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Lake Tanganyika (LT) is the largest tropical freshwater lake, and the largest body of anoxic freshwater on Earth’s surface. LT’s mixed oxygenated surface waters float atop a permanently anoxic layer and host rich animal biodiversity. However, little is known about microorganisms inhabiting LT’s 1470 meter deep water column and their contributions to nutrient cycling, which affect ecosystem-level function and productivity. Here, we applied genome-resolved metagenomics and environmental analyses to link specific taxa to key biogeochemical processes across a vertical depth gradient in LT. We reconstructed 523 unique metagenome-assembled genomes (MAGs) from 34 bacterial and archaeal phyla, including many rarely observed in freshwater lakes. We identified sharp contrasts in community composition and metabolic potential with an abundance of typical freshwater taxa in oxygenated mixed upper layers, and Archaea and uncultured Candidate Phyla in deep anoxic waters. Genomic capacity for nitrogen and sulfur cycling was abundant in MAGs recovered from anoxic waters, highlighting microbial contributions to the productive surface layers via recycling of upwelled nutrients, and greenhouse gases such as nitrous oxide. Overall, our study provides a blueprint for incorporation of aquatic microbial genomics in the representation of tropical freshwater lakes, especially in the context of ongoing climate change, which is predicted to bring increased stratification and anoxia to freshwater lakes.

Abstract Cichlid fishes of the genus Oreochromis (tilapia) are among the most important fish for inland capture fisheries and global aquaculture. Deliberate introductions of non-native species for fisheries improvement and accidental escapees from farms have resulted in admixture with indigenous species. Such hybridization may be detrimental to native biodiversity, potentially leading to genomic homogenization of populations and the loss of important genetic material associated with local adaptation. By contrast, introgression may fuel diversification when combined with ecological opportunity, by supplying novel genetic combinations. To date, the role of introgression in the evolutionary history of tilapia has not been explored. Here we studied both ancient and recent hybridization in tilapia, using whole genome resequencing of 575 individuals from 23 species. We focused on Tanzania, a natural hotspot of tilapia diversity, and a country where hybridization between exotic and native species in the natural environment has been previously reported. We reconstruct the first genome-scale phylogeny of the genus and reveal prevalent ancient gene flow across the Oreochromis phylogeny. This has likely resulted in the hybrid speciation of one species, O. chungruruensis. We identify multiple cases of recent hybridization between native and introduced species in the wild, linked to the use of non-native species in both capture fisheries improvement and aquaculture. This has potential implications for both conservation of wild populations and the development of the global tilapia aquaculture industry.

Hybridization between introduced and indigenous species can lead to loss of unique genetic resources and precipitate extinction. In Tanzania, the Nile tilapia (Oreochromis niloticus) and blue-spotted tilapia (Oreochromis leucostictus) have been widely introduced to non-native habitats for aquaculture and development of capture fisheries. Here, we aimed to quantify interspecific hybridization between these introduced species and the indigenous species Oreochromis esculentus, Oreochromis jipe and Oreochromis korogwe. In the Pangani basin, several hybrids were observed (O. niloticus × O. jipe, O. leucostictus × O. jipe, O. niloticus × O. korogwe), although hybrids were relatively uncommon within samples relative to purebreds. Hybrids between the native O. jipe × O. korogwe were also observed. In the Lake Victoria basin, no evidence of hybrids was found. Analysis of body shape using geometric morphometrics suggested that although purebreds could be discriminated from one another, hybrids could not be readily identified on body and head shape alone. These results provide the first evidence of hybridization between the introduced species and the Critically Endangered O. jipe in Tanzania. Given uncertainty regarding benefits of introduced species over large-bodied indigenous species in aquaculture and capture fisheries, we suggest that future introductions of hybridization-prone species should be carefully evaluated.

