Identification and functional characterization of liposome tubulation protein from magnetotactic bacteria

Magnetotactic bacteria synthesize intracellular magnetosomes that are comprised of membrane‐enveloped magnetic crystals. In this study, to identify the early stages of magnetosome formation, we isolated magnetosomes containing small magnetite crystals and those containing regular‐sized magnetite crystals from Magnetospirillum magneticum AMB‐1. This was achieved by using a novel size fractionation technique, resulting in the identification of a characteristic protein (Amb1018/MamY) from the small magnetite crystal fraction. The gene encoding MamY was located in the magnetosome island. Like the previously reported membrane deformation proteins, such as bin/amphiphysin/Rvs (BAR) and the dynamin family proteins, recombinant MamY protein bound directly to the liposomes, causing them to form long tubules. We established a mamY gene deletion mutant (ΔmamY) and analysed MamY protein localization in it for functional characterization of the protein in vivo. The ΔmamY mutant was found to have expanded magnetosome vesicles and a greater number of small magnetite crystals relative to the wild‐type strain, suggesting that the function of the MamY protein is to constrict the magnetosome membrane during magnetosome vesicle formation, following which, the magnetite crystals grow to maturity within them.     

Perfluorinated Compounds in Aquatic Products from Bohai Bay,Tianjin, China

To understand concentrations of perfluorinated compounds (PFCs) in aquatic products, and risks to human health, concentrations of 12 PFCs were measured in edible tissues of aquatic products collected from Tianjin, China, a typical industrial area on the western Bohai Sea. Perfluorooctane sulfonate (PFOS) was the predominant PFC. Concentrations of PFOS in aquatic products from Tianjin Binhai New Area (TBNA) ranged from <0.10 to 241 ng/g wet weight, with the greatest concentration observed in the edible portions of mullet (Mugil so-iuy Basilewsky). Concentrations of PFOS in mullet from the TBNA were greater than those in other species of lower trophic levels, which suggests biomagnification. Concentrations of PFOS in aquatic products from markets were greater than those of locally farmed or wild marine products. Relatively great concentrations of PFOS were not only observed in products from the rapidly growing industrial areas such as Tangu District (TG) and Hangu District (HG), but also in less industrialized areas like the Dagang District (DG). The results of the hazard assessment indicated that consumption of seawater-farmed fish and market fish posed a greater hazard than wild marine fish or freshwater-farmed fish, but the risk to human health was not great.     

Risk Assessment of Rotavirus Infection in Surface Seawater from Bohai Bay,China

Dose-response data indicate that rotavirus (RV) may be one of the more infective agents among enteric viruses. The major limitation at present in the assessment of infection from rotavirus is lack of quantitative data on viral infectivity. In this work, an integrated cell culture and real-time quantitative polymerase chain reaction (ICC-qPCR) method and a Beta-Poisson model for risk assessment were employed. A set of 28 surface seawater samples was collected from December 2010 to September 2011 in Bohai Bay, China, to enable a seasonal risk assessment of infective RV at recreational beaches. Thirty-two percent of the samples were positive for rotavirus, and the estimated concentration range of infectious human rotavirus was 1 to 279 PFU/L. We further confirmed that the contamination of seawater with rotavirus was higher in autumn and winter, which was in reasonable agreement with the trend observed in a prior epidemiological study. Our preliminary risk assessment indicated the daily risk of illness at almost all the contaminated sites exceeded an acceptable threshold of marine recreational water quality (19 illnesses per 1000 swimmers). The detection method and dose-response model in the current work appear useful for evaluating pathogenic risks of seawater to vacationers and can inform management actions.     

