Hyperspectral imaging of the microscale distribution and dynamics of microphytobenthos in intertidal sediments
Authors : Arjun Chennu, Paul Färber, Nils Volkenborn, Mohammad A. A. Al-Najjar, Felix Janssen, Dirk de Beer and Lubos Polerecky
Abstract : We describe a novel, field-deployable hyperspectral imaging system, called Hypersub, that allows noninvasive in situ mapping of the microphytobenthos (MPB) biomass distribution with a high spatial (sub-millimeter) and temporal (minutes) resolution over areas of 1 × 1 m. The biomass is derived from a log-transformed and near-infrared corrected reflectance hyperspectral index, which exhibits a linear relationship (R2 > 0.97) with the chlorophyll a (Chl a) concentration in the euphotic zone of the sediment and depends on the sediment grain size. Deployments of the system revealed that due to factors such as sediment topography, bioturbation, and grazing, the distribution of MPB in intertidal sediments is remarkably heterogeneous, with Chl a concentrations varying laterally by up to 400% of the average value over a distance of 1 cm. Furthermore, due to tidal cycling and diel light variability, MPB concentrations in the top 1 mm of sediments are very dynamic, changing by 40- 80% over a few hours due to vertical migration. We argue that the high-resolution hyperspectral imaging method overcomes the inadequate resolution of traditional methods based on sedimentary Chl a extraction, and thus helps improve our understanding of the processes that control benthic primary production in coastal sediments.
Keywords : microbial mats, hyperspectral imaging, pigments
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Modular Spectral Imaging System for Discrimination of Pigments in Cells and Microbial Communities
Authors : Lubos Polerecky, Andrew Bissett, Mohammad Al-Najjar, Paul Faerber, 1 Harald Osmers, Peter A. Suci, Paul Stoodley and Dirk de Beer
Abstract : Here we describe a spectral imaging system for minimally invasive identification, localization, and relative quantification of pigments in cells and microbial communities. The modularity of the system allows pigment detection on spatial scales ranging from the single-cell level to regions whose areas are several tens of square centimeters. For pigment identification in vivo absorption and/or autofluorescence spectra are used as the analytical signals. Along with the hardware, which is easy to transport and simple to assemble and allows rapid measurement, we describe newly developed software that allows highly sensitive and pigment-specific analyses of the hyperspectral data. We also propose and describe a number of applications of the system for microbial ecology, including identification of pigments in living cells and high-spatial-resolution imaging of pigments and the associated phototrophic groups in complex microbial communities, such as photosynthetic endolithic biofilms, microbial mats, and intertidal sediments. This system provides new possibilities for studying the role of spatial organization of microorganisms in the ecological functioning of complex benthic microbial communities or for noninvasively monitoring changes in the spatial organization and/or composition of a microbial community in response to changing environmental factors.
Keywords : microbial mats, hyperspectral imaging, pigments
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Light utilization efficiency in photosynthetic microbial mats
Authors : Mohammad AA Al‐Najjar, Dirk de Beer, Michael Kühl, Lubos Polerecky
Abstract : Based on combined microsensor measurements of irradiance, temperature and O2, we compared light energy budgets in photosynthetic microbial mats, with a special focus on the efficiency of light energy conservation by photosynthesis. The euphotic zones in the three studied mats differed in their phototrophic community structure, pigment concentrations and thickness. In all mats, < 1% of the absorbed light energy was conserved via photosynthesis at high incident irradiance, while the rest was dissipated as heat. Under light-limiting conditions, the photosynthetic efficiency reached a maximum, which varied among the studied mats between 4.5% and 16.2% and was significantly lower than the theoretical maximum of 27.7%. The maximum efficiency correlated linearly with the light attenuation coefficient and photopigment concentration in the euphotic zone. Higher photosynthetic efficiency was found in mats with a thinner and more densely populated euphotic zone. Microbial mats exhibit a lower photosynthetic efficiency compared with ecosystems with a more open canopy-like organization of photosynthetic elements, where light propagation is not hindered to the same extent by photosynthetically inactive components; such components contributed about 40–80% to light absorption in the investigated microbial mats, which is in a similar range as in oceanic planktonic systems.
