Articles: Department of Biological Sciences
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Item The Latitudinal Biotic Interaction Hypothesis revisited contrasting latitudinal richness gradients in actively vs. passively accumulated interaction partners of honey bees(UoEm, 2025) Cirtwill, Alyssa R.; Roslin, Tomas; Peña‑Aguilera, Pablo; Agboto, Agathe; Bercê, William; Bondarchuk, Svetlana N.; Brodschneider, Robert; Heidari, Behzad; Kaizirege, Camara; Nyaga, Justine Muhoro; Ojonugwa, Ekpah; Gomez, Gonzalo Ossa; Paz, Claudia; Pirk, Christian; Salehi‑Najafabadi, Amir; Salonen, Anneli; Soloniaina, Chantal; Wirta, HelenaContrasting hypotheses suggest that the number of biotic interactions per species couldeither increase towards the equator due to the increasing richness of potential interaction partners (Neutral theory),or decrease in the tropics due to increased biotic competition (Latitudinal Biotic Interaction Hypothesis). Empiricaltesting of these hypotheses remains limited due to practical limitations, differences in methodology, and speciesturnover across latitudes. Here, we focus on a single species with a worldwide distribution, the honey bee (Apis mellif-era L.), to assess how the number of different types of interactions vary across latitudes. Foraging honey bees interactwith many organisms in their local environment, including plants they actively select to visit and microbes that theylargely encounter passively (i.e., unintentionally and more or less randomly). Tissue pieces and spores of these organ‑isms are carried to the hive by foraging honey bees and end up preserved within honey, providing a rich recordof the species honey bees encounter in nature.Item Geographic Distribution of Rabies Virus and Genomic Sequence Alignment of Wild and Vaccine Strains, Kenya(UoEm, 2024-08-08) Wambugu, Evalyne N.; Kimita, Gathii; Kituyi, Sarah N.; Washington, Michael A.; Masakhwe, Clement; Mutunga, Lucy M.; Jaswant, Gurdeep; Thumbi, S.M.; Schaefer, Brian C.; Waitumbi, John N.Rabies, a viral disease that causes lethal encephalitis, kills ≈59,000 persons worldwide annually, despite availability of effective countermeasures. Rabies is endemic in Kenya and is mainly transmitted to humans through bites from rabid domestic dogs. We analyzed 164 brain stems collected from rabid animals in western and eastern Kenya and evaluated the phylogenetic relationships of rabies virus (RABV) from the 2 regions. We also analyzed RABV genomes for potential amino acid changes in the vaccine antigenic sites of nucleoprotein and glycoprotein compared with RABV vaccine strains commonly used in Kenya. We found that RABV genomes from eastern Kenya overwhelmingly clustered with the Africa-1b subclade and RABV from western Kenya clustered with Africa-1a. We noted minimal amino acid variances between the wild and vaccine virus strains. These data confirm minimal viral migration between the 2 regions and that rabies endemicity is the result of limited vaccine coverage rather than limited efficacy.Item Nutritional status of people who inject drugs in Coastal Kenya: a cross-sectional study(UoeM, 2024) Budambula, Valentine ; Ngari, Moses ; Budambula, Nancy L.M. ; Ahmed, Abid A. ; Were, TomIntroduction Despite documentation on injection drug use (IDU) in Kenya, the nutritional status of people who inject drugs (PWIDs) is under-explored. Elsewhere studies report under-nutrition among PWIDs which is attributed to food insecurity; competing priorities between drugs and food supply; chaotic lifestyle; reduced food intake; substance use induced malnutrition due to inflammation and comorbidities. Methods This was a cross-sectional study that sought to assess the nutritional status of PWIDs in Coastal Kenya. We recruited 752 participants of whom 371(49%) were on IDUs and 75 non-IDUs and 306 non-drug users using respondent driven sampling, traditional snowball, makeshift outreach and purposive sampling methods. Results More than one half of the participants (56%) had BMI classified as normal while 35% had BMI < 18.5. The proportion with BMI < 18.5 was higher among IDUs (46%) compared to the non-IDUs (33%) and non-drug users (23%) at P < 0.001. Using the mid upper arm circumference (MUAC), 17% were classified as underweight and the proportion was lowest (11%) among non- drugs users compared to 22% among IDUs (P < 0.001). However, the IDUs had lower proportion of overweight (8.1%) compared to 55% among the non- drug users. The proportion with low waist-for-hip ratio was highest among the IDUs (74%) while high waist-for-hip ratio was lowest in the same group of IDUs (11%) at P < 0.001. One half (50%), of the participants had no signs of anaemia, (47%) had mild/moderate anaemia while 21 (2.8%) had severe anaemia. However, IDUs were more likely to be overweight based on waist circumference