Long-term warming and decreased precipitation regulated microbial community structure and potential function through enhanced predator-prey relationships in the Tibetan Plateau.

Global climate change can shape the interactions among soil microbes and, in turn, mediate ecosystem functions. However, how these interactions were regulated remains to be investigated. This study utilized 16S rRNA, ITS, and 18S rRNA high-throughput sequencing to investigate the effects of simulated warming and precipitation changes on the major components of soil micro-food webs in the Qinghai-Tibetan Plateau through a field experiment. Adonis and non-metric multidimensional scaling (NMDS) analyses showed that compositions of bacteria, fungi and protists were all affected by changes in temperature and precipitation. Correlation and cross-trophic network analyses revealed that warming and decreased precipitation, both separately and together, enhanced the relationships between bacteria and protists, especially protistan predators. We found that the modified stochasticity ratio of the bacterial community assembly was best predicted by protists. The potential functional structures of bacteria were positively correlated with protistan predators under warming and decreased precipitation condition, suggesting enhanced predator-prey relationships between protists and bacteria might further influence the potential functional characteristics of bacterial communities. Our study indicated that climate change altered bacterial compositional and functional structure via enhanced predator-prey interactions. Therefore, in the context of global climate change, broader and more comprehensive studies on protist-regulated soil bacterial and fungal communities are imperative.

Coexistence of adeno-associated virus 2 with adenovirus 18 or herpesvirus may be associated with severe lingual papillomatosis in an immunocompromised individual.

Next-generation sequencing (NGS) has significantly improved the accuracy and efficiency of pathogen diagnosis for a wide range of diseases. In this study, viral metagenomics analysis was conducted on fecal and tissue samples from a 13-year-old recipient of hematopoietic stem cell transplantation (HSCT) afflicted with severe lingual papillomatosis. The analysis revealed a high abundance of adeno-associated virus 2 (AAV2), alongside potential helper viruses, herpesvirus type 1 (HSV-1), and the uncommon adenovirus serotype 18 (AdV18). Although a direct causal relationship was not definitively established, the concurrence of these viruses indicated a plausible link to the development of severe lingual papillomatosis in immunocompromised individuals. Notably, the study generated a complete genome sequence of AdV18, offering insights into adenovirus genetic variability, origin, and pathogenicity. Noteworthy findings include three amino acid substitutions in the polymerase and one in the hexon, distinguishing them from previously published strains of AdV18. Phylogenetic analysis unveiled a close relationship between both the polymerase and hexon regions of AdV18 in our study and previously reported AdV18 sequences. This study underscores the pivotal role of comprehensive viral scrutiny in elucidating infections among HSCT patients with lingual papillomatosis.

The effects of grassland degradation on the genetic structure of a small mammal.

Grassland degradation is challenging the health of grassland ecosystems globally and causing biodiversity decline. Previous studies have demonstrated the impact of grassland degradation on the abundance and behavior of small mammals. Little is known about how it affects the genetic structure of gregarious mammals in the wild. This study explores the effects of grassland degradation on the genetic structure of a small burrowing mammal, plateau pika (Ochotona curzoniae). We used nine microsatellite loci to analyze the genetic diversity and genetic differentiation between colonies and genetic relatedness between individuals within the colony. We found that pikas in severely degraded grasslands had a significantly higher genetic diversity within colonies, a higher level of gene flow between colonies, and a lower genetic differentiation between colonies compared to pikas in less degraded grasslands. Individuals within colonies had a significantly lower genetic relatedness in severely degraded grasslands than in less degraded grasslands. This study has provided potential evidence of a significant impact of grassland degradation on the genetic structure of pikas, which has caused a breakdown of their kin-selected colony structure.

Whole-soil warming leads to substantial soil carbon emission in an alpine grassland.

The sensitivity of soil organic carbon (SOC) decomposition in seasonally frozen soils, such as alpine ecosystems, to climate warming is a major uncertainty in global carbon cycling. Here we measure soil CO2 emission during four years (2018-2021) from the whole-soil warming experiment (4 °C for the top 1 m) in an alpine grassland ecosystem. We find that whole-soil warming stimulates total and SOC-derived CO2 efflux by 26% and 37%, respectively, but has a minor effect on root-derived CO2 efflux. Moreover, experimental warming only promotes total soil CO2 efflux by 7-8% on average in the meta-analysis across all grasslands or alpine grasslands globally (none of these experiments were whole-soil warming). We show that whole-soil warming has a much stronger effect on soil carbon emission in the alpine grassland ecosystem than what was reported in previous warming experiments, most of which only heat surface soils.