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Conversion and conservation of light energy in a photosynthetic microbial mat ecosystem
Authors : Mohammad AA Al-Najjar, Dirk De Beer, Bo Barker Jørgensen, Michael Kühl, Lubos Polerecky
Abstract : Here we present, to the best of our knowledge, the first balanced light energy budget for a benthic microbial mat ecosystem, and show how the budget and the spatial distribution of the local photosynthetic efficiencies within the euphotic zone depend on the absorbed irradiance (Jabs). Our approach uses microscale measurements of the rates of heat dissipation, gross photosynthesis and light absorption in the system, and a model describing light propagation and conversion in a scattering–absorbing medium. The energy budget was dominated by heat dissipation on the expense of photosynthesis: in light-limiting conditions, 95.5% of the absorbed light energy dissipated as heat and 4.5% was channeled into photosynthesis. This energy disproportionation changed in favor of heat dissipation at increasing irradiance, with >99% of the absorbed light energy being dissipated as heat and <1% used by photosynthesis at Jabs>700 μmol photon m−2 s−1 (>150 J m−2 s−1). Maximum photosynthetic efficiencies varied with depth in the euphotic zone between 0.014−0.047 O2 per photon. Owing to steep light gradients, photosynthetic efficiencies varied differently with increasing irradiances at different depths in the euphotic zone; for example, at Jabs>700 μmol photon m−2 s−1, they reached around 10% of the maximum values at depths 0−0.3 mm and progressively increased toward 100% below 0.3 mm. This study provides the base for addressing, in much more detail, the photobiology of densely populated photosynthetic systems with intense absorption and scattering. Furthermore, our analysis has promising applications in other areas of photosynthesis research, such as plant biology and biotechnology.
Keywords : efficiency; light conversion; microbial mats; microsensors; photosynthesis
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Anoxygenic Photosynthesis Controls Oxygenic Photosynthesis in a Cyanobacterium from a Sulfidic Spring
Authors : Judith M Klatt, Mohammad AA Al-Najjar, Pelin Yilmaz, Gaute Lavik, Dirk de Beer, Lubos Polerecky
Abstract : Before the Earth's complete oxygenation (0.58 to 0.55 billion years [Ga] ago), the photic zone of the Proterozoic oceans was probably redox stratified, with a slightly aerobic, nutrient-limited upper layer above a light-limited layer that tended toward euxinia. In such oceans, cyanobacteria capable of both oxygenic and sulfide-driven anoxygenic photosynthesis played a fundamental role in the global carbon, oxygen, and sulfur cycle. We have isolated a cyanobacterium, Pseudanabaena strain FS39, in which this versatility is still conserved, and we show that the transition between the two photosynthetic modes follows a surprisingly simple kinetic regulation controlled by this organism's affinity for H2S. Specifically, oxygenic photosynthesis is performed in addition to anoxygenic photosynthesis only when H2S becomes limiting and its concentration decreases below a threshold that increases predictably with the available ambient light. The carbon-based growth rates during oxygenic and anoxygenic photosynthesis were similar. However, Pseudanabaena FS39 additionally assimilated NO3− during anoxygenic photosynthesis. Thus, the transition between anoxygenic and oxygenic photosynthesis was accompanied by a shift of the C/N ratio of the total bulk biomass. These mechanisms offer new insights into the way in which, despite nutrient limitation in the oxic photic zone in the mid-Proterozoic oceans, versatile cyanobacteria might have promoted oxygenic photosynthesis and total primary productivity, a key step that enabled the complete oxygenation of our planet and the subsequent diversification of life.
Keywords : oxygenic photosynthesis, sulfidic springs, cyanobacteria
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Community Structure and Activity of a Highly Dynamic and Nutrient-Limited Hypersaline Microbial Mat in Um Alhool Sabkha, Qatar
Authors : Roda Al-Thani, Mohammad AA Al-Najjar, Abdul Munem Al-Raei, Tim Ferdelman, Nguyen M Thang, Ismail Al Shaikh, Mehsin Al-Ansi, Dirk de Beer
Abstract : The Um Alhool area in Qatar is a dynamic evaporative ecosystem that receives seawater from below as it is surrounded by sand dunes. We investigated the chemical composition, the microbial activity and biodiversity of the four main layers (L1–L4) in the photosynthetic mats. Chlorophyll a (Chl a) concentration and distribution (measured by HPLC and hyperspectral imaging, respectively), the phycocyanin distribution (scanned with hyperspectral imaging), oxygenic photosynthesis (determined by microsensor), and the abundance of photosynthetic microorganisms (from 16S and 18S rRNA sequencing) decreased with depth in the euphotic layer (L1). Incident irradiance exponentially attenuated in the same zone reaching 1% at 1.7-mm depth. Proteobacteria dominated all layers of the mat (24%–42% of the identified bacteria). Anoxygenic photosynthetic bacteria (dominated by Chloroflexus) were most abundant in the third red layer of the mat (L3), evidenced by the spectral signature of Bacteriochlorophyll as well as by sequencing. The deep, black layer (L4) was dominated by sulfate reducing bacteria belonging to the Deltaproteobacteria, which were responsible for high sulfate reduction rates (measured using 35S tracer). Members of Halobacteria were the dominant Archaea in all layers of the mat (92%–97%), whereas Nematodes were the main Eukaryotes (up to 87%). Primary productivity rates of Um Alhool mat were similar to those of other hypersaline microbial mats. However, sulfate reduction rates were relatively low, indicating that oxygenic respiration contributes more to organic material degradation than sulfate reduction, because of bioturbation. Although Um Alhool hypersaline mat is a nutrient-limited ecosystem, it is interestingly dynamic and phylogenetically highly diverse. All its components work in a highly efficient and synchronized way to compensate for the lack of nutrient supply provided during regular inundation periods.
