Environmental impacts of cage aquaculture in the southeast arm of Lake Malawi: water and sediment quality and food web changes

Lake Malawi is a great lake not only because of its size (30,800 km2) but also because of its unique fish diversity. The lake contains the highest number of freshwater fish species in the world. The fish species are hypothesized to have radiated within the lake, which is 1-2 million years old. The collapse of the capture fishery in Lake Malawi between the 1970s and 1990s led to the launch of cage culture of indigenous fish species in 2004 in the south east arm of the lake. While cage culture has been practiced for many years in temperate lakes and seas, the fish farm in Lake Malawi is the first in the African Great Lakes and, therefore, not much information currently exists that is relevant to the impact of cage culture on such a large, species-rich tropical lake. Consequently, a study was done between January and December, 2007, at the fish farm in Lake Malawi to determine potential impacts of cage wastes on the environment. The study found that, just like in temperate systems where 70-87% of C, N and P added through feed get dispersed into the environment, discharges from fish cages in Lake Malawi were between 71-88% of the nutrients added through feed. The discharges were proportional to the amount of feed added so that as production and feed supply increase over time, more cage wastes would be generated and released into the environment. The discharges were exacerbated by poor stocking and feeding regimes. Production periods were longer (mean of 376±42 days) than if recommended stocking and feeding rates were followed. Feed quality may also have affected production performance and waste generation in the cages, but was not studied. The cage wastes were incorporated into the food web and support the wild fishes in the vicinity of the fish farm. Impacts of the cage wastes on the water column and sediments in the vicinity of the cages were minimal during the study period, probably because of rapid and efficient dispersion of the wastes by strong water currents, that averaged 9.3 cm s-1, through the cages and high consumption of the cage wastes by large numbers of wild fishes which aggregated around the cages. The wild fishes also helped to disperse the cage wastes over a larger area through consumption, translocation and defecation. However, as production increases, the amount of cage wastes generated may overwhelm mitigation by dispersion by water currents and consumption by wild fishes, particularly if many cages are deployed close together and interfere with current flows. Based on my observations, a fish farm that produces 15,000 tonnes fish/yr in Lake Malawi would generate 1249, 113 and 21 megamoles/yr of C, N and P, respectively, that are comparable or higher than DOC, TDN and TDP loadings observed in the most disturbed large river systems draining into Lake Malawi. The impacts of these river systems in Lake Malawi have been well documented, particularly around river mouths and in the more densely populated and shallower southern portion of the lake, where algal communities and their sedimentation rates have begun to change. Cage culture discharges may accelerate these changes

From sink to source: high inter-annual variability in the carbon budget of a southern African wetland

We report on three years of continuous monitoring of carbon dioxide (CO2) and methane (CH4) emissions in two contrasting wetland areas of the Okavango Delta, Botswana: a perennial swamp and a seasonal floodplain. The hydrographic zones of the Okavango Delta possess distinct attributes (e.g. vegetation zonation, hydrology) which dictate their respective greenhouse gas (GHG) temporal emission patterns and magnitude. The perennial swamp was a net source of carbon (expressed in CO2-eq units), while the seasonal swamp was a sink in 2018. Despite differences in vegetation types and lifecycles, the net CO2 uptake was comparable at the two sites studied in 2018/2020 (−894.2 ± 127.4 g m−2 yr−1 at the perennial swamp, average of the 2018 and 2020 budgets, and −1024.5 ± 134.7 g m−2 yr−1 at the seasonal floodplain). The annual budgets of CH4 were however a factor of three larger at the permanent swamp in 2018 compared to the seasonal floodplain. Both ecosystems were sensitive to drought, which switched these sinks of atmospheric CO2 into sources in 2019. This phenomenon was particularly strong at the seasonal floodplain (net annual loss of CO2 of 1572.4 ± 158.1 g m−2), due to a sharp decrease in gross primary productivity. Similarly, drought caused CH4 emissions at the seasonal floodplain to decrease by a factor of 4 in 2019 compared to the previous year, but emissions from the perennial swamp were unaffected. Our study demonstrates that complex and divergent processes can coexist within the same landscape, and that meteorological anomalies can significantly perturb the balance of the individual terms of the GHG budget. Seasonal floodplains are particularly sensitive to drought, which exacerbate carbon losses to the atmosphere, and it is crucial to improve our understanding of the role played by such wetlands in order to better forecast how their emissions might evolve in a changing climate. Studying such hydro-ecosystems, particularly in the data-poor tropics, and how natural stressors such as drought affect them, can also inform on the potential impacts of man-made perturbations (e.g. construction of hydro-electric dams) and how these might be mitigated. Given the contrasting effects of drought on the CO2 and CH4 flux terms, it is crucial to evaluate an ecosystem's complete carbon budget instead of treating these GHGs in isolation

Phenology is the dominant control of methane emissions in a tropical non-forested wetland

