Publications by authors named "Andreas Schramm"

110 Publications

The importance of environmental microbes for Drosophila melanogaster during seasonal macronutrient variability.

Sci Rep 2021 Sep 22;11(1):18850. Epub 2021 Sep 22.

Department of Chemistry and Bioscience, Aalborg University, 9220, Aalborg, Denmark.

Experiments manipulating the nutritional environment and the associated microbiome of animals have demonstrated their importance for key fitness components. However, there is little information on how macronutrient composition and bacterial communities in natural food sources vary across seasons in nature and on how these factors affect the fitness components of insects. In this study, diet samples from an orchard compost heap, which is a natural habitat for many Drosophila species and other arthropods, were collected over 9 months covering all seasons in a temperate climate. We developed D. melanogaster on diet samples and investigated stress resistance and life-history traits as well as the microbial community of flies and compost. Nutrient and microbial community analysis of the diet samples showed marked differences in macronutrient composition and microbial community across seasons. However, except for the duration of development on these diet samples and Critical Thermal maximum, fly stress resistance and life-history traits were unaffected. The resulting differences in the fly microbial community were also more stable and less diverse than the microbial community of the diet samples. Our study suggests that when D. melanogaster are exposed to a vastly varying nutritional environment with a rich, diverse microbial community, the detrimental consequences of an unfavourable macronutrient composition are offset by the complex interactions between microbes and nutrients.
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http://dx.doi.org/10.1038/s41598-021-98119-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8458401PMC
September 2021

Antimicrobial Compounds in the Volatilome of Social Spider Communities.

Front Microbiol 2021 24;12:700693. Epub 2021 Aug 24.

Department of Cellular Biochemistry and Metabolomics, University of Greifswald, Greifswald, Germany.

Social arthropods such as termites, ants, and bees are among others the most successful animal groups on earth. However, social arthropods face an elevated risk of infections due to the dense colony structure, which facilitates pathogen transmission. An interesting hypothesis is that social arthropods are protected by chemical compounds produced by the arthropods themselves, microbial symbionts, or plants they associate with. is an African social spider species, inhabiting communal silk nests. Because of the complex three-dimensional structure of the spider nest antimicrobial volatile organic compounds (VOCs) are a promising protection against pathogens, because of their ability to diffuse through air-filled pores. We analyzed the volatilomes of , their nests, and capture webs in three locations in Namibia and assessed their antimicrobial potential. Volatilomes were collected using polydimethylsiloxane (PDMS) tubes and analyzed using GC/Q-TOF. We showed the presence of 199 VOCs and tentatively identified 53 VOCs. More than 40% of the tentatively identified VOCs are known for their antimicrobial activity. Here, six VOCs were confirmed by analyzing pure compounds namely acetophenone, 1,3-benzothiazole, 1-decanal, 2-decanone, 1-tetradecene, and docosane and for five of these compounds the antimicrobial activity were proven. The nest and web volatilomes had many VOCs in common, whereas the spider volatilomes were more differentiated. Clear differences were identified between the volatilomes from the different sampling sites which is likely justified by differences in the microbiomes of the spiders and nests, the plants, and the different climatic conditions. The results indicate the potential relevance of the volatilomes for the ecological success of .
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http://dx.doi.org/10.3389/fmicb.2021.700693DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8422909PMC
August 2021

Phyllobacterium calauticae sp. nov. isolated from a microaerophilic veil transversed by cable bacteria in freshwater sediment.

Antonie Van Leeuwenhoek 2021 Sep 7. Epub 2021 Sep 7.

Section for Microbiology, Center for Electromicrobiology, Department of Biology, Aarhus University, Ny Munkegade 114, Building 1540, 8000, Aarhus C, Denmark.

Microaerophilic veils of swimming microorganisms form at oxic-anoxic interfaces, mostly described in sediments where sulfide from below meets oxygen diffusing in from the water phase. However, microaerophilic veils form even when these gradients do not overlap, for example when cable bacteria activity leads to a suboxic zone. This suggests that veil microorganisms can use electron donors other than sulfide. Here we describe the extraction of microorganisms from a microaerophilic veil that formed in cable-bacteria-enriched freshwater sediment using a glass capillary, and the subsequent isolation of a motile, microaerophilic, organoheterotrophic bacterium, strain R2-JL, unable to oxidize sulfide. Based on phenotypic, phylogenetic, and genomic comparison, we propose strain R2-JL as a novel Phyllobacterium species, P. calauticae sp. nov.. The type strain is R2-JL (= LMG 32286 = DSM 112555). This novel isolate confirms that a wider variety of electron donors, including organic compounds, can fuel the activity of microorganisms in microaerophilic veils.
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http://dx.doi.org/10.1007/s10482-021-01647-yDOI Listing
September 2021

Spatial separation of ribosomes and DNA in Asgard archaeal cells.

ISME J 2021 Aug 31. Epub 2021 Aug 31.

Department of Biology, Section for Microbiology, Aarhus University, Aarhus, Denmark.

The origin of the eukaryotic cell is a major open question in biology. Asgard archaea are the closest known prokaryotic relatives of eukaryotes, and their genomes encode various eukaryotic signature proteins, indicating some elements of cellular complexity prior to the emergence of the first eukaryotic cell. Yet, microscopic evidence to demonstrate the cellular structure of uncultivated Asgard archaea in the environment is thus far lacking. We used primer-free sequencing to retrieve 715 almost full-length Loki- and Heimdallarchaeota 16S rRNA sequences and designed novel oligonucleotide probes to visualize their cells in marine sediments (Aarhus Bay, Denmark) using catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). Super-resolution microscopy revealed 1-2 µm large, coccoid cells, sometimes occurring as aggregates. Remarkably, the DNA staining was spatially separated from ribosome-originated FISH signals by 50-280 nm. This suggests that the genomic material is condensed and spatially distinct in a particular location and could indicate compartmentalization or membrane invagination in Asgard archaeal cells.
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http://dx.doi.org/10.1038/s41396-021-01098-3DOI Listing
August 2021

How to grow your cable bacteria: Establishment of a stable single-strain culture in sediment and proposal of Candidatus Electronema aureum GS.

