Ivaylo Kostadinov

Metagenome and mRNA expression analyses of anaerobic methanotrophic archaea of the ANME‐1 group

Microbial consortia mediating the anaerobic oxidation of methane with sulfate are composed of methanotrophic Archaea (ANME) and Bacteria related to sulfate-reducing Deltaproteobacteria. Cultured representatives are not available for any of the three ANME clades. Therefore, a metagenomic approach was applied to assess the genetic potential of ANME-1 archaea. In total, 3.4 Mbp sequence information was generated based on metagenomic fosmid libraries constructed directly from a methanotrophic microbial mat in the Black Sea. These sequence data represent, in 30 contigs, about 82-90% of a composite ANME-1 genome. The dataset supports the hypothesis of a reversal of the methanogenesis pathway. Indications for an assimilatory, but not for a dissimilatory sulfate reduction pathway in ANME-1, were found. Draft genome and expression analyses are consistent with acetate and formate as putative electron shuttles. Moreover, the dataset points towards downstream electron-accepting redox components different from the ones known from methanogenic archaea. Whereas catalytic subunits of [NiFe]-hydrogenases are lacking in the dataset, genes for an [FeFe]-hydrogenase homologue were identified, not yet described to be present in methanogenic archaea. Clustered genes annotated as secreted multiheme c-type cytochromes were identified, which have not yet been correlated with methanogenesis-related steps. The genes were shown to be expressed, suggesting direct electron transfer as an additional possible mode to shuttle electrons from ANME-1 to the bacterial sulfate-reducing partner.

Fosmids of novel marine Planctomycetes from the Namibian and Oregon coast upwelling systems and their cross-comparison with planctomycete genomes

Planctomycetes are widely distributed in marine environments, where they supposedly play a role in carbon recycling. To deepen our understanding about the ecology of this sparsely studied phylum six planctomycete fosmids from two marine upwelling systems were investigated and compared with all available planctomycete genomic sequences including the as yet unpublished near-complete genomes of Blastopirellula marina DSM 3645T and Planctomyces maris DSM 8797T. High numbers of sulfatase genes (41–109) were found on all marine planctomycete genomes and on two fosmids (2). Furthermore, C1 metabolism genes otherwise only known from methanogenic Archaea and methylotrophic Proteobacteria were found on two fosmids and all planctomycete genomes, except for ‘Candidatus Kuenenia stuttgartiensis’. Codon usage analysis indicated high expression levels for some of these genes. In addition, novel large families of planctomycete-specific paralogs with as yet unknown functions were identified, which are notably absent from the genome of ‘Candidatus Kuenenia stuttgartiensis’. The high numbers of sulfatases in marine planctomycetes characterizes them as specialists for the initial breakdown of sulfatated heteropolysaccharides and indicate their importance for recycling carbon from these compounds. The almost ubiquitous presence of C1 metabolism genes among Planctomycetes together with codon usage analysis and information from the genomes suggest a general importance of these genes for Planctomycetes other than formaldehyde detoxification. The notable absence of these genes in Candidatus K. stuttgartiensis plus the surprising lack of almost any planctomycete-specific gene within this organism reveals an unexpected distinctiveness of anammox bacteria from all other Planctomycetes.

JCoast – A biologist-centric software tool for data mining and comparison of prokaryotic (meta)genomes

BackgroundCurrent sequencing technologies give access to sequence information for genomes and metagenomes at a tremendous speed. Subsequent data processing is mainly performed by automatic pipelines provided by the sequencing centers. Although, standardised workflows are desirable and useful in many respects, rational data mining, comparative genomics, and especially the interpretation of the sequence information in the biological context, demands for intuitive, flexible, and extendable solutions.ResultsThe JCoast software tool was primarily designed to analyse and compare (meta)genome sequences of prokaryotes. Based on a pre-computed GenDB database project, JCoast offers a flexible graphical user interface (GUI), as well as an application programming interface (API) that facilitates back-end data access. JCoast offers individual, cross genome-, and metagenome analysis, and assists the biologist in exploration of large and complex datasets.ConclusionJCoast combines all functions required for the mining, annotation, and interpretation of (meta)genomic data. The lightweight software solution allows the user to easily take advantage of advanced back-end database structures by providing a programming and graphical user interface to answer biological questions. JCoast is available at the project homepage.

