Ulrike R. Fischer

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

ABSTRACT 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.

Vibrio calviensis sp. nov., a halophilic, facultatively oligotrophic 0.2 microm-fiIterabIe marine bacterium.

A gram-negative, facultatively anaerobic, straight to slightly curved rod-shaped bacterium (RE35F/12T) sensitive to vibriostatic agent O/129 was previously isolated from sea water (Western Mediterranean Sea, Bay of Calvi, Corsica, France) by 0.2 microm-membrane filtration. Strain RE35/F12T (= CIP 107077T = DSM 14347T) was facultatively oligotrophic, halophilic, required Na+ for growth and produced acid but no gas from D-glucose under anaerobic conditions. Comparative 165 rRNA gene-sequence analyses demonstrated that the bacterium is most closely related (94.3%) to Vibrio scophthalmi. Similarities to the sequences of all other established Vibrio species ranged from 93.6% (with Vibrio aestuarianus) to 90.7% (with Vibrio rumoiensis). Strain RE35/F12T occupies a distinct phylogenetic position; this is similar to the case of Vibrio hollisae, because RE35F/12T represents a relatively long subline of descent sharing a branching point with the outskirts species V. hollisae. The G+C content of the DNA was 49.5 mol%. Ubiquinone Q-8 was the main respiratory lipoquinone, and 16:1omega9cis, 16:0 and 18:1trans9, cis11 were the major cellular fatty acids, 16:1omega9cis being predominant. The polyamine pattern was characterized by the presence of the triamine sym-norspermidine. On the basis of the polyphasic information summarized above, a new Vibrio species is described for which the name Vibrio calviensis sp. nov. is proposed.

Benthic and Pelagic Viral Decay Experiments: a Model-Based Analysis and Its Applicability

ABSTRACT The viral decay in sediments, that is, the decrease in benthic viral concentration over time, was recorded after inhibiting the production of new viruses. Assuming that the viral abundance in an aquatic system remains constant and that viruses from lysed bacterial cells replace viruses lost by decay, the decay of viral particles can be used as a measure of viral production. Decay experiments showed that this approach is a useful tool to assess benthic viral production. However, the time course pattern of the decay experiments makes their interpretation difficult, regardless of whether viral decay is determined in the water column or in sediments. Different curve-fitting approaches (logarithmic function, power function, and linear regression) to describe the time course of decay experiments found in the literature are used in the present study and compared to a proposed “exponential decay” model based on the assumption that at any moment the decay is proportional to the amount of viruses present. Thus, an equation of the form dVA/dt = −k × VA leading to the time-integrated form VAt = VA0 × e−k×t was used, where k represents the viral decay rate (h−1), VAt is the viral abundance (viral particles ml−1) at time t (h), and VA0 is the initial viral abundance (viral particles ml−1). This approach represents the best solution for an accurate curve fitting based on a mathematical model for a realistic description of viral decay occurring in aquatic systems. Decay rates ranged from 0.0282 to 0.0696 h−1 (mean, 0.0464 h−1). Additionally, a mathematical model is presented that enables the quantification of the viral control of bacterial production. The viral impact on bacteria based on decay rates calculated from the different mathematical approaches varied widely within one and the same decay experiment. A comparison of the viral control of bacterial production in different aquatic environments is, therefore, improper when different mathematical formulas are used to interpret viral decay experiments.

Benthic Bacterial Production and Protozoan Predation in a Silty Freshwater Environment

The interrelation of heterotrophic bacteria with bacterivorous protists has been widely studied in pelagic environments, but data on benthic habitats, especially in freshwater systems, are still scarce. We present a seasonal study focusing on bacterivory by heterotrophic nanoflagellates (HNF) and ciliates in the silty sediment of a temperate macrophyte-dominated oxbow lake. From January 2001 to February 2002 we monitored the standing stock of bacteria and protozoa, bacterial secondary production (BSP, 3H-thymidine, and 14C-leucine incorporation), and grazing rates of HNF and ciliates on bacteria (FLB uptake) in the oxic sediment of the investigated system. BSP ranged from 470 to 4050 µg C L−1 wet sediment h−1. The bacterial compartment turned out to be highly dynamic, indicated by population doubling times (0.6–10.0 d), which were comparable to those in the water column of the investigated system. Yet, the control mechanisms acting upon the bacterial population led to a relative constancy of bacterial standing stock during a year. Ingestion rates of protozoan grazers were 0–20.0 bacteria HNF−1 h−1 and 0–97.6 bacteria ciliate−1 h−1. HNF and ciliates together cropped 0–14 (mean 4)% of BSP, indicating that they did not significantly contribute to benthic bacterial mortality during any period of the year. The low impact of protozoan grazing was due to the low numbers of HNF and ciliates in relation to bacteria (1.8–3.5 × 104 bacteria HNF−1, 0.9–3.1 × 106 bacteria ciliate−1). Thus, grazing by HNF and ciliates could be ruled out as a parameter regulating bacterial standing stock or production in the sediment of the investigated system, but the factors responsible for the limitation of benthic protistan densities and the fate of benthic BSP remained unclear.

