The impact of conventional and organic farming on soil biodiversity conservation: a case study on termites in the long-term farming systems comparison trials in Kenya

A long-term experiment at two trial sites in Kenya has been on-going since 2007 to assess the effect of organic and conventional farming systems on productivity, profitability and sustainability. During these trials the presence of significant numbers of termites (Isoptera) was observed. Termites are major soil macrofauna and within literature they are either depict as ‘pests’ or as important indicator for environmental sustainability. The extent by which termites may be managed to avoid crop damage, but improve sustainability of farming systems is worthwhile to understand. Therefore, a study on termites was added to the long-term experiments in Kenya. The objectives of the study were to quantify the effect of organic (Org) and conventional (Conv) farming systems at two input levels (low and high) on the abundance, incidence, diversity and foraging activities of termites. The results showed higher termite abundance, incidence, activity and diversity in Org-High compared to Conv-High, Conv-Low and Org-Low. However, the termite presence in each system was also dependent on soil depth, trial site and cropping season. During the experiment, nine different termite genera were identified, that belong to three subfamilies: (i) Macrotermitinae (genera: Allodontotermes, Ancistrotermes, Macrotermes, Microtermes, Odontotermes and Pseudocanthotermes), (ii) Termitinae (Amitermes and Cubitermes) and (iii) Nasutitiermitinae (Trinervitermes). We hypothesize that the presence of termites within the different farming systems might be influenced by the types of input applied, the soil moisture content and the occurrence of natural enemies. Our findings further demonstrate that the organic high input system attracts termites, which are an important, and often beneficial, component of soil fauna. This further increases the potential of such systems in enhancing sustainable agricultural production in Kenya

Insecticide contamination in organic agriculture: Evidence from a long-term farming systems comparison trial

Synthetic pesticides applied in conventional agriculture to control pests tend to compromise ecosystem services, and their residues may contaminate organic agriculture. To understand the significance of this contamination, also in small-scale farming systems in sub-Saharan Africa, quantitative data is required. Therefore, we compared synthetic insecticide and botanical/biopesticide residues in conventional and organic agricultural production systems after nine years of continuous cultivation of a maize-based crop rotation system at two sites in Kenya. Our results show high detectable concentrations of synthetic insecticide residues (imidacloprid, acetamiprid, chlorpyrifos, and chlorantraniliprole) in conventional plant produce and soil. Furthermore, the organophosphate chlorpyrifos was detected at concentrations above European Union Maximum Residue Limits (MRL) for plant produce, indicating potential risks for human health. Additionally, we detected imidacloprid, acetamiprid, chlorpyrifos, and chlorantraniliprole concentrations in the soil, indicating potential environmental harm. No residues of biopesticide/botanicals were detected in any of the production systems. However, we detected imidacloprid and chlorantraniliprole in organic plots. The findings indicate that the MRLs can be crossed even if synthetic insecticides are applied according to or below the recommended rates on the conventional plots. Thus, synthetic insecticides potentially risk human health and the environment, while botanicals and bio-pesticides represent a safe alternative

Evolution of fungal and non-fungal eukaryotic communities in response to thermophilic co-composting of various nitrogen-rich green feedstocks

Thermophilic composting is a promising soil and waste management approach involving diverse micro and macro-organisms, including eukaryotes. Due to sub-optimal amounts of nutrients in manure, supplemental feedstock materials such as Lantana camara, and Tithonia diversifolia twigs are used in composting. These materials have, however, been reported to have antimicrobial activity in in-vitro experiments. Furthermore, the phytochemical analysis has shown differences in their complexities, thus possibly requiring various periods to break down. Therefore, it is necessary to understand these materials’ influence on the biological and physical-chemical stability of compost. Most compost microbiome studies have been bacterial-centric, leaving out eukaryotes despite their critical role in the environment. Here, the influence of different green feedstock on the fungal and non-fungal eukaryotic community structure in a thermophilic compost environment was examined. Total community fungal and non-fungal eukaryotic DNA was recovered from triplicate compost samples of four experimental regimes. Sequencing for fungal ITS and non-fungal eukaryotes; 18S rDNA was done under the Illumina Miseq platform, and bioinformatics analysis was done using Divisive Amplicon Denoising Algorithm version 2 workflow in R version 4.1. Samples of mixed compost and composting day 84 recorded significantly (P<0.05) higher overall fungal populations, while Lantana-based compost and composting day 84 revealed the highest fungal community diversity. Non-fungal eukaryotic richness was significantly (P< 0.05) more abundant in Tithonia-based compost and composting day 21. The most diverse non-fungal eukaryotic biome was in the Tithonia-based compost and composting day 84. Sordariomycetes and Holozoa were the most contributors to the fungal and non-fungal community interactions in the compost environment, respectively. The findings of this study unravel the inherent influence of diverse composting materials and days on the eukaryotic community structure and compost’s biological and chemical stability

Seroprevalence of anti-SARS-CoV-2 IgG antibodies in Kenyan blood donors.

