Publications by authors named "Kasper U Kjeldsen"

30 Publications

  • Page 1 of 1

Response to substrate limitation by a marine sulfate-reducing bacterium.

ISME J 2021 Jul 20. Epub 2021 Jul 20.

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

Sulfate-reducing microorganisms (SRM) in subsurface sediments live under constant substrate and energy limitation, yet little is known about how they adapt to this mode of life. We combined controlled chemostat cultivation and transcriptomics to examine how the marine sulfate reducer, Desulfobacterium autotrophicum, copes with substrate (sulfate or lactate) limitation. The half-saturation uptake constant (K) for lactate was 1.2 µM, which is the first value reported for a marine SRM, while the K for sulfate was 3 µM. The measured residual lactate concentration in our experiments matched values observed in situ in marine sediments, supporting a key role of SRM in the control of lactate concentrations. Lactate limitation resulted in complete lactate oxidation via the Wood-Ljungdahl pathway and differential overexpression of genes involved in uptake and metabolism of amino acids as an alternative carbon source. D. autotrophicum switched to incomplete lactate oxidation, rerouting carbon metabolism in response to sulfate limitation. The estimated free energy was significantly lower during sulfate limitation (-28 to -33 kJ mol sulfate), suggesting that the observed metabolic switch is under thermodynamic control. Furthermore, we detected the upregulation of putative sulfate transporters involved in either high or low affinity uptake in response to low or high sulfate concentration.
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http://dx.doi.org/10.1038/s41396-021-01061-2DOI Listing
July 2021

Identity and hydrocarbon degradation activity of enriched microorganisms from natural oil and asphalt seeps in the Kurdistan Region of Iraq (KRI).

Biodegradation 2021 06 29;32(3):251-271. Epub 2021 Mar 29.

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

A previous cultivation-independent investigation of the microbial community structure of natural oil and asphalt seeps in the Kurdistan Region of Iraq (KRI) revealed the dominance of uncultured bacterial taxa belonging to the phyla Deferribacterota and Coprothermobacterota and the orders Thermodesulfobacteriales, Thermales, and Burkholderiales. Here we report on a cultivation-dependent approach to identify members of these groups involved in hydrocarbon degradation in the KRI oil and asphalt seeps. For this purpose, we set up anoxic crude oil-degrading enrichment cultures based on cultivation media known to support the growth of members of the above-mentioned taxonomic groups. During 100-200 days incubation periods, nitrate-reducing and fermentative enrichments showed up to 90% degradation of C-C alkanes and up to 28% degradation of C-C alkanes along with aromatic hydrocarbons. Community profiling of the enrichment cultures showed that they were dominated by diverse bacterial taxa, which were rare in situ community members in the investigated seeps. Groups initially targeted by our approach were not enriched, possibly because their members are slow-growing and involved in the degradation of recalcitrant hydrocarbons. Nevertheless, the enriched taxa were taxonomically related to phylotypes recovered from hydrocarbon-impacted environments as well as to characterized bacterial isolates not previously known to be involved in hydrocarbon degradation. Marker genes (assA and bssA), diagnostic for fumarate addition-based anaerobic hydrocarbon degradation, were not detectable in the enrichment cultures by PCR. We conclude that hydrocarbon biodegradation in our enrichments occurred via unknown pathways and synergistic interactions among the enriched taxa. We suggest, that although not representing abundant populations in situ, studies of the cultured close relatives of these taxa will reveal an unrecognized potential for anaerobic hydrocarbon degradation, possibly involving poorly characterized mechanisms.
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http://dx.doi.org/10.1007/s10532-021-09931-4DOI Listing
June 2021

Physicochemical and biological controls of sulfide accumulation in a high temperature oil reservoir.

Appl Microbiol Biotechnol 2020 Oct 21;104(19):8467-8478. Epub 2020 Aug 21.

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

In order to maintain the reservoir pressure during secondary oil production large volumes of seawater are injected into reservoirs. This practice introduces high concentrations of sulfate into the reservoir promoting the growth of sulfate-reducing microorganisms (SRM) and results in the production of an increasing volume of produced water (PW) that needs to be discharged. SRM reduce sulfate to sulfide causing reservoir souring and as a mitigation strategy nitrate is injecting along with the seawater into the reservoir. We used PW from the Halfdan oil field (North Sea) to set up microcosms to determine the best reinjection strategy in order to inhibit SRM activity and minimize the environmental impact of PW during secondary oil production. We discuss the effect of temperature, electron donor, and sulfate and nitrate availability on sulfide production and microbial community composition. Temperature and the terminal electron acceptor played a key role in shaping the microbial community of the microcosms. PW reinjection at 62 °C inhibited SRM activity due to nitrite toxicity by encouraging nitrate reduction to nitrite by thermophilic nitrate reducers, while at 74 °C we observed complete absence of any microbial activity over the course of 150 days. KEY POINTS: • Temperature and the presence/ absence of nitrate shaped the microbial community structure. • Thermophilic nitrate reducers convert nitrate to ammonia with the accumulation of nitrite that inhibits sulfide production. • Nitrite inhibition is the most effective nitrate-based souring mitigation mechanisms. • The reinjection of hot produced water to oil reservoirs is a promising souring mitigation approach.
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http://dx.doi.org/10.1007/s00253-020-10828-0DOI Listing
October 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

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

Environmental filtering determines family-level structure of sulfate-reducing microbial communities in subsurface marine sediments.

