Community Structure of Nitrifying and Denitrifying Bacteria from Effluents Discharged into Lake Victoria, Kenya.

An active microbial community of nitrifying and denitrifying bacteria is needed for efficient utilization of nitrogenous compounds from wastewater. In this study, we explored the bacterial community diversity and structure within rivers, treated and untreated wastewater treatment plants (WWTPs) discharging into Lake Victoria. Water samples were collected from rivers and WWTPs that drain into Lake Victoria. Physicochemical analysis was done to determine the level of nutrients or pollutant loading in the samples. Total community DNA was extracted, followed by Illumina high throughput sequencing to determine the total microbial community and abundance. Enrichment and isolation were then done to recover potential nitrifiers and denitrifiers. Physicochemical analysis pointed to high levels total nitrogen and ammonia in both treated and untreated WWTPs as compared to the samples from the lake and rivers. A total of 1,763 operational taxonomic units (OTUs) spread across 26 bacterial phyla were observed with the most dominant phylum being Proteobacteria. We observed a decreasing trend in diversity from the lake, rivers to WWTPs. The genus Planktothrix constituted 19% of the sequence reads in sample J2 collected from the lagoon. All the isolates recovered in this study were affiliated to three genera: Pseudomonas, Klebsiella and Enterobacter in the phylum Proteobacteria. A combination of metagenomic analysis and a culture-dependent approach helped us understand the relative abundance as well as potential nitrifiers and denitrifiers present in different samples. The recovered isolates could be used for in situ removal of nitrogenous compounds from contaminated wastewater.

The Phosphate Inhibition Paradigm: Host and Fungal Genotypes Determine Arbuscular Mycorrhizal Fungal Colonization and Responsiveness to Inoculation in Cassava With Increasing Phosphorus Supply.

A vast majority of terrestrial plants are dependent on arbuscular mycorrhizal fungi (AMF) for their nutrient acquisition. AMF act as an extension of the root system helping phosphate uptake. In agriculture, harnessing the symbiosis can potentially increase plant growth. Application of the AMF Rhizophagus irregularis has been demonstrated to increase the yields of various crops. However, there is a paradigm that AMF colonization of roots, as well as the plant benefits afforded by inoculation with AMF, decreases with increasing phosphorus (P) supply in the soil. The paradigm suggests that when fertilized with sufficient P, inoculation of crops would not be beneficial. However, the majority of experiments demonstrating the paradigm were conducted in sterile conditions without a background AMF or soil microbial community. Interestingly, intraspecific variation in R. irregularis can greatly alter the yield of cassava even at a full application of the recommended P dose. Cassava is a globally important crop, feeding 800 million people worldwide, and a crop that is highly dependent on AMF for P uptake. In this study, field trials were conducted at three locations in Kenya and Tanzania using different AMF and cassava varieties under different P fertilization levels to test if the paradigm occurs in tropical field conditions. We found that AMF colonization and inoculation responsiveness of cassava does not always decrease with an increased P supply as expected by the paradigm. The obtained results demonstrate that maximizing the inoculation responsiveness of cassava is not necessarily only in conditions of low P availability, but that this is dependent on cassava and fungal genotypes. Thus, the modeling of plant symbiosis with AMF under different P levels in nature should be considered with caution.

Reconciling yield gains in agronomic trials with returns under African smallholder conditions.

Increased adoption of improved agricultural technologies is considered an essential step to address global poverty and hunger, and agronomic trials suggest intensification in developing countries could result in large yield gains. Yet the promise of new technologies does not always carry over from trials to real-life conditions, and diffusion of many technologies remains limited. We show how parcel and farmer selection, together with behavioural responses in agronomic trials, can explain why yield gain estimates from trials may differ from the yield gains of smallholders using the same inputs under real-life conditions. We provide quantitative evidence by exploiting variation in farmer selection and detailed data collection from research trials in Western Kenya on which large yield increments were observed from improved input packages for maize and soybean. After adjusting for selection, behavioural responses, and other corrections, estimates of yield gains fall to being not significantly different from zero for the input package tested on one of the crops (soybean), but remain high for the other (maize). These results suggest that testing new agricultural technologies in real-world conditions and without researcher interference early in the agricultural research and development process might help with identifying which innovations are more likely to be taken up at scale.

