Characterization of a homogeneous taxonomic group of marine magnetotactic cocci within a low tide zone in the China Sea

Magnetotactic bacteria are a heterologous group of motile prokaryotes, ubiquitous in aquatic habitats and cosmopolitan in distribution. Here, we studied the diversity of magnetotactic bacteria in a seawater pond within an intertidal zone at Huiquan Bay in the China Sea. The pond is composed of a permanently submerged part and a low tide subregion. The magnetotactic bacteria collected from the permanently submerged part display diversity in morphology and taxonomy. In contrast, we found a virtually homogenous population of ovoid-coccoid magnetotactic bacteria in the low tide subregion of the pond. They were bilophotrichously flagellated and exhibited polar magnetotactic behaviour. Almost all cells contained two chains of magnetosomes composed of magnetite crystals. Intriguingly, the combination of restriction fragment length polymorphism analysis (RFLP) and sequencing of cloned 16S rDNA genes from the low tide subregion samples as well as fluorescence in situ hybridization (FISH) revealed the presence of a homogenous population. Moreover, phylogenetic analysis indicated that the Qingdao Huiquan low tide magnetotactic bacteria belong to a new genus affiliated with the alpha-subclass of Proteobacteria. This finding suggests the adaptation of the magnetotactic bacterial population to the marine tide.

Isolation and characterization of a marine magnetotactic spirillum axenic culture QH-2 from an intertidal zone of the China Sea

Magnetotactic bacteria (MTB) are ubiquitous in aquatic habitats. Because of their fastidious requirements for growth conditions, only very few axenic MTB cultures have been obtained worldwide. In this study, we report a novel marine magnetotactic spirillum axenic culture, designated as QH-2, isolated from the China Sea. It was able to grow in semi-solid or liquid chemically defined medium. The cells were amphitrichously flagellated and contained one single magnetosome chain with an average number of 16 magnetosomes per cell. Phosphate and lipid granules were also observed in the cells. Both rock magnetism and energy-dispersive X-ray spectroscopy characterizations indicated that the magnetosomes in QH-2 were single-domain magnetites (Fe3O4). QH-2 cells swam mostly in a straight line at a velocity of 20-50 mu m/s and occasionally changed to a helical motion. Unlike other magnetotactic spirilla. QH-2 cells responded to light illumination. As a consequence of illumination, the cells changed the direction in which they swam from parallel to the magnetic field to antiparallel. This response appears to be similar to the effect of an increase in [O-2]. Analysis of the QH-2 16S rRNA sequence showed that it had greater than 11% sequence divergence from freshwater magnetotactic spirilla. Thus, the marine QH-2 strain seems to be both phylogenetically and magnetotactically distinct from the freshwater Magnetospirillum spp. studied previously. (C) 2010 Elsevier Masson SAS. All rights reserved.

