Paleometagenomics reveals environmental microbiome response to vegetation changes in northern Siberia over the millennia

The study of environmental ancient DNA provides us with the unique opportunity to link environmental with ecosystem change over a millennial timescale. Paleorecords such as lake sediments contain genetic pools of past living organisms that are a valuable source of information to reconstruct how ecosystems were and how they changed in response to climate in the past. Here, we report on paleometagenomics of a sedimentary record in northern Siberia covering the past 6700 years. We integrated taxonomic with functional gene analysis, which enabled to shed light not only on community compositions but also on eco-physiological adaptations and ecosystem functioning. We reconstructed the presence of an open boreal forest 6700 years ago that over time was gradually replaced by tundra. This vegetation change had major consequences on the environmental microbiome, primarily enriching bacterial and archaeal ammonia oxidizers (e.g., Nitrospira, Nitrosopumilus, and Ca. Nitrosocosmicus) in the tundra ecosystem. We identified a core microbiome conserved through time and largely consisting of heterotrophic bacteria of the Bacteroidetes phylum (e.g., Mucilaginibacter) harboring numerous functional genes for degradation of plant-biomass and abiotic and biotic stress resistance. Archaea were also a key functional guild, involved in nitrogen and carbon cycling, not only methanogenesis but possibly also degradation of plant material via enzymes such as cellulases and amylases. Overall, the paleo-perspective offered by our study can have a profound impact on modern climate change biology, by helping to explain and predict the ecological interplay among multiple ecosystem levels based on past experiences

Progress towards the eradication of Tsetse from the Loos islands, Guinea

Background: The tsetse fly Glossina palpalis gambiensis is the main vector of sleeping sickness (Human African Trypanosomiasis - HAT) in West Africa, in particular in littoral Guinea where this disease is currently very active. The Loos islands constitute a small archipelago some 5 km from mainland Guinea, where G. p. gambiensis is well known as a nuisance and potential disease vector by inhabitants of the three main islands, Fotoba, Room, and Kassa. The National Control Program against HAT of Guinea has decided to eradicate tsetse in Loos islands in order to sustainably protect humans and economic activities. After baseline data collection, tsetse control began on the islands in 2006. On each of the three islands a specific combination of control methods was implemented according to the entomological situation found. Results: Starting densities before control operations were 10, 3 and 1 tsetse/trap/day in Kassa, Room and Fotoba respectively, but by July 2010, tsetse were no longer caught in any of the sentinel traps used for monitoring. The reduction rate was faster where several control methods were implemented as a combination (impregnated traps and targets ITT, selective groundspraying, epicutaneous insecticide treatment of pigs, and impregnated fences around pig pens), whereas it was slower when ITT were used as the only control method. Conclusions: This 100% suppression is a promising step in the eradication process, but G. p. gambiensis may still occur at very low, undetectable, densities on the archipelago. Next step will consist in assessing a 0.05 probability of tsetse absence to ascertain a provisional eradication status. Throughout these operations, a key factor has been the involvement of local teams and local communities without whom such results would be impossible to obtain. Work will continue thanks to the partners involved until total eradication of the tsetse on Loos islands can be declared

Landforms and degradation pattern of the Batagay thaw slump, Northeastern Siberia

Thaw slumps are clear indicators of rapid permafrost degradation. They form preferentially in near-surface ice-rich permafrost of northern high latitudes after initial thermal disturbance by the subsequent interplay of thermal (thawing of frozen deposits and melting of ice) and mechanical (slumping and erosion) processes. The largest known thaw slump on Earth – the Batagay megaslump – has been identified in sloping terrain on the Yana Upland in northern Yakutia. Its initiation began in the 1980s, with a current area of >0.8 km2. It continues to grow and has headwall retreat rates of up to 15 m per year. While various satellite remote sensing studies of the Batagay thaw slump have been undertaken, on-site studies characterizing internal landforms, terrain changes, and geomorphic processes have not yet been conducted. To fill this knowledge gap and to enhance our understanding of the dynamics of very large thaw slumps, our study employs on-site observations and detailed permafrost sampling combined with unoccupied aerial vehicle data from 2019. The latter were used to generate an orthomosaic, a digital surface model, hypsometric slope profiles and a map of relief types in the thaw slump. Within the Batagay thaw slump, the dynamic relationship between headwall morphology and slump floor is largely determined by the cryolithological structure of the permafrost horizons exposed across the headwall rising up to 55 m above the slump floor. Factors include the thickness and overall high volumetric ground-ice content (up to 87 %) of the cryostratigraphic horizons. Furthermore, the diurnal and seasonal insolation exposure of the headwall perimeter superimposes both thermal denudation activity and meltwater transport of eroded material. Thus, recent degradation patterns are linked to permafrost properties. Therefore, the Batagay thaw slump is not only a window into Earth's past as it reveals ancient permafrost, but its modern dynamics highlight that ongoing rapid permafrost thaw under present Arctic warming is directly influenced by its Quaternary geological and permafrost history

Restricted Application of Insecticides: A Promising Tsetse Control Technique, but What Do the Farmers Think of It?

