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1.
Front Microbiol. 2018 Nov 21;9:2787. doi: 10.3389/fmicb.2018.02787. eCollection 2018.

Influence of CO2 Degassing on the Microbial Community in a Dry Mofette Field in Hartoušov, Czech Republic (Western Eger Rift).

Author information

1
GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany.
2
GFZ German Research Centre for Geosciences, Section Organic Geochemistry, Potsdam, Germany.
3
Institute of Applied Geosciences, Technische Universität Berlin, Berlin, Germany.
4
Institute for Geophysics and Geology, University of Leipzig, Leipzig, Germany.
5
GFZ German Research Centre for Geosciences, Section Climate Dynamics and Landscape Evolution, Potsdam, Germany.
6
Institute of Earth and Environmental Science, University of Potsdam, Potsdam, Germany.

Abstract

The Cheb Basin (CZ) is a shallow Neogene intracontinental basin filled with fluvial and lacustrine sediments that is located in the western part of the Eger Rift. The basin is situated in a seismically active area and is characterized by diffuse degassing of mantle-derived CO2 in mofette fields. The Hartoušov mofette field shows a daily CO2 flux of 23-97 tons of CO2 released over an area of 0.35 km2 and a soil gas concentration of up to 100% CO2. The present study aims to explore the geo-bio interactions provoked by the influence of elevated CO2 concentrations on the geochemistry and microbial community of soils and sediments. To sample the strata, two 3-m cores were recovered. One core stems from the center of the degassing structure, whereas the other core was taken 8 m from the ENE and served as an undisturbed reference site. The sites were compared regarding their geochemical features, microbial abundances, and microbial community structures. The mofette site is characterized by a low pH and high TOC/sulfate contents. Striking differences in the microbial community highlight the substantial impact of elevated CO2 concentrations and their associated side effects on microbial processes. The abundance of microbes did not show a typical decrease with depth, indicating that the uprising CO2-rich fluid provides sufficient substrate for chemolithoautotrophic anaerobic microorganisms. Illumina MiSeq sequencing of the 16S rRNA genes and multivariate statistics reveals that the pH strongly influences microbial composition and explains around 38.7% of the variance at the mofette site and 22.4% of the variance between the mofette site and the undisturbed reference site. Accordingly, acidophilic microorganisms (e.g., OTUs assigned to Acidobacteriaceae and Acidithiobacillus) displayed a much higher relative abundance at the mofette site than at the reference site. The microbial community at the mofette site is characterized by a high relative abundance of methanogens and taxa involved in sulfur cycling. The present study provides intriguing insights into microbial life and geo-bio interactions in an active seismic region dominated by emanating mantle-derived CO2-rich fluids, and thereby builds the basis for further studies, e.g., focusing on the functional repertoire of the communities. However, it remains open if the observed patterns can be generalized for different time-points or sites.

KEYWORDS:

Acidithiobacillus; Acidobacteriaceae; Acidothermus; acidophilic microorganisms; deep biosphere; elevated CO2 concentration; geo–bio interaction; paleo-sediment

2.
Front Microbiol. 2018 Sep 20;9:2082. doi: 10.3389/fmicb.2018.02082. eCollection 2018.

Desiccation- and Saline-Tolerant Bacteria and Archaea in Kalahari Pan Sediments.

Author information

1
GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, Potsdam, Germany.
2
GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 3.2 Organic Geochemistry, Potsdam, Germany.
3
Institute of Earth and Environmental Science, University of Potsdam, Potsdam, Germany.

Abstract

More than 41% of the Earth's land area is covered by permanent or seasonally arid dryland ecosystems. Global development and human activity have led to an increase in aridity, resulting in ecosystem degradation and desertification around the world. The objective of the present work was to investigate and compare the microbial community structure and geochemical characteristics of two geographically distinct saline pan sediments in the Kalahari Desert of southern Africa. Our data suggest that these microbial communities have been shaped by geochemical drivers, including water content, salinity, and the supply of organic matter. Using Illumina 16S rRNA gene sequencing, this study provides new insights into the diversity of bacteria and archaea in semi-arid, saline, and low-carbon environments. Many of the observed taxa are halophilic and adapted to water-limiting conditions. The analysis reveals a high relative abundance of halophilic archaea (primarily Halobacteria), and the bacterial diversity is marked by an abundance of Gemmatimonadetes and spore-forming Firmicutes. In the deeper, anoxic layers, candidate division MSBL1, and acetogenic bacteria (Acetothermia) are abundant. Together, the taxonomic information and geochemical data suggest that acetogenesis could be a prevalent form of metabolism in the deep layers of a saline pan.

