Comparative genomics of 274 Vibrio cholerae genomes reveals mobile functions structuring three niche dimensions

Background

Vibrio cholerae is a globally dispersed pathogen that has evolved with humans for centuries, but also includes non-pathogenic environmental strains. Here, we identify the genomic variability underlying this remarkable persistence across the three major niche dimensions space, time, and habitat.

Results

Taking an innovative approach of genome-wide association applicable to microbial genomes (GWAS-M), we classify 274 complete V. cholerae genomes by niche, including 39 newly sequenced for this study with the Ion Torrent DNA-sequencing platform. Niche metadata were collected for each strain and analyzed together with comprehensive annotations of genetic and genomic attributes, including point mutations (single-nucleotide polymorphisms, SNPs), protein families, functions and prophages.

Conclusions

Our analysis revealed that genomic variations, in particular mobile functions including phages, prophages, transposable elements, and plasmids underlie the metadata structuring in each of the three niche dimensions. This underscores the role of phages and mobile elements as the most rapidly evolving elements in bacterial genomes, creating local endemicity (space), leading to temporal divergence (time), and allowing the invasion of new habitats. Together, we take a data-driven approach for comparative functional genomics that exploits high-volume genome sequencing and annotation, in conjunction with novel statistical and machine learning analyses to identify connections between genotype and phenotype on a genome-wide scale.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-654) contains supplementary material, which is available to authorized users.     

A molecular study of microbe transfer between distant environments

Background

Environments and their organic content are generally not static and isolated, but in a constant state of exchange and interaction with each other. Through physical or biological processes, organisms, especially microbes, may be transferred between environments whose characteristics may be quite different. The transferred microbes may not survive in their new environment, but their DNA will be deposited. In this study, we compare two environmental sequencing projects to find molecular evidence of transfer of microbes over vast geographical distances.

Methodology

By studying synonymous nucleotide composition, oligomer frequency and orthology between predicted genes in metagenomics data from two environments, terrestrial and aquatic, and by correlating with phylogenetic mappings, we find that both environments are likely to contain trace amounts of microbes which have been far removed from their original habitat. We also suggest a bias in direction from soil to sea, which is consistent with the cycles of planetary wind and water.

Conclusions

Our findings support the Baas-Becking hypothesis formulated in 1934, which states that due to dispersion and population sizes, microbes are likely to be found in widely disparate environments. Furthermore, the availability of genetic material from distant environments is a possible font of novel gene functions for lateral gene transfer.     

Horizontal gene transfer in an acid mine drainage microbial community

Background

Horizontal gene transfer (HGT) has been widely identified in complete prokaryotic genomes. However, the roles of HGT among members of a microbial community and in evolution remain largely unknown. With the emergence of metagenomics, it is nontrivial to investigate such horizontal flow of genetic materials among members in a microbial community from the natural environment. Because of the lack of suitable methods for metagenomics gene transfer detection, microorganisms from a low-complexity community acid mine drainage (AMD) with near-complete genomes were used to detect possible gene transfer events and suggest the biological significance.

Results

Using the annotation of coding regions by the current tools, a phylogenetic approach, and an approximately unbiased test, we found that HGTs in AMD organisms are not rare, and we predicted 119 putative transferred genes. Among them, 14 HGT events were determined to be transfer events among the AMD members. Further analysis of the 14 transferred genes revealed that the HGT events affected the functional evolution of archaea or bacteria in AMD, and it probably shaped the community structure, such as the dominance of G-plasma in archaea in AMD through HGT.

Conclusions

Our study provides a novel insight into HGT events among microorganisms in natural communities. The interconnectedness between HGT and community evolution is essential to understand microbial community formation and development.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1720-0) contains supplementary material, which is available to authorized users.     

Differential Nutrient Limitation of Soil Microbial Biomass and Metabolic Quotients (qCO2): Is There a Biological Stoichiometry of Soil Microbes?

