Response to Interpreting the results of oceanic mesoscale enrichment experiments: Caveats and lessons from limnology and coastal ecology

Peer Reviewe

Effect of CO2 enrichment on bacterial metabolism in an Arctic fjord

he anthropogenic increase of carbon dioxide (CO2) alters the seawater carbonate chemistry, with a decline of pH and an increase in the partial pressure of CO2 (pCO2). Although bacteria play a major role in carbon cycling, little is known about the impact of rising pCO2 on bacterial carbon metabolism, especially for natural bacterial communities. In this study, we investigated the effect of rising pCO2 on bacterial production (BP), bacterial respiration (BR) and bacterial carbon metabolism during a mesocosm experiment performed in Kongsfjorden (Svalbard) in 2010. Nine mesocosms with pCO2 levels ranging from ca. 180 to 1400 μatm were deployed in the fjord and monitored for 30 days. Generally BP gradually decreased in all mesocosms in an initial phase, showed a large (3.6-fold average) but temporary increase on day 10, and increased slightly after inorganic nutrient addition. Over the wide range of pCO2 investigated, the patterns in BP and growth rate of bulk and free-living communities were generally similar over time. However, BP of the bulk community significantly decreased with increasing pCO2 after nutrient addition (day 14). In addition, increasing pCO2 enhanced the leucine to thymidine (Leu : TdR) ratio at the end of experiment, suggesting that pCO2 may alter the growth balance of bacteria. Stepwise multiple regression analysis suggests that multiple factors, including pCO2, explained the changes of BP, growth rate and Leu : TdR ratio at the end of the experiment. In contrast to BP, no clear trend and effect of changes of pCO2 was observed for BR, bacterial carbon demand and bacterial growth efficiency. Overall, the results suggest that changes in pCO2 potentially influence bacterial production, growth rate and growth balance rather than the conversion of dissolved organic matter into CO2

Production of individual marine organic aggregates using paramagnetic microspheres : a new tool for examining microbial associations with aggregates

We describe a new method to produce marine aggregates from natural organic material based on the sticking properties of transparent exopolymeric particles. Seawater samples were prescreened and ultrafiltered to concentrate the 30 kDa to 10 mu m size fraction. First, we produced small magnetizable aggregates by combining glass microfibers and paramagnetic 1-mu m beads with the organic matter present in the concentrated solution. The second step involved clustering the small aggregates into a single macro-aggregate, using a small ring-shaped magnet as an aggregation nucleus. Viral and bacterial densities, determined after dissolution of the newly formed aggregates with methanol, averaged 13.8 x 10(6) +/- 3.6 x 10(6) vir. agg.(-1) and 4.1 x 10(6) +/- 1.1 x10(6) bact. agg.(-1). Bacterial respiration and production measurements of single aggregates averaged 8.47 +/- 1.72 nmol O-2 agg.(-1) h(-1) and 1.54 +/- 0.45 ng C agg.(-1) h(-1), respectively. Particulate organic carbon and nitrogen content of the newly formed macro-aggregates averaged 31.92 +/- 2.67 mu g C agg.(-1) and 3.44 +/- 0.43 mu g N agg.(-1), respectively. This approach allows the concentration and isolation of the organic matter precursors that compose natural aggregates and provides a simple protocol for recombining those precursors into single newly formed macro-aggregates, which can then be easily manipulated for further investigation. This method is a new tool for investigations into the interactions between microorganisms and marine aggregates and their implications at the ecosystem level, but also into the interactions between aggregates and dissolved organic or inorganic substances

Effects of Noise on Ecological Invasion Processes: Bacteriophage-mediated Competition in Bacteria

Pathogen-mediated competition, through which an invasive species carrying and transmitting a pathogen can be a superior competitor to a more vulnerable resident species, is one of the principle driving forces influencing biodiversity in nature. Using an experimental system of bacteriophage-mediated competition in bacterial populations and a deterministic model, we have shown in [Joo et al 2005] that the competitive advantage conferred by the phage depends only on the relative phage pathology and is independent of the initial phage concentration and other phage and host parameters such as the infection-causing contact rate, the spontaneous and infection-induced lysis rates, and the phage burst size. Here we investigate the effects of stochastic fluctuations on bacterial invasion facilitated by bacteriophage, and examine the validity of the deterministic approach. We use both numerical and analytical methods of stochastic processes to identify the source of noise and assess its magnitude. We show that the conclusions obtained from the deterministic model are robust against stochastic fluctuations, yet deviations become prominently large when the phage are more pathological to the invading bacterial strain.Comment: 39 pages, 7 figure