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.

Comparative study of the abundance of various bacterial morphotypes in an eutrophic freshwater environment determined by AODC and TEM.

Transmission electron microscopy (TEM) and epifluorescence microscopy were used to obtain comparative measurements of total bacterial counts, and to enumerate abundances of various bacterial morphotypes in an eutrophic freshwater habitat. Although particulate matter would have been expected to interfere with counting by obscuring large areas of the electron microscope grids, estimates of total bacterial abundance made by TEM were on average 1.2 times greater than those obtained using the acridine orange direct counting method (AODC). However, the precision of the AODC method was greater than that for TEM, with a coefficient of variation (C.V.) of 4.0% versus 8.8%, respectively. The total bacterial abundance ranged from 1.1 to 3.2 x 10(6) ml(-1). As was the case for total bacterial density, the numbers of rod- and vibrio-shaped cells were lower when counted in the epifluorescence microscope, indicating the presence of potential starvation forms or ultramicrobacteria. Greatest variations in counts made by TEM and AODC were found for filamentous and coccoid bacteria. Counts of filamentous bacteria made by AODC were only about half of those detected by TEM. In contrast, cocci were on average 1.5 times greater when counted by AODC compared to TEM estimates. Both counting differences were probably caused by the morphology and low density of filamentous and coccoid bacteria (1.7 and 1.4 x 10(5) ml(-1), respectively), which led to an uneven distribution on polycarbonate filters as well as on electron microscope grids. Besides, cocci might easily be mistaken for large viral particles when counted by AODC. Hence, the study supports the use of TEM over AODC for obtaining accurate estimates of total bacterial abundance and especially bacterial morphotypes in natural waters.

Growth Response of Soda Lake Bacterial Communities to Simulated Rainfall

Moderately saline soda lakes harbor extremely abundant and fast growing bacterial communities. An interesting phenomenon of an explosive bacterial growth in shallow soda lakes in Eastern Austria after dilution with rainwater, concomitantly with a significant decrease in temperature was observed in a former study. In the present study, we tried to identify the factors being responsible for this enhanced bacterial growth in laboratory batch cultures. Three experiments were performed with water taken from two different lakes at different seasons. Natural soda lake water was diluted with distilled water, artificial lake water, sterile filtered soda lake water, and grazer-free water to test (1) for the influence of compatible solutes released to the environment and reduced salt stress after osmotic down-shock, (2) for the influence of nutrients, which may be washed in from the dry areas of the lake bottom after rainfall and (3) for the decrease of grazing pressure due to dilution. The potential influence of (4) viruses was indirectly deduced. The response of the bacterial community to the manipulations was measured by changes in bacterial numbers, the incorporation of 3H-leucine and the concomitant determination of the amount of 3H-leucine uptaking bacteria by microautoradiography. The influence of the environmental factors enhancing bacterial growth after a simulated rainfall event showed variations between the lakes and over the seasons. The addition of nutrients was, in all experiments, the main factor triggering bacterial growth. The decrease in grazing pressure and viral lysis after dilution was of significant importance in two of three experiments. In the experiment with the highest salinity, we could show that either compatible solutes released after osmotic down-shock and used as a source of nutrients for the soda lake bacterial populations or reduced salt stress were most probably responsible for the observed marked enhancement of bacterial growth.

Dynamics of natural prokaryotes, viruses, and heterotrophic nanoflagellates in alpine karstic groundwater

Seasonal dynamics of naturally occurring prokaryotes, viruses, and heterotrophic nanoflagellates in two hydro‐geologically contrasting alpine karst springs were monitored over three annual cycles. To our knowledge, this study is the first to shed light on the occurrence and possible interrelationships between these three groups in karstic groundwater. Hydrological and microbiological standard indicators were recovered simultaneously in order to estimate surface influence, especially during rainfall events. Data revealed a strong dependence of the microbial communities on the prevailing hydrological situation. Prokaryotic numbers averaged 5.1 × 107 and 1.3 × 107 cells L−1, and heterotrophic nanoflagellate abundance averaged 1.1 × 104 and 3 × 103 cells L−1 in the limestone spring type (LKAS2) and the dolomitic spring type (DKAS1), respectively. Viral abundance in LKAS2 and DKAS1 averaged 9.4 × 108 and 1.1 × 108 viruses L−1. Unlike in DKAS1, the dynamic spring type LKAS2 revealed a clear difference between base flow and high discharge conditions. The virus‐to‐prokaryotes ratio was generally lower by a factor of 2–3, at higher average water residence times. Furthermore, the high prokaryotes‐to‐heterotrophic nanoflagellate ratios, namely about 4700 and 5400 for LKAS2 and DKAS1, respectively, pointed toward an uncoupling of these two groups in the planktonic fraction of alpine karstic aquifers.