ISME J 2019 08 20;13(8):1920-1932. Epub 2019 Mar 20.

Section for Microbiology and Center for Geomicrobiology, Department of Bioscience, Aarhus University, Ny Munkegade 114, Aarhus, 8000, Denmark.

Recent work has shown that subsurface microbial communities assemble by selective survival of surface community members during sediment burial, but it remains unclear to what extent the compositions of the subsurface communities are a product of their founding population at the sediment surface or of the changing geochemical conditions during burial. Here we investigate this question for communities of sulfate-reducing microorganisms (SRMs). We collected marine sediment samples from the upper 3-5 m at four geochemically contrasting sites in the Skagerrak and Baltic Sea and measured SRM abundance (quantitative PCR of dsrB), metabolic activity (radiotracer rate measurements), and community composition (Illumina sequencing of dsrB amplicons). These data showed that SRM abundance, richness, and phylogenetic clustering as determined by the nearest taxon index peaked below the bioturbation zone and above the depth of sulfate depletion. Minimum cell-specific rates of sulfate reduction did not vary substantially between sites. SRM communities at different sites were best distinguished based on their composition of amplicon sequence variants (ASVs), while communities in different geochemical zones were best distinguished based on their composition of SRM families. This demonstrates environmental filtering of SRM communities in sediment while a site-specific fingerprint of the founding community is retained.
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http://dx.doi.org/10.1038/s41396-019-0387-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6658220PMC
August 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

Bacterial interactions during sequential degradation of cyanobacterial necromass in a sulfidic arctic marine sediment.

Environ Microbiol 2018 08 3;20(8):2927-2940. Epub 2018 Sep 3.

Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria.

Seafloor microorganisms impact global carbon cycling by mineralizing vast quantities of organic matter (OM) from pelagic primary production, which is predicted to increase in the Arctic because of diminishing sea ice cover. We studied microbial interspecies-carbon-flow during anaerobic OM degradation in arctic marine sediment using stable isotope probing. We supplemented sediment incubations with C-labeled cyanobacterial necromass (spirulina), mimicking fresh OM input, or acetate, an important OM degradation intermediate and monitored sulfate reduction rates and concentrations of volatile fatty acids (VFAs) during substrate degradation. Sequential 16S rRNA gene and transcript amplicon sequencing and fluorescence in situ hybridization combined with Raman microspectroscopy revealed that only few bacterial species were the main degraders of C-spirulina necromass. Psychrilyobacter, Psychromonas, Marinifilum, Colwellia, Marinilabiaceae and Clostridiales species were likely involved in the primary hydrolysis and fermentation of spirulina. VFAs, mainly acetate, produced from spirulina degradation were mineralized by sulfate-reducing bacteria and an Arcobacter species. Cellular activity of Desulfobacteraceae and Desulfobulbaceae species during acetoclastic sulfate reduction was largely decoupled from relative 16S rRNA gene abundance shifts. Our findings provide new insights into the identities and physiological constraints that determine the population dynamics of key microorganisms during complex OM degradation in arctic marine sediments.© 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.
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http://dx.doi.org/10.1111/1462-2920.14297DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6175234PMC
August 2018

Bacterial community succession and degradation patterns of hydrocarbons in seawater at low temperature.

J Hazard Mater 2018 07 7;353:127-134. Epub 2018 Apr 7.

Arctic Research Centre, Department of Bioscience, Aarhus University, Aarhus, Denmark; Center for Earth and Observation Science, University of Manitoba, Winnipeg, Canada.

The risk of oil spills in cold marine environments is expected to increase in response to trans-Arctic shipping and as Arctic oil reserves get exploited. Marine hydrocarbon-degrading microbes can reduce the impact of spilled hydrocarbons, but their degradation capabilities at low temperature are yet to be uncovered. We combined DNA amplicon sequencing and chemometrics to investigate the effect of decreasing temperature (0-15 °C) on the succession and function of hydrocarbon-degrading bacteria in seawater. The bacterial community and degradation patterns were investigated at time points when a similar amount of hydrocarbons was mineralised at the different temperatures. This allowed decomposing the effect of temperature into a main component related to the reduced microbial activity at low temperature and a secondary effect. The reduced microbial activity at low temperature delayed the microbial community succession and degradation rates. The secondary effect of temperature was most pronounced at 0 °C, where (1) degradation of the least water-soluble n-alkanes (>C12) was suppressed in contrast to a relative stronger degradation of the most water-soluble n-alkanes (
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http://dx.doi.org/10.1016/j.jhazmat.2018.03.051DOI Listing
July 2018

Sulfate Transporters in Dissimilatory Sulfate Reducing Microorganisms: A Comparative Genomics Analysis.

Front Microbiol 2018 2;9:309. Epub 2018 Mar 2.

