[Show abstract][Hide abstract] ABSTRACT: Microbial communities from hypersaline ponds, dominated by halophilic archaea, are considered to be specific of such extreme conditions. The associated viral communities have accordingly been shown to display specific features, such as similar morphologies among different sites. However, little is known about the genetic diversity of these halophilic viral communities across the Earth. Here, we studied viral communities in hypersaline ponds sampled on the coast of Senegal (8 to 36% of salinity) using metagenomics approach, and compared them to hypersaline viromes from Australia and Spain. The specificity of hyperhalophilic viruses could first be demonstrated at a community scale, salinity being a strong discriminating factor between communities. For the major viral group detected in all samples (Caudovirales), only a limited number of halophilic Caudovirales clades were highlighted. These clades gather viruses from different continents and display consistent genetic composition, indicating that they represent related lineages with a world-wide distribution. Non-tailed hyperhalophilic viruses display a greater rate of gene transfer and recombination, with uncharacterized genes conserved across different kind of viruses and plasmids. Thus, hypersaline viral communities around the world appear to form a genetically consistent community that are likely to harbor new genes coding for enzymes specifically adapted to these environments.
No preview · Article · Oct 2015 · Environmental Microbiology
[Show abstract][Hide abstract] ABSTRACT: The impact of fish and oysters on components of the pelagic microbial food web (MFW) was studied in a 10 d mesocosm experiment using Mediterranean coastal waters. Two mesocosms contained natural water only ('Controls'), 2 contained natural water with Crassostrea gigas ('Oyster'), and 2 contained natural water with Atherina spp. ('Fish'). Abundances and biomasses of microorganisms (viruses, bacteria, phytoplankton, heterotrophic flagellates, and ciliates) were measured to estimate their contribution to the total microbial carbon biomass. Two MFW indices, the microbial autotroph: heterotroph C biomass ratio (A:H) structural index and the gross primary production: respiration ratio (GPP:R) functional index, were defined. In the Fish mesocosms, selective predation on zooplankton led to a trophic cascade with 51% higher phytoplankton C biomass and consequently higher A: H and GPP: R than in the Controls. By the end of the experiment, the Oyster mesocosms had a bacterial C biomass 87% higher and phytoplankton C biomass 93% lower than the Controls, giving significantly lower A: H and GPP: R (<1). Overall, the results showed that wild zooplanktivorous fish had a cascading trophic effect, making the MFW more autotrophic (both indices >1), whereas oyster activities made the MFW more heterotrophic (both indices <1). These MFW indices can therefore be used to assess the impact of multiple local and global forcing factors on the MFW. The results presented here also have implications for sustainable management of coastal environments, suggesting that intense cultivation of filter feeders can be coupled with management to encourage wild local zooplanktivorous fishes to maintain a more resilient system and preserve the equilibrium of the MFW.
[Show abstract][Hide abstract] ABSTRACT: Using three different microscopy techniques (epifluorescence, electronic and atomic force microscopy), we showed that high-Mg calcite grains in calcifying microbial mats from the hypersaline lake “La Salada de Chiprana”, Spain, contain viruses with a diameter of 50–80 nm. Energy-dispersive X-ray spectrometer analysis revealed that they contain nitrogen and phosphorus in a molar ratio of ~9, which is typical for viruses. Nucleic acid staining revealed that they contain DNA or RNA. As characteristic for hypersaline environments, the concentrations of free and attached viruses were high (>1010 viruses per g of mat). In addition, we showed that acid treatment (dissolution of calcite) resulted in release of viruses into suspension and estimated that there were ~15 × 109 viruses per g of calcite. We suggest that virus-mineral interactions are one of the possible ways for the formation of nano-sized structures often described as “nanobacteria” and that viruses may play a role in initiating calcification.
[Show abstract][Hide abstract] ABSTRACT: Abstract. Size fractionation was performed using water from the Great Reef of Toliara (Madagascar) taken from two
different habitats (ocean and lagoon) during the dry and wet seasons, to study the growth and mortality rates of
bacterioplankton. Experiments were conducted with 1 and 100% of heterotrophic nanoflagellate (HNF) concentrations
and virus-free water was obtained by tangential filtration (10 kDa). During the dry season, in both environments, bacterial
abundance and production were significantly lower than values recorded during the wet season. Bacterial growth rates
without grazers were 0.88 day
�1 in the lagoon and 0.58 day
�1 in the ocean. However, growth rates were statistically higher
without grazers and viruses (1.58 day
�1 and 1.27 day
�1). An estimate of virus-induced bacterial mortality revealed the
important role played by viruses in the lagoon (0.70 day
�1) and the ocean (0.69 day
�1). During the wet season, bacterial
growth rates without grazers were significantly higher in both environments than were values obtained in the dry season.
