The uptake of urea and dissolved organic nitrogen by a Lyngbya gracialis dominated microbial mat ... more The uptake of urea and dissolved organic nitrogen by a Lyngbya gracialis dominated microbial mat was studied in a double chambered continuous flow-through system in a 12:12 h 1ight:dark cycle experiment and during a prolonged dark incubation. In addition, the fluxes of total inorganic carbon, oxygen, dissolved free amino acids, nitrate and ammonium across the microbial mat were studied. In the 12:12 h 1ight:dark cycle, the microbial mats grew exponentially (0.5 d-') with dis-solved organic nitrogen as a nitrogen source. Dark urea uptakes were 50 to 85 % of the urea uptakes in light. The uptake of urea continued during the 2 wk of prolonged dark incubation. Natural microbial mats may be important regulators of urea dynamics in shallow marine environments, as the microbial mat efficiently took up urea at concentrations somewhat higher than in situ urea concentrations in sur-face sedirnents.
Bacterial biomarkers (D-amino acids and muramic acid) were investigated in surface sediments (0-1... more Bacterial biomarkers (D-amino acids and muramic acid) were investigated in surface sediments (0-1 cm) at 22 stations in the Peru margin. Concentrations were used to quantitatively estimate the relative importance of peptidoglycan in the preservation of prokaryotic remains during diagenesis. The bacterial imprint in organic matter was also evident from low molar ratios (average of 1.6) of glucosamine and galactosamine. Estimates of the fraction of biomarkers associated with intact peptidoglycan showed that peptidoglycan became a progressively less important component of prokaryotic remains with ongoing diagenesis, whereas other prokaryotic biomolecules increased in importance. The exact nature of these biomolecules remains unknown, but constant ratios between individual D-amino acids and amino sugars observed in this study provide novel information on their molecular composition. Examination of total hydrolyzable amino acids revealed systematic compositional changes with increasing water depth and age of the sediment, reflecting increased diagenetic alteration of the organic matter. The time scale integrated in the upper 1 cm of the sediment was ca. 2 yr at the shallow sites and up to 20 yr at the deeper stations. The alteration stages of organic matter ranged from coastal and ocean margin sediments at shallow water depth to organic matter as degraded as hemipelagic surface sediments at greater water depths.
The ratios of D-versus L-amino acids can be used to infer the sources and composition of sediment... more The ratios of D-versus L-amino acids can be used to infer the sources and composition of sedimentary organic matter. Such inferences, however, rely on knowing the rates at which amino acids in sedimentary organic matter racemize abiotically between the D-and the L-forms. Based on a heating experiment, we report kinetic parameters for racemization of aspartic acid, glutamic acid, serine, and alanine in bulk sediment from Aarhus Bay, Denmark, taken from the surface, 30 cm, and 340 cm depth below seafloor. Extrapolation to a typical cold deep sea sediment temperature of 3uC suggests racemization rate constants of 0.50610 25 -11610 25 yr 21 . These results can be used in conjunction with measurements of sediment age to predict the ratio of D:L amino acids due solely to abiotic racemization of the source material, deviations from which can indicate the abundance and turnover of active microbial populations.
Because of the similarities between Earth and Mars early history the hypothesis was forwarded tha... more Because of the similarities between Earth and Mars early history the hypothesis was forwarded that Mars is a site where extraterrestrial life might have and/or may still occur(red). Sample-return missions are planned by NASA and ESA to test this hypothesis. The enormous economic costs and the logistic challenges of these missions make earth-based model facilities inevitable. The Mars simulation system
Two decades of scientific ocean drilling have demonstrated widespread microbial life in deep sub-... more Two decades of scientific ocean drilling have demonstrated widespread microbial life in deep sub-seafloor sediment, and surprisingly high microbial-cell numbers. Despite the ubiquity of life in the deep biosphere, the large community sizes and the low energy fluxes in this vast buried ecosystem are not yet understood 1,2 . It is not known whether organisms of the deep biosphere are specifically adapted to extremely low energy fluxes or whether most of the observed cells are in a dormant, spore-like state 3 . Here we apply a new approach-the D:L-amino-acid model-to quantify the distributions and turnover times of living microbial biomass, endospores and microbial necromass, as well as to determine their role in the sub-seafloor carbon budget. The approach combines sensitive analyses of unique bacterial markers (muramic acid and D-amino acids) and the bacterial endospore marker, dipicolinic acid, with racemization dynamics of stereo-isomeric amino acids. Endospores are as abundant as vegetative cells and microbial activity is extremely low, leading to microbial biomass turnover times of hundreds to thousands of years. We infer from model calculations that biomass production is sustained by organic carbon deposited from the surface photosynthetic world millions of years ago and that microbial necromass is recycled over timescales of hundreds of thousands of years.
