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Background: Trypanosomatid parasites are widely distributed in nature, evolving monoxenous and dixenous cycles. These parasites thrive in a wide number of Insect Orders, some of them with an important economic and environmental value, such as bees. The objective of this work was to develop a robust and sensitive qPCR assay for detecting trypanosomatid parasites in any kind of parasitized insect sample. Methods: A TaqMan qPCR assay based on a trypanosomatid-conserved region of the α-tubulin gene was standardized and evaluated. The limits of detection, sensitivity, and versatility of the α-tub TaqMan assay have been tested and validated using field samples from honeybee workers, wild bees, bumblebees, and grasshoppers as well as in the human infective trypanosomatid Leishmania major. Results: This assay showed a detection limit of 1 parasite equivalent/µL and successfully detected trypanosomatids in 10 different hosts belonging to the Hymenoptera and Orthoptera. The methodology was also tested using honeybee samples from 4 apiaries (n= 224 worker honeybees) located in Alpujarra region (Granada, Spain). Trypanosomatids were detected in 2.7% of the honeybees, with an intra colony prevalence of 0 to 13%. Parasite loads in 4 different classes of insects ranged from 40.6 to up to 1.1 x 108 cell equivalents per host. Conclusions: These results showed that α-tubulin TaqMan qPCR assay is a versatile diagnostic tool for the accurate detection and quantification of trypanosomatid parasites in a wide range of environmental settings.

The success of second-generation (2G) ethanol technology relies on the efficient transformation of hemicellulose into monosaccharides and, particularly, on the full conversion of xylans into xylose for over 18% of fermentable sugars. We sought new hemicellulases using ruminal liquid, after enrichment of microbes with industrial lignocellulosic substrates and preparation of metagenomic libraries. Among 150 000 fosmid clones tested, we identified 22 clones with endoxylanase activity and 125 with bxylosidase activity. These positive clones were sequenced en masse, and the analysis revealed open reading frames with a low degree of similarity with known glycosyl hydrolases families. Among them, we searched for enzymes that were thermostable (activity at > 50°C) and that operate at high rate at pH around 5. Upon a wide series of assays, the clones exhibiting the highest endoxylanase andb-xylosidase activities were identified. The fosmids were sequenced, and the corresponding genes cloned, expressed and proteins purified. We found that the activity of the most active b-xylosidase was at least 10-fold higher than that in commercial enzymatic fungal cocktails. Endoxylanase activity was in the range of fungal enzymes. Fungal enzymatic cocktails supplemented with the bacterial hemicellulases exhibited enhanced release of sugars from pretreated sugar cane straw, a relevant agricultural residue.

A series of N-monosubstituted and N,N’-disubstituted derivatives of the indolo[3,2-b]carbazole chromophore have been prepared, and their binding affinity for duplex DNA has been evaluated by ultraviolet and fluorescence spectroscopies. It has been found that indolo[3,2-b]carbazoles bearing basic N-alkyl substituents are intercalators that bind DNA with affinities in the micromolar and submicromolar range and a preference for associating with sequences of mixed composition and purine-pyrimidine steps.

Petroleum waste sludges are toxic and dangerous that is why environmental protection agencies have declared their treatment top priority. Physicochemical treatments are expensive and environmentally unfriendly, while alternative biological treatments are less costly but, in general, work at a slower pace. An in situ bioremediation and rhizoremediation field scale trial was performed in an area contaminated with oil refinery sludge under semiarid climate. The bioremediation and rhizoremediation treatments included the use of an artificial consortium made up of plant growth-promoting rhizobacteria and polycyclic aromatic hydrocarbon-degrading bacteria,and the combined use of the mentioned consortium along with pasture plants respectively. Rhizoremediation revealed that the development of vegetation favoured the evolution of indigenous microbiota with potential to remove petroleum wastes. This was inferred as the decline of total petroleum hydrocarbons 7 months after the biological treatment.

This study presents the results of the physicochemical characterization of particulate matter associated with an important dust event from the Sahara area that occurred in the South of Spain in 2010. The chemical composition of the samples reflected the dominance of the crustal component of sand from the Sahara desert, although the presence of Mo, Ti, and V trace elements indicated that the dust contained industrial material; probably collected in its transport from Africa. Microbial biodiversity associated with the dust was low, but dominated by Firmicutes and Proteobacteria. Some Firmicutes (belonging to the genus Bacillus and Sporosarcina) were cultured on solid and liquid medium, which suggested that the transported microbes were alive or present as spores that germinated under favorable conditions. These cultivable microbes in the form of spores were highly resistant to desiccation, heat, and UV light.

