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Wang, Shi

Publications and source records attributed to Wang, Shi.

10 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Multi-omics reveals nitrogen dynamics associated with soil microbial blooms during snowmelt

Snowmelt triggers a soil microbial bloom and crash that affects nitrogen (N) export in high-elevation watersheds. The mechanisms underlying these microbial dynamics are uncertain, making soil nitrogen processes difficult to predict as snowpack declines globally. Here, integration of genome-resolved metagenomics, metatranscriptomics and metabolomics in a high-elevation watershed revealed ecologically distinct soil microorganisms linked across the snowmelt time-period by their unique nitrogen cycling capacities. The molecular properties and transformations of dissolved organic N suggested that degradation or recycling of microbial biomass provided N for biosynthesis during the microbial bloom. Winter-adapted Bradyrhizobia spp. oxidized amino acids anaerobically and had the highest gene expression for denitrification during the microbial bloom. A pulse of nitrate was driven by spring-adapted Nitrososphaerales after snowmelt, but dissimilatory nitrate reduction to ammonia (DNRA) gene expression indicated significant nitrate retention potential. These findings inform our understanding of nitrogen cycling in environments sensitive to snowpack decline due to global change.

Sorensen, Patrick O↗
DOE OSTI2023

Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem

Background: Viruses impact nearly all organisms on Earth, including microbial communities and their associated biogeochemical processes. In soils, highly diverse viral communities have been identified, with a global distribution seemingly driven by multiple biotic and abiotic factors, especially soil temperature and moisture. However, our current understanding of the stability of soil viral communities across time and their response to strong seasonal changes in environmental parameters remains limited. Here, we investigated the diversity and activity of environmental soil DNA and RNA viruses, focusing especially on bacteriophages, across dynamics’ seasonal changes in a snow-dominated mountainous watershed by examining paired metagenomes and metatranscriptomes. Results: We identified a large number of DNA and RNA viruses taxonomically divergent from existing environmental viruses, including a significant proportion of fungal RNA viruses, and a large and unsuspected diversity of positive single-stranded RNA phages ( Leviviricetes ), highlighting the under-characterization of the global soil virosphere. Among these, we were able to distinguish subsets of active DNA and RNA phages that changed across seasons, consistent with a “seed-bank” viral community structure in which new phage activity, for example, replication and host lysis, is sequentially triggered by changes in environmental conditions. At the population level, we further identified virus-host dynamics matching two existing ecological models: “Kill-The-Winner” which proposes that lytic phages are actively infecting abundant bacteria, and “Piggyback-The-Persistent” which argues that when the host is growing slowly, it is more beneficial to remain in a dormant state. The former was associated with summer months of high and rapid microbial activity, and the latter with winter months of limited and slow host growth. Conclusion: Taken together, these results suggest that the high diversity of viruses in soils is likely associated with a broad range of host interaction types each adapted to specific host ecological strategies and environmental conditions. As our understanding of how environmental and host factors drive viral activity in soil ecosystems progresses, integrating these viral impacts in complex natural microbiome models will be key to accurately predict ecosystem biogeochemistry.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Ultrarapid crystallization of low-dimensional perovskite with excellent stability for future high-throughput fabrication

We report perovskite solar cells (PSCs) as an emerging photovoltaic technique have achieved exceptional power conversion efficiency (PCE) up to 25.7% after fast development over the past decade. But currently some critical issues are still not well addressed in terms of realizing large-scale fabrication, for example, fast fabrication of high-quality perovskite film with good stability. Here, we demonstrate the use of stable and fast-crystallizing low-dimensional (LD) perovskite thin films as the light absorber with only a 10 s annealing time at 250 °C, delivering a PCE of 18.16%. The crystallization and photoelectric properties of LD perovskite are well illustrated. The reduction in the annealing time will dramatically increase the productivity of PSCs. The PSCs based on rapidly annealed LD perovskite thin films exhibit excellent stability, with only 12% loss of PCE after 1000 h storage at 85 °C and 40-70% relative humidity.

