Herein, we propose a convenient method to enable pretreatment of target objects using digital holographic microscopy (DHM). As a test sample, we used diatom frustules (Nitzschia sp.) as the target objects. In the generally used sample preparation method, the frustule suspension is added dropwise onto a glass substrate or into a glass chamber. While our work confirms good observation of purified frustules using the typical sample preparation method, we also demonstrate a new procedure to observe unseparated structures of frustules prepared by baking them on a mica surface. The baked frustules on the mica surface were transferred to a glass chamber with 1% sodium dodecyl sulfate solution. In this manner, the unseparated structures of the diatom frustules were clearly observed. Furthermore, metal-coated frustules prepared by sputtering onto them on a mica surface were also clearly observed using the same procedure. Our method can be applied for the observation of any target object that is pretreated on a solid surface. We expect our proposed method to be a basis for establishing DHM techniques for microscopic observations of biomaterials.

The study of the sinking phenomenon of diatom cells, which have a slightly larger specific gravity (~1.3) compared to that of water, is an important research topic for understanding photosynthetic efficiency. In this study, we successfully demonstrated the observation of the sinking behaviors of four different species of diatom using a homemade “tumbled” optical microscope. A homemade 1 mm3 microchamber was employed to decrease the effects of convection currents. In the microchamber, diatom cells were basically settled in a linear manner without floating, although some of the cells were rotated during their sinking. Sinking speeds of the four species of diatom cells, Nitzschia sp., Pheodactylum tricornutum, Navicula sp., and Odontella aurita, were 0.81 ± 5.56, 3.03 ± 10.17, 3.29 ± 7.39, and 11.22 ± 21.42 μm/s, respectively, based on the automatic tracking analysis of the centroids of each cell. Manual analysis of a vector between two longitudinal ends of the cells (two-point analysis) was effective for quantitatively characterizing the rotation phenomenon; therefore, angles and angular velocities of rotating cells were well determined as a function of time. The effects of the cell shapes on sinking velocity could be explained by simulation analysis using the modified Stokes’ law proposed by Miklasz et al.

To help characterise the palaeogeographic and lacustrine environmental changes that resulted from the Holocene transgression and residual subsidence in the eastern Kanto Plain of central Japan, we analysed four drill cores and reviewed other core data from the southern part of the Lake Inba area. Fossil diatom assemblages yielded evidence of centennial-scale palaeogeographic and salinity responses to sea-level changes since the late Pleistocene. We determined that the seawater incursion into the Lake Inba area during the Holocene transgression occurred at approximately 9000 yr. We also recognised a late Holocene regression event corresponding to the Yayoi regression, considered to have occurred from ca. 3000 to ca. 2000 yr, and a subsequent transgression. Our data clarify some of the palaeogeographic changes that occurred in the Lake Inba area and document an overall trend toward lower salinity in the lake during the regression. In particular, the environment in Lake Inba changed from brackish to freshwater no later than 1000 yr. From the detailed palaeogeographic and palaeo-sea-level reconstruction, we recognised that residual subsidence occurred during the Holocene in this area. Thus, comparison of sea-level reconstructions based on modelling and fossil diatom assemblages is effective in interpreting Holocene long-term subsidence.

Diatom assemblages in lake sediments of Lac Noir, southwestern Québec, were studied at a resolution of 10 yr to determine principal drivers of primary producers for the past ~1000 yr. Generalized additive modeling revealed strong links between broadscale climate intervals of the late Holocene, forest composition, and diatom flora. During the Medieval Warm Period (~AD 1200) and onset of the Little Ice Age (~AD 1450), increases in Tabellaria flocculosa str. IIIp at the expense of Discostella stelligera reflected low lake productivity. At AD 1630, an abrupt shift to cooler temperatures and dry conditions triggered a decline in hemlock (Tsuga), replaced by disturbance and cool-adapted taxa. Greater nutrient availability and soil erosion in the catchment led to a corresponding and rapid increase in diatoms with higher optima for nitrogen, such as Asterionella formosa and Fragilaria crotonensis. After AD 1870, an increase in pollen of taxa associated with disturbances signaled the arrival of Euro-Canadians, and associated nutrient inputs to the lake triggered increases in Stephanodiscus minutulus and Achnanthidium minutissimum. Overall results of the study indicate that climate played an important underlying role in lake-ecosystem dynamics; however, disturbances affecting forest composition had more direct influences on the diatom communities of Lac Noir.