Androgens and spermatogenesis: lessons from transgenic mouse models

Transgenic mouse models have contributed considerably to our understanding of the cellular and molecular mechanisms by which androgens control spermatogenesis. Cell-selective ablation of the androgen receptor (AR) in Sertoli cells (SC) results in a complete block in meiosis and unambiguously identifies the SC as the main cellular mediator of the effects of androgens on spermatogenesis. This conclusion is corroborated by similar knockouts in other potential testicular target cells. Mutations resulting in diminished expression of the AR or in alleles with increased length of the CAG repeat mimick specific human forms of disturbed fertility that are not accompanied by defects in male sexual development. Transcriptional profiling studies in mice with cell-selective and general knockouts of the AR, searching for androgen-regulated genes relevant to the control of spermatogenesis, have identified many candidate target genes. However, with the exception of Rhox5, the identified subsets of genes show little overlap. Genes related to tubular restructuring, cell junction dynamics, the cytoskeleton, solute transportation and vitamin A metabolism are prominently present. Further research will be needed to decide which of these genes are physiologically relevant and to identify genes that can be used as diagnostic tools or targets to modulate the effects of androgens in spermatogenesis

Climate Change and the Potential Spreading of Marine Mucilage and Microbial Pathogens in the Mediterranean Sea

Background: Marine snow (small amorphous aggregates with colloidal properties) is present in all oceans of the world. Surface water warming and the consequent increase of water column stability can favour the coalescence of marine snow into marine mucilage, large marine aggregates representing an ephemeral and extreme habitat. Marine mucilage characterize aquatic systems with altered environmental conditions. Methodology/Principal Findings: We investigated, by means of molecular techniques, viruses and prokaryotes within the mucilage and in surrounding seawater to examine the potential of mucilage to host new microbial diversity and/or spread marine diseases. We found that marine mucilage contained a large and unexpectedly exclusive microbial biodiversity and hosted pathogenic species that were absent in surrounding seawater. We also investigated the relationship between climate change and the frequency of mucilage in the Mediterranean Sea over the last 200 years and found that the number of mucilage outbreaks increased almost exponentially in the last 20 years. The increasing frequency of mucilage outbreaks is closely associated with the temperature anomalies. Conclusions/Significance: We conclude that the spreading of mucilage in the Mediterranean Sea is linked to climate-driven sea surface warming. The mucilage can act as a controlling factor of microbial diversity across wide oceanic regions and could have the potential to act as a carrier of specific microorganisms, thereby increasing the spread of pathogenic bacteria

Population Dynamics and Diversity of Viruses, Bacteria and Phytoplankton in a Shallow Eutrophic Lake

We have studied the temporal variation in viral abundances and community assemblage in the eutrophic Lake Loosdrecht through epifluorescence microscopy and pulsed field gel electrophoresis (PFGE). The virioplankton community was a dynamic component of the aquatic community, with abundances ranging between 5.5 × 107 and 1.3 × 108 virus-like particles ml−1 and viral genome sizes ranging between 30 and 200 kb. Both viral abundances and community composition followed a distinct seasonal cycle, with high viral abundances observed during spring and summer. Due to the selective and parasitic nature of viral infection, it was expected that viral and host community dynamics would covary both in abundances and community composition. The temporal dynamics of the bacterial and cyanobacterial communities, as potential viral hosts, were studied in addition to a range of environmental parameters to relate these to viral community dynamics. Cyanobacterial and bacterial communities were studied applying epifluorescence microscopy, flow cytometry, and denaturing gradient gel electrophoresis (DGGE). Both bacterial and cyanobacterial communities followed a clear seasonal cycle. Contrary to expectations, viral abundances were neither correlated to abundances of the most dominant plankton groups in Lake Loosdrecht, the bacteria and the filamentous cyanobacteria, nor could we detect a correlation between the assemblage of viral and bacterial or cyanobacterial communities during the overall period. Only during short periods of strong fluctuations in microbial communities could we detect viral community assemblages to covary with cyanobacterial and bacterial communities. Methods with a higher specificity and resolution are probably needed to detect the more subtle virus–host interactions. Viral abundances did however relate to cyanobacterial community assemblage and showed a significant positive correlation to Chl-a as well as prochlorophytes, suggesting that a significant proportion of the viruses in Lake Loosdrecht may be phytoplankton and more specific cyanobacterial viruses. Temporal changes in bacterial abundances were significantly related to viral community assemblage, and vice versa, suggesting an interaction between viral and bacterial communities in Lake Loosdrecht

