Freshwater Ecology Research Articles

A Fluorescence and Surface-Enhanced Raman Spectroscopic Dual-Modal Aptasensor for Sensitive Detection of Cyanotoxins.

The ability to detect trace analytes without necessitating solid surface attachment or complicated processing steps would facilitate the translation of sensors for monitoring environmental toxins in the field. To address a critical unmet need in fresh water ecology, we have developed a dual-modal aptamer-based biosensor (aptasensor), featuring fluorescence and surface-enhanced Raman spectroscopy (SERS), for sensitive and selective detection of hepatotoxin microcystin-LR (MC-LR). The rational sensor design is based on the high affinity of the cyanine (Cy3) dye-modified complementary DNA (Cy3-cDNA) strand toward the plasmonic gold nanostars (GNSs) in comparison to the Cy3-cDNA/aptamer duplex. The preferential binding of MC-LR toward the MC-LR-specific aptamer triggers the dissociation of Cy3-cDNA/aptamer duplexes, which switches the Cy3's fluorescence "off" and SERS "on" due to the proximity of Cy3 dye to the GNS surface. Both fluorescence and SERS intensities are observed to vary linearly with the MC-LR concentration over the range of investigation. We have achieved high sensitivity and excellent specificity with the aptasensor toward MC-LR, which can be attributed to the fluorescence quenching effect, significant SERS enhancement by the GNSs, and the high affinity of the aptamer toward the MC-LR analytes. We further demonstrate the applicability of the present aptasensor for detection of MC-LR in a diverse set of real water samples with high accuracy and excellent reproducibility. With further refinement, we believe that the aptamer-driven complementary assembly of the SERS and fluorescence sensing constructs can be applied for rapid, multiplexed, and robust measurements of environmental toxins in the field.

Growth and rapid succession of methanotrophs effectively limit methane release during lake overturn

Lakes and reservoirs contribute substantially to atmospheric concentrations of the potent greenhouse gas methane. Lake sediments produce large amounts of methane, which accumulate in the oxygen-depleted bottom waters of stratified lakes. Climate change and eutrophication may increase the number of lakes with methane storage in the future. Whether stored methane escapes to the atmosphere during annual lake overturn is a matter of controversy and depends critically on the response of the methanotroph assemblage. Here we show, by combining 16S rRNA gene and pmoA mRNA amplicon sequencing, qPCR, CARD-FISH and potential methane-oxidation rate measurements, that the methanotroph assemblage in a mixing lake underwent both a substantial bloom and ecological succession. As a result, methane oxidation kept pace with the methane supplied from methane-rich bottom water and most methane was oxidized. This aspect of freshwater methanotroph ecology represents an effective mechanism limiting methane transfer from lakes to the atmosphere.

Goose and hare faeces as a source of nutrients and dissolved organic matter for bacterial communities in the newly formed proglacial lake Ventisquero Negro (Patagonia, Argentina)

Fil: Vega, Evelyn Nathalie. Universidad Nacional del Comahue. Centro Regional Universitario Bariloche. Laboratorio de Limnologia; Argentina. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Conicet - Patagonia Norte. Instituto de Investigaciones en Biodiversidad y Medioambiente. Universidad Nacional del Comahue. Centro Regional Universidad Bariloche. Instituto de Investigaciones en Biodiversidad y Medioambiente; Argentina

Potential impacts of non‐native fish on the threatened mahseer (Tor) species of the Indian Himalayan biodiversity hot spot

Abstract Mahseer (Tor) fish species are critical components of locally adapted freshwater food webs across the Indian Himalayan biodiversity hotspot; however, multiple human stressors compounded by climate change have significantly depleted their populations over recent decades. Mahseer species are now considered locally vulnerable or endangered in many regions. Hydropower projects in particular have fragmented populations, impairing genetic exchange, obstructing migratory paths, and changing the structure and functioning of riverine habitats, especially of formerly fast‐flowing rivers. Worryingly, a literature survey and group discussions reveal that the increasing spread of non‐native fish species further compounds threats to mahseer and overall freshwater ecology. A better understanding of the current distribution, habitat requirement, and dispersal of non‐native fish is therefore essential to manage the growing threats to mahseer in the Indian Himalayan region.