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

The first step in the sulfate reduction pathway is the transport of sulfate across the cell membrane. This uptake has a major effect on sulfate reduction rates. Much of the information available on sulfate transport was obtained by studies on assimilatory sulfate reduction, where sulfate transporters were identified among several types of protein families. Despite our growing knowledge on the physiology of dissimilatory sulfate-reducing microorganisms (SRM) there are no studies identifying the proteins involved in sulfate uptake in members of this ecologically important group of anaerobes. We surveyed the complete genomes of 44 sulfate-reducing bacteria and archaea across six phyla and identified putative sulfate transporter encoding genes from four out of the five surveyed protein families based on homology. We did not find evidence that ABC-type transporters (SulT) are involved in the uptake of sulfate in SRM. We speculate that members of the CysP sulfate transporters could play a key role in the uptake of sulfate in thermophilic SRM. Putative CysZ-type sulfate transporters were present in all genomes examined suggesting that this overlooked group of sulfate transporters might play a role in sulfate transport in dissimilatory sulfate reducers alongside SulP. Our analysis highlights several targets for further molecular studies in order to understand this key step in the metabolism of SRMs.
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http://dx.doi.org/10.3389/fmicb.2018.00309DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5840216PMC
March 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

Microbial turnover times in the deep seabed studied by amino acid racemization modelling.

Sci Rep 2017 07 18;7(1):5680. Epub 2017 Jul 18.

Center for Geomicrobiology, Department of Bioscience, Aarhus University, Ny Munkegade 114, 8000, Aarhus C, Denmark.

The study of active microbial populations in deep, energy-limited marine sediments has extended our knowledge of the limits of life on Earth. Typically, microbial activity in the deep biosphere is calculated by transport-reaction modelling of pore water solutes or from experimental measurements involving radiotracers. Here we modelled microbial activity from the degree of D:L-aspartic acid racemization in microbial necromass (remains of dead microbial biomass) in sediments up to ten million years old. This recently developed approach (D:L-amino acid modelling) does not require incubation experiments and is highly sensitive in stable, low-activity environments. We applied for the first time newly established constraints on several important input parameters of the D:L-amino acid model, such as a higher aspartic acid racemization rate constant and a lower cell-specific carbon content of sub-seafloor microorganisms. Our model results show that the pool of necromass amino acids is turned over by microbial activity every few thousand years, while the turnover times of vegetative cells are in the order of years to decades. Notably, microbial turnover times in million-year-old sediment from the Peru Margin are up to 100-fold shorter than previous estimates, highlighting the influence of microbial activities on element cycling over geologic time scales.
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http://dx.doi.org/10.1038/s41598-017-05972-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5516024PMC
July 2017

Concurrent Methane Production and Oxidation in Surface Sediment from Aarhus Bay, Denmark.

Front Microbiol 2017 30;8:1198. Epub 2017 Jun 30.

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

Marine surface sediments, which are replete with sulfate, are typically considered to be devoid of endogenous methanogenesis. Yet, methanogenic archaea are present in those sediments, suggesting a potential for methanogenesis. We used an isotope dilution method based on sediment bag incubation and spiking with C-CH to quantify CH turnover rates in sediment from Aarhus Bay, Denmark. In two independent experiments, highest CH production and oxidation rates (>200 pmol cm d) were found in the top 0-2 cm, below which rates dropped below 100 pmol cm d in all other segments down to 16 cm. This drop in overall methane turnover with depth was accompanied by decreasing rates of organic matter mineralization with depth. Molecular analyses based on quantitative PCR and MiSeq sequencing of archaeal 16S rRNA genes showed that the abundance of methanogenic archaea also peaked in the top 0-2 cm segment. Based on the community profiling, hydrogenotrophic and methylotrophic methanogens dominated among the methanogenic archaea in general, suggesting that methanogenesis in surface sediment could be driven by both CO reduction and fermentation of methylated compounds. Our results show the existence of elevated methanogenic activity and a dynamic recycling of CH at low concentration in sulfate-rich marine surface sediment. Considering the common environmental conditions found in other coastal systems, we speculate that such a cryptic methane cycling can be ubiquitous.
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http://dx.doi.org/10.3389/fmicb.2017.01198DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5492102PMC
June 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

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

Identity, Abundance, and Reactivation Kinetics of Thermophilic Fermentative Endospores in Cold Marine Sediment and Seawater.

Front Microbiol 2017 6;8:131. Epub 2017 Feb 6.

