Microbial biogeography: putting microorganisms on the map

Distinct protistan assemblages characterize the euphotic zone and deep sea (2500 m) of the western North Atlantic (Sargasso Sea and Gulf Stream)

Protistan diversity was characterized at three locations in the western North Atlantic (Sargasso Sea and Gulf Stream) by sequencing 18S rRNA genes in samples from euphotic (< or = 125 m) and bathypelagic depths (2500 m). A total of 923 partial-length protistan sequences were analysed, revealing 324 distinct operational taxonomic units (OTUs) determined by an automated OTU-calling program set to 95% sequence similarity. Most OTUs were comprised of only one or two sequences suggesting a large but rare pool of protistan diversity. Many OTUs from both depth strata were associated with recently described novel alveolate and stramenopile lineages while many OTUs from the bathypelagic were affiliated with Acantharea, Polycystinea and Euglenozoa and were not observed in euphotic zone libraries. Protistan assemblages from the euphotic zone and the deep sea were largely composed of distinct OTUs; only 28 of the 324 protistan OTUs were detected in both shallow and deep sea clone libraries. The diversity of protistan assemblages in the deep sea was distinctly lower than the diversity of euphotic zone assemblages. Protistan assemblages from the Gulf Stream were the most diverse for either depth strata. Overall, protistan assemblages from different stations but comparable depths were more similar than the assemblages from different depths at the same station. These data suggest that particular groups of protistan OTUs formed distinct 'shallow' and 'deep-sea' assemblages across widely spaced oceanic locales.

Multiscale responses of microbial life to spatial distance and environmental heterogeneity in a patchy ecosystem

Spatial distance (SD) and environmental heterogeneity (EH) are currently thought to represent major factors shaping genetic variation and population abundance, but their relative importance is still poorly understood. Because EH varies at multiple spatial scales, so too are microbial variables expected to vary. The determination of SD x EH interactions at multiple scales is, however, not a trivial exercise, especially when one examines their effects on microbial abundance and genomic similarities. Here we assessed those interactions at all scales perceptible in a patchy environment composed of known plant species and of heterogeneous soil physical and chemical parameters. For free-living, soil-borne Burkholderia ambifaria, genomic similarities responded to most of the spatial scales that the experimental sampling scheme could reveal, despite limited dispersal of the individuals. Species abundance and community composition were, however, responding to much smaller scales more consistent with local responses to EH. Our results suggest that whole-genome similarities may reflect the simultaneous effects of both SD and EH in microbial populations, but the pure effects of each factor only contributed to < 2% of the total genetic variation. The large amount of unexplained variation that remains after considering most environmental, spatial, and biological interactions is then posited to be the result of noise introduced by unmeasured environmental and spatial variability, sampling effects, and neutral ecological drift.

The marine viromes of four oceanic regions

Viruses are the most common biological entities in the marine environment. There has not been a global survey of these viruses, and consequently, it is not known what types of viruses are in Earth's oceans or how they are distributed. Metagenomic analyses of 184 viral assemblages collected over a decade and representing 68 sites in four major oceanic regions showed that most of the viral sequences were not similar to those in the current databases. There was a distinct "marine-ness" quality to the viral assemblages. Global diversity was very high, presumably several hundred thousand of species, and regional richness varied on a North-South latitudinal gradient. The marine regions had different assemblages of viruses. Cyanophages and a newly discovered clade of single-stranded DNA phages dominated the Sargasso Sea sample, whereas prophage-like sequences were most common in the Arctic. However most viral species were found to be widespread. With a majority of shared species between oceanic regions, most of the differences between viral assemblages seemed to be explained by variation in the occurrence of the most common viral species and not by exclusion of different viral genomes. These results support the idea that viruses are widely dispersed and that local environmental conditions enrich for certain viral types through selective pressure.

