Under the sea: microbial life in volcanic oceanic crust

Exploration of the microbiology in igneous, 'hard rock' oceanic crust represents a major scientific frontier. The igneous crust harbours the largest aquifer system on Earth, most of which is hydrologically active, resulting in a substantial exchange of fluids, chemicals and microorganisms between oceanic basins and crustal reservoirs. Study of the deep-subsurface biosphere in the igneous crust is technically challenging. However, technologies have improved over the past decade, providing exciting new opportunities for the study of deep-seated marine life, including in situ and cross-disciplinary experimentation in microbiology, geochemistry and hydrogeology. In this Progress article, we describe the recent advances, available technology and remaining challenges in the study of the marine intraterrestrial microbial life that is harboured in igneous oceanic crust.     

Marine Dadabacteria exhibit genome streamlining and phototrophy-driven niche partitioning

The remineralization of organic material via heterotrophy in the marine environment is performed by a diverse and varied group of microorganisms that can specialize in the type of organic material degraded and the niche they occupy. The marine Dadabacteria are cosmopolitan in the marine environment and belong to a candidate phylum for which there has not been a comprehensive assessment of the available genomic data to date. Here in, we assess the functional potential of the marine pelagic Dadabacteria in comparison to members of the phylum that originate from terrestrial, hydrothermal, and subsurface environments. Our analysis reveals that the marine pelagic Dadabacteria have streamlined genomes, corresponding to smaller genome sizes and lower nitrogen content of their DNA and predicted proteome, relative to their phylogenetic counterparts. Collectively, the Dadabacteria have the potential to degrade microbial dissolved organic matter, specifically peptidoglycan and phospholipids. The marine Dadabacteria belong to two clades with apparent distinct ecological niches in global metagenomic data: a clade with the potential for photoheterotrophy through the use of proteorhodopsin, present predominantly in surface waters up to 100 m depth; and a clade lacking the potential for photoheterotrophy that is more abundant in the deep photic zone.Subject terms: Water microbiology, Marine microbiology, Metagenomics, Microbial ecology     

Genome-wide expression analysis in Corynebacterium glutamicum using DNA microarrays

DNA microarray technology has become an important research tool for microbiology and biotechnology as it allows for comprehensive DNA and RNA analyses to characterize genetic diversity and gene expression in a genome-wide manner. DNA microarrays have been applied extensively to study the biology of many bacteria including Mycobacterium tuberculosis, but only recently have they been used for the related high-GC Gram-positive Corynebacterium glutamicum, which is widely used for biotechnological amino acid production. Besides the design and generation of microarrays as well as their use in hybridization experiments and subsequent data analysis, recent applications of DNA microarray technology in C. glutamicum including the characterization of ribose-specific gene expression and the valine stress response will be described. Emerging perspectives of functional genomics to enlarge our insight into fundamental biology of C. glutamicum and their impact on applied biotechnology will be discussed.     

Developments in aquatic microbiology.

Major discoveries in marine microbiology over the past 4-5 decades have resulted in the recognition of bacteria as a major biomass component of marine food webs. Such discoveries include chemosynthetic activities in deep-ocean ecosystems, survival processes in oligotrophic waters, and the role of microorganisms in food webs coupled with symbiotic relationships and energy flow. Many discoveries can be attributed to innovative methodologies, including radioisotopes, immunofluorescent-epifluorescent analysis, and flow cytometry. The latter has shown the key role of marine viruses in marine system energetics. Studies of the components of the "microbial loop" have shown the significance of various phagotrophic processes involved in grazing by microinvertebrates. Microbial activities and dissolved organic carbon are closely coupled with the dynamics of fluctuating water masses. New biotechnological approaches and the use of molecular biology techniques still provide new and relevant information on the role of microorganisms in oceanic and estuarine environments. International interdisciplinary studies have explored ecological aspects of marine microorganisms and their significance in biocomplexity. Studies on the origins of both life and ecosystems now focus on microbiological processes in the marine environment. This paper describes earlier and recent discoveries in marine (aquatic) microbiology and the trends for future work, emphasizing improvements in methodology as major catalysts for the progress of this broadly-based field.     

