Shifts in phylogenetic diversity of archaeal communities in mangrove sediments at different sites and depths in southeastern Brazil

This study focused on the structure and composition of archaeal communities in sediments of tropical mangroves in order to obtain sufficient insight into two Brazilian sites from different locations (one pristine and another located in an urban area) and at different depth levels from the surface. Terminal restriction fragment length polymorphism (T-RFLP) of PCR-amplified 16S rRNA gene fragments was used to scan the archaeal community structure, and 16S rRNA gene clone libraries were used to determine the community composition. Redundancy analysis of T-RFLP patterns revealed differences in archaeal community structure according to location, depth and soil attributes. Parameters such as pH, organic matter, potassium and magnesium presented significant correlation with general community structure. Furthermore, phylogenetic analysis revealed a community composition distributed differently according to depth where, in shallow samples, 74.3% of sequences were affiliated with Euryarchaeota and 25.7% were shared between Crenarchaeota and Thaumarchaeota, while for the deeper samples, 24.3% of the sequences were affiliated with Euryarchaeota and 75.7% with Crenarchaeota and Thaumarchaeota. Archaeal diversity measurements based on 16S rRNA gene clone libraries decreased with increasing depth and there was a greater difference between depths (<18% of sequences shared) than sites (>25% of sequences shared). Taken together, our findings indicate that mangrove ecosystems support a diverse archaeal community; it might possibly be involved in nutrient cycles and are affected by sediment properties, depth and distinct locations. (C) 2012 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Evaluation of microorganisms with sulfidogenic metabolic potential under anaerobic conditions

The aim of this work was to identify groups of microorganisms that are capable of degrading organic matter utilizing sulfate as an electron acceptor. The assay applied for this purpose consisted of running batch reactors and monitoring lactate consumption, sulfate reduction and sulfide production. A portion of the lactate added to the batch reactors was consumed, and the remainder was converted into acetic, propionic and butyric acid after 111 hours of operation These results indicate the presence of sulfate-reducing bacteria (SRB) catalyzing both complete and incomplete oxidation of organic substrates. The sulfate removal efficiency was 49.5% after 1335 hours of operation under an initial sulfate concentration of 1123 mg/L. The SRB concentrations determined by the most probable number (MPN) method were 9.0x10(7) cells/mL at the beginning of the assay and 8.0x10(5) cells/mL after 738 hours of operation.

Biometanazione della frazione organica di rifiuti solidi urbani da raccolta indifferenziata mediante codigestione con refluo zootecnico o addizione di solfuro di sodio

Il presente elaborato è stato finalizzato allo sviluppo di un processo di digestione anaerobica della frazione organica dei rifiuti solidi urbani (FORSU oppure, in lingua inglese OFMSW, Organic Fraction of Municipal Solid Waste) provenienti da raccolta indifferenziata e conseguente produzione di biogas da impiegarsi per il recupero energetico. Questo lavoro rientra nell’ambito di un progetto, cofinanziato dalla Regione Emilia Romagna attraverso il Programma Regionale per la Ricerca Industriale, l’Innovazione e il Trasferimento Tecnologico (PRRIITT), sviluppato dal Dipartimento di Chimica Applicata e Scienza dei Materiali (DICASM) dell’Università di Bologna in collaborazione con la Facoltà di Ingegneria dell’Università di Ferrara e con la società Recupera s.r.l. che applicherà il processo nell’impianto pilota realizzato presso il proprio sito di biostabilizzazione e compostaggio ad Ostellato (FE). L’obiettivo è stato la verifica della possibilità di impiegare la frazione organica dei rifiuti indifferenziati per la produzione di biogas, e in particolare di metano, attraverso un processo di digestione anaerobica previo trattamento chimico oppure in codigestione con altri substrati organici facilmente fermentabili. E’ stata inoltre studiata la possibilità di impiego di reattori con biomassa adesa per migliorare la produzione specifica di metano e diminuire la lag phase. Dalla sperimentazione si può concludere che è possibile giungere allo sviluppo di metano dalla purea codigerendola assieme a refluo zootecnico. Per ottenere però produzioni significative la quantità di solidi volatili apportati dal rifiuto non deve superare il 50% dei solidi volatili complessivi. Viceversa, l’addizione di solfuri alla sola purea si è dimostrata ininfluente nel tentativo di sottrarre gli agenti inibitori della metanogenesi. Inoltre, l’impiego di supporti di riempimento lavorando attraverso processi batch sequenziali permette di eliminare, nei cicli successivi al primo, la lag phase dei batteri metanogeni ed incrementare la produzione specifica di metano.

