On the Stability of Clathrate Hydrates Encaging Polar Guest Molecules: Contrast in the Hydrogen Bonds of Methylamine and Methanol Hydrates

Abstract

The stability of clathrate hydrates encaging highly polar guests has been investigated in order to explain the experimental observation that some amines form clathrate hydrates but alcohols act as inhibitor to hydrate formation. We choose methylamine and methanol as guest species and examine the stable structure, at which the total potential energy has a minimum value. At the local minima of those two hydrates, the potential energies of water-water and guest-water, and their hydrogen bonded networks are compared. It is found that methanol does not retain the host lattice structure, while the host-network structure is kept in the presence of methylamine. It is shown that the difference in the magnitude of the partial charge on the hydrogen atom between the hydroxyl and amino groups plays a much more significant role on the stability of both clathrate hydrates than the difference in molecular geometry. This is supported from the result of a methylamine-like model that has the same partial charges on the atoms in the hydrophilic site as methanol.     

The Stability of Clathrate Hydrates: Temperature Dependence of Dissociation Pressure in Xe and Ar Hydrate

Abstract

The thermodynamic stability of clathrate hydrates I and II encaging xenon or argon has been investigated by examining the temperature dependence of the dissociation pressure. The evaluation of the stability is made based on the generalized van der Waals and Platteeuw theory developed by Tanaka and Kiyohara [J. Chem. Phys. 98, 4098 (1993)]. In the new treatment, the free energy of formation of hydrates in equilibrium with ice is calculated by taking the coupling of the host lattice vibrations with guests into consideration. The predicted dissociation pressures of Xe and Ar hydrates agree well with experiments in higher temperature range. A poor agreement between experiment and calculation for Ar clathrate hydrate at low temperature is improved by the use of a quantum mechanical partition function for a harmonic oscillator in evaluating the free energy difference between ice and empty hydrate.     

Vibrational spectra of deuterated methane and water molecules in structure I clathrate hydrate from ab initio MD simulation

The deuteration of the lattice molecules in clathrate hydrates is a widely used experimental technique to clearly separate the vibrational modes. However, the effect of the deuteration on the vibrational spectra and molecular motions is not fully understood. Since the guest–host coupling may change the vibrational spectra, a detailed analysis of the vibrational spectra of deuterated clathrate hydrate is significant in the understanding of the mechanism of the vibrational shift. In this study, the vibrational spectra of the deuterated methane hydrates were calculated by ab initio molecular dynamics simulation. The intramolecular vibrational frequency of the methane in D₂O lattice and deuterated methane in H₂O lattice was calculated and compared with the pure methane hydrate. The bending, rocking and overtone of the bending mode was also reported. The effect of coupling of the rattling motions of guest and host molecules on the vibrational spectra was revealed.     

The thermal properties of binary structure sI clathrate hydrate from molecular dynamics simulation

In this work, we present temperature dependence of lattice parameter and normalised lattice parameter in the atmospheric pressure and 120 bar and also pressure dependence of unit cell volume and normalised unit cell volume at 150 and 250?K for variety guests with different size, polarity and guest–host hydrogen bonding capability such as trimethylene oxide (TMO), ethylene oxide (EO), formaldehyde (FA), cyclobutane (CB), cyclopropane (CP) and ethane (Et) in the large cages with CH₄ in small cages of sI clathrate hydrates by molecular dynamics simulations. The obtained values of lattice parameters for the guest species are compatible with the experimental values. These clathrate hydrates are simulated with TIP4P/ice four-site water potential. Herein, isobaric thermal expansivity and isothermal compressibility are calculated at a temperature range of 50–250?K and a wide pressure range. These structural properties have been compared for guests which they are isoelectronic and have similar masses but with different size and polarity. We use molecular dynamics simulations to relate microscopic guest properties, like guest–host hydrogen bonding to macroscopic sI clathrate hydrate properties. The temperature dependence of thermodynamic properties such as constant-volume and constant-pressure heat capacity is presented in the atmospheric pressure for these guest species.     

