Gernot Arp

Biofilm exopolymers control microbialite formation at thermal springs discharging into the alkaline Pyramid Lake, Nevada, USA

Calcium carbonate precipitation and microbialite formation at highly supersaturated mixing zones of thermal spring waters and alkaline lake water have been investigated at Pyramid Lake, Nevada. Without precipitation, pure mixing should lead to a nearly 100-fold supersaturation at 40oC. Physicochemical precipitation is modified or even inhibited by the properties of biofilms, dependent on the extent of biofilm development and the current precipitation rate. Mucus substances (extracellular polymeric substances, EPS, e.g., of cyanobacteria) serve as effective Ca 2C -buffers, thus preventing seed crystal nucleation even in a highly supersaturated macroenvironment. Carbonate is then preferentially precipitated in mucus-free areas such as empty diatom tests or voids. After the buffer capacity of the EPS is surpassed, precipitation is observed at the margins of mucus areas. Hydrocarbon biomarkers extracted from (1) a calcifying Phormidium-biofilm, (2) the stromatolitic carbonate below, and (3) a fossil ‘tufa’ of the Pleistocene pinnacles, indicate that the cyanobacterial primary producers have been subject to significant temporal changes in their species distribution. Accordingly, the species composition of cyanobacterial biofilms does not appear to be relevant for the formation of microbial carbonates in Pyramid Lake. The results demonstrate the crucial influence of mucus substances on carbonate precipitation in highly supersaturated natural environments.

Calcification in cyanobacterial biofilms of alkaline salt lakes

Geomicrobiological analysis of calcifying biofilms of three alkaline salt lakes characterized by moderate to high carbonate alkalinity indicates that microbial carbonate rock formation is not directly linked to cyanobacterial carbon fixation. The present review summarizes results from two published case studies that have been carried out at Pyramid Lake, USA, and Lake Nuoertu, PR China. New observations and data are presented for a current project on Satonda Crater Lake, Indonesia, that revise previous conclusions concerning the relationship between cyanobacteria and biofilm calcification. Extracellular polymeric substances (EPS) in the investigated lakes are mostly produced by cyanobacteria; their properties are discussed as key factors in biofilm calcification. In particular, EPS are capable of binding divalent cations (e.g. Ca2+) from the liquid phase by their carboxylate and sulphate groups. Therefore, despite a high supersaturation of the lake water with respect to calcium carbonate minerals, precipi...

Widefield deconvolution epifluorescence microscopy combined with fluorescence in situ hybridization reveals the spatial arrangement of bacteria in sponge tissue

Widefield deconvolution epifluorescence microscopy (WDEM) combined with fluorescence in situ hybridization (FISH) was performed to identify and characterize single bacterial cells within sections of the mediterranean sponge Chondrosia reniformis. Sponges were embedded in paraffin wax or plastic prior to the preparation of thin sections, in situ hybridization and microscopy. Serial digital images generated by widefield epifluorescence microscopy were visualized using an exhaustive photon reassignment deconvolution algorithm and three-dimensional rendering software. Computer processing of series of images taken at different focal planes with the deconvolution technique provided deblurred three-dimensional images with high optical resolution on a submicron scale. Results from the deconvolution enhanced widefield microscopy were compared with conventional epifluorescent microscopical images. By the application of the deconvolution algorithm on digital image data obtained with widefield epifluorescence microscopy after FISH, the occurrence and spatial arrangement of Desulfovibrionaceae closely associated with micropores of Chondrosia reniformis could be visualized.

