Evolution Of Microbial Populations Research Articles

Study on the effect of alkali on the production of volatile fatty acids from rhamnolipid‐alkali‐thermal pretreated waste activated sludge

AbstractThis article systematically explores the strengthening effect of NaOH dosage on the fermentation acid production of Waste Activated Sludge (WAS) by the rhamnolipids‐alkali‐thermal combined pretreatment. Analyzed the dissolution characteristics of organic matter in sludge, changes in total volatile fatty acids (VFAs) content and components, and microbial community structure. Research has shown that increasing the amount of NaOH can promote the dissolution of sludge extracellular polymeric substances (EPS) and cell lysis. When NaOH dose was 60 mg/g VS, the dissolution of SCOD was the largest, reaching 5427.78 mg/L. It provides high‐quality substrate for anaerobic flora through the decomposition of refractory humus‐like substances and macromolecular substances, thus improving the production of VFAs. When NaOH dose was 80 mg/g VS, the maximum VFAs yield was 1663.76 mg C/L, and the fermentation type was butyric acid. The increase of NaOH dose promotes the effective enrichment of bacteria, and the dominant bacteria are Proteobacteria, Firmicutes, and Bacteroides at the gate level, with different abundance. The fermentation time plays a decisive role in the evolution of microbial population, and the increase of NaOH dose promotes the enrichment of acid‐producing bacteria, thus improving the production of VFAs.

Evaluation of 10 Different Pipelines for Bacterial Single-Nucleotide Variant Detection

Abstract Bacterial genome sequencing is a powerful technique for studying the genetic diversity and evolution of microbial populations. However, the detection of genomic variants from sequencing data is challenging due to the presence of contamination, sequencing errors and multiple strains within the same species. Several bioinformatics tools have been developed to address these issues, but their performance and accuracy have not been systematically evaluated. In this study, we compared 10 variant detection pipelines using 18 simulated and 17 real datasets of high-throughput sequences from a bundle of representative bacteria. We assessed the sensitivity of each pipeline under different conditions of coverage, simulation and strain diversity. We also demonstrated the application of these tools to identify consistent mutations in a 30-time repeated sequencing dataset of Staphylococcus hominis. We found that HaplotypeCaller, but not Mutect2, from the GATK tool set showed the best performance in terms of accuracy and robustness. CFSAN and Snippy performed not as well in several simulated and real sequencing datasets. Our results provided a comprehensive benchmark and guidance for choosing the optimal variant detection pipeline for high-throughput bacterial genome sequencing data.

The analysis of the function, diversity, and evolution of the Bacillus phage genome

BackgroundPhages play a pivotal role in the evolution of microbial populations. The interactions between phages and their hosts are complex and may vary in response to host physiology and environmental conditions. Here, we have selected the genomes of some representative Bacillus prophages and lysosomes from the NCBI database for evolutionary analysis. We explored their evolutionary relationships and analyzed the protein information encoded by hundreds of Bacillus phages.ResultsWe obtained the following conclusions: First, Bacillus phages carried some known functional gene fragments and a large number of unknown functional gene fragments, which might have an important impact on Bacillus populations, such as the formation of spores and biofilms and the transmission of virulence factors. Secondly, the Bacillus phage genome showed diversity, with a clear genome boundary between Bacillus prophages and Bacillus lytic phages. Furthermore, genetic mutations, sequence losses, duplications, and host-switching have occurred during the evolution of the Bacillus phage, resulting in low genome similarity between the Bacillus phages. Finally, the lysis module played an important influence on the process of Bacillus phage cross-species infestation.ConclusionsThis study systematically described their protein function, diversity, and genome evolution, and the results of this study provide a basis for evolutionary diversity, horizontal gene transfer and co-evolution with the host in Bacillus phages.

