Environmental DNA detects a rare large river crayfish but with little relation to local abundance

相似文献   

Factors influencing biomass and nutrient content of the submersed macrophyte Egeria densa Planch. in a pampasic stream

We identified factors influencing biomass and nutrient content in E. densa in an enriched pampean stream of Argentina. Physical (current velocity, temperature), chemical (pH, conductivity, dissolved oxygen, nutrient content in water and sediments), and biological variables (biomass and nutrient content of E. densa, biomass of periphyton and other macrophytes) were estimated at each sampling occasion, and mean monthly values estimated. Biomass and nutrient content in E. densa were correlated with these physical-chemical and biological variables. Biomass was positively correlated with ammonium in stream water (P<0.05) and sediment total nitrogen (P<0.01). Nitrogen showed a positive relationship with ammonium (P<0.01), and a negative one with nitrate and periphyton biomass (P<0.05). Phosphorus was positively correlated with soluble reactive phosphorus (P<0.01). The growth of other macrophyte species in the stream seemed to influence E. densa biomass, probably through competition for light. Current velocity was low and not significantly related with E. densa biomass, however, a flood at the beginning of the study washed the macrophyte stand downstream.     

Effects of macrophyte heterogeneity and food availability on structural parameters of the macroinvertebrate community in a Pampean stream

Environmental heterogeneity in natural ecosystems influences several parameters at the population and community levels. In freshwater ecosystems, habitat heterogeneity can be provided by macrophyte species with different structural shapes. Previous studies suggest that aquatic plants with more complex architectures will support higher number, biomass, and taxon richness of macroinvertebrates than plants with simpler shape. We investigated the influence of macrophyte structural heterogeneity (quantified by fractal dimension) and food availability (represented by epiphytic biomass) on several parameters (number of individuals, biomass, body size distribution, taxon richness, and diversity) of the macroinvertebrate community in a Pampean stream. Four submerged macrophyte species (Egeria densa, Elodea ernstae, Ceratophyllum demersum, and Stuckenia striata) and associated macroinvertebrates were sampled in late spring, summer, and autumn. Plants were photographed and fractal dimension was estimated from the images by the box-counting method. Fractal dimension was independent of plant surface area per unit of macrophyte biomass and differed significantly among species. Mean fractal dimension varied between 1.29 and 1.62, and increased following the sequence E. densa → S. striata → E. ernstae → C. demersum. Macrophyte species with higher fractal dimension supported a greater abundance of macroinvertebrates, especially those of small body size (500–1,000 μm); but fractal dimension was unrelated to macroinvertebrate biomass, richness, and diversity. However, overall animal biomass was significantly associated to the epiphytic abundance. Consequently, macrophyte heterogeneity influences macroinvertebrate density and body size distribution, while animal biomass depends on epiphytic food resources provided by plants.     

Riverine distribution of mussel environmental DNA reflects a balance among density,transport, and removal processes

相似文献   

Identifying spawning sites and other critical habitat in lotic systems using eDNA “snapshots”: A case study using the sea lamprey Petromyzon marinus L.

Many aquatic species of conservation concern exist at low densities and are inherently difficult to detect or monitor using conventional methods. However, the introduction of environmental (e)DNA has recently transformed our ability to detect these species and enables effective deployment of limited conservation resources. Identifying areas for breeding, as well as the ecological distribution of species, is vital to the survival or recovery of a conservation species (i.e., areas of critical habitat). In many species, spawning events are associated with a higher relative abundance of DNA released within an aquatic system (i.e., gametes, skin cells etc.), making this the ideal time to monitor these species using eDNA techniques. This study aims to examine whether a “snapshot” eDNA sampling approach (i.e., samples taken at fixed points in chronological time) could reveal areas of critical habitat including spawning sites for our target species Petromyzon marinus. We utilized a species‐specific qPCR assay to monitor spatial and temporal patterns in eDNA concentration within two river catchments in Ireland over three consecutive years. We found that eDNA concentration increased at the onset of observed spawning activity and patterns of concentration increased from downstream to upstream over time, suggesting dispersal into the higher reaches as the spawning season progressed. We found P. marinus to be present upstream of several potential barriers to migration, sometimes in significant numbers. Our results also show that the addition of a lamprey‐specific fish pass at an “impassable” weir, although assisting in ascent, did not have any significant impact on eDNA concentration upstream after the pass had been installed. eDNA concentration was also found to be significantly correlated with both the number of fish and the number of nests encountered. The application of snapshot sampling techniques for species monitoring therefore has substantial potential for the management of low‐density species in fast‐moving aquatic systems.     