Exploiting Biological Nitrogen Fixation: A Route Towards a Sustainable Agriculture.

For all living organisms, nitrogen is an essential element, while being the most limiting in ecosystems and for crop production. Despite the significant contribution of synthetic fertilizers, nitrogen requirements for food production increase from year to year, while the overuse of agrochemicals compromise soil health and agricultural sustainability. One alternative to overcome this problem is biological nitrogen fixation (BNF). Indeed, more than 60% of the fixed N on Earth results from BNF. Therefore, optimizing BNF in agriculture is more and more urgent to help meet the demand of the food production needs for the growing world population. This optimization will require a good knowledge of the diversity of nitrogen-fixing microorganisms, the mechanisms of fixation, and the selection and formulation of efficient N-fixing microorganisms as biofertilizers. Good understanding of BNF process may allow the transfer of this ability to other non-fixing microorganisms or to non-leguminous plants with high added value. This minireview covers a brief history on BNF, cycle and mechanisms of nitrogen fixation, biofertilizers market value, and use of biofertilizers in agriculture. The minireview focuses particularly on some of the most effective microbial products marketed to date, their efficiency, and success-limiting in agriculture. It also highlights opportunities and difficulties of transferring nitrogen fixation capacity in cereals.

Genetically Different Isolates of the Arbuscular Mycorrhizal Fungus Rhizophagus irregularis Induce Differential Responses to Stress in Cassava.

Water scarcity negatively impacts global crop yields and climate change is expected to greatly increase the severity of future droughts. The use of arbuscular mycorrhizal fungi (AMF) can potentially mitigate the effects of water stress in plants. Cassava is a crop that feeds approximately 800 million people daily. Genetically different isolates of the AMF R. irregularis as well as their clonal progeny have both been shown to greatly alter cassava growth in field conditions. Given that cassava experiences seasonal drought in many of the regions in which it is cultivated, we evaluated whether intraspecific variation in R. irregularis differentially alters physiological responses of cassava to water stress. In a first experiment, conducted in field conditions in Western Kenya, cassava was inoculated with two genetically different R. irregularis isolates and their clonal progeny. All cassava plants exhibited physiological signs of stress during the dry period, but the largest differences occurred among plants inoculated with clonal progeny of each of the two parental fungal isolates. Because drought had not been experimentally manipulated in the field, we conducted a second experiment in the greenhouse where cassava was inoculated with two genetically different R. irregularis isolates and subjected to drought, followed by re-watering, to allow recovery. Physiological stress responses of cassava to drought differed significantly between plants inoculated with the two different fungi. However, plants that experienced higher drought stress also recovered at a faster rate following re-watering. We conclude that intraspecific genetic variability in AMF significantly influences cassava physiological responses during water stress. This highlights the potential of using naturally existing variation in AMF to improve cassava tolerance undergoing water stress. However, the fact that clonal progeny of an AMF isolate can differentially affect how cassava copes with natural drought stress in field conditions, highlights the necessity to understand additional factors, beyond genetic variation, which can account for such large differences in cassava responses to drought.

Variability of soybean response to rhizobia inoculant, vermicompost, and a legume-specific fertilizer blend in Siaya County of Kenya.

Rhizobia inoculation can increase soybean yield, but its performance is influenced by among others soybean genotype, rhizobia strains, environment, and crop management. The objective of the study was to assess soybean response to rhizobia inoculation when grown in soils amended with urea or vermicompost to improve nitrogen levels. Two greenhouse experiments and one field trial at two sites were carried out. The first greenhouse experiment included soils from sixty locations, sampled from smallholder farms in Western Kenya. The second greenhouse experiment consisted of one soil selected among soils used in the first experiment where inoculation response was poor. The soil was amended with vermicompost or urea. In the two greenhouse experiments, Legumefix (inoculant) + Sympal (legume fertilizer blend) were used as a standard package. Results from the second greenhouse experiment were then validated in the field. Analysis of variance was done using SAS statistical software and mean separation was done using standard error of the difference for shoot biomass, grain yield nodulation, nodule effectiveness and nutrient uptake. In the first greenhouse trial, soybean response to inoculation was significantly affected by soil fertility based on nodule fresh weight and shoot biomass. Soils with low nitrogen had low to no response to inoculation. After amendment, nodule fresh weight, nodule effectiveness, nodule occupancy, and shoot dry biomass were greater in the treatment amended with vermicompost than those amended with urea (Legumefix + Sympal + vermicompost and Legumefix + Sympal + urea) respectively. Under field conditions, trends were similar to the second experiment for nodulation, nodule occupancy and nitrogen uptake resulting in significantly greater grain yields (475, 709, 856, 880, 966 kg ha-1) after application of vermicompost at 0, 37, 74, 111, and 148 kg N ha-1 respectively. It was concluded that soybean nodulation and biological nitrogen fixation in low fertility soils would not be suppressed by organic amendments like vermicompost up to 148 kg N ha-1.

