Codon usage in the vertebrate hemoglobins and its implications

A study of codon usage in vertebrate hemoglobins revealed an evolutionary trend toward elevated numbers of CpG codon boundary pairs in mammalian hemoglobin alpha genes. Selection for CpG codon boundaries countering the generally observed CpG suppression is strongly suggested by these data. These observations parallel recently published experimental results that indicate that constitutive expression of the human alpha-globin gene appears to be determined by regulatory information encoded within the structural gene. The possibility is raised that, in the absence of selection, CpG decay can be used to date the evolutionary origin of a mammalian alpha pseudogene from its active alpha gene.      

Are viruses important partners in pelagic fend webs?

Viruses have been assumed to play a rather negligible role as partners in microbial food web dynamics. However, recent discoveries suggest that the rate of virally induced lysis of marine microbial populations may be significant. This, in turn, may have important consequences for the developing conceptual framework of the microbial food web.     

Trade-Offs between Competition and Defense Specialists among Unicellular Planktonic Organisms: the “Killing the Winner” Hypothesis Revisited

Summary: A trade-off between strategies maximizing growth and minimizing losses appears to be a fundamental property of evolving biological entities existing in environments with limited resources. In the special case of unicellular planktonic organisms, the theoretical framework describing the trade-offs between competition and defense specialists is known as the “killing the winner” hypothesis (KtW). KtW describes how the availability of resources and the actions of predators (e.g., heterotrophic flagellates) and parasites (e.g., viruses) determine the composition and biogeochemical impact of such organisms. We extend KtW conceptually by introducing size- or shape-selective grazing of protozoans on prokaryotes into an idealized food web composed of prokaryotes, lytic viruses infecting prokaryotes, and protozoans. This results in a hierarchy analogous to a Russian doll, where KtW principles are at work on a lower level due to selective viral infection and on an upper level due to size- or shape-selective grazing by protozoans. Additionally, we critically discuss predictions and limitations of KtW in light of the recent literature, with particular focus on typically neglected aspects of KtW. Many aspects of KtW have been corroborated by in situ and experimental studies of isolates and natural communities. However, a thorough test of KtW is still hampered by current methodological limitations. In particular, the quantification of nutrient uptake rates of the competing prokaryotic populations and virus population-specific adsorption and decay rates appears to be the most daunting challenge for the years to come.     

Bacterial community composition in an Arctic phytoplankton mesocosm bloom: the impact of silicate and glucose

In order to study interactions between microorganisms at different nutrient conditions in an arctic environment, a mesocosm experiment was performed in Kongsfjorden, Svalbard (79°N). A phytoplankton bloom was initiated by daily additions of mineral nutrients (ammonium and phosphate) to all mesocosm units. The addition of silicate and glucose, forming a factorial design (+Si/+C, +Si/−C, −Si/+C, −Si/−C), was intended to produce different types of growth rate limitation for the bacterial community. We here focus on the response in bacterial community composition to different nutrient situations. Phytoplankton, bacteria and viruses were enumerated by flow cytometry, while denaturing gradient gel electrophoresis (DGGE) was used to track changes in the bacterial community composition. Our results showed that both glucose and silicate addition affected the bacterial community composition, with the largest effect from glucose. The initial increase in bacterial abundance was most pronounced in the glucose units. After silicate addition, highest bacterial abundance was observed in the silicate treatments where mineral nutrient competition by diatoms was expected to be highest. The major effect of glucose was expressed by the significant separation of the +C and the −C samples at the end of the experiment, while silicate addition resulted in a more stable bacterial community structure. In the unit, given both silicate and glucose, the diatoms were totally outcompeted by the bacterial community. The competitive success of the heterotrophic bacteria in C-replete situations allows the conclusion that the bacteria were not more negatively affected by low temperatures than phytoplankton.     

Bacterioplankton groups involved in the uptake of phosphate and dissolved organic phosphorus in a mesocosm experiment with P-starved Mediterranean waters

The use of inorganic phosphate (Pi) and dissolved organic phosphorus (DOP) by different bacterial groups was studied in experimental mesocosms of P-starved eastern Mediterranean waters in the absence (control mesocosms) and presence of additional Pi (P-amended mesocosms). The low Pi turnover times in the control mesocosms and the increase in heterotrophic prokaryotic abundance and production upon Pi addition confirmed that the bacterial community was originally P-limited. The bacterioplankton groups taking up Pi and DOP were identified by means of microautoradiography combined with catalysed reporter deposition fluorescence in situ hybridization. Incubations with leucine were also performed for comparative purposes. All the probe-identified groups showed a high percentage of cells taking up Pi and DOP in the control, P-limited, mesocosms throughout the experiment. However, in response to Pi addition two contrasting scenarios in Pi use were observed: (i) on day 1 of the experiment Pi addition caused a clear reduction in the percentage of SAR11 cells taking up Pi, whereas Gammaproteobacteria, Roseobacter and Bacteroidetes showed similar percentages to the ones in the control mesocosms and (ii) on day 4 of the experiment, probably when the bacterial community had fully responded to the P input, all the probe-identified groups showed low percentages of cells taking up the substrate as compared with the control mesocosms. These differences are likely related to different P requirements among the bacterial groups and point out to the existence of two contrasting strategies in P use.     

