Microbial difference and its influencing factors in ice-covered lakes on the three poles.

Most lakes in the world are permanently or seasonally covered with ice. However, little is known about the distribution of microbes and their influencing factors in ice-covered lakes worldwide. Here we analyzed the microbial community composition in the waters of 14 ice-covered lakes in the Hoh Xil region of northern Qing-Tibetan Plateau (QTP), and conducted a meta-analysis by integrating published microbial community data of ice-covered lakes in the tripolar regions (the Arctic, Antarctica and QTP). The results showed that there were significant differences in microbial diversity, community composition and distribution patterns in the ice-covered tripolar lakes. Microbial diversity and richness were lower in the ice-covered QTP lakes (including the studied lakes in the Hoh Xil region) than those in the Arctic and Antarctica. In the ice-covered lakes of Hoh Xil, prokaryotes are mainly involved in S-metabolic processes, making them more adaptable to extreme environmental conditions. In contrast, prokaryotes in the ice-covered lakes of the Arctic and Antarctica were predominantly involved in carbon/nitrogen metabolic processes. Deterministic (salinity and nutrients) and stochastic processes (dispersal limitation, homogenizing dispersal and drift) jointly determine the geographical distribution patterns of microorganisms in ice-covered lakes, with stochastic processes dominating. These results expand the understanding of microbial diversity, distribution patterns, and metabolic processes in polar ice-covered lakes.

Bacterial isolation and genome analysis of a novel Klebsiella quasipneumoniae phage in southwest China's karst area.

BACKGROUND: Southwest China is one of the largest karst regions in the world. Karst environment is relatively fragile and vulnerable to human activities. Due to the discharge of sewage and domestic garbage, the karst system may be polluted by pathogenic bacteria. The detection of bacterial distribution and identification of phage capable of infecting them is an important approach for environmental assessment and resource acquisition. METHODS: Bacteria and phages were isolated from karst water in southwest China using the plate scribing and double plate method, respectively. Isolated phage was defined by transmission electron microscopy, one-step growth curve and optimal multiplicity of infection (MOI). Genomic sequencing, phylogenetic analysis, comparative genomic and proteomic analysis were performed. RESULTS: A Klebsiella quasipneumoniae phage was isolated from 32 isolates and named KL01. KL01 is morphologically identified as Caudoviricetes with an optimal MOI of 0.1, an incubation period of 10 min, and a lysis period of 60 min. The genome length of KL01 is about 45 kb, the GC content is 42.5%, and it contains 59 open reading frames. The highest average nucleotide similarity between KL01 and a known Klebsiella phage 6939 was 83.04%. CONCLUSIONS: KL01 is a novel phage, belonging to the Autophagoviridae, which has strong lytic ability. This study indicates that there were not only some potential potentially pathogenic bacteria in the karst environment, but also phage resources for exploration and application.

Critical role of multiple antibiotics on the denitrification rate in groundwater: Field investigative proof.

The impact of antibiotics on denitrification has emerged as a significant topic; however, there is a dearth of mechanistic understanding regarding the effects of multiple antibiotics at the ng/L level on denitrification in groundwater. This study conducted five field samplings between March 2019 and July 2021 at two representative monitoring wells. The investigation utilized metagenomic sequencing to unveil the antibiotic mechanisms influencing denitrification. Results revealed the detection of 16 out of 64 antibiotics, with a maximum detection frequency and total concentration of 100 % and 187 ng/L, respectively. Additionally, both nitrate and total antibiotic concentrations exhibited a gradual decrease along the groundwater flow direction. Metagenomic evidence indicated that denitrification served as the dominant biogeochemical process controlling nitrate attenuation in groundwater. However, the denitrification capacity experienced significant inhibition in the presence of multiple antibiotics at the ng/L level. This inhibition was attributed to decreases in the relative abundance of dominant denitrifying bacteria (Candidatus_Scalindua, Herminiimonas and unclassified_p_Planctomycetes) and denitrifying functional genes (narGH, nirKS and norB), signifying the pressure exerted by antibiotics on denitrifying bacteria. The variation in antibiotic concentration (∆Cantibiotics) indicated a change in antibiotic pressure on denitrifying bacteria. A larger ∆Cantibiotics corresponded to a greater rebound in the relative abundance of denitrifying functional genes, resulting in a faster denitrification rate (Kdenitrification). Field observations further demonstrated a positive correlation between Kdenitrification and ∆Cantibiotics. Comparatively, a higher Kdenitrification observed at higher ∆Cantibiotics was primarily due to the enrichment of more nondominant denitrifying bacteria carrying key denitrifying functional genes. In conclusion, this study underscores that multiple antibiotics at the ng/L level in groundwater inhibited denitrification, and the degree of inhibition was closely related to ∆Cantibiotics.

