Saturnispora sinensis sp. nov., a new ascomycetous yeast species from soil and rotten wood.

A yeast strain (CGMCC 2.6937T) belonging to the ascomycetous yeast genus Saturnispora was recently isolated from soil collected in Xinghuacun, Shanxi Province, PR China. The strain produces one or two ellipsoid or spherical ascospores in asci formed by the conjugation between a cell and its bud. Phylogenetic analyses of the internal transcribed spacer (ITS) region and the D1/D2 domain of the large subunit rRNA gene suggest that this strain is conspecific with strains NYNU 14639 isolated from rotten wood collected in Funiu Mountain, Henan province and ES13S05 from soil collected in Nantou County, Taiwan. The CGMCC 2.6937T group is most closely related to Saturnispora dispora and Saturnispora zaruensis. However, strain CGMCC 2.6937T differs from S. dispora by 17 (3.2 %, 13 substitutions and four gaps) and 77 (18.8 %, 52 substitutions and 25 gaps) mismatches, and from S. zaruensis by 15 (2.9 %, 12 substitutions and three gaps) and 64 (15.6 %, 44 substitutions and 20 gaps) mismatches, in the D1/D2 domain and ITS region, respectively. The results suggest that the CGMCC 2.6937T group represents an undescribed species in the genus Saturnispora, for which the name Saturnispora sinensis sp. nov. is proposed. The holotype strain is CGMCC 2.6937T.

Confined Cu-OH single sites in SSZ-13 zeolite for the direct oxidation of methane to methanol.

The direct oxidation of methane to methanol (MTM) remains a significant challenge in heterogeneous catalysis due to the high dissociation energy of the C-H bond in methane and the high desorption energy of methanol. In this work, we demonstrate a breakthrough in selective MTM by achieving a high methanol space-time yield of 2678 mmol molCu-1 h-1 with 93% selectivity in a continuous methane-steam reaction at 400 °C. The superior performance is attributed to the confinement effect of 6-membered ring (6MR) voids in SSZ-13 zeolite, which host isolated Cu-OH single sites. Our results provide a deeper understanding of the role of Cu-zeolites in continuous methane-steam to methanol conversion and pave the way for further improvement.

Identification of dominant functional microbes that contribute to the characteristic aroma of Msalais, traditional wine fermented from boiled local grape juice in China.

Msalais is a traditional wine produced from naturally fermented boiled local grape juice in China. It has characteristic dried fruit and caramel odors, mainly attributed to aromatic compounds, such as furaneol and 5-methylfurfural. However, it is unclear how microbes involved in the natural fermentation of Msalais contribute to this characteristic aroma. Here, we analyzed the Msalais-fermenting microbes and aromatic compounds formed during natural Msalais fermentation by using high-throughput sequencing and gas chromatography-mass spectrometry, respectively. The analysis revealed that Saccharomyces cerevisiae, Kazachstania humilis, Lactobacillus plantarum, and Lactobacillus farraginis are the dominant and key functional species that produce high amounts of furaneol and 5-methylfurfural during Msalais fermentation. Of these, K. humilis and L. farraginis are rarely detected during regular wine fermentation. The identified functional species could be used to control typical aromatic characteristics of Msalais.

Yueomyces silvicola sp. nov., a novel ascomycetous yeast species unable to utilize ammonium, glutamate, and glutamine as sole nitrogen sources.

Five yeast strains isolated from tree bark and rotten wood collected in central and southwestern China, together with four Brazilian strains (three from soil and rotting wood collected in an Amazonian rainforest biome and one from Bromeliad collected in Alagoas state) and one Costa Rican strain isolated from a flower beetle, represent a new species closely related with Yueomyces sinensis in Saccharomycetaceae, as revealed by the 26S ribosomal RNA gene D1/D2 domain and the internal transcribed spacer region sequence analysis. The name Yueomyces silvicola sp. nov. is proposed for this new species with the holotype China General Microbiological Culture Collection Center 2.6469 (= Japan Collection of Microorganisms 34885). The new species exhibits a whole-genome average nucleotide identity value of 77.8% with Y. sinensis. The two Yueomyces species shared unique physiological characteristics of being unable to utilize ammonium and the majority of the amino acids, including glutamate and glutamine, as sole nitrogen sources. Among the 20 amino acids tested, only leucine and tyrosine can be utilized by the Yueomyces species. Genome sequence comparison showed that GAT1, which encodes a GATA family protein participating in transcriptional activation of nitrogen-catabolic genes in Saccharomyces cerevisiae, is absent in the Yueomyces species. However, the failure of the Yueomyces species to utilize ammonium, glutamate, and glutamine, which are generally preferred nitrogen sources for microorganisms, implies that more complicated alterations in the central nitrogen metabolism pathway might occur in the genus Yueomyces.