海洋趋磁细菌多样性和特性研究及其分离纯化培养

趋磁细菌是一类革兰氏阴性的原核生物，广泛分布于淡水和海水环境中的有氧-无氧过渡区。本文研究了青岛汇泉湾沿岸一个海水养殖池塘中两个不同亚区内趋磁细菌的多样性。一个是常年水深在0.5 ~ 3 m，类似潮下带区域；另一个是在落大潮的时候沉积物能暴露在空气中，类似潮间带区域。 在该池塘类似潮下带区域的沉积物中发现了大量海洋趋磁细菌，最大丰度可达105 cells/cm3。透射电镜观察发现该菌菌体形态多样，有球形或卵球形、长短杆状、弧状和螺旋状，其中球形或卵球形趋磁细菌占绝对优势。电镜观察还发现该菌磁小体的排列方式呈多样化，大多数呈链状排列，有单链、双链及多链，还有的呈环状或者成簇排列。磁小体的形态也多种多样，有正方体、棱柱体、立方八面体、子弹头状、片状和齿状。用RFLP方法分析了70个克隆，测序得到10条不同序列。经16S rDNA系统发育分析，发现9个属于α-变形菌亚纲，1个属于γ-变形菌亚纲，共有8个不同的属，优势种属于未培养的海洋趋磁球菌。所有克隆与最接近的海洋趋磁球菌的相似性并不高（76.4% ~ 89.4%），表明该区域的趋磁细菌为新发现的微生物资源。 而在该池塘类似潮间带区域的沉积物中发现了单一种群结构的趋磁细菌。透射电镜观察显示菌体形态为球形至卵球形，大小为1.8 ~ 2.3 × 2.0 ~ 2.8 μm，细胞侧生两簇鞭毛，极性趋磁运动，每个细胞内都含有两条磁小体链。统计结果显示，两条磁小体链上的磁小体数目60%都相差1个。单个菌体中磁小体数目从7到31个不等，平均为18个，其中包含19个磁小体的菌体占多数。磁小体的形状多为长方体，平均长度和宽度分别为101 + 24 nm和83 + 21 nm，形态因子约为0.83 + 0.09，为单磁畴晶体。能谱显示磁小体的成分为Fe3O4。磁滞回线的测量得到单个磁小体的磁距为2.6 × 10-13 emu。用RFLP方法分析了98个克隆，测序得到3条不同序列，而三条序列之间的相似性都在98%以上，可认为是同一个种，FISH也证实了该处趋磁细菌为单一种群。经16S rDNA系统发育分析显示，该处趋磁细菌隶属于α-变形菌亚纲中的一个新属。初步结果显示了趋磁细菌对潮间带环境的适应性。 本文还采用半固体培养基培养了一株海洋趋磁螺菌，电镜下观察，菌体大小约为3 × 0.8 μm，体内包含一条磁小体链，磁小体形态不规则，大小分布不均。目前，纯化工作正在进行。

趋磁细菌AMB-1培养条件优化及磁小体变化过程研究

趋磁细菌(Magnetotactic bacteria)的研究是国际微生物学研究热点之一。趋磁细菌体内含有纳米单磁畴的氧化铁/硫化铁(Fe3O4或Fe3S4)晶体，称为磁小体。由于趋磁细菌营养条件要求苛刻，在环境中需要微好氧条件，且营养类型属于化能自养，使得培养趋磁细菌时常遇到问题。 本研究首先通过正交试验优化趋磁细菌AMB-1菌株培养条件，在培养条件铁源为奎尼酸铁0.02 mmol/L，装瓶量75% ，pH值6.7，温度25 ℃时，AMB-1 OD600达到0.440(1.166×109 cells/ml)。同时运用磁收集传代法，使带有磁小体的AMB-1细胞比例占95％以上(Cmag值稳定在1.9-2.0)。 在AMB-1具有较好的生物量，同时又具有较好的含磁小体细胞比例后，研究磁小体的变化过程。通过透射电镜观察磁小体变化过程，发现培养24 h细菌体内已有较小晶体形成(平均27 nm，n=188)且沿长轴分布；48 h晶体长大(平均43 nm，n=203)且形成分段链沿长轴排列；72 h晶体进一步成熟(平均50 nm，n=191)仍以分段链沿长轴排列；随后细菌逐渐衰亡磁小体变小，168 h可见部分自溶细菌中仍有磁小体链(平均37 nm，n=186)；192 h细菌自溶磁小体链(平均33 nm，n=184)分散到环境中。 通过透射电镜在细胞水平上研究趋磁细菌细胞分裂时发现，磁小体在细菌分裂时采用两种分离方式：一种为磁小体分配到两个子细胞；另一种为磁小体只分配到一个子细胞。无磁小体的子细胞，在随后的生长过程又分为两种情况：一种为细胞逐渐产生磁小体，另一种为不再产生磁小体。这种现象的发现，解释了随着传代次数的增多，细菌磁性有所下降的原因(Cmag值降低)。 在对趋磁细菌磁小体合成机制的研究中，常使用基因敲除的办法获得缺陷型，并与野生型对比进行研究。但是，利用基因敲除获得缺陷型不仅操作繁琐并且所得缺陷型不稳定。本研究利用特殊的磁富集传代法，先将带有磁小体的菌体收集并连续传代，筛选获得了高磁菌株；利用这种方法，收集不含磁小体的菌体并连续传代，筛选获得了无磁菌株。 趋磁细菌磁小体在医疗、环保等领域具有广阔应用价值，但是目前由于趋磁细菌难以大规模培养，并且磁小体纯化存在成本高等原因，将磁小体真正实际应用尚有一段距离。通过研究磁小体在趋磁细菌中的变化过程发现，AMB-1菌株在培养192 h后自溶，并且磁小体随着细胞的破碎释放到环境中去。