Warming and altered precipitation independently and interactively suppress alpine soil microbial growth in a decadal-long experiment.

Warming and precipitation anomalies affect terrestrial carbon balance partly through altering microbial eco-physiological processes (e.g., growth and death) in soil. However, little is known about how such processes responds to simultaneous regime shifts in temperature and precipitation. We used the 18O-water quantitative stable isotope probing approach to estimate bacterial growth in alpine meadow soils of the Tibetan Plateau after a decade of warming and altered precipitation manipulation. Our results showed that the growth of major taxa was suppressed by the single and combined effects of temperature and precipitation, eliciting 40-90% of growth reduction of whole community. The antagonistic interactions of warming and altered precipitation on population growth were common (~70% taxa), represented by the weak antagonistic interactions of warming and drought, and the neutralizing effects of warming and wet. The members in Solirubrobacter and Pseudonocardia genera had high growth rates under changed climate regimes. These results are important to understand and predict the soil microbial dynamics in alpine meadow ecosystems suffering from multiple climate change factors.

More enhanced non-growing season methane exchanges under warming on the Qinghai-Tibetan Plateau.

Uncertainty in methane (CH4) exchanges across wetlands and grasslands in the Qinghai-Tibetan Plateau (QTP) is projected to increase due to continuous permafrost degradation and asymmetrical seasonal warming. Temperature plays a vital role in regulating CH4 exchange, yet the seasonal patterns of temperature dependencies for CH4 fluxes over the wetlands and grasslands on the QTP remain poorly understood. Here, we demonstrated a stronger warming response of CH4 exchanges during the non-growing season compared to the growing season on the QTP. Analyzing 9745 daily observations and employing four methods -regression fitting of temperature-CH4 flux, temperature dependence calculations, field-based and model-based control experiments-we found that warming intensified CH4 emissions in wetlands and uptakes in grasslands. Specifically, the average reaction intensity in the non-growing season surpasses that in the growing season by 1.89 and 4.80 times, respectively. This stronger warming response of CH4 exchanges during the non-growing season significantly increases the regional CH4 exchange on the QTP. Our research reveals that CH4 exchanges in the QTP have a higher warming sensitivity in non-growing seasons, which meanwhile are dominated by a larger warming rate than the annual average. The combined effects of these two factors will significantly alter the CH4 source/sink on the QTP. Neglecting these impacts would lead to inaccurate estimations of CH4 source/sink over the QTP under climate warming.

Alpine grassland degradation intensifies the burrowing behavior of small mammals: evidence for a negative feedback loop.

Globally, grassland degradation is an acute ecological problem. In alpine grassland on the Tibetan Plateau, increased densities of various small mammals in degraded grassland are assumed to intensify the degradation process and these mammals are subject to lethal control. However, whether the negative impact of small mammals is solely a result of population size or also a result of activity and behavior has not been tested. In this study, we use plateau pika as a model to compare population size, core area of colony, and the number of burrow entrances and latrines between lightly and severely degraded grassland. We test whether the alleged contribution of pika to grassland degradation is a result of increased population size or increased burrowing activities of individuals in response to lower food abundance. We found that grassland degradation resulted in lower plant species richness, plant height, and biomass. Furthermore, the overall population size of pika was not significantly affected by location in lightly and severely degraded grassland. However, pika core areas in severely grassland degradation were significantly larger and had significantly higher densities of burrows and latrines. Our study provides convincing evidence that habitat-induced changes in the behavior of small, burrowing mammals, such as pika, can exacerbate grassland degradation. This finding has significant implications for managing small mammals and restoring degraded grassland ecosystems.

Comparative analysis of human respiratory syncytial virus evolutionary patterns during the COVID-19 pandemic and pre-pandemic periods.

The COVID-19 pandemic has resulted in the implementation of strict mitigation measures that have impacted the transmission dynamics of human respiratory syncytial virus (HRSV). The measures also have the potential to influence the evolutionary patterns of the virus. In this study, we conducted a comprehensive analysis comparing genomic variations and evolving characteristics of its neutralizing antigens, specifically F and G proteins, before and during the COVID-19 pandemic. Our findings showed that both HRSV A and B exhibited an overall chronological evolutionary pattern. For the sequences obtained during the pandemic period (2019-2022), we observed that the HRSV A distributed in A23 genotype, but formed into three subclusters; whereas the HRSV B sequences were relatively concentrated within genotype B6. Additionally, multiple positively selected sites were detected on F and G proteins but none were located at neutralizing antigenic sites of the F protein. Notably, amino acids within antigenic site III, IV, and V of F protein remained strictly conserved, while some substitutions occurred over time on antigenic site Ø, I, II and VIII; substitution S389P on antigenic site I of HRSV B occurred during the pandemic period with nearly 50% frequency. However, further analysis revealed no substitutions have altered the structural conformations of the antigenic sites, the vial antigenicity has not been changed. We inferred that the intensive public health interventions during the COVID-19 pandemic did not affect the evolutionary mode of HRSV.

