Bremen, Germany

The Max Planck Institute for Marine Microbiology is located in Bremen, Germany. It was founded in 1992, almost a year after the foundation of its sister institute, the Max Planck Institute for Terrestrial Microbiology at Marburg. In 1996, the institute moved into new buildings at the campus of the University of Bremen. It is one of 80 institute in the Max Planck Society . Currently, the institute consists of three departments with several associated research groups:Microbiology )Biogeochemistry Molecular Ecology Additionally, three independent Max-Planck research groups and a joint research group between the Max-Planck-Society and the Helmholtz-Society reside in the institute. Wikipedia.

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Reintjes G.,Max Planck Institute for Marine Microbiology
ISME Journal | Year: 2017

Heterotrophic microbial communities process much of the carbon fixed by phytoplankton in the ocean, thus having a critical role in the global carbon cycle. A major fraction of the phytoplankton-derived substrates are high-molecular-weight (HMW) polysaccharides. For bacterial uptake, these substrates must initially be hydrolysed to smaller sizes by extracellular enzymes. We investigated polysaccharide hydrolysis by microbial communities during a transect of the Atlantic Ocean, and serendipitously discovered—using super-resolution structured illumination microscopy—that up to 26% of total cells showed uptake of fluorescently labelled polysaccharides (FLA-PS). Fluorescence in situ hybridisation identified these organisms as members of the bacterial phyla Bacteroidetes and Planctomycetes and the gammaproteobacterial genus Catenovulum. Simultaneous membrane staining with nile red indicated that the FLA-PS labelling occurred in the cell but not in the cytoplasm. The dynamics of FLA-PS staining was further investigated in pure culture experiments using Gramella forsetii, a marine member of Bacteroidetes. The staining patterns observed in environmental samples and pure culture tests are consistent with a ‘selfish’ uptake mechanisms of larger oligosaccharides (>600 Da), as demonstrated for gut Bacteroidetes. Ecologically, this alternative polysaccharide uptake mechanism secures substantial quantities of substrate in the periplasmic space, where further processing can occur without diffusive loss. Such a mechanism challenges the paradigm that hydrolysis of HMW substrates inevitably yields low-molecular-weight fragments that are available to the surrounding community and demonstrates the importance of an alternative mechanism of polysaccharide uptake in marine bacteria.The ISME Journal advance online publication, 21 March 2017; doi:10.1038/ismej.2017.26. © 2017 The Author(s)

News Article | March 2, 2017

On Friday, The Association for the Sciences of Limnology and Oceanography (ASLO) honors Danish Professor Bo Barker Jørgensen with the prestigious 2017 A.C. Redfield Award at the Aquatic Sciences Meeting in Honolulu, Hawaii 26 February - 03 March, 2017. Dr. Bo Barker Jørgensen receives the prize for his lifelong and groundbreaking work advancing our understanding of marine sediment microbial ecology and biogeochemistry. His work has ranged from surface sediments to the deep biosphere, several kilometers into the seabed. ASLO is an international aquatic science society founded in 1948. For more information about ASLO, please visit their website: http://www. . In their press release, ASLO writes, "Bo Barker Jørgensen has led the way in advancing our understanding of the biogeochemistry and microbial ecology of marine sediments. His papers have been cited more than 32,000 times, with two of his papers having over one thousand citations each. Colleagues say these statistics are evidence of Jørgensen's "jaw dropping" influence on science and a tribute to the huge impact of his lifelong work." ASLO also highlights Bo Barker Jørgensen's early research on the sulfur cycle in marine sediments presented in a paper in 1977. The method he developed for determining the rate of bacterial sulfate reduction in marine sediments is still in use today and his paper is of one of the most highly cited papers in marine sediment biogeochemistry. Another highlight in a long and illustrious science career is the work of Bo Barker Jørgensen and then graduate student, Niels Peter Revsbech who is now a professor and colleague at Aarhus University, Denmark. During the late 70's and early 80's they used oxygen microelectrodes for the first time to measure the distribution of oxygen in sediments, "...shocking the scientific community with their discovery that oxygen penetrates only a few millimeters into coastal sediments. Their introduction of microelectrodes revolutionized our understanding of the distribution and dynamics of oxygen and oxidants in marine sediments," ASLO writes in their nomination. Bo Barker Jørgensen is famous not only for developing techniques, instruments and publishing influential papers, but the A. C. Redfield award also recognizes his work achievements as a mentor. Many of the young scientists he advised have established successful scientific careers of their own. "The list of students, postdoctoral fellows and colleagues who have been mentored by Jørgensen reads like a virtual 'who's who' of marine microbiology," the nomination reads. Bo Barker Jørgensen's vision for microbial research is credited by colleagues as central for the establishment of Max Planck Institute for Marine Microbiology in Bremen, Germany. Bo Barker Jørgensen served as director of the Institute from 1992-2011, and helped to establish it as a world leader in research on marine microbes. In 2007, Bo Barker Jørgensen established the Center for Geomicrobiology in Aarhus, where he has built an international team of leading scientists focused on sediments in the deep biosphere. "He and his team are 'providing fundamental and new insights into the nature of what may be the largest, yet least known, biosphere on Earth,'" it is written in the nomination. Contact: Bo Barker Jørgensen is at the moment in Hawaii but can be reached on mail: The ASLO Lifetime Achievement award is given to those that have excelled in limnologic and oceanographic research, education, service to the community and society throughout a lifetimes work. The prize was first presented in 1994 and has since 2004 been named after Alfred Clarence Redfield, an American oceanographer whose major discovery was the atomic ratio between nitrogen, phosphorus, and carbon found in marine plankton (phytoplankton), also known as the Redfield ratio. Dr. Jørgensen is Professor and Head of the Center for Geomicrobiology at Aarhus University in Denmark. In his long career, Bo Barker Jørgensen has received numerous prizes and honors for his impressive work: Fellow of the American Academy of Microbiology, 2009 Fellow of the European Academy of Microbiology, 2009

