Michael W Friedrich

Michael W Friedrich
Universität Bremen | Uni Bremen · MARUM - Center for Marine Environmental Sciences

Prof. Dr.

About

197
Publications
28,469
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Introduction
Current research interests: - Microbial metal reduction in sediments - Inorganic carbon metabolism in sediments - Anaerobic methane oxidation in sediments - Functional diversity of microorganisms Methods and techniques: - Stable isotope probing of nucleic acids - High-trough-put analysis of microbial communities - Metagenomics of isotopically enriched DNA - Quantitative analysis of methanogens and anaerobic methanotrophs
Additional affiliations
November 2012 - present
Universität Bremen
Position
  • Professor
October 2008 - present
Universität Bremen
Position
  • Professor

Publications

Publications (197)
Article
Full-text available
Metagenomic analysis has facilitated prediction of a variety of carbon utilization potentials by uncultivated archaea including degradation of protein, which is a widespread carbon polymer in marine sediments. However, the activity of detrital catabolic protein degradation is mostly unknown for the vast majority of archaea. Here, we show actively e...
Article
Full-text available
Acidobacteria occur in a large variety of ecosystems worldwide and are particularly abundant and highly diverse in soils. In spite of their diversity, only few species have been characterized to date which makes Acidobacteria one of the most poorly understood phyla among the domain Bacteria. We used a culture-independent niche modeling approach to...
Article
Full-text available
Permanently cold marine sediments are heavily influenced by increased input of iron as a result of accelerated glacial melt, weathering, and erosion. The impact of such environmental changes on microbial communities in coastal sediments is poorly understood. We investigated geochemical parameters that shape microbial community compositions in anoxi...
Article
Colonization of newly ice-free areas by marine benthic organisms intensifies burial of macroalgae detritus in Potter Cove coastal surface sediments (Western Antarctic Peninsula). Thus, fresh and labile macroalgal detritus serves as primary organic matter (OM) source for microbial degradation. Here, we investigated the effects on post-depositional m...
Article
Full-text available
Anaerobic methane oxidizing archaea (ANME) mediate anaerobic oxidation of methane (AOM) in marine sediments and are therefore important for controlling atmospheric methane concentrations in the water column and ultimately the atmosphere. Numerous previous studies have revealed that AOM is coupled to the reduction of different electron acceptors suc...
Article
Full-text available
Elevated dissolved iron concentrations in the methanic zone are typical geochemical signatures of rapidly accumulating marine sediments. These sediments are often characterized by co-burial of iron oxides with recalcitrant aromatic organic matter of terrigenous origin. Thus far, iron oxides are predicted to either impede organic matter degradation,...
Article
Full-text available
Asgard is a recently discovered archaeal superphylum, closely linked to the emergence of eukaryotes. Among Asgard archaea, Lokiarchaeota are abundant in marine sediments, but their in situ activities are largely unknown except for Candidatus 'Prometheoarchaeum syntrophicum'. Here, we tracked the activity of Lokiarchaeota in incubations with Helgola...
Article
Asgard is a newly proposed archaeal superphylum, which has been suggested to hold the key to decipher the origin of Eukaryotes. However, their ecology remains largely unknown. Here, we conducted a meta-analysis of publicly available Asgard-associated 16S rRNA gene fragments, and found that just three previously proposed clades (Lokiarchaeota, Thora...
Article
Full-text available
In many organisms two component systems have evolved to discriminate self from nonself. While the molecular function of the two components has been elucidated in several systems, the evolutionary events leading to the large number of different specificities for self/nonself recognition found in most systems remain obscure. We have investigated the...
Article
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Spatial and temporal processes shaping microbial communities are inseparably linked but rarely studied together. By Illumina 16S rRNA sequencing, we monitored soil bacteria in 360 stations on a 100 square meter plot distributed across six intra-annual samplings in a rarely managed, temperate grassland. Using a multi-tiered approach, we tested the e...
