Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances

Resolution of phenotypically distinct strains of Enterococcus spp. in a complex microbial community using cpn60 universal target sequencing

Characterization of complex microbial communities is frequently based on the examination of polymerase chain reaction amplified sequences from a single phylogenetic marker, usually the 16S rRNA gene. However, this commonly used target often does not offer robust resolution of species or sub-species and is thus not a sufficiently informative target for understanding microbial population dynamics occurring at the strain level. We have used the cpn60 universal target sequence to characterize Enterococcus isolates from feces of growing pigs and have shown that sub-species groups, not detected using 16S rRNA sequences, can be resolved. Furthermore, groups resolved by cpn60-based phylogenetic analysis have distinct phenotypes. We report changes in the structure and function of Enterococcus communities in pig feces sampled from individual animals at three times, from suckling through to maturity. Enterococcus faecalis was largely replaced by Enterococcus hirae between suckling and 9 weeks of age, and a shift from one sub-species group of E. hirae to another was observed in all animals between 9 and 15 weeks. Conversely, E. faecalis strains remained consistent throughout the study period. Our results demonstrate that cpn60 sequences can be used to detect strain level changes in Enterococcus populations during succession in the fecal microbiota of growing pigs.

The oral microbiota: general overview, taxonomy, and nucleic acid techniques

Application of nucleic acid technology to the analysis of the bacterial diversity in the oral cavity in conditions of health and disease has not only confirmed the findings from early culture studies but also significantly expanded the list of oral inhabitants and candidate pathogens associated with the major oral diseases. Over 800 bacterial distinct species-level taxa have been detected in the oral cavity and recent studies using high-throughput technology suggest that the breadth of bacterial diversity can be much larger. This chapter provides an overview of the diversity and taxonomy of oral bacteria. Emphasis is also given on nucleic acid technologies that have been widely used for the study of the oral microbiota.

Microbial architecture of environmental sulfur processes: a novel syntrophic sulfur-metabolizing consortia

Microbial oxidation of sulfur-rich mining waste materials drives acid mine drainage (AMD) and affects the global sulfur biogeochemical cycle. The generation of AMD is a complex, dynamic process that proceeds via multiple reaction pathways. The role of natural consortia of microbes in AMD generation, however, has received very little attention despite their widespread occurrence in mining environments. Through a combination of geochemical experimentation and modeling, scanning transmission X-ray microscopy, and fluorescent in situ hybridization, we show a novel interdependent metabolic arrangement of two ubiquitous and abundant AMD bacteria: chemoautotrophic sulfur-oxidizing Acidithiobacillus sp. and heterotrophic Acidiphilium sp. Highly reminiscent of anaerobic methane oxidation (AOM) consortia, these bacteria are spatially segregated within a planktonic macrostructure of extracellular polymeric substance in which they syntrophically couple sulfur oxidation and reduction reactions in a mutually beneficial arrangement that regenerates their respective sulfur substrates. As discussed here, the geochemical impacts of microbial metabolism are linked to the consortial organization and development of the pod structure, which affects cell-cell interactions and interactions with the surrounding geochemical microenvironment. If these pods are widespread in mine waters, echoing the now widespread discovery of AOM consortia, then AMD-driven CO(2) atmospheric fluxes from H(2)SO(4) carbonate weathering could be reduced by as much as 26 TgC/yr. This novel sulfur consortial discovery indicates that organized metabolically linked microbial partnerships are likely widespread and more significant in global elemental cycling than previously considered.

Sewage Disposal and Wildlife Health in Antarctica

Sewage and its microbiology, treatment and disposal are important to the topic of Antarctic wildlife health because disposal of untreated sewage effluent into the Antarctic marine environment is both allowed and commonplace. Human sewage contains enteric bacteria as normal flora, and has the potential to contain parasites, bacteria and viruses which may prove pathogenic to Antarctic wildlife. Treatment can reduce levels of micro-organisms in sewage effluent, but is not a requirement of the Environmental Protocol to the Antarctic Treaty (the Madrid Protocol). In contrast, the deliberate release of non-native organisms for any other reason is prohibited. Hence, disposal of sewage effluent to the marine environment is the only activity routinely undertaken in Antarctica knowing that it will likely result in the release of large numbers of potentially non-native species.