Cowpea (Vigna unguiculata L. Walp) hosts several widespread bradyrhizobial root nodule symbionts across contrasting agro-ecological production areas in Kenya.

Cowpea (Vigna unguiculata L. Walp.) is an important African food legume suitable for dry regions. It is the main legume in two contrasting agro-ecological regions of Kenya as an important component of crop rotations because of its relative tolerance to unpredictable drought events. This study was carried out in an effort to establish a collection of bacterial root nodule symbionts and determine their relationship to physicochemical soil parameters as well as any geographical distributional patterns. Bradyrhizobium spp. were found to be widespread in this study and several different types could be identified at each site. Unique but rare symbionts were recovered from the nodules of plants sampled in a drier in-land region, where there were also overall more different bradyrhizobia found. Plants raised in soil from uncultivated sites with a natural vegetation cover tended to also associate with more different bradyrizobia. The occurrence and abundance of different bradyrhizobia correlated with differences in soil texture and pH, but did neither with the agro-ecological origin, nor the origin from cultivated (n = 15) or uncultivated (n = 5) sites. The analytical method, protein profiling of isolated strains by Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS), provided higher resolution than 16S rRNA gene sequencing and was applied in this study for the first time to isolates recovered directly from field-collected cowpea root nodules. The method thus seems suitable for screening isolate collections on the presence of different groups, which, provided an appropriate reference database, can also be assigned to known species.

Evaluation of MALDI-TOF mass spectrometry for the competitiveness analysis of selected indigenous cowpea (Vigna unguiculata L. Walp.) Bradyrhizobium strains from Kenya.

Cowpea N2 fixation and yield can be enhanced by selecting competitive and efficient indigenous rhizobia. Strains from contrasting agro-ecologies of Kilifi and Mbeere (Kenya) were screened. Two pot experiments were established consisting of 13 Bradyrhizobium strains; experiment 1 (11 Mbeere + CBA + BK1 from Burkina Faso), experiment 2 (12 Kilifi + CBA). Symbiotic effectiveness was assessed (shoot biomass, SPAD index and N uptake). Nodule occupancy of 13 simultaneously co-inoculated strains in each experiment was analyzed by matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) mass spectrometry (MS) to assess competitiveness. Strains varied in effectiveness and competitiveness. The four most efficient strains were further evaluated in a field trial in Mbeere during the 2014 short rains. Strains from bacteroids of cowpea nodules from pot and field experiments were accurately identified as Bradyrhizobium by MALDI-TOF based on the SARAMIS™ database. In the field, abundant indigenous populations 7.10 × 103 rhizobia g-1 soil, outcompeted introduced strains. As revealed by MALDI-TOF, indigenous strains clustered into six distinct groups (I, II, III, IV, V and VI), group III were most abundant occupying 80% of nodules analyzed. MALDI-TOF was rapid, affordable and reliable to identify Bradyrhizobium strains directly from nodule suspensions in competition pot assays and in the field with abundant indigenous strains thus, its suitability for future competition assays. Evaluating strain competitiveness and then symbiotic efficacy is proposed in bioprospecting for potential cowpea inoculant strains.

Combined Application of Biofertilizers and Inorganic Nutrients Improves Sweet Potato Yields.