Revealing discrepancies and drivers in the impact of lomefloxacin on groundwater denitrification throughout microbial community growth and succession.

The coexistence of antibiotics and nitrates has raised great concern about antibiotic's impact on denitrification. However, conflicting results in these studies are very puzzling, possibly due to differences in microbial succession stages. This study investigated the effects of the high-priority urgent antibiotic, lomefloxacin (LOM), on groundwater denitrification throughout microbial growth and succession. The results demonstrated that LOM's impact on denitrification varied significantly across three successional stages, with the most pronounced effects exhibited in the initial stage (53.8% promotion at 100 ng/L-LOM, 84.6% inhibition at 100 µg/L-LOM), followed by the decline stage (13.3-18.2% inhibition), while no effect in the stable stage. Hence, a distinct pattern encompassing susceptibility, insusceptibility, and sub-susceptibility in LOM's impact on denitrification was discovered. Microbial metabolism and environment variation drove the pattern, with bacterial numbers and antibiotic resistance as primary influencers (22.5% and 15.3%, p < 0.01), followed by carbon metabolism and microbial community (5.0% and 3.68%, p < 0.01). The structural equation model confirmed results reliability. Bacterial numbers and resistance influenced susceptibility by regulating compensation and bacteriostasis, while carbon metabolism and microbial community impacted energy, electron transfer, and gene composition. These findings provide valuable insights into the complex interplay between antibiotics and denitrification patterns in groundwater.

Creation of a High-Throughput Microfluidic Platform for Single-Cell Transcriptome Sequencing of Cell-Cell Interactions.

Cell-cell interaction is one of the major modalities for transmitting information between cells and activating the effects of functional cells. However, the construction of high-throughput analysis technologies from cell omics focusing on the impact of interactions of functional cells on targets has been relatively unexplored. Here, they propose a droplet-based microfluidic platform for cell-cell interaction sequencing (c-c-seq) and screening in vitro to address this challenge. A class of interacting cells is pre-labeled using cell molecular tags, and additional single-cell sequencing reagents are introduced to quickly form functional droplet mixes. Lastly, gene expression analysis is used to deduce the impact of the interaction, while molecular sequence tracing identifies the type of interaction. Research into the active effect between antigen-presenting cells and T cells, one of the most common cell-to-cell interactions, is crucial for the advancement of cancer therapy, particularly T cell receptor-engineered T cell therapy. As it allows for high throughput, this platform is superior to well plates as a research platform for cell-to-cell interactions. When combined with the next generation of sequencing, the platform may be able to more accurately evaluate interactions between epitopes and receptors and verify their functional relevance.

Recent developments in applications of physical fields for microbial decontamination and enhancing nutritional properties of germinated edible seeds and sprouts: a review.

Germinated edible seeds and sprouts have attracted consumers because of their nutritional values and health benefits. To ensure the microbial safety of the seed and sprout, emerging processing methods involving physical fields (PFs), having the characteristics of high efficiency and environmental safety, are increasingly proposed as effective decontamination processing technologies. This review summarizes recent progress on the application of PFs to germinating edible seeds, including their impact on microbial decontamination and nutritional quality and the associated influencing mechanisms in germination. The effectiveness, application scope, and limitation of the various physical techniques, including ultrasound, microwave, radio frequency, infrared heating, irradiation, pulsed light, plasma, and high-pressure processing, are symmetrically reviewed. Good application potential for improving seed germination and sprout growth is also described for promoting the accumulation of bioactive compounds in sprouts, and subsequently enhancing the antioxidant capacity under favorable PFs processing conditions. Moreover, the challenges and future directions of PFs in the application to germinated edible seeds are finally proposed. This review also attempts to provide an in-depth understanding of the effects of PFs on microbial safety and changes in nutritional properties of germinating edible seeds and a theoretical reference for the future development of PFs in processing safe sprouted seeds.