The types of bioreactors used for shoots and embryos

Plant regenerated organs such as shoots, bulbs, microtubers, corms, embryos, etc. have been successfully proliferated in the bioreactor. The use of a bioreactor leads to the development of technology suitable for large scale plant propagation. The basic construction and characteristics of various types of bioreactor systems are reviewed in relation to shoot and embryo cultures. A pilot scale 500 liter bioreactor system was applied to the production of large scale Stevia rebaudiana shoots.Abbreviations DW dry weight - EC electrical conductivity - FW fresh weight - ORP oxidation-reduction potential     

Wireless bioreactor for anaerobic cultivation of bacteria

Anaerobic cultivation methods of bacteria are indispensable in microbiology. One methodology is to cultivate the microbes in anaerobic enclosure with oxygen-adosrbing chemicals. Here, we report an electronic extension of such strategy for facultative anaerobic bacteria. The technique is based a bioreactor with entire operation including turbidity measurement, fluidic mixing, and gas delivery in an anaerobic enclosure. Wireless data transmission is employed and the anaerobic condition is achieved with gas pack. Although the technique is not meant to completely replace the anaerobic chamber for strict anaerobic bacteria, it provides a convenient way to bypass the cumbersome operation in anaerobic chamber for facultative anaerobic bacteria. Such a cultivation strategy is demonstrated with Escherichia coli with different carbon sources and hydrogen as energy source.     

When Pasteurian Science Went to Sea: The Birth of Marine Microbiology

In the late nineteenth century, French naturalists were global leaders in microbial research. Louis Pasteur advanced sterilization techniques and demonstrated that dust particles in the air could contaminate a putrefiable liquid. Pasteur’s discoveries prompted a new research program for the naturalists of the Talisman and Travailleur expeditions: to recover uncontaminated water and mud samples from the deep sea. French naturalists Adrien Certes and Paul Regnard both independently conducted experiments to address the question of whether microorganisms inhabited the oceans and whether organic material in the deep sea was subject to decomposition. The experiments of Certes and Regnard have largely been omitted from histories of microbiology and marine science. However, an examination of their work is crucial for understanding the context in which marine microbiology first developed. At the end of the nineteenth century, marine microbiology emerged from the disciplinary melding of terrestrial microbial ecology, experimental physiology, and the then-nascent field of deep-sea biology.     

Biodiversity characterisation and hydrodynamic consequences of marine fouling communities on marine renewable energy infrastructure in the Orkney Islands Archipelago,Scotland, UK

As part of ongoing commitments to produce electricity from renewable energy sources in Scotland, Orkney waters have been targeted for potential large-scale deployment of wave and tidal energy converting devices. Orkney has a well-developed infrastructure supporting the marine energy industry; recently enhanced by the construction of additional piers. A major concern to marine industries is biofouling on submerged structures, including energy converters and measurement instrumentation. In this study, the marine energy infrastructure and instrumentation were surveyed to characterise the biofouling. Fouling communities varied between deployment habitats; key species were identified allowing recommendations for scheduling device maintenance and preventing spread of invasive organisms. A method to measure the impact of biofouling on hydrodynamic response is described and applied to data from a wave-monitoring buoy deployed at a test site in Orkney. The results are discussed in relation to the accuracy of the measurement resources for power generation. Further applications are suggested for future testing in other scenarios, including tidal energy.     

转基因动物克隆技术的应用及生物反应器的建立

利用转基因克隆技术实现外源基因的导入宿主染色体基因组内稳定整合,并能遗传给后代,已在基因表达与调控的理论研究、人类遗传病动物模型的建立、药用蛋白的生产、抗病育种、人类移植用的器官的研究等方面得到广泛应用。转基因动物的研究与应用也已经成为21世纪生命科学领域最活跃、最具有实际应用价值的方向之一,尤其是作为生物反应器和医学上为人类提供所用器官方面,其经济价值和社会效益将是不可估量。在查阅大量近年来国内外相关资料的基础上,本文以转基因动物克隆为中心,对转基因动物克隆所采用显微注射技术、核移植技术、基因打靶与真核BAC表达载体制备等主要研究技术,以及转基因动物克隆在异种器官移植、构建生物反应器等方面的应用进行了综合性论述与分析,同时阐述了各种转基因技术的优点与缺点,以其为转基因动物克隆研究提供理论基础与技术支撑。     

