Identity, abundance and reactivation kinetics of thermophilic fermentative endospores in cold marine sediment and seawater

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 degrees 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-2 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 similar to 105-106 inducible TFEs cm(-3). 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 X 109 anaerobic thermophilic endospores are deposited on the seafloor per m2 per year in Aarhus Bay, and that these thermophiles represent >10% of the total endospore community in the surface sediment

Nitrate Reduction Functional Genes and Nitrate Reduction Potentials Persist in Deeper Estuarine Sediments. Why?

Denitrification and dissimilatory nitrate reduction to ammonium (DNRA) are processes occurring simultaneously under oxygen-limited or anaerobic conditions, where both compete for nitrate and organic carbon. Despite their ecological importance, there has been little investigation of how denitrification and DNRA potentials and related functional genes vary vertically with sediment depth. Nitrate reduction potentials measured in sediment depth profiles along the Colne estuary were in the upper range of nitrate reduction rates reported from other sediments and showed the existence of strong decreasing trends both with increasing depth and along the estuary. Denitrification potential decreased along the estuary, decreasing more rapidly with depth towards the estuary mouth. In contrast, DNRA potential increased along the estuary. Significant decreases in copy numbers of 16S rRNA and nitrate reducing genes were observed along the estuary and from surface to deeper sediments. Both metabolic potentials and functional genes persisted at sediment depths where porewater nitrate was absent. Transport of nitrate by bioturbation, based on macrofauna distributions, could only account for the upper 10 cm depth of sediment. A several fold higher combined freeze-lysable KCl-extractable nitrate pool compared to porewater nitrate was detected. We hypothesised that his could be attributed to intracellular nitrate pools from nitrate accumulating microorganisms like Thioploca or Beggiatoa. However, pyrosequencing analysis did not detect any such organisms, leaving other bacteria, microbenthic algae, or foraminiferans which have also been shown to accumulate nitrate, as possible candidates. The importance and bioavailability of a KCl-extractable nitrate sediment pool remains to be tested. The significant variation in the vertical pattern and abundance of the various nitrate reducing genes phylotypes reasonably suggests differences in their activity throughout the sediment column. This raises interesting questions as to what the alternative metabolic roles for the various nitrate reductases could be, analogous to the alternative metabolic roles found for nitrite reductases

Is there a common water-activity limit for the three domains of life?

Archaea and Bacteria constitute a majority of life systems on Earth but have long been considered inferior to Eukarya in terms of solute tolerance. Whereas the most halophilic prokaryotes are known for an ability to multiply at saturated NaCl (water activity (a w) 0.755) some xerophilic fungi can germinate, usually at high-sugar concentrations, at values as low as 0.650-0.605 a w. Here, we present evidence that halophilic prokayotes can grow down to water activities of <0.755 for Halanaerobium lacusrosei (0.748), Halobacterium strain 004.1 (0.728), Halobacterium sp. NRC-1 and Halococcus morrhuae (0.717), Haloquadratum walsbyi (0.709), Halococcus salifodinae (0.693), Halobacterium noricense (0.687), Natrinema pallidum (0.681) and haloarchaeal strains GN-2 and GN-5 (0.635 a w). Furthermore, extrapolation of growth curves (prone to giving conservative estimates) indicated theoretical minima down to 0.611 a w for extreme, obligately halophilic Archaea and Bacteria. These were compared with minima for the most solute-tolerant Bacteria in high-sugar (or other non-saline) media (Mycobacterium spp., Tetragenococcus halophilus, Saccharibacter floricola, Staphylococcus aureus and so on) and eukaryotic microbes in saline (Wallemia spp., Basipetospora halophila, Dunaliella spp. and so on) and high-sugar substrates (for example, Xeromyces bisporus, Zygosaccharomyces rouxii, Aspergillus and Eurotium spp.). We also manipulated the balance of chaotropic and kosmotropic stressors for the extreme, xerophilic fungi Aspergillus penicilloides and X. bisporus and, via this approach, their established water-activity limits for mycelial growth (∼0.65) were reduced to 0.640. Furthermore, extrapolations indicated theoretical limits of 0.632 and 0.636 a w for A. penicilloides and X. bisporus, respectively. Collectively, these findings suggest that there is a common water-activity limit that is determined by physicochemical constraints for the three domains of life