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Effect of temperature on photosynthesis, oxygen consumption and sulfide production in an extremely hypersaline cyanobacterial mat
Authors : Raeid MM Abed, Lubos Polerecky, Mohammad Al Najjar, Dirk De Beer
Abstract : We used microsensors to study short-term temperature effects on gross photosynthesis, oxygen consumption and sulfate reduction in an extremely hypersaline (salinity 200‰) cyanobacterial mat. In situ, the mat surface can reach high temperatures (ca. 50°C in summer), and experiences daily temperature fluctuations due to tidal inundation. A mat sample was incubated in the laboratory at 25, 35, 45, 50 and 60°C. Areal rates of gross and net photosynthesis increased with increasing temperature, and maximum rates were detected at 45°C. The photosynthetic zone (i.e. the depth zone in which oxygenic photosynthesis was detectable by the light–dark shift method) decreased from 3 to 1.75 mm with increasing temperature. Above 50°C, photosynthesis was completely inhibited, probably due to high sulfide concentrations. This inhibition was confirmed by the pH profiles, where the peak in the top 2 to 4 mm at 25 to 45°C disappeared at 50 to 60°C. Between 25 and 45°C, areal oxygen consumption rates in the light did not change significantly but showed a decreasing trend in the photosynthetic zone, suggesting a decoupling between photosynthesis and oxygen consumption in the light. In both the light and dark, sulfide production was strongly enhanced by increasing temperature to a maximum flux at 50°C, above which it became inhibited. At 50 to 60°C, the sulfide produced could not be completely removed by sulfide oxidation, resulting in sulfide leakage to the overlying water. Our data demonstrate that these mat ecosystems are well adapted to high ambient temperatures. Photosynthesis, oxygen consumption in the light and sulfide production are differentially controlled by temperature. However, the individual processes in this complex community are not only directly controlled by temperature, but also by the temperaturedependent response of other processes.
Keywords : Cyanobacterial mats · Temperature · Microsensors · Arabian Gulf · Photosynthesis . Oxygen consumption
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Rapid Reactivation of Cyanobacterial Photosynthesis and Migration upon Rehydration of Desiccated Marine Microbial Mats
Authors : Arjun Chennu, Alistair Grinham, Lubos Polerecky, Dirk De Beer, Mohammad AA Al-Najjar
Abstract : Desiccated cyanobacterial mats are the dominant biological feature in the Earth’s arid zones. While the response of desiccated cyanobacteria to rehydration is well-documented for terrestrial systems, information about the response in marine systems is lacking. We used high temporal resolution hyperspectral imaging, liquid chromatography, pulse-amplitude fluorometry, oxygen microsensors, and confocal laser microscopy to study this response in a desiccated microbial mat from Exmouth Gulf, Australia. During the initial 15 min after rehydration chlorophyll a concentrations increased 2–5 fold and cyanobacterial photosynthesis was re-established. Although the mechanism behind this rapid increase of chlorophyll a remains unknown, we hypothesize that it involves resynthesis from a precursor stored in desiccated cyanobacteria. The subsequent phase (15 min–48 h) involved migration of the reactivated cyanobacteria toward the mat surface, which led, together with a gradual increase in chlorophyll a, to a further increase in photosynthesis. We conclude that the response involving an increase in chlorophyll a and recovery of photosynthetic activity within minutes after rehydration is common for cyanobacteria from desiccated mats of both terrestrial and marine origin. However, the response of upward migration and its triggering factor appear to be mat-specific and likely linked to other factors.
