Abstract:

Abstract:Ammonium oxidation coupled to Fe(III) reduction (Feammox), as a nitrogen metabolic pathway connecting N cycle and Fe cycle, plays an important role in the process of ammonia nitrogen conversion in nature. A systematic study of the biogeochemical coupling process of nitrogen and iron driven by Feammox and its controlling factors will help to understand microbial mechanism of earth’s element cycle in depth, and also avail to reveal of the role of Feammox in the evolution of the nitrogen pool and the formation of iron-bearing minerals in Paleo-ocean. This review mainly summarized the development history, related microorganisms, influencing factors and potential geological significance of Feammox, followed by prospect on the future research of Feammox.

Abstract:As the second most abundant greenhouse gas in the world, methane is a typical renewable energy source and an important material component in the key link of the carbon cycle. About 74% of atmospheric methane is produced by syntrophy between methanogenic archaea and other microorganisms, and interspecies electron transfer (IET) is the core process of methanogenic microbial communities to overcome the thermodynamic energy barrier. IET can be sorted into mediated interspecies electron transfer (MIET) and direct interspecies electron transfer (DIET). During MIET, microorganisms rely on electron shuttles such as hydrogen and formate for long-distance electron transport. However, during DIET, microbial communities establish direct connections and transport electrons through electrically conductive pili, cytochrome c and other membrane-bound proteins. This review will start from the research history of IET and then compare MIET and DIET in terms of electron transfer mechanism, related microbial species, and ecological distribution. Finally, we will summarize the future research directions. This review is expected to help deepen the understanding of IET during microbial syntrophic methanogenesis and lay a theoretical basis for solving ecological problems such as global warming caused by methane.

Abstract:[Objective] Antarctica is a unique habitat harboring diverse microorganisms because of its extreme environmental conditions. The aim of this study is to promote the growth of microorganisms that are difficult to culture by changing the culture conditions to isolate lesser-known microorganisms. This study provides a better understanding of the unique microbial groups and their diversity in Antarctic cryoconites and provides guidance for the development of culture methods for uncultured microorganisms in the extreme environments of Antarctica. [Methods] We added resuscitation-promoting factor (Rpf) in different media to improve the culture efficiency of microorganisms from the cryoconite of the Collins Glacier, Antarctica, and explore the diversity of microorganisms in this habitat. Four media with different nutrient levels were used for strain culture, and Rpf was added in parallels. After isolation, purification, and 16S rRNA sequencing, the diversity of culturable microorganisms in the cryoconite and the influence of culture conditions on the diversity were analyzed. [Results] A total of 407 bacterial strains were isolated and cultured, covering 29 genera, 18 families of 5 phyla. Actinomycetota, Microbacteriaceae, and Lacisediminihabitans were the dominant phylum, family, and genus with the relative abundance of 72.73%, 69.78%, and 45.70%, respectively. According to the number of strains cultured, different media followed the trend of R2A medium (188 strains)>1/2 R2A+Rpf medium (144 strains)>1/2 R2A medium (46 strains)>R2A+Rpf medium (14 strains)>TSB+Rpf medium (9 strains)>TSB medium (3 strains)=LB medium (3 strains). No microorganism was cultured in LB+Rpf medium. According to the threshold of 16S rRNA sequence similarity below 98.65%, which indicates potential new species, 69 out of the isolated strains belonged to 19 potential new species. The media with high isolation rates of potential new species were R2A, 1/2 R2A, and 1/2 R2A+Rpf. [Conclusion] Eight different media were used to recover bacteria from the Antarctic cryoconite samples, and the addition of Rpf can generally promote the growth of strains. A relatively diverse collection of strains including several putative novel species has been isolated, which inspires the future use of different media for the isolation of microorganisms difficult to culture in extreme polar environments.

Abstract:[Objective] Bacteria of Exiguobacterium are ubiquitous in marine and non-marine environments and display versatile metabolism pathways to adapt to complex and diverse habitats. In this study, we explored the adaptability of Exiguobacterium to different habitats from the perspective of energy metabolism pathways. [Methods] The genomes of a total 146 Exiguobacterium strains available at National Center for Biotechnology Information (NCBI) database were downloaded for the mining of the genes encoding key enzymes of multiple energy metabolism pathways. The encoded enzymes mainly included rhodopsin for phototrophy, molybdenum cofactor synthesis protein for anaerobic respiration, and isocitrate lyase and malate synthase for glyoxylate shunt. We then built the phylogenetic trees based on the amino acid sequences of rhodopsin, MoaC, and isocitrate lyase to analyze the conservation of different energy metabolism pathways. [Results] Fifty percent of Exiguobacterium species possessed rhodopsin gene. The strains isolated from non-marine habitats tended to carry rhodopsin gene, accounting for about 70%, while the strains carrying rhodopsin gene from marine habitats accounted for only 19%. Approximately 27% of species possessed the gene encoding molybdenum cofactor synthesis protein, and the strains isolated from marine habitats (32%) carrying this gene were more than those from non-marine habitats (21%). The strains with complete molybdenum cofactor synthesis pathway concentrated in several species, sharing the same branch on the phylogenetic tree. The glyoxylate shunt existed in approximately 61% of the species, which clustered in the same branch of the phylogenetic tree. All the strains of such species possessed related genes, which indicated that this pathway had species specificity in Exiguobacterium. [Conclusion] The key genes for energy metabolism vary in different species or different strains of Exiguobacterium. The diversity of energy metabolism pathways may, to some extent, facilitate the adaptation of these bacteria to complex habitats. Furthermore, the distribution of most energy metabolism pathways is not species-specific for this genus. This finding suggests that the prediction of metabolic types of targeted strains by 16S rRNA gene-based species identification alone may be biased and limited.

