Pelin Yilmaz

Pelin Yilmaz
b.value AG

PhD

About

100
Publications
34,780
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22,510
Citations
Additional affiliations
December 2017 - December 2018
Max Planck Institute for Marine Microbiology
Position
  • PostDoc Position
December 2011 - December 2017
Max Planck Institute for Marine Microbiology
Position
  • PostDoc Position

Publications

Publications (100)
Article
Full-text available
Symbiotic N2-fixing microorganisms have a crucial role in the assimilation of nitrogen by eukaryotes in nitrogen-limited environments1–3. Particularly among land plants, N2-fixing symbionts occur in a variety of distantly related plant lineages and often involve an intimate association between host and symbiont2,4. Descriptions of such intimate sym...
Article
Full-text available
The sulfur cycle is an important, although understudied facet of today's modern oxygen minimum zones (OMZs). Sulfur cycling is most active in highly productive coastal OMZs where sulfide‐rich sediments interact with the overlying water column, forming a tightly coupled benthic‐pelagic sulfur cycle. In such productive coastal systems, highly eutroph...
Article
Full-text available
The class Deltaproteobacteria comprises an ecologically and metabolically diverse group of bacteria best known for dissimilatory sulphate reduction and predatory behaviour. Although this lineage is the fourth described class of the phylum Proteobacteria , it rarely affiliates with other proteobacterial classes and is frequently not recovered as a m...
Article
Full-text available
Cyanobacterial mats were hotspots of biogeochemical cycling during the Precambrian. However, mechanisms that controlled O2 release by these ecosystems are poorly understood. In an analog to Proterozoic coastal ecosystems, the Frasassi sulfidic springs mats, we studied the regulation of oxygenic and sulfide-driven anoxygenic photosynthesis (OP and A...
Article
Full-text available
The taxonomy and associated nomenclature of many taxa of rumen bacteria are poorly defined within databases of 16S rRNA genes. This lack of resolution results in inadequate definition of microbial community structures, with large parts of the community designated as incertae sedis, unclassified, or uncultured within families, orders, or even classe...
Article
Full-text available
With the advent of advanced molecular meta-omics techniques and methods, a new era commenced for analysing and characterizing historic collection specimens, as well as recently collected environmental samples. Nucleic acid and protein sequencing-based analyses are increasingly applied to determine the origin, identity and traits of environmental (b...
Article
Full-text available
We present an extension of the Minimum Information about any (x) Sequence (MIxS) standard for reporting sequences of uncultivated virus genomes. Minimum Information about an Uncultivated Virus Genome (MIUViG) standards were developed within the Genomic Standards Consortium framework and include virus origin, genome quality, genome annotation, taxon...
Article
The phylum Acidobacteria was created in 1997 in order to accommodate a large number of 16S rRNA gene sequences retrieved from various environments in cultivation-independent studies. At present, 26 major sequence clades or subdivisions (SDs) are recognized within this phylum, but only seven of them (SDs 1, 3, 4, 6, 8, 10 and 23) are commonly addres...
Article
Full-text available
Naming of uncultured Bacteria and Archaea is often inconsistent with the International Code of Nomenclature of Prokaryotes. The recent practice of proposing names for higher taxa without designation of lower ranks and nomenclature types is one of the most important inconsistencies that needs to be addressed to avoid nomenclatural instability. The C...
Article
Full-text available
In the version of this article initially published, the following acknowledgment was omitted: A.L. was supported by the Russian Science Foundation (grant number 14-50-00069). The error has been corrected in the HTML and PDF versions of the article. © 2018 Nature America, Inc., part of Springer Nature. All rights reserved.
Article
Full-text available
Nitrite-oxidizing bacteria (NOB) have conventionally been regarded as a highly specialized functional group responsible for the production of nitrate in the environment. However, recent culture-based studies suggest that they have the capacity to lead alternative lifestyles, but direct environmental evidence for the contribution of marine nitrite o...
Article
Full-text available
Background Phylogenetic trees are an important tool to study the evolutionary relationships among organisms. The huge amount of available taxa poses difficulties in their interactive visualization. This hampers the interaction with the users to provide feedback for the further improvement of the taxonomic framework. ResultsThe SILVA Tree Viewer is...
Article
Full-text available
We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum Information about a Metagenome-Assembled G...
Article
Full-text available
The usage of molecular phylogenetic approaches is critical to advance the understanding of systematics and community processes in the kingdom Fungi. Among the possible phylogenetic markers (or combinations of them), the 18S rRNA gene appears currently as the most prominent candidate due to its large availability in public databases and informative...
Article
Full-text available
SILVA (lat. forest) is a comprehensive web resource, providing services around up to date, high-quality datasets of aligned ribosomal RNA gene (rDNA) sequences from the Bacteria, Archaea, and Eukaryota domains. SILVA dates back to the year 1991 when Dr. Wolfgang Ludwig from the Technical University Munich started the integrated software workbench A...