Microbial communities and their correlation with flavor compound formation during the mechanized production of light-flavor Baijiu.

Light-flavor Baijiu fermentation is a typical spontaneous solid-state fermentation process fueled by a variety of microorganisms. Mechanized processes have been increasingly employed in Baijiu production to replace traditional manual operation processes, however, the microbiological and physicochemical dynamics in mechanized processes remain largely unknown. Here, we investigated the microbial community succession and flavor compound formation during a whole mechanized fermentation process of light-flavor Baijiu using the conventional dilution plating method, PacBio single-molecule real-time (SMRT) sequencing and headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry. The results showed that largely different fungal and bacterial communities were involved in the soaking and fermentation processes. A clear succession from Pantoea agglomerans to Bacillus (B.) smithii and B. coagulans in dominant bacterial species and from Cladosporium exasperatum to Saccharomyces cerevisiae and Lichtheimia ramosa in dominant fungal species occurred in the soaking processes. In the fermentation process, the most dominant bacterial species was shifted from Pantoea agglomerans to Lactobacillus (La.) acetotolerans and the most dominant fungal species were shifted from Lichtheimia ramose and Rhizopus arrhizus to Saccharomyces cerevisiae. The bacterial and fungal species positively associated with acidity and the formation of ethanol and different flavor compounds were specified. The microbial species exhibited strong co-occurrence or co-exclusion relationships were also identified. The results are helpful for the improvement of mechanized fermentation process of light-flavor Baijiu production.

Distinct Selectivity Control in Solar-Driven Bio-Based α-Hydroxyl Acid Conversion: A Comparison of Pt Nanoparticles and Atomically Dispersed Pt on CdS.

Solar-driven photocatalytic lignocellulose conversion is a promising strategy for the sustainable production of high-value chemicals, but selectivity control remains a challenging goal in this field. Here, we report efficient and selective conversion of lignocellulose-derived α-hydroxyl acids to tartaric acid derivatives, α-keto acids, and H2 using Pt-modified CdS catalysts. Pt nanoparticles on CdS selectively produce tartaric acid derivatives via C-C coupling, while atomically dispersed Pt on CdS switches product selectivity to the oxidation reaction to produce α-keto acids. The atomically dispersed Pt species stabilized by Pt-S bonds promote the activation of the hydroxyl group and thus switch product selectivity from tartaric acid derivatives to α-keto acids. A broad range of lignocellulose-derived α-hydroxyl acids was applied for preparing the corresponding tartaric acid derivatives and α-keto acids over the two Pt-modified CdS catalysts. This work highlights the unique performance of metal sulfides in coupling reactions and demonstrates a strategy for rationally tuning product selectivity by engineering the interaction between metal sulfide and cocatalyst.

Microbial Community Affects Daqu Quality and the Production of Ethanol and Flavor Compounds in Baijiu Fermentation.

Daqu is a traditional starter for Baijiu fermentation and is produced by spontaneous fermentation of ground and moistened barley or wheat. The quality of Daqu is traditionally evaluated based on physicochemical and subjective sensory parameters without microbiological analysis. Here, we compared the physicochemical characteristics of qualified (QD) and inferior (ID) Daqu, their microbial communities based on plate counting and PacBio SMRT sequencing of rRNA gene libraries, and their impacts on Baijiu fermentation. The results showed that the glucoamylase and α-amylase activities of QD were significantly higher than those of ID. The counts of yeasts and relative abundances of functional microbes, especially the amylolytic bacterium Bacillus licheniformis and fungi Saccharomycopsis fibuligera and Lichtheimia ramosa, were significantly higher in QD than in ID. The laboratory-scale Baijiu fermentation tests showed that the relative abundances of the amylolytic microbes were higher in the QD than the ID fermentation set, resulting in more efficient fermentation, as indicated by more weight loss and higher moisture content in the former. Consequently, more glycerol, acetic acid, ethanol, and other volatile compounds were produced in the QD than in the ID fermentation set. The results suggest that Daqu quality is determined by, and can be evaluated based on, its microbial community.