Tropical wetlands are a significant source of atmospheric methane (CH4), but their importance to the global CH4 budget is uncertain due to a paucity of direct observations. Net wetland emissions result from complex interactions and co-variation between microbial production and oxidation in the soil, and transport to the atmosphere. Here we show that phenology is the overarching control of net CH4 emissions to the atmosphere from a permanent, vegetated tropical swamp in the Okavango Delta, Botswana, and we find that vegetative processes modulate net CH4 emissions at sub-daily to inter-annual timescales. Without considering the role played by papyrus on regulating the efflux of CH4 to the atmosphere, the annual budget for the entire Okavango Delta, would be under- or over-estimated by a factor of two. Our measurements demonstrate the importance of including vegetative processes such as phenological cycles into wetlands emission budgets of CH4

δ13C methane source signatures from tropical wetland and rice field emissions

The atmospheric methane (CH4) burden is rising sharply, but the causes are still not well understood. One factor of uncertainty is the importance of tropical CH4 emissions into the global mix. Isotopic signatures of major sources remain poorly constrained, despite their usefulness in constraining the global methane budget. Here, a collection of new δ13CCH4 signatures is presented for a range of tropical wetlands and rice fields determined from air samples collected during campaigns from 2016 to 2020. Long-term monitoring of δ13CCH4 in ambient air has been conducted at the Chacaltaya observatory, Bolivia and Southern Botswana. Both long-term records are dominated by biogenic CH4 sources, with isotopic signatures expected from wetland sources. From the longer-term Bolivian record, a seasonal isotopic shift is observed corresponding to wetland extent suggesting that there is input of relatively isotopically light CH4 to the atmosphere during periods of reduced wetland extent. This new data expands the geographical extent and range of measurements of tropical wetland and rice δ13CCH4 sources and hints at significant seasonal variation in tropical wetland δ13CCH4 signatures which may be important to capture in future global and regional models. This article is part of a discussion meeting issue ‘Rising methane: is warming feeding warming? (part 2)’

Gap-filling eddy covariance methane fluxes : Comparison of machine learning model predictions and uncertainties at FLUXNET-CH4 wetlands

Time series of wetland methane fluxes measured by eddy covariance require gap-filling to estimate daily, seasonal, and annual emissions. Gap-filling methane fluxes is challenging because of high variability and complex responses to multiple drivers. To date, there is no widely established gap-filling standard for wetland methane fluxes, with regards both to the best model algorithms and predictors. This study synthesizes results of different gap-filling methods systematically applied at 17 wetland sites spanning boreal to tropical regions and including all major wetland classes and two rice paddies. Procedures are proposed for: 1) creating realistic artificial gap scenarios, 2) training and evaluating gap-filling models without overstating performance, and 3) predicting halfhourly methane fluxes and annual emissions with realistic uncertainty estimates. Performance is compared between a conventional method (marginal distribution sampling) and four machine learning algorithms. The conventional method achieved similar median performance as the machine learning models but was worse than the best machine learning models and relatively insensitive to predictor choices. Of the machine learning models, decision tree algorithms performed the best in cross-validation experiments, even with a baseline predictor set, and artificial neural networks showed comparable performance when using all predictors. Soil temperature was frequently the most important predictor whilst water table depth was important at sites with substantial water table fluctuations, highlighting the value of data on wetland soil conditions. Raw gap-filling uncertainties from the machine learning models were underestimated and we propose a method to calibrate uncertainties to observations. The python code for model development, evaluation, and uncertainty estimation is publicly available. This study outlines a modular and robust machine learning workflow and makes recommendations for, and evaluates an improved baseline of, methane gap-filling models that can be implemented in multi-site syntheses or standardized products from regional and global flux networks (e.g., FLUXNET).Peer reviewe

Methane and carbon dioxide fluxes from a permanent wetland in the Okavango Delta, Botswana, 2018-2020.

The data resource consists of half hourly time series of heat (latent and sensible) and trace gas (carbon dioxide and methane) fluxes obtained by eddy-covariance, gas concentrations and ancillary meteorological data (e.g. air temperature, relative humidity, pressure, photosynthetically active radiation, total incoming radiation, wind speed and direction). The data were collected at Guma Lagoon (18°57'53.01"S; 22°22'16.20"E), in the perennially flooded area of the Okavango Delta, Botswana, for the purpose of quantifying greenhouse gas fluxes over a Cyperus papyrus stand. The measurement period was 01/01/2018 to 31/12/2020. The instrumentation was installed the UK Centre for Ecology and Hydrology; monthly maintenance and data collection visits were effected by the Okavango Research Institute, University of Botswana. The research was funded through NERC grant reference NE/N015746/2 - The Global Methane Budget

Methane and carbon dioxide fluxes from a seasonal wetland in the Okavango Delta, Botswana, 2018-2020.

