小月菌属放线菌的研究进展

小月菌属(Microlunatus)菌株在治理磷元素造成的环境污染方面呈现优势,具有广阔的研究与开发前景。1995年Nakamura等以积磷小月菌(Microlunatus phosphovorus)为模式种建立了小月菌属。目前,该属包含7个有效描述种,分离自多种生态环境。小月菌属在分类学上的典型特征是:细胞壁含有LL-二氨基庚二酸,优势甲基萘醌成分为MK-9(H_4),磷酸类脂主要包括双磷脂酰甘油和磷脂酰甘油。本文结合我们对新近分离得到的2株小月菌属菌株的分类研究结果和相关文献资料,就小月菌属的建立、分类学特征、属内各成员的分布、及其在化工和医药业上的应用研究进展和开发前景进行了综述。     

环磷酸腺苷对太湖界面沉积物可培养细菌多样性的影响

【背景】环境细菌可培养率只有1%,菌间的信息交流是限制培养效率的一个重要原因。细胞间信息传递的"第二信使"——环磷酸腺苷(cAMP)是细菌感知和应对外界变化时使用广泛的物质。【目的】研究cAMP诱导培养下的细菌种群组成变化,以探讨对微生物可培养性的影响,为提高细菌可培养率和菌种资源开发提供参考。【方法】以太湖沉积物为对象,结合高通量测序和分离培养方法解析样品中细菌的多样性。【结果】高通量测序的物种组成分析结果表明,cAMP作用下诱导出60个不同于对照组的OTU(Operational taxonomic unit),其中显著差异的是变形菌门和拟杆菌门,前者提高4.08%,后者降低3.36%,非常显著差异的是疣微菌门。在属分类水平有8个显著差异的菌属,2个非常显著差异的菌属(气单胞菌属和Trichococcus)。分离培养结果显示,cAMP诱导下CFU(Colony-forming unit)提高至1.6倍,诱导培养出微小杆菌属(Exiquobacterium)、微杆菌属(Microbacterium)、热单胞菌属(Thermomonas)、Lacibacter、Pedobacter、Massilia、Kocuria和Arthrobacter。【结论】从高通量结果可知cAMP对变形菌门的菌株生长有显著促进作用,而分离培养结果表明,cAMP提高微小杆菌属、微杆菌属、热单胞菌属、Lacibacter、Pedobacter、Massilia、Kocuria和Arthrobacter的可培养性。     

杭州市西湖景区春季空气细菌多样性特征

选取了杭州市西湖景区4个典型样点,利用高通量测序方法研究了其空气细菌多样性特征。结果表明,在细菌门水平上,各样点优势细菌为变形菌门(Proteobacteria)、放线菌门(Actinobacteria)、厚壁菌门(Firmicutes)和拟杆菌门(Bacteroidetes),其总相对含量在断桥残雪(MSBB)、柳浪闻莺(OSW)、宝石流霞(PSHFRC)和三潭印月(TPMM)分别为88.31%、86.03%、85.06%和89.28%,且不同样点优势菌群存在一定的差异,OSW和TPMM厚壁菌门分别占9.65%和11.6%,拟杆菌门分别占6.86%和5.55%,MSBB和PSHFRC拟杆菌门分别占7.31%和7.86%,厚壁菌门分别占7.09%和5.32%。在细菌属水平上,各样点优势菌属及含量差异显著,MSBB、TPMM、OSW和PSHFRC相对含量最高的菌属分别为马赛菌属(Massilia)、两面神菌属(Janibacter)、鞘氨醇单胞菌属(Sphingomonas)和甲基杆菌属(Methylobacterium),分别占6.22%、6.45%、6.05%和11.5%,各样点相对含量高于2%的细菌属有鞘氨醇单胞菌属、甲基杆菌属、薄层菌属(Hymenobacter)和异常球菌属(Deinococcus),这些菌属是西湖景区各样点共有的优势菌群;通过空气细菌OTU及多样性分析可知,MSBB空气细菌丰富度较高,均匀度较低,而PSHFRC丰富度较低,均匀度较高。杭州西湖景区不同样点空气细菌群落特征差异显著,且其丰富度和均匀度明显不同。     