Influence of alternative electron acceptors on the anaerobic biodegradation of polycyclic aromatic hydrocarbons

Polycyclic aromatic hydrocarbons are chemicals produced by both human activities and natural sources and they have been present in the biosphere since millions of years. For this reason microorganisms should have developed, during the world history, the capacity of metabolized them under different electron acceptors and redox conditions. The deep understanding of these natural attenuation processes and of microbial degradation pathways has a main importance in the cleanup of contaminated areas. Anaerobic degradation of aromatic hydrocarbons is often presumed to be slow and of a minor ecological significance compared with the aerobic processes; however anaerobic bioremediation may play a key role in the transformation of organic pollutants when oxygen demand exceeds supply in natural environments. Under such conditions, anoxic and anaerobic degradation mediated by denitrifying or sulphate-reducing bacteria can become a key pathway for the contaminated lands clean up. Actually not much is known about anaerobic bioremediation processes. Anaerobic biodegrading techniques may be really interesting for the future, because they give the possibility of treating contaminated soil directly in their natural status, decreasing the costs concerning the oxygen supply, which usually are the highest ones, and about soil excavations and transports in appropriate sites for a further disposal. The aim of this dissertation work is to characterize the conditions favouring the anaerobic degradation of polycyclic aromatic hydrocarbons. Special focus will be given to the assessment of the various AEA efficiency, the characterization of degradation performance and rates under different redox conditions as well as toxicity monitoring. A comparison with aerobic and anaerobic degradation concerning the same contaminated material is also made to estimate the different biodegradation times.

Phylogenetische Charakterisierung von Mikroorganismen aus dem Intestinaltrakt von Insekten

Zusammenfassung Die komplexe Lebensgemeinschaft des Termitendarms fasziniert die Biologen schon seit langem. Es ist bekannt, dass Termiten ihre Nahrung mit Hilfe von symbiontischen Bakterien und Protozoen verdauen können. Ohne ihre Symbionten würden sie verhungern. Das Zusammenspiel von Termiten und darmbewohnenden Mikroorganismen, zu denen Flagellaten, Bakterien, Archaebakterien und Hefen gehören, ist trotz moderner Untersuchungstechniken keineswegs vollständig aufgeklärt. In der vorliegenden Arbeit wurden:1) Einige kultivierte und nicht-kultivierte Bakterien charakterisiert, die an der Darmwand von Mastotermes darwiniensis lokalisiert sind. Die Darmwandbakterien wurden entweder nach Kultivierung oder direkt von der Darmwand für die Analyse der 16S rDNA verwendet. Die Sequenzierung erfolgte entweder nach DGGE oder nach Klonierung der PCR-Produkte. Die identifizierten Bakterien kann man in 7 Gruppen teilen:1: Gram-positive Bakterien mit hohem GC-Gehalt 2: Gram-positive Bakterien mit niedrigem GC-Gehalt 3: Fusobakterien-ähnliche Bakterien 4: ß-Proteobakterien5: Verrucomicrobien6: Bacteroides-ähnliche Bakterien7: Methanogene Bakterien 2) Aufgrund des Vorhandenseins des Coenzyms Deazaflavin-Derivats F420, kann man Methanbakterien mikroskopisch identifizieren und von anderen Bakterien unterscheiden, weil Methanbakterien im kurzwelligen Blaulicht blaugrün aufleuchten. Untersuchungen haben gezeigt, dass mindestens zwei Morphotypen von Methanbakterien an der Darmwand von M. darwiniensis vorkommen. Sie wurden auch über 16S rDNA Sequenzanalyse identifiziert. Ihre Lokalisierung an der Darmwand wurde durch Fluoreszenz-in-situ-Hybridsierung mit spezifischen Oligonukleotiden nachgewiesen. Schließlich konnte gezeigt werden, dass pro Gramm Termite 2,6 µg Methan pro Stunde produziert werden. 3) Bis jetzt wurden aus verschiedenen Termiten sulfatreduzierende Bakterien (SRB) isoliert. Deshalb wurde in dieser Arbeit die Verbreitung der SRB in verschiedenen Insekten untersucht. Insgesamt wurden zwei Sequenzen aus Libellenlarven (FSBO4 und FSBRO2), drei Sequenzen aus Zuckmückenlarven (FSCI, FSCII und FSC4), eine Sequenz aus Rosenkäfern (FSPa4-5) und ebenfalls eine Sequenz aus Eintagsfliegenlarven (FSB6) identifiziert. Alle identifizierten Bakterien ausser Klon FSB6, gehören zur Gattung Desulfovibrio. Klon FSB6 gehört zu der Gram-positiven Gattung Desulfotomaculum.Außerdem wurde die Sulfatreduktionsrate der SRB im Darm von Rosenkäfern (Pachnoda marginata), Holz- bzw. Sulfat-gefütterten Termiten (Mastotermes darwiniensis) und einer Reinkultur von Desulfovibrio intestinalis gemessen. Dabei konnte gezeigt werden, dass die Aktivität pro Zelle in Holz-gefütterten Termite am höchsten ist (4,9 nmol/107 Bakterien x h).

