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Exemplarily selected results of the PCR – DGGE analysis covering 768km of the upstream section of the German (lane numbers 1, 2, 3, 4, 6) Austrian (lane numbers 7 –15) and Slovakian (16 – 21) River Danube JDS 2001 sampling stations (from km2580 to km1812). Lanes 5,13,16 are tributaries (see below for details). Lane 41 is given as an “outgroup” band pattern of the given upstream sequences, representing a downstream location at km1533. Given DGGE band patterns of the analysed sampling locations are a result of the encountered bacterial 328
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... methodical details are given in Winter et al. (2006) Results During the JDS 2001, all 98 filtrations of 50ml to 150ml of River Danube water followed by DNA extraction and PCR -DGGE analysis resulted in complex and well focused 16S rRNA gene DGGE band patterns (c.f. Fig.1). Apparent bacterial richness (i.e. ...
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... to the number of observable DGGE bands. 1, 2, 3, 4, 6) Austrian (lane numbers 7 -15) and Slovakian (16 -21) River Danube JDS 2001 sampling stations (from km2580 to km1812). Lanes 5,13,16 are tributaries (see below for details). ...
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... bacterioplankton including taxa of Cyanobacteria, α-, β-, γ-Proteobacteria, Cytophaga - Flavobacterium -Bacteroides group and Actinobacteria. Analysis of the longitudinal development of the DGGE profiles in the River Danube during the JDS 2001 indicated that the bacterial community developed gradually over the studied distance of over 2500km (see Fig. 1 bands 1-24 as selected example of the gradual development of the upstream sections km2580 to km1812). The similarity of the bacterial communities related to the first sampling station decreased with increasing distance and the Jaccard dissimilarity index ranged from approximately 0,25 (2412 km) to 0,65 (12 km). However, the gradual ...
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... Despite efforts to preserve its ecosystem, the Danube faces severe physical, chemical, and biological pollution, especially in its upper part, the Pokutsko-Bukovynian Carpathians (Pall et al., 2013;Kolarevich et al., 2011). Researchers have classified the microbiological quality of water in the Danube basin into different classes based on standard indicators of fecal and organic pollution (Eiler et al., 2022;Kavka et al., 2006;Winter et al., 2007;Kirschner et al., 2009;Kirschner et al., 2017). The Siret and Prut rivers, originating in the Ukrainian Carpathians, were categorized as critical and strongly fecal pollution classes, respectively. ...
... Despite efforts to preserve its ecosystem, the Danube faces severe physical, chemical, and biological pollution, especially in its upper part, the Pokutsko-Bukovynian Carpathians (Pall et al., 2013;Kolarevich et al., 2011). Researchers have classified the microbiological quality of water in the Danube basin into different classes based on standard indicators of fecal and organic pollution (Eiler et al., 2022;Kavka et al., 2006;Winter et al., 2007;Kirschner et al., 2009;Kirschner et al., 2017). The Siret and Prut rivers, originating in the Ukrainian Carpathians, were categorized as critical and strongly fecal pollution classes, respectively. ...
... In another study, the total bacterial number exhibited significantly increased trend along the complete length of the Danube River, but the bacterial activity did not follow a continuous trend because of the input of sewage from large cities in the midstream (Velimirov et al., 2011). Some previous studies on large rivers, as the Danube River, have reported that the bacterial community compositions developed gradually, in general, based on the data of Joint Danube Survey 2001(Winter et al., 2007Kirschner et al., 2008;Savio et al., 2015). Differently, the compositions of the bacterial communities at the upper-middle-reach sites differed significantly from those at downstream sites in this study (Figure 4 and Supplementary Figure S2). ...
Sediment microbes play major roles in riparian ecosystems; however, little is known about their longitudinal distribution pattern and their responses to dam construction, the most severe human disturbance in river basins. Here, we investigated the variability of sediment bacterial communities along a large-scale longitudinal gradient and between dam-controlled and dam-affected sites in riparian zone of the Lancang River, China. The abundance, activity and diversity of sediment bacteria gradually increased in a downstream direction, but were significantly lower in the dam-affected sites than in the dam-controlled sites. The bacterial community compositions differed significantly between the upper-middle-reach and downstream sites at all control sites, and also between the dam-affected and dam-controlled sites. In the cascade dam area, the relative importance of spatial distance and environmental heterogeneity for bacterial distribution differed between the dam-controlled and dam-affected sites. Spatial distance was the primary cause of variations in bacterial community in dam-controlled site. By contrast, the environmental heterogeneity had more control over the bacterial communities than did the spatial distance in dam-affected site. Network analysis showed that the bacterial community in the dam-affected sites had lower connectivity and stability when compared with that in dam-controlled sites. These results suggest the distinct variations in sediment bacterial community in dam-affected sites, which could enhance our understanding of potential ecological effects caused by dam construction.