Evolution of microbial populations and impacts of microbial activity in the anaerobic-oxic-settling-anaerobic process for simultaneous sludge reduction and dyeing wastewater treatment

In-situ sludge reduction is an important process in the biological treatment of dyeing wastewater. In this study, an anaerobic-oxic-settling-anaerobic process (A + OSA) was employed for dyeing wastewater treatment under the condition of sludge return to investigate the efficiency of dyeing wastewater treatment and sludge reduction performance. This was compared with an anaerobic-anaerobic-oxic process (AAO) without sludge return. Results showed that treatment of dyeing wastewater with the A + OSA process gave a 30% reduction in sludge and a 90% decolourisation efficiency, which was more efficient than the AAO process. Interestingly, the effluent chemical oxygen demand from the A + OSA process was higher than that from the AAO process. This was due to the inhibition of microbial activity due to the accumulation of intermediate compounds―aromatic amines―caused by long-term sludge return. Moreover, the returned sludge may have been degraded as a co-metabolism substrate, which resulted in the concentration of extracellular polymeric substances in the A + OSA process was higher than that in the AAO process. Additionally, high-throughput sequencing analysis indicated that sludge reduction performance was correlated with the growth of Saccharibacteria. Furthermore, analysis of the enzyme activity showed that dehydrogenase and catalase content decreased in the A + OSA process. This A + OSA process could be further scaled-up and optimized to serve as a promising and effective technology for the treatment of dyeing wastewater.

Bioaugmentation Treatment of a PAH-Polluted Soil in a Slurry Bioreactor

A bioslurry reactor was designed and used to treat loamy clay soil polluted with polycyclic aromatic hydrocarbons (PAHs). To this end, biostimulation alone, or combined with bioaugmentation with two bacterial strains (Rhodocccus erythropolis and Pseudomonas stuzeri) previously isolated from the polluted site, was applied. The PAH concentrations decreased notably after 15 days in all of the treatments. The concentrations of the two- and three-ring compounds fell by >80%, and, remarkably, the four- to six-ring PAHs also showed a marked decrease (>70%). These results thus indicate the capacity of bioslurry treatments to improve, notably, the degradation yields obtained in a previous real-scale remediation carried out using biopiles. In this sense, the remarkable results for recalcitrant PAHs can be attributed to the increase pollutants’ bioavailability achieves in the slurry bioreactors. Regarding bioaugmentation, although treatment with R. erythropolis led to a somewhat greater reduction of lighter PAHs at 15 days, the most time-effective treatment was achieved using P. stutzeri, which led to an 84% depletion of total PAHs in only three days. The effects of microbial degradation of other organic compounds were also monitored by means of combined qualitative and quantitative gas chromatography mass spectrometry (GC–MS) tools, as was the evolution of microbial populations, which was analyzed by culture and molecular fingerprinting experiments. On the basis of our findings, bioslurry technology emerges as a rapid and operative option for the remediation of polluted sites, especially for fine soil fractions with a high load of recalcitrant pollutants.

Computer Simulation of the Evolution of Microbial Population: Overcoming Local Minima When Reaching a Peak on the Fitness Landscape

The study focuses on the mechanisms of crossing the valleys of fitness by a population of haploid microorganisms, whose fitness depends on allelic values at two different loci and is determined by a complex landscape, the shape of which corresponds to the pattern “a mountain in the field surrounded by a trench”; these mechanisms are analyzed using computer modeling. We have studied the influence of various biological factors on the evolutionary perspective of microbial colonies, the reproduction rate of which is controlled by a protein consisting of two subunits encoded at different loci. Molecular genetic (mutation rate, affinity of subunits), population (fitness function landscape and population density), and ecological (concentration of available substrate in the habitat, flow intensity) factors have been considered. Our results demonstrate that the difference in fitness for various allelic combinations, while determining the shape of the fitness landscape, sets the optimal mutation rates to overcome its valleys and opens a window of opportunity for the evolution of the population toward the state of the highest average fitness. Moreover, depending on the fitness landscape type, either gradual or saltational evolutionary regimes are optimal for reaching the peak.

Evolution of the Natural Transformation Protein, ComEC, in Bacteria.

Natural transformation enables the incorporation of exogenous DNA into host genomes and plays a fundamental role in the evolution of microbial populations. At the center of the natural transformation machinery, the ComEC protein mediates DNA import and serves potential functions in DNA recognition and single strand degradation. Despite its importance, the evolution of ComEC is not fully understood. Here, we aim to fill this knowledge gap by surveying putative ComEC proteins across 5,574 bacteria that span diverse phyla. We first derived the presence of a universal, core Competence domain through the analysis of ComEC proteins from known naturally competent species. Then, we followed this observation to identify Competence domain containing proteins (CDCPs) from all bacteria and used CDCPs as putative ComEC proteins for evolutionary analysis. A near universal presence of CDCPs was revealed, with 89% of the proteomes and 96% of the genomes encoding a single CDCP or a CDCP-like fragment. Two domains, DUF4131 and Lactamase_B, were found to commonly co-occur with the Competence domain. Ancestral state reconstruction of CDCPs over the bacterial species phylogeny suggested an origin of a Competence-only domain profile, while multiple gains and losses of the DUF4131 and Lactamase_B domains were observed among diverse bacterial lineages.