Lake Ejagham is a small, shallow lake in Cameroon, West Africa, which supports five endemic species of cichlid fishes in two distinct lineages. Genetic evidence suggests a relatively young age for the species flocks, but supporting geologic evidence has thus far been unavailable. Here we present diatom, geochemical, mineralogical, and radiocarbon data from two sediment cores that provide new insights into the age and origin of Lake Ejagham and its endemic fishes. Radiocarbon ages at the base of the longer core indicate that the lake formed approximately 9 ka ago, and the diatom record of the shorter core suggests that hydroclimate variability during the last 3 millennia was similar to that of other lakes in Cameroon and Ghana. These findings establish a maximum age of ca. 9 cal ka BP for the lake and its endemic species and suggest that repeated cichlid speciation in two distinct lineages occurred rapidly within the lake. Local geology and West African paleoclimate records argue against a volcanic, chemical, or climatic origin for Lake Ejagham. Although not conclusive, the morphometry of the lake and possible signs of impact-induced effects on quartz grains are instead more suggestive of a bolide impact.

Late-Holocene environmental and climatic conditions were reconstructed from diatom assemblages in sediment cores from four western Montana lakes: Crevice Lake, Foy Lake, Morrison Lake, and Reservoir Lake. The lakes show synchroneity in timing of shifts in diatom community structure, but the nature of these changes differs among the lakes. Two of the sites provide highly resolved records of hydrologic balance, while the other two stratigraphic sequences primarily record temperature impact on lake thermal structure. All four lakes show significant change in five discrete intervals: 2200–2100, 1700–1600, 1350–1200, 800–600, and 250 cal yr BP. The similarities in the timing of change suggest overlying regional climatic influences on lake dynamics. The 800–600 cal yr BP shift is evident in other paleorecords throughout the Great Plains and western US, associated with the transition from the Medieval Climate Anomaly to the Little Ice Age. Large-scale climatic mechanisms that influence these lake environments may result from atmospheric circulation patterns that are driven by interactions between Pacific and Atlantic sea-surface temperatures, which are then locally modified by topography.

The relationships among internally consistent records of summer sea-surface temperature (SSST), winter sea ice (WSI), and diatomaceous stable isotopes were studied across seven terminations over the last 660 ka in sedimentary cores from ODP sites 1093 and 1094. The sequence of events at both sites indicates that SSST and WSI changes led the carbon and nitrogen isotopic changes in three Terminations (TI, TII and TVI) and followed them in the other four Terminations (TIII, TIV, TV and TVII). In both TIII and TIV, the leads and lags between the proxies were related to weak glacial mode, while in TV and TVII they were due to the influence of the mid-Pleistocene transition. We show that the sequence of events is not unique and does not follow the same pattern across terminations, implying that the processes that initiated climate change in the Southern Ocean has varied through time.

Reconstructions of past environmental changes are critical for understanding the natural variability of Earth's climate system and for providing a context for present and future global change. Radiocarbon-dated lake sediments from Lake CF3, northeastern Baffin Island, Arctic Canada, are used to reconstruct past environmental conditions over the last 11,200 years. Numerous proxies, including chironomid-inferred July air temperatures, diatom-inferred lakewater pH, and sediment organic matter, reveal a pronounced Holocene thermal maximum as much as 5°C warmer than historic summer temperatures from ∼10,000 to 8500 cal yr B.P. Following rapid cooling ∼8500 cal yr B.P., Lake CF3 proxies indicate cooling through the late Holocene. At many sites in northeastern Canada, the Holocene thermal maximum occurred later than at Lake CF3; this late onset of Holocene warmth is generally attributed to the impacts of the decaying Laurentide Ice Sheet on early Holocene temperatures in northeastern Canada. However, the lacustrine proxies in Lake CF3 apparently responded to insolation-driven warmth, despite the proximity of Lake CF3 to the Laurentide Ice Sheet and its meltwater. The magnitude and timing of the Holocene thermal maximum at Lake CF3 indicate that temperatures and environmental conditions at this site are highly sensitive to changes in radiative forcing.

