Six steps towards operationalising freshwater ecoacoustic monitoring

1. Applications in bioacoustics and its sister discipline ecoacoustics have increased exponentially over the last decade. However, despite knowledge about aquatic bioacoustics dating back to the times of Aristotle and a vast amount of background literature to draw upon, freshwater applications of ecoacoustics have been lagging to date.
2. In this special issue, we present nine studies that deal with underwater acoustics, plus three acoustic studies on water-dependent birds and frogs. Topics include automatic detection of freshwater organisms by their calls, quantifying habitat change by analysing entire soundscapes, and detecting change in behaviour when organisms are exposed to noise.
3. We identify six major challenges and review progress through this special issue. Challenges include characterisation of sounds, accessibility of archived sounds as well as improving automated analysis methods. Study design considerations include characterisation analysis challenges of spatial and temporal variation. The final key challenge is the so far largely understudied link between ecological condition and underwater sound.
4. We hope that this special issue will raise awareness about underwater soundscapes as a survey tool. With a diverse array of field and analysis tools, this issue can act as a manual for future monitoring applications that will hopefully foster further advances in the field.

     

Spatio-temporal heterogeneity in river sounds: Disentangling micro- and macro-variation in a chain of waterholes

1. Passive acoustic monitoring is gaining momentum as a viable alternative method to surveying freshwater ecosystems. As part of an emerging field, the spatio-temporal replication levels of these sampling methods need to be standardised. However, in shallow waters, acoustic spatio-temporal patchiness remains virtually unexplored.
2. In this paper, we specifically investigate the spatial heterogeneity in underwater sounds observed within and between waterholes of an ephemeral river at different times of the day and how it could affect sampling in passive acoustic monitoring.
3. We recorded in the Einasleigh River, Queensland in August 2016, using a linear transect of hydrophones mounted on frames. We recorded four times a day: at dawn, midday, dusk, and midnight. To measure different temporal and spectral attributes of the recorded sound, we investigated the mean frequency spectrum and computed acoustic indices.
4. Both mean frequency spectrum and index analyses revealed that the site and diel activity patterns significantly influenced the sounds recorded, even for adjacent sites with similar characteristics along a single river. We found that most of the variation was due to temporal patterns, followed by between-site differences, while within-site differences had limited influence.
5. This study demonstrates high spatio-temporal acoustic variability in freshwater environments, linked to different species or species groups. Decisions about sampling design are vital to obtain adequate representation. This study thus emphasises the need to tailor spatio-temporal settings of a sampling design to the aim of the study, the species and the habitat.

     

SILIC: A cross database framework for automatically extracting robust biodiversity information from soundscape recordings based on object detection and a tiny training dataset

• 1.Passive acoustic monitoring (PAM) offers many advantages comparing with other survey methods and gains an increasing use in terrestrial ecology, but the massive effort needed to extract species information from a large number of recordings limits its application. The convolutional neural network (CNN) has been demonstrated with its high performance and effectiveness in identifying sound sources automatically. However, requiring a large amount of training data still constitutes a challenge.
• 2.Object detection is used to detect multiple objects in photos or videos and is effective at detecting small objects in a complex context, such as animal sounds in a spectrogram and shows the opportunity to build a good performance model with a small training dataset. Therefore, we developed the Sound Identification and Labeling Intelligence for Creatures (SILIC), which integrates online animal sound databases, PAM databases and an object detection-based model, for extracting information on the sounds of multiple species from complex soundscape recordings.
• 3.We used the sounds of six owl species in Taiwan to demonstrate the effectiveness, efficiency and application potential of the SILIC framework. Using only 786 sound labels in 133 recordings, our model successfully identified the species' sounds from the recordings collected at five PAM stations, with a macro-average AUC of 0.89 and a mAP of 0.83. The model also provided the time and frequency information, such as the duration and bandwidth, of the sounds.
• 4.To our best knowledge, this is the first time that the object detection algorithm has been used to identify sounds of multiple wildlife species. With an online sound-labeling platform embedded and a novel data preprocessing approach (i.e., rainbow mapping) applied, the SILIC shows its good performance and high efficiency in identifying wildlife sounds and extracting robust species, time and frequency information from a massive amount of soundscape recordings based on a tiny training dataset acquired from existing animal sound databases. The SILIC can help expand the application of PAM as a tool to evaluate the state of and detect the change in biodiversity by, for example, providing high temporal resolution and continuous information on species presence across a monitoring network.

