Microbial metabolomics: toward a platform with full metabolome coverage

Achieving metabolome data with satisfactory coverage is a formidable challenge in metabolomics because metabolites are a chemically highly diverse group of compounds. Here we present a strategy for the development of an advanced analytical platform that allows the comprehensive analysis of microbial metabolomes. Our approach started with in silico metabolome information from three microorganisms-Escherichia coli, Bacillus subtilis, and Saccharomyces cerevisiae-and resulted in a list of 905 different metabolites. Subsequently, these metabolites were classified based on their physicochemical properties, followed by the development of complementary gas chromatography-mass spectrometry and liquid chromatography-mass spectrometry methods, each of which analyzes different metabolite classes. This metabolomics platform, consisting of six different analytical methods, was applied for the analysis of the metabolites for which commercial standards could be purchased (399 compounds). Of these 399 metabolites, 380 could be analyzed with the platform. To demonstrate the potential of this metabolomics platform, we report on its application to the analysis of the metabolome composition of mid-logarithmic E. coli cells grown on a mineral salts medium using glucose as the carbon source. Of the 431 peaks detected, 235 (=176 unique metabolites) could be identified. These include 61 metabolites that were not previously identified or annotated in existing E. coli databases.     

Biotechnological production of gluconic acid: future implications

Gluconic acid (GA) is a multifunctional carbonic acid regarded as a bulk chemical in the food, feed, beverage, textile, pharmaceutical, and construction industries. The favored production process is submerged fermentation by Aspergillus niger utilizing glucose as a major carbohydrate source, which accompanied product yield of 98%. However, use of GA and its derivatives is currently restricted because of high prices: about US$ 1.20–8.50/kg. Advancements in biotechnology such as screening of microorganisms, immobilization techniques, and modifications in fermentation process for continuous fermentation, including genetic engineering programmes, could lead to cost-effective production of GA. Among alternative carbohydrate sources, sugarcane molasses, grape must show highest GA yield of 95.8%, and banana must may assist reducing the overall cost of GA production. These methodologies would open new markets and increase applications of GA. Authors’ contributions OVS and RK are the sole contributors of this original review article. This review is based upon the published research in the area of gluconic acid fermentation.     

气调包装生鲜冷却牛肉贮藏的微生物种类变化

在冷却牛肉的贮藏过程中,微生物的生长繁殖是导致其腐败变质的主要原因。在低温冷藏条件下,大多数微生物的生长受到抑制,但仍有一些嗜冷菌可以生长繁殖,从而对冷却肉的品质及人类健康安全造成威胁。因此,研究和分析生鲜冷却牛肉中菌群构成及其演替规律,不但具有重要的     

Cultivating the uncultured: limits, advances and future challenges

Since the invention of the Petri dish, there have been continuous efforts to improve efficiency in microbial cultivation. These efforts were devoted to the attainment for diverse growth conditions, simulation of in situ conditions and achievement of high-throughput rates. As a result, prokaryotes catalysing novel redox reactions as well as representatives of abundant, but not-yet cultured taxa, were isolated. Significant insights into microbial physiology have been made by studying the small number of prokaryotes already cultured. However, despite these numerous breakthroughs, microbial cultivation is still a low-throughput process. The main hindrance to cultivation is likely due to the prevailing lack of knowledge on targeted species. In this review, we focus on the limiting factors surrounding cultivation. We discuss several cultivation obstacles, including the loss of microbial cell–cell communication following species isolation. Future research directions, including the refinement of culture media, strategies based on cell–cell communication and high-throughput innovations, are reviewed. We further propose that a combination of these approaches is urgently required to promote cultivation of uncultured species, thereby dawning a new era in the field.     

Microbial fuel cells meet with external resistance

The influence of external load on the composition of the anodic biofilm microbial community and biomass yield was investigated in a microbial fuel cell fed with glucose and domestic wastewater was used as source of electrogens. Denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR) amplified 16S rRNA gene fragments revealed distinct differences in anodic bacterial communities formed at the anode of each MFC operated under a different external load. These results implied that in an MFC, electrogenic bacteria were enriched under higher current densities, i.e., low external load, and were able to sustain better current and effluent quality. The influence of the external resistance applied to the MFCs during formation of the bacterial communities from sewage wastewater was shown to have no significant effect on power performance of the MFCs nor to have a significant influence on their anodic activity with both glucose and brewery wastewater as fuel. As expected, current generation, COD removal and the biomass yield were all directly influenced by the external load. Significantly, when operated under lower external load, the biomass yield in the MFC was less than that in conventional anaerobic digestion (i.e., control).     