Positive biotic interactions in freshwaters: A review and research directive

AbstractPositive interspecific interactions such as mutualism, commensalism, and facilitation are globally ubiquitous. Although research on positive interactions in terrestrial and marine systems has progressed over the past few decades, comparatively little is known about them in freshwater ecosystems. However, recent advances have brought the study of positive interactions in freshwater systems to a point where synthesis is warranted.In this review, we catalogue the variety of direct positive interactions described to date in freshwater ecosystems, discuss factors that could influence prevalence and impact of these interactions, and provide a framework for future research.In positive interactions, organisms exchange key resources such as nutrients, protection, transportation, or habitat to a net benefit for at least one participant. A few mutualistic relationships have received research attention to date, namely seed‐dispersing fishes, crayfishes and their ectosymbiotic cleaners, and communal‐spawning stream fishes. Similarly, only a handful of commensalisms have been studied, primarily phoretic relationships. Facilitation via ecosystem engineering has received more attention, for example habitat modification by beavers and bioturbation by salmon.It is well known that interaction outcomes vary with abiotic and biotic context. However, only a few of studies have examined context dependency in positive interactions in freshwater systems. Likewise, positive interactions incur costs as well as benefits; conceptualising interactions in terms of net cost/benefit to participants will help to clarify complex interactions.It is likely that there are many positive interactions that have yet to be discovered in freshwater systems. To identify these interactions, we encourage inductive natural history studies combined with hypotheses deduced from general ecological models. Research on positive interactions must move beyond small‐scale experiments and observational studies and adopt a cross‐scale approach. Likewise, we must progress from reducing systems to oversimplified pairwise interactions, toward studying positive interactions in broader community contexts. Positive interactions have been greatly overlooked in applied freshwater ecology, but have great potential for conservation, restoration, and aquaculture.

Near-bed velocity and shear stress of open-channel flow over surface roughness

Near-bed flows in rough-bed open-channels are of relevance to river engineering, freshwater ecology and hydraulic design. Detailed measurements of near-bed flow velocity and turbulence distributions are rarely available. This paper aims to improve our understanding of near-bed flow characteristics. We performed experiments of turbulent open-channel flow over roughness elements, and made fine-scale measurements of three-dimensional velocity and turbulence quantities, using an acoustic Doppler velocimeter. The experiments allowed for the d-type, the intermediate-type and the k-type of surface roughness. The fine scale measurements covered the entire flow region in the bed vicinity, including cavities below the crests of roughness elements. Below the crests, the longitudinal velocity field displays one weak eddy in the cavity between adjacent elements for the d-type of roughness, two eddies of different strengths for the intermediate-type of roughness, and boundary-layer velocity structures for the k-type of roughness. Above the crests, the main (or longitudinal) flow velocity shows a variety of vertical structures for the three types of surface roughness. At the elevation equal to one half the roughness height above the crests, there is a lack of longitudinal variations in the main flow velocity over the length of element—cavity sequence. In other words, main-flow velocity fluctuations are small; the velocity distributions have a standard deviation equal to 5%, 6% and 7% of their mean values for the d-type, the intermediate-type, and the k-type of roughness, respectively. Practically the influence of roughness surface may be considered as capped at that elevation. The secondary flow has the highest intensity nearest the bed. Turbulence shear has the highest average value at the crest level of roughness elements.

Editorial: Freshwater sustainability and aquatic ecology in a fast-changing world

Editorial: Freshwater sustainability and aquatic ecology in a fast-changing world

Network Analysis Reveals Seasonal Patterns of Bacterial Community Networks in Lake Taihu under Aquaculture Conditions