Niche differentiation and influencing factors of nitrite oxidation bacteria Nitrospira in sediments of the Luan River estuary in China.

In the estuarine sediment, the nitrite oxidation process mediated by bacteria significantly influences nitrification. Nitrospira is the most widely distributed nitrite-oxidizing bacteria (NOB) and can adapt to various environments. In this study, the Nitrospira-specific primer nxrB 169F-638R was used to analyze the microbial communities in the sediments of low-, middle-, and high-level zones in the Luan River estuary. The structure of the microbial community and its response to environmental factors were also assessed. The abundance and diversity of Nitrospira were the highest in the low-level zone and lowest in the high-level zone. Lineage II and lineage IV were the dominant Nitrospira at 43.58% and 32.09%, respectively. The distribution pattern of Nitrospira was also affected by complex environmental factors, such as the concentration of NH4+, Fe, and Cu cations. This study provides novel insights into the niche differentiation and adaptation strategies of Nitrospira in an estuarine sediment environment and will help to facilitate single-step nitrification.

Effect of radio frequency energy on buckwheat quality: An insight into structure and physicochemical properties of protein and starch.

Radio frequency (RF) heating as an emerging technology is widely used to improve cereal-based food quality. To further investigate effects of RF treatment on buckwheat quality, structures and physicochemical properties of protein and starch in buckwheat were evaluated under various temperatures (80, 90, and 100 °C) and holding times (0, 5, and 10 min). Results showed that protein-starch complexes were reaggregated with the increases of RF heating temperature and time, as well as the values of R1047/1022, crystallinity, random coil, and α-helix significantly decreased, and the values of ß-sheet obviously increased. Moreover, viscosities and rheological properties of buckwheat were reduced by the raised RF treatment intensity. Besides, the RF processing had a mostly positive effect on swelling power at low temperature of 30 °C, but contrary effect at high temperatures of 60 °C and 90 °C. However, changes of water solubility index, emulsifying capacity, and emulsion stability depended on the RF processing intensity. These results of the study suggested that buckwheat quality was affected by multiple RF treatment conditions, which can be tailored to develop a RF process having the potential to improve the function of buckwheat flour.

High-Throughput Screening of Functional Neo-Antigens and Their Specific T-Cell Receptors via the Jurkat Reporter System Combined with Droplet Microfluidics.

T-cell receptor (TCR)-engineered T cells can precisely recognize a broad repertoire of targets derived from both intracellular and surface proteins of tumor cells. TCR-T adoptive cell therapy has shown safety and promising efficacy in solid tumor immunotherapy. However, antigen-specific functional TCR screening is time-consuming and expensive, which limits its application clinically. Here, we developed a novel integrated antigen-TCR screening platform based on droplet microfluidic technology, enabling high-throughput peptide-major histocompatibility complex (pMHC)-to-TCR paired screening with a high sensitivity and low background signal. We introduced DNA barcoding technology to label peptide antigen candidate-loaded antigen-presenting cells and Jurkat reporter cells to check the specificity of pMHC-TCR candidates. Coupled with the next-generation sequencing pipeline, interpretation of the DNA barcodes and the gene expression level of the Jurkat T-cell activation pathway provided a clear peptide-MHC-TCR recognition relationship. Our proof-of-principle study demonstrates that the platform could achieve pMHC-TCR paired high-throughput screening, which is expected to be used in the cross-reactivity and off-target high-throughput paired testing of candidate pMHC-TCRs in clinical applications.

Identification of two novel T cell epitopes on the E2 protein of classical swine fever virus C-strain.