KEYWORDS:

Firmicutes; Gemmatimonadetes; Halobacteria; Kalahari; saline pan

3.
Environ Microbiol. 2018 Dec;20(12):4297-4313. doi: 10.1111/1462-2920.14343. Epub 2018 Oct 16.

Metabolic potential of microbial communities from ferruginous sediments.

Author information

1
GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3: Geomicrobiology, Potsdam, Germany.
2
Department of Earth & Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany.
3
University of Potsdam, Faculty of Mathematics and Natural Sciences, Institute of Earth and Environmental Sciences, Potsdam, Germany.
4
Research Center for Limnology (LIPI), Indonesian Institute of Sciences, Division of Inland Waterways Dynamics, Cibinong-Bogor, Indonesia.
5
Geobio-CenterLMU, Ludwig-Maximilians-Universität München, Munich, Germany.
6
Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada.
7
Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, Canada.

Abstract

Ferruginous (Fe-rich, SO4 -poor) conditions are generally restricted to freshwater sediments on Earth today, but were likely widespread during the Archean and Proterozoic Eons. Lake Towuti, Indonesia, is a large ferruginous lake that likely hosts geochemical processes analogous to those that operated in the ferruginous Archean ocean. The metabolic potential of microbial communities and related biogeochemical cycling under such conditions remain largely unknown. We combined geochemical measurements (pore water chemistry, sulfate reduction rates) with metagenomics to link metabolic potential with geochemical processes in the upper 50 cm of sediment. Microbial diversity and quantities of genes for dissimilatory sulfate reduction (dsrAB) and methanogenesis (mcrA) decrease with increasing depth, as do rates of potential sulfate reduction. The presence of taxa affiliated with known iron- and sulfate-reducers implies potential use of ferric iron and sulfate as electron acceptors. Pore-water concentrations of acetate imply active production through fermentation. Fermentation likely provides substrates for respiration with iron and sulfate as electron donors and for methanogens that were detected throughout the core. The presence of ANME-1 16S and mcrA genes suggests potential for anaerobic methane oxidation. Overall our data suggest that microbial community metabolism in anoxic ferruginous sediments support coupled Fe, S and C biogeochemical cycling.

4.
FEMS Microbiol Ecol. 2018 Apr 1;94(4). doi: 10.1093/femsec/fiy029.

Microbial community composition along a 50 000-year lacustrine sediment sequence.

Author information

1
Department of Earth & Environmental Science, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333 Munich, Germany.
2
Section of Earth & Environmental Sciences, University of Geneva, rue des Maraichers 13, 1205 Geneva, Switzerland.
3
GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3: Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany.
4
Geobio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333 Munich, Germany.

Abstract

For decades, microbial community composition in subseafloor sediments has been the focus of extensive studies. In deep lacustrine sediments, however, the taxonomic composition of microbial communities remains undercharacterized. Greater knowledge on microbial diversity in lacustrine sediments would improve our understanding of how environmental factors, and resulting selective pressures, shape subsurface biospheres in marine and freshwater sediments. Using high-throughput sequencing of 16S rRNA genes across high-resolution climate intervals covering the last 50 000 years in Laguna Potrok Aike, Argentina, we identified changes in microbial populations in response to both past environmental conditions and geochemical changes of the sediment during burial. Microbial communities in Holocene sediments were most diverse, reflecting a layering of taxa linked to electron acceptors availability. In deeper intervals, the data show that salinity, organic matter and the depositional conditions over the Last Glacial-interglacial cycle were all selective pressures in the deep lacustrine assemblage resulting in a genetically distinct biosphere from the surface dominated primarily by Bathyarchaeota and Atribacteria groups. However, similar to marine sediments, some dominant taxa in the shallow subsurface persisted into the subsurface as minor fraction of the community. The subsequent establishment of a deep subsurface community likely results from a combination of paleoenvironmental factors that have shaped the pool of available substrates, together with substrate depletion and/or reworking of organic matter with depth.

