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Open Access Publications from the University of California

Scholarly Works (9 results)

  • Article
Journal of Citrus Pathology, Volume 1, Issue 1 (2014)

Citrus huanglongbing (HLB) associated with the pathogen Candidatus Liberibacter asiaticus (Las) is a devastating disease for the US citrus industry (1, 2). To gain knowledge on the mechanism(s) by which Las evades host defense responses, we first expressed salicylate hydroxylase (sahA) of Las in Escherichia coli. Our data indicate that Las encodes a functional salicylate hydroxylase, which converts salicylic acid (SA) into catechol, a product that does not induce resistance. The sahA gene was highly induced in planta compared to psyllid vector suggesting its important role in disease progression. To determine expression level of defense related genes after Las infection, Xanthomonas axonopodis pv. citri strain AW (Xac AW) was used to induce PR gene expression. The PR-1 gene expression in Xac Aw-challenged plants, which were previously infected with Las, was lower than Xac Aw-challenged healthy plants. Using SA biosensor strain (Acinetobacter sp. ADPWH_lux), 4 fold reduction in SA accumulation was observed in the Las-infected as compared to healthy plants. To understanda possible synergistic effect of the presence of Las on the citrus canker [caused by X. citri subsp. citri (Xcc)] we inoculated Xcc in Las-infected and healthy leaves of grapefruit. The population levels of Xcc were significantly higher during all the observation time points (up to 14 days) in Las-infected as compared to healthy citrus indicating that modulation of SA production and subsequent regulation of defense related genes such as PR-1 gene could be one of the mechanisms deployed by Las to evade plant defense responses. The Las-infected plants compromised with defense responses could further succumb to the infection by other pathogens. We also conducted experiments to restore the SA level in Las infected plants using SA hydroxylase inhibitors and test their effect in controlling HLB.

    Cover page: Modulation of plant defense responses by Salicylate hydroxylase of Candidatus Liberibacter asiaticusCreative Commons 'BY' version 4.0 license
    • Article
    Journal of Citrus Pathology, Volume 1, Issue 1 (2014)

    Huanglongbing is the most devastating disease of citrus caused by Candidatus Liberibacter asiaticus (Las) (1, 2). In the present study, we report the discovery of novel small molecule inhibitors against SecA ATPase of Las by using structure based design methods. We built the homology model of SecA protein structure of Las based on the SecA of Escherichia coli. The model was used for in-silico screening of commercially available compounds from ZINC database. Using the glide flexible molecular docking method, twenty structures were chosen for in vitro studies. Five compounds were found to inhibit the ATPase activity of SecA of Las at nano molar concentrations and showed antimicrobial activities against Agrobacterium tumefaciens with MBC ranging from 128 to 256 g/mL.  These compounds appear to be suitable as lead compounds for further development of antimicrobial compounds against Las. To test the application potential of those compounds on plants, the phytotoxicity studies were performed on the five compounds against citrus.  In addition, we are optimizing these five antimicrobial compounds to identify compounds higher antimicrobial activity.