C-strain, also known as the HCLV strain, is a well-known live attenuated vaccine against classical swine fever (CSF), a devastating disease caused by classical swine fever virus (CSFV). Vaccination with C-strain induces a rapid onset of protection, which is associated with virus-specific gamma interferon (IFN-γ)-secreting CD8+ T cell responses. The E2 protein of CSFV is a major protective antigen. However, the T cell epitopes on the E2 protein remain largely unknown. In this study, eight overlapping nonapeptides of the E2 protein were predicted and synthesized to screen for potential T cell epitopes on the CSFV C-strain E2 protein. Molecular docking was performed on the candidate epitopes with the swine leukocyte antigen-1*0401. The analysis obtained two highly conserved T cell epitopes, 90STEEMGDDF98 and 331ATDRHSDYF339, which were further identified by enzyme-linked immunospot assay. Interestingly, the mutants deleting or substituting the epitopes are nonviable. Further analysis demonstrated that 90STEEMGDDF98 is crucial for the E2 homodimerization, while CSFV infection is significantly inhibited by the 331ATDRHSDYF339 peptide treatment. The two novel T cell epitopes can be used to design new vaccines that are able to provide rapid-onset protection.

Transfer route and driving forces of antibiotic resistance genes from reclaimed water to groundwater.

The infiltration of reclaimed water has created a significant environmental risk due to the spread of antibiotic resistance genes (ARGs) in riparian groundwater. Reclaimed water from wastewater treatment plants (WWTPs) had been identified as a source of both antibiotics and ARGs in groundwater, based on their spatial and temporal distribution. The assembly process of microbial communities in the groundwater of the infiltration zone was more influenced by deterministic processes. Co-occurrence network analysis revealed that Thermotoga, Desulfotomaculum, Methanobacterium, and other such genera were dominant shared genera. These were considered core genera and hosts of ARGs for transport from reclaimed water to groundwater. The most abundant ARG in these shared genera was MacB, enriched in groundwater point G3 and potentially transferred from reclaimed water to groundwater by Acidovorax, Hydrogenophaga, Methylotenera, Dechloromonas, and Nitrospira. During the infiltration process, environmental factors and the tradeoff between energy metabolism and antibiotic defense strategy may have affected ARG transfer. Understanding the transfer route and driving forces of ARGs from reclaimed water to groundwater provided a new perspective for evaluating the spread risk of ARGs in reclaimed water infiltration.

Succession and environmental response of sediment bacterial communities in the Liao River Estuary at the centenary scale.

Microbial community succession in turbulent estuarine environments is key to the understanding of microbial community development in estuaries. Centennial-scale sediment core samples collected from the Liao River Estuary (LRE) channel bar and side beaches were studied for geochemistry and 16S rRNA gene-based bacterial analyses. The results showed that bacterial community composition significantly differed between the sediments of the two sides of the channel bar, with Campilobacterota and Bacteroidota being dominant bacterial phyla in the tributary (T1, T2) and mainstream (MS1, MS2) sediment, respectively. Co-occurrence network of the bacterial community at the genus level showed more centralized and compacted topological features in tributary with weaker hydrodynamic, and the keystone taxas were Halioglobus, Luteolibacter, and Lutibacter in the bacterial community. The bacterial network structure had more edges and larger average degree in LRE sediments from the stage of the year 2016-2009 and the stage before 1939, which was possibly related to hydrodynamic conditions and nutrients. Stochastic processes (dispersal limitation) were the key factors driving bacterial community assembly in the LRE sediments. In addition, total organic carbon (TOC), total sulfur (TS), and grain size were the main deterministic factors affecting the change of bacterial community structure. Relative microbial abundance has the potential to indicate geologically historical environmental changes. This study provided a new perspective to reveal the succession and response of bacterial communities under frequent fluctuation environments.

Seasonal variations of microbial community structure, assembly processes, and influencing factors in karst river.

The physicochemical properties and microbial communities have significant annual and seasonal changes in karst aquifers. To explore the changes of microbial community and their relationships with environmental factors, water samples were collected from a typical karst river. Microbial communities in winter (Jan-2017 and Jan-2019) were stable with high similarity in spite of the 2 years sampling interval, but the microbial communities in Aug-2017 was different from that in Aug-2018. In four sampling times, there were 275 shared genera, whose average relative abundance ranging from 89.04 to 96.27%. The winter and summer specific genera were mainly from the recharge of tributary site K6 and discharge of waste water treatment plant (K2 and K3), respectively. The deterministic processes had a more significant effect on the microbial community assembly in winter than that in summer, which was affected by environmental pressure from pollution. Furthermore, antibiotics and inorganic nitrogen pollution affected element cycles of nitrogen and sulfur indirectly through microbial ecological modules in karst river, and the denitrification and desulfurization processes were potentially inhibited. These findings contributed to understand the changes and its assembly mechanism of microbial community, as well as the feedback to environment in polluted karst river.