赤杆菌科微生物分类研究进展

赤杆菌科微生物隶属于细菌域(Bacteria)、变形菌门(Proteobacteria)、α-变形菌纲(Alphaproteobacteria)、鞘脂单胞菌目(Sphingomonadales)。依据16S rRNA基因序列的系统发育分析结果,2005年赤杆菌科被提议建立,成立之初由3个属5个种组成;在过去10年中,该科的物种数量增加迅速;截止2015年10月,赤杆菌科合格发表6个属44个种。赤杆菌科微生物在土壤、热泉、海水和沉积物等环境中广泛分布,其在环境修复、食品工程及生物医药等领域具有重要的应用前景。此外,部分菌株具有细菌叶绿素a,营好氧异养生长兼具光合作用功能,是好养不产氧光合异养菌的一个重要类群,近年来其在全球海洋碳循环和能量代谢过程中的重要作用日益凸显,得到了国内外学者的关注。本文综述了赤杆菌科微生物的分类特征、生态分布和应用基础等方向的研究进展,并对其分类研究趋势做了分析。     

类诺卡氏属放线菌的研究进展

Prauser H.最初于1976年从土壤中分离到17株诺卡氏形态放线菌,综合形态、生理生化特性和部分化学分类特征的研究结果,提议建立了一个新属——类诺卡氏属(Nocardioides),并以新种白色类诺卡氏菌(N.albus)为典型种。之后,随着分离、纯培养和分类方法的发展,越来越多的新成员从各种不同环境中分离得到。尽管这些菌来源广泛,形态和生理生化等特征各异,但他们拥有共同的属的特征。过去的50年中,随着放线菌研究的发展,该属中部分成员历经了分类地位的变迁和修订。到目前为止,该属共收纳了56个有效描述种。类诺卡氏属(Nocardioides)放线菌在农业、工业、化工业等方面也曾有应用研究报道。本文就类诺卡氏属放线菌的建立依据,属的特征,属内种的分布和变更以及它们在工农业上的应用研究前景及进展进行了综述。     

青岛市秋季空气微生物群落多样性

采用KC-6120空气综合采样器采集空气微生物样品,通过构建16S/18SrDNA克隆文库方法分析青岛市市区街道秋季空气微生物群落结构特征.结果表明： 空气细菌分布在6大类,分别为变形菌门(78.8%)、厚壁菌门(14.6%)、放线菌门(4.0%)、浮霉菌门(1.3%)、蓝藻门(0.7%)和栖热菌门(0.6%),优势菌属为不动杆菌属(39.7%)、葡萄球菌属(11.3%)、鞘脂单胞菌属(8.6%)和副球菌属(6.0%).空气真菌分布在子囊菌门(97.5%)和担子菌门(2.5%),优势菌属为核腔菌属(76.5%)、炭角菌属(13.6%)和外瓶霉属(2.5%).空气微生物中存在不动杆菌属、鞘脂单胞菌、葡萄球菌等致病菌或条件致病菌,以及引发多种农作物枯萎死亡的麦类核腔菌、团炭角菌和角状平脐疣孢等真菌.     