Background

Variation in microbial metabolism poses one of the greatest current uncertainties in models of global carbon cycling, and is particularly poorly understood in soils. Biological Stoichiometry theory describes biochemical mechanisms linking metabolic rates with variation in the elemental composition of cells and organisms, and has been widely observed in animals, plants, and plankton. However, this theory has not been widely tested in microbes, which are considered to have fixed ratios of major elements in soils.

Methodology/Principal Findings

To determine whether Biological Stoichiometry underlies patterns of soil microbial metabolism, we compiled published data on microbial biomass carbon (C), nitrogen (N), and phosphorus (P) pools in soils spanning the global range of climate, vegetation, and land use types. We compared element ratios in microbial biomass pools to the metabolic quotient qCO₂ (respiration per unit biomass), where soil C mineralization was simultaneously measured in controlled incubations. Although microbial C, N, and P stoichiometry appeared to follow somewhat constrained allometric relationships at the global scale, we found significant variation in the C∶N∶P ratios of soil microbes across land use and habitat types, and size-dependent scaling of microbial C∶N and C∶P (but not N∶P) ratios. Microbial stoichiometry and metabolic quotients were also weakly correlated as suggested by Biological Stoichiometry theory. Importantly, we found that while soil microbial biomass appeared constrained by soil N availability, microbial metabolic rates (qCO₂) were most strongly associated with inorganic P availability.

Conclusions/Significance

Our findings appear consistent with the model of cellular metabolism described by Biological Stoichiometry theory, where biomass is limited by N needed to build proteins, but rates of protein synthesis are limited by the high P demands of ribosomes. Incorporation of these physiological processes may improve models of carbon cycling and understanding of the effects of nutrient availability on soil C turnover across terrestrial and wetland habitats.     

Physical,Chemical and Biological Characteristics in Habitats of High and Low Presence of Anopheline Larvae in Western Kenya Highlands

Background

Characteristics of aquatic habitats determine whether mosquitoes will oviposit, hatch, develop, pupate and successfully emerge into adults or not, thus influencing which mosquito species will occupy a habitat. This study determined whether physiochemical and biological characteristics differ between habitats with high and low presence of anopheline larvae.

Methods

Physical, chemical and biological characteristics were evaluated in selected habitats twice per month within three highland valleys in western Kenya. Aquatic macro-organisms were sampled using a sweep-net. Colorimetric methods were used to determine levels of iron, phosphate, nitrate, ammonium and nitrite in water samples. Generalized Estimating Equations (GEE) was used to compare parameters between the two categories of anopheline presence.

Results

Habitats with high anopheline presence had greater abundance of mosquito aquatic stages and tadpoles and two times more levels of nitrate in water, whereas habitats with low anopheline presence had wider biofilm cover and higher levels of iron in water.

Conclusion

Habitats of high and low presence of anopheline larvae, which differed in a number of physical, chemical and biological characteristics, were identified in valleys within western Kenya highlands. Differences in habitat characteristics are critical in determining the number of anopheline larvae that will fully develop and emerge into adults.     

Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes

Background

The influence of lateral gene transfer on gene origins and biology in eukaryotes is poorly understood compared with those of prokaryotes. A number of independent investigations focusing on specific genes, individual genomes, or specific functional categories from various eukaryotes have indicated that lateral gene transfer does indeed affect eukaryotic genomes. However, the lack of common methodology and criteria in these studies makes it difficult to assess the general importance and influence of lateral gene transfer on eukaryotic genome evolution.

Results

We used a phylogenomic approach to systematically investigate lateral gene transfer affecting the proteomes of thirteen, mainly parasitic, microbial eukaryotes, representing four of the six eukaryotic super-groups. All of the genomes investigated have been significantly affected by prokaryote-to-eukaryote lateral gene transfers, dramatically affecting the enzymes of core pathways, particularly amino acid and sugar metabolism, but also providing new genes of potential adaptive significance in the life of parasites. A broad range of prokaryotic donors is involved in such transfers, but there is clear and significant enrichment for bacterial groups that share the same habitats, including the human microbiota, as the parasites investigated.