An early warning signal for grassland degradation on the Qinghai-Tibetan Plateau.

Intense grazing may lead to grassland degradation on the Qinghai-Tibetan Plateau, but it is difficult to predict where this will occur and to quantify it. Based on a process-based ecosystem model, we define a productivity-based stocking rate threshold that induces extreme grassland degradation to assess whether and where the current grazing activity in the region is sustainable. We find that the current stocking rate is below the threshold in ~80% of grassland areas, but in 55% of these grasslands the stocking rate exceeds half the threshold. According to our model projections, positive effects of climate change including elevated CO2 can partly offset negative effects of grazing across nearly 70% of grasslands on the Plateau, but only in areas below the stocking rate threshold. Our analysis suggests that stocking rate that does not exceed 60% (within 50% to 70%) of the threshold may balance human demands with grassland protection in the face of climate change.

Asymmetric response of aboveground and belowground temporal stability to nitrogen and phosphorus addition in a Tibetan alpine grassland.

Anthropogenic eutrophication is known to impair the stability of aboveground net primary productivity (ANPP), but its effects on the stability of belowground (BNPP) and total (TNPP) net primary productivity remain poorly understood. Based on a nitrogen and phosphorus addition experiment in a Tibetan alpine grassland, we show that nitrogen addition had little impact on the temporal stability of ANPP, BNPP, and TNPP, whereas phosphorus addition reduced the temporal stability of BNPP and TNPP, but not ANPP. Significant interactive effects of nitrogen and phosphorus addition were observed on the stability of ANPP because of the opposite phosphorus effects under ambient and enriched nitrogen conditions. We found that the stability of TNPP was primarily driven by that of BNPP rather than that of ANPP. The responses of BNPP stability cannot be predicted by those of ANPP stability, as the variations in responses of ANPP and BNPP to enriched nutrient, with ANPP increased while BNPP remained unaffected, resulted in asymmetric responses in their stability. The dynamics of grasses, the most abundant plant functional group, instead of community species diversity, largely contributed to the ANPP stability. Under the enriched nutrient condition, the synchronization of grasses reduced the grass stability, while the latter had a significant but weak negative impact on the BNPP stability. These findings challenge the prevalent view that species diversity regulates the responses of ecosystem stability to nutrient enrichment. Our findings also suggest that the ecological consequences of nutrient enrichment on ecosystem stability cannot be accurately predicted from the responses of aboveground components and highlight the need for a better understanding of the belowground ecosystem dynamics.

Whole-soil-profile warming does not change microbial carbon use efficiency in surface and deep soils.

The paucity of investigations of carbon (C) dynamics through the soil profile with warming makes it challenging to evaluate the terrestrial C feedback to climate change. Soil microbes are important engines driving terrestrial biogeochemical cycles; their carbon use efficiency (CUE), defined as the proportion of metabolized organic C allocated to microbial biomass, is a key regulator controlling the fate of soil C. It has been theorized that microbial CUE should decline with warming; however, empirical evidence for this response is scarce, and data from deeper soils are particularly scarce. Here, based on soil samples from a whole-soil-profile warming experiment (0 to 1 m, +4 °C) and 18O tracing approach, we examined the vertical variation of microbial CUE and its response to ~3.3-y experimental warming in an alpine grassland on the Qinghai-Tibetan Plateau. Microbial CUE decreased with soil depth, a trend that was primarily controlled by soil C availability. However, warming had limited effects on microbial CUE regardless of soil depth. Similarly, warming had no significant effect on soil C availability, as characterized by extractable organic C, enzyme-based lignocellulose index, and lignin phenol-based ratios of vanillyls, syringyls, and cinnamyls. Collectively, our work suggests that short-term warming does not alter microbial CUE in either surface or deep soils, and emphasizes the regulatory role of soil C availability on microbial CUE.

Experimental warming causes mismatches in alpine plant-microbe-fauna phenology.