5.
Sci Rep. 2018 Jan 22;8(1):1291. doi: 10.1038/s41598-018-19505-9.

Anaerobic methanotrophic communities thrive in deep submarine permafrost.

Author information

1
GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, 14473, Potsdam, Germany. mwinkel@gfz-potsdam.de.
2
GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, 14473, Potsdam, Germany.
3
Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Periglacial Research, 14473, Potsdam, Germany.
4
Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Marine Geochemistry, 27570, Bremerhaven, Germany.
5
Mel'nikov Permafrost Institute, SB RAS, Yakutsk, 677010, Russia.
6
Institute of Soil Science, Universität Hamburg, 20146, Hamburg, Germany.
7
GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 3.2 Organic Geochemistry, 14473, Potsdam, Germany.

Abstract

Thawing submarine permafrost is a source of methane to the subsurface biosphere. Methane oxidation in submarine permafrost sediments has been proposed, but the responsible microorganisms remain uncharacterized. We analyzed archaeal communities and identified distinct anaerobic methanotrophic assemblages of marine and terrestrial origin (ANME-2a/b, ANME-2d) both in frozen and completely thawed submarine permafrost sediments. Besides archaea potentially involved in anaerobic oxidation of methane (AOM) we found a large diversity of archaea mainly belonging to Bathyarchaeota, Thaumarchaeota, and Euryarchaeota. Methane concentrations and δ13C-methane signatures distinguish horizons of potential AOM coupled either to sulfate reduction in a sulfate-methane transition zone (SMTZ) or to the reduction of other electron acceptors, such as iron, manganese or nitrate. Analysis of functional marker genes (mcrA) and fluorescence in situ hybridization (FISH) corroborate potential activity of AOM communities in submarine permafrost sediments at low temperatures. Modeled potential AOM consumes 72-100% of submarine permafrost methane and up to 1.2 Tg of carbon per year for the total expected area of submarine permafrost. This is comparable with AOM habitats such as cold seeps. We thus propose that AOM is active where submarine permafrost thaws, which should be included in global methane budgets.

PMID:
29358665
PMCID:
PMC5778128
DOI:
10.1038/s41598-018-19505-9
[Indexed for MEDLINE]
Free PMC Article
Icon for Nature Publishing Group Icon for PubMed Central
6.
Front Microbiol. 2017 Dec 11;8:2446. doi: 10.3389/fmicb.2017.02446. eCollection 2017.

Microbiological and Geochemical Survey of CO2-Dominated Mofette and Mineral Waters of the Cheb Basin, Czech Republic.

Author information

1
GFZ German Research Centre for Geosciences, Section 5.3 Geomicrobiology, Potsdam, Germany.
2
GFZ German Research Centre for Geosciences, Section 3.2 Organic Geochemistry, Potsdam, Germany.
3
Hydroisotop GmbH, Schweitenkirchen, Germany.
4
Institute for Earth and Environmental Sciences, University of Potsdam, Potsdam, Germany.

Abstract

The Cheb Basin (NW Bohemia, Czech Republic) is a shallow, neogene intracontinental basin. It is a non-volcanic region which features frequent earthquake swarms and large-scale diffuse degassing of mantle-derived CO2 at the surface that occurs in the form of CO2-rich mineral springs and wet and dry mofettes. So far, the influence of CO2 degassing onto the microbial communities has been studied for soil environments, but not for aquatic systems. We hypothesized, that deep-trenching CO2 conduits interconnect the subsurface with the surface. This admixture of deep thermal fluids should be reflected in geochemical parameters and in the microbial community compositions. In the present study four mineral water springs and two wet mofettes were investigated through an interdisciplinary survey. The waters were acidic and differed in terms of organic carbon and anion/cation concentrations. Element geochemical and isotope analyses of fluid components were used to verify the origin of the fluids. Prokaryotic communities were characterized through quantitative PCR and Illumina 16S rRNA gene sequencing. Putative chemolithotrophic, anaerobic and microaerophilic organisms connected to sulfur (e.g., Sulfuricurvum, Sulfurimonas) and iron (e.g., Gallionella, Sideroxydans) cycling shaped the core community. Additionally, CO2-influenced waters form an ecosystem containing many taxa that are usually found in marine or terrestrial subsurface ecosystems. Multivariate statistics highlighted the influence of environmental parameters such as pH, Fe2+ concentration and conductivity on species distribution. The hydrochemical and microbiological survey introduces a new perspective on mofettes. Our results support that mofettes are either analogs or rather windows into the deep biosphere and furthermore enable access to deeply buried paleo-sediments.