The effect of the seagrass Zostera capricorni on sediment microbial processes was studied in a ta... more The effect of the seagrass Zostera capricorni on sediment microbial processes was studied in a tank experiment, where vegetated and unvegetated control sedunents were incubated in 10 and 50% of incident light. Leaf and root-rhizome biomass, shoot density, and leaf productivity were significantly higher when plants were incubated in 50 % than in 10% of incident light. Nitrogen fixation, sulphate reduction, and urea turnover in the Z. capricorni vegetated sediment were higher in the 50 % than in the 10% light treatment and higher in the vegetated than in the unvegetated sediment. The stimulation of microbial processes in the Z, capricorni vegetated sedunent took place in the rhizosphere, where nitrogen fixation and sulphate reduction in particular were stimulated. The sediment studies were supplemented by measurements of nitrogen fixation, sulphate reduction, and urea turnover by microorganisms associated with the roots and rhizomes of Z, capricorni. The rates of nitrogen fixation and sulphate reduction associated with root-rhizomes were up to 40-and 7-fold higher, respectively, than the highest respective sediment rates, whereas the root-rhlzome associated urea turnover was lower than sediment rates. Nitrogen fixation and sulphate reduction associated with rootrhizomes could account for up to 39 and 4%, respectively, of the depth-integrated sediment rates. Nitrogen fixed by microorganisms associated with root-rhizomes could supply up to 65 % of the nitrogen needed for plant growth. Further, it was estimated that 8 to 18% of the carbon fixed by Z. capricorni was released to the sediment by the roots and rhizomes. Urea turnover was suggested to be an important intermediate in the gross production of ammonium, and a low net production of ammonium indicated rapid internal nitrogen cycling within the sediment.
ABSTRACT A high performance liquid chromatographic (HPLC) method for fluorescence detection of di... more ABSTRACT A high performance liquid chromatographic (HPLC) method for fluorescence detection of dipicolinic acid (DPA), a unique component of bacterial endospores, was developed for rapid and highly sensitive quantification of endospores. DPA was pre-column complexed to the lanthanide metal terbium (Tb3+). Surplus free Tb3+ and the Tb3+-DPA complex were separated by reverse-phase gradient chromatography and the fluorescence emission was read at 545 nm after exitation at 270 nm. The limits of quantification (LOQ) and detection (LOD) were 0.26 and 0.08 nM, respectively. The method was used to detect DPA extracted from Bacillus subtilis endospores, DPA extracted from B. subtilis endospores added to more complex substrates such as marine sediment and canned tuna and DPA extracted from indigenous endospores in a coastal marine sediment. Endospores represented 4% of the microbial community (bacterial cells + endospores) in active surface sediment from the Aarhus Bay.
The contribution of D-isomers of aspartate (Asp), glutamate (Glu), alanine (Ala), and serine (Ser... more The contribution of D-isomers of aspartate (Asp), glutamate (Glu), alanine (Ala), and serine (Ser) to the total concentrations of dissolved free amino acids (DFAA), dissolved combined amino acids (DCAA), and total hydrolyzable amino acids (THAA) was studied in a Ͻ2,300-yr-old coastal sediment. Concentrations of the different amino acid pools were typically 5 (DFAA), 100 (DCAA), and 20,000 nmol cm Ϫ3 (THAA), but variable amounts occurred, especially in the surface layer. D-amino acids were identified in all three amino acid fractions. The highest concentration of D-isomers occurred in the THAA fraction at a depth of 10 cm, where the maximum bacterial density has been observed Mar. Ecol. Prog. Ser. 59: 39-54). This coincidence suggests that the D-amino acids originated in peptidoglycan of bacterial cell walls. The proportion of D-Asp, D-Glu, D-Ala, and D-Ser increased through the pools of DFAA and DCAA to THAA, suggesting a selective removal of L-amino acids to D-amino acids. The percentage of the four D-amino acids in the THAA pool increased with sediment depth to at least 4.3 m (ϳ2,150 yr). This most likely indicated that peptidoglycan THAA were retained for a longer period of time in a particulate form compared to other proteinaceous material. The contribution of THAA from peptidoglycan to the THAA pool was estimated to range from Ͼ9% at the surface to at least 18% at 4.3 m deep, depending on the assumptions used in the calculation. The distribution of amino acid isomers in Aarhus Bay sediment demonstrated that bacterial peptidoglycan contributed to the pool of organic nitrogen (the four analyzed D-amino acids made up about 3% of particulate organic nitrogen [PON]). Although the peptidoglycan concentration increased with sediment depth, our observations do not indicate a long-term accumulation of peptidoglycan-derived amino acids.