as a parameter. The IDUs had the highest proportion (54%) of mild to moderate anaemia compared to non-IDUs (37%) and 40% non- drug users (P < 0.001). In the multivariable models, IDUs (aRRR 2.83 (95%CI 1.84‒4.35)) and non-IDUs (aRRR 1.42 (95%CI 1.07‒1.88)) compared to non- drug users were positively associated with BMI < 18.5. Being an IDU was positively associated with mild or moderate anaemia (aRRR 1.65 (95%CI 1.13‒2.41)) while non-IDUs were positively associated with severe anaemia (aRRR 1.69 (95%CI 1.16‒2.48)). Conclusion A significant proportion of the participants were under-nourished with those injecting drugs bearing the heaviest brunt. Being an IDU was positively associated with the low BMI, MUAC, waist for hip ratio and mild or moderate anaemia but high waist circumference. People who inject drugs have high risk for under-nutrition and should be targeted with appropriate interventions. Keywords Under nutrition, Injection drug use, BMI, MUAC and anaemiaItem Mapping brucellosis risk in Kenya and its implications for control strategies in sub‑Saharan Africa(UoEm, 2023-11-30) Akoko, James M.; Mwatondo, Athman; Muturi, Mathew; Wambua, Lillian; Abkallo, Hussein M.; Nyamota, Richard; Bosire, Caroline; Oloo, Stephen; Limbaso, Konongoi S.; Gakuya, Francis; Nthiwa, Daniel; Bartlow, Andrew; Middlebrook, Earl; Fair, Jeanne; Ogutu, Joseph O.; Gachohi, John; Njenga, Kariuki; Bett, BernardIn Sub-Saharan Africa (SSA), effective brucellosis control is limited, in part, by the lack of long-term commitments by governments to control the disease and the absence of reliable national human and livestock population-based data to inform policies. Therefore, we conducted a study to establish the national prevalence and develop a risk map for Brucella spp. in cattle to contribute to plans to eliminate the disease in Kenya by the year 2040. We randomly generated 268 geolocations and distributed them across Kenya, proportionate to the area of each of the five agroecological zones and the associated cattle population. Cattle herds closest to each selected geolocation were identified for sampling. Up to 25 cattle were sampled per geolocation and a semi-structured questionnaire was administered to their owners. We tested 6,593 cattle samples for Brucella immunoglobulin G (IgG) antibodies using an Enzyme-linked immunosorbent assay (ELISA). We assessed potential risk factors and performed spatial analyses and prevalence mapping using approximate Bayesian inference implemented via the integrated nested Laplace approximation (INLA) method. The national Brucella spp. prevalence was 6.8% (95% CI: 6.2–7.4%). Exposure levels varied significantly between agro-ecological zones, with a high of 8.5% in the very arid zone with the lowest agricultural potential relative to a low of 0.0% in the agro-alpine zone with the highest agricultural potential. Additionally, seroprevalence increased with herd size, and the odds of seropositivity were significantly higher for females and adult animals than for males or calves. Similarly, animals with a history of abortion, or with multiple reproductive syndromes had higher seropositivity than those without. At the herd level, the risk of Brucella spp. transmission was higher in larger herds, and herds with a history of reproductive problems such as abortion, giving birth to weak calves, or having swollen testes. Geographic localities with high Brucella seroprevalence occurred in northern, eastern, and southern regions of Kenya all primarily characterized by semi-arid or arid agro-ecological zones dominated by livestock pastoralism interspersed with vast areas with mixed livestock-wildlife systems. The large spatial extent of our survey provides compelling evidence for the widespread geographical distribution of brucellosis risk across Kenya in a manner easily understandable for policymakers. Our findings can provide a basis for risk-stratified pilot studies aiming to investigate the cost-effectiveness and efficacy of singular and combined preventive intervention strategies that seek to inform Kenya’s Brucellosis Control Policy.Item Seroprevalence and related risk factors of Brucella spp. in livestock and humans in Garbatula subcounty, Isiolo county, Kenya(Uoem, 2023-10-16) Mwatondo, Athman; Nthiwa, Daniel; Muturi, Mathew; Akoko, James; Nyamota, Richard; Bett, Bernard; Omolo, Jack; Gichuhi, Stephen; Mureit, Marianne W.Item Seroprevalence of Brucella spp. and Rift Valley fever virus among slaughterhouse workers in Isiolo County, northern Kenya(UoEm, 2023-10-05) Nyamota, Richard; Maina, Josphat; Mwatondo, Athman; Akoko, James; Nthiwa, Daniel; Bartlow, Andrew W.; Muturi, Mathew; Wambua, Lillian; Middlebrook, Earl A.; Bett, BernardBrucella spp. and Rift Valley fever virus (RVFV) are classified as priority zoonotic agents in Kenya, based on