Bacterial diversity along a 2600 km river continuum

The bacterioplankton diversity in large rivers has thus far been under‐sampled despite the importance of streams and rivers as components of continental landscapes. Here, we present a comprehensive dataset detailing the bacterioplankton diversity along the midstream of the Danube River and its tributaries. Using 16S rRNA‐gene amplicon sequencing, our analysis revealed that bacterial richness and evenness gradually declined downriver in both the free‐living and particle‐associated bacterial communities. These shifts were also supported by beta diversity analysis, where the effects of tributaries were negligible in regards to the overall variation. In addition, the river was largely dominated by bacteria that are commonly observed in freshwaters. Dominated by the acI lineage, the freshwater SAR11 (LD12) and the Polynucleobacter group, typical freshwater taxa increased in proportion downriver and were accompanied by a decrease in soil and groundwater‐affiliated bacteria. Based on views of the meta‐community and River Continuum Concept, we interpret the observed taxonomic patterns and accompanying changes in alpha and beta diversity with the intention of laying the foundation for a unified concept for river bacterioplankton diversity.     

Catchment-scale biogeography of riverine bacterioplankton

Lotic ecosystems such as rivers and streams are unique in that they represent a continuum of both space and time during the transition from headwaters to the river mouth. As microbes have very different controls over their ecology, distribution and dispersion compared with macrobiota, we wished to explore biogeographical patterns within a river catchment and uncover the major drivers structuring bacterioplankton communities. Water samples collected across the River Thames Basin, UK, covering the transition from headwater tributaries to the lower reaches of the main river channel were characterised using 16S rRNA gene pyrosequencing. This approach revealed an ecological succession in the bacterial community composition along the river continuum, moving from a community dominated by Bacteroidetes in the headwaters to Actinobacteria-dominated downstream. Location of the sampling point in the river network (measured as the cumulative water channel distance upstream) was found to be the most predictive spatial feature; inferring that ecological processes pertaining to temporal community succession are of prime importance in driving the assemblages of riverine bacterioplankton communities. A decrease in bacterial activity rates and an increase in the abundance of low nucleic acid bacteria relative to high nucleic acid bacteria were found to correspond with these downstream changes in community structure, suggesting corresponding functional changes. Our findings show that bacterial communities across the Thames basin exhibit an ecological succession along the river continuum, and that this is primarily driven by water residence time rather than the physico-chemical status of the river.     

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-PO(4) (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-NO(2) and P-PO(4) 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.     

Heterotrophic free-living and particle-bound bacterial cell size in the river Cauvery and its downstream tributaries

This is the first comprehensive study on planktonic heterotrophic bacterial cell size in the river Cauvery and its important tributaries in Karnataka State, India. The initial hypothesis that the mean cell size of planktonic heterotrophic bacteria in the four tributaries are markedly different from each other and also from that in the main river Cauvery was rejected, because all five watercourses showed similar planktonic heterotrophic bacterial cell size. Examination of the correlation between mean heterotrophic bacterial cell size and environmental variables showed four correlations in the river Arkavathy and two in the river Shimsha. Regression analysis revealed that 18% of the variation in mean heterotrophic free-living bacterial cell size was due to biological oxygen demand (BOD) in the river Arkavathy, 11% due to surface water velocity (SWV) in the river Cauvery and 11% due to temperature in the river Kapila. Heterotrophic particle-bound bacterial cell size variation was 28% due to chloride and BOD in the river Arkavathy, 11% due to conductivity in the river Kapila and 8% due to calcium in the river Cauvery. This type of relationship between heterotrophic bacterial cell size and environmental variables suggests that, though the mean heterotrophic bacterial cell size was similar in all the five water courses, different sets of environmental variables apparently control the heterotrophic bacterial cell size in the various water bodies studied in this investigation. The possible cause for this environmental (bottom-up) control is discussed.     