Maize represents one of the main cultivar for food and energy and crop yields are influenced by soil physicochemical and climatic conditions. To study how maize plants influence soil microbes we have examined microbial communities that colonize maize plants grown in carbonate-rich soil (pH 8.5) using culture-independent, PCR-based methods. We observed a low proportion of unclassified bacteria in this soil whether it was planted or unplanted. Our results indicate that a higher complexity of the bacterial community is present in bulk soil with microbes from nine phyla, while in the rhizosphere microbes from only six phyla were found. The predominant microbes in bulk soil were bacteria of the phyla Acidobacteria, Bacteroidetes and Proteobacteria, while Gammaproteobacteria of the genera Pseudomonas and Lysobacter were the predominant in the rhizosphere. As Gammaproteobacteria respond chemotactically to exudates and are efficient in the utilization of plants exudate products, microbial communities associated to the rhizosphere seem to be plant-driven. It should be noted that Gammaproteobacteria made available inorganic nutrients to the plants favouring plant growth and then the benefit of the interaction is common.

The industrial revolution, the first agricultural 'green revolution', and the development of antibiotics and therapeutic chemicals have brought significant and undeniable benefits to the human race. However, these advances demand high levels of energy, exploit natural resources and create large amounts of waste that creates an environmental burden for our planet. The pollution rate and character of many of the pollutants results in a rapid deterioration of the environment. Bioremediation functions to isolate and select microorganisms that operate under aerobic and anoxic conditions to remove these harmful pollutants. Current 'omics' technologies allow the exploitation of the catabolic potential of microbes without the need to cultivate them. Synthetic microbiology builds new catabolic pathways to remove recalcitrant pollutants from the environment.

We describe the characterization, purification, expression, and location of a 52-kDa protein secreted during interaction between the metacyclic form of Trypanosoma cruzi and its target host cell. The protein, which we have named MASP52, belongs to the family of mucin-associated surface proteins (MASPs). The highest levels of expression of both the protein and mRNA occur during the metacyclic and bloodstream trypomastigote stages, the forms that infect the vertebrate host cells. The protein is located in the plasma membrane and in the flagellar pockets of the epimastigote, metacyclic, and trypomastigote forms and is secreted into the medium at the point of contact between the parasite and the cell membrane, as well as into the host-cell cytosol during the amastigote stage. IgG antibodies specific against a synthetic peptide corresponding to the catalytic zone of MASP52 significantly reduce the parasite's capacity to infect the host cells. Furthermore, when the protein is adsorbed onto inert particles of bentonite and incubated with a nonphagocytic cell culture, the particles are able to induce endocytosis in the cells, which seems to demonstrate that MASP52 plays a role in a process whereby the trypomastigote forms of the parasite invade the host cell.

A monoclonal antibody (MAb) capable of detecting the gliadin in wheat flour has been developed. By immunoblot, the monoclonal antibody recognized three bands in the membranes after electrophoresis in an SDS PAGE of the alcohol-soluble proteins of wheat, and only one band in the alcohol extract of the oat flour. ELISA technique can be applied using this monoclonal antibody in the detection of gliadin and avenin in samples from wheat or triticale. The characterization of the antibody shows that it is an IgM class. Sensitivity by ELISA to the gliadin was 80 ng/ml.