Untersuchungen zur mikrobiellen Methylquecksilberbildung in Termiten und im Faulschlamm

Im Rahmen dieser Arbeit wurde erstmalig eine in vivo Methylierung von Quecksilber in Insekten nachgewiesen. Des Weiteren wurde die Kinetik der Quecksilbermethylierung im Faulschlamm untersucht und eine Identifizierung der für die Methylierung verantwortlichen Bakteriengruppe durchgeführt. Die Methylquecksilberbestimmung erfolgte mittels Purge&Trap Gaschromatographie-Atomfluoreszenzspektrometrie nach einer sauren Phasenextraktion. Zur Untersuchung einer in vivo Methylquecksilberbildung in Insekten wurde die australischen Termite Mastotermes darwiniensis als Modellorganismus verwandt. Den Tieren wurde über einen Zeitraum von vierzehn Tagen Quecksilber(II)chlorid in unterschiedlichen Konzentrationen mit der Nahrung zugeführt und anschließend die Methylquecksilberkonzentration in den Termiten bestimmt. Mit zunehmender Quecksilberkonzentration in der Nahrung (0 µg bis 150 µg Hg2+/g) stieg die Methylquecksilberkonzentration von ca. 5 ng auf 53,8 ng pro g Termite Trockengewicht. Bei höheren Quecksilberkonzentrationen in der Nahrung wurde kein weiterer Anstieg in der Methylquecksilberkonzentration in den Termiten festgestellt. Die Untersuchung der Methylquecksilberbildung im Faulschlamm des Klärwerks Mainz-Mombach zeigte, dass die Methylquecksilberkonzentration zu Beginn der Inkubationsphase rasch anstieg und mit zunehmender Inkubationsdauer eine Sätti-gung erreichte. Nach 164 Stunden waren insgesamt 2,6 % des eingesetzten Quecksilbers zu Methylquecksilber umgesetzt. Anhand von Hemmstoffversuchen wurden Sulfat-reduzierende Bakterien als hauptverantwortliche Organismengruppe für die Quecksilbermethylierung identifiziert.

Untersuchungen zur biotischen Bildung von Methylquecksilber aus anorganischem Quecksilber durch intestinale Sulfat-reduzierende Bakterien und die Bestimmung alkylierter Quecksilberverbindungen mittels GC-ICP-MS und Isotopenverdünnungsanalyse