The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Africa is poorly described. The first case of SARS-CoV-2 in Kenya was reported on 12 March 2020, and an overwhelming number of cases and deaths were expected, but by 31 July 2020, there were only 20,636 cases and 341 deaths. However, the extent of SARS-CoV-2 exposure in the community remains unknown. We determined the prevalence of anti-SARS-CoV-2 immunoglobulin G among blood donors in Kenya in April-June 2020. Crude seroprevalence was 5.6% (174 of 3098). Population-weighted, test-performance-adjusted national seroprevalence was 4.3% (95% confidence interval, 2.9 to 5.8%) and was highest in urban counties Mombasa (8.0%), Nairobi (7.3%), and Kisumu (5.5%). SARS-CoV-2 exposure is more extensive than indicated by case-based surveillance, and these results will help guide the pandemic response in Kenya and across Africa

Epidemiology of COVID-19 infections on routine polymerase chain reaction (PCR) and serology testing in Coastal Kenya [version 1; peer review: 2 approved]

Background: There are limited studies in Africa describing the epidemiology, clinical characteristics and serostatus of individuals tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. We tested routine samples from the Coastal part of Kenya between 17th March 2020 and 30th June 2021. Methods: SARS-CoV-2 infections identified using reverse transcription polymerase chain reaction (RT-PCR) and clinical surveillance data at the point of sample collection were used to classify as either symptomatic or asymptomatic. IgG antibodies were measured in sera samples, using a well validated in-house enzyme-linked immunosorbent assay (ELISA). Results: Mombasa accounted for 56.2% of all the 99,694 naso-pharyngeal/oro-pharyngeal swabs tested, and males constituted the majority tested (73.4%). A total of 7737 (7.7%) individuals were SARS-CoV-2 positive by RT-PCR. The majority (i.e., 92.4%) of the RT-PCR positive individuals were asymptomatic. Testing was dominated by mass screening and travellers, and even at health facility level 91.6% of tests were from individuals without symptoms. Out of the 97,124 tests from asymptomatic individuals 7,149 (7%) were positive and of the 2,568 symptomatic individuals 588 (23%) were positive. In total, 2458 serum samples were submitted with paired naso-pharyngeal/oro-pharyngeal samples and 45% of the RT-PCR positive samples and 20% of the RT-PCR negative samples were paired with positive serum samples. Symptomatic individuals had significantly higher antibody levels than asymptomatic individuals and become RT-PCR negative on repeat testing earlier than asymptomatic individuals. Conclusions: In conclusion, the majority of SARS-CoV-2 infections identified by routine testing in Coastal Kenya were asymptomatic. This reflects the testing practice of health services in Kenya, but also implies that asymptomatic infection is very common in the population. Symptomatic infection may be less common, or it may be that individuals do not present for testing when they have symptoms

COVID-19 transmission dynamics underlying epidemic waves in Kenya

Policy decisions on COVID-19 interventions should be informed by a local, regional and national understanding of SARS-CoV-2 transmission. Epidemic waves may result when restrictions are lifted or poorly adhered to, variants with new phenotypic properties successfully invade, or when infection spreads to susceptible sub-populations. Three COVID-19 epidemic waves have been observed in Kenya. Using a mechanistic mathematical model, we explain the first two distinct waves by differences in contact rates in high and low social-economic groups, and the third wave by the introduction of higher-transmissibility variants. Reopening schools led to a minor increase in transmission between the second and third waves. Socio-economic and urban/rural population structure are critical determinants of viral transmission in Kenya

Sero-surveillance for IgG to SARS-CoV-2 at antenatal care clinics in three Kenyan referral hospitals: Repeated cross-sectional surveys 2020-21.