青岛市秋季空气微生物群落多样性

采用KC-6120空气综合采样器采集空气微生物样品,通过构建16S/18SrDNA克隆文库方法分析青岛市市区街道秋季空气微生物群落结构特征.结果表明： 空气细菌分布在6大类,分别为变形菌门(78.8%)、厚壁菌门(14.6%)、放线菌门(4.0%)、浮霉菌门(1.3%)、蓝藻门(0.7%)和栖热菌门(0.6%),优势菌属为不动杆菌属(39.7%)、葡萄球菌属(11.3%)、鞘脂单胞菌属(8.6%)和副球菌属(6.0%).空气真菌分布在子囊菌门(97.5%)和担子菌门(2.5%),优势菌属为核腔菌属(76.5%)、炭角菌属(13.6%)和外瓶霉属(2.5%).空气微生物中存在不动杆菌属、鞘脂单胞菌、葡萄球菌等致病菌或条件致病菌,以及引发多种农作物枯萎死亡的麦类核腔菌、团炭角菌和角状平脐疣孢等真菌.     

印度洋深海沉积物石油烃降解菌分离、鉴定与多样性分析

烃类物质在海洋环境中广泛分布,深海可能含有特殊的烃降解微生物。本研究通过对西南印度洋中脊与印度洋中部深海沉积物中石油降解菌的富集培养和分离鉴定,从6个站点的样品中共分离得到800株菌,通过BOX-PCR去重复菌株后,对其中183株菌进行了16S rRNA基因序列分析,发现这些菌分属于23个属;其中,γ-变形菌纲的食烷菌属(Alcanivorax)和放线菌纲的微杆菌属(Microbacterium)占优势。此外,还发现了食烷菌属2个潜在的新种、假海栖菌属(Pseudooceanicola)1个潜在新种。高通量测序结果证明,富集菌群中γ-变形菌纲是优势菌,主要包括食烷菌属、盐单胞菌属(Halomonas)、海杆菌属(Marinobacter)等。结合可培养菌与高通量测序结果,食烷菌属、盐单胞菌属、海杆菌属、交替假单胞菌(Pseudoalteromonas)、海源菌属(Idiomarina)与微杆菌属(Microbacterium)是沉积物样品中常见的石油烃降解菌,迪茨氏菌属(Dietzia)、红球菌属(Rhodococcus),假单胞菌属(Pseudomonas)、赤杆菌属(Erythrobacter)与副球菌属(Paracoccus)等可能也参与了烃的降解。     

陇东旱作果园生草对土壤细菌群落组成的影响

以陇东旱塬13年生秦冠苹果园为对象,采用高通量测序技术分析鸭茅(Dactylis glomerata)、白三叶(Trifolium repens)和紫花苜蓿(Medicago sativa)生草模式下0~10 cm土壤细菌群落及特异菌属组成特征,明晰生草覆盖后土壤细菌群落多样性变化规律,为陇东旱作果园建立最优生草管理方式提供依据。结果表明:3种生草模式下,土壤细菌群落中相对丰度前3位的菌门为变形菌门(Proteobacteria)(48%~52%)、拟杆菌门(Bacteroidetes)(14%~19%)和酸杆菌门(Acidobacteria)(10%~17%);与对照相比,鸭茅、白三叶和紫花苜蓿处理土壤细菌β-变形菌纲(Betaproteobacteria)相对丰度分别增加19%~38%,黄杆菌纲(Flavobacteriia)相对丰度分别增加31%~65%,土壤溶杆菌属(Lysobacter)相对丰度分别增加37%~93%,苯基杆菌属(Phenylobacterium)相对丰度分别增加45%~52%;不同生草模式下土壤均发现特异菌属,梭菌属(Clostridium)出现在鸭茅模式中,该菌属促进土壤氮素积累;侏囊菌属(Nannocystis)存在于白三叶模式中,该菌属分布在有机质丰富环境中;芽孢杆菌属(Bacillus)主要出现在种植白三叶和紫花苜蓿的土壤中,该菌属与植物固氮有较强关联性;果园生草后土壤细菌多样性有增加趋势,可以促进土壤有益特异菌属产生,从而起到调节土壤微环境的作用。     