Abstract:[Objective] To explore the contributions of adjacent water bodies to the microbial communities in Gas Hure Salt Lake. [Methods] We collected the water and sediment samples from Gas Hure Salt Lake and the water samples from adjacent springs, river, and saltern for the measurement of geochemical parameters. Illumina MiSeq high-throughput sequencing was employed to explore the microbial community composition. [Results] Proteobacteria, Bacteroidetes, Actinobacteria, and Euryarchaeota were dominant phyla in the water and sediment samples of Gas Hure Salt Lake. Salinity and pH were the most influential factors driving the community composition in the survey region. The contribution rates of adjacent water bodies to the microbial communities in the water and sediment of Gas Hure Salt Lake were 12.94% and 7.53%, respectively. [Conclusion] The external water bodies have limited contributions to the microbial communities of Gas Hure Salt Lake.

Abstract:[Objective] The Xiaochaidan Lake on the Qinghai-Tibetan Plateau is rich in sulfate brine. The metagenomics study has demonstrated that Xiaochaidan Lake harbors abundant microorganisms with salt tolerance and the potential of carbon fixation and desulfurization. This paper aims to reveal the metabolic diversity and environmental adaptation mechanism of Desulfotignum via bioinformatics analysis. [Methods] The genomes of Desulfotignum in Xiaochaidan Lake were obtained via metagenomic analysis and public database. The global habitat distribution of Desulfotignum was revealed through literature tracking and 16S rRNA database retrieval. Desulfotignum subgroups were classified based on the phylogenetic analysis of 120 marker proteins in genome taxonomy database (GTDB). The environmental adaptation mechanism and metabolic diversity of Desulfotignum were analyzed through metabolic reconstruction. [Results] Desulfotignum is widely distributed in the world, and most of its habitats have high salinity. Eleven Desulfotignum genomes (nine from the sediments of Xiaochaidan Lake and two from the public database) were clustered into two groups (G1 and G2) according to the phylogenetic tree, average nucleotide identity (ANI), and average amino acid identity (AAI). Metabolic reconstruction indicated that Desulfotignum may be mixotrophic bacteria (using organic carbon and inorganic carbon as carbon sources) with Wood-Ljungdahl (WL) and reductive glycine (rGly) pathways for carbon fixation. The members in G1 can use nitrite, sulfate, and oxygen as electron receptors and carry out lactate fermentation, thiosulfate disproportionation, and chemotaxis through flagella. The members in G2 can use sulfate and oxygen as electron acceptors, participate in partial nitrification and thiosulfate disproportionation, and move via pilus twisting. Both G1 and G2 can take K⁺ through the Trk system to adapt to the high salt environment. [Conclusion] Our study expands new branches of Desulfotignum and predicts the potential metabolic diversity and environmental adaptation mechanism of Desulfotignum.

Abstract:Karst caves are important karst landforms, serving as natural laboratories to investigate deep biosphere. Despite the diverse microorganisms, little is known about microorganisms capable of fixing nitrogen in the permanent darkness and oligotrophic karst caves. [Objective] To reveal the composition of nitrogen-fixers and their correlation with biotic and abiotic factors in karst caves. [Methods] We collected samples from overlying soils, loose sediments, and weathered rock inside the Heshang Cave, Hubei Province, and conducted high-throughput sequencing of nifH responsible for nitrogen fixation. [Results] The nitrogen-fixing bacteria had the highest alpha diversity in the overlying soils and the lowest α diversity in the sediments. K⁺, NO₂^-, and NO₃^- were the main factors impacting the nitrogen-fixing bacteria, which showed high specificity for habitats. Bradyrhizobium widely distributed in all habitats with high relative abundance. Geobacter dominated in the overlaying soil, whereas Azotobacter was dominant in the sediments. Geobacter, Azotobacter, and Halorhodospira had similar relative abundance in weathered rock samples. The co-occurrence network analysis showed that the nitrogen fixers had closely positive correlations, suggesting their cooperative survival strategy under the oligotrophic conditions. It was noted that a large proportion of nitrogen fixers cannot be classified, which indicated rich novel nitrogen fixers in the caves, hot spots for studying microbial dark matter. [Conclusion] Our study revealed the composition and structure of the nitrogen-fixing microbial community and their correlations with environmental variables in the underground dark oligotrophic Heshang Cave. The findings are of great significance for the in-depth understanding of the nitrogen cycle in deep biosphere.

Abstract:[Objective] To investigate the variation of composition and abundance of microbial communities involved in the transformation of arsenic-bearing ferrihydrites under different humic acid concentrations and their effects on arsenic release, and to predict the role of functional microbial communities in participating the transformation processes of organic matter-arsenic-bearing iron minerals on arsenic release from high arsenic aquifers. [Methods] Iron-reducing microbial populations were enriched from a high arsenic groundwater and a high sediment sample from the same depth from Hetao Plain, Inner Mongolia Autonomous Region. Anaerobic microcosms were constructed by amendments of bacterial enrichment and different concentrations of humic acid (0, 1.5, 7, and 14 mg C/L) into arsenic-bearing ferrihydrites. The variation of arsenic and iron species during the 50-day incubation was monitored. The composition succession of microbial communities was analyzed by high-throughput sequencing, and the transformation of iron minerals was visualized by X-ray diffractometer (XRD). [Results] The iron-reducing functional communities enriched in the high arsenic groundwater group (group G) and the sediment group (group S) were significantly different, with Aeromonadaceae as the specific dominant family in group G while Shewanellaceae as the specific dominant family in group S. Results of microcosm experiments showed that the iron reduction rates and amount in group S were relatively faster and higher than those in group G. The liquid phase arsenic speciation in group G and group S were different. As(V) was the dominant arsenic form in group G throughout the incubation period. In contrast, in group S, As(V) was the main arsenic species in the early stage, and As(III) became dominant and was up to 3.4 μmol/L in the incubation of 20 d. It was assumed that the microbial communities capable of arsenic reduction were dominated at this time. In the final stage of incubation, the released arsenic in both group G and group S showed different degrees of fixation under the addition of humic acid. Different concentrations of humic acid led to different amounts of arsenic release. XRD results showed that the transformation of arsenic-bearing ferrihydrites was relatively higher in group S, with goethite the dominant secondary mineral in both groups. Redundancy analysis (RDA) indicated that the addition of arsenic and humic acid influenced the overall succession of microbial community composition. Comamonadaceae, Desulfobacteraceae, and Burkholderiaceae became the predominant populations in group G, while populations of Pseudomonadaceae, Comamonadaceae, and Burkholderiaceae were dominated in group S. [Conclusion] The amendments of different concentrations of humic acid into arsenic-bearing ferrihydrites led to differentiated successions of microbial communities, which might play different effects on iron mineral transformation and arsenic release.

