Application of Atomic Force Microscopy to Observation of Marine Bacteria

The atomic force microscopy (AFM) is a recently developed, bench-top instrument that can image the surface structures of biological specimens at high resolution with simultaneous measurement of their size. This paper describes the application of AFM to marine bacteria. Both natural and cultured bacteria were retained on a filter or placed on glass, washed, air-dried and observed by AFM. The instrumental condition, the choice of suitable filter, effect of fixation and filtration, comparison with epifluorescent microscopic (EFM) count, and the size and shape of bacterial cells were investigated. An Isopore filter was best for concentration and subsequent observation because of its surface flatness. Cross section images showed that both rod and coccoid cells were flattened, the former usually having a two-humped shape. Bacterial cells were differentiated from non-living particles based on their cross section shape and size. Bacterial counts by AFM and EFM showed good agreement. Although size measurement is easily done by the instrument, AFM tends to overestimate the size of microspheres. More work is thus needed on the size measurement of living organisms. Because AFM easily provides images of natural bacterial cells at high magnification, it can be used as a new tool to study the fine structures of marine bacteria. This revised version was published online in July 2006 with corrections to the Cover Date.     

Turbulent Flow at 190 m Height Above London During 2006–2008: A Climatology and the Applicability of Similarity Theory

Flow and turbulence above urban terrain is more complex than above rural terrain, due to the different momentum and heat transfer characteristics that are affected by the presence of buildings (e.g. pressure variations around buildings). The applicability of similarity theory (as developed over rural terrain) is tested using observations of flow from a sonic anemometer located at 190.3 m height in London, U.K. using about 6500 h of data. Turbulence statistics—dimensionless wind speed and temperature, standard deviations and correlation coefficients for momentum and heat transfer—were analysed in three ways. First, turbulence statistics were plotted as a function only of a local stability parameter z/Λ (where Λ is the local Obukhov length and z is the height above ground); the σ _i /u _* values (i = u, v, w) for neutral conditions are 2.3, 1.85 and 1.35 respectively, similar to canonical values. Second, analysis of urban mixed-layer formulations during daytime convective conditions over London was undertaken, showing that atmospheric turbulence at high altitude over large cities might not behave dissimilarly from that over rural terrain. Third, correlation coefficients for heat and momentum were analyzed with respect to local stability. The results give confidence in using the framework of local similarity for turbulence measured over London, and perhaps other cities. However, the following caveats for our data are worth noting: (i) the terrain is reasonably flat, (ii) building heights vary little over a large area, and (iii) the sensor height is above the mean roughness sublayer depth.     

Sulfur bacteria originating from the water and organisms in a hydrothermally active area of the mid-okinawa trough

Hydrothermal venting and associated fauna were observed in the mid-Okinawa Trough during deep-sea diving byShinkai 2000. Water and organisms were collected there for on-board cultivation of sulfur bacteria. Sulfur bacteria capable of growing on an inorganic medium containing thiosulfate were subcultured and isolated. The isolated chemoautotrophic sulfur bacteria were all rod- to beanshaped, nonsporing, and gram-negative. They could also grow on an organic medium and thus were shown to be facultative chemoautotrophs. Their facultative chemoautotrophy would result in synergetic metabolism of both inorganic and organic substrates; thus the sulfur bacteria could be highly adaptive to nutritional diversity of hydrothermal vent areas.     

Vertical distribution of bacterial abundance in the northwest pacific ocean

Mixed populations of free-living marine bacteria were collected at depths from the surface to the bottom (1,960m in Suruga Bay and 1,585 m in the Japan Sea) in the northwest Pacific during deep-sea diving by the submersible,Shinkai 2000. Their abundance in total cell counts and in lipopolysaccharide (LPS) concentration was found to decrease with increasing depth, and the decreasing profiles were shown to be linear on logarithmic scales. The total cell counts and the LPS concentration showed a linear relationship on arithmetic scales, and the LPS content per cell was found to be 1.02×10^–14 g.     

Field survey report on tsunami disasters caused by the 1993 Southwest Hokkaido earthquake

