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Catalytic regio-, diastereo- and enantioselective reductive coupling of 1,3-dienes and aldehydes through regio- and enantioselective oxidative cyclization followed by regio- and diastereoselective protonation promoted by a chiral phosphine-cobalt complex is presented. Such processes represent an unprecedented reaction pathway for cobalt catalysis that enable selective transformation of the more substituted alkene in 1,3-dienes, affording a broad scope of bishomoallylic alcohols without the need of pre-formation of stoichiometric amounts of sensitive organometallic reagents in up to 98% yield, >98:2 regioselectivity, >98:2 dr and 98:2 er. Application of this method to construction of axial stereogenicity and deuterated stereogenic center provided a wide range of multifunctional chiral building blocks that are otherwise difficult to access. DFT calculations revealed the origin of regio- and stereoselectivity as well as a unique oxidative cyclization mechanism for cobalt catalysis.
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Even in the vertical dimension, soil bacterial communities are spatially distributed in a distance-decay relationship (DDR). However, whether this pattern is universal among all soil microbial taxonomic groups, and how body size influences this distribution, remains elusive. Our study consisted of obtaining 140 soil samples from two adjacent ecosystems in the Yellow River Delta (YRD), both nontidal and tidal, and measuring the DDR between topsoil and subsoil for bacteria, archaea, fungi and protists (rhizaria). Our results showed that the entire community generally fitted the DDR patterns (P < 0.001), this was also true at the kingdom level (P < 0.001, with the exception of the fungal community), and for most individual phyla (47/75) in both ecosystems and with soil depth. Meanwhile, these results presented a general trend that the community turnover rate of nontidal soils was higher than tidal soils (P < 0.05), and that the rate of topsoil was also higher than that of subsoil (P < 0.05). Additionally, microbial spatial turnover rates displayed a negative relationship with body sizes in nontidal topsoil (R2 = 0.29, P = 0.009), suggesting that the smaller the body size of microorganisms, the stronger the spatial limitation was in this environment. However, in tidal soils, the body size effect was negligible, probably owing to the water's fluidity. Moreover, community assembly was judged to be deterministic, and heterogeneous selection played a dominant role in the different environments. Specifically, the spatial distance was much more influential, while the soil salinity in these ecosystems was the major environmental factor in selecting the distributions of microbial communities. Overall, this study revealed that microbial community compositions at different taxonomic levels followed relatively consistent distribution patterns and mechanisms in this coastal area.
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Bacterias , Microbiota , Bacterias/genética , Suelo , Microbiología del SueloRESUMEN
Although many studies have investigated the spatial scaling of microbial communities living in surface soils, very little is known about the patterns within deeper strata, nor is the mechanism behind them. Here, we systematically assessed spatial scaling of prokaryotic biodiversity within three different strata (Upper: 0-20 cm, Middle: 20-40 cm, and Substratum: 40-100 cm) in a typical grassland by examining both distance-decay (DDRs) and species-area relationships (SARs), taxonomically and phylogenetically, as well as community assembly processes. Each layer exhibited significant biogeographic patterns in both DDR and SAR (p < .05), with taxonomic turnover rates higher than phylogenetic ones. Specifically, the spatial turnover rates, ß and z values, respectively, ranged from 0.016 ± 0.005 to 0.023 ± 0.005 and 0.065 ± 0.002 to 0.077 ± 0.004 across soil strata, and both increased with depth. Moreover, the prokaryotic community in grassland soils assembled mainly according to deterministic rather than stochastic mechanisms. By using normalized stochasticity ratio (NST) based on null model, the relative importance of deterministic ratios increased from 48.0 to 63.3% from Upper to Substratum, meanwhile a phylogenetic based method revealed average ßNTI also increased with depth, from -5.29 to 19.5. Using variation partitioning and distance approaches, both geographic distance and soil properties were found to strongly affect biodiversity structure, the proportions increasing with depth, but spatial distance was always the main underlying factor. These indicated increasingly deterministic proportions in accelerating turnover rates for spatial assembly of prokaryotic biodiversity. Our study provided new insights on biogeography in different strata, revealing importance of assembly patterns and mechanisms of prokaryote communities in below-surface soils.
