Combined Earth observations reveal the sequence of conditions leading to a large algal bloom in Lake Geneva.

Freshwater algae exhibit complex dynamics, particularly in meso-oligotrophic lakes with sudden and dramatic increases in algal biomass following long periods of low background concentration. While the fundamental prerequisites for algal blooms, namely light and nutrient availability, are well-known, their specific causation involves an intricate chain of conditions. Here we examine a recent massive Uroglena bloom in Lake Geneva (Switzerland/France). We show that a certain sequence of meteorological conditions triggered this specific algal bloom event: heavy rainfall promoting excessive organic matter and nutrients loading, followed by wind-induced coastal upwelling, and a prolonged period of warm, calm weather. The combination of satellite remote sensing, in-situ measurements, ad-hoc biogeochemical analyses, and three-dimensional modeling proved invaluable in unraveling the complex dynamics of algal blooms highlighting the substantial role of littoral-pelagic connectivities in large low-nutrient lakes. These findings underscore the advantages of state-of-the-art multidisciplinary approaches for an improved understanding of dynamic systems as a whole.

A Comparative Study of the Dynamics and Diversity of Bdellovibrio and Like Organisms in Lakes Annecy and Geneva.

Bdellovibrio and like organisms (BALOs) are obligate bacterial predators of other Gram-negative bacteria. Here, we used quantitative PCR (qPCR) and recently developed specific primers which target the 16S rRNA gene to explore the abundance and distribution of three families of BALO belonging to the Oligoflexia class (i.e., Bdellovibrionaceae, Peredibacteraceae and Bacteriovoracaceae) over one year in the epilimnion and hypolimnion of Lakes Annecy and Geneva. Peredibacteraceae was the dominant group at all sampling points except at the bottom of Lake Geneva, where Bdellovibrionaceae was found in higher number. In addition, the abundance of BALOs increased significantly during the warmer months. Using high-throughput sequencing (Illumina Miseq), hundreds of OTUs were identified for Bdellovibrionaceae and Peredibacteraceae. Phylogenetic analysis suggests that Bdellovibrionaceae are more diverse than Peredibacteraceae and that some OTUs belong to new species of Bdellovibrionaceae. We also found that dominant OTUs were present simultaneously in the two lakes, while some others were specific to each lake, suggesting an adaptive pattern. Finally, both abundance and diversity of BALOs were poorly associated with abiotic factors except temperature, suggesting the importance of studying biotic relationships, assumed to play a greater role than physico-chemical variables in BALOs' dynamics and distribution.

Soil pH, Calcium Content and Bacteria as Major Factors Responsible for the Distribution of the Known Fraction of the DNA Bacteriophage Populations in Soils of Luxembourg.

Bacteriophages participate in soil life by influencing bacterial community structure and function, biogeochemical cycling and horizontal gene transfer. Despite their great abundance, diversity, and importance in microbial processes, they remain little explored in environmental studies. The influence of abiotic factors on the persistence of bacteriophages is now recognized; however, it has been mainly studied under experimental conditions. This study aimed to determine whether the abiotic factors well-known to influence bacteriophage persistence also control the natural distribution of the known DNA bacteriophage populations. To this end, soil from eight study sites including forests and grasslands located in the Attert River basin (Grand Duchy of Luxembourg) were sampled, covering different soil and land cover characteristics. Shotgun metagenomics, reference-based bioinformatics and statistical analyses allowed characterising the diversity of known DNA bacteriophage and bacterial communities. After combining soil properties with the identified DNA bacteriophage populations, our in-situ study highlighted the influence of pH and calcium cations on the diversity of the known fraction of the soil DNA bacteriophages. More interestingly, significant relationships were established between bacteriophage and bacterial populations. This study provides new insights into the importance of abiotic and biotic factors in the distribution of DNA bacteriophages and the natural ecology of terrestrial bacteriophages.

Bacterial, Phytoplankton, and Viral Distributions and Their Biogeochemical Contexts in Meromictic Lake Cadagno Offer Insights into the Proterozoic Ocean Microbial Loop.