Conclusions

Our data show that ecology and lifestyle strongly influence gene origins and opportunities for gene transfer and reveal that, although the outlines of the core eukaryotic metabolism are conserved among lineages, the genes making up those pathways can have very different origins in different eukaryotes. Thus, from the perspective of the effects of lateral gene transfer on individual gene ancestries in different lineages, eukaryotic metabolism appears to be chimeric.     

PCR primers for metazoan mitochondrial 12S ribosomal DNA sequences

Background

Assessment of the biodiversity of communities of small organisms is most readily done using PCR-based analysis of environmental samples consisting of mixtures of individuals. Known as metagenetics, this approach has transformed understanding of microbial communities and is beginning to be applied to metazoans as well. Unlike microbial studies, where analysis of the 16S ribosomal DNA sequence is standard, the best gene for metazoan metagenetics is less clear. In this study we designed a set of PCR primers for the mitochondrial 12S ribosomal DNA sequence based on 64 complete mitochondrial genomes and then tested their efficacy.

Methodology/Principal Findings

A total of the 64 complete mitochondrial genome sequences representing all metazoan classes available in GenBank were downloaded using the NCBI Taxonomy Browser. Alignment of sequences was performed for the excised mitochondrial 12S ribosomal DNA sequences, and conserved regions were identified for all 64 mitochondrial genomes. These regions were used to design a primer pair that flanks a more variable region in the gene. Then all of the complete metazoan mitochondrial genomes available in NCBI''s Organelle Genome Resources database were used to determine the percentage of taxa that would likely be amplified using these primers. Results suggest that these primers will amplify target sequences for many metazoans.

Conclusions/Significance

Newly designed 12S ribosomal DNA primers have considerable potential for metazoan metagenetic analysis because of their ability to amplify sequences from many metazoans.     

Spatial scales of bacterial diversity in cold-water coral reef ecosystems

Background

Cold-water coral reef ecosystems are recognized as biodiversity hotspots in the deep sea, but insights into their associated bacterial communities are still limited. Deciphering principle patterns of bacterial community variation over multiple spatial scales may however prove critical for a better understanding of factors contributing to cold-water coral reef stability and functioning.

Methodology/Principal Findings

Bacterial community structure, as determined by Automated Ribosomal Intergenic Spacer Analysis (ARISA), was investigated with respect to (i) microbial habitat type and (ii) coral species and color, as well as the three spatial components (iii) geomorphologic reef zoning, (iv) reef boundary, and (v) reef location. Communities revealed fundamental differences between coral-generated (branch surface, mucus) and ambient microbial habitats (seawater, sediments). This habitat specificity appeared pivotal for determining bacterial community shifts over all other study levels investigated. Coral-derived surfaces showed species-specific patterns, differing significantly between Lophelia pertusa and Madrepora oculata, but not between L. pertusa color types. Within the reef center, no community distinction corresponded to geomorphologic reef zoning for both coral-generated and ambient microbial habitats. Beyond the reef center, however, bacterial communities varied considerably from local to regional scales, with marked shifts toward the reef periphery as well as between different in- and offshore reef sites, suggesting significant biogeographic imprinting but weak microbe-host specificity.

Conclusions/Significance

This study presents the first multi-scale survey of bacterial diversity in cold-water coral reefs, spanning a total of five observational levels including three spatial scales. It demonstrates that bacterial communities in cold-water coral reefs are structured by multiple factors acting at different spatial scales, which has fundamental implications for the monitoring of microbial diversity and function in those ecosystems.     

Biogeography of the ecosystems of the healthy human body

Background

Characterizing the biogeography of the microbiome of healthy humans is essential for understanding microbial associated diseases. Previous studies mainly focused on a single body habitat from a limited set of subjects. Here, we analyzed one of the largest microbiome datasets to date and generated a biogeographical map that annotates the biodiversity, spatial relationships, and temporal stability of 22 habitats from 279 healthy humans.