Relationship between epipelon,epiphyton and phytoplankton in two limnological phases in a shallow tropical reservoir with high Nymphaea coverage

Macrophytes and phytoplankton are recognized as having roles in determining alternative stable states in shallow lakes and reservoirs, while the role of periphyton has been poorly investigated. Temporal and spatial variation of phytoplankton, epipelon and epiphyton was examined in a shallow reservoir with high abundance of aquatic macrophytes. The relationships between algae communities and abiotic factors, macrophyte coverage and zooplankton density were also analyzed. Monthly sampling was performed in three zones of the depth gradient of the reservoir. Two phases of algal dominance were found: a phytoplankton phase and epipelon phase. The phase of phytoplankton dominance was characterized by high macrophyte coverage. Rotifera was the dominant zooplankton group in all the zones. Flagellate algae were dominant in phytoplankton, epipelon and epiphyton. Macrophyte coverage was found to be a predictor for algal biomass. Changes in biomass and species composition were associated with macrophyte cover variation, mainly the Nymphaea. In addition to the abiotic factors, the macrophyte coverage was a determining factor for changes to the algal community, contributing to the alternation between dominance phases of phytoplankton and epipelon. The macrophyte–phytoplankton–periphyton relationship needs to be further known in shallow reservoirs, especially the role of epipelon as an alternate stable state.

     

Environmental DNA analysis for estimating the abundance and biomass of stream fish

相似文献   

Effects of Spirogyra arcta on biomass and structure of submerged macrophyte communities

The presence of algae can greatly reduce the amount of light that reaches submerged macrophytes, but few experimental studies have been conducted to examine the effects of algae on biomass and structure of submerged macrophyte communities. We constructed communities with four submerged macrophytes (Hydrilla verticillata, Egeria densa, Ceratophyllum demersum, and Chara vulgaris) in three environments in which 0 (control), 50 and 100% of the water surface was covered by Spirogyra arcta. Compared to the control treatment, the 100% spirogyra treatment decreased biomass of the submerged macrophyte communities and of all the four macrophytes except C. demersum. Compared to the control and 50% treatments, the 100% treatment significantly increased relative abundance of C. demersum and decreased that of E. densa. Therefore, the presence of S. arcta can greatly affect the productivity and alter the structure of submerged macrophyte communities. To restore submerged macrophyte communities in conditions with abundant algae, assembling communities consisting of C. demersum or similar species may be a good practice.     

Effects of a combined use of macronutrients nitrate,ammonium, and phosphate on cadmium absorption by <Emphasis Type="Italic">Egeria densa</Emphasis> Planch. and its phytoremediation applicability

Phosphorus and nitrogen fertilizers represent a source of cadmium (Cd) which may be leached into aquatic systems. Macrophytes accumulate contaminants, and Egeria densa has been shown to grow in aquatic environments polluted with trace elements. In this study, Cd accumulation by E. densa exposed to two Cd treatments (3 and 5 mg L^?1) was evaluated under increasing nutrient levels (NP as N–NO₃ ^?, N–NH₄ ⁺, and P–PO₄ ^3?, in concentrations 5-, 10- and 100-fold higher (NP₅, NP₁₀ and NP₁₀₀) than in the sampling site) to simulate different levels of eutrophication. Bioaccumulation factors and Cd recovery were calculated and effects on plants were evaluated based on chloroplastidic pigment concentrations (chlorophylls a and b, and carotenoids). We conclude that Cd accumulation by Egeria densa is positively influenced by increasing availability of N and P at the level of around NP₁₀ and probably at a broader concentration range not defined in this study. A further increase in N and P, however, does not generate a significant increase in Cd accumulation. Chloroplastidic pigment concentrations were not linearly correlated with Cd accumulation and the NP₁₀ experiment produced less damage to macrophyte when compared to NP₅ and NP₁₀₀ experiments. Under controlled conditions, it was possible to satisfactorily model Cd bioaccumulation over time, in order to provide essential data for E. densa use in phytoremediation processes. The Cd residence in the macrophyte tissue is increased in eutrophic environments, which puts at risk the whole food chain of the aquatic ecosystem, mainly the primary consumers.     