BPB1 regulates rice (Oryza sative L.) panicle length and panicle branch development by promoting lignin and inhibiting cellulose accumulation.

Panicle structure is one of the most important agronomic traits directly related to rice yield. This study identified a rice mutant basal primary branch 1 (bpb1), which exhibited a phenotype of reduced panicle length and arrested basal primary branch development. In addition, lignin content was found to be increased while cellulose content was decreased in bpb1 young panicles. Map-based cloning methods characterized the gene BPB1, which encodes a peptide transporter (PTR) family transporter. Phylogenetic tree analysis showed that the BPB1 family is highly conserved in plants, especially the PTR2 domain. It is worth noting that BPB1 is divided into two categories based on monocotyledonous and dicotyledonous plants. Transcriptome analysis showed that BPB1 mutation can promote lignin synthesis and inhibit cellulose synthesis, starch and sucrose metabolism, cell cycle, expression of various plant hormones, and some star genes, thereby inhibiting rice panicle length, resulting in basal primary branch development stagnant phenotypes. In this study, BPB1 provides new insights into the molecular mechanism of rice panicle structure regulation by BPB1 by regulating lignin and cellulose content and several transcriptional metabolic pathways. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-023-01389-x.

Mechanistic Insights into Radical-Induced Selective Oxidation of Methane over Nonmetallic Boron Nitride Catalysts.

Boron-based nonmetallic materials (such as B2O3 and BN) emerge as promising catalysts for selective oxidation of light alkanes by O2 to form value-added products, resulting from their unique advantage in suppressing CO2 formation. However, the site requirements and reaction mechanism of these boron-based catalysts are still in vigorous debate, especially for methane (the most stable and abundant alkane). Here, we show that hexagonal BN (h-BN) exhibits high selectivities to formaldehyde and CO in catalyzing aerobic oxidation of methane, similar to Al2O3-supported B2O3 catalysts, while h-BN requires an extra induction period to reach a steady state. According to various structural characterizations, we find that active boron oxide species are gradually formed in situ on the surface of h-BN, which accounts for the observed induction period. Unexpectedly, kinetic studies on the effects of void space, catalyst loading, and methane conversion all indicate that h-BN merely acts as a radical generator to induce gas-phase radical reactions of methane oxidation, in contrast to the predominant surface reactions on B2O3/Al2O3 catalysts. Consequently, a revised kinetic model is developed to accurately describe the gas-phase radical feature of methane oxidation over h-BN. With the aid of in situ synchrotron vacuum ultraviolet photoionization mass spectroscopy, the methyl radical (CH3•) is further verified as the primary reactive species that triggers the gas-phase methane oxidation network. Theoretical calculations elucidate that the moderate H-abstraction ability of predominant CH3• and CH3OO• radicals renders an easier control of the methane oxidation selectivity compared to other oxygen-containing radicals generally proposed for such processes, bringing deeper understanding of the excellent anti-overoxidation ability of boron-based catalysts.

Confinement-Enhanced Selective Oxidation of Lignin Derivatives to Formic Acid Over Fe-Cu/ZSM-5 Catalysts Under Mild Conditions.

Aqueous-phase oxidation by H2 O2 , known as the Fenton-type process, provides an attractive route to convert recalcitrant lignin derivatives to valuable chemicals under mild conditions. The development of this technology is, however, limited by the uncontrolled selectivity, resulting from the highly reactive nature of H2 O2 and the thermodynamically favored deep oxidation to form CO2 . This study demonstrated that formic acid could be produced with a high selectivity (up to 80.3 % at 313 K) from the Fenton-type oxidation of guaiacol and several other lignin derivatives over a bimetallic Fe-Cu catalyst supported on a ZSM-5 zeolite. Combined experimental and theoretical investigations unveiled that the micropores of the zeolite support, which contained active metal sites, preferred to adsorb C2 -C4 intermediates over formic acid because of its stronger dispersive interaction with the larger guest molecules. This confinement effect significantly suppressed the secondary oxidation of formic acid, accounting for the uniquely high formic acid selectivity over Fe-Cu/ZSM-5.