The initial benthic degradation of senescent Zostera marina leaves was studied in controlled flow... more The initial benthic degradation of senescent Zostera marina leaves was studied in controlled flowthrough microcosm chambers for 33 d. Sediment chambers without added eelgrass leaves served as control chambers. The inflowing artificial seawater and ouflowing seawater were analyzed for dissolved organic carbon and nitrogen (DOC and DON), total acid-hydrolyzable amino acids (THAA), dissolved free amino acids (DFAA), urea, NH , NO ,
Bioavailability and chemical composition of dissolved organic nitrogen (DON) in marine pore water... more Bioavailability and chemical composition of dissolved organic nitrogen (DON) in marine pore water were followed and related to bacterial activity in a 14-d anoxic decomposition experiment. For the experiment 0.2-m filtered pore water from a coastal marine sediment was inoculated with native sediment bacteria. The initial composition of DON was characterized by a high contribution of dissolved free amino acids (DFAA), dissolved combined amino acids (DCAA), and urea, which together accounted for 82% of the DON pool. During the experiment, 54% of the DON was used by bacteria, indicating that DON was readily available to bacterial degradation. The consumption of DFAA and DCAA accounted for more than half of the DON consumed. The unidentified DON pool accounted for 33% of the net DON consumption, and the unidentified DON pool was fully depleted by the end of the experiment. Systematic changes in the amino acid composition occurred with time of incubation, as demonstrated by use of a principal component analysis based on the mole percent contribution of amino acids. The results indicated that amino acids of both the DFAA and the DCAA pools were useful indicators of the diagenetic state of DON. The present study presents the first direct evidence of short-term (within 14 d) changes in DFAA and DCAA of the DON pool. These changes were similar to decompositional changes in the molecular composition of amino acids observed in traditional studies of bulk sediment diagenesis.
Journal of Experimental Marine Biology and Ecology, 2004
The initial benthic decomposition of Zostera marina roots was studied in a controlled flowthrough... more The initial benthic decomposition of Zostera marina roots was studied in a controlled flowthrough chamber experiment for 23 days. Sediment chambers without added roots served as controls. The inflowing and outflowing artificial seawater (ASW) was analyzed for O 2 , ACO 2 , urea-N, NH 4 + and NO 2 À +NO 3 À . Sediment profiles of Eh, particulate organic carbon (POC) and nitrogen, dissolved organic nitrogen (DON), dissolved free amino acids (DFAA), urea-N, NH 4 + , DFAA and urea turnover rates, sulfate reduction and counts of total anaerobic heterotrophic bacteria and different functional groups were determined. Fluxes of O 2 , ACO 2 , urea-N and NH 4 + were stimulated during root decomposition compared to the unamended control. There were indications of stimulated bacterial growth based on counts of total anaerobic heterotrophic bacteria, anaerobic phosphatase utilizers, 0022-0981/$ -see front matter D ammonifyers and sulfate reducers. Independent estimates of nitrogen and carbon incorporation into bacterial biomass during root decomposition indicate that a major fraction of the nitrogen for microbial growth was mobilized from the indigenous particulate organic nitrogen (PON) pool, whereas the energy source for bacterial growth was mainly obtained from the added eelgrass roots. Most of the nitrogen mineralized during root decomposition was incorporated into the bacterial biomass resulting in a low efflux of urea-N and inorganic nitrogen from the sediment to the water column. D
Journal of Experimental Marine Biology and Ecology, 2006
The benthic degradation of mussel tissue (Mytilus edulis) was studied in a continuous flow-throug... more The benthic degradation of mussel tissue (Mytilus edulis) was studied in a continuous flow-through system over a 32 day incubation period. Sediment chambers without mussels served as controls. The inflowing artificial seawater and the outflow water were analyzed for dissolved organic nitrogen (DON), short chain fatty acids (SCFA), dissolved inorganic nitrogen (DIN), ∑CO2 and O2 during the course of incubation. Sediment profiles of particulate organic carbon (POC), particulate organic nitrogen (PON), total hydrolyzable amino acids (THAA), pore water concentrations of DON and DIN and turnover rate of dissolved free amino acids (DFAA) were measured at four different times during the 32 day experiment. Immediately after the addition of mussel tissue, the chambers became completely