基于高通量测序方法分析荣成月湖潮间带趋磁细菌多样性

摘要:荣成月湖是一个典型天然潟湖,潮间带沉积物中存在多种形态趋磁细菌。通过Roche454高通量测序平台,对沉积物样品(B_S)和磁收样品(B_M)进行16SrRNA基因高通量测序,认识荣成潮间带沉积物的细菌群落结构,并了解趋磁细菌多样性及系统进化地位。研究结果表明沉积物样品中主要的细菌类群为δ-变形菌纲,占总细菌数的26.4%,其次是γ-变形菌纲和α-变形菌纲;而磁收样品中细菌多样性和种类明显降低,以α-变形菌纲占绝对优势,相对比例达72.6%。在磁收样品和沉积物样品分别发现了1612条和186条reads与趋磁细菌相关,分别占细菌总数的5.76%和0.85%,磁收样品中趋磁细菌数是沉积物样品的6.8倍。对两个样品中获得的趋磁细菌序列进行系统进化分析,发现这些序列多数属于变形菌门的α-变形菌纲,以趋磁球菌占绝对优势,少数属于δ-变形菌纲,与多细胞趋磁原核生物亲缘关系最近。海洋趋磁螺菌属仅在B_M样品中检出,趋磁弧菌属在B_M样品优势度高于B_S样品,而多细胞趋磁原核生物和趋磁螺菌属在B_S样品中优势度更高。通过分析样品间的差异OTUs,认为荣成潮间带沉积物中可能存在大量未知的趋磁细菌新类群。研究结果为下一步培养和开发趋磁细菌这一功能菌群,发现趋磁细菌新类群及趋磁细菌生态功能提供了基础资料。

Characterization of uncultivated magnetotactic bacteria from the sediments of Yuehu Lake, China

Marine magnetotactic bacteria were collected from the intertidal sediments of Yuehu Lake(China), where their abundance reached 103–104 ind./cm3. Diverse morphotypes of magnetotactic bacteria were observed, including cocci and oval, vibrio-, spirillum-, rod-, elliptical-, handle- and bar-shaped forms. The magnetococci were the most abundant, and had flagella arranged in parallel within a bundle. The majority of magnetosomes were arranged in one, two or multiple chains, although irregular arrangements were also evident. All the results of high-resolution transmission electron microscopy(HRTEM) analysis show that magnetosome crystals were composed of Fe3O4, and their morphology was specific to particular cell morphotypes. By the 16 S r RNA gene sequence analysis, we found fourteen operational taxonomic units(OTUs) which were related to magnetotactic bacteria. Among these, thirteen belonged to the Alphaproteobacteria and one to the Gammaproteobacteria.Compared with known axenic and uncultured marine magnetotactic bacteria, the 16 S r RNA gene sequences of most magnetotactic bacteria collected from the Yuehu Lake exhibited sequence identities ranging from 90.1% to96.2%(<97%). The results indicate that microbial communities containing previously unidentified magnetotactic bacteria occur in the Yuehu Lake.

Distinct influence of trimethylamine N-oxide and high hydrostatic pressure on community structure and culturable deep-sea bacteria

Trimethylamine N-oxide(TMAO)is one of the most important nutrients for bacteria in the deep-sea environment and is capable of improving pressure tolerance of certain bacterial strains.To assess the impact of TMAO on marine microorganisms,especially those dwelling in the deep-sea environment,we analyzed the bacterial community structure of deep-sea sediments after incubated under different conditions.Enrichments at 50 MPa and 0.1 MPa revealed that TMAO imposed a greater influence on bacterial diversity and community composition at atmospheric pressure condition than that under high hydrostatic pressure(HHP).We found that pressure was the primary factor that determines the bacterial community.Meanwhile,in total,238 bacterial strains were isolated from the enrichments,including 112 strains a ffiliated to 16 genera of 4 phyla from the Yap Trench and 126 strains a ffiliated to 11 genera of 2 phyla from the Mariana Trench.Treatment of HHP reduced both abundance and diversity of isolates,while the presence of TMAO mainly af fected the diversity of isolates obtained.In addition,certain genera were isolated only when TMAO was supplemented.Taken together,we demonstrated that pressure primarily defines the bacterial community and culturable bacterial isolates.Furthermore,we showed for the first time that TMAO had distinct influences on bacterial community depending on the pressure condition.The results enriched the understanding of the significance of TMAO in bacterial adaptation to the deep-sea environment.