Article
Full-text available
The bewildering organismal and functional complexity of microbial eukaryotes has long fascinated protistologists but exceeded the capacity of this research community to comprehensively study it. Lacking the critical mass for a strong scientific discipline, protistologists remain largely divided into various sub-communities (protozoology versus phyc...
Article
Full-text available
Here we introduce a MIxS extension to facilitate the recording and cataloguing of metadata from samples related to hydrocarbon resources. The proposed MIxS-HCR package incorporates the core features of the MIxS standard for marker gene (MIMARKS) and metagenomic (MIMS) sequences along with a hydrocarbon resources customized environmental package. Ad...
Article
Full-text available
The Compliance and Interoperability Working Group of the Genomic Standards Consortium facilitates the establishment of a community of experts and the development of recommendations to describe genomic data and associated information. Here we present our ongoing conation to harmonise the reporting of contextual plant specimen data associated with ge...
Article
Full-text available
Background Making forecasts about biodiversity and giving support to policy relies increasingly on large collections of data held electronically, and on substantial computational capability and capacity to analyse, model, simulate and predict using such data. However, the physically distributed nature of data resources and of expertise in advanced...
Article
Full-text available
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 t...
Article
Full-text available
Ocean Sampling Day is a simultaneous, global mega-sequencing campaign that takes place during the boreal summer solstice each year. The European-funded 7 Framework project Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) initiated the first sampling campaign in 2014 with the aim of generating the largest standardized global m...
Article
Microbial dinitrogen (N2) fixation, the nitrogenase enzyme-catalysed reduction of N2 gas into biologically available ammonia, is the main source of new nitrogen (N) in the ocean. For more than 50 years, oceanic N2 fixation has mainly been attributed to the activity of the colonial cyanobacterium Trichodesmium1,2. Other smaller N2-fixing microorgani...
Article
Full-text available
Molecular sequences in public databases are mostly annotated by the submitting authors without further validation. This procedure can generate erroneous taxonomic sequence labels. Mislabeled sequences are hard to identify, and they can induce downstream errors because new sequences are typically annotated using existing ones. Furthermore, taxonomic...
Preprint
Full-text available
Molecular sequences in public databases are mostly annotated by the submitting authors without further validation. This procedure can generate erroneous taxonomic sequence labels. Mislabeled sequences are hard to identify, and they can induce downstream errors because new sequences are typically annotated using existing ones. Furthermore, taxonomic...
Article
Full-text available
Determining which microbial taxa are out there, where they live, and what they are doing is a driving approach in marine microbial ecology. The importance of these questions is underlined by concerted, large-scale, and global ocean sampling initiatives, for example the International Census of Marine Microbes, Ocean Sampling Day, or Tara Oceans. Giv...
Data
Relative contribution of different phyla to SILVA SSU Ref 111 (all and only newly recognized clades) and ICoMM tag sequences.
Data
Average relative abundances of newly recognized clades in different marine environments.
Data
Number of sequences in known and newly recognized marine clades (Sheet 1), references and accession numbers for known clades (Sheet 2), taxonomic hierarchy of newly recognized clades (Sheet 3).
Data
Metadata and SILVAngs statistics for ICoMM and MIRADA samples (Sheet 1), and definitions of biomes and environments (Sheet 2).
Data
Indicator species analysis results for the new clades. Results are shown for those with a p-value of less than 0.05. The light green colored cells indicate that an order can be considered indicator of a given marine environment. LP, low productivity; MP, mid productivity; HP, high productivity.
Data
PICRUSt prediction results for newly recognized clades. The sheets are organized according to energy (Sheet 1), carbon (Sheet 2), nitrogen (Sheet 3), sulfur (Sheet 4), phosphate (Sheet 5), and other (Sheet 6) metabolism.
Data
World map showing the locations of ICoMM and MIRADA samples used in this study. The bounding boxes represent Longhurst regions.
Data
Keywords used for identifying marine water column sequences in SILVA SSU Ref 111 dataset.
Article
Ocean Sampling Day is a simultaneous, global mega-sequencing campaign that takes place during the boreal summer solstice each year. The European-funded 7 Framework project Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) initiated the first sampling campaign in 2014 with the aim of generating the largest standardized global m...
Article
Full-text available
A wide variety of enzymatic pathways that produce specialized metabolites in bacteria, fungi and plants are known to be encoded in biosynthetic gene clusters. Information about these clusters, pathways and metabolites is currently dispersed throughout the literature, making it difficult to exploit. To facilitate consistent and systematic deposition...
Article
Full-text available