pCO2/pH perturbation experiments were carried out under two different pCO2 levels to evaluate effects of CO2-driven ocean acidification on semi-continuous cultures of the marine diatom Skeletonema pseudocostatum CSA48. Under higher pCO2/lowered pH conditions, our results showed that CO2-driven acidification had no significant impact on growth rate, chlorophyll-a, cellular abundance, gross photosynthesis, dark respiration, particulate organic carbon and particulate organic nitrogen between CO2-treatments, suggesting that S. pseudocostatum is adapted to tolerate changes of ~0.5 units of pH under high pCO2 conditions. However, dissolved organic carbon (DOC) concentration and DOC/POC ratio were significantly higher at high pCO2, indicating that a greater partitioning of organic carbon into the DOC pool was stimulated by high CO2/low pH conditions. Total fatty acids (FAs) were significantly higher under low pCO2 conditions. The composition of FAs changed from low to high pCO2, with an increase in the concentration of saturated and a reduction of monounsaturated FAs. Polyunsaturated FAs did not show significant differences between pCO2 treatments. Our results lead to the conclusion that the balance between negative or null effect on S. pseudocostatum ecophysiology upon low pH/high pCO2 conditions constitute an important factor to be considered in order to evaluate the global effect of rising atmospheric CO2 on primary productivity in coastal ocean. We found a significant decrease in total FAs, however no indications were found for a detrimental effect of ocean acidification on the nutritional quality in terms of essential fatty acids.

Spatial and temporal variability and bloom formation of the potentially toxic diatom Pseudo-nitzschia spp. was investigated weekly to monthly from October 2009 to October 2010 in a eutrophic estuary, the Golden Horn. Pseudo-nitzschia spp. were detected in 195 of 512 samples (38%) collected throughout the year. Two species, P. calliantha and P. pungens, were identified based on the SEM examination. Blooms of Pseudo-nitzschia occurred in the lower and middle estuary in January and May. The bloom in January mainly comprised P. calliantha. In the bloom in early May, P. calliantha made up 72% of the Pseudo-nitzschia cells and P. pungens 28%. However, the contribution of P. pungens increased to 83% in late May. The Pseudo-nitzschia blooms occurred at low temperature (9–15°C) and moderate salinity (17–18), and for P. calliantha a significant negative correlation was found with temperature and a significant positive correlation with salinity. The percentage of Pseudo-nitzschia cells decreased gradually from lower to upper estuary (59–14%), correlating with a decrease in Secchi depth (5.5–0.5 m). Principal components analyses (PCA) were used to explore the spatial and temporal variability of environmental factors in relation to Pseudo-nitzschia abundances, and showed that NH4, pH, Secchi depth and DO values were the most important factors reflecting spatial differences, while temperature, salinity, Chl-a and Si:N were more important factors showing temporal differences. High abundances of P. pungens correlated mainly with pH, Secchi depth and DO values, whereas P. calliantha also correlated with NO3 + NO2. Low light availability due to high concentrations of suspended material and very variable environmental conditions (e.g. pH, DO and NH4) may have limited growth of Pseudo-nitzschia in the upper estuary. Regular monitoring of Pseudo-nitzschia is important for improving the understanding of the influence of environmental parameters on bloom dynamics in the study area.

Diatoms and geochemical stratigraphy were studied in sediment core samples collected from a heavily polluted urban lake (SE China) in order to track the history of eutrophication and heavy metal contamination. The sediment profile covered ca. 60 years (from ca. 1951 to 2011) based on 137Cs and Spheroidal carbonaceous particles (SCP) dating, and encompassed a period of rapid industrial development in this region. Diatoms experienced two visible shifts, including the replacement of benthic and epiphytic taxa by planktonic species (e.g., Cyclotella meneghiniana Kützing) in 1972, and the dominance of Cyclotella atomus Hustedt and Nitzschia palea (Kützing) W. Smith after 1999. Metals (i.e., Cd, Pb and Zn), total phosphorus, total nitrogen and total organic carbon all increased in the past 60 years. Redundancy analysis was used to correlate diatom with chemical change and explained 50.3–60% of total variation in diatom data for three periods (from 1951 to 1999, between 1951 and 2011 and from 1972 to 2011). The combined effects of nutrients and metals were the predominant factor, capturing 29.6–42.8% of the total variance. Nutrients alone accounted for little more variance than did metals alone for the first flora shift about 1972. The further shift after 1999 was more influenced by the sole effect of metals than that of nutrients. Increases in species (e.g., N. Palea) able to tolerate both nutrient-related and metal-related stressors were related to persistent nutrient and metal inputs. In addition, climate warming might exacerbate eutrophication and metal contamination in this lake.