Keywords : cyanobacteria, desiccation tolerance, extreme environment, rehydration, photosynthesis, reactivatio
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Spatial patterns and links between microbial community composition and function in cyanobacterial mats
Authors : Mohammad AA Al-Najjar, Alban Ramette, Michael Kühl, Waleed Hamza, Judith M Klatt, Lubos Polerecky
Abstract : We imaged reflectance and variable fluorescence in 25 cyanobacterial mats from four distant sites around the globe to assess, at different scales of resolution, spatial variabilities in the physiological parameters characterizing their photosynthetic capacity, including the absorptivity by chlorophyll a (Achl), maximum quantum yield of photosynthesis (Ymax), and light acclimation irradiance (Ik). Generally, these parameters significantly varied within individual mats on a sub-millimeter scale, with about 2-fold higher variability in the vertical than in the horizontal direction. The average vertical profiles of Ymax and Ik decreased with depth in the mat, while Achl exhibited a sub-surface maximum. The within-mat variability was comparable to, but often larger than, the between-sites variability, whereas the within-site variabilities (i.e., between samples from the same site) were generally lowest. When compared based on averaged values of their photosynthetic parameters, mats clustered according to their site of origin. Similar clustering was found when the community composition of the mats' cyanobacterial layers were compared by automated ribosomal intergenic spacer analysis (ARISA), indicating a significant link between the microbial community composition and function. Although this link is likely the result of community adaptation to the prevailing site-specific environmental conditions, our present data is insufficient to identify the main factors determining these patterns. Nevertheless, this study demonstrates that the spatial variability in the photosynthetic capacity and light acclimation of benthic phototrophic microbial communities is at least as large on a sub-millimeter scale as it is on a global scale, and suggests that this pattern of variability scaling is similar for the microbial community composition.
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Nutritive effect of dust on microbial biodiversity and productivity of the Arabian Gulf
Authors : Mohammad AA Al-Najjar, Christopher Munday, Artur Fink, Mohamed AR Abdel-Moati, Waleed Hamza, Laura Korte, Jan-Berend Stuut, Ibrahim S Al-Ansari, Ibrahim Al-Maslamani, Dirk de Beer
Abstract : The Arabian Gulf is exposed to intensive dust storms during summer until early winter. We investigated the nutritive effect of the dust on microbial biodiversity of the water column and the productivity of the Gulf. We collected samples from three sites in a transect perpendicular to the shore in March (before the strong dust storms) and in October (after the dust season) in 2013. At the three sites, we sampled the water column at three depths, and see-floor sediments using a HAPS corer. We also sampled the sand dunes that are the source of the dust. We analyzed the samples for pigments, microbial community composition using a 16S rRNA analysis, and nutrients. Our results showed that species richness and biodiversity were higher in October than in March. The relative abundances of key-player microorganisms were strongly pronounced in October. We assume that the dust rapidly sinks to the seafloor where the nutrients Fe and P are liberated through iron reduction. Assuming that all phosphate diffusing from the seafloor originates from the dust particles after deposition, we estimated a contribution of minimum 30,000 tons of fish produced every year in the Gulf. We found no close temporal coupling between dust storms and productivity. This is because nutrient liberation from the seafloor is slow and its transport from the seafloor to the photic zone by circulation processes is irregular. This study highlights the importance of dust as a source of nutrients in the Gulf ecosystem.
Keywords : dust, Arabian Gulf productivity, microbial loops
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Prevalence, knowledge of and attitude towards hepatitis B virus among pregnant females in Jordan
Authors : Bayan Othman, Mohammad AA Al‐Najjar, Dalia Othman, Rajaa Al‐Qudah, Iman Basheti
Abstract : This observational study was designed to assess the prevalence, knowledge and attitude of pregnant females towards hepatitis B infection, in addition to their perspective of the healthcare practice about HBV in Jordan. A randomly selected group of pregnant females visiting public gynaecology clinics in Jordan were approached to participate in the study. Blood samples were collected from the participants, and HBV markers were detected in their serum using specialized ELISA Kits to assess for the prevalence of infection. Knowledge and attitude of participants was assessed via a developed and validated questionnaire. Statistical analysis was conducted using the Statistical Package for the Social Sciences (SPSS) version 24. Blood samples (n = 300) from 330 pregnant females were collected. The prevalence of hepatitis B surface antigen (HBsAg) among the pregnant females was found to be 5%. Anti-HBs and anti-HBc were found to be 33.3% and 7%, respectively. No significant correlation between age, socio-economic status and educational level was found with HBsAg positivity. Limited knowledge regarding HBV was revealed among the pregnant females (9.1%-41.3%, P < .05). The majority had a positive attitude regarding HBV vaccination and antiviral medications in case of infectivity. More than 90% agreed on the present lack of counselling and screening of HBV they obtained during their first perinatal visit to the gynaecology clinics. This study revealed a lack of knowledge on HBV, and low counselling and screening received were reported. Policymakers need to introduce new interventions to improve the current awareness of patients and gynaecologists regarding hepatitis B infection.