When the Madrid Protocol was negotiated, the decision to allow release of untreated sewage effluent was considered the only pragmatic option, as a prohibition would have been costly, and may not have been achievable by many Antarctic operators. In addition, at that time the potential for transmission of pathogens to wildlife from sewage was not emphasised as a significant potential risk. Since then, the transmission of disease-causing agents between species is more widely recognised and it is now timely to consider the risks of continued discharge of sewage effluent in Antarctica and whether there are practical alternatives.

Investigation of the toxic effect of cadmium on Candida humicola and Bacillus subtilis using a microcalorimetric method

In this study, the technique of microcalorimetry based on heat-output by aerobic bacterial respiration was explored to evaluate the toxic effect of cadmium on Candida humicola, Bacillus subtilis, singularly or in a mixture of both. Power-time curves of the growth metabolism of C. humicola and B. subtilis and the effect of Cd(2+) were studied using the TAM III (the third generation thermal activity monitor) multi-channel microcalorimetric system, isothermal mode, at 28 degrees C. The differences in shape of the power-time curves and the thermodynamic and kinetic characteristics of microorganisms growth were compared. The effect of cadmium added into microorganism would significantly reduce the life cycle and change the thermal effect of microbial metabolic process with different concentrations of Cd(2+). The experimental results revealed that at the same concentration, the sequence of inhibitory ratio (I) and maximum thermal power (P(max)) of the Cd(2+) was: mixed microorganisms>C. humicola>B. subtilis. The sequence of total thermal effect (Q(total)) and growth rate constant (k) is mixed microorganisms>B. subtilis>C. humicola. These results are important to further studies of the physiology and pharmacology of C. humicola and B. subtilis and may support the theory of restoring contaminated soil.

A biological treasure metagenome: pave a way for big science

The trend of recent researches, in which synthetic biology and white technology through system approaches based on "Omics technology" are recognized as the ground of biotechnology, indicates the coming of the 'metagenome era' that accesses the genomes of all microbes aiming at the understanding and industrial application of the whole microbial resources. The remarkable advance of technologies for digging out and analyzing metagenome is enabling not only practical applications of metagenome but also system approaches on a mixed-genome level based on accumulated information. In this situation, the present review is purposed to introduce the trends and methods of research on metagenome and to examine big science led by related resources in the future.

Evidence for novel viruses by analysis of nucleic acids in virus-like particle fractions from Ambrosia psilostachya

To test the hypothesis that many viruses remain to be discovered in plants, a procedure was developed to sequence nucleic acids cloned randomly from virus-like particle fractions of plant homogenates. As a test of the efficiency of the procedure we targeted Ambrosia psilostachya, western ragweed, plants growing at the Tallgrass Prairie Preserve of northeastern Oklahoma. Amplifiable nucleic acid was found in the fractions from six of twelve specimens and sequences were characterized from four of them. Evidence was obtained for the presence of viruses belonging to two families (Caulimoviridae, Flexiviridae). Multiple viral species were found in two of the four specimens and their level within the isolated nucleic acid population varied from less than 1-37%. None of the sequences were derived from reported sequences of known viruses. Thus, the analysis of nucleic acid from virus-like particles is a useful tool to expand our knowledge of the universe of viruses to non-cultivated species.

Metagenomics in animal gastrointestinal ecosystem: a microbiological and biotechnological perspective

Metagenomics- the application of the genomics technologies to nonculturable microbial communities, is coming of age. These approaches can be used for the screening and selection of nonculturable rumen microbiota for assessing their role in gastrointestinal (GI) nutrition, plant material fermentation and the health of the host. The technologies designed to access this wealth of genetic information through environmental nucleic acid extraction have provided a means of overcoming the limitations of culture-dependent microbial genetic exploitation. The molecular procedures and techniques will result in reliable insights into the GI microbial structure and activity of the livestock gut microbes in relation to functional interactions, temporal and spatial relationships among different microbial consortia and dietary ingredients. Future developments and applications of these methods promise to provide the first opportunity to link distribution and identity of rumen microbes in their natural habitats with their genetic potential and in situ activities.