     

Salinisation reduces biodiversity in neighbouring freshwater patches in experimental metacommunities

1. Aquatic ecosystems are biodiversity hot spots across many landscapes; therefore, the degradation of these habitats can lead to decreases in biodiversity across multiple scales. Salinisation is a global issue that threatens freshwater ecosystems by reducing water quality and local biodiversity. The effects of salinity on local processes have been studied extensively; however, the effects of salinisation or similar environmental stressors within a metacommunity (a dispersal network of several distinct communities) have not been explored.
2. We tested how the spatial heterogeneity and the environmental contrast between freshwater and saline habitat patches influenced cladoceran biodiversity and species composition at local and regional scales in a metacommunity mesocosm experiment. We defined spatial heterogeneity as the proportion of freshwater to saltwater patches within the metacommunity, ranging from a freshwater-dominated metacommunity to a saltwater-dominated metacommunity. Environmental contrast was defined as the environmental distance between habitat patches along the salinity gradient in which low-contrast metacommunities consisted of freshwater and low-salinity patches and high-contrast metacommunities consisted of freshwater and high-salinity patches.
3. We hypothesised that the α-richness of freshwater patches and metacommunity γ-richness would decrease as freshwater patches became less abundant along the spatial heterogeneity gradient in both low- and high-contrast metacommunities, because there would be fewer freshwater patches that could serve as source populations for declining populations. We hypothesised that low-contrast metacommunities would support more species across the spatial heterogeneity gradient than high-contrast metacommunities, because, via dispersal, low-salinity patches can support halotolerant freshwater species that can mitigate population declines in neighbouring freshwater patches, whereas` high-salinity patches will mostly support halophilic species, providing fewer potential colonisers to freshwater patches.
4. We found that α-richness of freshwater mesocosms and metacommunity γ-richness declined in saline-dominated metacommunities regardless of the environmental contrast between the freshwater and saline mesocosms. We found that environmental contrast influenced freshwater and saline community composition in low-contrast metacommunities by increasing the abundances of species that could tolerate low-salinity environments through dispersal, whereas freshwater and high-salinity communities showed limited interactions through dispersal.
5. Freshwater mesocosms had a disproportionate effect on the local and regional biodiversity in these experimental metacommunities, indicating that habitat identity may be more important than habitat diversity for maintaining biodiversity in some metacommunities. This study further emphasises the importance in maintaining multiple species-rich habitat patches across landscapes, particularly those experiencing landscape-wide habitat degradation.

     

