Search Results (820)

Rhizosphere microbiota are key drivers of plant nutrition, immunity, and stress tolerance. Abies ziyuanensis L. K. Fu & S. L. Mo (Pinaceae) is an endangered conifer endemic to China, and its persistence may depend on its interactions with its belowground microbiome. However, how soil-borne bacterial functional groups respond to, and potentially support, A. ziyuanensis remains unclear. Based on amplicon high-throughput sequencing data of the 16S rRNA gene and soil physicochemical properties, the bacterial community structure in the rhizosphere soil of A. ziyuanensis in Yinzhu Laoshan National Nature Reserve in Guangxi Zhuang Autonomous Region, China, was analyzed, and the potential ecological functions and phenotypic characteristics of the bacterial community were predicted to determine the functional taxa characteristics (nitrogen cycle, phototrophy, and chemoheterotrophy) and dominant soil environmental factors. Proteobacteria, Acidobacteria, Actinobacteria, Planctomycetes, Verrucomicrobia, and Chloroflexi were the dominant bacterial taxa in the A. ziyuanensis rhizosphere soil, and all bacteria were significantly positively correlated with soil NO₃⁻-N (R = 0.47, p = 0.0079). Based on FAPROTAX, the A. ziyuanensis rhizosphere soil bacterial community had chemoheterotrophic-related functions, which were more prevalent than nitrogen cycle- and phototrophic-related functions, and the relative abundance of bacteria with nitrogen cycle-related functions was higher than that of those with phototrophic functions. The nitrogen nutrient- and phototrophic-related functional taxa in the rhizosphere soil bacterial community had significant correlations with soil physicochemical properties, whereas the chemoheterotrophic-related functional taxa did not show a significant correlation. Based on BugBase phenotype prediction, Acidobacteria, Proteobacteria, and Chloroflexi made the greatest contribution to the phenotype, with pathogenic and stress tolerance being the most important phenotypes. The pathogenic and stress-tolerant bacteria all belonged to Proteobacteria. The rhizosphere bacteria exhibited rich diversity and dominated several biogeochemical cycling processes. This study identifies beneficial rhizosphere bacteria of A. ziyuanensis, providing a theoretical basis for conserving soil bacterial diversity and guiding the targeted recruitment of functional bacteria by the endangered plant. Full article

Phytoplankton plays a pivotal role in marine ecosystems and global biogeochemical cycles. Accurate identification and monitoring of phytoplankton are essential for understanding environmental dynamics and climate variations. Despite the significant progress made in automatic phytoplankton identification, current datasets predominantly consist of idealized laboratory images, leading to models that demonstrate persistent limitations in the fine-grained differentiation of phytoplankton species. To achieve high accuracy and transferability for morphologically similar species and diverse ecosystems, we introduce a hybrid dataset by integrating laboratory-based observations with in situ marine environmental data. We evaluate the performance of our dataset on contemporary deep learning models, revealing that CNN-based architectures offer superior stability (85.27% mAcc., 93.76% oAcc.). Multimodal learning facilitates refined phytoplankton recognition through the integration of visual and textual representations, thereby enhancing the model’s semantic comprehension capabilities. We present a fine-tuned visual language model leveraging enhanced textual prompts augmented with expert-annotated morphological descriptions, significantly enhancing visual-semantic alignment and allowing for more accurate and interpretable recognition of closely related species (84.11% mAcc., 94.48% oAcc.). Our research establishes a benchmark dataset that facilitates real-time ecological monitoring and aquatic biodiversity research. Furthermore, it also contributes to the field by enhancing model robustness and transferability to diverse environmental contexts and taxonomically similar species. Full article