Restricted application of insecticides to cattle is a cheap and safe farmer-based method to control tsetse and the diseases they transmit, i.e. human and animal African trypanosomoses. The efficiency of this new control method has been demonstrated earlier but no data is available on its perception and adoption intensity by farmers. We studied these two features in Burkina Faso, where the method has diffused thanks to two development projects. The study allowed identifying three groups of farmers with various adoption intensities, of which one was modern and two traditional. The economic benefit and the farmers' knowledge of the epidemiological system appeared to have a low impact on the early adoption process whereas some modern practices, as well as social factors appeared critical. The quality of technical support provided to the farmers had also a great influence on the adoption rate. The study highlighted individual variations in risk perceptions and benefits, as well as the prominent role of the socio-technical network of cattle farmers. The results of the study are discussed to highlight the factors that should be taken into consideration, to move discoveries from bench to field for an improved control of trypanosomoses vectors

Contrasting Population Structures of Two Vectors of African Trypanosomoses in Burkina Faso: Consequences for Control

Tsetse flies are insects that transmit trypanosomes to humans (sleeping sickness) and animals (nagana). Controlling these vectors is a very efficient way to control these diseases. In Burkina Faso, a tsetse eradication campaign is presently targeting the northern part of the Mouhoun River Basin. To attain this objective, the approach has to be area-wide, i.e. the control effort targets an entire pest population within a circumscribed area. To assess the level of this isolation, we studied the genetic structure of Glossina palpalis gambiensis and Glossina tachinoides populations in the target area and in the adjacent river basins of the Comoé, the Niger and the Sissili River Basins. Our results suggest an absence of strong genetic isolation of the target populations. We therefore recommend establishing permanent buffer zones between the Mouhoun and the other river basin(s) to prevent reinvasion. This kind of study may be extended to other areas on other tsetse species

The impact of vector migration on the effectiveness of strategies to control gambiense human African trypanosomiasis

BACKGROUND: Several modeling studies have been undertaken to assess the feasibility of the WHO goal of eliminating gambiense human African trypanosomiasis (g-HAT) by 2030. However, these studies have generally overlooked the effect of vector migration on disease transmission and control. Here, we evaluated the impact of vector migration on the feasibility of interrupting transmission in different g-HAT foci. METHODS: We developed a g-HAT transmission model of a single tsetse population cluster that accounts for migration of tsetse fly into this population. We used a model calibration approach to constrain g-HAT incidence to ranges expected for high, moderate and low transmission settings, respectively. We used the model to evaluate the effectiveness of current intervention measures, including medical intervention through enhanced screening and treatment, and vector control, for interrupting g-HAT transmission in disease foci under each transmission setting. RESULTS: We showed that, in low transmission settings, under enhanced medical intervention alone, at least 70% treatment coverage is needed to interrupt g-HAT transmission within 10 years. In moderate transmission settings, a combination of medical intervention and a vector control measure with a daily tsetse mortality greater than 0.03 is required to achieve interruption of disease transmission within 10 years. In high transmission settings, interruption of disease transmission within 10 years requires a combination of at least 70% medical intervention coverage and at least 0.05 tsetse daily mortality rate from vector control. However, the probability of achieving elimination in high transmission settings decreases with an increased tsetse migration rate. CONCLUSION: Our results suggest that the WHO 2030 goal of G-HAT elimination is, at least in theory, achievable. But the presence of tsetse migration may reduce the probability of interrupting g-HAT transmission in moderate and high transmission foci. Therefore, optimal vector control programs should incorporate monitoring and controlling of vector density in buffer areas around foci of g-HAT control efforts

Paleometagenomics reveals environmental microbiome response to vegetation changes in northern Siberia over the millennia

