Michael Richter

• PhD
• Researcher at Ribocon GmbH

The phylum "Candidatus Omnitrophica"(candidate division OP3) is ubiquitous in anaerobic habitats but is currently characterized only by draft genomes from metagenomes and single cells. We had visualized cells of the phylotype OP3 LiM in methanogenic cultures on limonene as small epibiotic cells. In this study, we enriched OP3 cells by double densit...

At hydrothermal vent sites, chimneys consisting of sulfides, sulfates, and oxides are formed upon contact of reduced hydrothermal fluids with oxygenated seawater. The walls and surfaces of these chimneys are an important habitat for vent-associated microorganisms. We used community proteogenomics to investigate and compare the composition, metaboli...

Oceanic ecosystems are dominated by minute microorgan-isms that play a major role in food webs and biogeochemical cycles1. Many microorganisms thrive in the dilute environment due to their capacity to locate, attach to, and use patches of nutrients and organic matter2,3. We propose that some free-living planktonic bacteria have traded their ability...

In the version of this Letter originally published, the authors incorrectly stated that primers 28F-519R were reported in ref. 54 to underestimate the abundance of SAR11 in the ocean. This statement has now been amended in all versions of the Letter.

Cotylorhiza tuberculata is an important scyphozoan jellyfish producing population blooms in the Mediterranean probably due to pelagic ecosystem's decay. Its gastric cavity can serve as a simple model of microbial – animal digestive associations, yet poorly characterized. Using state-of-the-art metagenomic population binning and catalyzed reporter d...

The Gulf of Naples is a dynamical area with intense exchanges between offshore oligotrophic and coastal eutrophic waters with frequent freshwater inputs. The Sarno River, one of the most polluted rivers in Europe, strongly contributes to the pollution of the area, discharging high amounts of heavy metals and organic wastes from heavily cultivated a...

Thioalkalivibrio is a genus of obligate chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacteria. Their habitat are soda lakes which are dual extreme environments with a pH range from 9.5 to 11 and salt concentrations up to saturation. More than 100 strains of this genus have been isolated from various soda lakes all over the world, but onl...

Calculated ANIb, ANIm and TETRA values. Strains marked with a (T) are type strains. Genomic species classification based on ANIb and ANIm value (green: ANI > 96% (strains belong to the same genomic species); yellow: 94% < ANI < 96% (strains might belong to the same genomic species); black: ANI < 94% (strains do not belong to the same genomic specie...

Previous and current species affiliations. (XLSX)

Dendrogram based on ANIm. De novo species clusters obtained without consideration of type strains. Clusters are indicated by dots (green: ANI > 96% (strains belong to the same genomic species); yellow: 94% < ANI < 96% (strains might belong to the same genomic species); red: ANI < 94% (strains do not belong to the same genomic species). The origin o...

Genome characteristics of Thioalkalivibrio strains used in this study. (DOCX)

Genome characteristics of the other genera used in this study. (DOCX)

16S rRNA gene sequence identities. (XLSX)

Predicted dDDH values. Strains marked with a (T) are type strains. Genomic species classification based on dDDH shown by dots (green: dDDH ? 70% (strains belong to the same genomic species); black: dDDH < 70% (strains do not belong to the same genomic species). (XLSX)

Identity values based on MLSA. (XLSX)

OPTSIL de novo species clustering and affiliation, and type-based affiliation results of dDDH, ANIb, ANIm and TETRA. (XLSX)

Nucleotide- and amino acid-based GBDP distance matrices. (XLSX)

Single gene phylogenetic trees based on atpD, clpA, dnaJ, gyrB, rpoD, rpoH, rpoS and secF gene sequences. (PDF)

The anaerobic formation and oxidation of methane involve unique enzymatic mechanisms and cofactors that are believed to be all specific for C1-compounds. Here we found that an anaerobic thermophilic enrichment culture composed of dense consortia of archaea and bacteria apparently uses partly similar pathways to oxidize the C4-hydrocarbon butane. Th...

Large, colorless sulfur-oxidizing bacteria (LSB) of the family Beggiatoaceae form thick mats at sulfidic sediment surfaces, where they efficiently detoxify sulfide before it enters the water column. The genus Thiomargarita harbors the largest known free-living bacteria with cell sizes of up to 750 μm in diameter. In addition to their ability to oxi...

The anaerobic oxidation of methane (AOM) is mediated by consortia of anaerobic methane-oxidizing archaea (ANME) and their specific partner bacteria. In thermophilic AOM consortia enriched from Guaymas Basin, members of the ANME-1 clade are associated with bacteria of the HotSeep-1 cluster, which likely perform direct electron exchange via nanowires...

Deep-sea hydrothermal vents are highly dynamic habitats characterized by steep temperature and chemical gradients. The oxidation of reduced compounds dissolved in the venting fluids fuels primary production providing the basis for extensive life. Until recently studies of microbial vent communities have focused primarily on chemolithoautotrophic or...

Marine sediments are the largest carbon sink on earth. Nearly half of dark carbon fixation in the oceans occurs in coastal sediments, but the microorganisms responsible are largely unknown. By integrating the 16S rRNA approach, single-cell genomics, metagenomics and transcriptomics with (14)C-carbon assimilation experiments, we show that uncultured...