Syst Appl Microbiol 2021 Sep 22;44(5):126236. Epub 2021 Jul 22.

Section for Microbiology, Department of Biology, Aarhus University, Denmark; Center for Electromicrobiology, Aarhus University, Denmark; Center for Geomicrobiology, Aarhus University, Denmark; ECOBE, Department of Biology, University of Antwerp, Belgium.

Cable bacteria are multicellular filamentous bacteria within the Desulfobulbaceae that couple the oxidation of sulfide to the reduction of oxygen over centimeter distances via long distance electron transport (LDET). So far, none of the freshwater or marine cable bacteria species have been isolated into pure culture. Here we describe a method for establishing a stable single-strain cable bacterium culture in partially sterilized sediment. By repeated transfers of a single cable bacterium filament from freshwater pond sediment into autoclaved sediment, we obtained strain GS, identified by its 16S rRNA gene as a member of Ca. Electronema. This strain was further propagated by transferring sediment clumps, and has now been stable within its semi-natural microbial community for several years. Its metagenome-assembled genome was 93% complete, had a size of 2.76 Mbp, and a DNA G + C content of 52%. Average Nucleotide Identity (ANI) and Average Amino Acid Identity (AAI) suggest the affiliation of strain GS to Ca. Electronema as a novel species. Cell size, number of outer ridges, and detection of LDET in the GS culture are likewise consistent with Ca. Electronema. Based on these combined features, we therefore describe strain GS as a new cable bacterium species of the candidate genus Electronema, for which we propose the name Candidatus Electronema aureum sp.nov. Although not a pure culture, this stable single-strain culture will be useful for physiological and omics-based studies; similar approaches with single-cell or single-filament transfers into natural medium may also aid the characterization of other difficult-to-culture microbes.
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http://dx.doi.org/10.1016/j.syapm.2021.126236DOI Listing
September 2021

Dissimilatory nitrate reduction by a freshwater cable bacterium.

ISME J 2021 Jul 2. Epub 2021 Jul 2.

Center for Electromicrobiology, Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark.

Cable bacteria (CB) are filamentous Desulfobulbaceae that split the energy-conserving reaction of sulfide oxidation into two half reactions occurring in distinct cells. CB can use nitrate, but the reduction pathway is unknown, making it difficult to assess their direct impact on the N-cycle. Here we show that the freshwater cable bacterium Ca. Electronema sp. GS performs dissimilatory nitrate reduction to ammonium (DNRA). NO-amended sediment with Ca. Electronema sp. GS showed higher rates of DNRA and nitrite production than sediment without Ca. Electronema sp. GS. Electron flux from sulfide oxidation, inferred from electric potential (EP) measurements, matched the electron flux needed to drive CB-mediated nitrate reduction to nitrite and ammonium. Ca. Electronema sp. GS expressed a complete nap operon for periplasmic nitrate reduction to nitrite, and a putative octaheme cytochrome c (pOCC), whose involvement in nitrite reduction to ammonium remains to be verified. Phylogenetic analysis suggests that the capacity for DNRA was acquired in multiple events through horizontal gene transfer from different organisms, before CB split into different salinity niches. The architecture of the nitrate reduction system suggests absence of energy conservation through oxidative phosphorylation, indicating that CB primarily conserve energy through the half reaction of sulfide oxidation.
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http://dx.doi.org/10.1038/s41396-021-01048-zDOI Listing
July 2021

The bacterial and fungal nest microbiomes in populations of the social spider Stegodyphus dumicola.

Syst Appl Microbiol 2021 Jul 2;44(4):126222. Epub 2021 Jun 2.

Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark.

Social spiders of the species Stegodyphus dumicola live in communal nests with hundreds of individuals and are characterized by extremely low species-wide genetic diversity. The lack of genetic diversity in combination with group living imposes a potential threat for infection by pathogens. We therefore proposed that specific microbial symbionts inhabiting the spider nests may provide antimicrobial defense. To compare the bacterial and fungal diversity in 17 nests from three different locations in Namibia, we used 16S rRNA gene and internal transcribed spacer (ITS2) sequencing. The nest microbiomes differed between geographically distinct spider populations and appeared largely determined by the local environment. Nevertheless, we identified a core microbiome consisting of four bacterial genera (Curtobacterium, Modestobacter, Sphingomonas, Massilia) and four fungal genera (Aureobasidium, Didymella, Alternaria, Ascochyta), which likely are selected from surrounding soil and plants by the nest environment. We did not find indications for a strain- or species-specific symbiosis in the nests. Isolation of bacteria and fungi from nest material retrieved a few bacterial strains with antimicrobial activity but a number of antimicrobial fungi, including members of the fungal core microbiome. The significance of antimicrobial taxa in the nest microbiome for host protection remains to be shown.
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http://dx.doi.org/10.1016/j.syapm.2021.126222DOI Listing
July 2021

Cable bacteria at oxygen-releasing roots of aquatic plants: a widespread and diverse plant-microbe association.

New Phytol 2021 Apr 23. Epub 2021 Apr 23.

Section for Microbiology, Department of Biology, Center for Electromicrobiology, Aarhus University, Ny Munkegade 116, Aarhus C, DK-8000, Denmark.

