Browsing by Author "Sharaf, Hazem"

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    Compost applications increase bacterial community diversity in the apple rhizosphere
    Sharaf, Hazem; Thompson, Ashley A.; Williams, Mark A.; Peck, Gregory M. (2021-03-24)
    Sustainable practices are key to the improvement of soil fertility and quality in apple (Malus x domestica Borkh.) orchards. Rootstock genotype and fertilizer inputs can alter soil biology, as well as aboveground traits including nutrient acquisition. In this study, a factorial design was used to assess the interaction between two apple rootstocks, 'Geneva 41' ('G.41') and 'Malling 9' ('M.9') with four fertilizer treatments [chicken-litter compost, yardwaste compost, fertigation using Ca(NO3)(2), and an unamended control]. The bacterial community in the rhizosphere was assessed for its impact on both plant and soil properties for each rootstock x fertilizer treatment combination. The bacterial community was dominated by Acidobacteria, Proteobacteria, and Planctomycetes, but Verrucomicrobia and Chloroflexi were the most responsive to the fertilizer treatments. The chicken litter and yardwaste treatments had a greater effect on bacterial community structure than the control. Yardwaste, in particular, was associated with increased relative abundance of Chloroflexi, which was correlated with soil nutrient concentrations. Malling 9 had a greater bacterial diversity than G.41, but the rootstock treatment had no independent effect on the rhizosphere community structure. There was, however, a strong interaction between the rootstock and fertilizer treatments. Carbon cycling was the most prominent functional change associated with the soil bacterial community. These results suggest that compost amendments have a more positive effect on soil bacterial activity and nutrient availability than Ca(NO3)(2). Our work shows that waste-stream amendments can lead to multiple positive responses, such as increasing aboveground tree biomass, thus potentially improving orchard productivity.
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    Ecology of Root Nodule Bacterial Diversity: Implications for Soybean Growth
    Sharaf, Hazem (Virginia Tech, 2021-11-30)
    Diazotrophs supply legumes such as soybean (Glycine max L. Merr) with nitrogen (N) needed for protein synthesis through biological nitrogen fixation (BNF). Through BNF, these bacteria such as Bradyrhizobium that reside in soybean root nodules, convert atmospheric nitrogen (N2) into ammonia (NH3/ NH4), a form that is biologically available for use by the plants, in return for photosynthate carbon from the plant. Abiotic stresses such as drought disrupt BNF and subsequently affects soybean yield. In addition, increasing demand for soybean is leading to supplementing its growth with synthetic N fertilizer. However, fertilizer application is known for its detrimental effects on the environment causing waterways eutrophication contributing to global warming. On the other hand, diazotrophs can supply soybean with up to 90% of N need. As such, improving the understanding and exploiting the relationship between soybean and diazotrophs is key to promoting the sustainable growing of soybean. This dissertation here investigates three main questions. First, how the soybean-diazotrophs respond to changes in water such as rainfall and irrigation. Second, how changes in these bacterial diazotrophs are related to levels of BNF, and N-related soybean molecular markers. Finally, as my colleagues and I found non-diazotrophs in the nodules of some soybean plants, I was curious about the role they are playing inside the nodules in concert with the diazotrophs. The main hypotheses tested in this dissertation are that root nodule bacterial community (bacteriome) would (1) vary by plant type, (2) respond to changes in water, and (3) be related to BNF. To answer the research questions, I devised the dissertation as follows. In Chapter 2, my colleagues and I used nine commercial cultivars of soybean that vary in drought tolerance and agronomic traits. We show that soybean sometimes, but not always, harbor a consortium of non-nitrogen fixing bacteria belonging to Pseudomonadaceae and Enterobacteriaceae families. However, as expected, nodules diazotrophs rather than non-diazotrophs responded most to changes in soil water status. In chapter 3, I used a collection of 24 genotypes of soybean that vary in their ability to fix nitrogen. The results revealed that the bacteriome diazotroph alpha diversity metrics, phylogenetic richness and evenness, was correlated with changes in BNF. Moreover, few N-related molecular markers were associated with some of the bacteria. However, we have also observed a strong effect of the environment on the diazotroph driven process of BNF (i.e. 39%-75%). For chapter 4, we sequenced three of the Pseudomonas spp. strains that were subsequently recovered again from a diversity of soybean nodules in field trials. I found that one of the strains has the ability to adapt to the nodule's unique hypoxic conditions, supporting Bradyrhizobium nodulation and possibly nodule iron. The results include the draft assembly of the proposed Pseudomonas nodulensis sp. nov. as a novel species of nodule adapted bacteria belonging to the P. fluorescens complex. The results of this dissertation contribute to the basic knowledge needed to advance sustainable breeding and management of soybean. Nodule diazotrophs are sensitive to water status e.g. drought, and other experiments have shown that the nodule bacteriome is the driver of BNF. Thus, improving the understanding and exploiting the nodule bacteriome will support developing more resilient cultivars of soybean that are efficient in BNF, and tolerant of stress. Identifying and testing diazotrophs and atypical nodule bacteria will provide a platform for developing new inoculants and biofertilizers.
