CW-Department of Plant and Microbial Sciences
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Item Seasonal Variability in the Diversity of Microbial Assemblages and Antibiotic Resistance Determinants of an Estuary System(2015) Mariita, Richard M.; Mohammad J. Hossain; Mark R. Liles; Anthony G. MossAntibiotic resistance (AR) promoted by heavy metal pollution, is widely found in environmental microbes [1-3]. The mobility and acquisition of AR genes depends on mobile genetic elements (MGEs) [4]. Estuaries are metals sinks and aid with the comingling of AR genes [5,6]. In light of the food and recreational value of estuaries (6), it is important to understand estuarine AR dynamics. Here we demonstrate seasonal changes in 1) microbial assemblages and functional diversity, and 2) AR, for the Mobile Bay Estuary. Seasonal samples were sequenced using Illumina Miseq platform. Annotation was achieved via MG-RAST [7], taxonomic analysis via the SILVA SSU rDNA database [8], functional annotation via the SEED Project and functional graphical analysis via Krona [9]. Analysis revealed seasonal trends in abundance. The predominant microbes were Proteobacteria (1,000,738) reads. Abundances were β-proteobacteria (447,758)>α-proteobacteria (307,924)> γ-proteobacteria (209,704)>δ-proteobacteria (30,565)> ε-proteobacteria (4,340)> ζ-proteobacteria (447). α-diversity followed a similar trend: Sp (436.94), W (405.76); Su and F were <300. Chemotaxis and motility genes displayed similar trends: Sp (2728) > W (2221) > F (900) > Su (698). Co-Zn-Cd resistance genes were most abundant in the winter: W (1553) > Sp (1345) > F (494) ≈ Su (459). MvirDB [10] BLAST results revealed the greatest number of virulence and AR genes during Summer: Su (79) > Sp (59) > W (48) > F (23). Our study reveals that microbial taxonomic, functional, and AR gene diversity is highest during Sp, possibly because of expanded riverine input. In contrast, the greatest abundance of AR genes occurs summer, during reduced fresh water input. Thus, this study describes distinct trends in seasonal microbial and genetic populations, and forms a basis for future studies of the link between watershed management, estuaries, and public health. Supported in part by ALA-EPSCoR: NSF EPS-1158862, USDA-Hatch 370225-310100 (AGM, ML) and NSF0348327 (AGM). RMM support: Alabama EPSCoR fellowship, AU-CMB Peaks of Excellence summer graduate research award Seasonal Variability in the Diversity of Microbial Assemblages and Antibiotic Resistance Determinants of an Estuary SystemItem Use of agro-industrial waste and organic amendments in managing root- knot nematodes in black nightshade in selected parts of Kenya(African Crop Science Societ, 2011) Nchore, S. B.; Waceke, J.W.; Kariuki, G. M.A study was conducted in both greenhouse and field to determine the use of agro-industrial waste and organic amendments in the management of root-knot nematodes (RKN) in Solanum nigrum. Treatments included cattle manure (CM), goat manure (GM), Tithonia diversifolia (Td) and agro-industrial wastes of tea [Camellia sinensisresi due (Tres)] and pyrethrum [Chrysanthemumcineraria foliumVis.] pymarc (Pm) and vegetable waxy resins (VWR). They were incorporated in sterilized soil at their respective rates into 1 kg plastic pots and S. nigrum seedlings planted, across the treatments, two weeks later. Ten egg-masses were inoculated into three pots for each amendment with uninoculated and unamended pots serving as controls. Field experiment was also conducted on plots measuring 1.2x3.2 m in Kisii County, with unamended plots serving as control. The experiments were arranged in randomized complete block design with four replications. All experiments were terminated 60 days after inoculation and data on plant growth and disease parameters collected. The results revealed suppression of RKN population and reproduction by the various amendments compared to their controls in both field and greenhouse. Improved plant growth was also recorded in all the amendments in both tests except for Tres. However, higher levels of Tres and VWR application caused stunted growth despite significant reductions in GI,Rf and J2 populations. These organic amendments can be used as alternatives in eco-friendly management of Meloidogyne species and other plant parasitic nematodes.Item Optimizing pumpkin production and value addition in Kenya: baseline survey findings(2012) Muchugi, Alice Njeri; Ndegwa, R.; Nguthi, F. N.; Karembu, M. K.; Muli, B.; Mugendi, Jane Beatrice; Karanja, J.; Gichina, W.Traditionally considered a “poor man’s food”, the pumpkin is increasingly being recognized as an important food crop in Kenya mainly due to increased knowledge of its nutritional value and ease of crop cultivation in several agro-ecological zones. However, pumpkin production is faced with several challenges that have limited the exploitation of the crop particularly pests and diseases that currently do not have effective control methods. A participatory research project? was to find out solutions to these constraints with a goal of optimizing pumpkin production for food security and income generation.. The initial activity involved a baseline survey in four counties in eastern and central Kenya where farmers and traders were interviewed in order to capture the challenges and issues of concern in pumpkin growing and marketing in the region. On average, pumpkin were ranked fourth as an important food crop in the area and was mainly grown as an opportunistic crop mixed with other major food crops. Several pumpkin varieties recognized by their colour, shape, ridges, stripes and spots were grown in the region. Taste and cooked texture were the major desired characteristics for a good pumpkin. The main limitations to pumpkin growing were cited as limited availability of high quality seed and lack of markets. Farmers are willing to increase their pumpkin production for income