Formation of 3-Aminophenols from Cyclohexane-1,3-diones.

meta-Aminophenols are formed by the action of DBU on 3-amino-2-chlorocyclohex-2-en-1-ones at room temperature in MeCN. The chloro compounds are generated by treating 3-aminocyclohex-2-en-1-ones with the easily prepared halogenating agent BnNMe3·ICl2 in MeOH-CH2Cl2. The amino group must carry two substituents, either two aryl, one aryl and one alkyl, or two alkyl groups; 3-aminocyclohex-2-en-1-ones of this type are readily made from cyclohex-2-en-1-one and a primary or secondary amine.

Lipid Biomarker and Isotopic Study of Community Distribution and Biomarker Preservation in a Laminated Microbial Mat from Shark Bay, Western Australia.

Modern microbial mats from Shark Bay present some structural similarities with ancient stromatolites; thus, the functionality of microbial communities and processes of diagenetic preservation of modern mats may provide an insight into ancient microbial assemblages and preservation. In this study, the vertical distribution of microbial communities was investigated in a well-laminated smooth mat from Shark Bay. Biolipid and compound-specific isotopic analyses were performed to investigate the distribution of microbial communities in four distinct layers of the mat. Biomarkers indicative of cyanobacteria were more abundant in the uppermost oxic layer. Diatom markers (e.g. C25 HBI alkene, C20:4ω6 and C20:5ω3 polar lipid fatty acids (PLFAs)) were also detected in high abundance in the uppermost layer, but also in the deepest layer under conditions of permanent darkness and anoxia, where they probably used NO3 (-) for respiration. CycC19:0, an abundant PLFA of purple sulfur bacteria (PSB), was detected in all layers and presented the most (13)C-depleted values of all PLFAs, consistent with photoautotrophic PSB. Sulfur-bound aliphatic and aromatic biomarkers were detected in all layers, highlighting the occurrence of early sulfurisation which may be an important mechanism in the sedimentary preservation of functional biolipids in living and, thus, also ancient mats.

Characterizing microbial communities and processes in a modern stromatolite (Shark Bay) using lipid biomarkers and two-dimensional distributions of porewater solutes.

Modern microbial mats are highly complex and dynamic ecosystems. Diffusive equilibration in thin films (DET) and diffusive gradients in thin films (DGT) samplers were deployed in a modern smooth microbial mat from Shark Bay in order to observe, for the first time, two-dimensional distributions of porewater solutes during day and night time. Two-dimensional sulfide and alkalinity distributions revealed a strong spatial heterogeneity and a minor contribution of sulfide to alkalinity. Phosphate distributions were also very heterogeneous, while iron(II) distributions were quite similar during day and night with a few hotspots of mobilization. Lipid biomarkers from the three successive layers of the mat were also analysed in order to characterize the microbial communities regulating analyte distributions. The major hydrocarbon products detected in all layers included n-alkanes and isoprenoids, whilst other important biomarkers included hopanoids. Phospholipid fatty acid profiles revealed a decrease in cyanobacterial markers with depth, whereas sulfate-reducing bacteria markers increased in abundance in accordance with rising sulfide concentrations with depth. Despite the general depth trends in community structure and physiochemical conditions within the mat, two-dimensional solute distributions showed considerable small-scale lateral variability, indicating that the distributions and activities of the microbial communities regulating these solute distributions were equally heterogeneous and complex.

Formation of micro-spherulitic barite in association with organic matter within sulfidized stromatolites of the 3.48 billion-year-old Dresser Formation, Pilbara Craton.

The shallow marine and subaerial sedimentary and hydrothermal rocks of the ~3.48 billion-year-old Dresser Formation are host to some of Earth's oldest stromatolites and microbial remains. This study reports on texturally distinctive, spherulitic barite micro-mineralization that occur in association with primary, autochthonous organic matter within exceptionally preserved, strongly sulfidized stromatolite samples obtained from drill cores. Spherulitic barite micro-mineralization within the sulfidized stromatolites generally forms submicron-scale aggregates that show gradations from hollow to densely crystallized, irregular to partially radiating crystalline interiors. Several barite micro-spherulites show thin outer shells. Within stromatolites, barite micro-spherulites are intimately associated with petrographically earliest dolomite and nano-porous pyrite enriched in organic matter, the latter of which is a possible biosignature assemblage that hosts microbial remains. Barite spherulites are also observed within layered barite in proximity to stromatolite layers, where they are overgrown by compositionally distinct (Sr-rich), coarsely crystalline barite that may have been sourced from hydrothermal veins at depth. Micro-spherulitic barite, such as reported here, is not known from hydrothermal systems that exceed the upper temperature limit for life. Rather, barite with near-identical morphology and micro-texture is known from zones of high bio-productivity under low-temperature conditions in the modern oceans, where microbial activity and/or organic matter of degrading biomass controls the formation of spherulitic aggregates. Hence, the presence of micro-spherulitic barite in the organic matter-bearing Dresser Formation sulfidized stromatolites lend further support for a biogenic origin of these unusual, exceptionally well-preserved, and very ancient microbialites.

