Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics

High‐throughput DNA methods hold great promise for the study of taxonomically intractable mesofauna of the soil. Here, we assess species diversity and community structure in a phylogenetic framework, by sequencing total DNA from bulk specimen samples and assembly of mitochondrial genomes. The combination of mitochondrial metagenomics and DNA barcode sequencing of 1494 specimens in 69 soil samples from three geographic regions in southern Iberia revealed >300 species of soil Coleoptera (beetles) from a broad spectrum of phylogenetic lineages. A set of 214 mitochondrial sequences longer than 3000 bp was generated and used to estimate a well‐supported phylogenetic tree of the order Coleoptera. Shorter sequences, including cox1 barcodes, were placed on this mitogenomic tree. Raw Illumina reads were mapped against all available sequences to test for species present in local samples. This approach simultaneously established the species richness, phylogenetic composition and community turnover at species and phylogenetic levels. We find a strong signature of vertical structuring in soil fauna that shows high local community differentiation between deep soil and superficial horizons at phylogenetic levels. Within the two vertical layers, turnover among regions was primarily at the tip (species) level and was stronger in the deep soil than leaf litter communities, pointing to layer‐mediated drivers determining species diversification, spatial structure and evolutionary assembly of soil communities. This integrated phylogenetic framework opens the application of phylogenetic community ecology to the mesofauna of the soil, among the most diverse and least well‐understood ecosystems, and will propel both theoretical and applied soil science.     

Correction to: An automated iterative approach for protein structure refinement using pseudocontact shifts

Journal of Biomolecular NMR -     

An improved environmental index based on the relative abundance of oligochaete species

Howmiller & Scott (1977) presented an ‘Environmental Index’ based on thorough knowledge of the ecological demands of species of freshwater oligochaetes frequently found in North American waters. These authors emphasized the fact that common diversity measures do not utilize information about the ecological attributes of the constituent species but rather about community structure. A modification of the ‘Environmental Index’ is here presented with the aim of increasing its sensitivity in Europe and possibly also in North America. Four ecological groups are here preferred to the original three, and the ecological valence of the ‘key-species’ Tubifex tubifex is discussed at some length. Whereas most environmental and diversity indices remain little affected by changes in the total abundance of oligochaetes, the modified index is sensitive to such changes. Comparisons are made with two of the most popular diversity indices applied to specific situations, i.e. the Shannon-Weaver index and Simpson's index. In spite of recommendation in pollution manuals, indices of diversity may be inadequate in correctly characterizing situations of nutrient enrichment of freshwater environments. In the present study it is stressed that low diversity is usually found at both ends of the trophic scale and high diversity, which is supposed to characterize a clean and unstressed environment, is generally obtained in zones of transit between oligotrophic and eutrophic conditions — a likely result of the ‘nonequilibrium state’ described by Connell (1978) from coral reefs and rain forests in the tropics.     

The relative abundance and seawater requirements of gram-positive bacteria in near-shore tropical marine samples

The relative abundance of gram-positive bacteria in a variety of near-shore marine samples was determined using the KOH method. Gram-positive bacteria accounted for 14%, 25%, 31 %, and 12%, respectively, of the colony-forming bacteria obtained from seawater, sediments, and the surfaces of algae and invertebrates. A total of 481 gram-positive strains were isolated representing a wide range of morphological groups including regular and irregular rods, cocci, and actinomycetes. Seventy-seven percent of the strains characterized did not form spores and were aerobic, catalase-positive rods with regular to irregular cell morphologies. Eighty-two percent of the strains tested showed an obligate requirement of seawater for growth. None of the cocci tested required seawater or sodium for growth. This is the first report documenting that gram-positive bacteria can compose a large percentage of the culturable, heterotrophic bacteria associated with the surfaces of tropical marine algae. Correspondence to: P.R. Jensen     

Structure determination of asymmetric membrane profiles using an iterative Fourier method.