Highly diverged lineages of Saccharomyces paradoxus in temperate to subtropical climate zones in China.

The wild yeast Saccharomyces paradoxus has become a new model in ecology and evolutionary biology. Different lineages of S. paradoxus have been recognized across the world, but the distribution and genetic diversity of the species remain unknown in China, where the origin of its sibling species S. cerevisiae lies. In this study, we investigated the ecological and geographic distribution of S. paradoxus through an extensive field survey in China and performed population genomic analysis on a set of S. paradoxus strains, including 27 strains, representing different geographic and ecological origins within China, and 59 strains representing all the known lineages of the species recognized in the other regions of the world so far. We found two distinct lineages of S. paradoxus in China. The majority of the Chinese strains studied belong to the Far East lineage, and six strains belong to a novel highly diverged lineage. The distribution of these two lineages overlaps ecologically and geographically in temperate to subtropical climate zones in China. With the addition of the new China lineage, the Eurasian population of S. paradoxus exhibits higher genetic diversity than the American population. We observed more possible lineage-specific introgression events from the Eurasian lineages than from the American lineages. Our results expand the knowledge on ecology, genetic diversity, biogeography, and evolution of S. paradoxus.

Genetic diversity and population structure of the amylolytic yeast Saccharomycopsis fibuligera associated with Baijiu fermentation in China.

The amylolytic yeast Saccharomycopsis fibuligera is a predominant species in starters and the early fermentation stage of Chinese liquor (Baijiu). However, the genetic diversity of the species remains largely unknown. Here we sequenced the genomes of 97 S. fibuligera strains from different Chinese Baijiu companies. The genetic diversity and population structure of the strains were analyzed based on 1,133 orthologous genes and the whole genome single nucleotide polymorphisms (SNPs). Four main lineages were recognized. One lineage contains 60 Chinese strains which are exclusively homozygous with relatively small genome sizes (18.55-18.72 Mb) and low sequence diversity. The strains clustered in the other three lineages are heterozygous with larger genomes (21.85-23.72 Mb) and higher sequence diversity. The genomes of the homozygous strains showed nearly 100% coverage with the genome of the reference strain KPH12 and the sub-genome A of the hybrid strain KJJ81 at the above 98% sequence identity level. The genomes of the heterozygous strains showed nearly 80% coverage with both the sub-genome A and the whole genome of KJJ81, suggesting that the Chinese heterozygous strains are also hybrids with nearly 20% genomes from an unidentified source. Eighty-three genes were found to show significant copy number variation between different lineages. However, remarkable lineage specific variations in glucoamylase and α-amylase activities and growth profiles in different carbon sources and under different environmental conditions were not observed, though strains exhibiting relatively high glucoamylase activity were mainly found from the homozygous lineage.

Improved redox homeostasis owing to the up-regulation of one-carbon metabolism and related pathways is crucial for yeast heterosis at high temperature.

Heterosis or hybrid vigor is a common phenomenon in plants and animals; however, the molecular mechanisms underlying heterosis remain elusive, despite extensive studies on the phenomenon for more than a century. Here we constructed a large collection of F1 hybrids of Saccharomyces cerevisiae by spore-to-spore mating between homozygous wild strains of the species with different genetic distances and compared growth performance of the F1 hybrids with their parents. We found that heterosis was prevalent in the F1 hybrids at 40°C. A hump-shaped relationship between heterosis and parental genetic distance was observed. We then analyzed transcriptomes of selected heterotic and depressed F1 hybrids and their parents growing at 40°C and found that genes associated with one-carbon metabolism and related pathways were generally up-regulated in the heterotic F1 hybrids, leading to improved cellular redox homeostasis at high temperature. Consistently, genes related with DNA repair, stress responses, and ion homeostasis were generally down-regulated in the heterotic F1 hybrids. Furthermore, genes associated with protein quality control systems were also generally down-regulated in the heterotic F1 hybrids, suggesting a lower level of protein turnover and thus higher energy use efficiency in these strains. In contrast, the depressed F1 hybrids, which were limited in number and mostly shared a common aneuploid parental strain, showed a largely opposite gene expression pattern to the heterotic F1 hybrids. We provide new insights into molecular mechanisms underlying heterosis and thermotolerance of yeast and new clues for a better understanding of the molecular basis of heterosis in plants and animals.

