Interdependencies between Biotic and Abiotic Ferrous Iron Oxidation and Influence of pH,Oxygen and Ferric Iron Deposits

The effect of pH, oxygen and ferrous iron on growth and oxidation rates of iron-oxidizing bacteria (Gallionella spp and Leptothrix spp) as well as indirect effects, the most prominent being catalytic activity of the produced ferric iron deposits, were investigated. Deposits of biotic origin exhibit slightly lower surface oxidation rates compared to abiotically produced ferric iron. It was shown that the required habitat conditions of the studied species hardly overlap, but increase the pH/oxygen range of potential Fe(II) oxidation conditions. The study highlights the combined effect of microbial iron oxidation and catalytic properties of the Mn and Fe oxidation products.     

Growth of Iron-Oxidizing Bacteria Gallionella ferruginea and Leptothrix cholodnii in Oligotrophic Environments: Ca,Mg, and C as Limiting Factors and G. ferruginea Necromass as C-Source

Abstract

Iron-oxidizing bacteria (FeOB) can successively populate low-nutrient aquatic environments and adapt to a broad concentration range of alkaline earth metals, with optimum conditions widely differing from one species to another. For the most abundant known FeOB genera Gallionella and Leptothrix, there is a lack of reports on substrate affinity for calcium and magnesium and necromass assimilability. Single nutrient and combined affinity for Ca and Mg of a wild Gallionella ferruginea isolate and a Leptothrix cholodnii strain as well as growth of heterotrophic L. cholodnii on necromass of autotrophic G. ferruginea were determined by cell density measurements. G. ferruginea responds with Monod-shaped preferences and thus favors waters rich in Ca and Mg. Maximum growth occurred at Ca concentrations five times above those of commonly used modified mineral Wolfe’s medium. L. cholodnii showed a Monod-shaped preference in the low concentration range and an inhibitory response to increasing hardness: concentrations >2?mM Ca or >0.6?mM Mg allow only 50 or 75%, respectively, of maximum specific cell densities. Considering the concentration range with a Monod-shaped response (for L. cholodnii only lower concentration range), both FeOB show a type I independent colimitation for Ca and Mg with lower requirements of Mg than Ca. On a C-limited medium containing G. ferruginea necromass as the only C-source, L. cholodnii cell counts were higher by two orders of magnitude compared to pyruvate medium. Thus, the necromass may serve as a primary C-source for heterotrophic FeOB and other heterotrophic bacteria with technical and economical relevance.     

Diversity of Culturable Bacteria,from the Anaerobic Zone of the Meromictic Lake Pavin,Able to Perform Dissimilatory-Iron Reduction in Different in Vitro Conditions

A culture-dependent study was performed with the aim of assessing the carbon, electron and Fe(III) sources used for the dissimilatory Fe(III) reduction pathway and the diversity of culturable Fe(III)-reducers in the anoxic zone of the meromictic Lake Pavin. This metabolic pathway was investigated in enrichment cultures inoculated with water samples collected at 70 m depth in the anoxic zone of Lake Pavin. Combinations of different media, organic acids, and incubation gas phases were performed. The potential for Fe(III) reduction in the different growth conditions was assessed by measuring the accumulation of Fe(II) overtime. Bacterial community structure was determined in each growth conditions by Temporal Temperature gradient Gel Electrophoresis (TTGE) profiles of 16S rDNA genes and bands of interest in positive enrichments were sequenced. Comparisons of bacterial community structure between growth conditions revealed that the electron donor, the basal media as well as the Fe(III) source yielded to the selection of different bacterial populations, suggesting that Fe(III) reducers occupy different ecological niches in the anoxic zone of Lake Pavin. Facultative Fe(III) reducers, such as fermentative (e.g., Pseudomonas, Clostridium) and sulphate-reducing (e.g., Desulfovibrio sp.) bacteria, were retrieved in enrichments but well-known obligatory Fe(III) reducers (e.g., Geobacter) were not detected. A greater Fe(III) reduction was noted under H₂:CO₂ gas phase, suggesting that H₂ is used as an electron donor for Fe(III) reduction. Acetate was not used as a precursor for this terminal electron-accepting process, and a high Fe(III) reduction was observed with fumarate provided as the electron donor and carbon sources suggesting that this metabolite may be energetically more beneficial for Fe(III)-reducers.     