Results

We identified 929 genera from more than 24 million 16S rRNA gene sequences of 22 habitats, and we provide a baseline of inter-subject variation for healthy adults. The oral habitat has the most stable microbiota with the highest alpha diversity, while the skin and vaginal microbiota are less stable and show lower alpha diversity. The level of biodiversity in one habitat is independent of the biodiversity of other habitats in the same individual. The abundances of a given genus at a body site in which it dominates do not correlate with the abundances at body sites where it is not dominant. Additionally, we observed the human microbiota exhibit both cosmopolitan and endemic features. Finally, comparing datasets of different projects revealed a project-based clustering pattern, emphasizing the significance of standardization of metagenomic studies.

Conclusions

The data presented here extend the definition of the human microbiome by providing a more complete and accurate picture of human microbiome biogeography, addressing questions best answered by a large dataset of subjects and body sites that are deeply sampled by sequencing.     

Reducing assembly complexity of microbial genomes with single-molecule sequencing

Background

The short reads output by first- and second-generation DNA sequencing instruments cannot completely reconstruct microbial chromosomes. Therefore, most genomes have been left unfinished due to the significant resources required to manually close gaps in draft assemblies. Third-generation, single-molecule sequencing addresses this problem by greatly increasing sequencing read length, which simplifies the assembly problem.

Results

To measure the benefit of single-molecule sequencing on microbial genome assembly, we sequenced and assembled the genomes of six bacteria and analyzed the repeat complexity of 2,267 complete bacteria and archaea. Our results indicate that the majority of known bacterial and archaeal genomes can be assembled without gaps, at finished-grade quality, using a single PacBio RS sequencing library. These single-library assemblies are also more accurate than typical short-read assemblies and hybrid assemblies of short and long reads.

Conclusions

Automated assembly of long, single-molecule sequencing data reduces the cost of microbial finishing to $1,000 for most genomes, and future advances in this technology are expected to drive the cost lower. This is expected to increase the number of completed genomes, improve the quality of microbial genome databases, and enable high-fidelity, population-scale studies of pan-genomes and chromosomal organization.     

Productivity of malaria vectors from different habitat types in the western Kenya highlands

Background

Mosquito Larval Source Management (LSM) could be a valuable additional tool for integrated malaria vector control especially in areas with focal transmission like the highlands of western Kenya if it were not for the need to target all potential habitats at frequent intervals. The ability to determine the productivity of malaria vectors from identified habitats might be used to target LSM only at productive ones.

Methods

Each aquatic habitat within three highland sites in western Kenya was classified as natural swamp, cultivated swamp, river fringe, puddle, open drain or burrow pit. Three habitats of each type were selected in each site in order to study the weekly productivity of adult malaria vectors from February to May 2009 using a sweep-net and their habitat characteristics recorded.

Results

All surveyed habitat types produced adult malaria vectors. Mean adult productivity of Anopheles gambiae sensu lato in puddles (1.8/m²) was 11–900 times higher than in the other habitat types. However, puddles were the most unstable habitats having water at 43% of all sampling occasions and accounted for 5% of all habitats mapped in the study areas whereas open drains accounted for 72%. Densities of anopheline late instars larvae significantly increased with the presence of a biofilm but decreased with increasing surface area or when water was flowing. Taking stability and frequency of the habitat into account, puddles were still the most productive habitat types for malaria vectors but closely followed by open drains.

Conclusion

Even though productivity of An. gambiae s.l. was greatest in small and unstable habitats, estimation of their overall productivity in an area needs to consider the more stable habitats over time and their surface extension. Therefore, targeting only the highly productive habitats is unlikely to provide sufficient reduction in malaria vector densities.     

Contrasting diversity patterns of crenarchaeal, bacterial and fungal soil communities in an alpine landscape

Background

The advent of molecular techniques in microbial ecology has aroused interest in gaining an understanding about the spatial distribution of regional pools of soil microbes and the main drivers responsible of these spatial patterns. Here, we assessed the distribution of crenarcheal, bacterial and fungal communities in an alpine landscape displaying high turnover in plant species over short distances. Our aim is to determine the relative contribution of plant species composition, environmental conditions, and geographic isolation on microbial community distribution.