their public health and socioeconomic impact on the country. Data on the pathogen-specific and co-exposure levels is scarce due to limited active surveillance. This study investigated seroprevalence and co-exposure of Brucella spp. and RVFV and associated risk factors among slaughterhouse workers in Isiolo County, northern Kenya. A crosssectional serosurvey was done in all 19 slaughterhouses in Isiolo County, enrolling 378 participants into the study. The overall seroprevalences for Brucella spp. and RVFV were 40.2% (95% CI: 35.2–45.4) and 18.3% (95% CI: 14.5–22.5), respectively while 10.3% (95% CI 7.4%-13.8%) of individuals were positive for antibodies against both Brucella spp. and RVFV. Virus neutralisation tests (VNT) confirmed anti-RVFV antibodies in 85% of ELISApositive samples. Our seroprevalence results were comparable to community-level seroprevalences previously reported in the area. Since most of the study participants were not from livestock-keeping households, our findings attribute most of the detected infections to occupational exposure. The high exposure levels indicate slaughterhouse workers are the most at-risk population and there is need for infection, prevention, and control programs among this high-risk group. This is the first VNT confirmation of virus-neutralising antibodies among slaughterhouse workers in Isiolo County and corroborates reports of the area being a high-risk RVFV area as occasioned by previously reported outbreaks. This necessitates sensitization campaigns to enhance awareness of the risks involved and appropriate mitigation measures.Item Ecological and Subject‐Level Drivers of Interepidemic Rift Valley Fever Virus Exposure in Humans and Livestock in Northern Kenya(UoEm, 2023) Mathew, Muturi; Athman, Mwatondo; Nijhof, Ard M; Akoko, James; Nyamota, Richard; Makori, Anita; Mutono, Nyamai; Nthiwa, Daniel; Wambua, Lilian; Roesel, Kristina; Thumbi, S. M.; Bett, BernardItem Do afroalpine plants differ from other alpine plants by their leaf functional traits?(UoEm, 2023-06-16) Onipchenko, Vladimir G.; Kipkeev, Aliy M.; Kopylova, Natalia A.; Nyaga, Justine M.; Elumeeva, Tatiana G.; Dudova, Ksenia V.; Akhmetzhanova, Asem A.; Tiunov, Alexei V.; Karpukhin, Mikhail M.; Makarov, Mikhail I.Afroalpine plants develop under specific climate with great daily fluctuations and weak seasonal dynamics of temperature. Do leaf functional traits of the plants in Mt. Kenya differ from those of temperate plants in NW Caucasus? To answer this question, we conducted a comparative study at the Teleki valley (4000–4500 m a.s.l.), Mt. Kenya, Kenya, and Teberda national park (2600–2900 m a.s.l.), the Caucasus, Russia. We measured leaf area, fresh and dry mass, C, N, P, δ 13 C, δ 15 N and derivative traits (specific leaf area – SLA, leaf dry matter content – LDMC, C:N and N:P ratios) for 48 species at the Teleki valley, and the same traits, except for the δ 13 C and δ 15 N, for 141 species in the Teberda national park. The CSR-stra tegies scores were calculated. We applied the Principal Component Analysis to reveal the main patterns of trait variation. Leaf dry mass of Mt. Kenya alpine plants ranged from 0.27 mg (Sagina afroalpina) to 14.0 g (Dendrosenecio kenio den dron). Leaf area, mass and LDMC of alpine plants in both regions did not differ significantly. The SLA of Mt. Kenya’s plants varied about 20-fold: from 2.6 mm 2 mg -1 (Festuca pilgeri) to 39.8 mm 2 mg -1 (Cineraria deltoidea), and Caucasian plants had higher SLA. N and P leaf concentrations were higher, but C lower in Caucasian plants than in Kenyan. Leaf N:P ratio was similar for both regions, while C:N ratio was higher in Kenyan plants. Species of “rosette” trees (Dendrosenecio spp.) differed from other species by size characteristics (maximal leaf dry mass and area were in Dendrosenecio kenioden dron), as well as correspondingly higher investment to mechanical tissues (high C:N ratio, low SLA). By the other functional traits, “rosette” trees were similar to many other alpine plants. Thus, afroalpine plants of Mt. Kenya are close to temperate alpine plants by some leaf functional traits, but possess higher stress-tolerance.Item HIV Virologic Failure among Patients with Persistent Low-Level Viremia in Nairobi, Kenya: It Is Time to Review the >1000 Virologic Failure Threshold(Hindawi, 2023-04-27) Nzivo, Mirriam M.; Waruhiu, Cecilia N.; Kang’ethe, James M.; Budambula, Nancy L. M.Persistent low-level viremia (PLLV) of 200-999 copies/ml has been reported as a risk factor for HIV virologic failure (VF). This retrospective study was aimed at characterizing patients with PLLV, determining factors associated with VF, and determining the effect of regimen change. Data were extracted from electronic medical records for HIV care and treatment. Patients’ characteristics (N = 705) were as