Unlabelled: JSpecies Web Server (JSpeciesWS) is a user-friendly online service for in silico calculating the extent of identity between two genomes, a parameter routinely used in the process of polyphasic microbial species circumscription. The service measures the average nucleotide identity (ANI) based on BLAST+ (ANIb) and MUMmer (ANIm), as well...

The planctomycete strain K833 was isolated from cold waters at the coast of Island and is tentatively named 'Rhodopirellula islandica'. It has a lower temperature range for growth than other genome-sequenced Rhodopirellula strains affiliating to Rhodopirellula baltica and 'Rhodopirellula europaea'. The permanent draft genome of strain K833 was obta...

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...

Two of the largest crude oil-polluted areas in the world are the semi-enclosed Mediterranean and Red Seas, but the effect of chronic pollution remains incompletely understood on a large scale. We compared the influence of environmental and geographical constraints and anthropogenic forces (hydrocarbon input) on bacterial communities in eight geogra...

While magnetosome biosynthesis within the magnetotactic Proteobacteria is increasingly well understood, much less is known about the genetic control within deep-branching phyla which have a unique ultrastructure and biosynthesize up to several hundreds of bullet-shaped magnetite magnetosomes arranged in multiple bundles of chains, but have no cultu...

For magnetic orientation, magnetotactic bacteria biosynthesize magnetosomes, which consist of membrane-enveloped magnetic nanocrystals of either magnetite (Fe3 O4 ) or greigite (Fe3 S4 ). While magnetite formation is increasingly well understood, much less is known about the genetic control of greigite biomineralization. Recently, two related yet d...

Macroscopic growths at geographically separated acid mine drainages (AMDs) exhibit distinct populations. Yet, local heterogeneities are poorly understood. To gain novel mechanistic insights into this, we used OMICs tools to profile microbial populations coexisting in a single pyrite gallery AMD (pH ∼2) in three distinct compartments: two from a str...

Rhodopirellula baltica SH1(T) is a marine planctomycete with 7,325 genes in its genome. Ten strains of the genus Rhodopirellula were studied in whole genome microarray experiments to assess the extent of their genetic relatedness to R. baltica SH1(T). DNA of strains which were previously affiliated with the species R. baltica (OTU A) hybridized wit...

Half of the microbial cells in the Earth's oceans are found in sediments. Many of these cells are members of the Archaea, single-celled prokaryotes in a domain of life separate from Bacteria and Eukaryota. However, most of these archaea lack cultured representatives, leaving their physiologies and placement on the tree of life uncertain. Here we sh...

The majority of strains belonging to the genus Pseudovibrio have been isolated from marine invertebrates such as tunicates, corals and particularly sponges, but the physiology of these bacteria is poorly understood. In this study, we analyse for the first time the genomes of two Pseudovibrio strains - FO-BEG1 and JE062. The strain FO-BEG1 is a requ...

A metagenomic approach was carried out in order to study the genetic pool of a hypersaline microbial mat, paying more attention to the archaeal community and, specifically, to the putatively methanogenic members. The main aim of the work was to expand the knowledge of a likely ecologically important archaeal lineage, candidate division MSBL1, which...

Bacteroidetes are commonly assumed to be specialized in degrading high molecular weight (HMW) compounds and to have a preference for growth attached to particles, surfaces or algal cells. The first sequenced genomes of marine Bacteroidetes seemed to confirm this assumption. Many more genomes have been sequenced recently. Here, a comparative analysi...

The genome of Rhodopirellula sallentina SM41 was sequenced as a permanent draft to supplement the full genome sequence of the type strain Rhodopirellula baltica SH1T. This isolate is part of a larger study to gain insights into the biogeography of Rhodopirellula species in European marine waters, as well as to amend the genus description of R. balt...

The whole genome sequence of Rhodopirellula baltica SH1(T), published nearly 10years ago, already revealed a high amount of sulfatase genes. So far, little is known about the diversity and potential functions mediated by sulfatases in Planctomycetes. We combined in vivo and in silico techniques to gain insights into the ecophysiology of planktomyce...

Recent studies have indicated the existence of an extensive trans-genomic trans-mural co-metabolism between gut microbes and animal hosts that is diet-, host phylogeny- and provenance-influenced. Here, we analyzed the biodiversity at the level of small subunit rRNA gene sequence and the metabolic composition of 18 Mbp of consensus metagenome sequen...

A neighbor-joining tree of the proteobacterial SSU rRNA gene sequences representing the largest clostridia families affiliated with the phylum Firmicutes. (JPG)

A neighbor-joining tree of the proteobacterial SSU rRNA gene sequences affiliated with the phylum Firmicutes. The number of sequences in each identity cluster is specified. (JPG)

Small subunit (SSU) rRNA length distribution identified in raw (unassembled) sequences after direct pyrosequencing of the extracted DNA from lynx fecal samples. Sequences with a length ≥ 200 nucleotides are shown. (JPG)

Overview of the prokaryotic diversity of SSU rRNA tag sequences extracted from the lynx distal gut pyrosequences. (JPG)

A neighbor-joining tree of non-proteobacterial SSU rRNA gene sequences. The number of sequences in each identity cluster is specified. (JPG)

General features of the lynx gut metagenome sequences. (DOC)

Complete information regarding gene prediction and the annotation and taxonomic classification of lynx gut metagenome sequences. Panel ‘General features’ includes, total length of the metagenome, number of hypothetical, conserved hypothetical and functional conserved proteins, number of contigs, ORFs, tRNAs, RNAs, GC content and contig length distr...