The impacts of invasive ecosystem engineers in freshwaters: A review

1. Invasive species are a key stressor in freshwater ecosystems. When these species are also ecosystem engineers, their impacts are exacerbated because they modulate resource availability for a wide range of other species. The aim of this review is to synthesise existing knowledge of the impacts of invasive ecosystem engineers in freshwaters and identify knowledge gaps requiring further research.
2. The four questions explored in this review are: (1) What are the trends in research into invasive ecosystem engineers? (2) What are common negative effects of invasive ecosystem engineers in freshwater? (3) Do all impacts of invasive ecosystem engineers have negative consequences for biodiversity? (4) What happens when multiple ecosystem engineers interact? Four literature searches in Web of Science have been used to identify articles for the review and to estimate relative research effort between terrestrial, marine and freshwater ecosystems.
3. The number of research articles focusing on ecosystem engineers across all ecosystem types is increasing. Despite well-known examples of ecosystem engineer species in freshwaters (e.g. beaver), more research has focussed on terrestrial environments and invasive species.
4. The effects of invasive ecosystem engineers in freshwater systems are varied and often context dependent. Their effects on biodiversity or native ecosystem engineers are often shown to be negative; however, not all effects associated with these species are deleterious to native species. For instance, some invasive ecosystem engineers support native species through the provision of food or refuges.
5. Although freshwater ecosystems are often influenced by multiple species of ecosystem engineers (including native, invasive or both), little is known about interactions between these species or the combined effects of multiple ecosystem engineers. More research is also needed that relates the results of laboratory experiments to the field and develops methods for measuring factors that govern the impact of engineers on ecosystems. Understanding the spatial variability of the impacts of invasive ecosystem engineers as well as their interaction with anthropogenic stressors (e.g. hydrologic modification) is also necessary.
6. The lag in research surrounding invasive ecosystem engineers in freshwater compared to other biomes is concerning, as freshwater ecosystems support biodiversity disproportionate to the area they occupy. Creating predictive models of the impacts of freshwater ecosystem engineers would help anticipate the effects of invasive ecosystem engineers in freshwater and add to the broader understanding of their effects in other biomes.

     

Singing streams: Describing freshwater soundscapes with the help of acoustic indices

1. Understanding soundscapes, that is, the totality of sounds within a location, helps to assess nature in a more holistic way, providing a novel approach to investigating ecosystems. To date, very few studies have investigated freshwater soundscapes in their entirety and none across a broad spatial scale.
2. In this study, we recorded 12 freshwater streams in South East Queensland continuously for three days and calculated three acoustic indices for each minute in each stream. We then used principal component analysis of summary statistics for all three acoustic indices to investigate acoustic properties of each stream and spatial variation in their soundscapes.
3. All streams had a unique soundscape with most exhibiting diurnal variation in acoustic patterns. Across these sites, we identified five distinct groups with similar acoustic characteristics. We found that we could use summary statistics of AIs to describe daytimes across streams as well. Most difference in stream soundscapes was observed during the daytime with significant variation in soundscapes both between hours and among sites.
4. Synthesis and Application. We demonstrate how to characterize stream soundscapes by using simple summary statistics of complex acoustic indices. This technique allows simple and rapid investigation of streams with similar acoustic properties and the capacity to characterize them in a holistic and universal way. While we developed this technique for freshwater streams, it is also applicable to terrestrial and marine soundscapes.

     

Diurnal variation in freshwater ecoacoustics: Implications for site-level sampling design

1. Ecoacoustic methods are increasingly used to monitor the state of populations and ecosystems. In freshwater environments, they present the clear advantages of being non-invasive, reducing bias, and providing continuous observations instead of only limited sampling snapshots in time. However, similar to standard bioassessment methods, temporal variation and choice of indicators can greatly influence ecoacoustic assessments, highlighting the importance of sampling and analysis design.
2. In this study, we quantified diurnal variation in underwater sound and its effect on sampling regimes for two waterholes in the Einasleigh River, Northern Australia. Recording continuously for 6 days, and subsampling 5 s every 10 min, we found 22 distinct sounds that were emitted by fish, Hemiptera and Coleoptera as well as another 22 of abiotic or unknown origin.
3. Through rarefaction analyses, we found that subsampling the data to 60% of the recorded sound events resulted in capture of most of the 44 identified sound types. Temporal heterogeneity—patchy sound events through time—needs to be considered when maximising detected sound events. Reducing the sampling interval from every 10 min to half-hourly or hourly had a much greater effect on capturing all sound types compared to the number of days recorded or the length of the recording. Overall, only 10–20% of the sound events need to be annotated for most sound types to be described; for example, restricting analysis of the days recorded to only three and the recording interval to 0.5–1 s. Acoustic indices were dominated by three main event types—a diurnally flowing creek, a nocturnal chorus of Hemiptera, as well as a dawn chorus of terapontid fishes.
4. We conclude with two key messages: First, a select group of informative signals can be monitored using very simple methods—namely, converting an audio stream into indices using freely available software. Second, however, to detect less acoustically dominant sound events, manual annotation or single call processing will still be needed. While these findings are encouraging, similar analysis will need to be conducted within other freshwater ecosystems before general conclusions about optimal sampling regimes can be drawn.