Detailed field work at Okushiri Island and along the southwest coast of Hokkaido has revealed quantitatively (1) the advancing direction of tsunami on land, (2) the true tsunami height (i.e., height of tsunami, excluding its splashes, as measured from the ground) and (3) the flow velocity of tsunami on land, in heavily damaged areas. When a Japanese wooden house is swept away by tsunami, bolts that tie the house to its concrete foundation resist until the last moment and become bent towards the direction of the house being carried away. The orientations of more than 850 of those bent bolts and iron pipes (all that can be measured, mostly at Okushiri Island) and fell-down direction of about 400 trees clearly display how tsunami behaved on land and caused serious damage at various places. The true tsunami height was estimated by using several indicators, such as broken tree twigs and a window pane. The flow velocity of tsunami on land was determined by estimating the hydrodynamic force exerted on a bent handrail and a bent-down guardrail by the tsunami throughin situ strength tests.Contrary to the wide-spread recognition after the tsunami hazard, our results clearly indicate that only a few residential areas (i.e., Monai, eastern Hamatsumae, and a small portion at northern Aonae, all on Okushiri Island) were hit by a huge tsunami, with true heights reaching 10 m. Southern Aonae was completely swept away by tsunami that came directly from the focal region immediately to the west. The true tsunami height over the western sea wall of southern Aonae was estimated as 3 to 4 m. Northern Aonae also suffered severe damage due to tsunami that invaded from the corner zone of the sand dune (8 m high) and tide embankment at the northern end of the Aonae Harbor. This corner apparently acted as a tsunami amplifier, and tide embankment or breakwater can be quite dangerous when tsunami advances towards the corner it makes with the coast. The nearly complete devastation of Inaho at the northern end of Okushiri Island underscored the danger of tsunami whose propagation direction is parallel to the coast, since such tsunami waves tend to be amplified and tide embankment or breakwater is constructed low towards the coast at many harbors or fishing ports. Tsunami waves mostly of 2 to 4 m in true height swept away Hamatsumae on the southeast site of Okushiri Island where there were no coastal structures. Coastal structures were effective in reducing tsunami hazard at many sites. The maximum flow velocity at northern Aonae was estimated as 10 to 18 m/s (Tsutsumi et al., 1994), and such a high on-land velocity of tsunami near shore is probably due to the rapid shallowing of the deep sea near the epicentral region towards Okushiri Island. If the advancing direction, true height, and flow velocity of tsunami can be predicted by future analyses of tsunami generation and progagation, the analyses will be a powerful tool for future assessment of tsunami disasters, including the identification of blind spots in the tsunami hazard reduction.     

Modelling chemistry in the nocturnal boundary layer above tropical rainforest and a generalised effective nocturnal ozone deposition velocity for sub-ppbv NOx conditions

Measurements of atmospheric composition have been made over a remote rainforest landscape. A box model has previously been demonstrated to model the observed daytime chemistry well. However the box model is unable to explain the nocturnal measurements of relatively high [NO] and [O₃], but relatively low observed [NO₂]. It is shown that a one-dimensional (1-D) column model with simple O₃-NO_x chemistry and a simple representation of vertical transport is able to explain the observed nocturnal concentrations and predict the likely vertical profiles of these species in the nocturnal boundary layer (NBL). Concentrations of tracers carried over from the end of the night can affect the atmospheric chemistry of the following day. To ascertain the anomaly introduced by using the box model to represent the NBL, vertically-averaged NBL concentrations at the end of the night are compared between the 1-D model and the box model. It is found that, under low to medium [NO_x] conditions (NO_x?<?1 ppbv), a simple parametrisation can be used to modify the box model deposition velocity of ozone, in order to achieve good agreement between the box and 1-D models for these end-of-night concentrations of NO_x and O₃. This parametrisation would could also be used in global climate-chemistry models with limited vertical resolution near the surface. Box-model results for the following day differ substantially if this effective nocturnal deposition velocity for ozone is implemented; for instance, there is a 9% increase in the following days peak ozone concentration. However under medium to high [NO_x] conditions (NO_x > 1 ppbv), the effect on the chemistry due to the vertical distribution of the species means no box model can adequately represent chemistry in the NBL without modifying reaction rate coefficients.     

Onshore tsunami deposits caused by the 1993 Southwest Hokkaido and 1983 Japan Sea earthquakes

Onshore tsunami deposits resulting from the 1993 Southwest Hokkaido and 1983 Japan Sea earthquakes were described to evaluate the feasibility of tsunami deposits for inferring paleoseismic events along submarine faults. Tsunami deposits were divided into three types, based on their composition and aerial distribution: (A) deposits consisting only of floating materials, (B) locally distributed siliclastic deposits, and (C) widespread siliclastic deposits. The most widely distributed tsunami deposits consist of the first two types. Type C deposits are mostly limited to areas where the higher tsunami runup was observed. The scale of tsunami represented by vertical tsunami runup is an important factor controlling the volume of tsunami deposits. The thickest deposits, about 10 cm, occur behind coastal dunes. To produce thick siliclastic tsunami deposits, a suitable source area, such as sand bar or dune, must be available in addition to sufficient vertical tsunami runup. Estimation of the amounts of erosion and deposition indicates that tsunami deposits were derived from both onshore and shoreface regions. The composition and grain size of the tsunami deposits strongly reflect the nature of the sedimentary materials of their source area. Sedimentary structures of the tsunami deposits suggest both low and high flow régimes. Consequently, it seems very difficult to identify tsunami deposits based only on grain size distribution or sedimentary structure of a single site in ancient successions.