[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.
PLoS ONE 06/2015; 10(6). DOI:10.1371/journal.pone.0130552 · 3.23 Impact Factor
[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.
Marine and Freshwater Research 04/2015; DOI:10.1071/MF14253 · 1.47 Impact Factor
[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.
Frontiers in Microbiology 01/2015; 5:795. DOI:10.3389/fmicb.2014.00795 · 3.99 Impact Factor
[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.
[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.
[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.
[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.
[Show abstract][Hide abstract] ABSTRACT: a b s t r a c t The amendment of vermicompost is a management practice that may contribute to sustainable agro-ecosystems 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 T 0 and T 5). This study highlights the rapid development of D. bolaui after compost amendment. However, the low quality of vermicompost and the absence of organic amendment in the control treatment allowed the survival but not the development of D. bolaui. Higher bacterial and viral abundances in compost and vermicompost substrates led to more important transfer of these communities from the soil to the water system in comparison with the untreated soil, but no difference was observed between compost and vermicompost treatments. In terms of abundance, the bacterial to virus ratio was rather stable in the soil solution but no such a relation was observed in the soil. A reduction of bacterial diversity (OTU) was measured at the end of the incubation period for all the treatments. However, higher number of OTU at T 5 for the compost treatment suggested a better adaptation and/or resistance of soil bacteria to the aquatic system, in comparison with the control treatment. Vermicompost treatment led to intermediate conclusions. The presence of D. bolaui significantly reduced bacterial abundance in the soil organic layer (both compost and vermicompost treatments) but it did not influence bacterial and viral abundance in water, suggesting independent processes. Earthworms buffered bacterial DGGE patterns after five days of incubation, probably through a facilitation of soil bacterial groups more able to resist in solution.
[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.
[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.
[Show abstract][Hide abstract] ABSTRACT: Small size eukaryotes play a fundamental role in the functioning of coastal ecosystems, however, the way in which these micro-organisms respond to combined effects of water temperature, UVB radiations (UVBR) and nutrient availability is still poorly investigated.
We coupled molecular tools (18S rRNA gene sequencing and fingerprinting) with microscope-based identification and counting to experimentally investigate the short-term responses of small eukaryotes (<6 μm; from a coastal Mediterranean lagoon) to a warming treatment (+3°C) and UVB radiation increases (+20%) at two different nutrient levels. Interestingly, the increase in temperature resulted in higher pigmented eukaryotes abundances and in community structure changes clearly illustrated by molecular analyses. For most of the phylogenetic groups, some rearrangements occurred at the OTUs level even when their relative proportion (microscope counting) did not change significantly. Temperature explained almost 20% of the total variance of the small eukaryote community structure (while UVB explained only 8.4%). However, complex cumulative effects were detected. Some antagonistic or non additive effects were detected between temperature and nutrients, especially for Dinophyceae and Cryptophyceae.
This multifactorial experiment highlights the potential impacts, over short time scales, of changing environmental factors on the structure of various functional groups like small primary producers, parasites and saprotrophs which, in response, can modify energy flow in the planktonic food webs.
[Show abstract][Hide abstract] ABSTRACT: The distribution of viruses inhabiting the coral mucus remains undetermined, as there is no suitable standardized procedure for their separation from this organic matrix, principally owing to its viscosity and autofluorescence. Seven protocols were tested, and the most efficient separations were obtained from a chemical treatment requiring potassium citrate.
[Show abstract][Hide abstract] ABSTRACT: The ecological insurance hypothesis predicts a positive effect of species richness on ecosystem functioning in a variable environment. This effect stems from temporal and spatial complementarity among species within metacommunities coupled with optimal levels of dispersal. Despite its importance in the context of global change by human activities, empirical evidence for ecological insurance remains scarce and controversial. Here we use natural aquatic bacterial communities to explore some of the predictions of the spatial and temporal aspects of the ecological insurance hypothesis. Addressing ecological insurance with bacterioplankton is of strong relevance given their central role in fundamental ecosystem processes. Our experimental set up consisted of water and bacterioplankton communities from two contrasting coastal lagoons. In order to mimic environmental fluctuations, the bacterioplankton community from one lagoon was successively transferred between tanks containing water from each of the two lagoons. We manipulated initial bacterial diversity for experimental communities and immigration during the experiment. We found that the abundance and production of bacterioplankton communities was higher and more stable (lower temporal variance) for treatments with high initial bacterial diversity. Immigration was only marginally beneficial to bacterial communities, probably because microbial communities operate at different time scales compared to the frequency of perturbation selected in this study, and of their intrinsic high physiologic plasticity. Such local "physiological insurance" may have a strong significance for the maintenance of bacterial abundance and production in the face of environmental perturbations.
PLoS ONE 06/2012; 7(6):e37620. DOI:10.1371/journal.pone.0037620 · 3.23 Impact Factor