Niche differentiation among mat-forming, sulfide-oxidizing bacteria in chemosynthetic ecosystems of the Nile Deep Sea Fan (Eastern Mediterranean Sea)

Sulfidic muds of cold seeps on the Nile Deep Sea Fan are populated by different types of mat-forming sulfide-oxidizing bacteria. The predominant sulfide oxidizers of three different mats were identified by microscopic and phylogenetic analyses as (i) Arcobacter species producing cotton-ball-like sulfur precipitates, (ii) large filamentous sulfur bacteria including Beggiatoa species, or (iii) single, spherical cells resembling Thiomargarita species. High resolution in situ microprofiles revealed different geochemical settings selecting for different mat types. Arcobacter mats occurred where oxygen and sulfide overlapped at the bottom water interface. Filamentous sulfide oxidizers were associated with non-overlapping, steep gradients of oxygen and sulfide. A dense population of Thiomargarita was favored by temporarily changing supplies of oxygen and sulfide. These results indicate that the decisive factors in selecting for different mat-forming bacteria within one deep-sea province are spatial or temporal variations in energy supply. Furthermore, the occurrence of Arcobacter spp.-related 16S rRNA genes in the sediments below all three types of mats, as well as on top of brine lakes of the Nile Deep Sea Fan, indicates that this group of sulfide oxidizers can switch between different life modes depending on the geobiochemical habitat setting.

Element contents, sulfur and oxygen isotopes, and molecular biomarkers of phosphatic crust samples from the Chimbote Platform of the shelf off Peru

Authigenic phosphatic laminites enclosed in phosphorite crusts from the shelf off Peru (10°01' S and 10°24' S) consist of carbonate fluorapatite layers, which contain abundant sulfide minerals including pyrite (FeS2) and sphalerite (ZnS). Low d34Spyrite values (average -28.8 per mill) agree with bacterial sulfate reduction and subsequent pyrite formation. Stable sulfur isotopic compositions of sulfate bound in carbonate fluorapatite are lower than that of sulfate from ambient sea water, suggesting bacterial reoxidation of sulfide by sulfide-oxidizing bacteria. The release of phosphorus and subsequent formation of the autochthonous phosphatic laminites are apparently caused by the activity of sulfate-reducing bacteria and associated sulfide-oxidizing bacteria. Following an extraction-phosphorite dissolution-extraction procedure, molecular fossils of sulfate-reducing bacteria (mono-O-alkyl glycerol ethers, di-O-alkyl glycerol ethers, as well as the short-chain branched fatty acids i/ai-C15:0, i/ai-C17:0 and 10MeC16:0) are found to be among the most abundant compounds. The fact that these molecular fossils of sulfate-reducing bacteria are distinctly more abundant after dissolution of the phosphatic laminite reveals that the lipids are tightly bound to the mineral lattice of carbonate fluorapatite. Moreover, compared with the autochthonous laminite, molecular fossils of sulfate-reducing bacteria are: (1) significantly less abundant and (2) not as tightly bound to the mineral lattice in the other, allochthonous facies of the Peruvian crusts consisting of phosphatic coated grains. These observations confirm the importance of sulfate-reducing bacteria in the formation of the phosphatic laminite. Model calculations highlight that organic matter degradation by sulfate-reducing bacteria has the potential to liberate sufficient phosphorus for phosphogenesis.

Oxidation rate of thiosulfate and elemental sulfur in the Black Sea

Oxidation rate of 35S-thiosulfate under simulated natural conditions and abundance of thiosulfate-oxidizing bacteria in a redox zone of the Black Sea are lower during winter and spring than in summer, especially in halistatic regions. Oxidation of thiosulfate under natural conditions is performed chiefly by lithotropic thionic bacteria, whose activity is limited by low temperatures. Adding thiosulfate and readily available organic matter to water samples from the redox zone and raising temperature of water stimulated activity of heterotrophic thiosulfate-oxidizing bacteria. Oxidation of elemental sulfur tagged with 35S apparently invovled two stages: abiotic oxidation of thiosulfate and subsequent bacterial oxidation of thiosulfate to sulfate.

