Differences of heterotrophic 13CO2 assimilation by Pseudomonas knackmussii strain B13 and Rhodococcus opacus 1CP and potential impact on biomarker stable isotope probing

Motivated by the finding that Pseudomonas knackmussii B13 but not Rhodococcus opacus 1CP grows in the absence of externally provided CO(2), we investigated the assimilation of (13)CO(2) into active cells cultivated with non-labelled glucose as sole energy substrate. (13)C found in the bulk biomass indicated a substantial but different CO(2) assimilation by Pseudomonas and Rhodococcus, respectively (3500 per thousand and 2600 per thousand). Cellular fatty acids were labelled from -15 per thousand to 470 per thousand and amino acids from 500 per thousand to 24,000 per thousand demonstrating clear differences between various compound classes. 'You are what you eat plus 1 per thousand' is therefore only valid for the average bulk C without specific isotope signature deviation of the external CO(2) or carbonates. Odd-numbered and 10-methyl fatty acids, which are much more abundant in Rhodococcus or other Gram-positive bacteria, were up to fivefold higher enriched in (13)C relative to the Pseudomonas fatty acids. A high-level growth-phase-independent, labelling of the oxaloacetate-derived amino acids indicated heterotrophic CO(2) fixation by anaplerotic reactions known to replenish the tricarboxylic acid cycle. Although both strains assimilate CO(2) via similar general pathways, Rhodococcus depends to a much higher extent on carboxylations reactions with external CO(2) owing to the formation of odd-numbered fatty acids. As a general consequence, heterotrophic fixation of CO(2) should be taken into account in investigations of degradation experiments using isotope tracer compounds.     

Tracing the slow growth of anaerobic methane-oxidizing communities by 15N-labelling techniques

The anaerobic oxidation of methane (AOM) is an important methane sink in marine ecosystems mediated by still uncultured Archaea . We established an experimental system to grow AOM communities in different sediment samples. Approaches to show growth of the slow-growing anaerobic methanotrophs have been either via nucleic acids (quantitative PCR) or required long-term incubations. Previous long-term experiments with ¹³C-labelled methane led to an unspecific distribution of the ¹³C-label. Although quantitative PCR is a sensitive technique to detect small changes in community composition, it does not determine growth yield. Therefore, we tested an alternative method to detect a biomass increase of AOM microorganisms with ¹⁵N-labelled ammonium as N-source. After only 3 weeks, significant ¹⁵N-labelling became apparent in amino acids as major structural units of microbial proteins. This was especially evident in methane-containing incubations, showing the methane-dependent uptake of the ¹⁵N-labelled ammonium by microorganisms. Cell counts demonstrated a two- and fourfold increase at ambient or elevated methane concentrations. With denaturing gradient gel electrophoresis, over 6 months incubation no changes in community composition of sulphate-reducing bacteria and archaea were detected. These data indicate doubling times for AOM microorganisms between 2 and 3.4 months. In conclusion, the ¹⁵N-labelling approach proved to be a sensitive and fast way to show growth of extremely slow-growing microorganisms.     

Iron corrosion by methanogenic archaea characterized by stable isotope effects and crust mineralogy

Carbon and hydrogen stable isotope effects associated with methane formation by the corrosive archaeon Methanobacterium strain IM1 were determined during growth with hydrogen and iron. Isotope analyses were complemented by structural, elemental and molecular composition analyses of corrosion crusts. During growth with H₂, strain IM1 formed methane with average δ¹³C of −43.5‰ and δ²H of −370‰. Corrosive growth led to methane more depleted in ¹³C, with average δ¹³C ranging from −56‰ to −64‰ during the early and the late growth phase respectively. The corresponding δ²H were less impacted by the growth phase, with average values ranging from −316 to −329‰. The stable isotope fractionation factors, , were 1.026 and 1.042 for hydrogenotrophic and corrosive growth respectively. Corrosion crusts formed by strain IM1 have a domed structure, appeared electrically conductive and were composed of siderite, calcite and iron sulfide, the latter formed by precipitation of sulfide (from culture medium) with ferrous iron generated during corrosion. Strain IM1 cells were found attached to crust surfaces and encrusted deep inside crust domes. Our results may assist to diagnose methanogens-induced corrosion in the field and suggest that intrusion of sulfide in anoxic settings may stimulate corrosion by methanogenic archaea via formation of semiconductive crusts.     

