Hilal ERDOGAN1*, Pelin OZMEN 2, Hayrun Nisa BULBUL31 Nevsehir Haci Bektas Veli University, Faculty of Dentistry, Department of Endodontics, Nevsehir, Turkiye. ORCID: 0000-0001-5219-46932 Nevsehir Haci Bektas Veli University, Faculty of Dentistry, Department of Basic Sciences, Department of Medical Microbiology, Nevsehir, Turkiye. ORCID: 0000-0001-9496-30323 Nevsehir Haci Bektas Veli University, Institute of Science and Technology, Department of Molecular Biology and Genetics, Nevsehir, Turkiye. ORCID: 0000-0001-6843-417x* Corresponding authorCorrespondence author: Hilal ERDOGANNevsehir Haci Bektas Veli University, Faculty of Dentistry, Department of Endodontics, 2000 Evler Mah. Zübeyde Hanım Cad. 50300, Nevşehir/Turkiye. Email:firstname.lastname@example.orgTel: +90 (384) 228 10 00-22009ORCID ID: 0000-0001-5219-4693Acknowledgments: The authors deny any conflicts of interestFunding: This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.All authors have contributed significantly, and all authors are in agreement with the manuscript.
During NASA’s Apollo missions, inhalation of dust particles from lunar regolith was identified as a potential occupational hazard for astronauts. These fine particles adhered tightly to spacesuits and were brought accidentally into the living areas of the spacecraft. Apollo astronauts reported that exposure to the dust caused intense respiratory and ocular irritation. This problem is a potential challenge for the Artemis Program, which aims to return humans to the Moon for extended stays in this decade. Since lunar dust is “weathered” by space radiation, solar wind, and the incessant bombardment of micrometeorites, we investigated whether treatment of lunar regolith simulants to mimic space weathering enhanced their toxicity. Two such simulants were employed in this research, Lunar Mare Simulant-1 (LMS-1), and Lunar Highlands Simulant-1 (LHS-1), which were applied to human lung epithelial cells (A549). In addition to pulverization, previously shown to increase dust toxicity sharply, the simulants were exposed to hydrogen gas at high temperature as a proxy for solar wind exposure. This treatment further increased the toxicity of both simulants, as measured by the disruption of mitochondrial function, and damage to DNA both in mitochondria and in the nucleus. By testing the effects of supplementing the cells with an antioxidant (N-acetylcysteine), we showed that a substantial component of this toxicity arises from free radicals. It remains to be determined to what extent the radicals arise from the dust itself, as opposed to their active generation by inflammatory processes in the treated cells.
To integrate temporal and spatial dimensions of seasonal cycles, we combine two conceptual frameworks: ecological calendars and the “3Hs” model of the biocultural ethic. The latter values the vital links between human and other-than-human co-inhabitants, their life habits (e.g., cultural practices of human communities or life cycles of other-than-human species) and the structure, patterns and processes of their shared habitats. This integration enhances an understanding of core links between cultural practices and the life cycles of biocultural keystone species. As a synthesis, we use the term biocultural calendars to emphasize the co-constitutive nature of calendars that result from continuous interactions between dynamic biophysical and cultural processes. We apply biocultural calendars to examine cultural practices and socio-environmental changes in southwestern South America, specifically in Chile, spanning from (1) Cape Horn at the southern of the Americas in sub-Antarctic habitats inhabited by the Yagan indigenous community, (2) artisanal fisher communities in Chiloe; archipelagoes, (3) coastal regions of central-southern Chile inhabited by Lafkenche and Williche indigenous communities, to (4) high Andean habitats in northern Chile co-inhabited by Aymara communities along with domesticated camelids and a rich biodiversity. To illustrate biocultural calendars, we designed analemma diagrams that show the position of the Sun in the sky as seen from a fixed time and location, and linked to continuous renewal of astronomical, biological and cultural, seasonal cycles that sustain life. These biocultural calendars enhance the integration of indigenous and scientific knowledge to confront complex challenges of climate change faced by local communities and global society.