Integrating renewable energy requires robust, large-scale storage solutions to balance intermittent supply. Underground hydrogen storage (UHS) in geological formations, such as salt caverns, depleted hydrocarbon reservoirs, or aquifers, offers a promising way to store large volumes of energy for seasonal periods. This review focuses on the biological aspects of UHS, examining the biogeochemical interactions between H₂, reservoir minerals, and key hydrogenotrophic microorganisms such as sulfate-reducing bacteria, methanogens, acetogens, and iron-reducing bacteria within the gas–liquid–rock–microorganism system. These microbial groups use H₂ as an electron donor, triggering biogeochemical reactions that can affect storage efficiency through gas loss and mineral dissolution–precipitation cycles. This review discusses their metabolic pathways and the geochemical interactions driven by microbial byproducts such as H₂S, CH₄, acetate, and Fe²⁺ and considers biofilm formation by microbial consortia, which can further change the petrophysical reservoir properties. In addition, the review maps 76 ongoing European projects focused on UHS, showing 71% target salt caverns, 22% depleted hydrocarbon reservoirs, and 7% aquifers, with emphasis on potential biogeochemical interactions. It also identifies key knowledge gaps, including the lack of in situ kinetic data, limited field-scale monitoring of microbial activity, and insufficient understanding of mineral–microbe interactions that may affect gas purity. Finally, the review highlights the need to study microbial adaptation over time and the influence of mineralogy on tolerance thresholds. By analyzing these processes across different geological settings and integrating findings from European research initiatives, this work evaluates the impact of microbial and geochemical factors on the safety, efficiency, and long-term performance of UHS. Full article

Indonesia has 13.43 million hectares of tropical peatlands, the largest in Southeast Asia, which are crucial for carbon sequestration. This function is influenced by vegetation nutrient content, particularly carbon (C), nitrogen (N), phosphorus (P), and potassium (K), which regulate biogeochemical cycles and peat formation. This study analyzed stoichiometric profiles of tree species in South Sumatra peatlands based on (1) C:N ratios across roots, stems, twigs, and leaves, and identified species with traits associated with high carbon sequestration potential, and (2) leaf N:P:K stoichiometry to infer nutrient limitations. Research was conducted in a 1-hectare primary peatland plot within the PT. Tri Pupa Jaya conservation area. C, N, P, and K contents were measured using Kjeldahl distillation, spectrophotometry, flame photometry, and the Walkley–Black method following acid digestion. Stoichiometric distribution was visualized with violin-box plots and species grouped through hierarchical clustering. Among 153 identified species, stems showed the highest mean C:N ratio (314.9 ± 210.8), while leaves had the lowest (29.7 ± 13.0). Species were grouped into three clusters by C:N ratios across four organs, with six in clusters 1 and 2 showing high carbon sequestration potential. Leaf N:P:K stoichiometry suggested nitrogen, phosphorus, or combined N + P limitations. Full article

Plastic debris has become a persistent feature of deep-sea ecosystems, yet its role as a habitat for calcifying organisms remains poorly understood. Foraminifera colonization has been observed in significant numbers on plastic surfaces, suggesting that these materials serve as novel and significant deep-sea colonization sites for these abundant calcifying organisms. This study uses deep-sea experimental plastic substrates to examine the colonization and reproductive morphology of the benthic foraminifera Lobatula wuellerstorfi across three locations: Station M (4000 m), Oregon OOI (575 m), and Southern Hydrate Ridge (774 m). A total of 482 individuals were analyzed for morphometric traits, including proloculus diameter, to investigate reproductive morphotypes. The Oregon samples displayed a clear bimodal proloculus size distribution, consistent with alternating reproductive strategies, while Station M populations exhibited a broader, less defined bimodal distribution skewed toward megalospheric forms. A weak but significant increase in proloculus diameter over deployment duration was observed at Station M, suggesting a possible influence of experiment duration and/or substrate maturity and environmental conditions. These findings demonstrate that plastics can serve as persistent colonization sites for deep-sea foraminifera, offering a unique experimental platform to investigate benthic population dynamics, ecological plasticity, and potential geochemical implications, as well as the broader impacts of foraminifera on deep-sea biodiversity and biogeochemical cycling. Full article

Iron, an essential element for virtually all known organisms, serves not only as a micronutrient but also as an energy source for bacteria. Iron-oxidizing microorganisms mediate Fe(II) oxidation under diverse redox conditions, yielding amorphous iron (hydr)oxides or crystalline iron minerals. This globally significant biogeochemical process drives modern iron cycling across terrestrial and aquatic ecosystems. The resulting biomineralization not only produces secondary minerals but also effectively immobilizes heavy metals, offering a sustainable strategy for environmental remediation. This review systematically examines (1) the biogeochemical mechanisms and mineralogical signatures of Fe(II) oxidation by four distinct iron oxidizers: acidophilic aerobes (e.g., Acidithiobacillus), neutrophilic microaerophiles (e.g., Gallionella), nitrate-reducing anaerobes (e.g., Acidovorax), and anoxygenic phototrophs (e.g., Rhodobacter); (2) research advances in heavy metal immobilization by biogenic iron minerals: adsorption, coprecipitation, and structural incorporation; and (3) the impact of pH, temperature, organic matter, and coexisting ions on Fe(II) oxidation efficiency and iron mineral formation by iron-oxidizing bacteria. By characterizing iron-oxidizing bacterial species and their functional processes under varying pH and redox conditions, this study provides critical insights into microbial behaviors driving the evolution of acid mine drainage (AMD). Full article