The removal of pollutants from the environment has been declared a priority by a number of Environmental Protection Agencies (Roze et al., 2009). A great number of aerobic pathways have been deciphered and their relevance in microbiology and biotechnology has been reviewed several times (Garmendia et al., 2008; Siezen and Galardini, 2008; Govantes et al., 2008; Atlas and Bragg, 2009). In the area of biodegradation the role anaerobes and fungi play in removal of pollutants is of mounting interest. Microbial Biotechnology is publishing a number of new titles in this area, and here we have extracted some of the main conclusions. Tas and colleagues (2009) have dealt with mineralization of polychlorinated chemicals, which are harmful contaminants due to their persistence and their chronic toxicity to living organisms. Dehalococcoides spp. can anaerobically transform chlorinated xenobiotics to less‐ or even non‐noxious derivatives via reductive dechlorination. Tas and colleagues (2009) have reviewed the biology of this genus, focusing on its genetic peculiarities, its variability and, of course, its biodegradative properties. Dehalococcoides can replace chlorine by hydrogen atoms in recalcitrant halogenated compounds, using them as electron acceptors during anaerobic respiration. More than 100 16S rRNAs from environmental Dehalococcoides spp., are available, most of them corresponding to uncultured strains. In addition to the standard problems of cultivating anaerobic microbes, these coccoids usually grow in microbial communities where they can find a H2 supplier needed for thriving. The full genome sequences of several Dehalococcoides strains show that they have very small genomes which are highly similar. Moreover, they exhibit a large number of putative dehalogenase‐encoding genes (rdh), reaching up to 1.7% of the coding sequences in Dehalococcoides sp. Further work, combining transcriptional and proteomic techniques, will identify which proteins are really essential for the degradation of polychorinated xenobiotics. Jeon and colleagues (2009) also report in Microbial Biotechnology issues related with the attack of halogenated chemicals. They detail the discovery of four HAD (Halodehalogenases) defluorinases from different microbial genomes. Some of these dehalogenases have enhanced activities and this appears to arise from their sequence diversity (less than 30% sequence identity for HADs) (Prudnikova et al., 2009; Rye et al., 2009). The set of new dehalogenase were elucidated via biochemical characterization of 163 potential dehalogenases from the sequenced genomes of five common soil bacteria. Their discovery and characterization will be imperative to the future use of these enzymes in the biodegradation of halogenated chemicals. Another area of interest is the anaerobic degradation of monoaromatic compounds such as benzene, toluene, ethylbenzene and the xylene isomers (BTEX; Dou et al., 2008a; Wolicka et al., 2009). Anaerobic BTEX degradation has been shown to occur under denitrifying, sulfate‐reducing, iron‐reducing, manganese‐reducing and methanogenic conditions (Dou et al., 2008a,b; Barton and Fauque, 2009). These activities are of the relevance in removal of pollutants from contaminated aquifers and soils, and they are considered an important remediation strategy for hydrocarbon‐contaminated sites. New approaches based on isotopes are being taken, in fact, recently, compound‐specific isotope analysis was successfully used to distinguish between the effects of non‐degradative processes of mass loss such as sorption, volatilization, and dilution and those of biodegradation for aromatic hydrocarbons in the field (Fischer et al., 2008; Vogt et al., 2008). Compound‐specific isotope analysis is based on the fact that, in most chemical reactions, lighter isotopomers react faster than heavier ones, leading to a kinetic isotope effect. Herrmann and colleagues (2008) in Environmental Microbiology Reports, suggest that two‐dimensional isotope fractionation analyses are a valuable tool for identifying and monitoring anaerobic biodegradation of xylene isomers. They explored the carbon and hydrogen isotope fractionation of benzylsuccinate synthase (Bss)‐initiated degradation pathways for xylene isomers in order to obtain further information on the variability of isotope fractionation processes associated with Bss that might be important for the assessment of anaerobic degradation of xylene and toluene in the environment. The use of combined carbon and hydrogen isotope fractionation analyses may therefore be useful to monitor anaerobic xylene degradation at contaminated sites; this sort of technology will allow invaluable in situ monitoring of bioremediation processes.

