Strategies for accessing soil metagenome for desired applications

Most of the microorganisms in nature are inaccessible as they are uncultivable in the laboratory. Metagenomic approaches promise the accessibility of the genetic resources and their potential applications. Genetic resources from terrestrial environments can be accessed by exploring the soil metagenome. Soil metagenomic analyses are usually initiated by the isolation of environmental DNAs. Several methods have been described for the direct isolation of environmental DNAs from soil and sediments. Application of metagenomics largely depends on the construction of genomic DNA libraries and subsequent high-throughput sequencing or library screening. Thus, obtaining large quantities of pure cloneable DNA from the environment is a prerequisite. This review discusses the recent developments related to efficient extraction and purification of soil metagenome highlighting the considerations for various metagenomic applications.     

Screening of promoters from metagenomic DNA and their use for the construction of expression vectors

This study was focused on the screening of valuable genetic resources, such as promoters from metagenome, and describes a promoter trapping system with a bidirectional probe concept, which can select promoters or operons from various biological resources including metagenomic DNA. A pair of reporters, GFP and DsRed, facing the opposite direction without promoters, is an effective system that can function regardless of the direction of inserted promoters. The feasibility of this system was tested for the isolation of constitutively expressed promoters in E. coli from a soil metagenome, resulting in a potential pool of various promoters for practical application. The analyses of structural organization of the trapped genes demonstrated that constitutively expressible promoters in E. coli were broadly distributed within the metagenome, and suggested that some promoters were useful for the construction of expression vectors. Based on these observations, three constitutive promoters were employed in the expression vector system and their potentials for practical application were evaluated in terms of expression level, protein solubility, and effects on host growth.     

NeSSM: A Next-Generation Sequencing Simulator for Metagenomics

Background

Metagenomics can reveal the vast majority of microbes that have been missed by traditional cultivation-based methods. Due to its extremely wide range of application areas, fast metagenome sequencing simulation systems with high fidelity are in great demand to facilitate the development and comparison of metagenomics analysis tools.

Results

We present here a customizable metagenome simulation system: NeSSM (Next-generation Sequencing Simulator for Metagenomics). Combining complete genomes currently available, a community composition table, and sequencing parameters, it can simulate metagenome sequencing better than existing systems. Sequencing error models based on the explicit distribution of errors at each base and sequencing coverage bias are incorporated in the simulation. In order to improve the fidelity of simulation, tools are provided by NeSSM to estimate the sequencing error models, sequencing coverage bias and the community composition directly from existing metagenome sequencing data. Currently, NeSSM supports single-end and pair-end sequencing for both 454 and Illumina platforms. In addition, a GPU (graphics processing units) version of NeSSM is also developed to accelerate the simulation. By comparing the simulated sequencing data from NeSSM with experimental metagenome sequencing data, we have demonstrated that NeSSM performs better in many aspects than existing popular metagenome simulators, such as MetaSim, GemSIM and Grinder. The GPU version of NeSSM is more than one-order of magnitude faster than MetaSim.

Conclusions

NeSSM is a fast simulation system for high-throughput metagenome sequencing. It can be helpful to develop tools and evaluate strategies for metagenomics analysis and it’s freely available for academic users at http://cbb.sjtu.edu.cn/~ccwei/pub/software/NeSSM.php.     

Metagenomic Analysis of 0.2-μm-Passable Microorganisms in Deep-Sea Hydrothermal Fluid

