Articles Online (Volume 13, Issue 5)

Preface

The Value and Significance of Metagenomics of Marine Environments

Fangqing Zhao, Vladimir B. Bajic

Page 271–274


Research Highlight

The Tara Oceans Project: New Opportunities and Greater Challenges Ahead

Houjin Zhang , Kang Ning

本文总结了目前Tara Oceans Project项目中产生的数据和相关分析结果。指出相关研究可以作为大规模海洋微生物组学大数据深入挖掘的起点,服务于不同的研究层面,同时也提出了在数据易理解和易获取性、数据分析和挖掘方面潜在的问题。最后指出Tara Oceans Project作为近期的众多微生物组学项目中一项具有里程碑意义的项目,将会在不同层面影响对于微生物组学的深入理解和挖掘。

Page 275–277


Review

PacBio Sequencing and Its Applications

Anthony Rhoads, Kin Fai Au

Single-molecule, real-time sequencing developed by Pacific BioSciences offers longer read lengths than the second-generation sequencing (SGS) technologies, making it well-suited for unsolved problems in genome, transcriptome, and epigenetics research. The highly-contiguous de novo assemblies using PacBio sequencing can close gaps in current reference assemblies and characterize structural variation (SV) in personal genomes. With longer reads, we can sequence through extended repetitive regions and detect mutations, many of which are associated with diseases. Moreover, PacBio transcriptome sequencing is advantageous for the identification of gene isoforms and facilitates reliable discoveries of novel genes and novel isoforms of annotated genes, due to its ability to sequence full-length transcripts or fragments with significant lengths. Additionally, PacBio’s sequencing technique provides information that is useful for the direct detection of base modifications, such as methylation. In addition to using PacBio sequencing alone, many hybrid sequencing strategies have been developed to make use of more accurate short reads in conjunction with PacBio long reads. In general, hybrid sequencing strategies are more affordable and scalable especially for small-size laboratories than using PacBio Sequencing alone. The advent of PacBio sequencing has made available much information that could not be obtained via SGS alone.

Page 278–289


Review

Marine Metagenome as A Resource for Novel Enzymes

Amani D. Alma’abadi, Takashi Gojobori, Katsuhiko Mineta

More than 99% of identified prokaryotes, including many from the marine environment, cannot be cultured in the laboratory. This lack of capability restricts our knowledge of microbial genetics and community ecology. Metagenomics, the culture-independent cloning of environmental DNAs that are isolated directly from an environmental sample, has already provided a wealth of information about the uncultured microbial world. It has also facilitated the discovery of novel biocatalysts by allowing researchers to probe directly into a huge diversity of enzymes within natural microbial communities. Recent advances in these studies have led to a great interest in recruiting microbial enzymes for the development of environmentally-friendly industry. Although the metagenomics approach has many limitations, it is expected to provide not only scientific insights but also economic benefits, especially in industry. This review highlights the importance of metagenomics in mining microbial lipases, as an example, by using high-throughput techniques. In addition, we discuss challenges in the metagenomics as an important part of bioinformatics analysis in big data.

Page 290–295


Review

Web Resources for Metagenomics Studies

Pravin Dudhagara , Sunil Bhavsar, Chintan Bhagat, Anjana Ghelani, Shreyas Bhatt, Rajesh Patel

The development of next-generation sequencing (NGS) platforms spawned an enormous volume of data. This explosion in data has unearthed new scalability challenges for existing bioinformatics tools. The analysis of metagenomic sequences using bioinformatics pipelines is complicated by the substantial complexity of these data. In this article, we review several commonly-used online tools for metagenomics data analysis with respect to their quality and detail of analysis using simulated metagenomics data. There are at least a dozen such software tools presently available in the public domain. Among them, MGRAST, IMG/M, and METAVIR are the most well-known tools according to the number of citations by peer-reviewed scientific media up to mid-2015. Here, we describe 12 online tools with respect to their web link, annotation pipelines, clustering methods, online user support, and availability of data storage. We have also done the rating for each tool to screen more potential and preferential tools and evaluated five best tools using synthetic metagenome. The article comprehensively deals with the contemporary problems and the prospects of metagenomics from a bioinformatics viewpoint.

Page 296–303


Original Research

First Insights into the Viral Communities of the Deep-sea Anoxic Brines of the Red Sea

André Antunes, Intikhab Alam, Marta Filipa Simões, Camille Daniels, Ari J.S. Ferreira, Rania Siam, Hamza El-Dorry, Vladimir B. Bajic

The deep-sea brines of the Red Sea include some of the most extreme and unique environments on Earth. They combine high salinities with increases in temperature, heavy metals, hydrostatic pressure, and anoxic conditions, creating unique settings for thriving populations of novel extremophiles. Despite a recent increase of studies focusing on these unusual biotopes, their viral communities remain unexplored. The current survey explores four metagenomic datasets obtained from different brine–seawater interface samples, focusing specifically on the diversity of their viral communities. Data analysis confirmed that the particle-attached viral communities present in the brine–seawater interfaces were diverse and generally dominated by Caudovirales, yet appearing distinct from sample to sample. With a level of caution, we report the unexpected finding of Phycodnaviridae, which infects algae and plants, and trace amounts of insect-infecting Iridoviridae. Results from Kebrit Deep revealed stratification in the viral communities present in the interface: the upper-interface was enriched with viruses associated with typical marine bacteria, while the lower-interface was enriched with haloviruses and halophages. These results provide first insights into the unexplored viral communities present in deep-sea brines of the Red Sea, representing one of the first steps for ongoing and future sampling efforts and studies.