Geochemistry of sediment cores from METEOR cruise M76/1b

Marine sediments are the main sink in the oceanic phosphorus (P) cycle. The activity of benthic microorganisms is decisive for regeneration, reflux, or burial of inorganic phosphate (Pi), which has a strong impact on marine productivity. Recent formation of phosphorites on the continental shelf and a succession of different sedimentary environments make the Benguela upwelling system a prime region for studying the role of microbes in P biogeochemistry. The oxygen isotope signature of pore water phosphate (d18OP) carries characteristic information of microbial P cycling: Intracellular turnover of phosphorylated biomolecules results in isotopic equilibrium with ambient water, while enzymatic regeneration of Pi from organic matter produces distinct offsets from equilibrium. The balance of these two processes is the major control for d18OP. Our study assesses the importance of microbial P cycling relative to regeneration of Pi from organic matter from a transect across the Namibian continental shelf and slope by combining pore water chemistry (sulfate, sulfide, ferrous iron, Pi), steady-state turnover rate modeling, and oxygen isotope geochemistry of Pi. We found d18OP values in a range from 12.8 per mill to 26.6 per mill, both in equilibrium as well as pronounced disequilibrium with water. Our data show a trend towards regeneration signatures (disequilibrium) under low mineralization activity and low Pi concentrations, and microbial turnover signatures (equilibrium) under high mineralization activity and high Pi concentrations. These findings are opposite to observations from water column studies where regeneration signatures were found to coincide with high mineralization activity and high Pi concentrations. It appears that preferential Pi regeneration in marine sediments does not necessarily coincide with a disequilibrium d18OP signature. We propose that microbial Pi uptake strategies, which are controlled by Pi availability, are decisive for the alteration of the isotope signature. This hypothesis is supported by the observation of efficient microbial Pi turnover (equilibrium signatures) in the phosphogenic sediments of the Benguela upwelling system.

FISH analysis of biofilm samples from five CANON reactors in Beijing

Completely autotrophic nitrogen removal over nitrite (CANON) has been regarded as an efficient and economical process for nitrogen removal from wastewater. The distribution and genetic diversity of the functional microorganisms in five lab-scale CANON reactors have been investigated by using some molecular biology methods. Nitrosomonas-like aerobic ammonium oxidizing bacteria (AerAOB) and Candidatus Brocadia-related anaerobic ammonium oxidizing bacteria (AnAOB) were detected as predominant functional microbes in the five reactors while Nitrobacter-like nitrite oxidizing bacteria (NOB) existed only in the systems operated at ambient temperature. Communities of AerAOB and AnAOB were almost similar among the five reactors while the distribution of the functional microbes was either scattered or densely packed. Meanwhile, this study has demonstrated the feasibility of starting up CANON by inoculating conventional activated sludge in low ammonium content at ambient temperature.

Morphological descriptions from the recent bivalve of the genus Calyptogena (Vesicomyidae)