KEYWORDS:

Eger Rift; Gallionella; Sideroxydans; Sulfuricurvum; deep biosphere; elevated CO2 concentration; microbial ecology; paleo-sediment

7.
ACS Chem Biol. 2017 Dec 15;12(12):2927-2933. doi: 10.1021/acschembio.7b00814. Epub 2017 Nov 2.

Rewiring of the Austinoid Biosynthetic Pathway in Filamentous Fungi.

Author information

1
Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Adolf-Reichwein-Str. 23, 07745 Jena, Germany.
2
Friedrich Schiller University , 07745 Jena, Germany.
3
Leibniz Research Group - Biobricks of Microbial Natural Product Syntheses, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Adolf-Reichwein-Str. 23, 07745 Jena, Germany.
4
Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Adolf-Reichwein-Str. 23, 07745 Jena, Germany.
5
GFZ German Center for Geosciences , Section 5.3 Geomicrobiology, Telegrafenberg, 14471 Potsdam, Germany.
6
BASF SE , 67056 Ludwigshafen, Germany.

Abstract

Filamentous fungi produce numerous high-value natural products (NPs). The biosynthetic genes for NPs are normally clustered in the genome. A valuable NP class is represented by the insecticidal austinoids. We previously determined their biosynthesis in the fungus Aspergillus calidoustus. After further computational analysis looking into the austinoid gene clusters in two additional distantly related fungi, Aspergillus nidulans and Penicillium brasilianum, a rearrangement of the genes was observed that corresponded to the diverse austinoid derivatives produced by each strain. By advanced targeted combinatorial engineering using polycistronic expression of selected genes, we rewired the austinoid pathway in the fungus A. nidulans, which then produced certain compounds of interest under industrially favored conditions. This was possible by exploiting the presence of genes previously thought to be irrelevant. Our work shows that comparative analysis of genomes can be used to not only discover new gene clusters but unearth the hidden potential of known metabolic pathways.

PMID:
29076725
DOI:
10.1021/acschembio.7b00814
[Indexed for MEDLINE]
Icon for American Chemical Society
8.
Front Microbiol. 2017 Jul 27;8:1440. doi: 10.3389/fmicb.2017.01440. eCollection 2017.

Preservation and Significance of Extracellular DNA in Ferruginous Sediments from Lake Towuti, Indonesia.

Author information

1
GFZ German Research Centre for Geosciences, Section 5.3: GeomicrobiologyPotsdam, Germany.
2
Research Center for Limnology, Indonesian Institute of SciencesCibinong-Bogor, Indonesia.
3
Department of Microbiology and Immunology, University of British Columbia, VancouverBC, Canada.
4
Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, VancouverBC, Canada.

Abstract

Extracellular DNA is ubiquitous in soil and sediment and constitutes a dominant fraction of environmental DNA in aquatic systems. In theory, extracellular DNA is composed of genomic elements persisting at different degrees of preservation produced by processes occurring on land, in the water column and sediment. Extracellular DNA can be taken up as a nutrient source, excreted or degraded by microorganisms, or adsorbed onto mineral matrices, thus potentially preserving information from past environments. To test whether extracellular DNA records lacustrine conditions, we sequentially extracted extracellular and intracellular DNA from anoxic sediments of ferruginous Lake Towuti, Indonesia. We applied 16S rRNA gene Illumina sequencing on both fractions to discriminate exogenous from endogenous sources of extracellular DNA in the sediment. Environmental sequences exclusively found as extracellular DNA in the sediment originated from multiple sources. For instance, Actinobacteria, Verrucomicrobia, and Acidobacteria derived from soils in the catchment. Limited primary productivity in the water column resulted in few sequences of Cyanobacteria in the oxic photic zone, whereas stratification of the water body mainly led to secondary production by aerobic and anaerobic heterotrophs. Chloroflexi and Planctomycetes, the main degraders of sinking organic matter and planktonic sequences at the water-sediment interface, were preferentially preserved during the initial phase of burial. To trace endogenous sources of extracellular DNA, we used relative abundances of taxa in the intracellular DNA to define which microbial populations grow, decline or persist at low density with sediment depth. Cell lysis became an important additional source of extracellular DNA, gradually covering previous genetic assemblages as other microbial genera became more abundant with depth. The use of extracellular DNA as nutrient by active microorganisms led to selective removal of sequences with lowest GC contents. We conclude that extracellular DNA preserved in shallow lacustrine sediments reflects the initial environmental context, but is gradually modified and thereby shifts from its stratigraphic context. Discrimination of exogenous and endogenous sources of extracellular DNA allows simultaneously addressing in-lake and post-depositional processes. In deeper sediments, the accumulation of resting stages and sequences from cell lysis would require stringent extraction and specific primers if ancient DNA is targeted.