The Global Genome Biodiversity Network (GGBN) Data Standard specification

Genomic samples of non-model organisms are becoming increasingly important in a broad range of studies from developmental biology, biodiversity analyses, to conservation. Genomic sample definition, description, quality, voucher information and metadata all need to be digitized and disseminated across scientific communities. This information needs to be concise and consistent in today’s ever-increasing bioinformatic era, for complementary data aggregators to easily map databases to one another. In order to facilitate exchange of information on genomic samples and their derived data, the Global Genome Biodiversity Network (GGBN) Data Standard is intended to provide a platform based on a documented agreement to promote the efficient sharing and usage of genomic sample material and associated specimen information in a consistent way. The new data standard presented here build upon existing standards commonly used within the community extending them with the capability to exchange data on tissue, environmental and DNA sample as well as sequences. The GGBN Data Standard will reveal and democratize the hidden contents of biodiversity biobanks, for the convenience of everyone in the wider biobanking community. Technical tools exist for data providers to easily map their databases to the standard. Database URL: http://terms.tdwg.org/wiki/GGBN_Data_Standard

Metatranscriptome of marine bacterioplankton during winter time in the North Sea assessed by total RNA sequencing

Marine metatranscriptome data was generated as part of a study investigating the bacterioplankton communities towards the end of a diatom-dominated spring phytoplankton bloom. This genomic resource article reports a metatranscriptomic dataset from amidst the winter time prior to the occurrence of the spring diatom bloom. Up to 58% of all sequences could be assigned to predicted genes. Taxonomic analysis based on expressed 16S ribosomal RNA genes identified Alphaproteobacteria and Gammaproteobacteria as the most active community members.

Ecogenomic Perspectives on Domains of Unknown Function: Correlation-Based Exploration of Marine Metagenomes

Background The proportion of conserved DNA sequences with no clear function is steadily growing in bioinformatics databases. Studies of sequence and structural homology have indicated that many uncharacterized protein domain sequences are variants of functionally described domains. If these variants promote an organisms ecological fitness, they are likely to be conserved in the genome of its progeny and the population at large. The genetic composition of microbial communities in their native ecosystems is accessible through metagenomics. We hypothesize the co-variation of protein domain sequences across metagenomes from similar ecosystems will provide insights into their potential roles and aid further investigation. Methodology/Principal findings We calculated the correlation of Pfam protein domain sequences across the Global Ocean Sampling metagenome collection, employing conservative detection and correlation thresholds to limit results to well-supported hits and associations. We then examined intercorrelations between domains of unknown function (DUFs) and domains involved in known metabolic pathways using network visualization and cluster-detection tools. We used a cautious “guilty-by-association” approach, referencing knowledge-level resources to identify and discuss associations that offer insight into DUF function. We observed numerous DUFs associated to photobiologically active domains and prevalent in the Cyanobacteria. Other clusters included DUFs associated with DNA maintenance and repair, inorganic nutrient metabolism, and sodium-translocating transport domains. We also observed a number of clusters reflecting known metabolic associations and cases that predicted functional reclassification of DUFs. Conclusion/Significance Critically examining domain covariation across metagenomic datasets can grant new perspectives on the roles and associations of DUFs in an ecological setting. Targeted attempts at DUF characterization in the laboratory or in silico may draw from these insights and opportunities to discover new associations and corroborate existing ones will arise as more large-scale metagenomic datasets emerge.

CDinFusion - Submission-Ready, On-Line Integration of Sequence and Contextual Data

State of the art (DNA) sequencing methods applied in “Omics” studies grant insight into the ‘blueprints’ of organisms from all domains of life. Sequencing is carried out around the globe and the data is submitted to the public repositories of the International Nucleotide Sequence Database Collaboration. However, the context in which these studies are conducted often gets lost, because experimental data, as well as information about the environment are rarely submitted along with the sequence data. If these contextual or metadata are missing, key opportunities of comparison and analysis across studies and habitats are hampered or even impossible. To address this problem, the Genomic Standards Consortium (GSC) promotes checklists and standards to better describe our sequence data collection and to promote the capturing, exchange and integration of sequence data with contextual data. In a recent community effort the GSC has developed a series of recommendations for contextual data that should be submitted along with sequence data. To support the scientific community to significantly enhance the quality and quantity of contextual data in the public sequence data repositories, specialized software tools are needed. In this work we present CDinFusion, a web-based tool to integrate contextual and sequence data in (Multi)FASTA format prior to submission. The tool is open source and available under the Lesser GNU Public License 3. A public installation is hosted and maintained at the Max Planck Institute for Marine Microbiology at http://www.megx.net/cdinfusion. The tool may also be installed locally using the open source code available at http://code.google.com/p/cdinfusion.

Quantifying the effect of environment stability on the transcription factor repertoire of marine microbes.

BackgroundDNA-binding transcription factors (TFs) regulate cellular functions in prokaryotes, often in response to environmental stimuli. Thus, the environment exerts constant selective pressure on the TF gene content of microbial communities. Recently a study on marine Synechococcus strains detected differences in their genomic TF content related to environmental adaptation, but so far the effect of environmental parameters on the content of TFs in bacterial communities has not been systematically investigated.ResultsWe quantified the effect of environment stability on the transcription factor repertoire of marine pelagic microbes from the Global Ocean Sampling (GOS) metagenome using interpolated physico-chemical parameters and multivariate statistics. Thirty-five percent of the difference in relative TF abundances between samples could be explained by environment stability. Six percent was attributable to spatial distance but none to a combination of both spatial distance and stability. Some individual TFs showed a stronger relationship to environment stability and space than the total TF pool.ConclusionsEnvironmental stability appears to have a clearly detectable effect on TF gene content in bacterioplanktonic communities described by the GOS metagenome. Interpolated environmental parameters were shown to compare well to in situ measurements and were essential for quantifying the effect of the environment on the TF content. It is demonstrated that comprehensive and well-structured contextual data will strongly enhance our ability to interpret the functional potential of microbes from metagenomic data.