环洞庭湖四个淡水湖渔场底泥产几丁质酶细菌的筛选鉴定、分布和产酶量研究

为了解淡水湖渔场底泥中产几丁质酶菌株的产酶量和分布情况，对环洞庭湖的4个淡水湖渔场的表层底泥样品进行了无菌采集。利用稀释涂布平板法、点种法和摇瓶发酵法从底泥样品中筛选分离到26株产几丁质酶菌株，几丁质酶活在0.07～0.69 U/mL之间。对26株产几丁质酶菌株进行16S rRNA基因鉴定和系统发育分析。结果表明，26株菌株都分布于变形菌门(Proteobacteria)和厚壁菌门(Firmicutes)的芽胞杆菌属(Bacillus)、假单胞菌属(Pseudomonas)、不动杆菌属(Acinetobacter)和微小杆菌属(Exiguobacterium)。且产几丁质酶细菌在4个淡水湖渔场表层底泥中的分布情况为安乐湖>东湖>北民湖>西湖。对产几丁质酶菌株的降解活力、种类组成及数量分布的研究可为淡水湖渔场底泥中产几丁质酶微生物资源的开发及应用提供参考。     

香蕉植株内生细菌群落多态性研究

采用平板法对香蕉(Musa nana)植株的内生细菌进行分离纯化,并采用细菌脂肪酸法进行鉴定。结果表明,从香蕉的健康植株和感病植株中共分离得到内生细菌21属24种。从健株分离得到9种内生细菌,其中根、茎和叶分别分离到6种、2种和8种内生细菌。从病株分离得到15属17种内生细菌,其中根、茎和叶分别分离到3种、11种和6种。香蕉健株根部的内生细菌含量最高,达5.195×106cfu g-1,下部叶片内生细菌的含量最低,仅为30 cfu g-1;香蕉病株茎部内生细菌的数量显著高于其他部位,达1.05×107cfu g-1。这说明香蕉在不同生长状态下,其内生细菌的种类和数量存在多样性。     

内蒙古呼伦贝尔草原土壤氨氧化细菌多样性及群落结构

采用聚合酶链式反应-变性梯度凝胶电泳技术及扩增产物序列分析方法,研究了呼伦贝尔5种草地类型(线叶菊草原、贝加尔针茅草原、羊草草原、大针茅草原、克氏针茅草原)土壤氨氧化细菌多样性及群落结构特征.研究表明:不同草地类型间土壤氨氧化细菌群落结构组成差异显著,相似性均低于50%.线叶菊草原土壤氨氧化细菌群落多样性最高,其次是贝加尔针茅草原、羊草草原和克氏针茅草原,大针茅草原最低.5种草地类型土壤氨氧化细菌均以Nitrosospira cluster 3为优势种群,此外还发现有Nitrosospira cluster 1、2、4和Nitrosomonas.线叶菊草原土壤氨氧化细菌群落组成较其他草地类型复杂,而羊草草原和大针茅草原群落组成较简单.经相关性分析,土壤含水量、土壤全氮、有机碳、土壤C/N与土壤氨氧化细菌群落多样性显著正相关(P<0.05).     

