Metaproteomics for analysis of microbial function in the environment

This report briefly describes the approach of using proteomic analyses to examine protein expression directly from environmental samples (termed metaproteomics). This approach has potential for solving one of the major challenges facing microbial ecologists, by providing insight of microbial function directly within samples

The Ecology of Acidophilic Microorganisms in the Corroding Concrete Sewer Environment.

Concrete corrosion is one of the most significant problems affecting valuable sewer infrastructure on a global scale. This problem occurs in the aerobic zone of the sewer, where a layer of surface corrosion develops on the exposed concrete and the surface pH is typically lowered from around 11-10 (pristine concrete) to pH 2-4. Acidophilic microorganisms become established as biofilms within the concrete corrosion layer and enhance the loss of concrete mass. Until recently, the acidophilic community was considered to comprise relatively few species of microorganisms, however, the biodiversity of the corrosion community is now recognized as being extensive and varying from different sewer environmental conditions. The diversity of acidophiles in the corrosion communities includes chemolithoautotrophs, chemolithoheterotrophs, and chemoorganoheterotrophs. The activity of these microorganisms is strongly affected by H2S levels in the sewer gas phase, although CO2, organic matter, and iron in the corrosion layer influence this acidic ecosystem. This paper briefly presents the conditions within the sewer that lead to the development of concrete corrosion in that environment. The review focuses on the acidophilic microorganisms detected in sewer corrosion environments, and then summarizes their proposed functions and physiology, especially in relation to the corrosion process. To our knowledge, this is the first review of acidophilic corrosion microbial communities, in which, the ecology and the environmental conditions (when available) are considered. Ecological studies of sewer corrosion are limited, however, where possible, we summarize the important metabolic functions of the different acidophilic species detected in sewer concrete corrosion layers. It is evident that microbial functions in the acidic sewer corrosion environment can be linked to those occurring in the analogous acidic environments of acid mine drainage and bioleaching

Achieving Stable Nitritation for Mainstream Deammonification by Combining Free Nitrous Acid-Based Sludge Treatment and Oxygen Limitation.

Stable nitritation is a critical bottleneck for achieving autotrophic nitrogen removal using the energy-saving mainstream deammonification process. Herein we report a new strategy to wash out both the Nitrospira sp. and Nitrobacter sp. from the treatment of domestic-strength wastewater. The strategy combines sludge treatment using free nitrous acid (FNA) with dissolved oxygen (DO) control in the nitritation reactor. Initially, the nitrifying reactor achieved full conversion of NH4(+) to NO3(-). Then, nitrite accumulation at ~60% was achieved in the reactor when 1/4 of the sludge was treated daily with FNA at 1.82 mg N/L in a side-stream unit for 24 h. Fluorescence in-situ hybridization (FISH) revealed FNA treatment substantially reduced the abundance of nitrite oxidizing bacteria (NOB) (from 23.0 ± 4.3 to 5.3 ± 1.9%), especially that of Nitrospira sp. (from 15.7 ± 3.9 to 0.4 ± 0.1%). Nitrite accumulation increased to ~80% when the DO concentration in the mainstream reactor was reduced from 2.5-3.0 to 0.3-0.8 mg/L. FISH revealed the DO limitation further reduced the abundance of NOB (to 2.1 ± 1.0%), especially that of Nitrobacter sp. (from 4.9 ± 1.2 to 1.8 ± 0.8%). The strategy developed removes a major barrier for deammonification in low-strength domestic wastewater

Stochastic Species Turnover and Stable Coexistence in a Species-Rich, Fire-Prone Plant Community

Understanding the mechanisms that maintain diversity is important for managing ecosystems for species persistence. Here we used a long-term data set to understand mechanisms of coexistence at the local and regional scales in the Cape Floristic Region, a global hotspot of plant diversity. We used a dataset comprising 81 monitoring sites, sampled in 1966 and again in 1996, and containing 422 species for which growth form, regeneration mode, dispersal distance and abundances at both the local (site) and meta-community scales are known. We found that species presence and abundance were stable at the meta-community scale over the 30 year period but highly unstable at the local scale, and were not influenced by species' biological attributes. Moreover, rare species were no more likely to go extinct at the local scale than common species, and that alpha diversity in local communities was strongly influenced by habitat. We conclude that stochastic environmental fluctuations associated with recurrent fire buffer populations from extinction, thereby ensuring stable coexistence at the meta-community scale by creating a “neutral-like” pattern maintained by niche-differentiation

A Small Conductance Calcium-Activated K⁺ Channel in C. elegans, KCNL-2, Plays a Role in the Regulation of the Rate of Egg-Laying

In the nervous system of mice, small conductance calcium-activated potassium (SK) channels function to regulate neuronal excitability through the generation of a component of the medium afterhyperpolarization that follows action potentials. In humans, irregular action potential firing frequency underlies diseases such as ataxia, epilepsy, schizophrenia and Parkinson's disease. Due to the complexity of studying protein function in the mammalian nervous system, we sought to characterize an SK channel homologue, KCNL-2, in C. elegans, a genetically tractable system in which the lineage of individual neurons was mapped from their early developmental stages. Sequence analysis of the KCNL-2 protein reveals that the six transmembrane domains, the potassium-selective pore and the calmodulin binding domain are highly conserved with the mammalian homologues. We used widefield and confocal fluorescent imaging to show that a fusion construct of KCNL-2 with GFP in transgenic lines is expressed in the nervous system of C. elegans. We also show that a KCNL-2 null strain, kcnl-2(tm1885), demonstrates a mild egg-laying defective phenotype, a phenotype that is rescued in a KCNL-2-dependent manner. Conversely, we show that transgenic lines that overexpress KCNL-2 demonstrate a hyperactive egg-laying phenotype. In this study, we show that the vulva of transgenic hermaphrodites is highly innervated by neuronal processes and by the VC4 and VC5 neurons that express GFP-tagged KCNL-2. We propose that KCNL-2 functions in the nervous system of C. elegans to regulate the rate of egg-laying. © 2013 Chotoo et al