Recombination and genetic differentiation among natural populations of the ectomycorrhizal mushroom Tricholoma matsutake from southwestern China

Effective conservation and utilization strategies for natural biological resources require a clear understanding of the natural populations of the target organisms. Tricholoma matsutake is an ectomycorrhizal mushroom that forms symbiotic associations with plants and plays an important ecological role in natural forest ecosystems in many parts of the world. It is also an economically very important gourmet mushroom. Because no artificial cultivation is available, natural populations of this species are under increasing threats, primarily from habitat disturbance and destruction. Despite its economical and ecological importance, little is known about its genetics and population biology. Here, using 14 polymerase chain reaction-restriction fragment length polymorphism markers, we analysed 154 strains from 17 geographical locations in southwestern China, a region where over 25% of the global T. matsutake harvest comes from. Our results revealed abundant genetic variation within individual populations. The analyses of gene and genotype frequencies within populations indicated that most loci did not deviate from Hardy-Weinberg equilibrium in most populations and that alleles among loci were in linkage equilibrium in the majority of the local populations. These results are consistent with the hypothesis that sexual reproduction and recombination play an important role in natural populations of this species. Our analyses indicated low but significant genetic differentiation among the geographical populations, with a significant positive correlation between genetic distance and geographical distance. We discuss the implications of our results to the ecology and resource management of this species.

Metagenomics in animal gastrointestinal ecosystem: Potential biotechnological prospects

Microbial metagenomics---the applications of the genomics suit of technologies to nonculturable microorganisms, is coming of age. These approaches can be used for the screening and identification of nonculturable gastrointestinal (GI) microflora for assessing and exploiting them in nutrition and the health of the host. Advances in technologies designed to access this wealth of genetic information through environmental nucleic acids extraction and analysis have provided the means of overcoming the limitations of conventional culture-dependent microbial genetic exploitation. The molecular techniques and bioinformatics tools will result in reliable insights into the animals' GI microbial structure and activity of the livestock gut microbes in relation to functional interactions, temporal and spatial relationships among different microbial consortia and dietary ingredients. Further developments and applications of these methods promise to provide the opportunity to link distribution and identity of various GI microbes in their natural habitats, and explore their use for promoting livestock health and industrial development.

Effect of wastewater treatment plant effluent on microbial function and community structure in the sediment of a freshwater stream with variable seasonal flow

We investigated the effects of wastewater treatment plant (WWTP) discharge on the ecology of bacterial communities in the sediment of a small, low-gradient stream in South Australia. The quantification of genes involved in the biogeochemical cycling of carbon and nitrogen was used to assess potential impacts on ecosystem functions. The effects of disturbance on bacterial community structure were assessed by PCR-denaturing gradient gel electrophoresis of 16S rRNA genes, and clone library analysis was used to phylogenetically characterize significant shifts. Significant (P < 0.05) shifts in bacterial community structures were associated with alteration of the sediment's physicochemical properties, particularly nutrient loading from the WWTP discharge. The effects were greatest at the sampling location 400 m downstream of the outfall where the stream flow is reduced. This highly affected stretch of sediment contained representatives of the gammaproteobacteria that were absent from less-disturbed sites, including Oceanospirillales and Methylococcaceae. 16S rRNA gene sequences from less-disturbed sites had representatives of the Caulobacteraceae, Sphingomonadaceae, and Nitrospirae which were not represented in samples from disturbed sediment. The diversity was lowest at the reference site; it increased with proximity to the WWTP outfall and declined toward highly disturbed (400 m downstream) sites (P < 0.05). The potential for biological transformations of N varied significantly with the stream sediment location (P < 0.05). The abundance of amoA, narG, and nifH genes increased with the distance downstream of the outfall. These processes are driven by N and C availability, as well as redox conditions. Together these data suggest cause and effect between nutrient loading into the creek, shift in bacterial communities through habitat change, and alteration of capacity for biogeochemical cycling of N.

