Environmental proteomics: applications of proteome profiling in environmental microbiology and biotechnology

Landfill: An eclectic review on structure, reactions and remediation approach

Since the enactment of the Clean Water Act (1972), which was supplemented by increased accountability under Resource Conservation and Recovery Act (RCRA) Subtitle D (1991) and the Clean Air Act Amendments (1996), landfills have indeed been widely used all around the world for treating various wastes. The landfill's biological and biogeochemical processes are believed to be originated about 2 to 4 decades ago. Scopus and web of Science based bibliometric study reveals that there are few papers available in scientific domain. Further, till today not a single paper demonstrated the detailed landfills heterogenicity, chemistry and microbiological processes and their associated dynamics in a combined approach. Accordingly, the paper addresses the recent applications of cutting-edge biogeochemical and biological methods adopted by different countries to sketch an emerging perspective of landfill biological and biogeochemical reactions and dynamics. Additionally, the significance of several regulatory factors controlling the landfill's biogeochemical and biological processes is highlighted. Finally, this article emphasizes the future opportunities for integrating advanced techniques to explain landfill chemistry explicitly. In conclusion, this paper will provide a comprehensive vision of the diverse dimensions of landfill biological and biogeochemical reactions and dynamics to the scientific world and policymakers.

Sulfamethoxazole Enhances Specific Enzymatic Activities under Aerobic Heterotrophic Conditions: A Metaproteomic Approach

The growing concern about antibiotic-resistant microorganisms has focused on the sludge from wastewater treatment plants (WWTPs) as a potential hotspot for their development and spread. To this end, it seems relevant to analyze the changes on the microbiota as a consequence of the antibiotics that wastewater may contain. This study aims at determining whether the presence of sulfamethoxazole (SMX), even in relatively low concentrations, modifies the microbial activities and the enzymatic expression of an activated sludge under aerobic heterotrophic conditions. For that purpose, we applied a metaproteomic approach in combination with genomic and transformation product analyses. SMX was biotransformed, and the metabolite 2,4(1H,3H)-pteridinedione-SMX (PtO-SMX) from the pterin-conjugation pathway was detected at all concentrations tested. Metaproteomics showed that SMX at 50-2000 μg/L slightly affected the microbial community structure, which was confirmed by DNA metabarcoding. Interestingly, an enhanced activity of the genus Corynebacterium and specifically of five enzymes involved in its central carbon metabolism was found at increased SMX concentrations. Our results suggest a role of Corynebacterium genus on SMX risks mitigation in our bioreactors.

Microbial fuel cells: a comprehensive review for beginners

Microbial fuel cells (MFCs) have shown immense potential as a one-stop solution for three major sustainability issues confronting the world today-energy security, global warming and wastewater management. MFCs represent a cross-disciplinary platform for research at the confluence of the natural and engineering sciences. The diversity of variables influencing performance of MFCs has garnered research interest across varied scientific disciplines since the beginning of this century. The increasing number of research publications has made it necessary to keep track of work being carried out by research groups across the globe and consolidate significant findings on a regular basis. Review articles are often the nodal points for beginners who are required to undertake an exploratory survey of literature to identify a suitable research problem. This 'review of reviews' is a ready-reckoner that directs readers to relevant reviews and research articles reporting significant developments in MFC research in the last two decades. The article also highlights the areas needing research attention which when addressed could take this technology a few more steps closer to practical implementation.

A composite taxonomical and functional framework of microbiomes under acid mine drainage bioremediation systems

Mining-industry is one of the most important activities in the economic development of many countries and produces highly significant alterations on the environment, mainly due to the release of a strong acidic metal-rich wastewater called acid mine drainage (AMD). Consequently, the establishment of multiple wastewater treatment strategies remains as a fundamental challenge in AMD research. Bioremediation, as a constantly-evolving multidisciplinary endeavor had been complemented during the last decades by novel tools of increasingly higher resolution such as those based on omics approaches, which are providing detailed insights into the ecology, evolution and mechanisms of microbial communities acting in bioremediation processes. This review specifically addresses, reanalyzes and reexamines in a composite comparative manner, the available sequence information and associated metadata available in public databases about AMD impacted microbial communities; summarizing our understanding of its composition and functions, and proposing potential genetic enhancements for improved bioremediation strategies. 16 S rRNA gene-targeted sequencing data from 9 studies previously published including AMD systems reported and studied around the world, were collected and reanalyzed to compare and identify the core and most abundant genera in four distinct AMD ecosystems: surface biofilm, water, impacted soils/sediments and bioreactor microbiomes. We determined that the microbial communities of bioreactors were the most diverse in bacterial types detected. The metabolic pathways predicted strongly suggest the key role of syntrophic communities with denitrification, methanogenesis, manganese, sulfate and iron reduction. The perspectives to explore the dynamics of engineering systems by high-throughput sequencing and biochemical techniques are discussed and foreseen application of synthetic biology and omics exploration on improved AMD biotransformation are proposed.

