Jean-François Ghiglione

Pole-to-pole biogeography of surface and deep marine bacterial communities

The Antarctic and Arctic regions offer a unique opportunity to test factors shaping biogeography of marine microbial communities because these regions are geographically far apart, yet share similar selection pressures. Here, we report a comprehensive comparison of bacterioplankton diversity between polar oceans, using standardized methods for pyrosequencing the V6 region of the small subunit ribosomal (SSU) rRNA gene. Bacterial communities from lower latitude oceans were included, providing a global perspective. A clear difference between Southern and Arctic Ocean surface communities was evident, with 78% of operational taxonomic units (OTUs) unique to the Southern Ocean and 70% unique to the Arctic Ocean. Although polar ocean bacterial communities were more similar to each other than to lower latitude pelagic communities, analyses of depths, seasons, and coastal vs. open waters, the Southern and Arctic Ocean bacterioplankton communities consistently clustered separately from each other. Coastal surface Southern and Arctic Ocean communities were more dissimilar from their respective open ocean communities. In contrast, deep ocean communities differed less between poles and lower latitude deep waters and displayed different diversity patterns compared with the surface. In addition, estimated diversity (Chao1) for surface and deep communities did not correlate significantly with latitude or temperature. Our results suggest differences in environmental conditions at the poles and different selection mechanisms controlling surface and deep ocean community structure and diversity. Surface bacterioplankton may be subjected to more short-term, variable conditions, whereas deep communities appear to be structured by longer water-mass residence time and connectivity through ocean circulation.

Pronounced summer to winter differences and higher wintertime richness in coastal Antarctic marine bacterioplankton.

Marine bacterioplankton studies over the annual cycle in polar systems are limited due to logistic constraints in site access and support. Here, we conducted a comparative study of marine bacterioplankton sampled at several time points over the annual cycle (12 occasions each) at sub-Antarctic Kerguelen Islands (KI) and Antarctic Peninsula (AP) coastal sites in order to establish a better understanding of the extent and nature of variation in diversity and community structure at these different latitudes (49-64S). Molecular methods targeting the 16S rRNA gene (DGGE, CE-SSCP and tag pyrosequencing) suggest a strong seasonal pattern with higher richness in winter and a clear influence of phytoplankton bloom events on bacterioplankton community structure and diversity in both locations. The distribution of sequence tags within Gammaproteobacteria, Alphaproteobacteria and Bacteriodetes differed between the two regions. At both sites, several abundant Rhodobacteraceae, uncultivated Gammaproteobacteria and Bacteriodetes-associated tags displayed intense seasonal variation often with similar trends at both sites. This enhanced understanding of variability in dominant groups of bacterioplankton over the annual cycle contributes to an expanding baseline to understand climate change impacts in the coastal zone of polar oceans and provides a foundation for comparison with open ocean polar systems.

Role of Respiratory Nitrate Reductase in Ability of Pseudomonas fluorescens YT101 To Colonize the Rhizosphere of Maize

ABSTRACT Selection of the denitrifying community by plant roots (i.e., increase in the denitrifier/total heterotroph ratio in the rhizosphere) has been reported by several authors. However, very few studies to evaluate the role of the denitrifying function itself in the selection of microorganisms in the rhizosphere have been performed. In the present study, we compared the rhizosphere survival of the denitrifyingPseudomonas fluorescens YT101 strain with that of its isogenic mutant deficient in the ability to synthesize the respiratory nitrate reductase, coinoculated in nonplanted or planted soil. We demonstrated that under nonlimiting nitrate conditions, the denitrifying wild-type strain had an advantage in the ability to colonize the rhizosphere of maize. Investigations of the effect of the inoculum characteristics (density of the total inoculum and relative proportions of mutant and wild-type strains) on the outcome of the selection demonstrated that the selective effect of the plant was expressed only during the phase of bacterial multiplication and that the intensity of selection was dependent on the magnitude of this phase. Moreover, application of the de Wit replacement series technique to our results suggests that the advantage of the wild-type strain was maximal when the ratio between the two strains in the inoculum was close to 1:1. This work constitutes the first direct demonstration that the presence of a functional structural gene encoding the respiratory nitrate reductase confers higher rhizosphere competence to a microorganism.

