Controls on timescales of soil organic carbon persistence across sub-Saharan Africa.

Given the importance of soil for the global carbon cycle, it is essential to understand not only how much carbon soil stores but also how long this carbon persists. Previous studies have shown that the amount and age of soil carbon are strongly affected by the interaction of climate, vegetation, and mineralogy. However, these findings are primarily based on studies from temperate regions and from fine-scale studies, leaving large knowledge gaps for soils from understudied regions such as sub-Saharan Africa. In addition, there is a lack of data to validate modeled soil C dynamics at broad scales. Here, we present insights into organic carbon cycling, based on a new broad-scale radiocarbon and mineral dataset for sub-Saharan Africa. We found that in moderately weathered soils in seasonal climate zones with poorly crystalline and reactive clay minerals, organic carbon persists longer on average (topsoil: 201 ± 130 years; subsoil: 645 ± 385 years) than in highly weathered soils in humid regions (topsoil: 140 ± 46 years; subsoil: 454 ± 247 years) with less reactive minerals. Soils in arid climate zones (topsoil: 396 ± 339 years; subsoil: 963 ± 669 years) store organic carbon for periods more similar to those in seasonal climate zones, likely reflecting climatic constraints on weathering, carbon inputs and microbial decomposition. These insights into the timescales of organic carbon persistence in soils of sub-Saharan Africa suggest that a process-oriented grouping of soils based on pedo-climatic conditions may be useful to improve predictions of soil responses to climate change at broader scales.

Prolonged water limitation shifts the soil microbiome from copiotrophic to oligotrophic lifestyles in Scots pine mesocosms.

Reductions in soil moisture due to prolonged episodes of drought can potentially affect whole forest ecosystems, including soil microorganisms and their functions. We investigated how the composition of soil microbial communities is affected by prolonged episodes of water limitation. In a mesocosm experiment with Scots pine saplings and natural forest soil maintained at different levels of soil water content over 2 years, we assessed shifts in prokaryotic and fungal communities and related these to changes in plant development and soil properties. Prolonged water limitation induced progressive changes in soil microbial community composition. The dissimilarity between prokaryotic communities at different levels of water limitation increased over time regardless of the recurrent seasons, while fungal communities were less affected by prolonged water limitation. Under low soil water contents, desiccation-tolerant groups outcompeted less adapted, and the lifestyle of prokaryotic taxa shifted from copiotrophic to oligotrophic. While the abundance of saprotrophic and ligninolytic groups increased alongside an accumulation of dead plant material, the abundance of symbiotic and nutrient-cycling taxa decreased, likely impairing the development of the trees. Overall, prolonged episodes of drought appeared to continuously alter the structure of microbial communities, pointing to a potential loss of critical functions provided by the soil microbiome.

Correction: Combining organic and mineral fertilizers as a climate-smart integrated soil fertility management practice in sub-Saharan Africa: A meta-analysis.

[This corrects the article DOI: 10.1371/journal.pone.0239552.].

N2O emission factors for cattle urine: effect of patch characteristics and environmental drivers.

Urine patches from grazing cattle are hotspots of nitrous oxide (N2O) emissions. The default IPCC emission factor for urine patches (EFurine) is 0.77% for wet climates and 0.32% for dry climates. However, literature reports a considerable range of cattle urine EF values and urine characteristics used in experimental studies, revealing contrary results on the effects of urine patch characteristics and seasonal pattern. Therefore, we examined N2O emissions and corresponding EFurine values in relation to urine patch characteristics (urine N concentration, urine volume, patch area, urine composition) and environmental drivers (precipitation, water filled pore space, soil temperature). Ten artificial urine application experiments were performed from July 2020 to June 2022 on a pasture located in Eastern Switzerland. Urine N concentration, patch area, volume and urine N composition showed no significant effects on the EFurine value (p > 0.05). EFurine varied, however, strongly over time (0.17-2.05%). A large part of the variation could be predicted either by cumulative precipitation 20 days after urine application using a second order polynomial model (Adj. R2 = 0.60) or average WFPS 30 days after urine application using a linear model (Adj. R2 = 0.45). The derived precipitation model was used to simulate EFurine weekly over the last 20 years showing no significant differences between the seasons of a year. The resulting overall average EFurine was 0.67%. More field studies are needed across sites/regions differing in climate and soil properties to implement a country-specific EF3 for Switzerland and to improve the quantification of N2O emissions at the national scales.