generation (51%), food security (31%), market demand and availability (7%) among others. These findings will guide in pumpkin germplasm improvements through marker assisted breeding .Item Low cost tissue culture strategies for selected cassava and sweet potato varieties in Kenya(2012) Ombori, O.; Ogero, K. O.; Gitonga, N. M.; Mwangi, M.Tissue culture (TC) has gained prominence in propagation of vegetative crops. The technology is important as it enables production of disease-free planting materials on a timely basis. However, its adoption among small scale farmers is limited by the high cost of production. It is therefore important to develop strategies that will make TC products affordable. This project sought to develop low cost TC protocols for sweet potato and cassava varieties. The feasibility of using locally available fertilizers as an alternative source to Murashige and Skoog (MS) nutrients was evaluated. Two protocols were developed for each crop. Two varieties of each crop (Muchericheri and KME 1 for cassava; KEMB 36 and Tainung for sweet potato) were subjected to three treatments with different media composition and replicated nine times. In the first medium (LCM 1), Easygro ®vegetative fertilizer (27:10:16 (N: P: K) + microelements) was used as an alternative source for MS basal salts. In the second media (LCM 2), the conventional sources of four MS macronutrients were substituted individually with locally available fertilizers while Stanes Iodized Microfood® was used as the low cost source of micronutrients. Table sugar was used as an alternative source of carbon while conventional MS medium (CM) was used as the control. The use of LCM 1 for cassava micropropagation led to a reduction of 96.3% in the cost of the nutrient sources while LCM 2 led to savings of up to 95.5%. For sweet potato, a cost reduction of 96.9% was realized with LCM 1 while LCM 2 led to cost reduction of 94.4%. The two cassava varieties had regeneration indices of 3-7 nodes per plantlet on all the media. Sweet potato varieties had regeneration indices of 2.9-7.8 nodes per plantlet across the media. This study has shown that it is possible to reduce the cost of cassava and sweet potato tissue culture by adopting alternative nutrient sources.Item Levels of fumonisin b1 and aflatoxin b1 in sorghum and finger millet in western Kenya(2012) Mafurah, J. J.; Monda, E. O.; Amata, L. R.Sorghum and finger millet grains were collected from ten randomly selected farms in five locations in Nyamira, Kakamega, Busia and Teso districts. . Fumonisin B1 and Aflatoxin analyses were done using ELISA methods. The levels of fumonisin B1 detected in sorghum grains (48.81μg/g) were higher than those in finger millet grains (1.13μg/g). Sorghum from Nyamira district had the highest fumonisin B1 levels at 76.63μg/g while low levels were detected in Busia district at17.59μg/g. Sorghum varieties, Ochuti at 129.92μg/g and Wagiita 128.68 at μg/g, had the highest fumonisin B1 levels while no fumonisin B1 was detected in varieties KARI Mtama-1 and Esila. Variety Ikhumba had low levels at detection limits (1.75μg/g). Some finger millet varieties had the lowest levels of fumonisin B1 which were at the detection limit levels of 1.75μg/g each while some had no fumonisin B1 detected. The aflatoxin B1in sorghum from Busia and Teso districts had levels below the detection limit of 2ppb while no aflatoxin B1 was done for finger millet grains as no Aspergillus species had been isolated from the grains. From theresults, finger millet grains are safe for consumption but sorghum might cause mycotoxicoses. Some of the fumonisin levels found in this study coincide with levels associated with risks to humans and animals reported in other countries. There is need for continued surveillance of fumonisin B1 and aflatoxin B1 levels in Western Kenya in sorghum and finer millet grains as it may vary from year to year.Item Incidence of fusarium species in sorghum and finger millet from western Kenya(2012) Mafurah, J. J.; Monda, E. O.; Amata, L. R.Sorghu (Sorghum bicolor (L.) Moench), finger millet (Eleusine coracana (L.) Gaertn) and maize (Zea mays L.) comprise the major components of human diet in Africa. Other crops such as wheat, groundnuts, pulses(cowpeas and beans) and bananas are also important food crops but to a lesser extent. The objective of this study was to identifying Fusarium species associated with sorghum and finger millet grains in Western Kenya. There were 19 morphologically distinct Fusarium species isolated from sorghum and finger millet grains. These included; Fusarium compactum, F. equiseti, F.thapsinum, F. verticillioides, F. longipes, F. andiyazi, F. nygamai, F. pseudonygamai, F. brevicatenulatum, F. chlamydosporum, F. heterosporum, F. napiforme, F. graminearum, F. pseudograminearum, F. oxysporum, F.solani, F. subglutinans, F. semitectum and F. proliferatum. Fusarium compactum (14.40%) and F. equiseti (9.60%) were the mostisolatedspecies in all the districts in both grains while F. thapsinum and F. verticillioides were isolated in sorghum varieties from all the districts. The overall incidence of Fusarium species was 29.66% and 4.87% in sorghum and finger milletrespectively. Nyamira district had the highest incidences (62.23%) and Kakamega had the lowest (11.12%). Wagiita variety of sorghum had the highest incidences (28.92%) while Esila had no infection. All finger millet varieties had a low incidence of Fusarium of less than 8%. The Fusarium species isolated from sorghum in this study coincide with those isolated from other countries but finger millet had fewer Fusarium species than in other countries and this could be due to the traditional varieties sampled that have chemicals and a hard seed coat which prevents fungal penetration. The presence of fumonisin producing species like F. verticillioides and F. thapsinum could pose cancer related problems to the people consuming these grains.