An iterative Fourier method is applied to solving and refining the electron density profile projected into the line perpendicular to a membrane surface. Solutions to the continuous X-ray scattering pattern derived from swelling of multilayer systems or from membrane dispersions can be obtained by this technique. The method deals directly with the observed structure factors and does not rely on deconvolution of the Patterson function. We used this method previously to derive the electron density profile for acetylcholine receptor membranes (Ross et al., 1977). The present paper is an analysis of the theoretical basis for the procedure. In addition, the technique is tested on artificially generated continuous-scattering data, on the data for frog sciatic nerve myelin derived from swelling experiments by Worthington and McIntosh (1974), and on the data for purple membrane (Blaurock and Stoeckenius, 1971). Although the method applies to asymmetric membranes, the special case of centrosymmetric profiles is also shown to be solvable by the same technique. The limitations of the method and the boundary conditions that limit the degeneracy of the solution are analyzed.     

Bayesian shrinkage estimation of the relative abundance of mRNA transcripts using SAGE

Serial analysis of gene expression (SAGE) is a technology for quantifying gene expression in biological tissue that yields count data that can be modeled by a multinomial distribution with two characteristics: skewness in the relative frequencies and small sample size relative to the dimension. As a result of these characteristics, a given SAGE sample may fail to capture a large number of expressed mRNA species present in the tissue. Empirical estimators of mRNA species' relative abundance effectively ignore these missing species, and as a result tend to overestimate the abundance of the scarce observed species comprising a vast majority of the total. We have developed a new Bayesian estimation procedure that quantifies our prior information about these characteristics, yielding a nonlinear shrinkage estimator with efficiency advantages over the MLE. Our prior is mixture of Dirichlets, whereby species are stochastically partitioned into abundant and scarce classes, each with its own multivariate prior. Simulation studies reveal our estimator has lower integrated mean squared error (IMSE) than the MLE for the SAGE scenarios simulated, and yields relative abundance profiles closer in Euclidean distance to the truth for all samples simulated. We apply our method to a SAGE library of normal colon tissue, and discuss its implications for assessing differential expression.     

Statistical mechanics of relative species abundance

Statistical mechanics of relative species abundance (RSA) patterns in biological networks is presented. The theory is based on multispecies replicator dynamics equivalent to the Lotka–Volterra equation, with diverse interspecies interactions. Various RSA patterns observed in nature are derived from a single parameter related to productivity or maturity of a community. The abundance distribution is formed like a widely observed left-skewed lognormal distribution. It is also found that the “canonical hypothesis” is supported in some parameter region where the typical RSA patterns are observed. As the model has a general form, the result can be applied to similar patterns in other complex biological networks, e.g. gene expression.     

Tests of density dependence using indices of relative abundance in a deer population

A major question in animal ecology is explaining the causes of population fluctuations. Consensus about the most reliable method to detect density dependence (DD) or environmental effects from time‐series data, however, has not yet been achieved. Times series analyses have been used with indices of relative abundance in numerous studies, although these indices are rarely validated. Here, we used three different time series of relative abundance (number of deer seen per hunter per day, hunting success and proportion of males in the harvest) to explore direct and delayed DD in a white‐tailed deer Odocoileus virginianus population on Anticosti Island, Québec, Canada. Three mathematical approaches were tested: linear models, autoregressive (AR) models, and total DD in life history. Tests of DD using different indices of abundance on the same population should lead to similar results if all indices exhibit similar behaviour. Indices of relative abundance correlated with each other, although sometimes weakly, such that we obtained similar DD estimates with each index using detrended non‐stationary series. In most time series, linear regression of N_t?1 and N_t and AR models did not detect DD, while we obtained strong evidence for DD from the life‐history approach. This meant that contrasting conclusions about the role of density dependence within this population were reached depending on which method was used. We conclude that the method that incorporates most biological realism, the life‐history approach, provided a different result than classical interpretation of autoregressive coefficients. Only the life‐history interpretation supported our a priori belief that density dependence operating through competition for food regulates the Anticosti deer population. Phenomenological analysis aiming to investigate changes in abundance should be carefully conducted as the use of inappropriate indices or methods could lead to inappropriate conclusions or management strategies. Preferably, the method used should match the time scale of the population sampling regime and species life history.     