Cable bacteria are sulfide-oxidising, filamentous bacteria that reduce toxic sulfide levels, suppress methane emissions and drive nutrient and carbon cycling in sediments. Recently, cable bacteria have been found associated with roots of aquatic plants and rice (Oryza sativa). However, the extent to which cable bacteria are associated with aquatic plants in nature remains unexplored. Using newly generated and public 16S rRNA gene sequence datasets combined with fluorescence in situ hybridisation, we investigated the distribution of cable bacteria around the roots of aquatic plants, encompassing seagrass (including seagrass seedlings), rice, freshwater and saltmarsh plants. Diverse cable bacteria were found associated with roots of 16 out of 28 plant species and at 36 out of 55 investigated sites, across four continents. Plant-associated cable bacteria were confirmed across a variety of ecosystems, including marine coastal environments, estuaries, freshwater streams, isolated pristine lakes and intensive agricultural systems. This pattern indicates that this plant-microbe relationship is globally widespread and neither obligate nor species specific. The occurrence of cable bacteria in plant rhizospheres may be of general importance to vegetation vitality, primary productivity, coastal restoration practices and greenhouse gas balance of rice fields and wetlands.
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http://dx.doi.org/10.1111/nph.17415DOI Listing
April 2021

Oxygen consumption of individual cable bacteria.

Sci Adv 2021 Feb 10;7(7). Epub 2021 Feb 10.

Center for Electromicrobiology, Department of Biology, Aarhus University, 8000 Aarhus C, Denmark.

The electric wires of cable bacteria possibly support a unique respiration mode with a few oxygen-reducing cells flaring off electrons, while oxidation of the electron donor and the associated energy conservation and growth is allocated to other cells not exposed to oxygen. Cable bacteria are centimeter-long, multicellular, filamentous Desulfobulbaceae that transport electrons across oxic-anoxic interfaces in aquatic sediments. From observed distortions of the oxic-anoxic interface, we derived oxygen consumption rates of individual cable bacteria and found biomass-specific rates of unheard magnitude in biology. Tightly controlled behavior, possibly involving intercellular electrical signaling, was found to generally keep <10% of individual filaments exposed to oxygen. The results strengthen the hypothesis that cable bacteria indeed have evolved an exceptional way to take the full energetic advantages of aerobic respiration and let >90% of the cells metabolize in the convenient absence of oxidative stress.
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http://dx.doi.org/10.1126/sciadv.abe1870DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7875522PMC
February 2021

An antimicrobial Staphylococcus sciuri with broad temperature and salt spectrum isolated from the surface of the African social spider, Stegodyphus dumicola.

Antonie Van Leeuwenhoek 2021 Mar 4;114(3):325-335. Epub 2021 Feb 4.

Section for Microbiology, Department of Biology, Aarhus University, Ny Munkegade 114, Building 1540, 8000, Aarhus, Denmark.

Some social arthropods engage in mutualistic symbiosis with antimicrobial compound-producing microorganisms that provide protection against pathogens. Social spiders live in communal nests and contain specific endosymbionts with unknown function. Bacteria are also found on the spiders' surface, including prevalent staphylococci, which may have protective potential. Here we present the genomic and phenotypic characterization of strain i1, isolated from the surface of the social spider Stegodyphus dumicola. Phylogenomic analysis identified i1 as novel strain of Staphylococcus sciuri within subgroup 2 of three newly defined genomic subgroups. Further phenotypic investigations showed that S. sciuri i1 is an extremophile that can grow at a broad range of temperatures (4 °C-45 °C), high salt concentrations (up to 27%), and has antimicrobial activity against closely related species. We identified a lactococcin 972-like bacteriocin gene cluster, likely responsible for the antimicrobial activity, and found it conserved in two of the three subgroups of S. sciuri. These features indicate that S. sciuri i1, though not a specific symbiont, is well-adapted to survive on the surface of social spiders and may gain a competitive advantage by inhibiting closely related species.
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http://dx.doi.org/10.1007/s10482-021-01526-6DOI Listing
March 2021

Microbiomes and Specific Symbionts of Social Spiders: Compositional Patterns in Host Species, Populations, and Nests.

Front Microbiol 2020 31;11:1845. Epub 2020 Jul 31.

Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark.

Social spiders have remarkably low species-wide genetic diversities, potentially increasing the relative importance of microbial symbionts for host fitness. Here we explore the bacterial microbiomes of three species of social (, , and ), within and between populations, using 16S rRNA gene amplicon sequencing. The microbiomes of the three spider species were distinct but shared similarities in membership and structure. This included low overall diversity (Shannon index 0.5-1.7), strong dominance of single symbionts in individual spiders (McNaughton's dominance index 0.68-0.93), and a core microbiome (>50% prevalence) consisting of 5-7 specific symbionts. The most abundant and prevalent symbionts were classified as Chlamydiales, , and , all representing novel, presumably -specific lineages. - and -like symbionts were localized by fluorescence hybridization (FISH) in the spider midgut. The microbiomes of individual spiders were highly similar within nests but often very different between nests from the same population, with only the microbiome of consistently reflecting host population structure. The weak population pattern in microbiome composition renders microbiome-facilitated local adaptation unlikely. However, the retention of specific symbionts across populations and species may indicate a recurrent acquisition from environmental vectors or an essential symbiotic contribution to spider phenotype.
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http://dx.doi.org/10.3389/fmicb.2020.01845DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7412444PMC
July 2020

Electrogenic sulfide oxidation mediated by cable bacteria stimulates sulfate reduction in freshwater sediments.

ISME J 2020 05 10;14(5):1233-1246. Epub 2020 Feb 10.

Department of Bioscience, Section for Microbiology, Aarhus University, Aarhus, Denmark.

