Label-free quantitative proteomics of maize roots from different root zones provides insight into proteins associated with enhance water uptake.

BACKGROUND: Maize is one of the most important food crops worldwide. Roots play important role in maize productivity through water and nutrient uptake from the soil. Improving maize root traits for efficient water uptake will help to optimize irrigation and contribute to sustainable maize production. Therefore, we investigated the protein profiles of maize cv. Anyu308 root system divided into Upper root zone (UR), Middle root (MR), and Lower root (LR), by label free quantitative shotgun proteomic approach (LFQ). The aim of our study was to identify proteins and mechanisms associated with enhanced water uptake in different maize root zones under automatic irrigation system. RESULTS: At field capacity, MR had the highest water uptake than the UR and LR. We identified a total of 489 differentially abundant proteins (DAPs) by pairwise comparison of MR, LR, and UR. Cluster analysis of DAPs revealed MR and UR had similar protein abundance patterns different from LR. More proteins were differentially abundant in MR/UR compared to LR/MR and LR/UR. Comparisons of protein profiles indicate that the DAPs in MR increased in abundance, compared to UR and LR which had more downregulated DAPs. The abundance patterns, functional category, and pathway enrichment analyses highlight chromatin structure and dynamics, ribosomal structures, polysaccharide metabolism, energy metabolism and transport, induction of water channels, inorganic ion transport, intracellular trafficking, and vesicular transport, and posttranslational modification as primary biological processes related to enhanced root water uptake in maize. Specifically, the abundance of histones, ribosomal proteins, and aquaporins, including mitochondrion electron transport proteins and the TCA cycle, underpinned MR's enhanced water uptake. Furthermore, proteins involved in folding and vascular transport supported the radial transport of solute across cell membranes in UR and MR. Parallel reaction monitoring analysis was used to confirmed profile of the DAPs obtained by LFQ-based proteomics. CONCLUSION: The list of differentially abundant proteins identified in MR are interesting candidates for further elucidation of their role in enhanced water uptake in maize root. Overall, the current results provided an insight into the mechanisms of maize root water uptake.

Afforestation can lower microbial diversity and functionality in deep soil layers in a semiarid region.

Afforestation is an effective approach to rehabilitate degraded ecosystems, but often depletes deep soil moisture. Presently, it is not known how an afforestation-induced decrease in moisture affects soil microbial community and functionality, hindering our ability to understand the sustainability of the rehabilitated ecosystems. To address this issue, we examined the impacts of 20 years of afforestation on soil bacterial community, co-occurrence pattern, and functionalities along vertical profile (0-500 cm depth) in a semiarid region of China's Loess Plateau. We showed that the effects of afforestation with a deep-rooted legume tree on cropland were greater in deep than that of in top layers, resulting in decreased bacterial beta diversity, more responsive bacterial taxa and functional groups, increased homogeneous selection, and decreased network robustness in deep soils (120-500 cm). Organic carbon and nitrogen decomposition rates and multifunctionality also significantly decreased by afforestation, and microbial carbon limitation significantly increased in deep soils. Moreover, changes in microbial community and functionality in deep layer was largely related to changes in soil moisture. Such negative impacts on deep soils should be fully considered for assessing afforestation's eco-environment effects and for the sustainability of ecosystems because deep soils have important influence on forest ecosystems in semiarid and arid climates.

Modeling the effect of salt-affected soil on water balance fluxes and nitrous oxide emission using modified DNDC.