Phylogenetic Analysis of a Microbialite-Forming Microbial Mat from a Hypersaline Lake of the Kiritimati Atoll, Central Pacific

On the Kiritimati atoll, several lakes exhibit microbial mat-formation under different hydrochemical conditions. Some of these lakes trigger microbialite formation such as Lake 21, which is an evaporitic, hypersaline lake (salinity of approximately 170‰). Lake 21 is completely covered with a thick multilayered microbial mat. This mat is associated with the formation of decimeter-thick highly porous microbialites, which are composed of aragonite and gypsum crystals. We assessed the bacterial and archaeal community composition and its alteration along the vertical stratification by large-scale analysis of 16S rRNA gene sequences of the nine different mat layers. The surface layers are dominated by aerobic, phototrophic, and halotolerant microbes. The bacterial community of these layers harbored Cyanobacteria (Halothece cluster), which were accompanied with known phototrophic members of the Bacteroidetes and Alphaproteobacteria. In deeper anaerobic layers more diverse communities than in the upper layers were present. The deeper layers were dominated by Spirochaetes, sulfate-reducing bacteria (Deltaproteobacteria), Chloroflexi (Anaerolineae and Caldilineae), purple non-sulfur bacteria (Alphaproteobacteria), purple sulfur bacteria (Chromatiales), anaerobic Bacteroidetes (Marinilabiacae), Nitrospirae (OPB95), Planctomycetes and several candidate divisions. The archaeal community, including numerous uncultured taxonomic lineages, generally changed from Euryarchaeota (mainly Halobacteria and Thermoplasmata) to uncultured members of the Thaumarchaeota (mainly Marine Benthic Group B) with increasing depth.

Photosynthesis, Respiration and Exopolymer Calcium-Binding in Biofilm Calcification (Westerhöfer and Deinschwanger Creek, Germany)

The impact of microbial activity on biofilm calcification in aquatic environments is still a matter of debate, especially in settings where ambient water has high CaCO3 mineral supersaturation. In this study, biofilms of two CO2-degassing karst-water creeks in Germany, which attain high calcite supersaturation during their course downstream, were investigated with regard to water chemistry of the biofilm microenvironment. The biofilms mainly consisted of filamentous cyanobacteria (Phormidium morphotype) and heterotrophic bacteria (including sulfate-reducing bacteria), which affect the microenvironment and produce acidic exopolymers. In situ and ex situ microelectrode measurements showed that a strong pH increase, coupled with Ca2 + consumption, occurred in light conditions at the biofilm surface, while the opposite occurred in the dark. Calcite supersaturation at the biofilm surface, calculated from ex situ Ca2 + and CO3 2− microelectrode measurements, showed that photosynthesis resulted in high omega values during illumination, while respiration slightly lowered supersaturation values in the dark, compared to values in the water column. Dissociation calculation demonstrated that the potential amount of Ca2 + binding by exopolymers would be insufficient to explain the Ca2 + loss observed, although Ca2 + complexation to exopolymers might be crucial for calcite nucleation. No spontaneous precipitation occurred on biofilm-free limestone substrates under the same condition, regardless of high supersaturation. These facts indicate that photosynthesis is a crucial mechanism to overcome the kinetic barrier for CaCO3 precipitation, even in highly supersaturated settings.

Fluvival tufa formation in a hard-water creek (Deinschwanger Bach, Franconian Alb, Germany)

SummaryCyanobacteria-dominated biofilms involved in tufa deposition in the hardwater creek Deinschwanger Bach, Bavaria, were investigated with regard to their effect on the carbonate equilibrium and fabric formation. Current tufa deposition is evident by up to 1.5 mm thick crusts that have formed on substrate plates placed in the creek for 10 months. Hydrochemistry data indicate that carbonate precipitation along the creek is physicochemically driven by CO2 degassing, whereas photosynthetic carbon assimilation is without detectable effect on the macroscale carbonate equilibrium. However, stable isotope data indicate a minor photosynthetic effect, but only for the lower creek section where the pCO2 already drops to the two-fold of the atmospheric level. Though the initial process of external nucleation on cyanobacterial sheaths in the lower creck section might be promoted of by a photosynthetically-induced microscale pH gradient, the effect is not strong enough to cause a CaCO3 impregnation of the sheaths. The fabric of the laminated tufa crusts in the creek reflects the temporal alternation of porous microspariticPhormidium incrustatum-Phormidium foveolarum-diatom biofilms in spring, micrite-impregnatedPhormidium incrustatum-Phormidium foveolarum-diatom biofilms in summerautumn, and detritus-rich non-calcified diatom-biofilms in winter. By contrast, exopolymer-poor surfaces of cascade tufa mosses show large, euhedral spar crystals. Non-phototrophic bacteria, which occur in large numbers inPhormidium incrustatum-Phormidium foveolarums-diatom-communities, thrive on extracellular polymeric substances (EPS) and dead cells of the cyanobacteria and are unlikely to promote CaCO3 precipitation.