Carbon isotope fractionation during <Emphasis Type="Italic">cis</Emphasis>–<Emphasis Type="Italic">trans</Emphasis> isomerization of unsaturated fatty acids in <Emphasis Type="Italic">Pseudomonas putida</Emphasis>

The molecular mechanism of the unique cis to trans isomerization of unsaturated fatty acids in the solvent-tolerant bacterium Pseudomonas putida S12 was studied. For this purpose, the carbon isotope fractionation of the cis–trans isomerase was estimated. In resting cell experiments, addition of 3-nitrotoluene for activation of the cis–trans isomerase resulted in the conversion of the cis-unsaturated fatty acids into the corresponding trans isomers. For the conversion of C16:1 cis to its corresponding trans isomer, a significant fractionation was measured. The intensity of this fractionation strongly depended on the rate of cis–trans isomerization and the added concentration of 3-nitrotoluene, respectively. The presence of a significant fractionation provides additional indication for a transition from the sp² carbon linkage of the cis-double bond to an intermediate sp³ within an enzyme–substrate complex. The sp² linkage is reconstituted after rotation to the trans configuration has occurred. As cytochrome c plays a major role in the catabolism of Cti polypeptide, these findings favour a mechanism for the enzyme in which electrophilic iron (Fe³⁺), provided by a heme domain, removes an electron of the cis double bond thereby transferring the sp² linkage into sp³.     

Ethylene and methane in the upper water column of the subtropical Atlantic

The vertical distributions of ethylene and methane in the upper water column of the subtropical Atlantic were measured along a transect from Madeira to the Caribbean and compared with temperature, salinity, oxygen, nutrients, chlorophyll-a, and dissolved organic carbon (DOC).Methane concentrations between 41.6 and 60.7 nL L-1 were found in the upper 20 m of the water column giving a calculated average flux of methane into the atmosphere of 0.82 g m-2 h-1. Methane profiles reveal several distinct maxima in the upper 500 m of the water column and short-time variations which are presumably partly related to the vertical migration of zooplankton.Ethylene concentrations in near surface waters varied in the range of 1.8 to 8.2 nL L-1. Calculated flux rates for ethylene into the atmosphere were in the range of 0.41 to 1.35 g m-2 h-1 with a mean of 0.83 g m-2 h-1. Maximum concentrations of up to 39.2 nL L-1 were detected directly below the pycnocline in the western Atlantic. The vertical distributions of ethylene generally showed one maximum at the pycnocline (about 100 m depth) where elevated concentrations of chlorophyll-a, dissolved oxygen, and nutrients were also found; no ethylene was detected below 270 m depth. This suggests that ethylene release is mainly related to one, probably phytoplankton associated, source, while for methane, enhanced net production occurs at various depth horizons. For surface waters, a simple correlation between ethylene and chlorophyll-a or DOC concentrations could not be observed. No considerable diurnal variation was observed for the distribution and concentration of ethylene in the upper water column.     

Changing Feeding Regimes To Demonstrate Flexible Biogas Production: Effects on Process Performance,Microbial Community Structure,and Methanogenesis Pathways