Abstract:After undergoing weathering and being influenced by topography, vegetation, climate, time and biology, the carbonate rocks gradually evolved into black calcareous soil, brown calcareous soil, yellow calcareous soil and red calcareous soil. [Objective] This study aims to investigate the microbial community characteristics of particulate organic matter (POM) and mineral-associated organic matter (MAOM) in calcareous soil at different succession stages, providing a theoretical basis for the study of organic matter stability mechanism in karst soil. [Methods] Black calcareous soil, brown calcareous soil, yellow calcareous soil, and red calcareous soil from the Nonggang Nature Reserve in Guangxi were chosen as the research objects, and soil organic matter (SOM) was divided into POM and MAOM by using wet screening method. The soil physicochemical properties and soil microbial community characteristics were analyzed. [Results] During the succession process of calcareous soil, the soil organic carbon, total nitrogen, and exchangeable calcium contents of POM and MAOM showed a decreasing trend, and the C/N of MAOM was greater than that of POM, whereas the C/P of POM was greater than that of MAOM. The bacterial diversity was higher in black calcareous soil of POM and MAOM, and the diversity of bacteria and fungi in the four type calcareous soil of MAOM was higher than that in POM. Acidobacteria, Proteobacteria, and Ascomycota were the dominant phyla in POM and MAOM along the succession process of calcareous soil. Total phosphorus was a key factor affecting the changes of bacterial communities in POM and MAOM during calcareous soil succession, while dissolved organic carbon and soil organic carbon were key factors affecting the changes of fungal communities in POM and MAOM during calcareous soil succession, respectively. The microorganisms from black calcareous soil in POM and MAOM may have undergone ecological niche differentiation, and bacteria and fungi tend to cooperate more closely along calcareous soil succession. [Conclusion] During the succession process of calcareous soil, the nutrients and microbial diversity of POM and MAOM decrease. POM may be the main source for microbial nutrients, and MAOM is more conducive to be the long-term stable accumulation of carbon. This study can provide a theoretical basis for the role of microorganisms in the formation of organic matter during the succession process of karst soil.

Abstract:[Objective] The Liuzhong area of Xinjiang Oilfield is a typical ordinary heavy oil reservoir with poor water flooding effect and rich indigenous microorganisms. We studied the application potential of indigenous microbial flooding in this reservoir by analyzing the impact of indigenous microbial flooding on the microbial activities in the reservoir. [Methods] During the implementation of indigenous microbial flooding, we employed high-throughput sequencing and the techniques of analytical chemistry to systematically determine the microbial community structure, total bacterial count, number of functional microorganisms, and properties of the produced fluid. [Results] The injection of the activator and air into the reservoir in the field test significantly activated the indigenous microorganisms, changed the bacterial community structure, and increased the number of total bacteria and functional bacteria by 2-3 orders of magnitude. Moreover, it significantly enhanced the metabolic activities of indigenous microorganisms. After interaction with formation fluid, the crude oil was obviously emulsified, and the oil recovery was finally improved by 5.2%. [Conclusion] Indigenous microbial flooding significantly affects the microbial activities in the water drive ordinary heavy oil reservoirs with abundant indigenous microorganisms, demonstrating significant technical advantages and great application potential. The microbial community structure, number of functional microorganisms, and concentrations of related metabolites can be used as indicators to evaluate the on-site activation effect of indigenous microbial flooding. The findings of this study provide technical reference for other on-site experiments of indigenous microbial flooding.

Abstract:[Objective] To investigate the coal’s pyrite on the biological gas production. [Methods] In present work, we took the coal obtained from Yulin City, Shaanxi Province as substrate and the methanogenic microorganisms domesticated by our laboratory as inoculation flora. The simulation biological gas production of coal was carried out by dosing different content of pyrite into the anaerobic system. The changes of CH₄ content, total volatile fatty acids (VFAs) concentration, coenzyme F₄₂₀ content, organic functional groups of coal before and after gas production and microbial community structure were investigated by gas chromatograph, liquid chromatograph, microplate reader, Fourier infrared spectrometer and Illumina high-throughput sequencing platform. [Results] The addition of pyrite could promote the production of CH₄ in the early stage of gas production (15-22 d), while inhibited the production of CH₄ in the late stage (29-50 d). The gas production of 0.5% dosage pyrite in the early and middle stages was 48.1% higher than that of the control group, and the cumulative gas production reached 193.67 μmol/g-coal. The concentrations of VFAs and coenzyme F₄₂₀ in the experimental group were higher than those in the control group, indicating that the addition of pyrite promoted the activities of acid bacteria and methanogens in the reaction system. After adding pyrite, alcohol and phenol hydroxyl, -NH- and -NH₂ in coal were more easily utilized by microorganisms. Adding pyrite could influence the community diversity of bacteria and archaea, and greater effect on the latter. Adding a small amount of pyrite could improve the community abundance of Bacteroidota, while more pyrite could increase the community abundance of Bacillota. Pyrite had the most significant impact on Proteiniphilum, Desulfurella and JGI-0000079-D21 bacteria in the system. After addition of pyrite, the abundance of Halobacterota and Methanosarcina changed greatly. Pyrite had the most significant effect on Methanosarcina, Methanomassiliicoccus and Methanobacterium. [Conclusion] A small amount of pyrite can promote the biological gas production of coal, and affect the microbial community structure in fermentation liquid.

