Functional analysis of natural microbial consortia using community proteomics

Metaproteomics: harnessing the power of high performance mass spectrometry to identify the suite of proteins that control metabolic activities in microbial communities

The availability of extensive genome information for many different microbes, including unculturable species in mixed communities from environmental samples, has enabled systems-biology interrogation by providing a means to access genomic, transcriptomic, and proteomic information. To this end, metaproteomics exploits the power of high-performance mass spectrometry for extensive characterization of the complete suite of proteins expressed by a microbial community in an environmental sample.

Beyond the genome: community-level analysis of the microbial world

The development of culture-independent strategies to study microbial diversity and function has led to a revolution in microbial ecology, enabling us to address fundamental questions about the distribution of microbes and their influence on Earth's biogeochemical cycles. This article discusses some of the progress that scientists have made with the use of so-called "omic" techniques (metagenomics, metatranscriptomics, and metaproteomics) and the limitations and major challenges these approaches are currently facing. These 'omic methods have been used to describe the taxonomic structure of microbial communities in different environments and to discover new genes and enzymes of industrial and medical interest. However, microbial community structure varies in different spatial and temporal scales and none of the 'omic techniques are individually able to elucidate the complex aspects of microbial communities and ecosystems. In this article we highlight the importance of a spatiotemporal sampling design, together with a multilevel 'omic approach and a community analysis strategy (association networks and modeling) to examine and predict interacting microbial communities and their impact on the environment.

Proteomic analysis of an unculturable bacterial endosymbiont (Blochmannia) reveals high abundance of chaperonins and biosynthetic enzymes

Many insect groups have coevolved with bacterial endosymbionts that live within specialized host cells. As a salient example, ants in the tribe Camponotini rely on Blochmannia, an intracellular bacterial mutualist that synthesizes amino acids and recycles nitrogen for the host. We performed a shotgun, label-free, LC/MS/MS quantitative proteomic analysis to investigate the proteome of Blochmannia associated with Camponotus chromaiodes. We identified more than 330 Blochmannia proteins, or 54% coverage of the predicted proteome, as well as 244 Camponotus proteins. Using the average intensity of the top 3 "best flier" peptides along with spiking of a surrogate standard at a known concentration, we estimated the concentration (fmol/μg) of those proteins with confident identification. The estimated dynamic range of Blochmannia protein abundance spanned 3 orders of magnitude and covered diverse functional categories, with particularly high representation of metabolism, information transfer, and chaperones. GroEL, the most abundant protein, totaled 6% of Blochmannia protein abundance. Biosynthesis of essential amino acids, fatty acids, and nucleotides, and sulfate assimilation had disproportionately high coverage in the proteome, further supporting a nutritional role of the symbiosis. This first quantitative proteomic analysis of an ant endosymbiont illustrates a promising approach to study the functional basis of intimate symbioses.

Quantitative proteomic analysis of ibuprofen-degrading Patulibacter sp. strain I11

Ibuprofen is the third most consumed pharmaceutical drug in the world. Several isolates have been shown to degrade ibuprofen, but very little is known about the biochemistry of this process. This study investigates the degradation of ibuprofen by Patulibacter sp. strain I11 by quantitative proteomics using a metabolic labelling strategy. The whole-genome of Patulibacter sp. strain I11 was sequenced to provide a species-specific protein platform for optimal protein identification. The bacterial proteomes of actively ibuprofen-degrading cells and cells grown in the absence of ibuprofen was identified and quantified by gel based shotgun-proteomics. In total 251 unique proteins were quantitated using this approach. Biological process and pathway analysis indicated a number of proteins that were up-regulated in response to active degradation of ibuprofen, some of them are known to be involved in the degradation of aromatic compounds. Data analysis revealed that several of these proteins are likely involved in ibuprofen degradation by Patulibacter sp. strain I11.

Genome-based Modeling and Design of Metabolic Interactions in Microbial Communities

Biotechnology research is traditionally focused on individual microbial strains that are perceived to have the necessary metabolic functions, or the capability to have these functions introduced, to achieve a particular task. For many important applications, the development of such omnipotent microbes is an extremely challenging if not impossible task. By contrast, nature employs a radically different strategy based on synergistic combinations of different microbial species that collectively achieve the desired task. These natural communities have evolved to exploit the native metabolic capabilities of each species and are highly adaptive to changes in their environments. However, microbial communities have proven difficult to study due to a lack of suitable experimental and computational tools. With the advent of genome sequencing, omics technologies, bioinformatics and genome-scale modeling, researchers now have unprecedented capabilities to analyze and engineer the metabolism of microbial communities. The goal of this review is to summarize recent applications of genome-scale metabolic modeling to microbial communities. A brief introduction to lumped community models is used to motivate the need for genome-level descriptions of individual species and their metabolic interactions. The review of genome-scale models begins with static modeling approaches, which are appropriate for communities where the extracellular environment can be assumed to be time invariant or slowly varying. Dynamic extensions of the static modeling approach are described, and then applications of genome-scale models for design of synthetic microbial communities are reviewed. The review concludes with a summary of metagenomic tools for analyzing community metabolism and an outlook for future research.

