Analysis of diurnal and vertical microbial diversity of a hypersaline microbial mat

Microbial mats are prokaryotic communities that provide model systems to analyze microbial diversity and ecophysiological interactions. Community diversity of microbial mat samples was assessed at 8:00 a.m. and 3:00 p.m. in a combined analysis consisting of 16S rRNA-denaturing gradient gel electrophoresis (DGGE) and phospholipid fatty acid (PLFA) profiles. The divergence index determined from PLFA and DGGE data showed that depth-related differences have a greater influence on diversity than temporal variations. Shannon and Simpson indices yielded similar values in all samples, which suggested the stable maintenance of a structurally diverse microbial community. The increased diversity observed at 3:00 p.m. between 2.5 and 4 mm can be explained mainly by diversification of anaerobic microorganisms, especially sulfate-reducing bacteria. In the afternoon sampling, the diversity index reflected a higher diversity between 4 and 5.5 mm depth, which suggested an increase in the diversity of strict anaerobes and fermenters. The results are consistent with the conclusion that hypersaline microbial mats are characterized by high degree of diversity that shifts in response to the photobiological adaptations and metabolic status of the microbial community. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Dedicated to the memory of David C. White.     

Degradation of petroleum model compounds immobilized on clay by a hypersaline microbial mat

In this study the degradation of hydrophobic petroleum model compounds (phenanthrene, pristane, octadecane and dibenzothiophene) added to a submersed hypersaline microbial mat was investigated. Montmorillonite with an artificially altered, hydrophobic surface was used as carrier material, forming an organo-clay complex (OCC) with the attached mixture of petroleum model compounds. 6 mg/cm² OCC were applied to cyanobacterialmat pieces, containing 33.3 g/mg OCC of each compound. The degradationexperiment was performed under controlled laboratory conditions and accompanied bychemical analyses by GC/GC-MS, molecular analyses by PCR and DGGE as well asfunctional analyses by microsensor measurements of oxygen, photosynthesis, sulfide,pH and light. All applied model compounds were degraded, but residues were stillpresent after 18 weeks. The aromatic compounds phenanthrene (5.1 g/mg OCC)and dibenzothiophene (4.3 g/mg OCC) were preferentially degraded compared to the alkanes pristane (12.4 g/mg OCC) and n-octadecane (13.4 g/mg OCC). Metabolic changes during the degradation process could not be detected by microsensor measurements. The molecular population analyses did not reveal any significant community changes concomitant with the decrease of the petroleum model compounds. We conclude, that the pristine mats represent an intact, robust ecosystem in which the enzymatic requirements for the degradation of the applied pollutants exist. The slow degradation process did not affect the usual high internal turnover rates and did not favor a certain population in the community of the mats.     

A stochastic differential equation model of diurnal cortisol patterns

Circadian modulation of episodic bursts is recognized as the normal physiological pattern of diurnal variation in plasma cortisol levels. The primary physiological factors underlying these diurnal patterns are the ultradian timing of secretory events, circadian modulation of the amplitude of secretory events, infusion of the hormone from the adrenal gland into the plasma, and clearance of the hormone from the plasma by the liver. Each measured plasma cortisol level has an error arising from the cortisol immunoassay. We demonstrate that all of these three physiological principles can be succinctly summarized in a single stochastic differential equation plus measurement error model and show that physiologically consistent ranges of the model parameters can be determined from published reports. We summarize the model parameters in terms of the multivariate Gaussian probability density and establish the plausibility of the model with a series of simulation studies. Our framework makes possible a sensitivity analysis in which all model parameters are allowed to vary simultaneously. The model offers an approach for simultaneously representing cortisol's ultradian, circadian, and kinetic properties. Our modeling paradigm provides a framework for simulation studies and data analysis that should be readily adaptable to the analysis of other endocrine hormone systems.     

Effects of salinity and light on organic carbon and nitrogen uptake in a hypersaline microbial mat

Utilization of dissolved organic matter (DOM) is thought to be the purview of heterotrophic microorganisms, but photoautotrophs can take up dissolved organic nitrogen (DON) and dissolved organic carbon (DOC). This study investigated DOC and DON uptake in a laminated cyanobacterial mat community from hypersaline Salt Pond (San Salvador, Bahamas). The total community uptake of (3)H-labeled substrates was measured in the light and in the dark and under conditions of high and low salinity. Salinity was the primary control of DOM uptake, with increased uptake occurring under low-salinity, 'freshened' conditions. DOC uptake was also enhanced in the light as compared with the dark and in samples incubated with the photosystem II inhibitor 3(3,4-dichlorophenyl)-1, 1-dimethylurea, suggesting a positive association between photosynthetic activity and DOC uptake. Microautoradiography revealed that some DOM uptake was attributed to cyanobacteria. Cyanobacteria DOM uptake was negatively correlated with that of smaller filamentous microorganisms, and DOM uptake by individual coccoid cells was negatively correlated with uptake by colonial coccoids. These patterns of activity suggest that Salt Pond microorganisms are engaged in resource partitioning, and DOM utilization may provide a metabolic boost to both heterotrophs and photoautrophs during periods of lowered salinity.     