      Cover page: Identification of small molecule inhibitors against SecA of Candidatus Liberibacter asiaticus by structure based designCreative Commons 'BY' version 4.0 license
      • Article
      • Peer Reviewed
      LBL Publications (2016)
      A lack of empirical evidence for the microbial regulation of ecosystem processes, including carbon (C) degradation, hinders our ability to develop a framework to directly incorporate the genetic composition of microbial communities in the enzyme-driven Earth system models. Herein we evaluated the linkage between microbial functional genes and extracellular enzyme activity in soil samples collected across three geographical regions of Australia. We found a strong relationship between different functional genes and their corresponding enzyme activities. This relationship was maintained after considering microbial community structure, total C and soil pH using structural equation modelling. Results showed that the variations in the activity of enzymes involved in C degradation were predicted by the functional gene abundance of the soil microbial community (R2>0.90 in all cases). Our findings provide a strong framework for improved predictions on soil C dynamics that could be achieved by adopting a gene-centric approach incorporating the abundance of functional genes into process models.
        Cover page: Microbial regulation of the soil carbon cycle: evidence from gene–enzyme relationships
        • Article
        • Peer Reviewed
        Climate & Ecosystems (2015)
        Understanding the influence of long-term crop management practices on the soil microbial community is critical for linking soil microbial flora with ecosystem processes such as those involved in soil carbon cycling. In this study, pyrosequencing and a functional gene array (GeoChip 4.0) were used to investigate the shifts in microbial composition and functional gene structure in a medium clay soil subjected to various cropping regimes. Pyrosequencing analysis showed that the community structure (β-diversity) for bacteria and fungi was significantly impacted among different cropping treatments. Functional gene array-based analysis revealed that crop rotation practices changed the structure and abundance of genes involved in C degradation. Significant correlations were observed between the activities of four enzymes involved in soil C degradation and the abundance of genes responsible for the production of respective enzymes, suggesting that a shift in the microbial community may influence soil C dynamics. We further integrated physical, chemical, and molecular techniques (qPCR) to assess relationships between soil C, microbial derived enzymes and soil bacterial community structure at the soil micro-environmental scale (e.g. within different aggregate-size fractions). We observed a dominance of different bacterial phyla within soil microenvironments which was correlated with the amount of C in the soil aggregates suggesting that each aggregate represents a different ecological niche for microbial colonization. Significant effects of aggregate size were found for the activity of enzymes involved in C degradation suggesting that aggregate size distribution influenced C availability. The influence of cropping regimes on microbial and soil C responses declined with decreasing size of soil aggregates and especially with silt and clay micro-aggregates. Our results suggest that long term crop management practices influence the structural and functional potential of soil microbial communities and the impact of crop rotations on soil C turnover varies between different sized soil aggregates. These findings provide a strong framework to determine the impact of management practices on soil C and soil health.
          Cover page: Soil aggregate size mediates the impacts of cropping regimes on soil carbon and microbial communities
          • Article
          • Peer Reviewed
          UC Merced Previously Published Works (2020)
          Unlike plants and vertebrates, the ecological preferences, and potential vulnerabilities of soil invertebrates to environmental change, remain poorly understood in terrestrial ecosystems globally. We conducted a cross-biome survey including 83 locations across six continents to advance our understanding of the ecological preferences and vulnerabilities of the diversity of dominant and functionally important soil invertebrate taxa, including nematodes, arachnids and rotifers. The diversity of invertebrates was analyzed through amplicon sequencing. Vegetation and climate drove the diversity and dominant taxa of soil invertebrates. Our results suggest that declines in forest cover and plant diversity, and reductions in plant production associated with increases in aridity, can result in reductions of the diversity of soil invertebrates in a drier and more managed world. We further developed global atlases of the diversity of these important soil invertebrates, which were cross-validated using an independent database. Our study advances the current knowledge of the ecological preferences and vulnerabilities of the diversity and presence of functionally important soil invertebrates in soils from across the globe. This information is fundamental for improving and prioritizing conservation efforts of soil genetic resources and management policies.
            Cover page: Climatic vulnerabilities and ecological preferences of soil invertebrates across biomes
            • Article
            • Peer Reviewed
            UC Merced Previously Published Works (2020)
            The importance of soil age as an ecosystem driver across biomes remains largely unresolved. By combining a cross-biome global field survey, including data for 32 soil, plant, and microbial properties in 16 soil chronosequences, with a global meta-analysis, we show that soil age is a significant ecosystem driver, but only accounts for a relatively small proportion of the cross-biome variation in multiple ecosystem properties. Parent material, climate, vegetation and topography predict, collectively, 24 times more variation in ecosystem properties than soil age alone. Soil age is an important local-scale ecosystem driver; however, environmental context, rather than soil age, determines the rates and trajectories of ecosystem development in structure and function across biomes. Our work provides insights into the natural history of terrestrial ecosystems. We propose that, regardless of soil age, changes in the environmental context, such as those associated with global climatic and land-use changes, will have important long-term impacts on the structure and function of terrestrial ecosystems across biomes.
              Cover page: The influence of soil age on ecosystem structure and function across biomes
              • Article
              • Peer Reviewed
              UC Merced Previously Published Works (2019)
              Identifying the global drivers of soil priming is essential to understanding C cycling in terrestrial ecosystems. We conducted a survey of soils across 86 globally-distributed locations, spanning a wide range of climates, biotic communities, and soil conditions, and evaluated the apparent soil priming effect using 13C-glucose labeling. Here we show that the magnitude of the positive apparent priming effect (increase in CO2 release through accelerated microbial biomass turnover) was negatively associated with SOC content and microbial respiration rates. Our statistical modeling suggests that apparent priming effects tend to be negative in more mesic sites associated with higher SOC contents. In contrast, a single-input of labile C causes positive apparent priming effects in more arid locations with low SOC contents. Our results provide solid evidence that SOC content plays a critical role in regulating apparent priming effects, with important implications for the improvement of C cycling models under global change scenarios.
                Cover page: Global ecological predictors of the soil priming effect.
                • Article
                • Peer Reviewed
                UC Merced Previously Published Works (2020)
                The role of soil biodiversity in regulating multiple ecosystem functions is poorly understood, limiting our ability to predict how soil biodiversity loss might affect human wellbeing and ecosystem sustainability. Here, combining a global observational study with an experimental microcosm study, we provide evidence that soil biodiversity (bacteria, fungi, protists and invertebrates) is significantly and positively associated with multiple ecosystem functions. These functions include nutrient cycling, decomposition, plant production, and reduced potential for pathogenicity and belowground biological warfare. Our findings also reveal the context dependency of such relationships and the importance of the connectedness, biodiversity and nature of the globally distributed dominant phylotypes within the soil network in maintaining multiple functions. Moreover, our results suggest that the positive association between plant diversity and multifunctionality across biomes is indirectly driven by soil biodiversity. Together, our results provide insights into the importance of soil biodiversity for maintaining soil functionality locally and across biomes, as well as providing strong support for the inclusion of soil biodiversity in conservation and management programmes.
                  Cover page: Multiple elements of soil biodiversity drive ecosystem functions across biomes
                  • Article
                  • Peer Reviewed
                  UC Merced Previously Published Works (2019)
                  Identifying the global drivers of soil priming is essential to understanding C cycling in terrestrial ecosystems. We conducted a survey of soils across 86 globally-distributed locations, spanning a wide range of climates, biotic communities, and soil conditions, and evaluated the apparent soil priming effect using 13C-glucose labeling. Here we show that the magnitude of the positive apparent priming effect (increase in CO2 release through accelerated microbial biomass turnover) was negatively associated with SOC content and microbial respiration rates. Our statistical modeling suggests that apparent priming effects tend to be negative in more mesic sites associated with higher SOC contents. In contrast, a single-input of labile C causes positive apparent priming effects in more arid locations with low SOC contents. Our results provide solid evidence that SOC content plays a critical role in regulating apparent priming effects, with important implications for the improvement of C cycling models under global change scenarios.
                    Cover page: Global ecological predictors of the soil priming effect
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