We pyrosequenced the bulk DNA extracted from microorganisms that passed through 0.2-μm-pore-size filters and trapped by 0.1-μm-pore-size filters in the hydrothermal fluid of the Mariana Trough. Using the 454-FLX sequencer, we generated 202,648 sequences with an average length of 173.8 bases. Functional profiles were assigned by the SEED Annotation Engine. In the metagenome of the 0.2-μm-passable microorganisms, genes related to membrane function, including potassium homeostasis classified as membrane transport, and multidrug-resistance efflux pumps classified as virulence, were dominant. There was a higher proportion of genes pertinent to the subsystem of membrane transport in our metagenomic library than in other oceanic and hydrothermal vent metagenomes. Genes associated with a RND-type efflux transporter for exogenous substances were specifically identified in the present study. After a comparative analysis with the genome of the known ultramicrobacterium Sphingopyxis alaskensis RB2256, we discovered 1,542 cases of significant hits (E < 1 × 10⁻²) in our metagenome, and 1,172 of those were related to the DNA repair protein RadA. In this way, the microbial functional profile of 0.2-μm-passable fraction in the present study differs from oceanic metagenomes in the 0.2-μm-trapped fractions and hydrothermal vent metagenomes reported in previous research.     

A new approach to retrieve full lengths of functional genes from soil by PCR-DGGE and metagenome walking

Metagenomes are a vast genetic resource, and various approaches have been developed to explore them. Here, we present a new approach to retrieve full lengths of functional genes from soil DNA using PCR-denaturing gradient gel electrophoresis (DGGE) followed by metagenome walking. Partial fragments of benzoate 1,2-dioxygenase alpha subunit gene (benA) were detected from a 3-chlorobenzoate (3CB)-dosed soil by PCR-DGGE, and one DGGE band induced by 3CB was used as a target fragment for metagenome walking. The walking retrieved the flanking regions of the target fragment from the soil DNA, resulting in recovery of the full length of benA and also downstream gene (benB). The same strategy retrieved another gene, tfdC, and a complete tfdC and two downstream genes were obtained from the same soil. PCR-DGGE allows screening for target genes based on their potential for degrading contaminants in the environment. This feature provides an advantage over other existing metagenomic approaches.     

On-line feedback-based automatic resource configuration for distributed applications

A key problem in executing performance critical applications on distributed computing environments (e.g. the Grid) is the selection of resources. Research related to “automatic resource selection” aims to allocate resources on behalf of users to optimize the execution performance. However, most of current approaches are based on the static principle (i.e. resource selection is performed prior to execution) and need detailed application-specific information. In the paper, we introduce a novel on-line automatic resource selection approach. This approach is based on a simple control theory: the application continuously reports the Execution Satisfaction Degree (ESD) to the middleware Application Agent (AA), which relies on the reported ESD values to learn the execution behavior and tune the computing environment by adding/replacing/deleting resources during the execution in order to satisfy users’ performance requirements. We introduce two different policies applied to this approach to enable the AA to learn and tune the computing environment: the Utility Classification policy and the Desired Processing Power Estimation (DPPE) policy. Each policy is validated by an iterative application and a non-iterative application to demonstrate that both policies are effective to support most kinds of applications.     

MetCap: a bioinformatics probe design pipeline for large-scale targeted metagenomics

BackgroundMassive sequencing of genes from different environments has evolved metagenomics as central to enhancing the understanding of the wide diversity of micro-organisms and their roles in driving ecological processes. Reduced cost and high throughput sequencing has made large-scale projects achievable to a wider group of researchers, though complete metagenome sequencing is still a daunting task in terms of sequencing as well as the downstream bioinformatics analyses. Alternative approaches such as targeted amplicon sequencing requires custom PCR primer generation, and is not scalable to thousands of genes or gene families.ResultsIn this study, we are presenting a web-based tool called MetCap that circumvents the limitations of amplicon sequencing of multiple genes by designing probes that are suitable for large-scale targeted metagenomics sequencing studies. MetCap provides a novel approach to target thousands of genes and genomic regions that could be used in targeted metagenomics studies. Automatic analysis of user-defined sequences is performed, and probes specifically designed for metagenome studies are generated. To illustrate the advantage of a targeted metagenome approach, we have generated more than 300,000 probes that match more than 400,000 publicly available sequences related to carbon degradation, and used these probes for target sequencing in a soil metagenome study. The results show high enrichment of target genes and a successful capturing of the majority of gene families. MetCap is freely available to users from: http://soilecology.biol.lu.se/metcap/.ConclusionMetCap is facilitating probe-based target enrichment as an easy and efficient alternative tool compared to complex primer-based enrichment for large-scale investigations of metagenomes. Our results have shown efficient large-scale target enrichment through MetCap-designed probes for a soil metagenome. The web service is suitable for any targeted metagenomics project that aims to study several genes simultaneously. The novel bioinformatics approach taken by the web service will enable researchers in microbial ecology to tap into the vast diversity of microbial communities using targeted metagenomics as a cost-effective alternative to whole metagenome sequencing.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0501-8) contains supplementary material, which is available to authorized users.     