Archaeal community structure in sediments from a seamount in the Mariana Volcanic Arc

Seamounts are subsurface mountains in the ocean. Examination of the abundance and distribution of Archaea in seamount ecosystems may provide a better understanding of their ecological functions. Most studies of marine archaeal assemblages in seamount area have focused on hydrothermal vents or ferromanganese crusts. We investigated the archaeal communities from a seamount of the Mariana Volcanic Arc, in the tropical western Pacific Ocean by using high-throughput sequencing. Thaumarchaeota was dominant in the sediments of all sample stations. Community diversity and species richness were greatest at stations near the top of the seamount, and lowest at the deepest station. One sample station on the steep southeast slope that faced the Yap-Mariana trench had a unique composition of Archaea. In summary, depth has an important influence on archaeal community structure, and the geographic properties and sediment characteristics may explain the unique distribution patterns of Archaea in this seamount. This study provides a foundation for future research on Archaea in seamounts.

Morphological and phylogenetic diversity of magnetotactic bacteria and multicellular magnetotactic prokaryotes from a mangrove ecosystem in the Sanya River,South China

Magnetotactic bacteria(MTB)are morphologically and phylogenetically diverse prokaryotes commonly able to produce magnetic nanocrystals within intracellular membrane-bound organelles(i.e.,magnetosomes)and to swim along geomagnetic field lines.We studied the diversity of MTB in the samples collected from a mangrove area in the Sanya River,Hainan,South China,using microscopic and microbial phylogenetic methods.Results of microanalysis and observation in microscopy and energy dispersive X-ray spectroscopy(EDXS)reveal a highly morphological diversity of MTB including unicellular cocci,vibrios,rod-shaped bacteria,and three morphotypes of multicellular magnetotactic prokaryotes(MMPs).In addition,analysis of the 16S rRNA gene showed that these MTB were clustered into 16 operational taxonomic units affi liated to the Alpha-,Delta-,and Gamma-proteobacteria classes within the Proteobacteria phylum.Meanwhile,by using the coupled fluorescence and transmission electron microscopy analysis,rodshaped bacteria,vibrio,and cocci were phylogenetically and structurally identified at the single-cell level.This study demonstrated highly diverse MTB communities in the mangrove ecosystem and provide a new insight into the overall diversity of MTB.

Contribution of trimethylamine N-oxide on the growth and pressure tolerance of deep-sea bacteria

Trimethylamine N-oxide(TMAO) is widely dispersed in marine environments and plays an important role in the biogeochemical cycle of nitrogen. Diverse marine bacteria utilize TMAO as carbon and nitrogen sources or as electron acceptor in anaerobic respiration. Alteration of respiratory component according to the pressure is a common trait of deep-sea bacteria. Deep-sea bacteria from dif ferent genera harbor high hydrostatic pressure(HHP) inducible TMAO reductases that are assumed to be constitutively expressed in the deep-sea piezosphere and facilitating quick reaction to TMAO released from ?sh which is a potential nutrient for bacterial growth. However, whether deep-sea bacteria universally employ this strategy remains unknown. In this study, 237 bacterial strains affliated to 23 genera of Proteobacteria,Bacteroidetes, Firmicutes and Actinobacteria were isolated from seawater, sediment or amphipods collected at dif ferent depths. The pressure tolerance and the utilization of TMAO were examined in 74 strains. The results demonstrated no apparent correlation between the depth where the bacteria inhabit and their pressure tolerance, regarding to our samples. Several deep-sea strains from the genera of Alteromonas, Halomonas,Marinobacter, Photobacterium, and Vibrio showed capacity of TMAO utilization, but none of the isolated Acinebacter, Bacillus, Brevundimonas, Muricauda, Novosphingobium, Rheinheimera, Sphingobium and Stenotrophomonas did, indicating the utilization of TMAO is a species-speci?c feature. Furthermore, we noticed that the ability of TMAO utilization varied among strains of the same species. TMAO has greater impact on the growth of deep-sea isolates of Vibrio neocaledonicus than shallow-water isolates. Taken together, the results describe for the ?rst time the TMAO utilization in deep-sea bacterial strains, and expand our understanding of the physiological characteristic of marine bacteria.