Explore mediated co-varying dynamics in microbial community using integrated local similarity and liquid association analysis

Background

Discovering the key microbial species and environmental factors of microbial community and characterizing their relationships with other members are critical to ecosystem studies. The microbial co-occurrence patterns across a variety of environmental settings have been extensively characterized. However, previous studies were limited by their restriction toward pairwise relationships, while there was ample evidence of third-party mediated co-occurrence in microbial communities.

Methods

We implemented and applied the triplet-based liquid association analysis in combination with the local similarity analysis procedure to microbial ecology data. We developed an intuitive scheme to visualize those complex triplet associations along with pairwise correlations. Using a time series from the marine microbial ecosystem as example, we identified pairs of operational taxonomic units (OTUs) where the strength of their associations appeared to relate to the values of a third “mediator” variable. These “mediator” variables appear to modulate the associations between pairs of bacteria.

Results

Using this analysis, we were able to assess the OTUs’ ability to regulate its functional partners in the community, typically not manifested in the pairwise correlation patterns. For example, we identified Flavobacteria as a multifaceted player in the marine microbial ecosystem, and its clades were involved in mediating other OTU pairs. By contrast, SAR11 clades were not active mediators of the community, despite being abundant and highly correlated with other OTUs. Our results suggested that Flavobacteria are more likely to respond to situations where particles and unusual sources of dissolved organic material are prevalent, such as after a plankton bloom. On the other hand, SAR11s are oligotrophic chemoheterotrophs with inflexible metabolisms, and their relationships with other organisms may be less governed by environmental or biological factors.

Conclusions

By integrating liquid association with local similarity analysis to explore the mediated co-varying dynamics, we presented a novel perspective and a useful toolkit to analyze and interpret time series data from microbial community. Our augmented association network analysis is thus more representative of the true underlying dynamic structure of the microbial community. The analytic software in this study was implemented as new functionalities of the ELSA (Extended local similarity analysis) tool, which is available for free download (http://bitbucket.org/charade/elsa).

     

Marine microbial natural products in antifouling coatings

Ecological problems associated with current antifouling technologies have increased interest in the natural strategies that marine organisms use to keep their surfaces clean and free from fouling. Bacteria isolated from living surfaces in the marine environment have been shown to produce chemicals that are potential antifoulants. Active compounds from the cells and culture supernatant of two bacterial strains, FS‐55 and NudMB50–11, isolated from surface of the seaweed, Fucus serratus, and the nudibranch, Archidoris pseudoargus, respectively, were extracted using solid phase extraction. The extracts were combined with acrylic base paint resin and assayed for antifouling activity by measuring their ability to inhibit the growth of fouling bacteria. These formulations were found to be active against fouling bacteria isolated from marine surfaces. The formulation of antifouling paints that incorporate marine microbial natural products is reported here for the first time. This is a significant advance towards the production of an environmentally friendly antifouling paint that utilises a sustainable supply of natural biodegradable compounds.     

Reactivity of Iron Minerals in the Seabed Toward Microbial Reduction – A Comparison of Different Extraction Techniques

Abstract

Dissimilatory iron reduction and sulfate reduction are the most important processes for anaerobic mineralization of organic carbon in marine sediments. The thermodynamics and kinetics of microbial Fe(III) reduction depend on the characteristics of the Fe(III) minerals, which influence the potential of Fe(III)-reducers to compete with sulfate-reducers for common organic substrates. In the present study, we tested different methods to quantify and characterize microbially reducible Fe(III) in sediments from a transect in Kongsfjorden, Svalbard, using different standard sequential endpoint extractions and time-course extractions with either ascorbate or a Fe(III)-reducing microbial culture. Similar trends of increasing ‘reactive Fe’ content of the sediment along the fjord transect were found using the different extraction methods. However, the total amount of ‘reactive Fe’ extracted differed between the methods, due to different Fe dissolution mechanisms and different targeted Fe fractions. Time-course extractions additionally provided information on the reactivity and heterogeneity of the extracted Fe(III) minerals, which also impact the favorability for microbial reduction. Our results show which fractions of the existing Fe extraction protocols should be considered ‘reactive’ in the sense of being favorable for microbial Fe(III) reduction, which is important in studies on early diagenesis in marine sediments.     

