present in SL2. Whether each Sulfurospirillum population was catalyzing a different dechlorination step could however not be elucidated

The use of genomic signature distance between bacteriophages and their hosts displays evolutionary relationships and phage growth cycle determination

<p>Abstract</p> <p>Background</p> <p>Bacteriophage classification is mainly based on morphological traits and genome characteristics combined with host information and in some cases on phage growth lifestyle. A lack of molecular tools can impede more precise studies on phylogenetic relationships or even a taxonomic classification. The use of methods to analyze genome sequences without the requirement for homology has allowed advances in classification.</p> <p>Results</p> <p>Here, we proposed to use genome sequence signature to characterize bacteriophages and to compare them to their host genome signature in order to obtain host-phage relationships and information on their lifestyle. We analyze the host-phage relationships in the four most representative groups of Caudoviridae, the dsDNA group of phages. We demonstrate that the use of phage genomic signature and its comparison with that of the host allows a grouping of phages and is also able to predict the host-phage relationships (lytic <it>vs</it>. temperate).</p> <p>Conclusions</p> <p>We can thus condense, in relatively simple figures, this phage information dispersed over many publications.</p

Biocorrosion on nanofilms induces rapid bacterial motions via iron dissolution

International audienceStability and reactivity of solid metal or mineral surfaces in contact with bacteria are critical properties for development of biocorrosion protection and for understanding bacteria-solid environmental interactions. Here, we opted to work with nanosheets of iron nanolayers offering arbitrarily large and stable areas of contact that can be simply monitored by optical means. We focused our study on the sediments' bacteria, the strain Shewanella oneidensis WT MR-1, that served as models for previous research on electroactivity and iron-reduction effects. Data show that a sudden uniform corrosion appeared after an early electroactive period without specific affinities and that iron dissolution induced rapid bacterial motions. By extending the approach to mutant strains and three bacterial species, we established a correlation between corrosion onset and oxygen-depletion combined with iron reduction and demonstrated bacterial's extraordinary ability to transform their solid environments

Genetic studies of a thermoregulated gene in the psychrotrophic bacterium Pseudomonas fluorescens

International audienceIn the psychrotrophic bacterium Pseudomonas fluorescens, some genes are thermoregulated: they are maximally expressed at a particular temperature within the broad range of temperatures that allow growth of this bacterium. To study this regulation, random transcriptional insertion fusions were obtained by means of mini-Tn5lacZ1 or mini-Tn5luxAB transposition. One fusion was studied in which β-galactosidase production was maximal at a low-growth temperature. The mutated gene (that we call xsf) was highly homologous to xseA from Escherichia coli (and from other bacteria) which encodes the large subunit of exonuclease VII. Genetic tools were constructed in order to analyse and manipulate this fusion: a plasmid derived from R68.45 was used for chromosome transfer and a replacement vector was constructed to allow in situ marker exchange of the mini-Tn5lacZ1 by an Hgr interposon. This vector was used to make double mutants and hence to study the effect of the insertion in xsf on the expression of other fusions. Six genes were thereby identified with a decreased expression in an xsf – background and with different characteristics of thermoregulation.Études génétiques d'un gène thermorégulé de la bactérie psychrotrophique Pseudomonas fluorescens. Chez la bactérie psychrotrophe, Pseudomonas fluorescen, certains gènes sont thermorégulés (exprimés de façon maximale à une température particulière de leur large gamme de températures de croissance). Pour étudier cette régulation, des fusions transcriptionnelles ont été réalisées par insertion aléatoire de mini-transposons (mini-Tn5lacZ et mini-Tn5luxAB). Une fusion chez laquelle la production de β-galactosidase est maximale à basse température de croissance est étudiée ici. Le gène muté (que nous avons dénommé xsf) est fortement homologue du gène xseA de Escherichia coli (et d'autres bactéries), qui code la grande sous-unité de l'exonuclease VII. Des outils génétiques ont été construits pour analyser et manipuler cette fusion : l'utilisation d'un plasmide dérivé de R68.45 pour réaliser du transfert chromosomique, et la construction d'un vecteur de remplacement pour effectuer l'échange in situ de marqueurs. Des doubles mutants ont été construits pour étudier l'effet de la mutation dans xsf sur l'expression d'autres fusions. Six gènes, différant par leur thermorégulation, voient leur expression réduite dans un environnement xsf