Mn accumulation in a submerged plant Egeria densa (Hydrocharitaceae) is mediated by epiphytic bacteria

Many aquatic plants act as biosorbents, removing and recovering metals from the environment. To assess the biosorbent activity of Egeria densa, a submerged freshwater macrophyte, plants were collected monthly from a circular drainage area in Lake Biwa basin and the Mn concentrations of the plants were analysed. Mn concentrations in these plants were generally above those of terrestrial hyperaccumulators, and were markedly higher in spring and summer than in autumn. Mn concentrations were much lower in plants incubated in hydroponic medium at various pH levels with and without Mn supplementation than in field‐collected plants. The precipitation of Mn oxides on the leaves was determined by variable pressure scanning electron microscopy‐energy dispersive X‐ray analysis and Leucoberbelin blue staining. Several strains of epiphytic bacteria were isolated from the field‐collected E. densa plants, with many of these strains, including those of the genera Acidovorax, Comamonas, Pseudomonas and Rhizobium, found to have Mn‐oxidizing activity. High Mn concentrations in E. densa were mediated by the production of biogenic Mn oxide in biofilms on leaf surfaces. These findings provide new insights into plant epidermal bacterial flora that affect metal accumulation in plants and suggest that these aquatic plants may have use in Mn phytomining.     

Effects of invasive species on plant communities: an example using submersed aquatic plants at the regional scale

Submersed aquatic plants have a key role in maintaining functioning aquatic ecosystems through their effects on the hydrological regime, sedimentation, nutrient cycling and habitat of associated fauna. Modifications of aquatic plant communities, for example through the introduction of invasive species, can alter these functions. In the Sacramento-San Joaquin River Delta, California, a major invasive submersed plant, Brazilian waterweed Egeria densa, has become widespread and greatly affected the functionality of the submersed aquatic plant community. Rapid assessments of the distribution and abundance of this species are therefore crucial to direct management actions early in the season. Given the E. densa bimodal growth pattern (late spring and fall growth peaks), summer assessments of this species may indicate which and where other submersed species may occur and fall assessments may indicate where this and other species may occur in the following spring, primarily because the Delta’s winter water temperatures are usually insufficient to kill submersed aquatic plant species. We assessed community composition and distribution in the fall of 2007 and summer of 2008 using geostatistical analysis; and measured summer biomass, temperature, pH, salinity, and turbidity. In the fall of 2007, submersed aquatic plants covered a much higher proportion of the waterways (60.7%) than in the summer of 2008 (37.4%), with a significant overlap between the seasonal distribution of native and non-native species. Most patches were monospecific, and multispecies patches had significantly higher dominance by E. densa, co-occurring especially with Ceratophyllum demersum. As species richness of non-natives increased there was a significant decrease in richness of natives, and of native biomass. Sustained E. densa summer biomass negatively affected the likelihood of presence of Myriophyllum spicatum, Potamogeton crispus, and Elodea canadensis but not their biomass within patches. Depth, temperature and salinity were associated with biomass; however, the direction of the effect was species specific. Our results suggest that despite native and invasive non-native submersed plant species sharing available niches in the Delta, E. densa affects aquatic plant community structure and composition by facilitating persistence of some species and reducing the likelihood of establishment of other species. Successful management of this species may therefore facilitate shifts in existing non-native or native plant species.     

Relations between trophic state indicators and plant biomass in Florida lakes

We collected quantitative data on macrophyte abundance and water quality in 319 mostly shallow, polymictic, Florida lakes to look for relationships between trophic state indicators and the biomasses of plankton algae, periphyton, and macrophytes. The lakes ranged from oligotrophic to hypereutrophic with total algal chlorophylls ranging from 1 to 241 mg m^–3. There were strong positive correlations between planktonic chlorophylls and total phosphorus and total nitrogen, but there were weak inverse relationships between the densities of periphyton and the trophic state indicators total phosphorus, total nitrogen and algal chlorophyll and a positive relationship with Secchi depth. There was no predictable relationship between the abundance of emergent, floating-leaved, and submersed aquatic vegetation and the trophic state indicators. It was only at the highest levels of nutrient concentrations that submersed macrophytes were predictably absent and the lakes were algal dominated. Below these levels, macrophyte abundance could be high or low. The phosphorus–chlorophyll and phosphorus–Secchi depth relationships were not influenced by the amounts of aquatic vegetation present indicating that the role of macrophytes in clearing lakes may be primarily to reduce nutrient concentrations for a given level of loading. Rather than nutrient concentrations controlling macrophyte abundance, it seems that macrophytes acted to modify nutrient concentrations.     