14 SOLAR ENERGY↗
DOE OSTI2022

Alterations in soil pH emerge as a key driver of the impact of global change on soil microbial nitrogen cycling: Evidence from a global meta-analysis

Soil nitrogen (N) cycling is critical to the productivity of terrestrial ecosystems. However, the impact of global change factors (GCFs) on the microbial mediators of N cycling pathways has yet to be synthesized, and it also remains unclear whether the response of the abundance of N-cycling genes can predict changes in their corresponding processes. We synthesized 8322 paired observations of soil microorganisms related to N cycling from field experiments in which GCFs (climate change and nutrient addition) were manipulated. We found that the abundance of soil microbes and most N-cycling genes were resistant to elevated CO 2 , experimental warming and water addition/reduction; however, N addition and the combination of N addition with other GCFs significantly increased the abundance of ammonia oxidizer bacteria (amoA-AOB). The results indicated that in steady-state (natural) conditions, the main factors driving the global abundance of soil bacteria, archaea and N-cycling genes varied in terms of the contributions of climatic and edaphic factors. However, upon manipulation of GCFs, the induced change in soil pH was the most essential factor associated with changes in the abundance of soil microbes and N-cycling genes. Notably, the changes in ammonia-oxidizing archaea (amoA-AOA) and amoA-AOB genes, in addition to genes involved in denitrification (nirS and nirK), were significantly correlated with the rates of their corresponding processes, but GCF-induced shifts in the potential nitrification rate (PNR) were explained well by changes in the abundance of the amoA-AOB gene under GCFs. In conclusion, our study highlights how ongoing GCFs impact the abundance of soil microbes and N-cycling genes, which might have a profound impact on terrestrial N cycling. Our field-based results provide new insights into the drivers of the abundance of soil microbes and N-cycling genes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Risk assessment of engineering diseases of embankment–bridge transition section for railway in permafrost regions

Abstract The embankment–bridge transition section (EBTS) is one of the zones where railway diseases occur frequently in permafrost regions. Disease risk assessment of EBTSs can provide guidance for maintenance. In this study, considering the engineering geological conditions, climate characteristics, and embankment structure types along the Qinghai–Tibet Railway (QTR) as well as based on the disease inventory of the QTR from 2010 to 2019, the logistic regression (LR), support vector machine (SVM), and combination‐weight‐based gay relation analysis (GRA) were used for disease risk assessment of the EBTSs along the QTR in permafrost regions. The results indicate that the LR and SVM models have a better capability for EBTS disease prediction than the GRA model, and the SVM model can select more disease samples in relatively larger regions than the LR model. Based on the SVM and LR models, the risk level of EBTSs is divided into four classes: low‐ (29.9%), moderate‐ (39.6%), high‐ (22.1%), and very high (8.4%) risk. Finally, we selected 272 EBTSs in high‐ and very‐high‐risk classes for key observation during the maintenance of the QTR in permafrost regions. This study provides a reference for the risk assessment of railways built in permafrost regions using data‐driven methods.

Zhang, Saize↗
DOE OSTI2021

Microbial Phosphorus Mobilization Strategies Across a Natural Nutrient Limitation Gradient and Evidence for Linkage With Iron Solubilization Traits

Microorganisms have evolved several mechanisms to mobilize and mineralize occluded and insoluble phosphorus (P), thereby promoting plant growth in terrestrial ecosystems. However, the linkages between microbial P-solubilization traits and the preponderance of insoluble P in natural ecosystems are not well known. We tested the P solubilization traits of hundreds of culturable bacteria representative of the rhizosphere from a natural gradient where P concentration and bioavailability decline as soil becomes progressively more weathered. Aluminum, iron phosphate and organic P (phytate) were expected to dominate in more weathered soils. A defined cultivation medium with these chemical forms of P was used for isolation. A combination of soil chemical, spectroscopic analyses and 16S rRNA gene sequencing were used to understand the in situ ability for solubilization of these predominant forms of P. Locations with more occluded and organic P harbored the greatest abundance of P-mobilizing microorganisms, especially Burkholderiaceae ( Caballeronia and Paraburkholderia spp.). Nearly all bacteria utilized aluminum phosphate, however fewer could subsist on iron phosphate (FePO 4 ) or phytate. Microorganisms isolated from phytic acid were also most effective at solubilizing FePO 4 , suggesting that phytate solubilization may be linked to the ability to solubilize Fe. Significantly, we observed Fe to be co-located with P in organic patches in soil. Siderophore addition in lab experiments reinstated phytase mediated P-solubilization from Fe-phytate complexes. Taken together, these results indicate that metal-organic-P complex formation may limit enzymatic P solubilization from phytate in soil. Additionally, the linked traits of phytase and siderophore production were mostly restricted to specific clades within the Burkholderiaceae . We propose that Fe complexation of organic P (e.g., phytate) represents a major constraint on P turnover and availability in acidic soils, as only a limited subset of bacteria appear to possess the traits required to access this persistent pool of soil P.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Measurement of Volatile Compounds for Real-Time Analysis of Soil Microbial Metabolic Response to Simulated Snowmelt

