State Key Laboratory of Soil and Sustainable Agriculture

Abstract. The Intergovernmental Technical Panel on Soils has completed the first State of the World's Soil Resources Report. Globally soil erosion was identified as the gravest threat, leading to deteriorating water quality in developed regions and to lowering of crop yields in many developing regions. We need to increase nitrogen and phosphorus fertilizer use in infertile tropical and semi-tropical soils – the regions where the most food insecurity among us are found – while reducing global use of these products overall. Stores of soil organic carbon are critical in the global carbon balance, and national governments must set specific targets to stabilize or ideally increase soil organic carbon stores. Finally the quality of soil information available for policy formulation must be improved – the regional assessments in the State of the World's Soil Resources Report frequently base their evaluations on studies from the 1990s based on observations made in the 1980s or earlier.

This study investigated the role of the sugar transporter OsSWEET11 during the early stage of rice caryopsis development using β-glucoronidase (GUS) to represent its expression, together with clustered regularly interspaced short palindromic repeats-CRISPR-associated protein 9 (CRISPR-Cas9)-mediated knockout, cross-fertilization and RNA sequencing (RNA-seq) analyses. The results showed that OsSWEET11 was expressed strongly in developing caryopsis, particularly in the ovular vascular trace, nucellar epidermis and cross cells. The knockout of OsSWEET11 significantly decreased the sucrose concentration in the mutant embryo sacs and led to defective grain filling compared with that of the wild-type (WT) plant. Moreover, the expression of 2,549 genes in the mutant caryopsis was affected. The grain weight and seed setting percentage were also decreased in the mutants. The cross-fertilization of the mutant and WT rice revealed that the mutated maternal donor induced defective grain filling. These results strongly suggested that OsSWEET11 played an important role in sucrose release from maternal tissue to the maternal-filial interface during the early stage of caryopsis development. It might also induce sucrose release from the ovular vascular trace and cross cells of developing caryopsis. These findings bridge the gap in the understanding of post-phloem sugar transport during the early stage of rice caryopsis development.

BACKGROUND: Ribosomes are essential ribonucleoprotein complexes that are engaged in translation and thus indispensable for growth. Arabidopsis thaliana ribosomes are composed of 80 distinct ribosomal proteins (RPs), each of which is encoded by two to seven highly similar paralogous genes. Little information is available on how RP genes respond to a shortage of essential mineral nutrients such as phosphate (Pi) or iron (Fe). In the present study, the expression of RP genes and the differential accumulation of RPs upon Pi or Fe deficiency in Arabidopsis roots were comprehensively analyzed. RESULTS: Comparison of 3,106 Pi-responsive genes with 3,296 Fe-responsive genes revealed an overlap of 579 genes that were differentially expressed under both conditions in Arabidopsis roots. Gene ontology (GO) analysis revealed that these 579 genes were mainly associated with abiotic stress responses. Among the 247 RP genes retrieved from the TAIR10 release of the Arabidopsis genome (98 small subunit RP genes, 143 large subunit RP genes and six ribosome-related genes), seven RP genes were not detected in Arabidopsis roots by RNA sequencing under control conditions. Transcripts from 20 and 100 RP genes showed low and medium abundance, respectively; 120 RP genes were highly expressed in Arabidopsis roots. As anticipated, gene ontology (GO) analysis indicated that most RP genes were related to translation and ribosome assembly, but some of the highly expressed RP genes were also involved in the responses to cold, UV-B, and salt stress. Only three RP genes derived from three 'sets' of paralogous genes were differentially expressed between Pi-sufficient and Pi-deficient roots, all of which were induced by Pi starvation. In Fe-deficient plants, 81 RP genes from 51 'sets' of paralagous RP genes were significantly down-regulated in response to Fe deficiency. The biological processes 'translation' (GO: 0006412), 'ribosome biogenesis (GO: 0042254), and 'response to salt (GO: 0009651), cold (GO: 0009409), and UV-B stresses (GO: 0071493)' were enriched in this subset of RP genes. At the protein level, 21 and two RPs accumulated differentially under Pi- and Fe-deficient conditions, respectively. Neither the differentially expressed RP genes nor the differentially expressed RPs showed any overlap between the two growth types. CONCLUSIONS: In the present study three and 81 differentially expressed RP genes were identified under Pi and Fe deficiency, respectively. At protein level, 21 and two RP proteins were differentially accumulated under Pi- and Fe-deficient conditions. Our study shows that the expression of paralogous genes encoding RPs was regulated in a stress-specific manner in Arabidopsis roots, presumably resulting in an altered composition of ribosomes and biased translation. These findings may aid in uncovering an unexplored mechanism by which plants adapt to changing environmental conditions.