Bacterial communities play essential roles in multiple ecological processes, such as primary production and nutrient recycling in aquatic systems. However, although the composition, diversity and function of bacterial communities have been well studied, little is known about the interactions and co-occurrence characteristics of these communities, let alone their seasonal patterns. To investigate the seasonal variations of bacterial community interactions, we collected water samples from four seasons in Lake Taihu and applied network analysis to reveal bacterial community interactions. Bacterial community networks were non-random in structure, and interactions among bacterial taxa in the networks varied markedly in different seasons. The autumnal bacterial network was the largest and most complex among obtained networks, whereas the spring correlation network was the simplest, having no module hubs or connectors. The important species of the networks were the dominant bacterial phyla/classes (e.g., Alphaproteobacteria and Bacteroidetes), although their relative abundance varied among seasons. The relationships between species and measured environmental variables changed over seasons; fewer environmental factors were correlated with bacterial species in the spring bacterial network, while we observed a greater number of species-environment correlations in the winter network. Our study highlights the seasonal differences in bacterial community interactions and expands our understanding of freshwater microbial ecology in systems affected by aquaculture.

Designing Eco‐Friendly Water Intake Portfolios in a Tropical Andean Stream Network

AbstractIn view of the rapid proliferation of water infrastructures worldwide, balancing human and ecosystem needs for water resources is a critical environmental challenge of global significance. While there is abundant literature on the environmental impacts of individual water infrastructures, little attention has been paid to their cumulative effects in river networks, which may have basin‐to‐global impacts on freshwater ecology. Here we developed a methodological framework based on Pareto frontier analysis for optimizing trade‐offs between water withdrawal and ecological indicators. We applied this framework to a mountainous Ecuadorian headwater river network that is part of a continental water transfer for supply and demand management to optimize ecological conditions and the operation of 11 water intake structures used to provide potable water to the city of Quito. We found that the current water intake configuration has an important effect on the total length of fifth‐order stream sections (65% reduction compared to premanaged condition) and isolates 70.9% of the headwater stream length. The Pareto frontier analysis identified water intake portfolios (i.e., different combinations of intake sites) that decreased ecological impacts by 7.8% points (pp) and 13.0 pp for connectivity and stream order change, respectively, while meeting Quito's water demands. Additional portfolios accounting for monthly variability in water demand and resources further decrease the ecological impact up to 9.6 pp in connectivity and 13.4 pp in stream order. These eco‐friendly portfolios suggest that adaptive management at basin level may help optimize water withdrawal to fulfill urban demands while preserving ecological integrity.

Mixotrophic protists and a new paradigm for marine ecology: where does plankton research go now?

Abstract Many protist plankton are mixotrophs, combining phototrophy and phagotrophy. Their role in freshwater and marine ecology has emerged as a major developing feature of plankton research over recent decades. To better aid discussions, we suggest these organisms are termed “mixoplankton”, as “planktonic protist organisms that express, or have potential to express, phototrophy and phagotrophy”. The term “phytoplankton” then describes phototrophic organisms incapable of phagotrophy. “Protozooplankton” describes phagotrophic protists that do not engage in acquired phototrophy. The complexity of the changes to the conceptual base of the plankton trophic web caused by inclusion of mixoplanktonic activities are such that we suggest that the restructured description is termed the “mixoplankton paradigm”. Implications and opportunities for revision of survey and fieldwork, of laboratory experiments and of simulation modelling are considered. The main challenges are not only with taxonomic and functional identifications, and with measuring rates of potentially competing processes within single cells, but with decades of inertia built around the traditional paradigm that assumes a separation of trophic processes between different organisms. In keeping with the synergistic nature of cooperative photo- and phagotrophy in mixoplankton, a comprehensive multidisciplinary approach will be required to tackle the task ahead.

Passive acoustic monitoring as a potential tool to survey animal and ecosystem processes in freshwater environments