Compartment model for biological conversions of DMS in a microbial mat: Effect of pH on DMS fluxes

Abstract: A model has been developed to describe the biological conversions of five functional groups of microorganisms in a microbial mat. Microbial metabolism and transport of nutrients are the two dominant processes that were considered. The microbial activity was described with Michaelis-Menten kinetics. Transport of nutrients through the mat was described by simple transport processes. The model was validated using documented measurements, and was used to simulate the fluxes of compounds and concentrations in a microbial mat during a light period of 12 hours. Experimental data from Methylopila sulfovorans cultures (isolated from a microbial mat) were incorporated in the model in order to describe DMS oxidation under varying conditions in a mat.     

Insights into chemotaxonomic composition and carbon cycling of phototrophic communities in an artesian sulfur-rich spring (Zodletone, Oklahoma, USA), a possible analog for ancient microbial mat systems

Zodletone spring in Oklahoma is a unique environment with high concentrations of dissolved-sulfide (10 mm) and short-chain gaseous alkanes, exhibiting characteristics that are reminiscent of conditions that are thought to have existed in Earth's history, in particular the late Archean and early-to-mid Proterozoic. Here, we present a process-oriented investigation of the microbial community in two distinct mat formations at the spring source, (1) the top of the sediment in the source pool and (2) the purple streamers attached to the side walls. We applied a combination of pigment and lipid biomarker analyses, while functional activities were investigated in terms of oxygen production (microsensor analysis) and carbon utilization ((13)C incorporation experiments). Pigment analysis showed cyanobacterial pigments, in addition to pigments from purple sulfur bacteria (PSB), green sulfur bacteria (GSB) and Chloroflexus-like bacteria (CLB). Analysis of intact polar lipids (IPLs) in the source sediment confirmed the presence of phototrophic organisms via diacylglycerol phospholipids and betaine lipids, whereas glyceroldialkylglyceroltetraether additionally indicated the presence of archaea. No archaeal IPLs were found in the purple streamers, which were strongly dominated by betaine lipids. (13)C-bicarbonate- and -acetate-labeling experiments indicated cyanobacteria as predominant phototrophs in the source sediment, carbon was actively fixed by PSB/CLB/GSB in purple streamers by using near infrared light. Despite the presence of cyanobacteria, no oxygen could be detected in the presence of light, suggesting anoxygenic photosynthesis as the major metabolic process at this site. Our investigations furthermore indicated photoheterotrophy as an important process in both habitats. We obtained insights into a syntrophically operating phototrophic community in an ecosystem that bears resemblance to early Earth conditions, where cyanobacteria constitute an important contributor to carbon fixation despite the presence of high sulfide concentrations.     

A hypersaline microbial mat from the Pacific Atoll Kiritimati: insights into composition and carbon fixation using biomarker analyses and a 13C-labeling approach

Modern microbial mats are widely recognized as useful analogs for the study of biogeochemical processes relevant to paleoenvironmental reconstruction in the Precambrian. We combined microscopic observations and investigations of biomarker composition to investigate community structure and function in the upper layers of a thick phototrophic microbial mat system from a hypersaline lake on Kiritimati (Christmas Island) in the Northern Line Islands, Republic of Kiribati. In particular, an exploratory incubation experiment with ¹³C-labeled bicarbonate was conducted to pinpoint biomarkers from organisms actively fixing carbon. A high relative abundance of the cyanobacterial taxa Aphanocapsa and Aphanothece was revealed by microscopic observation, and cyanobacterial fatty acids and hydrocarbons showed ¹³C-uptake in the labeling experiment. Microscopic observations also revealed purple sulfur bacteria (PSB) in the deeper layers. A cyclic C_19:0 fatty acid and farnesol were attributed to this group that was also actively fixing carbon. Background isotopic values indicate Calvin–Benson cycle-based autotrophy for cyc C_19:0 and farnesol-producing PSBs. Biomarkers from sulfate-reducing bacteria (SRB) in the top layer of the mat and their ¹³C-uptake patterns indicated a close coupling between SRBs and cyanobacteria. Archaeol, possibly from methanogens, was detected in all layers and was especially abundant near the surface where it contained substantial amounts of ¹³C-label. Intact glycosidic tetraether lipids detected in the deepest layer indicated other archaea. Large amounts of ornithine and betaine bearing intact polar lipids could be an indicator of a phosphate-limited ecosystem, where organisms that are able to substitute these for phospholipids may have a competitive advantage.     