However, the bacterial growth rates were paradoxally lower in the absence of viruses than with viruses in both
environments. Our results suggest that changes in nutrient concentrations can play an important role in the balance
between viral lysis and HNF grazing in the bacterial mortality. However, virus-mediated bacterial mortality is likely to act
simultaneously with nanoflagellates pressure in their effects on bacterial communities.
Full-text · Article · Apr 2015 · Marine and Freshwater Research
[Show abstract][Hide abstract] ABSTRACT: N2-fixing cyanobacteria represent a major source of new nitrogen and carbon for marine microbial communities, but little is known about their ecological interactions with associated microbiota. In this study we investigated the interactions between the unicellular N2-fixing cyanobacterium Cyanothece sp. Miami BG043511 and its associated free-living chemotrophic bacteria at different concentrations of nitrate and dissolved organic carbon and different temperatures. High temperature strongly stimulated the growth of Cyanothece, but had less effect on the growth and community composition of the chemotrophic bacteria. Conversely, nitrate and carbon addition did not significantly increase the abundance of Cyanothece, but strongly affected the abundance and species composition of the associated chemotrophic bacteria. In nitrate-free medium the associated bacterial community was co-dominated by the putative diazotroph Mesorhizobium and the putative aerobic anoxygenic phototroph Erythrobacter and after addition of organic carbon also by the Flavobacterium Muricauda. Addition of nitrate shifted the composition toward co-dominance by Erythrobacter and the Gammaproteobacterium Marinobacter. Our results indicate that Cyanothece modified the species composition of its associated bacteria through a combination of competition and facilitation. Furthermore, within the bacterial community, niche differentiation appeared to play an important role, contributing to the coexistence of a variety of different functional groups. An important implication of these findings is that changes in nitrogen and carbon availability due to, e.g., eutrophication and climate change are likely to have a major impact on the species composition of the bacterial community associated with N2-fixing cyanobacteria.
Full-text · Article · Jan 2015 · Frontiers in Microbiology
[Show abstract][Hide abstract] ABSTRACT: Viruses inhabiting the surface mucus layer of scleractinian corals have received little ecological attention so far. Yet they have recently been shown to be highly abundant and could even play a pivotal role in coral health. A fundamental aspect that remains unresolved is whether their abundance and diversity change with the trophic state of their environment. The present study examined the variability in the abundance of viral and bacterial epibionts on 13 coral species collected from 2 different sites in the Ha Long Bay, Vietnam: one station heavily affected by anthropogenic activity (Cat Ba Island) and one protected offshore station (Long Chau Island). In general, viral abundance was significantly higher in coral mucus (mean = 10.6 +/- 2.0 x 10(7) virus-like particles ml(-1)) than in the surrounding water (5.2 +/- 1.3 x 10(7) virus-like particles ml(-1)). Concomitantly, the abundance and community diversity (inferred from phylogenetic and morphological analyses) of their mucosal bacterial hosts strongly differed from their planktonic counterparts. Surprisingly, despite large differences in water quality and nutrient concentrations between Cat Ba and Long Chau, there were no significant differences in the concentrations of epibiotic viruses and bacteria measured in the only 2 coral species (i.e. Pavona decussata and Lobophyllia flabelliformis) that were common at both sites. The ability of corals to shed bacteria to compensate for their fast growth in nutrient-rich mucus is questioned here.
Full-text · Article · Jan 2015 · Aquatic Microbial Ecology
[Show abstract][Hide abstract] ABSTRACT: Phytoplankton diversity and abundance in estuarine systems are controlled by many factors. Salinity, turbidity, and inorganic nutrient concentrations and their respective ratios have all been proposed as principal factors that structure phytoplankton diversity and influence the emergence of potentially toxic species. Although much work has been conducted on temperate estuaries, less is known about how phytoplankton diversity is controlled in tropical, monsoonal systems that are subject to large, seasonal shifts in hydrology and to rapidly changing land use. Here, we present the results of an investigation into the factors controlling phytoplankton species composition and distribution in a tropical, monsoonal estuary (Bach Dang estuary, North Vietnam). A total of 245 taxa, 89 genera from six algal divisions were observed. Bacillariophyceae were the most diverse group contributing to 51.4 % of the microalgal assemblage, followed by Dinophyceae (29.8 %), Chlorophyceae (10.2 %), Cyanophyceae (3.7 %), Euglenophyceae (3.7 %) and Dictyochophyceae (1.2 %). The phytoplankton community was structured by inorganic nutrient ratios (DSi:DIP and DIN:DIP) as well as by salinity and turbidity. Evidence of a decrease in phytoplankton diversity concomitant with an increase in abundance and dominance of certain species (e.g., Skeletonema costatum) and the appearance of some potentially toxic species over the last two decades was also found. These changes in phytoplankton diversity are probably due to a combination of land use change resulting in changes in nutrient ratios and concentrations and global change as both rainfall and temperature have increased over the last two decades. It is therefore probable in the future that phytoplankton diversity will continue to change, potentially favoring the emergence of toxic species in this system.