Deciphering the Functioning of Microbial Communities: Shedding Light on the Critical Steps in Metaproteomics

Unraveling the complex structure and functioning of microbial communities is essential to accurately predict the impact of perturbations and/or environmental changes. From all molecular tools available today to resolve the dynamics of microbial communities, metaproteomics stands out, allowing the establishment of phenotype-genotype linkages. Despite its rapid development, this technology has faced many technical challenges that still hamper its potential power. How to maximize the number of protein identification, improve quality of protein annotation, and provide reliable ecological interpretation are questions of immediate urgency. In our study, we used a robust metaproteomic workflow combining two protein fractionation approaches (gel-based versus gel-free) and four protein search databases derived from the same metagenome to analyze the same seawater sample. The resulting eight metaproteomes provided different outcomes in terms of (i) total protein numbers, (ii) taxonomic structures, and (iii) protein functions. The characterization and/or representativeness of numerous proteins from ecologically relevant taxa such as Pelagibacterales, Rhodobacterales, and Synechococcales, as well as crucial environmental processes, such as nutrient uptake, nitrogen assimilation, light harvesting, and oxidative stress response, were found to be particularly affected by the methodology. Our results provide clear evidences that the use of different protein search databases significantly alters the biological conclusions in both gel-free and gel-based approaches. Our findings emphasize the importance of diversifying the experimental workflow for a comprehensive metaproteomic study.

Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives

The sea represents a major source of biodiversity. It exhibits many different ecosystems in a huge variety of environmental conditions where marine organisms have evolved with extensive diversification of structures and functions, making the marine environment a treasure trove of molecules with potential for biotechnological applications and innovation in many different areas. Rapid progress of the omics sciences has revealed novel opportunities to advance the knowledge of biological systems, paving the way for an unprecedented revolution in the field and expanding marine research from model organisms to an increasing number of marine species. Multi-level approaches based on molecular investigations at genomic, metagenomic, transcriptomic, metatranscriptomic, proteomic, and metabolomic levels are essential to discover marine resources and further explore key molecular processes involved in their production and action. As a consequence, omics approaches, accompanied by the associated bioinformatic resources and computational tools for molecular analyses and modeling, are boosting the rapid advancement of biotechnologies. In this review, we provide an overview of the most relevant bioinformatic resources and major approaches, highlighting perspectives and bottlenecks for an appropriate exploitation of these opportunities for biotechnology applications from marine resources.

Alterations in the proteomic composition of Serratia marcescens in response to manganese (II)

Background

Proteomics is an important tool for the investigation of dynamic physiological responses of microbes under heavy metal stress. To gain insight into how bacteria respond to manganese (II) and identify the proteins involved in Mn (II) oxidation, the shotgun proteomics approach was applied to a potential Mn (II)-oxidizing Serratia marcescens strain cultivated in the absence and presence of Mn (II).

Results

The LG1 strain, which grew equally well in the two conditions, was found to express a set of proteins related to cellular processes vital for survival, as well as proteins involved in adaptation and tolerance to Mn (II). The multicopper oxidase CueO was identified, indicating its probable participation in the Mn (II) bio-oxidation; however, its expression was not modulated by the presence of Mn (II). A set of proteins related to cell and metabolic processes vital to the cells were downregulated in the presence of Mn (II), while cell membrane-related proteins involved in the maintenance of cell integrity and survival under stress were upregulated under this condition.

Conclusions

These findings indicate that the LG1 strain may be applied successfully in the bioremediation of Mn (II), and the shotgun approach provides an efficient means for obtaining the total proteome of this species.