Biotransformation of Ginsenosides (Rb1, Rb2, Rb3, Rc) in Human Intestinal Bacteria and Its Effect on Intestinal Flora

Ginsenosides, including Rb₁, Rb₂, Rb₃ and Rc, belong to protopanaxadiol-type saponins in Panax ginseng C. A. Mey. Their contents are high in P. ginseng. They could inhibit oxidant stress, enhance immunity, lower blood sugar, resist tumor cells and facilitate other physiological activities. This study aimed to explore the interaction between ginsenosides Rb₁, Rb₂, Rb₃ and Rc and the intestinal flora of healthy people. It also sought to analyse the biotransformation products and pathways of these ginsenosides in in-vitro human intestinal bacteria and their effects on the diversity of human intestinal flora. Human intestinal bacteria were incubated with ginsenosides Rb₁, Rb₂, Rb₃ and Rc at 37 °C under anaerobic conditions. Samples were taken at different timepoints. The transformed products were identified by rapid high-resolution liquid chromatography-quadrupole time-of-flight mass spectrometry. After 48 h of transformation, the transformed product of ginsenosides Rb₁, Rb₂, Rb₃ and Rc was ginsenoside compound K. The transformation rates were 83.5 %, 88.7 %, 85.6 %, and 84.2 %. 16S rRNA sequencing technology was applied to the bioinformatic analysis of faecal samples incubated for 48 h. Relative to the blank control, the relative abundance of Firmicutes and Proteobacteria significantly increased at the phylum level. Moreover, the relative abundance of Bacteroidetes significantly decreased in ginsenosides Rb₁, Rb₂, Rb₃ and Rc. At the genus level, the relative abundance of Escherichia significantly increased, whereas that of Dorea, Prevotella and Megasphaera significantly decreased in all groups. These results showed that Rb₁, Rb₂, Rb₃ and Rc could improve the structure and diversity of human intestinal flora and balance the metabolic process.     

Isolation and Characterization of Bile Acid 7-Dehydroxylating Bacteria from Human Feces

Methods for isolation of fecal 7α-dehydroxylating bacteria are presented. A total of 219 strains were isolated from feces of healthy humans, and their ability to 7-dehydroxylate cholic, chenodeoxycholic, and ursodeoxycholic acids were examined. Of all the isolates, 14 strains were found to be capable of eliminating the hydroxy group at C-7α and/or C-7β. All the isolates were strictly anaerobic, Gram-positive rods. Thirteen isolates were non-sporeforming bacteria showing certain saccharolytic properties with the production of acid and gas from dextrose, and were catalase-positive but indole-, lecithinase-, urease- and oxidase-negative. Based on the data available at present, it was concluded that they could be regarded as members of the genus Eubacterium. One strain, however was identified as Clostridium sordellii. The isolated strains capable of 7α-dehydroxylating cholic acid and chenodeoxycholic acid were also able to oxidize the hydroxy group at C-7α. Nine strains (10, 12, 36S, M-2, M-17, M-18, Y-98, Y-1112, and Y-1113) of the 7α-dehydroxylating bacteria were confirmed to have 7β-dehydroxylation ability, but five strains (O-51, O-52, O-71, O-72, and Y-67) could not transform ursodeoxycholic acid to lithocholic acid.     

Distribution and Diversity of Aerobic Carbon Monoxide-Oxidizing Bacteria in Geothermal Springs of China,the Philippines,and the United States

Accumulating genomic evidence suggests that a variety of thermophilic bacteria contain cox operons and may be capable of aerobic carbon monoxide (CO) oxidation. However, little is known about the distribution and diversity of the cox-encoding (COXE) bacteria in natural geothermal environments. In this study, we examined coxL gene (encoding the large subunit of carbon monoxide dehydrogenase: CoxL) sequences retrieved from the sediments of 25 geothermal sites located in the Qinghai-Tibetan Plateau (QTP) and Yunnan Province (YP) of China, the Bacon-Manito Geothermal Production Field (BGPF) of the Philippines, and the Great Basin of the United States (USGB). Temperature and pH ranges of the studied hot springs were 22.1 to 90.8°C and 2.7 to 9.4, respectively. Phylogenetic analyses showed that most CoxL sequences were closely related to the classes Actinobacteria, Deinococci, Ktedonobacteria, Thermomicrobia, and Clostridia, and hot springs from different regions hosted different COXE communities. In addition, these hot springs harbored some COXE bacteria that were phylogenetically distinct from those inhabiting nongeothermal ecosystems. This study revealed no significant correlation between temperature or pH and the composition or diversity of COXE communities at the global scale. However, within a given region, temperature was correlated with the COXE bacterial community composition.     