Soil metaproteomics - Comparative evaluation of protein extraction protocols

Metaproteomics and its potential applications are very promising to study microbial activity in environmental samples and to obtain a deeper understanding of microbial interactions. However, due to the complexity of soil samples the exhaustive extraction of proteins is a major challenge. We compared soil protein extraction protocols in terms of their protein extraction efficiency for two different soil types. Four different protein extraction procedures were applied based on (a) SDS extraction without phenol, (b) NaOH and subsequent phenol extraction, (c) SDS-phenol extraction and (d) SDS-phenol extraction with prior washing steps. To assess the suitability of these methods for the functional analysis of the soil metaproteome, they were applied to a potting soil high in organic matter and a forest soil. Proteins were analyzed by two-dimensional liquid chromatography/tandem mass spectrometry (2D-LC-MS/MS) and the number of unique spectra as well as the number of assigned proteins for each of the respective protocols was compared. In both soil types, extraction with SDS-phenol (c) resulted in "high" numbers of proteins. Moreover, a spiking experiment was conducted to evaluate protein recovery. To this end sterilized forest soil was amended with proteins from pure cultures of Pectobacterium carotovorum and Aspergillus nidulans. The protein recovery in the spiking experiment was almost 50%. Our study demonstrates that a critical evaluation of the extraction protocol is crucial for the quality of the metaproteomics data, especially in highly complex samples like natural soils.

Bacterial community composition in the water column of a lake formed by a former uranium open pit mine

Mining of pyrite minerals is a major environmental issue involving both biological and geochemical processes. Here we present a study of an artificial lake of a former uranium open pit mine with the aim to connect the chemistry and bacterial community composition (454-pyrosequencing of 16S rRNA genes) in the stratified water column. A shift in the water chemistry from oxic conditions in the epilimnion to anoxic, alkaline, and metal and sulfide-rich conditions in the hypolimnion was corresponded by a strong shift in the bacterial community, with few shared operational taxonomic units (OTU) between the water layers. The epilimnetic bacterial community of the lake (~20 years old) showed similarities to other temperate freshwater lakes, while the hypolimnetic bacterial community showed similarity to extreme chemical environments. The epilimnetic bacterial community had dominance of Actinobacteria and Betaproteobacteria. The hypolimnion displayed a higher bacterial diversity and was dominated by the phototrophic green sulphur bacterium of the genus Chlorobium (ca. 40 % of the total community). Deltaproteobacteria were only represented in the hypolimnion and the most abundant OTUs were affiliated with ferric iron and sulfate reducers of the genus Geobacter and Desulfobulbus, respectively. The chemistry is clearly controlling, especially the hypolimnetic, bacterial community but the community composition also indicates that the bacteria are involved in metal cycling in the lake.

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.

Community and proteomic analysis of methanogenic consortia degrading terephthalate

Degradation of terephthalate (TA) through microbial syntrophy under moderately thermophilic (46 to 50°C) methanogenic conditions was characterized by using a metagenomic approach (A. Lykidis et al., ISME J. 5:122-130, 2011). To further study the activities of key microorganisms responsible for the TA degradation, community analysis and shotgun proteomics were used. The results of hierarchical oligonucleotide primer extension analysis of PCR-amplified 16S rRNA genes indicated that Pelotomaculum, Methanosaeta, and Methanolinea were predominant in the TA-degrading biofilms. Metaproteomic analysis identified a total of 482 proteins and revealed a distinctive distribution pattern of microbial functions expressed in situ. The results confirmed that TA was degraded by Pelotomaculum spp. via the proposed decarboxylation and benzoyl-coenzyme A-dependent pathway. The intermediate by-products, including acetate, H(2)/CO(2), and butyrate, were produced to support the growth of methanogens, as well as other microbial populations that could further degrade butyrate. Proteins related to energy production and conservation, and signal transduction mechanisms (that is, chemotaxis, PAS/GGDEF regulators, and stress proteins) were highly expressed, and these mechanisms were important for growth in energy-limited syntrophic ecosystems.

Microbial metabolomics

Microbial metabolomics constitutes an integrated component of systems biology. By studying the complete set of metabolites within a microorganism and monitoring the global outcome of interactions between its development processes and the environment, metabolomics can potentially provide a more accurate snap shot of the actual physiological state of the cell. Recent advancement of technologies and post-genomic developments enable the study and analysis of metabolome. This unique contribution resulted in many scientific disciplines incorporating metabolomics as one of their “omics” platforms. This review focuses on metabolomics in microorganisms and utilizes selected topics to illustrate its impact on the understanding of systems microbiology.

