Publications

Fisheries resources face a confluence of socio-ecological challenges, the resolution of which requires interdisciplinary scientific information for sustainable utilization and management. The present study assessed gaps and challenges in Lake Victoria fisheries resources management for better research focus, policy formulation and improved governance of the fishery towards sustainability. Using key informant interviews and a plenary discussion with trans-disciplinary experts regarding Lake Victoria fisheries research, management and policy sectors, the present study identified current management challenges, gaps and priorities. The present study results indicate a constantly increasing fishing effort, poor enforcement of existing regulations and pollution and invasive weeds pose the greatest threats to the sustainability of Lake Victoria's fisheries resources. Policy gaps include a lack of regulations on emerging technologies (e.g. cage culture) and an absence of implementation guidelines and framework for some existing policies. The aspects and gaps of each challenge are discussed, using available literature for the lake, with policy and capacity interventions recommended under each section for sustainable management of Lake Victoria fisheries resources.

Among four extant and declining runs of Chinook Salmon Oncorhynchus tshawytscha in California’s Central Valley, none has declined as precipitously as the Sacramento River winter run. Migratory winter-run Chinook Salmon employ a life history strategy to reside and feed in stopover habitats on their way from freshwaters to the ocean. Migratory winter run, on their way from freshwaters to the ocean, employ a life history strategy to reside and feed in stopover habitats that have been affected by anthropogenic disturbance. Using acoustic telemetry, we examined conditions that influenced reach-specific movement and survival of out-migrating juveniles during a prolonged, multi-year drought from 2013 to 2016, followed by one of the wettest years on record (2017). We modeled how time-varying individual riverine covariates and reach-specific habitat features influenced smolt survival. Model selection favored a model with mean annual flow, intra-annual deviations from the mean flow at the reach scale, reach-specific channel characteristics, and travel time. Mean annual flow had the strongest positive effect on survival. A negative interaction between mean annual flow and intra-annual reach flow indicated that within-year deviations at the reach scale from annual mean flow had larger effects on survival in low-flow years. These factors resulted in higher survival during years with pulse flows or high flows. Changes in movement behavior in response to small-scale changes in velocity were negatively associated with survival. Covariates of revetment and wooded bank habitat were positively associated with survival, but the effect of these fixed habitat features changed depending on whether they were situated in the upper or lower part of the river. Fish exhibited density-dependent stopover behavior, with slowed downstream migration in the upper river in the wet years and extending to the lower river in the most critically dry year. This paper contributes two key findings for natural resource managers interested in flow management and targeted habitat restoration. The first is new insight into how the magnitude of pulse flows in dry and wet years affects survival of winter-run fish. The second is that density dependence influences where stopover habitat is used. Despite this, we identified an area of the river where fish consistently exhibited stopover behavior in all years.

In California (USA), seasonal lagoons provide important oversummer rearing habitat for juvenile steelhead trout (anadromous Oncorhynchus mykiss). However, key water quality parameters such as temperature and dissolved oxygen concentration can periodically approach or exceed the physiological tolerances of steelhead during the protracted dry season. A field study employing distributed temperature sensing technology, water quality monitoring, habitat mapping, and mark-recapture sampling was conducted to examine how shifting environmental conditions affected the performance and behavior of juvenile steelhead in the Scott Creek estuary/lagoon (Santa Cruz County). Abiotic conditions were driven by episodic inputs of seawater to the typically freshwater lagoon. During midsummer, the water column was vertically stratified which reduced suitable lagoon rearing habitat by approximately 40%. Nevertheless, steelhead abundance, growth, and condition factor were high during the summer and decreased in autumn following lagoon destratification and cooling. Unlike previous work, this study identified limited emigration from the lagoon to riverine habitat during the summer. Instead, juvenile steelhead exhibited crepuscular movement patterns within the lagoon, with peaks in upstream (to upper lagoon habitat) and downstream (to lower lagoon habitat) movement occurring at dawn and dusk, respectively. This study underscores that habitat complexity and connectivity are critical for juvenile steelhead production and persistence and provides insight into steelhead habitat use and behavior in seasonal lagoons.