海南岛不同林龄木麻黄凋落物内外细菌多样性及其化感潜力

凋落物在生态系统中具有重要作用。为了对比凋落物内外微生物的多样性和群落结构,选取海南省海口市桂林洋海滨区3个林龄木麻黄凋落物为研究对象,采用Illumina Miseq高通量测序,对凋落物内外微生物的多样性和组成进行分析。结果表明: 凋落物外生细菌的多样性高于内生细菌,中龄林凋落物内外细菌多样性和丰富度均最高,其次是幼龄林,成熟林最低。菌群群落组成分析表明: 在门分类水平上,变形菌门和放线菌门最为丰富(约占总数的80%);属水平上,短小杆菌属、Jatrophihabitans、分支杆菌属、放线孢菌属、Mucilaginibacter、假单孢菌属等在不同林龄间表现出显著差异。主坐标分析(PCoA)表明,凋落物内生细菌受林龄的影响较大,而外生细菌受环境因子的影响较大;解淀粉芽孢杆菌发酵液对木麻黄种子化感潜力最强,且其中含有2,2′-亚甲基双-(4-甲基-6-叔丁基苯酚)等化感物质,表明解淀粉芽孢杆菌参与了化感物质的合成。凋落物微生物群落多样性对木麻黄的化感作用有一定影响,这为探讨微生物在木麻黄凋落物降解过程中作用的研究奠定基础。     

轮作和连作对胡萝卜根际和非根际细菌多样性的影响

细菌是土壤最重要的组成部分,土壤细菌的群落结构对土壤的健康至关重要,可以直接影响植物的生长。胡萝卜的长年连作导致其产量低、质量差等一系列问题的发生,连作问题已成为不可忽视的问题。本研究通过HiSeq PE250高通量测序和生物信息学方法获得了玉米胡萝卜轮作种植和胡萝卜连作种植中胡萝卜根际和非根际土壤细菌的组成结构。研究结果表明,相较于胡萝卜连作,玉米胡萝卜轮作种植改变了胡萝卜根际土壤细菌的组成和群落多样性。RM.M (玉米胡萝卜轮作根际土壤样品)样品中的优势菌门为放线菌门和厚壁菌门,RM.R (胡萝卜连作根际土壤样品)的优势菌门是变形菌门;有益菌如芽孢杆菌属和根瘤菌属在玉米胡萝卜轮作种植中的胡萝卜根际富集。RM.M与RM.R的细菌类群差异显著,群落多样性较低;NRM.M(玉米胡萝卜轮作非根际土壤样品)和NRM.R (胡萝卜连作非根际土壤样)的细菌类群差异不明显,群落多样性较高。与连作根际土壤相比,轮作根际土壤中有益菌的相对丰度较大,细菌相对丰度明显增加。本研究结果对通过调节根际土壤细菌组成来保证胡萝卜产量和质量的稳定,解决连作问题具有重要的意义。     

植物铁吸收、转运和调控的分子机制研究进展

铁是植物正常生命活动所必需的微量矿质元素,铁离子的吸收、转运和利用是一个复杂的过程,很多基因参与了这一过程。本文对近10年来发现和分离的参与植物铁吸收、转运及调控的基因研究进展进行了综述。根据最近的研究结果,提出了植物控制铁吸收的分子调控模式(机理I)。     

Effects of logging and recruitment on community phylogenetic structure in 32 permanent forest plots of Kampong Thom,Cambodia