Characteristics and turnover of exopolymeric substances in a hypersaline microbial mat

The properties and microbial turnover of exopolymeric substances (EPS) were measured in a hypersaline nonlithifying microbial mat (Eleuthera, Bahamas) to investigate their potential role in calcium carbonate (CaCO₃) precipitation. Depth profiles of EPS abundance and enzyme activities indicated that c . 80% of the EPS were turned over in the upper 15–20 mm. Oxic and anoxic mat homogenates amended with low-molecular-weight (LMW) organic carbon, sugar monomers, and different types of EPS revealed rapid consumption of all substrates. When comparing the consumption of EPS with that of other substrates, only marginally longer lag times and lower rates were observed. EPS (5–8%) were readily consumed during the conversion of labile to refractory EPS. This coincided with a decrease in glucosidase activity and a decrease in the number of acidic functional groups on the EPS. Approximately half of the calcium bound to the EPS remained after 10 dialyses steps. This tightly bound calcium was readily available to precipitate as CaCO₃. We present a conceptual model in which LMW organic carbon complexed with the tightly bound calcium is released upon enzyme activity. This increases alkalinity and creates binding sites for carbonate and allows CaCO₃ to precipitate. Therefore, this model explains interactions between EPS and CaCO₃ precipitation, and underscores the critical role of aerobic and anaerobic microorganisms in early diagenesis and lithification processes.     

Rates of sulfate reduction and thiosulfate consumption in a marine microbial mat

Abstract The sulfur cycle in a microbial mat was studied by determining viable counts of sulfate-reducing bacteria, chemolithoautotrophic sulfur bacteria and anoxygenic phototrophic bacteria. All three functional groups of sulfur bacteria revealed a maximum population density in the uppermost 5 mm of the mat: 1.1 × 10⁸ cells of sulfate reducers cm⁻³ sediment, 2.0 × 10⁹ cells of chemolithoautotrophs cm⁻³ sediment, and 4.0 × 10⁷ cells of anoxygenic phototrophs cm⁻³ sediment. Bacterial dynamics were studied by sulfate reduction rate measurements, both under anoxic conditions (dark incubation) and oxic conditions (incubation in the light), and determination of the vertical distribution of the potential rate of thiosulfate consumption under oxic conditions. Sulfate reduction rates in the top 5 mm of the sediment were 566 nmol cm⁻³ d⁻¹ in the absence of oxygen, and 123 nmol cm⁻³ d⁻¹ in the presence of oxygen. In the latter case, the maximum rate was found in the 5–10-mm depth horizon (361 nmol cm⁻³ d⁻¹). Biological consumption of amended thiosulfate was rapid and decreased with depth, while in the presence of molybdate, thiosulfate consumption decreased to 10–30% of the original rate.     

Prediction of group patterns in social mammals based on a coalescent model

This study describes a statistical model which assumes that mammal group patterns match with groups of genetic relatives. Given a fixed sample size, recursive algorithms for the exact computation of the probability distribution of the number of groups are provided. The recursive algorithms are then incorporated into a statistical likelihood framework which can be used to detect and quantify departure from the null-model by estimating a clustering parameter. The test is then applied to ecological data from social herbivores and carnivores. Our findings support the hypothesis that genetic relatedness is likely to predict group patterns when large mammals have few or no predators.     

Oscillations in the perception of ambiguous patterns a model based on synergetics

An algorithm which can be realized by synergetic systems and which was introduced by one of us (Haken 1987) for the recognition of patterns is extended so that the perception of ambiguous patterns can be modelled. In this approach so-called attention parameters are subjected to a damping mechanism mimicking the effect of saturation of attention. In this way oscillations of perception arise quite naturally. Our approach takes also ambiguous patterns with bias into account which leads to different periods of the attention paid to the one or the other interpretation of the pattern. Our results are in good agreement with previous psycho-physical studies by other authors. Finally we show how hysteresis of perception can be modelled.     