follows: a mean age of 42 years, majority female (55%), and 51% married. A majority (78.7%) had a history of opportunistic infections in their ART lifetime. To determine factors associated with VF, 187 records on patients who maintained PLLV and 12 on deceased patients at the time of data review were eliminated from the analysis, leaving 506 patient records. Out of the 506, 89% (451/506) suppressed VL to nondetectable levels while 11% (55/506) had VF, and the difference was significant (P = 0:0001). Virologic failure was significantly associated with ages 10-30 years (P < 0:05). Baseline VL ≥ 1000 (OR 3.929; P = 0:002) and 200-999 copies/ml (OR 4.062; P = 0:004) were associated with VF. During PLLV, factors associated with VF included the following: PLLV of 200-999 copies/ml (P < 0:05), viral blips (OR 4.545; P = 0:0001), mean maximum VL (P < 0:05), and age (P = 0:043). Married marital status was inversely associated with VF (OR 0.318; P = 0:026). Regimen change was not significantly associated with virologic outcomes. However, patients who switched regimens to the second line had a high risk of VF (P = 0:028; OR 3.203). Regimen change was significantly high (P < 0:05) among adolescents and patients with a start regimen of 2NRTI+1NNRTI. Most of the PLLV patients (89%) achieved nondetectable VL after their continued ART monitoring for at least 12 months. Therefore, PLLV was not an indicator of VF. However, a consistent VL of ≥200-999 copies/ml at baseline and more than 12 months of ART care and treatment were significantly associated with VF. Patients with VL 200-999 copies/ml, adolescents, and young adults require intensive ART monitoring and support.Item Food web structure of nematode communities in irrigated rice fields(Heliyon, 2023-02) Mokuah, Dorcas; Karuri, Hannah W.; Nyaga, Justine M.Nematodes are a key component of the soil food web and they play an important role in the provision of ecosystem services. Rice cultivation in Mwea, Kenya involves the intensive use of fertilizers and pesticides which may affect the complexity of the nematode-based soil food web. This study examined the nematode diversity and food web structure in irrigated rice fields in Nyangati and Tebere in Mwea, Kirinyaga County, Kenya. Nematodes were identified up to the genus level and soil physico-chemical properties were also determined. Aphelenchoides and Longidorus occurred in significantly greater proportions in Tebere, while in Nyangati there was a high abundance of Helicotylenchus. Aphelenchoides was positively correlated to soil electrical conductivity. From additive diversity partitioning of genus richness, the α and β components contributed 33.7% and 66.3% of the γ diversity, respectively. For Shannon and Simpson diversity indices, the largest contribution to overall diversity was from α component. Soil food web indices were similar across the two regions. Channel and basal indices were below 30% while Enrichment (EI) and Structure (SI) indices were above 50%. There was no variation in metabolic footprints except for the fungivore footprint which was significantly higher in Tebere. Based on the EI and SI, the soil food web in paddy rice fields in Mwea was structured and enriched with moderate disturbance. Due to the high prevalence of economically damaging parasitic nematodes in the rice fields, appropriate management schemes that enhance specific components of the soil food web and increase the suppressive ability of soil against plant-parasitic nematodes should be implemented.Item Amplicon-based assessment of bacterial diversity and community structure in three tropical forest soils in Kenya(Heliyon, 2022-11) Kenya, Eucharia U.; Kinyanjui, Grace; Kipnyargis, Alex C.; Kinyua, Franklin; Mwangi, Mary; Khamis, Fathiya; Mwirichia, Romano K.Forest soils provide a multitude of habitats for diverse communities of bacteria. In this study, we selected three tropical forests in Kenya to determine the diversity and community structure of soil bacteria inhabiting these regions. Kakamega and Irangi are rainforests, whereas Gazi Bay harbors mangrove forests. The three natural forests occupy different altitudinal zones and differ in their environmental characteristics. Soil samples were collected from a total of 12 sites and soil physicochemical parameters for each sampling site were analyzed. We used an amplicon-based Illumina high-throughput sequencing approach. Total community DNA was extracted from individual samples using the phenol-chloroform method. The 16S ribosomal RNA gene segment spanning the V4 region was amplified using the Illumina MiSeq platform. Diversity indices, rarefaction curves, hierarchical clustering, principal component analysis (PCA), and non-metric multidimensional scaling (NMDS) analyses were performed in R software. A total of 13,410 OTUs were