Identification and characterization of a halocin-producing haloarchaeon isolated from Pachpadra salt lake

Haloarchaea are known to produce antimicrobial proteins, halocins which are generally stable at extreme conditions suggesting their potential biotechnological applications. Here, we report a halocin-producing haloarchaeon isolated from salt lake and identified as Haloferax larsenii HA4 using partial 16S rDNA sequence and biochemical properties. Whole-cell methanolysate showed ether-linked lipids, which is a characteristic feature of haloarchaea. Strain HA4 was able to grow at pH 6·0–10·0 and 15–30% NaCl. The growth response was normal but antimicrobial activity was detected only during the log-phase. Crude halocin HA4 was active in the pH range of pH 2·0–10·0 with stability up to 100°C. Cell-free supernatant (CFS) was also stable in different organic solvents and detergents tested. However, halocin activity was reduced after treatment with proteinase K suggesting the proteinaceous nature of the active compound. Concentrated CFS showed the presence of several proteins from 6·5–66 kDa but bioassay suggested ~14 kDa protein as halocin. Crude halocin preparation showed cytocidal activity against indicator strain, H. larsenii HA10 and inhibited the growth of other related strains such as H. larsenii HA3, HA8, HA9 and HA10.     

Length–weight relationships of five Gobiidae species from Bohai Bay,China

Length–weight relationships (LWR) for five Gobiidae species collected by trawl net in Bohai Bay, China, were determined. Parameter b in the LWR was 2.871, 2.664, 2.901, 3.237 and 2.882 for Amblychaeturichthys hexanema, Synechogobius ommaturus, Odontamblyopus rubicundus, Tridentiger barbatus and Paratrypauchen microcephalus, respectively. This is the first report in FishBase for the fitted LWRs of three of the Gobiidae species mentioned above.     

Isolation and characterization of a magnetotactic bacterial culture from the Mediterranean Sea

The widespread magnetotactic bacteria have the peculiar capacity of navigation along the geomagnetic field. Despite their ubiquitous distribution, only few axenic cultures have been obtained worldwide. In this study, we reported the first axenic culture of magnetotactic bacteria isolated from the Mediterranean Sea. This magneto‐ovoid strain MO‐1 grew in chemically defined O₂ gradient minimal media at the oxic–anoxic transition zone. It is phylogenetically related to Magnetococcus sp. MC‐1 but might represent a novel genus of Proteobacteria. Pulsed‐field gel electrophoresis analysis indicated that the genome size of the MO‐1 strain is 5 ± 0.5 Mb, with four rRNA operons. Each cell synthesizes about 17 magnetosomes within a single chain, two phosphorous‐oxygen‐rich globules and one to seven lipid storage granules. The magnetosomes chain seems to divide in the centre during cell division giving rise to two daughter cells with an approximately equal number of magnetosomes. The MO‐1 cell possesses two bundles of seven individual flagella that were enveloped in a unique sheath. They swam towards the north pole with a velocity up to 300 μm per second with frequent change from right‐hand to left‐hand helical trajectory. Using a magneto‐spectrophotometry assay we showed that MO‐1 flagella were powered by both proton‐motive force and sodium ion gradient, which is a rare feature among bacteria.     

Length–weight relationships of three fish species from Liaodong Bay,Bohai Sea,China

Length–weight relationships (LWRs) in the present study were determined for three fish species: Collichthys niveatus Jordan & Starks, 1906; Ctenotrypauchen chinensis Steindachner, 1867 and Liparis tanakae (Gilbert & Burke, 1912), collected from Liaodong Bay, Bohai Sea, China using bottom trawl nets from June to August 2014. The b parameters in the fitted LWRs for the three fish species were 2.882, 2.991 and 3.353, respectively. A new maximum total length (15.6 cm) for C. chinensis was recorded. The LWRs for the three fish species are first reported in FishBase.     