Understanding and Designing the Strategies for the Microbe-Mediated Remediation of Environmental Contaminants Using Omics Approaches

Rapid industrialization and population explosion has resulted in the generation and dumping of various contaminants into the environment. These harmful compounds deteriorate the human health as well as the surrounding environments. Current research aims to harness and enhance the natural ability of different microbes to metabolize these toxic compounds. Microbial-mediated bioremediation offers great potential to reinstate the contaminated environments in an ecologically acceptable approach. However, the lack of the knowledge regarding the factors controlling and regulating the growth, metabolism, and dynamics of diverse microbial communities in the contaminated environments often limits its execution. In recent years the importance of advanced tools such as genomics, proteomics, transcriptomics, metabolomics, and fluxomics has increased to design the strategies to treat these contaminants in ecofriendly manner. Previously researchers has largely focused on the environmental remediation using single omics-approach, however the present review specifically addresses the integrative role of the multi-omics approaches in microbial-mediated bioremediation. Additionally, we discussed how the multi-omics approaches help to comprehend and explore the structural and functional aspects of the microbial consortia in response to the different environmental pollutants and presented some success stories by using these approaches.

Proteomic studies on lactic acid bacteria: A review

Probiotics are amongst the most common microbes in the gastro-intestinal tract of humans and other animals. Prominent among probiotics are Lactobacillus and Bifidobacterium. They offer wide-ranging health promoting benefits to the host which include reduction in pathological alterations, stimulation of mucosal immunity and interaction with mediators of inflammation among others. Proteomics plays a vital role in understanding biological functions of a cell. Proteomics is also slowly and steadily adding to the existing knowledge on role of probiotics. In this paper, the proteomics of probiotics, with special reference to lactic acid bacteria is reviewed with a view to understand i) proteome map, ii) mechanism of adaptation to harsh gut environment such as low pH and bile acid, iii) role of cell surface proteins in adhering to intestinal epithelial cells, and iv) as a tool to answer basic cell functions. We have also reviewed various analytical methods used to carry out proteome analysis, in which 2D-MS and LC-MS/MS approaches were found to be versatile methods to perform high-throughput sample analyses even for a complex gut samples. Further, we present future road map of understanding gut microbes combining meta-proteomics, meta-genomics, meta-transcriptomics and -metabolomics.

Meta-proteomic analysis of protein expression distinctive to electricity-generating biofilm communities in air-cathode microbial fuel cells

BACKGROUND

Bioelectrochemical systems (BESs) harness electrons from microbial respiration to generate power or chemical products from a variety of organic feedstocks, including lignocellulosic biomass, fermentation byproducts, and wastewater sludge. In some BESs, such as microbial fuel cells (MFCs), bacteria living in a biofilm use the anode as an electron acceptor for electrons harvested from organic materials such as lignocellulosic biomass or waste byproducts, generating energy that may be used by humans. Many BES applications use bacterial biofilm communities, but no studies have investigated protein expression by the anode biofilm community as a whole.

RESULTS

To discover functional protein expression during current generation that may be useful for MFC optimization, a label-free meta-proteomics approach was used to compare protein expression in acetate-fed anode biofilms before and after the onset of robust electricity generation. Meta-proteomic comparisons were integrated with 16S rRNA gene-based community analysis at four developmental stages. The community composition shifted from dominance by aerobic Gammaproteobacteria (90.9 ± 3.3%) during initial biofilm formation to dominance by Deltaproteobacteria, particularly Geobacter (68.7 ± 3.6%) in mature, electricity-generating anodes. Community diversity in the intermediate stage, just after robust current generation began, was double that at the early stage and nearly double that of mature anode communities. Maximum current densities at the intermediate stage, however, were relatively similar (~ 83%) to those achieved by mature-stage biofilms. Meta-proteomic analysis, correlated with population changes, revealed significant enrichment of categories specific to membrane and transport functions among proteins from electricity-producing biofilms. Proteins detected only in electricity-producing biofilms were associated with gluconeogenesis, the glyoxylate cycle, and fatty acid β-oxidation, as well as with denitrification and competitive inhibition.