Bacterial community profiles of endodontic abscesses from Brazilian and USA subjects as compared by denaturing gradient gel electrophoresis analysis

This study compared the bacterial community profiles of the microbiota associated with acute apical abscesses from Brazilian and USA patients using denaturing gradient gel electrophoresis (DGGE). DNA was extracted from purulent exudate aspirates and part of the 16S rRNA gene was amplified by polymerase chain reaction and separated by DGGE. The resulting banding patterns, which were representative of the bacterial community structures in samples from the two locations, were then compared. Distinct DGGE banding patterns were observed from different samples. Ninety-nine bands with distinct positions in the gels were detected, of which 27 were found only in the USA samples and 13 were exclusive to Brazilian samples. Four of the 59 shared bands showed very discrepant findings with regard to prevalence in the two locations. Cluster analysis of DGGE banding profiles showed a great variability in the bacterial populations associated with teeth with abscesses regardless of the geographical location. Two big clusters, one for each location, were observed. Other clusters contained a mixture of samples from the two locations. The results of the present study demonstrated a great variability in the bacterial community profiles among samples. This indicates that the bacterial communities of abscesses are unique for each individual in terms of diversity. The composition of the microbiota in some samples showed a geography-related pattern. Furthermore, several bands were exclusive for each location and others were shared by the two locations and showed great differences in prevalence.

Quantitative phylogenetic assessment of microbial communities in diverse environments

The taxonomic composition of environmental communities is an important indicator of their ecology and function. We used a set of protein-coding marker genes, extracted from large-scale environmental shotgun sequencing data, to provide a more direct, quantitative, and accurate picture of community composition than that provided by traditional ribosomal RNA-based approaches depending on the polymerase chain reaction. Mapping marker genes from four diverse environmental data sets onto a reference species phylogeny shows that certain communities evolve faster than others. The method also enables determination of preferred habitats for entire microbial clades and provides evidence that such habitat preferences are often remarkably stable over time.

MEGAN analysis of metagenomic data

Metagenomics is the study of the genomic content of a sample of organisms obtained from a common habitat using targeted or random sequencing. Goals include understanding the extent and role of microbial diversity. The taxonomical content of such a sample is usually estimated by comparison against sequence databases of known sequences. Most published studies use the analysis of paired-end reads, complete sequences of environmental fosmid and BAC clones, or environmental assemblies. Emerging sequencing-by-synthesis technologies with very high throughput are paving the way to low-cost random "shotgun" approaches. This paper introduces MEGAN, a new computer program that allows laptop analysis of large metagenomic data sets. In a preprocessing step, the set of DNA sequences is compared against databases of known sequences using BLAST or another comparison tool. MEGAN is then used to compute and explore the taxonomical content of the data set, employing the NCBI taxonomy to summarize and order the results. A simple lowest common ancestor algorithm assigns reads to taxa such that the taxonomical level of the assigned taxon reflects the level of conservation of the sequence. The software allows large data sets to be dissected without the need for assembly or the targeting of specific phylogenetic markers. It provides graphical and statistical output for comparing different data sets. The approach is applied to several data sets, including the Sargasso Sea data set, a recently published metagenomic data set sampled from a mammoth bone, and several complete microbial genomes. Also, simulations that evaluate the performance of the approach for different read lengths are presented.

The bacterial species dilemma and the genomic-phylogenetic species concept

The number of species of Bacteria and Archaea (ca 5000) is surprisingly small considering their early evolution, genetic diversity and residence in all ecosystems. The bacterial species definition accounts in part for the small number of named species. The primary procedures required to identify new species of Bacteria and Archaea are DNA-DNA hybridization and phenotypic characterization. Recently, 16S rRNA gene sequencing and phylogenetic analysis have been applied to bacterial taxonomy. Although 16S phylogeny is arguably excellent for classification of Bacteria and Archaea from the Domain level down to the family or genus, it lacks resolution below that level. Newer approaches, including multilocus sequence analysis, and genome sequence and microarray analyses, promise to provide necessary information to better understand bacterial speciation. Indeed, recent data using these approaches, while meagre, support the view that speciation processes may occur at the subspecies level within ecological niches (ecovars) and owing to biogeography (geovars). A major dilemma for bacterial taxonomists is how to incorporate this new information into the present hierarchical system for classification of Bacteria and Archaea without causing undesirable confusion and contention. This author proposes the genomic-phylogenetic species concept (GPSC) for the taxonomy of prokaryotes. The aim is twofold. First, the GPSC would provide a conceptual and testable framework for bacterial taxonomy. Second, the GPSC would replace the burdensome requirement for DNA hybridization presently needed to describe new species. Furthermore, the GPSC is consistent with the present treatment at higher taxonomic levels.

