Yonatan Sher

Deep-rooting perennial grasses are promising feedstocks for biofuel production, especially in marginal soils lacking organic material, nutrients, and/or that experience significant water stress. Perennial grass roots influence surrounding soil conditions and microbial activities, and produce extracellular polymeric substances (EPS) composed primarily of extracellular polysaccharides (EPSac). These polymers can alleviate microbial moisture and nutrient stress, and enhance soil characteristics through improved water retention and aggregate stability—which may in turn enhance carbon persistence. In this study we used a 13CO2 greenhouse tracer experiment to examine the effect of switchgrass cultivation on EPSac production and origin in a marginal soil with five fertilization/water treatments (control, +N, +NP, +P, low water), and compared these results with measurements of field soils collected after long-term switchgrass cultivation. Soils with added nitrogen and phosphorus (+NP) had the highest root biomass, EPSac and percentage of water-stable soil aggregates. Multiple linear regression analyses revealed that root biomass and soil water potential were important determinants of soil EPSac production, potentially by controlling carbon supply and diurnal changes in moisture stress. Path analysis showed that soil aggregation was positively correlated with bulk soil EPSac content and also regulated by soil water potential. High mannose content indicated the majority of EPSac was of microbial origin and 13CO2 labeling indicated that 0.18% of newly fixed plant carbon was incorporated into EPSac. Analysis of field soils suggests that EPSac is significantly enhanced after long-term switchgrass cultivation. Taken as a whole, our greenhouse and field results demonstrate that switchgrass cultivation can promote microbial production of EPSac, providing a mechanism to enhance aggregation in marginal soils.

Besides water, nitrogen is the limiting factor for biomass production in arid ecosystems. Global climatic changes are exacerbating aridity levels, and the response of nitrogen-transforming microorganisms to these changes is not clear yet. Using semi-arid and arid ecosystems as surrogates for conditions of increased aridity, we investigated the activity, abundance, and diversity of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in arid and semi-arid soils. Ammonia oxidation potentials were higher during the winter in both sites than in the summer, and higher nitrate concentrations were measured in the arid soil than in the semi-arid soil. Denaturing gradient gel electrophoresis (DGGE) patterns of AOB 16S rRNA gene fragments were similar for the arid and semi-arid soils with no seasonal variations. In contrast, the DGGE patterns of the AOA amoA gene fragments differed between the sites and a soil transfer experiment suggested that these differences are possibly associated with soil type. AOB numbers were higher during the winter than in the summer, while AOA numbers were higher during the summer. The results indicate the resistance of AOB and AOA community structure to arid conditions, albeit with seasonal variations in their abundance. Together, the results suggest the resilience of nitrification activity to increased aridity level.

Microbes alter their transcriptomic profiles in response to the environment. The physiological conditions experienced by a microbial community can thus be inferred using meta-transcriptomic sequencing by comparing transcription levels of specifically chosen genes. However, this analysis requires accurate reference genomes to identify the specific genes from which RNA reads originate. In addition, such an analysis should avoid biases in transcript counts related to differences in organism abundance. In this study we describe an approach to address these difficulties. Sample-specific meta-genomic assembled genomes (MAGs) were used as reference genomes to accurately identify the origin of RNA reads, and transcript ratios of genes with opposite transcription responses were compared to eliminate biases related to differences in organismal abundance, an approach hereafter named the "diametric ratio" method. We used this approach to probe the environmental conditions experienced by Escherichia spp. in the gut of 4 premature infants, 2 of whom developed necrotizing enterocolitis (NEC), a severe inflammatory intestinal disease. We analyzed twenty fecal samples taken from four premature infants (4-6 time points from each infant), and found significantly higher diametric ratios of genes associated with low oxygen levels in samples of infants later diagnosed with NEC than in samples without NEC. We also show this method can be used for examining other physiological conditions, such as exposure to nitric oxide and osmotic pressure. These study results should be treated with caution, due to the presence of confounding factors that might also distinguish between NEC and control infants. Nevertheless, together with benchmarking analyses, we show here that the diametric ratio approach can be applied for evaluating the physiological conditions experienced by microbes in situ. Results from similar studies can be further applied for designing diagnostic methods to detect NEC in its early developmental stages.