Process Control as Ecosystem Management: Using the History of Sewage Treatment Plants to Analyze Ecosystem Management Practices

Industrial ecosystems are fruitful sites for examining ecosystem management. Sewage treatment plants, breweries, biotechnology reactors, and ethanol production plants are all ecosystems—complex biophysical systems in which communities of bacteria, yeast, fungi, and other organisms are maintained to extract services or resources. The industrial analog to ecosystem management is “process control”, where the industrial operator is the ecosystem manager. Process control is the management of a production process through the careful measurement and adjustment of its physical and chemical conditions. By analyzing the history of process control in activated sludge sewage treatment plants, I show the importance of craft knowledge in ecosystem management. Sewage treatment plant workers, through their experience in operating the plants, developed means of evaluating process conditions based on sight and smell rather than laboratory analysis. These craft techniques developed and persisted in spite of concerted efforts on the part of sanitary scientists to institute “scientific” control of the process based on laboratory analysis and models of microbial kinetics, suggesting that craft knowledge of ecosystem function can contribute to successful management. The craft knowledge of sewage plant workers is a kind of adaptive management, in which workers constantly adjust ecosystem parameters and observe the results. This approach is contrasted to “command and control” approaches to treatment plant automation, which have met with uneven success.     

Soil-specific limitations for access and analysis of soil microbial communities by metagenomics

Metagenomics approaches represent an important way to acquire information on the microbial communities present in complex environments like soil. However, to what extent do these approaches provide us with a true picture of soil microbial diversity? Soil is a challenging environment to work with. Its physicochemical properties affect microbial distributions inside the soil matrix, metagenome extraction and its subsequent analyses. To better understand the bias inherent to soil metagenome 'processing', we focus on soil physicochemical properties and their effects on the perceived bacterial distribution. In the light of this information, each step of soil metagenome processing is then discussed, with an emphasis on strategies for optimal soil sampling. Then, the interaction of cells and DNA with the soil matrix and the consequences for microbial DNA extraction are examined. Soil DNA extraction methods are compared and the veracity of the microbial profiles obtained is discussed. Finally, soil metagenomic sequence analysis and exploitation methods are reviewed.     

IMG/M-HMP: a metagenome comparative analysis system for the Human Microbiome Project

The Integrated Microbial Genomes and Metagenomes (IMG/M) resource is a data management system that supports the analysis of sequence data from microbial communities in the integrated context of all publicly available draft and complete genomes from the three domains of life as well as a large number of plasmids and viruses. IMG/M currently contains thousands of genomes and metagenome samples with billions of genes. IMG/M-HMP is an IMG/M data mart serving the US National Institutes of Health (NIH) Human Microbiome Project (HMP), focussed on HMP generated metagenome datasets, and is one of the central resources provided from the HMP Data Analysis and Coordination Center (DACC). IMG/M-HMP is available at http://www.hmpdacc-resources.org/imgm_hmp/.     