Bottom-Up versus Top-Down Control of Hypo- and Epilimnion Free-Living Bacterial Community Structures in Two Neighboring Freshwater Lakes

ABSTRACT Bacterioplankton plays a central role in the microbial functioning of lacustrine ecosystems; however, factors that constrain its structural variation are still poorly understood. Here we evaluated the driving forces exerted by a large set of environmental and biological parameters on the temporal and spatial dynamics of free-living bacterial community structures (BCS) in two neighboring perialpine lakes, Lake Bourget and Lake Annecy, which differ in trophic status. We analyzed monthly data from a 1-year sampling period at two depths situated in the epi- and hypolimnia for each lake. Overall, denaturing gradient gel electrophoresis (DGGE) revealed significant differences in the BCS in the two lakes, characterized by a higher number of bands in the oligotrophic ecosystem (i.e., Lake Annecy). The temporal dynamics of BCS differed greatly between depths and lakes, with temporal scale patterns being much longer in the mesotrophic Lake Bourget. Direct-gradient multivariate ordination analyses showed that a complex array of biogeochemical parameters was the driving force behind BCS shifts in both lakes. Our results indicated that 60 to 80% of the variance was explained only by the bottom-up factors in both lakes, indicating the importance of nutrients and organic matter from autotrophic origin in controlling the BCS. Top-down regulation by flagellates together with ciliates or viruses was found only in the hypolimnion and not in the epilimnion for both lakes and explained less than 18% of the bacterial community changes during the year. Our study suggests that the temporal dynamics of the free-living bacterial community structure in deep perialpine lakes are dependent mainly on bottom-up factors and to a lesser extent on top-down factors, whatever the specific environmental conditions of these lakes.

Effects of temperature and fertilization on total vs. active bacterial communities exposed to crude and diesel oil pollution in NW Mediterranean Sea

The dynamics of total and active microbial communities were studied in seawater microcosms amended with crude or diesel oil at different temperatures (25, 10 and 4 degrees C) in the presence/absence of organic fertilization (Inipol EAP 22). Total and hydrocarbon-degrading microbes were enumerated by fluorescence microscopy and Most Probable Number (MPN) method, respectively. Total (16S rDNA-based) vs. active (16S rRNA) bacterial community structure was monitored by Capillary-Electrophoresis Single Strand Conformation Polymorphism (CE-SSCP) fingerprinting. Hydrocarbons were analyzed after 12 weeks of incubation by gas chromatography-mass spectrometry. Total and hydrocarbon-degrading microbial counts were highly influenced by fertilization while no important differences were observed between temperatures. Higher biodegradation levels were observed in fertilized microcosms. Temperature and fertilization induced changes in structure of total bacterial communities. However, fertilization showed a more important effect on active bacterial structure. The calculation of Simpsons diversity index showed similar trends among temperatures whereas fertilization reduced diversity index of both total and active bacterial communities.

Effects of nutrient and temperature on degradation of petroleum hydrocarbons in sub-Antarctic coastal seawater

In an attempt to evaluate the potential of petroleum bioremediation at high latitudes environments, microcosm studies using Antarctic coastal seawater contaminated with diesel or crude oil were conducted in Kerguelen Archipelago (49°22′S, 70°12′E). Microcosms were incubated at three different temperatures (4, 10 and 20°C). During experiments, changes observed in microbial assemblages (total direct count, heterotrophic cultivable microorganisms and hydrocarbon-degrading microorganisms) were generally similar for all incubation temperatures, but chemical data showed only some slight changes in biodegradation indices [Σ(C12–C20)/Σ(C21–C32) and C17/pristane]. The complete data set provided strong evidence of the presence of indigenous hydrocarbon-degrading bacteria in Antarctic seawater and their high potential for hydrocarbon bioremediation. The rate of oil degradation could be increased by the addition of a commercial fertilizer, but water temperature had little effects on biodegradation efficiency which is in conflict with the typical temperature-related assumption predicting 50% rate reduction when temperature is reduced by 10°C. Global warming of Antarctic seawater should not increase significantly the rate of oil biodegradation in these remote regions.