anoxic and there was an increase in carbon oxidation and the efflux of DON, SCFA and NH4+ from the sediment+mussel layer to the overlaying water. During the first 9 days there was a net buildup of DON, and NH4+ in the sediment followed by a net consumption of the respective N-species during the remainder of the experiment. During the course of incubation 41% of the organic content of the added mussel tissue was released from the sediment as DON, whereas most of the other mussel-N effluxed the sediment as NH4+. Only 8% of the added mussel-N remained by the end of the experiment. There were indications of stimulated bacterial growth in both the mussel amended and the unamended sediments. This was measured as a net increase in THAA, which could only be explained by net bacterial growth and/or protein synthesis. During mussel decomposition both the estimated bacterial carbon incorporation efficiency and the C:N ratio of the substrates used by the bacteria were low. This resulted in a low bacterial nitrogen demand. As a consequence, almost all of the nitrogen mineralized within the sediment was released to the water column as NH4+.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2009
Two pigmented, Gram-negative, non-motile, pleomorphic rod-shaped bacteria (strains SPM-9 T and SP... more Two pigmented, Gram-negative, non-motile, pleomorphic rod-shaped bacteria (strains SPM-9 T and SPM-10 T ) were isolated from a permafrost soil collected from the Adventdalen valley, Spitsbergen, northern Norway. A third isolate (strain M5-H2) was recovered from the same soil sample after the sample had been exposed to simulated Martian environmental conditions. The three strains were characterized taxonomically by using a polyphasic approach. Phylogenetic, chemotaxonomic, physiological and morphological analyses demonstrated that the three isolates were most closely related to members of the genus Spirosoma. 16S rRNA gene sequence data indicated that the three isolates could be divided into two clusters: (i) strain SPM-9 T and (ii) strains SPM-10 T and M5-H2. This grouping was confirmed by DNA-DNA hybridization experiments. Strains SPM-9 T and SPM-10 T exhibited 92 % 16S rRNA gene sequence similarity to both Spirosoma linguale LMG 10896 T and Spirosoma rigui WPCB 118 T . The major fatty acids present in all three isolates were summed feature 3 (comprising iso-C 15:0 2-OH and/or C 16 : 1 v7c; 43.0-48.2 % of the total), C 16 : 1 v5c (19.1-21.3 %), C 16 : 0 (6.7-7.3 %), iso-C 17 : 0 3-OH (4.7-6.0 %) and iso-C 15 : 0 (2.6-5.7 %). On the basis of their phenotypic and genotypic characteristics, the new strains are assigned to two novel species of the genus Spirosoma, for which the names Spirosoma spitsbergense sp. nov. and Spirosoma luteum sp. nov. are proposed. The type strain of Spirosoma spitsbergense is SPM-9 T (5NCIMB 14407 T 5DSM 19989 T ) and the type strain of Spirosoma luteum is SPM-10 T (5NCIMB 14406 T 5DSM 19990 T ). An emended description of the genus Spirosoma is also proposed.
A simulation experiment with a complex bacterial soil community in a Mars simulation chamber was ... more A simulation experiment with a complex bacterial soil community in a Mars simulation chamber was performed to determine the effect of Martian conditions on community activity, stability and survival. At three different depths in the soil core short-term effects of Martian conditions with and without ultraviolet (UV) exposure corresponding to 8 Martian Sol were compared. Community metabolic activities and functional diversity, measured as glucose respiration and versatility in substrate utilization, respectively, decreased after UV exposure, whereas they remained unaffected by Martian conditions without UV exposure. In contrast, the numbers of culturable bacteria and the genetic diversity were unaffected by the simulated Martian conditions both with and without UV exposure. The genetic diversity of the soil community and of the colonies grown on agar plates were evaluated by denaturant gradient gel electrophoresis (DGGE) on DNA extracts. Desiccation of the soil prior to experimentation affected the functional diversity by decreasing the versatility in substrate utilization. The natural dominance of endospores and Gram-positive bacteria in the investigated Mars-analogue soil may explain the limited effect of the Mars incubations on the survival and community structure. Our results suggest that UV radiation and desiccation are major selecting factors on bacterial functional diversity in terrestrial bacterial communities incubated under simulated Martian conditions. Furthermore, these results suggest that forward contamination of Mars is a matter of great concern in future space missions.