黄海近岸海洋趋磁细菌的多样性研究

海洋趋磁细菌在黄海、东海的近岸海域沉积物中分布广泛，形态上以球菌为主，部分地区有杆菌、螺旋菌。在青岛汇泉湾发现大量的海洋趋磁细菌，趋磁球菌占优势，最大丰度可达105 cells/cm3。 透射电镜观察潮间带趋磁细菌以球菌或卵球菌占绝对优势；潮下带菌体形态多样，有球形或卵球形、长短杆状、弧状和螺旋状，其中球形或卵球形趋磁细菌占优势。电镜观察还发现磁小体的排列方式多样化，大多数呈链状排列，有单链、双链及多链，还有的呈环状或者成簇排列。磁小体的形态也多种多样，有正方体、棱柱体、立方八面体、子弹头状、片状和齿状。 PCR-RFLP分析RT收集潮间带得到的三个菌株同属于α-变形菌亚纲中的未培养的趋磁球菌，三者之间相似性都在98%以上，可能都属于同一个属。潮下带RT收集，测序分析得到10个菌株。发现9个属于α-变形菌亚纲，1个属于γ-变形菌亚纲，共有8个不同的属，优势种是MRT-81和MRT-82。目前尚未获得这些细菌的纯培养。 结合电镜观察的结果发现，潮间带形态单一，属于同一个属；潮下带形态多样，属于8个不同的属。电镜结果跟RFLP的结果一致。结合区域特点我们分析潮间带水深大约0.5-1 m，在大潮最低潮时可能暴露于空气中，且受潮汐的影响，物化环境变化较大。潮下带水深常年>2 m，物化环境比较稳定。这可能是造成两个区域多样性差别的主要原因。 我们得到的所有的序列与未培养和已纯培养的海洋趋磁球菌的16S rDNA相似性都不高于94%，两优势菌群与纯培养的MC-1相似性都不高于88%，可能为新发现的海洋趋磁细菌资源。

Diversity and abundance of ammonia-oxidizing bacteria in eutrophic and oligotrophic basins of a shallow Chinese lake (Lake Donghu)

Classical cultivation and molecular methods based on the ammonia monooxygenase gene (amoA) were used to study the abundance and diversity of beta-proteobacterial ammonia-oxidizing bacteria (AOB) in lake sediments. The eutrophic and oligotrophic basins of a Chinese shallow lake (Lake Donghu), in terms of ammonium (NH4+) concentrations, were sampled. The AOB number was significantly lower in the oligotrophic basin, but significantly higher in the eutrophic basin. In addition, using restriction fragment length polymorphism targeting the amoA, ten restriction patterns including six unique ones were found in the eutrophic basin, while five patterns were observed in the oligotrophic basin with only one unique restriction group. Phylogenetic analysis for AOB revealed that Nitrosomonas oligotropha- and Nitrosomonas ureae-related AOB and Nitrosospira-affiliated AOB were ubiquitous; the former dominated in the eutrophic basin (87.2%), while the latter dominated in the oligotrophic basin (65.5%). Furthermore, Nitrosomonas communis-related AOB was only detected in the eutrophic basin, at a small proportion (3.2%). These results indicate significant selection and adaptation of sediment AOB in lakes with differing trophic status. (C) 2009 Elsevier Masson SAS. All rights reserved.

