<Emphasis Type="Italic">Drosophila</Emphasis><Emphasis Type="Italic">P</Emphasis> transposons of the urochordata <Emphasis Type="Italic">Ciona intestinalis</Emphasis>

P transposons belong to the eukaryotic DNA transposons, which are transposed by a cut and paste mechanism using a P-element-coded transposase. They have been detected in Drosophila, and reside as single copies and stable homologous sequences in many vertebrate species. We present the P elements Pcin1, Pcin2 and Pcin3 from Ciona intestinalis, a species of the most primitive chordates, and compare them with those from Ciona savignyi. They showed typical DNA transposon structures, namely terminal inverted repeats and target site duplications. The coding region of Pcin1 consisted of 13 small exons that could be translated into a P-transposon-homologous protein. C. intestinalis and C. savignyi displayed nearly the same phenotype. However, their P elements were highly divergent and the assumed P transposase from C. intestinalis was more closely related to the transposase from Drosophila melanogaster than to the transposase of C. savignyi. The present study showed that P elements with typical features of transposable DNA elements may be found already at the base of the chordate lineage. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Does Virus-Induced Lysis Contribute Significantly to Bacterial Mortality in the Oxygenated Sediment Layer of Shallow Oxbow Lakes?

Despite the recognition that viruses are ubiquitous components of aquatic ecosystems, the number of studies on viral abundance and the ecological role of viruses in sediments is scarce. In this investigation, the interactions between viruses and bacteria were studied in the oxygenated silty sediment layer of a mesotrophic oxbow lake. A long-term study (13 months) and a diel study revealed that viruses are a numerically important and dynamic component of the microbial community. The abundance and decay rates ranged from 4.3 × 10⁹ to 7.2 × 10⁹ particles ml of wet sediment⁻¹ and from undetectable to 22.2 × 10⁷ particles ml⁻¹ h⁻¹, respectively, and on average the values were 2 orders of magnitude higher than the values for the overlying water. In contrast to our expectations, viruses did not contribute significantly to the bacterial mortality in the sediment, since on average only 6% (range, 0 to 25%) of the bacterial secondary production was controlled by viruses. The low impact of viruses on the bacterial community may be associated with the quantitatively low viral burden that benthic bacteria have to cope with compared to the viral burden with which bacterial assemblages in the water column are confronted. The virus-to-bacterium ratio of the sediment varied between 0.9 and 3.2, compared to a range of 5.0 to 12.4 obtained for the water column. We speculate that despite high numbers of potential hosts, the possibility of encountering a host cell is limited by the physical conditions in the sediment, which is therefore not a favorable environment for viral proliferation. Our data suggest that viruses do not play an important role in the processing and transfer of bacterial carbon in the oxygenated sediment layer of the environment investigated.     

Variability and predictability of the empirical conversion factor for converting 3H-thymidine uptake into bacterial carbon production for a eutrophic lake

To assess the variability and predictability of the empiricalconversion factor (CF) for converting the uptake of ³H-thymidine(TDR) to bacterial carbon production rates in eutrophic environments,we performed 11 dilution culture experiments and results wererelated to a set of important concomitantly recorded environmentalvariables. TDR incorporation data from a field study were thenconverted to carbon production with the established empiricalCF and a theoretical CF and compared to production estimatesderived from leucine incorporation. Mean empirical CF variedbetween 0.5 and 7.0 x 10⁶ cells (pmol TDR)^–1 over theyear and showed highly significant negative correlation withTDR incorporation rate and a highly significant positive correlationto temperature. Values of carbon production derived with thevariable empirical CF were lower than the values obtained bythe use of the theoretical CF of 1 x 10⁶ cells (pmol TDR)^–1.They showed less seasonal variation than values obtained byleucine incorporation, and periods of uncoupling were observed.However, when the empirical CF was calculated from the multipleregression equation including TDR incorporation and temperature,the resulting carbon production rates showed a high correspondencewith the leucine-derived production rates. Results of the analyseswere interpreted as an indication that under favourable conditions(resulting in high TDR incorporation) bacteria may be able tooptimize DNA duplication over protein synthesis as a possiblestrategy to persist and to maintain their potential to divideunder limiting conditions (e.g. decrease in temperature andsubstrate availability). In unfavourable conditions (resultingin low incorporation rates), bacteria may then use already producedDNA copies for rapid growth, when the environmental conditionsturn favourable again. Thus, an experimental set-up causingnutrient enrichment of the sampled water by autoclaving andfiltering, as generally used for dilution culture experiments,does not always reflect in situ situations, especially duringperiods of low nutrient concentrations.     