Microbial landscapes: new paths to biofilm research

It is the best of times for biofilm research. Systems biology approaches are providing new insights into the genetic regulation of microbial functions, and sophisticated modelling techniques are enabling the prediction of microbial community structures. Yet it is also clear that there is a need for ecological theory to contribute to our understanding of biofilms. Here, we suggest a concept for biofilm research that is spatially explicit and solidly rooted in ecological theory, which might serve as a universal approach to the study of the numerous facets of biofilms.

Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection

The gut microbiotas of zebrafish and mice share six bacterial divisions, although the specific bacteria within these divisions differ. To test how factors specific to host gut habitat shape microbial community structure, we performed reciprocal transplantations of these microbiotas into germ-free zebrafish and mouse recipients. The results reveal that communities are assembled in predictable ways. The transplanted community resembles its community of origin in terms of the lineages present, but the relative abundance of the lineages changes to resemble the normal gut microbial community composition of the recipient host. Thus, differences in community structure between zebrafish and mice arise in part from distinct selective pressures imposed within the gut habitat of each host. Nonetheless, vertebrate responses to microbial colonization of the gut are ancient: Functional genomic studies disclosed shared host responses to their compositionally distinct microbial communities and distinct microbial species that elicit conserved responses.

Can landscape ecology untangle the complexity of antibiotic resistance?

Bacterial resistance to antibiotics continues to pose a serious threat to human and animal health. Given the considerable spatial and temporal heterogeneity in the distribution of resistance and the factors that affect its evolution, dissemination and persistence, we argue that antibiotic resistance must be viewed as an ecological problem. A fundamental difficulty in assessing the causal relationship between antibiotic use and resistance is the confounding influence of geography: the co-localization of resistant bacterial species with antibiotic use does not necessarily imply causation and could represent the presence of environmental conditions and factors that have independently contributed to the occurrence of resistance. Here, we show how landscape ecology, which links the biotic and abiotic factors of an ecosystem, might help to untangle the complexity of antibiotic resistance and improve the interpretation of ecological studies.

The bacterial species definition in the genomic era

The bacterial species definition, despite its eminent practical significance for identification, diagnosis, quarantine and diversity surveys, remains a very difficult issue to advance. Genomics now offers novel insights into intra-species diversity and the potential for emergence of a more soundly based system. Although we share the excitement, we argue that it is premature for a universal change to the definition because current knowledge is based on too few phylogenetic groups and too few samples of natural populations. Our analysis of five important bacterial groups suggests, however, that more stringent standards for species may be justifiable when a solid understanding of gene content and ecological distinctiveness becomes available. Our analysis also reveals what is actually encompassed in a species according to the current standards, in terms of whole-genome sequence and gene-content diversity, and shows that this does not correspond to coherent clusters for the environmental Burkholderia and Shewanella genera examined. In contrast, the obligatory pathogens, which have a very restricted ecological niche, do exhibit clusters. Therefore, the idea of biologically meaningful clusters of diversity that applies to most eukaryotes may not be universally applicable in the microbial world, or if such clusters exist, they may be found at different levels of distinction.

Allopatric origins of microbial species

Although allopatric divergence is a well-accepted mechanism of speciation for eukaryotic macro-organisms, the importance of geographical barriers to divergence in microbial populations is a subject of great debate. Do geographically separated populations of micro-organisms diverge independently, or does their structure fit the often quoted Bass-Becking description 'everything is everywhere; the environment selects'? Aided by high-resolution genetic and genomic tools, the search for 'microbial marsupials' has revealed that in fact both are true; some species of micro-organisms demonstrate allopatric divergence, while others do not. This discovery opens the door for comparative analyses, where questions about the differences in evolutionary and ecological mechanisms that drive divergence and speciation in different microbial species can begin to be explored. Investigating these differences in evolutionary mechanisms will greatly enhance interest in, and understanding of, the dynamic processes that create and maintain the vast diversity of the microbial world.