Alkylierte Quecksilberspezies sind hundertfach toxischer als anorganisches Quecksilber (Hg) und werden in der Nahrungskette mit zunehmender Trophieebene im Gewebe von Tieren und dem Menschen akkumuliert. Aufgrund der Relevanz für die Umwelt und den Effekt auf die menschliche Gesundheit kommt der biotischen Transformation von anorganischem Hg zu Monomethylquecksilber (MeHg) eine große Bedeutung zu. Es ist bekannt, dass Sulfat-reduzierende Bakterien zu den Hauptproduzenten von MeHg gehören. Darüber hinaus gibt es jedoch nur wenige Untersuchungen über die biologischen Mechanismen und die Zusammenhänge in terrestrischen und insbesondere in intestinalen Systemen. Die vorliegende Arbeit leistet daher einen wichtigen Beitrag zur Abschätzung des Potentials zur Hg-Methylierung durch intestinale Bakterien und vertieft die Kenntnisse zu der damit verbundenen Akkumulation der organischen Schwermetallverbindung im Gewebe des Kompostwurms Eisenia foetida (E. foetida). rnIm Rahmen dieser Arbeit wurde erstmals unter Anwendung der Gas Chromatographie mit induktiv gekoppelter Massenspektrometrie (GC-ICP-MS) und Isotopenverdünnungsanalyse verschiedene Kulturen intestinaler Sulfat-reduzierender Bakterien auf die Bildung von organischem Monomethylquecksilber aus Hg(II) untersucht. Da in komplexen bakteriellen Nährlösungen mit hohem Sulfidgehalt Matrixeffekte auftreten und die Analyse von MeHg im Ultraspurenbereich erschweren können, erfolgte die Probenvorbereitung mittels der Methanol-Kaliumhydroxid-Extraktion unter Verwendung eines Maskierungsreagenzes und der Derivatisierung mit Natriumtetrapropylborat. Das Detektionslimit für MeHg in bakteriellen Nährlösungen betrug 0,03 ng/mL. Die Wiederfindung von zertifiziertem Referenzmaterial ERM® CE-464 Tuna Fish war sehr gut und lag in einem Bereich zwischen 98 – 105%. rnDie Resultate der Untersuchung von 14 verschiedenen Rein- und Anreicherungskulturen Sulfat-reduzierender Bakterien zeigten, dass neun Kulturen innerhalb von 12 h nach einer Inkubation mit 0,1 mg/L Hg2+ im Durchschnitt 100 bis 1200 pg/mL MeHg produzierten. Darunter waren zwei Desulfovibrio sp. Stämme, die Spezies Desulfovibrio piger, Desulfovibrio giganteus, Desulfovibrio termitidis, Desulfotomaculum ruminis, Desulfobulbus propionicus sowie Anreicherungskulturen aus dem Intestinaltrakt einer Zygoptera-Larve Zy1 und E. foetida EF4. Die Fähigkeit zur Hg-Methylierung durch eine Spezies der Ordnung Desulfotomaculum aus der Gruppe der Gram-positiven Firmicutes wurde hiermit erstmals beobachtet.rnWeiterhin wurde gezeigt, dass im Intestinaltrakt von E. foetida im Gegensatz zu mikrobiellen Bodenproben eine signifikante biotische Methylierung von Hg(II) durchgeführt wird. Dass diese Transformationen in hohem Maße von der intestinalen Region ausgeht und somit zur Akkumulation von MeHg im Gewebe beiträgt, konnte durch weiterführende Experimente mittels Laserablations-ICP-MS an histologischen Gefrierschnitten des Invertebraten darge-stellt werden. rn

Retrofitting boreholes contaminated with iron in rural Uganda

During my Peace Corps service as a community health liaison in rural Uganda I noticed that many improved water wells in our area had been abandoned. The communities described the water in these wells as being reddish in color, having a foul taste and odor, discoloring clothes and food, and not able to produce lather for washing. Personal investigations and an initial literature search suggested that the primary contaminant was iron. The water in these wells had a low pH and a rusty metallic smell. The water produced early in the morning appeared very red but the water became more transparent as pumping continued. The iron components of many of these wells experienced accelerated corrosion resulting in frequent pump failure. This rapid corrosion coupled with the timing of the onset of iron contamination (months to years after these wells were completed) suggests that the most likely cause of the poor quality water was iron related bacteria and/or sulphate reducing bacteria. This report describes a remedy for iron contamination employed at 5 wells. The remedy involved disinfecting the wells with chlorine and replacing iron pump components with plastic and stainless steel. Iron concentrations in the wells were less than 1 mg/L when the wells were drilled but ranged from 2.5 to 40 mg/L prior to the remedy. After the remedy was applied, the total iron concentrations returned to levels below 1 mg/L. The presence of iron related bacteria was measured in all of these wells using Biological Activity Reaction Tests. Although IRB are still present in all the wells, the dissolved iron concentrations remain less than 1 mg/L. This remedy is practical for rural areas because the work can be performed with only hand tools and costs less than US $850. Because the source of iron contamination is removed in this approach, substantial follow-up maintenance is not necessary.