Iron deficiency is a nutritional problem in plants and reduces crop productivity, quality and yield. With the goal of improving the iron (Fe) storage properties of plants, we have investigated the function of three Arabidopsis proteins with homology to Vacuolar Iron Transporter1 (AtVIT1). Heterologous expression of Vacuolar Iron Transporter-Like1 (AtVTL1; At1g21140), AtVTL2 (At1g76800) or AtVTL5 (At3g25190) in the yeast vacuolar Fe transport mutant, Δccc1, restored growth in the presence of 4 mM Fe. Isolated vacuoles from yeast expressing either of the VTL genes in the Δccc1 background had a three- to four-fold increase in Fe concentration compared to vacuoles isolated from the untransformed mutant. Transiently expressed GFP-tagged AtVTL1 was localized exclusively and AtVTL2 was localized primarily to the vacuolar membrane of onion epidermis cells. Seedling root growth of the Arabidopsis nramp3/nramp4 and vit1-1 mutants was decreased compared to the wild type when seedlings were grown under Fe deficiency. When expressed under the 35S promoter in the nramp3/nramp4 or vit1-1 backgrounds, AtVTL1, AtVTL2 or AtVTL5 restored root growth in both mutants. The seed Fe concentration in the nramp3/nramp4 mutant overexpressing AtVTL1, AtVTL2 or AtVTL5 was between 50 and 60% higher than in non-transformed double mutants or wild-type plants. We conclude that the VTL proteins catalyze Fe transport into vacuoles and thus contribute to the regulation of Fe homeostasis in planta.

A typical soil shrinkage curve is S-shaped and composed of four phases termed structural, proportional, residual, and zero shrinkage. However, many studies have not found all four soil shrinkage phases despite investigating the full spectrum of soil moisture content. The objectives of this paper were to determine different soil shrinkage types based on the presence of shrinkage phases and to define relationships between the parameters of different shrinkage types and soil properties. A total of 270 sets of shrinkage data were collected from published (N = 245) and our unpublished work (N = 25), covering a wide range of soil types, sample sizes, and measurement methods. According to the presence of different shrinkage phases, six types of soil shrinkage curves were classified using the shrinkage model proposed by Peng and Horn (2005). Soil shrinkage types generally depended on soil structure, but not on the measurement method. The coefficient of linear extensibility (COLE) had a positive relation with saturated soil bulk density (r = 0.50, P < 0.001), clay content (r = 0.20, P < 0.05), and soil organic carbon (SOC) content (r = 0.46, P < 0.001). This paper is the first to propose six soil shrinkage types that will improve our understanding of the relationship between soil structure and soil water content.

Rab GTPases are required for vesicle-vacuolar fusion during vacuolar biogenesis in fungi. To date, little is known about the biological functions of the Rab small GTPase components in Magnaporthe oryzae. In this study, we investigated MoYpt7 of M. oryzae, a homologue of the small Ras-like GTPase Ypt7 in Saccharomyces cerevisiae. Cellular localization assays showed that MoYpt7 was predominantly localized to vacuolar membranes. Using a targeted gene disruption strategy, a ΔMoYPT7 mutant was generated that exhibited defects in mycelial growth and production of conidia. The conidia of the ΔMoYPT7 mutant were malformed and defective in the formation of appressoria. Consequently, the ΔMoYPT7 mutant failed to cause disease in rice and barley. Furthermore, the ΔMoYPT7 mutant showed impairment in autophagy, breached cell wall integrity, and higher sensitivity to both calcium and heavy metal stress. Transformants constitutively expressing an active MoYPT7 allele (MoYPT7-CA, Gln67Leu) exhibited distinct phenotypes from the ΔMoYPT7 mutant. Expression of MoYPT7-CA in MoYpt7 reduced pathogenicity and produced more appressoria-forming single-septum conidia. These results indicate that MoYPT7 is required for fungal morphogenesis, vacuole fusion, autophagy, stress resistance and pathogenicity in M. oryzae.