Biocompatibility of marine magnetotactic ovoid strain MO-1 for in vivo application

Magnetotactic bacteria are capable of biosynthesizing magnetic nanoparticles,also called magnetosomes,and swimming along magnetic field lines.The abilities endow the whole cells of magnetotactic bacteria with such applications as targeted therapy and manipulation of microrobots.We have shown that the intact marine magnetotactic bacteria MO-1 kill efficiently antibiotic-resistant pathogen Staphylococcus aureus in vivo,but the biocompatibility of this marine bacterium is unknown.In this study,the strain MO-1 was chosen to analyze its biocompatibility and potential for biomedicine applications.Results showed that MO-1 cells could be guided at 37℃ under an external magnetic field and swim in the blood plasma and urine.They could keep active locomotivity within 40 min in the plasma and urine,although their velocity slowed down.When incubated with human cells,magnetotactic bacteria MO-1 had no obvious effects on cellular viability at low dose,while the cell toxicity increased with the augmentation of the quantity of the MO-1 cells added.In the in-vivo experiments,the median lethal dose of magnetotactic bacteria MO-1 in rats was determined to be 7.9×10^(10) bacteria/kg.These results provided the foundation for the biocompatibility and safety evaluations of magnetotactic bacteria MO-1 and suggested that they could be basically used in clinical targeted therapy.

Magnetotactic bacteria and magnetoreception

A broad range of organisms have evolved abilities to exploit the Earth’s magnetic field for orientation and navigation-a behavior known as magnetoreception(Nordmann et al.,2017).Magnetotactic bacteria(MTB),diverse microbes with a patchy distribution across the bacterial tree of life,are the best known and most extensively studied magnetosensitive microorganisms.In order to efficiently achieve magnetotactic behavior,MTB biomineralize intracellular chain-arranged magnetic single-domain crystals of magnetite(Fe_(3)O_(4))and/or greigite(Fe_(3)S_(4))called magnetosomes,which are unique prokaryotic organelles that confer a magnetic moment to the cell and act as an internal compass needle(Bazylinski and Frankel,2004).

Resazurin as an indicator of reducing capacity for analyzing the physiologic status of deep-sea bacterium Photobacterium phosphoreum ANT-2200

Resazurin(RZ)is a weakly fl uorescent blue dye and can be reduced irreversibly to highly fl uorescent pink resorufi n(RF)that is reduced reversibly to colorless dihydroresorufi n(hRF)by photodeoxygenation,chemical reaction and reductive organic compounds produced through cell metabolism.Because of the reliable and sensitive fl uorescence-color change and noninvasive features,RZ has been used widely as a redox indicator in cell viability/proliferation assays for bacteria,yeast,and mammalian cells.However,RZ is used rarely for physiological characterization of marine microorganisms.Here,we developed a custom-made irradiation and absorption-analysis device to assess the reducing capacity and physiologic status of marine bacterial cultures.We measured the absorption spectra of RZ,RF,and hRF in the presence of the reducing compound Na 2 S and under visible-light irradiation.After establishing appropriate parameters,we monitored the color changes of RZ and its reduced derivatives to evaluate the coherence between reducing capacity,bioluminescence and growth of the deep-sea bacterium Photobacterium phosphoreum strain ANT-2200 under various conditions.Emission of bioluminescence is an oxidation process dependent upon cellular reducing capacity.Growth and bioluminescence of ANT-2200 cell cultures were impeded progressively with increasing concentrations of RZ,which suggested competition for reducing molecules between RZ at high concentration with reductive metabolism.Therefore,caution should be applied upon direct addition of RZ to growth media to monitor redox reactions in cell cultures.Analyses of the instantaneous reduction velocity of RZ in ANT-2200 cell cultures showed a detrimental eff ect of high hydrostatic pressure and high coherence between the reducing capacity and bioluminescence of cultures.These data clearly demonstrate the potential of using RZ to characterize the microbial metabolism and physiology of marine bacteria.