The study of environmental ancient DNA provides us with the unique opportunity to link environmental with ecosystem change over a millennial timescale. Paleorecords such as lake sediments contain genetic pools of past living organisms that are a valuable source of information to reconstruct how ecosystems were and how they changed in response to climate in the past. Here, we report on paleometagenomics of a sedimentary record in northern Siberia covering the past 6700 years. We integrated taxonomic with functional gene analysis, which enabled to shed light not only on community compositions but also on eco-physiological adaptations and ecosystem functioning. We reconstructed the presence of an open boreal forest 6700 years ago that over time was gradually replaced by tundra. This vegetation change had major consequences on the environmental microbiome, primarily enriching bacterial and archaeal ammonia oxidizers (e.g., Nitrospira, Nitrosopumilus, and Ca. Nitrosocosmicus) in the tundra ecosystem. We identified a core microbiome conserved through time and largely consisting of heterotrophic bacteria of the Bacteroidetes phylum (e.g., Mucilaginibacter) harboring numerous functional genes for degradation of plant-biomass and abiotic and biotic stress resistance. Archaea were also a key functional guild, involved in nitrogen and carbon cycling, not only methanogenesis but possibly also degradation of plant material via enzymes such as cellulases and amylases. Overall, the paleo-perspective offered by our study can have a profound impact on modern climate change biology, by helping to explain and predict the ecological interplay among multiple ecosystem levels based on past experiences

Vegetation Changes in Southeastern Siberia During the Late Pleistocene and the Holocene

Relationships between climate, species composition, and species richness are of particular importance for understanding how boreal ecosystems will respond to ongoing climate change. This study aims to reconstruct changes in terrestrial vegetation composition and taxa richness during the glacial Late Pleistocene and the interglacial Holocene in the sparsely studied southeastern Yakutia (Siberia) by using pollen and sedimentary ancient DNA (sedaDNA) records. Pollen and sedaDNA metabarcoding data using the trnL g and h markers were obtained from a sediment core from Lake Bolshoe Toko. Both proxies were used to reconstruct the vegetation composition, while metabarcoding data were also used to investigate changes in plant taxa richness. The combination of pollen and sedaDNA approaches allows a robust estimation of regional and local past terrestrial vegetation composition around Bolshoe Toko during the last ∼35,000 years. Both proxies suggest that during the Late Pleistocene, southeastern Siberia was covered by open steppe-tundra dominated by graminoids and forbs with patches of shrubs, confirming that steppe-tundra extended far south in Siberia. Both proxies show disturbance at the transition between the Late Pleistocene and the Holocene suggesting a period with scarce vegetation, changes in the hydrochemical conditions in the lake, and in sedimentation rates. Both proxies document drastic changes in vegetation composition in the early Holocene with an increased number of trees and shrubs and the appearance of new tree taxa in the lake’s vicinity. The sedaDNA method suggests that the Late Pleistocene steppe-tundra vegetation supported a higher number of terrestrial plant taxa than the forested Holocene. This could be explained, for example, by the “keystone herbivore” hypothesis, which suggests that Late Pleistocene megaherbivores were able to maintain a high plant diversity. This is discussed in the light of the data with the broadly accepted species-area hypothesis as steppe-tundra covered such an extensive area during the Late Pleistocene

Pleistocene glacial and interglacial ecosystems inferred from ancient DNA analyses of permafrost sediments from Batagay megaslump, East Siberia

Pronounced glacial and interglacial climate cycles characterized northern ecosystems during the Pleistocene. Our understanding of the resultant community transformations and past ecological interactions strongly depends on the taxa found in fossil assemblages. Here, we present a shotgun metagenomic analysis of sedimentary ancient DNA (sedaDNA) to infer past ecosystem-wide biotic composition (from viruses to megaherbivores) from the Middle and Late Pleistocene at the Batagay megaslump, East Siberia. The shotgun DNA records of past vegetation composition largely agree with pollen and plant metabarcoding data from the same samples. Interglacial ecosystems at Batagay attributed to Marine Isotope Stage (MIS) 17 and MIS 7 were characterized by forested vegetation (Pinus, Betula, Alnus) and open grassland. The microbial and fungal communities indicate strong activity related to soil decomposition, especially during MIS17. The local landscape likely featured more open, herb-dominated areas, and the vegetation mosaic supported birds and small omnivorous mammals. Parts of the area were intermittently/partially flooded as suggested by the presence of water-dependent taxa. During MIS 3, the sampled ecosystems are identified as cold-temperate, periodically flooded grassland. Diverse megafauna (Mammuthus, Equus, Coelodonta) coexisted with small mammals (rodents). The MIS 2 ecosystems existed under harsher conditions, as suggested by the presence of cold-adapted herbaceous taxa. Typical Pleistocene megafauna still inhabited the area. The new approach, in which shotgun sequencing is supported by metabarcoding and pollen data, enables the investigation of community composition changes across a broad range of taxonomic groups and inferences about trophic interactions and aspects of soil microbial ecology.</p