Cable bacteria are filamentous members of the Desulfobulbaceae family that oxidize sulfide with oxygen or nitrate by transferring electrons over centimeter distances in sediments. Recent studies show that freshwater sediments can support populations of cable bacteria at densities comparable to those found in marine environments. This is surprising since sulfide availability is presumably low in freshwater sediments due to sulfate limitation of sulfate reduction. Here we show that cable bacteria stimulate sulfate reduction in freshwater sediment through promotion of sulfate availability. Comparing experimental freshwater sediments with and without active cable bacteria, we observed a three- to tenfold increase in sulfate concentrations and a 4.5-fold increase in sulfate reduction rates when cable bacteria were present, while abundance and community composition of sulfate-reducing microorganisms (SRM) were unaffected. Correlation and ANCOVA analysis supported the hypothesis that the stimulation of sulfate reduction activity was due to relieve of the kinetic limitations of the SRM community through the elevated sulfate concentrations in sediments with cable bacteria activity. The elevated sulfate concentration was caused by cable bacteria-driven sulfide oxidation, by sulfate production from an indigenous sulfide pool, likely through cable bacteria-mediated dissolution and oxidation of iron sulfides, and by enhanced retention of sulfate, triggered by an electric field generated by the cable bacteria. Cable bacteria in freshwater sediments may thus be an integral component of a cryptic sulfur cycle and provide a mechanism for recycling of the scarce resource sulfate, stimulating sulfate reduction. It is possible that this stimulation has implication for methanogenesis and greenhouse gas emissions.
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http://dx.doi.org/10.1038/s41396-020-0607-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7174387PMC
May 2020

On the evolution and physiology of cable bacteria.

Proc Natl Acad Sci U S A 2019 09 19;116(38):19116-19125. Epub 2019 Aug 19.

Section for Microbiology & Center for Geomicrobiology, Department of Bioscience, Aarhus University, 8000 Aarhus, Denmark;

Cable bacteria of the family Desulfobulbaceae form centimeter-long filaments comprising thousands of cells. They occur worldwide in the surface of aquatic sediments, where they connect sulfide oxidation with oxygen or nitrate reduction via long-distance electron transport. In the absence of pure cultures, we used single-filament genomics and metagenomics to retrieve draft genomes of 3 marine Electrothrix and 1 freshwater Electronema species. These genomes contain >50% unknown genes but still share their core genomic makeup with sulfate-reducing and sulfur-disproportionating Desulfobulbaceae, with few core genes lost and 212 unique genes (from 197 gene families) conserved among cable bacteria. Last common ancestor analysis indicates gene divergence and lateral gene transfer as equally important origins of these unique genes. With support from metaproteomics of a Electronema enrichment, the genomes suggest that cable bacteria oxidize sulfide by reversing the canonical sulfate reduction pathway and fix CO using the Wood-Ljungdahl pathway. Cable bacteria show limited organotrophic potential, may assimilate smaller organic acids and alcohols, fix N, and synthesize polyphosphates and polyglucose as storage compounds; several of these traits were confirmed by cell-level experimental analyses. We propose a model for electron flow from sulfide to oxygen that involves periplasmic cytochromes, yet-unidentified conductive periplasmic fibers, and periplasmic oxygen reduction. This model proposes that an active cable bacterium gains energy in the anodic, sulfide-oxidizing cells, whereas cells in the oxic zone flare off electrons through intense cathodic oxygen respiration without energy conservation; this peculiar form of multicellularity seems unparalleled in the microbial world.
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http://dx.doi.org/10.1073/pnas.1903514116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6754541PMC
September 2019

Draft Genome Sequence of Bacillus subtilis SB-14, an Antimicrobially Active Isolate from Namibian Social Spiders ().

Microbiol Resour Announc 2019 Jun 20;8(25). Epub 2019 Jun 20.

Department of Bioscience, Section for Microbiology, Aarhus University, Aarhus, Denmark

We present the high-quality draft genome sequence of SB-14, isolated from the Namibian social spider In accordance with its antimicrobial activity, both known and potentially novel antimicrobial biosynthetic gene clusters were identified in the genome of SB-14.
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http://dx.doi.org/10.1128/MRA.00156-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6588362PMC
June 2019

Marine Deep Biosphere Microbial Communities Assemble in Near-Surface Sediments in Aarhus Bay.

Front Microbiol 2019 12;10:758. Epub 2019 Apr 12.

Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark.

Analyses of microbial diversity in marine sediments have identified a core set of taxa unique to the marine deep biosphere. Previous studies have suggested that these specialized communities are shaped by processes in the surface seabed, in particular that their assembly is associated with the transition from the bioturbated upper zone to the nonbioturbated zone below. To test this hypothesis, we performed a fine-scale analysis of the distribution and activity of microbial populations within the upper 50 cm of sediment from Aarhus Bay (Denmark). Sequencing and qPCR were combined to determine the depth distributions of bacterial and archaeal taxa (16S rRNA genes) and sulfate-reducing microorganisms (SRM) ( gene). Mapping of radionuclides throughout the sediment revealed a region of intense bioturbation at 0-6 cm depth. The transition from bioturbated sediment to the subsurface below (7 cm depth) was marked by a shift from dominant surface populations to common deep biosphere taxa (e.g., Chloroflexi and Atribacteria). Changes in community composition occurred in parallel to drops in microbial activity and abundance caused by reduced energy availability below the mixed sediment surface. These results offer direct evidence for the hypothesis that deep subsurface microbial communities present in Aarhus Bay mainly assemble already centimeters below the sediment surface, below the bioturbation zone.
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http://dx.doi.org/10.3389/fmicb.2019.00758DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6474314PMC
April 2019

Single-Cell Genomics Reveals a Diverse Metabolic Potential of Uncultivated -Related Deltaproteobacteria Widely Distributed in Marine Sediment.

Front Microbiol 2018 3;9:2038. Epub 2018 Sep 3.

Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark.