Human gut microbiota and bifidobacteria: from composition to functionality

The human gut is the home of an estimated 10(18) bacterial cells, many of which are uncharacterized or unculturable. Novel culture-independent approaches have revealed that the majority of the human gut microbiota consists of members of the phyla Bacteroidetes and Firmicutes. Nevertheless the role of bifidobacteria in gut ecology illustrates the importance of Actinomycetes and other Actinobacteria that may be underestimated. The human gut microbiota represents an extremely complex microbial community the collective genome of which, the microbiome, encodes functions that are believed to have a significant impact on human physiology. The microbiome is assumed to significantly enhance the metabolism of amino and glycan acids, the turnover of xenobiotics, methanogenesis and the biosynthesis of vitamins. Co-colonisation of the gut commensals Bifidobacterium longum and Bacteroides thetaiotaomicron in a murine model system revealed that the presence of bifidobacteria induced an expansion in the diversity of polysaccharides targeted for degradation by Bacteroides and also induced host genes involved in innate immunity. In addition, comparative analysis of individual human gut microbiomes has revealed various strategies that the microbiota use to adapt to the intestinal environment while also pointing to the existence of a distinct infant and adult-type microbiota.

Recent fungal diseases of crop plants: is lateral gene transfer a common theme?

A cursory glance at old textbooks of plant pathology reveals that the diseases which are the current scourge of agriculture in many parts of the world are a different set from those that were prominent 50 or 100 years ago. Why have these new diseases arisen? The traditional explanations subscribe to the "nature abhors a vacuum" principle-that control of one disease creates the condition for the emergence of a replacement-but does little to explain why the new pathogen succeeds. The emergence of a new disease requires a series of conditions and steps, including the enhanced fecundity of the new pathogen, enhanced survival from season to season, and spread around the world. Recently, evidence was obtained that wheat tan spot emerged through a lateral gene transfer event some time prior to 1941. Although there have been sporadic and persistent reports of lateral gene transfer between and into fungal plant pathogens, most examples have been dismissed through incomplete evidence. The completion of whole genome sequences of an increasing number of fungal pathogens no longer allows such proposed cases of lateral gene transfer to be dismissed so easily. How frequent are lateral gene transfers involving fungal plant pathogens, and can this process explain the emergence of many of the new diseases of the recent past? Many of the apparently new diseases are dependant on the expression of host-specific toxins. These are enigmatic molecules whose action requires the presence of plant genes with products that specifically encode sensitivity to the toxin and susceptibility to the disease. It is also notable that many new diseases belong to the fungal taxon dothideomycetes. This review explores the coincidence of new diseases, interspecific gene transfer, host-specific toxins, and the dothideomycete class.

Predicting antibiotic resistance

The treatment of bacterial infections is increasingly complicated because microorganisms can develop resistance to antimicrobial agents. This article discusses the information that is required to predict when antibiotic resistance is likely to emerge in a bacterial population. Indeed, the development of the conceptual and methodological tools required for this type of prediction represents an important goal for microbiological research. To this end, we propose the establishment of methodological guidelines that will allow researchers to predict the emergence of resistance to a new antibiotic before its clinical introduction.

Metagenomics and biological ontology

Metagenomics is an emerging microbial systems science that is based on the large-scale analysis of the DNA of microbial communities in their natural environments. Studies of metagenomes are revealing the vast scope of biodiversity in a wide range of environments, as well as new functional capacities of individual cells and communities, and the complex evolutionary relationships between them. Our examination of this science focuses on the ontological implications of these studies of metagenomes and metaorganisms, and what they mean for common sense and philosophical understandings of multicellularity, individuality and organism. We show how metagenomics requires us to think in different ways about what human beings are and what their relation to the microbial world is. Metagenomics could also transform the way in which evolutionary processes are understood, with the most basic relationship between cells from both similar and different organisms being far more cooperative and less antagonistic than is widely assumed. In addition to raising fundamental questions about biological ontology, metagenomics generates possibilities for powerful technologies addressed to issues of climate, health and conservation. We conclude with reflections about process-oriented versus entity-oriented analysis in light of current trends towards systems approaches.