Riverine macrophytes control seasonal nutrient uptake via both physical and biological pathways

1. In low-gradient, macrophyte-rich rivers, we expect that the significant change in macrophyte biomass among seasons will strongly influence both biological activity and hydraulic conditions resulting in significant effects on nutrient dynamics. Understanding seasonal variation will improve modelling of nutrient transport in river networks, including annual estimations of export, which could optimise decision-making and management outcomes.
2. We explored the relationships among seasonal differences in reach-scale nutrient uptake, macrophyte abundance, solute transport and transient storage in the River Gudenå (Denmark), a large macrophyte-rich river. We used the minimal pulse addition technique to measure uptake of ammonium, nitrate, soluble reactive phosphorus, as well as reach-scale metabolism, and surface transient storage in spring, summer, and autumn.
3. We found that riverine uptake changed among seasons and was linked to macrophyte biomass via both biological activity, reflected in reach-scale metabolism, and through physical processes, as solute transport was influenced by longitudinal dispersion. In this macrophyte-rich river, seasonal changes in macrophyte biomass affected contact time between the water and biota, which influenced ammonium and soluble reactive phosphorus uptake. Using stoichiometric scaling of reach-scale metabolism, we found that seasonal variation also influenced the relative contributions of autotrophic and heterotrophic biota in assimilatory uptake.
4. In summary, riverine nutrient uptake was not static, highlighting the importance of seasonality, with significant implications for modelling of nutrient export in river networks. Moreover, current management strategies that remove macrophyte biomass (i.e. weed cutting and dredging) will short-circuit the positive effects of enhanced nutrient uptake resulting from abundant macrophytes in rivers.

     

Prediction of potential macrophyte development in response to restoration measures in an urban riverine wetland

Wetland restoration efforts require practical models for predicting the effects of various measures on ecosystem structure and function. The present study examined the species diversity and abundance of macrophytes in relation to hydrological parameters in the Alluvial Zone National Park along the Austrian Danube with a main focus on the Lobau, an urban riverine wetland within the city limits of Vienna. A macrophyte regression model was developed based on the output of a 2D hydraulic model for different wetland management options. These management options describe possible rehabilitation measures by re-connecting the riverine wetland with the Danube. Stepwise multiple regressions revealed that the most important predictors of macrophyte diversity and abundance were water velocity at bankfull discharge (maximum water velocity) and size of shallow water areas (<1 m depth) during the growing season. Macrophyte abundance and diversity increased with decreasing water velocity and increasing shallow water area. These parameters integrate information about environmental features such as nutrients, light availability and hydrological disturbance for macrophytes and explained between 65 and 85% of the macrophyte distribution in an analysis. The model results enabled us to predict quantitatively the development and spatial distribution of macrophytes for different management options in this urban riverine wetland. These predictions suggest that partial reconnection could be a compromise solution at the scale of the whole riverine wetland, increasing the availability of suitable aquatic habitats and diversifying the types of existing wetland water bodies to establish potential new habitats for macrophyte species.     

Estimating fish abundance and biomass from eDNA concentrations: variability among capture methods and environmental conditions

Environmental DNA (eDNA) promises to ease noninvasive quantification of fish biomass or abundance, but its integration within conservation and fisheries management is currently limited by a lack of understanding of the influence of eDNA collection method and environmental conditions on eDNA concentrations in water samples. Water temperature is known to influence the metabolism of fish and consequently could strongly affect eDNA release rate. As water temperature varies in temperate regions (both seasonally and geographically), the unknown effect of water temperature on eDNA concentrations poses practical limitations on quantifying fish populations using eDNA from water samples. This study aimed to clarify how water temperature and the eDNA capture method alter the relationships between eDNA concentration and fish abundance/biomass. Water samples (1 L) were collected from 30 aquaria including triplicate of 0, 5, 10, 15 and 20 Brook Charr specimens at two different temperatures (7 °C and 14 °C). Water samples were filtered with five different types of filters. The eDNA concentration obtained by quantitative PCR (qPCR) varied significantly with fish abundance and biomass and types of filters (mixed‐design ANOVA, P < 0.001). Results also show that fish released more eDNA in warm water than in cold water and that eDNA concentration better reflects fish abundance/biomass at high temperature. From a technical standpoint, higher levels of eDNA were captured with glass fibre (GF) filters than with mixed cellulose ester (MCE) filters and support the importance of adequate filters to quantify fish abundance based on the eDNA method. This study supports the importance of including water temperature in fish abundance/biomass prediction models based on eDNA.     