Methodology/Principal Findings

Eleven types of habitats that best represent the landscape heterogeneity were investigated. Crenarchaeal, bacterial and fungal communities were described by means of Single Strand Conformation Polymorphism. Relationships between microbial beta diversity patterns were examined by using Bray-Curtis dissimilarities and Principal Coordinate Analyses. Distance-based redundancy analyses and variation partitioning were used to estimate the relative contributions of different drivers on microbial beta diversity. Microbial communities tended to be habitat-specific and did not display significant spatial autocorrelation. Microbial beta diversity correlated with soil pH. Fungal beta-diversity was mainly related to soil organic matter. Though the effect of plant species composition was significant for all microbial groups, it was much stronger for Fungi. In contrast, geographic distances did not have any effect on microbial beta diversity.

Conclusions/Significance

Microbial communities exhibit non-random spatial patterns of diversity in alpine landscapes. Crenarcheal, bacterial and fungal community turnover is high and associated with plant species composition through different set of soil variables, but is not caused by geographical isolation.     

Genome size and DNA base composition of geophytes: the mirror of phenology and ecology?

Background and Aims

Genome size is known to affect various plant traits such as stomatal size, seed mass, and flower or shoot phenology. However, these associations are not well understood for species with very large genomes, which are laregly represented by geophytic plants. No detailed associations are known between DNA base composition and genome size or species ecology.

Methods

Genome sizes and GC contents were measured in 219 geophytes together with tentative morpho-anatomical and ecological traits.

Key Results

Increased genome size was associated with earliness of flowering and tendency to grow in humid conditions, and there was a positive correlation between an increase in stomatal size in species with extremely large genomes. Seed mass of geophytes was closely related to their ecology, but not to genomic parameters. Genomic DNA GC content showed a unimodal relationship with genome size but no relationship with species ecology.

Conclusions

Evolution of genome size in geophytes is closely related to their ecology and phenology and is also associated with remarkable changes in DNA base composition. Although geophytism together with producing larger cells appears to be an advantageous strategy for fast development of an organism in seasonal habitats, the drought sensitivity of large stomata may restrict the occurrence of geophytes with very large genomes to regions not subject to water stress.     

The role of seed traits in determining the phylogenetic structure of temperate plant communities

Background and Aims

Phylogenetic clustering of species within plant communities can be expected to result from environmental filtering acting on an evolutionary-conserved plant trait. One such a candidate trait is the embryo to seed-size ratio (E:S). A high E:S may allow faster germination immediately after imbibition, and is therefore assumed to be advantageous in dry habitats. In this study the hypothesis was tested that habitat filtering driven by soil moisture conditions and acting on seed germination and seedling establishment is an important ecological mechanism in structuring temperate plant communities.

Methods

Vegetation samplings were performed in three habitats located within 200 km of each other in western Europe: Ellenberg indicator values showed that the habitats selected differed substantially in terms of soil moisture and light availability. E.S ratio and seed mass data for all genera were obtained from literature. Data were analysed using recently developed phylogenetic methods.

Key Results

Genera with a similar E:S tend to co-occur, as low and high E:S genera dominate in moist and dry habitats, respectively. A phylogenetically clustered pattern of community structure was evident, and dispersion of E:S was positively related to phylogenetic dispersion.

Conclusions

The phenotypically and phylogenetically clustered pattern indicates that E:S-mediated habitat filtering is an important assembly process structuring the plant community of the temperate climate habitats studied.     

Relative Amino Acid Composition Signatures of Organisms and Environments

Background

Identifying organism-environment interactions at the molecular level is crucial to understanding how organisms adapt to and change the chemical and molecular landscape of their habitats. In this work we investigated whether relative amino acid compositions could be used as a molecular signature of an environment and whether such a signature could also be observed at the level of the cellular amino acid composition of the microorganisms that inhabit that environment.