     

Large-scale bioacoustic monitoring to elucidate the distribution of a non-native katydid

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Nonconsumptive predator effects modify crayfish‐induced bioturbation as mediated by limb loss: Field and mesocosm experiments

1. We addressed the implications of limb loss and regeneration for multispecies interactions and their impacts on ecosystem engineering in freshwater stream environments.
2. We included regenerative and nonregenerative crayfish as well as fish predators in a 2 × 2 factorial design to assess the effects on water turbidity of interactions between crayfish ecosystem engineers differing in regenerative status and their fish predators.
3. We demonstrated that crayfish limb loss and predation risks lead to more turbidity in field and mesocosm conditions. Moreover, ongoing regeneration of crayfish increased turbidity, while fish presence seemed to hinder crayfish turbidity‐inducing behaviors (such as tail‐flipping and burrowing) in the mesocosm experiment.
4. We confirmed that greater numbers of crayfish produce a greater amount of turbidity in situ in streams.
5. Although mechanical burrowing crayfish capacities may depend on crayfish burrowing classification (primary, secondary, or tertiary), our work emphasizes the implication for turbidity levels of crayfish autotomy in freshwater streams.

     

Monitoring the acoustic activity of an aquatic insect population in relation to temperature,vegetation and noise

1. Acoustic population monitoring is a noninvasive method that can be deployed continuously over long periods of time and at large spatial scales. One of the newly discovered threats acting on biological diversity is anthropogenic noise. High levels of anthropogenic noise occur in aquatic environments, yet their effects on animals living in freshwater habitats have very rarely been investigated.
2. Here, we used acoustic monitoring and automatic detection to assess the acoustic activity of a population of a soniferous freshwater insect.
3. The sounds emitted by the corixid Micronecta scholtzi were recorded in a Mediterranean pond with an array of 12 hydrophones. An automatic analysis based on a measure of the amplitude found in the frequency band of M. scholtzi was developed to assess the level of acoustic activity. We used functional linear models, accounting for the periodicity of the calling behaviour, to estimate the possible effect of temperature, vegetation and a noise due to an immersed engine.
4. The automatic analysis was validated as an efficient method to measure the acoustic activity. The monitoring revealed a clear 24-hr pattern in the acoustic activity of M. scholtzi and three peaks of activity during the morning. Functional linear models revealed negative effects of both temperature and vegetation and showed that an engine noise, played back for 2 hr during the night, elicited an increase in the level of acoustic activity of the population. Moreover, a cross-correlation procedure showed that noise delayed the acoustic activity of the population.
5. Our results suggest that acoustic survey and automatic detection are efficient methods to monitor the acoustic activity of an insect population especially in response to an anthropogenic disturbance.

     