The uptake of urea and dissolved organic nitrogen by a Lyngbya gracialis dominated microbial mat ... more The uptake of urea and dissolved organic nitrogen by a Lyngbya gracialis dominated microbial mat was studied in a double chambered continuous flow-through system in a 12:12 h 1ight:dark cycle experiment and during a prolonged dark incubation. In addition, the fluxes of total inorganic carbon, oxygen, dissolved free amino acids, nitrate and ammonium across the microbial mat were studied. In the 12:12 h 1ight:dark cycle, the microbial mats grew exponentially (0.5 d-') with dis-solved organic nitrogen as a nitrogen source. Dark urea uptakes were 50 to 85 % of the urea uptakes in light. The uptake of urea continued during the 2 wk of prolonged dark incubation. Natural microbial mats may be important regulators of urea dynamics in shallow marine environments, as the microbial mat efficiently took up urea at concentrations somewhat higher than in situ urea concentrations in sur-face sedirnents.
Bacterial biomarkers (D-amino acids and muramic acid) were investigated in surface sediments (0-1... more Bacterial biomarkers (D-amino acids and muramic acid) were investigated in surface sediments (0-1 cm) at 22 stations in the Peru margin. Concentrations were used to quantitatively estimate the relative importance of peptidoglycan in the preservation of prokaryotic remains during diagenesis. The bacterial imprint in organic matter was also evident from low molar ratios (average of 1.6) of glucosamine and galactosamine. Estimates of the fraction of biomarkers associated with intact peptidoglycan showed that peptidoglycan became a progressively less important component of prokaryotic remains with ongoing diagenesis, whereas other prokaryotic biomolecules increased in importance. The exact nature of these biomolecules remains unknown, but constant ratios between individual D-amino acids and amino sugars observed in this study provide novel information on their molecular composition. Examination of total hydrolyzable amino acids revealed systematic compositional changes with increasing water depth and age of the sediment, reflecting increased diagenetic alteration of the organic matter. The time scale integrated in the upper 1 cm of the sediment was ca. 2 yr at the shallow sites and up to 20 yr at the deeper stations. The alteration stages of organic matter ranged from coastal and ocean margin sediments at shallow water depth to organic matter as degraded as hemipelagic surface sediments at greater water depths.
The ratios of D-versus L-amino acids can be used to infer the sources and composition of sediment... more The ratios of D-versus L-amino acids can be used to infer the sources and composition of sedimentary organic matter. Such inferences, however, rely on knowing the rates at which amino acids in sedimentary organic matter racemize abiotically between the D-and the L-forms. Based on a heating experiment, we report kinetic parameters for racemization of aspartic acid, glutamic acid, serine, and alanine in bulk sediment from Aarhus Bay, Denmark, taken from the surface, 30 cm, and 340 cm depth below seafloor. Extrapolation to a typical cold deep sea sediment temperature of 3uC suggests racemization rate constants of 0.50610 25 -11610 25 yr 21 . These results can be used in conjunction with measurements of sediment age to predict the ratio of D:L amino acids due solely to abiotic racemization of the source material, deviations from which can indicate the abundance and turnover of active microbial populations.
Because of the similarities between Earth and Mars early history the hypothesis was forwarded tha... more Because of the similarities between Earth and Mars early history the hypothesis was forwarded that Mars is a site where extraterrestrial life might have and/or may still occur(red). Sample-return missions are planned by NASA and ESA to test this hypothesis. The enormous economic costs and the logistic challenges of these missions make earth-based model facilities inevitable. The Mars simulation system
Two decades of scientific ocean drilling have demonstrated widespread microbial life in deep sub-... more Two decades of scientific ocean drilling have demonstrated widespread microbial life in deep sub-seafloor sediment, and surprisingly high microbial-cell numbers. Despite the ubiquity of life in the deep biosphere, the large community sizes and the low energy fluxes in this vast buried ecosystem are not yet understood 1,2 . It is not known whether organisms of the deep biosphere are specifically adapted to extremely low energy fluxes or whether most of the observed cells are in a dormant, spore-like state 3 . Here we apply a new approach-the D:L-amino-acid model-to quantify the distributions and turnover times of living microbial biomass, endospores and microbial necromass, as well as to determine their role in the sub-seafloor carbon budget. The approach combines sensitive analyses of unique bacterial markers (muramic acid and D-amino acids) and the bacterial endospore marker, dipicolinic acid, with racemization dynamics of stereo-isomeric amino acids. Endospores are as abundant as vegetative cells and microbial activity is extremely low, leading to microbial biomass turnover times of hundreds to thousands of years. We infer from model calculations that biomass production is sustained by organic carbon deposited from the surface photosynthetic world millions of years ago and that microbial necromass is recycled over timescales of hundreds of thousands of years.
