Soil metatranscriptome demonstrates a shift in C, N, and S metabolisms of a grassland ecosystem in response to elevated atmospheric CO2

Hormonal and transcriptomic regulation of drought adaptation in barley roots and leaves

Drought poses a significant threat to global crop productivity and food security. In this study, we aimed to elucidate the impact of drought on transcriptional regulation and alternative splicing in barley (Hordeum vulgare), and to determine whether these transcriptomic alterations correlate with changes in hormonal profiles. We hypothesized that drought stress induces extensive reprogramming of gene expression, including alternative splicing events, and that these molecular responses are accompanied by tissue-specific shifts in hormone levels, ultimately underpinning adaptive responses in both leaves and roots. To test this, we performed RNA-seq and comprehensive hormone profiling on leaves and roots sampled at 25 days after planting under both optimal and drought conditions. Our analysis identified over 6,655 differentially expressed genes, with a substantial subset exhibiting differential alternative splicing. In leaves, drought primarily downregulated photosynthesis-related genes while upregulating pathways involved in water stress and abscisic acid (ABA) signaling. In contrast, roots displayed broader metabolic adjustments and significant isoform switching. Hormone analysis revealed marked ABA accumulation, particularly in roots, alongside organ-specific modulation of jasmonates and auxins. A limited assessment of the rhizosphere microbial community revealed low transcript abundance, underscoring the primacy of intrinsic plant responses. Collectively, these findings provide valuable insights into the multilayered adaptive strategies of barley under drought stress.

Metagenomics and plant-microbe symbioses: Microbial community dynamics, functional roles in carbon sequestration, nitrogen transformation, sulfur and phosphorus mobilization for sustainable soil health

Biogeochemical cycles are fundamental processes that regulate the flow of essential elements such as carbon, nitrogen, and phosphorus, sustaining ecosystem productivity and global biogeochemical equilibrium. These cycles are intricately influenced by plant-microbe symbioses, which facilitate nutrient acquisition, organic matter decomposition, and the transformation of soil nutrients. Through mutualistic interactions, plants and microbes co-regulate nutrient availability and promote ecosystem resilience, especially under environmental stress. Metagenomics has emerged as a transformative tool for deciphering the complex microbial communities and functional genes driving these cycles. By enabling the high-throughput sequencing and annotation of microbial genomes, metagenomics provides unparalleled insights into the taxonomic diversity, metabolic potential, and functional pathways underlying microbial contributions to biogeochemical processes. Unlike previous reviews, this work integrates recent advancements in metagenomics with complementary omics approaches to provide a comprehensive perspective on how plant-microbe interactions modulate biogeochemical cycles at molecular, genetic, and ecosystem levels. By highlighting novel microbial processes and potential biotechnological applications, this review aims to guide future research in leveraging plant-microbe symbioses for sustainable agriculture, ecosystem restoration, and climate change mitigation.

Impact of elevated CO2 on microbial communities and functions in riparian sediments: Role of pollution levels in modulating effects

The impact of elevated CO2 levels on microorganisms is a focal point in studying the environmental effects of global climate change. A growing number of studies have demonstrated the importance of the direct effects of elevated CO2 on microorganisms, which are confounded by indirect effects that are not easily identified. Riparian zones have become key factor in identifying the environmental effects of global climate change because of their special location. However, the direct effects of elevated CO2 levels on microbial activity and function in riparian zone sediments remain unclear. In this study, three riparian sediments with different pollution risk levels of heavy metals and nutrients were selected to explore the direct response of microbial communities and functions to elevated CO2 excluding plants. The results showed that the short-term effects of elevated CO2 did not change the diversity of the bacterial and fungal communities, but altered the composition of their communities. Additionally, differences were observed in the responses of microbial functions to elevated CO2 levels among the three regions. Elevated CO2 promoted the activities of nitrification and denitrification enzymes and led to significant increases in N2O release in the three sediments, with the greatest increase of 76.09 % observed in the Yuyangshan Bay (YYS). Microbial carbon metabolism was promoted by elevated CO2 in YYS but was significantly inhibited by elevated CO2 in Gonghu Bay and Meiliang Bay. Moreover, TOC, TN, and Pb contents were identified as key factors contributing to the different microbial responses to elevated CO2 in sediments with different heavy metal and nutrient pollution. In conclusion, this study provides in-depth insights into the responses of bacteria and fungi in polluted riparian sediments to elevated CO2, which helps elucidate the complex interactions between microbial activity and environmental stressors.