Article
Asgard is an archaeal superphylum that might hold the key to understand the origin of eukaryotes, but its diversity and ecological roles remain poorly understood. Here, we reconstructed 15 metagenomic-assembled genomes from coastal sediments covering most known Asgard archaea and a novel group, which is proposed as a new Asgard phylum named as the...
Article
Full-text available
The flux of methane, a potent greenhouse gas, from the seabed is largely controlled by anaerobic oxidation of methane (AOM) coupled to sulfate reduction (S-AOM) in the sulfate methane transition (SMT). S-AOM is estimated to oxidize 90% of the methane produced in marine sediments and is mediated by a consortium of anaerobic methanotrophic archaea (A...
Preprint
Full-text available
Asgard is an archaeal superphylum that might hold the key to understand the origin of eukaryotes, but its diversity and ecological roles remain poorly understood. Here, we reconstructed 15 metagenomic-assembled genomes (MAGs) from coastal sediments covering most known Asgard archaea and a novel group, which is proposed as a new Asgard phylum named...
Article
Full-text available
The active bacterial rhizobiomes and root exudate profiles of phytometers of six plant species growing in central European temperate grassland communities were investigated in three regions located up to 700 km apart, across diverse edaphic conditions and along a strong land use gradient. The recruitment process from bulk soil communities was ident...
Chapter
Methylotrophic methanogenic archaea are an integral part of the carbon cycle in various anaerobic environments. Different from methylotrophic bacteria, methylotrophic methanogens assimilate both, the methyl compound and dissolved inorganic carbon. Here, we present DNA- and RNA-stable isotope probing (SIP) methods involving an effective labeling str...
Article
Full-text available
Soil protists are increasingly appreciated as essential components of soil foodwebs; however, there is a dearth of information on the factors structuring their communities. Here we investigate the importance of different biotic and abiotic factors as key drivers of spatial and seasonal distribution of protistan communities. We conducted an intensiv...
Article
Full-text available
A new strain of Streptomyces sp., strain RFCAC02, was isolated from the gut of the Pacific chub mackerel Scomber japonicus peruanus This strain produces a variety of secondary metabolites. Further bioinformatic analysis revealed the presence of biosynthetic gene clusters putatively coding for compounds related to the polycyclic tetramate macrolacta...
Article
Full-text available
Methyl substrates are important compounds for methanogenesis in marine sediments but diversity and carbon utilization by methylotrophic methanogenic archaea have not been clarified. Here, we demonstrate that RNA-stable isotope probing (SIP) requires 13C-labeled bicarbonate as co-substrate for identification of methylotrophic methanogens in sediment...
Preprint
Full-text available
Methyl substrates are important compounds for methanogenesis in marine sediments but diversity and carbon utilization by methylotrophic methanogenic archaea have not been clarified. Here, we demonstrate that RNA-stable isotope probing (SIP) requires 13C-labeled bicarbonate as co-substrate for identification of methylotrophic methanogens in sediment...
Preprint
Full-text available
Soil protists are increasingly appreciated as essential components of soil foodwebs; however, there is a dearth of information on the factors structuring their communities. Here we investigate the importance of different biotic and abiotic factors as key drivers of spatial and seasonal distribution of protistan communities. We conducted an intensiv...
Article
Full-text available
Microorganisms can use crystalline iron minerals for iron reduction linked to organic matter degradation or as conduits for direct interspecies electron transfer (mDIET) to syntrophic partners, e.g., methanogens. The environmental conditions that lead either to reduction or conduit use are so far unknown. We investigated microbial community shifts...
Article
Full-text available
A new Vibrio strain, V7A, was isolated from the intestinal tract of the Peruvian scallop ( Argopecten purpuratus ). Strain V7A clusters within the Mediterranei clade of the genus Vibrio and has the potential to produce bacteriocin-like inhibitory substances (BLIS). Here, we report the draft genome sequence of Vibrio mediterranei strain V7A.