observed at 97% sequence similarity. Bacterial communities were dominated by Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, and Acidobacteria in both rainforest and mangrove sampling sites. Alpha diversity indices and species richness were higher in Kakamega and Irangi rainforests compared to mangroves in Gazi Bay. The composition of bacterial communities within and between the three forests was also significantly differentiated (R ¼ 0.559, p ¼ 0.007). Clustering in both PCA and NMDS plots showed that each sampling site had a distinct bacterial community profile. The NMDS analysis also indicated that soil EC, sodium, sulfur, magnesium, boron, and manganese contributed significantly to the observed variation in the bacterial community structure. Overall, this study demonstrated the presence of diverse taxa and heterogeneous community structures of soil bacteria inhabiting three tropical forests of Kenya. Our results also indicated that variation in soil chemical parameters was the major driver of the observed bacterial diversity and community structure in these forests.Item Poly-drug use among female and male commercial sex workers visiting a drop in centre in Mombasa County, Kenya(PLOS GLOBAL PUBLIC HEALTH, 2022-11-11) Budambula, Nancy L. M.; Kemunto, Phyllys; Ziro, Onesmus Wanje; Kissinger, George; Ngari, Moses; Budambula, ValentineThe relationship between commercial sex work and drug use is complex and the two exacerbate each other. In Kenya, Mombasa County has one of the highest populations of drug users and commercial sex workers. Despite documentation of drug use among sex workers, most of the studies are based on self-reported history which is prone to social desirability and memory recall biases. It is in this context that we sought to establish actual drug use is this sub-population. A cross-sectional study was conducted to determine self-reported and confirmed drug use among 224 commercial sex workers accessing services at Mvita Dropin. Actual drug use was determined qualitatively using 6 panel plus alcohol Saliva Test kit. The overall prevalence of self-reported and confirmed current use for at least one drug was 98% and 99% respectively. Regardless of the technique used, alcohol and tobacco products were the most consumed substances. Alcohol use increased significantly with age (P = 0.03). Risk of cigarette use and testing positive for cotinine was higher among those age 18 to 35 years compared to >35years at P = 0.001 and P = 0.002 respectively. Poly-drug use was common with 98% testing positive for more than one drug. The reason for drug use was sex work related pressure (88%) with 60% of the respondents reporting they cannot transact this business without drugs. Almost every commercial sex worker is a poly-drug user. We recommend targeted interventions for commercial sex workers.Item Vertical Distribution of Plant-Parasitic Nematodes in Sweet Potato(Sciendo., 2022) Kemboi, Bernard; Karuri, Hannah; Nyaga, Justine M.; Kingsbury, Aaron J.Plant-parasitic nematodes (PPN) are harmful pests that have become a severe threat to crop production worldwide. Diversity of PPN at horizontal and spatial scales influence the effectiveness of control strategies. This study evaluated the vertical distribution of PPN genera at 0 cm to 30 cm and 30 cm to 60 cm in sweet potato fields in Central, Manyatta, and Nembure regions of Embu County, Kenya. A significant region × depth interaction was observed for Tylenchus. For all the other nematode genera, there were no significant variations in the abundance at 0 cm to 30 cm and 30 cm to 60 cm depths. However, Helicotylenchus, Meloidogyne, and Scutellonema occurred in greater numbers at both depths in all regions. Shannon and Simpson diversity indices were higher at 0 cm to 30 cm depth while Pielou’s evenness was similar at both depths in the three regions. Diversity partitioning of genus richness, Shannon, and Simpson diversities across all regions at 0 cm to 30 cm, indicated that β component contributed 61.9%, 35.6%, and 22.6% of γ diversity, respectively. Coinertia analysis indicated a significant covariation between nematode genera and soil properties. The results show that management of PPN in sweet potato fields should be targeted at soil depths that are not less than 60 cm.Item Nematode diversity and its association with soil properties in monocrop pigeon pea(Elsevier Ltd, 202-07-03) Maina, Samuel; Karuri, Hannah; Mugweru, JuliusPigeon pea is a versatile pulse crop grown in semi-arid regions of Kenya; however, its production is affected by plant-parasitic nematodes. The current study was undertaken to investigate the diversity of nematodes and the influence of soil properties on their diversity in monocrop pigeon pea fields in Mbeere North, Embu County, Kenya. Soil samples were collected