Boron (B) alleviates aluminum (Al) toxicity in higher plants; however, the underlying mechanisms behind this phenomenon remain unknown. Here, we used bromocresol green pH indicator, noninvasive microtest, and microelectrode ion flux estimation techniques to demonstrate that B promotes root surface pH gradients in pea (Pisum sativum) roots, leading to alkalization in the root transition zone and acidification in the elongation zone, while Al inhibits these pH gradients. B significantly decreased Al accumulation in the transition zone (∼1.0–2.5 mm from the apex) of lateral roots, thereby alleviating Al-induced inhibition of root elongation. Net indole acetic acid (IAA) efflux detected by an IAA-sensitive platinum microelectrode showed that polar auxin transport, which peaked in the root transition zone, was inhibited by Al toxicity, while it was partially recovered by B. Electrophysiological experiments using the Arabidopsis (Arabidopsis thaliana) auxin transporter mutants (auxin resistant1-7; pin-formed2 [pin2]) and the specific polar auxin transporter inhibitor1-naphthylphthalamic acid showed that PIN2-based polar auxin transport is involved in root surface alkalization in the transition zone. Our results suggest that B promotes polar auxin transport driven by the auxin efflux transporter PIN2 and leads to the downstream regulation of the plasma membrane-H+-ATPase, resulting in elevated root surface pH, which is essential to decrease Al accumulation in this Al-targeted apical root zone. These findings provide a mechanistic explanation for the role of exogenous B in alleviation of Al accumulation and toxicity in plants.

Abstract. The Intergovernmental Technical Panel on Soils has completed the first State of the World's Soil Resources report. Globally soil erosion was identified as the gravest threat, leading to deteriorating water quality in developed regions and to lowering of crop yields in many developing regions. We need to increase nitrogen and phosphorus fertilizer use in infertile tropical and semi-tropical soils – the regions where the most food insecure among us are found – while reducing global use of these products overall. Stores of soil organic carbon are critical in the global carbon balance, and national governments must set specific targets to stabilize or ideally increase soil organic carbon stores. Finally the quality of soil information available for policy formulation must be improved – the regional assessments in the SWSR report frequently base their evaluations on studies from the 1990s based on observations made in the 1980s or earlier.

Exudates produced by plants and microorganisms can alter greatly the physical behaviour of soil. There is limited research that quantifies directly the underlying hydrological and mechanical mechanisms concerned, and so in this study we amended soils with a range of analogue biological exudate compounds with different physical and chemical properties: polygalacturonic acid (PGA), dextran, xanthan and lecithin. These were added to a structurally rigid soil (Plinthosol) and a non‐rigid soil (Gleysol) that were formed as repacked cores and exposed to five cycles of wetting and drying (WD). Aggregate stability, tensile strength, water sorptivity and water repellency were measured initially and after the first, third and fifth WD cycle. Improved aggregate stability was only found for some exudates and differed between the soils. Xanthan had the greatest impact on aggregate stability, causing a 95% increase in the Plinthosol and 75% increase in the Gleysol. Xanthan also caused the greatest increase in tensile strength (50% in the Plinthosol and 148% in the Gleysol) but had minimal impact on water repellency in both soils, indicating mechanical stabilization. Lecithin reduced tensile strength but caused the greatest increase in water repellency, indicating hydrological stabilization. Both PGA and dextran had clear positive impacts on soil stability, but the underlying processes were not detected in the hydrological and mechanical tests. Increasing the number of WD cycles diminished aggregate stability, tensile strength and water repellency more rapidly in the non‐rigid Gleysol than in the rigid Plinthosol. This study demonstrated that the effects of analogous biological exudates on aggregation and stabilization depend on the nature of exudate, the rigidity of soil structure and the number of WD cycles.

BACKGROUND: For achieving long-term sustainability of intensive agricultural practices, it is pivotal to understand belowground functional stability as belowground organisms play essential roles in soil biogeochemical cycling. It is commonly believed that resource availability is critical for controlling the soil biodiversity and belowground organism interactions that ultimately lead to the stabilization or collapse of terrestrial ecosystem functions, but evidence to support this belief is still limited. Here, we leveraged field experiments from the Chinese National Ecosystem Research Network (CERN) and two microcosm experiments mimicking high and low resource conditions to explore how resource availability mediates soil biodiversity and potential multi-trophic interactions to control functional trait stability. RESULTS: We found that agricultural practice-induced higher resource availability increased potential cross-trophic interactions over 316% in fields, which in turn had a greater effect on functional trait stability, while low resource availability made the stability more dependent on the potential within trophic interactions and soil biodiversity. This large-scale pattern was confirmed by fine-scale microcosm systems, showing that microcosms with sufficient nutrient supply increase the proportion of potential cross-trophic interactions, which were positively associated with functional stability. Resource-driven belowground biodiversity and multi-trophic interactions ultimately feedback to the stability of plant biomass. CONCLUSIONS: Our results indicated the importance of potential multi-trophic interactions in supporting belowground functional trait stability, especially when nutrients are sufficient, and also suggested the ecological benefits of fertilization programs in modern agricultural intensification. Video Abstract.