The effect of the seagrass Zostera capricorni on sediment microbial processes was studied in a ta... more The effect of the seagrass Zostera capricorni on sediment microbial processes was studied in a tank experiment, where vegetated and unvegetated control sedunents were incubated in 10 and 50% of incident light. Leaf and root-rhizome biomass, shoot density, and leaf productivity were significantly higher when plants were incubated in 50 % than in 10% of incident light. Nitrogen fixation, sulphate reduction, and urea turnover in the Z. capricorni vegetated sediment were higher in the 50 % than in the 10% light treatment and higher in the vegetated than in the unvegetated sediment. The stimulation of microbial processes in the Z, capricorni vegetated sedunent took place in the rhizosphere, where nitrogen fixation and sulphate reduction in particular were stimulated. The sediment studies were supplemented by measurements of nitrogen fixation, sulphate reduction, and urea turnover by microorganisms associated with the roots and rhizomes of Z, capricorni. The rates of nitrogen fixation and sulphate reduction associated with root-rhizomes were up to 40-and 7-fold higher, respectively, than the highest respective sediment rates, whereas the root-rhlzome associated urea turnover was lower than sediment rates. Nitrogen fixation and sulphate reduction associated with rootrhizomes could account for up to 39 and 4%, respectively, of the depth-integrated sediment rates. Nitrogen fixed by microorganisms associated with root-rhizomes could supply up to 65 % of the nitrogen needed for plant growth. Further, it was estimated that 8 to 18% of the carbon fixed by Z. capricorni was released to the sediment by the roots and rhizomes. Urea turnover was suggested to be an important intermediate in the gross production of ammonium, and a low net production of ammonium indicated rapid internal nitrogen cycling within the sediment.
ABSTRACT A high performance liquid chromatographic (HPLC) method for fluorescence detection of di... more ABSTRACT A high performance liquid chromatographic (HPLC) method for fluorescence detection of dipicolinic acid (DPA), a unique component of bacterial endospores, was developed for rapid and highly sensitive quantification of endospores. DPA was pre-column complexed to the lanthanide metal terbium (Tb3+). Surplus free Tb3+ and the Tb3+-DPA complex were separated by reverse-phase gradient chromatography and the fluorescence emission was read at 545 nm after exitation at 270 nm. The limits of quantification (LOQ) and detection (LOD) were 0.26 and 0.08 nM, respectively. The method was used to detect DPA extracted from Bacillus subtilis endospores, DPA extracted from B. subtilis endospores added to more complex substrates such as marine sediment and canned tuna and DPA extracted from indigenous endospores in a coastal marine sediment. Endospores represented 4% of the microbial community (bacterial cells + endospores) in active surface sediment from the Aarhus Bay.
The contribution of D-isomers of aspartate (Asp), glutamate (Glu), alanine (Ala), and serine (Ser... more The contribution of D-isomers of aspartate (Asp), glutamate (Glu), alanine (Ala), and serine (Ser) to the total concentrations of dissolved free amino acids (DFAA), dissolved combined amino acids (DCAA), and total hydrolyzable amino acids (THAA) was studied in a Ͻ2,300-yr-old coastal sediment. Concentrations of the different amino acid pools were typically 5 (DFAA), 100 (DCAA), and 20,000 nmol cm Ϫ3 (THAA), but variable amounts occurred, especially in the surface layer. D-amino acids were identified in all three amino acid fractions. The highest concentration of D-isomers occurred in the THAA fraction at a depth of 10 cm, where the maximum bacterial density has been observed Mar. Ecol. Prog. Ser. 59: 39-54). This coincidence suggests that the D-amino acids originated in peptidoglycan of bacterial cell walls. The proportion of D-Asp, D-Glu, D-Ala, and D-Ser increased through the pools of DFAA and DCAA to THAA, suggesting a selective removal of L-amino acids to D-amino acids. The percentage of the four D-amino acids in the THAA pool increased with sediment depth to at least 4.3 m (ϳ2,150 yr). This most likely indicated that peptidoglycan THAA were retained for a longer period of time in a particulate form compared to other proteinaceous material. The contribution of THAA from peptidoglycan to the THAA pool was estimated to range from Ͼ9% at the surface to at least 18% at 4.3 m deep, depending on the assumptions used in the calculation. The distribution of amino acid isomers in Aarhus Bay sediment demonstrated that bacterial peptidoglycan contributed to the pool of organic nitrogen (the four analyzed D-amino acids made up about 3% of particulate organic nitrogen [PON]). Although the peptidoglycan concentration increased with sediment depth, our observations do not indicate a long-term accumulation of peptidoglycan-derived amino acids.