-related organisms comprise one of the most abundant deltaproteobacterial lineages in marine sediments where they occur throughout the sediment column in a gradient of increasing sulfate and organic carbon limitation with depth. Characterized isolates are dissimilatory sulfate reducers able to grow by degrading aromatic hydrocarbons. The ecophysiology of environmental -populations is poorly understood, however, possibly utilization of aromatic compounds may explain their predominance in marine subsurface sediments. We sequenced and analyzed seven -related single-cell genomes (SAGs) from Aarhus Bay sediments to characterize their metabolic potential with regard to aromatic compound degradation and energy metabolism. The average genome assembly size was 1.3 Mbp and completeness estimates ranged between 20 and 50%. Five of the SAGs (group 1) originated from the sulfate-rich surface part of the sediment while two (group 2) originated from sulfate-depleted subsurface sediment. Based on 16S rRNA gene amplicon sequencing group 2 SAGs represent the more frequent types of -populations in Aarhus Bay sediments. Genes indicative of aromatic compound degradation could be identified in both groups, but the two groups were metabolically distinct with regard to energy conservation. Group 1 SAGs carry a full set of genes for dissimilatory sulfate reduction, whereas the group 2 SAGs lacked any genetic evidence for sulfate reduction. The latter may be due to incompleteness of the SAGs, but as alternative energy metabolisms group 2 SAGs carry the genetic potential for growth by acetogenesis and fermentation. Group 1 SAGs encoded reductive dehalogenase genes, allowing them to access organohalides and possibly conserve energy by their reduction. Both groups possess sulfatases unlike their cultured relatives allowing them to utilize sulfate esters as source of organic carbon and sulfate. In conclusion, the uncultivated marine populations are metabolically diverse, likely reflecting different strategies for coping with energy and sulfate limitation in the subsurface seabed.
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http://dx.doi.org/10.3389/fmicb.2018.02038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6129605PMC
September 2018

Transient bottom water oxygenation creates a niche for cable bacteria in long-term anoxic sediments of the Eastern Gotland Basin.

Environ Microbiol 2018 08 24;20(8):3031-3041. Epub 2018 Jul 24.

Department of Biology, Universiteit Antwerpen, Antwerpen, Belgium.

Cable bacteria have been reported in sediments from marine and freshwater locations, but the environmental factors that regulate their growth in natural settings are not well understood. Most prominently, the physiological limit of cable bacteria in terms of oxygen availability remains poorly constrained. In this study, we investigated the presence, activity and diversity of cable bacteria in relation to a natural gradient in bottom water oxygenation in a depth transect of the Eastern Gotland Basin (Baltic Sea). Cable bacteria were identified by FISH at the oxic and transiently oxic sites, but not at the permanently anoxic site. Three species of the candidate genus Electrothrix, i.e. marina, aarhusiensis and communis were found coexisting within one site. The highest filament density (33 m cm ) was associated with a 6.3 mm wide zone depleted in both oxygen and free sulphide, and the presence of an electric field resulting from the electrogenic sulphur oxidizing metabolism of cable bacteria. However, the measured filament densities and metabolic activities remained low overall, suggesting a limited impact of cable bacteria at the basin level. The observed bottom water oxygen levels (< 5 μM) are the lowest so far reported for cable bacteria, thus expanding their known environmental distribution.
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http://dx.doi.org/10.1111/1462-2920.14349DOI Listing
August 2018

Intracellular nitrate in sediments of an oxygen-deficient marine basin is linked to pelagic diatoms.

FEMS Microbiol Ecol 2018 08;94(8)

Center for Geomicrobiology and Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark.

Intracellular nitrate is an important electron acceptor in oxygen-deficient aquatic environments, either for the nitrate-storing microbes themselves, or for ambient microbial communities through nitrate leakage. This study links the spatial distribution of intracellular nitrate with the abundance and identity of nitrate-storing microbes in sediments of the Bornholm Basin, an environmental showcase for severe hypoxia. Intracellular nitrate (up to 270 nmol cm-3 sediment) was detected at all 18 stations along a 35-km transect through the basin and typically extended as deep as 1.6 cm into the sediment. Intracellular nitrate contents were particularly high at stations where chlorophyll contents suggested high settling rates of pelagic primary production. The depth distribution of intracellular nitrate matched that of the diatom-specific photopigment fucoxanthin in the upper 1.6 cm and calculations support that diatoms are the major nitrate-storing microbes in these sediments. In contrast, other known nitrate-storing microbes, such as sulfide-oxidizing bacteria and foraminifers, played only a minor role, if any. Strikingly, 18S rRNA gene sequencing revealed that the majority of the diatoms in the sediment were pelagic species. We conclude that intracellular nitrate stored by pelagic diatoms is transported to the seafloor by settling phytoplankton blooms, implying a so far overlooked 'biological nitrate pump'.
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http://dx.doi.org/10.1093/femsec/fiy122DOI Listing
August 2018

Long-distance electron transport in individual, living cable bacteria.

Proc Natl Acad Sci U S A 2018 05 7;115(22):5786-5791. Epub 2018 May 7.

Center for Electromicrobiology, Aarhus University, DK-8000 Aarhus C, Denmark;

Electron transport within living cells is essential for energy conservation in all respiring and photosynthetic organisms. While a few bacteria transport electrons over micrometer distances to their surroundings, filaments of cable bacteria are hypothesized to conduct electric currents over centimeter distances. We used resonance Raman microscopy to analyze cytochrome redox states in living cable bacteria. Cable-bacteria filaments were placed in microscope chambers with sulfide as electron source and oxygen as electron sink at opposite ends. Along individual filaments a gradient in cytochrome redox potential was detected, which immediately broke down upon removal of oxygen or laser cutting of the filaments. Without access to oxygen, a rapid shift toward more reduced cytochromes was observed, as electrons were no longer drained from the filament but accumulated in the cellular cytochromes. These results provide direct evidence for long-distance electron transport in living multicellular bacteria.
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http://dx.doi.org/10.1073/pnas.1800367115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5984516PMC
May 2018

Gene expression of terminal oxidases in two marine bacterial strains exposed to nanomolar oxygen concentrations.

FEMS Microbiol Ecol 2018 07;94(7)

Section for Microbiology, Department of Bioscience, Aarhus University, Denmark.