CONCLUSIONS

The results demonstrate that it is possible for an MFC microbial community to generate robust current densities while exhibiting high taxonomic diversity. Moreover, these data provide evidence to suggest that startup growth of air-cathode MFCs under conditions that promote the establishment of aerobic-anaerobic syntrophy may decrease startup times. This study represents the first investigation into protein expression of a complex BES anode biofilm community as a whole. The findings contribute to understanding of the molecular mechanisms at work during BES startup and suggest options for improvement of BES generation of bioelectricity from renewable biomass.

Metabolic pathway and cell adaptation mechanisms revealed through genomic, proteomic and transcription analysis of a Sphingomonas haloaromaticamans strain degrading ortho-phenylphenol

Ortho-phenylphenol (OPP) is a fungicide contained in agro-industrial effluents produced by fruit-packaging plants. Within the frame of developing bio-strategies to detoxify these effluents, an OPP-degrading Sphingomonas haloaromaticamans strain was isolated. Proteins/genes with a putative catabolic role and bacterium adaptation mechanisms during OPP degradation were identified via genomic and proteomic analysis. Transcription analysis of all putative catabolic genes established their role in the metabolism of OPP. The formation of key transformation products was verified by chromatographic analysis. Genomic analysis identified two orthologous operons encoding the ortho-cleavage of benzoic acid (BA) (ben/cat). The second ben/cat operon was located in a 92-kb scaffold along with (i) an operon (opp) comprising genes for the transformation of OPP to BA and 2-hydroxypenta-2,4-dienoate (and genes for its transformation) and (ii) an incomplete biphenyl catabolic operon (bph). Proteomics identified 13 up-regulated catabolic proteins when S. haloaromaticamans was growing on OPP and/or BA. Transcription analysis verified the key role of the catabolic operons located in the 92-kb scaffold, and flanked by transposases, on the transformation of OPP by S. haloaromaticamans. A flavin-dependent monoxygenase (OppA1), one of the most up-regulated proteins in the OPP-growing cells, was isolated via heterologous expression and its catabolic activity was verified in vitro.

Assessing the impact of long term frozen storage of faecal samples on protein concentration and protease activity

Background

The proteome is the second axis of the microbiome:host interactome and proteases are a significant aspect in this interaction. They interact with a large variety of host proteins and structures and in many situations are implicated in pathogenesis. Furthermore faecal samples are commonly collected and stored frozen so they can be analysed at a later date. So we were interested to know whether long term storage affected the integrity of proteases and total protein and whether historical native faecal samples were still a viable option for answering research questions around the functional proteome.

Methods

Faecal samples were collected from 3 healthy volunteers (3 biological replicates) and processed in order to be stored at both − 20 °C and − 80 °C and in a variety of storage buffers. Protein extraction, protein content and protease activity were assessed at the time of collection, after 24 h, 1 week, 1 month, 3 months 6 months and finally 1 year.

Results

Beadbeating impacted the quantity of protein extracted, while sodium azide did not impact protease assays. Long term storage of extracted proteins showed that both total protein and protease activity were affected when they were stored as extracted protein. Intact faecal samples were shown to maintain both protein levels and protease activity regardless of time and temperature.

Conclusions

Beadbeating increases the protein and protease activity when extracting from a faecal sample, however, the extracted protein is not stable and activity is lost, even with a suitable storage buffer. The most robust solution is to store the proteins in an intact frozen native faecal matrix and extract at the time of assay or analysis, this approach was shown to be suitable for samples in which, there are low levels of protease activity and which had been frozen for a year.

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Long term storage of protein in frozen faeces is viable.

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Protein concentration does not change if native samples are used.

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Protease activity is maintained in native frozen faeces.

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Both protein concentration and protease activity are reduced, in storage, once extracted from faeces.

Proteomic tools to decipher microbial community structure and functioning

Recent advances in microbial ecology allow studying microorganisms in their environment, without laboratory cultivation, in order to get access to the large uncultivable microbial community. With this aim, environmental proteomics has emerged as an appropriate complementary approach to metagenomics providing information on key players that carry out main metabolic functions and addressing the adaptation capacities of living organisms in situ. In this review, a wide range of proteomic approaches applied to investigate the structure and functioning of microbial communities as well as recent examples of such studies are presented.