The new tools revolutionizing Vibrio science

As microbiologists we live in exciting times. A variety of technical and conceptual developments, particularly in the last decade have revolutionized the field of microbiology, redrawing the landscape, and entirely redefining what is possible. Perhaps this paradigm shift is no more apparent than in the study of vibrios. The family Vibrionaceae are almost unique as a group of bacteria to study in microbiology: they are genomically, phylogenetically and functionally diverse yet a distinct group of environmental bacteria encompassing important human and animal pathogens as well as non-pathogenic species such as ecologically critical symbionts. Sensitive to physiochemical stimuli, they are among the fasting replicating bacteria studied, capable of responding almost immediately to favourable environmental conditions such as those afforded by climate warming. Characterized by an unusual double chromosome and frequently carrying numerous cryptic plasmids – their genomes are often pockmarked with insertion elements, transposons, prophages and integrases – paying testament to past genomic promiscuity. With a strong affinity for environmental niches in freshwater and marine systems, they are among the most numerous bacteria present in our oceans, coasts and freshwater environments. As such they offer something for almost anyone interested in microbiology and represent an excellent example of field of microbiology that has benefitted hugely by advances across a gamut of disciplines – not just microbiological – but encompassing genomics, genetics, oceanography, ecological, earth observations sciences and data visualization, among others. We will briefly outline some of the most exciting, innovative and translational scientific advances that are currently being applied to these ecologically, environmentally and clinically important bacteria.     

Use of flow cytometric methods for single-cell analysis in environmental microbiology

Flow cytometry (FCM) is emerging as an important tool in environmental microbiology. Although flow cytometry applications have to date largely been restricted to certain specialized fields of microbiology, such as the bacterial cell cycle and marine phytoplankton communities, technical advances in instrumentation and methodology are leading to its increased popularity and extending its range of applications. Here we will focus on a number of recent flow cytometry developments important for addressing questions in environmental microbiology. These include (i) the study of microbial physiology under environmentally relevant conditions, (ii) new methods to identify active microbial populations and to isolate previously uncultured microorganisms, and (iii) the development of high-throughput autofluorescence bioreporter assays.     

海洋环境中难培养微生物的寡营养培养

海洋中存在着丰富的微生物资源, 但迄今为止能够在实验室培养的微生物却不到1%, 而且能够通过培养得到的环境优势种更少, 这成为当代环境微生物学研究和海洋资源开发的最大障碍。过去十多年来, 通过不断改进培养方法和检测手段, 发明了许多新颖独特的技术, 提高了培养效率。特别是通过海洋微生物的寡营养培养技术, 分离并命名了一些难培养微生物, 给予人们极大的启发。海洋微生物资源的可持续性开发和利用, 是21世纪人类发展的重要方向, 是我们研究海洋微观世界的基础, 值得微生物学界同仁的共同关注。     

Bioreactor landfill technology in municipal solid waste treatment: An overview

In recent years, due to an advance in knowledge of landfill behaviour and decomposition processes of municipal solid waste, there has been a strong thrust to upgrade existing landfill technologies for optimizing these degradation processes and thereafter harness a maximum of the useful bioavailable matter in the form of higher landfill gas generation rates. Operating landfills as bioreactors for enhancing the stabilization of wastes is one such technology option that has been recently investigated and has already been in use in many countries. A few full-scale implementations of this novel technology are gaining momentum in landfill research and development activities. The publication of bioreactor landfill research has resulted in a wide pool of knowledge and useful engineering data. This review covers leachate recirculation and stabilization, nitrogen transformation and corresponding extensive laboratory- and pilot-scale research, the bioreactor landfill concept, the benefits to be derived from this bioreactor landfill technology, and the design and operational issues and research trends that form the basis of applied landfill research.     

Perspective: Microfluidic applications in microbiology

The application of microfluidics technology to microbiology research is an excellent platform for the analysis of microorganisms and their nucleic acids. This technology combines engineering, physics, chemistry, biology and computing to control the devices. In this perspective we discuss how microfluidics can be applied to microbiological research and used in diagnostic applications. We also summarize advantages and limitations of this technology, as well as highlight some recent microbiological applications.     