PaxDb, a database of protein abundance averages across all three domains of life

Although protein expression is regulated both temporally and spatially, most proteins have an intrinsic, "typical" range of functionally effective abundance levels. These extend from a few molecules per cell for signaling proteins, to millions of molecules for structural proteins. When addressing fundamental questions related to protein evolution, translation and folding, but also in routine laboratory work, a simple rough estimate of the average wild type abundance of each detectable protein in an organism is often desirable. Here, we introduce a meta-resource dedicated to integrating information on absolute protein abundance levels; we place particular emphasis on deep coverage, consistent post-processing and comparability across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. By aggregating and averaging over the various samples, conditions and cell-types, the resulting integrated data set achieves increased coverage and a high dynamic range. We score and rank each contributing, individual data set by assessing its consistency against externally provided protein-network information, and demonstrate that our weighted integration exhibits more consistency than the data sets individually. The current PaxDb-release 2.1 (at http://pax-db.org/) presents whole-organism data as well as tissue-resolved data, and covers 85,000 proteins in 12 model organisms. All values can be seamlessly compared across organisms via pre-computed orthology relationships.

Stable isotope peptide mass spectrometry to decipher amino acid metabolism in Dehalococcoides strain CBDB1

Dehalococcoides species are key players in the anaerobic transformation of halogenated solvents at contaminated sites. Here, we analyze isotopologue distributions in amino acid pools from peptides of Dehalococcoides strain CBDB1 after incubation with (13)C-labeled acetate or bicarbonate as a carbon source. The resulting data were interpreted with regard to genome annotations to identify amino acid biosynthesis pathways. In addition to using gas chromatography-mass spectrometry (GC-MS) for analyzing derivatized amino acids after protein hydrolysis, we introduce a second, much milder method, in which we directly analyze peptide masses after tryptic digest and peptide fragments by nano-liquid chromatography-electrospray ionization-tandem mass spectrometry (nano-LC-ESI-MS/MS). With this method, we identify isotope incorporation patterns for 17 proteinaceous amino acids, including proline, cysteine, lysine, and arginine, which escaped previous analyses in Dehalococcoides. Our results confirmed lysine biosynthesis via the α-aminoadipate pathway, precluding lysine formation from aspartate. Similarly, the isotopologue pattern obtained for arginine provided biochemical evidence of its synthesis from glutamate. Direct peptide MS/MS analysis of the labeling patterns of glutamine and asparagine, which were converted to glutamate and aspartate during protein hydrolysis, gave biochemical evidence of their precursors and confirmed glutamate biosynthesis via a Re-specific citrate synthase. By addition of unlabeled free amino acids to labeled cells, we show that in strain CBDB1 none of the 17 tested amino acids was incorporated into cell mass, indicating that they are all synthesized de novo. Our approach is widely applicable and provides a means to analyze amino acid metabolism by studying specific proteins even in mixed consortia.

Microbial metaproteomics: identifying the repertoire of proteins that microorganisms use to compete and cooperate in complex environmental communities

The availability of genome information for microbial consortia, including unculturable species, from environmental samples has enabled systems-biology interrogation by providing a means to access genomic, transcriptomic, and proteomic information. This provides a unique opportunity to characterize the molecular activities and interactions of these microbial systems at a comprehensive level never before possible. Such information not only provides details about the organizational, functional, and metabolic activities of such systems, but also the untapped reserve of molecular activities that might be invoked and exploited under certain environmental conditions. Since bacteria naturally exist in complex ecosystems, it is imperative to develop and utilize analytical approaches that can provide molecular level details on systems consisting of mixed microbial membership. This is the realm of metaproteomics-the characterization of the complement of proteins expressed by a microbial community in an environmental sample.

Exploring mixed microbial community functioning: recent advances in metaproteomics

System approaches to elucidate ecosystem functioning constitute an emerging area of research within microbial ecology. Such approaches aim at investigating all levels of biological information (DNA, RNA, proteins and metabolites) to capture the functional interactions occurring in a given ecosystem and track down characteristics that could not be accessed by the study of isolated components. In this context, the study of the proteins collectively expressed by all the microorganisms present within an ecosystem (metaproteomics) is not only crucial but can also provide insights into microbial functionality. Overall, the success of metaproteomics is closely linked to metagenomics, and with the exponential increase in the availability of metagenome sequences, this field of research is starting to experience generation of an overwhelming amount of data, which requires systematic analysis. Metaproteomics has been employed in very diverse environments, and this review discusses the recent advances achieved in the context of human biology, soil, marine and freshwater environments as well as natural and bioengineered systems.