Keywords : epidemiology, HBV tests, Hepatitis B virus (HBV), Jordan, pregnant females
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Shifts in microbial community composition in tannery-contaminated soil in response to increased gamma radiation
Authors : Mohammad AA Al-Najjar, Majed M Albokari
Abstract : Purpose: Contaminated sites from man-made activities such as old-fashioned tanneries are inhabited by virulent microorganisms that exhibit more resistance against extreme and toxic environmental conditions. We investigated the effect of different Gamma radiation doses on microbial community composition in the sediment of an old-fashioned tannery. Methods: Seven samples collected from the contaminated sites received different gamma radiation doses (I = 0.0, II = 5, III = 10, VI = 15, V = 20, VI = 25, and VII = 30 kGy) as an acute exposure. The shift in microbial community structure was assessed using the high throughput 454 pyrosequencing. Variations in diversity, richness, and the shift in operational taxonomic units (OTUs) were investigated using statistical analysis. Result: Our results showed that the control sample (I) had the highest diversity, richness, and OTUs when compared with the irradiated samples. Species of Halocella, Parasporobacterium, and Anaerosporobacter had the highest relative abundance at the highest radiation dose of 30 kGy. Members of the Firmicutes also increased by 20% at the highest radiation dose when compared with the control sample (0.0 kGy). Representatives of Synergistetes decreased by 25% while Bacteroidetes retained a steady distribution across the range of gamma radiation intensities. Conclusion: This study provides information about potential “radioresistant” and/or “radiotolerant” microbial species that are adapted to elevated level of chemical toxicity such as Cr and Sr in tannery. These species can be of a high biotechnological and environmental importance.
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Patterns of antibiotic use, knowledge, and perceptions among different population categories: A comprehensive study based in Arabic countries
Authors : Ahmad Alsayed, Feras Darwish El Hajji, Mohammad AA Al-Najjar, Husam Abazid, Abdullah Al-Dulaimi
Abstract : Background:Antibiotics are essential for the treatment of bacterial infections and are considered among the most commonly sold drug classes from the community pharmacy in the developing countries without a prescription in most cases. Purpose: This study aims to explore the knowledge, practices, and attitudes regarding antibiotic use. Materials and methods: This study employs a cross-sectional descriptive design that used a pre-validated survey. The participants were classified into three main mutually exclusive groups: healthcare professionals, medical students, and other adults in the community. Results: Of the 10,226 participants, 1157 (11%) were healthcare professionals; 2322 (23%) were medical students and 6747 (66%) were other adults in community. The majority of participants used antibiotic at least once during the past year. A total of 838 (72.4%) healthcare professionals and 800 (34.5%) medical students had prescribed an antibiotic during the last 6 months. Almost half of the medical students and adults in the community and almost one-third of healthcare professionals reported that the aim of antibiotics use is for fever. Furthermore, around one-quarter of participants reported that the aim of antibiotics use is for viral infection. Around one-quarter of respondents stated that the antibiotic will always be effective in the treatment of the same infection in the future. Around one-quarter of participants stated that 21 to 50% of antibiotics are considered to be unnecessary or inappropriate prescriptions. Different factors were perceived as being very important causes of antibiotic resistance among the participants. Conclusions: These findings indicated that this study participants showed unsatisfactory knowledge and perceptions of proper antibiotic use. Therefore, there is a requirement for a comprehensive and effective antibiotic-stewardship program to promote rational antibiotics use, and compensate for knowledge and perceptions gaps to prevent antibiotic resistance development.
