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Long-term regional evidence of the effects of livestock grazing on soil microbial community structure and functions in surface and deep soil layers
No full textGrazing by livestock can affect plant biodiversity and topsoil functions. However, experimental evidence on whether these impacts are limited to the topsoil or penetrate into deep layers (via changes in soil environment and resource locations) of soil is lacking, especially for soil microbial biomass and diversity. Here, we used paired grazed and ungrazed (fenced) plots at 10 locations across the Mongolian Plateau to investigate how long-term (>10 years) livestock grazing affects the biomass, diversity, composition, and function of microbial communities in surface (0-20 cm) and deep soil layers (40-60 cm). Livestock grazing increased bacterial diversity by 5-9% in both soil layers but increased fungal diversity by 10% only in the topsoil. Livestock grazing also strongly altered bacterial and fungal community composition in both soil layers. Livestock grazing decreased soil C mineralization rates by 11-25% in both soil layers, and decreased soil N mineralization rates by 16% and bacterial biomass by 20% only in the topsoil. The grazing-induced increase in microbial diversity in both soil layers was mainly explained by the changes in plant C:N ratio and plant biomass rather than by soil abiotic variables, especially for the deep soil layer. The grazing-induced negative effects on ecosystem functions (soil C and N mineralization) were mainly associated with soil abiotic variables together with plant variables or microbial diversity in the surface soil layer and were mainly associated with plant variables and soil microbial diversity in the deep soil layer. Overall, our regional field experiment provides the first evidence that the strong effects of livestock grazing on soil microbial biomass, diversity, composition, and function can penetrate the deep soil in arid and semi-arid grasslands. This knowledge suggests that models should consider the dynamic interactions between land use and both soil microbial diversity and biomass across soil depths in global drylands
Aboveground productivity and community stability tend to keep stable under long-term fencing and nitrogen fertilization on restoration of degraded grassland
No full textRestoration of degraded grassland is an essential issue which has been widely concerned but not effectively resolved. Fencing and nitrogen fertilization are common and efficient restoration practices. However, there are still controversy on the effectiveness and duration of fencing and nitrogen fertilization on the restoration of degraded grassland. To estimate the effects of fencing and nitrogen fertilization on the community above-ground net primary productivity (ANPP) and stability, and explore the underlying mechanism, an 18-year (from 2003 to 2020) fencing and nitrogen fertilization (8 g N m-2 yearxfffd; 1) field experiment was conducted on a degraded temperate steppe in Inner Mongolia. Community ANPP and species richness were measured at the peak of plant biomass in growing season (mid-August) from 2004 to 2020. Temporal stability of community ANPP were calculated to estimate the community stability under different restoration managements. We found that both fencing and nitrogen fertilization can significantly increase the ANPP. Nevertheless, ANPP tended to keep stable rather than continuously increase with the extension of restoration duration. Long-term fencing and nitrogen fertilization significantly reduced the stability of ANPP in early stage of restoration (2004-2010), but had no significant effect on the stability of ANPP in later stage (2011-2020). Moreover, the stability of ANPP maintained stable with extension of restoration duration. Furthermore, we found that the biological factors that regulate the community stability were similar between the two restoration measures. Specifically, the stability of ANPP was regulated by species asynchrony in early phase, while, it was mediated by both species asynchrony and dominant species stability in later phase. Overall, from the perspective of community ANPP, the degraded steppe reached optimal status after approximately seven years of fencing and nitrogen fertilization, appropriate utilization after seven years' restoration may be conducive to maintain ANPP and the stability of ANPP. This study provided valuable information for better restoring and managing the degraded temperate steppes
Plants Play Stronger Effects on Soil Fungal than Bacterial Communities and Co-Occurrence Network Structures in a Subtropical Tree Diversity Experiment