Microbial Allyl Rearrangement and Resolution of Acetates of Unsaturated Cyclic Terpene Alchols by Pseudomonas sp. NOF-5 Strain

Microbial hydrolysis of the acetates of unsaturated cyclic terpene alcohols by Pseudomonas sp. NOF-5 isolated from soil was investigated. (±)-trans-Carveyl acetate ((±)-trans-3) was enantio-selectively hydrolyzed with NOF-5 strain to give ( – )-trans-carveol (( – )-trans-2 of 86.6% optical purity). However, the hydrolysis of (±)-cis-3 was less enantioselective, while (±)-piperitylacetate ((±)-6, a cis and trans mixture) was hydrolyzed to give the ( – )-trans- and ( – )-cis-piperitols (( – )- trans-5 and ( – )-cis-5) in a poor optical yield. In this case, other tert-alcohols, ( + )-trans- and ( – )- ds-2-p-menthen-1-ols ((±)-trans-7 and ( – )-cis-7), were also produced. Furthermore, microbial and enzymic allyl rearrangements of ( + )-trans-6 and ( – )-trans-verbenylacetate (( – )-trans-11) were studied. Biological treatment of (+)-trans-6 and ( – )-trans-11 with NOF-5 or its esterase gave (+)-trans- and (-)-cis-1 and ( + )-cis-3-pinen-2-ol (( + )-cis-12), respectively.     

南海东海岛近海固氮细菌多样性及对菜心的促生作用

海洋固氮细菌在自然界氮循环中发挥着重要作用,筛选和开发海洋固氮促生的菌种资源,对于生物菌肥的开发应用和农业生产具有重要意义。[目的]研究海洋固氮细菌的生物多样性及对陆地作物的促生作用,筛选优良的植物根际促生菌株。[方法]通过形态特征、生理生化试验和16S rRNA基因序列比对进行菌属鉴定;将解磷、解钾、产蛋白酶和纤维素酶等性能优良的菌株作为菜心盆栽试验的组合菌液,探究对菜心能否起促生作用。[结果]本研究从南海东海岛的海岛沉积物中筛选出18株固氮菌,分布在6个属9种,不动杆菌属4株,假交替单胞菌属1株,芽孢杆菌属8株,嗜冷杆菌属1株,海单胞菌属1株,交替单胞菌属3株。菜心幼苗经过组合菌剂的浇灌,在茎高、茎粗、最大叶宽和最大叶长4个指标均表明对菜心有显著的促生作用。其中,以芽孢杆菌属和不动杆菌属的菌株在菜心的生长过程中起关键的促进作用,对菜心的促生性能最佳。[结论]南海近海具有种类丰富多样的固氮细菌,以芽孢杆菌属和不动杆菌属的菌株促生作用最为显著,具有开发成微生物菌肥的潜力,为优良的海洋促生微生物菌种资源的定向利用及蔬菜的无公害生产提供重要依据。     

Where in the world do bacteria experience oxidative stress?

Reactive oxygen species – superoxide, hydrogen peroxide and hydroxyl radicals – have long been suspected of constraining bacterial growth in important microbial habitats and indeed of shaping microbial communities. Over recent decades, studies of paradigmatic organisms such as Escherichia coli, Salmonella typhimurium, Bacillus subtilis and Saccharomyces cerevisiae have pinpointed the biomolecules that oxidants can damage and the strategies by which microbes minimize their injuries. What is lacking is a good sense of the circumstances under which oxidative stress actually occurs. In this MiniReview several potential natural sources of oxidative stress are considered: endogenous ROS formation, chemical oxidation of reduced species at oxic–anoxic interfaces, H₂O₂ production by lactic acid bacteria, the oxidative burst of phagocytes and the redox-cycling of secreted small molecules. While all of these phenomena can be reproduced and verified in the lab, the actual quantification of stress in natural habitats remains lacking – and, therefore, we have a fundamental hole in our understanding of the role that oxidative stress actually plays in the biosphere.     

Trichoderone, a novel cytotoxic cyclopentenone and cholesta-7, 22-diene-3β, 5α, 6β-triol, with new activities from the marine-derived fungus Trichoderma sp.