KEYWORDS:

GC content; ICDP drilling; Lake Towuti; cell lysis; environmental archive; extracellular DNA; ferruginous sediment; intracellular DNA

9.
Front Microbiol. 2017 Jul 18;8:1339. doi: 10.3389/fmicb.2017.01339. eCollection 2017.

Global Biogeographic Analysis of Methanogenic Archaea Identifies Community-Shaping Environmental Factors of Natural Environments.

Author information

1
Section 5.3 Geomicrobiology, GFZ German Research Centre for GeosciencesPotsdam, Germany.
2
College of Electrical Engineering, Northwest University for NationalitiesLanzhou, China.
3
State Key Laboratory of Frozen Soil Engineering, Northwest Institute of Eco-Environment and Resources, Chinese Academy of SciencesLanzhou, China.

Abstract

Methanogenic archaea are important for the global greenhouse gas budget since they produce methane under anoxic conditions in numerous natural environments such as oceans, estuaries, soils, and lakes. Whether and how environmental change will propagate into methanogenic assemblages of natural environments remains largely unknown owing to a poor understanding of global distribution patterns and environmental drivers of this specific group of microorganisms. In this study, we performed a meta-analysis targeting the biogeographic patterns and environmental controls of methanogenic communities using 94 public mcrA gene datasets. We show a global pattern of methanogenic archaea that is more associated with habitat filtering than with geographical dispersal. We identify salinity as the control on methanogenic community composition at global scale whereas pH and temperature are the major controls in non-saline soils and lakes. The importance of salinity for structuring methanogenic community composition is also reflected in the biogeography of methanogenic lineages and the physiological properties of methanogenic isolates. Linking methanogenic alpha-diversity with reported values of methane emission identifies estuaries as the most diverse methanogenic habitats with, however, minor contribution to the global methane budget. With salinity, temperature and pH our study identifies environmental drivers of methanogenic community composition facing drastic changes in many natural environments at the moment. However, consequences of this for the production of methane remain elusive owing to a lack of studies that combine methane production rate with community analysis.

KEYWORDS:

biogeography; environmental drivers; mcrA; methanogenic archaea; pH; salinity; temperature

10.
ACS Chem Biol. 2017 May 19;12(5):1227-1234. doi: 10.1021/acschembio.7b00003. Epub 2017 Mar 15.

Discovery of an Extended Austinoid Biosynthetic Pathway in Aspergillus calidoustus.

Author information

1
Friedrich Schiller University , 07745 Jena, Germany.
2
Institute of Biotechnology and Drug Research , Erwin-Schroedinger-Strasse 56, 67663 Kaiserslautern, Germany.
3
Johannes-Gutenberg-University Mainz , Institute of Biotechnology, Johann-Joachim-Becherweg 15, 55128 Mainz, Germany.
4
BASF SE , 67056 Ludwigshafen, Germany.

Abstract

Filamentous fungi produce a wide range of natural products that are commonly used in various industrial contexts (e.g., pharmaceuticals and insecticides). Meroterpenoids are natural products of interest because of their various biological activities. Among the meroterpenoids, there is a group of insecticidal compounds known as the austinoids. These compounds have also been studied because of their intriguing spiro-lactone ring formation along with various modifications. Here, we present an extension of the original austinol/dehydroaustinol biosynthesis pathway from Aspergillus nidulans in the recently identified filamentous fungus Aspergillus calidoustus. Besides the discovery and elucidation of further derivatives, genome mining led to the discovery of new putative biosynthetic genes. The genes involved in the biosynthesis of later austinoid products were characterized, and among them was a second polyketide synthase gene in the A. calidoustus cluster that was unusual because it was a noninterative polyketide synthase producing a diketide. This diketide product was then loaded onto the austinoid backbone, resulting in a new insecticidal derivative, calidodehydroaustin.