Evolutionary history of Salmonella typhi

For microbial pathogens, phylogeographic differentiation seems to be relatively common. However, the neutral population structure of Salmonella enterica serovar Typhi reflects the continued existence of ubiquitous haplotypes over millennia. In contrast, clinical use of fluoroquinolones has yielded at least 15 independent gyrA mutations within a decade and stimulated clonal expansion of haplotype H58 in Asia and Africa. Yet, antibiotic-sensitive strains and haplotypes other than H58 still persist despite selection for antibiotic resistance. Neutral evolution in Typhi appears to reflect the asymptomatic carrier state, and adaptive evolution depends on the rapid transmission of phenotypic changes through acute infections.

Biogeography of the marine actinomycete Salinispora

Marine actinomycetes belonging to the genus Salinispora were cultured from marine sediments collected at six geographically distinct locations. Detailed phylogenetic analyses of both 16S rRNA and gyrB gene sequences reveal that this genus is comprised of three distinct but closely related clades corresponding to the species Salinispora tropica, Salinispora arenicola and a third species for which the name 'Salinispora pacifica' is proposed. Salinispora arenicola was cultured from all locations sampled and provides clear evidence for the cosmopolitan distribution of an individual bacterial species. The co-occurrence of S. arenicola with S. tropica and S. pacifica suggests that ecological differentiation as opposed to geographical isolation is driving speciation within the genus. All Salinispora strains cultured to date share greater than 99% 16S rRNA gene sequence identity and thus comprise what has been described as a microdiverse ribotype cluster. The description of this cluster as a new genus, containing multiple species, provides clear evidence that fine-scale 16S rDNA sequence analysis can be used to delineate among closely related species and that more conservative operational taxonomic unit values may significantly underestimate global species diversity.

Nonrandom distribution of Burkholderia pseudomallei clones in relation to geographical location and virulence

Burkholderia pseudomallei is a soil-dwelling saprophyte and the causative agent of melioidosis, a life-threatening human infection. Most cases are reported from northeast Thailand and northern Australia. Using multilocus sequence typing (MLST), we have compared (i) soil and invasive isolates from northeast Thailand and (ii) invasive isolates from Thailand and Australia. A total of 266 Thai B. pseudomallei isolates were characterized (83 soil and 183 invasive). These corresponded to 123 sequence types (STs), the most abundant being ST70 (n=21), ST167 (n=15), ST54 (n=12), and ST58 (n=11). Two clusters of related STs (clonal complexes) were identified; the larger clonal complex (CC48) did not conform to a simple pattern of radial expansion from an assumed ancestor, while a second (CC70) corresponded to a simple radial expansion from ST70. Despite the large number of STs, overall nucleotide diversity was low. Of the Thai isolates, those isolated from patients with melioidosis were overrepresented in the 10 largest clones (P<0.0001). There was a significant difference in the classification index between environmental and disease isolates (P<0.001), confirming that genotypes were not distributed randomly between the two samples. MLST profiles for 158 isolates from Australia (mainly disease associated) contained a number of STs (96) similar to that seen with the Thai invasive isolates, but no ST was found in both populations. There were also differences in diversity and allele frequency distribution between the two populations. This analysis reveals strong genetic differentiation on the basis of geographical isolation and a significant differentiation on the basis of virulence potential.

Diversity of 16S rRNA gene, ITS region and aclB gene of the Aquificales

The Aquificales are prevalent members of the microbial communities inhabiting many marine and terrestrial hydrothermal systems. Numerous new strains were obtained from deep-sea and terrestrial hydrothermal systems. In order to resolve the phylogenetic relationships within this group, three different phylogenetic datasets were used, namely the 16S rRNA gene, the intergenic transcribed spacer region between the 16S rRNA and 23S rRNA genes (ITS) and the gene coding for the ATP citrate lyase (aclB), a key enzyme in the reductive TCA cycle. The data were analyzed using neighbor-joining, parsimony and maximum likelihood. The resulting phylogenies appeared to be consistent between the three markers. The three genes confirmed the presence of isolates that merit further characterization and descriptions as new species and perhaps even new genera. The detailed phylogenetic interrelationships of these isolates are described here.