Interspecific variation in the response of fish to anthropogenic noise

1. Elevated levels of anthropogenic noise, especially those observed through boating activity, can negatively impact fish species, but it remains unclear which species are most affected and which behavioural metrics are best used in assessing fish responses to underwater noise. The effects of boat sounds on freshwater species are of particular interest because freshwater environments are less studied than the marine realm despite comparably high levels of biodiversity.
2. In the current study, we examine the behavioural responses to boat noise in two freshwater species that differ in their hypothesised response to sound inputs: the spottail shiner (Notropis hudsonius), a species with known hearing specialisations, and the bluegill sunfish (Lepomis macrochirus), a species with more generalised hearing capabilities. Fish were presented with boat noise in a laboratory setting, and their swimming, escape and foraging behaviours were assessed to examine differential responses in relation to hypothesised hearing abilities.
3. Both species showed a decrease in general swimming behaviours but an increase in erratic movements in response to boat noise, indicative of stress responses for both species. Despite the similarities in response based on swimming behaviours however, only spottail shiners exhibited true escape responses to the onset of the noise stimulus, suggesting a more extreme reaction in the species with a more refined hearing ability.
4. Taken together, these results show that freshwater fish can respond to increased levels of anthropogenic noise, but that the severity of the response may differ based on auditory structures and therefore presumed hearing ability. The differences seen between behavioural metrics used (swimming vs. escape responses) also demonstrate how care must be taken in choosing a metric when developing exposure guidelines for underwater sound exposures, as different metrics could lead to differential impact assessments.

     

Positive biotic interactions in freshwaters: A review and research directive

1. Positive 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.
2. 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.
3. 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.
4. 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.
5. 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.

     

Acoustic monitoring reveals diversity and surprising dynamics in tropical freshwater soundscapes

1. Freshwater systems are globally threatened and in need of enhanced monitoring and assessment. We applied soundscape recording and analysis—which presents an opportunity for long-term, high-resolution animal community monitoring and assessment—to a freshwater context to better understand the acoustic diversity and dynamics of these systems.
2. We recorded the aquatic soundscape of a Neotropical freshwater swamp in Costa Rica for 23 days in January and February 2015 during the dry season. We classified biological sound types in these recordings and developed measurements of richness and occupancy based on this classification. We also calculated six complementary acoustic indices to assess soundscape diversity and daily and longer-term soundscape dynamics, and we examined correlations between these acoustic indices and sound type metrics.
3. We found rich soundscapes in which biological sounds were almost always present, and we classified 18 sound types that we attribute to aquatic insects. These sound types showed distinct daily patterns and exhibited temporal and spectral acoustic niche partitioning. Sound type richness was most correlated with the number of peaks index (correlation = .36; p < .001), while sound type occupancy was most correlated with the Bioacoustic Index (correlation = .92; p < .001). In contrast to generally high levels of acoustic activity, there were brief (approximately 1 hr), unexpected quiet periods around dawn and dusk.
4. This study represents an early attempt to comprehensively describe tropical freshwater soundscapes in a systematic and quantitative manner. We demonstrate that sound type classification and the quantification of acoustic occupancy capture aspects of soundscape diversity and dynamics that are complementary to those assessed by acoustic indices. Our analyses reveal that the soundscapes of this tropical wetland were diverse and exhibited daily dynamics that differed from those found in other ecosystems.

     

Omnivory and stability in freshwater habitats: Does theory match reality?

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Influence of acoustics on the collective behaviour of a shoaling freshwater fish

1. Understanding how collective behaviour of animals is influenced by anthropogenic activity is important for their conservation in an increasingly urbanised world. River infrastructure, e.g. for transport and electricity generation, and associated construction and operation, produces sound that can disrupt ecological processes.
2. Adopting a reductionist manipulative experimental approach using Eurasian minnow (Phoxinus phoxinus) as a model shoaling species, we compared the response of individuals and groups of five fish to a broadband acoustic stimulus in a tank containing still water.
3. Four metrics were calculated 10 min immediately before (control–sound stimulus absent) and during the acoustic treatment: (1) swimming speed, (2) persistence of swim paths, (3) cohesion of the group, and (4) orientation of group members.
4. On presentation of the stimulus, groups exhibited a consistent escape response compared to individuals for which behaviour was more variable. Thereafter, individuals swam faster and their swim paths were less persistent than during the control; no difference was observed for groups. Conversely, group integrity became more cohesive and members were more likely to orient in a common direction during the treatment compared to the control.
5. This study provides insight into the importance of collective behaviour of fish in relation to antipredator-like response to anthropogenic noise. Short-term shifts in behaviour are context specific and depend on whether fish are members of a shoal or solitary. The results indicate the potential for negative impacts of unnatural sound on the ecology of shoaling species that inhabit engineered freshwater environments.