From the 1950s onwards, programmes to promote aquaculture and improve capture fisheries in East Africa have relied heavily on the promise held by introduced species. In Tanzania these introductions have been poorly documented. Here we report the findings of surveys of inland water bodies across Tanzania between 2011 and 2017 that clarify distributions of tilapiine cichlids of the genus Oreochromis. We identified Oreochromis from 123 sampling locations, including 14 taxa restricted to their native range and three species that have established populations beyond their native range. Of these three species, the only exotic species found was blue-spotted tilapia (Oreochromis leucostictus), while Nile tilapia (Oreochromis niloticus) and Singida tilapia (Oreochromis esculentus), which are both naturally found within the country of Tanzania, have been translocated beyond their native range. Using our records, we developed models of suitable habitat for the introduced species based on recent (1960–1990) and projected (2050, 2070) East African climate. These models indicated that presence of suitable habitat for these introduced species will persist and potentially expand across the region. The clarification of distributions provided here can help inform the monitoring and management of biodiversity, and inform policy related to the future role of introduced species in fisheries and aquaculture.

Among the many negative impacts of invasive species, hybridization with indigenous species has increasingly become recognized as a major issue. However, relatively few studies have characterized the phenotypic outcomes of hybridization following biological invasions. Here we investigate the genetic and morphological consequences of stocking invasive tilapia species in two water bodies in central Tanzania. We sampled individuals from the Mindu Reservoir on the Ruvu river system, and at Kidatu on the Great Ruaha–Rufiji river system. We screened individuals at 16 microsatellite loci, and quantified morphology using geometric morphometrics and linear measurements. In both the Mindu and Kidatu systems, we identified evidence of hybridization between indigenous Wami tilapia (Oreochromis urolepis) and the introduced Nile tilapia (Oreochromis niloticus) or blue-spotted tilapia (Oreochromis leucostictus). At both sites, purebred individuals could largely be separated using geometric morphometric variables, with hybrids occupying a broad morphospace among the parental species. Our data demonstrate that the gene pools and phenotypic identity of the indigenous O. urolepis have been severely impacted by the stocking of the invasive species. Given the lack of evidence for clear commercial benefits from stocking invasive tilapia species in waters already populated by indigenous congenerics, we suggest further spread of introduced species should be undertaken with considerable caution.

Lake Tanganyika, the deepest and most voluminous lake in Africa, has warmed over the last century in response to climate change. Separate analyses of surface warming rates estimated from in situ instruments, satellites, and a paleolimnological temperature proxy (TEX86) disagree, leaving uncertainty about the thermal sensitivity of Lake Tanganyika to climate change. Here, we use a comprehensive database of in situ temperature data from the top 100 meters of the water column that span the lake's seasonal range and lateral extent to demonstrate that long-term temperature trends in Lake Tanganyika depend strongly on depth, season, and latitude. The observed spatiotemporal variation in surface warming rates accounts for small differences between warming rate estimates from in situ instruments and satellite data. However, after accounting for spatiotemporal variation in temperature and warming rates, the TEX86 paleolimnological proxy yields lower surface temperatures (1.46 °C lower on average) and faster warming rates (by a factor of three) than in situ measurements. Based on the ecology of Thaumarchaeota (the microbes whose biomolecules are involved with generating the TEX86 proxy), we offer a reinterpretation of the TEX86 data from Lake Tanganyika as the temperature of the low-oxygen zone, rather than of the lake surface temperature as has been suggested previously. Our analyses provide a thorough accounting of spatiotemporal variation in warming rates, offering strong evidence that thermal and ecological shifts observed in this massive tropical lake over the last century are robust and in step with global climate change.