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 production in the Lower Mississippi River: importance of suspended sediment and phytoplankton biomass

The roles and metabolic activity of heterotrophic bacteria, along with factors controlling their activity, are poorly known for large, turbid rivers. The aim of this study was to evaluate temporal patterns in heterotrophic bacterial production (BP) in the main channel of the Lower Mississippi River (LMR) in relation to several seasonally dynamic environmental factors. We hypothesized that whole-water BP would vary with levels of temperature, as well as phytoplankton biomass and suspended sediment concentration. Further, we hypothesized that bacteria attached to suspended sediment would comprise an important component of whole-water BP, their importance varying with sediment concentration. Measurements were made at three locations on the LMR for up to 29 months. Bacterial production in whole-water ranged over an order of magnitude between summer and winter, with little variation among sites. Peaks in whole-water BP were associated with periods of high suspended sediment concentrations in spring, and elevated phytoplankton biomass in summer. Attached BP was correlated with all the measures of sediment concentration, especially particulate phosphorus, and accounted for a large majority of water-column BP. After temperature, the only positive correlate of free-living cells was with phytoplankton biomass. Rates of BP in the LMR during summer were much higher than measurements made previously in the Mississippi River plume, similar to the Hudson River, but lower than in three large tributaries of the LMR. Determination of bacterial population dynamics is an essential step in analysis of the food web structure and biogeochemical processes of large rivers. This is the first study of heterotrophic bacterial production in the main channel of the LMR.     

Oligochaeta of the Danube River — a faunistical review

The aim of this work is to discuss the distribution of Oligochaeta (Annelida) in the Danube River using the collections made by the Joint Danube Survey 2007 (JDS2) on more than 2800 km of the river. The basic faunistical features of the oligochaete assemblages were analysed with regard to three main sectors of the Danube (upper, middle and lower reaches, the last with the Danube Delta). A total of 52 oligochaete taxa have been recorded. Most of the observed species are typical of the potamon-type rivers in the region, and are well adapted to moderate-to-high organic load. The highest taxa richness and frequency of occurrence were observed among the Tubificidae family. Naididae, Propappidae, Enchytraeidae and Haplotaxidae had also low frequency. The upper reach of the Danube showed the lowest species richness, while the middle reach is characterised by its highest species richness. Construction of dams and regulation of the riverbed have resulted in an increase of limno(rheo)philic taxa which prefer slow-flowing and lentic zones.     

Fungal community demonstrates stronger dispersal limitation and less network connectivity than bacterial community in sediments along a large river

Despite the essential functions of sedimentary bacterial and fungal communities in biogeochemical cycling, little is known about their biogeographic patterns and driving processes in large rivers. Here we investigated the biogeographic assemblies and co-occurrence patterns of sedimentary bacterial and fungal communities in the Jinsha River, one of the largest rivers in southwestern China. The mainstream of river was divided into upstream, midstream and downstream. The results showed that both bacterial and fungal communities differed significantly among three sections. For both communities, their composition variations in all sites or each river section were controlled by the combination of dispersal limitation and environmental selection, and dispersal limitation was the dominant factor. Compared with bacteria, fungi had stronger dispersal limitation. Co-occurrence network analyses revealed higher network connectivity but a lower proportion of positive interaction in the bacterial than fungal network at all sites. In particular, the keystone species belonging to bacterial phyla Proteobacteria and Firmicutes and fungal phyla Ascomycota and Chytridiomycota may play critical roles in maintaining community function. Together, these observations indicate that fungi have a stronger dispersal limitation influence and less network connectivity than bacteria, implying different community assembly mechanisms and ecological functions between bacteria and fungi in large rivers.     