Lake Cadagno, a permanently stratified high-alpine lake with a persistent microbial bloom in its chemocline, has long been considered a model for the low-oxygen, high-sulfide Proterozoic ocean. Although the lake has been studied for over 25 years, the absence of concerted study of the bacteria, phytoplankton, and viruses, together with primary and secondary production, has hindered a comprehensive understanding of its microbial food web. Here, the identities, abundances, and productivity of microbes were evaluated in the context of Lake Cadagno biogeochemistry. Photosynthetic pigments together with 16S rRNA gene phylogenies suggest the prominence of eukaryotic phytoplankton chloroplasts, primarily chlorophytes. Chloroplasts closely related to those of high-alpine-adapted Ankyra judayi persisted with oxygen in the mixolimnion, where photosynthetic efficiency was high, while chloroplasts of Closteriopsis-related chlorophytes peaked in the chemocline and monimolimnion. The anoxygenic phototrophic sulfur bacterium Chromatium dominated the chemocline along with Lentimicrobium, a genus of known fermenters. Secondary production peaked in the chemocline, which suggested that anoxygenic primary producers depended on heterotrophic nutrient remineralization. The virus-to-microbe ratio peaked with phytoplankton abundances in the mixolimnion and were at a minimum where Chromatium abundance was highest, trends that suggest that viruses may play a role in the modulation of primary production. Through the combined analysis of bacterial, eukaryotic, viral, and biogeochemical spatial dynamics, we provide a comprehensive synthesis of the Lake Cadagno microbial loop. This study offers a new ecological perspective on how biological and geochemical connections may have occurred in the chemocline of the Proterozoic ocean, where eukaryotic microbial life is thought to have evolved. IMPORTANCE As a window into the past, this study offers insights into the potential role that microbial guilds may have played in the production and recycling of organic matter in ancient Proterozoic ocean chemoclines. The new observations described here suggest that chloroplasts of eukaryotic algae were persistent in the low-oxygen upper chemocline along with the purple and green sulfur bacteria known to dominate the lower half of the chemocline. This study provides the first insights into Lake Cadagno's viral ecology. High viral abundances suggested that viruses may be essential components of the chemocline, where their activity may result in the release and recycling of organic matter. The integration of diverse geochemical and biological data types provides a framework that lays the foundation to quantitatively resolve the processes performed by the discrete populations that comprise the microbial loop in this early anoxic ocean analogue.

Bdellovibrio and like organisms: current understanding and knowledge gaps of the smallest cellular hunters of the microbial world.

Almost sixty years ago, Bdellovibrio and like organisms (BALOs) were discovered as the first obligate bacterial predators of other bacteria known to science. Since then, they were shown to be diverse and ubiquitous in the environment, and to bear astonishing ecological, physiological, and metabolic capabilities. The last decade has seen important strides made in understanding the mechanistic basis of their life cycle, the dynamics of their interactions with prey, along with significant developments towards their use in medicine, agriculture, and industry. This review details these achievements, identify current understanding and knowledge gaps to encourage and guide future BALO research.

Physico-chemical dataset from an in situ mesocosm experiment simulating extreme climate events in Lake Geneva (MESOLAC).

This dataset complement a previously published dataset [1] and corresponds to the physico-chemical parameters data series produced during the MESOLAC experimental project [2]. The presented dataset is composed of: 1. In situ profiles (0-3m) of temperature, conductivity, pH, dissolved oxygen (concentration and saturation). 2. In situ measurements of light spectral UV/VIS/IR irradiance (300-950 nm wavelength range) taken at 0, 0.25, 0.5, 1, 1.5, 2 and 2.5m. 3. Laboratory chemical analysis of samples collected at 0 and 2 m (conductivity, pH, total alkalinity, NH4, NO2, NO3, total and particulate nitrogen (Ntot, Npart), PO4, total and particulate phosphorus (Ptot, Ppart), total, organic particulate and total particulate carbon (Ctot, Cpart-org, Cpart-tot), Cl, SO4, SiO2. 4. Laboratory analysis of pigments extracted from samples collected at 0 and 2 m (Chla, Chlc, carotenoids, phaeopigments). The experimental design is the same as in Tran-Khac et al [1]. Briefly, it consisted of nine pelagic mesocosms (about 3000 L, 3m depth) deployed in July 2019 in Lake Geneva near the shore of Thonon les Bains (France) aiming to simulate predicted climate scenarios (i.e. extreme events) and assess the response of planktonic communities, ecosystem functioning and resilience. During the experiment, physical parameters were measured twice a week. At the same time, samples were collected at 0 and 2m of depth for subsequent chemical laboratory analyses. These data are presented in the dataset file, ordered by sampling event (numbered from S1 to S8), treatment (Control-C, High-H and Medium-M) and replicates (1 to 3). For each sampling point the measured parameters are listed in columns, missing data and values below the detection limit are marked as NA (not available). This data set aims to contribute to the understanding of the effect of environmental forcing on lake physico-chemical characteristics (such as temperature, oxygen and nutrient concentration) under simulated intense weather events. To a broader extent, the presented data can be used for a wide variety of applications, including monitoring of a large peri-alpine lake functioning under environmental stress and being included in further meta-analysis to generalise the effect of climate change on large lakes. The two complementary dataset differ in the acquired data and methods, temporal and spatial resolution. They complete each other in terms of physico-chemical characterization of the experimental treatments and together can allow comparison of the two different monitoring strategies (continuous vs punctual) during in situ experimental manipulations.