Key players and team play: anaerobic microbial communities in hydrocarbon-contaminated aquifers

Biodegradation of anthropogenic pollutants in shallow aquifers is an important microbial ecosystem service which is mainly brought about by indigenous anaerobic microorganisms. For the management of contaminated sites, risk assessment and control of natural attenuation, the assessment of in situ biodegradation and the underlying microbial processes is essential. The development of novel molecular methods, "omics" approaches, and high-throughput techniques has revealed new insight into complex microbial communities and their functions in anoxic environmental systems. This review summarizes recent advances in the application of molecular methods to study anaerobic microbial communities in contaminated terrestrial subsurface ecosystems. We focus on current approaches to analyze composition, dynamics, and functional diversity of subsurface communities, to link identity to activity and metabolic function, and to identify the ecophysiological role of not yet cultured microbes and syntrophic consortia. We discuss recent molecular surveys of contaminated sites from an ecological viewpoint regarding degrader ecotypes, abiotic factors shaping anaerobic communities, and biotic interactions underpinning the importance of microbial cooperation for microbial ecosystem services such as contaminant degradation.

Environmental proteomics, biodiversity statistics and food-web structure

Pioneering studies in environmental proteomics have revealed links between protein diversity and ecological function in simple ecological communities, such as microbial biofilms. In the near future, high-throughput proteomic methods will be applied to more complex ecological systems in which microbes and macrobes interact. Data structures in biodiversity and protein surveys have many similarities, so the statistical methods that ecologists use for analyzing biodiversity data should be adapted for use with quantitative surveys of protein diversity. However, increasing quantities of protein and bioinformatics data will not, by themselves, reveal the functional significance of proteins. Instead, ecologists should be measuring changes in the abundance of protein cohorts in response to replicated field manipulations, including nutrient enrichment and removal of top predators.

Targeted isolation of proteins from natural microbial communities living in an extreme environment

Microorganisms from extreme environments are often very difficult to cultivate, precluding detailed study by biochemical and physiological techniques. Recent advances in genomic sequencing and proteomic measurements of samples obtained from natural communities have allowed new access to these uncultivated extremophiles and identified abundant proteins that can be isolated directly from natural samples. Here we report the isolation of two abundant heme proteins from low-diversity biofilm microbial communities that thrive in very acidic (pH ~ 1), metal-rich water in a subsurface mine. Purification and detailed characterization of these proteins has afforded new insight into the possible mechanism of Fe(II) oxidation by Leptospirillum Group II, the dominant population in most of these biofilms, and demonstrated that the abundance and posttranslational modifications of one of these proteins is dependent on the lifecycle of the biofilm.

Global transcriptomic and proteomic responses of Dehalococcoides ethenogenes strain 195 to fixed nitrogen limitation

Bacteria of the genus Dehalococcoides play an important role in the reductive dechlorination of chlorinated ethenes. A systems-level approach was taken in this study to examine the global transcriptomic and proteomic responses of exponentially growing cells of Dehalococcoides ethenogenes strain 195 to fixed nitrogen limitation (FNL), as dechlorination activity and cell yield both decrease during FNL. As expected, the nitrogen-fixing (nif) genes were differentially upregulated in the transcriptome and proteome of strain 195 during FNL. Aside from the nif operon, a putative methylglyoxal synthase-encoding gene (DET1576), the product of which is predicted to catalyze the formation of the toxic electrophile methylglyoxal and is implicated in the uncoupling of anabolism from catabolism in bacteria, was strongly upregulated in the transcriptome and could potentially play a role in the observed growth inhibition during FNL. Carbon catabolism genes were generally downregulated in response to FNL, and a number of transporters were differentially regulated in response to nitrogen limitation, with some playing apparent roles in nitrogen acquisition, while others were associated with general stress responses. A number of genes related to the functions of nucleotide synthesis, replication, transcription, translation, and posttranslational modifications were also differentially expressed. One gene coding for a putative reductive dehalogenase (DET1545) and a number of genes coding for oxidoreductases, which have implications in energy generation and redox reactions, were also differentially regulated. Interestingly, most of the genes within the multiple integrated elements were not differentially expressed. Overall, this study elucidates the molecular responses of strain 195 to FNL and identifies differentially expressed genes that are potential biomarkers to evaluate environmental cellular nitrogen status.

Molecular musings in microbial ecology and evolution

A few major discoveries have influenced how ecologists and evolutionists study microbes. Here, in the format of an interview, we answer questions that directly relate to how these discoveries are perceived in these two branches of microbiology, and how they have impacted on both scientific thinking and methodology.

The first question is "What has been the influence of the 'Universal Tree of Life' based on molecular markers?" For evolutionists, the tree was a tool to understand the past of known (cultured) organisms, mapping the invention of various physiologies on the evolutionary history of microbes. For ecologists the tree was a guide to discover the current diversity of unknown (uncultured) organisms, without much knowledge of their physiology.

The second question we ask is "What was the impact of discovering frequent lateral gene transfer among microbes?" In evolutionary microbiology, frequent lateral gene transfer (LGT) made a simple description of relationships between organisms impossible, and for microbial ecologists, functions could not be easily linked to specific genotypes. Both fields initially resisted LGT, but methods or topics of inquiry were eventually changed in one to incorporate LGT in its theoretical models (evolution) and in the other to achieve its goals despite that phenomenon (ecology).