Keywords : Antibiotic, Arabic Countries, Knowledge, Perceptions
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Evaluation of the orally administered calcium alginate aerogel on the changes of gut microbiota and hepatic and renal function of Wistar rats
Authors : Mohammad A A Al-Najjar, Tamara Athamneh, Reem AbuTayeh, Iman Basheti, Claudia Leopold, Pavel Gurikov
Abstract : The present study evaluates the effect of calcium alginate aerogel as a potential drug carrier, on the liver and kidney functions, and on the gut microbiota of Wistar rats. The studied alginate aerogel was prepared in the form of nanoparticles using the jet cutting technique, and they were characterized in terms of specific surface areas, outer morphology and particle size distribution. For the in vivo study, calcium alginate aerogel was administered orally, and liver and kidney functions were tested for one week and for four weeks in two distinct studies. During the short-term in vivo study, feces samples were collected for bacterial DNA extraction followed by 16S rRNA gene sequencing analyses to detect changes in gut microbiota. Results showed that the prepared alginate aerogel has an average BET-specific surface area of around 540 m2/g, with a pore volume of 7.4 cc/g, and pore width of 30–50 nm. The in vivo study revealed that the levels of the studied kidney and liver enzymes didn’t exceed the highest level of the normal range. The study of gut microbiota showed different patterns; certain groups of bacteria, such as Clostridia and Bacteriodia, increased during the aerogels regime and continued to increase after the aerogel was stopped. While other groups such as Erysipelotrichia, and Candidatus saccharibacteria increased during aerogels treatment, and then decreased again after one month. Members of the Bacilli class showed a unique trend, that is, after being the most abundant group (63%) at time 0, their relative abundance decreased dramatically until it reached < 5%; which was the case even after stopping the aerogel treatment.
Keywords : aerogel, gut microbiota, 16S rRNA sequencing, nanoparticles
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Pore water gradients below microbial mat surface of Umm Alhool sabkha in Qatar
Authors : Abdul Munem Al-Raei, Mohammad Al-Najjar, Roda Al-Thani
Abstract : The mineralization of organic matter in marine sediments by microbial activity was studied in Umm Alhool sabkha. In intertidal surface sediments, the development of steep compositional and physico-chemical gradients was a common phenomenon. Rapidly, oxygen is consumed within the upper few mm of marine mats and sediments. In permeable sediments, however, oxygenated bottom waters may have flew through the upper part of the surface sediments leading to enhanced participation of oxygen in element cycling. Whereas in microbial mats, the surface sediments are locally formed, indicating a disturbance in the balance of the biogeochemical processes. Umm Alhool sabkha, situated between Umm Sa'id (Mesaieed) and Al Wakrah, drew our attention to study the biogeochemical cycling because both microbial mats and mangroves ecosystems affect its biogeochemistry. In the present study, the chemistry of pore water below mats surfaces of intertidal sandy sediments was investigated in winter 2011 using a number of different techniques. Pore water was sampled down to 20 cm below surface using pore water lances, diffusion samplers, and centrifugation of sediment core sections. Microsensor measurements of sulfide and pH were also performed on the upper 2 cm. Specifically, we measured salinity, dissolved O2, pH, SO4²¯, H2S, Cl¯, TN, TOC, PO4³¯, NO3¯, NH4+, H4SiO4, and microbial sulfate reduction rates have been analyzed using intact sediment cores. Sulfidic sediments were characterized by high sulfate reduction rates exhibiting maxima between about 5-15 cm, associated with decreased oxygen penetration depths, and proton activities. Anaerobic metabolic activity in pore waters below mat surface lead to significantly enhanced concentrations of sulfide, ammonium, dissolved inorganic carbon, phosphate, silica (steep gradients), and a net consumption of sulfate. They acted as windows for the liberation of reduced substances into the bottom water or the atmosphere. This study represents the first comprehensive investigation of the chemical composition and sulfate reduction rates in Umm Alhool microbial mat ecosystem. It shows how dynamic and self-fueling the system is.
Keywords : microbial mats, microsensors, pore water, physico-chemical gradients
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HYPER-SPECTRAL IMAGING OF BIOFILM GROWTH DYNAMICS
Authors : Lubos Polerecky, Judith M Klatt, Mohammad Al-Najjar, Dirk de Beer
Abstract : Spectrally resolved imaging was applied to study the growth dynamics of phototrophic biofilms comprizing a mixture of one cyanobacterial and one diatom species. Linear spectral unmixing was combined with liquid chromatography to quantitatively discriminate the areal biomass densities of the two populations. The grown biofilms exhibited highly heterogeneous distribution with patches of 1–2 mm in size, although the conditions provided for growth, including substrate roughness, illumination and flow of the overlying water, were homogeneous. The biomass was initially dominated by cyanobacteria, which exhibited an exponential-like growth phase during days 2–7. Their population declined during days 9–17, which coincided with the growth phase of the diatom population. By allowing non-invasive and real-time measurements and data evaluation, the spectral imaging approach constitutes a useful tool for microbial ecologists.