Bird abundance and species richness on Florida lakes: influence of trophic status,lake morphology,and aquatic macrophytes

Data from 46 Florida lakes were used to examine relationships between bird abundance (numbers and biomass) and species richness, and lake trophic status, lake morphology and aquatic macrophyte abundance. Average annual bird numbers ranged from 7 to 800 birds km^–2 and bird biomass ranged from 1 to 465 kg km^–2. Total species richness ranged from 1 to 30 species per lake. Annual average bird numbers and biomass were positively correlated to lake trophic status as assessed by total phosphorus (r = 0.61), total nitrogen (r = 0.60) and chlorophyll a (r = 0.56) concentrations. Species richness was positively correlated to lake area (r = 0.86) and trophic status (r = 0.64 for total phosphorus concentrations). The percentage of the total annual phosphorus load contributed to 14 Florida lakes by bird populations was low averaging 2.4%. Bird populations using Florida lakes, therefore, do not significantly impact the trophic status of the lakes under natural situations, but lake trophic status is a major factor influencing bird abundance and species richness on lakes. Bird abundance and species richness were not significantly correlated to other lake morphology or aquatic macrophyte parameters after the effects of lake area and trophic status were accounted for using stepwise multiple regression. The lack of significant relations between annual average bird abundance and species richness and macrophyte abundance seems to be related to changes in bird species composition. Bird abundance and species richness remain relatively stable as macrophyte abundance increases, but birds that use open-water habitats (e.g., double-crested cormorant, Phalacrocorax auritus) are replaced by species that use macrophyte communities (e.g., ring-necked duck, Aythya collaris).     

Seasonal Effects in the Hormonal Control of Growth in the Submerged Aquatic Macrophyte Ceratophyllum demersum

The season dependent changes in growth response to treatment with auxin or gibberellin were studied in the aquatic macrophyte Ceratophyllum demersum. Control plants show, under experimental conditions, a maximum growth in length in February. In the same period most of the lateral buds appear. Growth of the lateral buds occurs later. IAA causes a stimulation of growth in length from late November or December until February, in concentrations of 10^?9M and 10^?6M. There is almost no stimulation of lateral bud formation by IAA, only a slight increase from late November until December occurs by the lowest concentrations used. The highest concentration used, 10^?4M, is in most cases supraoptimal for lateral bud formation; only when plants become dormant (August), this high dose may stimulate the process. GA₃, in concentrations of 10^?9, 10^?6 or 10^?4M, exhibits a dose dependent increase of the response with respect to growth in length and lateral bud formation. The response occurs earlier than that for IAA: already early in November, or December, until February. Growth of the lateral buds may show only a slight stimulation by IAA as well as GA in winter. From February until April all GA concentrations used could cause a small increase of the growth of sprouts. In the case of IAA, however, only the lowest concentration could cause a small increase.     

Behavior and season affect crayfish detection and density inference using environmental DNA

Although the presence/absence of aquatic invertebrates using environmental DNA (eDNA) has been established for several species, inferring population densities has remained problematic. The invasive American signal crayfish, Pacifastacus leniusculus (Dana), is the leading cause of decline in the UK's only native crayfish species, Austropotamobius pallipes (Lereboullet). Methods to detect species at low abundances offer the opportunity for the early detection, and potential eradication, of P. leniusculus before population densities reach threatening levels in areas occupied by A. pallipes. Using a factorial experimental design with aquaria, we investigated the impacts of biomass, sex ratio, and fighting behavior on the amount of eDNA released by P. leniusculus, with the aim to infer density per aquarium depending on treatments. The amount of target eDNA in water samples from each aquarium was measured using the quantitative Polymerase Chain Reaction. We show that the presence of eggs significantly increases the concentration of crayfish eDNA per unit of mass, and that there is a significant relationship between eDNA concentration and biomass when females are egg‐bearing. However, the relationship between crayfish biomass and eDNA concentration is lost in aquaria without ovigerous females. Female‐specific tanks had significantly higher eDNA concentrations than male‐specific tanks, and the prevention of fighting did not impact the amount of eDNA in the water. These results indicate that detection and estimate of crayfish abundance using eDNA may be more effective while females are ovigerous. This information should guide further research for an accurate estimation of crayfish biomass in the field depending on the season. Our results indicate that detection and quantification of egg‐laying aquatic invertebrate species using eDNA could be most successful during periods when eggs are developing in the water. We recommend that practitioners consider the reproductive cycle of target species when attempting to study or detect aquatic species using eDNA in the field.     

Photosynthetic and growth responses of Egeria densa to photosynthetic active radiation

Egeria densa, a submerged aquatic macrophyte native to South America, has successfully invaded many reservoirs in Brazil and elsewhere. Ecophysiological responses of E. densa to light availability were assessed in microcosm experiments. Under low light conditions, we found that apical shoots expanded more rapidly than those under higher light exposure, allowing the plant to reach the higher light conditions of the surface. E. densa showed low k_m (15.6-34.8 μmol m⁻² s⁻¹ PAR) and light compensation point values (7.5-16.2 μmol m⁻² s⁻¹ PAR), indicating that it is able to effectively exploit the low radiation levels available at high depths and turbid waters. This may represent a competitive advantage over other submerged species, and it helps to explain the successful spread of E. densa in Brazilian reservoirs.     

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.