Groundwater, a critical source of drinking water, plays an essential role in global biogeochemical cycles, yet its microbial ecosystems remain insufficiently characterized, particularly in pristine karst aquifers. This study conducted high-resolution profiling of microbial communities and environmental parameters in two representative alpine karst aquifers in Slovenia: Idrijska Bela and Krajcarca. Monthly groundwater samples from the Krajcarca spring and Idrijska Bela borehole over a 14-month period were analyzed using whole-metagenome sequencing (WMS), UV-Vis spectroscopy, inductively coupled plasma mass spectrometry (ICP-MS), and isotopic analysis. The results revealed stable hydrochemical conditions with clear spatial differences driven by bedrock composition and groundwater residence time. Bacterial communities displayed strong correlations with hydrochemical parameters, while archaeal communities exhibited temporal stability. Functional gene profiles mirrored bacterial patterns, emphasizing the influence of environmental gradients on metabolic potential. No significant temporal changes were detected across two sampling campaigns (2016–2023), highlighting the resilience of these aquifers. This work establishes a valuable baseline for understanding pristine groundwater microbiomes and informs future monitoring and water quality management strategies. Full article

Microbial communities, as critical functional components of riverine ecosystems, play a pivotal role in biogeochemical cycles and water quality regulation. The South-to-North Water Diversion Middle Route Project (SNWD-MRP) is a major cross-basin water transfer initiative, and bacteria are essential for the stability of water quality in the project. This study employed environmental DNA (eDNA) metabarcoding targeting the 16S rRNA gene to investigate spatiotemporal variations in water quality and bacterial communities along the SNWD-MRP during summer and winter. Integrated analyses, including redundancy analysis (RDA), Mantel tests, and ecological network modeling, were applied to unravel the driving mechanisms of microbial succession. The water quality along the SNWD-MRP is generally classified as Grade I, with significant seasonal variations in water quality parameters and microbial community composition. In the summer, higher temperatures lead to an increased abundance of cyanobacteria. In contrast, during the winter, lower water temperatures and higher dissolved oxygen levels result in the dominance of Pseudomonas and Bacillota species. RDA identified the permanganate index as the primary driver of microbial composition across seasons, with total phosphorus and total nitrogen having a greater influence in winter. Mantel tests highlighted significant correlations between Cyanobacteria and total phosphorus during winter. Ecological network analysis revealed that the complexity and connectivity of the winter network increased, likely due to suitable nutrient levels rendering the microbial network more complex and stable. These findings underscore the synergistic effects of temperature and nutrient availability on microbial succession, providing actionable insights for optimizing water quality management and ecological stability in large-scale water diversion systems. Full article

Base Mine Lake (BML) is the first full-scale demonstration of water-capped tailing technology in a pit lake to reclaim lands impacted by surface mining in the Alberta Oil Sands Region (AOSR). Biogeochemical cycling and/or exchange near the fluid water interface (FWI) of the organic-rich fluid fine tailings (FFT) can hinder the reclamation process. To monitor this activity, sedimentary depth profiles were collected from three platforms (P1 to P3) at BML. Seventy-four chromatographically well-resolved petroleum hydrocarbon (PHC) isomers were quantified at each depth interval using comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry (GC × GC/TOFMS). The range of total concentrations of all isomers examined across the FFT was the highest at P1 (range = 3.6 × 10⁰–5.5 × 10³ ng/g TOC), second highest at P2 (range = 3.8 × 10⁰–1.9 × 10³ ng/g TOC), and lowest at P3 (range = 5.6 × 10⁰–7.1 × 10² ng/g TOC). The elevated levels of the same isomers across platforms suggest a consistent source fingerprint. While the source fingerprint was mostly consistent across the platforms and depths, Principal Component Analysis (PCA) identified small differences between geospatial locations caused by variations in specific isomer concentrations. Hierarchical Clustering Analysis (HCA) identified the isomers responsible for the PCA separation, showing that the concentrations of low-molecular-weight n-alkanes (C11–C13) and drimane varied compared to the heavier PHCs with depth. These alkanes are the most biodegradable of the compounds identified in this study, and their variations may reflect biogeochemical cycling within the FFT. Combining these statistical tools provided deeper insight into how isomer concentrations vary with depth, helping to identify possible influences like changing inputs, biogeochemical cycling, and species exchange with the water column. Full article