Molecular approaches: advantages and artifacts in assessing bacterial diversity

Bacteria account for a major proportion of Earth’s biological diversity. They play essential roles in quite diverse environments and there has been an increasing interest in bacterial biodiversity. Research using novel and efficient tools to identify and characterize bacterial communities has been the key for elucidating biological activities with potential for industrial application. The current approach used for defining bacterial species is based on phenotypic and genomic properties. Traditional and novel DNA-based molecular methods are improving our knowledge of bacterial diversity in nature. Advances in molecular biology have been important for studies of diversity, considerably improving our knowledge of morphological, physiological, and ecological features of bacterial taxa. DNA–DNA hybridization, which has been used for many years, is still considered the golden standard for bacteria species identification. PCR-based methods investigating 16S rRNA gene sequences, and other approaches, such as the metagenome, have been used to study the physiology and diversity of bacteria and to identify novel genes with potential pharmaceutical and other biotechnological applications. We examined the advantages and limitations of molecular methods currently used to analyze bacterial diversity; these are mainly based on the 16S rRNA gene. These methods have allowed us to examine microorganisms that cannot be cultivated by routine methods and have also been useful for phylogenetic studies. We also considered the importance of improvements in microbe culture techniques and how we can combine different methods to allow a more appropriate assessment of bacterial diversity and to determine their real potential for industrial applications.     

Use of nitro blue tetrazolium in the reaction of adrenaline autooxidation for the determination of superoxide dismutase activity

The addition of nitro blue tetrazolium (NBT) into the reaction of adrenaline autooxidation allows direct identification of superoxide anion formation (O₂^−⊙) as well as demonstration of kinetics of their accumulation in this superoxide-generating system. The kinetics of adrenochrome and O₂^−⊙ formation has been compared under the same conditions. Three possible approaches to the use of the adrenaline autooxidation reaction for the determination of superoxide dismutase activity (SOD) and revealing antioxidant properties of various compounds are discussed. Two of these approaches have been described previously: the spectro-photometric method of registration of adrenochrome, an end product of adrenaline autooxidation, at 347 nm (Sirota, 1999) and the polarographic method, which measures oxygen consumption used for O₂^−⊙ formation (Sirota, 2011). Here, a novel approach to this problem is presented; it is based on spectrophotometric determination of O₂^−⊙ using NBT. The employment of this approach results in a significant decrease of the pH value of carbonate buffer from 10.5 to 9.7 and a 4-fold decrease in the amounts of added adrenaline, thus creating milder conditions for the revealing and investigation of antioxidant properties of materials being examined.     

Sibling rivalry between seeds within a fruit: Some population genetic models

Competition between seeds within a fruit for parental resources is described using one-locus-two-allele models. While a “normal” allele leads to an equitable distribution of resources between seeds (a situation which also corresponds to the parental optimum), the “selfish” allele is assumed to cause the seed carrying it to usurp a higher proportion of the resources. The outcome of competition between “selfish” alleles is also assumed to lead to an asymmetric distribution of resources, the “winner” being chosen randomly. Conditions for the spread of an initially rare selfish allele and the optimal resource allocation corresponding to the evolutionarily stable strategy, derived for species with n-seeded fruits, are in accordance with expectations based on Hamilton’s inclusive fitness criteria. Competition between seeds is seen to be most intense when there are only two seeds, and decreases with increasing number of seeds, suggesting that two-seeded fruits would be rarer than one-seeded or many-seeded ones. Available data from a large number of plant species are consistent with this prediction of the model. Based on a talk given at the Haldane Centenary Symposium held on 6 November 1992 at Ahmedabad as part of the 58th Annual Meeting of the Indian Academy of Sciences.     

Potential and pitfalls of eukaryotic metagenome skimming: a test case for lichens