Page 304–309


Original Research

Soil and Rhizosphere Associated Fungi in Gray Mangroves (Avicennia marina) from the Red Sea — A Metagenomic Approach

Marta Filipa Simões, André Antunes, Cristiane A. Ottoni, Mohammad Shoaib Amini, Intikhab Alam, Hanin Alzubaidy, Noor-Azlin Mokhtar, John A.C. Archer, Vladimir B. Bajic

Covering a quarter of the world’s tropical coastlines and being one of the most threatened ecosystems, mangroves are among the major sources of terrestrial organic matter to oceans and harbor a wide microbial diversity. In order to protect, restore, and better understand these ecosystems, researchers have extensively studied their microbiology, yet few surveys have focused on their fungal communities. Our lack of knowledge is even more pronounced for specific fungal populations, such as the ones associated with the rhizosphere. Likewise, the Red Sea gray mangroves (Avicennia marina) remain poorly characterized, and understanding of their fungal communities still relies on cultivation-dependent methods. In this study, we analyzed metagenomic datasets from gray mangrove rhizosphere and bulk soil samples collected in the Red Sea coast, to obtain a snapshot of their fungal communities. Our data indicated that Ascomycota was the dominant phylum (76%–85%), while Basidiomycota was less abundant (14%–24%), yet present in higher numbers than usually reported for such environments. Fungal communities were more stable within the rhizosphere than within the bulk soil, both at class and genus level. This finding is consistent with the intrinsic patchiness in soil sediments and with the selection of specific microbial communities by plant roots. Our study indicates the presence of several species on this mycobiome that were not previously reported as mangrove-associated. In particular, we detected representatives of several commercially-used fungi, e.g., producers of secreted cellulases and anaerobic producers of cellulosomes. These results represent additional insights into the fungal community of the gray mangroves of the Red Sea, and show that they are significantly richer than previously reported.

Page 310–320


Application Note

CVTree3 Web Server for Whole-genome-based and Alignment-free Prokaryotic Phylogeny and Taxonomy

Guanghong Zuo, Bailin Hao

A faithful phylogeny and an objective taxonomy for prokaryotes should agree with each other and ultimately follow the genome data. With the number of sequenced genomes reaching tens of thousands, both tree inference and detailed comparison with taxonomy are great challenges. We now provide one solution in the latest Release 3.0 of the alignment-free and whole-genome-based web server CVTree3. The server resides in a cluster of 64 cores and is equipped with an interactive, collapsible, and expandable tree display. It is capable of comparing the tree branching order with prokaryotic classification at all taxonomic ranks from domains down to species and strains. CVTree3 allows for inquiry by taxon names and trial on lineage modifications. In addition, it reports a summary of monophyletic and non-monophyletic taxa at all ranks as well as produces print-quality subtree figures. After giving an overview of retrospective verification of the CVTree approach, the power of the new server is described for the mega-classification of prokaryotes and determination of taxonomic placement of some newly-sequenced genomes. A few discrepancies between CVTree and 16S rRNA analyses are also summarized with regard to possible taxonomic revisions. CVTree3 is freely accessible to all users at http://tlife.fudan.edu.cn/cvtree3/ without login requirements.
当前,对原核生物的分类现在越来越多的依赖生物的基因组,而物种的亲缘关系也是基于生物的基因组,故原核生物的亲缘关系与其分类系统具有可比拟性。也就是说一个可行的亲缘关系应该与其分类系统保持一定的一致性,另一方面也可以通过亲缘关系的分析来进行物种分类地位进行初步的鉴定。我们新开发的CVTree 3.0网络服务器(网址:http://tlife.fudan.edu.cn/cvtree3),通过组分矢量方法(CVTree)来得到原核生物的亲缘关系,然后基于高效的算法,将其与分类系统进行对比,并将结果以可交互的方式展示在网页上,从而方便广大生物工作者使用。通过使用CVTree网络服务器,用户可以快速的对未知的全基因组序列进行亲缘关系分析,并对其分类地位进行初步鉴定。由于合理利用全基因组信息,CVTree方法能对种以下的亲缘关系与分类具有高分辨力。我们希望,随着CVTree方法的深入与完善,CVTree方法能成为阐明原核生物亲缘关系与分类系统的定义性的工具。

Page 321–331