Viruses in the deep biosphere: A review

Viruses, the most abundant biological entities on the planet, are widely distributed in various environments, including the deep biosphere. Via infection, which is frequently followed by lysis of the host cells, viruses play an important role in shaping microbial population structure, impacting the ecological characteristics of their hosts, and breaking up cellular biomass into organic matter, thereby affecting microbial processes and nutrient cycling. Because of these activities, viruses are known as nano-scale drivers of global-scale processes. The deep biosphere, extending hundreds to thousands of meters below the seafloor, harbors by far the largest reservoir of organic carbon and more than half of the worlds prokaryotic organisms. However, it remains a black box in terms of the ecological characteristics and functions of its resident viruses. To date, only a few studies on viruses in the deep biosphere have been reported, and these mainly originate from the Ocean Drilling Program (ODP) and the Integrated Ocean Drilling Program (IODP). The limited results of these studies show that the abundance of viruses in the deep biosphere is much greater than that in marine environments (108–109 viruses g-1 in sediments versus 106–108 viruses mL-1 in seawater). In general, viral abundance decreases with an increase in depth, but the Virus-to-Prokaryote Ratio, which is used to predict the relationship between viral and prokaryotic communities, varies greatly among different deep habitats. Viral abundance is affected not only by in situ viral production and decay, processes that are usually tightly linked to the productivity of microbial hosts and the activity of extracellular enzymes, but also by the physical, chemical, and geological characteristics of the environment, including temperature, total organic carbon content, sediment porosity, and sedimentation rate, amongst other factors. In addition, virus assemblages in the deep biosphere appear to be both morphologically and genetically more diverse than their aquatic counterparts. Highly diverse morphotypes and unknown virus sequences indicate that there is a huge uncharacterized viral pool in the deep biosphere, which could represent a treasure trove for the future discovery of novel viruses and lifestyle mechanisms. In addition, analyses of prophage sequences deduced from prokaryotic genomes imply that lysogenic infection should be an important life strategy for viruses, making them more adaptable to the dynamic, and often extreme, deep biosphere environment. These findings have important implications for the potential interactions between viruses and their hosts and for the vital role of viruses in manipulating microbial community structure and evolution in the deep biosphere. However, technical difficulties, which have only recently been at least partially overcome, have limited our ability to study these elusive viruses. The fact is that we have barely begun to characterize the deep virosphere, which is the dark matter of the biological world and a tremendous source of future discoveries. The questions of what role viruses play in the deep biosphere, whether and to what extent viruses drive the metabolic functioning and evolution of microbial populations, and how virus populations adapt to deep environments are still open and answering them will require significant amounts of work. The purpose of this review is, therefore, to provide an overview of the current knowledge about viruses (e.g., distribution, diversity, and life cycles) in the deep biosphere. The relationships of viruses with microbial hosts and environmental parameters and the potential ecological importance of viruses in the deep biosphere are discussed. Finally, we put forward some suggestions regarding areas of research that need to be addressed in the future to establish a more complete picture of the ecological and evolutionary significance of viruses in the biosphere.

Granulation process in an expanded granular sludge blanket (EGSB) reactor for domestic sewage treatment: Impact of extracellular polymeric substances compositions and evolution of microbial population

In this study, an expanded granular sludge blanket (EGSB) reactor was used for the treatment of low-strength domestic sewage and the sludge granulation process was systematically investigated. At an optimized hydraulic retention time (HRT) of 5 h, up-flow velocity (Vup) of 1.9 m/h, and organic loading rate (OLR) of 2.16 kg COD/m3/d, the average COD removal efficiency was 71.5 ± 2.3%. Completely granular sludge can be observed after 107 d of continuous operation. Analysis of the distribution and composition of the extracellular polymeric substances (EPS) indicates that the tightly bound EPS (TB-EPS) content shows an increasing trend, while the loosely bound EPS (LB-EPS) content did not significantly alter after the granular sludge was formed. The three-dimensional excitation-emission matrix technique (3D-EEM) confirms that aromatic protein-like substances are of key importance to sludge granulation. High-throughput sequencing analysis indicates that the metabolism shifted from hydrogenotrophic (Methanobaterium) to aceticlastic methanogens (Methanosaeta) during sludge granulation.

