Ecophyiology of rare biosphere members

PI: Prof. Dr. Michael Pester

Most of microbial diversity worldwide is captured in the rare biosphere. These microorganisms are characterized by relative population sizes of <0.1% in their respective environment. The rare biosphere is opposed by a much smaller number of abundant microorganisms, which are typically made responsible for the major ecosystem functions in a habitat. However, there is accumulating evidence that the rare biosphere is not just a seed bank of microorganisms that are waiting to become active and numerically dominant upon environmental change, but harbors active microorganisms with important ecosystem functions. We study a Desulfosporosinus species as an important sulfate reducers in peatlands, which is able to compensate its very low natural abundance with high cell-specific sulfate reduction rates. This makes it an interesting model for highly active rare biosphere members that contribute to biogeochemical cycling of elements. Using comparative genomics and in situ metatranscriptomics, we aim to understand why Desulfosporosinus species are so successful as low abundance populations and what ecological forces prevent these microorganisms of becoming more abundant despite their success.

Selected references

  1. Hausmann, B.,Pelikan, C.,Rattei, T., Loy, A., Pester, M. (2019)Long-term transcriptional activity at zero growth by a cosmopolitan rare biosphere member.mBio. 10: e02189-02118.
  2. Hausmann, B., Knorr, K.-H., Schreck, K., Tringe, S.G., Glavina del Rio, T., Loy, A., Pester, M.(2016) Consortia of low-abundance bacteria drive sulfate reduction-dependent degradation of fermentation products in peat soil microcosms. The  ISME J. 10: 2365–2375.
  3. Pester, M., Bittner, N., Deevong, P., Wagner, M., and Loy, A. (2010). A 'rare biosphere' microorganism drives sulfate reduction in a peatland. The ISME J. 4:1591–1602.

Genomic Encyclopedia of Bacteria and Archaea

PIs: Dr. Markus Göker & Prof. Dr. Michael Pester

The GEBA (Genomic Encyclopedia of Bacteria and Archaea) project and its follow-up projects aim at systematically filling in genome gaps along the bacterial and archaeal branches of the tree of life. This is done in close collaboration between the Leibniz Institute DSMZ and the Joint Genome Institute, Department of Energy, USA. Within this effort, roughly 3,300 genomes of type strains present at the Leibniz Institute DSMZ were already sequenced.While the GEBA pilot phase included 250 type strains, the GEBA I (KMG, 1000 Microbial Genomes) phase was completed in 2014. The follow-up project GEBA II, which was also diversity-oriented and comprised 1000 type-strain genomes, was basically finished in 2018. The ACTINO 1000 project comprises up to 1000 actinobacterial strains of biotechnological and phylogenetic interest and is ongoing as of 2019, much like GEBA IV, which comprises 1000 type-strain genomes selected for improving metagenomic binning. The latest project, GEBA VI, has been established in 2019.

A steadily increasing number of newly isolated bacteria and archaea gets validly published each year. Microbiologists in an increasing number of countries engage in isolating strains and using them as type strains of newly described species. Improved cultivation technologies enable researchers to target difficult to grow microorganisms including oligotrophs and symbionts. Thus there is a widening gap between the number of newly proposed species and the number of newly genome-sequenced type strains. In the currently running GEBA VI project, DSMZ contributes to close this gap. GEBA VI is open to the whole scientific community and aims to sequence the genomes of 10,000 prokaryotes including 5,000 from type strains. An extension of these analysis to the transcriptome and exometabolome for up to 1,000 type strains is anticipated. See gold.jgi.doe.gov/gebaVI for more details on the program, sample preparation, and instructions on how to participate in the project.