Seasonal Dynamics of Abundance, Structure, and Diversity of Methanogens and Methanotrophs in Lake Sediments.

Understanding temporal and spatial microbial community abundance and diversity variations is necessary to assess the functional roles played by microbial actors in the environment. In this study, we investigated spatial variability and temporal dynamics of two functional microbial sediment communities, methanogenic Archaea and methanotrophic bacteria, in Lake Bourget, France. Microbial communities were studied from 3 sites sampled 4 times over a year, with one core sampled at each site and date, and 5 sediment layers per core were considered. Microbial abundance in the sediment were determined using flow cytometry. Methanogens and methanotrophs community structures, diversity, and abundance were assessed using T-RFLP, sequencing, and real-time PCR targeting mcrA and pmoA genes, respectively. Changes both in structure and abundance were detected mainly at the water-sediment interface in relation to the lake seasonal oxygenation dynamics. Methanogen diversity was dominated by Methanomicrobiales (mainly Methanoregula) members, followed by Methanosarcinales and Methanobacteriales. For methanotrophs, diversity was dominated by Methylobacter in the deeper area and by Methylococcus in the shallow area. Organic matter appeared to be the main environmental parameter controlling methanogens, while oxygen availability influenced both the structure and abundance of the methanotrophic community.

Exopolymeric Substances Control Microbial Community Structure and Function by Contributing to both C and Fe Nutrition in Fe-Limited Southern Ocean Provinces.

Organic ligands such as exopolymeric substances (EPS) are known to form complexes with iron (Fe) and modulate phytoplankton growth. However, the effect of organic ligands on bacterial and viral communities remains largely unknown. Here, we assessed how Fe associated with organic ligands influences phytoplankton, microbial, and viral abundances and their diversity in the Southern Ocean. While the particulate organic carbon (POC) was modulated by Fe chemistry and bioavailability in the Drake Passage, the abundance and diversity of microbes and viruses were not governed by Fe bioavailability. Only following amendments with bacterial EPS did bacterial abundances increase, while phenotypic alpha diversity of bacterial and viral communities decreased. The latter was accompanied by significantly enhanced POC, pointing toward the relief of C limitation or other drivers of the microbial loop. Based on the literature and our findings, we propose a conceptual framework by which EPS may affect phytoplankton, bacteria, and viruses. Given the importance of the Southern Ocean for Earth's climate as well as the prevalence of viruses and their increasingly recognized impact on marine biogeochemistry and C cycling; the role of microbe-virus interactions on primary productivity in the Southern Ocean needs urgent attention.

Advances in forecasting harmful algal blooms using machine learning models: A case study with Planktothrix rubescens in Lake Geneva.