Phylogenetic comparisons of bacterial communities from serpentine and nonserpentine soils

I present the results of a culture-independent survey of soil bacterial communities from serpentine soils and adjacent nonserpentine comparator soils using a variety of newly developed phylogenetically based statistical tools. The study design included site-based replication of the serpentine-to-nonserpentine community comparison over a regional scale ( approximately 100 km) in Northern California and Southern Oregon by producing 16S rRNA clone libraries from pairs of samples taken on either side of the serepentine-nonserpentine edaphic boundary at three geographical sites. At the division level, the serpentine and nonserpentine communities were similar to each other and to previous data from forest soils. Comparisons of both richness and Shannon diversity produced no significant differences between any of the libraries, but the vast majority of phylogenetically based tests were significant, even with only 50 sequences per library. These results suggest that most samples were distinct, consisting of a collection of lineages generally not found in other samples. The pattern of results showed that serpentine communities tended to be more similar to each other than they were to nonserpentine communities, and these differences were at a lower taxonomic scale. Comparisons of two nonserpentine communities generally showed differences, and some results suggest that the geographical site may control community composition as well. These results show the power of phylogenetic tests to discern differences between 16S rRNA libraries compared to tests that discard DNA data to bin sequences into operational taxonomic units, and they stress the importance of replication at larger scales for inferences regarding microbial biogeography.

Annually reoccurring bacterial communities are predictable from ocean conditions

Factors influencing patterns in the distribution and abundance of plant and animal taxa modulate ecosystem function and ecosystem response to environmental change, which is often taken to infer low functional redundancy among such species, but such relationships are poorly known for microbial communities. Using high-resolution molecular fingerprinting, we demonstrate the existence of extraordinarily repeatable temporal patterns in the community composition of 171 operational taxonomic units of marine bacterioplankton over 4.5 years at our Microbial Observatory site, 20 km off the southern California coast. These patterns in distribution and abundance of microbial taxa were highly predictable and significantly influenced by a broad range of both abiotic and biotic factors. These findings provide statistically robust demonstration of temporal patterning in marine bacterial distribution and abundance, which suggests that the distribution and abundance of bacterial taxa may modulate ecosystem function and response and that a significant subset of the bacteria exhibit low levels of functional redundancy as documented for many plant and animal communities.

Genetic population structure of the soil bacterium Myxococcus xanthus at the centimeter scale

Myxococcus xanthus is a gram-negative soil bacterium best known for its remarkable life history of social swarming, social predation, and multicellular fruiting body formation. Very little is known about genetic diversity within this species or how social strategies might vary among neighboring strains at small spatial scales. To investigate the small-scale population structure of M. xanthus, 78 clones were isolated from a patch of soil (16 by 16 cm) in Tübingen, Germany. Among these isolates, 21 genotypes could be distinguished from a concatemer of three gene fragments: csgA (developmental C signal), fibA (extracellular matrix-associated zinc metalloprotease), and pilA (the pilin subunit of type IV pili). Accumulation curves showed that most of the diversity present at this scale was sampled. The pilA gene contains both conserved and highly variable regions, and two frequency-distribution tests provide evidence for balancing selection on this gene. The functional domains in the csgA gene were found to be conserved. Three instances of lateral gene transfer could be inferred from a comparison of individual gene phylogenies, but no evidence was found for linkage equilibrium, supporting the view that M. xanthus evolution is largely clonal. This study shows that M. xanthus is surrounded by a variety of distinct conspecifics in its natural soil habitat at a spatial scale at which encounters among genotypes are likely.

Spatial scaling of microbial biodiversity

A central goal in ecology is to understand the spatial scaling of biodiversity. Patterns in the spatial distribution of organisms provide important clues about the underlying mechanisms that structure ecological communities and are central to setting conservation priorities. Although microorganisms comprise much of Earth's biodiversity, little is known about their biodiversity scaling relationships relative to that for plants and animals. Here, we discuss current knowledge of microbial diversity at local and global scales. We focus on three spatial patterns: the distance-decay relationship (how community composition changes with geographic distance), the taxa-area relationship, and the local:global taxa richness ratio. Recent empirical analyses of these patterns for microorganisms suggest that there are biodiversity scaling rules common to all forms of life.