Article
Full-text available
Chocolate Pots hot springs (CP) is a circumneutral-pH Fe-rich geothermal feature located in Yellowstone National Park. Previous Fe(III)-reducing enrichment culture studies with CP sediments identified close relatives of known dissimilatory Fe(III)-reducing bacterial (FeRB) taxa, including Geobacter and Melioribacter. However, the abundances and act...
Article
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Shallow-water hydrothermal systems represent extreme environments with unique biogeochemistry and high biological productivity, at which autotrophic microorganisms use both light and chemical energy for the production of biomass. Microbial communities of these ecosystems are metabolically diverse and possess the capacity to transform a large range...
Article
Full-text available
A new Vibrio strain, V1B, was isolated from the intestinal tract of the scallop Argopecten purpuratus . Strain V1B is closely related to the species Vibrio inhibens BFLP-10, which has been characterized as showing antagonistic activity against pathogenic Vibrio sp. We report here the draft genome of the isolated Vibrio sp. strain V1B.
Article
Full-text available
In this study, we investigated how co-occurrence patters of ammonia and nitrite oxidizers, which drive autotrophic nitrification, are influenced by tree species composition as well as soil pH in different forest soils. We expected that a decline of ammonia oxidizers in coniferous forests, as a result of excreted nitrification inhibitors and at acid...
Article
Full-text available
Sulfate‐reducing microorganisms (SRMs) are a phylogenetically and physiologically diverse group of microorganisms, responsible for the dissimilatory reduction of sulfate. SRMs thrive under anaerobic conditions with high availability of organic matter. Such conditions characterize lagoonal ecosystems which experience regular dystrophic crises. The a...
Article
Full-text available
In this study, we analysed metagenomes along with biogeochemical profiles from Skagerrak (SK) and Bothnian Bay (BB) sediments, to trace the prevailing nitrogen pathways. NO3⁻ was present in the top 5 cm below the sediment-water interface at both sites. NH4⁺ increased with depth below 5 cm where it overlapped with the NO3⁻ zone. Steady-state modelli...
Article
In many marine surface sediments, the reduction of manganese (Mn) and iron (Fe) oxides is obscured by sulfate reduction, which is regarded as the predominant anaerobic microbial respiration process. However, many dissimilatory sulfate and sulfur reducing microorganisms are known to utilize alternative electron acceptors such as metal oxides. In thi...
Article
Microbial methanotrophy is important in mitigating methane emissions to the atmosphere. Geochemical evidence suggests the occurrence of anaerobic methane oxidation with metal oxides in natural environments. A study has now identified, for the first time, novel freshwater archaea of the order Methanosarcinales that can oxidize methane with Fe(III) a...
Article
Full-text available
Plants shape distinct, species-specific microbiomes in their rhizospheres. A main premise for evaluating microbial communities associated with root-soil compartments is their successful separation into the rhizosphere (soil-root interface), the rhizoplane (root surface), and the endosphere (inside roots). We evaluated different approaches (washing,...
Conference Paper
Full-text available
In this study, we analysed metagenomes along with biogeochemical profiles from Skagerrak (North Sea) and Bothnian Bay (Baltic Sea) sediments, to trace the prevailing nitrogen pathways. NO 3-was present in the top 5 cm below the sediment-water interface at both sites. NH4+ increased with depth below 5 cm where it overlapped with the NO 3-zone. Stead...
Article
To gain insight into the bacterial communities involved in iron (Fe) cycling under marine conditions we analysed sediments with Fe-contents (0.5-1.5 wt %) from the suboxic zone at a marine site in the Skagerrak (SK) and a brackish site in the Bothnian Bay (BB) using 16S rRNA gene pyrosequencing. Several bacterial families, including Desulfobulbacea...
Article
Full-text available
57Fe Mössbauer spectroscopy (MS) and X-ray fluorescence spectroscopy (XRF) were used to determine the identity of iron(III) oxides in surface (top 30 cm) and subsurface (> 30 cm – 500 cm)sediments from the Helgoland mud area in the German Bight of the North Sea. A 500 cm-long sediment core was cut in 25 cm sections while only the top 10 cm of a 30...