Ecological communities including tropical rainforest are rapidly changing under various disturbances caused by increasing human activities. Recently in Cambodia, illegal logging and clear-felling for agriculture have been increasing. Here, we study the effects of logging, mortality and recruitment of plot trees on phylogenetic community structure in 32 plots in Kampong Thom, Cambodia. Each plot was 0.25 ha; 28 plots were established in primary evergreen forests and four were established in secondary dry deciduous forests. Measurements were made in 1998, 2000, 2004 and 2010, and logging, recruitment and mortality of each tree were recorded. We estimated phylogeny using rbcL and matK gene sequences and quantified phylogenetic α and β diversity. Within communities, logging decreased phylogenetic diversity, and increased overall phylogenetic clustering and terminal phylogenetic evenness. Between communities, logging increased phylogenetic similarity between evergreen and deciduous plots. On the other hand, recruitment had opposite effects both within and between communities. The observed patterns can be explained by environmental homogenization under logging. Logging is biased to particular species and larger diameter at breast height, and forest patrol has been effective in decreasing logging.     

甘肃天水麦积山风景名胜区土壤纤毛虫的物种多样性

用活体观察和固定染色方法对麦积山风景名胜区土壤纤毛虫物种多样性进行了研究。共鉴定到隶属于3纲12目41科55属的土壤纤毛虫115种,其中包括11个未定名种和26个中国土壤纤毛虫新纪录种。街子温泉景区、曲溪景区、麦积山石窟区、石门山和仙人崖景区各分布有47、46、44、33和26种,大弹跳虫、似织毛虫、膨大肾形虫、僧帽肾形虫、迅捷肾形虫、吻四膜虫、长刀口虫和苔藓刀口虫为广布物种。前口目和下毛目为风景名胜区土壤纤毛虫群落中的优势类群,肾形目和盾纤目为次优势类群,侧口目、吸管目和寡毛目为罕见类群。风景名胜区土壤纤毛虫物种多样性与我国已有研究报道的其他地区的均极不相似。研究结果表明,风景名胜区土壤纤毛虫物种十分丰富,特有和稀有物种繁多,群落结构复杂而特殊;土壤和水生纤毛虫群落物种组成极不相似,土壤和水生纤毛虫群落是不同的2个独立群落。     

Floristic composition and endemism pattern of vascular plants in Ethiopia and Eritrea

Traditional attempts to delineate floristic regions are typically based on the qualitative analysis of species distribution, often ignoring the phylogenetic relationships among their taxa. Ethiopia and Eritrea are in the Horn of Africa, known as one of the world's biodiversity hotspots. We quantitatively classified the flora of Ethiopia and Eritrea into meaningful geographical units by analyzing the taxonomic and phylogenetic β‐diversity at genera, total species, and endemic species levels at a scale of 0.5° × 0.5° grid cells. Hierarchical clustering was used to quantitatively delimitate the flora and analysis of similarities was used to test the significant difference between the derived groups in taxonomic composition and phylogenetic relatedness. In total, two floristic subprovinces, five floristic districts, and 13 floristic subdistricts, as well as three centers of species endemism associated with three floristic subdistricts were identified. Our results also showed that the species diversity, endemism, and turnover of the highlands in Ethiopia and Eritrea were much higher than the lowlands, indicating that the floristic differences are closely related to the topography of the East African Rift. In this study, we provided a scientific framework for the composition and relationships of the floristic units in the Horn of Africa, and similarly provided a scientific basis for better conservation of the diversity in this region.     