Abstract:[Objective] Soil contamination by heavy metal is a growing concern, of which vanadium is gradually becoming a research hotspot. Although leaching is an important tool for soil remediation, it can cause severe pollution and incur high cost. Bioleaching can be applied as an efficient soil remediation process because of its cost-effective and environmental- friendliness. However, current understanding of remediation of vanadium-contaminated soil is still limited. [Methods] In this study, we applied Acidithiobacillus ferrooxidans in the bioleaching of vanadium-contaminated soil. The optimal leaching conditions were investigated by changing the influencing factors. The scanning electron microscopy and energy dispersive X-ray spectroscopy were applied to analyze the changes of vanadium during the bioleaching process. The microbial metabolites were characterized. [Results] The microbial secondary metabolites could promote the leaching of vanadium from the soil. The leaching efficiency of vanadium from soil by Acidithiobacillus ferrooxidans was high, and the leaching rate of vanadium from soil reached 27.4% after 20 days. Further experiments on the influencing factors showed that the best leaching of vanadium from soil was achieved at a solid concentration of 3%, an inoculum volume of 10%, an initial pH of 1.8 and an initial Fe²⁺ concentration of 3.0 g/L. SEM-EDS analysis confirmed the reduction of vanadium content in the soil after leaching, and analysis of the vanadium morphology in the soil indicated that the vanadium present in the non-residue form in the soil was more easily leached. Metabolomic analyses showed that Acidithiobacillus ferrooxidans produced a large number of metabolites during the leaching process to cope with the high concentration of heavy metals in the environment. [Conclusion] The bioleaching technology can effectively remediate vanadium-contaminated soil. This study provides an environmentally friendly remediation approach for the restoration of vanadium-contaminated soil.

Abstract:[Objective] The environmental hazard of heavy metal vanadium is increasingly concerned. Microorganisms can achieve reductive immobilization of highly toxic pentavalent vanadium (V(V)), while electron donor is the key to this bioprocess. Although both natural Fe(II)-bearing minerals and natural biomass have been reported to independently support microbial V(V) reduction, the characteristics of microbial V(V) reduction under mixotrophic condition based on these two materials have not been revealed yet. [Methods] In this study, natural Fe(II) minerals and biomass were preferentially selected and compounded in combination to investigate the reduction mechanism of V(V) in a mixotrophic biological system. [Results] The results showed that the highest V(V) removal efficiencies of 54.2%±3.4% and 67.1%±3.1% were achieved for pyrrhotite and woodchips, respectively. The highest V(V) removal efficiency of 82.7%±3.1% was achieved when the preferred combination of pyrrhotite and woodchips was compounded at a ratio of 1:3. V(V) was reduced to insoluble V(IV) precipitate, while Fe(II) and S(-II) were oxidized to Fe(III) and SO₄^2-, respectively. In the mixotrophic system, chemolithoautotrophic bacterial genera such as Desulfurivibrio and Thiobacillus might be involved in the oxidation of pyrrhotite coupled to V(V) reduction and the synthesis of organic intermediate metabolites using inorganic carbon sources. Together with the decomposing products of woodchips by cellulose degrading bacteria such as Acholeplasma, these organics were utilized by chemoorganoheterotrophic V(V) reducers such as Bacteroidetes_vadinHA17 to reduce V(V). [Conclusion] This study provides a promising remediation method for groundwater V(V) contamination.

Abstract:[Objective] Constructed wetland fillers as denitrification electron donors can remove nitrogen and phosphorus efficiently and stably, but the selection method and mechanism of filler are still unclear. [Methods] In this study, pyrrhotite, siderite and agricultural waste (sawdust, etc.) were used as fillers in constructed wetlands, and their effects on denitrification, nitrogen and phosphorus removal in constructed wetlands were studied. [Results] The results show that the ore combination with a mass ratio of 1:1 and wood chips are used as a mixed filler with a mass ratio of 3:1, the removal rates of NO₃^--N and PO₄^3--P reached 88.6% and 88.9% after eight cycles of domestication. The results of scanning electron microscopy (SEM), X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD) and community analysis showed that the microorganisms could effectively use the ore and its secondary products and sawdust for efficient and lasting nitrogen and phosphorus removal, and the functional bacteria Thiobacillus, Romboutsia and Lysobacter were enriched. [Conclusion] This study provides theoretical basis and guiding significance for the selection of new fillers in the practical application of constructed wetlands.

Abstract:Carbon dioxide reduction and utilization is a key issue attracting increasing attention at present. Using carbon dioxide as the resource for the production of methane facilitates the environmental and social sustainability. By reviewing the studies of different technologies for the bio-conversion of carbon dioxide to methane, we summarized the pathways and influencing factors of carbon dioxide bio-conversion and the mechanisms and energy sources of the bio-conversion conducted by methylotrophic methanogens and hydrogenotrophic methanogens. Furthermore, we reviewed the studies about microbial electrosynthesis by different methanogens. We elaborated on the progress and existing problems in the reactor design, electrode material selection, parameter optimization, and result evaluation of carbon dioxide bio-conversion technologies, including microbial electrosynthesis, photosynthetic biohybrid systems, and anaerobic digestion. In particular, we put forward that enhancing microbial activity, improving hydrogen utilization efficiency, accelerating efficient electrode development, increasing energy efficiency, strengthening research on waste gas-stream, and reinforcing photo-electricity conversion can be the priorities and directions of the future research for improving microbial electrosynthesis. Moreover, this review deduced that strengthening interdisciplinary collaborative innovation, such as computer-based simulation, would be a new direction to promote the advances in carbon dioxide bio-conversion technology.

Abstract:Microplastics (MPs) are ubiquitous in the surface water of aquatic ecosystems. Generally, MPs can provide unique niches for microorganisms in the environment and pose potential threats to ecosystems and human health. China produces and uses a large amount of plastics, which results in serious plastic pollution. The pollution of MPs in aquatic ecosystems in China and the ecological effects of the microbial communities on MPs have aroused increasing concern. This review introduced the status of MP contamination in three major rivers (Pearl River, Yangtze River, and Yellow River) in China, the microorganisms on MPs, and the factors influencing the microbial community structure. Finally, we summarized the research progress in the microorganisms on MPs in China’s aquatic ecosystems and put forward the prospects.

