一株糖降解噬糖菌FZY0027的多糖水解活性及基因组分析

【目的】潮间带海水中分离获得一株具有水解多糖能力的菌株FZY0027,分析其对不同多糖的水解能力和基因组特征。【方法】通过形态观察、16S rRNA基因测序和基于Illumina NovaSeq和OxfordNanopore PromethION测序技术全基因组测序对菌株FZY0027进行鉴定。使用dbCAN、EasyCGTree、BRIG和Easyfig等生物信息学软件将菌株FZY0027和降解糖噬糖菌(Saccharophagus degradans) 2-40^T进行比较。使用3,5-二硝基水杨酸(3,5-dinitrosalicylic acid, DNS)法测定多糖水解活性。【结果】菌株FZY0027与S. degradans 2-40^T的16S rRNA基因序列相似度达到99.9%,初步鉴定为降解糖噬糖菌(S. degradans) FZY0027。该菌株在水解淀粉、木聚糖和甘露聚糖时产生的还原糖浓度最高,分别为2.28、1.75和1.10 mg/mL。菌株FZY0027基因组全长5 178 381 bp,共编码4 156个基因,G+C含量为45.8%。菌株FZY0027与S. degradans 2-40^T的平均核苷酸一致性(average nucleotide identity, ANI)、平均氨基酸一致性(average amino acid identity, AAI)和DNA-DNA分子杂交(digital DNA-DNA hybridization, dDDH)值分别为96.5%、96.7%和70.0%。经碳水化合物活性酶数据库注释获得303个基因,其中,菌株FZY0027和S. degradans 2-40^T分别有糖苷水解酶(glycoside hydrolases, GHs)结构域的基因137个和130个。菌株FZY0027具有多个参与淀粉、木聚糖等多糖水解的基因,这与菌株FZY0027对淀粉和木聚糖的水解能力强的结果一致。然而,与S. degradans 2-40^T相比,菌株FZY0027在实验条件下只能水解少数多糖,这可能需要特定的诱导条件才能充分发挥其多糖水解能力。【结论】菌株FZY0027是一株多能型多糖水解菌,具有潜在开发价值。     

从黑茶中分离和筛选产单宁酶菌株

茶叶中富含单宁化合物。从分离自黑茶的真菌菌株中,筛选高产单宁酶的菌株;进而分离纯化单宁酶,分析单宁酶对茶汤的转溶效果。从不同产地的3个黑茶样品中,共分离获得44个真菌分离物;经初步鉴定,这些真菌分离物以曲霉属（Aspergillus）、青霉属（Penicillium）和散囊菌属（Eurotium）的真菌居多。以单宁酸为底物的鉴别培养基初筛表明,其中26个真菌分离物在鉴别平板上产生透明圈,显示单宁水解酶活性;通过固体发酵复筛,筛选到1株产单宁酶活性较高的菌株,初步鉴定为青霉属（Penicillium）菌株,命名为青霉MP-24菌株。青霉MP-24可以以茶叶、茶梗和麸皮等农副产品作为原料固体发酵产生单宁酶。以麸皮为原料的发酵产物经过硫酸铵分级沉淀、DEAE阴离子交换层析和葡聚糖G-150凝胶层析等分离纯化步骤,得到分子量为70 kDa的单一蛋白质条带,单宁酶活力达到603.68 U/mg。纯化获得的单宁酶对茶汤有良好的转溶效果。研究结果表明,在黑茶相关微生物中含有丰富的产单宁酶菌株,是工业酶制剂的重要资源。     

一株粗糙脉孢菌的分离、鉴定及其基因组变异和功能分析

【背景】粗糙脉孢菌LY03是从武平传统"红菌豆腐"中分离得到的主要发酵菌株。【目的】研究粗糙脉孢菌LY03菌株的基因组信息,揭示武平传统"红菌豆腐"发酵特性。【方法】采用形态学观察、ITS鉴定、重测序及框架图测序对所分离的LY03菌株进行鉴定和基因组信息解析。【结果】武平传统"红菌豆腐"中分离得到的主要发酵菌株LY03确定为粗糙脉孢菌,将其在中国普通微生物菌种保藏管理中心进行专利保藏,保藏号为CGMCC3.19233。LY03菌株比对到参考基因组上的总Read数目为95.85%,测序对应深度的位点占全基因组76.13%;各变异类型在内含子区域均无变异,主要变异存在于基因组的外显子区域,具体变异数量为:单核苷酸多态性位点(single nucleotide polymorphism,SNP)位点变异总数203128个、插入缺失(insertion/deletion,In Del)突变总和26859个、拷贝数变异(copy number variation,CNV)增加和减少的拷贝总数1 039个、结构变异(structure variation,SV)注释的变异总数777个;LY03菌株...     