No full textIncreasing biodiversity loss profoundly affects community structure and ecosystem functioning. Therefore, revealing the mechanisms associated with community assembly and co-occurrence network structure of microbes along plant species diversity gradients is very important for understanding biodiversity maintenance and community stability in response to plant diversity loss. Increasing biodiversity loss profoundly affects community structure and ecosystem functioning. However, the differences in community assembly and potential drivers of the co-occurrence network structure of soil fungi and bacteria in association with tree species richness gradients are poorly documented. Here, we examined soil fungal and bacterial communities in a Chinese subtropical tree species richness experiment (from 1 to 16 species) using amplicon sequencing targeting the internal transcribed spacer 2 and V4 hypervariable region of the rRNA genes, respectively. Tree species richness had no significant effect on the diversity of either fungi or bacteria. In addition to soil and spatial distance, tree species richness and composition had a significant effect on fungal community composition but not on bacterial community composition. In fungal rather than bacterial co-occurrence networks, the average degree, degree centralization, and clustering coefficient significantly decreased, but the modularity significantly increased with increasing tree species richness. Fungal co-occurrence network structure was influenced by tree species richness and community composition as well as the soil carbon: nitrogen ratio, but the bacterial co-occurrence network structure was affected by soil pH and spatial distance. This study demonstrates that the community assembly and potential drivers of the co-occurrence network structure of soil fungi and bacteria differ in the subtropical forest. IMPORTANCE Increasing biodiversity loss profoundly affects community structure and ecosystem functioning. Therefore, revealing the mechanisms associated with community assembly and co-occurrence network structure of microbes along plant species diversity gradients is very important for understanding biodiversity maintenance and community stability in response to plant diversity loss. Here, we compared the differences in community assembly and potential drivers of the co-occurrence network structure of soil fungi and bacteria in a subtropical tree diversity experiment. In addition to soil and spatial distance, plants are more strongly predictive of the community and co-occurrence network structure of fungi than those of bacteria. The study highlighted that plants play more important roles in shaping community assembly and interactions of fungi than of bacteria in the subtropical tree diversity experiment
An Efficient Clearing Protocol for the Study of Seed Development in Tomato (Solanum lycopersicum L.)
No full textTomato (Solanum lycopersicum L.) is one of the major cash crops worldwide. The tomato seed is an important model for studying genetics and developmental biology during plant reproduction. Visualization of finer embryonic structure within a tomato seed is often hampered by seed coat mucilage, multi-cell-layered integument, and a thick-walled endosperm, which needs to be resolved by laborious embeddingsectioning. A simpler alternative is to employ tissue clearing techniques that turn the seed almost transparent using chemical agents. Although conventional clearing procedures allow deep insight into smaller seeds with a thinner seed coat, clearing tomato seeds continues to be technically challenging, especially in the late developmental stages. Presented here is a rapid and labor-saving clearing protocol to observe tomato seed development from 3 to 23 days after flowering when embryonic morphology is nearly complete. This method combines chloral hydrate-based clearing solution widely used in Arabidopsis with other modifications, including the omission of Formalin-Aceto-Alcohol (FAA) fixation, the addition of sodium hypochlorite treatment of seeds, removal of the softened seed coat mucilage, and washing and vacuum treatment. This method can be applied for efficient clearing of tomato seeds at different developmental stages and is useful in full monitoring of the developmental process of mutant seeds with good spatial resolution. This clearing protocol may also be applied to deep imaging of other commercially important species in the Solanaceae
Biotic colonization of subtropical East Asian caves through time