Abstract Biodiversity in freshwater habitats is decreasing faster than in any other type of environment, mostly as a result of human activities. Monitoring these losses can help guide mitigation efforts. In most studies, sampling strategies predominantly rely on collecting animal and vegetal specimens. Although these techniques produce valuable data, they are invasive, time‐consuming and typically permit only limited spatial and temporal replication. There is need for the development of complementary methods. As observed in other ecosystems, freshwater environments host animals that emit sounds, either to communicate or as a by‐product of their activity. The main freshwater soniferous groups are amphibians, fish, and macroinvertebrates (mainly Coleoptera and Hemiptera, but also some Decapoda, Odonata, and Trichoptera). Biophysical processes such as flow or sediment transport also produce sounds, as well as human activities within aquatic ecosystems. Such animals and processes can be recorded, remotely and autonomously, and provide information on local diversity and ecosystem health. Passive acoustic monitoring (PAM) is an emerging method already deployed in terrestrial environments that uses sounds to survey environments. Key advantages of PAM are its non‐invasive nature, as well as its ability to record autonomously and over long timescales. All these research topics are the main aims of ecoacoustics, a new scientific discipline investigating the ecological role of sounds. In this paper, we review the sources of sounds present in freshwater environments. We then underline areas of research in which PAM may be helpful emphasising the role of PAM for the development of ecoacoustics. Finally, we present methods used to record and analyse sounds in those environments. Passive acoustics represents a potentially revolutionary development in freshwater ecology, enabling continuous monitoring of dynamic bio‐physical processes to inform conservation practitioners and managers.

Lakes as Islands: Editor's Note

In this edition of the Paper Trail, two researchers are connected by water, which is vast in many ways, thus making their overlapping interest in the rusty crayfish seem all the more improbable. For the established researcher, he came to see that lake islands are like any other, except that they are surrounded by land and not by water. He and a colleague chose to study rusty crayfish, as a component of aquatic ecology, and because of this, their work influenced the next generation. Thus, the connection was made to the arising researcher, who was searching for direction following his thesis work in freshwater ecology. Both have added significantly to our scientific understanding of rusty crayfish (an invasive species) abundance in lakes. In addition, they share a great concern for helping others in scholarly pursuits, which is also part of the reason for the Paper Trail.

Diatoms (Bacillariophyta) as bio-indicators

Bio-indicators such as diatoms from algae considered to be key factors in ecological studies as an assessment of freshwater ecology. Algae are very sensitive to environmental changes and reflect the spatiotemporal changes on exists or biomass of diatoms in waters. Diatoms have been used not just for the assessment of water quality, but also can be used as an organic pollution indicator in the freshwater ecosystems, such as algal water bloom. The reason for using diatoms as bio-indicators was for several characteristics such as rapid growth, and represent high biomass in the freshwater ecosystem. Also, diatoms have high biodiversity among the other aquatic biota and energy flow and cycling. Compared with the other aquatic biota, diatoms reflect ecological disturbance due to high sensitivity to light, temperature, water flow, pH, and oxygen content. Additionally, diatoms are used as an assessment of eutrophication, organic pollution and climate change.

Celebrating women conducting research in freshwater ecology … and how the citation game is damaging them

We highlight women’s contributions to freshwater ecology by firstly considering the historical context and gender-based barriers faced by women attempting to gain an education and secure research jobs in science over the past 100+ years. The stories of four remarkable, pioneering women in freshwater ecology (Kathleen Carpenter, Ann Chapman, Rosemary Lowe-McConnell and Ruth Patrick) illustrate the impact of barriers, emphasise the significance of their contributions and provide inspiration for the challenges ahead. Women still face barriers to participation in science, and the second part of the paper focuses on a current form of discrimination, which is citation metrics used to measure the ‘quality’ or ‘impact’ of research. We show that arguments that citation metrics reflect research quality are logically flawed, and that women are directly disadvantaged by this practice. Women are also indirectly disadvantaged in ecology because they are more likely to carry out empirical than theoretical research, and publications are generated more slowly from empirical research. Surveys of citation patterns in ecology reveal also that women are less likely to be authors of review papers, which receive three times more citations than do original articles. Unless unfettered use of citation metrics is stopped, research will be damaged, and women will be prominent casualties.