from Gatunguru B, Gwakaithi, Itururi, Kambungu, Kanyueri, Karigiri, Mbangua and Njarange regions. From each field, soil samples were collected from a depth of 25 cm using W- shaped sampling pattern. The nematodes were identified to the genus level using morphological features. In total, 46 nematode genera assigned to five trophic levels were identified across the eight regions. Abundance of Meloidogyne, Rotylenchulus, Longidorus, Acrobeloides, Cervidellus, Panagrolaimus, Prismatolaimus and Wilsonema varied markedly among the eight regions. Bacterivores belonging to colonizer-persister group 2 were the most prevalent group. There were no differences in Pielou’s evenness, genus richness, Shannon and Simpson diversity indices across the regions. Canonical correspondence analysis indicated significant correlations between certain nematode genera and soil attributes with the first two axes accounting for 56.65% of the variance. Acrobeloides correlated positively with Mg, C, Mn and N, and negatively with Fe. The occurrence of Hoplolaimus and Meso- rhabditis was associated negatively with soil pH, clay and Ca, and positively with sand. The present work reveals a high abundance of economically important PPN in monocrop pigeon pea which necessitates that appropriate nematode management programs are implemented.Item Nematode assemblages, food web indices and metabolic footprints in maize-pigeon pea agro-ecosystems(Elsevier Ltd, 2022-08-02) Maina, Samuel; Karuri, Hannah; Mugweru, JuliusPigeon pea (Cajanus cajan L.) and maize (Zea mays L.) are important food crops in developing countries due to their multiple benefits. However, their production is constrained by plant-parasitic nematodes (PPN) which cause significant yield losses. Understanding the nematode-based soil food web structure in maize-pigeon pea agroecosystems will allow sustainable PPN management by improving soil health. This study explored nematode community assemblages, indices and metabolic footprints in maize-pigeon pea agroecosystems in Mbeere South, Embu County, Kenya. Soil samples were collected from Gachuriri, Irabari, Kanduu, Kangeta, Kangungi, Kaninwathiga, Karimari and Mutugu regions. The recovered nematodes were identified to the genus level. There were 41 nematode genera across the eight regions. Longidorus spp., Heterocephalobus spp., Cervidellus spp., Mesorhabditis spp. and Mononchus spp. differed significantly across the regions. Meloidogyne spp., Scutellonema spp., Rotylenchulus spp. and Pratylenchus spp. were the most prevalent genera although their abundance was not statistically different across the regions. Using the structure and enrichment indices, soil food web in Irabari was degraded, whereas the other seven regions were structured. The main energy channel of organic matter decomposition in the studied regions was dominated by fungivores. There were no differences in metabolic footprints expect for bacterivore footprint. The occurrence of Hoplolaimus spp. and Xiphinema spp. showed a negative correlation with N, C, Mg and Na. This work provides useful insights into the maize-pigeon pea nematode soil food web structure and function which can be used in improving their yields and soil healthItem The Contribution of Subtidal Seagrass Meadows to the Total Carbon Stocks of Gazi Bay, Kenya(Diversity, 2022-08-11) Wang’ondu, Virginia W.; Githaiga, Michael N.; Gorman, Daniel; Kairo, James G.; Omollo, Derrick J.Seagrass beds occur globally in both intertidal and subtidal zones within shallow marine environments, such as bays and estuaries. These important ecosystems support fisheries production, attenuate strong wave energies, support human livelihoods and sequester large amounts of CO2 that may help mitigate the effects of climate change. At present, there is increased global interest in understanding how these ecosystems could help alleviate the challenges likely to face humanity and the environment into the future. Unlike other blue carbon ecosystems, i.e., mangroves and saltmarshes, seagrasses are less understood, especially regarding their contribution to the carbon dynamics. This is particularly true in regions with less attention and limited resources. Paucity of information is even more relevant for the subtidal meadows that are less accessible. In Kenya, much of the available information on seagrasses comes from Gazi Bay, where the focus has been on the extensive intertidal meadows. As is the case with other regions, there remains a paucity of information on subtidal meadows. This limits our understanding of the overall contribution of seagrasses in carbon capture and storage. This study provides the first assessment of the species composition and variation in carbon storage capacity of subtidal seagrass meadows within Gazi Bay. Nine seagrass species, comprising of Cymodocea