Single nucleotide polymorphisms in the ectomycorrhizal mushroom Tricholoma matsutake

Single nucleotide polymorphisms (SNPs) are becoming increasingly popular markers for studying a variety of biological phenomena. This paper describes the development and analysis of a set of SNP markers for the basidiomycete fungus Tricholoma matsutake. T. matsutake is a gourmet mycorrhizal mushroom primarily associated with pine forests. However, little is known about its genetics and genomic variation, including SNP variation. To identify and analyse SNPs in T. matsutake, a genomic library was constructed and >72,000 nt were analysed from >200 random clones. Primers from 20 sequenced fragments were then designed to amplify and sequence >10,000 bp sequences from the original strain, from which the genomic library was constructed, as well as another strain from >350 km away; both strains were from south-western China. These two strains had similar intra-strain SNP frequencies (1.104 and 1.278 % per nucleotide, respectively). The combined analysis revealed that 14 of the 20 examined fragments contained SNPs, ranging from two to 47 per fragment, and yielding a total of 178 SNPs out of the 10 428 sequenced nucleotides (an SNP frequency of 1.707 %). Among the 178 SNPs, one site had three alternative nucleotides, while the remaining 177 had two each, with 148 transitions and 29 transversions, resulting in a combined transition to transversion ratio of 5.1. In addition, the haplotype phases of all SNPs within individual fragments for both strains were determined. Phylogenetic analyses of these haplotypes revealed three kinds of haplotype relationship, including haplotype sharing both within and between strains. Furthermore, a subset of the SNPs detectable by restriction enzyme digests was screened for its distribution among 31 additional wild strains from five distinct locations in south-western China. The implications of these SNPs and haplotypes for our understanding of the genetics, population history, ecology and evolution of this important mushroom species are discussed.

Characterization of a tightly controlled promoter of the halophilic archaeon Haloferax volcanii and its use in the analysis of the essential cct1 gene

A system where archaeal gene expression could be controlled by simple manipulation of growth conditions would enable the construction of conditional lethal mutants in essential genes, and permit the controlled overproduction of proteins in their native host. As tools for the genetic manipulation of Haloferax volcanii are well developed, we set out to identify promoters with a wide dynamic range of expression in this organism. Tryptophan is the most costly amino acid for the cell to make, so we reasoned that tryptophan-regulated promoters might be good candidates. Microarray analysis of H. volcanii gene expression in the presence and absence of tryptophan identified a tryptophanase gene (tna) that showed strong induction in the presence of tryptophan. qRT-PCR revealed a very fast response and an up to 100-fold induction after tryptophan addition. This result has been confirmed using three independent reporter genes (cct1, pyrE2 and bgaH). Vectors containing this promoter will be very useful for investigating gene function in H. volcanii and potentially in other halophilic archaea. To demonstrate this, we used the promoter to follow the consequences of depletion of the essential chaperonin protein CCT1, and to determine the ability of heterologous CCT proteins to function in H. volcanii.

Environmental variability and modularity of bacterial metabolic networks

BACKGROUND

Biological systems are often modular: they can be decomposed into nearly-independent structural units that perform specific functions. The evolutionary origin of modularity is a subject of much current interest. Recent theory suggests that modularity can be enhanced when the environment changes over time. However, this theory has not yet been tested using biological data.

RESULTS

To address this, we studied the relation between environmental variability and modularity in a natural and well-studied system, the metabolic networks of bacteria. We classified 117 bacterial species according to the degree of variability in their natural habitat. We find that metabolic networks of organisms in variable environments are significantly more modular than networks of organisms that evolved under more constant conditions.

CONCLUSION

This study supports the view that variability in the natural habitat of an organism promotes modularity in its metabolic network and perhaps in other biological systems.