Article
Full-text available
Interrelated successive transformation steps of nitrification are performed by distinct microbial groups – the ammonia-oxidizers, comprising ammonia-oxidizing archaea (AOA) and bacteria (AOB), and nitrite-oxidizers such as Nitrobacter and Nitrospira, which are the dominant genera in the investigated soils. Hence, not only their presence and activit...
Data
The role of microorganisms in the cycling of sedimentary organic carbon is a crucial one. To better understand relationships between molecular composition of a potentially bioavailable fraction of organic matter and microbial populations, bacterial and archaeal communities were characterized using pyrosequencing-based 16S rRNA gene analysis in surf...
Article
Full-text available
The role of microorganisms in the cycling of sedimentary organic carbon is a crucial one. To better understand relationships between molecular composition of a potentially bioavailable fraction of organic matter and microbial populations, bacterial and archaeal communities were characterized using pyrosequencing-based 16S rRNA gene analysis in surf...
Article
Full-text available
Remane?s Artenminimum (?species minimum?) concept was developed for the Baltic Sea, the world?s largest semi-enclosed brackish water body with a unique permanent salinity gradient. It argues that taxonomic diversity of macrobenthic organisms is lowest within the horohalinicum, which occurs at salinity 5 to 8, because the number of brackish speciali...
Article
Full-text available
Remane’s Artenminimum (“species minimum”) concept was developed for the Baltic Sea, the world’s largest semi-enclosed brackish water body with a unique permanent salinity gradient. It argues that taxonomic diversity of macrobenthic organisms is lowest within the horohalinicum, which occurs at salinity 5 to 8, because the number of brackish speciali...
Research
The role of microorganisms in the cycling of sedimentary organic carbon is a crucial one. To better understand relationships between molecular composition of a potentially bioavailable fraction of organic matter and microbial populations, bacterial and archaeal communities were characterized using pyrosequencing-based 16S rRNA gene analysis in surf...
Chapter
De.sul.fo.fus' tis. L. pref. de from; L. n. sulfur sulfur; L. n. fustis club; M.L. masc. n. Desulfofustis a clubshaped sulfate reducer. Proteobacteria / Deltaproteobacteria / Desulfobacterales / Desulfobulbaceae / Desulfofustis Straight or slightly curved rods, spore formation not observed. Gram negative. Metabolism anaerobic, respiratory. Organic...
Chapter
Syn.tro.pho.bo'tu.lus. Gr. pref. syn together; Gr. v. trophein to nourish; L. masc. n. botulus sausage; N.L. masc. n. Syntrophobotulus a syntrophic, sausage-like bacterium. Firmicutes / “Clostridia” / Clostridiales / Peptococcaceae / Syntrophobotulus Straight to slightly curved rods. Spores formed at the cell ends. Stains Gram-stain-negative; ultra...
Article
Full-text available
Reduction of crystalline Fe(III) oxides is one of the most important electron sinks for organic compound oxidation in natural environments. Yet a limited number of isolates makes it difficult to understand physiology and ecological impact of the microorganisms involved. Here, two-staged cultivation was implemented to selectively enrich and isolate...
Article
Full-text available
Iron reduction in subseafloor sulfate-depleted and methane-rich marine sediments is currently a subject of interest in subsurface geomicrobiology. While iron reduction and microorganisms involved have been well studied in marine surface sediments, little is known about microorganisms responsible for iron reduction in deep methanic sediments. Here,...
Article
Planted sediment microbial fuel cells (PMFC) couple the oxidation of root exudates in living rice plants to current production. We analyzed the composition of the microbial community on anodes from PMFC with natural rice field soil as substratum for rice by analyzing 16S rRNA as an indicator of microbial activity and diversity. TRFLP analysis indic...
Article
Stable isotope probing (SIP) of rRNA directly identifies microorganisms assimilating an isotopically labeled substrate. High-throughput DNA sequencing is available for label screening at high resolution and high sensitivity, yet its effectiveness and validity remain to be clarified. Here, we investigated whether the detection sensitivity of rRNA-SI...