No full textCaves are home to unique and fragile biotas with high levels of endemism. However, little is known about how the biotic colonization of caves has developed over time, especially in caves from middle and low latitudes. Subtropical East Asia holds the world's largest karst landform with numerous ancient caves, which harbor a high diversity of cave-dwelling organisms and are regarded as a biodiversity hotspot. Here, we assess the temporal dynamics of biotic colonization of subtropical East Asian caves through a multi-taxon analysis with representatives of green plants, animals, and fungi. We then investigate the consequences of paleonviromental changes on the colonization dynamics of these caves in combination with reconstructions of vegetation, temperature, and precipitation. We discover that 88% of cave colonization events occurred after the Oligocene-Miocene boundary, and organisms from the surrounding forest were a major source for subtropical East Asian cave biodiversity. Biotic colonization of subtropical East Asian caves during the Neogene was subject to periods of acceleration and decrease, in conjunction with large-scale, seasonal climatic changes and evolution of local forests. This study highlights the long-term evolutionary interaction between surface and cave biotas; our climate-vegetation-relict model proposed for the subtropical East Asian cave biota may help explain the evolutionary origins of other mid-latitude subterranean biotas
Autophagy targets Hd1 for vacuolar degradation to regulate rice flowering
No full textFlowering time (heading date) is a critical agronomic trait that determines the yield and regional adaptability of crops. Heading date 1 (Hd1) is a central regulator of photoperiodic flowering in rice (Oryza sativa). Howev-er, how the homeostasis of Hd1 protein is achieved is poorly understood. Here, we report that the nuclear autophagy pathway mediates Hd1 degradation in the dark to regulate flowering. Loss of autophagy function results in an accumulation of Hd1 and delays flowering under both short-day and long-day conditions. In the dark, nucleus-localized Hd1 is recognized as a substrate for autophagy and is subjected to vacuolar degra-dation via the autophagy protein OsATG8. The Hd1-OsATG8 interaction is required for autophagic degrada-tion of Hd1 in the dark. Our study reveals a new mechanism by which Hd1 protein homeostasis is regulated by autophagy to control rice flowering. Our study also indicates that the regulation of flowering by autophagic degradation of Hd1 orthologs may have arisen over the course of mesangiosperm evolution, which would have increased their flexibility and adaptability to the environment by modulating flowering time
Integrative species delimitation of Selaginella labordei and closely related species: Uncovering the mysterious identity of S. jugorum and S. tibetica, and description of a new species
No full textThe taxonomy of Selaginella has been historically problematic due to the indistinguishable morphological characters within species complexes. The S. labordei group contains (S. subg. Stachygynandrum) 4-7 species, distributed from the Himalayas to eastern China. The taxonomy of this group was problematic due to few collections that were available to delimitate S. jugorum and S. tibetica, and large variation of the widely distributed S. labordei in different ecological conditions. Here, we re-evaluate the species delimitation of the S. labordei group using morphological, molecular and cytological data. A total of 55 individuals representing five species of the S. labordei group were investigated using two nuclear markers (26S rDNA, pgiC), one plastid marker (rbcL), as well as 43 plastid-coding sequences obtained from assembled plastid genomes. Five species are recognized based on the phylogenetic analysis of nuclear genes and plastid-coding sequences. The plastid genomes phylogeny showed a good resolution at lower taxonomic levels. All the individuals of the broadly defined S. labordei formed a monophyletic group in our analyses of different datasets. However, samples of S. chrysocaulos were strongly supported as non-monophyletic and were divided into two clades. One clade of S. chrysocaulos is described as a new species, Selaginella parachrysocaulos sp. nov., which is a cryptic species morphologically almost indistinguishable from S. chrysocaulos but with the microspores covered by a honeycomb-like network microstructure. The nuclear pgiC phylogeny and flow cytometry evidence indicate that some individuals of S. parachrysocaulos may be derived from polyploidization. Based on molecular and morphological evidence, S. sichuanica and S. daozhenensis are treated as synonymous to S. labordei, and S. hengduanshanicola to S. tibetica. Our results uncover the previously mysterious affinities of S. jugorum and S. tibetica, which are members of the S. labordei group
Differential linkages between soil respiration components and microbial community structures under long-term forest conversion