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    Genomic characterization of NDM-1 and 5, and OXA-1 81 carbapenemases in uropathogenic Escherichia coli isolates from Riyadh, Saudi Arabia
    Abd El Ghany, Moataz; Sharaf, Hazem; Al-agamy, Mohamed H.; Shibi, Atef; Hill-Cawthorne, Grant A.; Hong, Pei-Ying (PLOS, 2018-08-15)
    Urinary tract infections (UTIs) associated with Escherichia coli are a growing threat with an increase in the prevalence of multidrug resistant (MDR) strains, particularly beta-lactamase producers, occurring globally. We investigated the presence of carbapenem-resistant uropathogenic E. coli clones in community-acquired UTIs in Riyadh, Kingdom of Saudi Arabia (KSA) to identify the virulence and resistance structures of the resistant clones and relate the isolates to those circulating globally. A combination of comparative genomics and phenotypic approaches were used to characterize ten MDR-uropathogenic Escherichia coli isolates recovered from UTI patients in Riyadh between November 2014 and January 2015. We report the presence of NDM-1 and 5, and OXA-181 in carbapenem-resistant UPEC strains from Riyadh, KSA. Single nucleotide polymorphism analyses demonstrated that these ten isolates fell into four phylogenetically distinct clades within the UPEC phylogeny. Comparative genomic analyses indicate that these diverse clones could be distinguished according to their multilocus sequencing type (MLST), serology, and virulence and antimicrobial gene architectures. These clones include the b/aNDm-i carrying isolates of the globally predominant MDR ST131 and ST69 types, previously identified as one of the most common UPEC strains in KSA. This is in addition to clones of ST23Cplx (ST410) and ST448Cplx (ST448) that have likely evolved from common intestinal strains, carrying copies of beta-lactamase genes including bla(NDM-5), bla(CTX-m-15), bla(TEM-1), bla(CMY-42), bla(OXA-1) and bla(OXA-181). These data have identified an emerging public health concern and highlight the need to use comprehensive approaches to detect the structure of MDR E. coli populations associated with community-acquired UTIs in KSA.
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    Unprecedented bacterial community richness in soybean nodules vary with cultivar and water status
    Sharaf, Hazem; Rodrigues, Richard R.; Moon, Jinyoung; Zhang, Bo; Mills, Kerri; Williams, Mark A. (2019-04-16)
    Background Soybean (Glycine max) and other legumes are key crops grown around the world, providing protein and nutrients to a growing population, in a way that is more sustainable than most other cropping systems. Diazotrophs inhabiting root nodules provide soybean with nitrogen required for growth. Despite the knowledge of culturable Bradyrhizobium spp. and how they can differ across cultivars, less is known about the overall bacterial community (bacteriome) diversity within nodules, in situ. This variability could have large functional ramifications for the long-standing scientific dogma related to the plant-bacteriome interaction. Water availability also impacts soybean, in part, as a result of water-deficit sensitive nodule diazotrophs. There is a dearth of information on the effects of cultivar and water status on in situ rhizobia and non-rhizobia populations of nodule microbiomes. Therefore, soybean nodule microbiomes, using 16S rRNA and nifH genes, were sampled from nine cultivars treated with different field water regimes. It was hypothesized that the nodule bacteriome, composition, and function among rhizobia and non-rhizobia would differ in response to cultivar and soil water status. Results 16S rRNA and nifH showed dominance by Bradyrhizobiaceae, but a large diversity was observed across phylogenetic groups with < 1% and up to 45% relative abundance in cultivars. Other groups primarily included Pseudomonadaceae and Enterobacteriaceae. Thus, nodule bacteriomes were not only dominated by rhizobia, but also described by high variability and partly dependent on cultivar and water status. Consequently, the function of the nodule bacteriomes differed, especially due to cultivar. Amino acid profiling within nodules, for example, described functional changes due to both cultivar and water status. Conclusions Overall, these results reveal previously undescribed richness and functional changes in Bradyrhizobiaceae and non-rhizobia within the soybean nodule microbiome. Though the exact role of these atypical bacteria and relative variations in Bradyrhizobium spp. is not clear, there is potential for exploitation of these novel findings of microbiome diversity and function. This diversity needs consideration as part of bacterial-inclusive breeding of soybean to improve traits, such as yield and seed quality, and environmental resilience.