Expressed sequences tags of the anther smut fungus, Microbotryum violaceum, identify mating and pathogenicity genes

Background

The basidiomycete fungus Microbotryum violaceum is responsible for the anther-smut disease in many plants of the Caryophyllaceae family and is a model in genetics and evolutionary biology. Infection is initiated by dikaryotic hyphae produced after the conjugation of two haploid sporidia of opposite mating type. This study describes M. violaceum ESTs corresponding to nuclear genes expressed during conjugation and early hyphal production.

Results

A normalized cDNA library generated 24,128 sequences, which were assembled into 7,765 unique genes; 25.2% of them displayed significant similarity to annotated proteins from other organisms, 74.3% a weak similarity to the same set of known proteins, and 0.5% were orphans. We identified putative pheromone receptors and genes that in other fungi are involved in the mating process. We also identified many sequences similar to genes known to be involved in pathogenicity in other fungi. The M. violaceum EST database, MICROBASE, is available on the Web and provides access to the sequences, assembled contigs, annotations and programs to compare similarities against MICROBASE.

Conclusion

This study provides a basis for cloning the mating type locus, for further investigation of pathogenicity genes in the anther smut fungi, and for comparative genomics.

Pathogen profiling for disease management and surveillance

The usefulness of rapid pathogen genotyping is widely recognized, but its effective interpretation and application requires integration into clinical and public health decision-making. How can pathogen genotyping data best be translated to inform disease management and surveillance? Pathogen profiling integrates microbial genomics data into communicable disease control by consolidating phenotypic identity-based methods with DNA microarrays, proteomics, metabolomics and sequence-based typing. Sharing data on pathogen profiles should facilitate our understanding of transmission patterns and the dynamics of epidemics.

Abundant sequence variation around the mitochondrial origin of replication in the human opportunistic yeast pathogen Candida albicans from a tropical island in China

Due to its haploid nature and its predominantly uniparental mode of inheritance, the mitochondrial genome has been analyzed extensively in population and evolutionary genetic studies of eukaryotes. Among the mitochondrial DNA (mtDNA) fragments, the region surrounding the origin of replication is the most commonly studied. However, most of the studies have focused on animals and little is known about the extent and patterns of sequence variation around the mtDNA origin of replication (mtOri) in fungi. In this study, we found abundant variation in a 597bp fragment surrounding the mtOri for 53 isolates of the pathogenic yeast Candida albicans obtained from a diverse group of hosts in Hainan, a tropical island of China. Within this DNA fragment, a total of 17 haplotypes were found for the 53 isolates. The extent of sequence variation for this group of strains was similar to that for 24 strains that represented the global nuclear genotype diversity. In contrast to those in animals where there were significant biases in favor of transitional mutations (e.g. the transition to transversion ratio is about 20 in human mtDNA), our data showed a transition to transversion ratio of approximately 0.5 around mtOri in C. albicans. Our analysis revealed no apparent geographic pattern of sequence variation based on the birthplaces of the analyzed hosts. However, the sample from patients had a lower genotypic diversity than those from healthy hosts borne either in Hainan or elsewhere in China. Our results suggest that C. albicans mtDNA has a base substitution pattern different from its nuclear genome and that sequences from the mtOri region could enhance our understanding of C. albicans genome evolution and population structuring.

The positive role of the ecological community in the genomic revolution

The exponential increase of genomic and metagenomic data, fueled in part by recent advancements in sequencing technology, are greatly expanding our understanding of the phylogenetic diversity and metabolic capacity present in the environment. Two of the central challenges that bioinformaticians and ecologists alike must face are the design of bioinformatic resources that facilitate the analysis of genomic and metagenomic data in a comparative context and the efficient capture and organization of the plethora of descriptive information required to usefully describe these data sets. In this commentary, we review three initiatives presented in the "new frontiers" session of the second SCOPE meeting on Microbial Environmental Genomics (MicroEnGen-II, Shanghai, June 12-15, 2006). These are (1) the Integrated Microbial Genomes Resources (IMG), (2) the Genomic Standards Consortium (GSC), and (3) the Natural Environment Research Council (NERC) Environmental Bioinformatics Centre (NEBC). These integrative bioinformatics and data management initiatives underscore the increasingly important role ecologists have to play in the genomic (metagenomic) revolution.

