真菌系统学大趋势：越来越多的分类单元

分子生物学技术与真菌系统学的有机融合,为真菌分类和系统发育研究带来了革命性的变化。最近20年来,真菌学家们建立了大量的新目、新科、新属和新种,掀开了真菌多样性及其起源进化研究的新纪元,但很多重要的系统发育问题仍没有解决,特别是大量目间、科间的亲缘关系并不清楚。细分是真菌系统学的主流趋势,野生食用菌和毒蘑菇的分类也是如此,近年涌现了越来越多的新分类单元,如在2010-2019年的10年间,中国发表大型真菌（含地衣）新种1 240余个。本专刊收载的15篇论文是对我国野生食用菌和毒蘑菇研究工作的部分总结,对真菌资源利用、毒蘑菇中毒预防与治疗具有较重要的科学意义和应用价值。     

产溶剂梭菌分子遗传操作技术研究进展

产溶剂梭菌是一类重要的工业微生物.通过遗传改造以优化产溶剂梭菌的发酵性能一直是溶剂制造技术研究的重要课题,但长期受限于该类菌并不完善的遗传操作工具,未见明显突破.近年来,随着TargeTron基因中断、大片段基因整合等新技术和新方法的出现,其分子遗传改造已取得较大进展.文中对产溶剂梭菌的分子遗传操作工具研究进展进行了总结,并指出了现有技术在效率及全面性方面的不足.基于此,今后应进一步优化现有的梭菌基因失活技术,如建立基于同源重组的基因删除和替换;同时也应发展新的分子操作技术,如基因组多位点共编辑、多拷贝定点和随机整合等.     

Metabolic regulation in solventogenic clostridia: regulators,mechanisms and engineering

Solventogenic clostridia, a group of important industrial microorganisms, have exceptional substrate and product diversity, capable of producing a series of two-carbon and even long-chain chemicals and fuels by using various substrates, including sugars, cellulose and hemicellulose, and C1 gases. For the sake of in-depth understanding and engineering these anaerobic microorganisms for broader applications, studies on metabolic regulation of solventogenic clostridia had been extensively carried out during the past ten years, based on the rapid development of various genetic tools. To date, a number of regulators that are essential for cell physiological and metabolic processes have been identified in clostridia, and the relevant mechanisms have also been dissected, providing a wealth of valuable information for metabolic engineering. Here, we reviewed the latest research progresses on the metabolic regulation for chemical production and substrate utilization in solventogenic clostridia, by focusing on three typical Clostridium species, the saccharolytic C. acetobutylicum and C. beijerinckii, as well as the gas-fermenting C. ljungdahlii. On this basis, future directions in the study and remodeling of clostridial regulation systems, were proposed for effective modification of these industrially important anaerobes.     

Identifying inflorescence phytoliths from selected species of wheat (Triticum monococcum, T. dicoccon, T. dicoccoides, and T. aestivum) and barley (Hordeum vulgare and H. spontaneum) (Gramineae)

Analysis of microfossil silica phytoliths is becoming an increasingly important research tool for taxonomists, archaeobotanists, and paleoecologists. Expanded use of phytolith analysis by researchers is dependent upon development of phytolith systematics. In this study phytoliths produced by the inflorescence bracts from four species of wheat, Triticum monoccocum, T. dicoccon, T. dicoccoides, and T. aestivum, and two species of barley, Hordeum vulgare, and H. spontaneum, were analyzed using computer-assisted image and statistical analysis with the intent to develop taxonomic tools to distinguish among the taxa. A classification key based on significant differences among the mean morphometries of the inflorescence phytoliths produced by each species was created and tested. Discriminant analysis of the morphometries of several morphotypes of phytoliths was also conducted to determine whether this computer-assisted statistical procedure could be used as another method to classify the taxa and to determine which morphotypes have measurements that can best be used in discriminant functions. Test results indicated that, at the genus level, both the classification key and discriminant analysis of certain morphotypes of phytoliths were relatively reliable tools for distinguishing among phytoliths produced in the inflorescence bracts of the taxa considered. For distinguishing among the taxa at the species level, the classification key was most reliable. Of the discriminant analyses tested, that based on all the phytolith morphotypes combined was more reliable than those based on only one morphotype.     