PMID:
28233494
DOI:
10.1021/acschembio.7b00003
[Indexed for MEDLINE]
Icon for American Chemical Society
12.
Genome Announc. 2016 Mar 10;4(2). pii: e00102-16. doi: 10.1128/genomeA.00102-16.

Draft Genome Sequences of Fungus Aspergillus calidoustus.

Author information

1
Department of Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Jena, Germany.
2
Department of Molecular and Applied Microbiology, HKI, Jena, Germany Institute for Microbiology, Friedrich Schiller University, Jena, Germany.
3
National Reference Center for Invasive Fungal Infections, HKI, Jena, Germany.
4
Department of Biomolecular Chemistry, HKI, Jena, Germany.
5
BASF SE, Ludwigshafen, Germany.
6
Bio Pilot Plant, HKI, Jena, Germany.
7
Leibniz Junior Research Group-Biobricks of Microbial Natural Product Syntheses, HKI, Jena, Germany vito.valiante@leibniz-hki.de.

Abstract

Here, we report the draft genome sequence of Aspergillus calidoustus (strain SF006504). The functional annotation of A. calidoustus predicts a relatively large number of secondary metabolite gene clusters. The presented genome sequence builds the basis for further genome mining.

13.
Genome Announc. 2015 Sep 3;3(5). pii: e00724-15. doi: 10.1128/genomeA.00724-15.

Draft Genome Sequence of the Fungus Penicillium brasilianum MG11.

Author information

1
Department of Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Jena, Germany vito.valiante@leibniz-hki.de.
2
Department of Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Jena, Germany.
3
Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Jena, Germany.
4
National Center for Invasive Mycoses, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Jena, Germany.
5
Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Jena, Germany Friedrich Schiller University, Institute for Microbiology, Jena, Germany.
6
Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Jena, Germany Leibniz Junior Research Group-Biobricks of Microbial Natural Product Syntheses, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Jena, Germany vito.valiante@leibniz-hki.de.

Abstract

The genus Penicillium belongs to the phylum Ascomycota and includes a variety of fungal species important for food and drug production. We report the draft genome sequence of Penicillium brasilianum MG11. This strain was isolated from soil, and it was reported to produce different secondary metabolites.

14.
Genome Announc. 2015 Apr 23;3(2). pii: e00270-15. doi: 10.1128/genomeA.00270-15.

Genome Sequence of Methanosarcina soligelidi SMA-21, Isolated from Siberian Permafrost-Affected Soil.

Author information

1
GFZ German Research Centre for Geosciences, Section 4.5 Geomicrobiology, Potsdam, Germany mashal.alawi@gfz-potsdam.de.
2
DOE Joint Genome Institute, Walnut Creek, California, USA.
3
GFZ German Research Centre for Geosciences, Section 4.5 Geomicrobiology, Potsdam, Germany.
4
Altoona College, The Pennsylvania State University, Altoona, Pennsylvania, USA.

Abstract

Here, we announce the genome sequence of Methanosarcina soligelidi SMA-21, an anaerobic methanogenic archaeon that was previously isolated from Siberian permafrost-affected soil. The sequencing of strain SMA-21 yielded a 4.06-Mb genome with 41.5% G+C content, containing a total of 2,647 open reading frames.

15.
Genome Announc. 2015 Jan 22;3(1). pii: e01439-14. doi: 10.1128/genomeA.01439-14.

Draft Genome Sequence and Gene Annotation of the Entomopathogenic Fungus Verticillium hemipterigenum.

Author information

1
Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany.
2
Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany.
3
Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany.
4
Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany joerg.linde@hki-jena.de christian.hertweck@hki-jena.de.
5
Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany joerg.linde@hki-jena.de christian.hertweck@hki-jena.de.

Abstract

Verticillium hemipterigenum (anamorph Torrubiella hemipterigena) is an entomopathogenic fungus and produces a broad range of secondary metabolites. Here, we present the draft genome sequence of the fungus, including gene structure and functional annotation. Genes were predicted incorporating RNA-Seq data and functionally annotated to provide the basis for further genome studies.

16.
Genome Announc. 2015 Jan 22;3(1). pii: e01370-14. doi: 10.1128/genomeA.01370-14.

Draft Genome Sequences of Symbiotic and Nonsymbiotic Rhizopus microsporus Strains CBS 344.29 and ATCC 62417.