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Biodiversidad , Microbiota , Microbiota/genética , Filogenia , Suelo , Microbiología del SueloRESUMEN
KEY MESSAGE: High-resolution multiplex oligonucleotide FISH revealed the frequent occurrence of structural chromosomal rearrangements and polymorphisms in widely grown wheat cultivars and their founders. Over 2000 wheat cultivars including 19 founders were released and grown in China from 1949 to 2000. To understand the impact of breeding selection on chromosome structural variations, high-resolution karyotypes of Chinese Spring (CS) and 373 Chinese cultivars were developed and compared by FISH (fluorescence in situ hybridization) using an oligonucleotide multiplex probe based on repeat sequences. Among them, 148 (39.7%) accessions carried 14 structural rearrangements including three single translocations (designated as T), eight reciprocal translocations (RT), one pericentric inversion (perInv), and two combined variations having both the deletion and single translocations. Five rearrangements were traced to eight founders, including perInv 6B detected in 57 cultivars originating from Funo, Abbondanza, and Fan 6, T 1RSâ1BL in 47 cultivars derived from the Lovrin series, RT 4ASâ4AL-1DS/1DLâ1DS-4AL in 31 varieties from Mazhamai and Bima 4, RT 1RSâ7DL/7DSâ1BL in three cultivars was from Aimengniu, and RT 5BSâ5BL-5DL/5DSâ5DL-5BL was only detected in Youzimai. In addition to structural rearrangements, 167 polymorphic chromosome blocks (defined as unique signal patterns of oligonucleotide repeat probes distributed within chromosomes) were identified, and 59 were present in one or more founders. Some specific types were present at high frequencies indicating selective blocks in Chinese wheat varieties. All cultivars and CS were clustered into four groups and 15 subgroups at chromosome level. Common block patterns occurred in the same subgroup. Origin, geographic distribution, probable adaptation to specific environments, and potential use of these chromosomal rearrangements and blocks are discussed.
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Inversión Cromosómica , Polimorfismo Genético , Translocación Genética , Triticum/genética , China , Cromosomas de las Plantas/genética , Hibridación Fluorescente in Situ , Cariotipo , OligonucleótidosRESUMEN
In comparison with general FISH for preparing probes in terms of time and cost, synthesized oligonucleotide (oligo hereafter) probes for FISH have many advantages such as ease of design, synthesis, and labeling. Low cost and high sensitivity and resolution of oligo probes greatly simplify the FISH procedure as a simple, fast, and efficient method of chromosome identification. In this study, we developed new oligo and oligo multiplex probes to accurately and efficiently distinguish wheat (Triticum aestivum, 2n = 6x, AABBDD) and Thinopyrum bessarabicum (2n = 2x = 14, JJ) chromosomes. The oligo probes contained more nucleotides or more repeat units that produced stronger signals for more efficient chromosome painting. Four Th. bessarabicum-specific oligo probes were developed based on genomic DNA sequences of Th. bessarabicum chromosome arm 4JL, and one of them (oligo DP4J27982) was pooled with the oligo multiplex #1 to simultaneously detect wheat and Th. bessarabicum chromosomes for quick and accurate identification of Chinese Spring (CS) - Th. bessarabicum alien chromosome introgression lines. Oligo multiplex #4 revealed chromosome variations among CS and eight wheat cultivars by a single round of FISH analysis. This research demonstrated the high efficiency of using oligos and oligo multiplexes in chromosome identification and manipulation.