Colorful niches of phytoplankton shaped by the spatial connectivity in a large river ecosystem: a riverscape perspective

Large rivers represent a significant component of inland waters and are considered sentinels and integrators of terrestrial and atmospheric processes. They represent hotspots for the transport and processing of organic and inorganic material from the surrounding landscape, which ultimately impacts the bio-optical properties and food webs of the rivers. In large rivers, hydraulic connectivity operates as a major forcing variable to structure the functioning of the riverscape, and--despite increasing interest in large-river studies--riverscape structural properties, such as the underwater spectral regime, and their impact on autotrophic ecological processes remain poorly studied. Here we used the St. Lawrence River to identify the mechanisms structuring the underwater spectral environment and their consequences on pico- and nanophytoplankton communities, which are good biological tracers of environmental changes. Our results, obtained from a 450 km sampling transect, demonstrate that tributaries exert a profound impact on the receiving river's photosynthetic potential. This occurs mainly through injection of chromophoric dissolved organic matter (CDOM) and non-algal material (tripton). CDOM and tripton in the water column selectively absorbed wavelengths in a gradient from blue to red, and the resulting underwater light climate was in turn a strong driver of the phytoplankton community structure (prokaryote/eukaryote relative and absolute abundances) at scales of many kilometers from the tributary confluence. Our results conclusively demonstrate the proximal impact of watershed properties on underwater spectral composition in a highly dynamic river environment characterized by unique structuring properties such as high directional connectivity, numerous sources and forms of carbon, and a rapidly varying hydrodynamic regime. We surmise that the underwater spectral composition represents a key integrating and structural property of large, heterogeneous river ecosystems and a promising tool to study autotrophic functional properties. It confirms the usefulness of using the riverscape approach to study large-river ecosystems and initiate comparison along latitudinal gradients.     

Free-Living and Particle-Associated Bacterioplankton in Large Rivers of the Mississippi River Basin Demonstrate Biogeographic Patterns

The different drainage basins of large rivers such as the Mississippi River represent interesting systems in which to study patterns in freshwater microbial biogeography. Spatial variability in bacterioplankton communities in six major rivers (the Upper Mississippi, Missouri, Illinois, Ohio, Tennessee, and Arkansas) of the Mississippi River Basin was characterized using Ion Torrent 16S rRNA amplicon sequencing. When all systems were combined, particle-associated (>3 μm) bacterial assemblages were found to be different from free-living bacterioplankton in terms of overall community structure, partly because of differences in the proportional abundance of sequences affiliated with major bacterial lineages (Alphaproteobacteria, Cyanobacteria, and Planctomycetes). Both particle-associated and free-living communities ordinated by river system, a pattern that was apparent even after rare sequences or those affiliated with Cyanobacteria were removed from the analyses. Ordination of samples by river system correlated with environmental characteristics of each river, such as nutrient status and turbidity. Communities in the Upper Mississippi and the Missouri and in the Ohio and the Tennessee, pairs of rivers that join each other, contained similar taxa in terms of presence-absence data but differed in the proportional abundance of major lineages. The most common sequence types detected in particle-associated communities were picocyanobacteria in the Synechococcus/Prochlorococcus/Cyanobium (Syn/Pro) clade, while free-living communities also contained a high proportion of LD12 (SAR11/Pelagibacter)-like Alphaproteobacteria. This research shows that while different tributaries of large river systems such as the Mississippi River harbor distinct bacterioplankton communities, there is also microhabitat variation such as that between free-living and particle-associated assemblages.     

Damming river shapes distinct patterns and processes of planktonic bacterial and microeukaryotic communities

Planktonic bacterial and microeukaryotic communities play important roles in biogeochemical cycles, but their biogeographic patterns and community assembly processes in large damming rivers still remain unclear. In this study, 16S rRNA and 18S rRNA coding genes were used for sample sequencing analysis of planktonic bacterial and microeukaryotic communities in the upper Yangtze River. The upper Yangtze River was divided into dam-affected zones and river zones based on the influence of dams. The results showed that there were significant differences in the bacterial and microeukaryotic communities between the two zones and that dams significantly reduced the α-diversity of the bacterial communities. Co-occurrence network analysis indicated that networks in the river zone were denser than those in the dam-affected zone. The relationships among species in bacterial networks were more complex than those in microeukaryotic networks. Dispersal limitation and ecological drift were the main processes influencing planktonic bacterial and microeukaryotic communities in the dam-affected zone respectively, whereas the role of deterministic processes increased in the river zone. Anthropogenic activities and hydraulic conditions affected suspended sediment and controlled microbial diversity in the river zone. These results suggest that dams impact planktonic bacteria more strongly than planktonic microeukaryotes, indicating that the distribution patterns and processes of the bacterial and microeukaryotic communities in large rivers are significantly different.     