Whole‐genome shotgun sequencing of multispecies communities using only a single library layout is commonly used to assess taxonomic and functional diversity of microbial assemblages. Here, we investigate to what extent such metagenome skimming approaches are applicable for in‐depth genomic characterizations of eukaryotic communities, for example lichens. We address how to best assemble a particular eukaryotic metagenome skimming data, what pitfalls can occur, and what genome quality can be expected from these data. To facilitate a project‐specific benchmarking, we introduce the concept of twin sets, simulated data resembling the outcome of a particular metagenome sequencing study. We show that the quality of genome reconstructions depends essentially on assembler choice. Individual tools, including the metagenome assemblers Omega and MetaVelvet, are surprisingly sensitive to low and uneven coverages. In combination with the routine of assembly parameter choice to optimize the assembly N50 size, these tools can preclude an entire genome from the assembly. In contrast, MIRA, an all‐purpose overlap assembler, and SPAdes, a multisized de Bruijn graph assembler, facilitate a comprehensive view on the individual genomes across a wide range of coverage ratios. Testing assemblers on a real‐world metagenome skimming data from the lichen Lasallia pustulata demonstrates the applicability of twin sets for guiding method selection. Furthermore, it reveals that the assembly outcome for the photobiont Trebouxia sp. falls behind the a priori expectation given the simulations. Although the underlying reasons remain still unclear, this highlights that further studies on this organism require special attention during sequence data generation and downstream analysis.     

Cambium: old challenges – new opportunities

 Trees represent a, probably the, major component of the biosphere and have a unique place in the history of Mankind. One of their most fascinating features is the process of secondary growth which is effected principally by the secondary vascular system, the developmental continuum of secondary phloem, vascular cambium, and secondary xylem. However, for too long assumptions about the developmental biology of trees have had to be based upon studies of primary growth systems within annual, herbaceous species because study of the secondary vascular system had been largely ignored. Even when attempts are made to understand some of the most fundamental features of the secondary vascular system, such as xylogenesis, the current model system, isolated Zinnia mesophyll cells, is not entirely appropriate to the situation in the intact tree. Some deficiencies of the Zinnia system are discussed, and the advantages of the genus Populus as a model for study of the hardwood secondary vascular system are considered. Some of the new approaches which are poised to lead to significant advances in our knowledge of the cell bio-logy of the secondary vascular system of trees – spe-cifically of the cell wall, the plasmalemma, and the cytoskeleton – are discussed. The value of one of these new techniques – immunocytochemistry – is demonstrated by a consideration of recent work on the role of the cytoskeleton in the hardwood secondary vascular system. Received: 23 December 1997 / Accepted: 13 May 1998     

Habitat use and mating system of the houbara bustard (Chlamydotis undulata undulata) in a semi-desertic area of North Africa: implications for conservation

Studies of the movements and home-ranges of houbara bustards (Chlamydotis undulata undulata) showed sexual and seasonal differences in the use of space, with a polygynous mating system similar to an ‘exploded-lek’ or a ‘resource-defence-polygyny’, that remains undefined. We used the arthropod biomass as an index of the trophic quality of six defined habitats and we radio-tracked 7 females and 13 males to test whether sexual and seasonal variations in habitat use were related to resource availability, and to verify if critical resources for breeding females were monopolised by males. We analysed habitat selection in both sexes separately. We used the habitat type composition of buffer zones around radio-locations to study annual and seasonal habitat selection and to identify preferred habitats, using the chi-square goodness-of-fit test. Habitat use between sexes and between seasons were compared using MANOVA based on log-ratios of habitat proportions. During the year, and in each season, both sexes appeared to be significantly selective for habitats in comparison to their availability. But males avoided esparto grass, while females used all habitats. Habitat use differed between sexes in the breeding season, but not in the non-breeding season. In spring, when food resources were abundant and uniformly distributed in space, males preferred ‘temporarily flooded areas’ and females preferred ‘reg with tall perennials’ that offered both food and cover for brooding. Critical resources were not monopolised by males and the mating system fulfilled the definition of the ‘exploded-lek’. Leks are key sites for reproduction and should be considered as priority areas in further conservation plans.     

Long-Term Foraging Expeditions (Molongo) among the Baka Hunter-Gatherers in the Northwestern Congo Basin, with Special Reference to the “Wild Yam Question”

While “Pygmy” hunter-gatherers have generally been assumed to be the original inhabitants of the central African rainforest, recent studies dispute the viability of subsistence in tropical rainforests through foraging alone. There are, however, few studies that are based on sound data of actual long-term foraging. This paper examines the viability of “pure” foraging in tropical rainforests, based on data from participant observation of a long-term foraging expedition among the Baka in the northwestern Congo Basin. The group was observed to subsist solely on wild food resources, particularly wild yams, for two-and-half months. The study was carried out during the dry season when food resources are generally thought to be scarce in tropical rainforests.     

