Biodiversity surveys of aquatic systems often include DNA metabarcoding analyses of environmental samples that are collected through filtration of large volumes of water. The standard practice of sterile collection and filtration in or near the field sites is challenging to implement in remote locations, and filtration of large volumes is a limiting step, especially for water from highly productive systems or with high suspended sediment loads. Recent trials have shown that passive samplers can be effective for aquatic metabarcoding to document metazoan diversity, but that this approach needs to be trialed under a wider variety of conditions and across more diverse taxa. Here we assess the utility of passive sampling for documenting the diversity of bacteria in six tropical aquatic environments (one lake, one reservoir, two mountain streams and two blackwater rivers). We find that passive collectors generally recover significantly higher diversity of Bacteria compared to filtered samples, despite capturing significantly less overall DNA than active water filtering. However, the communities captured by the two methods show significant differences within sites, with only 26% of the Bacteria ASVs recovered by both methods. These differences were largely driven by relative abundances of taxa within Actinobacteriota, Campilobacterota, Desulfobacterota, and Proteobacteria. Our results demonstrate that passive collectors can be a cost-effective solution for monitoring aquatic microbial diversity but that the two methods are not interchangeable. Additional work is necessary to understand the selectivity of both passive collectors and active water filtering for eDNA studies.

Freshwater harmful algal blooms (HABs) are a global environmental, economic, social, and public health hazard. While there is an increasing understanding of the ecological considerations of HABs, there is limited understanding of human dimensions and management needs. We conducted semi-structured key informant interviews with 28 water managers and researchers to better understand how they perceive current management and to identify future management priorities in regard to HABs. For this study, we interviewed 31 key informants from three regions of the United States (New England, Ohio, and the Mountain West). We solicited insights across aspects of HABs management, including prevention, forecasting, monitoring, response, and communication. Nutrient management was the main consideration for the prevention of HAB events. Key informants noted that forecasting has the potential to be a valuable tool in the future but is not yet accurate enough at a local scale for widespread use. Monitoring was found to be implemented in varying ways across and even within the states and regions, with a need for more funding and standardization. HAB event responses vary greatly from chemical and physical treatments that suppress toxins to no-swim advisories, all with a mix of strengths and weaknesses. Finally, an increase in and improvement of communication efforts was identified as critical for reducing public health risks. These findings provide perceptions of current management practices and future plans while including opportunities to improve current freshwater HAB management efforts.

The freshwater and saltwater aquatic food sector has experienced the most significant growth in recent years and is increasingly recognized as a sustainable alternative for fostering prosperous societies self-sufficiently and ecologically. One primary economic and health risk factor in aquaculture production is health control, with potentially more severe impacts observed in tropical and developing countries. While metagenomics holds great promise for application in agro-industrial fields like aquaculture, its adoption remains limited. Consequently, this study aimed to assess the prospects for developing and applying metagenomics in identifying pathogens in freshwater aquaculture. The WIPO database was used to search for patents developed using metagenomics to monitoring pathogens in freshwater aquaculture. Metagenomics methods have been extensively employed in different fields, such as, medicine, veterinary, biotechnology, agriculture, particularly in studies focusing on microbial communities in different ecosystems. In aquaculture, the utilization of metagenomics has predominantly revolved around investigating antibiotic resistance genes, primarily in saltwater farms. Despite this, freshwater aquaculture, particularly in fish and crustacean farming, aligns closely with sustainable development goals, notably (SDGs) 2, 3, 6, and 13. Countries such as the United States of America, South Korea, and Canada stand at the forefront of utilizing metagenomics for disease monitoring in freshwater aquaculture, evidenced by their active patent developments. The metagenomic analysis, coupled with bioinformatics tools and databases, represents a rapid, secure, and non-invasive approach to environmental monitoring for preventive purposes.Systematic review registrationhttps://osf.io/srpyz/, identifier 10.17605/OSF.IO/SRPYZ.

Fish from Cambodia's Tonle Sap Lake are economically, culturally, and nutritionally significant for people in the Lower Mekong Basin, providing income, livelihoods, and protein. Fish in this system generally migrate toward upstream Mekong River in dry season and return in early wet season. However, drivers of fish migration from Tonle Sap Lake to the Mekong River are not well-understood. In this paper, we utilized Mixed Effects Random Forest to predict the catch weight of six fish species migrating from the Tonle Sap Lake to the Mekong River using precipitation, lunar cycle, and hydrologic conditions like river stage, streamflow, flow magnitude, and timing as predictors. As a surrogate for fish migration, we used daily fish catch weight from 2002 through 2008 at the bagnet, or Dai, fisheries along Tonle Sap River, a migration corridor connecting Tonle Sap Lake to the Mekong River. We found that migration of large fish was mainly cued by streamflow and flow magnitude, while smaller fish migrate depending on the combination of streamflow and flow timing. Streamflow less than average cumulative flow was the most important driver for migration of Pangasianodon hypophthalmus, and Cirrhinus microlepis. Migration of Cyclocheilichthys enoplos and Osteochilus melanopleurus was highly dependent on the number of low- and minimum-flow days. Cumulative flows, period of high flow and water level were the main predictors of the small mud-carp Henicorhynchus entmema's migration, while individuals of Labiobarbus leptocheilus migrated out of the Tonle Sap Lake depending on the number of days after 7-, 30-, and 90-day minimum flows. These results suggest that flow characteristics can be used to aid conservation and adaptive management of Cambodia's Dai fisheries.