Soil organic matter (SOM) decomposition is a critical biogeochemical process that regulates the carbon cycle, nutrient availability, and agricultural sustainability of cropland systems. Recent progress in multi-omics and microbial network analyses has provided us with a better understanding of the decomposition process at different spatial and temporal scales. Climate factors, such as temperature and seasonal variations in moisture, play a critical role in microbial activity and enzyme kinetics, and their impacts are mediated by soil physical and chemical properties. Soil mineralogy, texture, and structure create different soil microenvironments, affecting the connectivity of microbial habitats, substrate availability, and protective mechanisms of organic matter. Moreover, different microbial groups (bacteria, fungi, and archaea) contribute differently to the decomposition of plant residues and SOM. Recent findings suggest the paramount importance of living microbial communities as well as necromass in forming soil organic carbon pools. Microbial functional traits such as carbon use efficiency, dormancy, and stress tolerance are essential drivers of decomposition in the soil. Furthermore, the role of microbial necromass, alongside live microbial communities, in the formation and stabilization of persistent SOM fractions is increasingly recognized. Based on this microbial perspective, feedback between local microbial processes and landscape-scale carbon dynamics illustrates the cross-scale interactions that drive agricultural productivity and regulate soil climate. Understanding these dynamics also highlights the potential for incorporating microbial functioning into sustainable agricultural management, which offers promising avenues for increasing carbon sequestration without jeopardizing soil nutrient cycling. This review explores current developments in intricate relationships between climate, soil characteristics, and microbial communities determining SOM decomposition, serving as a promising resource in organic fertilization and regenerative agriculture. Specifically, we examine how nutrient availability, pH, and oxygen levels critically influence these microbial contributions to SOM stability and turnover. Full article

Microbial carbon use efficiency (CUE) is an important indicator of soil organic carbon accumulation and loss and a key parameter in biogeochemical cycling models. Its regulatory mechanism is highly dependent on microbial communities and their dynamic mediation of abiotic factors. Land-use change (e.g., agricultural expansion, deforestation, urbanization) profoundly alter carbon input patterns and soil physicochemical properties, further exacerbating the complexity and uncertainty of CUE. Existing carbon cycle models often neglect microbial ecological processes, resulting in an incomplete understanding of how microbial traits interact with environmental factors to regulate CUE. This paper provides a comprehensive review of the microbial regulation mechanisms of CUE under land-use change and systematically explores how microorganisms drive organic carbon allocation through community compositions, interspecies interactions, and environmental adaptability, with particular emphasis on the synergistic response between microbial communities and abiotic factors. We found that the buffering effect of microbial communities on abiotic factors during land-use change is a key factor determining CUE change patterns. This review not only provides a theoretical framework for clarifying the microbial-dominated carbon turnover mechanism but also lays a scientific foundation for the precise implementation of sustainable land management and carbon neutrality goals. Full article

Rare earth elements and yttrium (REY) are critical metals underpinning high-technology industries. Marine deposits have attracted growing interest due to their abundant REY reserves and high grades. This review synthesizes current knowledge on sources, distribution, and enrichment mechanisms of marine REY, with a particular focus on the role of microorganisms in REY phase transitions, fractionation, and enrichment. We highlight the largely untapped potential of marine-specific microbial strains and critically assess their influence on REY cycling. Key research challenges are proposed, followed by actionable directions to advance understanding of microbial–REY interactions. This review aims to deepen insights into marine REY cycling and support the sustainable development of deep-sea REY resources, emphasizing the need to integrate molecular-scale microbial processes into marine REY biogeochemical models. Full article