Pico- and Nanoplankton in Aquatic Ecosystems in the Valley of the Lakes and Great Lakes Depression (Mongolia)

The abundance and biomass of bacterioplankton, phototrophic picoplankton, and heterotrophic nanoflagellates has been determined in lakes, rivers, and reservoirs located in the Valley of the Lakes and Great Lakes Depression (Mongolia). The species richness of the heterotrophic flagellates and their consumption of bacteria are estimated. Pico- and nanoplankton are the most abundant in shallow mineral lakes Orog and Tatsyn and in the freshwater Durgun Reservoir. Heterotrophic nanoflagellates consume 26–92% (on average 66%) of the daily bacterioplankton production. Thus, flagellates are important in the transfer of bacterial carbon to the higher levels of planktonic trophic webs. A total of 30 species and their forms of heterotrophic flagellates from 14 large taxa are identified. The highest species diversity of these protists are found in the Durgun and Taishyr reservoirs.     

Communities at the extreme: Aquatic food webs in desert landscapes

Studying food webs across contrasting abiotic conditions is an important tool in understanding how environmental variability impacts community structure and ecosystem dynamics. The study of extreme environments provides insight into community‐wide level responses to environmental pressures with relevance to the future management of aquatic ecosystems. In the western Lake Eyre Basin of arid Australia, there are two characteristic and contrasting aquatic habitats: springs and rivers. Permanent isolated Great Artesian Basin springs represent hydrologically persistent environments in an arid desert landscape. In contrast, hydrologically variable river waterholes are ephemeral in space and time. We comprehensively sampled aquatic assemblages in contrasting ecosystem types to assess patterns in community composition and to quantify food web attributes with stable isotopes. Springs and rivers were found to have markedly different invertebrate communities, with rivers dominated by more dispersive species and springs associated with species that show high local endemism. Qualitative assessment of basal resources shows autochthonous carbon appears to be a key basal resource in both types of habitat, although the particular sources differed between habitats. Food‐web variables such as trophic length, trophic breadth, and community isotopic niche size were relatively similar in the two habitat types. The basis for the similarity in food‐web structure despite differences in community composition appears to be broader isotopic niches for predatory invertebrates and fish in springs as compared with rivers. In contrast to published theory, our findings suggest that the food webs of the hydrologically variable river sites may show less dietary generalization and more compact food‐web modules than in springs.     

Correlations Between Predominant Heterotrophic Bacteria and Physicochemical Water Quality Parameters in Two Canadian Rivers

The heterotrophic bacterial populations in two contrasting rivers have been examined over a period of 1 year. The populations were analyzed (i) as total heterotrophic counts, (ii) as species numbers, using numerical taxonomy, (iii) by diversity indices, and (iv) by factor analysis. Isolates were obtained by plating directly from water samples and by chemostat enrichment. Four factors emerged which profiled the bacterial community and were common to both rivers. They were, in order of decreasing importance, fermentative metabolism, inorganic nitrogen metabolism, fluorescence-oxidative metabolism, and lack of starch hydrolysis. Several factors produced significant correlations with a range of physicochemical parameters, which were also measured. The correlations suggested an intricate algal-bacterial interaction. The oxidative metabolism factor correlated with rainfall in one river, suggesting that the oxidative bacteria may be washed in from the surrounding land. In the other river, the oxidative-fermentative factor correlated negatively with sunshine. Factor analysis was the most effective method for revealing correlations between bacterial characteristics and the environmental parameters; however, the use of a variety of methods provided more insight into the ecological aspects.     