Methodologies/Principal Findings

To address these questions we collected and analyzed environmental amino acid determinations from the literature, and estimated from complete genomic sequences the global relative amino acid abundances of organisms that are cognate to the different types of environment. Environmental relative amino acid abundances clustered into broad groups (ocean waters, host-associated environments, grass land environments, sandy soils and sediments, and forest soils), indicating the presence of amino acid signatures specific for each environment. These signatures correlate to those found in organisms. Nevertheless, relative amino acid abundance of organisms was more influenced by GC content than habitat or phylogeny.

Conclusions

Our results suggest that relative amino acid composition can be used as a signature of an environment. In addition, we observed that the relative amino acid composition of organisms is not highly determined by environment, reinforcing previous studies that find GC content to be the major factor correlating to amino acid composition in living organisms.     

Alternative Complement Activity in the Egg Cytosol of Amphioxus Branchiostoma belcheri: Evidence for the Defense Role of Maternal Complement Components

Background

The eggs in most invertebrates are fertilized externally, and therefore their resulting embryos are exposed to an environment full of microbes, many of which are pathogens capable of killing other organisms. How the developing embryos of invertebrates defend themselves against pathogenic attacks is an intriguing question to biologists, and remains largely unknown.

Methodology/Principal Findings

Here we clearly demonstrated that the egg cytosol prepared from the newly fertilized eggs of amphioxus Branchiostoma belcheri, an invertebrate chordate, was able to inhibit the growth of both the Gram-negative bacterium Vibrio anguillarum and the Gram-positive bacterium Staphylococcus aureus. All findings point to that it is the complement system operating via the alternative pathway that is attributable to the bacteriostatic activity.

Conclusions/Significance

This appears to be the first report providing the evidence for the functional role of the maternal complement components in the eggs of invertebrate species, paving the way for the study of maternal immunity in other invertebrate organisms whose eggs are fertilized in vitro. It also supports the notion that the early developing embryos share some defense mechanisms common with the adult species.     

Metagenomic comparison of two Thiomicrospira lineages inhabiting contrasting deep-sea hydrothermal environments

Background

The most widespread bacteria in oxic zones of carbonate chimneys at the serpentinite-hosted Lost City hydrothermal field, Mid-Atlantic Ridge, belong to the Thiomicrospira group of sulfur-oxidizing chemolithoautotrophs. It is unclear why Thiomicrospira-like organisms thrive in these chimneys considering that Lost City hydrothermal fluids are notably lacking in hydrogen sulfide and carbon dioxide.

Methodology/Principal Findings

Here we describe metagenomic sequences obtained from a Lost City carbonate chimney that are highly similar to the genome of Thiomicrospira crunogena XCL-2, an isolate from a basalt-hosted hydrothermal vent in the Pacific Ocean. Even though T. crunogena and Lost City Thiomicrospira inhabit different types of hydrothermal systems in different oceans, their genomic contents are highly similar. For example, sequences encoding the sulfur oxidation and carbon fixation pathways (including a carbon concentration mechanism) of T. crunogena are also present in the Lost City metagenome. Comparative genomic analyses also revealed substantial genomic changes that must have occurred since the divergence of the two lineages, including large genomic rearrangements, gene fusion events, a prophage insertion, and transposase activity.

Conclusions/Significance

Our results show significant genomic similarity between Thiomicrospira organisms inhabiting different kinds of hydrothermal systems in different oceans, suggesting that these organisms are widespread and highly adaptable. These data also indicate genomic processes potentially associated with the adaptation of these lineages into strikingly different habitats.     

Regulation of mariner transposition: the peculiar case of mos1

Background

Mariner elements represent the most successful family of autonomous DNA transposons, being present in various plant and animal genomes, including humans. The introduction and co-evolution of mariners within host genomes imply a strict regulation of the transposon activity. Biochemical data accumulated during the past decade have led to a convergent picture of the transposition cycle of mariner elements, suggesting that mariner transposition does not rely on host-specific factors. This model does not account for differences of transposition efficiency in human cells between mariners. We thus wondered whether apparent similarities in transposition cycle could hide differences in the intrinsic parameters that control mariner transposition.

