Plant microbiomes : do different preservation approaches and primer sets alter our capacity to assess microbial diversity and community composition?

The microbial communities associated with plants (the plant microbiome) play critical roles in regulating plant health and productivity. Because of this, in recent years, there have been significant increase in studies targeting the plant microbiome. Amplicon sequencing is widely used to investigate the plant microbiome and to develop sustainable microbial agricultural tools. However, performing large microbiome surveys at the regional and global scales pose several logistic challenges. One of these challenges is related with the preservation of plant materials for sequencing aiming to maintain the integrity of the original diversity and community composition of the plant microbiome. Another significant challenge involves the existence of multiple primer sets used in amplicon sequencing that, especially for bacterial communities, hampers the comparability of datasets across studies. Here, we aimed to examine the effect of different preservation approaches (snap freezing, fresh and kept on ice, and air drying) on the bacterial and fungal diversity and community composition on plant leaves, stems and roots from seven plant species from contrasting functional groups (e.g. C3, C4, N-Fixers, etc.). Another major challenge comes when comparing plant to soil microbiomes, as different primers sets are often used for plant vs. soil microbiomes. Thus, we also investigated if widely used 16S rRNA primer set (779F/1193R) for plant microbiome studies provides comparable data to those often used for soil microbiomes (341F/805R) using 86 soil samples. We found that the community composition and diversity of bacteria or fungi were robust to contrasting preservation methods. The primer sets often used for plants provided similar results to those often used for soil studies suggesting that simultaneous studies on plant and soil microbiomes are possible. Our findings provide novel evidence that preservation approaches do not significantly impact plant microbiome data interpretation and primer differences do not impact the treatment effect, which has significant implication for future large-scale and global surveys of plant microbiomes

Generalist taxa shape fungal community structure in cropping ecosystems

Fungi regulate nutrient cycling, decomposition, symbiosis, and pathogenicity in cropland soils. However, the relative importance of generalist and specialist taxa in structuring soil fungal community remains largely unresolved. We hypothesized that generalist fungi, which are adaptable to various environmental conditions, could potentially dominate the community and become the basis for fungal coexisting networks in cropping systems. In this study, we identified the generalist and habitat specialist fungi in cropland soils across a 2,200 kms environmental gradient, including three bioclimatic regions (subtropical, warm temperate, and temperate). A few fungal taxa in our database were classified as generalist taxa (~1%). These generalists accounted for >35% of the relative abundance of all fungal populations, and most of them are Ascomycota and potentially pathotrophic. Compared to the specialist taxa (5–17% of all phylotypes in three regions), generalists had a higher degree of connectivity and were often identified as hub within the network. Structural equation modeling provided further evidence that after accounting for spatial and climatic/ edaphic factors, generalists had larger contributions to the fungal coexistence pattern than habitat specialists. Taken together, our study provided evidence that generalist taxa are crucial components for fungal community structure. The knowledge of generalists can provide important implication for understanding the ecological preference of fungal groups in cropland systems

Synthetic community improves crop performance and alters rhizosphere microbial communities

Introduction: Harnessing synthetic communities (SynCom) of plant growth‐promoting (PGP) microorganisms is considered a promising approach to improve crop fitness and productivity. However, biotic mechanisms that underpin improved plant performance and the effects of delivery mode of synthetic community are poorly understood. These are critical knowledge gaps that constrain field efficacy of SynCom and hence large‐ scale adoption by the farming community. Material & Methods: In this study, a SynCom of four PGP microbial species was constructed and applied to either as seed dressing (treatment T1, applied at the time of sowing) or to soil (treatment T2, applied in soil at true leaf stage) across five different cotton (Gossypium hirsutum) cultivars. The impact of SynCom on plant growth, rhizosphere microbiome and soil nutrient availability, and how this was modified by plant variety and mode of applications, was assessed. Results: Results showed that the seed application of SynCom had the strongest positive impact on overall plant fitness, resulting in higher germination (14.3%), increased plant height (7.4%) and shoot biomass (5.4%). A significant increase in the number of flowers (10.4%) and yield (8.5%) was also observed in T1. The soil nitrate availability was enhanced by 28% and 55% under T1 and T2, respectively. Results further suggested that SynCom applications triggered enrichment of members from bacterial phyla Actinobacteria, Firmicutes and Cyanobacteria in the rhizosphere. A shift in fungal communities was also observed, with a significant increase in the relative abundance of fungi from phyla Chytridiomycota and Basidiomycota in SynCom treatments. A structural equation model suggested that SynCom directly increased crop productivity but also indirectly via impacting the alpha diversity of bacteria. Conclusion: Overall, this study provides mechanistic evidence that SynCom applications can shift rhizosphere microbial communities and improve soil fertility, plant growth, and crop productivity, suggesting that their use could contribute toward sustainable increase in farm productivity