Multiple gene genealogical analyses reveal both common and distinct population genetic patterns among replicons in the nitrogen-fixing bacterium Sinorhizobium meliloti

Sinorhizobium meliloti is a Gram-negative alpha-proteobacterium that can form symbiotic relationships with alfalfa and fix atmospheric nitrogen. The complete genome of a laboratory strain, Rm1021, was published in 2001, and the genome of this strain is arranged in three replicons: a chromosome of 3.65 million base pairs (Mb), and two megaplasmids, pSymA (1.35 Mb) and pSymB (1.68 Mb). However, the potential difference in genetic variation among the three replicons in natural strains remains poorly understood. In this study, a total of 16 gene fragments were sequenced, four from pSymA and six each from the chromosome and pSymB, for 49 natural S. meliloti strains. The analyses identified significant differences in divergence among genes, with the mean Hasegawa-Kishino-Yano-1985 (HKY85) distance ranging from 0.00157 to 0.04109 between pairs of strains. Overall, genes on pSymA showed the highest mean HKY85 distance, followed by those on pSymB and the chromosome. Although evidence for recombination was found, the authors' population genetic analyses revealed overall significant linkage disequilibria among genes within both pSymA and the chromosome. However, genes on pSymB were in overall linkage equilibrium, consistent with frequent recombination among genes on this replicon. Furthermore, the genealogical comparisons among the three replicons identified significant incongruence, indicating reassortment among the three replicons in natural populations. The results suggest both shared and distinct patterns of molecular evolution among the three replicons in the genomes of natural strains of S. meliloti.

The molecular ecologist's guide to expressed sequence tags

Genomics and bioinformatics have great potential to help address numerous topics in ecology and evolution. Expressed sequence tags (ESTs) can bridge genomics and molecular ecology because they can provide a means of accessing the gene space of almost any organism. We review how ESTs have been used in molecular ecology research in the last several years by providing sequence data for the design of molecular markers, genome-wide studies of gene expression and selection, the identification of candidate genes underlying adaptation, and the basis for studies of gene family and genome evolution. Given the tremendous recent advances in inexpensive sequencing technologies, we predict that molecular ecologists will increasingly be developing and using EST collections in the years to come. With this in mind, we close our review by discussing aspects of EST resource development of particular relevance for molecular ecologists.

Multiple gene genealogical analyses suggest divergence and recent clonal dispersal in the opportunistic human pathogen Candida guilliermondii

Candida guilliermondii is a haploid opportunistic pathogen accounting for about 2 % of human blood yeast infections. Recent analyses using multilocus enzyme electrophoresis and karyotyping suggest that strains from human sources traditionally designated C. guilliermondii in fact include at least two species, C. guilliermondii and Candida fermentati. However, the patterns of molecular variation within and between these two species remain largely unknown. In this study, DNA fragments were sequenced from five genes for each of 37 strains collected from Canada, China, the Philippines and Tanzania. The analyses identified significant sequence differences between C. guilliermondii and C. fermentati. The five gene genealogies showed no apparent incongruence, suggesting a predominantly clonal reproductive structure for both species in nature. Indeed, two large clones of C. guilliermondii were identified, with one from Ontario, Canada, and the other from China. Interestingly, the results indicate that strains currently designated C. guilliermondii may contain additional divergent lineages. On the practical side, the results revealed several diagnostic molecular markers that can be used in clinical microbiology laboratories to distinguish C. guilliermondii and C. fermentati. The multiple gene genealogical analyses conducted here revealed significant divergence and clonal dispersal in this important pathogenic yeast complex.

How do we compare hundreds of bacterial genomes?

The genomic revolution is fully upon us in 2006 and the pace of discovery is set to accelerate with the emergence of ultra-high-throughput sequencing technologies. Our complete genome collection of bacteria and archaea continues to grow in number and diversity, as genome sequencing is applied to an array of new problems, from the characterization of the pan-genome to the detection of mutation after experimentation and the exploration of microbial communities in unprecedented detail. The benefits of large-scale comparative genomic analyses are driving the community to think about how to manage our public collections of genomes in novel ways.