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

Cold marine sediments harbor endospores of fermentative and sulfate-reducing, thermophilic bacteria. These dormant populations of endospores are believed to accumulate in the seabed via passive dispersal by ocean currents followed by sedimentation from the water column. However, the magnitude of this process is poorly understood because the endospores present in seawater were so far not identified, and only the abundance of thermophilic sulfate-reducing endospores in the seabed has been quantified. We investigated the distribution of thermophilic fermentative endospores (TFEs) in water column and sediment of Aarhus Bay, Denmark, to test the role of suspended dispersal and determine the rate of endospore deposition and the endospore abundance in the sediment. We furthermore aimed to determine the time course of reactivation of the germinating TFEs. TFEs were induced to germinate and grow by incubating pasteurized sediment and water samples anaerobically at 50°C. We observed a sudden release of the endospore component dipicolinic acid immediately upon incubation suggesting fast endospore reactivation in response to heating. Volatile fatty acids (VFAs) and H began to accumulate exponentially after 3.5 h of incubation showing that reactivation was followed by a short phase of outgrowth before germinated cells began to divide. Thermophilic fermenters were mainly present in the sediment as endospores because the rate of VFA accumulation was identical in pasteurized and non-pasteurized samples. Germinating TFEs were identified taxonomically by reverse transcription, PCR amplification and sequencing of 16S rRNA. The water column and sediment shared the same phylotypes, thereby confirming the potential for seawater dispersal. The abundance of TFEs was estimated by most probable number enumeration, rates of VFA production, and released amounts of dipicolinic acid during germination. The surface sediment contained ∼10-10 inducible TFEs cm. TFEs thus outnumber thermophilic sulfate-reducing endospores by an order of magnitude. The abundance of cultivable TFEs decreased exponentially with sediment depth with a half-life of 350 years. We estimate that 6 × 10 anaerobic thermophilic endospores are deposited on the seafloor per m per year in Aarhus Bay, and that these thermophiles represent >10% of the total endospore community in the surface sediment.
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http://dx.doi.org/10.3389/fmicb.2017.00131DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5292427PMC
February 2017

Asgard archaea illuminate the origin of eukaryotic cellular complexity.

Nature 2017 01 11;541(7637):353-358. Epub 2017 Jan 11.

Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden.

The origin and cellular complexity of eukaryotes represent a major enigma in biology. Current data support scenarios in which an archaeal host cell and an alphaproteobacterial (mitochondrial) endosymbiont merged together, resulting in the first eukaryotic cell. The host cell is related to Lokiarchaeota, an archaeal phylum with many eukaryotic features. The emergence of the structural complexity that characterizes eukaryotic cells remains unclear. Here we describe the 'Asgard' superphylum, a group of uncultivated archaea that, as well as Lokiarchaeota, includes Thor-, Odin- and Heimdallarchaeota. Asgard archaea affiliate with eukaryotes in phylogenomic analyses, and their genomes are enriched for proteins formerly considered specific to eukaryotes. Notably, thorarchaeal genomes encode several homologues of eukaryotic membrane-trafficking machinery components, including Sec23/24 and TRAPP domains. Furthermore, we identify thorarchaeal proteins with similar features to eukaryotic coat proteins involved in vesicle biogenesis. Our results expand the known repertoire of 'eukaryote-specific' proteins in Archaea, indicating that the archaeal host cell already contained many key components that govern eukaryotic cellular complexity.
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http://dx.doi.org/10.1038/nature21031DOI Listing
January 2017

Endozoicomonas Are Specific, Facultative Symbionts of Sea Squirts.

Front Microbiol 2016 12;7:1042. Epub 2016 Jul 12.

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

Ascidians are marine filter feeders and harbor diverse microbiota that can exhibit a high degree of host-specificity. Pharyngeal samples of Scandinavian and Mediterranean ascidians were screened for consistently associated bacteria by culture-dependent and -independent approaches. Representatives of the Endozoicomonas (Gammaproteobacteria, Hahellaceae) clade were detected in the ascidian species Ascidiella aspersa, Ascidiella scabra, Botryllus schlosseri, Ciona intestinalis, Styela clava, and multiple Ascidia/Ascidiella spp. In total, Endozoicomonas was detected in more than half of all specimens screened, and in 25-100% of the specimens for each species. The retrieved Endozoicomonas 16S rRNA gene sequences formed an ascidian-specific subclade, whose members were detected by fluorescence in situ hybridization (FISH) as extracellular microcolonies in the pharynx. Two strains of the ascidian-specific Endozoicomonas subclade were isolated in pure culture and characterized. Both strains are chemoorganoheterotrophs and grow on mucin (a mucus glycoprotein). The strains tested negative for cytotoxic or antibacterial activity. Based on these observations, we propose ascidian-associated Endozoicomonas to be commensals, living off the mucus continuously secreted into the pharynx. Members of the ascidian-specific Endozoicomonas subclade were also detected in seawater from the Scandinavian sampling site, which suggests acquisition of the symbionts by horizontal transmission. The combined results indicate a host-specific, yet facultative symbiosis between ascidians and Endozoicomonas.
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http://dx.doi.org/10.3389/fmicb.2016.01042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4940369PMC
July 2016

A taxonomic framework for cable bacteria and proposal of the candidate genera Electrothrix and Electronema.

Syst Appl Microbiol 2016 Jul 6;39(5):297-306. Epub 2016 Jun 6.