Asymmetric responses of soil bacterial community and soil respiration to precipitation changes : a global meta-analysis

Changes in the frequency and intensity of precipitation altered the hydrological features, thereafter greatly affecting carbon (C) cycling in terrestrial ecosystems. Soil bacteria are pivotal drivers of the global C cycle in terrestrial ecosystems; however, the responses of soil bacterial communities and the C-cycle they regulated to precipitation changes remain unclear. Here, we conducted a global meta-analysis using 98 paired observations from 58 studies to explore the responses of soil bacteria (abundance and diversity) and their C-related functions (soil respiration) to increased/decreased precipitation. We found that the response of soil bacterial abundance was linearly correlated with precipitation changes, while the response of soil respiration was negatively asymmetric (concave-down). The relationship among soil bacterial abundance, alpha diversity, and soil respiration was weakened by decreased precipitation, indicating that decreased precipitation exhibited a stronger effect on soil bacterial community and soil respiration. Our study extends the understanding of soil bacteria and their functions in response to precipitation change and facilitates the prediction of soil carbon cycle-related functions by using soil microorganisms in terrestrial ecosystem models under future precipitation scenarios

Effects of remoulding and wetting-drying-freezing-thawing cycles on the pore structures of Yanji mudstones

The pore structure governs the physical and mechanical behaviours of geomaterials, thereby affecting the stability of the infrastructures built on these materials. This study investigated the effects of remoulding and wetting-drying-freezing-thawing (W–D–F–T) cycles on the pore structures of two Yanji mudstones using scanning electronic microscopy (SEM), mercury intrusion porosimetry (MIP) and nitrogen adsorption (NA) techniques. The results show that the pores of both the yellow-brown and magenta mudstones become rounder and more disordered after remoulding. Remoulding leads to an increase in the inter-aggregate pore volume and a decrease in the intra-aggregate pore volume because of the exposure of intra-aggregate pores after crushing and the compaction of aggregates during the compression process. The W-D-F-T cycles make the pores of the remoulded yellow-brown mudstone more disordered and flatter and induce an increase in the inter-aggregate pore volume due to the formation of cracks and large pores. Meanwhile, the intra-aggregate pore volume decreases owing to the contraction of aggregates during the drying process. According to the increased inter-aggregate pore volume and decreased intra-aggregate pore volume, an increase in the hydraulic conductivity and a decrease in the shear strength can be expected after remoulding and W-D-F-T cycles, which decrease the stability of mudstone slopes

(Succession of soil fungal and bacterial communities in a typical chronosequence of abandoned agricultural lands)

As pivotal components of belowground communities, soil fungi and bacteria are important indices for evaluating the ecological benefits of the Grain for Green program in China. In this study, we used a high-throughput sequencing approach to compare the succession of soil fungal and bacterial communities in a typical chronosequence of abandoned agricultural lands in Yunnan Province, southwest China. The results showed that bacterial diversity decreased significantly and then increased gradually after the soil was abandoned, while fungal diversity showed no significant change. However, when plant communities changed from herb to woodland via the shnib stage during reforestation, the proportion of Sordariomvcetes decreased significantly from 30% to approximately 10% and the proportion of Agaricomycetes increased from 5% to more than 20%; there was no obvious change in the bacterial community composition along the chronosequence. (Mustering analysis showed that the successional pattern of the fungi community was more consistent with plant communities than bacterial along successional stages. Both fungi and bacteria communities in undisturbed natural forest soil differed significantly from thosr in other stages, indicating that anthropogenic disturbance of soil microbial communities has long-term effects. These results revealed the succession characteristics of soil fungal and bacterial communities during reforestation in typical abandoned soil in Yunnan Province and provide essential data support for the comprehensive evaluation of the ecological benefits of the Grain for Green project in Southwest China

Archaea is more important than bacteria in driving soil stoichiometry in phosphorus deficient habitats

Phosphorus deficiency is a critical limit on the cycling of carbon (C), nitrogen (N) and phosphorus (P) in forest ecosystems. Despite the pivotal roles of microbes in driving the biogeochemical cycling of C/N/P, our knowledge on the relationships of soil bacteria and archaea to P deficiency in forest ecosystems remains scarce. Here, we studied 110 acidic soils (average pH4.5) collected across 700-kmsubtropical forests with a gradient of available phosphorus (AP) ranging from 0.21 to 17.6 mg/kg. We analyzed the soil C/N/P stoichiometry and studied soil bacterial and archaeal diversity/abundance via high throughput sequencing and qPCR approaches. Our results show that soil P decoupled with N or C when below 3 mg/kg but coupled with C and N when above 3 mg/kg. Archaeal diversity and abundance were significantly higher in low AP (3 mg/kg) soils, while bacterial were less changed. Compared with bacteria, archaea are more strongly related with soil stoichiometry (C:N, C:P, N:P), especially when AP was less than 3 mg/kg. Taxonomic and functional composition analysis further confirmed that archaeal rather than bacterial taxonomic composition was significantly related with functional composition of microbial communities. Taken together, our results show that archaea are more important than bacteria in driving soil stoichiometry in phosphorus deficient habitats and suggest a niche differentiation of soil bacteria and archaea in regulating the soil C/N/P cycling in subtropical forests

