Nitrogen and phosphorus limitation of oceanic microbial growth during spring in the Gulf of Aqaba

Bioassay experiments were performed to identify how growth of key groups within the microbial community was simultaneously limited by nutrient (nitrogen and phosphorus) availability during spring in the Gulf of Aqaba's oceanic waters. Measurements of chlorophyll a (chl a) concentration and fast repetition rate (FRR) fluorescence generally demonstrated that growth of obligate phototrophic phytoplankton was co-limited by N and P and growth of facultative aerobic anoxygenic photoheterotropic (AAP) bacteria was limited by N. Phytoplankton exhibited an increase in chl a biomass over 24 to 48 h upon relief of nutrient limitation. This response coincided with an increase in photosystem II (PSII) photochemical efficiency (F v /F m), but was preceded (within 24 h) by a decrease in effective absorption crosssection (σPSII) and electron turnover time (τ). A similar response for τ and bacterio-chl a was observed for the AAPs. Consistent with the up-regulation of PSII activity with FRR fluorescence were observations of newly synthesized PSII reaction centers via low temperature (77K) fluorescence spectroscopy for addition of N (and N + P). Flow cytometry revealed that the chl a and thus FRR fluorescence responses were partly driven by the picophytoplankton (æ10 μm) community, and in particular Synechococcus. Productivity of obligate heterotrophic bacteria exhibited the greatest increase in response to a natural (deep water) treatment, but only a small increase in response to N and P addition, demonstrating the importance of additional substrates (most likely dissolved organic carbon) in moderating the heterotrophs. These data support previous observations that the microbial community response (autotrophy relative to heterotrophy) is critically dependent upon the nature of transient nutrient enrichment. © Inter-Research 2009

Microbial rhodopsins on leaf surfaces of terrestrial plants

Author Posting. © The Author(s), 2011. This is the author's version of the work. It is posted here by permission of John Wiley & Sons for personal use, not for redistribution. The definitive version was published in Environmental Microbiology 14 (2012): 140-146, doi:10.1111/j.1462-2920.2011.02554.x.The above-ground surfaces of terrestrial plants, the phyllosphere, comprise the main interface between the terrestrial biosphere and solar radiation. It is estimated to host up to 1026 microbial cells that may intercept part of the photon flux impinging on the leaves. Based on 454- pyrosequencing generated metagenome data, we report on the existence of diverse microbial rhodopsins in five distinct phyllospheres from tamarisk (Tamarix nilotica), soybean (Glycine max), Arabidopsis (Arabidopsis thaliana), clover (Trifolium repens) and rice (Oryza sativa). Our findings, for the first time describing microbial rhodopsins from non-aquatic habitats, point toward the potential coexistence of microbial rhodopsin-based phototrophy and plant chlorophyll-based photosynthesis, with the different pigments absorbing non-overlapping fractions of the light spectrum.This work was supported in part by a grant from Bridging the Rift Foundation (O.B. & S.B.), Israel Science Foundation grant 1203/06 (O.B.), the Gruss-Lipper Family Foundation at MBL (O.M.F., S.B. & A.F.P.), a US-Israel Binational Science Foundation grant 2006324 (S.B.), and DOE National Institutes of Health Grant R37GM27750, Department of Energy Grant DE-FG02-07ER15867, and endowed chair AU-0009 from the Robert A. Welch Foundation (J.L.S.)

A global atlas of artificial light at night under the sea

The impacts of artificial light at night (ALAN) on marine ecosystems have emerged as a focus for ecological light pollution research in recent years, yet the global prevalence of ALAN in underwater marine ecosystems is unknown. We have derived a global atlas of ALAN throughout the marine water column that will accelerate our understanding of its sources and environmental impacts. At a depth of 1 m, 1.9 million km2 of the world’s coastal seas are exposed to biologically important ALAN, which equates to around 3.1% of the global exclusive economic zones.This area decreases to 1.6 million km2 (2.7%) at a depth of 10 m, and to 840,000 km2 (1.4%) at 20 m.The most heavily exposed regions are those that experience intensive offshore development in addition to coastal urbanization.The atlas highlights that ALAN as a global change issue is not exclusive to land but is also widespread in the world’s underwater habitats at irradiances that elicit biological responses in marine organisms

Freezing of gait and fall detection in Parkinson’s disease using wearable sensors:a systematic review

Despite the large number of studies that have investigated the use of wearable sensors to detect gait disturbances such as Freezing of gait (FOG) and falls, there is little consensus regarding appropriate methodologies for how to optimally apply such devices. Here, an overview of the use of wearable systems to assess FOG and falls in Parkinson’s disease (PD) and validation performance is presented. A systematic search in the PubMed and Web of Science databases was performed using a group of concept key words. The final search was performed in January 2017, and articles were selected based upon a set of eligibility criteria. In total, 27 articles were selected. Of those, 23 related to FOG and 4 to falls. FOG studies were performed in either laboratory or home settings, with sample sizes ranging from 1 PD up to 48 PD presenting Hoehn and Yahr stage from 2 to 4. The shin was the most common sensor location and accelerometer was the most frequently used sensor type. Validity measures ranged from 73–100% for sensitivity and 67–100% for specificity. Falls and fall risk studies were all home-based, including samples sizes of 1 PD up to 107 PD, mostly using one sensor containing accelerometers, worn at various body locations. Despite the promising validation initiatives reported in these studies, they were all performed in relatively small sample sizes, and there was a significant variability in outcomes measured and results reported. Given these limitations, the validation of sensor-derived assessments of PD features would benefit from more focused research efforts, increased collaboration among researchers, aligning data collection protocols, and sharing data sets

