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Browsing by Author "Moon, Jinyoung"

Now showing 1 - 4 of 4
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    Microbial communities and diazotrophic activity differ in the root-zone of Alamo and Dacotah switchgrass Feedstocks
    Rodrigues, Richard R.; Moon, Jinyoung; Zhao, Bingyu; Williams, Mark A. (Wiley, 2016-08-22)
    Nitrogen (N) bioavailability is a primary limiting nutrient for crop and feedstock productivity. Associative nitrogen fixation (ANF) by diazotrophic bacteria in root-zone soil microbial communities have been shown to provide significant amounts of N to some tropical grasses, but this potential in switchgrass, a warm-season, temperate, US native, perennial tallgrass has not been widely studied. ‘Alamo’ and ‘Dacotah’ are cultivars of switchgrass, adapted to the southern and northern regions of the United States, respectively, and offer an opportunity to better describe this plant–bacterial association. The nitrogenase enzyme activity, microbial communities, and amino acid profiles in the root-zones of the two ecotypes were studied at three different plant growth stages. Differences in the nitrogenase enzyme activity and free soluble amino acid profiles indicated the potential for greater nitrogen fixation in the high productivity Alamo compared with the lower productivity Dacotah. Changes in the amino acid profiles and microbial community structure (rRNA genes) of the root-zone suggest different plant–bacterial interactions can help to explain differences in nitrogenase activity. PICRUSt analysis revealed functional differences, especially nitrogen metabolism, that supported ecotype differences in root-zone nitrogenase enzyme activity. It is thought that the greater productivity of Alamo increased the belowground flow of carbon into roots and root-zone habitats, which in turn support the high energy demands needed to support nitrogen fixation. Further research is thus needed to understand plant ecotype and cultivar trait differences that can be used to breed or genetically modify crop plants to support root-zone associations with diazotrophs.
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    Plant - Microbial and mineral contributions to amino acid and protein organic matter accumulation during 4000 years of pedogenesis
    Moon, Jinyoung; Ma, Li; Xia, Kang; Williams, Mark A. (2016-09)
    The dynamics and persistence of proteinaceous compounds during pedogenesis are major mechanisms of soil formation and determinants of organic matter (OM) turnover. We investigated the accumulation patterns of proteinogenic amino acids associated with minerals dominated by permanently negative charges (primary silica minerals) and related these to vegetative and belowground microbial succession during soil ecosystem development. Positively-charged amino acids (arginine, lysine, histidine), extracted from whole soil pool using 6 M HCl, showed clear patterns of accumulation, increasing similar to 65% during 4010 years of development, while negatively charged amino acids (glutamic acid, aspartic acid) decreased similar to 13%. In the mineral associated sub-pool, positively charged amino acids were approximately similar to 431% more enriched, while negatively charged amino acids were similar to 38% depleted as compared to the whole soil pool. The multivariate ordination of soil bacterial community structure based on a 16s ribosomal RNA gene analysis and that of the aboveground plant community structure predicted 71% (p < 0.0001) and 66% (p < 0.0001) of the amino acid dynamics, respectively, during soil ecosystem development. Ala-rich Actinobacteria abundance declined with the year of development, concomitant with the decrease of Ala content in soil (r(2) = 0.82, p = 0.0019). His-rich Acidobacteria and His in soil both increased with the year of development (r(2) = 0.92, p = 0.0022). In support of the main hypothesis, the relative distribution of proteinogenic amino acids changed during pedogenesis with evidence indicating that biological communities and minerals play roles as source and sink of OM in soil, respectively.
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    Selective accrual and dynamics of proteinaceous compounds during pedogenesis: testing source and sink selection hypotheses
    Moon, Jinyoung (Virginia Tech, 2015-10-12)
    The emerging evidence of preferential accumulation and long residence time of proteinaceous compounds in soil are counter to the traditional view that their structure is readily broken down through microbial activity. The shift in thinking of their residence time is, however, heavily influenced by physical and chemical protections in soil, representing an important change for understanding global biogeochemical carbon and nitrogen cycling. We investigated the accumulation patterns of proteinogenic amino acids for a long term (thousands of years) related to their sources and sinks. We found clear patterns of change in the amino acids in a 4000 year-chronosequence adjacent to Lake Michigan, USA (Michigan chronosequence) and they were tightly related to the shifts in their biological sources, namely aboveground vegetative community (r2=0.66, p<0.0001) and belowground microbial community (r2=0.71, p<0.0001). Results also showed great variations of approximately 49% between seasons (summer and winter). Moreover, seasonal dynamic patterns (22% variations) of the amino acids in soil mineral associated fraction were rather counter to the conceptual view that it represents a slow soil organic pool with long residence times. The amino acids enriched in the mineral associated fraction, (e.g., positively charged, aromatic, and sulfur containing amino acids), tended to preferentially accumulate in whole soil pool during the 4000 years of ecosystem development. Their interaction with soil minerals, therefore, may play a critical role in the long-term sink and selective accumulation of proteinaceous compounds with some degree of the displacement. This was further confirmed by another chronosequence system near Haast River, New Zealand, which is geologically separated and climatically- and ecologically- different from the Michigan chronosequence. Common trends between two chronosequences suggested that either polar interactions or redox reactions may be relatively more important in the mineral interaction of amino acids than non-polar interactions. The consistency of results at two disparate locations in the southern and northern hemispheres is strong evidence that the processes of pedogenesis and ecosystem development are parsimonious and predictable. Our research demonstrated fundamental understanding of behavior of proteinaceous compounds at the molecular species level, and further provided their partitioning mechanisms associated with soil components.
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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.