The historical paradigm of the deep ocean as a biological ‘desert’ has shifted to one of a ‘rainforest’ owing to the isolation of many novel microbes and their associated bioactive compounds. To explore the potential of the bioactive compounds in our marine microbial natural product library, we screened it for the selective cytotoxicity of six different cancer cell lines to human normal lung fibroblast cell line HLF. The crude extract from a marine-derived fungal strain showed notable selectivity against cancer cell lines. For a bioactivity-guided fractionation and purification, a novel cyclopentenone, (−)-(4R ^*, 5S ^*)-3-ethyl-4,5-dihydroxycyclopent-2-enone (1, trichoderone), and a known compound with new activity, cholesta-7,22- diene-3β,5α,6β-triol (2), were identified from a marine Trichoderma sp. that was isolated from the deep sea sediment of the South China Sea. Their structures were determined by NMR and MS data analyses. Trichoderone (1) displayed potent cytotoxicity against a panel of six cancer cell lines, whereas it did not show much cytotoxicity against normal human lung fibroblast cell line HLF even at a concentration of 7.02 mM. The selectivity index (SI) value for 1 was greater than 100. To the best of our knowledge, both compounds were isolated from marine fungi for the first time. They also exhibited bioactivities against HIV protease and Taq DNA polymerase. Optimization of the compounds would shed new light on treating cancer and infectious diseases.     

纳帕海高原湿地噬藻体g20基因系统发育多样性分析

【背景】噬藻体是感染蓝藻的病毒,是水生系统的重要组成部分。它们对宿主种群死亡率有重要影响,是控制蓝藻水华生消的潜在因子,对蓝藻群落结构的调控具有重要意义。大量研究揭示了海洋和淡水环境中噬藻体的高度多样性,但目前对高原湿地中噬藻体的多样性知之甚少。【目的】阐明我国纳帕海高原湿地噬藻体g20基因的遗传多样性,为进一步开展高原湿地微生物资源及其生态功能研究提供理论基础。【方法】采集雨季的水体样品,以衣壳蛋白基因g20为标记基因,利用特异性引物Cps1和Cps8对其进行PCR扩增,得到26条不同的g20基因有效序列,并将其与其他生境中g20基因序列进行主坐标分析和系统发育分析。【结果】与其他海洋和淡水的噬藻体序列相比,纳帕海高原湿地中噬藻体的序列与其他稻田序列更为相近;但也存在部分序列单独聚簇,这可能为纳帕海高原湿地中独有的噬藻体类型。【结论】表明该地区的噬藻体较丰富,并具有一定的独特性。     

Estimates of biogenic methane production rates in deep marine sediments at Hydrate Ridge, Cascadia margin

Methane hydrate found in marine sediments is thought to contain gigaton quantities of methane and is considered an important potential fuel source and climate-forcing agent. Much of the methane in hydrates is biogenic, so models that predict the presence and distribution of hydrates require accurate rates of in situ methanogenesis. We estimated the in situ methanogenesis rates in Hydrate Ridge (HR) sediments by coupling experimentally derived minimal rates of methanogenesis to methanogen biomass determinations for discrete locations in the sediment column. When starved in a biomass recycle reactor, Methanoculleus submarinus produced ca. 0.017 fmol methane/cell/day. Quantitative PCR (QPCR) directed at the methyl coenzyme M reductase subunit A gene (mcrA) indicated that 75% of the HR sediments analyzed contained <1,000 methanogens/g. The highest numbers of methanogens were found mostly from sediments <10 m below seafloor. By considering methanogenesis rates for starved methanogens (adjusted to account for in situ temperatures) and the numbers of methanogens at selected depths, we derived an upper estimate of <4.25 fmol methane produced/g sediment/day for the samples with fewer methanogens than the QPCR method could detect. The actual rates could vary depending on the real number of methanogens and various seafloor parameters that influence microbial activity. However, our calculated rate is lower than rates previously reported for such sediments and close to the rate derived using geochemical modeling of the sediments. These data will help to improve models that predict microbial gas generation in marine sediments and determine the potential influence of this source of methane on the global carbon cycle.     