Vegetation acts as a critical link between the geosphere, biosphere, and atmosphere, regulating the flux of water to the atmosphere via transpiration (E) and the input of carbon from the atmosphere to plants and soil via photosynthetic carbon assimilation (A). The rate of A is known to be seasonally dynamic, however, few studies have investigated how the ratio between E and A, known as the water use efficiency (WUE), changes with phenology. WUE directly impacts regional to global carbon and water cycles and lack of knowledge regarding the dynamics of WUE remains among the largest uncertainties in current earth system model (ESM) projections of carbon and water exchange in temperate forests. Here we attempt to reduce this knowledge gap by studying these dynamics across a range of eight deciduous tree species common to temperate forests of North America. Using gas exchange and spectroscopic measurements, we investigated seasonal patterns in leaf level physiological, biochemical, and anatomical properties, including the seasonal progress of WUE and foliar capacity for carbon assimilation, which corollate with seasonal leaf phenology. We incorporate these findings into a modeling framework that contains the same representation of A, E, and canopy scaling found in ESMs to explore the impact of parameterization, which tracks phenological status, on model forecasts. Our results indicate that both photosynthetic capacity and WUE are seasonally dynamic processes which are not synchronized. WUE increased from a minimum at leaf out toward a more conservative behavior at the mid-summer growth peak. This pattern was explained by a decreased stomatal aperture and a decrease in cuticular leakage with leaf aging. We also observed a seasonal increase in maximum carboxylation capacity, with maximum rates of A and modeled tree net primary productivity (NPP) occurring later toward the end of the summer. This change was primarily driven by an increase in foliar nitrogen content, and a shift in the ratio of Vcmax to Jmax between expanding and mature leaves. By applying our revised parameterization, which captures seasonal dynamics of gas exchange, into our model framework we aim to improve the process representation of leaf function in a temperate forest, and more faithfully represent dynamics of NPP and E in the early and late growth season.
[This presentation is published at https://doi.org/10.1111/1440-1703.12317] Dead organic matter (DOM), which consists of leaf litter, fine woody debris (FWD; < 3 cm diameter), downed coarse woody debris (CWDlog), and standing or suspended coarse woody debris (CWDsnag), plays a crucial role in forest carbon cycling. However, the contributions of each DOM type on stand-scale carbon storage (necromass) and stand-scale CO2 efflux (Rstand) estimates are not well understood. In addition, there is little knowledge of the effect of each DOM type on the accuracy of stand-scale estimates of total necromass and Rstand. This study investigated characteristics of necromass and Rstand from DOM in a subtropical forest in Okinawa island, Japan, to quantify the effect of each DOM type on total necromass, total Rstand, and estimate error of total necromass and Rstand. The CWDsnag accounted for the highest proportion (54%) of total necromass (1499.7 g C m–2), followed by CWDlog (24%), FWD (11%), and leaf litter (11%). Leaf litter accounted for the highest proportion (37%) of total Rstand (340.6 g C m–2 yr–1), followed by CWDsnag (25%), CWDlog (20%), and FWD (17%). The CWDsnag was distributed locally with 173% of the coefficient of variation for necromass, which was approximately two times higher than those of leaf litter and FWD (72–73%). Our spatial analysis revealed, for accurate estimates of CWDsnag and CWDlog necromass, sampling areas of ≥ 28750 m2 and ≥ 2058‒42875 m2 were required, respectively, under the condition of 95% confidence level and 0.1 of accepted error. In summary, CWD considerably contributed to stand-scale carbon storage and efflux in this subtropical forest, resulting in a major source of errors in the stand-scale estimates. In forests where frequent tree death is likely to occur, necromass and Rstand of CWD are not negligible in considering the carbon cycling as in this study, and therefore need to be estimated accurately.