Author information

1
Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany.
2
Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany.
3
Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany joerg.linde@hki-jena.de christian.hertweck@hki-jena.de.
4
Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany joerg.linde@hki-jena.de christian.hertweck@hki-jena.de.

Abstract

Specific Rhizopus microsporus pathovars harbor bacterial endosymbionts (Burkholderia rhizoxinica) for the production of a phytotoxin. Here, we present the draft genome sequences of two R. microsporus strains, one symbiotic (ATCC 62417), and one endosymbiont-free (CBS 344.29). The gene predictions were supported by RNA sequencing (RNA-seq) data. The functional annotation sets the basis for comparative analyses.

17.
Nucleic Acids Res. 2015 Feb 18;43(3):1392-406. doi: 10.1093/nar/gku1357. Epub 2015 Jan 13.

Defining the transcriptomic landscape of Candida glabrata by RNA-Seq.

Author information

1
Research Group Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, Jena, Germany joerg.linde@hki-jena.de.
2
Septomics Research Center, Fungal Septomics, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, Jena, Germany.
3
Research Group Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, Jena, Germany.
4
Research Group Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, Jena, Germany Department of Bioinformatics, Faculty of Biology and Pharmacy, Friedrich Schiller University, Jena, Germany.
5
Research Group Bioinformatics and High Throughput Analysis, Faculty of Mathematics and Computer Sciences, Friedrich Schiller University, Jena, Germany.
6
Septomics Research Center, Fungal Septomics, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, Jena, Germany National Reference Center for Invasive Mycoses, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, Jena, Germany.

Abstract

Candida glabrata is the second most common pathogenic Candida species and has emerged as a leading cause of nosocomial fungal infections. Its reduced susceptibility to antifungal drugs and its close relationship to Saccharomyces cerevisiae make it an interesting research focus. Although its genome sequence was published in 2004, little is known about its transcriptional dynamics. Here, we provide a detailed RNA-Seq-based analysis of the transcriptomic landscape of C. glabrata in nutrient-rich media, as well as under nitrosative stress and during pH shift. Using RNA-Seq data together with state-of-the-art gene prediction tools, we refined the annotation of the C. glabrata genome and predicted 49 novel protein-coding genes. Of these novel genes, 14 have homologs in S. cerevisiae and six are shared with other Candida species. We experimentally validated four novel protein-coding genes of which two are differentially regulated during pH shift and interaction with human neutrophils, indicating a potential role in host-pathogen interaction. Furthermore, we identified 58 novel non-protein-coding genes, 38 new introns and condition-specific alternative splicing. Finally, our data suggest different patterns of adaptation to pH shift and nitrosative stress in C. glabrata, Candida albicans and S. cerevisiae and thus further underline a distinct evolution of virulence in yeast.

PMID:
25586221
PMCID:
PMC4330350
DOI:
10.1093/nar/gku1357
[Indexed for MEDLINE]
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18.
PLoS Genet. 2014 Dec 4;10(12):e1004824. doi: 10.1371/journal.pgen.1004824. eCollection 2014 Dec.

Microevolution of Candida albicans in macrophages restores filamentation in a nonfilamentous mutant.

Author information

1
Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute Jena (HKI), Jena, Germany.
2
Research Group Systems Biology & Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute Jena (HKI), Jena, Germany.
3
Septomics Research Center, Friedrich Schiller University and Leibniz Institute for Natural Product Research and Infection Biology -Hans Knoell Institute, Jena, Germany.
4
Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute Jena (HKI), Jena, Germany; Research Group Microbial Immunology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute Jena (HKI), Jena, Germany.
5
Medical University Vienna, Max F. Perutz Laboratories, Department of Medical Biochemistry, Vienna, Austria.
6
Department of Biology, Bowdoin College, Brunswick, Maine, United States of America.
7
Institut Pasteur, Unité Biologie et Pathogénicité Fongiques, Département Génomes et Génétique, Paris, France; INRA, USC2019, Paris, France.
8
Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute Jena (HKI), Jena, Germany; Integrated Research and Treatment Center, Sepsis und Sepsisfolgen, Center for Sepsis Control and Care (CSCC), Universitätsklinikum Jena, Germany.
9
Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute Jena (HKI), Jena, Germany; Integrated Research and Treatment Center, Sepsis und Sepsisfolgen, Center for Sepsis Control and Care (CSCC), Universitätsklinikum Jena, Germany; Friedrich Schiller University, Jena, Germany.