西藏鹅膏菌属的分布特征

西藏地区已知鹅膏菌属(Amanita)真菌28种。西藏东南部的生态环境有利于该属种类的繁殖生长,约有90%以上的种集中分布在这里,同时反映了十分明显的垂直分布和对高山的适应特征。绝大多数种分布在海拔2500～3500m的森林带。另外该属全部种均属树木的外生菌根菌。本文还将鹅膏菌属的菌托初步划分为袋状型(Saccate type)、浅杯型(Vadosocupulatetype)、领口型(Collared type)、颗粒型(易碎型Granulate type)、小托型(Microvolvate type)、粉托型(Pulverulent type)等六种类型,并简要讨论了各种菌托类型与所处生态环境的适应性。     

拟诺卡氏菌属放线菌研究进展

拟诺卡氏菌属是一个经典的丝状放线菌类群,在近十余年来获得了快速发展,目前已合格发表42个种、2个亚种。该菌群在土壤环境,尤其是天然高盐碱土样生境中广泛分布,同时从海洋、人居环境、临床样本、堆肥等生境中也能分离到。拟诺卡氏菌不仅能合成抗生素、酶抑制剂、生物表面活性剂等多种结构新颖的活性物质,而且还能产生多种具有潜在工业用途的酶,因此近年来引起了国内外学者的广泛关注。本文综述了拟诺卡氏菌分类学、生态分布与适应机制、代谢产物及遗传转化的研究进展,并对其研究趋势做了分析。     

Diversity of N-acyl homoserine lactone-producing and -degrading bacteria in soil and tobacco rhizosphere

In Gram-negative bacteria, quorum-sensing (QS) communication is mostly mediated by N-acyl homoserine lactones (N-AHSL). The diversity of bacterial populations that produce or inactivate the N-AHSL signal in soil and tobacco rhizosphere was investigated by restriction fragment length polymorphism (RFLP) analysis of amplified 16S DNA and DNA sequencing. Such analysis indicated the occurrence of N-AHSL-producing strains among the alpha-, beta- and gamma-proteobacteria, including genera known to produce N-AHSL (Rhizobium, Sinorhizobium and Pseudomonas) and novel genera with no previously identified N-AHSL-producing isolates (Variovorax, Sphingomonas and Massilia). The diversity of N-AHSL signals was also investigated in relation to the genetic diversity of the isolates. However, N-AHSL-degrading strains isolated from soil samples belonged to the Bacillus genus, while strains isolated from tobacco rhizospheres belonged to both the Bacillus genus and to the alpha subgroup of proteobacteria, suggesting that diversity of N-AHSL-degrading strains may be modulated by the presence of the tobacco plant. Among these rhizospheric isolates, novel N-AHSL-degrading genera have been identified (Sphingomonas and Bosea). As the first simultaneous analysis of both N-AHSL-degrading and -producing bacterial communities in a complex environment, this study revealed the coexistence of bacterial isolates, belonging to the same genus or species that may produce or degrade N-AHSL.     

Molecular phylogeny of the genus Dactylopius (Hemiptera: Dactylopiidae) and identification of the symbiotic bacteria

Phylogenetic analyses, from polymerase chain reaction (PCR)-amplified 12S rRNA and 18S rRNA gene sequences from cochineal insects of the genus Dactylopius present in Mexico, showed that D. ceylonicus, D. confusus, and D. opuntiae are closely related. D. coccus constitutes a separate clade, and D. tomentosus is the most distantly related. Bacterial 16S rRNA sequences from all the Dactylopius species sampled showed a common β-proteobacteria, related to Azoarcus, also found in eggs and in bacteriocytes in D. coccus. We propose the name "Candidatus Dactylopiibacterium carminicum" for this endosymbiont. Other bacterial sequences recovered from the samples were close to those from soil or plant associated bacteria, like Massilia, Herbaspirillum, Acinetobacter, Mesorhizobium, and Sphingomonas, suggesting a possible horizontal transmission from Cactaceae plant sap to Dactylopius spp. during feeding. This is the first molecular analysis of Dactylopius species and of their associated bacteria.     