海洋低温几丁质酶菌株筛选、鉴定及酶谱分析

以胶体几丁质为唯一碳源,从大连渤海湾的底泥样品中分离到1株高产低温几丁质酶的海洋细菌,命名为DL-06。由菌株的形态特征结合16S rDNA系统发育分析,初步确定该菌株属于交替假单胞菌(Pseudoalteromonas sp. DL-06)。该菌株经30 h摇瓶发酵后测定粗酶液几丁质酶酶活为9.184 U/mL,最适反应温度为15 ℃,60 ℃孵育1 h仍保持50%以上的酶活性,表明该低温酶具有一定热稳定性。经SDS-PAGE及酶谱分析,该菌株能够产生至少3种以上不同分子质量的几丁质酶组分。Pseudoalteromonas sp. DL-06产几丁质酶在低温下高活性与热稳定特点,使其具有潜在的工业应用价值。     

蝉虫草子实体与发酵菌丝体胞内多糖成分分析

比较蝉虫草子实体、孢梗束、虫体以及蝉虫草发酵菌丝体的胞内多糖含量、单糖组成和分子量差异,结果表明,蝉虫草子实体与发酵菌丝中胞内多糖的含量和组成均存在差异。葡萄糖、半乳糖和甘露糖是蝉虫草发酵菌丝体和子实体粗多糖中主要的3种单糖,阿拉伯糖和木糖是子实体粗多糖中的特征性单糖,而果糖属于菌丝体的特征性单糖。子实体粗多糖中高分子量组分（>1×10 ⁶Da）的相对含量明显高于菌丝体粗多糖。本研究对提升蝉虫草发酵多糖产品品质、促进蝉虫草开发应用具有参考价值。     

假单胞菌产脂肪酶条件的初步探索

对假单胞菌（Pseudomonassp）2106菌株产脂肪酶条件的初步探索表明,该菌株脂肪酶为组成型,不受油脂类底物的诱导。碳源的种类（单糖、双糖、多糖）和浓度对产酶影响不大,氮源以豆饼粉和玉米浆混合添加最好。最适发酵温度为32℃,摇瓶转速140r／min。实验中还通过正交试验优化了产酶培养基组成。     

诺卡氏菌形放线菌β-甘露聚糖酶的水解特性*

诺卡氏菌形放线菌(Nocardioform actinomycetes)NA3-540产生的β-甘露聚糖酶(ManNA)能不同程度地水解槐豆胶、瓜胶、田菁胶和魔芋胶等甘露多聚糖为组分的植物胶,生成系列甘露寡糖;该酶只轻微地水解香豆胶,不能水解β-甘露聚糖、黄原胶、海藻胶;ManNA对槐豆胶、瓜胶和魔芋胶多糖的K_m值和V_max分别为1.75、6.13、3.9mg/mL和2485、1303、853μmol/(min/mg),     