Alleviation of chronic venous leg ulcers with a hand-held dielectric barrier discharge plasma generator (PlasmaDerm(®) VU-2010): results of a monocentric, two-armed, open, prospective, randomized and controlled trial (NCT01415622).

BACKGROUND Cold atmospheric plasma (CAP, i.e. ionized air) is an innovating promising tool in reducing bacteria. OBJECTIVE We conducted the first clinical trial with the novel PlasmaDerm(®) VU-2010 device to assess safety and, as secondary endpoints, efficacy and applicability of 45 s/cm(2) cold atmospheric plasma as add-on therapy against chronic venous leg ulcers. METHODS From April 2011 to April 2012, 14 patients were randomized to receive standardized modern wound care (n = 7) or plasma in addition to standard care (n = 7) 3× per week for 8 weeks. The ulcer size was determined weekly (Visitrak(®) , photodocumentation). Bacterial load (bacterial swabs, contact agar plates) and pain during and between treatments (visual analogue scales) were assessed. Patients and doctors rated the applicability of plasma (questionnaires). RESULTS The plasma treatment was safe with 2 SAEs and 77 AEs approximately equally distributed among both groups (P = 0.77 and P = 1.0, Fisher's exact test). Two AEs probably related to plasma. Plasma treatment resulted in a significant reduction in lesional bacterial load (P = 0.04, Wilcoxon signed-rank test). A more than 50% ulcer size reduction was noted in 5/7 and 4/7 patients in the standard and plasma groups, respectively, and a greater size reduction occurred in the plasma group (plasma -5.3 cm(2) , standard: -3.4 cm(2) ) (non-significant, P = 0.42, log-rank test). The only ulcer that closed after 7 weeks received plasma. Patients in the plasma group quoted less pain compared to the control group. The plasma applicability was not rated inferior to standard wound care (P = 0.94, Wilcoxon-Mann-Whitney test). Physicians would recommend (P = 0.06, Wilcoxon-Mann-Whitney test) or repeat (P = 0.08, Wilcoxon-Mann-Whitney test) plasma treatment by trend. CONCLUSION Cold atmospheric plasma displays favourable antibacterial effects. We demonstrated that plasma treatment with the PlasmaDerm(®) VU-2010 device is safe and effective in patients with chronic venous leg ulcers. Thus, larger controlled trials and the development of devices with larger application surfaces are warranted.

Plant Adenosine 5′-phosphosulfate Reductase Is a Novel Iron-Sulfur Protein

Adenosine 5′-phosphosulfate reductase (APR) catalyzes the two-electron reduction of adenosine 5′-phosphosulfate to sulfite and AMP, which represents the key step of sulfate assimilation in higher plants. Recombinant APRs from both Lemna minorand Arabidopsis thaliana were overexpressed inEscherichia coli and isolated as yellow-brown proteins. UV-visible spectra of these recombinant proteins indicated the presence of iron-sulfur centers, whereas flavin was absent. This result was confirmed by quantitative analysis of iron and acid-labile sulfide, suggesting a 4Fe-4S cluster as the cofactor. EPR spectroscopy of freshly purified enzyme showed, however, only a minor signal at g = 2.01. Therefore, Mössbauer spectra of 57Fe-enriched APR were obtained at 4.2 K in magnetic fields of up to 7 tesla, which were assigned to a diamagnetic 4Fe-4S2+ cluster. This cluster was unusual because only three of the iron sites exhibited the same Mössbauer parameters. The fourth iron site gave, because of the bistability of the fit, a significantly smaller isomer shift or larger quadrupole splitting than the other three sites. Thus, plant assimilatory APR represents a novel type of adenosine 5′-phosphosulfate reductase with a 4Fe-4S center as the sole cofactor, which is clearly different from the dissimilatory adenosine 5′-phosphosulfate reductases found in sulfate reducing bacteria.