Temporal change in culturable phenanthrene degraders in response to long-term exposure to phenanthrene in a soil column system

Widespread environmental contamination by polycyclic aromatic hydrocarbons (PAH) has led to increased interest in the use of natural attenuation as a clean-up strategy. However, few bioremediation studies have investigated the behaviour of the indigenous PAH-degrading community after long-term exposure to a PAH. In this study, a column packed with sandy loam soil was exposed to a solution saturated with phenanthrene ( approximately 1.2 mg l-1) for a 6-month period to examine the temporal response of the indigenous phenanthrene-degrading community. Initial soil, effluent, and final soil samples were collected and analysed for phenanthrene concentration and culturable phenanthrene degraders. Phenanthrene-degrading isolates were grouped by colony morphology. For each unique group, 16S rDNA polymerase chain reaction was performed, and then sequencing analysis was used to identify the isolate at the genus level. Twenty-five phenanthrene-degrading isolates, potentially representing 19 genera, were obtained from this analysis. Of these, eight genera have not been reported previously to degrade phenanthrene, including Afipia, Janthinobacterium, Leptothrix, Massilia, Methylobacterium, Rhizobium, Sinorhizobium and Thiobacillus. Results indicate that the dominant phenanthrene-degrading population changed over the course of this 6-month experiment. Specifically, the isolates obtained initially from the soil were not subsequently found in either effluent samples or the soil at the end of the experiment. Furthermore, several isolates that were found in the soil at the end of the experiment were not observed in the soil initially or in the effluent samples. This study confirms earlier findings indicating that a diverse community participates in phenanthrene degradation in the environment, and also suggests that the composition of this community is temporally variable.     

Genus Pseudonocardia: What we know about its biological properties,abilities and current application in biotechnology

The genus Pseudonocardia belongs to a group of Actinomycetes, and is a member of the family Pseudonocardiacea. The members of this genus are aerobic, Gram-positive, non-motile bacteria that are commonly found in soil, plant and environment. Although this genus has a low clinical significance; however, it has an important role in biotechnology due to the production of secondary metabolites, some of which have anti-bacterial, anti-fungal and anti-tumour effects. The use of phenotypic tests, such as gelatinase activity, starch hydrolysis, catalase and oxidase tests, as well as molecular methods, such as polymerase chain reaction, are necessary for Pseudonocardia identification at the genus and species levels.     

The use of a functional approach as surrogate of Collembola species richness in European perennial crops and forests

Collembolans are known indicators of soil disturbance, used in several soil biodiversity monitoring programmes. As for other groups of soil microarthropods, taxonomic determination of Collembola species requires a huge effort and expert knowledge. In this study, we evaluated whether identification of Collembola species to the morphotype level, using an eco-morphological index which classifies individuals based on their adaptation to the soil, can be used as a surrogate of species richness in extensive monitoring schemes. The same evaluation was performed for higher taxa surrogates, using taxonomic categories at the genus and family levels. Additionally, sampling effort for perennial crops and forest systems was determined. Species data were collected from 35 sites sampled within different projects with the same number of samples (16 per site). Results showed that, on average, 8–12 samples are enough to have a good estimate of species richness for this type of systems, averaging 80–90%, but varying considerably with site habitat heterogeneity and local Collembola species pool. GLM models (using species richness as response variable) fitted for family, genus or morphotype levels (explanatory variables) were all significant (p < 0.05) but only the latter two had a pseudo R² higher than 0.75. This indicates that when a rapid, cost-effective assessment of Collembola richness in different sites is required, this eco-morphological trait approach, as well as the determination to the genus level, could be used.     