The proteome of Atlantic herring (Clupea harengus L.) larvae is resistant to elevated pCO2

Elevated anthropogenic pCO2 can delay growth and impair otolith structure and function in the larvae of some fishes. These effects may concurrently alter the larva's proteome expression pattern. To test this hypothesis, Atlantic herring larvae were exposed to ambient (370 μatm) and elevated (1800 μatm) pCO2 for one-month. The proteome structure of the larvae was examined using a 2-DE and mass spectrometry. The length of herring larvae was marginally less in the elevated pCO2 treatment compared to the control. The proteome structure was also different between the control and treatment, but only slightly: the expression of a small number of proteins was altered by a factor of less than 2-fold at elevated pCO2. This comparative proteome analysis suggests that the proteome of herring larvae is resilient to elevated pCO2. These observations suggest that herring larvae can cope with levels of CO2 projected for near future without significant proteome-wide changes.

Novel and cost-effective 6-plex isobaric tagging reagent, DiART, is effective for identification and relative quantification of complex protein mixtures using PQD fragmentation

Deuterium isobaric Amine Reactive Tag (DiART) reagents facilitate relative quantification during proteomic analysis in a functionally similar manner to commercially available isobaric tag for relative and absolute quantitation (iTRAQ) and tandem mass tag (TMT) reagents. In contrast to iTRAQ and TMT, DiART reagents incorporate deuterium isotopes which significantly reduce the number of required synthesis steps and hence have potential to significantly reduce reagent production cost. We examined the capability of DiART for performing quantitative proteomic experiments using a linear ion-trap mass spectrometer with Pulsed Q Dissociation (PQD) fragmentation. Using a synthetic peptide tagged with DiART reagent, we observed a precise mass shift of 144.79 Da on the triply charged precursor ion, which shows complete derivatization of the N-terminus and ε-amino group of lysine. A DiART tagged tryptic digest of bovine serum albumin showed a sequence coverage of 57.99% which was very comparable to that showed by iTRAQ, 54.77%. Furthermore, a ten protein mixture tagged with DiART reagents and mixed in 1:1:1:1:1:1 exhibited < 15% error, whereas a linear trend (slope of 1.085) was observed when tagged proteins were mixed in the ratio 2:1:2:4:10:14 and plotted against theoretical ratios. Finally, when complex cell-wall protein mixtures from the model fungus A. nidulans were tagged with DiART reagents and mixed in different ratios, they exhibited similar trends. We conclude that DiART reagents are capable of performing quantitative proteomic experiments using PQD on a linear ion trap mass spectrometer.

Metaproteomics of our microbiome - developing insight in function and activity in man and model systems

We are all colonized by a large microbiome, a complex set of microbes that have intimate associations with us. Culture-based approaches have provided insights in the complexity of the microbial communities living on surfaces inside and outside the body. However, the application of high-throughput sequencing technologies has identified large numbers of community members at both the phylogenetic and the (meta-)genome level. The latter allowed defining a reference set of several millions of mainly bacterial genes and provided the basis for developing approaches to target the activity and function of the human microbiome with proteomic techniques. Moreover, recent improvements in protein and peptide separation efficiencies and highly accurate mass spectrometers have promoted the field of metaproteomics, the study of the collective proteome of microbial communities. We here review the approaches that have been developed to study the human metaproteomes, focusing on intestinal tract and body fluids. Moreover, we complement these by considering metaproteomic studies in mouse and other model systems offering the option to study single species or simple consortia. Finally, we discuss present and future avenues that may be used to advance the application of metaproteomic approaches to further improve our understanding of the microbes inside and around our body. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.

In silico description of cobalt and nickel assimilation systems in the genomes of methanogens

Methanogens are a diverse group of organisms that can live in a wide range of environments. Herein, cobalt and tungsten assimilation pathways have proposed to be established in the genomes of Methanococcus maripaludies C5 and Methanosarcina mazei Go1, respectively. All of the proteins involved in the proposed pathways were identified from public domain databases and then complied manually to reconstruct the pathways. The function of proteins with unknown function was assigned by a combined prediction approach. Totally, 17 proteins were identified to cobalt transport and assimilation processes whereas 7 proteins reported to tungsten assimilation system. Phylogenetic analysis of this study revealed that heavy metal transporter of methanogens could be evolved from closely related members in the different genera of methanogens. Nevertheless, genes encoding for metal resistance proteins could be originated from thermophilic and sulfur reducing bacteria. Many metalloenzymes in methanogens were very unique to the species of methanogens. It implied that these metal ions were utilized to produce the precursors for energy driven processes of methanogens. This study suggested that in combination of systems models and evolutionary inference can only correlate metabolic fluxes and physiological changes in methanogens. In silico models of this study will provide insights to design experiments for heavy metal assimilation processes of methanogens growing under heavy metal-rich environments and or in a laboratory condition.

