Direct observations of North Pacific ventilation: brine rejection in the Okhotsk Sea

Brine rejection that accompanies ice formation in coastal polynyas is responsible for ventilating several globally important water masses in the Arctic and Antarctic. However, most previous studies of this process have been indirect, based on heat budget analyses or on warm-season water column inventories. Here, we present direct measurements of brine rejection and formation of North Pacific Intermediate Water in the Okhotsk Sea from moored winter observations. A steady, nearly linear salinity increase unambiguously caused by local ice formation was observed for more than a month.     

Pore-scale view of microbial turnover: Combining 14C imaging, μCT and zymography after adding soluble carbon to soil pores of specific sizes

The location of microorganisms and substrates within soil pore networks plays a crucial role in organic carbon (C) processing, and its microbial utilization and turnover, and has direct consequences for C and nutrient cycling. An optimal approach to quantify responses to new C inputs from microorganisms residing in specific pores is the addition of new C to pores of target sizes in undisturbed soil cores. We used the matric potential approach to add ¹⁴C-labelled glucose to small (< 40 μm, root free) or large (60–180 μm, potentially inhabited by roots) pores of undisturbed soil cores. Localization of glucose-derived C via ¹⁴C imaging was related to pore size distributions and connectivity, characterized via X-ray computed microtomography (μCT), and to β-glucosidase activity, characterized via zymography. After 2-week incubations, 1.3 times more glucose was mineralized (¹⁴CO₂) when it was added to the large pores; however, more ¹⁴C remained in microbial biomass when glucose was added to the small pores. Consequently, although utilizing the same amounts of easily available C, the microorganisms localized in the large pores had faster turnover compared to microorganisms in small pores. Stronger associations between β-glucosidase activity and glucose-derived C were observed when glucose was added to the large pores. We conclude that (a) the matric potential approach allows placing, albeit not exactly, of soluble substrates into pores of target diameter range, and (b) microorganisms localized in large pores respond to new C inputs with faster turnover, greater growth and more intensive enzyme production compared to those inhabiting the small pores.     

Applications of chemical shift imaging to marine sciences

The successful applications of magnetic resonance imaging (MRI) in medicine are mostly due to the non-invasive and non-destructive nature of MRI techniques. Longitudinal studies of humans and animals are easily accomplished, taking advantage of the fact that MRI does not use harmful radiation that would be needed for plain film radiographic, computerized tomography (CT) or positron emission (PET) scans. Routine anatomic and functional studies using the strong signal from the most abundant magnetic nucleus, the proton, can also provide metabolic information when combined with in vivo magnetic resonance spectroscopy (MRS). MRS can be performed using either protons or hetero-nuclei (meaning any magnetic nuclei other than protons or 1H) including carbon (13C) or phosphorus (31P). In vivo MR spectra can be obtained from single region of interest (ROI or voxel) or multiple ROIs simultaneously using the technique typically called chemical shift imaging (CSI). Here we report applications of CSI to marine samples and describe a technique to study in vivo glycine metabolism in oysters using 13C MRS 12 h after immersion in a sea water chamber dosed with [2-13C]-glycine. This is the first report of 13C CSI in a marine organism.     

Nectar sugars and bird visitation define a floral niche for basidiomycetous yeast on the Canary Islands

Background

Studies on the diversity of yeasts in floral nectar were first carried out in the late 19^th century. A narrow group of fermenting, osmophilous ascomycetes were regarded as exclusive specialists able to populate this unique and species poor environment. More recently, it became apparent that microorganisms might play an important role in the process of plant pollination. Despite the importance of these nectar dwelling yeasts, knowledge of the factors that drive their diversity and species composition is scarce.

Results

In this study, we linked the frequencies of yeast species in floral nectars from various host plants on the Canary Islands to nectar traits and flower visitors. We estimated the structuring impact of pollination syndromes (nectar volume, sugar concentration and sugar composition) on yeast diversity.The observed total yeast diversity was consistent with former studies, however, the present survey yielded additional basidiomycetous yeasts in unexpectedly high numbers. Our results show these basidiomycetes are significantly associated with ornithophilous flowers. Specialized ascomycetes inhabit sucrose-dominant nectars, but are surprisingly rare in nectar dominated by monosaccharides.

