Successful cryopreservation of Quercus robur plumules

Successful cryopreservation of Q. robur germplasm as plumules (i.e. shoot apical meristems of embryos) is described in this paper. After excision from the recalcitrant seeds and preliminary storage in 0.5 M sucrose solution (18 h), the plumules were subjected to cryoprotection (in 0.75 M sucrose, followed by 1.0 M sucrose and 1.5 M glycerol solutions), and next to desiccation (over silica gel or in nitrogen gas) and cooling (in slush at –210°C or in vials filled with liquid nitrogen, LN, −196°C), and were then cryostored for 24 h. High percentage of survival was obtained after cryostorage (21–67%, depending on pretreatment, assessed in vitro by greening plumules that increased in size). Desiccation of plumules over silica gel resulted in significantly higher survival after cryopreservation (58%) in comparison with desiccation in nitrogen gas (29%), with regrowth (shoots with leaves) 5–18%. The extent of plumule desiccation was comparable in both methods, in which drying of plumules for 20 min decreased the water content to 0.5–0.6 g H₂O g⁻¹ dry weight before LN exposure. The type of LN exposure did not significantly influence plumule survival and regrowth after cryostorage. Plumules isolated from acorns of four provenances survived cryostorage after cryoprotection followed by desiccation over silica gel and direct cooling in vials with LN (survival 51–76%, regrowth 8–20%). Normal plants developed from the recovered shoots after rooting. The presented protocol for Q. robur plumule cryopreservation may offer a potential approach for establishing germplasm conservation in gene banks for Quercus species.     

Different biogeographic patterns of prokaryotes and microbial eukaryotes in epilithic biofilms

Microbial biogeography studies expend much effort in determining whether environmental selection or stochastic processes related to dispersal are more important in shaping community composition. While both types of factors are possibly influential, it is tacitly assumed that protists, or microbial eukaryotes in general, behave biogeographically as prokaryotes because of their small physical size. However, direct evidence for this in exactly the same environment and at the same phylogenetic depth is lacking. In this study, we compared the structure of both prokaryotic and eukaryotic components of microbial communities forming biofilms on mineral substrates in different geographic locations at the level of small-subunit (SSU) rRNA-based operational taxonomic units (OTUs). These microbial communities are subjected to strong environmental selection and contain significant proportions of extremophilic microorganisms adapted to desiccation and UV radiation. We find that the nature of the substrate as well as climatic variables and geography influences microbial community structure. However, constrained correspondence analyses and distance-decay curves showed that, whereas the substrate type was the most significant factor structuring bacterial communities, geographic location was the most influential factor for microbial eukaryote communities. Biological explanations implying a higher dispersal success for bacteria combined with more mobile lifestyles for predatory protists may underlie these different prokaryote versus microbial eukaryote biogeographic patterns.     

Fossilization of Acidophilic Microorganisms

This study examines fossil microorganisms found in iron-rich deposits in an extreme acidic environment, the Tinto River in SW Spain. Both electron microscopy (SEM and TEM) and non-destructive in situ microanalytical techniques (EDS, EMP and XPS) were used to determine the role of permineralization and encrustation in preserving microorganisms forming biofilms in the sediments. Unicellular algae were preserved by silica permineralization of their cell walls. Bacterial biofilms were preserved as molds by epicellular deposition of schwertmannite around them. In the case of fungi and filamentous algae, we observed permineralization of cell structures by schwertmannite in the sediments. The extracellular polymeric matrix around the cells was also preserved through permineralization of the fibrillar component. The process of permineralization and deposition of iron-rich precipitates present in the acidic waters of Rio Tinto served to preserve many microfossils in an oxidizing environment, in which organic compounds would not normally be expected to persist. Studies of microbial fossil formation mechanisms in modern extreme environments should focus on defining criteria to identify inorganic traces of microbial life in past environments on Earth or other planets.     

Studies on Biosynthesis on Biotin by Microorganisms

The accumulation of biotin-vitamers in the culture media of a large number of microorganisms (about 700 strains) was studied. The contents of the biotin-vitamers were quantitatively determined by microbiological assays with Lactobacillus arabinosus and Saccharomyces cerevisiae.