Identification and biotechnological characterization of lactic acid bacteria isolated from chickpea sourdough in northwestern Argentina

Chickpea, a relevant legume worldwide, can be nutritional and functionally improved by fermentation with lactic acid bacteria (LAB). In order to select suitable autochthonous starter cultures, we isolated and identified LAB from kabuli chickpeas cultivated and consumed in northwestern Argentina, and screened their relevant techno-functional properties. Chickpeas were milled and spontaneously fermented with daily back-slopping at 37 °C for 6 days and evolution of microbial populations were followed by plate counting. Phenotypic and genotypic methods including (GTG)5-based PCR fingerprinting and 16S rDNA sequencing were used to differentiate and identify the isolates to species level. A marked increase of LAB counts was observed throughout fermentation raising from 0.88 ± 0.35 log CFU/g of unfermented flours to 9.61 ± 0.21 log CFU/g after 5 back-slopping steps with a concomitant pH decline from 6.09 ± 0.05 to 4.40 ± 0.03. Eighteen strains belonging to four LAB genera and six species: Enterococcus durans, E. mundtii, Lactococcus garvieae, Pediococcus pentosaceus, Weissella cibaria and W. paramesenteroides were identified in chickpea sourdoughs. Based on their abilities, Weissella cibaria CRL 2205 (acidification capacity), W. paramesenteroides CRL 2191 (proteolytic activity), Pediococcus pentosaceus CRL 2145 (gallate decarboxylase and peptidase activities), Lactococcus garviae CRL 2199 (α-galactosidase activity) and E. durans CRL 2193 (antimicrobial activity), were selected to design novel fermented chickpea products.

Massive Sequencing: A New Tool for the Control of Alcoholic Fermentation in Wine?

In wine industry, there is a prevalent use of starter cultures to promote a controlled and efficient alcoholic fermentation preventing the growth of spoilage microbes. However, current trends in enology aim to combine the guaranteed success of monitored process and the complexity of fermentations either by inoculating autochthonous starters or by performing spontaneously to produce distinctive wines. To understand the complex roles of microorganisms on wine fermentation, we must understand their population dynamics and their relationships with wine quality and metabolome. Current metagenomics techniques based on massive sequencing are gaining relevance to study the diversity and evolution of microbial population on every stage of the wine making process. This new tool and technique increases the throughput and sensitivity to study microbial communities. This review focuses on the current knowledge about wine alcoholic fermentation, the contribution of massive sequencing techniques and the possibility of using this tool for microbial control.

Sulfolobus islandicus meta-populations in Yellowstone National Park hot springs.

Abiotic and biotic forces shape the structure and evolution of microbial populations. We investigated forces that shape the spatial and temporal population structure of Sulfolobus islandicus by comparing geochemical and molecular analysis from seven hot springs in five regions sampled over 3 years in Yellowstone National Park. Through deep amplicon sequencing, we uncovered 148 unique alleles at two loci whose relative frequency provides clear evidence for independent populations in different hot springs. Although geography controls regional geochemical composition and population differentiation, temporal changes in population were not explained by corresponding variation in geochemistry. The data suggest that the influence of extinction, bottleneck events and/or selective sweeps within a spring and low migration between springs shape these populations. We suggest that hydrologic events such as storm events and surface snowmelt runoff destabilize smaller hot spring environments with smaller populations and result in high variation in the S. islandicus population over time. Therefore, physical abiotic features such as hot spring size and position in the landscape are important factors shaping the stability and diversity of the S. islandicus meta-population within Yellowstone National Park.

Iron Kinetics and Evolution of Microbial Populations in Low-pH, Ferrous Iron-Oxidizing Bioreactors