Soil salinity restricts plant growth, affects soil water balance and nitrous oxide (N2O) fluxes and can contaminate surface and groundwater. In this study, the Denitrification Decomposition (DNDC) model was modified to couple salt and water balance equations (SALT-DNDC) to investigate the effect of salinity on water balance and N2O fluxes. The model was examined against four growing seasons (2008-11) of observed data from Lethbridge, Alberta, Canada. Then, the model was used to simulate water filled pore space (WFPS), salt concentration and the N2O flux from agricultural soils. The results show that the effects of salinity on WFPS vary in different soil layers. Within shallow soil layers (<20 cm from soil surface) the salt concentration does not affect the average WFPS when initial salt concentrations range from 5 to 20 dS/m. However, in deeper soil layers (>20 cm from soil surface), when the initial salt concentration ranges from 5 to 20 dS/m it could indirectly affect the average WFPS due to changes of osmotic potential and transpiration. When AW is greater than 40%, the average growing season N2O emissions increase to a range of 0.6-1.0 g-N/ha/d at initial salt concentrations (5-20 dS/m) from a range of 0.5-0.7 g-N/ha/d when the salt concentrations is 0 dS/m. The newly developed SALT-DNDC model provides a unique tool to help investigate interactive effects among salt, soil, water, vegetation, and weather conditions on N2O fluxes.

Vertical distribution of microbial communities in chromium-contaminated soil and isolation of Cr(â ¥)-Reducing strains.

Soil ecosystems surrounding chromium slag undergo continuous harsh physicochemical conditions due to multiple heavy metals contamination. Previous studies of soil microbial communities mainly focused on surface soil layer, while little was known about the depth-related distributions of the microbial communities in chromium (Cr)-contaminated soil. In this study, a comprehensive analysis of depth-related distributions of microbial communities in Cr-contaminated soil was carried out by Illumina sequencing of 16s rRNA genes. The results revealed that bacterial diversities at 0 cm depth layer were significantly higher than those below 20 cm depths. And there was a remarkable difference in bacterial compositions along with the sampling depths especially for the dominant phyla of Proteobacteria, Actinobacteria, Chloroflexi and Fimicutes (p < 0.05). While the archaea accounted for a relatively low proportion of the microbes and showed stability in the compositions with the predominant phyla of Thaumarchaeota and Euryarchaeota. The linear discriminate analysis (LDA) and effect size (LEfSe) analysis showed that there were thirty-seven kinds of biomarker microbes existing in the five soil layers with LDA threshold of 4.0, and each layer showed distinct microbial divisions, indicating that microbes with different biological functions might survive along with the sampling depths. The environmental variables including total chromium (Cr), Cr(Ⅵ), Mn, Ni, and Zn had considerable influences on microbial community composition in the contaminated soil. A total of 25 Cr(Ⅵ)-reducing strains were further isolated and identified, which were phylogenetically affiliated to Proteobacteria, Actinobacteria and Firmicutes. Among the isolated Cr(Ⅵ)-reducing strains, Bacillus stratosphericus was the first time to be reported with Cr(Ⅵ) reducing capacity.

Topography- and depth-dependent rhizosphere microbial community characteristics drive ecosystem multifunctionality in Juglans mandshurica forest.

Rhizosphere microbial community characteristics and ecosystem multifunctionality (EMF), both affected by topographic factors, are closely correlated. However, more targeted exploration is yet required to fully understand the variations of rhizosphere microbial communities along topographic gradients in different soil layers, as well as whether and how they regulate EMF under specific site conditions. Here, we conducted relevant research on Juglans mandshurica forests at six elevation gradients and two slope positions ranging from 310 to 750 m in Tianjin Baxian Mountain. Results demonstrated that rhizosphere soil physicochemical properties and enzyme activities of both layers (0-20 cm and 20-40 cm) varied significantly with elevation, while only at top layer did slope position have significant impacts on most indicators. Bacterial richness and diversity were higher in the top layer at slope bottom and middle-high elevation, the difference in fungi was not as noticeable. Both topographic factors and soil depth significantly impacted microbial community structure, with Candidatus_Udaeobacter of bacteria, Mortierella, Sebacina, and Hygrocybe of fungi mainly contributing to the dissimilarity between communities. EMF rose with increasing elevation, bacteria were more critical drivers of this process than fungi, and topographic factors could affect EMF by altering bacterial diversity and dominant taxa abundance. For evaluating EMF, the aggregate structure of sub layer and the carbon cycle-related indicators of top layer were of higher importance. Our results revealed the depth-dependent characteristics of the rhizosphere microbial community along topographic gradients in studied stands, as well as the pivotal regulatory role of bacteria on EMF, while also highlighting depth as an important variable for analyzing soil properties and EMF. This work helps us better understand the response of individuals and communities of J. mandshurica to changing environmental conditions, further providing a scientific reference for the management and protection of secondary forests locally and in North China.