The development of anthropic activities during the 20th century increased the nutrient fluxes in freshwater ecosystems, leading to the eutrophication phenomenon that most often promotes harmful algal blooms (HABs). Recent years have witnessed the regular and massive development of some filamentous algae or cyanobacteria in Lake Geneva. Consequently, important blooms could result in detrimental impacts on economic issues and human health. In this study, we tried to lay the foundation of an HAB forecast model to help scientists and local stakeholders with the present and future management of this peri-alpine lake. Our forecast strategy was based on pairing two machine learning models with a long-term database built over the past 34 years. We created HAB groups via a K-means model. Then, we introduced different lag times in the input of a random forest (RF) model, using a sliding window. Finally, we used a high-frequency dataset to compare the natural mechanisms with numerical interaction using individual conditional expectation plots. We demonstrate that some HAB events can be forecasted over a year scale. The information contained in the concentration data of the cyanobacteria was synthesized in the form of four intensity groups that directly depend on the P. rubescens concentration. The categorical transformation of these data allowed us to obtain a forecast with correlation coefficients that stayed above a threshold of 0.5 until one year for the counting cells and two years for the biovolume data. Moreover, we found that the RF model predicted the best P. rubescens abundance for water temperatures around 14°C. This result is consistent with the biological processes of the toxic cyanobacterium. In this study, we found that the coupling between K-means and RF models could help in forecasting the development of the bloom-forming P. rubescens in Lake Geneva. This methodology could create a numerical decision support tool, which should be a significant advantage for lake managers.

In situ pelagic dataset from continuous monitoring: A mesocosm experiment in Lake Geneva (MESOLAC).

This dataset corresponds to a data series produced from automated data loggers during the MESOLAC experimental project. Nine pelagic mesocosms (about 3000 L, 3 m depth) were deployed in July 2019 in Lake Geneva near the shore of Thonon les Bains (France), simulating predicted climate scenarios (i.e. intense weather events) by applying a combination of forcing. The design consisted of three treatments each replicated three times: a control treatment (named C - no treatment applied) and two different treatments simulating different intensities of weather events. The high intensity treatment (named H) aimed to reproduce short and intense weather events such as violent storms. It consisted of a short-term stress applied during the first week, with high pulse of dissolved organic carbon (5x increased concentration, i.e. total DOC ∼ 6 mg L-1), transmitted light reduced to 15% and water column manual mixing. The medium intensity treatment (named M) simulated less intense and more prolonged exposures such as during flood events. It was maintained during the 4 weeks of the experiment and consisted of 1.5x increased concentration of dissolved organic carbon (i.e. total DOC ∼ 2 mg L-1), 70% transmitted light and water column manual mixing. Automated data loggers were placed for the entire period of the experiment in the mesocosms and in the lake for comparison with natural conditions. Temperature, conductivity, dissolved oxygen and CO2 were monitored every 15 min at different depths (0.15, 0.25, 1 and 2 m). This data set aims to contribute our understanding of the effect of environmental forcing on lake ecosystem processes (such as production, respiration and CO2 exchange) under simulated intense weather events and the ability of the planktonic community to recover after perturbation. To a broader extent, the presented data can be used for a wide variety of applications, including monitoring of lake community functioning during a period of high productivity on a large peri-alpine lake and being included in further meta-analysis aiming at generalising the effect of climate change on large lakes.

New 16S rRNA primers to uncover Bdellovibrio and like organisms diversity and abundance.

Appropriate use and specific primers are important in assessing the diversity and abundance of microbial groups of interest. Bdellovibrio and like organisms (BALOs), that refer to obligate Gram-negative bacterial predators of other Gram-negative bacteria, evolved in terms of taxonomy and classification over the past two decades. Hence, some former primers have become inadequate while others are yet to be designed, for both PCR (especially with the advent of NGS) and qPCR approaches. Thus, to study BALOs' abundance and diversity in a variety of aquatic ecosystems, we designed in silico specific primer sets for each BALO genera and tested them in vitro on a variety of cultures and environmental samples. Also, we performed Sanger and Nano Miseq sequencing to reveal the exact degree of specificity of the most promising primers set. Here we report our success in designing specific primers for some BALOs genera, i.e. Bdellovibrio (PCR), Bacteriovorax (qPCR), Peredibacter (PCR).

Bdellovibrio and Like Organisms in Lake Geneva: An Unseen Elephant in the Room?

When considering microbial biotic interactions, viruses as well as eukaryotic grazers are known to be important components of aquatic microbial food webs. It might be the same for bacterivorous bacteria but these groups have been comparatively less studied. This is typically the case of the Bdellovibrio and like organisms (BALOs), which are obligate bacterial predators of other bacteria. Recently, the abundance and distribution of three families of this functional group were investigated in perialpine lakes, revealing their presence and quantitative importance. Here, a more in-depth analysis is provided for Lake Geneva regarding the diversity of these bacterial predators at different seasons, sites and depths. We reveal a seasonal and spatial (vertical) pattern for BALOs. They were also found to be relatively diverse (especially Bdellovibrionaceae) and assigned to both known and unknown phylogenetic clusters. At last we found that most BALOs were positively correlated to other bacterial groups, mainly Gram-negative, in particular Myxococcales (among which many are predators of other microbes). This study is the first shedding light on this potentially important bacterial killing group in a large and deep lake.