Sulfate-reducing bacteria unearthed: ecological functions of the diverse prokaryotic group in terrestrial environments

Sulfate-reducing prokaryotes (SRPs) are essential microorganisms that play crucial roles in various ecological processes. Even though SRPs have been studied for over a century, there are still gaps in our understanding of their biology. In the past two decades, a significant amount of data on SRP ecology has been accumulated. This review aims to consolidate that information, focusing on SRPs in soils, their relation to the rare biosphere, uncultured sulfate reducers, and their interactions with other organisms in terrestrial ecosystems. SRPs in soils form part of the rare biosphere and contribute to various processes as a low-density population. The data reveal a diverse range of sulfate-reducing taxa intricately involved in terrestrial carbon and sulfur cycles. While some taxa like Desulfitobacterium and Desulfosporosinus are well studied, others are more enigmatic. For example, members of the Acidobacteriota phylum appear to hold significant importance for the terrestrial sulfur cycle. Many aspects of SRP ecology remain mysterious, including sulfate reduction in different bacterial phyla, interactions with bacteria and fungi in soils, and the existence of soil sulfate-reducing archaea. Utilizing metagenomic, metatranscriptomic, and culture-dependent approaches will help uncover the diversity, functional potential, and adaptations of SRPs in the global environment.

Rhizosphere and detritusphere habitats modulate expression of soil N-cycling genes during plant development

IMPORTANCE

Plant roots modulate microbial nitrogen (N) cycling by regulating the supply of root-derived carbon and nitrogen uptake. These differences in resource availability cause distinct micro-habitats to develop: soil near living roots, decaying roots, near both, or outside the direct influence of roots. While many environmental factors and genes control the microbial processes involved in the nitrogen cycle, most research has focused on single genes and pathways, neglecting the interactive effects these pathways have on each other. The processes controlled by these pathways determine consumption and production of N by soil microorganisms. We followed the expression of N-cycling genes in four soil microhabitats over a period of active root growth for an annual grass. We found that the presence of root litter and living roots significantly altered gene expression involved in multiple nitrogen pathways, as well as tradeoffs between pathways, which ultimately regulate N availability to plants.

Soil organic carbon stability and exogenous nitrogen fertilizer influence the priming effect of paddy soil under long-term exposure to elevated atmospheric CO2

Soil organic carbon (SOC) stability and dynamics are greatly influenced by long-term elevated atmospheric CO2 [CO2]. The priming effect (PE) is vital in SOC stability and dynamics, but its role in paddy soil under long-term elevated [CO2] remains unclear. To examine how SOC stability changed in paddy soil after long-term elevated atmospheric CO2 enrichment, the PE was quantified through a 13C-glucose-induced experiment with different N levels for topsoil (0-20 cm) from paddy free-air CO2 enrichment (FACE) platform. Compared with the ambient CO2 concentration ([CO2]), 10 years of elevated [CO2] (500 µmol·mol-1) significantly increased SOC and TN content by 18.4% and 19.0%, respectively, while the C/N ratio was not changed. The labile C fractions including dissolved organic carbon (DOC) and readily oxidizable organic carbon (ROC), but excluding microbial biomass C (MBC), accumulated faster than SOC in paddy soil, which implied the reduced SOC stability for long-term elevated [CO2] enrichment. With the decline of SOC stability, the exogenously induced cumulative specific PE (PE per gram of SOC) remarkably increased by 41.1-72.7% for elevated [CO2] fumigation. The cumulative PE, especially the cumulative specific PE, was found significantly linearly correlated with the ROC content or ROC/SOC ratio (labile SOC pool). Furthermore, the application of nitrogen fertilizer slowed down the PE under elevated [CO2] condition. Our results showed that long-term elevated [CO2] enrichment reduced SOC stability and, together with exogenous nitrogen fertilizer, regulated the PE in paddy soil.