absent

Soil-borne Fusarium wilt disease causes damage to certain crops, but crop rotation may be an effective management strategy for this pest. Soil microbes may play an important role in this strategy, but the response of the soil microbial community to crop rotation is unclear. In a field experiment, we used high-throughput sequencing to study the effects of banana rotation with one of four other crops (pepper, sugarcane, wax gourd and pumpkin) or continuous cultivation of banana as a single crop on soil microbial community. Compared with monocropping, all crop rotation strategies led to a decrease in the incidence of Fusarium wilt of banana, while an increase in banana yields. The main bacterial phyla were Proteobacteria (24.96%), Acidobacteria (21.25%), Gemmatimonadetes (12.98%), and the fungal phyla was Ascomycota (72.54%), across the soil. These four crop rotation treatments also increased bacterial richness and the relative abundance of Acidobacteria, Gemmatimonadetes, Firmicutes, and Actinobacteria, while reducing the relative abundance of Proteobacteria, Chloroflexi, Parcubacteria, Cyanobacteria and Fusarium. Redundancy analysis showed that soil pH, organic matter and available phosphorus were the main factors affecting the composition of bacterial and fungal communities. Overall, we show that crop rotation can inhibit banana wilt and change soil microbial community composition.

Zinc isotopes have been increasingly applied in cosmochemistry, geochemistry, and environmental sciences.

In shallow lakes, different primary producers might impact the physiochemical characteristics of the sediment and the associated microbial communities. Until now, little was known about the features of sediment Archaea and their variation across different primary producer-dominated ecosystems. Lake Taihu provides a suitable study area with cyanobacteria- and macrophyte-dominated zones co-occurring in one ecosystem. The composition of the sediment archaeal community was assessed using 16S rRNA gene amplicon sequencing technology, based on which the potential variation with respect to the physiochemical characteristics of the sediment was analyzed. Euryarchaeota (30.19% of total archaeal sequences) and Bathyarchaeota (28.00%) were the two most abundant phyla, followed by Crenarchaeota (11.37%), Aigarchaeota (10.24%) and Thaumarchaeota (5.98%). The differences found in the composition of the archaeal communities between the two zones was significant (p = 0.005). Sediment from macrophyte-dominated zones had high TOC and TN content and an abundance of archaeal lineages potentially involved in the degradation of complex organic compounds, such as the order Thermoplasmatales. In the area dominated by cyanobacteria, archaeal lineages related to sulfur metabolism, for example, Sulfolobales and Desulfurococcales, were significantly enriched. Among Bathyarchaeota, subgroups MCG-6 and MCG-15 were significantly accumulated in the sediment of areas dominated by macrophytes whereas MCG-4 was consistently dominant in both type of sediments. The present study contributes to the knowledge of sediment archaeal communities with different primary producers and their possible biogeochemical functions in sediment habitats.

Summary Root exudates help drive the formation of the rhizosphere by binding soil particles, but the underlying physical mechanisms have not been quantified. This was addressed by measuring the impact of a major component of root exudates, polygalacturonic acid (PGA), on the interparticle bond energy and fracture toughness of clay. Pure kaolinite was mixed with 0, 1.2, 2.4, 4.9 or 12.2 g PGA kg −1 to form test specimens. Half of the specimens were washed repeatedly to remove unbound PGA and evaluate the persistence of the effects, similar to weathering in natural soils. Fracture toughness, K IC , increased exponentially with added PGA, with washing increasing this trend. In unwashed specimens K IC ranged from 54.3 ± 2.5 kPa m −1/2 for 0 g PGA kg −1 to 86.9 ± 4.7 kPa m −1/2 for 12.2 g PGA kg −1 . Washing increased K IC to 61.3 ± 1.2 kPa m −1/2 for 0 g PGA kg −1 and 132.1 ± 4.9 kPa m −1/2 for 12.2 g PGA kg −1 . The apparent bond energy, γ, of the fracture surface increased from 5.9 ± 0.6 J m −2 for 0 g kg −1 to 12.0 ± 1.1 J m −2 for 12.2 g kg −1 PGA in the unwashed specimens. The washed specimens had γ of 13.0 ± 1.9 J m −2 for 0 g kg −1 and 21.3 ± 2.6 J m −2 for 12.2 g PGA kg −1 . Thus PGA, a major component of root exudates, has a large impact on the fracture toughness and bond energy of clay, and is likely to be a major determinant in the formation of the rhizosphere. This quantification of the thermodynamics of fracture will be useful for modelling rhizosphere formation and stability.