Observations on a magnetotactic bacteria-grazing ciliate in sediment from the intertidal zone of Huiquan Bay,China

Magnetotactic bacteria(MTB)are a group of prokaryotes having the ability to orient and swim along geomagnetic field lines because they contain intracellular magnetosomes that are synthesized through a biomineralization process.Magnetosomes have recently also been found in unicellular eukaryotes,which are referred to as magnetically responsive protists(MRPs).The magnetosomes have three origins in MRPs.In this study,we characterized a MTB-grazing ciliated MRP that was magnetically collected from intertidal sediment of Huiquan Bay,Qingdao,China.Based on 18S rRNA gene sequence analysis,the ciliated MRP was tentatively identified as Uronemella parafi lificum HQ.Using transmission electron microscopy,we observed that magnetosomes having 2-3 shapes were randomly distributed within this ciliate.Energydispersive X-ray spectroscopy and high-resolution transmission electron microscopy images of the magnetosomes were consistent with them being composed of magnetite.Magnetosomes having the same shape and mineral composition were also detected in MTB that occurred in the same environment as the ciliated MRP.Statistical analysis showed that the size and shape of the magnetosomes in the ciliated MRP were similar to those in MTB.The results suggest that this ciliated MRP can graze,ingest,and digest various types of MTB.It is certainly worth noting that this is the first record of MRPs in Asian aquatic sediment and suggesting they might be widely distributed.These results also support the assertion that MRPs probably contribute to the ecological cycles of iron,and expand possibilities for research into the mechanism of magnetoreception in eukaryotes.

Characterization and diversity of magnetotactic bacteria from sediments of Caroline Seamount in the Western Pacific Ocean

Magnetotactic bacteria(MTB)are a group of microorganisms capable of orientating and swimming along magnetic fields because they contain intracellular biomineralized magnetosomes composed of magnetite(Fe 3 O 4)or/and greigite(Fe_(3)S_(4)).They are ubiquitous in freshwater,brackish,and marine habitats,and are cosmopolitan in distribution.However,knowledge of their occurrence and distribution in seamount ecosystems is limited.We investigated the diversity and distribution of MTB in the Caroline Seamount(CM4).The abundance of living MTB in 12 stations in depth varying from 90 to 1545 m was 1.1×10^(3)-43.7×10^(3) inds./dm 3.Despite diverse shapes of MTB observed,magnetotactic cocci were the dominant morphotype and could be categorized into two types:1)typical cocci that appeared to have peritrichous fl agella;and 2)those characterized by having a drop-shaped form and one bundle of fl agella located at the thin/narrow end of the cell.Transmission electron microscopy(TEM)analysis revealed that the magnetosomes formed by those magnetotactic cocci are magnetite(Fe 3 O 4)with octahedral crystal habit.A total of 41 operational taxonomic units(OTUs)of putative MTB(2702 reads)were acquired from nine stations,based on high-throughput sequencing.Of these,40 OTUs belonged to the Proteobacteria phylum and one belonged to the Nitrospirae phylum.We found apparent connectivity between the MTB populations on the Caroline and Kexue(Science in Chinese)seamounts,although the diversity of MTB on Caroline was much richer than on the Kexue Seamount.Our results imply that the unique topography of seamounts and other as-yet unclear environmental factors could lead to evolution of different fl agella arrangements in magnetotactic cocci,and the occurrence of octahedral magnetite magnetosomes.