... This first survey of microbial communities along the riverocean continuum of the largest river in the world revealed that seasonal and spatial patterns were not fundamentally different than those previously observed in smaller rivers ( Levine and Crump, 2002;Sekiguchi et al., 2002;Crump and Hobbie, 2005;Winter et al., 2007;Crump et al., 2009), river plumes ( King et al., 2013;Mason et al., 2016), and riverocean continuums ( Fortunato et al., 2012;Ortega-Retuerta et al., 2013;Ma et al., 2016), suggesting globally consistent patterns in microbial community composition across river-ocean gradients. We found that river communities varied among tributaries, but mainstem river communities were spatially homogeneous over ∼675 km, and tracked seasonal changes in river discharge. ...
... Communities in the mainstem Amazon River did not vary spatially over the ∼675 river kilometers between Óbidos and Macapá, suggesting homogeneity in microbially relevant environmental conditions and little influence of tributaries. Similar results were found in long reaches of the lower Changjiang and Danube rivers ( Sekiguchi et al., 2002;Winter et al., 2007), but these results contrast with longitudinal surveys of other rivers in which tributary inputs and environmental changes significantly altered microbial communities (Winter et al., 2007;Jackson et al., 2014;Kolmakova et al., 2014;Gladyshev et al., 2015;Read et al., 2015). In the Amazon River, DOM analyses suggest a transition from higher plant-derived DOM to more algal/microbial-derived DOM between Óbidos and Macapá ( Seidel et al., 2016), and an associated enhancement in microbial activity and organic matter decomposition rates ( Ward et al., 2016). ...
... Communities in the mainstem Amazon River did not vary spatially over the ∼675 river kilometers between Óbidos and Macapá, suggesting homogeneity in microbially relevant environmental conditions and little influence of tributaries. Similar results were found in long reaches of the lower Changjiang and Danube rivers ( Sekiguchi et al., 2002;Winter et al., 2007), but these results contrast with longitudinal surveys of other rivers in which tributary inputs and environmental changes significantly altered microbial communities (Winter et al., 2007;Jackson et al., 2014;Kolmakova et al., 2014;Gladyshev et al., 2015;Read et al., 2015). In the Amazon River, DOM analyses suggest a transition from higher plant-derived DOM to more algal/microbial-derived DOM between Óbidos and Macapá ( Seidel et al., 2016), and an associated enhancement in microbial activity and organic matter decomposition rates ( Ward et al., 2016). ...
Spatial and temporal patterns in microbial biodiversity across the Amazon river-ocean continuum were investigated along ∼675 km of the lower Amazon River mainstem, in the Tapajós River tributary, and in the plume and coastal ocean during low and high river discharge using amplicon sequencing of 16S rRNA genes in whole water and size-fractionated samples (0.2–2.0 µm and >2.0 µm). River communities varied among tributaries, but mainstem communities were spatially homogeneous and tracked seasonal changes in river discharge and co-varying factors. Co-occurrence network analysis identified strongly interconnected river assemblages during high (May) and low (December) discharge periods, and weakly interconnected transitional assemblages in September, suggesting that this system supports two seasonal microbial communities linked to river discharge. In contrast, plume communities showed little seasonal differences and instead varied spatially tracking salinity. However, salinity explained only a small fraction of community variability, and plume communities in blooms of diatom-diazotroph assemblages were strikingly different than those in other high salinity plume samples. This suggests that while salinity physically structures plumes through buoyancy and mixing, the composition of plume-specific communities is controlled by other factors including nutrients, phytoplankton community composition, and dissolved organic matter chemistry. Co-occurrence networks identified interconnected assemblages associated with the highly productive low salinity near-shore region, diatom-diazotroph blooms, and the plume edge region, and weakly interconnected assemblages in high salinity regions. This suggests that the plume supports a transitional community influenced by immigration of ocean bacteria from the plume edge, and by species sorting as these communities adapt to local environmental conditions. Few studies have explored patterns of microbial diversity in tropical rivers and coastal oceans. Comparison of Amazon continuum microbial communities to those from temperate and arctic systems suggest that river discharge and salinity are master variables structuring a range of environmental conditions that control bacterial communities across the river-ocean continuum.
... For instance, microbial communities inhabiting pineland soils exhibited changes in diversity on a seasonal basis, but exhibit no differences in the micro- bial biomass (Rogers and Tate 2001). Environmental fac- tors have been shown to shape the microbial communities inhabiting different river ecosystems ( Liu et al. 2011Liu et al. , 2013Winter et al. 2007;Wu et al. 2011). Changes in water tem- perature and conductivity, for example, were identified to influence temporal partitioning in bacterial communities of a subtropical river. ...
Stability of microbial communities can impact the ability of dispersed cells to colonize a new habitat. Saturated brines and their halophile communities are presumed to be steady state systems due to limited environmental perturbations. In this study, the bacteriorhodopsin-containing fraction of the haloarchaeal community from Eilat salt crystallizer ponds was sampled five times over 3 years. Analyses revealed the existence of a constant core as several OTUs were found repeatedly over the length of the study: OTUs comprising 52 % of the total cloned and sequenced PCR amplicons were found in every sample, and OTUs comprising 89 % of the total sequences were found in more than one, and often more than two samples. LIBSHUFF and UNIFRAC analyses showed statistical similarity between samples and Spearman’s coefficient denoted significant correlations between OTU pairs, indicating non-random patterns in abundance and co-occurrence of detected OTUs. Further, changes in the detected OTUs were statistically linked to deviations in salinity. We interpret these results as indicating the existence of an ever-present core bacteriorhodopsin-containing Eilat crystallizer community that fluctuates in population densities, which are controlled by salinity rather than the extinction of some OTUs and their replacement through immigration and colonization.