Section for Microbiology & Center for Geomicrobiology, Department of Bioscience, Aarhus University, Ny Munkegade 114, 8000 Aarhus C, Denmark. Electronic address:

Cable bacteria are long, multicellular filaments that can conduct electric currents over centimeter-scale distances. All cable bacteria identified to date belong to the deltaproteobacterial family Desulfobulbaceae and have not been isolated in pure culture yet. Their taxonomic delineation and exact phylogeny is uncertain, as most studies so far have reported only short partial 16S rRNA sequences or have relied on identification by a combination of filament morphology and 16S rRNA-targeted fluorescence in situ hybridization with a Desulfobulbaceae-specific probe. In this study, nearly full-length 16S rRNA gene sequences of 16 individual cable bacteria filaments from freshwater, salt marsh, and marine sites of four geographic locations are presented. These sequences formed a distinct, monophyletic sister clade to the genus Desulfobulbus and could be divided into six coherent, species-level clusters, arranged as two genus-level groups. The same grouping was retrieved by phylogenetic analysis of full or partial dsrAB genes encoding the dissimilatory sulfite reductase. Based on these results, it is proposed to accommodate cable bacteria within two novel candidate genera: the mostly marine "Candidatus Electrothrix", with four candidate species, and the mostly freshwater "Candidatus Electronema", with two candidate species. This taxonomic framework can be used to assign environmental sequences confidently to the cable bacteria clade, even without morphological information. Database searches revealed 185 16S rRNA gene sequences that affiliated within the clade formed by the proposed cable bacteria genera, of which 120 sequences could be assigned to one of the six candidate species, while the remaining 65 sequences indicated the existence of up to five additional species.
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http://dx.doi.org/10.1016/j.syapm.2016.05.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4958695PMC
July 2016

A Novel Extracellular Gut Symbiont in the Marine Worm Priapulus caudatus (Priapulida) Reveals an Alphaproteobacterial Symbiont Clade of the Ecdysozoa.

Front Microbiol 2016 26;7:539. Epub 2016 Apr 26.

Section for Genetics, Ecology, and Evolution, Department of Bioscience, Aarhus University Aarhus, Denmark.

Priapulus caudatus (phylum Priapulida) is a benthic marine predatory worm with a cosmopolitan distribution. In its digestive tract we detected symbiotic bacteria that were consistently present in specimens collected over 8 years from three sites at the Swedish west coast. Based on their 16S rRNA gene sequence, these symbionts comprise a novel genus of the order Rickettsiales (Alphaproteobacteria). Electron microscopy and fluorescence in situ hybridization (FISH) identified them as extracellular, elongate bacteria closely associated with the microvilli, for which we propose the name "Candidatus Tenuibacter priapulorum". Within Rickettsiales, they form a phylogenetically well-defined, family-level clade with uncultured symbionts of marine, terrestrial, and freshwater arthropods. Cand. Tenuibacter priapulorum expands the host range of this candidate family from Arthropoda to the entire Ecdysozoa, which may indicate an evolutionary adaptation of this bacterial group to the microvilli-lined guts of the Ecdysozoa.
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http://dx.doi.org/10.3389/fmicb.2016.00539DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4844607PMC
May 2016

Ubiquitous Presence and Novel Diversity of Anaerobic Alkane Degraders in Cold Marine Sediments.

Front Microbiol 2015 17;6:1414. Epub 2015 Dec 17.

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

Alkanes are major constituents of crude oil and are released to the marine environment by natural seepage and from anthropogenic sources. Due to their chemical inertness, their removal from anoxic marine sediments is primarily controlled by the activity of anaerobic alkane-degrading microorganisms. To facilitate comprehensive cultivation-independent surveys of the diversity and distribution of anaerobic alkane degraders, we designed novel PCR primers that cover all known diversity of the 1-methylalkyl succinate synthase gene (masD/assA), which catalyzes the initial activation of alkanes. We studied masD/assA gene diversity in pristine and seepage-impacted Danish coastal sediments, as well as in sediments and alkane-degrading enrichment cultures from the Middle Valley (MV) hydrothermal vent system in the Pacific Northwest. MasD/assA genes were ubiquitously present, and the primers captured the diversity of both known and previously undiscovered masD/assA gene diversity. Seepage sediments were dominated by a single masD/assA gene cluster, which is presumably indicative of a substrate-adapted community, while pristine sediments harbored a diverse range of masD/assA phylotypes including those present in seepage sediments. This rare biosphere of anaerobic alkane degraders will likely increase in abundance in the event of seepage or accidental oil spillage. Nanomolar concentrations of short-chain alkanes (SCA) were detected in pristine and seepage sediments. Interestingly, anaerobic alkane degraders closely related to strain BuS5, the only SCA degrader in pure culture, were found in mesophilic MV enrichments, but not in cold sediments from Danish waters. We propose that the new masD/assA gene lineages in these sediments represent novel phylotypes that are either fueled by naturally occurring low levels of SCA or that metabolize medium- to long-chain alkanes. Our study highlights that masD/assA genes are a relevant diagnostic marker to identify seepage and microseepage, e.g., during prospecting for oil and gas, and may act as an indicator of anthropogenic oil spills in marine sediments.
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http://dx.doi.org/10.3389/fmicb.2015.01414DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4681840PMC
January 2016

Methanogenic archaea and sulfate reducing bacteria co-cultured on acetate: teamwork or coexistence?

Front Microbiol 2015 27;6:492. Epub 2015 May 27.

Agrotechnology and Food Sciences, Laboratory of Microbiology, Wageningen University Wageningen, Netherlands.