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Pintura Cromosómica , Cromosomas de las Plantas , Poaceae/genética , Triticum/genética , Pintura Cromosómica/métodos , Genes de Plantas , Variación Genética , Hibridación Fluorescente in Situ/métodos , Cariotipo , Familia de Multigenes , Secuencias Repetitivas de Ácidos NucleicosRESUMEN
The inoculum has a crucial impact on bioreactor initialization and performance. However, there is currently a lack of guidance on selecting appropriate inocula for applications in environmental biotechnology. In this study, we applied microbial electrolysis cells (MECs) as models to investigate the differences in the functional potential of electroactive microorganisms (EAMs) within anodic biofilms developed from four different inocula (natural or artificial), using shotgun metagenomic techniques. We specifically focused on extracellular electron transfer (EET) function and stress resistance, which affect the performance and stability of MECs. Community profiling revealed that the family Geobacteraceae was the key EAM taxon in all biofilms, with Geobacter as the dominant genus. The c-type cytochrome gene imcH showed universal importance for Geobacteraceae EET and was utilized as a marker gene to evaluate the EET potential of EAMs. Additionally, stress response functional genes were used to assess the stress resistance potential of Geobacter species. Comparative analysis of imcH gene abundance revealed that EAMs with comparable overall EET potential could be enriched from artificial and natural inocula (P > 0.05). However, quantification of stress response gene copy numbers in the genomes demonstrated that EAMs originating from natural inocula possessed superior stress resistance potential (196 vs. 163). Overall, this study provides novel perspectives on the inoculum effect in bioreactors and offers theoretical guidance for selecting inoculum in environmental engineering applications.
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Biopelículas , Reactores Biológicos , Reactores Biológicos/microbiología , Geobacter/fisiología , Geobacter/genética , Metagenómica , Estrés Fisiológico , Fuentes de Energía Bioeléctrica , Transporte de ElectrónRESUMEN
BACKGROUND: Microbial anaerobic metabolism is a key driver of biogeochemical cycles, influencing ecosystem function and health of both natural and engineered environments. However, the temporal dynamics of the intricate interactions between microorganisms and the organic metabolites are still poorly understood. Leveraging metagenomic and metabolomic approaches, we unveiled the principles governing microbial metabolism during a 96-day anaerobic bioreactor experiment. RESULTS: During the turnover and assembly of metabolites, homogeneous selection was predominant, peaking at 84.05% on day 12. Consistent dynamic coordination between microbes and metabolites was observed regarding their composition and assembly processes. Our findings suggested that microbes drove deterministic metabolite turnover, leading to consistent molecular conversions across parallel reactors. Moreover, due to the more favorable thermodynamics of N-containing organic biotransformations, microbes preferentially carried out sequential degradations from N-containing to S-containing compounds. Similarly, the metabolic strategy of C18 lipid-like molecules could switch from synthesis to degradation due to nutrient exhaustion and thermodynamical disadvantage. This indicated that community biotransformation thermodynamics emerged as a key regulator of both catabolic and synthetic metabolisms, shaping metabolic strategy shifts at the community level. Furthermore, the co-occurrence network of microbes-metabolites was structured around microbial metabolic functions centered on methanogenesis, with CH4 as a network hub, connecting with 62.15% of total nodes as 1st and 2nd neighbors. Microbes aggregate molecules with different molecular traits and are modularized depending on their metabolic abilities. They established increasingly positive relationships with high-molecular-weight molecules, facilitating resource acquisition and energy utilization. This metabolic complementarity and substance exchange further underscored the cooperative nature of microbial interactions. CONCLUSIONS: All results revealed three key rules governing microbial anaerobic degradation. These rules indicate that microbes adapt to environmental conditions according to their community-level metabolic trade-offs and synergistic metabolic functions, further driving the deterministic dynamics of molecular composition. This research offers valuable insights for enhancing the prediction and regulation of microbial activities and carbon flow in anaerobic environments. Video Abstract.