Quantifying CaCO3 Microprecipitates Within Developing Surface Mats of Marine Stromatolites Using GIS and Digital Image Analysis

The unique geochemical coupling of organic molecules and mineral CaCO₃ provides a fluorescence signature detectable using conventional confocal scanning laser microscopy (CSLM). The surface microbial mats of open-water marine stromatolites (Bahamas) exist in a continuum of states ranging from a Type 1 (i.e., nonlithifying) to Type 2 (i.e., lithified micritic laminae present) to Type 3 (i.e., fused grain layer). An approach was developed here, that utilizes geographical information systems (GIS) and digital image analysis, coupled with CSLM to estimate concentrations of calcium carbonate precipitates in developing marine stromatolites. We propose that the area occupied by particles within each image can be used to estimate concentrations of precipitates. Fluorescent polymeric microbeads and bacteria were used to calibrate the approach. We used this approach to demonstrate that CaCO₃ precipitates in lithifying layers were quantifiable and significantly different (p < 0.0001) from those in nonlithifying layers. The approach provided a useful tool for the unambiguous assessment of relative changes in microbial precipitates occurring over small ( μ m to mm) spatial scales, and that characterize the formation of lithified layers (micritic laminae) in open-water marine stromatolites.     

Diversity and distribution of a key sulpholipid biosynthetic gene in marine microbial assemblages

Sulphoquinovosyldiacylglycerols (SQDG) are polar sulphur‐containing membrane lipids, whose presence has been related to a microbial strategy to adapt to phosphate deprivation. In this study, we have targeted the sqdB gene coding the uridine 5′‐diphosphate‐sulphoquinovose (UDP‐SQ) synthase involved in the SQDG biosynthetic pathway to assess potential microbial sources of SQDGs in the marine environment. The phylogeny of the sqdB‐coding protein reveals two distinct clusters: one including green algae, higher plants and cyanobacteria, and another one comprising mainly non‐photosynthetic bacteria, as well as other cyanobacteria and algal groups. Evolutionary analysis suggests that the appearance of UDP‐SQ synthase occurred twice in cyanobacterial evolution, and one of those branches led to the diversification of the protein in members of the phylum Proteobacteria. A search of homologues of sqdB‐proteins in marine metagenomes strongly suggested the presence of heterotrophic bacteria potential SQDG producers. Application of newly developed sqdB gene primers in the marine environment revealed a high diversity of sequences affiliated to cyanobacteria and Proteobacteria in microbial mats, while in North Sea surface water, most of the detected sqdB genes were attributed to the cyanobacterium Synechococcus sp. Lipid analysis revealed that specific SQDGs were characteristic of microbial mat depth, suggesting that SQDG lipids are associated with specific producers.     

Who is where in the Plastisphere,and why does it matter?

To fully understand how plastic is affecting the ocean, we need to understand how marine life interacts directly with it. Besides their ecological relevance, microbes can affect the distribution, degradation and transfer of plastics to the rest of the marine food web. From amplicon sequencing and scanning electron microscopy, we know that a diverse array of microorganisms rapidly associate with plastic marine debris in the form of biofouling and biofilms, also known as the “Plastisphere.” However, observation of multiple microbial interactions in situ, at small spatial scales in the Plastisphere, has been a challenge. In this issue of Molecular Ecology Resources, Schlundt et al. apply the combination labelling and spectral imaging – fluorescence in situ hybridization to study microbial communities on plastic marine debris. The images demonstrate the colocalization of abundant bacterial groups on plastic marine debris at a relatively high taxonomic and spatial resolution while also visualizing biofouling of eukaryotes, such as diatoms and bryozoans. This modern imaging technology provides new possibilities to address questions regarding the ecology of marine microbes on plastic marine debris and describe more specific impacts of plastic pollution in the marine food webs.     

