Marine microbial genomics in Europe: current status and perspectives

The oceans are the Earth's largest ecosystem, covering 70% of our planet and providing goods and services for the majority of the world's population. Understanding the complex abiotic and biotic processes on the micro- to macroscale is the key to protect and sustain the marine ecosystem. Marine microorganisms are the ‘gatekeepers’ of the biotic processes that control the global cycles of energy and organic matter. A multinational, multidisciplinary approach, bringing together research on oceanography, biodiversity and genomics, is now needed to understand and finally predict the complex responses of the marine ecosystem to ongoing global changes. Such an integrative approach will not only bring better understanding of the complex interplay of the organisms with their environment, but will reveal a wealth of new metabolic processes and functions, which have a high potential for biotechnological applications. This potential has already been recognized by the European commission which funded a series of workshops and projects on marine genomics in the sixth and seventh framework programme. Nevertheless, there remain many obstacles to achieving the goal – such as a lack of bioinformatics tailored for the marine field, consistent data acquisition and exchange, as well as continuous monitoring programmes and a lack of relevant marine bacterial models. Marine ecosystems research is complex and challenging, but it also harbours the opportunity to cross the borders between disciplines and countries to finally create a rewarding marine research era that is more than the sum of its parts.     

In situ bacterial colonization of compacted bentonite under deep geological high-level radioactive waste repository conditions

Subsurface microorganisms are expected to invade, colonize, and influence the safety performance of deep geological spent nuclear fuel (SNF) repositories. An understanding of the interactions of subsurface dwelling microbial communities with the storage is thus essential. For this to be achieved, experiments must be conducted under in situ conditions. We investigated the presence of groundwater microorganisms in repository bentonite saturated with groundwater recovered from tests conducted at the Äspö underground Hard Rock Laboratory in Sweden. A 16S ribosomal RNA and dissimilatory bisulfite reductase gene distribution between the bentonite and groundwater samples suggested that the sulfate-reducing bacteria widespread in the aquifers were not common in the clay. Aerophilic bacteria could be cultured from samples run at ≤55°C but not at ≥67°C. Generally, the largely gram-negative groundwater microorganisms were poorly represented in the bentonite while the gram-positive bacteria commonly found in the clay predominated. Thus, bentonite compacted to a density of approximately 2 g cm^?3 together with elevated temperatures might discourage the mass introduction of the predominantly mesophilic granitic aquifer bacteria into future SNF repositories in the long run.     

Properties and applications of microbial D-amino acid oxidases: current state and perspectives

D-Amino acid oxidase (DAAO) is a biotechnologically relevant enzyme that is used in a variety of applications. DAAO is a flavine adenine dinucleotide-containing flavoenzyme that catalyzes the oxidative deamination of D-isomer of uncharged aliphatic, aromatic, and polar amino acids yielding the corresponding imino acid (which hydrolyzes spontaneously to the α-keto acid and ammonia) and hydrogen peroxide. This enzymatic activity is produced by few bacteria and by most eukaryotic organisms. In the past few years, DAAO from mammals has been the subject of a large number of investigations, becoming a model for the dehydrogenase-oxidase class of flavoproteins. However, DAAO from microorganisms show properties that render them more suitable for the biotechnological applications, such as a high level of protein expression (as native and recombinant protein), a high turnover number, and a tight binding of the coenzyme. Some important DAAO-producing microorganisms include Trigonopsis variabilis, Rhodotorula gracilis, and Fusarium solani. The aim of this paper is to provide an overview of the main biotechnological applications of DAAO (ranging from biocatalysis to convert cephalosporin C into 7-amino cephalosporanic acid to gene therapy for tumor treatment) and to illustrate the advantages of using the microbial DAAOs, employing both the native and the improved DAAO variants obtained by enzyme engineering.      

Retention of the Gram-negative bacterium SW8 on surfaces under conditions relevant to the subsurface environment: Effects of conditioning films and substratum nature

Abstract Shallow (5–13 m) and deep (35–65 m) groundwaters were evaluated for their ability to generate conditioning films which affect bacterial adhesion to natural (sandstone, shale, andesite) and man-made substrata (polypropylene, stainless steel). Water contact angles indicated that all water samples produced conditioning films. Most films modified retention of the nonmotile Gram-negative bacterium SW8, but attachment of the organism did not correlate with water contact angles. Each borewater produced conditioning films with a characteristic attachment profile of SW8. Films adsorbed from standing borewaters often retained SW8 in different numbers than coatings derived from pumped bores. Groundwater chemistry was very heterogeneous and microbiological data indicated the presence of a diverse aerobic and anaerobic microbial community. These results indicate that conditioning films derived from dissolved compounds may play a significant role in controlling the interaction of bacteria with substrata in the subsurface.     

Proteomic profiling of exosomes: current perspectives

Exosomes are 40-100 nm membrane vesicles of endocytic origin secreted by most cell types in vitro. Recent studies have shown that exosomes are also found in vivo in body fluids such as blood, urine, amniotic fluid, malignant ascites, bronchoalveolar lavage fluid, synovial fluid, and breast milk. While the biological function of exosomes is still unclear, they can mediate communication between cells, facilitating processes such as antigen presentation and in trans signaling to neighboring cells. Exosome-like vesicles identified in Drosophila (referred to as argosomes) may be potential vehicles for the spread of morphogens in epithelia. The advent of current MS-based proteomic technologies has contributed significantly to our understanding of the molecular composition of exosomes. In addition to a common set of membrane and cytosolic proteins, it is becoming increasingly apparent that exosomes harbor distinct subsets of proteins that may be linked to cell-type associated functions. The secretion of exosomes by tumor cells and their implication in the transport and propagation of infectious cargo such as prions and retroviruses such as HIV suggest their participation in pathological situations. Interestingly, the recent observation that exosomes contain both mRNA and microRNA, which can be transferred to another cell, and be functional in that new environment, is an exciting new development in the unraveling exosome saga. The present review aims to summarize the physical properties that define exosomes as specific cell-type secreted membrane vesicles.     