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Biodegradación Ambiental , Reactores Biológicos , Metabolómica , Microbiota , Anaerobiosis , Reactores Biológicos/microbiología , Bacterias/metabolismo , Bacterias/genética , Bacterias/clasificación , Metagenómica , Metano/metabolismo , Termodinámica , MultiómicaRESUMEN
BACKGROUND: Leakages of cold, methane-rich fluids from subsurface reservoirs to the sea floor are termed cold seeps. Recent exploration of the deep sea has shed new light on the microbial communities in cold seeps. However, conventional metagenomic methods largely rely on reference databases and neglect the phylogeny of functional genes. RESULTS: In this study, we developed the REMIRGE program to retrieve the full-length functional genes from shotgun metagenomic reads and fully explored the phylogenetic diversity in cold seep sediments. The abundance and diversity of functional genes involved in the methane, sulfur, and nitrogen cycles differed in the non-seep site and five cold seep sites. In one Haima cold seep site, the divergence of functional groups was observed at the centimeter scale of sediment depths, with the surface layer potentially acting as a reservoir of microbial species and functions. Additionally, positive correlations were found between specific gene sequence clusters of relevant genes, indicating coupling occurred within specific functional groups. CONCLUSION: REMIRGE revealed divergent phylogenetic diversity of functional groups and functional pathway preferences in a deep-sea cold seep at finer scales, which could not be detected by conventional methods. Our work highlights that phylogenetic information is conducive to more comprehensive functional profiles, and REMIRGE has the potential to uncover more new insights from shotgun metagenomic data. Video Abstract.
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Sedimentos Geológicos , Microbiota , Océanos y Mares , Metano/metabolismo , Filogenia , ARN Ribosómico 16S/genética , Metagenómica , FríoRESUMEN
Ecological and evolutionary processes simultaneously regulate microbial diversity, but the evolutionary processes and their driving forces remain largely unexplored. Here we investigated the ecological and evolutionary characteristics of microbiota in hot springs spanning a broad temperature range (54.8-80 °C) by sequencing the 16S rRNA genes. Our results demonstrated that niche specialists and niche generalists are embedded in a complex interaction of ecological and evolutionary dynamics. On the thermal tolerance niche axis, thermal (T) sensitive (at a specific temperature) versus T-resistant (at least in five temperatures) species were characterized by different niche breadth, community abundance and dispersal potential, consequently differing in potential evolutionary trajectory. The niche-specialized T-sensitive species experienced strong temperature barriers, leading to completely species shift and high fitness but low abundant communities at each temperature ("home niche"), and such trade-offs thus reinforced peak performance, as evidenced by high speciation across temperatures and increasing diversification potential with temperature. In contrast, T-resistant species are advantageous of niche expansion but with poor local performance, as shown by wide niche breadth with high extinction, indicating these niche generalists are "jack-of-all-trades, master-of-none". Despite of such differences, the T-sensitive and T-resistant species are evolutionarily interacted. Specifically, the continuous transition from T-sensitive to T-resistant species insured the exclusion probability of T-resistant species at a relatively constant level across temperatures. The co-evolution and co-adaptation of T-sensitive and T-resistant species were in line with the red queen theory. Collectively, our findings demonstrate that high speciation of niche specialists could alleviate the environmental-filtering-induced negative effect on diversity.
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Manantiales de Aguas Termales , ARN Ribosómico 16S/genética , Adaptación Fisiológica , Clima , Temperatura , Ecosistema , Evolución BiológicaRESUMEN
Quantitative real-time PCR (qPCR) has been widely used in quantifying bacterial and fungal populations in various ecosystems, as well as the fungi to bacteria ratio (F:B ratio). Recently, researchers have begun to apply droplet digital PCR (ddPCR) to this area; however, no study has systematically compared qPCR and ddPCR for quantitating both bacteria and fungi in environmental samples at the same time. Here, we designed probe-primer pair combinations targeting the 16S rRNA gene and internal transcribed spacer (ITS) for the detection of bacteria and fungi, respectively, and tested both SYBR Green and TaqMan approaches in qPCR and ddPCR methods for mock communities and in real environmental samples. In mock communities, the quantification results of ddPCR were significantly closer to expected values (p < .05), and had smaller coefficients of variations (p < .05) than qPCR, suggesting ddPCR was more accurate and repeatable. In environmental samples, ddPCR consistently quantified ITS and 16S rRNA gene concentrations in all four habitats without abnormal overestimation or underestimation, and the F:B ratio obtained by ddPCR was consistent with phospholipid fatty acid analysis. Our results indicated that ddPCR had better precision, repeatability, sensitivity, and stability in bacterial and fungal quantitation than qPCR. Although ddPCR has high cost, complicated processes and restricted detection range, it shows insensitivity to PCR inhibitors and the potential of quantifying long target fragments. We expect that ddPCR, which is complementary to qPCR, will contribute to microbial quantification in environmental monitoring and evaluation.