The deformation and permeability of Yanji mudstone under cyclic loading and unloading

During the constructions of motorways and high-speed railway lines in the Yanji Basin, large amounts of excess mudstones due to the enormous tunnel excavations and slope cuts would be deposited as landfills. Assessing the deformation and permeability of Yanji mudstone became important for the design, construction and operation of the landfills. This paper presents an experimental study on the deformation and permeability of Yanji mudstone by carrying out a series of oedometer tests with loading/unloading cycles. The results show that the sample with a lower initial water content exhibited greater swelling deformation after inundation, a lower yield stress, greater deformation and a higher hydraulic conductivity during the loading/unloading cycles. As the number of loading/unloading cycles increased, the yield stress and accumulated plastic deformation increased, while the compression index, rebound index and hydraulic conductivity decreased. The samples became stiffer and their hydromechanical behaviour tended to be stable after three cycles. The compression curves could be divided into pre-yield and post-yield zones. The post-yield zones of compression curves and the rebound curves could be normalized into a unique line, and the pre-yield zones of the compression curves could be described as lines. Basic equations were developed to predict mudstone deformation under cyclic loading and unloading. Additionally, an empirical relationship between the hydraulic conductivity and void ratio was also proposed. The ability of the proposed methods was verified by the overall good agreement between the experimental results and predicted values

Ecosystem functions are related to tree diversity in forests but soil biodiversity in open woodlands and shrublands

Millions of trees are expected to be planted in forested and non-forested ecosystems during the United Nations Decade of Restoration. Trees and soil organisms are known to interact, and are both crucial for maintaining multiple ecosystem functions. However, little is known about how the bidirectional relationships among above- and below-ground diversity and ecosystem functions differ across forested and non-forested ecosystems. We collected data from 126 sites from humid to arid areas in eastern Australia to explore bidirectional relationships among above-ground (richness of trees and other plants) and below-ground (richness of bacteria, fungi, invertebrate, protist) diversity and multiple ecosystem functions (multifunctionality, litter and labile carbon storage, nutrient pools, decomposition, groundstorey plant biomass production, soil stability) in forested (tree cover >10%) and non-forested (tree cover ≤10%, open woodlands, shrublands) systems. We found that the relative importance of above- and below-ground diversity differed among forested and non-forested systems. Ecosystem functions, such as litter and labile carbon storage and soil stability, were associated mainly with tree richness in forested systems. By comparison, ecosystem functions of non-forests were related to the richness of soil organisms. Such bidirectional biodiversity–ecosystem function relationships varied with the target function, and the relationships among ecosystem functions and the relative abundance of species varied with tree and soil taxa. The richness of other plants (i.e. all plants excluding trees) and soil organisms was positively coupled in forests only, but there were no linkages among above- and below-ground diversity and ecosystem functions in non-forests for groundstorey plant biomass production. Furthermore, increases in aridity and soil pH further weakened the biodiversity–ecosystem function relationships in forested and non-forested systems, by suppressing above-ground diversity and bacterial richness, respectively. Synthesis. Our study provides strong empirical evidence that the bidirectional relationships among above- and below-ground diversity and ecosystem functions are highly variable across ecosystem and function types. Moreover, our study demonstrates that soil biodiversity is relatively more important than tree diversity in supporting ecosystem functions in non-forested systems. This suggests that conservation of soil biodiversity is critical for maintaining the functioning of open woodland and shrubland systems

Soil pH determines fungal diversity along an elevation gradient in Southwestern China

Fungi play important roles in ecosystem processes, and the elevational pattern of fungal diversity is still unclear. Here, we examined the diversity of fungi along a 1,000 m elevation gradient on Mount Nadu, Southwestern China. We used MiSeq sequencing to obtain fungal sequences that were clustered into operational taxonomic units (OTUs) and to measure the fungal composition and diversity. Though the species richness and phylogenetic diversity of the fungal community did not exhibit significant trends with increasing altitude, they were significantly lower at mid-altitudinal sites than at the base. The Bray-Curtis distance clustering also showed that the fungal communities varied significantly with altitude. A distance-based linear model multivariate analysis (DistLM) identified that soil pH dominated the explanatory power of the species richness (23.72%), phylogenetic diversity (24.25%) and beta diversity (28.10%) of the fungal community. Moreover, the species richness and phylogenetic diversity of the fungal community increased linearly with increasing soil pH (P<0.05). Our study provides evidence that pH is an important predictor of soil fungal diversity along elevation gradients in Southwestern China