Isolation and Characterization of a Microorganism from Groundwater that Reduces Arsenate

This is an investigation into the microbially mediated processes involved in the transformation of arsenic. With the recent change in the Federal Maximum Contaminant Level for arsenic in drinking water, an increasing amount of resources are being devoted to understanding the mechanisms involved in the movement of arsenic. Arsenic in drinking water typically comes from natural sources, but the triggers that result in increased release of arsenic from parent material are poorly understood. Knowledge of these processes is necessary in order to make sound engineering decisions regarding drinking water management practices. Recent years have brought forth the idea that bacteria play a significant role in arsenic cycling. Groundwater is a major source of potable water in this and many other countries. To date, no reports have been made indicating the presence and activity of arsenate reducing bacteria in groundwater settings, which may increase dissolved arsenic concentrations. This research was designed to address this question and has shown that these bacteria are present in Maine groundwater. Two Maine wells were sampled in order to culture resident bacteria that are capable of dissimilatory arsenate reduction. Samples were collected using anaerobic techniques fiom wells in Northport and Green Lake. These samples were amended with specific compounds to enrich the resident population of arsenate utilizing bacteria. These cultures were monitored over time to establish rates of arsenate reduction. Cultures fiom both sites exhibited arsenate reduction in initial enrichment cultures. Isolates obtained fiom the Green Lake enrichments, however, did not reduce arsenate. This indicates either that a symbiotic relationship was required for the observed arsenate reduction or that fast-growing fermentative organisms that could survive in high arsenate media were picked in the isolation procedure. The Northport cultures exhibited continued arsenate reduction after isolation and successive transfers into fiesh media. The cultured bacteria reduced the majority of 1 a arsenate solutions in less than one week, accompanied by a corresponding oxidation of lactate. The 16s rRNA fiom the isolate was arnplifled and sequenced. The results of the DNA sequence analysis indicate that the rRNA sequence of the bacteria isolated at the Northport site is unique. This means that this strain of bacteria has not been reported before. It is in the same taxonomic subgroup as two previously described arsenate respirers. The implications of this study are significant. The fact that resident bacteria are capable of reducing arsenate has implications for water management practices. Reduction of arsenate to arsenite increases the mobility of the compound, as well as the toxicity. An understanding of the activity of these types of organisms is necessary in order to understand the contribution they are making to arsenic concentrations in drinking water. The next step in this work would be to quantitj the actual loading of dissolved arsenic present in aquifers because of these organisms.

Pasteurization of Apple Cider with UV Irradiation

In a period of increasing concern about food safety, food poisoning outbreaks where unpasterurized apple cider or apple juice was found contaminated with Escherichia coli 0157:H7 reinforces the need for using the best technologies in apple cider production. Most apple cider is sold as an unpasteurized raw product. Because of their acidity, it was believed that juice products do not usually contain microorganisms such as E. coli 0157:H7, Salmonella, and Crytosporidium. Yet all of these foodborne pathogens are capable of being transmitted in unpasteurized juices. It is known that these pathogens can survive for several weeks in a variety of acidic juices. Although heat pasteurization is probably the best method to eliminate these pathogens, it is not the most desirable method as it changes sensory properties and also is very costly for small to mid-sized apple cider processors. Pasteurization of apple cider with Ultraviolet Irradiation (UV) is a potential alternative to heat pasteurization. Germicidal W irradiation is effective in inactivating microorganisms without producing undesirable by-products and changing sensory properties. Unpasteurized raw apple cider from a small local processor was purchased for this study. The effects of physical parameters, exposure time and dosage on the W treatment efficacy were examined as well as the effects of the UV light on apple cider quality. W light with principal energy at a wavelength of 254.7 nm, was effective in reducing bacteria (E .coli, ATCC 25922) inoculated apple cider. The W dosage absorbed by the apple cider was mathematically calculated. A radiation dose of 8,777 μW-s/cm2 reduced bacteria an average of 2.20 logs and in multiple passes, the FDA mandated 5-log reduction was achieved. Sensory analysis showed there was no significant difference between the W treated and non-treated cider. Experiments with W treated apple cider indicated a significant (p < 0.01) extension of product shelf life through inhibition of yeast and mold growth. The extension of the researched performed is applicable to other fruit juice processing operations.