Complexity of Bacterial Communities in a River-Floodplain System (Danube, Austria)

Natural floodplains play an essential role in the processing and decomposition of organic matter and in the self-purification ability of rivers, largely due to the activity of bacteria. Knowledge about the composition of bacterial communities and its impact on organic-matter cycling is crucial for the understanding of ecological processes in river-floodplain systems. Particle-associated and free-living bacterial assemblages from the Danube River and various floodplain pools with different hydrological characteristics were investigated using terminal restriction fragment length polymorphism analysis. The particle-associated bacterial community exhibited a higher number of operational taxonomic units (OTUs) and was more heterogeneous in time and space than the free-living community. The temporal dynamics of the community structure were generally higher in isolated floodplain pools. The community structures of the river and the various floodplain pools, as well as those of the particle-associated and free-living bacteria, differed significantly. The compositional dynamics of the planktonic bacterial communities were related to changes in the algal biomass, temperature, and concentrations of organic and inorganic nutrients. The OTU richness of the free-living community was correlated with the concentration and origin of organic matter and the concentration of inorganic nutrients, while no correlation with the OTU richness of the particle-associated assemblage was found. Our results demonstrate the importance of the river-floodplain interactions and the influence of damming and regulation on the bacterial-community composition.     

Invasive Silver Carp movement patterns in the predominantly free-flowing Wabash River (Indiana,USA)

Many organisms must move among habitats to fulfill life history requirements. Fish movements have been widely studied and tend to be either fine-scale (i.e., routine) and governed by factors such as food availability and cover, or broad-scale and associated with spawning migrations. However, movements of invasive fishes in non-native ecosystems are comparatively poorly understood despite the often critical importance of fish movement and dispersal for invasion success. We examined invasive Silver Carp (Hypophthalmichthys molitrix) movements using acoustic telemetry to monitor the timing, distance, and direction of fish movements and assessed movements in relation to seasonal, annual, environmental, and individual factors in the Wabash River (Indiana, USA), a largely unregulated Midwestern river. Silver Carp exhibited highly variable movements that could be rapid and large in magnitude; however, tagged individuals remained stationary most of the time. Despite high variability, several trends emerged, indicating the importance of backwater habitats, avoidance of small tributaries, and tendencies of tagged fish to exhibit directed spring and fall broad-scale movements. Summer movements were smaller in magnitude, characterized by lower movement rates, and evenly split between upstream and downstream directions, although tagged Silver Carp moved more frequently during summer months. Our results indicate that specific seasons (i.e., spring and early fall) and locations (i.e., backwaters) are likely targets for Silver Carp control in the Wabash River and should also be useful targets for early detection and control in other largely unconstrained rivers over a broad geographic range (e.g., Great Lakes tributaries and upper Mississippi River mainstem and tributaries).     

Characterisation of the potamal Danube River and the Delta: connectivity determines indicative macrophyte assemblages

The complexity of water bodies in the eu-potamal river corridor and the main delta channels of the Romanian Danube is exemplified by the macrophyte vegetation. Two hypotheses provided the background for our study: (a) is the macrophyte vegetation of large, permanently connected branches significantly separated from that of the main river channel; (b) is the macrophyte composition of the Danube main stem significantly altered when the river divides into the three large navigable Delta channels. Water bodies considered were two contiguous sections of the main river channel, two large branches remaining from the historical floodplain, and the three main Delta channels. We quantified macrophyte diversity and floristic variation. Our data set was prepared from the MIDCC-project data base, in which macrophyte occurrence, abundance and habitat parameters are stored for contiguous survey units of the whole Danube river corridor. Field survey method followed that of Kohler and the European Standard EN14184. Results confirmed our first hypothesis: permanently connected side branches still support significantly different macrophyte assemblages, making them important indicators of floodplain connectivity. The diversion of the Danube into its three large navigable delta channels significantly alters the macrophyte vegetation from the c. 300 km of main stem up-river, substantially supporting our second hypothesis. Our results largely enhance the knowledge on aquatic plant biodiversity in the eu-potamal Danube, forming a solid base for long-term studies. We also discuss the relevance of our results regarding the ecological, as well as the conservational, quality of rivers and their floodplains.     