Water limitation intensity shifts carbon allocation dynamics in Scots pine mesocosms.

Background and aims: Tree species worldwide suffer from extended periods of water limitation. These conditions not only affect the growth and vitality of trees but also feed back on the cycling of carbon (C) at the plant-soil interface. However, the impact of progressing water loss from soils on the transfer of assimilated C belowground remains unresolved. Methods: Using mesocosms, we assessed how increasing levels of water deficit affect the growth of Pinus sylvestris saplings and performed a 13C-CO2 pulse labelling experiment to trace the pathway of assimilated C into needles, fine roots, soil pore CO2, and phospholipid fatty acids of soil microbial groups. Results: With increasing water limitation, trees partitioned more biomass belowground at the expense of aboveground growth. Moderate levels of water limitation barely affected the uptake of 13C label and the transit time of C from needles to the soil pore CO2. Comparatively, more severe water limitation increased the fraction of 13C label that trees allocated to fine roots and soil fungi while a lower fraction of 13CO2 was readily respired from the soil. Conclusions: When soil water becomes largely unavailable, C cycling within trees becomes slower, and a fraction of C allocated belowground may accumulate in fine roots or be transferred to the soil and associated microorganisms without being metabolically used. Supplementary Information: The online version contains supplementary material available at 10.1007/s11104-023-06093-5.

Impact of salinity gradient, water pollution and land use types on greenhouse gas emissions from an urbanized estuary.

Estuaries have been recognized as one of the major sources of greenhouse gases (GHGs) in aquatic systems; yet we still lack insights into the impact of both anthropogenic and natural factors on the dynamics of GHG emissions. Here, we assessed the spatiotemporal dynamics and underlying drivers of the GHG emissions from the Scheldt Estuary with a focus on the effects of salinity gradient, water pollution, and land use types, together with their interaction. Overall, we found a negative impact of salinity on carbon dioxide (CO2) and nitrous oxide (N2O) emissions which can be due to the decrease of both salinity and water quality when moving upstream. Stronger impact of water pollution on the GHG emissions was found at the freshwater sites upstream compared to saline sites downstream. In particular, when water quality of the sites reduced from good, mainly located in the mouth and surrounded by arable sites, to polluted, mainly located in the upstream and surrounded by urban sites, CO2 emissions from the sites doubled while N2O emissions tripled. Similarly, the effects of water pollution on methane (CH4) emissions became much stronger in the freshwater sites compared to the saline sites. These decreasing effects from upstream to the mouth were associated with the increase in urbanization as sites surrounded by urban areas released on average almost two times more CO2 and N2O than sites surrounded by nature and industry areas. Applied machine learning methods also revealed that, in addition to salinity effects, nutrient and organic enrichment stimulated the GHG emissions from the Scheldt Estuary. These findings highlight the importance of the interaction between salinity, water pollution, and land use in order to understand their influences on GHG emissions from dynamic estuarine systems.

Contrasting sensitivity of soil bacterial and fungal community composition to one year of water limitation in Scots pine mesocosms.

The soil microbiome is crucial for regulating biogeochemical processes and can, thus, strongly influence tree health, especially under stress conditions. However, little is known about the effect of prolonged water deficit on soil microbial communities during the development of saplings. We assessed the response of prokaryotic and fungal communities to different levels of experimental water limitation in mesocosms with Scots pine saplings. We combined analyses of physicochemical soil properties and tree growth with DNA metabarcoding of soil microbial communities throughout four seasons. Seasonal changes in soil temperature and soil water content and a decreasing soil pH strongly influenced the composition of microbial communities but not their total abundance. Contrasting levels of soil water contents gradually altered the soil microbial community structure over the four seasons. Results indicated that prokaryotic communities were less resistant to water limitation than fungal communities. Water limitation promoted the proliferation of desiccation tolerant, oligotrophic taxa. Moreover, water limitation and an associated increase in soil C/N ratio induced a shift in the potential lifestyle of taxa from symbiotic to saprotrophic. Overall, water limitation appeared to alter soil microbial communities involved in nutrient cycling, pointing to potential consequences for forest health affected by prolonged episodes of drought.

