Recovery of oleate‐inhibited anaerobic digestion by addition of simple substrates

Four laboratory‐scale anaerobic digesters were deliberately and completely inhibited by feeding sodium oleate to such an extent that no methane was produced from the digesters. Three of them were then respectively fed glucose, cysteine or glucose and cysteine along with sodium oleate, while the remaining digester was operated as control reactor and continued to be fed with only sodium oleate. Oligonucleotide probes ARC915, EUB338, MB310, MC1109, MSMX860 and MG1200 were used to target and quantify specific groups of microbes, Archaea, Bacteria, Methanobacteriales, Methanococcales, Methanosarcinaceae, and Methanomicrobiaceae, Methanocorpusculaceae and Methanoplanaceae respectively throughout the operation of reactors. Addition of glucose and/or cysteine assisted with the recovery of methane production from oleate inhibition. The addition of glucose was more effective than cysteine, while the combination of glucose and cysteine was most effective on this recovery. The addition of these substrates also stimulated the degradation of oleate in the reactor. Daily methane production from the digesters correlated negatively with residual oleate concentration and positively with Archaea counts. Addition of glucose was more effective than cysteine on increasing the number of Archaea cells, while cysteine was more effective in increasing the number of Bacteria cells. All microbial populations recovered to pre‐inhibition levels within 40 days when glucose together with cysteine was fed. Copyright © 2006 Society of Chemical Industry     

Assessment of nitrification in groundwater filters for drinking water production by qPCR and activity measurement

In groundwater treatment for drinking water production, the causes of nitrification problems and the effectiveness of process optimization in rapid sand filters are often not clear. To assess both issues, the performance of a full-scale groundwater filter with nitrification problems and another filter with complete nitrification and pretreatment by subsurface aeration was monitored over nine months. Quantitative real-time polymerase chain reaction (qPCR) targeting the amoA gene of bacteria and archaea and activity measurements of ammonia oxidation were used to regularly evaluate water and filter sand samples. Results demonstrated that subsurface aeration stimulated the growth of ammonia-oxidizing prokaryotes (AOP) in the aquifer. Cell balances, using qPCR counts of AOP for each filter, showed that the inoculated AOP numbers from the aquifer were marginal compared with AOP numbers detected in the filter. Excessive washout of AOP was not observed and did not cause the nitrification problems. Ammonia-oxidizing archaea grew in both filters, but only in low numbers compared to bacteria. The cell-specific nitrification rate in the sand and backwash water samples was high for the subsurface aerated filter, but systematically much lower for the filter with nitrification problems. From this, we conclude that incomplete nitrification was caused by nutrient limitation.     

Identification and antioxidative properties of transglycosylated puerarins synthesised by an archaeal maltogenic amylase

Puerarin is helpful for the prevention and treatment of various cardiovascular diseases. However, its insolubility often limits its uses. Transglycosylation reaction between 1% puerarin and 10% β-CD was catalysed by maltogenic amylase from archaeon Thermofilum pendens (TfMA) at 0.2 U/mg β-CD, 90 °C and pH 5.5, for 1 h in order to obtain puerarin glucosides of high water solubility. Seven puerarin derivatives with different number of additional α-glucosyl in the reaction solution were identified by HPLC–UV–MS analysis. Although less than puerarin, the transglycosylated puerarins still fully maintained their antioxidant activities, assessed by a radical scavenging test and a reducing power assay. Therefore, the transglycosylated puerarins exhibit a greater potential to be developed into new medicines and foods. This is the first report on the flavonoids glycosylation using the transglycosylation activity of archaeal maltogenic amylase.     

Microorganisms in landfill bioreactors for accelerated stabilization of solid wastes

Landfill bioreactors (LBRs) with management of leachate and biogas have presented numerous advantages such as accelerated stabilization of solid wastes, reduced amount of leachate, and in situ leachate treatment. Such advantages have minimized environmental risks, have allowed extension of the useful life of the landfill site, and have fostered cost reduction. LBRs of three types have been developed using both anaerobic and aerobic modes: anaerobic, aerobic, and hybrid. Microorganisms in landfills cause various reactions related with organic fractions and heavy metals. Such functions have been stimulated in LBRs by recirculation of leachate with or without aeration. To date, most studies of microorganisms in LBRs have analyzed bacteria and archaea based on 16S rRNA genes and have analyzed fungi based on 18S rRNA genes from a taxonomical viewpoint. Indicator genes for specific functions in LBRs such as nitrification, denitrification, and methane production have also been monitored. The population dynamics of microorganisms in LBRs have been partially clarified, but the obtained data remain limited because of highly heterogeneous features of solid wastes inside LBRs. Systematic monitoring of microorganisms should be established to improve LBR performance.     