The third and last question we ask is "What are the implications of the unexpected extent of diversity?" The variation in the extent of diversity between organisms invalidated the universality of species definitions based on molecular criteria, a major obstacle to the adaptation of models developed for the study of macroscopic eukaryotes to evolutionary microbiology. This issue has not overtly affected microbial ecology, as it had already abandoned species in favor of the more flexible operational taxonomic units. This field is nonetheless moving away from traditional methods to measure diversity, as they do not provide enough resolution to uncover what lies below the species level.

The answers of the evolutionary microbiologist and microbial ecologist to these three questions illustrate differences in their theoretical frameworks. These differences mean that both fields can react quite distinctly to the same discovery, incorporating it with more or less difficulty in their scientific practice.

Reviewers

This article was reviewed by W. Ford Doolittle, Eugene V. Koonin and Maureen A. O'Malley.

Examination of microbial proteome preservation techniques applicable to autonomous environmental sample collection

Improvements in temporal and spatial sampling frequency have the potential to open new windows into the understanding of marine microbial dynamics. In recent years, efforts have been made to allow automated samplers to collect microbial biomass for DNA/RNA analyses from moored observatories and autonomous underwater vehicles. Measurements of microbial proteins are also of significant interest given their biogeochemical importance as enzymes that catalyze reactions and transporters that interface with the environment. We examined the influence of five preservatives solutions (SDS-extraction buffer, ethanol, trichloroacetic acid, B-PER, and RNAlater) on the proteome integrity of the marine cyanobacterium Synechococcus WH8102 after 4 weeks of storage at room temperature. Four approaches were used to assess degradation: total protein recovery, band integrity on an SDS detergent polyacrylamide electrophoresis (SDS-PAGE) gel, and number of protein identifications and relative abundances by 1-dimensional LC–MS/MS proteomic analyses. Total protein recoveries from the preserved samples were lower than the frozen control due to processing losses, which could be corrected for with internal standardization. The trichloroacetic acid preserved sample showed significant loss of protein band integrity on the SDS-PAGE gel. The RNAlater preserved sample showed the highest number of protein identifications (103% relative to the control; 520 ± 31 identifications in RNAlater versus 504 ± 4 in the control), equivalent to the frozen control. Relative abundances of individual proteins in the RNAlater treatment were quite similar to that of the frozen control (average ratio of 1.01 ± 0.27 for the 50 most abundant proteins), while the SDS-extraction buffer, ethanol, and B-PER all showed significant decreases in both number of identifications and relative abundances of individual proteins. Based on these findings, RNAlater was an effective proteome preservative, although further study is warranted on additional marine microbes.

Proteomic insights into the lifestyle of an environmentally relevant marine bacterium

In terms of lifestyle, free-living bacteria are classified as either oligotrophic/specialist or opportunist/generalist. Heterogeneous marine environments such as coastal waters favour the establishment of marine generalist bacteria, which code for a large pool of functions. This is basically foreseen to cope with the heterogeneity of organic matter supplied to these systems. Nevertheless, it is not known what fraction of a generalist proteome is needed for house-keeping functions or what fraction is modified to cope with environmental changes. Here, we used high-throughput proteomics to define the proteome of Ruegeria pomeroyi DSS-3, a model marine generalist bacterium of the Roseobacter clade. We evaluated its genome expression under several natural environmental conditions, revealing the versatility of the bacterium to adapt to anthropogenic influence, poor nutrient concentrations or the presence of the natural microbial community. We also assayed 30 different laboratory incubations to increase proteome coverage and to dig further into the functional genomics of the bacterium. We established its core proteome and the proteome devoted to adaptation to general cellular physiological variations (almost 50%). We suggest that the other half of its theoretical proteome is the opportunist genetic pool devoted exclusively to very specific environmental conditions.

Glycoside hydrolase activities of thermophilic bacterial consortia adapted to switchgrass

Industrial-scale biofuel production requires robust enzymatic cocktails to produce fermentable sugars from lignocellulosic biomass. Thermophilic bacterial consortia are a potential source of cellulases and hemicellulases adapted to harsher reaction conditions than commercial fungal enzymes. Compost-derived microbial consortia were adapted to switchgrass at 60°C to develop thermophilic biomass-degrading consortia for detailed studies. Microbial community analysis using small-subunit rRNA gene amplicon pyrosequencing and short-read metagenomic sequencing demonstrated that thermophilic adaptation to switchgrass resulted in low-diversity bacterial consortia with a high abundance of bacteria related to thermophilic paenibacilli, Rhodothermus marinus, and Thermus thermophilus. At lower abundance, thermophilic Chloroflexi and an uncultivated lineage of the Gemmatimonadetes phylum were observed. Supernatants isolated from these consortia had high levels of xylanase and endoglucanase activities. Compared to commercial enzyme preparations, the endoglucanase enzymes had a higher thermotolerance and were more stable in the presence of 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]), an ionic liquid used for biomass pretreatment. The supernatants were used to saccharify [C2mim][OAc]-pretreated switchgrass at elevated temperatures (up to 80°C), demonstrating that these consortia are an excellent source of enzymes for the development of enzymatic cocktails tailored to more extreme reaction conditions.