细胞焦亡法破碎微生物细胞在合成生物学与代谢工程的应用

【背景】细胞焦亡是一种细胞程序性死亡。在古菌和细菌中,gasdermin同源蛋白（GSDM）能够被特定的活化caspase （protease）酶切,从而激活类似于细胞焦亡的效应,产生细胞破碎效果。【目的】合成生物学、代谢工程和生物制造等应用过程中,细胞破碎是不可或缺的一步。利用细胞焦亡法破碎细胞取代传统的破碎方法,可以简化操作、提高生产效益。【方法】在大肠杆菌（Escherichia coli） BW25113中共表达protease和不同来源的GSDM,选择有明显细胞焦亡效应即来源Runella sp.的GSDM进行蛋白截短改造,使其在诱导表达蛋白截短体GSDMJD后能直接激活细胞焦亡效应。对GSDMJD进行过表达优化,获得可控大肠杆菌细胞焦亡菌株。进一步以重组表达蔗糖磷酸化酶为研究模型,验证本系统应用于细胞破碎释放蛋白的效果。【结果】实现了大肠杆菌中细胞焦亡的人为可控。焦亡菌株在诱导表达焦亡相关蛋白2 h后大肠杆菌细胞破碎死亡,内容物释放。将上述系统和超声法应用于制备蔗糖磷酸化酶粗酶液,细胞焦亡法制备的粗酶液的相对酶活显著高于超声法制备的粗酶液。在制备粗酶液的菌液OD₆₀₀值为2.0时,细胞焦亡法制备的粗酶液相对酶活最高并且相较于超声法制备粗酶液,提高了60%的相对酶活。【结论】细胞焦亡提供了一种更加简单快捷、绿色环保的微生物细胞破碎方式,为合成生物学与代谢工程的发展奠定了基础。     

一株多糖降解菌的分离、鉴定与琼脂糖降解能力

【目的】筛选海洋来源的多糖降解菌,分析其多糖降解能力并初探机制。【方法】碘液染色法从海泥中初筛琼脂糖降解菌,唯一碳源生长法分析菌株的多糖利用能力,克隆16S rRNA基因以分析系统分类地位。用硫酸铵沉淀法制备胞外粗酶制剂,DNS-还原糖法测定琼胶酶活性,活性染色法分析胞外琼胶酶系的组成特征。分离、纯化琼脂糖的酶解产物,通过TLC测定寡糖Rf值、阳离子质谱测定分子量。【结果】分离到1株能液化琼脂糖的海洋细菌JZB09,鉴定至桃色杆菌属(Persicobacter)。JZB09能利用11种不同的多糖为唯一碳源生长,在利用琼脂糖、纤维素和木聚糖时生长较好。胞外粗酶制剂的琼胶酶活力约77.2U/mg,含有至少2条琼胶酶,大小约45kDa、70kDa。酶制剂降解琼脂糖后的产物是系列新琼寡糖,四糖是主产物,表明β-琼胶酶在胞外琼胶酶系降解琼脂糖时起关键作用。【结论】海洋细菌Persicobacter sp.JZB09是1株多能型多糖降解菌,可分泌β-琼胶酶降解琼脂糖且活性显著,具有潜在开发价值。     

灵芝液态发酵高产胞外多糖菌株筛选及多糖特性分析

对10株灵芝菌株发酵菌丝体生物量、胞内多糖含量、胞外粗多糖得率及其多糖含量和单糖组成特征进行了系统分析。结果表明,随着培养时间的延长,10株菌株的生物量均有不同程度增加,但不同菌株胞内多糖含量和胞外粗多糖得率变化趋势有所不同。在培养至7d时,G0023和G0160菌株胞外粗多糖得率均较高,分别为3.02g/L和3.14g/L,其多糖含量分别达到了84.11%和91.03%,可作为发酵高产胞外多糖的优良菌株。分级醇沉胞外多糖分析结果表明,各菌株胞外液20%乙醇沉淀所得20E组分的得率和多糖含量均高于50%乙醇沉淀所得的50E组分,说明胞外液中主要以大分子量多糖为主。20E主要由葡萄糖组成,含有少量木糖和甘露糖;50E主要由葡萄糖和甘露糖组成,含有少量木糖和半乳糖。胞外液表观粘度随剪切速率变化曲线分析结果显示,各菌株胞外液均呈现剪切变稀非牛顿流体特性,其表观粘度大小与菌株对应20E组分的得率及多糖含量呈正相关。     

Phylogeny of cardinalfishes (Teleostei: Gobiiformes: Apogonidae) and the evolution of visceral bioluminescence