Microplastics (MPs) and per- and polyfluoroalkyl substances (PFASs) are ubiquitous contaminants in environments, yet their co-occurrence and interactions remain insufficiently understood. In this study, we confirmed the concurrent presence of MPs and PFASs and their distinct distribution patterns in a wastewater treatment plant (WWTP) through a comprehensive sampling and analysis effort. Significant correlations (p < 0.05) were observed between specific types of MPs and PFASs, suggesting their shared sources. Moreover, MPs were identified as carriers of PFASs, with PFAS concentration ranging between 122 and 166 ng/g, predominantly consisting of perfluorooctanoic acid (PFOA) and perfluorobutanoic acid (PFBA). The laboratory verification experiment revealed that PFASs could be leached from MPs in aqueous environments, in which commercial MPs exhibited higher leaching potential, with the highest combined concentration of perfluorooctanesulfonate (PFOS), PFOA, and PFBA reaching 10.4 ng/mL. PFOS demonstrated a desorption efficiency exceeding 120% in sorption/desorption experiments, confirming its release from the MPs themselves. These results highlighted the dual roles of MPs as both carriers and sources of PFASs. The identified contaminant profiles and correlations between MPs and PFASs across different matrices in WWTP provide valuable insights and form a basis for further research into proactive measures to effectively mitigate their environmental contamination.

Straw return is a promising strategy for managing soil organic carbon (SOC) and improving yield stability. However, the optimal straw return strategy for sustainable crop production in the wheat (Triticum aestivum L.)-cotton (Gossypium hirsutum L.) cropping system remains uncertain. The objective of this study was to quantify the long-term (10 years) impact of C input on SOC sequestration, soil aggregation and crop yields in a wheat–cotton cropping system in the Yangtze River Valley. Five treatments were arranged with a single-factor randomized design as follows: no straw return (Control), return of wheat straw only (Wt), return of cotton straw only (Ct), return of 50% wheat and 50% cotton straw (Wh-Ch) and return of 100% wheat and 100% cotton straw (Wt-Ct). In comparison to the Control, the SOC content increased by 8.4 to 20.2% under straw return. A significant linear positive correlation between SOC sequestration and C input (1.42-7.19 Mg ha−1 yr−1) (P<0.05) was detected. The percentages of aggregates of sizes >2 and 1–2 mm at the 0–20 cm soil depth were also significantly elevated under straw return, with the greatest increase of the aggregate stability in the Wt-Ct treatment (28.1%). The average wheat yields increased by 12.4–36.0% and cotton yields increased by 29.4–73.7%, and significantly linear positive correlations were also detected between C input and the yields of wheat and cotton. The average sustainable yield index (SYI) reached a maximum value of 0.69 when the C input was 7.08 Mg ha−1 yr−1, which was close to the maximum value (SYI of 0.69, C input of 7.19 Mg ha−1 yr-1) in the Wt-Ct treatment. Overall, the return of both wheat and cotton straw was the best strategy for improving SOC sequestration, soil aggregation, yields and their sustainability in the wheat-cotton rotation system.

The aim of this study was to investigate the burrowing activity of two earthworm species: the endogeic Drawida sinica and one undescribed Amynthas species incubated in Vertisol and Ultisol presenting different soil organic C content. Because of their contrasting feeding behaviours, we hypothesised that soil type would have a bigger influence on the burrowing activity of the endogeic than the anecic species. Repacked soil columns inoculated with earthworms for 30 days were scanned using X-ray tomography and the compiled images used to characterise the burrow systems. After scanning, the saturated hydraulic conductivity (K sat) was also measured. The Amynthas species burrows were less numerous (30 vs. 180), more vertically oriented (57 vs. 37°), more connected from the surface to the bottom of the columns (73 vs. 5 cm3) and had a higher global connectivity index (83 vs. 28%) than those of D. sinica. The K sat was threefold faster in columns incubated with Amynthas and was linked to the volume of percolating burrows (R 2 = 0.81). The soil type did not influence Amynthas burrow characteristics. In contrast, there were 30% more D. sinica burrows in the Vertisol than in the Ultisol while other burrow characteristics were not affected. This result suggests that these burrows were more refilled with casts leading to shorter and discontinuous burrows. The K sat was negatively related to the number of burrows (R 2 = 0.44) but was not statistically different between the Vertisol and the Ultisol, suggesting a constant impact of this species on the K sat. We found that a decrease in the amount of soil organic C by 50% had only a small influence on earthworm burrowing activity and no effect on the K sat.

The key role of NOM heterogeneity in inhibiting the dissolution and consequently the uptake of total Ag.

Poor breakdown of lipids is a major barrier to the anaerobic treatment of domestic wastewater at low temperatures.