Adaptive Gene Content and Allele Distribution Variations in the Wild and Domesticated Populations of Saccharomyces cerevisiae.

Recent studies on population genomics of Saccharomyces cerevisiae have substantially improved our understanding of the genetic diversity and domestication history of the yeast. However, the origin of the domesticated population of S. cerevisiae and the genomic changes responsible for ecological adaption of different populations and lineages remain to be fully revealed. Here we sequenced 64 African strains from various indigenous fermented foods and forests in different African countries and performed a population genomic analysis on them combined with a set of previously sequenced worldwide S. cerevisiae strains representing the maximum genetic diversity of the species documented so far. The result supports the previous observations that the wild and domesticated populations of S. cerevisiae are clearly separated and that the domesticated population diverges into two distinct groups associated with solid- and liquid-state fermentations from a single ancestor. African strains are mostly located in basal lineages of the two domesticated groups, implying a long domestication history of yeast in Africa. We identified genes that mainly or exclusively occur in specific groups or lineages and genes that exhibit evident group or lineage specific allele distribution patterns. Notably, we show that the homing endonuclease VDE is generally absent in the wild but commonly present in the domesticated lineages of S. cerevisiae. The genes with group specific allele distribution patterns are mostly enriched in functionally similar or related fundamental metabolism processes, including the evolutionary conserved TOR signaling pathway.

Two New Sexual Talaromyces Species Discovered in Estuary Soil in China.

In the survey of mycobiota of mudflats in China, two new sexually reproducing Talaromyces sect. Talaromyces species were discovered and studied using a polyphasic approach. These species are named here Talaromyces haitouensis (ex-type AS3.160101T) and Talaromyces zhenhaiensis (ex-type AS3.16102T). Morphologically, T. haitouensis is distinguished by moderate growth, green-yellow gymnothecia, orange-brown mycelium, and echinulate ellipsoidal ascospores. T. zhenhaiensis is characterized by fast growth, absence of sporulation, cream yellow to naphthalene yellow gymnothecia and mycelium, and smooth-walled ellipsoidal ascospores with one equatorial ridge. The two novelties are further confirmed by phylogenetic analyses based on either individual sequences of BenA, CaM, Rpb2, and ITS1-5.8S-ITS2 or the concatenated BenA-CaM-Rpb2 sequences.

Direct conversion of methane to formaldehyde and CO on B2O3 catalysts.

Direct oxidation of methane to value-added C1 chemicals (e.g. HCHO and CO) provides a promising way to utilize natural gas sources under relatively mild conditions. Such conversions remain, however, a key selectivity challenge, resulting from the facile formation of undesired fully-oxidized CO2. Here we show that B2O3-based catalysts are selective in the direct conversion of methane to HCHO and CO (~94% selectivity with a HCHO/CO ratio of ~1 at 6% conversion) and highly stable (over 100 hour time-on-stream operation) conducted in a fixed-bed reactor (550 °C, 100 kPa, space velocity 4650 mL gcat-1 h-1). Combined catalyst characterization, kinetic studies, and isotopic labeling experiments unveil that molecular O2 bonded to tri-coordinated BO3 centers on B2O3 surfaces acts as a judicious oxidant for methane activation with mitigated CO2 formation, even at high O2/CH4 ratios of the feed. These findings shed light on the great potential of designing innovative catalytic processes for the direct conversion of alkanes to fuels/chemicals.

Visible-light-driven amino acids production from biomass-based feedstocks over ultrathin CdS nanosheets.