Compost derived from olive mill cake: Effects on isohumic soil quality based on humic acids characterization.

The compost effects on soil organic matter (SOM) stability were evaluated. Manure at 10 % ratio and compost at 10 %, 20 % and 40 % ratios (v/v) were added to the soil and their effects were compared to unamended control soil after 90-days of greenhouse-experiment. Humic acids (HA) and fulvic acids (FA) were extracted from two different soil-sample layers at 0-15 and 15-30 cm depth. The CHA/CFA ratio and the humification parameters were determined, and the soil-HA were characterized by spectroscopic methods (E4/E6 and FTIR). The humification parameters progress with time were affected by the amendment concentration. After 90 days, the treated soils HA' FTIR spectra showed an increase in aromatic carbon polycondensation and O-containing groups reflecting the high degrees of molecular associations and humification of soil HA. Compared to 10 % manure application and 40 % compost ratio use, the applications of 10 % and 20 % compost ratios induced higher humification level and highly oxidized HA structure. Moreover, changes in the HA compositional and functional groups were noticed at the upper layer which exhibited higher reactivity compared to the lower layer which displayed more humified SOM. Through the humification process, the HA fraction was improved to reach more stable and complex macromolecules, where aromatic structures were bio-converted into highly functionalized compounds.

Biochar and Manure Co-Application Increases Rice Yield in Low Productive Acid Soil by Increasing Soil pH, Organic Carbon, and Nutrient Retention and Availability.

In recent years, overuse of chemical fertilization has led to soil acidification and decreased rice yield productivity in southern China. Biochar and manure co-application remediation may have positive effects on rice yield and improve acid paddy soil fertility. This study was conducted to understand the effects of co-application of wood biochar and pig manure on rice yield and acid paddy soil quality (0-40 cm soil layers) in a 5-year field experiment. The experiment consisted of six treatments: no biochar and no fertilizer (CK); biochar only (BC); mineral fertilizer (N); mineral fertilizer combined with biochar (N + BC); manure (25% manure N replacing fertilizer N) combined with mineral fertilizer (MN); and manure combined with mineral fertilizer and biochar (MN + BC). Total nitrogen application for each treatment was the same at 270 kg nitrogen ha-1y-1, and 30 t ha-1 biochar was added to the soil only in the first year. After five years, compared with N treatments, N + BC, MN, and MN + BC treatments increased the rice yield rate to 2.8%, 4.3%, and 6.3%, respectively, by improving soil organic matter, total nitrogen, and available phosphate under a 0-40 cm soil layer. MN + BC had the strongest resistance to soil acidification among all the treatments. The interaction between fertilizers and biochar application was significant (p < 0.05) in rice yield, soil electrical conductivity (10-20 cm), and soil available phosphate (20-40 cm). Principal component analysis indicated that the effect of manure on soil property was stronger than that of biochar in the 0-40 cm soil layer. The overall rice yield and soil fertility decreased in the order of biochar + mineral fertilizer + manure > mineral fertilizer + manure > biochar + mineral fertilizer > mineral fertilizer > biochar > control. These results suggest that biochar and manure co-application is a long-term viable strategy for improving acid soil productivity due to its improvements in soil pH, organic carbon, nutrient retention, and availability.

Depth-dependent effects of tree species identity on soil microbial community characteristics and multifunctionality.