It was found that large amounts of biotin-vitamers were accumulated by various microorganisms such as Streptomyces, molds and bacteria, and that the yield of biotin-vitamers was enhanced by the addition of pimelic acid or azelaic acid to the media. It was also found that the main portion of the vitamers accumulated by many microorganisms did not support the growth of Lactobacillus arabinosus, while it did support that of Saccharomyces cerevisiae. The small amounts of true biotin were observed in the culture media of various Streptomyces and molds, but hardly in the culture media of bacteria.

The identification of biotin-vitamers accumulated by various microorganisms is described, and the distribution of the vitamers in microorganisms is also described.

The results presented in this paper show that the main component of the vitamers accumulated by many microorganisms is identified as desthiobiotin by anion exchange column chromatography, paper chromatography and chemical analysis. Small amounts of fraction B (unidentified vitamers) and Fraction D (biotin) were also detected in the culture media of various molds and Streptomyces. However, these fractions were not observed in the culture media of any bacteria tested.

It was also found that large amounts of an unknown biotin-vitamer was accumulated by various bacteria. The vitamer was avidin-uncombinable, and, from the paper electrophoretic studies, it was assumed that the vitamer might be an analogue of pelargonic acid.     

Alternative methods for sampling and preservation of photosynthetic pigments and tocopherols in plant material from remote locations

Current methods for the study of pigments involve freezing in liquid nitrogen and storage at −80°C or lyophilization until HPLC analysis. These requirements greatly restrict ecophysiological research in remote areas where such resources are hardly available. We aimed to overcome such limitations by developing several techniques not requiring freezing or lyophilization. Two species with contrasting foliar characteristics (Olea europaea and Taraxacum officinale) were chosen. Seven preservation methods were designed, optimized and tested in a field trial. These protocols were compared with a control immediately frozen after collection. Pigments and tocopherols were analysed by HPLC. Main artefacts were chlorophyll epimerization or phaeophytinization, carotenoid isomerization, altered de-epoxidation index and tocopherol degradation. Among all methods, sample desiccation in silica gel provides robust samples (pigment composition was unaffected by storage time or temperature) and almost unaltered pigment profiles, except for a shift in epoxidation state. Although liquid nitrogen freezing and subsequent lyophilization or freezer storage were preferred, when these facilities are either not available or not suitable for long-distance transport, desiccation with silica gel, passive extraction in acetone and/or storage of fresh samples in water vapour saturated atmospheres enable a complete pigment characterization. Silica gel is advisable for long-term sample conservation.     

Avoidance of protein oxidation correlates with the desiccation and radiation resistance of hot and cold desert strains of the cyanobacterium Chroococcidiopsis

To investigate the relationship between desiccation and the extent of protein oxidation in desert strains of Chroococcidiopsis a selection of 10 isolates from hot and cold deserts and the terrestrial cyanobacterium Chroococcidiopsis thermalis sp. PCC 7203 were exposed to desiccation (air-drying) and analyzed for survival. Strain CCMEE 029 from the Negev desert and the aquatic cyanobacterium Synechocystis sp. PCC 6803 were further investigated for protein oxidation after desiccation (drying over silica gel), treatment with H₂O₂ up to 1 M and exposure to γ-rays up to 25 kGy. Then a selection of desert strains of Chroococcidiopsis with different survival rates after prolonged desiccation, as well as Synechocystis sp. PCC 6803 and Chroococcidiopsis thermalis sp. PCC 7203, were analyzed for protein oxidation after treatment with 10 and 100 mM of H₂O₂. Results suggest that in the investigated strains a tight correlation occurs between desiccation and radiation tolerance and avoidance of protein oxidation.

     

A common garden experiment with Porphyra umbilicalis (Rhodophyta) evaluates methods to study spatial differences in the macroalgal microbiome

While macroalgal microbiomes are the focus of many recent studies, there is little information about microbial spatial diversity across the thallus. Reliance on field material makes it difficult to discern whether recovered microbiomes belong to the host or its epiphytes, and technical comparisons of macroalgal samples for microbial studies are needed. Here, we use a common garden approach that avoids the problem of epiphytes, particularly at holdfasts, to examine the microbiome of Porphyra umbilicalis (strain Pum1). We used the V6 hypervariable region of the 16S rDNA with Illumina HiSeq sequencing and developed PNA clamps to block recovery of organelle V6 sequences. The common garden approach allowed us to determine differences in the microbiome at the holdfast versus blade margin. We found a notable increase in the relative abundance of Planctomycetes and Alphaproteobacteria at the holdfast, particularly of the possible symbiont Sulfitobacter sp. Nonadjacent 1.5 cm² samples of blade margin had microbiomes that were not statistically different. The most abundant phylum in the overall microbiome was Proteobacteria, followed by Bacteroidetes. Because phycologists often work in remote sites, we compared three stabilization and preparation techniques and found silica gel desiccation/bead‐beating and flash‐freezing/lyophilization/bead‐beating to be interchangeable. Core taxa (≥0.1% of sequences) across treatments were similar and accounted for ≥95% of all sequences. Finally, statistical conclusions for all comparisons were the same, regardless of which microbial community analysis tool was used: mothur or minimum entropy decomposition.     