Keywords : Biofilm, Phototroph, Population dynamics, Spectral imaging
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Flow of Light Energy in Benthic Photosynthetic Microbial Mats
Authors : Mohammad Ahmad A Al-Najjar
Abstract : Spectrally resolved imaging was applied to study the growth dynamics of phototrophic biofilms comprising a mixture of one cyanobacterial and one diatom species. Linear spectral unmixing was combined with liquid chromatography to quantitatively discriminate the areal biomass densities of the two populations. The grown biofilms exhibited highly heterogeneous distribution with patches of 1-2 mm in size, although the conditions provided for growth, including substrate roughness, illumination and flow of the overlying water, were homogeneous. The biomass was initially dominated by cyanobacteria, which exhibited an exponential-like growth phase during days 2-7. Their population declined during days 9- 17, which coincided with the growth phase of the diatom population. By allowing noninvasive and real-time measurements and data evaluation, the spectral imaging approach constitutes a useful tool for microbial ecologists.
Keywords : efficiency / light conversion / microbial mats / microsensors / photosynthesis
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Changes in gut microbiota of alloxan-induced diabetic rats in response to orally administered combined aqueous extracts of olive leaves and ginger
Authors : Shatha Alshaer, Feras Darwish El-Hajji, Reem Abu-Tayeh, Iman Basheti, Mohammad AA Al-Najjar
Abstract : Olive leaves and ginger rhizomes are examples of medicinal plants that have been used, separately, for the management of different ailments. Diabetes mellitus is a chronic disease that is prevalent around the whole world and is significant among adults in Middle Eastern countries. The effect of the combined mixture of olive leaves and ginger rhizome aqueous extracts has not been previously studied for its hypoglycemic effect, nor for its effect on gut microbiota in the diabetes-induced rat model. This study aims to elucidate the potential effect of the orally ingested combination of the aqueous extract of olive leaves and ginger rhizome on the gut microbiota in both healthy and diabetic rats. Diabetes was induced by intraperitoneal injection of alloxan monohydrate, and the aqueous extracts were prepared in the same homemade preparation method. Each extract and subsequent combination were given separately at a dose of 500 mg/kg per day, with or without insulin (6 IU/kg) for 7 days, to every rat in the different groups. Fasting blood glucose was carried out to evaluate the diabetic state, and fecal samples were collected at different time points for 16s rRNA gene sequencing. The combination of extracts increased bacterial diversity in general and raised the Firmicutes/Bacteroidetes ratio in both healthy and diabetic rats. Moreover, while it increased the relative abundance of Lactobacillus and Prevotella, it decreased the relative abundance of Clostridium and Bacteroides in healthy rats. These results have positive effects on the management of diabetes, by increasing short-chain fatty acid production, which can suppress the appetite and prevent damage to pancreatic cells. This study underlines the additional benefits of using herbal extracts to retain dysbiosis and improve gut microbiota.
Keywords : Diabetes mellites, gut microbiota, olive leaves extracts, ginger rhizome extract, prebiotic effect, short-chain fatty acid production.
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Assessment of public knowledge and perception about the use of probiotics
Authors : Manal Ayyash, Mohammad AA Al-Najjar, Kamel Jaber, Layal Ayyash, Rana Abu-Farha
Abstract : Introduction In Jordan, there is a remarkable lack of public awareness about probiotics and available guidance on their use. This study was designed to evaluate Jordanians’ awareness and perception about probiotics and their willingness to use these nutritional supplements as a part of their daily diet. Methods This cross-sectional survey was conducted among the Jordanian public. During the study period, participants were invited to fill out an electronic-based questionnaire. Results A total of 508 people agreed to participate in the study. Among them, 64.0% (n = 325) reported that they were willing to take probiotics. Only 17.1% of the surveyed participants (n = 90) knew that probiotics were not dead microorganisms. Only 55.0% of participants (n = 279) believed that probiotics were safe to consume. In addition, 75.0% (n = 381) believed that community pharmacists had a limited role in improving public knowledge about probiotics. Regression analysis showed that participants with higher income (>500 JD/month) and those who had medical degrees had greater knowledge about probiotics compared to others (P <0.001). Conclusion This study demonstrated that there is inadequate knowledge about probiotics and their potential use. More effort is needed to provide more information about the benefits of probiotics. Greater knowledge could be achieved by encouraging medical doctors and pharmacists to inform the public about probiotics.