Occurrence of horizontal gene transfer of P(IB)-type ATPase genes among bacteria isolated from the uranium rich deposit of Domiasiat in North East India

Uranium (U) tolerant aerobic heterotrophs were isolated from the subsurface soils of one of the pre-mined U-rich deposits at Domiasiat located in the north-eastern part of India. On screening of genomic DNA from 62 isolates exhibiting superior U and heavy metal tolerance, 32 isolates were found to be positive for P(IB)-type ATPase genes. Phylogenetic incongruence and anomalous DNA base compositions revealed the acquisition of P(IB)-type ATPase genes by six isolates through horizontal gene transfer (HGT). Three of these instances of HGT appeared to have occurred at inter-phylum level and the other three instances indicated to have taken place at intra-phylum level. This study provides an insight into one of the possible survival strategies that bacteria might employ to adapt to environments rich in uranium and heavy metals.

Proteomic profiling of the acid tolerance response (ATR) during the enhanced biomethanation process from Taihu Blue Algae with butyrate stress on anaerobic sludge

Enhanced biomethanation with acid stress on anaerobic sludge, dehydrogenase activity, protein expression, and the primary proteomic profiling of microbial communities during the enhanced anaerobic digestion process from Taihu Blue Algae were investigated. It was found that the accumulation of organic acids and the specific biogas accumulation rate were 1.8 and 1.3 times of the control, when 10 g/L and 7.5 g/L of butyrate were selected for acid stress, respectively. Meanwhile, dehydrogenase activity of the 7.5 g/L acid stress group exhibited an increase of 1.6 times of the control, and protein expression was also found to be enhanced sharply as revealed by 1D-PAGE. Finally, twenty of the matched protein spots through 2D-PAGE from both the control and the 7.5 g/L stress groups were identified by MALDI-TOF MS, and five of which were proved to be involved in bioenergy metabolism. Significantly, ATR related proteins might be induced as the pIs of which were acidic as 5.92, 5.51 and 5.54, respectively.

Microbiology and proteomics, getting the best of both worlds!

High-throughput identification of proteins with the latest generation of hybrid high-resolution mass spectrometers is opening new perspectives in microbiology. I present, here, an overview of tandem mass spectrometry technology and bioinformatics for shotgun proteomics that make 2D-PAGE approaches obsolete. Non-labelling quantitative approaches have become more popular than labelling techniques on most proteomic platforms because they are easier to carry out while their quantitative outcome is rather robust. Parameters for recording mass spectrometry data, however, need to be chosen carefully and statistics to assess the confidence of the results should not be neglected. Interestingly, next-generation sequencing methodologies make any microbial model quickly amenable to proteomics, leading to the documentation of a wide range of organisms from diverse environments. Some recent discoveries made using microbial proteomics have challenged some biological dogma, such as: (i) initiation of the translation does not occur predominantly from ATG codons in some microorganisms, (ii) non-canonical initiation codons are used to regulate the production of specific but important proteins and (iii) a gene may code for multiple polypeptide species, heterogeneous in terms of sequences. Microbial diversity and microbial physiology can now be revisited by means of exhaustive comparative proteomic surveys where thousands of proteins are detected and quantified. Proteogenomics, consisting of better annotating of genomes with the help of proteomic evidence, is paving the way for integrated multi-omic approaches in microbiology. Finally, meta-proteomic tools and approaches are emerging for tackling the high complexity of the microbial world as a whole, opening new perspectives for assessing how microbial communities function.