Widespread diminishing anthropogenic effects on calcium in freshwaters.

Calcium (Ca) is an essential element for almost all living organisms. Here, we examined global variation and controls of freshwater Ca concentrations, using 440 599 water samples from 43 184 inland water sites in 57 countries. We found that the global median Ca concentration was 4.0 mg L-1 with 20.7% of the water samples showing Ca concentrations ≤ 1.5 mg L-1, a threshold considered critical for the survival of many Ca-demanding organisms. Spatially, freshwater Ca concentrations were strongly and proportionally linked to carbonate alkalinity, with the highest Ca and carbonate alkalinity in waters with a pH around 8.0 and decreasing in concentrations towards lower pH. However, on a temporal scale, by analyzing decadal trends in >200 water bodies since the 1980s, we observed a frequent decoupling between carbonate alkalinity and Ca concentrations, which we attributed mainly to the influence of anthropogenic acid deposition. As acid deposition has been ameliorated, in many freshwaters carbonate alkalinity concentrations have increased or remained constant, while Ca concentrations have rapidly declined towards or even below pre-industrial conditions as a consequence of recovery from anthropogenic acidification. Thus, a paradoxical outcome of the successful remediation of acid deposition is a globally widespread freshwater Ca concentration decline towards critically low levels for many aquatic organisms.

Diversity, Dynamics, and Distribution of Bdellovibrio and Like Organisms in Perialpine Lakes.

Microbes drive a variety of ecosystem processes and services, but many of them remain largely unexplored because of a lack of knowledge on both the diversity and functionality of some potentially crucial microbiological compartments. This is the case with and within the group of bacterial predators collectively known as Bdellovibrio and like organisms (BALOs). Here, we report the abundance, distribution, and diversity of three families of these obligate predatory Gram-negative bacteria in three perialpine lakes (Lakes Annecy, Bourget, and Geneva). The study was conducted at different depths (near-surface versus 45 or 50 m) from August 2015 to January 2016. Using PCR-denaturing gradient gel electrophoresis (PCR-DGGE) and cloning-sequencing approaches, we show that the diversity of BALOs is relatively low and very specific to freshwaters or even the lakes themselves. While the Peredibacteraceae family was represented mainly by a single species (Peredibacter starrii), it could represent up to 7% of the total bacterial cell abundances. Comparatively, the abundances of the two other families (Bdellovibrionaceae and Bacteriovoracaceae) were significantly lower. In addition, the distributions in the water column were very different between the three groups, suggesting various life strategies/niches, as follows: Peredibacteraceae dominated near the surface, while Bdellovibrionaceae and Bacteriovoracaceae were more abundant at greater depths. Statistical analyses revealed that BALOs seem mainly to be driven by depth and temperature. Finally, this original study was also the opportunity to design new quantitative PCR (qPCR) primers for Peredibacteraceae quantification.IMPORTANCE This study highlights the abundance, distribution, and diversity of a poorly known microbial compartment in natural aquatic ecosystems, the Bdellovibrio and like organisms (BALOs). These obligate bacterial predators of other bacteria may have an important functional role. This study shows the relative quantitative importance of the three main families of this group, with the design of a new primer pair, and their diversity. While both the diversity and the abundances of these BALOs were globally low, it is noteworthy that the abundance of the Peredibacteraceae could reach important values.

A New Freshwater Cyanosiphovirus Harboring Integrase.