Bacterial adaptation to life in association with plants - A proteomic perspective from culture to in situ conditions

Diverse bacterial taxa that live in association with plants affect plant health and development. This is most evident for those bacteria that undergo a symbiotic association with plants or infect the plants as pathogens. Proteome analyses have contributed significantly toward a deeper understanding of the molecular mechanisms underlying the development of these associations. They were applied to obtain a general overview of the protein composition of these bacteria, but more so to study effects of plant signaling molecules on the cytosolic proteome composition or metabolic adaptations upon plant colonization. Proteomic analyses are particularly useful for the identification of secreted proteins, which are indispensable to manipulate a host plant. Recent advances in the field of proteome analyses have initiated a new research area, the analysis of more complex microbial communities. Such studies are just at their beginning but hold great potential for the future to elucidate not only the interactions between bacteria and their host plants, but also of bacteria-bacteria interactions between different bacterial taxa when living in association with plants. These include not only the symbiotic and pathogenic bacteria, but also the commensal bacteria that are consistently found in association with plants and whose functions remain currently largely uncovered.

Quantitative tracking of isotope flows in proteomes of microbial communities

Stable isotope probing (SIP) has been used to track nutrient flows in microbial communities, but existing protein-based SIP methods capable of quantifying the degree of label incorporation into peptides and proteins have been demonstrated only by targeting usually less than 100 proteins per sample. Our method automatically (i) identifies the sequence of and (ii) quantifies the degree of heavy atom enrichment for thousands of proteins from microbial community proteome samples. These features make our method suitable for comparing isotopic differences between closely related protein sequences, and for detecting labeling patterns in low-abundance proteins or proteins derived from rare community members. The proteomic SIP method was validated using proteome samples of known stable isotope incorporation levels at 0.4%, ∼50%, and ∼98%. The method was then used to monitor incorporation of (15)N into established and regrowing microbial biofilms. The results indicate organism-specific migration patterns from established communities into regrowing communities and provide insights into metabolism during biofilm formation. The proteomic SIP method can be extended to many systems to track fluxes of (13)C or (15)N in microbial communities.

Do nutrient-gut-microbiota interactions play a role in human obesity, insulin resistance and type 2 diabetes?

The current obesity and type 2 diabetes pandemics have causes beyond changes in eating and exercise habits against a susceptible genetic background. Gut bacteria seem to additionally contribute to the differences in body weight, fat distribution, insulin sensitivity and glucose- and lipid-metabolism. Data, mostly derived from preclinical studies, suggest that gut microbiota play an important role in conditions such as obesity, diabetes, metabolic syndrome and non-alcoholic fatty liver disease. Regulation of energy uptake from the gut, by digesting otherwise indigestible common polysaccharides in our diet, production or activation of signalling molecules involved in host metabolism, modification of gut permeability, the release of gut hormones and inflammation, are among the mechanisms by which gut microbiota may influence the host cardiometabolic phenotype. Recent evidence suggests that quantitative and qualitative differences in gut microbiota exist between lean and obese, and between diabetic and non-diabetic individuals. Modification of the gut microbiota composition and/or its biochemical capacity by specific dietary or pharmacological interventions may favourably affect host metabolism. Large-scale intervention trials, investigating the potential benefit of prebiotics and probiotics in improving cardiometabolic health in high-risk populations, are eagerly awaited.

Dynamic flux balance modeling of microbial co-cultures for efficient batch fermentation of glucose and xylose mixtures

Sequential uptake of pentose and hexose sugars that compose lignocellulosic biomass limits the ability of pure microbial cultures to efficiently produce value-added bioproducts. In this work, we used dynamic flux balance modeling to examine the capability of mixed cultures of substrate-selective microbes to improve the utilization of glucose/xylose mixtures and to convert these mixed substrates into products. Co-culture simulations of Escherichia coli strains ALS1008 and ZSC113, engineered for glucose and xylose only uptake respectively, indicated that improvements in batch substrate consumption observed in previous experimental studies resulted primarily from an increase in ZSC113 xylose uptake relative to wild-type E. coli. The E. coli strain ZSC113 engineered for the elimination of glucose uptake was computationally co-cultured with wild-type Saccharomyces cerevisiae, which can only metabolize glucose, to determine if the co-culture was capable of enhanced ethanol production compared to pure cultures of wild-type E. coli and the S. cerevisiae strain RWB218 engineered for combined glucose and xylose uptake. Under the simplifying assumption that both microbes grow optimally under common environmental conditions, optimization of the strain inoculum and the aerobic to anaerobic switching time produced an almost twofold increase in ethanol productivity over the pure cultures. To examine the effect of reduced strain growth rates at non-optimal pH and temperature values, a break even analysis was performed to determine possible reductions in individual strain substrate uptake rates that resulted in the same predicted ethanol productivity as the best pure culture.