Indications for Acquisition of Reductive Dehalogenase Genes through Horizontal Gene Transfer by Dehalococcoides ethenogenes Strain 195

The genome of Dehalococcoides ethenogenes strain 195, an anaerobic dehalorespiring bacterium, contains 18 copies of putative reductive dehalogenase genes, including the well-characterized tceA gene, whose gene product functions as the key enzyme in the environmentally important dehalorespiration process. The genome of D. ethenogenes was analyzed using a bioinformatic tool based on the frequency of oligonucleotides. The results in the form of a genomic signature revealed several local disruptions of the host signature along the genome sequence. These fractures represent DNA segments of potentially foreign origin, so-called atypical regions, which may have been acquired by an ancestor through horizontal gene transfer. Most interestingly, 15 of the 18 reductive dehalogenase genes, including the tceA gene, were found to be located in these regions, strongly indicating the foreign nature of the dehalorespiration activity. The GC content and the presence of recombinase genes within some of these regions corroborate this hypothesis. A hierarchical classification of the atypical regions containing the reductive dehalogenase genes indicated that these regions were probably acquired by several gene transfer events

Indication for horizontal transfer of reductive dehalogenase genes

Tetra- (PCE) and trichloroethene (TCE) are major groundwater pollutants due to their extensive industrial use. Several anaerobic bacteria have been isolated using chloroethenes as terminal electron acceptor. Most of these bacteria dechlorinate PCE and TCE to cis-1,2-dichloroethene (cis-1,2-DCE). A few Dehalococcoides strains are able to dechlorinate cis-1,2-DCE and vinyl chloride (VC) to the ethene. Identification of the key enzyme, the reductive dehalogenase, has revealed a new class of enzymes containing a corrinoid and two iron-sulfur clusters as cofactors. The PCE reductive dehalogenase (PceAB) of Dehalobacter restrictus and Desulfitobacterium hafniense strain TCE1 showed 100% sequence identity which raised the question of a possible horizontal gene transfer. The flanking regions of the reductive dehalogenase genes (pceAB) revealed the presence of a composite transposon (named Tn-Dha1) in strain TCE1 bordered with two identical insertion sequences ISDha1 and containing besides the already characterized pceAB, two genes (pceCT) related to members of the o-chlorophenol reductive dehalogenase gene cluster of Desulfitobacterium dehalogenans. In contrast, only the pceABCT gene cluster (i.e. without the transposon structure) was present in Dehalobacter restrictus. Various circular molecules of Tn-Dha1 indicated that Tn-Dha1 is an active mobile genetic element. The genome of Dehalococcoides ethenogenes was shown to contain eighteen copies of putative reductive dehalogenase genes. A genomic signature of D. ethenogenes was obtained by calculating the frequency of 4-letter DNA words along the genome. Local disruptions of the genomic signature were observed, corresponding to DNA, which may have been acquired by horizontal gene transfer. Fifteen putative reductive dehalogenase genes were located in such atypical regions. Moreover, several genes encoding for recombinases (transposase, integrase) were found within these atypical regions, strongly indicating that these may have been acquired horizontally

A novel bacteriophage morphotype with a ribbon-like structure at the tail extremity

7 pagesInternational audienceWe have isolated a novel Siphoviridae phage (named Sol-P11) morphotype from the surface sands of the Sahara Desert with a ribbon-like structure at the tail extremity. Sol-P11 was found to grow on a Bacillus subtilis strain isolated from the same environment and to contain a double stranded DNA genome of approximately 120 kb in length incapable of being hydrolysed by a wide variety of restriction endonucleases. The major constituent proteins of CsCl-purified Sol-P11 virions were 65, 50, 30, and 24 kDa in size, with the 30 kDa polypeptide being the major protein of the 85 nm diameter icosahedral capsid, and the other three proteins comprising the major polypeptides of the tail (320 nm in length) and ribbon-like structure. Moreover, different sized phages displaying a Sol-P11 morphology were observed in phage preparations from the Death Valley and Namib deserts. Sol-P11-like phage morphotypes have been previously described, including PBPI, a flagellum-specific phage that infects B. pumilis and phage BcP15 infecting the marine bacterium, Burkholderia cepacia DR11. We thus propose that Sol-P11 represents a member of a novel morphotype of Siphoviridae phages that use a ribbon-like structure, instead of caudal fibers, to attach to their host cell