Nutrition in City Ecosystems (NICE): Protocol of a multi-sectoral development project to improve food and nutrition security of secondary city populations in Bangladesh, Kenya and Rwanda.

Background: Secondary cities tend to be better linked with local food systems than primate cities, acting as important platforms to trade agricultural produce with rural surrounding. COVID-19, conflicts and climate change continue to expose inefficiencies in food systems and have further exacerbated malnutrition, calling for substantial food systems transformations. However, tackling current food systems' challenges requires new approaches to ensure food and nutrition security. Nutritious and agroecologically produced food offer the potential to transform food systems by improving diets and alleviating pressure on the environment, as well as by creating jobs and reducing poverty. This paper describes the design of a project by a Swiss public-private consortium to improve food and nutrition security and to reduce poverty in city ecosystems in six secondary cities in Bangladesh, Kenya and Rwanda through governance/policy and supply and demand side interventions. Methods: The Nutrition in City Ecosystems (NICE) project promotes well-balanced nutrition for city populations through interdisciplinary agricultural, food, and health sector collaborations along city-specific value chains. Adopting a transdiciplinary systems approach, the main interventions of NICE are (i) advocacy and policy dialogue, (ii) building of decentralized institutional capacity in multi-sectoral collaborations, (iii) support of data-driven planning, coordination and resource mobilization, (iv) anchoring of innovations and new approaches in city-level partnerships, (v) capacity building in the agricultural, retail, health and education sectors, as well as (vi) evidence generation from putting policies into practice at the local level. NICE is coordinated by in-country partners and local offices of the Swiss public-private consortium partners. Discussion: The NICE project seeks to contribute to urban food system resilience and enhanced sustainable nutrition for city populations by (A) strengthening urban governance structures involving key stakeholders including women and youth, (B) generating income for producers along the supply chain, (C) triggering change in producers' and consumers' behavior such that nutritious and agroecologically produced foods are both in demand as well as available and affordable in urban markets, and (D) allowing a scale up of successful approaches to other national and international cities and city networks.

Soil carbon stocks in stable tropical landforms are dominated by geochemical controls and not by land use.

Soil organic carbon (SOC) dynamics depend on soil properties derived from the geoclimatic conditions under which soils develop and are in many cases modified by land conversion. However, SOC stabilization and the responses of SOC to land use change are not well constrained in deeply weathered tropical soils, which are dominated by less reactive minerals than those in temperate regions. Along a gradient of geochemically distinct soil parent materials, we investigated differences in SOC stocks and SOC (Δ14 C) turnover time across soil profile depth between montane tropical forest and cropland situated on flat, non-erosive plateau landforms. We show that SOC stocks and soil Δ14 C patterns do not differ significantly with land use, but that differences in SOC can be explained by the physicochemical properties of soils. More specifically, labile organo-mineral associations in combination with exchangeable base cations were identified as the dominating controls over soil C stocks and turnover. We argue that due to their long weathering history, the investigated tropical soils do not provide enough reactive minerals for the stabilization of C input in either high input (tropical forest) or low-input (cropland) systems. Since these soils exceeded their maximum potential for the mineral related stabilization of SOC, potential positive effects of reforestation on tropical SOC storage are most likely limited to minor differences in topsoil without major impacts on subsoil C stocks. Hence, in deeply weathered soils, increasing C inputs may lead to the accumulation of a larger readily available SOC pool, but does not contribute to long-term SOC stabilization.

Soil biodiversity needs policy without borders.

Soil health laws should account for global soil connections.

Residues from black soldier fly (Hermetia illucens) larvae rearing influence the plant-associated soil microbiome in the short term.