Pelagic cyanobacteria are key players in the functioning of aquatic ecosystems, and their viruses (cyanophages) potentially affect the abundance and composition of cyanobacterial communities. Yet, there are few well-described freshwater cyanophages relative to their marine counterparts, and in general, few cyanosiphoviruses (family Siphoviridae) have been characterized, limiting our understanding of the biology and the ecology of this prominent group of viruses. Here, we characterize S-LBS1, a freshwater siphovirus lytic to a phycoerythrin-rich Synechococcus isolate (Strain TCC793). S-LBS1 has a narrow host range, a burst size of ∼400 and a relatively long infecting step before cell lysis occurs. It has a dsDNA 34,641 bp genome with putative genes for structure, DNA packing, lysis, replication, host interactions, DNA repair and metabolism. S-LBS1 is similar in genome size, genome architecture, and gene content, to previously described marine siphoviruses also infecting PE-rich Synechococcus, e.g., S-CBS1 and S-CBS3. However, unlike other Synechococcus phages, S-LBS1 encodes an integrase, suggesting its ability to establish lysogenic relationships with its host. Sequence recruitment from viral metagenomic data showed that S-LBS1-like viruses are diversely present in a wide range of aquatic environments, emphasizing their potential importance in controlling and structuring Synechococcus populations. A comparative analysis with 16 available sequenced cyanosiphoviruses reveals the absence of core genes within the genomes, suggesting high degree of genetic variability in siphoviruses infecting cyanobacteria. It is likely that cyanosiphoviruses have evolved as distinct evolutionary lineages and that adaptive co-evolution occurred between these viruses and their hosts (i.e., Synechococcus, Prochlorococcus, Nodularia, and Acaryochloris), constituting an important driving force for such phage diversification.

Development and implementation of eco-genomic tools for aquatic ecosystem biomonitoring: the SYNAQUA French-Swiss program.

The effectiveness of environmental protection measures is based on the early identification and diagnosis of anthropogenic pressures. Similarly, restoration actions require precise monitoring of changes in the ecological quality of ecosystems, in order to highlight their effectiveness. Monitoring the ecological quality relies on bioindicators, which are organisms revealing the pressures exerted on the environment through the composition of their communities. Their implementation, based on the morphological identification of species, is expensive because it requires time and experts in taxonomy. Recent genomic tools should provide access to reliable and high-throughput environmental monitoring by directly inferring the composition of bioindicators' communities from their DNA (metabarcoding). The French-Swiss program SYNAQUA (INTERREG France-Switzerland 2017-2019) proposes to use and validate the tools of environmental genomic for biomonitoring and aims ultimately at their implementation in the regulatory bio-surveillance. SYNAQUA will test the metabarcoding approach focusing on two bioindicators, diatoms, and aquatic oligochaetes, which are used in freshwater biomonitoring in France and Switzerland. To go towards the renewal of current biomonitoring practices, SYNAQUA will (1) bring together different actors: scientists, environmental managers, consulting firms, and biotechnological companies, (2) apply this approach on a large scale to demonstrate its relevance, (3) propose robust and reliable tools, and (4) raise public awareness and train the various actors likely to use these new tools. Biomonitoring approaches based on such environmental genomic tools should address the European need for reliable, higher-throughput monitoring to improve the protection of aquatic environments under multiple pressures, guide their restoration, and follow their evolution.

Effects of temperature and UVR on organic matter fluxes and the metabolic activity of Acropora muricata.

Coral bleaching events are predicted to occur more frequently in the coming decades with global warming. The susceptibility of corals to bleaching during thermal stress episodes depends on many factors, including the magnitude of thermal stress and irradiance. The interactions among these two factors, and in particular with ultra-violet radiation (UVR), the most harmful component of light, are more complex than assumed, and are not yet well understood. This paper explores the individual and combined effects of temperature and UVR on the metabolism of Acropora muricata, one of the most abundant coral species worldwide. Particulate and dissolved organic matter (POM/DOM) fluxes and organic matter (OM) degradation by the mucus-associated bacteria were also monitored in all conditions. The results show that UVR exposure exacerbated the temperature-induced bleaching, but did not affect OM fluxes, which were only altered by seawater warming. Temperature increase induced a shift from POM release and DOM uptake in healthy corals to POM uptake and DOM release in stressed ones. POM uptake was linked to a significant grazing of pico- and nanoplankton particles during the incubation, to fulfil the energetic requirements of A. muricata in the absence of autotrophy. Finally, OM degradation by mucus-associated bacterial activity was unaffected by UVR exposure, but significantly increased under high temperature. Altogether, our results demonstrate that seawater warming and UVR not only affect coral physiology, but also the way corals interact with the surrounding seawater, with potential consequences for coral reef biogeochemical cycles and food webs.

[Bdellovibrio and like organisms: outstanding predators!] / Bdellovibrio et organismes apparentés - Des prédateurs bactériens hors du commun !