Conclusions

There are two conclusions from this study: (i) a shift of floral visitors towards ornithophily alters the likelihood of yeast inoculation in flowers, and (ii) low concentrated hexose-dominant nectar promotes colonization of flowers by basidiomycetes. In the studied floral system, basidiomycete yeasts are acknowledged as regular members of nectar. This challenges the current understanding that nectar is an ecological niche solely occupied by ascomycetous yeasts.

Electronic supplementary material

The online version of this article (doi:10.1186/s12898-015-0036-x) contains supplementary material, which is available to authorized users.     

Conformational Analysis of the Oligosaccharides Related to Side Chains of Holothurian Fucosylated Chondroitin Sulfates

Anionic polysaccharides fucosylated chondroitin sulfates (FCS) from holothurian species were shown to affect various biological processes, such as metastasis, angiogenesis, clot formation, thrombosis, inflammation, and some others. To understand the mechanism of FCSs action, knowledge about their spatial arrangement is required. We have started the systematic synthesis, conformational analysis, and study of biological activity of the oligosaccharides related to various fragments of these types of natural polysaccharides. In this communication, five molecules representing distinct structural fragments of chondroitin sulfate have been studied by means of molecular modeling and NMR. These are three disaccharides and two trisaccharides containing fucose and glucuronic acid residues with one sulfate group per each fucose residue or without it. Long-range C–H coupling constants were used for the verification of the theoretical models. The presence of two conformers for both linkage types was revealed. For the Fuc–GlA linkage, the dominant conformer was the same as described previously in a literature as the molecular dynamics (MD) average in a dodechasaccharide FCS fragment representing the backbone chain of the polysaccharide including GalNAc residues. This shows that the studied oligosaccharides, in addition to larger ones, may be considered as reliable models for Quantitative Structure-Activity Relationship (QSAR) studies to reveal pharmacophore fragments of FCS.     

Identification of virulence factors by multiplex PCR in Escherichia coli isolated from calves in Minas Gerais, Brazil

In this study, multiplex PCR was employed to investigate the virulence factors of Escherichia coli strains isolated from 60-day-old calves. Faecal samples were collected from 54 calves at 12 dairy farms in the state of Minas Gerais, Brazil. A total of 156 isolates were obtained after culture and microbiological isolation and were tested by multiplex PCR for the presence of genes encoding toxins (Stx1, Stx2 and STa) and adherence factors (intimin, F41 and F5). Seventy of 156 isolates were positive for at least one virulence factor: ten (14.3?%) from diarrhoeic animals and 60 (85.7?%) from healthy calves. The virulence markers identified were: Stx1 (82.8?%), eae (24.3?%), F41 (11.4?%), F5 (10?%), STa (4.28?%) and Stx2 (4?%). In diarrhoeic animals, Stx1 (70?%) and F41 (30?%) were identified, while Stx1 (83.3?%), eae (28.3?%), F41 (8.3?%), F5 (11.6?%), STa (5?%) and Stx2 (1.6?%) were detected in isolates from healthy calves. Mixed infections with pathotypes Shiga toxin-producing E. coli (STEC)/enteropathogenic E. coli, STEC/enterohaemorrhagic E. coli and STEC/other (eae/F5, Stx1/STa) were detected in five healthy calves. Pathogenic E. coli were identified in 59.26?% of all calves and on 75?% of the dairy farms studied, not only in diarrhoeic (five of six) but also in healthy calves (27 of 48), which demonstrates the importance of this agent in the aetiology of diarrhoea in calves in the state of Minas Gerais.     

The Efficiency of Moldboard Plowing upon Deactivation and Rehabilitation of Radioactively Contaminated Pastures in the North of Japan