News Article | February 10, 2017

Short bouts of suffocating conditions can desolate swaths of seafloor for decades, new research suggests. That devastation could spread in the future, as rising temperatures and agricultural runoff enlarge oxygen-poor dead zones in the world’s oceans. Monitoring sections of the Black Sea, researchers discovered that even days-long periods of low oxygen drove out animals and altered microbial communities. Those ecosystem changes slow decomposition that normally recycles plant and animal matter back into the ecosystem after organisms die, resulting in more organic matter accumulating in seafloor sediments, the researchers report February 10 in Science Advances. Carbon is included among that organic matter. Over a long enough period of time, the increased carbon burial could help offset a small fraction of carbon emitted by human activities such as fossil fuel burning, says study coauthor Antje Boetius, a marine biologist at the Max Planck Institute for Marine Microbiology in Bremen, Germany. That silver lining comes at a cost, though. “It means your ecosystem is fully declining,” she says. “We need to pay more attention to the bottom of the ocean,” says Lisa Levin, a biological oceanographer at the Scripps Institution of Oceanography in La Jolla, Calif. “There’s a lot happening down there.” The new work shows that scientists need to consider oxygen conditions when tracking how carbon moves around the environment, says Levin, who was not involved in the research. Some oxygen-poor, or hypoxic, waters form naturally, such as the suffocating conditions caused by a lack of churning in the deep realms of the Black Sea (SN Online: 10/9/15). Other regions lose their oxygen to human activities; fertilizer washing in from farms nourishes algal blooms, for example, and the bacteria that later decompose that algal influx suck up oxygen. Rising sea-surface temperatures could worsen these problems by decreasing the amount of dissolved oxygen that water can hold and making it harder for ocean layers to mix, as warmer waters remain on top (SN: 3/5/16, p. 11). Scientists have noticed increased carbon burial in hypoxic waters before. The mechanism behind that increase was unclear, though. Boetius and colleagues headed out to the Black Sea, the world’s largest oxygen-poor body of water, and studied sites along a 40-kilometer-long stretch of seafloor. (Military activities in the region following Russia’s annexation of Crimea limited where the researchers could study, Boetius says.) Some sites were always flush with oxygen, some occasionally suffered a few days of low oxygen, and others were permanently oxygen-free. The ecological difference between the sites was stark. In oxygen-rich waters, animals such as fish and starfish flourished, and little organic matter was deposited on the seafloor. In areas with perpetually or sporadically low oxygen, the researchers reported that oxygen-dependent animals were nowhere to be seen, and organic matter burial rates were 50 percent higher. Bottom-dwelling animals are particularly important, the researchers observed, helping recycle organic matter by eating larger bits of debris sinking from the surface ocean and by mixing oxygen into sediments during scavenging. What’s more, the researchers found that the microbial community in oxygen-poor waters shifted toward those microbes that don’t depend on oxygen to live. Such microbes further limit decomposition by producing sulfur-bearing compounds that make organic matter harder to break down. Depending on the size of the area affected, animals could take years or decades to return to previously hypoxic waters, Boetius says. Some of the studied sites experienced low-oxygen conditions for only a few days a year yet remained barren even when oxygen returned. The absence of animals prolongs the effects of hypoxic conditions beyond the times when oxygen is scarce, she says.