Accumulation of prokaryotic remains during organic matter diagenesis in surface sediments off Peru

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

Contrasting effects of nitrogen limitation and amino acid imbalance on carbon and nitrogen turnover in three species of Collembola

11 páginas, 5 figuras, 4 tablas.Soil animal detritivores play an important role in facilitating decomposition processes but little information is available on how the quality of dietary resources affects their stoichiometry of carbon (C) nitrogen (N) and phosphorus (P), and turnover of C and N. This study investigated how a fungal diet, Fusarium culmorum, with a low N content and imbalanced amino acid (AA) composition affected the physiology of three soil-dwelling collembolans (Folsomia candida, Protaphorura fimata and Proisotoma minuta) in comparison to a control diet, Saccharomyces cerevisiae, with a high N content and balanced AA composition. We compared the elemental composition of animals, their growth rates and tissue replacement of C and N.We also measured the individual AA d13C to investigate the extent that Collembola may rely on endogenous sources to compensate for scarcity of essential AAs. The results showed that animal’s N content tracked closely the composition of their diets, decreasing from around 10 to 7% N from the high to low N diet. They also had a significant increase of C and a decrease of P. P. fimata was less affected than F. candida and P. minuta. The total incorporation of C and N in the animals due to growth and tissue replacement decreased from 11e17 to 6e12% DM d 1 on the high and low N diet respectively with P. fimata experiencing the smallest change. Essential AAs d13C did not always match perfectly between Collembola species and their diets; particularly on the low N diet. Isotope patterns of AAs indicate that bacteria may have been the alternative source of essential AAs. While the results of this study cannot be extrapolated directly to the dynamics of Collembola populations in the field, they serve to demonstrate their flexibility in adapting physiologically to the temporal and spatial patchiness of the soil environment.This study was conducted with support from DARCOF (Danish Research Centre for Organic Farming). Partial support to TL and MV was also provided by the Spanish Ministry of Science and Innovation (Ref. CGL2010-14841/BOS).Peer reviewe

Beneficial Effect of Verminephrobacter Nephridial Symbionts on the Fitness of the Earthworm Aporrectodea tuberculata▿ †

Almost all lumbricid earthworms (Oligochaeta: Lumbricidae) harbor species-specific Verminephrobacter (Betaproteobacteria) symbionts in their nephridia (excretory organs). The function of the symbiosis, and whether the symbionts have a beneficial effect on their earthworm host, is unknown; however, the symbionts have been hypothesized to enhance nitrogen retention in earthworms. The effect of Verminephrobacter on the life history traits of the earthworm Aporrectodea tuberculata (Eisen) was investigated by comparing the growth, development, and fecundity of worms with and without symbionts given high (cow dung)- and low (straw)-nutrient diets. There were no differences in worm growth or the number of cocoons produced by symbiotic and aposymbiotic worms. Worms with Verminephrobacter symbionts reached sexual maturity earlier and had higher cocoon hatching success than worms cured of their symbionts when grown on the low-nutrient diet. Thus, Verminephrobacter nephridial symbionts do have a beneficial effect on their earthworm host. Cocoons with and without symbionts did not significantly differ in total organic carbon, total nitrogen, or total hydrolyzable amino acid content, which strongly questions the hypothesized role of the symbionts in nitrogen recycling for the host

Effect of the seagrass Zostera capricorni on sediment microbial processes

The effect of the seagrass Zostera capricorni on sediment microbial processes was studied in a tank experiment, where vegetated and unvegetated control sediments 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 sediment 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-rhizome associated urea turnover was lower than sediment rates. Nitrogen fixation and sulphate reduction associated with root-rhizomes 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