rotundata, Cymodocea serrulata, Enhalus acoroides, Halodule uninervis, Halophila ovalis, Halophila stipulacea, Syringodium isoetifolium, Thalassia hemprichii, and Thalassodendron ciliatum, were found. Organic carbon stocks varied between species and pools, with the mean below ground vegetation carbon (bgc) stocks (5.1 ± 0.7 Mg C ha−1 ) being more than three times greater than above ground carbon (agc) stocks (0.5 ± 0.1 Mg C ha−1 ). Mean sediment organic carbon stock (sed Corg) of the subtidal seagrass beds was 113 ± 8 Mg C ha−1 . Combining this new knowledge with existing data from the intertidal and mangrove fringed areas, we estimate the total seagrass ecosystem organic carbon stocks in the bay to be 196,721 Mg C, with the intertidal seagrasses storing about 119,790 Mg C (61%), followed by the subtidal seagrasses 55,742 Mg C (28%) and seagrasses in the mangrove fringed creeks storing 21,189 Mg C (11%). These findings are important in highlighting the need to protect subtidal seagrass meadows and for building a national and global data base on seagrass contribution to global carbon dynamics.Item Genetic diversity and population structure of wild and cultivated Crotalaria species based on genotyping-by-sequencing(Plos One, 2022-09) Muli, Joshua K.; Neondo, Johnstone O.; Kamau, Peter K.; Michuki, George N.; Budambula, Nancy L.Crotalaria is a plant genus that is found all over the world, with over 700 species of herbs and shrubs. The species are potential alternative food and industrial crops due to their adaptability to different environments. Currently, information on the genetic diversity and population structure of these species is scanty. Genotyping-by-sequencing (GBS) is a costeffective high-throughput technique in diversity evaluation of plant species that have not been fully sequenced. In the current study, de novo GBS was used to characterize 80 Crotalaria accessions from five geographical regions in Kenya. A total of 9820 single nucleotide polymorphism (SNP) markers were obtained after thinning and filtering, which were then used for the analysis of genetic diversity and population structure in Crotalaria. The proportion of SNPs with a minor allele frequency (maf) > = 0.05 was 45.08%, while the GuanineCytosine (GC) content was 0.45, from an average sequence depth of 455,909 reads per base. The transition vs transversion ratio was 1.81 and Heterozygosity (He) ranged between 0.01–0.07 in all the sites and 0.04 to 0.52 in the segregating sites. The mean Tajima’s D value for the population was -0.094, suggesting an excess of rare alleles. The fixation index (Fst) between the different populations based on the Wright Fst (1943) ranged from 0.0119 to 0.066 for the Eastern-Western and Nairobi-Western populations. Model based techniques of population structure analysis including structure, k-means and cross-entropy depicted eight clusters in the study accessions. Non-model based techniques especially DAPC depicted poor population stratification. Correspondence Analysis (CA), Principal coordinate analyses (PCoA) and phylogenetic analysis identified a moderate level of population stratification. Results from this study will help conservationists and breeders understand the genetic diversity of Crotalaria. The study also provides valuable information for genetic improvement of domesticated species.Item Annotations of novel antennae-expressed genes in male Glossina morsitans morsitans tsetse flies(Plos 1, 2022-08) Bwana, Billiah K.; Mireji, Paul O.; Obiero, George F.; Gakii, Consolata; Akoth, Modesta O.; Mugweru, Julius N.; Nyabuga, Franklin N.; Wachira, Benson M.; Bateta, Rosemary; Ng’ang’a, Margaret M.; Hassanali, AhmedTsetse flies use antennal expressed genes to navigate their environment. While most canonical genes associated with chemoreception are annotated, potential gaps with important antennal genes are uncharacterized in Glossina morsitans morsitans. We generated antennae-specific transcriptomes from adult male G. m. morsitans flies fed/unfed on bloodmeal and/or exposed to an attractant (ε-nonalactone), a repellant (δ-nonalactone) or paraffin diluent. Using bioinformatics approach, we mapped raw reads onto G. m. morsitans geneset from VectorBase and collected un-mapped reads (constituting the gaps in annotation). We de novo assembled these reads (un-mapped) into transcript and identified corresponding genes of the transcripts in G. m. morsitans gene-set and protein homologs in UniProt protein database to further annotate the gaps. We predicted potential protein-coding gene regions associated with these transcripts in G. m. morsitans genome, annotated/curated these genes and identified their putative annotated orthologs/homologs in Drosophila melanogaster, Musca domestica or Anopheles gambiae genomes. We finally evaluated differential