The final step of aerobic respiration is carried out by a terminal oxidase transporting electrons to oxygen (O2). Prokaryotes harbor diverse terminal oxidases that differ in phylogenetic origin, structure, biochemical function, and affinity for O2. Here we report on the expression of high-affinity (cytochrome cbb3 oxidase), low-affinity (cytochrome aa3 oxidase), and putative low-affinity (cyanide-insensitive oxidase (CIO)) terminal oxidases in the marine bacteria Idiomarina loihiensis L2-TR and Marinobacter daepoensis SW-156 upon transition to very low O2 concentrations (<200 nM), measured by RT-qPCR. In both strains, high-affinity cytochrome cbb3 oxidase showed the highest expression levels and was significantly up-regulated upon transition to low O2 concentrations. Low-affinity cytochrome aa3 oxidase showed very low transcription levels throughout the incubation. Surprisingly, however, it was also up-regulated upon transition to low O2 concentrations. In contrast, putative low-affinity CIO had much lower expression levels and markedly different regulation patterns between the two strains. These results demonstrate that exposure to low O2 concentrations regulates the gene expression of different types of terminal oxidases, but also that the type and magnitude of transcriptional response is species-dependent. Therefore, in situ transcriptome data cannot, without detailed knowledge of the transcriptional regulation of the species involved, be translated into relative respiratory activity.
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http://dx.doi.org/10.1093/femsec/fiy072DOI Listing
July 2018

Genomic insights into the Agromyces-like symbiont of earthworms and its distribution among host species.

FEMS Microbiol Ecol 2018 06;94(6)

Section for Microbiology, Department of Bioscience, Aarhus University, Denmark Ny Munkegade 116 8000 Aarhus, Denmark.

The nephridia (excretory organs) of lumbricid earthworms generally harbor symbiotic bacteria. In the compost worms Eisenia fetida and E. andrei, these comprise Verminephrobacter, Ca. Nephrothrix and an Agromyces-like symbiont. While diversity, transmission, and function of the first two symbionts has been unraveled in recent years, little is known about the biology of the uncultured Agromyces-like symbiont or about its distribution within lumbricid earthworms.In this study, we sequenced a cocoon metagenome of E. andrei and assembled a 96.3% complete genome of the Agromyces-like symbiont, which indicates a heterotrophic and potentially microaerophilic lifestyle. A 16S rRNA gene based survey showed that the Agromyces-like symbiont has a narrow host range (present in 10 out of 51 investigated lumbricid earthworm species) and is likely species-specific or at least specific for groups of closely related host species. The Agromyces-like symbionts form a monophyletic group and feature a reduced genome with AT-bias and very low genome-wide similarity to closely related Agromyces spp. (average amino acid identity of 64%); therefore, we suggest establishing a novel genus for the Agromyces-like symbionts of earthworms, for which we propose the name Candidatus Lumbricidophila, with the specific symbiont of Eisenia andrei as novel species Ca. L. eiseniae.
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http://dx.doi.org/10.1093/femsec/fiy068DOI Listing
June 2018

Male spiders control offspring sex ratio through greater production of female-determining sperm.

Proc Biol Sci 2018 03;285(1875)

Department of Bioscience, Section for Genetics, Ecology and Evolution, Aarhus University, Ny Munkegade 114, Building 1540, 8000 Aarhus C, Denmark

Sex allocation theory predicts that when sons and daughters have different reproductive values, parents should adjust offspring sex ratio towards the sex with the higher fitness return. Haplo-diploid species directly control offspring sex ratio, but species with chromosomal sex determination (CSD) were presumed to be constrained by Mendelian segregation. There is now increasing evidence that CSD species can adjust sex ratio strategically, but the underlying mechanism is not well understood. One hypothesis states that adaptive control is more likely to evolve in the heterogametic sex through a bias in gamete production. We investigated this hypothesis in males as the heterogametic sex in two social spider species that consistently show adaptive female-biased sex ratio and in one subsocial species that is characterized by equal sex ratio. We quantified the production of male (0) and female (X) determining sperm cells using flow cytometry, and show that males of social species produce significantly more X-carrying sperm than 0-sperm, on average 70%. This is consistent with the production of more daughters. Males of the subsocial species produced a significantly lower bias of 54% X-carrying sperm. We also investigated whether inter-genomic conflict between hosts and their endosymbionts may explain female bias. Next generation sequencing showed that five common genera of bacterial endosymbionts known to affect sex ratio are largely absent, ruling out that endosymbiont bacteria bias sex ratio in social spiders. Our study provides evidence for paternal control over sex allocation through biased gamete production as a mechanism by which the heterogametic sex in CSD species adaptively adjust offspring sex ratio.
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http://dx.doi.org/10.1098/rspb.2017.2887DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5897641PMC
March 2018

Distinct effects of the nephridial symbionts Verminephrobacter and Candidatus Nephrothrix on reproduction and maturation of its earthworm host Eisenia andrei.

FEMS Microbiol Ecol 2018 02;94(2)

Section for Microbiology, Department of Bioscience, Aarhus University, 8000 Aarhus, Denmark.

Verminephrobacter, the most common specific symbionts in the nephridia (excretory organs) of lumbricid earthworms, have been shown to improve reproduction of the garden earthworm Aporrectodea tuberculata under nutrient limitation. It is unknown how general this beneficial trait is in the Verminephrobacter-earthworm symbiosis, whether other nephridial symbionts also affect host fitness and what the mechanism of the fitness increase is. Here we report beneficial effects of Verminephrobacter and Candidatus Nephrothrix on life history traits of the compost worm Eisenia andrei, which in addition to these two symbionts also hosts Agromyces-like bacteria in its mixed nephridial community: while growth was identical between control, Verminephrobacter-free and aposymbiotic worms, control worms produced significantly more cocoons and offspring than both Verminephrobacter-free and aposymbiotic worms, confirming the reproductive benefit of Verminephrobacter in a second host with different ecology and feeding behavior. Furthermore, worms with Verminephrobacter and Ca. Nephrothrix, or with only Ca. Nephrothrix present, reached sexual maturity significantly earlier than aposymbiotic worms; this is the first evidence for a beneficial role of Ca. Nephrothrix in earthworms. Riboflavin content in cocoons and whole earthworms was unaffected by the presence or absence of nephridial symbionts, suggesting that nutritional supplementation with this vitamin does not play a major role in this symbiosis.
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http://dx.doi.org/10.1093/femsec/fix178DOI Listing
February 2018

Depth Distribution and Assembly of Sulfate-Reducing Microbial Communities in Marine Sediments of Aarhus Bay.