Sweet potato [Ipomoea batatas (L) Lam] yields currently stand at 4.5 t ha-1 on smallholder farms in Uganda, despite the attainable yield (45-48 t ha-1) of NASPOT 11 cultivar comparable to the potential yield (45 t ha-1) in sub-Saharan Africa (SSA). On-farm field experiments were conducted for two seasons in the Mt Elgon High Farmlands and Lake Victoria Crescent agro-ecological zones in Uganda to determine the potential of biofertilizers, specifically arbuscular mycorrhizal fungi (AMF), to increase sweet potato yields (NASPOT 11 cultivar). Two kinds of biofertilizers were compared to different rates of phosphorus (P) fertilizer when applied with or without nitrogen (N) and potassium (K). The sweet potato response to treatments was variable across sites (soil types) and seasons, and significant tuber yield increase (p < 0.05) was promoted by biofertilizer and NPK treatments during the short-rain season in the Ferralsol. Tuber yields ranged from 12.8 to 20.1 t ha-1 in the Rhodic Nitisol (sandy-clay) compared to 7.6 to 14.9 t ha-1 in the Ferralsol (sandy-loam) during the same season. Root colonization was greater in the short-rain season compared to the long-rain season. Biofertilizers combined with N and K realized higher biomass and tuber yield than biofertilizers alone during the short-rain season indicating the need for starter nutrients for hyphal growth and root colonization of AMF. In this study, N0.25PK (34.6 t ha-1) and N0.5PK (32.9 t ha-1) resulted in the highest yield during the long and the short-rain season, respectively, but there was still a yield gap of 11.9 and 13.6 t ha-1 for the cultivar. Therefore, a combination of 90 kg N ha-1 and 100 kg K ha-1 with either 15 or 30 kg P ha-1 can increase sweet potato yield from 4.5 to >30 t ha-1. The results also show that to realize significance of AMF in nutrient depleted soils, starter nutrients should be included.

Co-inoculation Effect of Rhizobia and Plant Growth Promoting Rhizobacteria on Common Bean Growth in a Low Phosphorus Soil.

Nitrogen (N) fixation through legume-Rhizobium symbiosis is important for enhancing agricultural productivity and is therefore of great economic interest. Growing evidence indicates that other soil beneficial bacteria can positively affect symbiotic performance of rhizobia. Nodule endophytic plant growth promoting rhizobacteria (PGPR) were isolated from common bean nodules from Nakuru County in Kenya and characterized 16S rDNA partial gene sequencing. The effect of co-inoculation of rhizobium and PGPR, on nodulation and growth of common bean (Phaseolus vulgaris L.) was also investigated using a low phosphorous soil under greenhouse conditions. Gram-positive nodule endophytic PGPR belonging to the genus Bacillus were successfully isolated and characterized. Two PGPR strains (Paenibacillus polymyxa and Bacillus megaterium), two rhizobia strains (IITA-PAU 987 and IITA-PAU 983) and one reference rhizobia strain (CIAT 899) were used in the co-inoculation study. Two common bean varieties were inoculated with Rhizobium strains singly or in a combination with PGPR to evaluate the effect on nodulation and growth parameters. Co-inoculation of IITA-PAU 987 + B. megaterium recorded the highest nodule weight (405.2 mg) compared to IITA-PAU 987 alone (324.8 mg), while CIAT 899 + B. megaterium (401.2 mg) compared to CIAT 899 alone (337.2 mg). CIAT 899 + B. megaterium recorded a significantly higher shoot dry weight (7.23 g) compared to CIAT 899 alone (5.80 g). However, there was no significant difference between CIAT 899 + P. polymyxa and CIAT 899 alone. Combination of IITA-PAU 987 and B. megaterium led to significantly higher shoot dry weight (6.84 g) compared to IITA-PAU 987 alone (5.32 g) but no significant difference was observed when co-inoculated with P. polymyxa. IITA-PAU 983 in combination with P. polymyxa led to significantly higher shoot dry weight (7.15 g) compared to IITA-PAU 983 alone (5.14 g). Plants inoculated with IITA-PAU 987 and B. megaterium received 24.0 % of their nitrogen demand from atmosphere, which showed a 31.1% increase compared to rhizobium alone. Contrast analysis confirmed the difference between the co-inoculation of rhizobia strains and PGPR compared to single rhizobia inoculation on the root dry weight. These results show that co-inoculation of PGPR and Rhizobia has a synergistic effect on bean growth. Use of PGPR may improve effectiveness of Rhizobium biofertilizers for common bean production. Testing of PGPR under field conditions will further elucidate their effectiveness on grain yields of common bean.