Finding a Needle in the Virus Metagenome Haystack - Micro-Metagenome Analysis Captures a Snapshot of the Diversity of a Bacteriophage Armoire

Viruses are ubiquitous in the oceans and critical components of marine microbial communities, regulating nutrient transfer to higher trophic levels or to the dissolved organic pool through lysis of host cells. Hydrothermal vent systems are oases of biological activity in the deep oceans, for which knowledge of biodiversity and its impact on global ocean biogeochemical cycling is still in its infancy. In order to gain biological insight into viral communities present in hydrothermal vent systems, we developed a method based on deep-sequencing of pulsed field gel electrophoretic bands representing key viral fractions present in seawater within and surrounding a hydrothermal plume derived from Loki's Castle vent field at the Arctic Mid-Ocean Ridge. The reduction in virus community complexity afforded by this novel approach enabled the near-complete reconstruction of a lambda-like phage genome from the virus fraction of the plume. Phylogenetic examination of distinct gene regions in this lambdoid phage genome unveiled diversity at loci encoding superinfection exclusion- and integrase-like proteins. This suggests the importance of fine-tuning lyosgenic conversion as a viral survival strategy, and provides insights into the nature of host-virus and virus-virus interactions, within hydrothermal plumes. By reducing the complexity of the viral community through targeted sequencing of prominent dsDNA viral fractions, this method has selectively mimicked virus dominance approaching that hitherto achieved only through culturing, thus enabling bioinformatic analysis to locate a lambdoid viral “needle" within the greater viral community “haystack". Such targeted analyses have great potential for accelerating the extraction of biological knowledge from diverse and poorly understood environmental viral communities

Viruses in extreme environments

The original publication is available at www.springerlink.comInternational audienceThe tolerance limits of extremophiles in term of temperature, pH, salinity, desiccation, hydrostatic pressure, radiation, anaerobiosis far exceed what can support non-extremophilic organisms. Like all other organisms, extremophiles serve as hosts for viral replication. Many lines of evidence suggest that viruses could no more be regarded as simple infectious ‘‘fragments of life'' but on the contrary as one of the major components of the biosphere. The exploration of niches with seemingly harsh life conditions as hypersaline and soda lakes, Sahara desert, polar environments or hot acid springs and deep sea hydrothermal vents, permitted to track successfully the presence of viruses. Substantial populations of double-stranded DNA virus that can reach 109 particles per milliliter were recorded. All these viral communities, with genome size ranging from 14 kb to 80 kb, seem to be genetically distinct, suggesting specific niche adaptation. Nevertheless, at this stage of the knowledge, very little is known of their origin, activity, or importance to the in situ microbial dynamics. The continuous attempts to isolate and to study viruses that thrive in extreme environments will be needed to address such questions. However, this topic appears to open a new window on an unexplored part of the viral world

Statistical Mechanics of Horizontal Gene Transfer in Evolutionary Ecology

The biological world, especially its majority microbial component, is strongly interacting and may be dominated by collective effects. In this review, we provide a brief introduction for statistical physicists of the way in which living cells communicate genetically through transferred genes, as well as the ways in which they can reorganize their genomes in response to environmental pressure. We discuss how genome evolution can be thought of as related to the physical phenomenon of annealing, and describe the sense in which genomes can be said to exhibit an analogue of information entropy. As a direct application of these ideas, we analyze the variation with ocean depth of transposons in marine microbial genomes, predicting trends that are consistent with recent observations using metagenomic surveys.Comment: Accepted by Journal of Statistical Physic