Interactions with livestock in public settings such as county and state fairs can expose people and other livestock to faecal material capable of spreading zoonotic enteric pathogens. The goal of this study was to understand these risks by screening livestock faeces (n = 245) and livestock bedding (n = 155) for common zoonotic pathogens (Giardia, Cryptosporidium, Salmonella and Campylobacter spp.) and by measuring faecal indicator, Escherichia coli, concentrations in drinking water (n = 153), feed containers (n = 124) and bedding material (n = 157) in four livestock species (cattle, sheep, goats and swine) from county fairs in California, USA. Results indicated that sheep were most likely to have pathogens detected in faeces and that Giardia was the most frequently detected pathogen in both faeces (11%) and bedding (21%) across all livestock species. Additionally, increasing the number of animals in a holding pen at fairs, increasing the stocking density of animals in transport trailers to fairs, and having access to water in transport trailers significantly increased the odds of detecting pathogens in livestock faeces of any animal species. Observing solid material in water, stale feed and soiled bedding was associated with detecting higher E. coli concentrations. These findings provide evidence of faecal pathogens present at county fairs and suggest that site observations can aid in assessing levels of faecal exposure. The findings also indicate that the use of biosecurity measures such as (a) routine changing of livestock drinking water, feed and bedding, (b) not overstocking animals in holding pens and trailers and (c) keeping species in separate holding areas may reduce the risk of humans and livestock being exposed to faecal pathogens.

Temperature is a fundamental aspect of water quality in rivers, controlling the rate of many ecological processes. By disrupting the flow of water, large reservoirs and dams can fundamentally alter downstream temperature regimes by resetting the water temperature and flow boundary conditions at the dam release point. Therefore, it is critically important to understand how the volume and temperature of these releases interact with meteorological conditions to influence downstream temperature dynamics. In this study, we modeled temperature dynamics in a large regulated river (Sacramento River, CA, USA) to better understand how heat fluxes, and ultimately river temperatures, responded to different physical drivers connected to meteorology and the upstream boundary conditions established by dam operations. We used a quantitative process-based model of river temperature (RAFT), combined with sensitivity analysis, to identify the dominant physical drivers of temperature in the Sacramento River, and explored how these drivers varied over space and time. The physical drivers that had the greatest influence on temperature dynamics were dam discharge temperature, air temperature, and solar radiation. The primary controlling factors were dam discharge temperature in the most upstream reaches and air temperature in the most downstream reaches. When isolating the effect of boundary conditions on downstream river temperature, we observed that temperatures closer to the dam under all but low flow conditions responded more to changes in dam discharge temperature than dam discharge volume. Understanding the spatial and temporal extents of drivers of heat flux and their relative importance is critical when managing for river temperature.

Life cycle models (LCMs) provide a quantitative framework that allows evaluation of how management actions targeting specific life stages can have population-level impacts on a species. The LCM building process is also a powerful tool that can be used to identify data gaps existing in the knowledge of the target species, and that might strongly influence overall population dynamics. LCMs are particularly useful for species such as salmon that are highly migratory and use multiple aquatic ecosystems throughout their life. Furthermore, they are lacking for threatened Central Valley spring-run Chinook (Oncorhynchus tshawytscha; CVSC). Here, we developed a CVSC LCM to describe the dynamics of Mill, Deer and Butte Creek CVSC populations. We used model construction, calibration and a global sensitivity analysis to highlight important data gaps in the monitoring of those populations. In particular, we found strong model sensitivity and high uncertainty in various egg, juvenile and adult ocean life stages’ biological processes. We concluded that the current CVSC monitoring network is insufficient to support using a LCM to inform how future management actions (e.g., hydrology and habitat restoration) influence CVSC dynamics. We propose a series of monitoring recommendations, such as the development of an enhanced juvenile tracking monitoring program and the implementation of juvenile trapping efficiency methodology combined with genetic identification tools, to help fill highlighted data gaps. These additional data collection efforts will provide critical quantitative information about the status of this imperiled species at key life stages (e.g., CVSC juvenile abundance estimates), and create a more comprehensive monitoring framework fundamental for working on the recovery of the entire stock. Furthermore, additional data collection will strengthen the LCM parameterization and calibration process, and ultimately improve the model’s predictive performance.