Biology of Amaranths

Amaranthus, a cosmopolitan genus including endangered species, restricted endemics and widespread weeds, is often difficult to characterize taxonomically and thus has generally been considered by systematists as a “difficult” genus. Species in this genus have high genetic variability, with diversity in growth form, plant height, number of inflorescences, seed colour, protein content, seed yield, resistance to pests and diseases, and adaptation to soil type, pH, climate, rainfall and day-length. The combination of various anatomical characteristics of Amaranthus, such as Kranz anatomy, well developed root system, stomatal conductance, and maintenance of leaf area, results in increased efficiency of using CO₂ under a wide range of temperatures, and higher light intensity and moisture stress environments which enables this plant to adapt under diverse geographic and environmental conditions. Buried seeds of Amaranthus constitute an important part of the soil seed bank and position, distribution and dormancy type of these seeds in the soil play an important role in their germination and subsequent emergence, which is further influenced by factors like temperature, soil moisture, and light availability. The current review highlights the positive as well as negative role of the various species of genus Amaranthus. Many species of the genus are medicinally important and bear antiallergic, anticancer, antihypertensive and antioxidant properties, thus being used in the treatment of several aliments. Amaranthus being a rich source of fatty acids, proteins, micronutrients, vitamins and squalene, are used as cereals, dye plants, forages, medicinal plants, ornamentals, and as vegetables. However some of the Amaranthus species are noxious weeds which are known to compete with many economic crops in different parts of the world and cause great yield losses. Thus, further research is warranted to strike a balance between the beneficial and harmful species of this Pseudocereal. Moreover, understanding the weedy behaviour of these plants would provide valuable information for improving our mechanistic models of crop-weed competition and weed population dynamics.     

Massilia sp. BS-1, a novel violacein-producing bacterium isolated from soil

A novel bacterium, Massilia sp. BS-1, producing violacein and deoxyviolacein was isolated from a soil sample collected from Akita Prefecture, Japan. The 16S ribosomal DNA of strain BS-1 displayed 93% homology with its nearest violacein-producing neighbor, Janthinobacterium lividum. Strain BS-1 grew well in a synthetic medium, but required both L-tryptophan and a small amount of L-histidine to produce violacein.     

Description of Massilia rubra sp. nov., Massilia aquatica sp. nov., Massilia mucilaginosa sp. nov., Massilia frigida sp. nov., and one Massilia genomospecies isolated from Antarctic streams,lakes and regoliths

Bacteria of the genus Massilia often colonize extreme ecosystems, however, a detailed study of the massilias from the Antarctic environment has not yet been performed. Here, sixty-four Gram-stain-negative, aerobic, motile rods isolated from different environmental samples on James Ross Island (Antarctica) were subjected to a polyphasic taxonomic study. The psychrophilic isolates exhibited slowly growing, moderately slimy colonies revealing bold pink-red pigmentation on R2A agar. The set of strains exhibited the highest 16S rRNA gene sequence similarities (99.5–99.9%) to Massilia violaceinigra B2^T and Massilia atriviolacea SOD^T and formed several phylogenetic groups based on the analysis of gyrB and lepA genes. Phenotypic characteristics allowed four of them to be distinguished from each other and from their closest relatives. Compared to the nearest phylogenetic neighbours the set of six genome-sequenced representatives exhibited considerable phylogenetic distance at the whole-genome level. Bioinformatic analysis of the genomic sequences revealed a high number of putative genes involved in oxidative stress response, heavy-metal resistance, bacteriocin production, the presence of putative genes involved in nitrogen metabolism and auxin biosynthesis. The identification of putative genes encoding aromatic dioxygenases suggests the biotechnology potential of the strains. Based on these results four novel species and one genomospecies of the genus Massilia are described and named Massilia rubra sp. nov. (P3094^T = CCM 8692^T = LMG 31213^T), Massilia aquatica sp. nov. (P3165^T = CCM 8693^T = LMG 31211^T), Massilia mucilaginosa sp. nov. (P5902^T = CCM 8733^T = LMG 31210^T), and Massilia frigida sp. nov. (P5534^T = CCM 8695^T = LMG 31212^T).