Lipid biomarkers, pigments and cyanobacterial diversity of microbial mats across intertidal flats of the arid coast of the Arabian Gulf (Abu Dhabi, UAE)

Variations in morphology, fatty acids, pigments and cyanobacterial community composition were studied in microbial mats across intertidal flats of the arid Arabian Gulf coast. These mats experience combined extreme conditions of salinity, temperature, UV radiation and desiccation depending on their tidal position. Different mat forms were observed depending on the topology of the coast and location. The mats contained 63 fatty acids in different proportions. The increased amounts of unsaturated fatty acids (12–39%) and the trans/cis ratio (0.6–1.6%) of the cyanobacterial fatty acid n- 18:1ω9 in the higher tidal mats suggested an adaptation of the mat microorganisms to environmental stress. Chlorophyll a concentrations suggested lower cyanobacterial abundance in the higher than in the lower intertidal mats. Scytonemin concentrations were dependent on the increase in solar irradiation, salinity and desiccation. The mats showed richness in cyanobacterial species, with Microcoleus chthonoplastes and Lyngbya aestuarii morphotypes as the dominant cyanobacteria. Denaturing gradient gel electrophoresis patterns suggested shifts in the cyanobacterial community dependent on drainage efficiency and salinity from lower to higher tidal zones. We conclude that the topology of the coast and the variable extreme environmental conditions across the tidal flat determine the distribution of microbial mats as well as the presence or absence of different microorganisms.     

Diversity and novelty of the gut microbial community of an herbivorous rodent (Neotoma bryanti)

Mammalian herbivores host diverse microbial communities to aid in fermentation and potentially detoxification of dietary compounds. However, the microbial ecology of herbivorous rodents, especially within the largest superfamily of mammals (Muroidea) has received little attention. We conducted a preliminary inventory of the intestinal microbial community of Bryant’s woodrat (Neotoma bryanti), an herbivorous Muroidea rodent. We collected woodrat feces, generated 16S rDNA clone libraries, and obtained sequences from 171 clones. Our results demonstrate that the woodrat gut hosts a large number of novel microorganisms, with 96% of the total microbial sequences representing novel species. These include several microbial genera that have previously been implicated in the metabolism of plant toxins. Interestingly, a comparison of the community structure of the woodrat gut with that of other mammals revealed that woodrats have a microbial community more similar to foregut rather than hindgut fermenters. Moreover, their microbial community was different to that of previously studied herbivorous rodents. Therefore, the woodrat gut may represent a useful resource for the identification of novel microbial genes involved in cellulolytic or detoxification processes.     

Experimental fossilization of the Thermophilic Gram-positive Bacterium Geobacillus SP7A: A Long Duration Preservation Study

Recent experiments to fossilize microorganisms using silica have shown that the fossilization process is far more complex than originally thought; microorganisms not only play an active role in silica precipitation but may also remain alive while silica is precipitating on their cell wall. To better understand the mechanisms that lead to the preservation of fossilized microbes in recent and ancient rocks, we experimentally silicified a Gram-positive bacterium, Geobacillus SP7A, over a period of five years. The microbial response to experimental fossilization was monitored with the use of LIVE/DEAD staining to assess the structural integrity of the cells during fossilization. It documented the crucial role of silicification on the preservation of the cells and of their structural integrity after several years. Electron microscopy observations showed that initial fossilization of Gram-positive bacteria was extremely rapid, thus allowing very good preservation of Geobacillus SP7A cells. A thick layer of silica was deposited on the outer surface of cell walls in the earliest phase of silicification before invading the cytoplasmic space. Eventually, the cell wall was the only recognizable feature. Heavily mineralized cells thus showed morphological similarities with natural microfossils found in the rock record.     