Phylogeny of the leech family Glossiphoniidae based on mitochondrial gene sequences and morphological data

The phylogenetic relationships of the Glossiphoniidae (Rhynchobdellida) were investigated using morphological characters and the mitochondrial genes cytochrome c oxidase subunit I and nicotinamide adenine dinucleotide dehydrogenase subunit 1. Thirty-five taxa representing 10 of the 23 currently recognized glossiphoniid genera were sampled, including more than 70% of known North American species, as well as others from Europe, South America, Africa, and a species endemic to Lake Baikal. Outgroup taxa included species from the Piscicolidae and Ozobranchidae. Cladistic analysis resulted in 1 most-parsimonious tree. Subfamily distinctions, i.e., Haementeriinae, Theromyzinae, and Glossiphoniinae, that have been based on eye morphology and reproductive biology are not corroborated. Results also provide insights into several problematic genus-level classifications. For example, relationships of Placobdella and Haementeria are clarified and elimination of Desserobdella may be necessary. Bloodfeeding from vertebrates is seen to be a primitive characteristic that has been lost twice within the clade. The hypothesis that the biannulate leech, Oligobdella biannulata, represents an important transitional form is re-evaluated in a phylogenetic context.     

Genome Size and Species Diversification

Theoretically, there are reasons to believe that large genome size should favour speciation. Several major factors contributing to genome size, such as duplications and transposable element activity have been proposed to facilitate the formation of new species. However, it is also possible that small genome size promotes speciation. For example, selection for genome reduction may be resolved in different ways in incipient species, leading to incompatibilities. Mutations and chromosomal rearrangements may also be more stably inherited in smaller genomes. Here I review the following lines of empirical evidence bearing on this question: (i) Correlations between genome size and species richness of taxa are often negative. (ii) Fossil evidence in lungfish shows that the accumulation of DNA in the genomes of this group coincided with a reduction in species diversity. (iii) Estimates of speciation interval in mammals correlate positively with genome size. (iv) Genome reductions are inferred at the base of particular species radiations and genome expansions at the base of others. (v) Insect clades that have been increasing in diversity up to the present have smaller genomes than clades that have remained stable or have decreased in diversity. The general pattern emerging from these observations is that higher diversification rates are generally found in small-genome taxa. Since diversification rates are the net effect of speciation and extinction, large genomes may thus either constrain speciation rate, increase extinction rate, or both. I argue that some of the cited examples are unlikely to be explained by extinction alone.     

Taxonomic surrogacy in biodiversity assessments,and the meaning of Linnaean ranks

The majority of biodiversity assessments use species as the base unit. Recently, a series of studies have suggested replacing numbers of species with higher ranked taxa (genera, families, etc.); a method known as taxonomic surrogacy that has an important potential to save time and resources in assesments of biological diversity. We examine the relationships between taxa and ranks, and suggest that species/higher taxon exchanges are founded on misconceptions about the properties of Linnaean classification. Rank allocations in current classifications constitute a heterogeneous mixture of various historical and contemporary views. Even if all taxa were monophyletic, those referred to the same rank would simply denote separate clades without further equivalence. We conclude that they are no more comparable than any other, non‐nested taxa, such as, for example, the genus Rattus and the phylum Arthropoda, and that taxonomic surrogacy lacks justification. These problems are also illustrated with data of polychaetous annelid worms from a broad‐scale study of benthic biodiversity and species distributions in the Irish Sea. A recent consensus phylogeny for polychaetes is used to provide three different family‐level classifications of polychaetes. We use families as a surrogate for species, and present Shannon‐Wiener diversity indices for the different sites and the three different classifications, showing how the diversity measures rely on subjective rank allocations.     