Abstract:The gut microbiota of animals plays a crucial role in bridging host and ecosystem functions. [Objective] We aimed at assessing the effects of ryegrass application and different sampling periods of rice growth stages on the composition and structure of soil bacterial and nematode gut bacterial communities and exploring their potential linkages. [Methods] Based on a pot experiment, soil bacterial and nematode gut bacterial communities in the early (green returning period) and later (harvest period) stages of rice growth under ryegrass application and control treatments were analyzed by using 16S rRNA gene high-throughput sequencing technology. The potential impact of soil bacterial interactions on nematode gut bacterial communities was further studied with the network analysis. [Results] Ryegrass application did not significantly affect the composition and structure of soil and nematode gut bacterial communities (P>0.05). The later samples had higher alpha diversity than earlier ones. Extensive and significant correlations between soil bacterial and nematode gut bacterial biomarkers were obtained based on random forest machine learning, providing strong evidence that soil bacterial community changes regulate intestinal bacterial community composition of nematodes. Co-occurrence network-based analysis showed that positive interactions among soil bacteria were significantly (P<0.01) positively correlated with positive interactions between soil and nematode gut bacteria, thereby influencing network interactions among nematode gut bacteria. Structural equation modeling (SEM) further showed that the reduction of soil nutrients indirectly affected the network interactions among nematode gut bacteria mainly by reducing the positive network interactions among soil bacteria. [Conclusion] Soil bacterial interactions may play important roles in regulating network interactions and community composition of nematode gut bacteria.

Abstract:[Objective] To explore the organic carbon composition in lake sediments and the influence on the composition of lake microbial communities. [Methods] We collected 81 sediment samples from 29 lakes on the Qinghai-Tibet Plateau. The concentration of labile and recalcitrant organic carbon in the studied lake sediments was determined after sulfuric acid hydrolysis, and the correlation with environmental variables was analyzed. Meanwhile, the diversity and composition of prokaryotic and fungal communities in the sediments and their correlation with the concentration of labile and recalcitrant organic carbon were investigated by Illumina sequencing and ecological statistics. [Results] The concentration of labile organic carbon I (LOC Ⅰ), labile organic carbon Ⅱ (LOC Ⅱ), and recalcitrant organic carbon (ROC) in the studied lake sediments was 0.03-29.62 mg/g, 0.02-23.38 mg/g, and 0.64-75.72 mg/g, respectively. ROC was the major component of organic carbon in the studied lake sediments, accounting for 54.97%±19.50%. Concentration of LOC Ⅰ was significantly correlated with elevation, and concentration of total nitrogen, total phosphorus, calcium ion, active calcium, and iron (P<0.05). Concentration of LOC Ⅱ was significantly correlated with concentration of total nitrogen, calcium ion, and active calcium. ROC concentration was significantly correlated with elevation, concentration of total nitrogen, total phosphorus, calcium ion, and active calcium. Among them, the concentration of calcium ion and active calcium was positively correlated with the concentration of LOC Ⅰ, LOC Ⅱ, and ROC, suggesting that organic matter binding with calcium may be an important mechanism for the preservation of organic carbon in lake sediments on the Qinghai-Tibet Plateau. The alpha diversity of prokaryotic community was positively correlated with the concentration of LOC Ⅰ, LOC Ⅱ, and ROC, while the α diversity of fungal community was only positively correlated with ROC concentration. The relative abundance of Alphaproteobacteria, Actinobacteria, Anaerolineae, Phycisphaerae, and Rhodothermes was significantly correlated with LOC Ⅰ concentration. The relative abundance of Anaerolineae, Gammaproteobacteria, and Phycisphaerae was significantly correlated with the concentration of LOC Ⅱ. The relative abundance of Actinobacteria and Anaerolineae was significantly correlated with ROC concentration. The concentration of LOC Ⅰ significantly affected both prokaryotic and fungal community composition in the studied lake sediments with the variance explained of 1.1% and 0.3%, respectively. Environmental factors explained 7.2% and 3.9% of the variation in prokaryotic and fungal community composition among samples, respectively, while spatial factors explained 14.6% and 6.4%, separately. The contributions of stochastic process to prokaryotic and fungal community assembly were 50% and 47%, respectively. [Conclusion] Organic carbon preservation in the studied lake sediments was controlled by the chemical protection of iron and calcium. Organic carbon components significantly affected the diversity and composition of prokaryotic and fungal community, but the variance explained was low. Physicochemical variables, spatial factors, and stochastic processes exhibited important influence on prokaryotic and fungal community composition in the studied lake sediments. This study advances our understanding of organic carbon components in sediments and their impact on microbial community composition in lakes.

Abstract:[Objective] To investigate the response of geochemistry and bacterial communities to water-level rise in the soil and sediment of the coastal zone of Qinghai Lake. [Methods] Surface samples were collected from the onshore soil (soil: S1, S2), littoral zone (transition: E0, E6, E17) and deep sediment (sediment: D1, D2) along the direction perpendicular to the shoreline near the Bird Island of Qinghai Lake. The water depth of the soil and sediment samples (soil water depths were expressed as negative numbers) was employed to characterize the transformation of shoreline soil into sediment caused by inundation. Geochemical analysis and 16S rRNA gene high-throughput sequencing were employed to explore the geochemical characteristics and microbial community composition in the collected soil and sediment samples. [Results] (1) The water level rise of Qinghai Lake significantly affects the geochemical characteristics, nutrient levels, and organic carbon types in the soils and sediments of the coastal zone. Specifically, the pH and mineral associated organic carbon contents of the soil and sediment in the shore zone increased significantly while the C/N value and the contents of dissolved organic carbon (DOC) and particulate organic carbon decreased significantly with the increase of water level; (2) The water level rise of Qinghai Lake will reduce the diversity of bacterial communities and change their community structure in the coastal soils and sediments. These changes in bacterial communities are closely related to changes in environmental factors caused by water level rise. Specifically, after the onshore soil was inundated by water level rise, the bacterial communities inhabiting it exhibited a decrease in the number of operational taxonomic unit (OTU) and Shannon diversity index; the changes of bacterial community diversity was closely related to the content of organic carbon bound with active metal; the important environmental factors that affect bacterial community structure included physicochemical properties (pH), nutrient level (total organic carbon content), and organic carbon quality (C/N value, organic carbon pool II, and mineral associated organic carbon content). Physicochemical properties, nutrient level, and organic carbon quality contributed equally to the differences in bacterial community structure. [Conclusion] The water level rise of Qinghai Lake has significantly affected the physiochemical characteristics, nutrient levels, and organic carbon quality of coastal soil and sediment, and reshaped the bacterial community structure. This implies that the regional carbon cycle homeostasis of the Qinghai-Tibetan lakes will change in the context of the extensive expansion of lakes on the Qinghai-Tibet Plateau. This study provides a data base and theoretical support for the evolution of soil and sediment microbial communities and the evaluation of ecosystem carbon stability in response to lake expansion.