Identification of Major Facilitator Transporters Involved in Cellulase Production during Lactose Culture of Trichoderma reesei PC-3-7

A compound showing antimicrobial activity was isolated from an oil-macerated garlic extract by silica gel column chromatography and preparative TLC. On basis of the results of NMR and MS analyses, it was identified as Z-4,5,9-trithiadeca-1,6-diene-9-oxide (Z-10-devinylajoene; Z-10-DA). Z-10-DA exhibited a broad spectrum of antimicrobial activity against such microorganisms as gram-positive and gram-negative bacteria and yeasts. The antimicrobial activity of Z-10-DA was comparable to that of Z-ajoene, but was superior to that of E-ajoene. Z-10-DA and Z-ajoene are different in respect of substitution of the allyl group by the methyl group flanking a sulfinyl group. This result suggests that substitution by the methyl group would also be effective for the inhibition of microbial growth.     

Desiccation of sediments affects assimilate transport within aquatic plants and carbon transfer to microorganisms

• With the projected increase in drought duration and intensity in future, small water bodies, and especially the terrestrial–aquatic interfaces, will be subjected to longer dry periods with desiccation of the sediment. Drought effects on the plant–sediment microorganism carbon continuum may disrupt the tight linkage between plants and microbes which governs sediment carbon and nutrient cycling, thus having a potential negative impact on carbon sequestration of small freshwater ecosystems. However, research on drought effects on the plant–sediment carbon transfer in aquatic ecosystems is scarce. We therefore exposed two emergent aquatic macrophytes, Phragmites australis and Typha latifolia, to a month‐long summer drought in a mesocosm experiment.
• We followed the fate of carbon from leaves to sediment microbial communities with ¹³CO₂ pulse labelling and microbial phospholipid‐derived fatty acid (PLFA) analysis.
• We found that drought reduced the total amount of carbon allocated to stem tissues but did not delay the transport. We also observed an increase in accumulation of ¹³C‐labelled sugars in roots and found a reduced incorporation of ¹³C into the PLFAs of sediment microorganisms.
• Drought induced a switch in plant carbon allocation priorities, where stems received less new assimilates leading to reduced starch reserves whilst roots were prioritised with new assimilates, suggesting their use for osmoregulation. There were indications that the reduced carbon transfer from roots to microorganisms was due to the reduction of microbial activity via direct drought effects rather than to a decrease in root exudation or exudate availability.

     

Characterisation and metabolic studies of Saccharomyces cerevisiae and Kluyveromyces fragilis by flow microcalorimetry

The use of microcalorimetry in the routine identification of microorganisms is critically discussed and assessed. By use of flow microcalorimetric studies on Saccharomyces cerevisiae and Kluyveromyces fragilis the role of physical parameters and that of oxygen tension are discussed. The conclusion reached is that identification of microorganisms by microcalorimetry and subsequent discussion of metabolic events revealed by the thermogram, except under restrictive conditions, is inappropriate. However flow microcalorimetry, in contrast to batch microcalorimetry which has been used in the published material on microorganism identification, may allow characterization of yeasts suitable for particular industrial processes.     

Cryopreservation of protocorm-like bodies (PLBs) of <Emphasis Type="Italic">Phalaenopsis bellina</Emphasis> (Rchb.f.) christenson by encapsulation-dehydration

Protocorm-like bodies (PLBs) of Phalaenopsis bellina were successfully cryopreserved by the encapsulation-dehydration approach. Various stages in obtaining successful cryopreservation using this method were optimized. Encapsulated PLBs precultured in half-strength MS medium supplemented with 0.75 M sucrose for 3 days exhibited the highest viability in terms of 2,3,5-triphenyltetrazoliumchloride (TTC) reduction. The amount of sucrose in the PLBs after incubation in different concentrations of sucrose for different periods of time determined by HPLC. The highest sucrose concentration was 7 mg/g of PLBs for the PLBs treated with 0.75 M sucrose for 3 days as compared to the control which had only 1 mg/g sucrose. After sucrose preculture, the PLBs were subjected to desiccation using one of two methods. Desiccation using silica gel was more efficient in reducing PLBs moisture content. After 6 h of desiccation, PLBs desiccated using laminar air flow had 43.5% moisture content while for those desiccated using silica gel had 32% moisture content. PLBs desiccated to different moisture contents were plunged into LN. After storage in LN the encapsulated PLBs were re-warmed. Two weeks after re-warming PLBs viability was determined by TTC reduction and re-growth assessed. Encapsulated PLBs precultured with 0.75 M sucrose for 3 days followed by desiccated using silica gel for 5 h resulting in a moisture content of 39% lead to the highest post re-warming viability in terms of TTC reduction (46.6% of control PLBs) and 30% re-growth.     