Batrachology of Japan and adjacent regions - a systematic review

As is the case with most other organisms, studies of amphibians started with systematics as the basis for many other biological fields, but systematics itself has endured a slower progress than other fields of biology have enjoyed for a long time. Nevertheless, philosophical and methodological 'revolutions' in the past 30 years, combined with more recent progress in biochemical and molecular techniques, have been forcing current systematics into a great change. Stejneger's (1907) monumental book, the first thorough review of amphibians from Japan and adjacent regions, was published nearly a century ago, and since then, the increase in number of areas that have been closely surveyed, together with the application of new theories and methods, have greatly enlarged our knowledge of the amphibian fauna in this region. For example, extensive experiments by the Hiroshima School using artificial hybridization techniques greatly contributed to our understandings of relationships among some groups of amphibians that had been taxonomically confusing. In addition to this, new species discovered by more detailed field surveys in a wider area and cryptic species revealed by analyses of isozymes and acoustic properties have made for a great increment in the number of taxa in this region. Further, analyses of DNA sequences now enable us to infer the affinities of taxa with few phylogenetically informative phenotypic properties, and the resultant phylogenetic hypotheses further contribute to our understandings of biogeography and many other issues on amphibian evolution. From these advances, it has been clarified that the amphibian species diversity is far greater than was previously expected, which in turn means a high endemism within particular regions. It is expected that future studies will also reveal exact systematic relationships of wide-ranging species, both those occurring within this region and those extending outside of it. For that purpose, international and interdisciplinary studies are indispensable. But what is also necessary is to conserve amphibian populations so that they will not disappear before their true relationships are realized. Knowledge of systematics among young amphibian biologists is also a matter of high priority.     

Clostridia in premature neonates' gut: incidence, antibiotic susceptibility, and perinatal determinants influencing colonization

Background

Although premature neonates (PN) gut microbiota has been studied, data about gut clostridial colonization in PN are scarce. Few studies have reported clostridia colonization in PN whereas Bacteroides and bifidobacteria have been seldom isolated. Such aberrant gut microbiota has been suggested to be a risk factor for the development of intestinal infections. Besides, PN are often treated by broad spectrum antibiotics, but little is known about how antibiotics can influence clostridial colonization based on their susceptibility patterns. The aim of this study was to report the distribution of Clostridium species isolated in feces from PN and to determine their antimicrobial susceptibility patterns. Additionally, clostridial colonization perinatal determinants were analyzed.

Results

Of the 76 PN followed until hospital discharge in three French neonatal intensive care units (NICUs), 79% were colonized by clostridia. Clostridium sp. colonization, with a high diversity of species, increased throughout the hospitalization. Antibiotic courses had no effect on the clostridial colonization incidence although strains were found susceptible (except C. difficile) to anti-anaerobe molecules tested. However, levels of colonization were decreased by either antenatal or neonatal (during more than 10 days) antibiotic courses (p = 0.006 and p = 0.001, respectively). Besides, incidence of colonization was depending on the NICU (p = 0.048).

Conclusion

This study shows that clostridia are part of the PN gut microbiota. It provides for the first time information on the status of clostridia antimicrobial susceptibility in PN showing that strains were susceptible to most antibiotic molecules. Thus, the high prevalence of this genus is not linked to a high degree of resistance to antimicrobial agents or to the use of antibiotics in NICUs. The main perinatal determinant influencing PN clostridia colonization appears to be the NICU environment.     

Clostridial iron-sulphur proteins

Iron-sulfur proteins are ubiquitous catalysts of a wide range of biological reactions, and are particularly abundant in clostridia which lack the ability to synthesize hemes. The development of research on these metalloproteins has therefore been strongly associated with biochemical investigations of clostridial metabolism. Major breakthroughs in the field, from the first isolation of an iron-sulfur protein in 1962, to the recent determination of an Fe-hydrogenase structure, have been made with clostridia. These data, as well as others obtained through studies on clostridia, are transferable to many other bioenergetic machineries, due to the strong phylogenetic conservation of some important components. For instance, clear homologies exist between constituents of the anaerobic electron transfer chains in clostridia and aerobic respiratory chains. The contribution of iron-sulfur proteins to the biotechnological and medical significance of clostridia is also discussed. Structural and functional genomics are expected to bring forth a wealth of novel data on clostridia and iron-sulfur proteins.     

A Retrospective Approach to Testing the DNA Barcoding Method

A decade ago, DNA barcoding was proposed as a standardised method for identifying existing species and speeding the discovery of new species. Yet, despite its numerous successes across a range of taxa, its frequent failures have brought into question its accuracy as a short-cut taxonomic method. We use a retrospective approach, applying the method to the classification of New Zealand skinks as it stood in 1977 (primarily based upon morphological characters), and compare it to the current taxonomy reached using both morphological and molecular approaches. For the 1977 dataset, DNA barcoding had moderate-high success in identifying specimens (78-98%), and correctly flagging specimens that have since been confirmed as distinct taxa (77-100%). But most matching methods failed to detect the species complexes that were present in 1977. For the current dataset, there was moderate-high success in identifying specimens (53-99%). For both datasets, the capacity to discover new species was dependent on the methodological approach used. Species delimitation in New Zealand skinks was hindered by the absence of either a local or global barcoding gap, a result of recent speciation events and hybridisation. Whilst DNA barcoding is potentially useful for specimen identification and species discovery in New Zealand skinks, its error rate could hinder the progress of documenting biodiversity in this group. We suggest that integrated taxonomic approaches are more effective at discovering and describing biodiversity.     