Lipidomic Analysis: From Archaea to Mammals

Lipids are among the most important organic compounds found in all living cells, from primitive archaebacteria to flowering plants or mammalian cells. They form part of cell walls and constitute cell storage material. Their biosynthesis and metabolism play key roles in faraway topics such as biofuel production (third‐generation biofuels produced by microorganisms, e.g. algae) and human diseases such as adrenoleukodystrophy, Zellweger syndrome, or Refsum disease. Current lipidomic analysis requires fast and accurate processing of samples and especially their characterization. Because the number of possible lipids and, more specifically, molecular species of lipids is of the order of hundreds to thousands, it is necessary to process huge amounts of data in a short time. There are two basic approaches to lipidomic analysis: shotgun and liquid chromatography–mass spectometry. Both methods have their pros and cons. This review deals with lipidomics not according to the type of ionization or the lipid classes analyzed but according to the types of samples (organisms) under study. Thus, it is divided into lipidomic analysis of archaebacteria, bacteria, yeast, fungi, algae, plants, and animals.     

A portable cryo-plunger for on-site intact cryogenic microscopy sample preparation in natural environments

We present a modern, light portable device specifically designed for environmental samples for cryogenic transmission-electron microscopy (cryo-TEM) by on-site cryo-plunging. The power of cryo-TEM comes from preparation of artifact-free samples. However, in many studies, the samples must be collected at remote field locations, and the time involved in transporting samples back to the laboratory for cryogenic preservation can lead to severe degradation artifacts. Thus, going back to the basics, we developed a simple mechanical device that is light and easy to transport on foot yet effective. With the system design presented here we are able to obtain cryo-samples of microbes and microbial communities not possible to culture, in their near-intact environmental conditions as well as in routine laboratory work, and in real time. This methodology thus enables us to bring the power of cryo-TEM to microbial ecology.     

The Finely Coordinated Action of SSB and NurA/HerA Complex Strictly Regulates the DNA End Resection Process in Saccharolobus solfataricus

Generation of the 3′ overhang is a critical step during homologous recombination (HR) and replication fork rescue processes. This event is usually performed by a series of DNA nucleases and/or helicases. The nuclease NurA and the ATPase HerA, together with the highly conserved MRE11/RAD50 proteins, play an important role in generating 3′ single-stranded DNA during archaeal HR. Little is known, however, about HerA-NurA function and activation of this fundamental and complicated DNA repair process. Herein, we analyze the functional relationship among NurA, HerA and the single-strand binding protein SSB from Saccharolubus solfataricus. We demonstrate that SSB clearly inhibits NurA endonuclease activity and its exonuclease activities also when in combination with HerA. Moreover, we show that SSB binding to DNA is greatly stimulated by the presence of either NurA or NurA/HerA. In addition, if on the one hand NurA binding is not influenced, on the other hand, HerA binding is reduced when SSB is present in the reaction. In accordance with what has been observed, we have shown that HerA helicase activity is not stimulated by SSB. These data suggest that, in archaea, the DNA end resection process is governed by the strictly combined action of NurA, HerA and SSB.     

Biohydrogen production characteristics of Desulfurococcus amylolyticus DSM 16532

Desulfurococcus amylolyticus DSM 16532 is a hyperthermophilic archaeon that can grow on cellulose. Due to the relevance of cellulose as a second generation biofuel production substrate this carbon compound was selected for molecular hydrogen (H₂) production studies.D. amylolyticus has several genes that are necessary for H₂ production, such as pyruvate ferredoxin oxidoreductase, formate dehydrogenase, glyceraldehyde-3-phosphate ferredoxin oxidoreductase and two membrane-bound hydrogenases. Moreover, D. amylolyticus comprises many physiological features that could promote H₂ production. Here, the biohydrogen production potential of D. amylolyticus was analysed in batch cultivation mode in bioreactors on cellulose and fructose. Analysing the cell specific biohydrogen production rates revealed that the organism possesses an intriguing physiological potential to produce H₂, at rates higher or equal to other known biohydrogen producing strains. However, with respect to the volumetric H₂ production rate the limiting factor could be related to low cell densities.Given the physiological capacity of D. amylolyticus the organism could still be envisioned to be optimized as a second generation H₂ cell factory.