The cardinalfishes (Apogonidae) are a diverse clade of small, mostly reef-dwelling fishes, for which a variety of morphological data have not yielded a consistent phylogeny. We use DNA sequence to hypothesize phylogenetic relationships within Apogonidae and among apogonids and other acanthomorph families, to examine patterns of evolution including the distribution of a visceral bioluminescence system. In conformance with previous studies, Apogonidae is placed in a clade with Pempheridae, Kurtidae, Leiognathidae, and Gobioidei. The apogonid genus Pseudamia is recovered outside the remainder of the family, not as sister to the superficially similar genus Gymnapogon. Species sampled from the Caribbean and Western Atlantic (Phaeoptyx, Astrapogon, and some Apogon species) form a clade, as do the larger-bodied Glossamia and Cheilodipterus. Incidence of visceral bioluminescence is found scattered throughout the phylogeny, independently for each group in which it is present. Examination of the fine structure of the visceral bioluminescence system through histology shows that light organs exhibit a range of morphologies, with some composed of complex masses of tubules (Siphamia, Pempheris, Parapriacanthus) and others lacking tubules but containing chambers formed by folds of the visceral epithelium (Acropoma, Archamia, Jaydia, and Rhabdamia). Light organs in Siphamia, Acropoma, Pempheris and Parapriacanthus are distinct from but connected to the gut; those in Archamia, Jaydia, and Rhabdamia are simply portions of the intestinal tract, and are little differentiated from the surrounding tissues. The presence or absence of symbiotic luminescent bacteria does not correlate with light organ structure; the tubular light organs of Siphamia and chambered tubes of Acropoma house bacteria, those in Pempheridae and the other Apogonidae do not.     

Foreign exploration for Scirtothrips perseae Nakahara (Thysanoptera: Thripidae) and associated natural enemies on avocado (Persea americana Miller)

Scirtothrips perseae Nakahara was discovered attacking avocados in California, USA, in 1996. Host plant surveys in California indicated that S. perseae has a highly restricted host range with larvae being found only on avocados, while adults were collected from 11 different plant species. As part of a management program for this pest, a “classical” biological control program was initiated and foreign exploration was conducted to delineate the home range of S. perseae, to survey for associated natural enemies and inventory other species of phytophagous thrips on avocados grown in Mexico, Guatemala, Costa Rica, the Dominican Republic, Trinidad, and Brazil. Foreign exploration efforts indicate that S. perseae occurs on avocados grown at high altitudes (>1500 m) from Uruapan in Mexico south to areas around Guatemala City in Guatemala. In Costa Rica, S. perseae is replaced by an undescribed congener as the dominant phytophagous thrips on avocados grown at high altitudes (>1300 m). No species of Scirtothrips were found on avocados in the Dominican Republic, Trinidad, or Brazil. In total, 2136 phytophagous thrips were collected and identified, representing over 47 identified species from at least 19 genera. The significance of these species records is discussed. Of collected material 4% were potential thrips biological control agents. Natural enemies were dominated by six genera of predatory thrips (Aeolothrips, Aleurodothrips, Franklinothrips, Leptothrips, Scolothrips, and Karnyothrips). One genus each of parasitoid (Ceranisus) and predatory mite (Balaustium) were found. Based on the results of our sampling techniques, prospects for the importation of thrips natural enemies for use in a “classical” biological control program in California against S. perseae are not promising.     

Molecular phylogeny of Phebalium (Rutaceae: Boronieae) and related genera based on the nrDNA regions ITS 1+2

Parsimony analyses of the internal transcribed spacer regions of nuclear ribosomal DNA (ITS 1 & ITS 2) for 38 taxa sampled from the Phebalium group (Rutaceae: Boronieae) and two outgroups confirm that, with the exception of Phebalium sensu stricto and Rhadinothamnus, six of the currently recognised genera within the group are monophyletic. The data indicate that Phebaliums. str. is paraphyletic with respect to Microcybe, and Rhadinothamnus is paraphyletic with respect to Chorilaena. Rhadinothamnus and Chorilaena together are the sister group to Nematolepis. Drummondita, included as an outgroup taxon, clustered within the ingroup as sister to Muiriantha and related to Asterolasia.The phylogeny suggests that the evolution of major clades within a number of these genera (e.g. Phebalium) relates to vicariance events between eastern and south-western Australia. Leionema is an eastern genus, with the most basal taxon being the morphologically distinct Leionema ellipticum from northern Queensland. Leionema also includes one species from New Zealand, but this species (as with some others) proved difficult to sequence and its phylogenetic position remains unknown. Taxonomic changes at the generic level are recommended.The authors wish to thank Paul G.Wilson, PERTH, for advice and discussion, and Paul Forster, BRI, for collecting and providing material of Leionema ellipticum. The project was supported by a Melbourne University Postgraduate Award (to BM), the Australian Biological Resources Study (ABRS), Australian Systematic Botany Society and Wolf Den (Australia) Investments.     