活性污泥微生物组：去除污浊，只留清淡

活性污泥法诞生一百多年来,在污水处理特别是城市污水处理中发挥了不可替代的作用。活性污泥微生物是去除污染物包括新型有机和无机污染物的关键角色,活性污泥微生物组为微生物分离培养、功能鉴定和生态互作等方面的研究带来新的活力。     

Ground cover and slope exposure effects on micro- and mesobiota in forest soils

The interrelation of Alpine topography with the micro − and mesobiota is still poorly understood. We investigated the effects of ground cover type and slope exposure on the soil microbial biomass (double-stranded DNA, dsDNA) and abundances (real time PCR, qPCR); hydrolytic enzyme activities; and enchytraeid community structure in top soils (2.5-cm increments depth) in subalpine forests in the Italian Alps. Dominant ground covers were grass, moss, litter and woody debris at the north- and the south-facing slopes. The autochthonous soil microbiota (bacteria, fungi and archaea) was quantified by qPCR in the extracellular (eDNA) and intracellular fraction (iDNA) of the total soil DNA pool. A higher eDNA/iDNA ratio indicative of lower microbial activity was recorded in the deepest layer of the grass plots at the north-facing slope. This can be related to a lower degradation of eDNA and/or to an accumulation of eDNA with increasing depth as a result of leaching. The exposure effect was enzyme-specific and higher activities occurred under woody debris primarily at the south-facing slope. These plots also showed a higher nutrient content and a greater microbial biomass assessed as dsDNA yields. Total microannelid abundance was elevated on north-facing slopes on account of strong acidity indicator species. This was related to soil pH being one unit lower compared to the south-facing slope. The thickness of the organic layer (OL + OF + OH) was elevated at the north-facing slope due to a considerably thicker OH-horizon. The vast majority of microannelids at this slope occurred in the organic layer, while at south exposure they were almost evenly distributed between the organic layer and the mineral soil (A-horizon). Exposure was found to be more determinative for the composition of microannelid assemblages than the ground cover type.     

The effect of internal capacitance on power quality and energy efficiency in a tubular microbial fuel cell

The pseudo-capacitive behaviour of a high surface area carbon veil electrode in a tubular microbial fuel cell (MFC) was investigated as a mechanism to enhance power quality and energy efficiency. Accumulated charge and energy from the anodic biofilm after prolonged open circuit times (1–120 min) were compared against equivalent periods of steady state loading (R = 100–3000 Ω). A significant difference in the amount of accumulated charge with different loads was observed, resulting in 1.051 C (R = 100 Ω) compared to 0.006 C (R = 3 kΩ). The automated application of short open and closed circuit (0.5–10 s) cycles resulted in an increase of power/current production (closed circuit alone), but presented lower efficiency considering entire open and closed period. The cumulative charge on the carbon veil electrode with biofilm was 39,807 C m⁻² at 100 Ω. Electrochemical Impedance Spectroscopy (EIS) showed that the Helmholtz layer presented a double layer capacitance of more than ten times the biofilm on electrode. The results indicate that the capacitive behaviour could be utilized to increase the power quality, i.e. its availability/applicability with respect to the operation of low power consuming devices.     

Luminometric measurement of population activity of genetically modified Pseudomonas fluorescens in the soil

Genetically modified cells of Pseudomonas fluorescens, chromosomally marked with genes for bioluminescence, were inoculated into sterile soil microcosms. During incubation for 90 days, viable cell concentration did not change significantly but light output, measured by luminometry, decreased, indicating reduced metabolic activity due to lack of substrates. Amendment with nutrients resulted in parallel increases in both luminescence and dehydrogenase activity. Luminometry therefore enables rapid monitoring of the activity of populations of luminescence-marked microbial inocula in the soil, with greater sensitivity and selectivity than traditional techniques.     

Facile synthesis and antimicrobial activity of CdS-Ag2S nanocomposites

In this study CdS-Ag₂S nanocomposites for antibacterial activity were synthesized via facile co-precipitation method using PVP as capping agent. The prepared nanocomposites have particle sizes in the range of 50–100 nm (SEM) and PVP addition has good influence on the morphology of nanocomposites. The antimicrobial activity of pure Ag₂S, CdS and CdS-Ag₂S composites was evaluated against Pseudomonas aeruginosa, Staphylococcus aureus and Escherichia coli. The results demonstrate that antibacterial activity was significantly improved due to increasing ratio of CdS into CdS-Ag₂S nanocomposites in comparison to pure Ag₂S and CdS.