Appl Environ Microbiol 2017 Dec 16;83(23). Epub 2017 Nov 16.

Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark

Most sulfate-reducing microorganisms (SRMs) present in subsurface marine sediments belong to uncultured groups only distantly related to known SRMs, and it remains unclear how changing geochemical zones and sediment depth influence their community structure. We mapped the community composition and abundance of SRMs by amplicon sequencing and quantifying the gene, which encodes dissimilatory sulfite reductase subunit beta, in sediment samples covering different vertical geochemical zones ranging from the surface sediment to the deep sulfate-depleted subsurface at four locations in Aarhus Bay, Denmark. SRMs were present in all geochemical zones, including sulfate-depleted methanogenic sediment. The biggest shift in SRM community composition and abundance occurred across the transition from bioturbated surface sediments to nonbioturbated sediments below, where redox fluctuations and the input of fresh organic matter due to macrofaunal activity are absent. SRM abundance correlated with sulfate reduction rates determined for the same sediments. Sulfate availability showed a weaker correlation with SRM abundances and no significant correlation with the composition of the SRM community. The overall SRM species diversity decreased with depth, yet we identified a subset of highly abundant community members that persists across all vertical geochemical zones of all stations. We conclude that subsurface SRM communities assemble by the persistence of members of the surface community and that the transition from the bioturbated surface sediment to the unmixed sediment below is a main site of assembly of the subsurface SRM community. Sulfate-reducing microorganisms (SRMs) are key players in the marine carbon and sulfur cycles, especially in coastal sediments, yet little is understood about the environmental factors controlling their depth distribution. Our results suggest that macrofaunal activity is a key driver of SRM abundance and community structure in marine sediments and that a small subset of SRM species of high relative abundance in the subsurface SRM community persists from the sulfate-rich surface sediment to sulfate-depleted methanogenic subsurface sediment. More generally, we conclude that SRM communities inhabiting the subsurface seabed assemble by the selective survival of members of the surface community.
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http://dx.doi.org/10.1128/AEM.01547-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5691419PMC
December 2017

Visualizing the dental biofilm matrix by means of fluorescence lectin-binding analysis.

J Oral Microbiol 2017 9;9(1):1345581. Epub 2017 Jul 9.

Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark.

The extracellular matrix is a poorly studied, yet important component of dental biofilms. Fluorescence lectin-binding analysis (FLBA) is a powerful tool to characterize glycoconjugates in the biofilm matrix. This study aimed to systematically investigate the ability of 75 fluorescently labeled lectins to visualize and quantify extracellular glycoconjugates in dental biofilms. Lectin binding was screened on pooled supragingival biofilm samples collected from 76 subjects using confocal microscopy. FLBA was then performed with 10 selected lectins on biofilms grown for 48 h in the absence of sucrose. For five lectins that proved particularly suitable, stained biovolumes were quantified and correlated to the bacterial composition of the biofilms. Additionally, combinations of up to three differently labeled lectins were tested. Of the 10 lectins, five bound particularly well in 48-h-biofilms: (AAL), (Calsepa), (LEA), (MNA-G) and (HPA). No significant correlation between the binding of specific lectins and bacterial composition was found. Fluorescently labeled lectins enable the visualization of glycoconjugates in the dental biofilm matrix. The characterization and quantification of glycoconjugates in dental biofilms require a combination of several lectins. For 48-h-biofilms grown in absence of sucrose, AAL, Calsepa, HPA, LEA, and MNA-G are recommendable.
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http://dx.doi.org/10.1080/20002297.2017.1345581DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5508396PMC
July 2017

Disguised as a Sulfate Reducer: Growth of the Deltaproteobacterium by Sulfide Oxidation with Nitrate.

mBio 2017 07 18;8(4). Epub 2017 Jul 18.

Center for Geomicrobiology, Aarhus University, Aarhus, Denmark

This study demonstrates that the deltaproteobacterium can grow chemolithotrophically by coupling sulfide oxidation to the dissimilatory reduction of nitrate and nitrite to ammonium. Key genes of known sulfide oxidation pathways are absent from the genome of Instead, the genome contains all of the genes necessary for sulfate reduction, including a gene for a reductive-type dissimilatory bisulfite reductase (DSR). Despite this, growth by sulfate reduction was not observed. Transcriptomic analysis revealed a very high expression level of sulfate-reduction genes during growth by sulfide oxidation, while inhibition experiments with molybdate pointed to elemental sulfur/polysulfides as intermediates. Consequently, we propose that initially oxidizes sulfide to elemental sulfur, which is then either disproportionated, or oxidized by a reversal of the sulfate reduction pathway. This is the first study providing evidence that a reductive-type DSR is involved in a sulfide oxidation pathway. Transcriptome sequencing further suggests that nitrate reduction to ammonium is performed by a novel type of periplasmic nitrate reductase and an unusual membrane-anchored nitrite reductase. Sulfide oxidation and sulfate reduction, the two major branches of the sulfur cycle, are usually ascribed to distinct sets of microbes with distinct diagnostic genes. Here we show a more complex picture, as , with the genomic setup of a sulfate reducer, grows by sulfide oxidation. The high expression of genes typically involved in the sulfate reduction pathway suggests that these genes, including the reductive-type dissimilatory bisulfite reductases, are also involved in as-yet-unresolved sulfide oxidation pathways. Finally, is closely related to cable bacteria, which grow by electrogenic sulfide oxidation. Since there are no pure cultures of cable bacteria, may represent an exciting model organism in which to study the physiology of this process.
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http://dx.doi.org/10.1128/mBio.00671-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5516251PMC
July 2017

The novel bacterial phylum Calditrichaeota is diverse, widespread and abundant in marine sediments and has the capacity to degrade detrital proteins.