Oncoproteomics: current trends and future perspectives

Oncoproteomics is the application of proteomics technologies in oncology. Functional proteomics is a promising technique for the rational identification of biomarkers and novel therapeutic targets for cancers. Recent progress in proteomics has opened new avenues for tumor-associated biomarker discovery. With the advent of new and improved proteomics technologies, such as the development of quantitative proteomic methods, high-resolution, -speed and -sensitivity mass spectrometry and protein arrays, as well as advanced bioinformatics for data handling and interpretation, it is now possible to discover biomarkers that can reliably and accurately predict outcomes during cancer management and treatment. However, there are several difficulties in the study of proteins/peptides that are not inherent in the study of nucleic acids. New challenges arise in large-scale proteomic profiling when dealing with complex biological mixtures. Nevertheless, oncoproteomics offers great promise for unveiling the complex molecular events of tumorigenesis, as well as those that control clinically important tumor behaviors, such as metastasis, invasion and resistance to therapy. In this review, the development and advancement of oncoproteomics technologies for cancer research in recent years are expounded.     

聚乙烯塑料生物降解研究进展

聚乙烯(polyethylene,PE)塑料是全球通用合成树脂中产量最丰富的品种,也是最难降解的塑料之一,其在环境中大量积累已造成严重的生态污染。传统的垃圾填埋、堆肥和焚烧处理技术难以满足生态环境的保护要求,生物降解是解决塑料污染问题的一种生态友好、成本低廉、前景可期的方法。本文对PE塑料的化学结构、降解微生物的种类、降解酶和代谢途径等方面进行了综述,结合国内外PE塑料生物降解的前沿和热点问题,建议重点开展高效降解菌株筛选、人工合成菌群构建、降解酶的挖掘与改造等方面的研究,为PE塑料生物降解研究提供路径选择和理论借鉴。     

Super-SILAC: current trends and future perspectives

Stable isotope labeling with amino acids in cell culture (SILAC) has risen as a powerful quantification technique in mass spectrometry (MS)–based proteomics in classical and modified forms. Previously, SILAC was limited to cultured cells because of the requirement of active protein synthesis; however, in recent years, it was expanded to model organisms and tissue samples. Specifically, the super-SILAC technique uses a mixture of SILAC-labeled cells as a spike-in standard for accurate quantification of unlabeled samples, thereby enabling quantification of human tissue samples. Here, we highlight the recent developments in super-SILAC and its application to the study of clinical samples, secretomes, post-translational modifications and organelle proteomes. Finally, we propose super-SILAC as a robust and accurate method that can be commercialized and applied to basic and clinical research.     

Real-time monitoring and control of microbial bioprocesses with focus on the specific growth rate: current state and perspectives

Understanding the growth characteristics of microorganisms is an essential step in bioprocessing, not only because product formation may be growth-associated but also because they might influence cell physiology and thereby product quality. The specific growth rate, a key variable of many bioprocesses, cannot be measured directly and relies on the estimation through other measurable variables such as biomass, substrate, or product concentrations. Techniques for real-time estimation of the specific growth rate in microbial fed-batch cultures are discussed in the present paper. The advantages and limitations of different models and various monitoring techniques are discussed, highlighting the importance of the specific growth rate in the development of fast, reliable, and robust processes for the production of high-value products such as recombinant proteins.     

Exploration of the effects of high hydrostatic pressure on microbial growth, physiology and survival: perspectives from piezophysiology

The discovery of piezophiles (previously referred to as barophiles) prompted researchers to investigate the survival strategies they employ in high-pressure environments. There have been innovative high-pressure studies on biological processes applying modern techniques of genetics and molecular biology in bacteria and yeasts as model organisms. Recent advanced studies in this field have shown unexpected outcomes in microbial growth, physiology and survival when living cells are subjected to high hydrostatic pressure. The effects are conceptually dependent on the sign and magnitude of volume changes associated with any chemical reaction in the cells. Nevertheless, it is difficult to explain the pressure effects on complex metabolic networks based on a simple volume law. The challenges in piezophysiology are to discover whether the physiological responses of living cells to high pressure are relevant to their growth and to identify the critical factors in cell viability and lethality under high pressure from the general and organism-specific viewpoints.     

Biodegradation of sulfamethoxazole: current knowledge and perspectives

Antibiotic compounds, like sulfamethoxazole (SMX), have become a concern in the aquatic environment due to the potential development of antibacterial resistances. Due to extensive consumption, excretion and disposal, SMX has been frequently detected in wastewaters and surface waters. This has led to numerous studies investigating the nature of SMX, with many researchers focusing on the biodegradation and persistence of SMX during wastewater treatment and in the environment. This review provides a summary of recent developments, outlines the discrepancies in observations and results, and demonstrates the need for further research to determine optimal biological removal strategies for SMX and other antibiotics.