Soil bacteria drive biogeochemical cycles and influence disease suppression, playing pivotal roles in sustainable agriculture. Using Illumina MiSeq sequencing, we assessed how six ridge-furrow film mulching patterns affect soil bacterial diversity in a continuous potato system. The Shannon index showed significantly higher diversity in fully mulched treatments (T2–T3) versus controls (CK), suggesting mulching enhances microbial community richness. This result suggests that complete mulching combined with ridge planting (T2) may significantly enhance bacterial proliferation in soil. The bacterial communities were predominantly composed of Acidobacteria, Pseudomonadota, Bacteroidota, Chloroflexota, and Planctomycetota. Among these, Acidobacteria showed the highest abundance, with ridge planting patterns favoring greater Acidobacteria richness compared to furrow planting. In contrast, Pseudomonadota exhibited higher abundance under half-mulching conditions than under complete mulching. At class level, Acidobacteria and Proteobacteria emerged as the most abundant groups, with Proteobacteria constituting 22.6–35.7% of total microbial populations. Notably, Proteobacteria demonstrated particular dominance under the complete mulching with ridge planting pattern (T2). At the genus level, Subgroup_6_norank represented the most dominant taxon among the 439 identified bacterial genera, accounting for 14.0–20.2% of communities across all treatments, with half-mulching ridge planting (T4) showing the highest relative abundance. Our findings demonstrate that different ridge-furrow film mulching patterns significantly influence soil microbial diversity. While traditional non-mulched (CK) and mulched flat plots (T1) exhibited similar impacts on bacterial community structure, other treatments displayed distinct taxonomic profiles. Complete mulching patterns, particularly ridge planting (T2), appear most conducive to microbial development, suggesting their potential to enhance soil biogeochemical cycling in continuous cropping systems. These results provide valuable insights for optimizing mulching practices to improve soil health in agricultural ecosystems. Full article

This article presents a review of several non-exclusive pathways for the sequestration of soil organic carbon, which can be classified into two large classical groups: the modification of plant and microbial macromolecules and the abiotic and microbial neoformation of humic substances. Classical studies have established a causal relationship between aromatic structures and the stability of soil humus (traditional hypotheses regarding lignin and aromatic microbial metabolites as primary precursors for soil organic matter). However, further evidence has emerged that underscores the significance of humification mechanisms based solely on aliphatics. The precursors may be carbohydrates, which may be transformed by the effects of fire or catalytic dehydration reactions in soil. Furthermore, humic-type structures may be formed through the condensation of unsaturated fatty acids or the alteration of aliphatic biomacromolecules, such as cutins, suberins, and non-hydrolysable plant polyesters. In addition to the intrinsic value of understanding the potential for carbon sequestration in diverse soil types, biogeochemical models of the carbon cycle necessitate the assessment of the total quantity, nature, provenance, and resilience of the sequestered organic matter. This emphasises the necessity of applying specific techniques to gain insights into their molecular structures. The application of appropriate analytical techniques to soil organic matter, including sequential chemolysis or thermal degradation combined with isotopic analysis and high-resolution mass spectrometry, derivative spectroscopy (visible and infrared), or ¹³C magnetic resonance after selective degradation, enables the simultaneous assessment of the concurrent biophysicochemical stabilisation mechanisms of C in soils. Full article

Inland waters, serving as crucial carbon sinks and pivotal conduits within the global carbon cycle, are essential targets for carbon assessment under global warming and carbon neutrality initiatives. However, the extensive spatial distribution and inherent sampling challenges pose fundamental difficulties for monitoring dissolved organic carbon (DOC) in these systems. Since 2010, remote sensing has catalyzed a technological revolution in inland water DOC monitoring, leveraging its advantages for rapid, cost-effective long-term observation. In this critical review, we systematically evaluate research progress over the past two decades to assess the performance of remote sensing products and existing methodologies in DOC retrieval. We provide a detailed examination of diverse remote sensing data sources, outlining their application characteristics and limitations. By tracing uncertainties in retrieval outcomes, we identify atmospheric correction, spatial heterogeneity, and model and data deficiencies as primary sources of uncertainty. Current retrieval approaches—direct, indirect, and machine learning (ML) methods—are thoroughly scrutinized for their features, effectiveness, and application contexts. While ML offers novel solutions, its application remains nascent, constrained by limited waterbody-specific samples and model constraints. Furthermore, we discuss current challenges and future directions, focusing on data optimization, feature engineering, and model refinement. We propose that future research should (1) employ integrated satellite–air–ground observations and develop tailored atmospheric correction for inland waters to reduce data noise; (2) develop deep learning architectures with branch networks to extract DOC’s intrinsic shortwave absorption and longwave anti-interference features; and (3) incorporate dynamic biogeochemical processes within study regions to refine retrieval frameworks using biogeochemical indicators. We also advocate for multi-algorithm collaborative prediction to overcome the spectral paradox and unphysical solutions arising from the single data-driven paradigm of traditional ML, thereby enhancing retrieval reliability and interpretability. Full article