Marmulla R.,Max Planck Institute for Marine Microbiology | Harder J.,Max Planck Institute for Marine Microbiology
Frontiers in Microbiology | Year: 2014

Isoprene and monoterpenes constitute a significant fraction of new plant biomass. Emission rates into the atmosphere alone are estimated to be over 500 Tg per year. These natural hydrocarbons are mineralized annually in similar quantities. In the atmosphere, abiotic photochemical processes cause lifetimes of minutes to hours. Microorganisms encounter isoprene, monoterpenes, and other volatiles of plant origin while living in and on plants, in the soil and in aquatic habitats. Below toxic concentrations, the compounds can serve as carbon and energy source for aerobic and anaerobic microorganisms. Besides these catabolic reactions, transformations may occur as part of detoxification processes. Initial transformations of monoterpenes involve the introduction of functional groups, oxidation reactions, and molecular rearrangements catalyzed by various enzymes. Pseudomonas and Rhodococcus strains and members of the genera Castellaniella and Thauera have become model organisms for the elucidation of biochemical pathways. We review here the enzymes and their genes together with microorganisms known for a monoterpene metabolism, with a strong focus on microorganisms that are taxonomically validly described and currently available from culture collections. Metagenomes of microbiomes with a monoterpene-rich diet confirmed the ecological relevance of monoterpene metabolism and raised concerns on the quality of our insights based on the limited biochemical knowledge. © 2014 Marmulla and Harder.

Ruff S.E.,Max Planck Institute for Marine Microbiology
PloS one | Year: 2013

The methane-emitting cold seeps of Hikurangi margin (New Zealand) are among the few deep-sea chemosynthetic ecosystems of the Southern Hemisphere known to date. Here we compared the biogeochemistry and microbial communities of a variety of Hikurangi cold seep ecosystems. These included highly reduced seep habitats dominated by bacterial mats, partially oxidized habitats populated by heterotrophic ampharetid polychaetes and deeply oxidized habitats dominated by chemosynthetic frenulate tubeworms. The ampharetid habitats were characterized by a thick oxic sediment layer that hosted a diverse and biomass-rich community of aerobic methanotrophic Gammaproteobacteria. These bacteria consumed up to 25% of the emanating methane and clustered within three deep-branching groups named Marine Methylotrophic Group (MMG) 1-3. MMG1 and MMG2 methylotrophs belong to the order Methylococcales, whereas MMG3 methylotrophs are related to the Methylophaga. Organisms of the groups MMG1 and MMG3 are close relatives of chemosynthetic endosymbionts of marine invertebrates. The anoxic sediment layers of all investigated seeps were dominated by anaerobic methanotrophic archaea (ANME) of the ANME-2 clade and sulfate-reducing Deltaproteobacteria. Microbial community analysis using Automated Ribosomal Intergenic Spacer Analysis (ARISA) showed that the different seep habitats hosted distinct microbial communities, which were strongly influenced by the seep-associated fauna and the geographic location. Despite outstanding features of Hikurangi seep communities, the organisms responsible for key ecosystem functions were similar to those found at seeps worldwide. This suggests that similar types of biogeochemical settings select for similar community composition regardless of geographic distance. Because ampharetid polychaetes are widespread at cold seeps the role of aerobic methanotrophy may have been underestimated in seafloor methane budgets.

Pruesse E.,Max Planck Institute for Marine Microbiology | Pruesse E.,Jacobs University Bremen | Peplies J.,Ribocon GmbH | Glockner F.O.,Max Planck Institute for Marine Microbiology | Glockner F.O.,Jacobs University Bremen
Bioinformatics | Year: 2012

Motivation: In the analysis of homologous sequences, computation of multiple sequence alignments (MSAs) has become a bottleneck. This is especially troublesome for marker genes like the ribosomal RNA (rRNA) where already millions of sequences are publicly available and individual studies can easily produce hundreds of thousands of new sequences. Methods have been developed to cope with such numbers, but further improvements are needed to meet accuracy requirements.Results: In this study, we present the SILVA Incremental Aligner (SINA) used to align the rRNA gene databases provided by the SILVA ribosomal RNA project. SINA uses a combination of k-mer searching and partial order alignment (POA) to maintain very high alignment accuracy while satisfying high throughput performance demands. SINA was evaluated in comparison with the commonly used high throughput MSA programs PyNAST and mothur. The three BRAliBase III benchmark MSAs could be reproduced with 99.3, 97.6 and 96.1 accuracy. A larger benchmark MSA comprising 38 772 sequences could be reproduced with 98.9 and 99.3% accuracy using reference MSAs comprising 1000 and 5000 sequences. SINA was able to achieve higher accuracy than PyNAST and mothur in all performed benchmarks. © The Author(s) 2012. Published by Oxford University Press.