Snowmelt dynamics are a significant determinant of microbial metabolism in soil and regulate global biogeochemical cycles of carbon and nutrients by creating seasonal variations in soil redox and nutrient pools. With an increasing concern that climate change accelerates both snowmelt timing and rate, obtaining an accurate characterization of microbial response to snowmelt is important for understanding biogeochemical cycles intertwined with soil. However, observing microbial metabolism and its dynamics non-destructively remains a major challenge for systems such as soil. Microbial volatile compounds (mVCs) emitted from soil represent information-dense signatures and when assayed non-destructively using state-of-the-art instrumentation such as Proton Transfer Reaction-Time of Flight-Mass Spectrometry (PTR-TOF-MS) provide time resolved insights into the metabolism of active microbiomes. In this study, we used PTR-TOF-MS to investigate the metabolic trajectory of microbiomes from a subalpine forest soil, and their response to a simulated wet-up event akin to snowmelt. Using an information theory approach based on the partitioning of mutual information, we identified mVC metabolite pairs with robust interactions, including those that were non-linear and with time lags. The biological context for these mVC interactions was evaluated by projecting the connections onto the Kyoto Encyclopedia of Genes and Genomes (KEGG) network of known metabolic pathways. Simulated snowmelt resulted in a rapid increase in the production of trimethylamine (TMA) suggesting that anaerobic degradation of quaternary amine osmo/cryoprotectants, such as glycine betaine, may be important contributors to this resource pulse. Unique and synergistic connections between intermediates of methylotrophic pathways such as dimethylamine, formaldehyde and methanol were observed upon wet-up and indicate that the initial pulse of TMA was likely transformed into these intermediates by methylotrophs. Increases in ammonia oxidation signatures (transformation of hydroxylamine to nitrite) were observed in parallel, and while the relative role of nitrifiers or methylotrophs cannot be confirmed, the inferred connection to TMA oxidation suggests either a direct or indirect coupling between these processes. Overall, it appears that such mVC time-series from PTR-TOF-MS combined with causal inference represents an attractive approach to non-destructively observe soil microbial metabolism and its response to environmental perturbation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Geochemistry, RNA radiocarbon signature, and metatranscriptome data from Rifle, Colorado groundwater well

Understanding the different sources of carbon subsurface microbes use is highly informative yet remains challenging. The goal of this work was to develop and test a cultivation-independent method that analyzes both the radiocarbon and ribosomal RNA (rRNA) signature of unamplified RNA from the same environmental sample, and that collectively characterizes community carbon utilization under in situ conditions. The method was applied to a filtered groundwater sample from a geochemically reduced zone of a shallow alluvial aquifer near Rife, Colorado (CO), where multiple potential carbon sources co-occur. The radiocarbon and RNA-Seq results, while addressing diverse sample properties, indicated a strikingly similar conclusion about the quantitative role of autotrophy in the subsurface microbial community.This data package provides (1) ribosomal RNA (rRNA) sequences for groundwater microbial populations, (2) the taxonomic identity and relative abundance of groundwater microbial populations based on these rRNA sequences, (3) radiocarbon signatures of the rRNA indicating the source of carbon used by the groundwater microbial populations (provided in both Word docx file and pdf file), (4) geochemical measurements for the monitoring well corresponding to these measurements.

54 ENVIRONMENTAL SCIENCES↗