No full textPurpose Soil respiration (Rs) can be significantly impacted by land-use change (LUC). This study aimed to determine the response of Rs components (i.e., heterotrophic respiration (Rh) and autotrophic respiration (Ra)) to long-term forest conversion and explore their associations with soil microbial community (SMC) structures. Materials and methods Three plantations converted from natural forest 36 years ago were investigated: Cryptomeria fortune (CF), Cunninghamia lanceolata (CL), and Metasequoia glyptostroboides (MG), with the control of an adjacent natural forest (NF). In each forest site, Rh and Ra were measured using the root trenching method during the growing season. SMC structures in trenched and rhizosphere soils (0-10 cm depth) were analyzed. Results We observed an evident differentiation between SMC structures in trenched and rhizosphere soils across forest types. SMC structural dynamic in trenched soil was primarily driven by the ratio of dissolved organic carbon (c) to dissolved organic nitrogen (DON) and bulk density, whereas that in rhizosphere soil was primarily driven by DON and pH. During the growing season, both Rh and Ra were greater in MG than in NF, but they showed non-significant differences among NF, CF, and CL. The Rh pattern was primarily modified by the SMC structure (e.g., arbuscular mycorrhizal fungi (AMF)) and soil temperature, whereas the Ra pattern was primarily modified by the SMC structure in rhizosphere soil (e.g., gram-positive bacteria (GP)) in addition to fine root quality and soil temperature. Conclusions Rh and Ra patterns were jointly modified by SMC structure and microenvironment over long-term forest conversion, emphasizing the underlying roles of plant community attributes and forest management in soil C emission into the atmosphere
Climatic niche comparisons of eastern North American and eastern Asian disjunct plant genera
No full textAim While the floras of eastern Asia (EA) and eastern North America (ENA) share numerous genera, they have drastically different species richness. Despite an overall similarity in the quality of their temperate climates, the climate of EA is more spatially heterogeneous than that of ENA. Spatial environmental heterogeneity has been found to play a key role in influencing species richness in some regions. Here, we tested the following hypotheses: (a) EA species will occupy larger climatic niches than their ENA congeners, (b) congeners of EA-ENA disjunct genera will occupy statistically equivalent climatic niches, and (c) congeners of EA-ENA disjunct genera will occupy more similar climatic niches than expected by their respective physiographic context. Location North America and Asia. Time period Present. Major taxa studied Seed plants. Methods Predictions generated by ecological niche models (ENMs) were compared for 88 species across 31 EA-ENA disjunct genera. ENM predictions were assessed for geographic and ecological breadth. Tests for niche equivalency and similarity were performed for congeneric species pairs to determine if species of disjunct genera have experienced niche conservatism or divergence. Results EA species tend to occupy greater amounts of climatic niche space than their close relatives in ENA. Over two-thirds of the conducted niche comparisons show that EA-ENA congeners either occupy equivalent climatic niche space within these broader climatic regimes or occupy non-equivalent niches that are as similar as expected given their physiographic contexts. Main conclusions EA species tend to occupy larger climatic niches, and congeners of EA-ENA disjunct genera tend to occupy equivalent/similar niche space within their respective distributions, with differences in occupied niches possibly due to their respective physiographic contexts, highlighting how niche-neutral processes and niche conservatism may affect the distributions of disjunct species
Exploring key developmental phases and phase-specific genes across the entirety of anther development in maize
No full textAnther development from stamen primordium to pollen dispersal is complex and essential to sexual reproduction. How this highly dynamic and complex developmental process is controlled genetically is not well understood, especially for genes involved in specific key developmental phases. Here we generated RNA sequencing libraries spanning 10 key stages across the entirety of anther development in maize (Zea mays). Global transcriptome analyses revealed distinct phases of cell division and expansion, meiosis, pollen maturation, and mature pollen, for which we detected 50, 245, 42, and 414 phase-specific marker genes, respectively. Phase-specific transcription factor genes were significantly enriched in the phase of meiosis. The phase-specific expression of these marker genes was highly conserved among the maize lines Chang7-2 and W23, indicating they might have important roles in anther development. We explored a desiccation-related protein gene, ZmDRP1, which was exclusively expressed in the tapetum from the tetrad to the uninucleate microspore stage, by generating knockout mutants. Notably, mutants in ZmDRP1 were completely male-sterile, with abnormal Ubisch bodies and defective pollen exine. Our work provides a glimpse into the gene expression dynamics and a valuable resource for exploring the roles of key phase-specific genes that regulate anther development