The initial benthic degradation of senescent Zostera marina leaves was studied in controlled flow... more The initial benthic degradation of senescent Zostera marina leaves was studied in controlled flowthrough microcosm chambers for 33 d. Sediment chambers without added eelgrass leaves served as control chambers. The inflowing artificial seawater and ouflowing seawater were analyzed for dissolved organic carbon and nitrogen (DOC and DON), total acid-hydrolyzable amino acids (THAA), dissolved free amino acids (DFAA), urea, NH , NO ,
Bioavailability and chemical composition of dissolved organic nitrogen (DON) in marine pore water... more Bioavailability and chemical composition of dissolved organic nitrogen (DON) in marine pore water were followed and related to bacterial activity in a 14-d anoxic decomposition experiment. For the experiment 0.2-m filtered pore water from a coastal marine sediment was inoculated with native sediment bacteria. The initial composition of DON was characterized by a high contribution of dissolved free amino acids (DFAA), dissolved combined amino acids (DCAA), and urea, which together accounted for 82% of the DON pool. During the experiment, 54% of the DON was used by bacteria, indicating that DON was readily available to bacterial degradation. The consumption of DFAA and DCAA accounted for more than half of the DON consumed. The unidentified DON pool accounted for 33% of the net DON consumption, and the unidentified DON pool was fully depleted by the end of the experiment. Systematic changes in the amino acid composition occurred with time of incubation, as demonstrated by use of a principal component analysis based on the mole percent contribution of amino acids. The results indicated that amino acids of both the DFAA and the DCAA pools were useful indicators of the diagenetic state of DON. The present study presents the first direct evidence of short-term (within 14 d) changes in DFAA and DCAA of the DON pool. These changes were similar to decompositional changes in the molecular composition of amino acids observed in traditional studies of bulk sediment diagenesis.
Journal of Experimental Marine Biology and Ecology, 2004
The initial benthic decomposition of Zostera marina roots was studied in a controlled flowthrough... more The initial benthic decomposition of Zostera marina roots was studied in a controlled flowthrough chamber experiment for 23 days. Sediment chambers without added roots served as controls. The inflowing and outflowing artificial seawater (ASW) was analyzed for O 2 , ACO 2 , urea-N, NH 4 + and NO 2 À +NO 3 À . Sediment profiles of Eh, particulate organic carbon (POC) and nitrogen, dissolved organic nitrogen (DON), dissolved free amino acids (DFAA), urea-N, NH 4 + , DFAA and urea turnover rates, sulfate reduction and counts of total anaerobic heterotrophic bacteria and different functional groups were determined. Fluxes of O 2 , ACO 2 , urea-N and NH 4 + were stimulated during root decomposition compared to the unamended control. There were indications of stimulated bacterial growth based on counts of total anaerobic heterotrophic bacteria, anaerobic phosphatase utilizers, 0022-0981/$ -see front matter D ammonifyers and sulfate reducers. Independent estimates of nitrogen and carbon incorporation into bacterial biomass during root decomposition indicate that a major fraction of the nitrogen for microbial growth was mobilized from the indigenous particulate organic nitrogen (PON) pool, whereas the energy source for bacterial growth was mainly obtained from the added eelgrass roots. Most of the nitrogen mineralized during root decomposition was incorporated into the bacterial biomass resulting in a low efflux of urea-N and inorganic nitrogen from the sediment to the water column. D
Journal of Experimental Marine Biology and Ecology, 2006
The benthic degradation of mussel tissue (Mytilus edulis) was studied in a continuous flow-throug... more The benthic degradation of mussel tissue (Mytilus edulis) was studied in a continuous flow-through system over a 32 day incubation period. Sediment chambers without mussels served as controls. The inflowing artificial seawater and the outflow water were analyzed for dissolved organic nitrogen (DON), short chain fatty acids (SCFA), dissolved inorganic nitrogen (DIN), ∑CO2 and O2 during the course of incubation. Sediment profiles of particulate organic carbon (POC), particulate organic nitrogen (PON), total hydrolyzable amino acids (THAA), pore water concentrations of DON and DIN and turnover rate of dissolved free amino acids (DFAA) were measured at four different times during the 32 day experiment. Immediately after the addition of mussel tissue, the chambers became completely anoxic and there was