Canada’s boreal forests and tundra ecosystems are responding to unprecedented climate change with implications for the global carbon (C) cycle and global climate. However, our ability to model the response of Canada’s terrestrial ecosystems to climate change is limited and there has been no comprehensive, process-based assessment of Canada’s terrestrial C cycle. We tailor the Canadian Land Surface Scheme Including Biogeochemical Cycles (CLASSIC) to Canada and evaluate its C cycling performance against independent reference data. We utilize skill scores to assess model performance against reference data alongside benchmark scores that quantify the level of agreement between the reference data sets to aid in interpretation. Our results demonstrate CLASSIC’s sensitivity to prescribed vegetation cover. They also show that the addition of five region-specific PFTs improves CLASSIC’s skill at simulating the Canadian C cycle. CLASSIC performs well when tailored to Canada, falls within the range of the reference data sets, and meets or exceeds the benchmark scores for most C cycling processes. New region-specific land cover products, well-informed plant functional type (PFT) parameterizations, and more detailed reference data sets will facilitate improvements to the representation of the terrestrial C cycle in regional and global land surface models (LSMs). Incorporating a parameterization for boreal disturbance processes and explicitly representing peatlands and permafrost soils will improve CLASSIC’s future performance in Canada and other boreal regions. This is an important step toward a comprehensive process-based assessment of Canada’s terrestrial C cycle and evaluating Canada’s net C balance under climate change.
Antarctic landfast sea ice (fast ice) is stationary sea ice that is attached to the coast, grounded icebergs, ice shelves, or other protrusions on the continental shelf. Fast ice forms in narrow (generally up to 200 km wide) bands, and ranges in thickness from centimeters to tens of meters. In most regions, it forms in autumn, persists through the winter and melts in spring/summer, but can remain throughout the summer in particular locations. Despite its relatively limited horizontal extent (comprising between about 4 and 13 \% of overall sea ice), its presence, variability and seasonality are drivers of a wide range of physical, biological and biogeochemical processes, with both local and far-ranging ramifications for various Earth systems. Antarctic fast ice has, until quite recently, been overlooked in studies, likely due to insufficient knowledge of its distribution, leading to its reputation as a “missing piece of the Antarctic puzzle”. This review presents a synthesis of current knowledge of the physical, biogeochemical and biological aspects of fast ice, based on the sub-domains of: fast ice growth, properties and seasonality; remote-sensing and distribution; interactions with the atmosphere and the ocean; biogeochemical interactions; its role in primary production; and fast ice as a habitat for grazers. Finally, we consider the potential state of Antarctic fast ice at the end of the 21st Century, underpinned by Coupled Model Intercomparison Project model projections. This review also gives recommendations for targeted future work to increase our understanding of this critically-important element of the global cryosphere.
The end-Permian mass extinction event resulted in the loss of approximately 80% to 90% of marine animal species due to drastic changes in climate. Because warming was a major factor in the extinction, it has been theorized the organisms that did survive were able to do so because they moved to higher latitudes and this hypothesis is consistent with tetrapod data. We hypothesized that this relationship holds true for marine mollusks and arthropods as well. Using Changhsingian (Late Permian) and Induan (Early Triassic) data from the Paleobiology Database, we extracted occurrences of classes Bivalvia, Cephalopoda, Gastropoda, and Ostracoda, which had 2433, 395, 379, and 1717 genus occurrences, respectively. Then, we used the paleolatitude data for each genus occurrence to characterize the latitude distribution of each class before and after the Permian/Triassic transition. We compared the paleolatitude medians before and after the mass extinction for each class to quantify the latitude shift for each class: 23.18° for Bivalvia, 37.45° for Cephalopoda, 29.82° for Gastropoda, and 6.29° for Ostracoda. This finding indicates that each individual class had a different latitudinal shift, with all classes exhibiting a poleward shift north. We also conducted Welch t-tests to compare the differences in latitudinal ranges and found that they were significant (Bivalvia: p < 2.2e-16, Cephalopoda: p = 3.83e-6, Gastropoda: p < 2.2e-16, Ostracoda: p = 0.0030). In addition, we ran multiple randomized models to compare them with our original results and found a significant difference between them via the Kolmogorov-Smirnov test, which means that the northward migration could be a biological response. Moreover, the results of our study show that the overall latitudinal range of most classes contracted after the extinction event, with the exception of the Cephalopoda class.