Chemical synthesis of amino acids from renewable sources is an alternative route to the current processes based on fermentation. Here, we report visible-light-driven amination of biomass-derived α-hydroxyl acids and glucose into amino acids using NH3 at 50 °C. Ultrathin CdS nanosheets are identified as an efficient and stable catalyst, exhibiting an order of magnitude higher activity towards alanine production from lactic acid compared to commercial CdS as well as CdS nanoobjects bearing other morphologies. Its unique catalytic property is attributed mainly to the preferential formation of oxygen-centered radicals to promote α-hydroxyl acids conversion to α-keto acids, and partially to the poor H2 evolution which is an undesired side reaction. Encouragingly, a number of amino acids are prepared using the current protocol, and one-pot photocatalytic conversion of glucose to alanine is also achieved. This work offers an effective catalytic system for amino acid synthesis from biomass feedstocks under mild conditions.

Wickerhamomyces kurtzmanii sp. nov. An Ascomycetous Yeast Isolated From Crater Lake Water, Da Hinggan Ling Mountain, China.

One novel ascomycetous yeast strain TF5-16-2 was isolated from water samples of Tuofengling crater lake located in Da Hinggan Ling Mountain, in the Inner Mongolia province of China. Morphological, physiological characteristics, as well as phylogenetic analyses of D1/D2 domains of the large subunit rRNA (LSU), ITS region, small subunit rRNA (SSU), and elongation factor-1α (EF-1α) were performed and finally confirmed the phylogenetic placement of strain TF5-16-2 in the genus Wickerhamomyces. Sequences analysis revealed that strain TF5-16-2 differed from its most closely related phylogenetic neighbors 'Candida' silvicultrix CBS 6269T and Wickerhamomyces anomalus CBS 5759T by 8.0% (including 2.3% gaps), 8.5% (including 2.4% gaps) divergences in D1/D2 domains of LSU, and 11% (including 4.3% gaps) and 13% (including 4.4% gaps) divergences in ITS region, respectively. As the considerable sequence divergence and distinguishable physiological characteristics, strain TF5-16-2 was proposed as a new species of the genus Wickerhamomyces, with the name Wickerhamomyces kurtzmanii sp. nov. (holotype = CGMCC 2.5597, Mycobank number is MB829959).

Reverse Evolution of a Classic Gene Network in Yeast Offers a Competitive Advantage.

Glucose repression is a central regulatory system in yeast that ensures the utilization of carbon sources in a highly economical manner. The galactose (GAL) metabolism network is stringently regulated by glucose repression in yeast and has been a classic system for studying gene regulation. We show here that a Saccharomyces cerevisiae (S. cerevisiae) lineage in spontaneously fermented milk has swapped all its structural GAL genes (GAL2 and the GAL7-10-1 cluster) with early diverged versions through introgression. The rewired GAL network has abolished glucose repression and conversed from a strictly inducible to a constitutive system through polygenic changes in the regulatory components of the network, including a thymine (T) to cytosine (C) and a guanine (G) to adenine (A) transition in the upstream repressing sequence (URS) sites of GAL1 and GAL4, respectively, which impair Mig1p-mediated repression, loss of function of the repressor Gal80p through a T146I substitution in the protein, and subsequent futility of GAL3. Furthermore, the milk lineage of S. cerevisiae has achieved galactose-utilization rate elevation and galactose-over-glucose preference switch through the duplication of the introgressed GAL2 and the loss of function of the main glucose transporter genes HXT6 and HXT7. In addition, we demonstrate that GAL2 requires GAL7 or GAL10 for its expression, and Gal2p likely requires Gal1p for its transportation function in the milk lineage of S. cerevisiae. We show a clear case of reverse evolution of a classic gene network for ecological adaptation and provide new insights into the regulatory model of the canonical GAL network.

The origin and adaptive evolution of domesticated populations of yeast from Far East Asia.

The yeast Saccharomyces cerevisiae has been an essential component of human civilization because of its long global history of use in food and beverage fermentation. However, the diversity and evolutionary history of the domesticated populations of the yeast remain elusive. We show here that China/Far East Asia is likely the center of origin of the domesticated populations of the species. The domesticated populations form two major groups associated with solid- and liquid-state fermentation and appear to have originated from heterozygous ancestors, which were likely formed by outcrossing between diverse wild isolates primitively for adaptation to maltose-rich niches. We found consistent gene expansion and contraction in the whole domesticated population, as well as lineage-specific genome variations leading to adaptation to different environments. We show a nearly panoramic view of the diversity and life history of S. cerevisiae and provide new insights into the origin and evolution of the species.