Acetate is a major product of fermentation processes and an important substrate for sulfate reducing bacteria and methanogenic archaea. Most studies on acetate catabolism by sulfate reducers and methanogens have used pure cultures. Less is known about acetate conversion by mixed pure cultures and the interactions between both groups. We tested interspecies hydrogen transfer and coexistence between marine methanogens and sulfate reducers using mixed pure cultures of two types of microorganisms. First, Desulfovibrio vulgaris subsp. vulgaris (DSM 1744), a hydrogenotrophic sulfate reducer, was cocultured together with the obligate aceticlastic methanogen Methanosaeta concilii using acetate as carbon and energy source. Next, Methanococcus maripaludis S2, an obligate H2- and formate-utilizing methanogen, was used as a partner organism to M. concilii in the presence of acetate. Finally, we performed a coexistence experiment between M. concilii and an acetotrophic sulfate reducer Desulfobacter latus AcSR2. Our results showed that D. vulgaris was able to reduce sulfate and grow from hydrogen leaked by M. concilii. In the other coculture, M. maripaludis was sustained by hydrogen leaked by M. concilii as revealed by qPCR. The growth of the two aceticlastic microbes indicated co-existence rather than competition. Altogether, our results indicate that H2 leaking from M. concilii could be used by efficient H2-scavengers. This metabolic trait, revealed from coculture studies, brings new insight to the metabolic flexibility of methanogens and sulfate reducers residing in marine environments in response to changing environmental conditions and community compositions. Using dedicated physiological studies we were able to unravel the occurrence of less obvious interactions between marine methanogens and sulfate-reducing bacteria.
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http://dx.doi.org/10.3389/fmicb.2015.00492DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4445324PMC
June 2015

The earthworm-Verminephrobacter symbiosis: an emerging experimental system to study extracellular symbiosis.

Front Microbiol 2014 28;5:128. Epub 2014 Mar 28.

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

Almost All Lumbricid Earthworms (oligochaeta: Lumbricidae) harbor extracellular species-specific bacterial symbionts of the genus Verminephrobacter (Betaproteobacteria) in their nephridia. The symbionts have a beneficial effect on host reproduction and likely live on their host's waste products. They are vertically transmitted and presumably associated with earthworms already at the origin of Lumbricidae 62-136 million years ago. The Verminephrobacter genomes carry signs of bottleneck-induced genetic drift, such as accelerated evolutionary rates, low codon usage bias, and extensive genome shuffling, which are characteristic of vertically transmitted intracellular symbionts. However, the Verminephrobacter genomes lack AT bias, size reduction, and pseudogenization, which are also common genomic hallmarks of vertically transmitted, intracellular symbionts. We propose that the opportunity for genetic mixing during part of the host-symbiont life cycle is the key to evade drift-induced genome erosion. Furthermore, we suggest the earthworm-Verminephrobacter association as a new experimental system for investigating host-microbe interactions, and especially for understanding genome evolution of vertically transmitted symbionts in the presence of genetic mixing.
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http://dx.doi.org/10.3389/fmicb.2014.00128DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3975124PMC
June 2014

Succession of cable bacteria and electric currents in marine sediment.

ISME J 2014 Jun 23;8(6):1314-22. Epub 2014 Jan 23.

1] Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark [2] Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark.

Filamentous Desulfobulbaceae have been reported to conduct electrons over centimetre-long distances, thereby coupling oxygen reduction at the surface of marine sediment to sulphide oxidation in sub-surface layers. To understand how these 'cable bacteria' establish and sustain electric conductivity, we followed a population for 53 days after exposing sulphidic sediment with initially no detectable filaments to oxygen. After 10 days, cable bacteria and electric currents were established throughout the top 15 mm of the sediment, and after 21 days the filament density peaked with a total length of 2 km cm(-2). Cells elongated and divided at all depths with doubling times over the first 10 days of <20 h. Active, oriented movement must have occurred to explain the separation of O2 and H2S by 15 mm. Filament diameters varied from 0.4-1.7 μm, with a general increase over time and depth, and yet they shared 16S rRNA sequence identity of >98%. Comparison of the increase in biovolume and electric current density suggested high cellular growth efficiency. While the vertical expansion of filaments continued over time and reached 30 mm, the electric current density and biomass declined after 13 and 21 days, respectively. This might reflect a breakdown of short filaments as their solid sulphide sources became depleted in the top layers of the anoxic zone. In conclusion, cable bacteria combine rapid and efficient growth with oriented movement to establish and exploit the spatially separated half-reactions of sulphide oxidation and oxygen consumption.
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http://dx.doi.org/10.1038/ismej.2013.239DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4030233PMC
June 2014

Predominant archaea in marine sediments degrade detrital proteins.

Nature 2013 Apr 27;496(7444):215-8. Epub 2013 Mar 27.

Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus 8000, Denmark.