Genomic analysis of a pure culture of magnetotactic bacterium Terasakiella sp.SH-1

Magnetotactic bacteria(MTB)display magnetotaxis ability because of biomineralization of intracellular nanometer-sized,membrane-bound organelles termed magnetosomes.Despite having been discovered more than half a century,only a few representatives of MTB have been isolated and cultured in the laboratory.In this study,we report the genomic characterization of a novel marine magnetotactic spirillum strain SH-1 belonging to the genus Terasakiella that was recently isolated.A gene encoding haloalkane dehalogenase,which is involved in the degradation of chlorocyclohexane,chlorobenzene,chloroalkane,and chloroalkene,was identified.SH-1 genome contained cysCHI and soxBAZYX genes,thus potentially capable of assimilatory sulfate reduction to H_(2)S and using thiosulfate as electron donors and oxidizing it to sulfate.Genome of SH-1 also contained genes encoding periplasmic dissimilatory nitrate reductases(napAB),assimilatory nitrate reductase(nasA)and assimilatory nitrite reductases(nasB),suggesting that it is capable of gaining energy by converting nitrate to ammonia.The pure culture of Terasakiella sp.SH-1 together with its genomic results off ers new opportunities to examine biology,physiology,and biomineralization mechanisms of MTB.

How light affect the magnetotactic behavior and reproduction of ellipsoidal multicellular magnetoglobules?

Magnetotactic bacteria(MTB)synthesize intracellular magnetic organelles,magnetosomes,which consist of magnetic crystals that are enveloped in a membrane.Magnetosomes are organized into a chain(s)and confer on cells a magnetic dipolar moment.This magnetic property allows MTB cells to align and swim along geomagnetic field lines,a movement referred to as magnetotaxis.Some MTB species change their swim direction in response to illumination by UV,violet and blue light.Here we analyzed the polarity of morphology,magnetism,and motion in Mediterranean multicellular magnetotactic prokaryotes,also called,magnetoglobules or MMP.The magnetoglobules were assembled from 60-80 cells into an asymmetric ellipsoidal morphology with a relative narrow and large end.They swam dominantly northward,parallel to the direction of the magnetic field,with the narrow-end as the leading side.In response to a reversal in the direction of the magnetic field,they aligned quickly along the magnetic field lines and kept swimming northward.Interestingly,under constant illumination,385-nm UV light,magnetoglobules changed their swimming direction southward anti-parallel to the direction of the magnetic field,with the large-end as the leading side.The change from a northward to southward direction occurred along with an increase of swimming speed.A minimum of 35-mW/cm^(2) irradiance of UV light was sufficient to trigger the swimming re-orientation.UV radiation also triggered the unidirectional division of magnetoglobules.Together these results revealed a coordination of the polarity of magnetoglobule morphology,magnetic moment,and swimming orientation,in response to magnetic and optical stimuli.The UV triggered the reversal of magnetotaxis and magnetoglobule division indicating the ecological significance of light for multicellular magnetotactic prokaryotes.

Effect of Water Stress Induced by Polyethylene Glycol 6000 on Somatic Embryogenesis in Cocoa (<i>Theobroma cacao</i>L.)

Climate change, coupled with insufficient and irregular rains, led to a decline in the productivity of Ivorian cocoa production. The present study aimed to screen three cocoa (Theobroma cacao L.) genotypes in order to evaluate their response to water stress at callus and somatic embryos induction and proliferation stages. Staminode and petal explants of the genotypes C1, C14 and C16 from the collection of National Center of Agronomic Research (CNRA) of Ivory Coast, were placed on medium DKW (Driver & Kuniyuki Walnut) in the presence of different concentrations of Polyethylene glycol (PEG) 6000 (0, 25, 50, 75, 100 and 125 g/l). This polymer was used as osmoticum to stimulate water stress. Data were recorded for callus induction frequency, callus fresh weight, embryogenic callus percentage and average number of somatic embryos. The results obtained showed that intensity of callus proliferation decreased with increasing concentration of PEG 6000. In all genotypes tested, only the petal explants underwent somatic embryogenesis. The induction rates and average number of somatic embryos per explant were reduced with the increase in the concentration of PEG 6000. Among the tested genotypes, C1 produced somatic embryos with all concentrations of PEG 6000 and expressed highest frequencies of induction (62%) and average number of somatic embryos per explant (6.22). This genotype would be the most tolerant to water stress. Somatic embryos obtained with high concentrations of PEG 6000 in this study provide an important basis for the selection and further production of water stress-tolerant varieties of cocoa.