INTRODUCTION: The high proportion of SARS-CoV-2 infections that have remained undetected presents a challenge to tracking the progress of the pandemic and estimating the extent of population immunity. METHODS: We used residual blood samples from women attending antenatal care services at three hospitals in Kenya between August 2020 and October 2021and a validated IgG ELISA for SARS-Cov-2 spike protein and adjusted the results for assay sensitivity and specificity. We fitted a two-component mixture model as an alternative to the threshold analysis to estimate of the proportion of individuals with past SARS-CoV-2 infection. RESULTS: We estimated seroprevalence in 2,981 women; 706 in Nairobi, 567 in Busia and 1,708 in Kilifi. By October 2021, 13% of participants were vaccinated (at least one dose) in Nairobi, 2% in Busia. Adjusted seroprevalence rose in all sites; from 50% (95%CI 42-58) in August 2020, to 85% (95%CI 78-92) in October 2021 in Nairobi; from 31% (95%CI 25-37) in May 2021 to 71% (95%CI 64-77) in October 2021 in Busia; and from 1% (95% CI 0-3) in September 2020 to 63% (95% CI 56-69) in October 2021 in Kilifi. Mixture modelling, suggests adjusted cross-sectional prevalence estimates are underestimates; seroprevalence in October 2021 could be 74% in Busia and 72% in Kilifi. CONCLUSIONS: There has been substantial, unobserved transmission of SARS-CoV-2 in Nairobi, Busia and Kilifi Counties. Due to the length of time since the beginning of the pandemic, repeated cross-sectional surveys are now difficult to interpret without the use of models to account for antibody waning

Seroprevalence of Antibodies to Severe Acute Respiratory Syndrome Coronavirus 2 Among Healthcare Workers in Kenya.

BACKGROUND: Few studies have assessed the seroprevalence of antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) among healthcare workers (HCWs) in Africa. We report findings from a survey among HCWs in 3 counties in Kenya. METHODS: We recruited 684 HCWs from Kilifi (rural), Busia (rural), and Nairobi (urban) counties. The serosurvey was conducted between 30 July and 4 December 2020. We tested for immunoglobulin G antibodies to SARS-CoV-2 spike protein, using enzyme-linked immunosorbent assay. Assay sensitivity and specificity were 92.7 (95% CI, 87.9-96.1) and 99.0% (95% CI, 98.1-99.5), respectively. We adjusted prevalence estimates, using bayesian modeling to account for assay performance. RESULTS: The crude overall seroprevalence was 19.7% (135 of 684). After adjustment for assay performance, seroprevalence was 20.8% (95% credible interval, 17.5%-24.4%). Seroprevalence varied significantly (P < .001) by site: 43.8% (95% credible interval, 35.8%-52.2%) in Nairobi, 12.6% (8.8%-17.1%) in Busia and 11.5% (7.2%-17.6%) in Kilifi. In a multivariable model controlling for age, sex, and site, professional cadre was not associated with differences in seroprevalence. CONCLUSION: These initial data demonstrate a high seroprevalence of antibodies to SARS-CoV-2 among HCWs in Kenya. There was significant variation in seroprevalence by region, but not by cadre

What is the contribution of organic agriculture to sustainable development? Results from the Long-term Farming Systems Comparisons Trials

The farming systems comparisons trials in Kenya have been running since 2007 at two trial sites (Chuka and Thika). The trials compare the economic, ecological, and sustainable performance of organic and conventional farming systems at a high and low input level. Results showed comparable productivity in conventional and organic systems for cereals but lower yields in organic for potatoes and leafy vegetables. Production costs are generally higher in organic due to the higher labor costs. However, soil fertility and biodiversity are better in organic systems. To fully exploit the potential of organic systems, further innovations in organic pest and input management have to be developed, and capacity building has to be strengthened

Nitrogen release and synchrony in organic and conventional farming systems of the Central Highlands of Kenya

To match Nitrogen (N) supply to crop N demand, it is essential to understand N release and uptake patterns in different farming systems and crops. To assesses the dynamics of N released in organic and conventional systems and potential synchrony and asynchrony in crop N uptake, a study was conducted over three cropping seasons (potato, maize and leafy vegetables) at two sites in the Central Highlands of Kenya. Mineral-N release and synchrony were monitored in conventional and organic systems at high (recommended N, P, pesticides and irrigation) and low input (low N, P, pesticide use and rainfed) systems. Mineral-N release was assessed using in situ buried bags and N synchrony was measured by the daily differences in N fluxes. The percentage of N applied released during potato (38%) and vegetable (44%) cropping seasons were similar between systems. However, under maize strong temporal N immobilization from inputs occurred, particularly at Thika, related to the poor quality of manure and compost (lignin:N ratio > 13). In all systems, excess-asynchrony of available N was pronounced during vegetative stages and at harvest, while insufficient-asynchrony occurred at reproductive stages. During potato cropping season at Thika, Org-High showed highest positive N fluxes (> 20 kg N ha−1 day−1) at planting and tuber bulking stage. At early stages of maize and vegetables Org-Low and Org-High experienced up to 5 times larger negative N fluxes (insufficiency) compared to conventional treatments at Chuka site. The study recommends reducing N applications at planting and increasing N dosages at reproductive stages of crops