expression of the novel genes in relation to odor exposures relative to no-odor control (unfed flies). About 45.21% of the sequenced reads had no corresponding transcripts within G. m. morsitans gene-set, corresponding to the gap in existing annotation of the tsetse fly genome. The total reads assembled into 72,428 unique transcripts, most (74.43%) of which had no corresponding genes in the UniProt database. We annotated/curated 592 genes from these transcripts, among which 202 were novel while 390 were improvements of existing genes in the G. m. morsitans genome. Among the novel genes, 94 had orthologs in D. melanogaster, M. domestica or An. gambiae while 88 had homologs in UniProt. These orthologs were putatively associated with oxidative regulation, protein synthesis, transcriptional and/or translational regulation, detoxification and metal ion binding, thus providing insight into their specific roles in antennal physiological processes in male G. m. morsitans. A novel gene (GMOY014237.R1396) was differentially expressed in response to the attractant. We thus established significant gaps in G. m. morsitans genome annotation and identified novel male antennae-expressed genes in the genome, among which > 53% (108) are potentially G. m. morsitans specific.Item Value chain and sustainability of mangrove wood harvesting in Lamu, Kenya(Elsevier, 2022-08) Riungu, Purity M.; Nyaga, Justine M.; Githaiga, Michael N.; Kairo, James G.Mangrove forests provide harvestable wood and non-wood resources to human society globally. The current study evaluated value chain of mangrove wood products from Lamu, Kenya, and how these impacts on resources’ sustainability. Results show that, exploitation of mangrove wood products in Kenya involves several actors, including national regulator, licensees, cutters, transporters, stockists and the consumers. Based on the differences between allowable and harvest data, Lamu mangroves can be said to be under-exploited. For the 1992–2018 period, an average of 223.5 scores ha of mangrove poles were target for harvesting from Lamu. During the same period, the harvest data indicate an average of 6.2 scores ha 1 1 yr of mangrove poles were removed. However, based on stand level data generated as part of this study, mangroves in Lamu are over- exploited and stocked with non-merchantable poles. There are differentiated net income among various actors in mangrove trade in Kenya. Mangrove cutters are among the ‘losers’ in mangrove trade value chain earning a monthly net income of USD118.6 ± 17.9. Winners in mangrove trade is the Kenya Forest Service, Licensees, transporters, and mangrove dealers (or stockists) in urban centers. The findings of this study are critical in development of the harvesting plan for Lamu mangroves. The results will provide insights toward streamlining mangrove trade for community development, revenue generation and environmental sustainability.Item Nematode assemblages, food web indices and metabolic footprints in maize-pigeon pea agro-ecosystems.(Elsevier, 2022-08) Maina, Samuel; Karuri, Hannah W.; Mugweru, JuliusPigeon pea (Cajanus cajan L.) and maize (Zea mays L.) are important food crops in developing countries due to their multiple benefits. However, their production is constrained by plant-parasitic nematodes (PPN) which cause significant yield losses. Understanding the nematode-based soil food web structure in maize-pigeon pea agroecosystems will allow sustainable PPN management by improving soil health. This study explored nematode community assemblages, indices and metabolic footprints in maize-pigeon pea agroecosystems in Mbeere South, Embu County, Kenya. Soil samples were collected from Gachuriri, Irabari, Kanduu, Kangeta, Kangungi, Kaninwathiga, Karimari and Mutugu regions. The recovered nematodes were identified to the genus level. There were 41 nematode genera across the eight regions. Longidorus spp., Heterocephalobus spp., Cervidellus spp., Mesorhabditis spp. and Mononchus spp. differed significantly across the regions. Meloidogyne spp., Scutellonema spp., Rotylenchulus spp. and Pratylenchus spp. were the most prevalent genera although their abundance was not statistically different across the regions. Using the structure and enrichment indices, soil food web in Irabari was degraded, whereas the other seven regions were structured. The main energy channel of organic matter decomposition in the studied regions was dominated by fungivores. There were no differences in metabolic footprints expect for bacterivore footprint. The occurrence of Hoplolaimus spp. and Xiphinema spp. showed a negative correlation with N, C, Mg and Na. This work provides useful insights into the maize-pigeon pea nematode soil food web structure and function which can be used in improving their yields and soil health.