Longitudinal Changes in the Bacterial Community Composition of the Danube River: a Whole-River Approach

The Danube River is the second longest river in Europe, and its bacterial community composition has never been studied before over its entire length. In this study, bacterial community composition was determined by denaturing gradient gel electrophoresis (DGGE) analysis of PCR-amplified portions of the bacterial 16S rRNA gene from a total of 98 stations on the Danube River (73 stations) and its major tributaries (25 stations), covering a distance of 2,581 km. Shifts in the bacterial community composition were related to changes in environmental conditions found by comparison with physicochemical parameters (e.g., temperature and concentration of nutrients) and the concentration of chlorophyll a (Chl a). In total, 43 distinct DGGE bands were detected. Sequencing of selected bands revealed that the phylotypes were associated with typical freshwater bacteria. Apparent bacterial richness in the Danube varied between 18 and 32 bands and correlated positively with the concentration of P-PO₄ (r = 0.56) and negatively with Chl a (r = −0.52). An artificial neural network-based model explained 90% of the variation of apparent bacterial richness using the concentrations of N-NO₂ and P-PO₄ and the distance to the Black Sea as input parameters. Between the cities of Budapest and Belgrade, apparent bacterial richness was significantly lower than that of other regions of the river, and Chl a showed a pronounced peak. Generally, the bacterial community composition developed gradually; however, an abrupt and clear shift was detected in the section of the phytoplankton bloom. Large impoundments did not have a discernible effect on the bacterial community of the water column. In conclusion, the riverine bacterial community was largely influenced by intrinsic factors.     

Bacterial metabolism in the River Danube: parameters influencing bacterial production

1. Microbial parameters were determined at five sampling sites in the River Danube up-and downstream of Vienna, Austria, twice monthly over an annual cycle. Bacterial production (BP) was estimated from thymidine and leucine incorporations; additionally, the effect of turbulence on BP and the conversion factors for converting incorporation rates into bacterial cell production were determined using the cumulative approach. 2. BP under turbulent conditions was not significantly different from that under stagnant conditions. For thymidine, a mean annual conversion factor of 3.2 ± 10¹⁸ cells mol^?1 thymidine incorporated was calculated. For leucine, the corresponding factor was 0.07 ± 10¹⁸ cells mol^?1 leucine. Average annual BP calculated by thymidine incorporation was significantly higher than BP calculated from leucine incorporation and ranged from 47.2 to 77.5 μg C 1-^?1 day^?1 depending on the tracer and the conversion factor used. 3. Bacterial growth rates ranged from 0.1 day^?1 during winter to 1.7 day^?1 in the summer. A strong correlation was found between temperature as well as chlorophyll a and bacterial growth when temperature was greater than 5 °C; a major spring phytoplankton bloom at a temperature below 5 °C did not increase BP. 4. Dissolved organic carbon (DOC) concentrations varied between 2 and 7.2 mg C 1-^?1 and comprised between 50 and 92% of the total organic carbon pool in the River Danube, Based on the DOC concentration and an assumed bacterial growth yield of 20% we calculated mean DOC turnover times of around 60 days in the winter and less than 8 days during the summer.     

Longitudinal changes in the benthic bacterial community of the Mahoning River (Ohio, U.S.A.)

To examine spatial differences in bacterial communities along the Mahoning River in Northeast Ohio (USA), sediment samples were collected on two dates from three sites. Downstream portions (sites 2 and 3, in this study) of the Mahoning River have been highly impacted by human activities. Two approaches were used to characterize the bacterial community: fluorescent in situ hybridization (FISH) with taxon specific probes and denaturing gradient gel electrophoresis (DGGE). Bacterial numbers (per g ash free dry mass), based on staining with DAPI (4′, 6-diamidino-2-phenylindole) or FISH with Domain Bacteria, Acinetobacter calcoaceticus or Pseudomonas putida-specific probes, were higher at the most upstream site (site 1) compared to the more disturbed downstream sites (sites 2 and 3). In addition, the number of bands based on DGGE was higher at the upstream site (site 1) compared to the two downstream sites (2 and 3) during spring. However, in summer, the number of bands was similar among sites and the most upstream (1) and the middle site (2) had the same average number of bands. In spring, the percent similarity (based on the presence/absence of bands) among the three sites was relatively low compared to summer. In general, differences in the bacterial community were found among the sites with differing levels of anthropogenic disturbance but varied between the two dates examined.     

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.     