Lipid biomarkers and carbon isotope signatures of a microbial (Beggiatoa) mat associated with gas hydrates in the gulf of Mexico

White and orange mats are ubiquitous on surface sediments associated with gas hydrates and cold seeps in the Gulf of Mexico. The goal of this study was to determine the predominant pathways for carbon cycling within an orange mat in Green Canyon (GC) block GC 234 in the Gulf of Mexico. Our approach incorporated laser-scanning confocal microscopy, lipid biomarkers, stable carbon isotopes, and 16S rRNA gene sequencing. Confocal microscopy showed the predominance of filamentous microorganisms (4 to 5 mum in diameter) in the mat sample, which are characteristic of Beggiatoa. The phospholipid fatty acids extracted from the mat sample were dominated by 16:1omega7c/t (67%), 18:1omega7c (17%), and 16:0 (8%), which are consistent with lipid profiles of known sulfur-oxidizing bacteria, including Beggiatoa. These results are supported by the 16S rRNA gene analysis of the mat material, which yielded sequences that are all related to the vacuolated sulfur-oxidizing bacteria, including Beggiatoa, Thioploca, and Thiomargarita. The delta13C value of total biomass was -28.6 per thousand; those of individual fatty acids were -29.4 to -33.7 per thousand. These values suggested heterotrophic growth of Beggiatoa on organic substrates that may have delta13C values characteristic of crude oil or on their by-products from microbial degradation. This study demonstrated that integrating lipid biomarkers, stable isotopes, and molecular DNA could enhance our understanding of the metabolic functions of Beggiatoa mats in sulfide-rich marine sediments associated with gas hydrates in the Gulf of Mexico and other locations.     

Microorganism-immobilized carbon nanoparticle anode for microbial fuel cells based on direct electron transfer

A fast and convenient bacterial immobilization method was proposed as an attempt to improve the anode efficiency of a microbial fuel cell, in which bacteria were entrapped into carbon nanoparticle matrix. The direct electron transfer from the entrapped bacterial cells to the anode was verified using cyclic voltammogram (CV). Using the immobilized bioanode, the start-up time of the MFC was greatly reduced. Meanwhile, the maximum power density of 1,947 mW m⁻² with the modified anode was much higher than that with the biofilm-based carbon cloth anode (1,479 mW m⁻²). Impedance measurements suggested that performance improvement resulted from the decrease in charge transfer and diffusion resistances. The results demonstrated that bacteria immobilization using carbon nanoparticle matrix was a simple and efficient approach for improving the anodes performances in MFCs.     

A stochastic model for eye movements during fixation on a stationary target

A stochastic model describing small eye movements occurring during steady fixation on a stationary target is presented. Based on eye movement data for steady gaze, the model has a hierarchical structure; the principal level represents the random motion of the image point within a local area of fixation while the higher level mimics the jump processes involved in transitions from one local area to another. Target image motion within a local area is described by a Langevinlike stochastic differential equation taking into consideration, the microsaccadic jumps pictured as being due to point processes and the high frequency muscle tremor, represented as a white noise. The transform of the probability density function for local area motion is obtained, leading to explicit expressions for their means and moments. Evaluation of these moments based on the model are comparable with experimental results. A physiologically based criterion for the occurrence of local area changes is assumed and the renewal density of these transitions is obtained. These transitions are brought about by the occurrence of large saccades. Hence, our analysis leads us to derive expressions for the mean and moments of the occurrence of large saccades in a given time T. These predictions may be checked against experimental results.This investigation was supported by National Institutes of Health under Grants Numbers GM 16197-03, GM 16437, and RR-0712-04, by the National Science Foundation under Grant Number GK-1834X, and by the National Aeronautics and Space Administration under Grant Number NGL-05-018-022.R.Vasudevan and J.D. Smith are with the Department of Electrical Engineering, University of Southern California, Los Angeles, California. —R.Vasudevan is on leave of absence from the Institute of Mathematical Sciences, Madras, India.A.V. Phatak is now with Systems Control, Inc. in Palo Alto, California.     

A kinetic model for microbial growth on liquid hydrocarbons

A kinetic model is presented to explain microbial growth using liquid n-alkanes as substrate. The model is based on the assumption that growth occurs on the soluble alkane and that the metabolite produced by the growing cells helps the dissolution of liquid alkanes in the aqueous medium. Growth curves based on that model fit well with growth data for batch and continuous culture reported by various authors. The model also explains the differences between the relative length of exponential and linear phases of growth reported earlier.