Long-term observations have shown that many plants and aboveground animals have changed their phenology patterns due to warmer temperatures over the past decades. However, empirical evidence for phenological shifts in alpine organisms, particularly belowground organisms, is scarce. Here, we investigate how the activities and phenology of plants, soil microbes, and soil fauna will respond to warming in an alpine meadow on the Tibetan Plateau, and whether their potential phenological changes will be synchronized. We experimentally simulate an increase in soil temperature by 2-4 °C according to future projections for this region. We find that warming promotes plant growth, soil microbial respiration, and soil fauna feeding by 8%, 57%, and 20%, respectively, but causes dissimilar changes in their phenology during the growing season. Specifically, warming advances soil faunal feeding activity in spring and delays it in autumn, while their peak activity does not change; whereas warming increases the peak activity of plant growth and soil microbial respiration but with only minor shifts in their phenology. Such phenological asynchrony in alpine organisms may alter ecosystem functioning and stability.

Molecular 14 C evidence for contrasting turnover and temperature sensitivity of soil organic matter components.

Climate projection requires an accurate understanding for soil organic carbon (SOC) decomposition and its response to warming. An emergent view considers that environmental constraints rather than chemical structure alone control SOC turnover and its temperature sensitivity (i.e., Q10 ), but direct long-term evidence is lacking. Here, using compound-specific radiocarbon analysis of soil profiles along a 3300-km grassland transect, we provide direct evidence for the rapid turnover of lignin-derived phenols compared with slower-cycling molecular components of SOC (i.e., long-chain lipids and black carbon). Furthermore, in contrast to the slow-cycling components whose turnover is strongly modulated by mineral association and exhibits low Q10 , lignin turnover is mainly regulated by temperature and has a high Q10 . Such contrasts resemble those between fast-cycling (i.e., light) and mineral-associated slow-cycling fractions from globally distributed soils. Collectively, our results suggest that warming may greatly accelerate the decomposition of lignin, especially in soils with relatively weak mineral associations.

Carbon-biodiversity relationships in a highly diverse subtropical forest.

Carbon-focused climate mitigation strategies are becoming increasingly important in forests. However, with ongoing biodiversity declines we require better knowledge of how much such strategies account for biodiversity. We particularly lack information across multiple trophic levels and on established forests, where the interplay between carbon stocks, stand age, and tree diversity might influence carbon-biodiversity relationships. Using a large dataset (>4600 heterotrophic species of 23 taxonomic groups) from secondary, subtropical forests, we tested how multitrophic diversity and diversity within trophic groups relate to aboveground, belowground, and total carbon stocks at different levels of tree species richness and stand age. Our study revealed that aboveground carbon, the key component of climate-based management, was largely unrelated to multitrophic diversity. By contrast, total carbon stocks-that is, including belowground carbon-emerged as a significant predictor of multitrophic diversity. Relationships were nonlinear and strongest for lower trophic levels, but nonsignificant for higher trophic level diversity. Tree species richness and stand age moderated these relationships, suggesting long-term regeneration of forests may be particularly effective in reconciling carbon and biodiversity targets. Our findings highlight that biodiversity benefits of climate-oriented management need to be evaluated carefully, and only maximizing aboveground carbon may fail to account for biodiversity conservation requirements.

Tracking of Mutational Signature of SARS-CoV-2 Omicron on Distinct Continents and Little Difference was Found.

The Omicron variant is currently ravaging the world, raising serious concern globally. Monitoring genomic variations and determining their influence on biological features are critical for tracing its ongoing transmission and facilitating effective measures. Based on large-scale sequences from different continents, this study found that: (i) The genetic diversity of Omicron is much lower than that of the Delta variant. Still, eight deletions (Del 1-8) and 1 insertion, as well as 130 SNPs, were detected on the Omicron genomes, with two deletions (Del 3 and 4) and 38 SNPs commonly detected on all continents and exhibiting high-occurring frequencies. (ii) Four groups of tightly linked SNPs (linkage I-IV) were detected, among which linkage I, containing 38 SNPs, with 6 located in the RBD, increased its occurring frequency remarkably over time. (iii) The third codons of the Omicron shouldered the most mutation pressures, while the second codons presented the least flexibility. (iv) Four major mutants with amino acid substitutions in the RBD were detected, and further structural analysis suggested that the substitutions did not alter the viral receptor binding ability greatly. It was inferred that though the Omicron genome harbored great changes in antigenicity and remarkable ability to evade immunity, it was immune-pressure selected. This study tracked mutational signatures of Omicron variant and the potential biological significance of the SNPs, and the linkages await further functional verification.

Simulated climate warming decreases fruit number but increases seed mass.