Lacustrine bioherms, spring mounds, and marginal carbonates of the Ries-impact-crater (Miocene, Southern Germany)

SummaryThe petrographic investigation of the Miocene Rieslake-carbonates gave rise to a modifiedDunham-scheme for classifying non-marine carbonates. If the fabric is not exclusively the result of hydromechanical or biogenic effects,Dunham-terms were extended by interpretative attributes describing processes responsible for the secondary fabric development (pedogenesis, early meteoric diagenesis). The lowermost investigated section reveals a distinct zonation of the lake shore during humid stages (carbonates of the infra-, eu-, and supralittoral), interrupted by playa-like interstages of arid conditions (desiccated mudflat). Dolomitic successions of sinter-veneered bioherms, built by green algae and cyanobacteria, form an incomplete ‘reef belt’ at the northern crater rim. Bioherm sequences were controlled by a seasonally oscillating lake level and fluctuations of higher order, which correspond to small-scale climatic fluctuations in the range of several hundreds to thousands of years. A superposed facies trend is recognized, which is the result of the decreasing eutrophy, alkalinity, and carbonate supersaturation. This reflects the climatic change to generally humid conditions at the end of Miocene. Originally thrombolitic sublacustrine spring mounds were caused by upwelling groundwater from permeable bedrock. Cement framestones of the mound core are considered to result from fabric alteration within the upwelling ground water and by emersions. Marginal carbonates of the Ries basin, inclusively bioherms, probably were originally Mg-calcitic. Aragonite was restricted to gastropod shells and sublacustrine spring mounds. Dolomitization is interpreted as essentially due to a fluctuating phreatic mixing-zone caused by meteoric groundwater, which underflowed saline water at the soda lake margin. The algal flora comprises cyanobacteria, possible cyanobacteria, green algae, few charophytes, endoliths, and problematic forms. A Recent contamination by endolithic fungi and lichens is evident. Occasionally preserved insect larval tubes, mass accumulations of pupal cases of flies, and arthropod eggs demonstrate that these groups were once a prominent part of the fossil soda lake ecosystem of the Nördlinger Ries.

Metabolic Microenvironmental Control by Photosynthetic Biofilms under Changing Macroenvironmental Temperature and pH Conditions

ABSTRACT Ex situ microelectrode experiments, using cyanobacterial biofilms from karst water creeks, were conducted under various pH, temperature, and constant-alkalinity conditions to investigate the effects of changing environmental parameters on cyanobacterial photosynthesis-induced calcification. Microenvironmental chemical conditions around calcifying sites were controlled by metabolic activity over a wide range of photosynthesis and respiration rates, with little influence from overlying water conditions. Regardless of overlying water pH levels (from 7.8 to 8.9), pH at the biofilm surface was approximately 9.4 in the light and 7.8 in the dark. The same trend was observed at various temperatures (4°C and 17°C). Biological processes control the calcium carbonate saturation state (Ω) in these and similar systems and are able to maintain Ω at approximately constant levels over relatively wide environmental fluctuations. Temperature did, however, have an effect on calcification rate. Calcium flux in this system is limited by its diffusion coefficient, resulting in a higher calcium flux (calcification and dissolution) at higher temperatures, despite the constant, biologically mediated pH. The ability of biological systems to mitigate the effects of environmental perturbation is an important factor that must be considered when attempting to predict the effects of increased atmospheric partial CO2 pressure on processes such as calcification and in interpreting microfossils in the fossil record.