Abstract:Carbohydrate-binding module (CBM) are important components of carbohydrate-active enzymes. CBMs recognize and bind to specific polysaccharides (substrates) to increase the concentration of catalytic domains near the substrates and improve catalytic efficiency, facilitating the degradation of macromolecular compounds such as cellulose, xylan, chitin, and xanthan. The substrate-binding characteristics of CBM vary because of the different sources or structures. This paper summarizes the studies of CBM in recent years from the aspects of family, structure, and function, especially the application in the degradation of polysaccharides and the modification of glycoside hydrolases.

Abstract:Adhesins and enterotoxins are the main virulence factors produced by enterotoxigenic Escherichia coli (ETEC), one of the major pathogens causing diarrhea in both humans and animals. Adhesins mediate the initial adhesion of ETEC to intestinal epithelial cells, which leads to ETEC colonization of the host small intestine. Subsequently, the ETEC produces enterotoxins, which result in the loss of electrolytes and culminates in watery diarrhea. ETEC is typically regarded as a non-invasive pathogen, which does not induce the apoptosis of intestinal epithelial cells or destroy intestinal barrier structure. However, more and more evidence indicates that ETEC is able to induce the apoptosis of intestinal epithelial cells in vitro and in vivo. The cell apoptosis would destroy the integrity of the intestinal mucosal barrier of the host and lead to ETEC-caused diarrhea. We introduce the mechanisms of apoptosis induced by different virulence determinants produced by ETEC, the correlation between intestinal epithelial cell apoptosis and ETEC-caused diarrhea, and the potential of using anti-apoptosis therapy to prevent ETEC infection in piglets, aiming to provide a reference for deciphering the molecular pathogenic mechanism of ETEC and provide new measures for preventing and treating diarrhea caused by the pathogen.

Abstract:Proteasomes play a vital role in the intracellular proteolysis of eukaryotes, archaea, and some bacteria (mainly actinobacteria). Although similar in structure, bacterial proteasomes are distinguished from the eukaryotic and archaeal proteasomes in assembly, regulation, and physiological functions. Studying bacterial proteasomes helps understand their origin and evolutionary processes and guides the mining of proteasome inhibitors (PI) with broad medical application prospects. This review summarized the current research status of the structure, function, and evolution of bacterial proteasomes and the latest progress on bacterial proteasome inhibitors, hoping to provide references for related research.

Abstract:Arbuscular mycorrhizal fungi (AMF) and dark septate endophytes (DSE) are the two key types of root symbiotic fungi that enhance plant growth and resistance of plants to heavy metal stress. Arsenic (As) and As compounds are highly toxic, which accumulate in plants and then enter biologic chain. Our team has been committed to the study of relationship between endophytic fungi and the growth, synthesis of active substances, and arsenic absorption and accumulation of medicinal plants and has made some progress. According to our previous research outcomes and available research results, we summarized the role of AMF colonization in the growth and As uptake and accumulation in host plants under As stress, expounded the responses of host plants to AMF regulation under As stress in terms of physiological activities, antioxidant system, hormone level, and transcription level. In addition, 7 synergistic regulatory mechanisms involved in improving the As resistance were summarized at cellular level: ‘growth dilution effect’, ‘isolation of hyphae’, ‘chelating and filtration’, ‘mycorrhizal immobilization’, ‘transporter inhibition’, ‘biotransformation’, and ‘protecting the host and reducing oxidative stress’. The interaction among mechanisms was plotted. There are limited studies on the regulation of As stress by DSE-host plants. We found that the mechanism of DSE in enhancing arsenic tolerance of plants is similar to that of AMF. Our work has important reference value for studying synergistic antagonistic mechanism of endophytic fungi and host plants against As stress, alleviating As-polluted soil, implementing ecological agriculture or ecological planting of Chinese medicinal materials, and reducing As accumulation in key parts of plants.

Abstract:[Objective] Due to the difference in production process, conventional Yongchuan Douchi (fermented soybean product) and rapid Yongchuan Douchi are remarkably different in flavor quality. We explored the effect of koji-making process on the quality of Douchi. [Methods] Yongchuan Douchi was prepared with the rapid process but different koji-making methods (conventional natural process and artificial inoculation of Aspergillus oryzae, respectively). Then we compared the physicochemical properties and microbial community of the products. [Results] The Douchi prepared with the natural koji-making process had higher content of amino acid nitrogen and darker color (P<0.05), lower content of reducing sugar (P<0.05), and higher microbial richness and diversity (P<0.05) than the product prepared with the artificial inoculation of A. oryzae. The two products showed no significant difference in the titratable acid content (P>0.05). The dominant bacterial genera of the Douchi prepared with the natural koji-making process were Mucor, Bacillus, Enterobacter, Enterococcus, Pseudomonas, Staphylococcus, Wickerhamomyces, Penicillium, and those of the Douchi prepared with the artificial inoculation of A. oryzae were Bacillus, Corynebacterium, Aspergillus, and Candida. In addition, a small number of Debaryomyces sp. was found on both of the two products. [Conclusion] The koji-making process had significant influence on the physicochemical properties and microbial community structure of rapid Yongchuan Douchi. The key physicochemical indexes of Douchi prepared with the natural koji-making process were significantly better than those of the Douchi prepared with artificial inoculation of A. oryzae.