1. The construction of dams on large rivers has negative impacts on native species. Environmental flows have been proposed as a tool to mitigate these impacts, but in order for these strategies to be effective they must account for disparate temperature and flow needs of different species.

2. We applied a multi-objective approach to identify trade-offs in dam release discharge and temperature for imperiled fishes with contrasting habitat requirements, while simultaneously meeting the needs of human water users.

3. Using the Sacramento River (California, USA) as a case study, our model suggests that current management aimed at providing high discharge for downstream water users and cold water for endangered winter-run Chinook salmon (Oncorhynchus tshawytscha) has detrimental impacts on threatened green sturgeon (Acipenser medirostris), which require warm water for juvenile growth.

4. We developed an optimal dam release scenario that can be used to meet the needs of salmon, sturgeon and human water users. Our results show that dam releases can be managed to successfully achieve these multiple objectives in all but the most severe drought years.

5. Synthesis and applications. This study shows that managing dam releases to meet the needs of a single species can have detrimental effects on other native species with different flow and temperature requirements. We applied a multi-objective approach to balance environmental requirements of multiple species with the needs of human water users. Our findings can be used to guide management of Shasta Dam and our approach can be applied to achieve multi-object management goals in other impounded rivers.

Indigenous Mayangna and Miskitu inhabit Nicaragua’s remote Bosawás Biosphere Reserve, located in the North Caribbean Coast Autonomous Region. They are sedentary horticulturists who supplement their diet with wild game, hunting with the assistance of dogs. To test whether hunting dogs increased the risk of human exposure to protozoal zoonotic neglected tropical diseases (NTDs), we sampled dogs from three communities varying in population size and level of contact with other communities. We screened dog feces (n = 58) for Giardia and Cryptosporidium DNA and sera (n = 78) for Trypanosoma cruzi antibodies and DNA. Giardia DNA was detected in 22% (13/58) of samples; sequencing revealed the presence of both zoonotic genotypes (assemblages A and B) and dog-specific genotypes (assemblages C and D). Giardia shedding was associated with community and age. Older dogs and those in the two, more accessible communities had greater odds of shedding parasites. Seroprevalence of T. cruzi antibodies, indicating prior exposure, was 9% (7/78). These results contribute to the limited literature on NTDs in indigenous populations, and suggest hunting dogs can both serve as sentinels of environmental NTDs and pose zoonotic risk for their owners and communities.

Water, sanitation, and hygiene (WASH) interventions aimed at reducing exposure to enteric pathogens have produced mixed health impacts, with some interventions finding no significant difference in health outcomes between intervention and control groups. While there are many explanations why individual WASH interventions may not achieve improved health outcomes, one reason is an incomplete understanding of the conditions that favor perpetuation and transmission of enteric pathogens in a given population and region. In this study, we developed a set of diarrhea-causing disease transmission models using measurements of drinking water contamination and child diarrhea over the same time period in the same study population. Using the disease transmission models, we examined how much of the observed diarrhea in children was due to waterborne transmission of enteric pathogens in a program in rural India that improved household sanitation but failed to produce improvements in child health. We focused on the role of two enteric protozoal pathogens, Cryptosporidium and Giardia, and diarrhea rates among children < 5 years of age in these communities. We found that Cryptosporidium and Giardia infections from drinking water contaminated with these enteric protozoa may have together caused as much as 65.8% (IQR 63.4–68.2%) or as little as 2.9% (IQR 2.3–3.4%) of the observed diarrhea in children depending on modeling assumptions about which protozoa species were present. These findings suggest implementing a single barrier, such as only sanitation, to disrupt the multiple pathways of fecal-oral transmission of enteric pathogens, rather than multiple barriers, such as sanitation and safe drinking water, may lead some interventions to fall short of achieving measurable health improvements. Finally, our research suggests that Cryptosporidium and Giardia may cause significant amounts of child diarrhea morbidity even at low levels of concentration when present in improved drinking water sources and their measurement should be including in community drinking water quality monitoring programs.