Heterotrophic denitrification at extremely high salt and pH by haloalkaliphilic Gammaproteobacteria from hypersaline soda lakes

In this paper we describe denitrification at extremely high salt and pH in sediments from hypersaline alkaline soda lakes and soda soils. Experiments with sediment slurries demonstrated the presence of acetate-utilizing denitrifying populations active at in situ conditions. Anaerobic enrichment cultures at pH 10 and 4 M total Na(+) with acetate as electron donor and nitrate, nitrite and N(2)O as electron acceptors resulted in the dominance of Gammaproteobacteria belonging to the genus Halomonas. Both mixed and pure culture studies identified nitrite and N(2)O reduction as rate-limiting steps in the denitrification process at extremely haloalkaline conditions.     

Avian communities in baylands and artificial salt evaporation ponds of the San Francisco Bay estuary

San Francisco Bay wetlands, seasonal and tidal marshes between the historic low and high tide lines, are now highly fragmented because of development during the past 150 years. Artificial salt pond systems in the Bay are hypersaline and typically support simple assemblages of algae and invertebrates. In order to establish the value of salt ponds for migratory waterbirds, we used datasets to conduct a meta-analysis of avian communities in the baylands and salt ponds of San Pablo Bay. Fifty-three species of waterbirds in the salt ponds represented six foraging guilds: surface feeders, shallow probers, deep probers, dabblers, diving benthivores and piscivores. The total number of species and the Shannon-Weiner diversity index was higher in baylands than in salt ponds during all four seasons. However, overall bird density (number/ha) was higher in salt ponds compared with baylands in the winter and spring, primarily because of large concentrations of benthivores. Cessation of salt production in 1993 and subsequent reduction in water depth resulted in a decline of some diving duck populations that used the salt ponds.     

渤海湾浮游纤毛虫丰度和生物量的周年变化

为了解渤海湾浮游纤毛虫丰度、生物量和种类组成的周年变化,于2019年7月-2020年6月在渤海湾一个站位进行每月1次共12个航次浮游纤毛虫样品的采集。样品按照Utermöhl方法进行分析,通过倒置显微镜镜检,计算纤毛虫的丰度和生物量。无壳纤毛虫和砂壳纤毛虫出现峰值的时间不同,无壳纤毛虫丰度和生物量均在4月和8月呈现双峰值,砂壳纤毛虫丰度和生物量均在7月出现单峰值。周年砂壳纤毛虫丰度占纤毛虫总丰度的比例平均为(28.6±32.6)%,5-7月较高,均超过50%。共鉴定砂壳纤毛虫6属21种,其中拟铃虫属(Tintinnopsis)种类最多,6-8月砂壳纤毛虫种类数最高。砂壳纤毛虫种类组成呈现明显的周年变化,温度是驱动砂壳纤毛虫群落周年变化的主要环境因子。砂壳纤毛虫群落Shannon指数的平均值为0.95±0.78,Pielou指数的平均值为0.52±0.34,均在6-8月较高。除无壳纤毛虫外,砂壳纤毛虫丰度、纤毛虫总丰度和砂壳纤毛虫丰度占纤毛虫总丰度的比例均与温度、Chl a浓度呈显著的正相关,与盐度呈显著的负相关。     

Culture-independent characterization of a novel, uncultivated magnetotactic member of the Nitrospirae phylum

A magnetotactic bacterium, designated strain LO-1, of the Nitrospirae phylum was detected and concentrated from a number of freshwater and slightly brackish aquatic environments in southern Nevada. The closest phylogenetic relative to LO-1 is Candidatus Magnetobacterium bavaricum based on a 91.2% identity in their 16S rRNA gene sequence. Chemical and cell profiles of a microcosm containing water and sediment show that cells of strain LO-1 are confined to the oxic-anoxic interface and the upper regions of the anaerobic zone which in this case, occurred in the sediment. This microorganism is relatively large, ovoid in morphology and usually biomineralizes three braid-like bundles of multiple chains of bullet-shaped magnetosomes that appeared to be enclosed in a magnetosome membrane. Cells of LO-1 had an unusual three-layered unit membrane cell wall and contained several types of inclusions, some of which are sulfur-rich. Strain LO-1 is motile by means of a single bundle of sheathed flagella and exhibits the typical 'wobbling' motility and helical swimming ('flight') path of the magnetotactic cocci. This study and reports from others suggest that LO-1-like organisms are widespread in sediments of freshwater to brackish natural aquatic environments.     