[Show abstract][Hide abstract] ABSTRACT: A recent hypothesis considers that many coral pathologies are the result of a sudden structural alteration of the epibiotic bacterial communities in response to environmental disturbances. However, the ecological mechanisms that lead to shifts in their composition are still unclear. In the ocean, viruses represent a major bactericidal agent but little is known on their occurrence within the coral holobiont. Recent reports have revealed that viruses are abundant and diversified within the coral mucus and therefore could be decisive for coral health. However, their mode of action is still unknown, and there is now an urgent need to shed light on the nature of the relationships they might have with the other prokaryotic and eukaryotic members of the holobiont. In this opinion letter, we are putting forward the hypothesis that coral-associated viruses (mostly bacterial and algal viruses), depending on the environmental conditions might either reinforce coral stability or conversely fasten their decline. We propose that these processes are presumably based on an environmentally driven shift in infection strategies allowing viruses to regulate, circumstantially, both coral symbionts (bacteria or Symbiodinium) and surrounding pathogens.
No preview · Article · Aug 2014 · Environmental Microbiology
[Show abstract][Hide abstract] ABSTRACT: Viruses attract increasing interest from environmental microbiologists seeking to understand their function and role in coral health. However, little is known about their main ecological traits within the coral holobiont. In this study, a quantitative and qualitative characterization of viral and bacterial communities was conducted on the mucus of 7 different coral species of the Van Phong Bay (Viet Nam). On average, the concentrations of viruses and bacteria were respectively 17 and 2-fold higher in the mucus than in the surrounding water. The examination of bacterial community composition also showed remarkable differences between mucus and water samples. The percentage of active respiring cells was nearly 3-fold higher in mucus (m= 24.8%) than in water (m= 8.6%). Interestingly, a positive and highly significant correlation was observed between the proportion of active cells and viral abundance in the mucus, suggesting that the metabolism of the bacterial associates is probably a strong determinant of the distribution of viruses within the coral holobiont. Overall, coral mucus, given its unique physico-chemical characteristics and sticking properties, can be regarded as a highly selective biotope for abundant, diversified and specialized symbiotic microbial and viral organisms.
Full-text · Article · Jun 2014 · Environmental Microbiology Reports
[Show abstract][Hide abstract] ABSTRACT: The effects of grazing pressure and inorganic nutrient availability on the direct carbon transfer from freshly produced phytoplankton exudates to heterotrophic bacteria biomass production were studied in Mediterranean coastal waters. The short-term incorporation of ¹³C (H¹³CO₃) in phytoplankton and bacterial lipid biomarkers was measured as well as the total bacterial carbon production (BP), viral lysis and the microbial community structure under three experimental conditions: (1) High inorganic Nutrient and High Grazing (HN + HG), (2) High inorganic Nutrient and Low Grazing (HN + LG) and (3) under natural in situ conditions with Low inorganic Nutrient and High Grazing (LN + HG) during spring. Under phytoplankton bloom conditions (HN + LG), the bacterial use of freshly produced phytoplankton exudates as a source of carbon, estimated from ¹³C enrichment of bacterial lipids, contributed more than half of the total bacterial production. However, under conditions of high grazing pressure on phytoplankton with or without the addition of inorganic nutrients (HN + HG and LN + HG), the ¹³C enrichment of bacterial lipids was low compared with the high total bacterial production. BP therefore seems to depend mainly on freshly produced phytoplankton exudates during the early phase of phytoplankton bloom period. However, BP seems mainly relying on recycled carbon from viral lysis and predators under high grazing pressure.