Microphytobenthos (MPB) contributes up to half the primary production of estuaries. These microorganisms are sensitive to changes in sediment temperatures, particularly the extreme temperatures during exposure periods. This study investigates the physiological responses of MPB to freezing temperatures at two locations near Hobart, Tasmania during winter. Photosynthetic parameters were measured at 2 mm intervals to a depth of 10 mm. FV/FM values at three different distances from the shoreline at Kings Beach and Browns River in winter were between 0.584 and 0.617. rETRmax values were between 24.696 and 20.773. Maximum α values peaked in the subsurface rather than at the sediment surface. In vitro laboratory experiments (down to −5°C) showed little difference in response between the control and treatment groups, indicating no apparent effects of short term freezing on the MPB. Little change in photosynthetic parameters in response to freezing was probably associated with the resistance of light-harvesting reactions to freezing temperatures, recovery of the plasmalemma integrity or cryoprotection. Sediment composition and species composition were similar at both sampling sites. Therefore, responses of MPB were not due to species and grain size composition.

In order to clarify the mechanisms underlying high efficiency of the silica sink in monomictic Lake Biwa in Japan, vertical flux of biogenic silica (BSi) was measured using sediment traps over a period of 15 months. The sediment traps were deployed at depths of 30 and 70 m. On a global scale, BSi fluxes in Lake Biwa were very high, ranging from 20 to 1087 mg Si.m−2.d−1 at the 30 m trap and 12–999 mg Si.m−2.d−1 at the 70 m trap throughout the observation period. The BSi fluxes at both traps increased significantly during the winter period and the ratio of BSi fluxes in the winter period to annual BSi fluxes ranged from 27 to 62%. In the winter period, when nutrients are supplied from the hypolimnion to the epilimnion, the distribution of photosynthetically active diatoms was almost homogeneous in all layers, including the aphotic layer. At this time, the diatoms assimilated dissolved silica (DSi) in a wider layer containing a part of aphotic layer in order to produce rigid frustules, which accumulated rapidly in bottom sediments as DSi concentration in the water column decreased. Thus, size of the silica sink in Lake Biwa is enhanced during the winter holomictic mixing period through interaction between physical (thermocline disruption: transfer of diatoms to deep layers by vertical convection), chemical (nutrient supply from deep layers) and biological (dominance of active diatoms in all layers) processes.

Past environmental changes based on diatom relative abundances have been inferred from the maar Lake Erlongwan in northeast China. The limnology of Lake Erlongwan is affected by the strongly seasonal regional climate. The composition of diatom assemblages, in turn, responds to changes in the seasonal duration of ice cover in winter, water-column turnover in spring and autumn, and thermal stratification in summer. Statistical analysis of the sedimentary diatom assemblages reveals three significant stratigraphic zones over the past 1000 yr. The highest abundance of the planktonic species Discostella species occurs between AD 1050 and 1400 and suggests an annual ice-free period of long duration and well-developed summer stratification of the water column. This planktonic diatom peak between ca. AD 1150 and 1200 suggests that this period was the warmest over the past 1000 yr. The interval between AD 1400 and 1800 is marked by a decline in planktonic diatoms and suggests shorter duration of the ice-free season, weaker water stratification and possibly generally cold conditions. After AD 1800 relative abundances of planktonic diatoms, including Puncticulata praetermissa and Asterionella formosa, increase again, which indicates lengthening of the duration of the annual ice-free period and a stronger overturn of the water column. All these data imply that the pattern of the seasons is different between the MWP and the 20th century.

The nanostructural features of the gas-phase displacement reaction 2Mg(g)+SiO2→2MgO(s)+{Si}, where SiO2 is in the form of diatom shells were studied via X-ray diffraction and Fourier methods. Diatomaceous powder heated to 700 °C in a sealed graphite cell in the presence of Mg vapor formed MgO via a displacement reaction. Warren-Averbach analysis performed on samples reacted for different times showed an initial sharp MgO grain size distribution which broadened with time. New MgO crystallization was shown to occur until about 60 min, whereafter only MgO grain growth occurred. Median MgO crystallite size increased from 7.5 to 24.9 nm during this period, whereas microstrain decreased dramatically past 60 min annealing time.

Ile de la Possession is one of the few islands in the southern Indian Ocean, making the island a valuable place to reconstruct past environmental and climatic changes. In this study a peat sediment core was analysed to reconstruct the changes that occurred before, during and after the eruption of the Morne Rouge (10 000–5500 14C yr bp) volcano. In addition to sedimentological analyses, diatom communities were used to reconstruct humidity and altitude, based on existing transfer functions. Radiocarbon dating of a tephra layer showed that the Morne Rouge volcano erupted between 6700–6600 cal. yr bp, giving a much more precise time scale for this event. The eruption was preceded by a tsunami flooding, indicated by the high numbers of marine diatoms found immediately before the tephra layer. After the eruption pioneer diatom species recolonized the coring site. Evidence is presented of the late climatic optimum around 3050 cal. yr bp, preceded by a cooling event until 6600 cal. yr bp. Nutrient input from elephant seals and wandering albatrosses obscured the climate signal for the last 600 cal yr bp.