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.

Using genomics to develop novel antibacterial therapeutics

As the genomics era matures, the availability of complete microbial genome sequences is facilitating computational approaches to understand bacterial genomes and DNA structure/function relationships. From the genome of pathogens, we can derive invaluable information on potential targets for new antimicrobial agents. Advancements in high-throughput 'omics' technologies and the availability of multiple isolates of the same species have significantly changed the time frame and scope for identifying novel therapeutic targets. This article aims to discuss selected aspects of the bacterial genome, and advocates 'omics'-based techniques to advance the discovery of new therapeutic targets against extracellular bacterial pathogens.

Direct cellular lysis/protein extraction protocol for soil metaproteomics

We present a novel direct protocol for deep proteome characterization of microorganisms in soil. The method employs thermally assisted detergent-based cellular lysis (SDS) of soil samples, followed by TCA precipitation for proteome extraction/cleanup prior to liquid chromatography-mass spectrometric characterization. This approach was developed and optimized using different soils inoculated with genome-sequenced bacteria (Gram-negative Pseudomonas putida or Gram-positive Arthrobacter chlorophenolicus). Direct soil protein extraction was compared to protein extraction from cells isolated from the soil matrix prior to lysis (indirect method). Each approach resulted in identification of greater than 500 unique proteins, with a wide range in molecular mass and functional categories. To our knowledge, this SDS-TCA approach enables the deepest proteome characterizations of microbes in soil to date, without significant biases in protein size, localization, or functional category compared to pure cultures. This protocol should provide a powerful tool for ecological studies of soil microbial communities.

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.

Systems approaches to microbial communities and their functioning

Recent advances in molecular microbial ecology and systems biology enhance insight into microbial community structure and functioning. They provide conceptual and technical bases for the translation of species-data and community-data into a model framework accounting for the functioning of and interactions between metabolic networks of species in multispecies environments. Function-directed and single cell-directed approaches supplement and improve metagenomics-derived community information. The topology of the metabolic network, reconstructed from a species' genome sequence, provides insight into its metabolic environments and interactions with other microorganisms. Progress in the theoretical and experimental analysis of flux through metabolic networks paves the way for their application at the community level, contributing to understanding of material flows between and within species and their resilience toward perturbations.

Ecological distribution and population physiology defined by proteomics in a natural microbial community

An important challenge in microbial ecology is developing methods that simultaneously examine the physiology of organisms at the molecular level and their ecosystem level interactions in complex natural systems. We integrated extensive proteomic, geochemical, and biological information from 28 microbial communities collected from an acid mine drainage environment and representing a range of biofilm development stages and geochemical conditions to evaluate how the physiologies of the dominant and less abundant organisms change along environmental gradients. The initial colonist dominates across all environments, but its proteome changes between two stable states as communities diversify, implying that interspecies interactions affect this organism's metabolism. Its overall physiology is robust to abiotic environmental factors, but strong correlations exist between these factors and certain subsets of proteins, possibly accounting for its wide environmental distribution. Lower abundance populations are patchier in their distribution, and proteomic data indicate that their environmental niches may be constrained by specific sets of abiotic environmental factors. This research establishes an effective strategy to investigate ecological relationships between microbial physiology and the environment for whole communities in situ.

Thiamine biosynthesis can be used to dissect metabolic integration

The emergence of systems biology has re-emphasized the advantages of understanding biological processes with a global perspective. One biological process amenable to global approaches is microbial metabolism. This review describes a model system that contributes to the goals of systems biology by experimentally defining metabolic integration found in a bacterial cell and thus providing data needed for implementation and interpretation of systems approaches. We have taken a largely unbiased in vivo approach centered on thiamine biosynthesis to identify new metabolic components and connections, and to explore uncharacterized paradigms of the integration between them. This article summarizes recent results from this approach that include the identification of the function of unknown genes, connections between cofactors biosynthesis and thiamine biosynthesis, and how metabolites from one biosynthetic pathway can be used in thiamine biosynthesis.

Recent progress and new challenges in metagenomics for biotechnology

A brief historical perspective on metagenomics is given followed by a discussion of the rapid progress in this field largely defined by transition to the next generation sequencing technologies. Problems and challenges connected to this transition are also addressed. The review focuses on recent literature describing metagenomic approaches connecting sequence information to functionality that are especially relevant to biotechnological applications, including metagenomics of specialized or enriched microbial communities, metagenomics combined with specific labeling techniques, metatranscriptomics and metaproteomics.