Identification and quantification of microbial populations in activated sludge and anaerobic digestion processes

Eight different phenotypes were studied in an activated sludge process (AeR) and anaerobic digester AnD) in a full-scale wastewater treatment plant by means of fluorescent in situ hybridization (FISH) and automated FISH quantification software. The phenotypes were ammonia-oxidizing bacteria, nitrite-oxidizing bacteria, denitrifying bacteria, phosphate-accumulating organisms (PAO), glycogen-accumulating organisms (GAO), sulphate-reducing bacteria (SRB), methanotrophic bacteria and methanogenic archaea. Some findings were unexpected: (a) Presence of PAO, GAO and denitrifiers in the AeR possibly due to unexpected environmental conditions caused by oxygen deficiencies or its ability to survive aerobically; (b) presence of SRB in the AeR due to high sulphate content of wastewater intake and possibly also due to digested sludge being recycled back into the primary clarifier; (c) presence of methanogenic archaea in the AeR, which can be explained by the recirculation of digested sludge and its ability to survive periods of high oxygen levels; (d) presence of denitrifying bacteria in the AnD which cannot be fully explained because the nitrate level in the AnD was not measured. However, other authors reported the existence of denitrifiers in environments where nitrate or oxygen was not present suggesting that denitrifiers can survive in nitrate-free anaerobic environments by carrying out low-level fermentation; (e) the results of this paper are relevant because of the focus on the identification of nearly all the significant bacterial and archaeal groups of microorganisms with a known phenotype involved in the biological wastewater treatment.This study was realized with support from the Universitat Politecnica de Valencia, Universitat de Valencia and CONACYT (National Council of Science and Technology of Mexico).Reyes Sosa, MB.; Borrás Falomir, L.; Seco Torrecillas, A.; Ferrer, J. (2015). Identification and quantification of microbial populations in activated sludge and anaerobic digestion processes. Environmental Technology. 36(1):45-53. doi:10.1080/09593330.2014.934745S455336

Comparative Toxicity of Fumigants and a Phosphine Synergist Using a Novel Containment Chamber for the Safe Generation of Concentrated Phosphine Gas

BACKGROUND: With the phasing out of ozone-depleting substances in accordance with the United Nations Montreal Protocol, phosphine remains as the only economically viable fumigant for widespread use. However the development of high-level resistance in several pest insects threatens the future usage of phosphine; yet research into phosphine resistance mechanisms has been limited due to the potential for human poisoning in enclosed laboratory environments. PRINCIPAL FINDINGS: Here we describe a custom-designed chamber for safely containing phosphine gas generated from aluminium phosphide tablets. In an improvement on previous generation systems, this chamber can be completely sealed to control the escape of phosphine. The device has been utilised in a screening program with C. elegans that has identified a phosphine synergist, and quantified the efficacy of a new fumigant against that of phosphine. The phosphine-induced mortality at 20°C has been determined with an LC(50) of 732 ppm. This result was contrasted with the efficacy of a potential new botanical pesticide dimethyl disulphide, which for a 24 hour exposure at 20°C is 600 times more potent than phosphine (LC(50) 1.24 ppm). We also found that co-administration of the glutathione depletor diethyl maleate (DEM) with a sublethal dose of phosphine (70 ppm, <LC(5)), results in a doubling of mortality in C. elegans relative to DEM alone. CONCLUSIONS: The prohibitive danger associated with the generation, containment, and use of phosphine in a laboratory environment has now been substantially reduced by the implementation of our novel gas generation chamber. We have also identified a novel phosphine synergist, the glutathione depletor DEM, suggesting an effective pathway to be targeted in future synergist research; as well as quantifying the efficacy of a potential alternative to phosphine, dimethyl disulphide

SECRET domain of variola virus CrmB protein can be a member of poxviral type II chemokine-binding proteins family

<p>Abstract</p> <p>Background</p> <p>Variola virus (VARV) the causative agent of smallpox, eradicated in 1980, have wide spectrum of immunomodulatory proteins to evade host immunity. Recently additional biological activity was discovered for VARV CrmB protein, known to bind and inhibit tumour necrosis factor (TNF) through its N-terminal domain homologous to cellular TNF receptors. Besides binding TNF, this protein was also shown to bind with high affinity several chemokines which recruit B- and T-lymphocytes and dendritic cells to sites of viral entry and replication. Ability to bind chemokines was shown to be associated with unique C-terminal domain of CrmB protein. This domain named SECRET (Smallpox virus-Encoded Chemokine Receptor) is unrelated to the host proteins and lacks significant homology with other known viral chemokine-binding proteins or any other known protein.</p> <p>Findings</p> <p><it>De novo </it>modelling of VARV-CrmB SECRET domain spatial structure revealed its apparent structural homology with cowpox virus CC-chemokine binding protein (vCCI) and vaccinia virus A41 protein, despite low sequence identity between these three proteins. Potential ligand-binding surface of modelled VARV-CrmB SECRET domain was also predicted to bear prominent electronegative charge which is characteristic to known orthopoxviral chemokine-binding proteins.</p> <p>Conclusions</p> <p>Our results suggest that SECRET should be included into the family of poxviral type II chemokine-binding proteins and that it might have been evolved from the vCCI-like predecessor protein.</p