Molecular identification of Taenia spp. in wolves (Canis lupus), brown bears (Ursus arctos) and cervids from North Europe and Alaska

Taenia tapeworms of Finnish and Swedish wolves (Canis lupus) and Finnish brown bears (Ursus arctos), and muscle cysticerci of Svalbard reindeer (Rangifer tarandus platyrhynchus), Alaskan Grant's caribou (Rangifer tarandus granti) and Alaskan moose (Alces americanus) were identified on the basis of the nucleotide sequence of a 396 bp region of the mitochondrial cytochrome c oxidase subunit 1 gene. Two species were found from wolves: Taenia hydatigena and Taenia krabbei. The cysticerci of reindeer, caribou and one moose also represented T. krabbei. Most of the cysticercal specimens from Alaskan moose, however, belonged to an unknown T. krabbei-like species, which had been reported previously from Eurasian elks (Alces alces) from Finland. Strobilate stages from two bears belonged to this species as well. The present results suggest that this novel Taenia sp. has a Holarctic distribution and uses Alces spp. as intermediate and ursids as final hosts.     

Planting densities and bird and rodent absence affect size distributions of four dicots in synthetic tallgrass communities

Variability in the size distributions of populations is usually studied in monocultures or in mixed plantings of two species. Variability of size distributions of populations in more complex communities has been neglected. The effects of seeding density (35 or 350 seeds/species/m²) and presence of small vertebrates on the variability of size distributions were studied for a total of 1,920 individuals of 4 species in replicated synthetic communities of 18 species in northern Illinois. End-of season height and above-ground biomass were measured for prairie perennials Dalea purpurea (purple prairie clover), Echinacea purpurea (purple coneflower), Desmanthus illinoensis (Illinois bundleflower) and Heliopsis helianthoides (early sunflower). Variability in biomass distribution of the four target species was twice as great at low than at high densities when small vertebrates were excluded. Our results suggest that inter- and intraspecific competition may affect all individuals more under high-density conditions, thereby reducing the variability in their biomass distributions within this community. This result, a consequence of plant-plant interaction, is obscured when small birds or mammals are present, presumably because either or both add variance that overwhelms the pattern.     

Phylogeny and Megasystematics of Phagotrophic Heterokonts (Kingdom Chromista)