Comparative metaproteomics and diversity analysis of human intestinal microbiota testifies for its temporal stability and expression of core functions

The human intestinal tract is colonized by microbial communities that show a subject-specific composition and a high-level temporal stability in healthy adults. To determine whether this is reflected at the functional level, we compared the faecal metaproteomes of healthy subjects over time using a novel high-throughput approach based on denaturing polyacrylamide gel electrophoresis and liquid chromatography–tandem mass spectrometry. The developed robust metaproteomics workflow and identification pipeline was used to study the composition and temporal stability of the intestinal metaproteome using faecal samples collected from 3 healthy subjects over a period of six to twelve months. The same samples were also subjected to DNA extraction and analysed for their microbial composition and diversity using the Human Intestinal Tract Chip, a validated phylogenetic microarray. Using metagenome and single genome sequence data out of the thousands of mass spectra generated per sample, approximately 1,000 peptides per sample were identified. Our results indicate that the faecal metaproteome is subject-specific and stable during a one-year period. A stable common core of approximately 1,000 proteins could be recognized in each of the subjects, indicating a common functional core that is mainly involved in carbohydrate transport and degradation. Additionally, a variety of surface proteins could be identified, including potential microbes-host interacting components such as flagellins and pili. Altogether, we observed a highly comparable subject-specific clustering of the metaproteomic and phylogenetic profiles, indicating that the distinct microbial activity is reflected by the individual composition.

Fourier transform infrared spectroscopy as a metabolite fingerprinting tool for monitoring the phenotypic changes in complex bacterial communities capable of degrading phenol

The coking process produces great volumes of wastewater contaminated with pollutants such as cyanides, sulfides and phenolics. Chemical and physical remediation of this wastewater removes the majority of these pollutants; however, these processes do not remove phenol and thiocyanate. The removal of these compounds has been effected during bioremediation with activated sludge containing a complex microbial community. In this investigation we acquired activated sludge from an industrial bioreactor capable of degrading phenol. The sludge was incubated in our laboratory and monitored for its ability to degrade phenol over a 48 h period. Multiple samples were taken across the time-course and analysed by Fourier transform infrared (FT-IR) spectroscopy. FT-IR was used as a whole-organism fingerprinting approach to monitor biochemical changes in the bacterial cells during the degradation of phenol. We also investigated the ability of the activated sludge to degrade phenol following extended periods (2-131 days) of storage in the absence of phenol. A reduction was observed in the ability of the microbial community to degrade phenol and this was accompanied by a detectable biochemical change in the FT-IR fingerprint related to cellular phenotype of the microbial community. In the absence of phenol a decrease in thiocyanate vibrations was observed, reflecting the ability of these communities to degrade this substrate. Actively degrading communities showed an additional new band in their FT-IR spectra that could be attributed to phenol degradation products from the ortho- and meta-cleavage of the aromatic ring. This study demonstrates that FT-IR spectroscopy when combined with chemometric analysis is a very powerful high throughput screening approach for assessing the metabolic capability of complex microbial communities.

An iterative workflow for mining the human intestinal metaproteome

BACKGROUND

Peptide spectrum matching (PSM) is the standard method in shotgun proteomics data analysis. It relies on the availability of an accurate and complete sample proteome that is used to make interpretation of the spectra feasible. Although this procedure has proven to be effective in many proteomics studies, the approach has limitations when applied on complex samples of microbial communities, such as those found in the human intestinal tract. Metagenome studies have indicated that the human intestinal microbiome contains over 100 times more genes than the human genome and it has been estimated that this ecosystem contains over 5000 bacterial species. The genomes of the vast majority of these species have not yet been sequenced and hence their proteomes remain unknown. To enable data analysis of shotgun proteomics data using PSM, and circumvent the lack of a defined matched metaproteome, an iterative workflow was developed that is based on a synthetic metaproteome and the developing metagenomic databases that are both representative for but not necessarily originating from the sample of interest.

RESULTS

Two human fecal samples for which metagenomic data had been collected, were analyzed for their metaproteome using liquid chromatography-mass spectrometry and used to benchmark the developed iterative workflow to other methods. The results show that the developed method is able to detect over 3,000 peptides per fecal sample from the spectral data by circumventing the lack of a defined proteome without naive translation of matched metagenomes and cross-species peptide identification.

CONCLUSIONS

The developed iterative workflow achieved an approximate two-fold increase in the amount of identified spectra at a false discovery rate of 1% and can be applied in metaproteomic studies of the human intestinal tract or other complex ecosystems.