Dyksma S.,Max Planck Institute for Marine Microbiology
ISME Journal | Year: 2016

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 14C-carbon assimilation experiments, we show that uncultured Gammaproteobacteria account for 70–86% of dark carbon fixation in coastal sediments. First, we surveyed the bacterial 16S rRNA gene diversity of 13 tidal and sublittoral sediments across Europe and Australia to identify ubiquitous core groups of Gammaproteobacteria mainly affiliating with sulfur-oxidizing bacteria. These also accounted for a substantial fraction of the microbial community in anoxic, 490-cm-deep subsurface sediments. We then quantified dark carbon fixation by scintillography of specific microbial populations extracted and flow-sorted from sediments that were short-term incubated with 14C-bicarbonate. We identified three distinct gammaproteobacterial clades covering diversity ranges on family to order level (the Acidiferrobacter, JTB255 and SSr clades) that made up >50% of dark carbon fixation in a tidal sediment. Consistent with these activity measurements, environmental transcripts of sulfur oxidation and carbon fixation genes mainly affiliated with those of sulfur-oxidizing Gammaproteobacteria. The co-localization of key genes of sulfur and hydrogen oxidation pathways and their expression in genomes of uncultured Gammaproteobacteria illustrates an unknown metabolic plasticity for sulfur oxidizers in marine sediments. Given their global distribution and high abundance, we propose that a stable assemblage of metabolically flexible Gammaproteobacteria drives important parts of marine carbon and sulfur cycles.The ISME Journal advance online publication, 12 February 2016; doi:10.1038/ismej.2015.257. © 2016 International Society for Microbial Ecology

Lam P.,Max Planck Institute for Marine Microbiology | Kuypers M.M.M.,Max Planck Institute for Marine Microbiology
Annual Review of Marine Science | Year: 2011

Oxygen minimum zones (OMZs) harbor unique microbial communities that rely on alternative electron acceptors for respiration. Conditions therein enable an almost complete nitrogen (N) cycle and substantial N-loss. N-loss in OMZs is attributable to anammox and heterotrophic denitrification, whereas nitrate reduction to nitrite along with dissimilatory nitrate reduction to ammonium are major remineralization pathways. Despite virtually anoxic conditions, nitrification also occurs in OMZs, converting remineralized ammonium to N-oxides. The concurrence of all these processes provides a direct channel from organic N to the ultimate N-loss, whereas most individual processes are likely controlled by organic matter. Many microorganisms inhabiting the OMZs are capable of multiple functions in the N- and other elemental cycles. Their versatile metabolic potentials versus actual activities present a challenge to ecophysiological and biogeochemical measurements. These challenges need to be tackled before we can realistically predict how N-cycling in OMZs, and thus oceanic N-balance, will respond to future global perturbations. Copyright © 2011 by Annual Reviews. All rights reserved.

Sulfate reduction has been suggested as a mechanism to induce precipitation of calcium and magnesium carbonates in marine sediments and microbial mats through most of Earth's history. However, sulfate reduction also causes a drop in pH that favors dissolution rather than precipitation of carbonates. Model results obtained in this study show that in modern seawater, modern hypersaline water, and assumed Precambrian alkaline seawater, sulfate reduction initially lowers the saturation of carbonates due to a rapid decrease in pH. With continuing sulfate reduction, the pH stabilizes between 6.5 and 7, and carbonate saturation slowly increases as a result of increasing dissolved inorganic carbon concentration. However, sulfate reduction in surface microbial mats is not suffi cient to cause such an increase in saturation. With increasing salinity, sulfate reduction becomes even less effi cient to induce carbonate precipitation. In an alkaline Precambrian ocean, where large amounts of carbonate were formed, induction through sulfate reduction was entirely ineffective. Other metabolic pathways or abiotic factors must be responsible for inducing carbonate formation in microbial mats through Earth's history. © 2013 Geological Society of America.

Teeling H.,Max Planck Institute for Marine Microbiology | Glockner F.O.,Jacobs Engineering
Briefings in Bioinformatics | Year: 2012

Metagenomics has become an indispensable tool for studying the diversity and metabolic potential of environmental microbes, whose bulk is as yet non-cultivable. Continual progress in next-generation sequencing allows for generating increasingly large metagenomes and studying multiple metagenomes over time or space. Recently, a new type of holistic ecosystem study has emerged that seeks to combine metagenomics with biodiversity, meta-expression and contextual data. Such 'ecosystems biology' approaches bear the potential to not only advance our understanding of environmental microbes to a new level but also impose challenges due to increasing data complexities, in particular with respect to bioinformatic post-processing. This mini review aims to address selected opportunities and challenges of modern metagenomics from a bioinformatics perspective and hopefully will serve as a useful resource for microbial ecologists and bioinformaticians alike. © The Author 2012. Published by Oxford University Press.

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