Mg2+ as an indicator of nutritional status in marine bacteria

Cells maintain an osmotic pressure essential for growth and division, using organic compatible solutes and inorganic ions. Mg²⁺, which is the most abundant divalent cation in living cells, has not been considered an osmotically important solute. Here we show that under carbon limitation or dormancy native marine bacterial communities have a high cellular concentration of Mg²⁺ (370–940 m) and a low cellular concentration of Na⁺ (50–170 m). With input of organic carbon, the average cellular concentration of Mg²⁺ decreased 6–12-fold, whereas that of Na⁺ increased ca 3–4-fold. The concentration of chlorine, which was in the range of 330–1200 m and was the only inorganic counterion of quantitative significance, balanced and followed changes in the concentration of Mg²⁺+Na⁺. In an osmotically stable environment, like seawater, any major shift in bacterial osmolyte composition should be related to shifts in growth conditions, and replacing organic compatible solutes with inorganic solutes is presumably a favorable strategy when growing in carbon-limited condition. A high concentration of Mg²⁺ in cells may also serve to protect and stabilize macromolecules during periods of non-growth and dormancy. Our results suggest that Mg²⁺ has a major role as osmolyte in marine bacteria, and that the [Mg²⁺]/[Na⁺] ratio is related to its physiological condition and nutritional status. Bacterial degradation is a main sink for dissolved organic carbon in the ocean, and understanding the mechanisms limiting bacterial activity is therefore essential for understanding the oceanic C-cycle. The [Mg²⁺]/[Na⁺]-ratio in cells may provide a physiological proxy for the transitions between C-limited and mineral nutrient-limited bacterial growth in the ocean''s surface layer.     

Changes in Morphology and Elemental Composition of <Emphasis Type="Italic">Vibrio splendidus</Emphasis> Along a Gradient from Carbon-limited to Phosphate-limited Growth

We examined morphology, elemental composition (C, N, P), and orthophosphate-uptake efficiency in the marine heterotrophic bacterium Vibrio splendidus grown in continuous cultures. Eight chemostats were arranged along a gradient of increasing glucose concentrations in the reservoirs, shifting the limiting factor from glucose to phosphate. The content of carbon, nitrogen, and phosphorus was measured in individual cells by x-ray microanalysis using a transmission electron microscope (TEM). Cell volumes (V) were estimated from length and width measurements of unfixed, air-dried cells in TEM. There was a transition from coccoid cells in C-limited cultures toward rod-shaped cells in P-limited cultures. Cells in P-limited cultures with free glucose in the media were significantly larger than cells in glucose-depleted cultures (P < 0.0001). We found functional allometry between cellular C-, N-, and P content (in femtograms) and V (in cubic micrometers) in V. splendidus (C = 224 × V ^0.89, N = 52.5 × V ^0.80, P = 2 × V ^0.65); i.e., larger bacteria had less elemental C, N, and P per V than smaller cells, and also less P relative to C. Biomass-specific affinity for orthophosphate uptake in large P-limited V. splendidus approached theoretical maxima predicted for uptake limited by molecular diffusion toward the cells. Comparing these theoretical values to respective values for the smaller, coccoid, C-limited V. splendidus indicated, contrary to the traditional view, that large size did not represent a trade-off when competing for the non-C-limiting nutrients.     

Viral control of bacterial biodiversity – evidence from a nutrient-enriched marine mesocosm experiment

We demonstrate here results showing that bottom-up and top-down control mechanisms can operate simultaneously and in concert in marine microbial food webs, controlling prokaryote diversity by a combination of viral lysis and substrate limitation. Models in microbial ecology predict that a shift in the type of bacterial growth rate limitation is expected to have a major effect on species composition within the community of bacterial hosts, with a subsequent shift in the composition of the viral community. Only moderate effects would, however, be expected in the absolute number of coexisting virus–host pairs. We investigated these relationships in nutrient-manipulated systems, under simulated in situ conditions. There was a strong correlation in the clustering of the viral and bacterial community data supporting the existence of an important link between the bacterial and viral communities. As predicted, the total number of viral populations was the same in all treatments, while the composition of the viral community varied. Our results support the theoretical prediction that there is one control mechanism for the number of niches for coexisting virus–host pairs (top-down control), and another mechanism that controls which virus–host pairs occupy these niches (bottom-up control).     

Dynamics of chemostat culture:the effect of a delay in cell response

The effect of introducing a delay between a change in concentration of limiting nutrient and the response in division rate of the population is investigated. It is shown that this might or might not introduce a delay in the control of the chemostat system, depending upon how the uptake rate is assumed to double during the cell cycle. An area in the parameter space where autonomous oscillations will occur for one specific model is found analytically. This result is confirmed by computer simulations.