Length–weight and length–length relationships of eight fish species from Bohai Bay,China

Length–weight and length–length relationships (LWRs and LLRs) for eight fish species collected quarterly by trawl net in Bohai Bay, China, were estimated in a total of 1,395 specimens from 2012 to 2015. These were Pholis fangi, Setipinna taty, Engraulis japonicus, Larimichthys polyactis, Thryssa kammalensis, Scomberomorus niphonius, Johnius grypotus and Sardinella zunasi. The LWRs for the last two fish species are first reports for FishBase.     

Isolation of magnetotactic bacterium WM-1 from freshwater sediment and phylogenetic characterization

The magnetotactic bacterium was isolated from freshwater sediment from North Lake of Wuhan. The isolate, designated WM-1, was Gram-negative, helical shaped, and studied by means of electron microscopy. The strain WM-1 was 0.2-0.4 μm in diameter and 3–4 μm in length. The DNA G + C content was found to be 65.7 mol%. Phylogenetic analysis of the 16S rDNA gene (Accession number DQ899734 in GeneBank) revealed that this isolate was a member ofαsubdivision of the Proteobacteria. Strain WM-1 was closely related (97.7%) to Magnetospirillum sp. AMB-1. Randomly amplified polymorphic DNA analysis showed that these two strains were in fact different strains. Electron diffraction patterns of WM-1 magnetosomes indicated that the magnetosomes were composed of magnetite. The magnetosomes from WM-1 were cuboidal in shape as observed by electron microscopy. Statistical analysis of magnetite crystals from WM-1 showed narrow asymmetric size distribution. The average number of magnetosomes in each WM-1 bacterium was 8 ± 3.4. The average length of magnetosomes in WM-1 was 54 ± 12.3 nm and the average width is 43 ± 10.9 nm. These data showed that the grains in WM-1 were single-domain crystals.     

青岛太平湾潮间带趋磁细菌多样性

在青岛太平湾潮间带沉积物中发现了一定量的海洋趋磁细菌,最大丰度可达350个/cm~3。透射电镜观察发现该区域趋磁细菌均为趋磁球菌。磁小体个体形状单一,皆是立方体状;磁小体排列方式多样,以链状排列为主,包括单链、双链与多链,也有少数成簇排列。EDS结果表明,磁小体成分为四氧化三铁。据估算,趋磁细菌的铁元素含量(干重)范围在0.40%—6.91%之间,平均为2.19%。通过16S rRNA基因文库的构建与测序得到了47个趋磁细菌序列,分属13个OTU。系统发育分析结果表明,它们都属于α-变形菌纲,其中9个OTU与已知最相似序列的相似性低于97%,有5个OTU与已知最相似序列的相似性低于93%,可能代表了趋磁细菌的9个新种、5个新属,说明该区域潜在的微生物新种质资源十分可观。     

Spatiotemporal distribution of marine magnetotactic bacteria in a seasonally stratified coastal salt pond

The occurrence and distribution of magnetotactic bacteria (MB) were studied as a function of the physical and chemical conditions in meromictic Salt Pond, Falmouth, Mass., throughout summer 2002. Three dominant MB morphotypes were observed to occur within the chemocline. Small microaerophilic magnetite-producing cocci were present at the top of the chemocline, while a greigite-producing packet-forming bacterium occurred at the base of the chemocline. The distributions of these groups displayed sharp changes in abundance over small length scales within the water column as well as strong seasonal fluctuations in population abundance. We identified a novel, greigite-producing rod in the sulfidic hypolimnion that was present in relatively constant abundance over the course of the season. This rod is the first MB that appears to belong to the gamma-Proteobacteria, which may suggest an iron- rather than sulfur-based respiratory metabolism. Its distribution and phylogenetic identity suggest that an alternative model for the ecological and physiological role of magnetotaxis is needed for greigite-producing MB.     

