The protist community mirrors seasonality and mesoscale hydrographic features in the oligotrophic Sargasso Sea

Protists represent the majority of the eukaryotic diversity in the oceans. They have different functions in the marine food web, playing essential roles in the biogeochemical cycles. Meanwhile the available data is rich in horizontal and temporal coverage, little is known on their vertical structuring, particularly below the photic zone. The present study applies DNA metabarcoding to samples collected over three years in conjunction with the BATS time-series to assess marine protist communities in the epipelagic and mesopelagic zones. The protist community showed a dynamic seasonality in the epipelagic, responding to hydrographic yearly cycles. Mixotrophic lineages dominated throughout the year; however, autotrophs bloomed during the rapid transition between the winter mixing and the stratified summer, and heterotrophs had their peak at the end of summer, when the base of the thermocline reaches its deepest depth. Below the photic zone, the community, dominated by Rhizaria, is depth-stratified and relatively constant throughout the year, mirroring local hydrographic and biological features such as the oxygen minimum zone. The results suggest a dynamic partitioning of the water column, where the niche vertical position for each community changes throughout the year, likely depending on nutrient availability, the mixed layer depth, and other hydrographic features. Finally, the protist community closely followed mesoscale events (eddies), where the communities mirrored the hydrographic uplift, raising the deeper communities for hundreds of meters, and compressing the communities above.

Denitrification in foraminifera has ancient origins and is complemented by associated bacteria

Benthic foraminifera are unicellular eukaryotes that inhabit sediments of aquatic environments. Several foraminifera of the order Rotaliida are known to store and use nitrate for denitrification, a unique energy metabolism among eukaryotes. The rotaliid Globobulimina spp. has been shown to encode an incomplete denitrification pathway of bacterial origins. However, the prevalence of denitrification genes in foraminifera remains unknown and the missing denitrification pathway components are elusive. Analysing transcriptomes and metagenomes of ten foraminifera species from the Peruvian oxygen minimum zone, we show that denitrification genes are highly conserved in foraminifera. We infer of the last common ancestor of denitrifying foraminifera, which enables us to predict further denitrifying species. Additionally, an examination of the foraminifera microbiota reveals evidence for a stable interaction with Desulfobacteracea, which harbour genes that complement the foraminifera denitrification pathway. Our results provide evidence that foraminiferal denitrification is complemented by the foraminifera microbiome. The interaction of Foraminifera with their resident bacteria is at the basis of foraminifera adaptation to anaerobic environments that manifested in ecological success within oxygen depleted habitats.

Impact of climate induced hypoxia on calcifying biota in the Arabian Sea : An evaluation from the micropaleontological records of the Indian margin

High biological productivity combined with the poor ventilation produces severe oxygen depletion (hypoxia) in upper intermediate waters of the Arabian Sea. The naturally developed Arabian Sea oxygen minimum zone (OMZ) is one of the most pronounced low oxygen ocean environments known today. The OMZ impinges the Indian margin where oxygen concentration reaches values less than 0.05 ml/l leading denitrification. In recent studies, it has been observed that the OMZ strength has varied considerably in the past, in tune with the global climate change. But the effect of changes in natural mid-water hypoxic environment on the marine biota particularly of the eastern Arabian Sea is unknown. Here, we analyzed 30,000 yr record of temporal changes in two major groups of marine calcifying microfauna pteropods secreting aragonitic shells and foraminifera secreting calcitic shells in terms of abundance and diversity variations. This study will provide an insight into our understanding of potential impact of rising atmospheric CO2 on marine ecosystem.

Research on Micro/Nano Surface Flatness Evaluation Method Based on Improved Particle Swarm Optimization Algorithm

Flatness error is an important factor for effective evaluation of surface quality. The existing flatness error evaluation methods mainly evaluate the flatness error of a small number of data points on the micro scale surface measured by CMM, which cannot complete the flatness error evaluation of three-dimensional point cloud data on the micro/nano surface. To meet the needs of nano scale micro/nano surface flatness error evaluation, a minimum zone method on the basis of improved particle swarm optimization (PSO) algorithm is proposed. This method combines the principle of minimum zone method and hierarchical clustering method, improves the standard PSO algorithm, and can evaluate the flatness error of nano scale micro/nano surface image data point cloud scanned by atomic force microscope. The influence of the area size of micro/nano surface topography data on the flatness error evaluation results is analyzed. The flatness evaluation results and measurement uncertainty of minimum region method, standard least squares method, and standard PSO algorithm on the basis of the improved PSO algorithm are compared. Experiments show that the algorithm can stably evaluate the flatness error of micro/nano surface topography point cloud data, and the evaluation result of flatness error is more reliable and accurate than standard least squares method and standard PSO algorithm.

Generation of Reference Softgauges for Minimum Zone Fitting Algorithms: Case of Aspherical and Freeform Surfaces

Optical aspherical lenses with high surface quality are increasingly demanded in several applications in medicine, synchrotron, vision, etc. To reach the requested surface quality, most advanced manufacturing processes are used in closed chain with high precision measurement machines. The measured data are analysed with least squares (LS or L2-norm) or minimum zone (MZ) fitting (also Chebyshev fitting or L∞-norm) algorithms to extract the form error. Performing data fitting according to L∞-norm is more accurate and challenging than L2-norm, since it directly minimizes peak-to-valley (PV). In parallel, reference softgauges are used to assess the performance of the implemented MZ fitting algorithms, according to the F1 algorithm measurement standard, to guarantee their traceability, accuracy and robustness. Reference softgauges usually incorporate multiple parameters related to manufacturing processes, measurement errors, points distribution, etc., to be as close as possible to the real measured data. In this paper, a unique robust approach based on a non-vertex solution is mathematically formulated and implemented for generating reference softgauges for complex shapes. Afterwards, two implemented MZ fitting algorithms (HTR and EPF) were successfully tested on a number of generated reference pairs. The evaluation of their performance was carried out through two metrics: degree of difficulty and performance measure.