Zooplankton biomass and community structure in a Danube River floodplain system: effects of hydrology

1. Zooplankton density and biomass was examined in a Danube River floodplain section with highly variable hydrological dynamics. Temporal patterns were analysed to assess the effects of hydrological conditions on zooplankton community structure and the differential response of the two major zooplankton taxa, rotifers and crustaceans.
2. Calculated floodplain water age was used as an integrated parameter describing hydrological conditions and connectivity.
3. Total zooplankton biomass, crustacean biomass and crustacean species number were significantly positively related to water age. Rotifer biomass followed a hump-shaped relationship with water age, and rotifer species number decreased with increasing water age.
4. Rotifers dominated the community in periods of low to medium water ages. In periods of higher water ages the community was dominated by crustaceans.
5. We propose that the hydrological regime of floodplains is crucial for zooplankton biomass patterns and succession, through the alternation of washing-out effects, taxon-specific potential of reproduction and biological interactions. Flood events and high water levels reset the community to an early successional phase.     

Characterizing seasonal changes in physicochemistry and bacterial community composition in hyporheic sediments

The hyporheic zone of stream ecosystems is a critical habitat for microbial communities. However, the factors influencing hyporheic bacterial communities along spatial and seasonal gradients remain poorly understood. We sought to characterize patterns in bacterial community composition among the sediments of a small stream in southern Ontario, Canada. We used sampling cores to collect monthly hyporheic water and sediment microbial communities in 2006 and 2007. We described bacterial communities terminal-restriction fragment length polymorphism (TRFLP) and tested for spatial and seasonal relationships with physicochemical parameters using multivariate statistics. Overall, the hyporheic zone appears to be a DOC, oxygen, and nitrogen sink. Microbial communities were distinct from those at the streambed surface and from soil collected in the adjacent watershed. In the sediments, microbial communities were distinct between the fall, spring, and summer seasons, and bacterial communities were more diverse at streambed surface and near-surface sites compared with deeper sites. Moreover, bacterial communities were similar between consecutive fall seasons despite shifting throughout the year, suggesting recurring community assemblages associated with season and location in the hyporheic zone. Using canonical correspondence analysis, seasonal patterns in microbial community composition and environmental parameters were correlated in the following way: temperature was related to summer communities; DOC (likely from biofilm and allochthonous inputs) influenced most fall communities; and nitrogen associated strongly with winter and spring communities. Our results also suggest that labile DOC entering the hyporheic zone occurred in concert with shifts in the bacterial community. Generally, seasonal patterns in hyporheic physicochemistry and microbial biodiversity remain largely unexplored. Therefore, we highlight the importance of seasonal and spatial resolution when assessing surface- and groundwater interactions in stream ecosystems.     

Shrub encroachment is associated with changes in soil bacterial community composition in a temperate grassland ecosystem

Plant and Soil - The growth and root morphology responses to soil phosphorus (P) fertility by five cultivars of Trifolium subterraneum (a temperate annual pasture legume) were examined to assess...     

Flagellate predation on a bacterial model community: interplay of size-selective grazing, specific bacterial cell size, and bacterial community composition.

The influence of grazing by the bacterivorous nanoflagellate Ochromonas sp. strain DS on the taxonomic and morphological structures of a complex bacterial community was studied in one-stage chemostat experiments. A bacterial community, consisting of at least 30 different strains, was fed with a complex carbon source under conditions of low growth rate (0.5 day(-1) when nongrazed) and low substrate concentration (9 mg liter(-1)). Before and after the introduction of the predator, the bacterial community composition was studied by in situ techniques (immunofluorescence microscopy and fluorescent in situ hybridization), as well as by cultivation on agar media. The cell sizes of nonspecifically stained and immunofluorescently labeled bacteria were measured by image analysis. Grazing by the flagellate caused a bidirectional change in the morphological structure of the community. Medium-size bacterial cells, which dominated the nongrazed community, were largely replaced by smaller cells, as well as by cells contained in large multicellular flocs. Cell morphological changes were combined with community taxonomic changes. After introduction of the flagellate, the dominating strains with medium-size cells were largely replaced by single-celled strains with smaller cells on the one hand and, on the other hand, by Pseudomonas sp. strain MWH1, which formed the large, floc-like forms. We assume that size-selective grazing was the major force controlling both the morphological and the taxonomic structures of the model community.     

Matrix composition and community structure analysis of a novel bacterial pyrite leaching community

Here we describe a novel bacterial community that is embedded in a matrix of carbohydrates and bio/geochemical products of pyrite (FeS₂) oxidation. This community grows in stalactite-like structures – snottites – on the ceiling of an abandoned pyrite mine at pH values of 2.2–2.6. The aqueous phase in the matrix contains 200 mM of sulfate and total iron concentrations of 60 mM. Micro-X-ray diffraction analysis showed that jarosite [(K,Na,H₃O)Fe₃(SO₄)₂(OH)₆] is the major mineral embedded in the snottites. X-ray absorption near-edge structure experiments revealed three different sulfur species. The major signal can be ascribed to sulfate, and the other two features may correspond to thiols and sulfoxides. Arabinose was detected as the major sugar component in the extracellular polymeric substance. Via restriction fragment length polymorphism analysis, a community was found that mainly consists of iron oxidizing Leptospirillum and Ferrovum species but also of bacteria that could be involved in dissimilatory sulfate and dissimilatory iron reduction. Each snottite can be regarded as a complex, self-contained consortium of bacterial species fuelled by the decomposition of pyrite.     