Abstract:[Objective] To analyze the effects of the addition of exogenous plant growth-promoting bacteria (PGPB) on plant growth, arsenic (As) accumulation, and rhizosphere microorganisms, and provide references for plant-microbial remediation of As-contaminated soil. [Methods] By adding exogenous PGPB into the soil, the relationships between the plant biomass and As content of Pteris vittata and the plant growth-promoting characteristics of PGPB were investigated. The high-throughput sequencing was also used to analyze the change in the rhizosphere microbial community of P. vittata with the intervention of exogenous PGPB. [Results] Two rhizobacteria Pseudomonas sp. PG12 and Bacillus sp. R19, and one endophytic bacterium P. putida S6 had typical plant growth-promoting characteristics, and the order of the growth-promoting effects on P. vittata was PG12>S6>R19. As compared with the control group, PG12, S6, and R19 increased the plant biomass by 234% (P<0.01), 136% (P<0.01), and 67%, respectively. The addition of exogenous PGPB increased the As content of P. vittata from 18.50 mg to 31.25−46.95 mg, being an increased percentage of 153% in PG12 and 139% in S6, respectively. The corresponding concentration of As in P. vittata decreased from 2 616.34 mg/kg to 1 348.04−2 156.23 mg/kg, showing a typical As “dilution effect”. Moreover, the α diversity indexes including Sobs, Chao, and Ace revealed that only R19 significantly improved the diversity of the rhizosphere microbial community, while the beta diversity analysis based on principal component analysis (PCA), principal co-ordinates analysis (PCoA), and partial least squares-discriminant analysis (PLS-DA) showed that there were significant clustering differences among all treatments. Furthermore, species composition analysis showed that the exogenous PGPB affected the distribution of the rhizosphere microbial community with an increase in the relative abundance of Arthrobacter and Solirubrobacter, etc., and a decrease in the relative abundance of Acidibacter, Dongia, and MND1. These microbial communities were presumedly associated with the growth and As uptake of P. vittata. [Conclusion] Exogenous PGPB addition shows positive effects on the growth, As uptake, and rhizosphere microbial community of P. vittata. The results of this study provide important clues for revealing the mechanism of arsenic remediation enhanced by microorganisms in plants, thereby promoting the associated studies on the plant-microbial remediation of As-contaminated soil.

Abstract:[Objective] To determine whether the byssochlamic acid (BA) gene cluster exists in the genome of Monascus ruber M7, and to explore the effect of polyketide synthase gene mr-Bys and 3-hydroxyacyl-CoA dehydrogenase gene mr-hdh in BA gene cluster on BA production. [Methods] The M7 genome was analyzed by bioinformatics methods to identify the BA candidate gene clusters. The effects of mr-Bys and mr-hdh on BA production were studied by the gene knockout and over-expression methods. BA was analyzed by ultra-performance liquid chromatography (UPLC) and mass spectrometry (MS). [Results] A BA gene cluster was found in the genome of M. ruber M7. After knocking out mr-Bys, BA disappeared, while both knockout and over-expression of mr-hdh affected BA production by M. ruber M7. [Conclusion] There is a BA gene cluster in the genome of M. ruber M7, which can produce BA. The research results enrich the research on the secondary metabolites of Monascus spp. and their synthetic pathways and lay a foundation for the development of new products using Monascus spp.

Abstract:[Objective] Isoniazid (INH) and ethambutol (EMB) are the two main first-line drugs for the treatment of tuberculosis (TB), while the underlying synergistic mechanism remains unclear. [Methods] The Ms0606 gene was cloned from Mycobacterium smegmatis and its expression was induced by the addition of 0.5 mmol/L isopropyl β-d-1-thiogalactopyranoside (IPTG) at 37 °C for 4 h. The interaction between Ms0606 protein and EMB was studied by isothermal titration calorimetry (ITC). The effect of EMB on the DNA binding activity of Ms0606 was examined by electrophoretic mobility shift assay (EMSA). The growth curves of the Ms0606-overexpressing strain treated with INH and INH+EMB were established. [Results] Ms0606 protein was purified with high purity. EMB can bind with Ms0606 at a ratio of 1:1 and specifically enhance the DNA binding activity of Ms0606. In the presence of a non-lethal dose of EMB, the overexpression of Ms0606 enhanced the effect of INH on M. smegmatis MC²155. [Conclusion] The TetR family transcriptional regulator encoded by Ms0606 plays a role in the synergistic effect of EMB and INH, the further research on which will help us to understand the regulatory mechanism of bacterial resistance.

Abstract:The function of CD630_27900 gene at the slpA-cwp66 locus of Clostridioides difficile is still unclear. The encoded enzyme is putatively regarded as a member of Lmbe family. [Objective] To construct CD630_27900 gene-deleted mutant, compare the phenotypes of the wild-type strain (CD630) and the mutant, and discuss the effect of CD630_27900 gene on the infection of C. difficile. [Methods] The CD630_27900-deleted mutant and the complementary strain were constructed by allele-coupled exchange (ACE). The growth curves, expression of autolysin genes (cwp19, Acd), cytotoxicity, expression of major toxin genes, and sensitivity to antibiotics and pH were compared among the three strains. [Results] The mutant strain ∆CD630_27900 and the complementary strain ::CD630_27900 were successfully constructed. At the decline phase, the autolysis rate of ∆CD630_27900 was significantly lower than that of CD630, and the autolysis rate of ::CD630_27900 was restored. The real-time fluorescence quantitative polymerase chain reaction(RT-qPCR) results showed that the expression of cwp19 and Acdwas decreased in ∆CD630_27900 and increased in ::CD630_27900 compared with that in the wild type. The cytotoxicity assay showed that the cytotoxicity of ∆CD630_27900 was significantly reduced compared with that of CD630 and the complementary strain, which is consistent with reduced expression levels of thetoxin genes tcdA and tcdB. Furthermore, ∆CD630_27900 showed significantly stronger sensitivity to ampicillin, metronidazole, amoxicillin, vancomycin, norfloxacin, cefoxitin, and kanamycin than CD630 and ::CD630_27900. Strain ∆CD630_27900 was more sensitive to acid than strain CD630 and ::CD630_27900. However, the sensitivity of ∆CD630_27900 to the alkaline environment was comparable to that of CD630. [Conclusion] Upon the deletion of CD630_27900 gene, C. difficile demonstrated slow autolysis, low expression of autolys in genes cwp19 and Acd, low cytotoxicity, and low expression of toxin genes tcdA and tcdB. Thus, CD630_27900 may influence the autolysis and virulence of C. difficile. ∆CD630_27900 was more sensitive to the antibiotics commonly used in clinical settings than the wild type. These changes were reversed after the complementation of the gene. Thus, CD630_27900 can be a potential target in the treatment of C. difficile infection (CDI) with antibiotics.