The interphase technique: a simple method of cell immobilization in gel-beads

A variation of the emulsion techniques for microbial cell immobilization by encapsulation in gel beads is described. The utilized gels are silica gel or natural polymers like agar, agarose, phytagel or carrageenan. This technique utilizes the interfacial tension that is formed between two liquids of different polarity. The gel-beads are easily obtained and homogeneous in size.     

A silica sands-based method for faithful analysis of microbial communities and DNA isolation from a wide range of species

A silica sands-based method has been developed to isolate high quality genomic DNAs from cells of animals, plants and microorganisms, such as Hemisalanx prognathus, Spinacia oleracea, Pichia pastoris, Bacillus licheniformis and Escherichia coli. To the best of our knowledge, no DNA isolation method has so wide application until now. In addition, this method and a commercially available kit were compared in analysis of microbial communities using high-throughput 16s rDNA sequencing. As a result, the silica sands-based method was found to be even more efficient in isolating genomic DNA from gram-positive bacteria than the kit, indicating that it would become a very valuable choice to faithfully reflect the composition of microbial communities.     

基于流式细胞仪高通量分选的深海微生物单细胞培养

【目的】建立适用于海洋微生物的流式细胞分选与高通量单细胞培养的方法,通过该方法从印度洋深海样品中分离微生物纯培养菌株。【方法】利用流式细胞仪单细胞分选功能,以前向角(FSC)和侧向角(SSC)散射光信号代替荧光信号作为分选逻辑,对深海水体和沉积物样品中微生物进行单细胞高通量分选和培养。【结果】确定了流式细胞分选的区域和条件,发现所建立方法适于分离海洋水体微生物,而不是沉积物微生物。从印度洋深海水体样品中获得61个潜在新菌株,分属于6个新属种,占分离菌株总数的26.29%,其16S rRNA基因序列与已培养的模式菌株相似性为89.79%–95.37%。【结论】本研究所建立的方法有助于提高发现海洋微生物新物种的效率,获得更多新的海洋微生物资源。     

Monitoring of accelerated naphthalene-biodegradation in a bioaugmented soil slurry

The effect of microbial inoculation on the mineralization of naphthalene in a bioslurry treatment was evaluated in soil slurry microcosms. Inoculation by Pseudomonas putida G7 carrying the naphthalene dioxygenase (nahA) gene resulted in rapid mineralization of naphthalene, whereas indigenous microorganisms in the PAH-contaminated soil required a 28 h adaptation period before significant mineralization occurred. The number of nahA-like gene copies increased in both the inoculated and non-inoculated soil as mineralization proceeded, indicating selection towards naphthalene dioxygenase producing bacteria in the microbial community. In addition, 16S rRNA analysis by denaturing gradient gel electrophoresis (DGGE) analysis showed that significant selection occurred in the microbial community as a result of biodegradation. However, the indigenous soil bacteria were not able to compete with the P. putida G7 inoculum adapted to naphthalene biodegradation, even though the soil microbial community slightly suppressed naphthalene mineralization by P. putida G7.     

Stability of plasmid DNA of Escherichia coli C600 and Alcaligenes eutrophus CH34 inoculated in desiccating soil

Abstract Molecular methods based on detection of specific DNA sequences are increasingly used to monitor microbial strains and communities in soils. Here, we report that desiccation of soil, a condition that frequently occurs in nature, may contribute considerably to dissimilarity between DNA levels and colony forming units of introduced bacteria. Three types of soil samples were supplemented with Escherichia coli or Alcaligenes eutrophus suspensions and incubated at 30°C in the presence or absence of dehydrating silica gel. Alternatively, seeded soil samples were desiccated by freeze-drying. At regular time points cells and total DNA were extracted and colony forming units and plasmid DNA were determined, respectively. These analyses showed that the decrease of the number of colony forming units was faster in desiccating than in control soil. Both in desiccating and in control soil, plasmid DNA levels were more stable than culturable counts. Long-term incubation experiments showed that in desiccating soil but not in control soil E. coli plasmid DNA remained intact and biologically active for at least 17 days after disappearance of E. coli culturable counts.