The genus Calyptogena (Bivalvia: Vesicomyidae) comprises highly specialized bivalves living in symbiosis with sulphur-oxidizing bacteria in reducing habitats. In this study, the genus is revised using shell and anatomical features. The work is based on type material, as well as on the extensive collection of vesicomyids obtained during twelve expeditions to the Pacific and Indian Oceans. Nine Recent species are ascribed to the genus Calyptogena, four of which are new: C. pacifica Dall, 1891, C. fausta Okutani, Fujikura & Hashimoto, 1993, C. rectimargo Scarlato, 1981, C. valdiviae (Thiele & Jaeckel, 1931), C. gallardoi Sellanes & Krylova, 2005, C. goffrediae n. sp., C. starobogatovi n. sp., C. makranensis n. sp. and C. costaricana n. sp. The characteristic features of Calyptogena are: shell up to 90 mm in length, elongate-elliptical or elongate; presence of escutcheon; presence of broad posterior ramus (3b) of right subumbonal cardinal tooth as well as right posterior nymphal ridge; absence of pallial sinus as a result of attachment of intersiphonal septal retractor immediately adjacent to ventral surface of posterior adductor; absence of processes on inner vulva of inhalant siphon; presence of inner demibranch only, with descending and ascending lamellae with interlamellar septa not divided into separate tubes. The most closely related taxa to Calyptogena are probably the genus Isorropodon Sturany, 1896, and the group of species represented by 'Calyptogena' phaseoliformis Métivier, Okutani & Ohta, 1986. These groups have several characters in common, namely absence of pallial sinus, presence of single inner pair of demibranchs and absence of processes on inner vulva of inhalant siphon. The worldwide distribution of the genus Calyptogena suggests that methane seeps at continental margins are the major dispersal routes and that speciation was promoted by geographical isolation. Recent species diversity and fossil records indicate that the genus originated in the Pacific Ocean. Sufficient data to discuss the distribution at species level exist only for C. pacifica, which has a remarkably narrow bathymetric range. Published studies on the physiology of C. pacifica suggest that adaptation to a specific geochemical environment has led to coexisting vesicomyid genera. The bacteria-containing gill of C. pacifica and other Calyptogena species is one of the most specialized in the family Vesicomyidae and may reflect these ecological adaptations.

(Table 1) List of studied samples with vestimentiferan tubes

Vestimentiferan tube worms are prominent members of modern methane seep communities and are totally reliant as adults on symbiotic sulphide-oxidizing bacteria for their nutrition. The sulphide is produced in the sediment by a biochemical reaction called the anaerobic oxidation of methane (AOM). A well-studied species from the Gulf of Mexico shows that seep vestimentiferans 'mine' sulphide from the sediment using root-like, thin walled, permeable posterior tube extensions, which can also be used to pump sulphate and possibly hydrogen ions from the soft tissue back into the sediment to increase the local rate of AOM. The 'root-balls' of exhumed seep vestimentiferans are intimately associated with carbonate nodules, which are a result of AOM. We have studied vestimentiferan specimens and associated carbonates from seeps at the Kouilou pockmark field on the Congo deep-sea fan and find that some of the posterior 'root' tubes of living specimens are enclosed with carbonate indurated sediment and other, empty examples are partially or completely replaced by the carbonate mineral aragonite. This replacement occurs from the outside of the tube wall inwards and leaves fine-scale relict textures of the original organic tube wall. The process of mineralization is unknown, but is likely a result of post-mortem microbial decay of the tube wall proteins by microorganisms or the precipitation from locally high flux of AOM derived carbonate ions. The aragonite-replaced tubes from the Kouilou pockmarks show similar features to carbonate tubes in ancient seep deposits and make it more likely that many of these fossil tubes are those of vestimentiferans. These observations have implications for the supposed origination of this group, based on molecular divergence estimates.

Lipid biomarkers of shelf sediments from upwelling regions off Namibia, Peru, and Chile

Sediments of upwelling regions off Namibia, Peru, and Chile contain dense populations of large nitrate-storing sulfide-oxidizing bacteria, Thiomargarita, Beggiatoa, and Thioploca. Increased contents of monounsaturated C16 and C18 fatty acids have been found at all stations studied, especially when a high density of sulfide oxidizers in the sediments was observed. The distribution of lipid biomarkers attributed to sulfate reducers (10MeC16:0 fatty acid, ai-C15:0 fatty acid, and mono-O-alkyl glycerol ethers) compared to the distribution of sulfide oxidizers indicate a close association between these bacteria. As a consequence, the distributions of sulfate reducers in sediments of Namibia, Peru, and Chile are closely related to differences in the motility of the various sulfide oxidizers at the three study sites. Depth profiles of mono-O-alkyl glycerol ethers have been found to correlate best with the occurrence of large sulfide-oxidizing bacteria. This suggests a particularly close link between mono-O-alkyl glycerol ether-synthesizing sulfate reducers and sulfide oxidizers. The interaction between sulfide-oxidizing bacteria and sulfate-reducing bacteria reveals intense sulfur cycling and degradation of organic matter in different sediment depths.