北京维管植物编目和分布数据集

区域性维管植物编目对于该区域内植物多样性保护及植物资源可持续利用具有重要意义。北京作为中国首都, 尽管编目工作早在20世纪60年代就得以开展, 但近30年来没有进行系统更新。现有数据零散、不系统, 相关编目进展甚至已经落后于周边地区。本文在《北京植物志(1992年修订版)》的基础上, 结合多年实际野外调查, 通过系统检索文献资料对现有编目数据进行查漏补缺(补充新分类群、新记录)、修订名称(基于新分类修订成果)、更新分类系统(采用基于分子数据的新分类系统), 并添加物种等级、分布状态、生长状态、室内/室外、分布区、了解程度及保护状况等相关信息, 最终完成北京维管植物编目和分布数据集(分为本土植物和外来植物两个表单, 其中外来植物主要基于志书和文献记载)。截至2021年12月31日, 该数据集共有数据2,883条(本土1,680条, 外来1,203条), 其中包含北京本土野生维管植物134科611属1,597个类群(1,440种3天然杂交种46亚种97变种11变型), 与《北京植物志(1992年修订版)》相比增加3科26属173种4亚种28变种11变型, 其中列入《国家重点保护野生植物名录(2021)》的有16种(一级仅1种), 列入《北京市重点保护野生植物名录(2008)》的有90种3亚种4变种; 收录外来维管植物137科581属1,184个类群(含992种及其他种下等级), 其中栽培植物854种19杂交种15亚种29变种2变型87栽培品种38栽培群, 逸生植物132种1亚种, 归化植物77种2变种, 入侵植物27种。编目数据显示, 北京本土野生维管植物多样性整体上并不高, 主要以广泛分布的常见种为主, 特有种、狭域种以及珍稀濒危种数量不多; 同时, 北京存在大量的外来植物(许多种类在《北京植物志》各版中已经收录), 这些植物也是北京维管植物多样性的重要组成部分, 但现有数据尚不完整。     

The growing contributions of molecular biology and immunology to protistan ecology: molecular signatures as ecological tools

Modern genetic and immunological techniques have become important tools for assessing protistan species diversity for both the identification and quantification of specific taxa in natural microbial communities. Although these methods are still gaining use among ecologists, the new approaches have already had a significant impact on our understanding of protistan diversity and biogeography. For example, genetic studies of environmental samples have uncovered many protistan phylotypes that do not match the DNA sequences of any cultured organisms, and whose morphological identities are unknown at the present time. Additionally, rapid and sensitive methods for detecting and enumerating taxa of special importance (e.g. bloom-forming algae, parasitic protists) have enabled much more detailed distributional and experimental studies than have been possible using traditional methods. Nevertheless, while the application of molecular approaches has advanced some aspects of aquatic protistan ecology, significant issues still thwart the widespread adoption of these approaches. These issues include the highly technical nature of some of the molecular methods, the reconciliation of morphology-based and sequence-based species identifications, and the species concept itself.     

Differentiation of the main species of Clostridium by gas chromatography

For the first time in the USSR the properties of microorganisms of the genus Clostridium have been studied with the use of the gas-chromatographic techniques. The analysis of the quantitative and qualitative composition of extracellular alcohols and carboxylic acids in 99 museum and newly isolated strains of 18 Clostridium species has made it possible to classify these microorganisms with 7 sharply differing groups. The above techniques permit the classification of clostridia with one of the groups within 2 hours if the microbial cultures have been grown in glucose-containing peptone yeast medium.     

Biodiversity: molecular biological domains, symbiosis and kingdom origins.