中国北部湾光裸方格星虫可培养微生物的分离鉴定及其活性代谢物产生菌筛选

【目的】本研究从北部湾海域光裸方格星虫(Sipunculus nudus)肠道中分离鉴定可培养微生物,并对筛选菌株的代谢物活性进行研究,为后续开发和利用光裸方格星虫肠道微生物代谢产物提供理论支持。【方法】通过微生物培养、菌株分离纯化和16S rRNA基因序列分析,分析鉴定湛江、北海、防城港三地光裸方格星虫肠道可培养微生物;采用透明圈法、可见分光光度法、平板打孔法等对产胞外活性代谢物的菌株进行筛选和活性分析。【结果】中国北部湾不同海域光裸方格星虫肠道可培养微生物包括弧菌属(Vibrio)、希瓦氏菌属(Shewanella)、假交替单胞菌属(Pseudoalteromonas)、发光杆菌属(Photobacterium)和芽孢杆菌属(Bacillus)等12个细菌属。弧菌属(Vibrio)是3个地区样本共有的优势菌群。具有产胞外水解蛋白酶、壳聚糖酶、多糖以及抑菌活性等能力的菌株主要来自假交替单胞菌属(Pseudoalteromonas)、发光杆菌属(Photobacterium)和芽孢杆菌属(Bacillus)。【结论】中国北部湾不同海域光裸方格星虫肠道可培养微生物在属的种类上存在显著性差异,且光裸方格星虫肠道菌株具有产生多种胞外活性代谢物的能力,是一种良好的海洋活性代谢物来源。     

东南极达尔克冰川-183m深处冰层融水细菌多样性研究

【目的】目前对于南极冰层微生物研究较少,而且研究手段多为纯培养和高通量测序,对于其中的微生物群落多样性仍知之甚少。本研究拟研究东南极达尔克冰川冰层中微生物群落组成。【方法】采用纯培养法、单细胞分选和高通量测序3种方法对东南极达尔克冰川冰层微生物进行研究,探究该生境中微生物的群落组成。【结果】从达尔克冰川中分离出10门19纲94属。其中,变形菌门(Proteobacteria)为优势菌门,α-变形菌纲(Alphaproteobacteria)为优势纲,鞘氨醇单胞菌属(Sphingomonas)为优势属,结果显示冰层中存在较为丰富的微生物多样性。其中,纯培养法分离出25株细菌。单细胞分选方法分离得到24株细菌。高通量测序共得到55 183条序列,聚类出116个操作分类单元(operational taxonomic unit, OTU)。3种研究方法得出的优势种群不尽相同。通过单细胞分选和纯培养法共获得7株细菌,它们与数据库最近源16S rRNA基因序列的相似度小于98.65%,其中有2株菌株与最近源16S rRNA基因序列的相似度小于95.00%,推测可能有2个潜在新属,5个潜在新种。【结论】本研究通过纯培养法、单细胞分选以及高通量测序3种方法对东南极达尔克冰川冰层微生物多样性进行研究发现,该生境中细菌多样性复杂。对比3种方法,其各有优势和局限性。这意味着结合使用多种研究方法研究微生物多样性,可获得更加全面的微生物群落组成。研究结果可为挖掘南极微生物资源提供数据基础。     

Biochemical characteristics of cellulose and a green alga degradation by Gilvimarinus japonicas 12-2T,and its application potential for seaweed saccharification

ABSTRACT

Cellulose is one of the major constituents of seaweeds, but reports of mechanisms in microbial seaweed degradation in marine environment are limited, in contrast to the multitude of reports for lignocellulose degradation in terrestrial environment. We studied the biochemical characteristics for marine cellulolytic bacterium Gilvimarinus japonicas 12-2^T in seaweed degradation. The bacterial strain was found to degrade green and red algae, but not brown algae. It was shown that the bacterial strain employs various polysaccharide hydrolases (endocellulase, agarase, carrageenanase, xylanase, and laminarinase) to degrade seaweed polysaccharides. Electrophoretic analysis and peptide sequencing showed that the major protein bands on the electrophoresis gel were homologous to known glucanases and glycoside hydrolases. A seaweed hydrolysate harvested from the bacterial culture was found useful as a substrate for yeasts to produce ethanol. These findings will provide insights into possible seaweed decomposition mechanisms of Gilvimarinus, and its biotechnological potential for ethanol production from inedible seaweeds.