Flexible biogas production that adapts biogas output to energy demand can be regulated by changing feeding regimes. In this study, the effect of changes in feeding intervals on process performance, microbial community structure, and the methanogenesis pathway was investigated. Three different feeding regimes (once daily, every second day, and every 2 h) at the same organic loading rate were studied in continuously stirred tank reactors treating distiller''s dried grains with solubles. A larger amount of biogas was produced after feeding in the reactors fed less frequently (once per day and every second day), whereas the amount remained constant in the reactor fed more frequently (every 2 h), indicating the suitability of the former for the flexible production of biogas. Compared to the conventional more frequent feeding regimes, a methane yield that was up to 14% higher and an improved stability of the process against organic overloading were achieved by employing less frequent feeding regimes. The community structures of bacteria and methanogenic archaea were monitored by terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA and mcrA genes, respectively. The results showed that the composition of the bacterial community varied under the different feeding regimes, and the observed T-RFLP patterns were best explained by the differences in the total ammonia nitrogen concentrations, H₂ levels, and pH values. However, the methanogenic community remained stable under all feeding regimes, with the dominance of the Methanosarcina genus followed by that of the Methanobacterium genus. Stable isotope analysis showed that the average amount of methane produced during each feeding event by acetoclastic and hydrogenotrophic methanogenesis was not influenced by the three different feeding regimes.     

Essential Role of the Disulfide-bonded Loop of Chromogranin B for Sorting to Secretory Granules Is Revealed by Expression of a Deletion Mutant in the Absence of Endogenous Granin Synthesis

Sorting of regulated secretory proteins in the TGN to immature secretory granules (ISG) is thought to involve at least two steps: their selective aggregation and their interaction with membrane components destined to ISG. Here, we have investigated the sorting of chromogranin B (CgB), a member of the granin family present in the secretory granules of many endocrine cells and neurons. Specifically, we have studied the role of a candidate structural motif implicated in the sorting of CgB, the highly conserved NH₂-terminal disulfide– bonded loop. Sorting to ISG of full-length human CgB and a deletion mutant of human CgB (Δcys-hCgB) lacking the 22–amino acid residues comprising the disulfide-bonded loop was compared in the rat neuroendocrine cell line PC12. Upon transfection, i.e., with ongoing synthesis of endogenous granins, the sorting of the deletion mutant was only slightly impaired compared to full-length CgB. To investigate whether this sorting was due to coaggregation of the deletion mutant with endogenous granins, we expressed human CgB using recombinant vaccinia viruses, under conditions in which the synthesis of endogenous granins in the infected PC12 cells was shut off. In these conditions, Δcys-hCgB, in contrast to full-length hCgB, was no longer sorted to ISG, but exited from the TGN in constitutive secretory vesicles. Coexpression of full-length hCgB together with Δcys-hCgB by double infection, using the respective recombinant vaccinia viruses, rescued the sorting of the deletion mutant to ISG. In conclusion, our data show that (a) the disulfide-bonded loop is essential for sorting of CgB to ISG and (b) the lack of this structural motif can be compensated by coexpression of loop-bearing CgB. Furthermore, comparison of the two expression systems, transfection and vaccinia virus–mediated expression, reveals that analyses under conditions in which host cell secretory protein synthesis is blocked greatly facilitate the identification of sequence motifs required for sorting of regulated secretory proteins to secretory granules.     

Sulfidic acetate mineralization at 45°C by an aquifer microbial community: key players and effects of heat changes on activity and community structure

High-Temperature Aquifer Thermal Energy Storage (HT-ATES) is a sustainable approach for integrating thermal energy from various sources into complex energy systems. Temperatures ≥45°C, which are relevant in impact zones of HT-ATES systems, may dramatically influence the structure and activities of indigenous aquifer microbial communities. Here, we characterized an acetate-mineralizing, sulfate-reducing microbial community derived from an aquifer and adapted to 45°C. Acetate mineralization was strongly inhibited at temperatures ≤25°C and 60°C. Prolonged incubation at 12°C and 25°C resulted in acetate mineralization recovery after 40–80 days whereas acetate was not mineralized at 60°C within 100 days. Cultures pre-grown at 45°C and inhibited for 28 days by incubation at 12°C, 25°C, or 60°C recovered quickly after changing the temperature back to 45°C. Phylotypes affiliated to the order Spirochaetales and to endospore-forming sulfate reducers of the order Clostridiales were highly abundant in microcosms being active at 45°C highlighting their key role. In summary, prolonged incubation at 45°C resulted in active microbial communities mainly consisting of organisms adapted to temperatures between the typical temperature range of mesophiles and thermophiles and being resilient to temporary heat changes.