The influence of light on nitrogen cycling and the primary nitrite maximum in a seasonally stratified sea

Author Posting. © The Author(s), 2011. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Progress In Oceanography 91 (2011): 545–560, doi:10.1016/j.pocean.2011.09.001.In the seasonally stratified Gulf of Aqaba Red Sea, both NO2- release by phytoplankton and NH4+ oxidation by nitrifying microbes contributed to the formation of a primary nitrite maximum (PNM) over different seasons and depths in the water column. In the winter and during the days immediately following spring stratification, NO2- formation was strongly correlated (R2=0.99) with decreasing irradiance and chlorophyll, suggesting that incomplete NO3- reduction by light limited phytoplankton was a major source of NO2-. However, as stratification progressed, NO2- continued to be generated below the euphotic depth by microbial NH4+ oxidation, likely due to differential photoinhibition of NH4+ and NO2- oxidizing populations. Natural abundance stable nitrogen isotope analyses revealed a decoupling of the δ15N and δ18O in the combined NO3- and NO2- pool, suggesting that assimilation and nitrification were co-occurring in surface waters. As stratification progressed, the δ15N of particulate N below the euphotic depth increased from -5‰ to up to +20‰. N uptake rates were also influenced by light; based on 15N tracer experiments, assimilation of NO3-, NO2-, and urea was more rapid in the light (434±24, 94±17, and 1194±48 nmol N L-1 day-1 respectively) than in the dark (58±14, 29±14, and 476±31 nmol N L-1 day-1 respectively). Dark NH4+ assimilation was 314±31 nmol N L-1 day-1, while light NH4+ assimilation was much faster, resulting in complete consumption of the 15N spike in less than 7 hour from spike addition. The overall rate of coupled urea mineralization and NH¬4+ oxidation (14.1±7.6 nmol N L-1 day-1) was similar to that of NH¬4+ oxidation alone (16.4±8.1 nmol N L-1 day-1), suggesting that for labile dissolved organic N compounds like urea, mineralization was not a rate limiting step for nitrification. Our results suggest that assimilation and nitrification compete for NH4+ and that N transformation rates throughout the water column are influenced by light over diel and seasonal cycles, allowing phytoplankton and nitrifying microbes to contribute jointly to PNM formation. We identify important factors that influence the N cycle throughout the year, including light intensity, substrate availability, and microbial community structure. These processes could be relevant to other regions worldwide where seasonal variability in mixing depth and stratification influence the contributions of phytoplankton and non-photosynthetic microbes to the N cycle.This research was supported under the North Atlantic Treaty Organization (NATO) Science for Peace Grant SfP 982161 to AP and AFP, a grant from the Koret Foundation to AP, a National Science Foundation Biological Oceanography grant to AP, the Israel Science Foundation grant 135/05 to AFP, and research grant 8330-06 from the Geological Society of America to KRMM

Chasing feet in the wild: A proposed egocentric motion-aware gait assessment tool

Despite advances in gait analysis tools, including optical motion capture and wireless electrophysiology, our understanding of human mobility is largely limited to controlled conditions in a clinic and/or laboratory. In order to examine human mobility under natural conditions, or the 'wild', this paper presents a novel markerless model to obtain gait patterns by localizing feet in the egocentric video data. Based on a belt-mounted camera feed, the proposed hybrid FootChaser model consists of: 1) the FootRegionProposer, a ConvNet that proposes regions with high probability of containing feet in RGB frames (global appearance of feet), and 2) LocomoNet, which is sensitive to the periodic gait patterns, and further examines the temporal content in the stacks of optical low corresponding to the proposed region. The LocomoNet signicantly boosted the overall model's result by ltering out the false positives proposed by the FootRegionProposer. This work advances our long-term objective to develop novel markerless models to extract spatiotemporal gait parameters, particularly step width, to complement existing inertial measurement unit (IMU) based methods

Phytoplankton dynamics in the Gulf of Aqaba (Eilat, Red Sea): a simulation study of mariculture effects

The northern Gulf of Aqaba is an oligotrophic water body hosting valuable coral reefs. In the Gulf, phytoplankton dynamics are driven by an annual cycle of stratification and mixing. Superimposed on that fairly regular pattern was the establishment of a shallow-water fish-farm initiative that increased gradually until its activity was terminated in June 2008. Nutrient, water temperature, irradiation, phytoplankton data gathered in the area during the years 2007-2009, covering the peak of the fish-farm activity and its cessation, were analyzed by means of statistical analyses and ecological models of phytoplankton dynamics. Two datasets, one from an open water station and one next to the fish farms, were used. Results show that nutrient concentrations and, consequently, phytoplankton abundance and seasonal succession were radically altered by the pollution originating from the fish-farm in the sampling station closer to it, and also that the fish-farm might even have influenced the open water station