Zooplankton-mediated changes of bacterial community structure

Enclosure experiments in the mesotrophic Schöhsee in northern Germany were designed to study the impact of metazooplankton on components of the microbial food web (bacteria, flagellates, ciliates). Zooplankton was manipulated in 500-liter epilimnetic mesocosms so that either Daphnia or copepods were dominating, or metazooplankton was virtually absent. The bacterial community responded immediately to changes in zooplankton composition. Biomass, productivity, and especially the morphology of the bacteria changed drastically in the different treatments. Cascading predation effects on the bacterioplankton were transmitted mainly by phagotrophic protozoans which had changed in species composition and biomass. When Daphnia dominated, protozoans were largely suppressed and the original morphological structure of the bacteria (mainly small rods and cocci) remained throughout the experiment. Dominance of copepods or the absence of metazoan predators resulted in a mass appearance of bacterivorous protists (flagellates and ciliates). They promoted a fast decline of bacterial abundance and a shift to the predominance of morphologically inedible forms, mainly long filaments. After 3 days they formed 80–90% of the bacterial biomass. The results indicate that metazooplankton predation on phagotrophic protozoans is a key mechanism for the regulation of bacterioplankton density and community structure.Correspondence to: K. Jürgens.     

Assessment of bacterial community composition in response to uranium levels in sediment samples of sacred Cauvery River

Applied Microbiology and Biotechnology - Global industrialization is a major cause of effluent discharge from industries up to alarming concentrations. Especially, uranium concentrations in water...     

Intertidal community composition along rocky shores in South-west Greenland: a quantitative approach

The intertidal communities on rocky shores are directly subjected to climatic changes in air and water temperatures and to derived effects of climate change, such as changes in freshwater run-off and ice dynamics. Global warming occurs at elevated rates in Greenland and results in changing species distributions with range expansions to the north and new species entering terrestrial habitats from the south. There is, however, no quantitative knowledge of past or present species distribution in the littoral zone of Southern Greenland, an area which represents an important gateway for northern range expansions of temperate species. This study provides baseline information on abundances of macroorganisms in the eulittoral Southern Greenland. This knowledge will pave the way for future studies on the impact of climate change and anthropogenic activities on these communities. Nine sites, situated at different exposure levels, were investigated. A total of 22 taxa were recorded, suggesting low species richness. Patellid limpets and predators such as dogwhelks, starfish and crabs were absent. Total standing stock ranged from 0 to 31,898 g m^?2. Species composition and biomasses were related to locally generated wave exposure, oceanic swells and ice scouring. The high standing stock at sheltered sites indicated that neither light, temperature nor nutrients, constrained buildup of biomass in this environment. Inshore seasonal measurements of water and air temperatures were recorded for the first time in the region, displaying low water temperatures and high variation in air temperatures, indicating lack of insulating stable sea ice in the area. Possible impacts of ongoing temperature changes are discussed based on recorded temperatures and meteorological data from the past 30 years.     

Changes in freshwater bacterial community composition during measurements of microbial and community respiration

The respiration rates of a pelagic community and of its microbialfraction (< 1.2 µm) were measured at two depths inthe oxic layer of a meromictic alpine lake (Cadagno, Switzerland)using the oxygen technique. The duration of the incubationswere 12, 24 and 55 h. Bacterioplankton abundance (DAPI counts)and composition (whole cell hybridization using 11 group-specificrRNA-targeted oligonucleotide probes) were measured during theincubations. Respiration generally increased with time, especiallyin the microbial fraction, or remained similar. This resultwas not always consistent with changes in bacterial abundanceand cell volume. The composition of the community also changedduring the incubations. The abundance of ß-Proteobacteriaincreased during the course of all the experiments. These resultsextend the previous conclusions drawn in marine environmentsto fresh waters and demonstrate that, in addition to changesin bacterial abundance, cell volume and biomass, changes inthe taxonomic composition of the bacterial community can occurduring discrete incubations of freshwater planktonic communities.     