Improved algorithm for minimum zone of roundness error evaluation using alternating exchange approach

Based on the computational geometry technique, an improved algorithm for minimum zone of roundness error evaluation using an alternating exchange method is presented. A minimum zone fitting function was created to enhance the roundness error evaluation. The function uses three candidate points to determine the initial solution: the expected centre, the mean circle radius, and the corresponding zone half-width. The best solution function is designed to use the initial solution as the input to determine the optimum solution for the minimum zone circle. The proposed algorithm was validated using data available in the literature. The roundness error evaluation comparison results demonstrate that the proposed method accurately detects both the centre error magnitude and minimum zone circle and overcomes the insufficiency of using selected colinear points for four selected points.

Deoxygenation of the eastern Indonesian waters and its variability

Long-term ocean deoxygenation could lead to decline biological productivity and alter biogeochemical cycles. Ocean warming contributions to ocean deoxygenation are reasonably understood, however, there is a challenge to reveal the gaps about other modifying factors to explain different regional patterns and predicts the condition in the coming century. This study aimed to identify the deoxygenation areas in the eastern Indonesian waters, understand the variability of physical and chemical parameters as the deoxygenation drivers, and investigate the correlation between parameters. In-situ and satellite-derived data from 1995 to 2020 were analyzed with statistical methods and remote sensing techniques to enhance deoxygenation measures in higher spatial and temporal resolutions. Our findings revealed that significant deoxygenation was detected around the Arafura Sea. The oxygen minimum zone extended at 133.5° – 136.8° E in the depth of 350 – 1,000 meters, with less than 20 mmol/m3 of dissolved oxygen concentration. Nitrate, phosphate, and temperature were identified to have a strong reversed relationship with the oxygen concentration in the study area. This study also developed multiple regression model algorithms to estimate the oxygen concentration in specified depths.

The Diversity and Nitrogen Metabolism of Culturable Nitrate-Utilizing Bacteria Within the Oxygen Minimum Zone of the Changjiang (Yangtze River) Estuary

The nitrogen cycle is an indispensable part of the biogeochemical cycle, and the reactions that occur in the ocean oxygen minimum zone (OMZ) mediate much of the loss of nitrogen from oceans worldwide. Here, nitrate-utilizing bacteria were isolated from the water column at 17 stations within the OMZ of the Changjiang (Yangtze River) Estuary using selective media and a culture-dependent method. The microbial diversity, nitrogen metabolism and nitrate reduction test of culturable heterotrophic bacteria were examined. A total of 164 isolates were obtained; they were mostly affiliated with Proteobacteria (81.1%), Actinobacteria (5.5%), Bacteroidetes (12.3%), and Firmicutes (0.6%). Pseudomonas aeruginosa, Sphingobium naphthae, and Zunongwangia profunda were found at most stations. Among 24 tested representative strains, 8 were positive for nitrate reduction; they belonged to genera Aurantimonas, Halomonas, Marinobacter, Pseudomonas, Thalassospira, and Vibrio. Pseudomonas aeruginosa contained the genes (napAB, norBC, nirS, and nosZ) for complete denitrification and may be responsible for mediating denitrification. 66% representative isolates (16/24) contained genes for reducing nitrate to nitrite (nasA, napAB, or narGHI) and 79% representative isolates (19/24) possessed genes for converting nitrite to ammonia (nirA or nirBD), suggesting that nitrate and nitrite could act as electron acceptors to generate ammonium, subsequently being utilized as a reduced nitrogen source. This study improves our understanding of the microbial diversity within the OMZ of Changjiang Estuary and may facilitate the cultivation and exploitation of bacteria involved in the nitrogen cycle.

COMPARATIVE STUDY OF ANTIBIOTICS, TOOTHPASTE AND PLANT EXTRACTS AGAINST BACTERIAL PATHOGENS ISOLATED FROM HUMAN GUMS

This study was conducted to find out the effectiveness of some antibiotics, toothpastes, and medicinal plant extracts against the bacterial species isolated from human gums. A total of 125 samples were collected. The male and female patients were with the age from 15-60 years. A total of 27 species were isolated and identified. Among those bacterial species, Streptococcus mutans was most prevalent 29.62%, followed by Lactobacillus acidophilus 22.22%, Streptococcus sobrinus 18.51% and S aureus 14.81% respectively. While Micrococcus spp. 3.7%, Streptococcus sanguinis 3.7%, Actinomyces viscosus 3.7% and Aeromonas were least prevalent. To observe the most effective treatment for gum infections, the isolated strains were subjected to the sensitivity tests against antibiotics, toothpastes and plant extracts. The maximum zone of inhibition formed by Sulfamethoxazole was found against Staph aurus 33mm, while the minimum zone by Amoxicillin was observed against Streptococcus sobrinus (6mm). The maximum zone of inhibition by Toothpaste 1 (Fluoride and salt) was against Micrococcus spp. 34mm. The maximum zone of inhibition by Curcuma longa against S. mutans was 22mm, while the minimum zone by Ajuga bracteosa against S. mutans was 11mm. The data obtained through this study revealed that antibiotics were more effective for the treatment of oral bacterial pathogens as compared to toothpaste and plant extracts with moderate and low activity, respectively. Therefore, it is strongly suggested that use of antibiotics during infection and toothpaste with fluoride and salt contents in daily routine could help in the elimination of bacterial pathogens to maintain oral health.