The number of extant species of organisms is estimated to be from fewer than 3 to more than 30 x 10(6) (May, 1992). Molecular biology, comparative genetics and ultrastructural analyses provide new insights into evolutionary relationships between these species, including increasingly precise ideas of how species and higher taxa have evolved from common ancestors. Accumulation of random mutations and large macromolecular sequence change in all organisms since the Proterozoic Eon has been importantly supplemented by acquisition of inherited genomes ('symbiogenesis'). Karyotypic alterations (polyploidization and karyotypic fissioning) have been added to these other mechanisms of species origin in plants and animals during the Phanerozoic Eon. The new evolution concepts (coupled with current rapid rates of species extinction and ignorance of the extent of biodiversity) prompted this analysis of the field of systematic biology and its role in the reorganization of extant species into higher taxa. Two superkingdoms (= Domains: Prokaryotae and Eukaryotae) and five kingdoms (Monera = Procaryotae or Bacteria; Protoctista: algae, amoebae, ciliates, foraminifera, oomycetes, slime molds, etc.; Mychota: 'true' fungi; Plantae: one phylum (division) of bryophytes and nine phyla of tracheophytes; and Animalia) are recognized. Two subkingdoms comprise the monera: the great diverse lineages are Archaebacteria and Eubacteria. The criteria for classification using molecular, ultrastructural and genetic data for this scheme are mentioned. For the first time since the nineteenth century, logical, technical definitions for each group are given with their time of appearance as inferred from the fossil record in the primary scientific literature. This classification scheme, which most closely reflects the evolutionary history, molecular biology, genetics and ultrastructure of extant life, requires changes in social organization of biologists, many of whom as botanists and zoologists, still behave as if there were only two important kingdoms (plants and animals).     

The contribution of recombination to heterozygosity differs among plant evolutionary lineages and life-forms

Background  

Despite its role as a generator of haplotypic variation, little is known about how the rates of recombination evolve across taxa. Recombination is a very labile force, susceptible to evolutionary and life trait related processes, which have also been correlated with general levels of genetic diversity. For example, in plants, it has been shown that long-lived outcrossing taxa, such as trees, have higher heterozygosity (H _e) at SSRs and allozymes than selfing or annual species. However, some of these tree taxa have surprisingly low levels of nucleotide diversity at the DNA sequence level, which points to recombination as a potential generator of genetic diversity in these organisms. In this study, we examine how genome-wide and within-gene rates of recombination evolve across plant taxa, determine whether such rates are influenced by the life-form adopted by species, and evaluate if higher genome-wide rates of recombination translate into higher H _e values, especially in trees.     

Lipid diversity in clostridia

Studies of the lipidomes of twenty-one species of clostridia have revealed considerable diversity. Even among those species now defined as Clostridium sensu stricto, which are related to Clostridium butyricum, the type species, lipid analysis has shown that a number of distinct clades have characteristic polar lipids. All species of Clostridium sensu stricto have phosphatidylethanolamine, phosphatidylglycerol and cardiolipin which are present as all acyl or alk-1′-enyl acyl (plasmalogen) species. In addition, almost every clade has specialized polar lipids. For example, the group closely related to Clostridium beijerinckii and several other solventogenic species has glycerol acetals of plasmenylethanolamine, which protects the membrane bilayer arrangement when the lipids are highly unsaturated or in the presence of solvents. The group related to Clostridium novyi has aminoacyl-phosphatidylglycerol, which protects these pathogens from cationic antimicrobial peptides (CAMPs) of innate immunity. Clostridium botulinum species, which fall into several groups, align with these clades, and have the same specific lipids. This review will present the current state of knowledge on clostridial lipids.     

Molecular Phylogeny of Microsporidians with Particular Reference to Species that Infect the Muscles of Fish

Ribosomal DNA from eight species of microsporidians infecting fish have been sequenced. Seven of these species infect the skeletal muscle of fish ( Pleistophora spp.) and one species infects migratory mesenchyma cells ( Glugea anomala ). These sequences, in addition to other available microsporidian rDNA sequences from a broad range of host taxa, have been used in phylogenetic analysis. This analysis revealed that muscle-infecting microsporidians from fish are a polyphyletic group, indicating that characters supposed to be important in the classification of the genus Pleistophora have to be re-evaluated. One character that probably has a polyphyletic origin is the amorphous coat, which has been extensively used in the definition of this genus. Furthermore, our results showed that the insect parasitizing Pleistophora spp. are not related to the true pleistophorans parasitic in skeletal muscle of fish. Phylogenetic analysis of small subunit rDNA sequences revealed disagreements between the molecular phylogeny and classifications based upon ultrastruclure. Many of the morphological characters claimed to be important in microsporidian classifications appeared to have arisen several times during evolution: for example, the diplokaryon and sporophorous vesicles.