The larvae of the black soldier fly (BSFL, Hermetia illucens) efficiently close resource cycles. Next to the nutrient-rich insect biomass used as animal feed, the residues from the process are promising plant fertilizers. Besides a high nutrient content, the residues contain a diverse microbial community and application to soil can potentially promote soil fertility and agricultural production through the introduction of beneficial microbes. This research assessed the application of the residues on plant-associated bacterial and fungal communities in the rhizosphere of a grass-clover mix in a 42-day greenhouse pot study. Potted soil was amended with BSFL residues (BR+) or conventional compost (CC+) produced by Rwandan waste management companies in parallel to residues and compost sterilized (BR-, CC-) by high-energy electron beam (HEEB) as abiotic controls. The fertilizers were applied at a rate of 150 kg N ha-1. Soil bacterial and fungal communities in both fertilizer and soil were assessed by high-throughput sequencing of ribosomal markers at different times after fertilizer application. Additionally, indicators for soil fertility such as basal respiration, plant yield and soil physicochemical properties were analyzed. Results showed that the application of BSFL residues influenced the soil microbial communities, and especially fungi, stronger than CC fertilizers. These effects on the microbial community structure could partly be attributed to a potential introduction of microbes to the soil by BSFL residues (e.g., members of genus Bacillus) since untreated and sterilized BSFL residues promoted different microbial communities. With respect to the abiotic effects, we emphasize a potential driving role of particular classes of organic matter like fiber and chitin. Indeed, especially taxa associated with decomposition of organic matter (e.g., members of the fungal genus Mortierella) were promoted by the application of BSFL residues. Soil fertility with respect to plant yield (+17% increase compared to unamended control) and basal respiration (+16% increase compared to unamended control) tended to be improved with the addition of BSFL residues. Findings underline the versatile opportunities for soil fertility arising from the application of BSFL residues in plant production and point to further research on quantification of the described effects.

Circular bioeconomy in African food systems: What is the status quo? Insights from Rwanda, DRC, and Ethiopia.

Increasing global food insecurity amidst a growing population and diminishing production resources renders the currently dominant linear production model insufficient to combat such challenges. Hence, a circular bioeconomy (CBE) model that ensures more conservative use of resources has become essential. Specifically, a CBE model that focuses on recycling and reusing organic waste is essential to close nutrient loops and establish more resilient rural-urban nexus food systems. However, the CBE status quo in many African food systems is not established. Moreover, scientific evidence on CBE in Africa is almost inexistent, thus limiting policy guidance to achieving circular food systems. Using a sample of about 2,100 farmers and consumers from key food value chains (cassava in Rwanda, coffee in DRC, and bananas in Ethiopia), we explored existing CBE practices; awareness, knowledge, and support for CBE practices; consumers' opinions on eating foods grown on processed organic waste (CBE fertilizers), and determinants of such opinions. We analysed data in Stata, first descriptively, and then econometrically using the ordered logistic regression, whose proportional odds assumption was violated, thus resorting to the generalized ordered logistic regression. Results show that communities practice aspects of CBE, mainly composting, and are broadly aware, knowledgeable, supportive of CBE practices, and would broadly accept eating foods grown CBE fertilizers. Households with heads that used mobile phones, or whose heads were older, or married, or had a better education and agricultural incomes were more likely to strongly agree that they were knowledgeable and supportive of CBE practices and would eat CBE foods (foods grown on processed organic waste). However, the reverse was true for households that were severely food insecure or lived farther from towns. Rwandan and Ethiopian households compared to DRC were less likely to eat CB foods. Policies to stimulate CBE investments in all three countries were largely absent, and quality scientific evidence to guide their development and implementation is currently insufficient.

Cassava-maize intercropping systems in southern Nigeria: Radiation use efficiency, soil moisture dynamics, and yields of component crops.