Soil microbes play key roles that support forest ecosystem functioning, while their community characteristics are strongly determined by tree species identity. However, the majority studies primarily focus on soil microorganisms in the topsoil, resulting in limited understanding of the linkages between tree species identity and the microbial communities that inhabit deep soils. Here we investigated the diversity, structure, function, and co-occurrence networks of soil bacterial and fungal communities, as well as related soil physicochemical properties, to a depth of two meters in dryland forests dominated by either Pinus tabuliformis, a native coniferous species, Robinia pseudoacacia, an exotic broadleaf and nitrogen-fixing species, or both. Tree species identity had stronger effects on soil multifunctionality and microbial community structure in the deep layers (80-200 cm) than in the top layers (0-60 cm). In addition, fungal communities were more responsive to tree species identity, whereas bacteria were more sensitive to soil depth. Tree species identity strongly influenced microbial network stability and complexity, with higher quantities in R. pseudoacacia than the other plantations, by affecting microbial composition and their associations. The increased in microbial network complexity and the relative abundance of keystone taxa enhance the soil multifunctionality of microbial productivity, sugar and chitin degradation, and nutrient availability and cycling. Meanwhile, the relative abundance of keystone taxa was more representative of soil multifunctionality than microbial diversity. Our study highlights that tree species identity significantly influences soil microbial community characteristics and multifunctionality, especially in deep soils, which will help us understand soil nutrients processed in plantation forest ecosystem and provide a reference for tree species selection in ecological restoration.

Coupling time-lapse ground penetrating radar surveys and infiltration experiments to characterize two types of non-uniform flow.

Understanding linkages between heterogeneous soil structures and non-uniform flow is fundamental for interpreting infiltration processes and improving hydrological simulations. Here, we utilized ground-penetrating radar (GPR) as a non-invasive technique to investigate those linkages and to complement current traditional methods that are labor-intensive, invasive, and non-repeatable. We combined time-lapse GPR surveys with different types of infiltration experiments to create three-dimensional (3D) diagrams of the wetting dynamics. We carried out the GPR surveys and validated them with in situ observations, independent measurements and field excavations at two experimental sites. Those sites were selected to represent different mechanisms that generate non-uniform flow: (1) preferential water infiltration initiated by tree trunk and root systems; and (2) lateral subsurface flow due to soil layering. Results revealed links between different types of soil heterogeneity and non-uniform flow. The first experimental site provided evidence of root-induced preferential flow paths along coarse roots, emphasizing the important role of coarse roots in facilitating preferential water movement through the subsurface. The second experimental site showed that water infiltrated through the restrictive layer mainly following the plant root system. The presented approach offers a non-invasive, repeatable and accurate way to detect non-uniform flow.

Influence of environmental factors on soil organic carbon in different soil layers for Chinese Mollisols under intensive maize cropping.

The Mollisol region of Northeast China has a large soil organic carbon (SOC) storage which is important for maintaining soil fertility. SOC is susceptible to various environmental factors; however, the responses of SOC content to environmental factors in different soil layers of cropland remain unclear, particularly in deep soil layers. In this study, we collected 138 soil samples from the surface, subsurface, and subsoil layers among 46 sample sites with monocropping maize and intensive conventional tillage in this region. We assessed the relative importance and effect paths of 12 environmental factors (including geography, climate, and soil properties) on SOC content in different layers using redundancy analysis (RDA), structural equation model (SEM), and variation partitioning analysis (VPA). The VPA results showed that SOC content was mainly affected by climatic factors that explained 68% and 57% for the surface and subsurface layers, respectively. However, SOC content in the subsoil layer was greatly affected by soil properties that explained 27%. Furthermore, the SEMs results suggested that geographical factors indirectly affected SOC content by influencing the climatic factors. Mean annual temperature was the most important factor affecting SOC content directly or indirectly, and its negative effects significantly diminished with soil depth, as it explained 63%, 52%, and 17% of the variation in SOC content for the surface, subsurface and subsoil layers, respectively. In addition, the effects of soil water-holding capacity on SOC content also decreased with soil depth, whereas pH and clay content showed a contrasting pattern. This implies that pH and clay content play important roles in the sequestration of SOC in deep soil layers. Moreover, the organic C content within >53 µm aggregates was more sensitive to environmental factors. This study can be useful for forecasting SOC dynamics and establishing reasonable C management strategies under climate change conditions.