Principal Findings

We find that Mos1 transposase concentrations in excess to the Mos1 ends prevent the paired-end complex assembly. However, we observe that Mos1 transposition is not impaired by transposase high concentration, dismissing the idea that transposase over production plays an obligatory role in the down-regulation of mariner transposition. Our main finding is that the paired-end complex is formed in a cooperative way, regardless of the transposase concentration. We also show that an element framed by two identical ITRs (Inverted Terminal Repeats) is more efficient in driving transposition than an element framed by two different ITRs (i.e. the natural Mos1 copy), the latter being more sensitive to transposase concentration variations. Finally, we show that the current Mos1 ITRs correspond to the ancestral ones.

Conclusions

We provide new insights on intrinsic properties supporting the self-regulation of the Mos1 element. These properties (transposase specific activity, aggregation, ITR sequences, transposase concentration/transposon copy number ratio…) could have played a role in the dynamics of host-genomes invasion by Mos1, accounting (at least in part) for the current low copy number of Mos1 within host genomes.     

Serpentine Soils Do Not Limit Mycorrhizal Fungal Diversity

Background

Physiologically stressful environments tend to host depauperate and specialized biological communities. Serpentine soils exemplify this phenomenon by imposing well-known constraints on plants; however, their effect on other organisms is still poorly understood.

Methodology/Principal Findings

We used a combination of field and molecular approaches to test the hypothesis that serpentine fungal communities are species-poor and specialized. We conducted surveys of ectomycorrhizal fungal diversity from adjacent serpentine and non-serpentine sites, described fungal communities using nrDNA Internal Transcribed Spacer (ITS) fragment and sequence analyses, and compared their phylogenetic community structure. Although we detected low fungal overlap across the two habitats, we found serpentine soils to support rich fungal communities that include representatives from all major fungal lineages. We failed to detect the phylogenetic signature of endemic clades that would result from specialization and adaptive radiation within this habitat.

Conclusions/Significance

Our results indicate that serpentine soils do not constitute an extreme environment for ectomycorrhizal fungi, and raise important questions about the role of symbioses in edaphic tolerance and the maintenance of biodiversity.     

Highly local environmental variability promotes intrapopulation divergence of quantitative traits: an example from tropical rain forest trees

Background and Aims

In habitat mosaics, plant populations face environmental heterogeneity over short geographical distances. Such steep environmental gradients can induce ecological divergence. Lowland rainforests of the Guiana Shield are characterized by sharp, short-distance environmental variations related to topography and soil characteristics (from waterlogged bottomlands on hydromorphic soils to well-drained terra firme on ferralitic soils). Continuous plant populations distributed along such gradients are an interesting system to study intrapopulation divergence at highly local scales. This study tested (1) whether conspecific populations growing in different habitats diverge at functional traits, and (2) whether they diverge in the same way as congeneric species having different habitat preferences.

Methods

Phenotypic differentiation was studied within continuous populations occupying different habitats for two congeneric, sympatric, and ecologically divergent tree species (Eperua falcata and E. grandiflora, Fabaceae). Over 3000 seeds collected from three habitats were germinated and grown in a common garden experiment, and 23 morphological, biomass, resource allocation and physiological traits were measured.

Key Results

In both species, seedling populations native of different habitats displayed phenotypic divergence for several traits (including seedling growth, biomass allocation, leaf chemistry, photosynthesis and carbon isotope composition). This may occur through heritable genetic variation or other maternally inherited effects. For a sub-set of traits, the intraspecific divergence associated with environmental variation coincided with interspecific divergence.

Conclusions

The results indicate that mother trees from different habitats transmit divergent trait values to their progeny, and suggest that local environmental variation selects for different trait optima even at a very local spatial scale. Traits for which differentiation within species follows the same pattern as differentiation between species indicate that the same ecological processes underlie intra- and interspecific variation.