an increase in carbon oxidation and the efflux of DON, SCFA and NH4+ from the sediment+mussel layer to the overlaying water. During the first 9 days there was a net buildup of DON, and NH4+ in the sediment followed by a net consumption of the respective N-species during the remainder of the experiment. During the course of incubation 41% of the organic content of the added mussel tissue was released from the sediment as DON, whereas most of the other mussel-N effluxed the sediment as NH4+. Only 8% of the added mussel-N remained by the end of the experiment. There were indications of stimulated bacterial growth in both the mussel amended and the unamended sediments. This was measured as a net increase in THAA, which could only be explained by net bacterial growth and/or protein synthesis. During mussel decomposition both the estimated bacterial carbon incorporation efficiency and the C:N ratio of the substrates used by the bacteria were low. This resulted in a low bacterial nitrogen demand. As a consequence, almost all of the nitrogen mineralized within the sediment was released to the water column as NH4+.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2009
Two pigmented, Gram-negative, non-motile, pleomorphic rod-shaped bacteria (strains SPM-9 T and SP... more Two pigmented, Gram-negative, non-motile, pleomorphic rod-shaped bacteria (strains SPM-9 T and SPM-10 T ) were isolated from a permafrost soil collected from the Adventdalen valley, Spitsbergen, northern Norway. A third isolate (strain M5-H2) was recovered from the same soil sample after the sample had been exposed to simulated Martian environmental conditions. The three strains were characterized taxonomically by using a polyphasic approach. Phylogenetic, chemotaxonomic, physiological and morphological analyses demonstrated that the three isolates were most closely related to members of the genus Spirosoma. 16S rRNA gene sequence data indicated that the three isolates could be divided into two clusters: (i) strain SPM-9 T and (ii) strains SPM-10 T and M5-H2. This grouping was confirmed by DNA-DNA hybridization experiments. Strains SPM-9 T and SPM-10 T exhibited 92 % 16S rRNA gene sequence similarity to both Spirosoma linguale LMG 10896 T and Spirosoma rigui WPCB 118 T . The major fatty acids present in all three isolates were summed feature 3 (comprising iso-C 15:0 2-OH and/or C 16 : 1 v7c; 43.0-48.2 % of the total), C 16 : 1 v5c (19.1-21.3 %), C 16 : 0 (6.7-7.3 %), iso-C 17 : 0 3-OH (4.7-6.0 %) and iso-C 15 : 0 (2.6-5.7 %). On the basis of their phenotypic and genotypic characteristics, the new strains are assigned to two novel species of the genus Spirosoma, for which the names Spirosoma spitsbergense sp. nov. and Spirosoma luteum sp. nov. are proposed. The type strain of Spirosoma spitsbergense is SPM-9 T (5NCIMB 14407 T 5DSM 19989 T ) and the type strain of Spirosoma luteum is SPM-10 T (5NCIMB 14406 T 5DSM 19990 T ). An emended description of the genus Spirosoma is also proposed.
A simulation experiment with a complex bacterial soil community in a Mars simulation chamber was ... more A simulation experiment with a complex bacterial soil community in a Mars simulation chamber was performed to determine the effect of Martian conditions on community activity, stability and survival. At three different depths in the soil core short-term effects of Martian conditions with and without ultraviolet (UV) exposure corresponding to 8 Martian Sol were compared. Community metabolic activities and functional diversity, measured as glucose respiration and versatility in substrate utilization, respectively, decreased after UV exposure, whereas they remained unaffected by Martian conditions without UV exposure. In contrast, the numbers of culturable bacteria and the genetic diversity were unaffected by the simulated Martian conditions both with and without UV exposure. The genetic diversity of the soil community and of the colonies grown on agar plates were evaluated by denaturant gradient gel electrophoresis (DGGE) on DNA extracts. Desiccation of the soil prior to experimentation affected the functional diversity by decreasing the versatility in substrate utilization. The natural dominance of endospores and Gram-positive bacteria in the investigated Mars-analogue soil may explain the limited effect of the Mars incubations on the survival and community structure. Our results suggest that UV radiation and desiccation are major selecting factors on bacterial functional diversity in terrestrial bacterial communities incubated under simulated Martian conditions. Furthermore, these results suggest that forward contamination of Mars is a matter of great concern in future space missions.
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