山西文峪河上中游森林群落多样性

基于山西文峪河上中游森林群落的野外调查数据,选取植物生活型、生活史、固氮类型、传粉途径、种子传播途径等14个植物功能性状,计算丰富度指数(R)、多样性指数(H')、均匀度指数(E)等物种多样性指数和功能丰富度指数(FRic)、功能均匀度指数(FEve)、功能分歧度指数(FDiv)等功能多样性指数,并用TWINSPAN对森林群落进行分类,Spearman秩相关分析多样性指数间及其与环境因子间的相关性,对山西文峪河上中游森林群落多样性进行研究。结果表明:青杄林种数最多(R=27),辽东栎油松林和油松林种数最少(R=16);白桦林的H'和E最大,油松林的H'和E最小。山杨白桦林的FRic值最大,白杄林的FRic值最小;青杄林的FEve值最大,山杨白桦林的FEve值最小;山杨林的FDiv值最大,白桦林的FDiv值最小。文峪河上中游森林群落物种多样性指数与功能多样性指数间相关性不显著(P0.05),仅FDiv与H'呈显著负相关关系(P0.05);物种多样性指数间呈极显著相关关系(P0.01),功能多样性指数间相关性不显著(P0.05),仅FRic与FEve呈显著负相关关系(P0.05);随着海拔增加,物种多样性指数增加(P0.05或P0.01),但功能多样性指数减小(P0.01或P0.05)。     

甘肃白水江国家级自然保护区土壤肉鞭虫物种多样性

2004年2月～2006年5月,用"非淹没培养皿法"和活体观察法对甘肃白水江国家级自然保护区土壤肉鞭虫的物种多样性进行了研究。共鉴定到肉鞭类原生动物84种,其中包括2个未定名种和23个国内土壤肉鞭虫新纪录种,隶属于2亚门5纲13目32科49属。鞭毛亚门以动基体目的物种占优势,肉足亚门以变形目的物种占优势。研究结果表明,保护区土壤肉鞭虫物种丰富,特有和稀有物种较多,物种组成具有独特性。分析了保护区土壤肉鞭虫物种多样性与自然环境的关系。     

洮河上游不同海拔紫果云杉根际与非根际土壤细菌多样性及影响因子

【背景】紫果云杉天然林在维护洮河上游生态环境安全方面发挥着重要作用,不同海拔梯度如何影响紫果云杉根际与非根际细菌多样性、土壤养分因子及三者之间的相关性尚不清楚。【目的】深入探索紫果云杉根际与非根际土壤细菌群落结构组成及受控因子。【方法】采用Illumina Miseq平台对洮河上游不同海拔紫果云杉天然林根际与非根际土壤细菌进行测序分析,分析土壤理化因子与细菌多样性随海拔的变化趋势,并通过相关性与冗余分析探究环境因子对细菌群落的影响。【结果】土壤养分因子随海拔升高呈先增加后降低趋势;根际土养分因子组间差异显著(P<0.05),非根际组间差异不显著(P>0.05)。随海拔升高根际微生物物种多样性指数(H)、均匀度指数(E)、丰富度指数(Chao1/ACE)和OTU数目呈单峰型变化趋势;非根际多样性指数随海拔升高呈双峰型变化趋势。土壤细菌多样性与养分因子密切相关,其中有机质、全氮和碱解氮呈显著正相关(P<0.05),而土壤pH和有效磷与细菌多样性呈负相关但不显著(P>0.05)。不同海拔梯度下紫果云杉天然林细菌群落结构一致性较高,从30个样本中获得7 159个细菌OTU,注释到37个门;细菌优势类群为放线菌门、变形菌门、酸杆菌门和绿弯菌门。不同细菌门对土壤养分因子的响应各不相同,有机质、全氮和碱解氮与变形菌门呈显著正相关(P<0.05)。【结论】土壤理化因子能够显著影响紫果云杉根际与非根际细菌多样性和组成,海拔和水热条件等环境因子对植物和土壤的驱动影响是细菌群落结构稳定组成的重要原因。本研究有助于深入理解紫果云杉天然林土壤细菌多样性的变化和驱动机制,为洮河上游天然林恢复与生态恢复提供借鉴。