Selected publications

  1. Hahnke, R.L., Meier-Kolthoff, J.P., García-López, M., Mukherjee, S., Huntemann, M., Ivanova, N.N., Woyke, T., Kyrpides, N.C., Klenk, H.-P., Göker, M. Genome-based Taxonomic Classification of Bacteroidetes. Frontiers in Microbiology 7: 2003, 2016 (doi:10.3389/fmicb.2016.02003).
  2. Kyrpides, N.C., Hugenholtz, P., Eisen, J.A., Woyke, T., Göker, M., et al . Genomic Encyclopedia of Bacteria and Archaea: sequencing a myriad of type strains. PLoS Biology 12: e1001920, 2014 (doi:10.1371/journal.pbio.1001920).
  3. Mukherjee, S., Seshadri, R., Varghese, N., Eloe-Fadrosh, E.A., Meier-Kolthoff, J.P., Göker, M., et al., 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. Nature Biotechnology 35: 676-683, 2017 (doi:10.1038/nbt.3886).
  4. Nouioui, I., Carro, L., García-López, M., Meier-Kolthoff, J-P., Woyke, T., Kyrpides, N.C., Pukall, R., Klenk, H.-P., Goodfellow, M., Göker, M. Genome-based taxonomic classification of the phylum Actinobacteria. Frontiers in Microbiology 9: 2007, 2018 (doi:10.3389/fmicb.2018.02007).
  5. Sczyrba, A., Hofmann, P., Belmann, P., Koslicki, D., Janssen, S., et al., Critical Assessment of Metagenome Interpretation − a benchmark of computational metagenomics software. Nature Methods 14: 1063-1071, 2017 (doi:10.1038/nmeth.4458).

Microbe-Mineral-Interactions

PI: Prof. Dr. Michael Pester

Pyrite, better known as fool’s gold, is the most abundant iron-sulfur mineral in sediments. Over geological times, its burial in sediments controlled oxygen levels in the atmosphere and sulfate concentrations in seawater. The conversion of iron sulfide and hydrogen sulfide to pyrite was also postulated as the energy-delivering process to drive auto-catalytic synthesis of organic matter in micro-compartments of marine hydrothermal vents. The latter are currently regarded as the most likely place for life to have emerged on Earth. To date, pyrite formation was considered to be a pure (geo)chemical reaction. Currently, we study the first enrichment culture capable of converting of iron sulfide and hydrogen sulfide to pyrite when coupled to a methanogenic partner. Our research has impact on the understanding of global biogeochemical cycles on geological time scales and provides an experimental window in a postulated primordial iron-sulfur world predating the origin of life.

Selected references

  1. Thiel, J., Byrne, J.M., Kappler, A., Schink, B., and Pester, M. (2019) Pyrite formation from FeS and H2S is mediated through microbial redox activity. Proc Natl Acad Sci USA.116: 6897-6902

Nitrification in lake ecosystem

PI: Prof. Dr. Michael Pester

In this project, we study the influence of changing lake ecosystems on microorganisms driving the conversion of ammonia to nitrate. Our study site is Lake Constance as an important prealpine lake and drinking water reservoir. Using process measurements of ammonia conversion, high-throughput 16S rRNA gene amplicon sequencing, metagenomics and metatranscriptomics, we are aiming to understand how the steadily increasing water temperatures in lakes influence population dynamics of nitrifying microorganisms and as a consequence the process of nitrification itself.

Selected references

  1. Pester, M., Maixner, F., Berry, D., Rattei, T., Koch, H., Lücker, S., Nowka, B., Richter, A., Spieck, E., Lebedeva, E., Loy, A., Wagner, M., and Daims, H. (2014NxrBencoding the beta subunit of nitrite oxidoreductase as novel functional and phylogenetic marker for nitrite-oxidizing NitrospiraEnviron. Microbiol.16: 3055–3071.
  2. Pester, M., Rattei, T., Flechl, S., Gröngröft, A., Richter, A., Overmann, J., Reinhold-Hurek, B., Loy, A., and Wagner, M. (2012amoA-based consensus phylogeny of ammonia-oxidizing archaea and deep sequencing of amoAgenes from soils of four different geographic regions. Environ. Microbiol.14: 525–539.
  3. Pester, M., Schleper, C., Wagner, M. (2011). The Thaumarchaeota: An emerging view of their phylogeny and ecophysiology. Curr. Opin. Microbiol. 14: 300–306.

The cryptic freshwater sulfur cycle

PI: Prof. Dr. Michael Pester

Freshwater wetlands are not only important for sustainability of biodiversity, water quality, flood protection, and recreational value but play an integral part in Earth’s biogeochemical cycles. In particular, they are considered key habitats in the upcoming climate change, influencing both positive and negative climate feedback cycles to the atmosphere in a warmer world. We study the cryptic sulfur cycle in freshwater wetlands, which plays an important role in controlling the emission of the greenhouse gas methane from these environments. Our aim is to identify microorganisms that drive the hidden sulfur cycle in wetlands using amplicon sequencing and genome-centric metagenomics and to study their ecophysiology using metatranscriptomics and metaproteomics.