How many damaged corals in Red Sea reef systems? A quantitative survey

Quantitative coral damage assessment by means of line transects was performed in several northern Red Sea coral reef sites in Israel (Eilat) and Egypt (Hurghada area). Reefs with high and low visitor frequency were compared. For both reef systems, breakage was found to be the most common damage category, being significantly higher on highly frequented reefs. Also, all observed damage (breakage, tissue loss, algal overgrowth) was most frequent within the first ten meters depth. A significant difference in the amount of corals overgrown by algae was found on the reefs near Hurghada as compared to all other reefs. Algal overgrowth was correlated with the occurrence of tissue loss and breakage, being considered as a consequence of pollution or the former damage types. In all cases of damage, Acropora was the most frequently affected genus, while Millepora dichotoma was the most affected species.     

Development of the bacterial compartment along the Danube River: a continuum despite local influences

Microbial food webs dominate heterotrophic food webs in large rivers with bacterial metabolism being a key component of carbon processing. Thus, analysis of bacterial population dynamics is critical to understanding patterns and mechanisms of material cycling and energy fluxes in large rivers. Within the frame of the Joint Danube Survey (JDS) 2007, the longitudinal development of the natural bacterial community in the Danube in terms of bacterial numbers, morphotype composition, and heterotrophic production of the suspended and particle-attached fractions was followed at a fine spatial resolution of approximately 30 km for the first time in such a large river along a 2,600-km stretch. Twenty-one major tributaries and branches were also included. This allowed us to investigate whether bacterial standing stock and production undergo continuous, linear changes or whether discontinuities and local processes like the merging of tributaries or the potential impact of sewage input drive the bacterial population in the Danube. The presented investigation revealed surprising continuous patterns of changes of bacterial parameters along the Danube River. Despite the presence of impoundments or hydropower plants, large municipalities, and the discharge of large tributaries, most bacterial parameters (standing stock, morphotype succession, and attached bacterial production) developed gradually, indicating that mainly broad-scale drivers and not local conditions shape and control the bacterial community in the midstream of this large river. As most important broad-scale drivers, nutrients (inorganic and organic) and changes in particle concentrations were identified. These data are also in remarkable accordance with the patterns of changes of the genetic bacterial community composition, observed during the first JDS (2001) 6 years before. In contrast, bacterial activity did not follow a continuous trend and was mainly controlled by the input of sewage from large cities in the middle section, leading to a bloom of phytoplankton. The observed patterns and the comparison between the Danube, its tributaries and other large rivers worldwide indicate that the bacterial community in rivers has a powerful indicator function for estimating the ecological status of large river ecosystems once enough information has been collected at various temporal and spatial scales.     

Bacterial lipolytic activity in a hypertrophic dead arm of the river Danube in Vienna

The kinetic parameters of lipase, bacterial secondaryproduction (BSP) and bacterial numbers (BN) were determined fortnightlyduringthe development of the summer phytoplankton bloom at twostationsof Alte Donau, a hypertrophic stagnant dead arm of the riverDanubein Vienna. Until the middle of August we observed a gradualincrease in lipase activity as well as BN and BSP rates tothe maximum of 19.9 nmol l^–1 h^–1,4.5×10⁹cells l^–1 and 8.1 g C l^–1 h^–1,respectively. Atthe end of August and during September we found a markeddecreasein all bacterial parameters, coinciding with a progressingincreaseof chlorophyll a concentrations at both sampling sites. Themaximalvalues of lipase V^max were determined in the bottom waterlayer (avg. 13.7±6.5 nmol l^–1 h^–1) probablyowingto the predominating importance of polymeric matter in thesubstrate pool for microheterotrophs in this water zone.Differential filtration experiments showed that 20.1% to56.3% ofthe total lipase activity and 4.2% to 9.0% of the totalbacterialnumbers in Alte Donau water samples occurred in 0.2-mfiltrate. Further experiments indicated that the highcontributionto lipase activity in the 0.2-m filtrate was rather dueto thepresence of 0.2 m filterable bacteria than to solubleenzymemolecules. Moreover, we observed higher bacterial lipaseactivityin 0.2 m filtrate than in unfiltered samples. Thepossibleinfluence of limiting factors on the metabolism of insitubacteria is discussed.     