Following the ‘Volgoneft-248’ oil spill, phytoplankton distribution within the affected area was investigated for two years. Simultaneously measured physical variables such as salinity, temperature, Secchi disc, current speed and direction, and total petroleum hydrocarbons (TPH) were evaluated together with phytoplankton data. At the time of the accident, the TPH concentration in surface water was measured as 2.17 mg l−1 and decreased to 88.5 µg l−1 after five days. In the first sampling period, no diatoms were detected in surface water, while dinoflagellates were dominant in the phytoplankton community. The species composition of phytoplankton changed rapidly in two months and the diatoms increased in terms of abundance and diversity. This indicated that the diatoms might be more sensitive to oil pollution than the dinoflagellates. In comparison with the historical datasets, the low phytoplankton abundance following the oil spill should be considered as the small effect of oil on the phytoplankton rather than natural variability of the ecosystem. High oil concentration in the water column caused stress on the phytoplankton and influenced the species composition negatively depending on the sensitivity of groups and the natural variability of the ecosystem.

The diatom, Phaeodactylum tricornutum is a common inhabitant of inshore waters and can exist in different morphotypes that are thought to be adapted for survival in different habitats. Despite this diatom being widely used for physiological and genetic studies of microalgae, little is known about biochemical or physiological differences between the cell morphotypes. The present study was aimed at comparing differences in the antibacterial properties of the fusiform and oval morphotypes, the dominant cell types found in laboratory cultures of most strains of P. tricornutum. In cultures differing in proportions of fusiform and oval cells, there is a significant and positive correlation between the proportion of cells in the fusiform morphotype and the antibacterial activity of cell extracts. Extracts prepared from cultures enriched for fusiform cells (~76%) show greater antibacterial activity against the Gram-positive bacterium, Staphylococcus aureus, than those prepared from pure (100%) oval cultures. Thus fusiform cells contain greater antibacterial activity per cell compared to the ovals. Gas–liquid chromatographic analyses of the extracts reveal that those from enriched fusiform populations contain significantly greater levels of the free fatty acids, eicosapentaenoic acid (EPA), hexadecatrienoic acid (HTA) and palmitoleic acid (PA) than the pure oval cell cultures. These free fatty acids from P. tricornutum have been previously shown by us to have potent antibacterial activity against S. aureus. Free fatty acids, released from damaged microalgal cells, defend the microalgal population against grazing predators but, here, we suggest that these free fatty acids could also act against pathogenic bacteria in the vicinity of the algae. As cell extracts from the fusiform cells contain greater quantities of these fatty acids, fusiform cells may have greater potential than the ovals for this type of protection.

Microphytobenthos need photoadaptive strategies to survive the highly dynamic light environment in which they reside. Xanthophyll pigments can provide photoprotection by cycling electrons between epoxide and de-epoxide forms, dissipating excess light energy as heat. This study examined the xanthophyll cycle in microphytobenthos on a tidally exposed substrate at Browns River, Tasmania. Fv/Fm decreased from 0.52±0.01 to 0.47±0.01 at noon in surface samples and a decrease in the diadinoxanthin:chlorophyll-a ratio from 0.022±0.003 to 0.015±0.005 also suggests that the microphytobenthos was under physiological stress at noon. The results indicate that the cells exposed to light at the surface migrated deeper into the sediments and replenished the epoxide form of their xanthophylls. The results suggest that micrphytobenthos utilizes both behavioural and physiological strategies to survive in the dynamic intertidal environment.

Local knowledge is increasingly seen as a critical information source for environmental management and habitat restoration, particularly in Australia. To assess the reliability of this information source, community perceptions of the salinity history of Lake Ainsworth (New South Wales, Australia) were investigated. Lake Ainsworth is a coastal dune lake classified as ‘permanently’ freshwater, although diatom evidence indicates a saline phase that ended in the 1930s. Local accounts of the Lake's history rarely reached consensus and local perceptions frequently contrasted with alternate evidence, including that derived from historical maps and aerial photographs. Given there was an inconsistent and unreliable local perspective about a relatively simple environmental issue, calls for environmental management and restoration to be based on local priorities should be viewed with scepticism.