Redefining the role of intestinal microbes in the pathogenesis of necrotizing enterocolitis

Neonatal necrotizing enterocolitis (NEC) remains an important cause of morbidity and mortality among very low birth weight infants. It has long been suspected that intestinal microbes contribute to the pathogenesis of NEC, but the details of this relationship remain poorly understood. Recent advances in molecular biology and enteric microbiology have improved our ability to characterize intestinal microbes from infants with NEC and from healthy unaffected newborns. The lack of diversity within the neonatal intestine makes it possible to study gut microbial communities at a high level of resolution not currently possible in corresponding studies of the adult intestinal tract. Here, we summarize clinical and laboratory evidence that supports the hypothesis that NEC is a microbe-mediated disorder. In addition, we detail recent technologic advances that may be harnessed to perform high-throughput, comprehensive studies of the gut microbes of very low birth weight infants. Methods for characterizing microbial genotype are discussed, as are methods of identifying patterns of gene expression, protein expression, and metabolite production. Application of these technologies to biological samples from affected and unaffected newborns may lead to advances in the care of infants who are at risk for the unabated problem of NEC.

Proteomic analysis of ethene-enriched groundwater microcosms from a vinyl chloride-contaminated site

Contamination of groundwater with vinyl chloride (VC), a known human carcinogen, is a common environmental problem at plastics manufacturing, dry cleaning, and military sites. At many sites, there is the potential to cleanup VC groundwater plumes with aerobic VC-oxidizing microorganisms (e.g., methanotrophs, etheneotrophs, and VC-assimilating bacteria). Environmental biotechnologies that reveal the presence and activity of VC-oxidizing bacteria in contaminated groundwater samples would provide valuable lines of evidence that bioremediation of VC is occurring at a site. We applied targeted shotgun mass spectrometry-based proteomic methods to ethene-enriched groundwater microcosms from a VC-contaminated site. Polypeptides from the enzymes alkene monooxygenase (EtnC) and epoxyalkane:CoM transferase (EtnE), both of which are expressed by aerobic etheneotrophs and VC-assimilating bacteria, were identified in 7 of the 14 samples analyzed. Bioinformatic analysis revealed that 2 EtnC and 5 EtnE peptides were unique to deduced EtnC and EtnE sequences from two different cultivated strains. In addition, several partial EtnE genes sequenced from microcosms matched with observed EtnE peptides. Our results have revealed broader etheneotroph functional gene diversity and demonstrate the feasibility, speed, and accuracy of applying a targeted metaproteomics approach to identifying protein biomarkers from etheneotrophs in complex environmental samples.

Comparative metaproteomics reveals ocean-scale shifts in microbial nutrient utilization and energy transduction

Bacteria and Archaea play critical roles in marine energy fluxes and nutrient cycles by incorporating and redistributing dissolved organic matter and inorganic nutrients in the oceans. How these microorganisms do this work at the level of the expressed protein is known only from a few studies of targeted lineages. We used comparative membrane metaproteomics to identify functional responses of communities to different nutrient concentrations on an oceanic scale. Comparative analyses of microbial membrane fractions revealed shifts in nutrient utilization and energy transduction along an environmental gradient in South Atlantic surface waters, from a low-nutrient gyre to a highly productive coastal upwelling region. The dominant membrane proteins identified (19%) were TonB-dependent transporters (TBDTs), which are known to utilize a proton motive force to transport nutrients across the outer membrane of Gram-negative bacteria. The ocean-wide importance of TonB-dependent nutrient acquisition in marine bacteria was unsuspected. Diverse light-harvesting rhodopsins were detected in membrane proteomes from every sample. Proteomic evidence of both TBDTs and rhodopsins in the same lineages suggest that phototrophic bacterioplankton have the potential to use energy from light to fuel transport activities. We also identified viral proteins in every sample and archaeal ammonia monooxygenase proteins in the upwelling region, suggesting that Archaea are important nitrifiers in nutrient-rich surface waters.

AMD biofilms: using model communities to study microbial evolution and ecological complexity in nature

Similar to virtually all components of natural environments, microbial systems are inherently complex and dynamic. Advances in cultivation-independent molecular methods have provided a route to study microbial consortia in their natural surroundings and to begin resolving the community structure, dominant metabolic processes and inter-organism interactions. However, the utility of these methods generally scales inversely with community complexity. By applying genomics-enabled methods to the study of natural microbial communities with reduced levels of species richness, a relatively comprehensive understanding of the metabolic networks and evolutionary processes within these communities can be attained. In such well-defined model systems, it is also possible to link emergent ecological patterns to their molecular and evolutionary underpinnings, facilitating construction of predictive ecosystem models. In this study, we review over a decade of research on one such system-acid mine drainage biofilm communities. We discuss the value and limitations of tractable model microbial communities in developing molecular methods for microbial ecology and in uncovering principles that may explain behavior in more complex systems.