Half of the microbial cells in the Earth's oceans are found in sediments. Many of these cells are members of the Archaea, single-celled prokaryotes in a domain of life separate from Bacteria and Eukaryota. However, most of these archaea lack cultured representatives, leaving their physiologies and placement on the tree of life uncertain. Here we show that the uncultured miscellaneous crenarchaeotal group (MCG) and marine benthic group-D (MBG-D) are among the most numerous archaea in the marine sub-sea floor. Single-cell genomic sequencing of one cell of MCG and three cells of MBG-D indicated that they form new branches basal to the archaeal phyla Thaumarchaeota and Aigarchaeota, for MCG, and the order Thermoplasmatales, for MBG-D. All four cells encoded extracellular protein-degrading enzymes such as gingipain and clostripain that are known to be effective in environments chemically similar to marine sediments. Furthermore, we found these two types of peptidase to be abundant and active in marine sediments, indicating that uncultured archaea may have a previously undiscovered role in protein remineralization in anoxic marine sediments.
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http://dx.doi.org/10.1038/nature12033DOI Listing
April 2013

Purifying selection and molecular adaptation in the genome of Verminephrobacter, the heritable symbiotic bacteria of earthworms.

Genome Biol Evol 2012 14;4(3):307-15. Epub 2012 Feb 14.

Department of Bioscience, Microbiology, Aarhus University, Denmark.

While genomic erosion is common among intracellular symbionts, patterns of genome evolution in heritable extracellular endosymbionts remain elusive. We study vertically transmitted extracellular endosymbionts (Verminephrobacter, Betaproteobacteria) that form a beneficial, species-specific, and evolutionarily old (60-130 Myr) association with earthworms. We assembled a draft genome of Verminephrobacter aporrectodeae and compared it with the genomes of Verminephrobacter eiseniae and two nonsymbiotic close relatives (Acidovorax). Similar to V. eiseniae, the V. aporrectodeae genome was not markedly reduced in size and showed no A-T bias. We characterized the strength of purifying selection (ω = dN/dS) and codon usage bias in 876 orthologous genes. Symbiont genomes exhibited strong purifying selection (ω = 0.09 ± 0.07), although transition to symbiosis entailed relaxation of purifying selection as evidenced by 50% higher ω values and less codon usage bias in symbiont compared with reference genomes. Relaxation was not evenly distributed among functional gene categories but was overrepresented in genes involved in signal transduction and cell envelope biogenesis. The same gene categories also harbored instances of positive selection in the Verminephrobacter clade. In total, positive selection was detected in 89 genes, including also genes involved in DNA metabolism, tRNA modification, and TonB-dependent iron uptake, potentially highlighting functions important in symbiosis. Our results suggest that the transition to symbiosis was accompanied by molecular adaptation, while purifying selection was only moderately relaxed, despite the evolutionary age and stability of the host association. We hypothesize that biparental transmission of symbionts and rare genetic mixing during transmission can prevent genome erosion in heritable symbionts.
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http://dx.doi.org/10.1093/gbe/evs014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3318438PMC
July 2012

Verminephrobacter aporrectodeae sp. nov. subsp. tuberculatae and subsp. caliginosae, the specific nephridial symbionts of the earthworms Aporrectodea tuberculata and A. caliginosa.

Antonie Van Leeuwenhoek 2012 Mar 22;101(3):507-14. Epub 2011 Oct 22.

Department of Bioscience, Microbiology, Aarhus University, Ny Munkegade 114, Aarhus C, Denmark.

Clone library-based studies have shown that almost all lumbricid earthworm species harbour host-specific symbiotic bacteria belonging to the novel genus Verminephrobacter in their nephridia (excretory organs). To date the only described representative from this genus is Verminephrobacter eiseniae, the specific symbiont of the earthworm Eisenia fetida. In this study two novel rod-shaped, non-endosporeforming, betaproteobacterial symbionts were isolated from the nephridia of two closely related earthworm species. Both isolates were affiliated with the genus Verminephrobacter by 16S rRNA gene sequence analysis. Similarly to V. eiseniae, the two isolates grew aerobically with a preference for low oxygen concentrations on a range of sugars, fatty acids and amino acids and fermentatively on glucose and pyruvate. These phenotypes match well with the conditions reported or inferred for the nephridial environment. Based on 16S rRNA gene similarity, DNA-DNA hybridization value and phenotypic characteristics the two isolates are clearly distinct from V. eiseniae. Phenotypic characteristics could not clearly differentiate the two strains as separate species but a low DNA-DNA hybridization value of 57.3%, their earthworm host specificity, differing temperature ranges and pH optima suggest that they represent two subspecies of a novel species of Verminephrobacter. For this species, the name V. aporrectodeae sp. nov. is proposed, with the two subspecies V. aporrectodeae subsp. tuberculatae (type strain, At4(T) = DSM 21361(T) = LMG 25313(T)) and V. aporrectodeae subsp. caliginosae (type strain, Ac9(T) = DSM 21895(T) = LMG 25312(T)) isolated from the nephridia of the earthworms Aporrectodea tuberculata and A. caliginosa, respectively.
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http://dx.doi.org/10.1007/s10482-011-9659-xDOI Listing
March 2012

Diversity and host specificity of the Verminephrobacter-earthworm symbiosis.

Environ Microbiol 2010 Aug 14;12(8):2142-51. Epub 2009 Oct 14.

Department of Biological Sciences, Microbiology, Aarhus University, Aarhus, Denmark.