Future of Coastal Lagoons in Arid Zones under Climate Change and Anthropogenic Pressure. A Case Study from San Jose Lagoon, Mexico

In arid and semiarid zones, groundwater plays a key role in the ecology and availability of freshwater. Coastal lagoons in arid zones have great importance as a refuge for species of flora and fauna, as a source of freshwater, and for recreational purposes for local communities and tourism. In addition, as environments under natural stress, they are suffering pressure from anthropogenic activities and climate change, especially in zones with intense touristic development as in the case of the Baja California Peninsula in northwest Mexico. In this paper, we analyze the future of a coastal lagoon impacted by climate change and anthropogenic pressures. We constructed a groundwater MODFLOW-SWI2 model to predict changes in freshwater–saltwater inputs and correlated them with the geospatial analysis of the distribution and evolution of the water body and surrounding vegetation. The methodology was applied to the San Jose lagoon, one of the most important wetlands in the Baja California peninsula, which had been affected by anthropogenic activities and endangered by climate change. According to our water balance, the deficit of the San Jose aquifer will increase by 2040 as a result of climate change. The water table north of the lagoon will drop, affecting the amount of freshwater inflow. This reduction, together with an increase of evapotranspiration and the sea-level rise, will favor an increase of mineralization, reducing the surface water and groundwater quality and in consequence affecting the vegetation cover. Without proper management and adequate measures to mitigate these impacts, the lagoon may disappear as a freshwater ecosystem. Results of this research indicate that the use of a groundwater flow model, together with a geospatial analysis provide effective tools to predict scenarios for the future of coastal lagoons, and serve as a basis for land planning, nature conservation, and sustainable management of these ecosystems.

Effects of Riparian Invasive Nonindigenous Plants on Freshwater Quantity and Ecological Functioning in Mesic Temperate Landscapes

As invasive nonindigenous plants colonize streamside ecosystems, they can transform ecological functioning by replacing native species, altering interspecific interactions, and reducing biodiversity. As a result of the intimate relationship between the riparian areas and their associated freshwater ecosystems, alteration of the riparian community may be reflected in the freshwater ecosystem. Research conducted in arid climates repeatedly has demonstrated that invasive nonindigenous plants can reduce water quantity, but far fewer studies have investigated the effects on water quantity and aquatic ecosystem functions when nonindigenous plants invade mesic temperate riparian areas. We identified 35 studies published since 1981 documenting impacts to freshwater ecosystems in mesic temperate climates attributable to invasions of riparian areas by nonindigenous plants. These studies revealed impacts on water quantity and on ecosystem function related to water temperature, edaphic characteristics, and physical and chemical alteration in allochthonous inputs. However, our assessment of the results found great variability in hydrological and ecological responses, with the strongest evidence for changes to (1) the timing of allochthonous organic matter inputs, (2) organic matter decomposition rates in aquatic ecosystems, and (3) aquatic community structure. In addition, in watersheds densely colonized by nitrogen-fixing invasive species, stream eutrophication is likely to occur. Because of the variability in the existing research results, more studies need to be focused specifically on invaded mesic temperate riparian ecosystems. Furthermore, more research is needed to consider the impact of additional problematic plant species that have yet to be studied, the correlation between invasive plant density and aquatic ecosystem response, the relationship between the length of time a plant community has been invaded and the aquatic community's reaction, and if invasive plant management and native species reintroduction can help restore the aquatic ecosystem.

The Water Hyacinth Microbiome: Link Between Carbon Turnover and Nutrient Cycling.

Water hyacinth (WH), a large floating plant, plays an important role in the biogeochemistry and ecology of many freshwaters globally. Its biogeochemical impact on wetland functioning is strongly mediated by the microbiome associated with its roots. However, little is known about the structure and function of this WH rhizobiome and its relation to wetland ecosystem functioning. Here, we unveil the core and transient rhizobiomes of WH and their key biogeochemical functions in two of the world's largest wetlands: the Amazon and the Pantanal. WH hosts a highly diverse microbial community shaped by spatiotemporal changes. Proteobacteria lineages were most common, followed by Actinobacteria and Planctomycetes. Deltaproteobacteria and Sphingobacteriia predominated in the core microbiome, potentially associated with polysaccharide degradation and fermentation of plant-derived carbon. Conversely, a plethora of lineages were transient, including highly abundant Acinetobacter, Acidobacteria subgroup 6, and methanotrophs, thus assuring diverse taxonomic signatures in the two different wetlands. Our findings point out that methanogenesis is a key driver of, and proxy for, community structure, especially during seasonal plant decline. We provide ecologically relevant insights into the WH microbiome, which is a key element linking plant-associated carbon turnover with other biogeochemical fluxes in tropical wetlands.