Iron-rich, acidic wastewaters are commonplace pollutants associated with metal and coal mining. Continuous-flow bioreactors were commissioned and tested for their capacities to oxidize ferrous iron in synthetic and actual acid mine drainage waters using (initially) pure cultures of the recently described acidophilic, iron-oxidizing heterotrophic bacterium Acidithrix ferrooxidans grown in the presence of glucose and yeast extract. The bioreactors became rapidly colonized by this bacterium, which formed macroscopic streamer growths in the flowing waters. Over 97% of ferrous iron in pH 2.0-2.2 synthetic mine water was oxidized (at up to 225 mg L(-1) h(-1)) at dilution rates (D) of 0.6 h(-1). Rates of iron oxidation decreased with pH but were still significant, with influent liquors as low as pH 1.37. When fed with actual mine water, >90% of ferrous iron was oxidized at D values of 0.4 h(-1), and microbial communities within the bioreactors changed over time, with Atx. ferrooxidans becoming increasingly displaced by the autotrophic iron-oxidizing acidophiles Ferrovum myxofaciens, Acidithiobacillus ferrivorans, and Leptospirillum ferrooxidans (which were all indigenous to the mine water), although this did not have a negative impact on net ferrous-iron oxidation. The results confirmed the potential of using a heterotrophic acidophile to facilitate the rapid commissioning of iron-oxidizing bioreactors and illustrated how microbial communities within them can evolve without compromising the performances of the bioreactors.

Genetic variation among Escherichia coli isolates from human and calves by using RAPD PCR

Background: Various strains of Escherichia coli (E. coli) are known as major causes of intestinal and extraintestinal infections in humans and various animal species. Molecular methods are important for the identification of bacterial isolates and nucleotide sequence variations, as well as information on tracking bacterial agents related to the outbreaks, the frequency of the bacterial genetic structure, and the evolution of microbial populations. Objectives: The purpose of the present study was to evaluate the efficiency of the RAPD method to differentiate E. coli strains. Methods: In this study, 110 isolates of E. coli were analyzed by the RAPD PCR method using two 10bp oligonucleotides. These strains were isolated from humans with urinary tract infections and neonatal calves affected by diarrhea or septicemia. Results: Data analysis showed that 87.5% of human E. coli isolates were correctly classified in the human host group, while 94.3% of calf E. coli isolates were correctly placed in calf groups. It also demonstrated that 100% and 93.3% of isolates were accurately assigned to diarrheic and septicemic calf groups, respectively. ConclusionS: Genetic variation analysis indicated that the percentage of polymorphism among E. coli isolates from humans with urinary tract infections, diarrheic calves, and septicemic neonatal calves were 54.71%, 61.22%, and 62.5%, respectively.

Evaluation of microbial population and attachment study during bio-heap leaching at Malanjkhand copper project

Microbial analysis of a 2X1000-tonne bio-heap leaching plant of Malanjkhand copper ore was done. Continuous monitoring of the micro-organism profi le was done through conventional methods. The evolution of microbial population was done at quarterly intervals. The bacterial cultures were allowed to grow on Feo medium and FeSo medium. Three iron-oxidising acidophiles, namely, Acidithiobacillus ferrooxidans, Acidithiobacillus thiooxidans and Leptospirillum ferrooxidans and three sulphur-oxidising acidophilic bacteria, namely, Acidithiobacillus caldus, Acidiphilum sps and Sulfobacillus sps were present in the heap leach liquor. AFM studies were conducted for estimation of bacterial cell dimensions and evaluation of possible mechanism for bio-leaching of copper ore.

Effect of the lactic acid bacteria on the control of listerial activity and shelf life of smoked salmon scraps

SummaryThe potential protective activity of lactic acid bacteria (LAB) from cold smoked salmon scraps was evaluated towards Listeria monocytogenes. Seventy‐three LAB strains were isolated and identified by biomolecular methods; Lactobacillus curvatus and Lactobacillus sakei prevailed. Three of the strains tested, identified as L. sakei, profile O, had a significant inhibitory activity against L. monocytogenes ATCC 19115 and clones DUP‐1042 and DUP‐18596. The evolution of microbial populations and chemical parameters were determined at time intervals to verify the shelf life. Listeria monocytogenes was isolated in half the packages also exceeding the legal limit. The shelf life of scraps was set at 30 days. Clonal characterisation of L. monocytogenes was performed by ribotyping. DUP‐1042, one of the human pathogen clones, was the most represented pattern. The results suggest further studies aimed at the selection of autochthonous nonspoilage LAB strains as bioprotective agents for cold smoked salmon.