Fatty acids and intact polar lipids of laminated microbial sediments from St. Peter Ording, German Wadden Sea

Hidden for the untrained eye through a thin layer of sand, laminated microbial sediments occur in supratidal beaches along the North Sea coast. The inhabiting microbial communities organize themselves in response to vertical gradients of light, oxygen or sulfur compounds. We performed a fine-scale investigation on the vertical zonation of the microbial communities using a lipid biomarker approach, and assessed the biogeochemical processes using a combination of microsensor measurements and a 13C-labeling experiment. Lipid biomarker fingerprinting showed the overarching importance of cyanobacteria and diatoms in these systems, and heterocyst glycolipids revealed the presence of diazotrophic cyanobacteria even in 9 to 20 mm depth. High abundance of ornithine lipids (OL) throughout the system may derive from sulfate reducing bacteria, while a characteristic OL profile between 5 and 8 mm may indicate presence of purple non-sulfur bacteria. The fate of 13C-labeled bicarbonate was followed by experimentally investigating the uptake into microbial lipids, revealing an overarching importance of cyanobacteria for carbon fixation. However, in deeper layers, uptake into purple sulfur bacteria was evident, and a close microbial coupling could be shown by uptake of label into lipids of sulfate reducing bacteria in the deepest layer. Microsensor measurements in sediment cores collected at a later time point revealed the same general pattern as the biomarker analysis and the labeling experiments. Oxygen and pH-microsensor profiles showed active photosynthesis in the top layer. The sulfide that diffuses from deeper down and decreases just below the layer of active oxygenic photosynthesis indicates the presence of sulfur bacteria, like anoxygenic phototrophs that use sulfide instead of water for photosynthesis.

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.

(Table 1) Stable isotope data of chemoherm carbonates at Hydrate Ridge on the Cascadia continental margin

Two active chemoherm build-ups growing freely up into the oceanic water column, the Pinnacle and the South East-Knoll Chemoherms, have been discovered at Hydrate Ridge on the Cascadia continental margin. These microbially-mediated carbonate formations rise above the seafloor by several tens of meters and display a pinnacle-shaped morphology with steep flanks. The recovered rocks are pure carbonates dominated by aragonite. Based on fabric and mineralogic composition different varieties of authigenic aragonite can be distinguished. Detailed visual and petrographic investigations unambiguously reveal the involvement of microbes during the formation of the carbonates. The fabric of the cryptocrystalline and fibrous aragonite can be described as thrombolitic. Fossilized microbial filaments in the microcrystalline aragonite indicate the intimate relationship between microbes and carbonates. The strongly 13C-depleted carbon isotope values of the samples (as low as -48.1 per mill PDB) are characteristic of methane as the major carbon source for the carbonate formation. The methane-rich fluids from which the carbonates are precipitated originate most probably from a gas reservoir below the bottom-simulating reflector (BSR) and rise through fault systems. The d18O values of the aragonitic chemoherm carbonates are substantially higher (as high as 5.0 per mill PDB) than the expected equilibrium value for an aragonite forming from ambient seawater (3.5 per mill PDB). As a first approximation this indicates formation from glacial ocean water but other factors are considered as well. A conceptual model is presented for the precipitation of these chemoherm carbonates based on in situ observations and the detailed petrographic investigation of the carbonates. This model explains the function of the consortium of archaea and sulfate-reducing bacteria that grows on the carbonates performing anaerobic oxidation of methane (AOM) and enabling the precipitation of the chemoherms above the seafloor surrounded by oxic seawater. Beggiatoa mats growing on the surface of the chemoherms oxidize the sulfide provided by sulfate-dependent anaerobic oxidation of methane within an oxic environment. The contact between Beggiatoa and the underlying microbial consortium represents the interface between the overlying oxic water column and an anoxic micro-environment where carbonate formation takes place.