Potamoplankton and primary productivity in the River Danube

Autochthonous production of potamoplankton has recently attracted greater interest as it was incorporated into expanded river concepts such as the flow pulse concept or the riverine productivity model (RPM). This review assembles data on primary production from the River Danube to evaluate the importance of productivity in large rivers. Results indicate positive net production in the middle reach of the river and in impoundments. These sections are characterised by favourable conditions for algal growth. Reduction in flow, reduced concentrations of suspended solids and improved under-water light result in significant increase in plankton biomass. Maximum chlorophyll concentrations were below 20 mg m^?3 in 2007 but concentrations up to 130 mg m^?3 have been recorded in the past. Since nutrients are not limiting, as in most large rivers, net primary production is largely controlled by availability of photosynthetic active radiation under water, chlorophyll-a, water depth and discharge. Hourly carbon uptake rates of 3–130 mg C m^?3 h^?1 observed in the Danube are well within the range of 0–790 mg C m^?3 h^?1 for large rivers of the world. Autochthonous autotrophic production must be regarded as an important feature of large rivers supporting the RPM concept.     

Seasonal differences in bacterial community composition following nutrient additions in a eutrophic lake

We examined the effects of nutrient amendments on epilimnetic freshwater bacteria during three distinct periods in the eutrophic Lake Mendota's seasonal cycle (spring overturn, summer stratification and autumn overturn). Microcosm treatments enriched solely with phosphorus containing compounds did not result in a large bacterial community composition (BCC) change or community activity response (assessed via alkaline phosphatase activity, APA) relative to the controls during any season. Treatments enriched with carbon‐ and nitrogen‐containing compounds resulted in a dramatic BCC change and a large APA increase in the autumn and spring seasons, but only treatments receiving carbon, nitrogen and phosphorus (CNP) exhibited similar responses in the summer season. Despite the fact that the amendments created similar CNP concentration conditions across seasons, the BCC following amendment greatly varied among seasons. 16S rRNA gene sequence analysis indicated that many common freshwater bacterial lineages from the Alpha‐ and Betaproteobacteria class and Bacteroidetes phylum were favoured following nutrient (CNP) addition, but individual taxa were generally not favoured across all seasons. Targeted quantitative PCR analysis revealed that the abundance of the Actinobacteria acIB1 cluster decreased in all microcosms during all three seasons, while the Flavobacterium aquatile (spring) and ME‐B0 (summer) clusters of Bacteroidetes increased following CNP addition. These results suggest a particular bacterial group is not universally favoured by increased nutrient loads to a lake; therefore, efforts to predict which bacteria are involved in nutrient cycling during these periods must take into account the seasonality of freshwater bacterial communities.     

Dynamics of bacterial community composition and activity during a mesocosm diatom bloom

Bacterial community composition, enzymatic activities, and carbon dynamics were examined during diatom blooms in four 200-liter laboratory seawater mesocosms. The objective was to determine whether the dramatic shifts in growth rates and ectoenzyme activities, which are commonly observed during the course of phytoplankton blooms and their subsequent demise, could result from shifts in bacterial community composition. Nutrient enrichment of metazoan-free seawater resulted in diatom blooms dominated by a Thalassiosira sp., which peaked 9 days after enrichment ( approximately 24 microg of chlorophyll a liter(-1)). At this time bacterial abundance abruptly decreased from 2.8 x 10(6) to 0.75 x 10(6) ml(-1), and an analysis of bacterial community composition, by denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA gene fragments, revealed the disappearance of three dominant phylotypes. Increased viral and flagellate abundances suggested that both lysis and grazing could have played a role in the observed phylotype-specific mortality. Subsequently, new phylotypes appeared and bacterial production, abundance, and enzyme activities shifted from being predominantly associated with the <1.0-microm size fraction towards the >1.0-microm size fraction, indicating a pronounced microbial colonization of particles. Sequencing of DGGE bands suggested that the observed rapid and extensive colonization of particulate matter was mainly by specialized alpha-Proteobacteria- and Cytophagales-related phylotypes. These particle-associated bacteria had high growth rates as well as high cell-specific aminopeptidase, beta-glucosidase, and lipase activities. Rate measurements as well as bacterial population dynamics were almost identical among the mesocosms indicating that the observed bacterial community dynamics were systematic and repeatable responses to the manipulated conditions.     

Long term functional changes within the Oligochaeta communities within the Danube River Delta,Romania

Within the Danube River delta's lakes the Oligochaeta communities comprise between 7.9% and 36.2% of the total biomass of benthic fauna. Their importance in energy flow at the ecosystem level changed in relation to fast trophic transition of all shallow lakes to the hypertrophic state. The parameters of the energy budget of the dominant populations and the potential production of benthivorous fish species assessed during 1976–1994 interval support this conclusion. P/B ratio, K ₁ and K ₂ coefficients assessed for both the 1976–1980 and 1991–1994 intervals revealed different functional patterns of response of Potamothrix hammoniensis (Michaelsen, 1901) and Limnodrilus hoffmeisteri (Claparede, 1862) to varying trophic conditions. Changes in communities structure, size of the constituent populations and their age distribution, as well as the quantity and quality of food supply and level of hypoxia at the sediment/water interface were the main factors that affected the role of these populations as energy carrier from the huge energy pool represented by sedimented organic carbon to benthivorous fish species.