Mechanistic-based water temperature models simulating how environmental and operational conditions affect water temperature dynamics in the Shasta/Sacramento system can aid water resource management in the region. This report outlines the process of linking two water temperature models (an upstream reservoir model to a downstream river model), including calibration and validation from 2000 to 2015 and the procedures used to run the models operationally. Validation results (even years) indicated the reservoir model matched observed vertical temperature distribution and discharge temperature well, with a RMSE on the order of 1° C. When ran with known upstream boundary conditions, the river model accurately matched daily average river temperatures, with a RMSE near 0.5° C. Running the models in series (i.e. the reservoir model supplying boundary conditions to the river model) resulted in the RMSE of daily average river temperatures to increase to approximately 1° C. Both the reservoir and river models tended to perform poorer from May to October during the temperature management season and predict warmer temperatures than observed. While further model refinement is needed, the linked model framework represents a useful tool to evaluate temperature dynamics of the system under past and future environmental and operational conditions.

Efforts to eradicate open defecation and improve sanitation access are unlikely to achieve health benefits unless interventions reduce microbial exposures. This study assessed human fecal contamination and pathogen exposures in rural India, and the effect of increased sanitation coverage on contamination and exposure rates. In a cross-sectional study of 60 villages of a cluster-randomized controlled sanitation trial in Odisha, India, human and domestic animal fecal contamination was measured in community tubewells and ponds (n = 301) and via exposure pathways in homes (n = 354), using Bacteroidales microbial source tracking fecal markers validated in India. Community water sources were further tested for diarrheal pathogens (rotavirus, adenovirus and Vibrio cholerae by quantitative PCR; pathogenic Escherichia coli by multiplex PCR; Cryptosporidium and Giardia by immunomagnetic separation and direct fluorescent antibody microscopy). Exposure pathways in intervention and control villages were compared and relationships with child diarrhea examined. Human fecal markers were rarely detected in tubewells (2.4%, 95%CI: 0.3–4.5%) and ponds (5.6%, 95%CI: 0.8–10.3%), compared to homes (35.4%, 95%CI: 30.4–40.4%). In tubewells, V. cholerae was the most frequently detected pathogen (19.8%, 95%CI: 14.4–25.2%), followed by Giardia (14.8%, 95%CI: 10.0–19.7%). In ponds, Giardia was most often detected (74.5%, 95%CI: 65.7–83.3%), followed by pathogenic E. coli (48.1%, 95%CI: 34.8–61.5%) and rotavirus (44.4%, 95%CI: 34.2–54.7%). At village-level, prevalence of fecal pathogen detection in community drinking water sources was associated with elevated prevalence of child diarrhea within 6 weeks of testing (RR 2.13, 95%CI: 1.25–3.63) while within homes, higher levels of human and animal fecal marker detection were associated with increased risks of subsequent child diarrhea (P = 0.044 and 0.013, respectively). There was no evidence that the intervention, which increased functional latrine coverage and use by 27 percentage points, reduced human fecal contamination in any tested pathway, nor the prevalence of pathogens in water sources. In conclusion, the study demonstrates that (1) improved sanitation alone may be insufficient and further interventions needed in the domestic domain to reduce widespread human and animal fecal contamination observed in homes, (2) pathogens detected in tubewells indicate these sources are microbiologically unsafe for drinking and were associated with child diarrhea, (3) domestic use of ponds heavily contaminated with multiple pathogens presents an under-recognized health risk, and (4) a 27 percentage point increase in improved sanitation access at village-level did not reduce detectable human fecal and pathogen contamination in this setting.