Nile tilapia (Oreochromis niloticus) is one of the most important species in Tanzania for inland fisheries and aquaculture. Although indigenous to the country, it is only naturally distributed within the margins of Lake Tanganyika and peripheral water bodies. The widespread distribution across other parts of the country is a consequence of introductions that started in the 1950s. We investigated the population genetic structure of Nile tilapia across Tanzania using nuclear microsatellite markers, and compared the head and body morphology of populations using geometric morphometric analyses. We found the Lake Tanganyika population to be genetically distinct from the introduced populations. However, there were no clear morphological differences in head and body shape that distinguished the Lake Tanganyika population from the others. We conclude that the Lake Tanganyika population of Nile tilapia represents a unique genetic resource within the country. We suggest that Nile tilapia aquaculture within the Lake Tanganyika catchment should be restricted to the indigenous strain.

Due to an unfortunate turn of events, four rows in Table 2 were transposed. Hence, the original article has been corrected. The corrected section (part of ‘Minor catchments’) of Table 2 is also published here.

Land use changes and mounting water demands reduce freshwater inflows into estuaries, impairing estuarine ecosystems and accelerating coastal seawater intrusion. However, determining minimum river inflows for management guidelines is hampered by a lack of ecosystem-flow link data. This study describes the development of freshwater inflow guidelines for the Wami Estuary, combining scarce river flow data, hydrological modeling, inferring natural salinity regime from vegetation zonation and investigating freshwater requirements of people/wildlife. By adopting the Building Blocks Methodology, a detailed Environmental Flows Assessment was performed to know the minimum water depth/quality seasonal requirements for vegetation, terrestrial/aquatic wildlife and human communities. Water depth requirements were assessed for drought and normal rainfall years; corresponding discharges were obtained by a hydrological model (HEC-RAS) developed for the river channel upstream of estuary. Recommended flows were well within historically occurring flows. However, given the rapidly increasing water demand coupled with reduction in basin water storage due to deforestation/wetland loss, it is critical to ensure these minimum flows are present, without which essential ecosystem services (fisheries, water quality, mangrove forest resources and wildlife/tourism) will be jeopardized. The EFA process is described in painstaking detail to provide a reference for undertaking similar studies in data-poor regions worldwide.

Seeds and feeds are among the most important inputs required for sustainable aquaculture industry development in any country worldwide. However, the value chain analysis of seeds and feeds in most developing countries including Tanzania has not been mapped, and the key actors are not identified and characterized. To address this knowledge gap, we mapped the fish seed and feed value chains in Morogoro, Dar es Salaam, Coast and Lindi regions in Tanzania, evaluated their performances, analyzed their contributions to aquaculture growth and finally assessed the critical factors impending aquaculture development before proposing appropriate strategies for upgrading. We found that the fish seed value chain comprised broodstock suppliers, seed producers, seed marketers, traders and fish farmers. Tilapia (Oreochromis sp.) and African sharptooth catfish (Clarias gariepinus) seeds produced were primarily sold to farmers at an advanced fry stage (1 to 5 g) at a price ranging from USD 0.09 to 0.13 and USD 0.22 to 0.27, respectively. The feed value chain consisted of suppliers, producers, importers, traders and fish farmers. The feeds produced were powdered, compressed and extruded pellets and granules sold at an average price of USD 2.50/kg. The seed and feed value chains in the four regions drive the aquaculture development and employ 137 and 109 people, respectively. The fish farming was mainly affected by insufficient seeds and feeds; inadequate extension services, inadequate technical skills in seed and feed production; limited farming equipment; insufficient capital and limited access to market. We propose increasing seed and feed production through collaborative research between researchers and the private sector, enhancing delivery of extension services to all fish farmers, providing fiscal incentives to hatchery and feed investors, organizing hatchery owners into associations, and undertaking marketing awareness campaign for aquaculture growth in the country for food, income and employment generation. The findings of this research reveal key players in Tanzanian seed and feed value chains, their contributions to aquaculture development and direct employment in Tanzania. Such knowledge does not exist in the Tanzania and other low income countries in sub‐Saharan Africa and elsewhere with diverse aquaculture systems leading to variations in domestic quantity and quality of inputs and services required for the aquaculture value chains.