Keywords : Probiotics, Knowledge, Perception, Jordan, Willingness
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Nutritive effect of dust on microbial biodiversity and productivity of the Arabian Gulf
Authors : Dirk de Beer Mohammad Alnajjar, Christopher Munday, Artur Fink, Mohamed A.R. Abdel-Moati, Waleed Hamza, Laura Korte, Jan-Berend Stuut, Ibrahim S. Al-Ansari, Ibrahim Al-Maslamani
Abstract : The Arabian Gulf is exposed to intensive dust storms during summer until early winter. We investigated the nutritive effect of the dust on microbial biodiversity of the water column and the productivity of the Gulf. We collected samples from three sites in a transect perpendicular to the shore in March (before the strong dust storms) and in October (after the dust season) in 2013. At the three sites, we sampled the water column at three depths, and see-floor sediments using a HAPS corer. We also sampled the sand dunes that are the source of the dust. We analyzed the samples for pigments, microbial community composition using a 16S rRNA analysis, and nutrients. Our results showed that species richness and biodiversity were higher in October than in March. The relative abundances of key-player microorganisms were strongly pronounced in October. We assume that the dust rapidly sinks to the seafloor where the nutrients Fe and P are liberated through iron reduction. Assuming that all phosphate diffusing from the seafloor originates from the dust particles after deposition, we estimated a contribution of minimum 30,000 tons of fish produced every year in the Gulf. We found no close temporal coupling between dust storms and productivity. This is because nutrient liberation from the seafloor is slow and its transport from the seafloor to the photic zone by circulation processes is irregular. This study highlights the importance of dust as a source of nutrients in the Gulf ecosystem.
Keywords : dust, Arabian Gulf productivity, microbial loops
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Niche for high abundant extremophilic microbial communities in an ancient crater
Authors : Majed Albokari, Mohammad AA Al-Najjar, Ibrahim Mashhour, Abdulaziz Huraysi
Abstract : Al Wahbah Crater, located in a remote area in western Saudi Arabia as part of The Harrat extinct volcanic chain, is 2 km wide with a depth of 250 m. It is registered by the General Commission for Tourism and National Heritage as an ancient and archaeological site. The crater is subjected to extreme environmental conditions as its bottom is rarely subjected to rainfall and mudflows. Because of high temperature, high evaporation rates and extremely limited rainfall, the crater leaves behind dried thick white sodium phosphate crystals. Here, we studied the chemical composition and the microbial community composition using 16S rRNA pyrosequencing in different vertical layers (2, 20, 40, 60, 80 and 100 cm) of the crater sediment. Total sodium concentrations s were 28 000– 46 700 ppm and calcium levels were 31 400– 56 500 ppm. In addition, samples were very sulphuric, with sulphate and sulphite levels exceeding 2157 ppm and 5.54 ppm, respectively. Ferric ions concentrations were
Keywords : Al Wahbah Crater, halophiles, 454 pyrosequencing, Salinibacter iranicus
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Unravelling Hidden Metabolic Capabilities in Microbial Mat Ecosystems by Combining In Situ Measurements and Omic Approaches
Authors : Mohammad Al-Najjar AA
Abstract : Microbial mats are unique ecosystems that harbor diversified metabolic capabilities raging from photosynthesis in the upper layer to fermentation and organic material degradation accompanied with methane production in the deepest layer. Microorganisms in a microbial mat are successful to flourish in extreme environments because they can shift their metabolism in response to the changes in their environment. These metabolic flexibility and capabilities of the microorganisms are underestimated because most of the studies so far have focused on measuring changing in the behavior of the inhabiting microorganisms, or on certain biochemical indicators, or on the shift of microbial community structure. However, to be able to broaden our understanding of the metabolic capabilities, an intensive study of the underlying molecular mechanisms should be carried out. Therefore, the best approach to be adopted is by combining in situ measurements with omics analysis (i.e., matatranscriptomic and/or metaproteomic) in response to changes in the environmental conditions.
Keywords : Microbial mats, OMICs, microsensors
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