Mixed organic and inorganic amendments enhance soil microbial interactions and environmental stress resistance of Tibetan barley on plateau farmland.

Sufficient crop yield while maintaining soil health and sustainable agricultural development is a global objective, serving a special challenge to certain climate-sensitive plateau areas. Despite conducting trails on a variety of soil amendments in plateau areas, systematic research is lacking regarding the influences of organic and inorganic amendments on soil quality, particularly soil microbiome. To our knowledge, this was the first study that compared the effects of inorganic, organic, and mixed amendments on typical plateau crop hulless barley (Hordeum vulgare L. var. Nudum, also known as "Qingke" in Chinese) over the course of tillering, jointing, and ripening. Microbial communities and their responses to amendments, soil properties and Tibetan hulless barley growth, yield were investigated. Results indicated that mixed organic and inorganic amendments promoted the abundance of rhizosphere microorganisms, enhancing the rhizosphere root-microbes interactions and resistance to pathogenic bacteria and environmental stresses. The rhizosphere abundant and significantly different genera Arthrobacter, Rhodanobacter, Sphingomona, Nocardioides and so on demonstrated their unique adaptation to the plateau environment based on the results of metagenomic binning. The abundance of 23 genes about plant growth and environmental adaptations in the mixed amendment soil were significantly higher than other treatments. Findings from this study suggest that the mixed organic/inorganic amendments can help establish a healthy microbiome and increase soil quality while achieving sufficient hulless barley yields in Tibet and presumably other similar geographic areas of high altitude.

Effects of sequential treatments using radio frequency energy and ultraviolet light on inactivation of Bacillus cereus spores and quality attributes of buckwheat.

Buckwheat kernels were susceptible to be contaminated by heat-resistant spores. This study aimed to investigate effects of radio frequency (RF) heating, ultraviolet (UV) light and their combination treatment on the inactivation of B. cereus spores and quality attributes of buckwheat kernels. Results showed that Weibull model well fitted the inactivation curves of B. cereus spores under RF heating or UV light, and both of the two techniques had a tailing phenomenon (n < 1) in the decontamination process. But the inactivation levels of spores significantly increased by the combined treatments of RF and UV, regardless of the treatment sequence. Treatment by individual RF heating at 105 °C for 30 min or UV exposure at 5.00 mW/cm2 for 60 min resulted in >2.0 log CFU/g reduction of B. cereus spores. The similar inactivation effect could be achieved with shorter processing times by combined treatments (RF temperature-holding time + UV intensity-irradiation time: 85-10 + 3.50-10, 90-0 + 2.25-10, and 95-5 + 1.00-10). Besides, the colors, antioxidant compounds and antioxidant activities of buckwheat were not significantly deteriorated after these combined treatments, but the enzymatic activities were reduced, which was beneficial for long-term storage. Therefore, the proposed sequential treatment of RF heating and UV light in this study holds great potential to assure the food safety of grains.

Identification of the p34 Protein of African Swine Fever Virus as a Novel Viral Antigen with Protection Potential.

African swine fever (ASF) is a highly contagious disease caused by African swine fever virus (ASFV), affecting domestic and wild boars. The polyprotein pp220 of ASFV is responsible for producing the major structural proteins p150, p37, p14, p34, and p5 via proteolytic processing. The p34 protein is the main component of the ASFV core shell. However, the immunologic properties of the p34 protein in vitro and in vivo remain unclear. The results showed that the recombinant p34 protein expressed in prokaryotes and eukaryotes could react with convalescent swine sera to ASFV, suggesting that p34 is an immunogenic protein. Significantly, anti-p34 antibodies were found to inhibit the replication of ASFV in target cells. Furthermore, rabbits immunized with the recombinant C-strain of classical swine fever virus containing p34 produced both anti-p34 humoral and cellular immune responses. In addition, the p34 protein could induce a cell-mediated immune response, and a T-cell epitope on the p34 protein was identified using immunoinformatics and enzyme-linked immunospot (ELIspot) assay. Our study demonstrates that the p34 protein is a novel antigen of ASFV with protective potential.