微小杆菌属(Exiguobacterium)细菌的能量代谢途径分析

【目的】微小杆菌属(Exiguobacterium)细菌广泛分布于海洋及非海洋环境中,具有多种代谢途径以适应复杂多样的生境。本研究从能量代谢途径角度出发,探究该属菌株对不同生境的适应能力。【方法】从美国国家生物科技数据中心(National Center for Biotechnology Information, NCBI)数据库中获取146个Exiguobacterium属菌株的基因组,查找并统计光营养、厌氧呼吸和底物代谢等多种能量代谢途径的关键蛋白或关键酶基因在各菌株基因组中的分布,包括光营养型的视紫红质基因、厌氧呼吸营养型的钼辅因子合成蛋白基因,以及底物代谢营养型中乙醛酸分流途径的异柠檬酸裂解酶及苹果酸合酶基因等。根据对应的氨基酸序列构建视紫红质、MoaC和异柠檬酸裂解酶的系统发育树,分析不同能量代谢途径在该属菌株进化过程中的保守性,推测其对于该属菌株的重要性。【结果】Exiguobacterium属中50%的种具有视紫红质基因,其中分离自非海洋生境的菌株更趋向于含有视紫红质基因。本研究所统计的全部非海洋生境菌株中,含有视紫红质基因的菌株占比约为70%,而在海洋生境菌株中该比例仅为19%。Exiguobacterium属约27%的种存在钼辅因子合成蛋白基因,分离自海洋环境的菌株有该类蛋白的可能性更高(32%:21%),具有完整钼辅因子合成途径的菌株集中于进化树同一分支上的少数种。该属约61%的种存在乙醛酸分流途径相关酶基因,这些种隶属进化树的同一分支,且种内所有菌株都具备相关基因,表明乙醛酸分流途径在Exiguobacterium属的分布具有种特异性。【结论】Exiguobacterium属细菌具有多种能量代谢途径相关基因,包括基于视紫红质的光营养型能量代谢途径、基于钼酶的厌氧呼吸型能量代谢途径和底物代谢营养型能量代谢途径中的乙醛酸分流途径。能量代谢途径多样性可能是Exiguobacterium属细菌适应复杂多样生境的机制之一。此外,本研究发现Exiguobacterium属中不同种、同种不同菌株间存在能量代谢途径差异,且能量代谢途径在该属内的分布多不具备种特异性,表明仅通过16S rRNA基因种属鉴定来预测目标菌株的代谢类型可能有较大偏差和局限性。

夏热冬冷地区绿化屋顶节能与生态效益研究

【目的】研究夏热冬冷地区绿化屋顶的节能效益,分析包括固碳释氧、空气净化、水源涵养和节能减排4个方面的生态效益。【方法】以无锡地区有无绿化的屋顶为研究对象,对比绿化屋顶的保温隔热及节电效果,并进行屋顶绿化生态效益的量化分析。【结果】在冬季,绿化屋顶内、外表面平均温度比非绿化屋顶分别高2. 5℃和5. 5℃,通过屋顶的热流相对减少36. 4%,绿化房间空调日平均节电量为0. 90 (kW·h);在夏季,绿化屋顶内、外表面平均温度比非绿化屋顶分别低3. 1℃、5. 6℃,通过屋顶的热流相对减少48. 6%,日平均空调节电量为4. 23(kW·h)。计算可得,绿化屋顶每年可节约空调用电量15. 39 (kW·h)/m^2;佛甲草屋顶绿化可创造的固碳释氧效益为1. 887元/(m^2·a),净化空气效益为2. 45×10-2元/(m^2·a),涵养水源效益为0. 957元/(m^2·a),节能效益可达到12. 875元/(m^2·a),减排效益达9. 613元/(m^2·a),综合生态效益是25. 357元/(m^2·a),动态投资回收期为7 a。【结论】屋顶绿化在冬季可提高屋顶内外表面温度,在夏季降低屋顶内外表面温度,减少通过屋面的热流,达到保温隔热和降低空调能耗的节能效果。屋顶绿化的生态效益显著,投资回收期短,应予以政策鼓励和支持。