Palaeobiology of red and white blood cell-like structures, collagen and cholesterol in an ichthyosaur bone.

Carbonate concretions are known to contain well-preserved fossils and soft tissues. Recently, biomolecules (e.g. cholesterol) and molecular fossils (biomarkers) were also discovered in a 380 million-year-old concretion, revealing their importance in exceptional preservation of biosignatures. Here, we used a range of microanalytical techniques, biomarkers and compound specific isotope analyses to report the presence of red and white blood cell-like structures as well as platelet-like structures, collagen and cholesterol in an ichthyosaur bone encapsulated in a carbonate concretion from the Early Jurassic (~182.7 Ma). The red blood cell-like structures are four to five times smaller than those identified in modern organisms. Transmission electron microscopy (TEM) analysis revealed that the red blood cell-like structures are organic in composition. We propose that the small size of the blood cell-like structures results from an evolutionary adaptation to the prolonged low oxygen atmospheric levels prevailing during the 70 Ma when ichthyosaurs thrived. The δ13C of the ichthyosaur bone cholesterol indicates that it largely derives from a higher level in the food chain and is consistent with a fish and cephalopod diet. The combined findings above demonstrate that carbonate concretions create isolated environments that promote exceptional preservation of fragile tissues and biomolecules.

Biodiversity inventories in high gear: DNA barcoding facilitates a rapid biotic survey of a temperate nature reserve.

BACKGROUND: Comprehensive biotic surveys, or 'all taxon biodiversity inventories' (ATBI), have traditionally been limited in scale or scope due to the complications surrounding specimen sorting and species identification. To circumvent these issues, several ATBI projects have successfully integrated DNA barcoding into their identification procedures and witnessed acceleration in their surveys and subsequent increase in project scope and scale. The Biodiversity Institute of Ontario partnered with the rare Charitable Research Reserve and delegates of the 6th International Barcode of Life Conference to complete its own rapid, barcode-assisted ATBI of an established land trust in Cambridge, Ontario, Canada. NEW INFORMATION: The existing species inventory for the rare Charitable Research Reserve was rapidly expanded by integrating a DNA barcoding workflow with two surveying strategies - a comprehensive sampling scheme over four months, followed by a one-day bioblitz involving international taxonomic experts. The two surveys resulted in 25,287 and 3,502 specimens barcoded, respectively, as well as 127 human observations. This barcoded material, all vouchered at the Biodiversity Institute of Ontario collection, covers 14 phyla, 29 classes, 117 orders, and 531 families of animals, plants, fungi, and lichens. Overall, the ATBI documented 1,102 new species records for the nature reserve, expanding the existing long-term inventory by 49%. In addition, 2,793 distinct Barcode Index Numbers (BINs) were assigned to genus or higher level taxonomy, and represent additional species that will be added once their taxonomy is resolved. For the 3,502 specimens, the collection, sequence analysis, taxonomic assignment, data release and manuscript submission by 100+ co-authors all occurred in less than one week. This demonstrates the speed at which barcode-assisted inventories can be completed and the utility that barcoding provides in minimizing and guiding valuable taxonomic specialist time. The final product is more than a comprehensive biotic inventory - it is also a rich dataset of fine-scale occurrence and sequence data, all archived and cross-linked in the major biodiversity data repositories. This model of rapid generation and dissemination of essential biodiversity data could be followed to conduct regional assessments of biodiversity status and change, and potentially be employed for evaluating progress towards the Aichi Targets of the Strategic Plan for Biodiversity 2011-2020.

Representative measurement of two-dimensional reactive phosphate distributions and co-distributed iron(II) and sulfide in seagrass sediment porewaters.

The high degree of heterogeneity within sediments can make interpreting one-dimensional measurements difficult. The recent development and use of in situ techniques that measure two-dimensional distributions of porewater solutes have facilitated investigation of the role of spatial heterogeneity in sediment biogeochemistry. A colourimetric diffusive equilibration in thin films method has been developed that allows two-dimensional, high-resolution measurement of reactive phosphate in sediment porewaters. A method detection limit of 0.22 µM, an effective upper limit of ~1000 µM and relative standard deviations typically below 5% were achieved. This method was evaluated by deployment in seagrass (Zostera capricorni) colonised sediments, as part of combined probes with similar colourimetric methods for sulfide and iron(II). The two-dimensional, high resolution distributions obtained provide a highly representative measurement of the co-distributions of porewater solutes, allowing heterogeneous features and biogeochemical processes to be observed and interpreted. Microniches of high phosphate concentration >100 µM were observed throughout the distributions and were interpreted to be due to localised zones of rapid organic matter mineralisation, possibly using electron acceptors other than iron(III) oxyhydroxides (e.g. aerobic respiration) as often they did not correspond with microniches of higher Fe(II) concentration.