An ecologically constrained procedure for sensitivity analysis of Artificial Neural Networks and other empirical models.

Sensitivity analysis applied to Artificial Neural Networks (ANNs) as well as to other types of empirical ecological models allows assessing the importance of environmental predictive variables in affecting species distribution or other target variables. However, approaches that only consider values of the environmental variables that are likely to be observed in real-world conditions, given the underlying ecological relationships with other variables, have not yet been proposed. Here, a constrained sensitivity analysis procedure is presented, which evaluates the importance of the environmental variables considering only their plausible changes, thereby exploring only ecological meaningful scenarios. To demonstrate the procedure, we applied it to an ANN model predicting fish species richness, as identifying relationships between environmental variables and fish species occurrence in river ecosystems is a recurring topic in freshwater ecology. Results showed that several environmental variables played a less relevant role in driving the model output when that sensitivity analysis allowed them to vary only within an ecologically meaningful range of values, i.e. avoiding values that the model would never handle in its practical applications. By comparing percent changes in MSE between constrained and unconstrained sensitivity analysis, the relative importance of environmental variables was found to be different, with habitat descriptors and urbanization factors that played a more relevant role according to the constrained procedure. The ecologically constrained procedure can be applied to any sensitivity analysis method for ANNs, but obviously it can also be applied to other types of empirical ecological models.

Integrating catchment land cover data to remotely assess freshwater quality: a step forward in heterogeneity analysis of river networks

Attempts to obtain information from geospatial data in freshwater ecology is a highly challenging task requiring the development of new concepts and adequate tools. Conventionally, river networks are represented as collections of vectors, but they can also be thought of as a succession of raster cells corresponding to the digital elevation model of the landscape they traverse. Based on the principle that each cell in the river raster collects environmental influences from its upstream drainage basin, we defined a remote measure of the potential of pollution named RWQ (Remote Water Quality). We used the CORINE Land Cover categories found in the catchment area of each cell in the river network grouped by ecological relevance and weighted by their respective areas in the catchment. To refine the index to account for the proximity of potential pollution sources, we tested successive buffers of 1 km up to the full catchment of each investigated point, concluding that the RWQ calculated for the full catchment is the most suitable index. For implementation, we developed RIVERenhancer, a free Python-based ArcGIS tool making possible the enhancement of raster river networks with data extracted from various files. The reliability of RWQ was tested with the aid of in situ measurements of chemical and biological water quality obtained from several sources in Danube basin (Romania and Hungary). The strong correlation with field data shows that this index can be considered a surrogate to depict the quality of freshwater habitats and to analyse network heterogeneity. The strength of this concept comes from taking advantage of the dendritic nature of river networks, opening new directions of operations for large scale approaches concerning important issues in global ecology, biogeography and conservation.

Growth and toxicity of Halomicronema metazoicum (Cyanoprokaryota, Cyanophyta) at different conditions of light, salinity and temperature.

ABSTRACTCyanobacteria may live in the water column and in the benthos of aquatic environments, or be symbionts of other organisms, as in the case of Phormidium-like cyanobacteria, known to influence the ecology of freshwater and marine ecosystems. A strain of Phormidium-like cyanobacteria has been recently isolated as a free-living epiphyte of leaves of Posidonia oceanica (L.) Delile in the Mediterranean sea and its biology and ecology are herein investigated. It was identified as Halomicronema metazoicum, previously known uniquely as a symbiont of marine sponges. We cultivated it in a range of light irradiances, temperatures and salinities, to establish the most suitable conditions for the production of allelopathic and toxic compounds. The bioactivity of its spent culture medium was measured by means of standard toxicity tests performed on two model organisms. Our results indicate that at least two bioactive compounds are produced, at low and high irradiance levels and at two temperatures. The main compounds influencing the survival of model organisms are produced at the highest temperature and high or intermediate irradiance levels. The present research contributes to the understanding of critical toxigenic relationships among cyanobacteria and invertebrates, possibly influencing the ecology of such a complex environment as P. oceanica. Future isolation, identification and production of bioactive compounds will permit their exploitation for biotechnologies in the field of ecological conservation and medical applications.