Spatial comparison of total vs. active bacterial populations by coupling genetic fingerprinting and clone library analyses in the NW Mediterranean Sea

Spatial distributions of both total (i.e. 16S rDNA-based fingerprints) and active (i.e. 16S rRNA-based fingerprints) bacterial populations, together with total bacterial activity measured by 3H-leucine incorporation, were studied along a 98 km transect in the NW Mediterranean Sea. Capillary electrophoresis-single strand conformation polymorphism (CE-SSCP) fingerprinting was coupled to a clone library, allowing CE-SSCP peaks identification and the monitoring of the spatial variation of bacterial phylotypes. Up to 80% of the community peaks matched those obtained from clone library sequences, accounting for 86.7% of the total fingerprinting area. A good agreement was found between the relative abundance of Prochlorococcus in the CE-SSCP fingerprints and flow cytometry counts (r2=0.66, P<0.05). The largest differences between total and active bacterial populations distribution were found at depths with higher bacterial activity (i.e. surface and deep chlorophyll maximum, DCM). SAR11 at the surface and Gammaproteobacteria at the DCM were the most abundant groups on the 16S rDNA-based fingerprints. However, their ratio of relative importance between rRNA : rDNA was <1 in most cases. Conversely, ratios observed for Prochlorococcus, were consistently >1 both at the surface and at the DCM. These results emphasize the need for combining rDNA- and rRNA-based analyses to better understand the functional role of individual bacterial populations in situ.

Genome Sequence of the Marine Bacterium Marinobacter hydrocarbonoclasticus SP17, Which Forms Biofilms on Hydrophobic Organic Compounds

Marinobacter hydrocarbonoclasticus SP17 forms biofilms specifically at the interface between water and hydrophobic organic compounds (HOCs) that are used as carbon and energy sources. Biofilm formation at the HOC-water interface has been recognized as a strategy to overcome the low availability of these nearly water-insoluble substrates. Here, we present the genome sequence of SP17, which could provide further insights into the mechanisms of enhancement of HOCs assimilation through biofilm formation.

Effect of soil type and plant species on the fluorescent pseudomonads nitrate dissimilating community

The distribution of nitrogen dissimilative abilities among 618 isolates of fluorescent pseudomonads was studied. These strains were isolated from two uncultivated soils (C and D; collected at Châteaurenard and Dijon, France, respectively) and from rhizosphere, rhizoplane and root tissue of two plant species (flax and tomato) cultivated on these two soils. According to their ability to dissimilate nitrogen, the isolates have been distributed into three metabolic types: non-dissimilators, NO2- accumulators and denitrifiers. While the three metabolic types were recovered in all the compartments of soil D experiments, only two (non-dissimilators and denitrifiers) were recovered in all the compartments of soil C experiments. Even under the contrasting conditions of the two soil types, both plants were able to select the nitrate dissimilating community among the total community of fluorescent Pseudomonas, but the mode of this selection seems to be dependent on both plant and soil type. The soil type appears to be unable to significantly modulate the strong selective effect of tomato. Indeed, similar dissimilator to non-dissimilator ratios were found in the root tissue of this plant species cultivated in both soils. In contrast, the different dissimilator to non-dissimilator ratios observed in flax roots between soils C and D suggest that the selective effect of flax was modulated by the soil type. Taxonomic identifications showed that the 618 isolates were distributed among three species (P. chlororaphis, P. fluorescens, P. putida) plus an intermediate type between P. fluorescens and P. putida. However, no clear relationship between the distribution of the metabolic types (functional diversity) and the distribution of bacterial species has been found.

Evidence of heterotrophic prokaryotic activity limitation by nitrogen in the Western Arctic Ocean during summer

Global warming in the Arctic Ocean may result in changes to the stock and dynamics of nutrients that drive the activity of heterotrophic prokaryotes, a key component of the microbial food web. We performed 14 enrichment experiments during summer in the Beaufort and Chukchi Seas (Western Arctic Ocean), with C (acetate and/or glucose), N (nitrate and/or ammonium) and P (phosphate) amendments. In 8 out of 11 experiments performed with surface waters, prokaryotic heterotrophic production was limited by N, either alone (5 experiments) or in co-limitation with C (3 experiments). This contrasted with the experiments performed using waters from the chlorophyll maxima, where N was never limiting. Diversity analyses (DNA- and RNA-based fingerprinting) suggest that limitation was not restricted to specific operational taxonomic units but common to the different groups. This is the first report of N limitation of prokaryotic heterotrophic production in Arctic surface waters. This control by N may gain importance in future scenarios of higher productivity in the area.