Full-text · Article · Mar 2014 · FEMS Microbiology Ecology
[Show abstract][Hide abstract] ABSTRACT: a b s t r a c t Vermicompost and biochar amendments are management practices which may contribute to sustain-able agroecosystems by reducing dependence on inorganic fertilizers. However, little is known about their impacts on soil microorganisms and their transfer and evolution in connected aquatic systems. The aim of this study was to determine the influence of organic manure (buffalo manure, compost or ver-micompost) and biochar amendments on bacterial and viral properties in soil and water. A three year experiment was carried out with terrestrial mesocosms which were used to test the effect of organic matter amendment on maize growth. In the last year of the experiment, runoff and infiltration waters from the terrestrial mesocosms were transferred to aquatic mesocosms. Organic fertilization improved soil properties (higher C, N content and pH H 2 O) and as a consequence increased soil bacterial and viral abundance. Bacterial diversity (Shannon 'H' and richness 'S' indices calculated from DGGE fingerprint) was also enhanced after the continuous application of organic amendments. Compared with compost, vermicompost reduced viral abundance and S but similar H and bacterial abundance were observed. The pH H 2 O , C content and bacterial and viral abundance increased in the aquatic mesocosms following organic fertilization. As a consequence, bacterial and viral diversity also increased in the water, although no dif-ferences were found between compost and vermicompost. Biochar increased soil bacterial abundance for the mineral fertilizer treatment but did not influence bacterial and viral abundance in water. However, the combination of biochar and vermicompost led to an increase of viruses in soil and a reduction of bacteria in water. Similarity dendrograms from the DGGE banding patterns showed that the structure of bacterial communities was mainly influenced by the fertilizer treatments in soil but by the presence of biochar in water. In conclusion, this study demonstrated that the nature of the organic amendment has important consequences on both soil and water microbial abundance and diversity.
Full-text · Article · Jan 2014 · Applied Soil Ecology
[Show abstract][Hide abstract] ABSTRACT: The amendment of vermicompost is a management practice that may contribute to sustainable agroecosystems by making them less dependent on inorganic fertilizers. However, little is known about the impact of this practice on soil biota and the flow of microbes to the water system. Using a 30-days laboratory experiment, we investigated the development of the peregrine earthworm species, Dichogaster bolaui, in presence of compost or vermicompost, and assessed its impact on the flow of bacteria and viruses to the water system. The dynamics of soil bacterial diversity (assessed by DGGE) and concentration in water together with their viral parasites were also assessed through an incubation of solution during 5 days (comparison between T0 and T5).
Full-text · Article · Aug 2013 · Soil Biology and Biochemistry
[Show abstract][Hide abstract] ABSTRACT: Recent developments of molecular tools have revolutionized our knowledge of microbial biodiversity by allowing detailed exploration of its different facets and generating unprecedented amount of data. One key issue with such large datasets is the development of diversity measures that cope with different data outputs and allow comparison of biodiversity across different scales. Diversity has indeed three components: local (α), regional (γ) and the overall difference between local communities (β). Current measures of microbial diversity, derived from several approaches, provide complementary but different views. They only capture the β component of diversity, compare communities in a pairwise way, consider all species as equivalent or lack a mathematically explicit relationship among the α, β and γ components. We propose a unified quantitative framework based on the Rao quadratic entropy, to obtain an additive decomposition of diversity (γ = α + β), so the three components can be compared, and that integrate the relationship (phylogenetic or functional) among Microbial Diversity Units that compose a microbial community. We show how this framework is adapted to all types of molecular data, and we highlight crucial issues in microbial ecology that would benefit from this framework and propose ready-to-use R-functions to easily set up our approach.
Full-text · Article · May 2013 · Environmental Microbiology
[Show abstract][Hide abstract] ABSTRACT: Changes in environmental conditions and prokaryote physiology can strongly affect the dynamics of both the lysogenic and lytic bacteriophage replication cycles in aquatic systems. However, it remains unclear whether it is the nature, amplitude or frequency of these changes that alter the phage replication cycles. We performed an annual survey of three Mediterranean lagoons with contrasting levels of chlorophyll a concentration and salinity to explore how these cues and their variability influence either replication cycle. The lytic cycle was always detected and showed seasonal patterns, whereas the lysogenic cycle was often undetected and highly variable. The lytic cycle was influenced by environmental and prokaryotic physiological cues, increasing with concentrations of dissolved organic carbon, chlorophyll a, and the proportion of respiring cells, and decreasing with the proportion of damaged cells. In contrast, lysogeny was not explained by the magnitude of any environmental or physiological parameter, but increased with the amplitude of change in prokaryote physiology. Our study suggests that both cycles are regulated by distinct factors: the lytic cycle is dependent on environmental parameters and host physiology, while lysogeny is dependent on the variability of prokaryote physiology. This could lead to the contrasting patterns observed between both cycles in aquatic systems.
Full-text · Article · Mar 2013 · Environmental Microbiology