Abstract

Following antifungal treatment, Candida albicans, and other human pathogenic fungi can undergo microevolution, which leads to the emergence of drug resistance. However, the capacity for microevolutionary adaptation of fungi goes beyond the development of resistance against antifungals. Here we used an experimental microevolution approach to show that one of the central pathogenicity mechanisms of C. albicans, the yeast-to-hyphae transition, can be subject to experimental evolution. The C. albicans cph1Δ/efg1Δ mutant is nonfilamentous, as central signaling pathways linking environmental cues to hyphal formation are disrupted. We subjected this mutant to constant selection pressure in the hostile environment of the macrophage phagosome. In a comparatively short time-frame, the mutant evolved the ability to escape macrophages by filamentation. In addition, the evolved mutant exhibited hyper-virulence in a murine infection model and an altered cell wall composition compared to the cph1Δ/efg1Δ strain. Moreover, the transcriptional regulation of hyphae-associated, and other pathogenicity-related genes became re-responsive to environmental cues in the evolved strain. We went on to identify the causative missense mutation via whole genome- and transcriptome-sequencing: a single nucleotide exchange took place within SSN3 that encodes a component of the Cdk8 module of the Mediator complex, which links transcription factors with the general transcription machinery. This mutation was responsible for the reconnection of the hyphal growth program with environmental signals in the evolved strain and was sufficient to bypass Efg1/Cph1-dependent filamentation. These data demonstrate that even central transcriptional networks can be remodeled very quickly under appropriate selection pressure.

PMID:
25474009
PMCID:
PMC4256171
DOI:
10.1371/journal.pgen.1004824
[Indexed for MEDLINE]
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19.
Bioinformatics. 2015 Feb 1;31(3):445-6. doi: 10.1093/bioinformatics/btu627. Epub 2014 Oct 7.

FungiFun2: a comprehensive online resource for systematic analysis of gene lists from fungal species.

Author information

1
Research Group Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute, Beutenbergstraße 11a, 07745 Jena, Germany.

Abstract

SUMMARY:

Systematically extracting biological meaning from omics data is a major challenge in systems biology. Enrichment analysis is often used to identify characteristic patterns in candidate lists. FungiFun is a user-friendly Web tool for functional enrichment analysis of fungal genes and proteins. The novel tool FungiFun2 uses a completely revised data management system and thus allows enrichment analysis for 298 currently available fungal strains published in standard databases. FungiFun2 offers a modern Web interface and creates interactive tables, charts and figures, which users can directly manipulate to their needs.

AVAILABILITY AND IMPLEMENTATION:

FungiFun2, examples and tutorials are publicly available at https://elbe.hki-jena.de/fungifun/.

CONTACT:

steffen.priebe@hki-jena.de or joerg.linde@hki-jena.de.

PMID:
25294921
PMCID:
PMC4308660
DOI:
10.1093/bioinformatics/btu627
[Indexed for MEDLINE]
Free PMC Article
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20.
Genome Announc. 2014 Sep 11;2(5). pii: e00888-14. doi: 10.1128/genomeA.00888-14.

De Novo Whole-Genome Sequence and Genome Annotation of Lichtheimia ramosa.

Author information

1
Systems Biology/Bioinformatics, Hans-Knöll-Institut, Jena, Germany.
2
Jena Microbial Resource Collection, Hans-Knöll-Institut, Jena, Germany.
3
Division of Hygiene and Medical Microbiology, Innsbruck Medical University, Innsbruck, Austria.
4
Jena Microbial Resource Collection, Hans-Knöll-Institut, Jena, Germany kerstin.voigt@hki-jena.de fabian.horn@hki-jena.de.
5
Systems Biology/Bioinformatics, Hans-Knöll-Institut, Jena, Germany kerstin.voigt@hki-jena.de fabian.horn@hki-jena.de.

Abstract

We report the annotated draft genome sequence of Lichtheimia ramosa (JMRC FSU:6197). It has been reported to be a causative organism of mucormycosis, a rare but rapidly progressive infection in immunocompromised humans. The functionally annotated genomic sequence consists of 74 scaffolds with a total number of 11,510 genes.

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