Ocean Sampling Day : Genomische Schatzsuche im Meer

Bedeutung der Mikroorganismen im Ökosystem Meer ó Mikroorganismen bilden einen wichtigen Bestandteil des marinen Planktons. Bereits in einem Tropfen Meerwasser befinden sich über eine Million Mikroorganismen. Als älteste Lebensform der Erde haben sie in den letzten vier Milliarden Jahren sämtliche ökologischen Nischen der Weltmeere besiedelt. Durch ihre große Vielfalt sind sie an allen biologischen Stoffkreisläufen beteiligt und beeinflussen somit direkt das Leben im Meer und an Land. Das Phytoplankton, zu denen auch Cyanobakterien zählen, ist maßgeblich an der Sauerstoffproduktion und Kohlendioxidverwertung auf der Erde beteiligt [1, 2]. Man geht davon aus, dass Phytoplankton für die Produktion von über 50 Prozent des atmosphärischen Sauerstoffs verantwortlich ist, obwohl es nur knapp ein Prozent der weltweiten photosynthetischen Biomasse stellt. Darüber hinaus ist Phytoplankton ein essenzieller Bestandteil der Nahrungskette. Obwohl die zentrale Rolle der marinen Mikroorganismen bekannt ist, steckt unser Wissen über diese, für das bloße Auge unsichtbaren, Meeresbewohner noch in den Kinderschuhen. Der Grund dafür liegt nicht nur in der mikroskopischen Größe der Organismen, sondern darin, dass nur zwischen ein und zehn Prozent von ihnen im Labor kultiviert werden können [3]. Als Revolution erwies sich die Anwendung von kultivierungsunabhängigen Methoden, wie z. B. 16S/18S-rRNA-Gen-Analysen oder die Sequenzierung der gesamten genomischen DNA einer Probe, Metagenomik genannt. Lange Zeit wurden diese Analysen mit dem klassischen Sanger-Sequenzierverfahren durchgeführt, welches jedoch weit entfernt von einem Hochdurchsatzverfahren ist. Noch vor wenigen Jahren konnte man deshalb nur erahnen, welches ungeheure Reservoir an genetischer, physiologischer und synthetischer Vielfalt marine Mikroorganismen besitzen. Durch den Fortschritt im Bereich Next Generation Sequencing (NGS) können Meeresforscher heute in vergleichsweise kurzer Zeit sehr viele Proben sequenzieren. In den wenigen Jahren seit der Einführung des NGS haben Meeresforschungseinrichtungen aus Europa bereits enorme Mengen an genetischen und genomischen Daten aus dem Meer gewonnen. Um ein besseres Verständnis des marinen Ökosystems zu generieren und dieses Wissen für neue biotechnologische Produkte zu nutzen, müssen diese Daten nun gemeinsam mit einer Vielzahl von Umweltparametern analysiert werden. Während vor wenigen Jahren noch die Datengenerierung der limitierende Faktor war, fehlen heute geeignete bioinformatische Infrastrukturen und Analysesoftware um diese großen multidimensionalen Datensätze auszuwerten. Interdisziplinarität und Integration: das Micro B3-Projekt Im Januar 2012 startete das internationale The Ocean of Tomorrow-EU-Projekt Micro B3 (Marine Mikrobielle Biodiversität, Bioinformatik, Biotechnologie). Prof. Dr. Frank Oliver Glöckner von der Jacobs University und dem Max-Planck-Institut für Marine Mikrobiologie in Bremen koordiniert das Konsortium aus 32 akademischen und industriellen Partnern, das sich aus neun interdisziplinären Expertenteams aus den Bereichen Bioinformatik, Informatik, Biologie, Ökologie, Ozeanografie, Bioprospektion, Biotechnologie, Ethik und Recht zusammensetzt. Micro B3 hat das Ziel, die großen Mengen an Sequenzund kontextuellen Daten – auch Metadaten genannt – aus dem Meer für Forscher und Endnutzer verfügbar zu machen sowie die rechtlichen Rahmenbedingungen für die Nutzung mariner genetischer Ressourcen zu entwickeln. Dabei gilt es, biotechnologisch relevante Gensequenzen zu

Applying graph theoretic approaches to microbial metagenomes: ecological perspectives on function

Graph theoretic approaches offer a powerful means to visualise and examine data arising from microbial environmental metagenomes. Here, inter-correlations of protein domains with no known function detected in marine microbial metagenomes were visualised as networks. The topology of these networks combined with putative functional assignments of some participant protein domains allowed the generation of hypotheses concerning the ecological functions these networks may reveal. These methods may be employed to offer an ecological perspective in future attempts to describe the function of uncharacterised protein domains.