Complete information regarding the hierarchical clustering of the lynx gut metagenome and other gut metagenomes based on functional composition. The metagenomes used for comparative analysis are specifically shown. Panel ‘List’ includes the list of metagenomes used for comparative analysis; Panel ‘Subset 2nd Class’ includes the comparative analysis...

Presence of glycoside hydrolases (GHs) in the lynx metagenome sample compared to that found in the metagenomes of other representative herbivores and carnivores. Panel ‘GH distribution’ includes the total number and the relative percentage of different GHs in the metagenomes as well as the putative function associated to each GH protein family (bas...

Location of the Guarrizas Iberian lynx reintroduction area. (JPG)

Recent research has disclosed a tight connection between obesity, metabolic gut microbial activities and host health. Obtaining a complete understanding of this relationship remains a major goal. Here, we conducted a comparative metagenomic and metaproteomic investigation of gut microbial communities in faecal samples taken from an obese and a lean...

Roseobacter clade bacteria (RCB) are abundant in marine bacterioplankton worldwide and central to pelagic sulfur cycling. Very little is known about their abundance and function in marine sediments. We investigated the abundance, diversity and sulfur oxidation potential of RCB in surface sediments of two tidal flats. Here, RCB accounted for up to 9...

Schematic illustration of methods for generation of deletions within the MAI. (A) Allelic replacement of target genes using double cross-over followed by removal of selection marker with Cre-lox mediated excision. (B) Cre-lox recombination using the modified sequences lox71 and lox66 for specific excision of large chromosomal regions and constructi...

Constructed suicide plasmids (pAL01 to pAL11_term) for integration of modified lox sequences. Regions (AL01 to AL11) within the MAI of M. gryphiswaldense used for site-specific plasmid insertion via homologous recombination to enable subsequent excision between lox sites of double insertions. (TIF)

Strains and plasmids used in this study. (DOC)

Annotation and characteristics of MAI genes of M. gryphiswaldense. (DOC)

Construction of integrative plasmids and deletion mutagenesis/Conjugation experiments. (DOC)

DNA oligonucleotides used in this work. (DOC)

Bacterial magnetosomes are membrane-enveloped, nanometer-sized crystals of magnetite, which serve for magnetotactic navigation. All genes implicated in the synthesis of these organelles are located in a conserved genomic magnetosome island (MAI). We performed a comprehensive bioinformatic, proteomic and genetic analysis of the MAI in Magnetospirill...

Bacteroidetes are widespread in marine systems where they play a crucial role in organic matter degradation. Whole genome analysis of several strains has revealed a broad glycolytic and proteolytic potential. In this study, we used a targeted metagenomic approach to investigate the degradation capabilities of distinct Bacteroidetes clades from two...

The phylogenetic and functional structure of the microbial community residing in a Ca2+-rich anoxic sediment of a sub-saline shallow lake (Laguna de Carrizo, initially operated as a gypsum (CaSO4 × 2 H2O) mine) was estimated by analyzing the diversity of 16S rRNA amplicons and a 3.1 Mb of consensus metagenome sequence. The lake has about half the s...

In this study, we present a single-cell genomics approach for the functional characterization of the candidate phylum Poribacteria, members of which are nearly exclusively found in marine sponges. The microbial consortia of the Mediterranean sponge Aplysina aerophoba were singularized by fluorescence-activated cell sorting, and individual microbial...

The prokaryotic communities inhabiting hypersaline sediments underlying a crystallizer pond of a Mediterranean solar saltern have been studied in a polyphasic approach including 16S rRNA and dsrAB gene libraries analysis [the last encoding for dissimilatory (bi)sulfite reductase], most probable number of cultivable counts, and metabolic measurement...

Symbioses between bacteria and eukaryotes are ubiquitous, yet our understanding of the interactions driving these associations is hampered by our inability to cultivate most host-associated microbes. Here we use a metagenomic approach to describe four co-occurring symbionts from the marine oligochaete Olavius algarvensis, a worm lacking a mouth, gu...

DNA-DNA hybridization (DDH) has been used for nearly 50 years as the gold standard for prokaryotic species circumscriptions at the genomic level. It has been the only taxonomic method that offered a numerical and relatively stable species boundary, and its use has had a paramount influence on how the current classification has been constructed. How...

Sulfate-reducing bacteria (SRB) belonging to the metabolically versatile Desulfobacteriaceae are abundant in marine sediments and contribute to the global carbon cycle by complete oxidation of organic compounds. Desulfobacterium autotrophicum HRM2 is the first member of this ecophysiologically important group with a now available genome sequence. W...