Combined approach for characterization of uncultivated magnetotactic bacteria from various aquatic environments

Both magnetic collection and "race track" purification techniques were highly effective for selective enrichment of magnetotactic bacteria (MTB) from complex communities, as suggested by amplified ribosomal DNA restriction analysis and denaturing gradient gel electrophoresis combined with sequence analysis of 16S rRNA genes. Using these purification methods, the occurrence and diversity of MTB in microcosms from various marine and freshwater environments were assayed by using a combined microscopic, molecular, and cultivation approach. Most microcosms were dominated by magnetotactic cocci. Consistently, the majority of retrieved 16S RNA sequences were affiliated with a distinct cluster in the Alphaproteobacteria. Within this lineage the levels of sequence divergence were <1 to 11%, indicating genus-level diversity between magnetotactic cocci from various microcosms, as well as between MTB from different stages of succession of the same microcosms. The community composition in microscosms underwent drastic succession during incubation, and significant heterogeneities were observed between microcosms from the same environmental sources. A novel magnetotactic rod (MHB-1) was detected in a sediment sample from a lake in northern Germany by fluorescence in situ hybridization. MHB-1 falls into the Nitrospira phylum, displaying 91% 16S rRNA sequence similarity to "Magnetobacterium bavaricum." In extensive cultivation attempts, we failed to isolate MHB-1, as well as most other MTB present in our samples. However, although magnetotactic spirilla were not frequently observed in the enrichments, 10 novel isolates of the genus Magnetospirillum which had not routinely been isolated in pure culture before were obtained.     

Newly isolated but uncultivated magnetotactic bacterium of the phylum Nitrospirae from Beijing, China

Magnetotactic bacteria (MTB) in the phylum Nitrospirae synthesize up to hundreds of intracellular bullet-shaped magnetite magnetosomes. In the present study, a watermelon-shaped magnetotactic bacterium (designated MWB-1) from Lake Beihai in Beijing, China, was characterized. This uncultivated microbe was identified as a member of the phylum Nitrospirae and represents a novel phylogenetic lineage with ≥6% 16S rRNA gene sequence divergence from all currently described MTB. MWB-1 contained 200 to 300 intracellular bullet-shaped magnetite magnetosomes and showed a helical swimming trajectory under homogeneous magnetic fields; its magnetotactic velocity decreased with increasing field strength, and vice versa. A robust phylogenetic framework for MWB-1 and all currently known MTB in the phylum Nitrospirae was constructed utilizing maximum-likelihood and Bayesian algorithms, which yielded strong evidence that the Nitrospirae MTB could be divided into four well-supported groups. Considering its population densities in sediment and its high numbers of magnetosomes, MWB-1 was estimated to account for more than 10% of the natural remanent magnetization of the surface sediment. Taken together, the results of this study suggest that MTB in the phylum Nitrospirae are more diverse than previously realized and can make important contributions to the sedimentary magnetization in particular environments.     

Improved technique for the isolation of magnetotactic spirilla from a freshwater sediment and their phylogenetic characterization.

An improved technique for the isolation of magnetotactic bacteria was used for the axenic cultivation of microaerophilic magnetotactic spirilla. Magnetotactic bacteria were first separated from non-magnetic contaminants by exploiting their active migration along magnetic field lines by a capillary "racetrack" method. The purified magnetic cells were then inoculated into a two-layer isolation medium with opposing oxygen and sulfide gradients. Several strains of magnetotactic spirilla were isolated from a freshwater sediment sample using this method. Based on their morphology, physiology and comparative analysis of almost complete 16S rRNA gene sequences, all newly isolated strains were identified as members of the genus Magnetospirillum. While five of the isolates were closely related to previously described species (> 99% sequence similarity), two isolates appear to represent a third phylogenetic cluster within the genus Magnetospirillum.