Efficient utilization of incident solar radiation and rainwater conservation in rain-fed smallholder cropping systems require the development and adoption of cropping systems with high resource use efficiency. Due to the popularity of cassava-maize intercropping and the food security and economic importance of both crops in Nigeria, we investigated options to improve interception of photosynthetically active radiation (IPAR), radiation use efficiency (RUE), soil moisture retention, and yields of cassava and maize in cassava-maize intercropping systems in 8 on-farm researcher-managed multi-location trials between 2017 and 2019 in different agro-ecologies of southern Nigeria. Treatments were a combination of (1) maize planting density (low density at 20,000 maize plants ha-1 versus high density at 40,000 maize plants ha-1, intercropped with 12,500 cassava plants ha-1); (2) fertilizer application and management targeting either the maize crop (90 kg N, 20 kg P and 37 kg K ha-1) or the cassava crop (75 kg N, 20 kg P and 90 kg K ha-1), compared with control without fertilizer application. Cassava and maize development parameters were highest in the maize fertilizer regime, resulting in the highest IPAR at high maize density. The combined intercrop biomass yield was highest at high maize density in the maize fertilizer regime. Without fertilizer application, RUE was highest at low maize density. However, the application of the maize fertilizer regime at high maize density resulted in the highest RUE, soil moisture content, and maize grain yield. Cassava storage root yield was higher in the cassava fertilizer regime than in the maize fertilizer regime. We conclude that improved IPAR, RUE, soil moisture retention, and grain yield on nutrient-limited soils of southern Nigeria, or in similar environments, can be achieved by intercropping 40,000 maize plants ha-1 with 12,500 cassava plants ha-1 and managing the system with the maize fertilizer regime. However, for higher cassava storage root yield, the system should be managed with the cassava fertilizer regime.

Increasing calcium scarcity along Afrotropical forest succession.

Secondary forests constitute an increasingly important component of tropical forests worldwide. Although cycling of essential nutrients affects recovery trajectories of secondary forests, the effect of nutrient limitation on forest regrowth is poorly constrained. Here we use three lines of evidence from secondary forest succession sequences in central Africa to identify potential nutrient limitation in regrowing forests. First, we show that atmospheric phosphorus supply exceeds demand along forest succession, whereas forests rely on soil stocks to meet their base cation demands. Second, soil nutrient metrics indicate that available phosphorus increases along the succession, whereas available cations decrease. Finally, fine root, foliar and litter stoichiometry show that tissue calcium concentrations decline relative to those of nitrogen and phosphorus during succession. Taken together, these observations suggest that calcium becomes an increasingly scarce resource in central African forests during secondary succession. Furthermore, ecosystem calcium storage shifts from soil to woody biomass over succession, making it a vulnerable nutrient in the wake of land-use change scenarios that involve woody biomass export. Our results thus call for a broadened focus on elements other than nitrogen and phosphorus regarding tropical forest biogeochemical cycles and identify calcium as a scarce and potentially limiting nutrient in an increasingly disturbed and dynamic tropical forest landscape.

Improving Soil Resource Uptake by Plants Through Capitalizing on Synergies Between Root Architecture and Anatomy and Root-Associated Microorganisms.

Root architectural and anatomical phenotypes are highly diverse. Specific root phenotypes can be associated with better plant growth under low nutrient and water availability. Therefore, root ideotypes have been proposed as breeding targets for more stress-resilient and resource-efficient crops. For example, root phenotypes that correspond to the Topsoil Foraging ideotype are associated with better plant growth under suboptimal phosphorus availability, and root phenotypes that correspond to the Steep, Cheap and Deep ideotype are linked to better performance under suboptimal availability of nitrogen and water. We propose that natural variation in root phenotypes translates into a diversity of different niches for microbial associations in the rhizosphere, rhizoplane and root cortex, and that microbial traits could have synergistic effects with the beneficial effect of specific root phenotypes. Oxygen and water content, carbon rhizodeposition, nutrient availability, and root surface area are all factors that are modified by root anatomy and architecture and determine the structure and function of the associated microbial communities. Recent research results indicate that root characteristics that may modify microbial communities associated with maize include aerenchyma, rooting angle, root hairs, and lateral root branching density. Therefore, the selection of root phenotypes linked to better plant growth under specific edaphic conditions should be accompanied by investigating and selecting microbial partners better adapted to each set of conditions created by the corresponding root phenotype. Microbial traits such as nitrogen transformation, phosphorus solubilization, and water retention could have synergistic effects when correctly matched with promising plant root ideotypes for improved nutrient and water capture. We propose that elucidation of the interactive effects of root phenotypes and microbial functions on plant nutrient and water uptake offers new opportunities to increase crop yields and agroecosystem sustainability.