Marine sponges as microbial fermenters

The discovery of phylogenetically complex, yet highly sponge-specific microbial communities in marine sponges, including novel lineages and even candidate phyla, came as a surprise. At the same time, unique research opportunities opened up, because the microorganisms of sponges are in many ways more accessible than those of seawater. Accordingly, we consider sponges as microbial fermenters that provide exciting new avenues in marine microbiology and biotechnology. This review covers recent findings regarding diversity, biogeography and population dynamics of sponge-associated microbiota, and the data are discussed within the larger context of the microbiology of the ocean.     

Electrical stimulation of human embryonic stem cells: Cardiac differentiation and the generation of reactive oxygen species

Exogenous electric fields have been implied in cardiac differentiation of mouse embryonic stem cells and the generation of reactive oxygen species (ROS). In this work, we explored the effects of electrical field stimulation on ROS generation and cardiogenesis in embryoid bodies (EBs) derived from human embryonic stem cells (hESC, line H13), using a custom-built electrical stimulation bioreactor. Electrical properties of the bioreactor system were characterized by electrochemical impedance spectroscopy (EIS) and analysis of electrical currents. The effects of the electrode material (stainless steel, titanium-nitride-coated titanium, titanium), length of stimulus (1 and 90 s) and age of EBs at the onset of electrical stimulation (4 and 8 days) were investigated with respect to ROS generation. The amplitude of the applied electrical field was 1 V/mm. The highest rate of ROS generation was observed for stainless steel electrodes, for signal duration of 90 s and for 4-day-old EBs. Notably, comparable ROS generation was achieved by incubation of EBs with 1 nM H₂O₂. Cardiac differentiation in these EBs was evidenced by spontaneous contractions, expression of troponin T and its sarcomeric organization. These results imply that electrical stimulation plays a role in cardiac differentiation of hESCs, through mechanisms associated with the intracellular generation of ROS.     

Microbioreactor arrays with parametric control for high-throughput experimentation

A scalable array technology for parametric control of high-throughput cell cultivations is demonstrated. The technology makes use of commercial printed circuit board (PCB) technology, integrated circuit sensors, and an electrochemical gas generation system. We present results for an array of eight 250 microl microbioreactors. Each bioreactor contains an independently addressable suite that provides closed-loop temperature control, generates feed gas electrochemically, and continuously monitors optical density. The PCB technology allows for the assembly of additional off-the-shelf components into the microbioreactor array; we demonstrate the use of a commercial ISFET chip to continuously monitor culture pH. The electrochemical dosing system provides a powerful paradigm for reproducible gas delivery to high-density arrays of microreactors. Growth data are presented for Escherichia coli cultured in the array with varying microaerobic conditions using electrochemically generated oxygen. Additionally, we present data on carbon dioxide generation for pH dosing.     

Squalene production in the cell suspension cultures of Indian sandalwood (<Emphasis Type="Italic">Santalum album</Emphasis> L.) in shake flasks and air lift bioreactor

Squalene has emerged as a specialty chemical being important in nutraceutical, pharmaceutical, vaccine and cosmetic industries due to the anticancer, antioxidant, skin hydrating, immune stimulating and emollient activities. The main source of squalene is shark liver oil, but alternate sources are being sought to secure sustainable supply of squalene and conserve the marine sources. The present work was carried out with the aim of generation of this compound in the cell suspension cultures of sandalwood, a medicinally important plant rich in sesquiterpenes. To achieve this, highly proliferating cell lines of sandalwood were generated by medium optimization. Accumulation of squalene in the cells was studied in a time dependent manner in shake flasks and bioreactor. In shake flask experiments, a significant amount of 3.2 mg/g dry weight was accumulated in 6 weeks of culture whereas the cells performed much better in bioreactor where squalene accumulation was found to be 5.5 mg/g dry weight in 4 weeks. Enzymes of lower terpenoid pathway namely hydroxy-3 methylglutaryl-coenzyme A reductase, farnesyl diphosphate synthase and squalene synthase showed a positive correlation with the product accumulation as evident from GC analysis of the reaction products and terpenoids accumulated. The findings of present work describe a high potential for commercial application since the marine sources have pollution concerns, vegetal sources are limited and the compound offers great hope in prevention of human chronic diseases like cancer. To our knowledge this is the first report about squalene generation in medicinally important sandalwood plant cell suspensions.