The nuclear disaster at the Fukushima-1 nuclear power plant resulted in the widespread contamination of agrocenoses with radiocesium (¹³⁴Cs and ¹³⁷Cs) on the Honshu Island. Our study was performed on four agricultural fields located on gentle slopes of southern aspect 150 km to the northwest from the nuclear power plant. Three plots were tilled in different periods (in 2012–2013), and one plot remained untilled. The density of soil contamination and the specific activity of radiocesium in plants (June 2014) on tilled plots appeared to be permissible. Thus, the density of soil contamination varied within the range of 1.3–6.5 kBq/m², and the specific radioactivity of plants did not exceed 100 Bq/kg in plants. Such areas may be used as pastures without restrictions. At the same time, an increased density of the soil contamination (13–32 kBq/m²) and the concentration of radiocesium in plants (up to 138 Bq/kg) were detected in some areas not subjected to reclamation works. Such fallow lands are suitable as pastures only for feeding cattle for meat and for milk with their obligatory subsequent processing. On all the plots, the concentration of radiocesium in soils decreased down the soil profile. In general, radiocesium was accumulated on the middle and lower parts of slopes, which is associated with the development of water erosion and initial distribution of radiocesium during the snowmelt season. The air dose rate on the studied plots did not exceed the permissible safety level (0.2 μSv/h) and varied within the range 0.05–0.10 μSv/h. The maximum level of γ-radiation was determined on the fallow (untilled) plot. On tilled plots, γ-radiation was 30–50% lower. Therefore, soil moldboard plowin tillage to the depth of 20 cm with or without shallow cultivation is an efficient measure to reclaim agricultural lands with the initially low level of radiocesium contamination (up to 32 kBq/m²).     

Irreversible sorption of humic substances causes a decrease in wettability of clay surfaces as measured by a sessile drop contact angle method

Purpose

The objective of the study was to obtain quantitative assessments of the hydrophobic impact of irreversible sorption of humic substances (HSs) onto clay mineral surfaces using a sessile drop contact angle method.

Materials and methods

Two clays (kaolin and montmorillonite) were modified with four humic materials: (1) sod podzolic soil, (2) chernozem, (3) peat, and (4) coal (leonardite). The humic materials were characterized using elemental analysis, size exclusion chromatography, and ¹³C NMR spectroscopy. Both clay samples were saturated with Ca²⁺ prior to modification with HS using a sorption isotherm technique. Contact angles (CAs) of the obtained HS-clay complexes were determined using a static sessile drop method after drying the obtained HS-clay complexes in the form of a thin film.

Results and discussion

HS modification rendered both clays under study—kaolin and montmorillonite—more hydrophobic. In case of Ca-kaolin, the CA values increased from 27° (Ca-kaolin) up to 31°–32° (all HS-kaolin complexes) with no significant difference among the HS types used for modification. In the case of Ca-montmorillonite, the CA values increased from 41° (Ca-montmorillonite) up to 51°–83° with the following ascending trend for the humic types investigated: chernozem HS < coal HS < peat HS < sod-podzolic HS. This trend is in reverse to the degree of aromaticity of the HS, expressed as the content of aromatic carbon, and it is directly proportional to the molecular weight of each HS.

Conclusions

Application of a sessile drop method showed increased surface hydrophobicity of HS-modified clays. Much more substantial hydrophobization was observed for montmorillonite as compared to kaolin, which was explained by the differences in the sorption mechanism.

     

Auxin production by rhizobacteria was associated with improved yield of wheat (Triticum aestivum L.) under drought stress

Drought tolerant rhizobacteria of the genus Bacillus, Enterobacter, Moraxella and Pseudomonas colonizing the root system of Acacia arabica were isolated to mitigate the drought stress of wheat (Triticum aestivum L.). In vitro auxin production by rhizobacteria was quantified by Ultra High Performance Liquid Chromatography (UPLC). Analysis of the crude extracts detected the indole-3-acetic acid (IAA), indole-3-carboxylic acid (ICA) and indole-3-lactic acid (ILA). Highest IAA production of 25.9 µg ml^?1 was observed for Bacillus amyloliquefaciens S-134. Pot trials were conducted to evaluate the role of rhizobacteria to enhance the growth of wheat at different water regimes. At highest water stress i.e. 10% field capacity (FC), significant improvement of shoot length was observed with B. amyloliquefaciens S-134. For yield parameters, B. muralis D-5 and E. aerogenes S-10 recorded 34% and 1 fold increases for spike length and seed weight, over respective control at 10% FC. Mixed culture combinations of M-2 (B. thuringiensis S-26, D-2, B. amyloliquefaciens S-134, B. simplex D-11) and M-3 (M. pluranimalium S-29, B. simplex D-1, B. muralis D-5, P. stutzeri S-80) showed significant improvement for tillers and number of spikelets. In conclusion, application of the drought tolerant rhizobacteria can help to overcome productivity losses in drought prone areas.