Particulate organic matter (POM) characteristics and variability have been widely studied along the land-ocean aquatic continuum, yet, gaps remain in quantifying its source composition, fluxes, and dynamics at the river-estuary interface. POM in rivers consists of a complex mixture of sources, derived both from locally produced (i.e. phytoplankton) and from adjacent ecosystems (e.g. terrestrial POM). Each source differ in its trophic and biogeochemical characteristics, hence impacting its integration into local food webs, its transfer to estuaries and sea, and its contribution to biogeochemical processes. In this study, we use a robust approach based on in situ POM to characterize river POM end-members, to quantify POM composition and dynamics, and to identify the related key drivers. This study was performed at the River-Estuary interface of one of the main rivers in Western Europe (the Loire River, France). For 3 years, we conducted bimonthly measurements of carbon and nitrogen isotopic (δ13C, δ15N) and elemental (C/N) ratios to quantify the contribution of two sources (phytoplankton and terrestrial POM) to the POM mixture and calculated annual fluxes of particulate organic carbon (POC) and nitrogen (PN) sources. Throughout the year, POM consisted of ~65% phytoplankton and 35% terrestrial POM. The mean annual export fluxes were 40.6 tPOC/year and 2.45 tPN/year over the studied period, with half of it originating from phytoplankton (53 and 55% for POC and PN, respectively). We observed a clear seasonal pattern in POM composition: phytoplankton predominated from March to October, in relation to high primary production, while terrestrial contributions were the highest from November to February, driven by greater autumn-winter hydrodynamics. Our study illustrate the interest of such an approach to quantify POM composition in aquatic system and estimate source fluxes, and provide fundamental results for estimating seasonal baselines in food webs, establishing biogeochemical budgets, and quantifying POM exports to estuarine and marine environments. Applying this methodology across a broad spectrum of aquatic systems should enhance our understanding of biogeochemical processes and organic matter transformation along the land-ocean continuum and illustrates the contribution of these ecosystems to global biogeochemical cycles.

IntroductionDeterrents that use acoustics to guide fish away from dangerous areas (e.g., water intakes) depend on the elicitation of avoidance in the target species. Background noise is often neglected when testing acoustic deterrents, but it is important to account for its effects as freshwater environments present a wide variety of ambient soundscapes.MethodsUsing the widely studied goldfish (Carassius auratus) as a suitable experimental model, this study adopted a reductionist approach to investigate the relationship between the startle response to a pure tone signal and background noise. Under laboratory conditions, the startle responses of individual goldfish exposed to 120 ms tones at 250 Hz and four Sound Pressure Levels (SPLs: 115, 125, 135, 145 dB re 1 μPa) were quantified in the presence (treatment) and absence (ambient - control) of band-limited random noise (105 dB re 1 μPa).Results and discussionWhen observing the dose-response relationship, the proportion of fish that startled to the signal increased with SPL in both the treatment and control, although there was no difference between them, suggesting that the signal-to-noise ratio was not influential under the conditions tested. However, further analysis using Signal Detection Theory indicated that the was higher in the noisy treatment than the control when responding to both false alarms (startle during a pre-signal period) and hits (startle to an external stimulus during the pre-signal period). Furthermore, fish were better able to discriminate (d?) external stimuli over time (during the pre-signal period) in the treatment than control. There is a need to consider the role of background noise when designing acoustic fish deterrents that depend on the exhibition of avoidance behaviors.

The effects of agriculture and flood control practices accrued over more than a century have impaired aquatic habitats and their fish communities in the Mississippi Alluvial Valley, the historic floodplain of the Lower Mississippi River prior to leveeing. As a first step to conservation planning and adaptive management, we developed and tested a conceptual model of how changes to this floodplain have affected stream environments and fish assemblages. The model is deliberately simple in structure because it needs to be understood by stakeholders ranging from engineers to farmers who must remain engaged to ensure effective conservation. Testing involved multivariate correlative analyses that included descriptors of land setting, water quality, and fish assemblages representing 376 stream samples taken over two decades and ranging in Strahler stream order from 1 to 8. The conceptual model was adequately corroborated by empirical data, but with unexplained variability that is not uncommon in field surveys where gear biases, temporal biases, and scale biases prevent accurate characterizations. Our conceptual model distinguishes three types of conservation actions relevant to large agricultural floodplains: reforestation of large parcels and riparian zone conservation, in-channel interventions and connectivity preservation, and flow augmentation. Complete restoration of the floodplain may not be an acceptable option to the agriculture community. However, in most cases the application of even the most basic measures can support the return of sensitive aquatic species. We suggest that together these types of conservation actions can bring improved water properties to impacted reaches, higher reach biodiversity, more intolerant species, and more rheophilic fishes.