Phylogenetic skew: an index of community diversity

The distribution of divergence times between member species of a community reflects the pattern of species composition. In this study, we contrast the species composition of a community against the meta‐community, which we define as the species composition of a set of target communities. We regard the collection of species that comprise a community as a sample from the set of member species of the meta‐community, and interpret the pattern of the community species composition in terms of the type of species sampled from the meta‐community. A newly defined effective species sampling proportion explains the amount of the difference between the divergence time distributions of the community and that of the meta‐community, assuming random sampling. We propose a new index of phylogenetic skew (PS), as the ratio of the maximum‐likelihood estimate of the effective species sampling proportion to the observed sampling proportion. A PS value of 1 is interpreted as random sampling. If the value is >1, the sampling is suspected to be phylogenetically skewed. If it is <1, systematic thinning of species is likely. Unlike other indices, the PS does not depend on species richness as long as the community has more than a few members of a species. Because it is possible to compare partially observed communities, the index may be effectively used in exploratory analysis to detect candidate communities with unique species compositions from a large number of communities.     

Estimating the relative abundance of emperor penguins at inaccessible colonies using satellite imagery

Emperor penguin (Aptenodytes forsteri) populations are useful environmental indicators due to the bird’s extreme reliance on sea ice. We used remote sensing technology to estimate relative adult bird abundance at two inaccessible emperor penguin colonies in the Ross Sea, Antarctica. We performed supervised classification of 12 panchromatic satellite images of the seven known Ross Sea colonies. We used regression to predict adult bird counts at the inaccessible colonies by relating the number of pixels classified as “penguin” in the satellite images of the accessible colonies to corresponding known adult bird counts from aerial photographs or ground counts. While our analysis was hampered by excessive guano and shadows, we used satellite imagery to differentiate between relatively small (<3,000 adult birds) and larger colonies (>5,000 adult birds). Remote sensing technology is logistically less intense and less costly than aerial or ground censuses when the objective is to document penguin presence and/or large emperor penguin population changes (e.g., catastrophic changes). Improvements expected soon in the resolution of the satellite images should allow for more accurate abundance estimates.     

Phylogenetic classification of Eudorylini (Diptera: Pipunculidae)

Abstract. The phylogenetic relationships of members of Eudorylini (Diptera: Pipunculidae: Pipunculinae) were explored. Two hundred and fifty-seven species of Eudorylini from all biogeographical regions and all known genera were examined. Sixty species were included in an exemplar-based phylogeny for the tribe. Two new genera are described, Clistoabdominalis and Dasydorylas . The identity of Eudorylas Aczél, the type genus for Eudorylini, has been obscure since its inception. The genus is re-diagnosed and a proposal to stabilize the genus and tribal names is discussed. An illustrated key to the genera of Pipunculidae is presented and all Eudorylini genera are diagnosed. Numerous new generic synonyms are proposed. Moriparia nigripennis Kozánek & Kwon is preoccupied by Congomyia nigripennis Hardy when both are transferred to Claraeola , so Cla. koreana Skevington is proposed as a new name for Mo. nigripennis .     

Functional metagenomics of oil-impacted mangrove sediments reveals high abundance of hydrolases of biotechnological interest

Mangroves are located in coastal wetlands and are susceptible to the consequences of oil spills, what may threaten the diversity of microorganisms responsible for the nutrient cycling and the consequent ecosystem functioning. Previous reports show that high concentration of oil favors the incidence of epoxide hydrolases and haloalkane dehalogenases in mangroves. This finding has guided the goals of this study in an attempt to broaden the analysis to other hydrolases and thereby verify whether oil contamination interferes with the prevalence of particular hydrolases and their assigned microorganisms. For this, an in-depth survey of the taxonomic and functional microbial diversity recovered in a fosmid library (Library_Oil Mgv) constructed from oil-impacted Brazilian mangrove sediment was carried out. Fosmid DNA of the whole library was extracted and submitted to Illumina HiSeq sequencing. The resulting Library Oil_Mgv dataset was further compared with those obtained by direct sequencing of environmental DNA from Brazilian mangroves (from distinct regions and affected by distinct sources of contamination), focusing on hydrolases with potential use in biotechnological processes. The most abundant hydrolases found were proteases, esterases and amylases, with similar occurrence profile in all datasets. The main microbial groups harboring such hydrolase-encoding genes were distinct in each mangrove, and in the fosmid library these enzymes were mainly assigned to Chloroflexaceae (for amylases), Planctomycetaceae (for esterases) and Bradyrhizobiaceae (for proteases). Assembly and analysis of Library_Oil Mgv reads revealed three potentially novel enzymes, one epoxide hydrolase, one xylanase and one amylase, to be further investigated via heterologous expression assays.     