Oxygen sufficiency controls TOP mRNA translation via the TSC-Rheb-mTOR pathway in a 4E-BP-independent manner

Cells encountering hypoxic stress conserve resources and energy by downregulating the protein synthesis. Here we demonstrate that one mechanism in this response is the translational repression of TOP mRNAs that encode components of the translational apparatus. This mode of regulation involves TSC and Rheb, as knockout of TSC1 or TSC2 or overexpression of Rheb rescued TOP mRNA translation in oxygen-deprived cells. Stress-induced translational repression of these mRNAs closely correlates with the hypophosphorylated state of 4E-BP, a translational repressor. However, a series of 4E-BP loss- and gain-of-function experiments disprove a cause-and-effect relationship between the phosphorylation status of 4E-BP and the translational repression of TOP mRNAs under oxygen or growth factor deprivation. Furthermore, the repressive effect of anoxia is similar to that attained by the very efficient inhibition of mTOR activity by Torin 1, but much more pronounced than raptor or rictor knockout. Likewise, deficiency of raptor or rictor, even though it mildly downregulated basal translation efficiency of TOP mRNAs, failed to suppress the oxygen-mediated translational activation of TOP mRNAs. Finally, co-knockdown of TIA-1 and TIAR, two RNA-binding proteins previously implicated in translational repression of TOP mRNAs in amino acid-starved cells, failed to relieve TOP mRNA translation under other stress conditions. Thus, the nature of the proximal translational regulator of TOP mRNAs remains elusive

Nitrite dynamics in the open ocean - clues from seasonal and diurnal variations

Two alternative mechanisms are suggested for nitrite accumulation in the oxygenated oligotrophic water column: (1) excretion by phytoplankton or (2) microbial oxidation of ammonium (nitrification). This study assessed the role of these 2 mechanisms, based on seasonal and high-resolution diurnal depth profiles of the dissolved inorganic nitrogen (DIN) species (nitrite, ammonium, nitrate) and chlorophyll a in the Gulf of Aqaba, Red Sea. Both mechanisms operated in the water column, but in different seasons; nitrification was the prime process responsible for nitrite accumulation during the stratified summer season and phytoplankton nitrite excretion operated during winter mixing. At the onset of summer stratification two N peaks developed below the photic zone, an ammonium maximum (AM) and below it the primary nitrite maximum (PNM). Both peaks were located at a depth range where phytoplankton are thought to be inactive and not excreting nitrite. During summer stratification, the water column deep chlorophyll maximum (DCM), AM, PNM and the nitracline were ordered by a downward increase in N oxidation state similar to the temporal order of the N-species during nitrification. This similarity, together with the diurnal stability of the PNM and its co-existence with oscillating chlorophyll profiles above the DCM, is consistent with nitrification as the key process forming the PNM. We suggest that transport and reaction control the vertical order and separation of N-species in the water column. The ratios between the rate constants for ammonification, ammonium oxidation, nitrite oxidation and nitrate assimilation were estimated by a simple box model to be 1:3:1.5:0.15, respectively. These field estimates are similar to the ratios between the rate constants measured in laboratory experiments

Nitrite dynamics in the open ocean—clues from seasonal and diurnal variations

Two alternative mechanisms are suggested for nitrite accumulation in the oxygenated oligotrophic water column: (1) excretion by phytoplankton or (2) microbial oxidation of ammonium (nitrification). This study assessed the role of these 2 mechanisms, based on seasonal and high-resolution diurnal depth profiles of the dissolved inorganic nitrogen (DIN) species (nitrite, ammonium, nitrate) and chlorophyll a in the Gulf of Aqaba, Red Sea. Both mechanisms operated in the water column, but in different seasons; nitrification was the prime process responsible for nitrite accumulation during the stratified summer season and phytoplankton nitrite excretion operated during winter mixing. At the onset of summer stratification two N peaks developed below the photic zone, an ammonium maximum (AM) and below it the primary nitrite maximum (PNM). Both peaks were located at a depth range where phytoplankton are thought to be inactive and not excreting nitrite. During summer stratification, the water column deep chlorophyll maximum (DCM), AM, PNM and the nitracline were ordered by a downward increase in N oxidation state similar to the temporal order of the N-species during nitrification. This similarity, together with the diurnal stability of the PNM and its co-existence with oscillating chlorophyll profiles above the DCM, is consistent with nitrification as the key process forming the PNM. We suggest that transport and reaction control the vertical order and separation of N-species in the water column. The ratios between the rate constants for ammonification, ammonium oxidation, nitrite oxidation and nitrate assimilation were estimated by a simple box model to be 1:3:1.5:0.15, respectively. These field estimates are similar to the ratios between the rate constants measured in laboratory experiments