We would like to begin this editorial by paying a modest but sincere tribute to Professor Kenneth Timmis for his recent nomination as a member of the Royal Society of the United Kingdom. Kenneth Timmis has pioneered science fields related to plasmid replication, biodegradation, microbial ecology, biodiversity and most recently metagenomics. In addition, to these many relevant scientific contributions, his services to the scientific community have been of paramount importance at the level of training for new generations of scientists and promotion of excellence in science through his role in journal editorial. Initially, as Editor for the Journal of Bacteriology (1989–1997) and then with the creation of two journals; one, Environmental Microbiology, that 10 years after the first issue came to light is the fifth journal in the area of microbiology and probably the leading journal in the field of environmental microbiology; the other, Microbial Biotechnology, that reflects his vision of microbes as useful biotechnological tools. Although Microbial Biotechnology is in its early infancy it has already attracted the attention of a specialized audience. The title of this editorial also entertains the idea that the future of Microbial Biotechnology will not only be based on food, energy, pharmaceutical and clinical microbiology, but will bring into the equation the many relevant aspects of environmental microbiology which contribute to the diversity of processes biotechnology can offer to society. An excellent example of Environmental Microbiology meeting Microbial Biotechnology comes from the publications by Kamilova and colleagues (2008) and Pechy‐Tarr and colleagues (2008). These articles emphasize two very relevant features in environmental microbiology, namely, the identification of new genes that encode proteins with potential to control insect pests and the phytopathogen Fusarium. Biotechnological exploitation of biocontrol properties of microbes requires an in‐depth knowledge of microbial genetics and physiology and/or the dissection in the lab of these properties, as well as specific training in designing and performance of field trials in which to test the microbes’ new potential. Plant–microbe interactions constitute a fascinating field of inter‐kingdom communication, some novel aspects of how bacteria sense plant signals and vice versa have been summarized by van Dillewijn (2008) in his highlight article entitled: what gets turned on in the rhizosphere? The field of plant–microbe interactions is extremely important to biotechnology; for this reason Microbial Biotechnology will dedicate an entire special issue to this area, which is expected to be published mid‐2009 with the assistance of invited guest editors with expertise in a number of fields (see announcing flyer). A set of articles published in this first volume of Microbial Biotechnology have dealt with microbial biofuel production (Maeda et al., 2008; Vardar‐Schara et al., 2008; Wackett, 2008a,b). The scientific community recognizes the potential of hydrogen as an alternative fuel due to its higher energy content than fossil fuels, its renewable nature, and because its product of oxidation is water. These advantages were already envisaged some 25 years ago (Takakuwa et al., 1983); however, not until recently have social demands for a cleaner environment led to a renewed interest in the theme. A relevant question regarding hydrogen production is its production limits. Limitations can arise from physical constraints – which could be solved via improvements in process development and/or fermentor design, or from the thermodynamic limits that govern reactions that lead to hydrogen production. In relation to this issue, Veit and colleagues (2008) explore the thermodynamic aspects limiting hydrogen yield in microbial fermentations; key reactions NAD(P)H + H+ ↔ NAD(P)+ + H2 hypothetically achieve equilibrium at very low partial hydrogen pressure, and the authors probe this through the design and thermodynamic analysis of a synthetic NAD(P)H:H2 pathway in Escherichia coli BL21 (DE3). The system consists of a ferredoxin‐dependent hydrogenase, ferredoxin as electron acceptor/donor intermediate, and a NAD(P)H:ferredoxin oxidoreductase. Results revealed that in both cases these pathways are influenced by partial headspace hydrogen pressure under closed bath conditions and that the NADPH:H2 system allows higher hydrogen accumulation than the NADH:H2 pathway. Novel molecules are the panacea for survival of large and small companies in the Biotech area. New methods that lead to more efficient synthesis of added value molecules are needed. This may involve the discovery of new molecules or the continuous improvement of a process through the identification of new enzymes. Both aspects are under consideration in this issue. Thiwthong and colleagues (2008) report on new aldehyde dehydrogenases for the synthesis of glyoxylic acid, an important compound in the pharmaceutical industry. They have purified and characterized two aldehyde oxidases, F10 and F13, from Pseudomonas sp. MX‐058. Both catalyse the oxidation of glyoxal to glyoxilic acid, and their kinetic properties hold potential for being economically and industrially exploitable. The authors claim these novel enzymes overcame limitations found earlier with aldehyde dehydrogenases from different eukaryotes. A unique feature is that the quaternary structure of the F13 enzyme revealed it to be heteropentameric. Expression of heterologous genes for use in a number of biotechnological applications has been the subject of intense research over the last 20 years (for a review see Bertram and Hillen, 2008). In this issue Fisher and colleagues (2008) systematically examined the twin‐arginine translocation system for secretion of heterologous proteins. The system is superior in yield and specific activity for secreted proteins than the ‘classical’ SEC pathway. One of the beauties of the system is that only properly folded proteins are exported to the periplasm; a screening process that guarantees correct protein properties. Medical and pharmaceutical industries are searching new cell targets for drug discovery. Glutamate racemase, a member of the cofactor‐independent, two thiol‐based family of amino acid racemases, has been implicated in maintaining sufficient d‐glutamate pool levels required for peptidoglycan cross‐linking; which in turn is of critical importance for bacterial growth. Fisher (2008) reviews the history of this enzyme, the recent biochemical and structural characterization of several isoenzymes and how a set of new inhibitors have been found. This research is of upmost significance for the pharmaceutical sector because peptidoglycan synthesis has long been an important antimicrobial drug target. Continuing on the theme of biotechnological applications of medical importance is the article published by Barbuddhe and Chakraborty (2008). Here the authors give a comprehensive review of the current and potential uses for the human pathogen Listeria monocytogenes in biotechnology. Because L. monocytogenes is capable of subverting host cell function and is able to survive and replicate within numerous eukaryotic cells during the infection process, it is an attractive delivery vehicle for use in both clinical and biotechnological applications. In fact Listeria are already being used to facilitate heterologous antigen presentation on the surface of antigen presenting cells and the Listeriolysin O protein has been used to assist DNA delivery by cell transfection for use in cell biology studies. The authors also consider the potential use of Listeria in the development of novel vaccine and drug delivery systems by exploiting their sophisticated approach to infection. Undoubtedly, future research allowing the development of these so‐called ‘patho‐biotechnology’ approaches will be of great interest over the coming years. Biosensors have also been the subject of mini‐review in Microbial Biotechnology, and a model for internal calibration of biosensors was recently published (Wackwitz et al., 2008). In the current issue a type of cell‐based biosensor is reported that permits one to distinguish pathogenic from non‐pathogenic strains of Bacillus cereus, a technology that holds promise for detection of pathogenic bacteria in food (Hutchison et al., 2008). The whole‐cell sensor system consists of erytrophore cells of Betta splendeus. The extension of the system to detect other pathogens is of major interest and of great importance in food biosafety.

