Microbial Ecology

Changes in the composition of viral communities were investigated along a salinity gradient and at different times by means of transmission electron microscopy (TEM) and pulsed field gel electrophoresis (PFGE). Samples were collected in fresh (Charente River), estuarine (Charente Estuary), and coastal (Pertuis d'Antioche, French Atlantic coast) waters. Both methods revealed similar patterns in viral community structure with a dominance of small viral particles (capsid and genome size). Viruses with a head size below 65 nm made up 71 ± 5% of total virus-like particles, and virus-like genomes (VLG) below 100 kb accounted for 89 ± 9% of total VLG. Despite this apparent stability of virioplankton composition over spatial scale (salinity gradient), the occurrence of large viruses (capsid and genome size) in estuarine and seawater samples indicated the presence of viral populations specific to a geographical location. Temporal changes in the structure (capsid and genome size) of viral communities were more pronounced than those reported at the spatial scale. From January to May 2003, seasonal changes in viral abundance and bacterial production occurred concomitantly with an increase in viral genomic diversity (richness), suggesting that virioplankton composition was strongly linked to changes in microbial activity and/or in the structure of the host communities. Although PFGE and TEM yielded complementary results in the description of virioplankton structures, it seems that the use of PFGE alone should be enough for the monitoring of community changes.

Inland saline-alkaline wetlands distributed in the mid-high latitude have repeatedly experienced freezing and thawing. However, the response of greenhouse gas (GHG) emission and microbially-mediated carbon and nitrogen cycle to freezing and thawing remains unclear. We monitored the GHG flux in an inland saline-alkaline wetland and found that, compared with the growth period, the average CO2 flux decreased from 171.99 to 76.61–80.71 mg/(m2‧h), the average CH4 flux decreased from 10.72 to 1.96–3.94 mg/(m2‧h), and the average N2O flux decreased from 56.17 to − 27.14 to − 20.70 μg/(m2‧h). Freezing and thawing significantly decreased the relative abundance of functional genes involved in carbon and nitrogen cycles. The aceticlastic methanogenic pathway was the main methanogenic pathway, whereas the Candidatus Methylomirabilis oxyfera was the most abundant methane oxidizer in the wetland. Ammonia-oxidizing archaea and denitrifier belonging to proteobacteria was the major microbial N2O source, while bacteria within clade II nosZ was the major microbial N2O sink. Freezing and thawing reduced the relative abundance of these genes, leading to a decrease in GHG flux.

Claims that organisms can be cultured from amber, if substantiated, would be significant contributions to our understanding of the evolution, tenacity, and potential spread of life. Three reports on the isolation of organisms from amber have been published. Cano and Borucki recently reported the isolation of Bacillus sphaericus and Lambert et al. have described a new species designated Staphylococcus succinus from 25–40 million year old Dominican amber. These characterized organisms were phylogenetically distant from extant relatives and the Staphylococcus sp. sufficiently far removed from other extant staphylococci to be considered a new species. Here we report the culture of bacteria from Dominican and previously untested 120 million year old Israeli (Lebanese lode) amber. Twenty-seven isolates from the amber matrix have been characterized by fatty-acid profiles (FAME) and/or 16S rRNA sequencing. We also performed a terminal restriction fragment pattern (TRF) analysis of the original amber before prolonged culture by consensus primer amplification of the 16S rRNA followed by restriction enzyme digestion of the amplicons. Sample TRFs were consistent with a sparse bacterial assemblage and included at least five of the isolated organisms. Finally, we microscopically mapped the internal topography of an amber slice.

Archaea inhabiting marine and freshwater sediments have a relevant role in organic carbon mineralization, affecting carbon fluxes at a global scale. Despite current evidences suggesting that freshwater sediments largely contribute to this process, few large-scale surveys have been addressed to uncover archaeal diversity and abundance in freshwater sedimentary habitats. In this work, we quantified and high-throughput sequenced the archaeal 16S rRNA gene from surficial sediments collected in 21 inland waterbodies across the Iberian Peninsula differing in typology and trophic status. Whereas methanogenic groups were dominant in most of the studied systems, especially in organic-rich sediments, archaea affiliated to widespread marine lineages (the Bathyarchaeota and the Thermoplasmata) were also ubiquitous and particularly abundant in euxinic sediments. In these systems, Bathyarchaeota communities were dominated by subgroups Bathyarchaeota-6 (87.95 ± 12.71%) and Bathyarchaeota-15 (8.17 ± 9.2%) whereas communities of Thermoplasmata were mainly composed of members of the order Thermoplasmatales. Our results also indicate that Archaea accounted for a minor fraction of sedimentary prokaryotes despite remarkable exceptions in reservoirs and some stratified lakes. Copy numbers of archaeal and bathyarchaeotal 16S rRNA genes were significantly different when compared according to system type (i.e., lakes, ponds, and reservoirs), but no differences were obtained when compared according to their trophic status (from oligotrophy to eutrophy). Interestingly, we obtained significant correlations between the abundance of reads (Spearman r = 0.5, p = 0.021) and OTU richness (Spearman r = 0.677, p < 0.001) of Bathyarchaeota and Thermoplasmata across systems, reinforcing the hypothesis of a potential syntrophic interaction between members of both lineages.