Climate warming is changing plant sexual reproduction, having consequences for species distribution and community dynamics. However, the magnitude and direction of plant reproductive efforts (e.g., number of flowers) and success (e.g., number and mass of fruits or seeds) in response to warming have not been well-characterized. Here, we generated a global dataset of simulated warming experiments, consisting of 477 pairwise comparisons for 164 terrestrial species. We found evidence that warming overall decreased fruit number and increased seed mass, but little evidence that warming influenced flower number, fruit mass, or seed number. The warming effects on seed mass were regulated by the pollination type, and insect-pollinated plants exhibited a stronger response to warming than wind-pollinated plants. We found strong evidence that warming increased the mass of seeds for the nondominant species but no evidence of this for the dominant species. There was no evidence that phylogenetic relatedness explained the effects of warming on plant reproductive effort and success. In addition, the effects of warming on flowering onset negatively related to the responses in terms of the number of fruits and seeds to warming, revealing a cascading effect of plant reproductive development. These findings provide the first quantification of the response of terrestrial plant sexual reproduction to warming and suggest that plants may increase their fitness by producing heavier seeds under a warming climate.

Carbon fluxes and soil carbon dynamics along a gradient of biogeomorphic succession in alpine wetlands of Tibetan Plateau.

Hydrological changes under climate warming drive the biogeomorphic succession of wetlands and may trigger substantial carbon loss from the carbon-rich ecosystems. Although many studies have explored the responses of wetland carbon emissions to short-term hydrological change, it remains poorly understood how the carbon cycle evolves with hydrology-driven wetland succession. Here, we used a space-for-time approach across hydrological gradients on the Tibetan Plateau to examine the dynamics of ecosystem carbon fluxes (carbon dioxide (CO2) and methane (CH4)) and soil organic carbon pools during alpine wetland succession. We found that the succession from mesic meadow to fen changed the seasonality of both CO2 and CH4 fluxes, which was related to the shift in plant community composition, enhanced regulation of soil hydrology and increasing contribution of spring-thaw emission. The paludification caused a switch from net uptake of gaseous carbon to net release on an annual timescale but produced a large accumulation of soil organic carbon. We attempted to attribute the paradox between evidence from the carbon fluxes and pools to the lateral carbon input and the systematic changes of historical climate, given that the wetlands are spatially low-lying with strong temporal climate-carbon cycle interactions. These findings demonstrate a systematic change in the carbon cycle with succession and suggest that biogeomorphic succession and lateral carbon flows are both important for understanding the long-term dynamics of wetland carbon footprints.

The protective immunity induced by intranasally inoculated serotype 63 chimpanzee adenovirus vector expressing human respiratory syncytial virus prefusion fusion glycoprotein in BALB/c mice.

Human respiratory syncytial virus (RSV) is a ubiquitous pediatric pathogen causing serious lower respiratory tract disease worldwide. No licensed vaccine is currently available. In this work, the coding gene for mDS-Dav1, the full-length and prefusion conformation RSV fusion glycoprotein (F), was designed by introducing the stabilized prefusion F (preF) mutations from DS-Cav1 into the encoding gene of wild-type RSV (wtRSV) F protein. The recombinant adenovirus encoding mDS-Cav1, rChAd63-mDS-Cav1, was constructed based on serotype 63 chimpanzee adenovirus vector and characterized in vitro. After immunizing mice via intranasal route, the rChAd63-mDS-Cav1 induced enhanced neutralizing antibody and F-specific CD8+ T cell responses as well as good immune protection against RSV challenge with the absence of enhanced RSV disease (ERD) in BALB/c mice. The results indicate that rChAd63-mDS-Cav1 is a promising mucosal vaccine candidate against RSV infection and warrants further development.

Progresses of CRISPR/Cas9 genome editing in forage crops.

The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) mediated-genome editing has evolved into a powerful tool that is widely used in plant species to induce editing in the genome for analyzing gene function and crop improvement. CRISPR/Cas9 is an RNA-guided genome editing tool consisting of a Cas9 nuclease and a single-guide RNA (sgRNA). The CRISPR/Cas9 system enables more accurate and efficient genome editing in crops. In this review, we summarized the advances of the CRISPR/Cas9 technology in plant genome editing and its applications in forage crops. We described briefly about the development of CRISPR/Cas9 technology in plant genome editing. We assessed the progress of CRISPR/Cas9-mediated targeted-mutagenesis in various forage crops, including alfalfa, Medicago truncatula, Hordeum vulgare, Sorghum bicolor, Setaria italica and Panicum virgatum. The potentials and challenges of CRISPR/Cas9 in forage breeding were discussed.