The dataset consists of a continuous time series of heat (latent and sensible) and trace gas (carbon dioxide and methane) fluxes obtained by eddy-covariance, gas concentrations and some ancillary meteorological data (e.g. air temperature, relative humidity, pressure, photosynthetically active radiation, total incoming radiation, wind speed and direction). The data were collected at Nxaraga, on the south edge of Chief’s Island (19°32'53''S; 23°10'45"E), in the seasonally flooded area of the Okavango Delta, Botswana, for the purpose of quantifying greenhouse gas fluxes from seasonal floodplains. The data is reported at half-hourly interval for the measurement period 01/01/2018 to 31/12/2020. Missing data were caused by instrumentation downtime and are reported as -999

Tracking methane fluxes using intact polar and core lipids in an aridity transect of the Okavango Delta (Botswana)

Wetland methane (CH4) emissions are the largest natural source in the global CH4 budget, contributing to roughly one third of total natural and anthropogenic emissions. As the second most important anthropogenic greenhouse gas in the atmosphere after CO2, CH4 is strongly associated with climate feedbacks. The different pathways of biochemical cycling of CH4, which exert a primary control on atmospheric CH4 concentrations through its production and biological consumption, remain poorly constrained. It is therefore crucial to understand and, if possible, quantify these variable CH4 sources to natural climate variability. We studied a soil transect (up to seven sites, 250 m long) across a seasonal floodplain at Nxaraga on the south-west part of the Chief’s Island, Okavango Delta, Botswana, over three years (2018 – 2020, 50 samples in total). Previous studies showed a clear link between CH4 fluxes and soil water content in the area, with CH4 fluxes in the seasonally flooded soils of up to 492 nmol m-2 s-1. To constrain biomass active in CH4 production (specifically, methanogenic archaea) intact and core isoprenoid lipids (and their stable carbon isotope signature) were quantified on a High Performance Liquid Chromatograph (HPLC) and on an high-resolution mass spectrometer ("Orbitrap"). To constrain biomass of CH4 oxidizers (i.e. bacterial methanotrophs), core (hopanol) and intact lipids (i.e., bacteriohopanepolyols (BHPs)) were analyzed non-derivatized on an Orbitrap. Confirming their proposed methanotroph source, BHP-aminopentol and methylcarbamate-BHP were detected and their variation correlated positively with those of hopanols and archaeol lipids. Methyl-amino BHPs however were not detected in the soils. In-depth study of their environmental variation points towards two bacterial communities depending on the pH, EC and water content of the soils. This will be confirmed or refuted by bacterial community profiling based on 16S RNA genes, and functional genes for methane oxidatio

Methane emissions from a pristine southern African wetland

We present one year of continuous monitoring of methane emissions at two contrasting sites in the Okavango Delta, a UNESCO World Heritage site located in North-Western Botswana. The wetlands of the Okavango Delta are in pristine condition and can be separated into three categories: permanently flooded, seasonally flooded (3-6 months per year) and occasionally flooded (typically once per decade). We set up two eddy-covariance systems in August 2017, one at Guma Lagoon (18°57'53.01" S; 22°22'16.20" E) at the edge of an extensive papyrus bed in the permanently-flooded section of the delta, and the second one at Nxaraga on the SW edge of Chief’s Island (19°32'53'' S; 23°10'45'' E) in the seasonal floodplain. We also conduct monthly measurements of methane and carbon dioxide fluxes by using a clear dynamic chamber at Nxaraga along transects chosen to span the natural soil moisture gradient (very dry to waterlogged soils). We observed contrasting spatial and temporal patterns of methane emissions between the sites as well as significant differences in emission intensities. Methane hotspots were observed in the Guma Lagoon papyrus swamp whereas fluxes at Nxaraga increased gradually with distance into the floodplain, which correlates with the spatial gradient of soil moisture in the seasonal floodplain. The differences observed at the two measurement sites suggest different controls, with soil moisture likely to be the dominant one at the seasonal floodplain. In contrast, we expect the emissions from the permanent wetland to be driven by a complex set of mechanisms, which could include plant-mediated transport, diffusion at the water-air interface, bubbling and convective flow within the water column

A review of the limnology of the Okavango Delta, Botswana

Water quantity and quality are important aspects in the management of aquatic ecosystems, including wetlands. This paper has integrated available knowledge from literature on the limnology of the Okavango Delta, Botswana. The current near-natural solute concentrations in the inflow waters can be attributed to low chemical weathering of the quartz basin substrate and nearly absent anthropogenic nutrient sources within the Okavango Delta.  The concentration of solutes in endorheic ecosystems is a natural phenomenon. In the Okavango Delta, this concentration is offset by the accumulation of solutes in groundwater beneath numerous treed-islands, due to evapotranspiration by evergreen trees. The freshwater environment has fostered high abundance and diversity of flora and fauna in a semi-arid environment. However, there are several aspects of the Okavango Delta that need more rigorous researched for management purposes. Some of the important knowledge gaps include the role of atmospheric deposition and animal excretion as sources of nutrients and trace elements into the system, and the influence of hydro-period on the distribution of trace elements especially in floodplain sediments, flora and fauna across the Okavango Delta. The issue of bioaccumulation of trace elements is also an important knowledge gap for the Okavango Delta particularly for wildlife and human health