     

Linking disturbances in neotropical landscapes with ecosystem functional traits: A preliminary assessment using epigaeic and leaf-litter ant communities

1. Environmental stressors and changes in land use have led to rapid and dramatic species losses and a reduction in associated ecosystem services.
2. Functional diversity has increasingly been suggested as an alternative for evaluating anthropogenic disturbances and restoration programs because it reflects different aspects of the relationship between biological diversity, ecosystem functioning and environmental constraints.
3. Ants are important components of terrestrial food webs and a key group associated with diverse interactions and ecosystem processes.
4. Additionally, their sensitiveness and rapid response to environmental changes pave the way for their use as informative metrics for monitoring several processes that threaten biodiversity and ecosystem services.
5. Consequently, ants' functional diversity might be considered leading edge indicators to assess ecosystem changes to ongoing anthropogenic disturbances.
6. The purpose of this study was to gauge the usefulness of epigaeic and leaf-litter ants' functional responses towards measuring ecosystem degradation (and/or restoration) in the Brazilian Amazon.
7. Our results demonstrate that functional traits exhibited sensitivity to ongoing changes, as well as different responses to specific environmental disturbances.
8. Communities supporting ants with specialised functional traits associated with pristine ecosystems suffered high species loss and were correlated with specific anthropogenic stressors.
9. The results obtained pinpoint the importance of pristine ecosystems for conserving unique functional attributes and biodiversity in neotropical forest landscapes.
10. We highlight the significance of further studies in this scope to guide environmental managers and practitioners in applying the best policies for integrated neotropical landscapes conservation, considering the competing interests of farmers, foresters and conservationists, but also the unpredictable effects of local and regional environmental changes.

     

Vegetation state changes in the course of shrub encroachment in an African savanna since about 1850 CE and their potential drivers

1. Shrub encroachment has far‐reaching ecological and economic consequences in many ecosystems worldwide. Yet, compositional changes associated with shrub encroachment are often overlooked despite having important effects on ecosystem functioning.
2. We document the compositional change and potential drivers for a northern Namibian Combretum woodland transitioning into a Terminalia shrubland. We use a multiproxy record (pollen, sedimentary ancient DNA, biomarkers, compound‐specific carbon (δ¹³C) and deuterium (δD) isotopes, bulk carbon isotopes (δ¹³Corg), grain size, geochemical properties) from Lake Otjikoto at high taxonomical and temporal resolution.
3. We provide evidence that state changes in semiarid environments may occur on a scale of one century and that transitions between stable states can span around 80 years and are characterized by a unique vegetation composition. We demonstrate that the current grass/woody ratio is exceptional for the last 170 years, as supported by n‐alkane distributions and the δ¹³C and δ¹³Corg records. Comparing vegetation records to environmental proxy data and census data, we infer a complex network of global and local drivers of vegetation change. While our δD record suggests physiological adaptations of woody species to higher atmospheric pCO₂ concentration and drought, our vegetation records reflect the impact of broad‐scale logging for the mining industry, and the macrocharcoal record suggests a decrease in fire activity associated with the intensification of farming. Impact of selective grazing is reflected by changes in abundance and taxonomical composition of grasses and by an increase of nonpalatable and trampling‐resistant taxa. In addition, grain‐size and spore records suggest changes in the erodibility of soils because of reduced grass cover.
4. Synthesis. We conclude that transitions to an encroached savanna state are supported by gradual environmental changes induced by management strategies, which affected the resilience of savanna ecosystems. In addition, feedback mechanisms that reflect the interplay between management legacies and climate change maintain the encroached state.