Symbiotic bacteria of the genus Verminephrobacter (Betaproteobacteria) were detected in the nephridia of 19 out of 23 investigated earthworm species (Oligochaeta: Lumbricidae) by 16S rRNA gene sequence analysis and fluorescence in situ hybridization (FISH). While all four Lumbricus species and three out of five Aporrectodea species were densely colonized by a mono-species culture of Verminephrobacter, other earthworm species contained mixed bacterial populations with varying proportions of Verminephrobacter; four species did not contain Verminephrobacter at all. The Verminephrobacter symbionts could be grouped into earthworm species-specific sequence clusters based on their 16S rRNA and RNA polymerase subunit B (rpoB) genes. Closely related host species harboured more closely related symbionts than did distantly related hosts. Co-diversification of the symbiotic partners could not be demonstrated unambiguously due to the poor resolution of the host phylogeny [based on histone H3 and cytochrome c oxidase subunit I (COI) gene sequence analyses]. However, there was a pattern of symbiont diversification within four groups of closely related hosts. The mean rate of symbiont 16S rRNA gene evolution was determined using a relaxed clock model, and the rate was calibrated with paleogeographical estimates of the time of origin of Lumbricid earthworms. The calibrated rates of symbiont 16S rRNA gene evolution are 0.012-0.026 substitutions per site per 50 million years and thus similar to rates reported from other symbiotic bacteria.
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http://dx.doi.org/10.1111/j.1462-2920.2009.02084.xDOI Listing
August 2010

Desulfovibrio oceani subsp. oceani sp. nov., subsp. nov. and Desulfovibrio oceani subsp. galateae subsp. nov., novel sulfate-reducing bacteria isolated from the oxygen minimum zone off the coast of Peru.

Antonie Van Leeuwenhoek 2010 Mar 11;97(3):221-9. Epub 2009 Dec 11.

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

Two deltaproteobacterial sulfate reducers, designated strain I.8.1(T) and I.9.1(T), were isolated from the oxygen minimum zone water column off the coast of Peru at 400 and 500 m water depth. The strains were Gram-negative, vibrio-shaped and motile. Both strains were psychrotolerant, grew optimally at 20 degrees C at pH 7.0-8.0 and at 2.5-3.5% NaCl (w/v). The strains grew by utilizing hydrogen/acetate, C(3-4) fatty acids, amino acids and glycerol as electron acceptors for sulfate reduction. Fumarate, lactate and pyruvate supported fermentative growth. Sulfate, sulfite, thiosulfate and taurin supported growth as electron acceptors. Both strains were catalase-positive and highly oxygen-tolerant, surviving 24 days of exposure to atmospheric concentrations. MK6 was the only respiratory quinone. The most prominent cellular fatty acid was iso-17:1-omega9c (18%) for strain I.8.1(T) and iso-17:0-omega9c (14%) for strain I.9.1(T). The G+C contents of their genomic DNA were 45-46 mol%. Phylogenetic analysis of 16S rRNA and dsrAB gene sequences showed that both strains belong to the genus Desulfovibrio. Desulfovibrio acrylicus DSM 10141(T) and Desulfovibrio marinisediminis JCM 14577(T) represented their closest validly described relatives with pairwise 16S rRNA gene sequence identities of 98-99%. The level of DNA-DNA hybridization between strains I.8.1(T) and I.9.1(T) was 30-38%. The two strains shared 10-26% DNA-DNA relatedness with D. acrylicus. Based on a polyphasic investigation it is proposed that strains I.8.1(T) and I.9.1(T) represent a novel species for which the name Desulfovibrio oceani sp. nov. is proposed with the two subspecies D. oceani subsp. oceani (type strain, I.8.1(T) = DSM 21390(T) = JCM 15970(T)) and D. oceani subsp. galateae (type strain, I.9.1(T) = DSM 21391(T) = JCM 15971(T)).
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http://dx.doi.org/10.1007/s10482-009-9403-yDOI Listing
March 2010

Oxygen tolerance of sulfate-reducing bacteria in activated sludge.

Environ Sci Technol 2004 Apr;38(7):2038-43

Department of Microbiology, Aarhus University, Building 540, Ny Munkegade, 8000 Aarhus C., Denmark.

The oxygen tolerance of sulfate-reducing bacteria (SRB) present in activated sludge was studied in batch incubations using radiolabeled [35S]sulfate and a most probable number (MPN) technique employing activated sludge medium. Sulfate reduction (SR) could not be detected in activated sludge during oxic incubation or in the presence of nitrate. However, upon anoxic incubation of both freshly sampled activated sludge and activated sludge preaerated for 40 min, SR resumed immediately at an initial rate of 2 microM h(-1). During long-term aeration of activated sludge, the number of viable and culturable SRB remained constant at around 10(6) SRB mL(-1) throughout a 121 h aeration period. During the first 9 h of the 121 h aeration period, the anaerobic SR activitywas unaffected, as compared to that of an unaerated control sample, and recommenced instantaneously upon anoxic incubation. Even after 121 h of continuous aeration, SR took place within 1.5 h after anoxic incubation albeit at a rate less than 20% that of the unaerated control. As suggested by MPN estimates and the observed kinetics of SR, oxygen exposure resulted in temporary metabolic inactivation of SRB but did not cause cell death. Consequently, SRB have the potential for quick proliferation during anoxic storage of activated sludge.
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http://dx.doi.org/10.1021/es034777eDOI Listing
April 2004
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