Antimicrobial activity-specific to Gram-negative bacteria and immune modulation-mediated NF-kappa B and Sp1 of a medaka beta-defensin

Defensins are a group of cationic antimicrobial peptides which play an important role in the innate immune system by exerting their antimicrobial activity against pathogens. In this study, we cloned a novel beta-defensin cDNA from medaka (Oryzias latipes) by rapid amplification of cDNA ends (RACE) technique. The full-length cDNA consists of 480 bp, and the open reading frame (CRF) of 189 bp encodes a polypeptide of 63 amino acids (aa) with a predicted molecular weight of 7.44 kDa. Its genomic organization was analyzed, and Southern blot detection confirmed that only one copy of beta-defensin exists in the medaka HNI strain. RT-PCR, Western blot and immunohistochemistry detections showed that the beta-defensin transcript and protein could be detected in eyes, liver, kidney, blood, spleen and gill, and obviously prevalent expression was found in eyes. Antimicrobial activity of the medaka beta-defensin was evaluated, and the antibacterial activity-specific to Gram-negative bacteria was revealed. Furthermore, the lipopolysaccharide (LPS), a major component of the outer membrane of Gram-negative bacteria, was demonstrated to be able to induce about 13-fol up-regulation of the beta-defensin within first 12 h. In addition, promoter and promoter mutagenesis analysis were performed in the medaka beta-defensin. A proximal 100 base pair(bp) sequence (+26 to -73)and the next 1700 bp sequence (-73 to -1755) were demonstrated to be responsible for the basal promoter activity and for the transcription regulation. Three nuclear factor kappa B (NF-kappa B) cis-elements and a Sp1 cis-element were revealed by mutagenesis analysis to exist in the 5' flanking sequence, and they were confirmed to be responsible for the up-regulation of medaka beta-defensin stimulated by LPS. And, the Sp1 cis-element was further revealed to be related to the basal promoter activity, and transcriptional factor II D (TFIID) was found to be in charge of the gene transcription initiation. All the obtained data suggested that the novel medaka beta-defensin should have antimicrobial activity-specific to Gram-negative bacteria, and the antibacterial immune function should be modulated by NF-kappa B and Sp1. (C) 2008 Elsevier Ltd. All rights reserved.

Comparing the Performance of Biomimetic Pattern Recognition with W8 and SVM on Prediction of Horizontal Gene Transfers in Bacteria Genomes

National Natural Science Foundation of China 60753001

Establishment and characterization of dual-species biofilms formed between a 3,5-dinitrobenzoic-degrading strain and bacteria with high biofilm-forming capabilities

In this study, the possibility of establishing a dual-species biofilm from a bacterium with a high biofilm-forming capability and a 3,5-dinitrobenzoic acid (3,5-DNBA)-degrading bacterium, Comamonas testosteroni A3, was investigated. Our results showed that the combinations of strain A3 with each of five strains with a high biofilm-forming capability (Pseudomonas sp. M8, Pseudomonas putida M9, Bacillus cereus M19, Pseudomonas plecoglossicida M21 and Aeromonas hydrophila M22) presented different levels of enhancement regarding biofilm-forming capability. Among these culture combinations, the 24-h dual-species biofilms established by C. testosteroni A3 with P. putida M9 and A. hydrophila M22 showed the strongest resistance to 3,5-DNBA shock loading, as demonstrated by six successive replacements with DMM2 synthetic wastewater. The degradation rates of 3,5-DNBA by these two culture combinations reached 63.3-91.6% and 70.7-89.4%, respectively, within 6 h of every replacement. Using the gfp-tagged strain M22 and confocal laser scanning microscopy, the immobilization of A3 cells in the dual-species biofilm was confirmed. We thus demonstrated that, during wastewater treatment processes, it is possible to immobilize degrader bacteria with bacteria with a high biofilm-forming capability and to enable them to develop into the mixed microbial flora. This may be a simple and economical method that represents a novel strategy for effective bioaugmentation.