Tufa-forming biofilms of German karstwater streams: microorganisms, exopolymers, hydrochemistry and calcification

Abstract To understand mechanisms of tufa biofilm calcification, selected karstwater stream stromatolites in Germany have been investigated with regard to their hydrochemistry, biofilm community, exopolymers, physicochemical microgradients, calcification pattern and lamination. In stream waters, CO2 degassing drives the increase in calcite saturation to maximum values of approximately 10-fold, independent from the initial Ca2+/alkalinity ratio. For the cyanobacteria of tufa biofilms, a culture-independent molecular approach showed that microscopy of resin-embedded biofilm thin sections underestimated the actual diversity of cyanobacteria, i.e. the six cyanobacteria morphotypes were opposed to nine different lineages of the 16S rDNA phylogeny. The same morphotype may even represent two genetically distant cyanobacteria and the closest relatives of tufa biofilm cyanobacteria may be from quite different habitats. Diatom diversity was even higher in the biofilm at the studied exemplar site than that of the cyanobacteria, i.e. 13 diatom species opposed to 9 cyanobacterial lineages. The non-phototrophic prokaryotic biofilm community is clearly different from the soil-derived community of the stream waters, and largely composed of flavobacteria, firmicutes, proteobacteria and actinobacteria. The exopolymeric biofilm matrix can be divided into three structural domains by fluorescence lectin-binding analysis. Seasonal and spatial variability of these structural EPS domains is low in the investigated streams. As indicated by microsensor data, biofilm photosynthesis is the driving mechanism in tufa stromatolite formation. However, photosynthesis-induced biofilm calcification accounts for only 10–20% of the total Ca2+ loss in the streams, and occurs in parallel to inorganic precipitation driven by CO2-degassing within the water column and on biofilm-free surfaces. Annual stromatolite laminae reflect seasonal changes in temperature and light supply. The stable carbon isotope composition of the laminae is not affected by photosynthesis-induced microgradients, but mirrors that of the bulk water body only reflecting climate fluctuations. Tufa stromatolites with their cyanobacterial–photosynthesis-related calcification fabrics form an analogue to porostromate cyanobacterial stromatolites in fossil settings high in CaCO3 mineral supersaturation but comparatively low in dissolved inorganic carbon. Here, the sum-effect of heterotrophic exopolymer-degradation and secondary Ca2+-release rather decreases calcite saturation, contrary to settings high in dissolved inorganic carbon such as soda lakes.

A Cryptoendolithic Community in Volcanic Glass

Fluorescent in situ hybridization (FISH) and 16S rDNA analysis were used to characterize the endolithic colonization of silica-rich rhyolitic glass (obsidian) in a barren terrestrial volcanic environment in Iceland. The rocks were inhabited by a diverse eubacterial assemblage. In the interior of the rock, we identified cyanobacterial and algal 16S (plastid) sequences and visualized phototrophs by FISH, which demonstrates that molecular methods can be used to characterize phototrophs at the limits of photosynthetically active radiation (PAR). Temperatures on the surface of the dark rocks can exceed 40 degrees C but are below freezing for much of the winter. The rocks effectively shield the organisms within from ultraviolet radiation. Although PAR sufficient for photosynthesis cannot penetrate more than approximately 250 mum into the solid rock, the phototrophs inhabit cavities; and we hypothesize that by weathering the rock they may contribute to the formation of cavities in a feedback process, which allows them to acquire sufficient PAR at greater depths. These observations show how pioneer phototrophs can colonize the interior of volcanic glasses and rocks, despite the opaque nature of these materials. The data show that protected microhabitats in volcanic rocky environments would have been available for phototrophs on early Earth.