Принцип инвариантности Ла-Салля и математические модели эволюции микробных популяций

Построена математическая модель эволюции микробных популяций при длительном непрерывном культивировании на протоке. Модель представляет собой обобщение целого ряда известных математических моделей эволюции, в которых учитываются такие факторы генетической изменчивости как хромосомные мутации, мутации плазмидных генов, перенос плазмид между клетками микроорганизмов, потери плазмид при делении клеток и др. Для общей модели эволюции построена функция Ляпунова и на основании теоремы Ла-Салля доказано существование в пространстве состояний математической модели ограниченного, положительно инвариантного и глобально притягивающего множества. Дано аналитическое описание этого множества. Обсуждаются перспективы применения численных методов для оценки числа, местоположения и последующего исследования предельных множеств в математических моделях эволюции на протоке.

Effectiveness of Edible Coatings Combined with Mild Heat Shocks on Microbial Spoilage and Sensory Quality of Fresh Cut Broccoli (Brassica oleracea L.)

The use of edible coatings and mild heat shocks is proposed as postharvest treatments to prevent microbial deterioration of refrigerated broccoli. Minimally processed broccoli was coated with either chitosan or carboxymethyl-cellulose (CMC) combined or not with a previous application of a mild heat shock. The evolution of microbial populations (mesophilic, psycrotrophic, Enterobacteriaceae, molds and yeast, and lactic acid bacteria) was studied during 20 d of storage and fitted to Gompertz and logistic models. Results revealed that, at the end of the storage, chitosan coating significantly reduced all microbiological population counts, except lactic acid bacteria; while higher reduction was observed with chitosan coating combined with a heat shock treatment. A significant delay at the beginning of the exponential phase was observed for all the bacterial populations analyzed. On the other hand, CMC coating, with and without a previous thermal treatment, did not exert any antibacterial effect. Excellent agreement was found between experimental microbial counts and predicted values obtained from Gompertz and logistic models. Kinetic modeling was found to be valuable for prediction of microbiological shelf life of broccoli during storage. Results showed that the application of chitosan coating effectively maintained microbiological quality and extended shelf life of minimally processed broccoli. According to these results, the use of the edible chitosan coating alone or in combination with a heat mild shock appear to be a viable alternative for controlling microbiological growth and sensory attributes in minimally processed broccoli. The continuous consumer interest in high quality and food safety, combined with environmental concern has induced to the development and study of edible coatings that avoid the use of synthetic materials. The edible coatings, formed from generally recognized as safe materials, have the potential to reduce weight loss, respiration rate, and improve food appearance and integrity. It is one of the most effective methods to maintain food quality. On the other hand, heat treatments have been demonstrated to be effective as a nonchemical means of improving postharvest quality for a variety of horticultural products. The applications of mild heat shocks combined with edible coatings constitute an alternative for the natural preservation of crops for which the use of synthetic chemicals is objectionable.

Full-Scale Remediation of a Jet Fuel-Contaminated Soil: Assessment of Biodegradation, Volatilization, and Bioavailability

Here, we addressed biodegradation vs. volatilization processes, and also bioavailability limitations during biopile remediation of soil initially contaminated by more than 5,000 mg/kg of hydrocarbons. In order to select bioremediation strategies, we first conducted a biotreatability study, which included geochemical, textural, and microbiological characterization of the soil matrix. Next, we implemented five bioremediation approaches onsite in real-scale biopiles. In order to monitor hydrocarbon depletion and to distinguish between biological and non-biological processes, we analyzed chemical biomarkers by means of gas chromatography–mass spectrometry. In addition, a comprehensive study of soil grain size and its implications on bioavailability were studied. Furthermore, the evolution of microbial populations was also examined. Two of the strategies implemented in the biopiles (the combination of a slow-release fertilizer and a surfactant, and the use of an oleophilic fertilizer respectively) reduced the soil hydrocarbon content to under 500 mg/kg in 5 months. Additional results from this study indicate that volatilization was the predominant degradation process for light hydrocarbons (below 12 carbon atoms), whereas heavier compounds were mainly biodegraded. However, even in the most favorable situation, a residual concentration of hydrocarbons linked to the finer fraction of the soil was found.

Functional analysis of natural microbial consortia using community proteomics

We know very little about the metabolic functioning and evolutionary dynamics of microbial communities. Recent advances in comprehensive, sequencing-based methods, however, are laying a molecular foundation for new insights into how microbial communities shape the Earth's biosphere. Here we explore the convergence of microbial ecology, genomics, biological mass spectrometry and informatics that form the new field of microbial community proteogenomics. We discuss the first applications of proteogenomics and its potential for studying the physiology, ecology and evolution of microbial populations and communities.