Surface and groundwater contamination with fecal pathogens is a public health concern especially in low-income settings where these sources are used untreated. We modeled observed Cryptosporidium and Giardia contamination in community ponds (n = 94; 79% contaminated), deep tubewells (DTWs) (n = 107; 17%), and shallow tubewells (STWs) (n = 96; 19%) during the 2012 and 2013 monsoon seasons (June–August) in 60 villages in Puri District, India to understand sources and processes of contamination. Detection of Cryptosporidium and/or Giardia in a tubewell was positively associated with damage to the well pad for DTWs, the amount of human loading into pour-flush latrine pits nearby (≤15 m) for STWs, and the village literacy rate (for Giardia in STWs). Pond concentration levels were positively associated with the number of people practicing open defecation within 50 m and the sheep population for Cryptosporidium, and with the village illiteracy rate for Giardia. Recent rainfall increased the risk of Cryptosporidium in STWs (an extreme event) and ponds (any), while increasing seasonal rainfall decreased the risk of Giardia in STWs and ponds. Full latrine coverage in this setting is expected to marginally reduce pond Cryptosporidium contamination (16%) while increasing local groundwater protozoal contamination (87–306%), with the largest increases predicted for Cryptosporidium in STWs.

Cryptosporidium parvum and Giardia lamblia are zoonotic enteric protozoa of significant health concern where sanitation, hygiene, and water supplies are inadequate. We examined 85 stool samples from diarrhea patients, 111 pooled fecal samples by species across seven domestic animal types, and water from tube wells (N = 207) and ponds (N = 94) across 60 villages in coastal Odisha, India, for Cryptosporidium oocysts and Giardia cysts to measure occurrence, concentration/shedding, and environmental loading rates. Oocysts/cysts were detected in 12% of diarrhea patients. Detection ranged from 0% to 35% for Cryptosporidium and 0% to 67% for Giardia across animal hosts. Animal loading estimates indicate the greatest contributors of environmental oocysts/cysts in the study region are cattle. Ponds were contaminated with both protozoa (oocysts: 37%, cysts: 74%), as were tube wells (oocysts: 10%, cysts: 14%). Future research should address the public health concern highlighted from these findings and investigate the role of domestic animals in diarrheal disease transmission in this and similar settings.

Background As part of the Total Sanitation Campaign (1999–2012), the Indian Government promoted construction and use of tens of millions of household latrines to improve public health in rural communities, areas where tubewells are often the main source of drinking water. In this study, we aimed to identify causes of tubewell contamination with the protozoal diarrhoeal pathogens, Cryptosporidium spp and Giardia spp in a coastal area in Puri District, Odisha, India. 

Methods We used data from a large-scale cluster randomised controlled trial of health eff ects of improved household sanitation in Puri District, gathered in 60 villages during the 2012 and 2013 monsoon seasons from June to August. We used multivariable modelling to identify associations between Cryptosporidium spp and Giardia spp contamination and variables such as tubewell characteristics, village socioeconomic characteristics, spatial densities of human and livestock faecal sources around each tubewell including leaching from latrine pits and cowsheds, and meteorological conditions. 

Findings We included data for 107 deep public and 96 shallow private tubewells of which 36 (18%) were contaminated. We found strong evidence that latrines were the source of contamination of local shallow groundwater used for drinking. Each 10 additional person-years of latrine loading, within 10–15 m of a shallow tubewell increased the odds of Cryptosporidium spp and Giardiaspp detection by 21% (OR 1·21, 95% CI 1·06–1·38) and 44% (1·44, 1·12–1·85), respectively. For deep groundwater, the risk of latrine contamination was raised by 1% if the latrines were situated within 150m for Giardia or within 500 m for Cryptosporidium of a deep tubewell (OR 1·01, 95% CI 0·998–1·012, and 1·01, 1·000–1·027, respectively). In deep tubewells, both protozoa were more often detected when the well pad was cracked or missing than when intact (OR 7·10, 95% CI 1·92–20·57 for Cryptosporidium; 5·91, 1·18–29·60 for Giardia). For every three goats in a village, we noted an increased OR of 1·09 (95% CI 1·03–1·14) for Cryptosporidium spp contamination in shallow tubewells. Antecedent rainfall also showed important mediating eff ects on contamination in shallow tubewells, depending on protozoan species and rainfall mechanism.