Ligand-Info,searching for similar small compounds using index profiles

MOTIVATION: The Ligand-Info system is based on the assumption that small molecules with similar structure have similar functional (binding) properties. The developed system enables a fast and sensitive index based search for similar compounds in large databases. Index profiles, constructed by averaging indexes of related molecules are used to increase the specificity of the search. The utilization of index profiles helps to focus on frequent, common features of a family of compounds. RESULTS: A Java-based tool for clustering and scanning of small molecules has been created. The tool can interactively cluster sets of molecules and create index profiles on the user side and automatically download similar molecules from a databases of 250 000 compounds. The results of the application of index profiles demonstrate that the profile based search strategy can increase the quality of the selection process. AVAILABILITY: The system is available at http://Ligand.Info. The application requires the Java Runtime Environment 1.4, which can be automatically installed during the first use on desktop systems, which support it. A standalone version of the program is available from the authors upon request.     

Recognition of related proteins by iterative template refinement (ITR).

Predicting the structural fold of a protein is an important and challenging problem. Available computer programs for determining whether a protein sequence is compatible with a known 3-dimensional structure fall into 2 categories: (1) structure-based methods, in which structural features such as local conformation and solvent accessibility are encoded in a template, and (2) sequence-based methods, in which aligned sequences of a set of related proteins are encoded in a template. In both cases, the programs use a static template based on a predetermined set of proteins. Here, we describe a computer-based method, called iterative template refinement (ITR), that uses templates combining structure-based and sequence-based information and employs an iterative search procedure to detect related proteins and sequentially add them to the templates. Starting from a single protein of known structure, ITR performs sequential cycles of database search to construct an expanding tree of templates with the aim of identifying subtle relationships among proteins. Evaluating the performance of ITR on 6 proteins, we found that the method automatically identified a variety of subtle structural similarities to other proteins. For example, the method identified structural similarity between arabinose-binding protein and phosphofructokinase, a relationship that has not been widely recognized.     

Serine-specific tRNAs in Escherichia coli: relative abundance and sequence

Serine isoaccepting tRNAs were isolated from bulk tRNA of Escherichia coli by affinity chromatography on immobilized bacterial elongation factor Tu and their relative abundance was determined. The three major species, which are sufficient to read all six serine codons, were identified by sequencing. The sequence of a novel tRNASer with the anticodon GGA was elucidated.     

Phylogenetic classification of short environmental DNA fragments

Metagenomics is providing striking insights into the ecology of microbial communities. The recently developed massively parallel 454 pyrosequencing technique gives the opportunity to rapidly obtain metagenomic sequences at a low cost and without cloning bias. However, the phylogenetic analysis of the short reads produced represents a significant computational challenge. The phylogenetic algorithm CARMA for predicting the source organisms of environmental 454 reads is described. The algorithm searches for conserved Pfam domain and protein families in the unassembled reads of a sample. These gene fragments (environmental gene tags, EGTs), are classified into a higher-order taxonomy based on the reconstruction of a phylogenetic tree of each matching Pfam family. The method exhibits high accuracy for a wide range of taxonomic groups, and EGTs as short as 27 amino acids can be phylogenetically classified up to the rank of genus. The algorithm was applied in a comparative study of three aquatic microbial samples obtained by 454 pyrosequencing. Profound differences in the taxonomic composition of these samples could be clearly revealed.