Contribution of virus-induced lysis and protozoan grazing to benthic bacterial mortality estimated simultaneously in microcosms

In contrast to the water column, the fate of bacterial production in freshwater sediments is still a matter of debate. Thus, the importance of virus-induced lysis and protozoan grazing of bacteria was investigated for the first time simultaneously in a silty sediment layer of a mesotrophic oxbow lake. Microcosms were installed in the laboratory in order to study the dynamics of these processes over 15 days. All microbial and physicochemical parameters showed acceptable resemblance to field data observed during a concomitant in situ study, and similar conclusions can be drawn with respect to the quantitative impact of viruses and protozoa on the bacterial compartment. Viral decay rates ranged from undetectable to 0.078 h⁻¹ (average, 0.033 h⁻¹), and the control of bacterial production from below the detection limit to 36% (average, 12%). The contribution of virus-induced lysis of bacteria to the dissolved organic matter pool as well as to benthic bacterial nutrition was low. Ingestion rates of protozoan grazers ranged from undetectable to 24.7 bacteria per heterotrophic nanoflagellate (HNF) per hour (average, 4.8 bacteria HNF⁻¹ h⁻¹) and from undetectable to 73.3 bacteria per ciliate per hour (average, 11.2 bacteria ciliate⁻¹ h⁻¹). Heterotrophic nanoflagellate and ciliates together cropped up to 5% (average, 1%) of bacterial production. The viral impact on bacteria prevailed over protozoan grazing by a factor of 2.5–19.9 (average, 9.5). In sum, these factors together removed up to 36% (average, 12%) of bacterial production. The high number of correlations between viral and protozoan parameters is discussed in view of a possible relationship between virus removal and the presence of protozoan grazers.     

Effects of Deposit-Feeding Macrofauna on Benthic Bacteria,Viruses, and Protozoa in a Silty Freshwater Sediment

In microcosm experiments, we simultaneously tested the effects of increased numbers of deposit-feeding macrofauna (chironomids, oligochaetes and cladocerans) on the standing stock, activities and interactions of heterotrophic bacteria, viruses, and bacterivorous protozoa (heterotrophic nanoflagellates and ciliates) in the aerobic layer of a silty littoral freshwater sediment. On average, bacterial secondary production was stimulated between 11 and 29% by all macrofaunal groups compared to control experiments without macrofauna addition. Bacterial standing stock increased significantly by 8 and 13% in case of chironomids and cladocerans, respectively. Oligochaetes and chironomids produced significant negative effects on viral abundance while the results with cladocerans were inconsistent. The addition of oligochaetes and chironomids resulted in a significant decrease by on average 68 and 32% of viral decay rates, respectively, used as a measure of viral production. The calculated contribution of virus-induced lysis to benthic bacterial mortality was low, with 2.8 to 11.8% of bacterial secondary production, and decreased by 39 to 81% after the addition of macrofauna compared to the control. The abundances of heterotrophic nanoflagellates were significantly reduced by 20% by all tested macrofauna groups, while ciliates showed inconsistent results. The importance of heterotrophic nanoflagellate grazing on benthic bacteria was very low (<1% of bacterial secondary production) and was further reduced by elevated numbers of macrofauna. Thus, the selected deposit feeding macrofauna groups seem to have several direct and indirect and partly antagonistic effects on the benthic bacterial compartment through the enhancement of bacterial production and the reduction of virus-induced cell lysis and protozoan grazing.     

Carbon fluxes in the microbial loop: Comments

The heterotrophic bacterial community of oceanic aggregates which mediates particle solubilization, displays features (low carbon demand and low turnover) that are difficult to reconcile with the observed high enzyme activities and cell numbers. Hypotheses are proposed to explain this discrepancy. Furthermore, production of both free and attached bacteria may have been underestimated by neglecting the ultramicrobacteria (UMB). Production of UMB may represent up to 28% of the total bacterial production.