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Bacterias , Ecosistema , Bacterias/genética , Hongos/genética , ARN Ribosómico 16S/genética , Reacción en Cadena en Tiempo Real de la Polimerasa/métodos , TecnologíaRESUMEN
The linkages between phytoplankton and zooplankton are crucial for the stability of complex food webs and the flow of energy within the marine ecosystem. Despite body size exhibiting multiple effects on the planktonic community assembly and the dispersal scale, its role in determining the stability of phyto-zooplanktonic co-occurrence patterns remains unclear. Here, we focused on more than 13,000 kilometers of the Chinese coast to study the diatom-dominated plankton ecosystem and to report the significant negative effects of zooplanktonic body sizes on the topological properties of phyto-zooplanktonic networks (PZNs) by using more than 500 species from 251 samples taken along the coastline. PZNs tended to be more complex and stable when phytoplankton associated with smaller zooplankton. Particularly, the subnetworks of dominant phytoplankton displayed differences with different zooplanktonic body sizes. The zooplankton with larger and smaller body sizes tended to interact with dinoflagellates and diatoms, respectively. Additionally, abiotic factors (i.e., water temperature, pH, salinity, and metal concentrations) displayed significant effects on PZNs via the shifting of zooplanktonic composition, and the zooplanktonic body sizes altered the network modules' associations with different environmental factors. Our study elucidated the general relationship between zooplanktonic body sizes and the stability of PZNs, which provides new insights into marine food webs. IMPORTANCE Body size is a key life trait of aquatic plankton that affects organisms' metabolic rates and ecological functions; however, its specific effects on interactions between phytoplankton and zooplankton are poorly understood. We collected planktonic species and their body size data along more than 13,000 kilometers of coastline to explore the role of zooplanktonic body size in maintaining the stability of phyto-zooplanktonic networks (PZNs). We found that zooplankton play a more important role in maintaining PZN stability than do phytoplankton as well as that the PZN would be more complex and stable with smaller zooplankton. Furthermore, this work revealed that body size significantly determined the relationships between environmental factors and network structure. Overall, these findings lay a general relationship between zooplanktonic body sizes and the stability of PZNs, which helps us further explore the micro food web of coastal ecosystems.
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Diatomeas , Ecosistema , Animales , Fitoplancton/metabolismo , Plancton , Zooplancton/metabolismo , ChinaRESUMEN
Integrated network analysis pipeline (iNAP) is an online analysis pipeline for generating and analyzing comprehensive ecological networks in microbiome studies. It is implemented in two sections, that is, network construction and network analysis, and integrates many open-access tools. Network construction contains multiple feasible alternatives, including correlation-based approaches (Pearson's correlation and Spearman's rank correlation along with random matrix theory, and sparse correlations for compositional data) and conditional dependence-based methods (extended local similarity analysis and sparse inverse covariance estimation for ecological association inference), while network analysis provides topological structures at different levels and the potential effects of environmental factors on network structures. Considering the full workflow, from microbiome data set to network result, iNAP contains the molecular ecological network analysis pipeline and interdomain ecological network analysis pipeline (IDENAP), which correspond to the intradomain and interdomain associations of microbial species at multiple taxonomic levels. Here, we describe the detailed workflow by taking IDENAP as an example and show the comprehensive steps to assist researchers to conduct the relevant analyses using their own data sets. Afterwards, some auxiliary tools facilitating the pipeline are introduced to effectively aid in the switch from local analysis to online operations. Therefore, iNAP, as an easy-to-use platform that provides multiple network-associated tools and approaches, can enable researchers to better understand the organization of microbial communities. iNAP is available at http://mem.rcees.ac.cn:8081 with free registration.