Macroscopic growths at geographically separated acid mine drainages (AMDs) exhibit distinct populations. Yet, local heterogeneities are poorly understood. To gain novel mechanistic insights into this, we used OMICs tools to profile microbial populations coexisting in a single pyrite gallery AMD (pH ∼2) in three distinct compartments: two from a stratified streamer (uppermost oxic and lowermost anoxic sediment-attached strata) and one from a submerged anoxic non-stratified mat biofilm. The communities colonising pyrite and those in the mature formations appear to be populated by the greatest diversity of bacteria and archaea (including ‘ARMAN’ (archaeal Richmond Mine acidophilic nano-organisms)-related), as compared with the known AMD, with ∼44.9% unclassified sequences. We propose that the thick polymeric matrix may provide a safety shield against the prevailing extreme condition and also a massive carbon source, enabling non-typical acidophiles to develop more easily. Only 1 of 39 species were shared, suggesting a high metabolic heterogeneity in local microenvironments, defined by the O2 concentration, spatial location and biofilm architecture. The suboxic mats, compositionally most similar to each other, are more diverse and active for S, CO2, CH4, fatty acid and lipopolysaccharide metabolism. The oxic stratum of the streamer, displaying a higher diversity of the so-called ‘ARMAN’-related Euryarchaeota, shows a higher expression level of proteins involved in signal transduction, cell growth and N, H2, Fe, aromatic amino acids, sphingolipid and peptidoglycan metabolism. Our study is the first to highlight profound taxonomic and functional shifts in single AMD formations, as well as new microbial species and the importance of H2 in acidic suboxic macroscopic growths., We gratefully acknowledge the financial support provided by the Spanish Ministry of Economy and Competitiveness (Projects CSD2007-00005, BIO2010-16303 and BIO2011-25012) and the European Regional Development Fund (ERDF). Partial support by the FP7-KBBE program through the projects Microme (Grant No. 222886-2) and MAGICPAH (FP7-KBBE-2009-245226) is also gratefully acknowledged. Proteomics analysis performed in the ONJ laboratory was supported by a research grant (FNU 09-072287) and an EliteForsk award to ONJ from the Danish Council for Independent Research.

The phylogenetic and functional structure of the microbial community residing in a Ca2+-rich anoxic sediment of a sub-saline shallow lake (Laguna de Carrizo, initially operated as a gypsum (CaSO4 × 2 H2O) mine) was estimated by analyzing the diversity of 16S rRNA amplicons and a 3.1 Mb of consensus metagenome sequence. The lake has about half the salinity of seawater and possesses an unusual relative concentration of ions, with Ca2+ and SO 4 2- being dominant. The 16S rRNA sequences revealed a diverse community with about 22% of the bacterial rRNAs being less than 94.5% similar to any rRNA currently deposited in GenBank. In addition to this, about 79% of the archaeal rRNA genes were mostly related to uncultured Euryarchaeota of the CCA47 group, which are often associated with marine and oxygen-depleted sites. Sequence analysis of assembled genes revealed that 23% of the open reading frames of the metagenome library had no hits in the database. Among annotated genes, functions related to (thio) sulfate and (thio) sulfonate-reduction and iron-oxidation, sulfur-oxidation, denitrification, synthrophism, and phototrophic sulfur metabolism were found as predominant. Phylogenetic and biochemical analyses indicate that the inherent physical–chemical characteristics of this habitat coupled with adaptation to anthropogenic activities have resulted in a highly efficient community for the assimilation of polysulfides, sulfoxides, and organosulfonates together with nitro-, nitrile-, and cyanide-substituted compounds. We discuss that the relevant microbial composition and metabolic capacities at Laguna de Carrizo, likely developed as an adaptation to thrive in the presence of moderate salinity conditions and potential toxic bio-molecules, in contrast with the properties of previously known anoxic sediments of shallow lakes., This research was supported by the Spanish CSD2007-00005 project and FEDER funds. M-E.G. thanks the CSIC for a JAE fellowship.