... Extracted DNA was purified with phenolchloroform before it was used as a template in PCR amplification. Partial 16S rDNA genes were amplified using the primer pair 341F (5 0 -CCT ACG GGA GGC AGC AG-3 0 ) and 907R (5 0 -CCG TCA ATT CCT TTG AGT TT-3 0 ) ( Winter et al. 2007). A 40-bp-long GC clamp (5 0 -CGC CCG CCG CGC CCC GCG CCC GTC CCG CCG CCC CCG CCC G-3 0 ) was attached to the 5 0 end of primer 341F. ...
We investigated the dynamics of attached and free-living bacterial abundance over a period of 18 months in tropical coastal waters of Malaysia. We measured the abundance at both oligotrophic coastal water (Port Dickson) and eutrophic estuary (Klang), and hypothesised that attached bacteria are predominant in eutrophic waters. We found that bacterial abundance was higher at Klang than Port Dickson (Student’s t-test: t = 4.87, d.f. = 19, P < 0.001). Attached bacteria also formed a large fraction of the total bacteria at Klang (75% ± 13 s.d.) relative to Port Dickson (56% ± 22), and showed preference for chlorophyll-a-based particles rather than total suspended solids. The bacterial community structure was clearly different between the two stations but was similar between the attached and free-living bacterial population. Our results showed the importance of attached bacteria in eutrophic water where they could play a major role in carbon and nutrient cycling.
Cyanobacteria and cyanotoxin producing cyanobacterial blooms are a trending focus of current research. Many studies focus on bloom events in lentic environments such as lakes or ponds. Comparatively few studies have explored lotic environments and fewer still have examined the cyanobacterial communities and potential cyanotoxin producers during ambient, non-bloom conditions. Here we used a metagenomics-based approach to profile non-bloom microbial communities and cyanobacteria in 12 major U.S. rivers at multiple time points during the summer months of 2019. Our data show that U.S. rivers possess microbial communities that are taxonomically rich, yet largely consistent across geographic location and time. Within these communities, cyanobacteria often comprise significant portions and frequently include multiple species with known cyanotoxin producing strains. We further characterized these potential cyanotoxin producing taxa by deep sequencing amplicons of the microcystin E (mcyE) gene. We found that rivers containing the highest levels of potential cyanotoxin producing cyanobacteria consistently possess taxa with the genetic potential for cyanotoxin production and that, among these taxa, the predominant genus of origin for the mcyE gene is Microcystis. Combined, these data provide a unique perspective on cyanobacteria and potential cyanotoxin producing taxa that exist in large rivers across the U.S. and can be used to better understand the ambient conditions that may precede bloom events in lotic freshwater ecosystems.
Waterborne pathogens have attracted a great deal of attention in the public health sector over the last several decades. However, little is known about the pathogenic microorganisms in urban water systems. In this study, the bacterial community structure of 16 typical surface waters in the city of Beijing were analyzed using Illumina MiSeq high-throughput sequencing based on 16S rRNA gene. The results showed that Bacteroidetes, Proteobacteria and Actinobacteria were the dominant groups in 16 surface water samples, and Betaproteobacteria, Alphaproteobacteria, Flavobacteriia, Sphingobacteriia and Actinobacteria were the most dominant classes. The dominant genus across all samples was Flavobacterium. In addition, fifteen genus level groups of potentialy pathogenic bacteria were detected within the 16 water samples, with Pseudomonas and Aeromonas the most frequently identified. Spearman correlation analysis demonstrated that richness estimators (OTUs and Chao1) were correlated with water temperature, nitrate and total nitrogen (p < 0.05), while ammonia-nitrogen and total nitrogen were significantly correlated with the percent of total potential pathogens (p ≤ 0.05). These results could provide insight into the ecological function and health risks of surface water bacterial communities during the process of urbanization.
Fecal microbial pollution is a major problem throughout the Danube River Basin, posing a threat to various types of water use, including drinking water production from river bank filtrates, water supply for agricultural and industrial use, and the role of the river as a recreational space. Fecal microbial pollution is introduced into the river by point sources, such as discharges of treated or untreated sewage from human sources or livestock, and by nonpoint sources, such as urban and agricultural runoff. In addition, fecal input from wildlife may be of importance in specific regions. Despite huge efforts to improve wastewater management in the past decade, in many sections, the river and its tributaries exhibit very high levels of fecal microbial pollution. To assess microbiological water quality, indicators of fecal pollution are used as surrogates for the potential presence of intestinal pathogens. However, the standard indicators cannot provide any reliable information regarding the origin of fecal pollution, nor can their concentration levels be directly related to human health risks for many types of exposure and situations.