Abstract:There are few studies about the functional genes involved in the microbial degradation of polycyclic aromatic hydrocarbons (PAHs) in crude oil-contaminated soils in Xinjiang, and the correlations between environmental factors and functional genes remain unclear. [Objective] To reveal the structures and dynamic characteristics of key PAH-degrading genes during the natural attenuation of crude oil-contaminated sandy soils in Xinjiang. [Methods] We studied the variations in the physicochemical properties and the content of PAHs in the soils contaminated by crude oil for different years in the same oil production area in Zhundong Oilfield in Xinjiang. Amplicon sequencing was employed to study the dynamic characteristics of genes involved in the degradation of PAHs during the natural attenuation of crude oil-contaminated soils. Mental test was performed to explore the environmental driving factors. [Results] The soils contaminated by crude oil for 1 and 3 years had several physicochemical properties significantly different from the background soils, while that contaminated for 5 years had only 2 physicochemical properties significantly different, which gradually returned to normal levels with the natural attenuation of crude oil. Among the 16 PAHs studied, the remaining 14 PAHs except acenaphthylene and chrysene in the soils contaminated by crude oil for 1 year had higher content than those in the soil contaminated by crude oil for 3 and 5 years. The total PAHs and crude oil content in the 1-year contaminated soils were significantly higher than those in the 3-year and 5-year contaminated soils, which indicated that PAHs could be rapidly degraded in a short time after contamination. The amplicon sequencing results showed that the operational taxonomic units (OTUs) of naphthalene dioxygenase gene gradually increased with the extension of pollution years. The OTUs of aromatic ring-hydroxylating dioxygenase gene were annotated by BLAST alignment into 6 types of PAH-degrading genes, which first increased and then decreased with the extension of contamination time. The OTUs of aromatic ring-hydroxylating dioxygenase gene presented dramatically decreased diversity within 5 years of contamination. The Mental test results showed that the functional gene structures were significantly affected by soil soluble organic carbon and water content and not by PAHs. [Conclusion] The structures of PAH-degrading genes are mainly affected by soil soluble organic carbon and water content during the natural attenuation of crude oil-contaminated sandy soil in the Zhundong Oilfield of Xinjiang.

Abstract:[Objective] Melanose caused by Diaporthe citri is one of the major fungal diseases in citrus. D. citri mainly undergoes three developmental stages, including mycelial growth stage (10 d, T1), pycnidium development stage (20 d, T2), and conidial sporulation stage (30 d, T3). The metabolomics analysis of the markers and key metabolites during the development of D. citri can provide clues for clarifying the sporulation mechanism and metabolic regulation of D. citri. [Methods] Ultra performance liquid chromatography/tandem mass spectrometry (UPLC-MS/MS) was employed to analyze the metabolic changes during the development of D. citri. Then, principal component analysis (PCA) and orthogonal partial least squares discriminant analysis (OPLS-DA) were performed to screen the differential metabolites. Finally, KEGG pathway enrichment analysis was conducted for the differential metabolites. [Results] A total of 1 090 metabolites were identified at the three developmental stages of D. citri. According to the thresholds of VIP≥1 and fold change≥2 or ≤0.5, 265, 456, and 580 differential metabolites were screened out for T1 vs. T2, T2 vs. T3, and T1 vs. T3, respectively. The differential metabolites mainly included organic acids, triglycerides, fatty acids, and amino acids, which were closely associated with the morphological development of the pathogen. Linoleic acid and its metabolites (13-HpODE, 9(S)-HODE, 9-oxoODE, 13-oxoODE, 9-HpODE, 9(S),12(S),13(S)-TriHOME, 9,10-DiHOME, and γ-linoleic acid), as well as arachidonic acid and its metabolites (20-COOH-AA, LXB4, 15-keto prostaglandin F2α, 20-carboxy LTB4, 15-deoxy-δ-12,14-PGJ2), might play a role in the sporulation of D. citri. [Conclusion] The morphological development of D. citri was closely associated with the changes of metabolites during different developmental stages, and the oxylipid metabolites (linoleic acid, arachidonic acid and their metabolites) were the key metabolites for sporulation.

Abstract:[Objective] Cell thermal shift assay (CETSA) is a biophysical technique allowing the direct study of drug (ligand) binding to proteins (targets) in cells and tissues by measuring variation in the proteins’ thermal stability upon ligand binding. In this paper, taking panobinostat, a drug targeting multiple myeloma, as an example, we developed a standard operating procedure for the identification of drug targets in K562 cells with Western blotting and CETSA. [Methods] Experimental procedures included treating cells with the drug, heat treatment of cells, cell lysis, total soluble protein extraction and quantitation by Western blotting with specific antibodies. [Results] Through quantification by Western blotting and curve fitting, we obtained the CETSA melting curve and isothermal dose-response curve of histone deacetylase (HDAC1), syntaxin-4 (STX4), and tetratricopeptide repeat protein 38 (TTC38) in K562 cells, respectively.[Conclusion] HDAC1, STX4, and TTC38 were the targets of panobinostat in K562 cells. A standard operating procedure for identifying the target proteins in living cells was established by CESTA and Western blotting. The experiment can be completed in 2-3 d.