Environ Microbiol Rep 2017 08 27;9(4):397-403. Epub 2017 Jun 27.

Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Denmark.

Calditrichaeota is a recently recognized bacterial phylum with three cultured representatives, isolated from hydrothermal vents. Here we expand the phylogeny and ecology of this novel phylum with metagenome-derived and single-cell genomes from six uncultivated bacteria previously not recognized as members of Calditrichaeota. Using 16S rRNA gene sequences from these genomes, we then identified 322 16S rRNA gene sequences from cultivation-independent studies that can now be classified as Calditrichaeota for the first time. This dataset was used to re-analyse a collection of 16S rRNA gene amplicon datasets from marine sediments showing that the Calditrichaeota are globally distributed in the seabed at high abundance, making up to 6.7% of the total bacterial community. This wide distribution and high abundance of Calditrichaeota in cold marine sediment has gone unrecognized until now. All Calditrichaeota genomes show indications of a chemoorganoheterotrophic metabolism with the potential to degrade detrital proteins through the use of extracellular peptidases. Most of the genomes contain genes encoding proteins that confer O tolerance, consistent with the relatively high abundance of Calditrichaeota in surficial bioturbated part of the seabed and, together with the genes encoding extracellular peptidases, suggestive of a general ecophysiological niche for this newly recognized phylum in marine sediment.
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http://dx.doi.org/10.1111/1758-2229.12544DOI Listing
August 2017

Biparental transmission of Verminephrobacter symbionts in the earthworm Aporrectodea tuberculata (Lumbricidae).

FEMS Microbiol Ecol 2017 05;93(5)

Section for Microbiology, Department of Bioscience, Aarhus University, Ny Munkegade 116, Building 1540, 8000 Aarhus-C, Denmark.

Most lumbricid earthworms harbor species-specific Verminephrobacter symbionts in their excretory organs (nephridia). These symbionts are vertically transmitted via the cocoon, where they colonize the embryos. Despite cospeciation for >100 million years with their hosts, Verminephrobacter lack genome reduction and AT bias typical of evolutionary old, vertically transmitted symbionts, caused by recurring bottlenecks. We hypothesized that biparental symbiont transmission into the cocoon enabled genetic mixing and relieved the bottleneck, and tested biparental transmission experimentally for V. aporrectodeae subsp. tuberculata, the specific symbiont of the earthworm Aporrectodea tuberculata, for which aposymbiotic worm lines are available. Virgin symbiotic and aposymbiotic adult worms were tagged, mated in pairs, separated before the start of cocoon production and their offspring assessed for Verminephrobacter. Specific PCR detected the symbionts in 41.5% of 188 juveniles produced by 20 aposymbiotic worms; fluorescence in situ hybridization showed a patchy but successful colonization of their nephridia. Symbionts were present in the mucus but absent in feed, soil, and spermatophora/nephridia of the aposymbiotic partner, suggesting symbiont transfer via mucus during mating. These results are consistent with the hypothesis that genome evolution in Verminephrobacter is distinct from other vertical-ly transmitted symbionts due to genetic mixing during transmission, partially facilitated by biparental transmission.
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http://dx.doi.org/10.1093/femsec/fix025DOI Listing
May 2017

Microbial community assembly and evolution in subseafloor sediment.

Proc Natl Acad Sci U S A 2017 03 27;114(11):2940-2945. Epub 2017 Feb 27.

Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, 8000 Aarhus C, Denmark;

Bacterial and archaeal communities inhabiting the subsurface seabed live under strong energy limitation and have growth rates that are orders of magnitude slower than laboratory-grown cultures. It is not understood how subsurface microbial communities are assembled and whether populations undergo adaptive evolution or accumulate mutations as a result of impaired DNA repair under such energy-limited conditions. Here we use amplicon sequencing to explore changes of microbial communities during burial and isolation from the surface to the >5,000-y-old subsurface of marine sediment and identify a small core set of mostly uncultured bacteria and archaea that is present throughout the sediment column. These persisting populations constitute a small fraction of the entire community at the surface but become predominant in the subsurface. We followed patterns of genome diversity with depth in four dominant lineages of the persisting populations by mapping metagenomic sequence reads onto single-cell genomes. Nucleotide sequence diversity was uniformly low and did not change with age and depth of the sediment. Likewise, there was no detectable change in mutation rates and efficacy of selection. Our results indicate that subsurface microbial communities predominantly assemble by selective survival of taxa able to persist under extreme energy limitation.
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http://dx.doi.org/10.1073/pnas.1614190114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5358386PMC
March 2017

High quality draft genome sequence of sp. nov., isolated from a frozen freshwater pond.

Stand Genomic Sci 2017 19;12. Epub 2017 Jan 19.

Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark.

Strain S3-2, isolated from sediment of a frozen freshwater pond, shares 99% 16S rRNA gene sequence identity with strains of the genus . Strain S3-2 is a facultative anaerobe that lacks the ability to produce violacein but shows antibiotic resistance, psychrotolerance, incomplete denitrification, and fermentation. The draft genome of strain S3-2 has a size of ~5.8 Mbp and contains 5,297 genes, including 115 RNA genes. Based on the phenotypic properties of the strain, the low DNA-DNA hybridization (DDH) values with related genomes (<35%), and the low whole genome-based average nucleotide identity (ANI) (<86%) with other strains within the genus we propose that strain S3-2 is the type strain (= DSM 102223 = LMG 29653) of a new species within this genus. We propose the name sp. nov. to emphasize the capability of the strain to grow at low temperatures.
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http://dx.doi.org/10.1186/s40793-017-0230-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5244535PMC
January 2017
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