Heterokonts are evolutionarily important as the most nutritionally diverse eukaryote supergroup and the most species-rich branch of the eukaryotic kingdom Chromista. Ancestrally photosynthetic/phagotrophic algae (mixotrophs), they include several ecologically important purely heterotrophic lineages, all grossly understudied phylogenetically and of uncertain relationships. We sequenced 18S rRNA genes from 14 phagotrophic non-photosynthetic heterokonts and a probable Ochromonas, performed phylogenetic analysis of 210–430 Heterokonta, and revised higher classification of Heterokonta and its three phyla: the predominantly photosynthetic Ochrophyta; the non-photosynthetic Pseudofungi; and Bigyra (now comprising subphyla Opalozoa, Bicoecia, Sagenista). The deepest heterokont divergence is apparently between Bigyra, as revised here, and Ochrophyta/Pseudofungi. We found a third universal heterokont signature sequence, and deduce three independent losses of ciliary hairs, several of 1-2 cilia, 10 of photosynthesis, but perhaps only two plastid losses. In Ochrophyta, heterotrophic Oikomonas is sister to the photosynthetic Chrysamoeba, whilst the abundant freshwater predator Spumella is biphyletic; neither clade is specifically related to Paraphysomonas, indicating four losses of photosynthesis by chrysomonads. Sister to Chrysomonadea (Chrysophyceae) is Picophagea cl. nov. (Picophagus, Chlamydomyxa). The diatom-parasite Pirsonia belongs in Pseudofungi. Heliozoan-like actinophryids (e.g. Actinosphaerium) are Opalozoa, not related to pedinellids within Hypogyristea cl. nov. of Ochrophyta as once thought. The zooflagellate class Bicoecea (perhaps the ancestral phenotype of Bigyra) is unexpectedly diverse and a major focus of our study. We describe four new biciliate bicoecean genera and five new species: Nerada mexicana, Labromonas fenchelii (=Pseudobodo tremulans sensu Fenchel), Boroka karpovii (=P. tremulans sensu Karpov), Anoeca atlantica and Cafeteria mylnikovii; several cultures were previously misidentified as Pseudobodo tremulans. Nerada and the uniciliate Paramonas are related to Siluania and Adriamonas; this clade (Pseudodendromonadales emend.) is probably sister to Bicosoeca. Genetically diverse Caecitellus is probably related to Anoeca, Symbiomonas and Cafeteria (collectively Anoecales emend.). Boroka is sister to Pseudodendromonadales/Bicoecales/Anoecales. Placidiales are probably divergent bicoeceans (the GenBank Placidia sequence is a basidiomycete/heterokont chimaera). Two GenBank ‘opalinid’ sequences are fungal; Pseudopirsonia is cercozoan; two previous GenBank ‘Caecitellus’ sequences are Adriamonas. Electronic Supplementary Material Electronic Supplementary material is available for this article at and accessible for authorised users. [Reviewing Editior: Patnck J. Keeling]     

Seven new calochroid and fulvoid species of Cortinarius

We describe seven new European species of Cortinarius. All species are based on analyses of morphological and DNA sequence data. They all belong to a well-supported clade comprising most species traditionally treated in Cortinarius subgenus Phlegmacium sections Fulvi and Calochroi (i.e. the/Calochroi clade). All taxa are either fulvoid (containing anthraquinoid pigments) or calochroid (without these pigments). Morphological and ecological data are presented for all species and compared with similar species. A dichotomous key is presented for C. calochrous and similar species, including all six newly described calochroid species. The calochroid species C. albertii, C. chailluzii, C. cisticola, C. sancti-felicis, C. selandicus and C. vesterholtii spp. nov., and the fulvoid species C. langeorum sp. nov. are described.     

New geographical distribution and host records of rust fungi from northern Thailand

Ten species of rust fungi (Crossopsora 2, Maravalia 1, Pileolaria 1, Puccinia 1, Ravenelia 1, Sphaerophragmium 1, Uredo 2, and Uromyces 1) are newly recorded together with six new host plants in Thailand.Contribution no. 194, Laboratory of Plant Parasitic Mycology, Graduate School of Life and Environmental Sciences, University of Tsukuba, Japan     

The hernandez and fernandez genes of Drosophila specify eye and antenna

The formation of different structures in Drosophila depends on the combined activities of selector genes and signaling pathways. For instance, the antenna requires the selector gene homothorax, which distinguishes between the leg and the antenna and can specify distal antenna if expressed ectopically. Similarly, the eye is formed by a group of "eye-specifying" genes, among them eyeless, which can direct eye development ectopically. We report here the characterization of the hernandez and fernandez genes, expressed in the antennal and eye primordia of the eye-antenna imaginal disc. The predicted proteins encoded by these two genes have 27% common amino acids and include a Pipsqueak domain. Reduced expression of either hernandez or fernandez mildly affects antenna and eye development, while the inactivation of both genes partially transforms distal antenna into leg. Ectopic expression of either of the two genes results in two different phenotypes: it can form distal antenna, activating genes like homothorax, spineless, and spalt, and it can promote eye development and activates eyeless. Reciprocally, eyeless can induce hernandez and fernandez expression, and homothorax and spineless can activate both hernandez and fernandez when ectopically expressed. The formation of eye by these genes seems to require Notch signaling, since the induction of ectopic eyes and the activation of eyeless by the hernandez gene are suppressed when the Notch function is compromised. Our results show that the hernandez and fernandez genes are required for antennal and eye development and are also able to specify eye or antenna ectopically.