Greenhouse gas dynamics in an urbanized river system: influence of water quality and land use.

Rivers act as a natural source of greenhouse gases (GHGs). However, anthropogenic activities can largely alter the chemical composition and microbial communities of rivers, consequently affecting their GHG production. To investigate these impacts, we assessed the accumulation of CO2, CH4, and N2O in an urban river system (Cuenca, Ecuador). High variation of dissolved GHG concentrations was found among river tributaries that mainly depended on water quality and land use. By using Prati and Oregon water quality indices, we observed a clear pattern between water quality and the dissolved GHG concentration: the more polluted the sites were, the higher were their dissolved GHG concentrations. When river water quality deteriorated from acceptable to very heavily polluted, the mean value of pCO2 and dissolved CH4 increased by up to ten times while N2O concentrations boosted by 15 times. Furthermore, surrounding land-use types, i.e., urban, roads, and agriculture, could considerably affect the GHG production in the rivers. Particularly, the average pCO2 and dissolved N2O of the sites close to urban areas were almost four times higher than those of the natural sites while this ratio was 25 times in case of CH4, reflecting the finding that urban areas had the worst water quality with almost 70% of their sites being polluted while this proportion of nature areas was only 12.5%. Lastly, we identified dissolved oxygen, ammonium, and flow characteristics as the main important factors to the GHG production by applying statistical analysis and random forests. These results highlighted the impacts of land-use types on the production of GHGs in rivers contaminated by sewage discharges and surface runoff.

Low N2O and variable CH4 fluxes from tropical forest soils of the Congo Basin.

Globally, tropical forests are assumed to be an important source of atmospheric nitrous oxide (N2O) and sink for methane (CH4). Yet, although the Congo Basin comprises the second largest tropical forest and is considered the most pristine large basin left on Earth, in situ N2O and CH4 flux measurements are scarce. Here, we provide multi-year data derived from on-ground soil flux (n = 1558) and riverine dissolved gas concentration (n = 332) measurements spanning montane, swamp, and lowland forests. Each forest type core monitoring site was sampled at least for one hydrological year between 2016 - 2020 at a frequency of 7-14 days. We estimate a terrestrial CH4 uptake (in kg CH4-C ha-1 yr-1) for montane (-4.28) and lowland forests (-3.52) and a massive CH4 release from swamp forests (non-inundated 2.68; inundated 341). All investigated forest types were a N2O source (except for inundated swamp forest) with 0.93, 1.56, 3.5, and -0.19 kg N2O-N ha-1 yr-1 for montane, lowland, non-inundated swamp, and inundated swamp forests, respectively.

Stable Isotope Analysis of Greenhouse Gases Requires Analyte Preconcentration.

Nitrous oxide (N2O) is an important trace gas contributing to global warming and depletion of ozone in the stratosphere. Its increasing abundance is caused mainly by anthropogenic sources, such as application of fertilizers in agriculture or emissions from industry. To understand the N2O global budget, its sources and sinks need to be well-described and quantified. In this project, a new method for N2O source appointment was developed that can help with this task. The method is based on analysis of the eight most abundant isotopic molecules of N2O, using quantum cascade laser absorption spectroscopy (QCLAS). The applicability of the method towards the N2O biogeochemical cycle was demonstrated on a prominent N2O source (bacterial denitrification) and the most important N2O sink (UV photolysis) on samples prepared in laboratory experiments. An extension of the QCLAS method to natural samples can be achieved by hyphenation with a preconcentration technique that increases concentration of the analyte and standardizes the sample matrix. This article provides an overview of currently applied preconcentration techniques in the field of greenhouse-gas analysis and a description of the preconcentration device TREX that will be employed in future projects with the developed QCLAS method.