一种基于PCR分析多样性的小鼠肠道微生物宏基因组提取方法

目的建立一种基于PCR分析分子多样性的小鼠肠道菌群宏基因组提取方法。方法比较、综合国内外小鼠肠道菌群宏基因组的提取方法后建立一种新方法,小鼠肠道内容物经丙酮洗涤,差速离心,溶菌酶、SDS裂解,CTAB处理,酚／氯仿抽提后可得到高质量的DNA,通过紫外分光光度计、琼脂糖凝胶电泳、细菌通用引物PCR和扩增核糖体限制性酶切片段分析（ARDRA）等检测该方法的实用性。结果该方法获得的小鼠肠道菌群宏基因组DNA大小在23kb左右,A260／A280在1．8—2．0,经细菌通用引物PCR后能得到适用于ARDRA的目的产物。结论该方法经济适用性较强,具备一定的应用价值。     

Impact assessment of abiotic resource consumption conceptual considerations

The impact assessment of the consumption of abiotic resources, such as fossil fuels or minerals, is usually part of the Life Cycle Impact Assessment (LCIA) in LCA studies. The problem with the consumption of such resources is their decreasing availability for future generations. In currently available LCA methods (e.g. Eco-indicator’ 99/Goedkoop and Spriensma 1999, CML/Guinée 2001), the consumption of various abiotic resources is aggregated into one summarizing indicator within the characterization phase of the LCIA. This neglects that many resources are used for different purposes and are not equivalent to each other. Therefore, the depletion of reserves of functionally non-equivalent resources should be treated as separate environmental problems, i.e. as separate impact sub-categories. Consequently, this study proposes assigning the consumption of abiotic resources to separate impact sub-categories and, if possible, integrating them into indicators only according to their primary function (e.g. coal, natural gas, oil → consumption of fossil fuels; phosphate rock → consumption of phosphate). Since this approach has been developed in the context of LCA studies on agricultural production systems, the impact assessment of the consumption of fossil fuels, phosphate rock, potash salt and lime is of particular interest and serves as an example. Following the general LCA framework (Consoli et al. 1993, ISO 1998), a normalization step is proposed separately for each of the subcategories. Finally, specific weighting factors have been calculated for the sub-categories based on the ’distance-to-target’ principle. The weighting step allows for further interpretation and enables the aggregation of the consumption of different abiotic resources to one summarizing indicator, called the Resource Depletion Index (RDI). The proposed method has been applied to a wheat production system in order to illustrate the conceptual considerations and to compare the approach to an established impact assessment method for abiotic resources (CML method, Guinée 2001).     

Fruit-feeding behaviour and use of olfactory cues by the fruit bat<Emphasis Type="Italic">Rousettus leschenaulti</Emphasis>: an experimental study

This paper describes the feeding behaviour ofRousettus leschenaulti Desmarest, 1820 on lychees, the preferred cultivated food of this bat in captive conditions. We found that feeding comprised 25–30% of the total activity of these animals in a flight cage and that feeding durations were not significantly different between two sexes. To evaluate the role of odor and vision in foraging behaviour, we provided animals with artificial lychees, real lychees and artificial lychees soaked in the juice of real lychees and we recorded the number of feeding approaches to the different “fruit” types. The results indicated that bats approached real fruit significantly more than artificial fruit, and that the number of approaches to the soaked artificial fruit was also significantly higher than to the unsoaked artificial fruit. There were no significant differences between sexes in approach rates to any “fruit” type. We discuss the role of different sensory cues in the foraging behaviour of these bats and emphasize that the olfactory cue is important in detecting food resources and discriminating between different kinds of food items.