Molecular diversity surveys have demonstrated that aquatic fungi are highly diverse, and that they play fundamental ecological roles in aquatic systems. Unfortunately, comparative studies of aquatic fungal communities are few and far between, due to the scarcity of adequate datasets. We combined all publicly available fungal 18S ribosomal RNA (rRNA...
Article
Full-text available
Quest for Orthologs (QfO) is a community effort with the goal to improve and benchmark orthology predictions. As quality assessment assumes prior knowledge on species phylogenies, we investigated the congruency between existing species trees by comparing the relationships of 147 QfO reference organisms from six Tree of Life (ToL) / species tree pro...
Article
Full-text available
We used microsensors to investigate the combinatory effect of H2S and light on oxygenic photosynthesis in biofilms formed by a cyanobacterium from sulphidic springs. We found that photosynthesis was both positively and negatively affected by H2S. (i) H2S accelerated the recovery of photosynthesis after prolonged exposure to darkness and anoxia. We...
Article
Full-text available
Before the Earth's complete oxygenation (0.58-0.55 Ga ago), the photic zone of the Proterozoic oceans was probably redox stratified and characterized by an upper slightly aerobic nutrient-limited layer above a light-limited layer that tended towards euxinia. In such oceans, cyanobacteria capable of both oxygenic and sulfide-driven anoxygenic photos...
Chapter
As an evolutionary marker, 23S ribosomal RNA (rRNA) offers more diagnostic sequence stretches and greater sequence variation than 16S rRNA. However, 23S rRNA is still not as widely used. Based on 80 metagenome samples from the Global Ocean Sampling (GOS) Expedition, the usefulness and taxonomic resolution of 23S rRNA were compared to those of 16S r...
Article
Full-text available
Publicly available sequence databases of the small subunit ribosomal RNA gene, also known as 16S rRNA in bacteria and archaea, are growing rapidly, and the number of entries currently exceeds 4 million. However, a unified classification and nomenclature framework for all bacteria and archaea does not yet exist. In this Analysis article, we propose...
Article
Full-text available
The Genomic Standards Consortium (GSC) is an open-membership community that was founded in 2005 to work towards the development, implementation and harmonization of standards in the field of genomics. Starting with the defined task of establishing a minimal set of descriptions the GSC has evolved into an active standards-setting body that currently...
Article
Full-text available
SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive resource for up-to-date quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. SILVA provides a manually curated taxonomy for all three domains of life, based on repres...
Article
Full-text available
SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive resource for up-to-date quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. SILVA provides a manually curated taxonomy for all three domains of life, based on repres...
Article
Full-text available
The ISME Journal: Multidisciplinary Journal of Microbial Ecology is the official Journal of the International Society for Microbial Ecology, publishing high-quality, original research papers, short communications, commentary articles and reviews in the rapidly expanding and diverse discipline of microbial ecology.
Article
The democratized world of sequencing is leading to numerous data analysis challenges; MG-RAST addresses many of these challenges for diverse datasets, including amplicon datasets, shotgun metagenomes, and metatranscriptomes. The changes from version 2 to version 3 include the addition of a dedicated gene calling stage using FragGenescan, clustering...
Article
Full-text available
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 organism's ecological fitness, they...
Data
Comments on selected transitivity clusters not discussed in text. (DOC)
Data
Pfam 24 domains categorized as photobiologically relevant in this analysis. (DOC)
Data
DUFs with correlative bias towards photobiologically relevant domains (unstandardized data). (DOC)
Data
Pfam domains contained in the second largest transitivity cluster derived from unstandardized domain abundances (Figure 3: TC2). Refer to Table 1, footnote for list of abbreviations. (DOC)
Data
Histogram of correlation strength between abundances of Pfam domains across GOS metagenomes, standardized by site maxima. The distribution's mean and standard deviation were ∼0.03 and ∼0.19 respectively. A normal distribution with equal mean and standard deviation is indicated by a blue contour. (TIF)
Data
High resolution, unannotated version of Figure 1 with individual node labels. (TIF)
Data
DUFs with correlative bias towards metabolic categories (standardized data). Refer to Table 1, footnote for list of abbreviations. (DOC)
Data
Domains present in a network region characterized by photobiologically relevant domains (unstandardized data; Figure 1, Box 2). Refer to Table 1, footnote for list of abbreviations. (DOC)
Data
DUFs with updated statuses in Pfam v26 and their location in transitivity clusters (TCs) from both the unstandardized (UM; Figure 3 ) and standardized (SM; Figure 4 ) datasets. (DOC)
Data
High resolution, unannotated version of Figure 2 with individual node labels. (TIF)
Data
High resolution, unannotated version of Figure 3 with individual node labels. (TIF)
Data
Domains present in a network region bridging two enmeshed regions (unstandardized data; Figure 1, Box 4). Refer to Table 1, footnote for list of abbreviations. (DOC)
Data
Domains present in the primary network generated from standardized Pfam abundances across GOS sites (Figure 2, i). Refer to Table 1, footnote for list of abbreviations. (DOC)