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Due to the massive quantity and broad phylogeny, an accurate measurement of microbial diversity is highly challenging in soil ecosystems. Initially, the deviation caused by sampling should be adequately considered. Here, we attempted to uncover the effect of different sampling strategies on α diversity measurement of soil prokaryotes. Four 1 m2 sampling quadrats in a typical grassland were thoroughly surveyed through deep 16S rRNA gene sequencing (over 11 million reads per quadrat) with numerous replicates (33 soil sampling cores with total 141 replicates per quadrat). We found the difference in diversity was relatively small when pooling soil cores before and after DNA extraction and sequencing, but they were both superior to a non-pooling strategy. Pooling a small number of soil cores (i.e., 5 or 9) combined with several technical replicates is sufficient to estimate diversities for soil prokaryotes, and there is great flexibility in pooling original samples or data at different experimental steps. Additionally, the distribution of local α diversity varies with sampling core number, sequencing depth, and abundance distribution of the community, especially for high orders of Hill diversity index (i.e., Shannon entropy and inverse Simpson index). For each grassland soil quadrat (1 m2), retaining 100,000 reads after taxonomic clustering might be a realistic option, as these number of reads can efficiently cover the majority of common species in this area. Our findings provide important guidance for soil sampling strategy, and the general results can serve as a basis for further studies.
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Microbiología del Suelo , Suelo , Bacterias/genética , Ecosistema , Filogenia , ARN Ribosómico 16S/genéticaRESUMEN
The SARS-CoV-2 virus, the causative agent of COVID-19, is undergoing constant mutation. Here, we utilized an integrative approach combining epidemiology, virus genome sequencing, clinical phenotyping, and experimental validation to locate mutations of clinical importance. We identified 35 recurrent variants, some of which are associated with clinical phenotypes related to severity. One variant, containing a deletion in the Nsp1-coding region (Δ500-532), was found in more than 20% of our sequenced samples and associates with higher RT-PCR cycle thresholds and lower serum IFN-ß levels of infected patients. Deletion variants in this locus were found in 37 countries worldwide, and viruses isolated from clinical samples or engineered by reverse genetics with related deletions in Nsp1 also induce lower IFN-ß responses in infected Calu-3 cells. Taken together, our virologic surveillance characterizes recurrent genetic diversity and identified mutations in Nsp1 of biological and clinical importance, which collectively may aid molecular diagnostics and drug design.
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COVID-19/inmunología , COVID-19/virología , Interferón Tipo I/inmunología , SARS-CoV-2/genética , SARS-CoV-2/inmunología , Proteínas no Estructurales Virales/genética , Células A549 , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Animales , Secuencia de Bases , COVID-19/sangre , Línea Celular , Niño , Preescolar , Chlorocebus aethiops , Femenino , Eliminación de Gen , Genómica , Células HEK293 , Humanos , Lactante , Interferón Tipo I/sangre , Interferón beta/sangre , Interferón beta/metabolismo , Masculino , Persona de Mediana Edad , Epidemiología Molecular , Genética Inversa , Células Vero , Proteínas no Estructurales Virales/inmunología , Adulto JovenRESUMEN
UNLABELLED: To evaluate the efficacy and safety of lactulose in the intervention treatment of postpartum women with constipation. METHODS: The study adopted the multicenter clinical survey with a big sample which enrolled 4781 valid questionnaires from postpartum women in 18 different districts. All of them were treated with lactulose oral solution. Their constipation-related symptoms and routine examination on blood, urine and stool were monitored before and after lactulose intervention. The treatment duration lasted 2 weeks and all the patients were followed for 4 weeks. RESULT: Their stool consistency, daily defecation frequencies, defecating time and dyschezia were improved significantly after lactulose intervention, and the good therapeutic effect was remained at the off-medication session. Furthermore, abnormal rate of each index in blood, urine and stool examination showed a decreased trend. CONCLUSION: Lactulose offered good therapeutic benefit and could be developed as an effective intervention to postpartum women with constipation.