Complexity of bacterial communities in a river-floodplain system (Danube, Austria)

Natural floodplains play an essential role in the processing and decomposition of organic matter and in the self-purification ability of rivers, largely due to the activity of bacteria. Knowledge about the composition of bacterial communities and its impact on organic-matter cycling is crucial for the understanding of ecological processes in river-floodplain systems. Particle-associated and free-living bacterial assemblages from the Danube River and various floodplain pools with different hydrological characteristics were investigated using terminal restriction fragment length polymorphism analysis. The particle-associated bacterial community exhibited a higher number of operational taxonomic units (OTUs) and was more heterogeneous in time and space than the free-living community. The temporal dynamics of the community structure were generally higher in isolated floodplain pools. The community structures of the river and the various floodplain pools, as well as those of the particle-associated and free-living bacteria, differed significantly. The compositional dynamics of the planktonic bacterial communities were related to changes in the algal biomass, temperature, and concentrations of organic and inorganic nutrients. The OTU richness of the free-living community was correlated with the concentration and origin of organic matter and the concentration of inorganic nutrients, while no correlation with the OTU richness of the particle-associated assemblage was found. Our results demonstrate the importance of the river-floodplain interactions and the influence of damming and regulation on the bacterial-community composition.     

The structure of food webs along river networks

Do changes in the species composition of riverine fish assemblages along river networks lead to predictable changes in food‐web structure? We assembled empirical “fish‐centered” river food webs for three rivers located along a latitudinal gradient in the South Saskatchewan River Basin (SSRB) that differ in land‐use impacts and geomorphology but flow through similar mountain, foothill, and prairie physiographic regions. We then calculated 17 food‐web properties to determine whether the nine river food webs differed according to physiographic region or river sub‐basin. There were no statistically significant differences in the 17 food‐web properties calculated among the rivers. In contrast, fish species richness, connectance, the proportion of herbivores, and the proportion of cannibals changed longitudinally along the river network. Our results suggest that regional changes in river geomorphology and physicochemistry play an important role in determining longitudinal variation in food‐web properties such as fish species richness and connectance. In contrast, the overall structure of river food webs may be relatively similar and insensitive to regional influences such as zoogeography. Further explorations of river and other food webs would greatly illuminate this suggestion.     

Seasonal dynamics of riverine fish communities using eDNA

As fish communities are a major concern in rivers ecosystems, we investigated if their environmental (e)DNA signals vary according to the sampling period or hydromorphological conditions. Three rivers were studied over a year using eDNA metabarcoding approach. The majority of the species (c. 80%) were detected all year round in two rivers having similar hydromorphological conditions, whereas in the river affected by an upstream lake waterflow, more species were detected sporadically (42%). For all the rivers, in more than 98% of the occasional detections, the reads abundance represented <0.4% of the total reads per site and per sampling session. Even if the majority of the fish communities remained similar over the year for each of the three rivers, specific seasonal patterns were observed. We studied if the waterflow or the reproduction period had an effect on the observed dynamics. Waterflow, which influences eDNA downstream transportation, had a global influence in taxonomic richness, while the fishes' reproductive period had only an influence on certain species. Our results may help selecting the best sampling strategy according to research objectives. To study fish communities at local scale, seasons of low waterflow periods are recommended. This particularly helps to restraint effects of external eDNA coming from connections with other aquatic environment (tributaries, lakes, wetlands, sewage effluents, etc.). To obtain a more integrative overview of the fish community living in a river basin, high waterflow or breeding seasons are preferable for enhancing species detection probability, especially for rare species.