Obligate predatory bacteria, i.e. bacteria requiring a Gram negative prey cell in order to complete their cell cycle, belong to the polyphyletic group referred to as the Bdellovibrio And Like Organisms (BALO). Predatory interactions between bacteria are complex, yet their dynamics and impact on bacterial communities in the environment are becoming better understood. BALO have unique life cycles: they grow epibiotically with the predator remaining attached to the prey's envelope, dividing in a binary manner or periplasmically, i.e. by penetrating the prey's periplasm to generate a number of progeny cells. The periplasmic life cycle includes unique gene and protein patterns and unique signaling features. These ecological and cellular features, along with applications of the BALO in the medical, agricultural and environmental fields are surveyed.

Temperature is a key factor in Micromonas-virus interactions.

The genus Micromonas comprises phytoplankton that show among the widest latitudinal distributions on Earth, and members of this genus are recurrently infected by prasinoviruses in contrasted thermal ecosystems. In this study, we assessed how temperature influences the interplay between the main genetic clades of this prominent microalga and their viruses. The growth of three Micromonas strains (Mic-A, Mic-B, Mic-C) and the stability of their respective lytic viruses (MicV-A, MicV-B, MicV-C) were measured over a thermal range of 4-32.5 °C. Similar growth temperature optima (Topt) were predicted for all three hosts but Mic-B exhibited a broader thermal tolerance than Mic-A and Mic-C, suggesting distinct thermoacclimation strategies. Similarly, the MicV-C virus displayed a remarkable thermal stability compared with MicV-A and MicV-B. Despite these divergences, infection dynamics showed that temperatures below Topt lengthened lytic cycle kinetics and reduced viral yield and, notably, that infection at temperatures above Topt did not usually result in cell lysis. Two mechanisms operated depending on the temperature and the biological system. Hosts either prevented the production of viral progeny or maintained their ability to produce virions with no apparent cell lysis, pointing to a possible switch in the viral life strategy. Hence, temperature changes critically affect the outcome of Micromonas infection and have implications for ocean biogeochemistry and evolution.

Deciphering the virus-to-prokaryote ratio (VPR): insights into virus-host relationships in a variety of ecosystems.

The discovery of the numerical importance of viruses in a variety of (aquatic) ecosystems has changed our perception of their importance in microbial processes. Bacteria and Archaea undoubtedly represent the most abundant cellular life forms on Earth and past estimates of viral numbers (represented mainly by viruses infecting prokaryotes) have indicated abundances at least one order of magnitude higher than that of their cellular hosts. Such dominance has been reflected most often by the virus-to-prokaryote ratio (VPR), proposed as a proxy for the relationship between viral and prokaryotic communities. VPR values have been discussed in the literature to express viral numerical dominance (or absence of it) over their cellular hosts, but the ecological meaning and interpretation of this ratio has remained somewhat nebulous or contradictory. We gathered data from 210 publications (and additional unpublished data) on viral ecology with the aim of exploring VPR. The results are presented in three parts: the first consists of an overview of the minimal, maximal and calculated average VPR values in an extensive variety of different environments. Results indicate that VPR values fluctuate over six orders of magnitude, with variations observed within each ecosystem. The second part investigates the relationship between VPR and other indices, in order to assess whether VPR can provide insights into virus-host relationships. A positive relationship was found between VPR and viral abundance (VA), frequency of visibly infected cells (FVIC), burst size (BS), frequency of lysogenic cells (FLC) and chlorophyll a (Chl a) concentration. An inverse relationship was detected between VPR and prokaryotic abundance (PA) (in sediments), prokaryotic production (PP) and virus-host contact rates (VCR) as well as salinity and temperature. No significant relationship was found between VPR and viral production (VP), fraction of mortality from viral lysis (FMVL), viral decay rate (VDR), viral turnover (VT) or depth. Finally, we summarize our results by proposing two scenarios in two contrasting environments, based on current theories on viral ecology as well as the present results. We conclude that since VPR fluctuates in every habitat for different reasons, as it is linked to a multitude of factors related to virus-host dynamics, extreme caution should be used when inferring relationships between viruses and their hosts. Furthermore, we posit that the VPR is only useful in specific, controlled conditions, e.g. for the monitoring of fluctuations in viral and host abundance over time.