Selected references

  1. Zecchin, S., Mueller, R.C., Seifert, J., Stingl, U., Anantharaman, K., von Bergen, M., Cavalca, L., Pester, M.(2018) Rice paddy Nitrospirae encode and express genes related to sulfate respiration: proposal of the new genus CandidatusSulfobium. Appl Environ Microbiol.84: e02224-17.
  2. Hausmann, B., Pelikan, C., Herbold, C.W., Koestlbacher, S., Albertsen, M., Eichorst, S.A., Glavina del Rio, T., Huemer, M., Nielsen, P.H., Rattei, T., Stingl, U., Tringe, S.G., Trojan, D., Wentrup, C., Woebken, D., Pester, M. (corresponding author), Loy, A. (2018). Peatland Acidobacteria with a dissimilatory sulfur metabolism. The ISME J.12: 1729–1742.
  3. Pester, M., Knorr, K.-H., Friedrich, M.W., Wagner, M., and Loy, M. (2012) Sulfate reducing microorganisms in wetlands – fameless actors in carbon cycling and climate change. Front. Microbiol.3: doi: 10.3389/fmicb.2012.00072.

The EcoGenomics Group

PI: Dr. David K. Ngugi

The research in my group adopts state-of-the-art approaches and techniques from molecular biology aimed at understanding the mechanistic basis for adaptation and phenotypic variation in non-model species of ecological relevance, focusing in particular, on the evolutionary basis of their interactions and significance in ecosystem functions. We use aquatic systems as model environments in combination with environmental genomics and analytics of massive metagenomic sequences to move this objective forward. Below, specific aspects of our on-going research work are highlighted:

Evolutionary dynamics of archaea-virus interactions in freshwater reservoirs 
Aquatic ecosystems teem with viruses that, in terms of biomass, are orders of magnitude higher than aquatic prokaryotes. Crucially, viruses are a key element of aquatic microbial life regulating bacterioplankton diversity and the biogeochemical processes that they catalyze. However, while most frequent targets of viral infections are typically the abundant and most active microbial communities, knowledge regarding the identity, the molecular mechanisms involved in host-viral life cycles, and the ecological importance of viruses that potentially interact with Thaumarchaeota are scarce; in turn, limiting the comprehensive understanding of the capacity of viruses to modulate global nitrogen cycles. Currently, we employ a mixture of genomic and experimental approaches to understand the evolution of archaea-virus interactions in freshwater reservoirs and the role the relationship plays in nitrification. In-depth understanding of thaumarchaea-virus interactions is vital for elucidating the impact of planktonic archaea on the N and C cycles in aquatic systems because thaumarchaea predominate the aquatic interior realm and are global players in nitrification and the cycling of scarce vitamins.

Ecological relevance of glycine betaine in aquatic biosystems 
Glycine betaine ranks among the few widespread biomolecules on Earth, abundant in all three domains of life. It protects membranes and proteins against abiotic stressors such as high salinity and photon stress. Significant amounts of glycine betaine—in the 100s of millimolar range—are stored in cells of cultured marine phytoplankton (macroalgae, dinoflagellates, and diatoms). Once excreted or released from lysed cells (e.g., via virus-mediated lysis), this organic compound represents a ubiquitous and dynamic constituent of dissolved organic matter readily available to aquatic microbial communities. However, ambient concentrations of glycine betaine in natural phytoplankton cells and the metabolic pathways underpinning the high intracellular stocks remain uncharacterized in species of ecological relevance. Our currents efforts work towards quantifying intracellular levels in native marine phytoplankton populations (at the single-cell level) and conducting genome-centric analysis to understand the producers and consumers better. Elucidating the metabolic and environmental determinants of glycine betaine fluxes in the aquatic system is vital for global nitrogen budgets since glycine betaine represents a significant allocation of intracellular nitrogen (up to 15% of total organic N in laboratory cultures) against the backdrop of N scarcity in large swaths of the ocean.