Filibacter limicola is a filamentous gliding bacterium isolated from the profundal sediment of a eutrophic lake. It is an obligate amino acid utilizer. The kinetic parameters for the metabolism of four amino acids byF. limicola, Vitreoscilla spp. and the bacterial populations of water and sediment samples were compared.F. limicola exhibited low half-saturation constants (K) which were of the same order as those obtained with water samples. The K values for theVitreoscilla spp. and the sediment were an order of magnitude higher. It would appear that the bacterium is a specialist, inhabiting a niche which is sufficiently nutrient rich to support an organism with a limited substrate range. It also possesses a high affinity uptake system for some amino acids which may permit it to compete effectively during periods of nutrient depletion.

Bdellovibrio bacteriovorus 109J is a predatory bacterium which lives by predating on other Gram-negative bacteria to obtain the nutrients it needs for replication and survival. Here, we evaluated the effects two classes of bacterial signaling molecules (acyl homoserine lactones (AHLs) and diffusible signaling factor (DSF)) have on B. bacteriovorus 109J behavior and viability. While AHLs had a non-significant impact on predation rates, DSF considerably delayed predation and bdelloplast lysis. Subsequent experiments showed that 50 μM DSF also reduced the motility of attack-phase B. bacteriovorus 109J cells by 50% (38.2 ± 14.9 vs. 17 ± 8.9 μm/s). Transcriptomic analyses found that DSF caused genome-wide changes in B. bacteriovorus 109J gene expression patterns during both the attack and intraperiplasmic phases, including the significant downregulation of the flagellum assembly genes and numerous serine protease genes. While the former accounts for the reduced speeds observed, the latter was confirmed experimentally with 50 μM DSF completely blocking protease secretion from attack-phase cells. Additional experiments found that 30% of the total cellular ATP was released into the supernatant when B. bacteriovorus 109J was exposed to 200 μM DSF, implying that this QS molecule negatively impacts membrane integrity.

Wolbachia are obligatory, cytoplasmatically inherited α-proteobacteria, which are common endosymbionts in arthropods where they may cause reproductive abnormalities. Many insects are well known to protect themselves from deleterious microorganisms by antibiotic components. In this study, we addressed the question whether Wolbachia are able to infect insects containing antimicrobial anthraquinones and anthrones, and if so, whether these genotypes of Wolbachia comprise a monophyletic cluster within one of the known supergroups. Leaf beetles of the taxon Galerucini (Galerucinae) are known to contain 1,8-dihydroxylated anthraquinones and anthrones. Also, the scale insect Dactylopius contains an anthraquinone glycoside, carminic acid. Our analyses revealed that a representative of the Galerucini, Galeruca tanaceti and Dactylopius, are indeed infected by endosymbiotic Wolbachia bacteria.Phylogenetic analysis of the wsp and ftsZ genes of these bacteria revealed that strains in G. tanaceti cluster in supergroup A, whereas those present in Dactylopius are distinctive from each other and from those of G. tanaceti. They are clustering in supergroups A and B. Wolbachia strains present in close, but anthraquinone-free relatives of G. tanaceti were shown to belong also to supergroup A. From these results, we can conclude (1) a double infection in Dactylopius, (2) that the presence of antimicrobial compounds such as anthraquinones does not necessarily protect insects from infection by Wolbachia, and (3) that genotypes of Wolbachia-infecting anthraquinone-containing insects most likely do not comprise a unique genotype. These results show that Wolbachia bacteria might be adapted to cope even with conditions usually detrimental to other bacteria and that these adaptations are widespread among Wolbachia supergroups.