Thermal and Dielectric Properties of Wolfberries as Affected by Moisture Content and Temperature Associated with Radio Frequency and Microwave Dehydrations.

Knowledge of the thermal and dielectric properties of wolfberries is essential for understanding the heat transfer and the interaction between the electromagnetic field (10-3000 MHz) and the sample during radio frequency (RF) and microwave (MW) drying. The thermal and dielectric properties of wolfberries were determined as influenced by moisture content from 15.1% to 75.2%, w.b.) and temperature from 25 to 85 °C. The results showed that as the moisture content increased from 15.1% to 75.2% (w.b.), the true density of wolfberries decreased, but the specific heat capacity and thermal conductivity increased with increasing temperature and moisture content. The dielectric properties (DPs) of wolfberries decreased with increasing frequency from 10 to 3000 MHz. The dielectric constant increased with increasing temperature at lower a moisture content (below 45% w.b.) but decreased with increasing temperature at a high moisture content (above 60% w.b.). The cubic and quadratic polynomial models (R2 = 0.977 - 0.997) were best for fitting the dielectric constant and loss factor at four representative frequencies of 27, 40, 915, and 2450 MHz, respectively. The penetration depth increased with the decreased frequency, temperature, and moisture content, and was greater at RF frequencies than MW range, making the RF heating more effective for drying bulk wolfberries. These findings offered essential data before optimizing RF or MW dehydration protocols for wolfberries via computer simulation.

Influence of the combination of cinnamon essential oil nanoemulsions and epsilon-polylysine on microbial community and quality of pork during refrigerated period and radio frequency cooking.

Pork preservation and cooking are common processes in food production. This study analyzed the influence of cinnamon essential oil nanoemulsions (CEON), ε-polylysine (ε-PL) and CEON/ε-PL on microbial community and quality of pork during refrigerated storage and radio frequency (RF) cooking. Results showed that a stable CEON was prepared with soybean lecithin (oil: lecithin = 1:1 w/w). CEON and ε-PL inhibited the growth of total bacteria counts (TBC) of raw pork, and caused Salmonella reduction at refrigerated storage of 12 d. Photobacterium and Pseudomonas were dominant spoilage bacteria of raw pork during refrigerated period. The 0.25 % CEON and 0.125 % CEON + 0.25 % ε-PL had good antimicrobial effects against Photobacterium while 0.5 % ε-PL had a small effect. Pork treated by CEON and CEON/ε-PL had better freshness than control and ε-PL treated samples. RF cooking lowered cooking time compared to water bath cooking at 80 °C and a similar quality of cooked pork was observed. CEON/ε-PL promoted Salmonella and TBC inactivation during RF cooking. TVB-N content, pH, cooking loss and appearance of RF cooked pork were not influenced by the addition of CEON/ε-PL, but the odor was slightly affected. The hardness, springiness and chewiness were enhanced by the addition of CEON/ε-PL. The results revealed that CEON/ε-PL could be used in raw pork preservation and promote bacteria inactivation during RF cooking.

Antibody-Dependent Enhancement: ″Evil″ Antibodies Favorable for Viral Infections.

The pandemics caused by emerging viruses such as severe acute respiratory syndrome coronavirus 2 result in severe disruptions to public health. Vaccines and antibody drugs play essential roles in the control and prevention of emerging infectious diseases. However, in contrast with the neutralizing antibodies (NAbs), sub- or non-NAbs may facilitate the virus to enter the cells and enhance viral infection, which is termed antibody-dependent enhancement (ADE). The ADE of most virus infections is mediated by the Fc receptors (FcRs) expressed on the myeloid cells, while others are developed by other mechanisms, such as complement receptor-mediated ADE. In this review, we comprehensively analyzed the characteristics of the viruses inducing FcRs-mediated ADE and the new molecular mechanisms of ADE involved in the virus entry, immune response, and transcription modulation, which will provide insights into viral pathogenicity and the development of safer vaccines and effective antibody drugs against the emerging viruses inducing ADE.