Liquid chromatography-mass spectrometry-based proteomics of Nitrosomonas

During the last century, the research on aerobic ammonium-oxidizing bacteria (AOB) lead to many exciting physiological and biochemical discoveries. Nevertheless the molecular biology of AOB is not well understood. The availability of the genome sequences of several Nitrosomonas species opened up new possiblities to use state of the art transcriptomic and proteomic tools to study AOB. With the currect technology, thousands of proteins can be analyzed in several hours of measurement and translated proteins can be detected at femtomole and attomole concentrations. Moreover, it is possible to use mass spectrometry-based proteomics approach to analyze the expression, subcellular localization, posttranslational modifications, and interactions of translated proteins. In this chapter, we describe our LC-MS/MS methodology and quality control strategy to study the protein complement of Nitrosomonas eutropha C91.

Stress induced cross-protection against environmental challenges on prokaryotic and eukaryotic microbes

Prokaryotic and eukaryotic microbes thrive successfully in stressful environments such as high osmolarity, acidic or alkali, solar heat and u.v. radiation, nutrient starvation, oxidative stress, and several others. To live under these continuous stress conditions, these microbes must have mechanisms to protect their proteins, membranes, and nucleic acids, as well as other mechanisms that repair nucleic acids. The stress responses in bacteria are controlled by master regulators, which include alternative sigma factors, such as RpoS and RpoH. The sigma factor RpoS integrates multiple signals, such as the general stress response regulators and the sigma factor RpoH regulates the heat shock proteins. These response pathways extensively overlap and are induced to various extents by the same environmental stresses. In eukaryotes, two major pathways regulate the stress responses: stress proteins, termed heat shock proteins (HSP), which appear to be required only for growth during moderate stress, and stress response elements (STRE), which are induced by different stress conditions and these elements result in the acquisition of a tolerant state towards any stress condition. In this review, the mechanisms of stress resistance between prokaryotic and eukaryotic microbes will be described and compared.

Environmental proteomics: analysis of structure and function of microbial communities

Prokaryotic and eukaryotic microorganisms make a vital contribution to biogeochemical cycles by decomposing virtually all natural compounds and thereby exert a lasting effect on biosphere and climate. The rapidly growing number of metagenomic sequences together with revolutionary advances in bioinformatics and protein analyses have opened completely new horizons to investigate the molecular basis of such complex processes. Proteomics has contributed substantially to our understanding of individual organisms at the cellular level as it offers excellent possibilities to probe many protein functions and responses simultaneously. However, it has not yet been widely applied in microbial ecology, although most proteins have an intrinsic metabolic function which can be used to relate microbial activities to the identity of defined organisms in multispecies communities. Albeit still in its infancy, environmental proteomics enables simple protein cataloging, comparative and semi-quantitative proteomics, analyses of protein localization, discovery of post-translational modifications, and even determination of amino-acid sequences and genotypes by strain-resolved proteogenomics. This review traces the historical development of environmental proteomics and summarizes milestone publications in the field. In conclusion, we briefly discuss current limitations of microbial community proteomics but also the potential of emerging technologies to shape the future of metaproteome analyses.

Integrating multiple 'omics' analysis for microbial biology: application and methodologies

Recent advances in various 'omics' technologies enable quantitative monitoring of the abundance of various biological molecules in a high-throughput manner, and thus allow determination of their variation between different biological states on a genomic scale. Several popular 'omics' platforms that have been used in microbial systems biology include transcriptomics, which measures mRNA transcript levels; proteomics, which quantifies protein abundance; metabolomics, which determines abundance of small cellular metabolites; interactomics, which resolves the whole set of molecular interactions in cells; and fluxomics, which establishes dynamic changes of molecules within a cell over time. However, no single 'omics' analysis can fully unravel the complexities of fundamental microbial biology. Therefore, integration of multiple layers of information, the multi-'omics' approach, is required to acquire a precise picture of living micro-organisms. In spite of this being a challenging task, some attempts have been made recently to integrate heterogeneous 'omics' datasets in various microbial systems and the results have demonstrated that the multi-'omics' approach is a powerful tool for understanding the functional principles and dynamics of total cellular systems. This article reviews some basic concepts of various experimental 'omics' approaches, recent application of the integrated 'omics' for exploring metabolic and regulatory mechanisms in microbes, and advances in computational and statistical methodologies associated with integrated 'omics' analyses. Online databases and bioinformatic infrastructure available for integrated 'omics' analyses are also briefly discussed.