Interpretation The promotion of latrines to increase the proportion of the population using an improved sanitation facility (MDG 7.9) might increase Cryptosporidium spp and Giardia spp contamination in groundwater drinking sources, especially shallow groundwater. If health gains are to be achieved from improved sanitation for all (SDG 6.2), piped supplies of centrally treated water might need to replace local groundwater drinking sources in settings which are vulnerable to faecal contamination from latrines 

Cryptosporidium parvum, Giardia lamblia, and Toxoplasma gondii are waterborne protozoal pathogens distributed worldwide and empirical evidence suggests that wetlands reduce the concentrations of these pathogens under certain environmental conditions. The goal of this study was to evaluate how protozoal removal in surface water is affected by the water temperature, turbidity, salinity, and vegetation cover of wetlands in the Monterey Bay region of California. To examine how protozoal removal was affected by these environmental factors, we conducted observational experiments at three primary spatial scales: settling columns, recirculating wetland mesocosm tanks, and an experimental research wetland (Molera Wetland). Simultaneously, we developed a protozoal transport model for surface water to simulate the settling columns, the mesocosm tanks, and the Molera Wetland. With a high degree of uncertainty expected in the model predictions and field observations, we developed the model within a Bayesian statistical framework. We found protozoal removal increased when water flowed through vegetation, and with higher levels of turbidity, salinity, and temperature. Protozoal removal in surface water was maximized (~ 0.1 hour− 1) when flowing through emergent vegetation at 2% cover, and with a vegetation contact time of ~ 30 minutes compared to the effects of temperature, salinity, and turbidity. Our studies revealed that an increase in vegetated wetland area, with water moving through vegetation, would likely improve regional water quality through the reduction of fecal protozoal pathogen loads.

Constructed wetland systems are used to reduce pollutants and pathogens in wastewater effluent, but comparatively little is known about pathogen transport through natural wetland habitats. Fecal protozoans, including Cryptosporidium parvum, Giardia lamblia, and Toxoplasma gondii, are waterborne pathogens of humans and animals, which are carried by surface waters from land-based sources into coastal waters. This study evaluated key factors of coastal wetlands for the reduction of protozoal parasites in surface waters using settling column and recirculating mesocosm tank experiments. Settling column experiments evaluated the effects of salinity, temperature, and water type (“pure” versus “environmental”) on the vertical settling velocities of C. parvum, G. lamblia, and T. gondii surrogates, with salinity and water type found to significantly affect settling of the parasites. The mesocosm tank experiments evaluated the effects of salinity, flow rate, and vegetation parameters on parasite and surrogate counts, with increased salinity and the presence of vegetation found to be significant factors for removal of parasites in a unidirectional transport wetland system. Overall, this study highlights the importance of water type, salinity, and vegetation parameters for pathogen transport within wetland systems, with implications for wetland management, restoration efforts, and coastal water quality.

Fecal pathogen contamination of watersheds worldwide is increasingly recognized, and natural wetlands may have an important role in mitigating fecal pathogen pollution flowing downstream. Given that waterborne protozoa, such as Cryptosporidium and Giardia, are transported within surface waters, this study evaluated associations between fecal protozoa and various wetland-specific and environmental risk factors. This study focused on three distinct coastal California wetlands: (i) a tidally influenced slough bordered by urban and agricultural areas, (ii) a seasonal wetland adjacent to a dairy, and (iii) a constructed wetland that receives agricultural runoff. Wetland type, seasonality, rainfall, and various water quality parameters were evaluated using longitudinal Poisson regression to model effects on concentrations of protozoa and indicator bacteria (Escherichia coli and total coliform). Among wetland types, the dairy wetland exhibited the highest protozoal and bacterial concentrations, and despite significant reductions in microbe concentrations, the wetland could still be seen to influence water quality in the downstream tidal wetland. Additionally, recent rainfall events were associated with higher protozoal and bacterial counts in wetland water samples across all wetland types. Notably, detection of E. coli concentrations greater than a 400 most probable number (MPN) per 100 ml was associated with higher Cryptosporidium oocyst and Giardia cyst concentrations. These findings show that natural wetlands draining agricultural and livestock operation runoff into human-utilized waterways should be considered potential sources of pathogens and that wetlands can be instrumental in reducing pathogen loads to downstream waters.