Graphene or graphene-based nanomaterials have emerged as novel scaffolds for developing robust bio-catalytic systems and a fast-developing promising contender for bioremediation. The interaction of bacteria and graphene is such an elusive issue that its implication in environmental biotechnology is unclear. The complexity and recalcitrant nature of the dyes make the conventional techniques inadequate and remain a challenge for industrial effluent treatment. Many scientists have developed hybrid processes and hybrid materials to enhance the treatment processes to satisfy increasingly stringent laws and criteria related to effluent discharge. The current study explicitly focuses on immobilization and growth of dye-degrading marine bacterial isolates on graphene oxide and their application in methylene blue dye degradation. The synergistic effects of adsorption and biodegradation achieved a unique clean-up performance that the counterpart-free bacteria could not fulfill. Further, toxicity analysis of intermediates also confirmed the non-toxic nature of the intermediates formed after synergistic treatment. This work has the potential to lead to zero effluent treatment processes.
The study was carried out to find significant lipid constituents of Sporotrichum schenckii (S. schenckii), purified lipid extract was assessed, and the ecology of S. schenckii was also studied. Phospholipids, triglycerides, and cholesterol were the three major lipid constituents of S. schenckii (77.9%). Other lipids (22.1%) were too few to be quantitated. 16 different types of fungi were isolated out of 120 samples processed; the maximum isolations were of Aspergillus spp., the most typical contaminant fungus. There was no particular correlation between the fungus isolate and the type of sample or its collection site. The pattern of various fungal isolates was almost identical irrespective of the sample and place. None of the samples processed was positive for S. schenckii. S. schenckii, though said to be a saprophyte, was not grown in the 120 samples studied. The endemicity of the disease, however, points towards the existence of the fungus in the area.
Understanding three-dimensional (3D) root traits is essential to improve water uptake, increase nitrogen capture, and raise carbon sequestration from the atmosphere. However, quantifying 3D root traits by reconstructing 3D root models for deeper field-grown roots remains a challenge due to the unknown tradeoff between 3D root-model quality and 3D root-trait accuracy. Therefore, we performed two computational experiments. We first compared the 3D model quality generated by five state-of-the-art open-source 3D model reconstruction pipelines on 12 contrasting genotypes of field-grown maize roots. These pipelines included COLMAP, COLMAP+PMVS (Patch-based Multi-view Stereo), VisualSFM, Meshroom, and OpenMVG+MVE (Multi-View Environment). The COLMAP pipeline achieved the best performance regarding 3D model quality versus computational time and image number needed. Thus, in the second test, we compared the accuracy of 3D root-trait measurement generated by the Digital Imaging of Root Traits 3D pipeline (DIRT/3D) using COLMAP-based 3D reconstruction with our current DIRT/3D pipeline that uses a VisualSFM-based 3D reconstruction (Liu et al., 2021) on the same dataset of 12 genotypes, with 5~10 replicates per genotype. The results revealed that, 1) the average number of images needed to build a denser 3D model was reduced from 3000~3600 (DIRT/3D [VisualSFM-based 3D reconstruction]) to 300~600 (DIRT/3D [COLMAP-based 3D reconstruction]); 2) denser 3D models helped improve the accuracy of the 3D root-trait measurement; 3) reducing the number of images can help resolve data storage capacity problems. The updated DIRT/3D (COLMAP-based 3D reconstruction) pipeline enables quicker image collection without compromising the accuracy of 3D root-trait measurements.
Lebanon’s natural water resources are facing serious problems and approaches exhaustion. One of these issues is deteriorating performance, which is linked to unregulated resource planning and rising demand. There are many different types of consumption, such as residential, industrial, and irrigation. Surface and groundwater are both referred to designate water resources. However, due to the obvious accessibility of exploitation, surface water resources such as rivers, lakes, and basins are primarily used. The Ras El-Ain basin is 6 km far south of Tyr, Lebanon. The Lebanese state dedicated it, along with other reservoirs, to supply potable water for Tyr and the surrounding villages. Today, these basins’ water quality has deteriorated significantly because of unrestricted liquid and soil waste dumping. As a result, contaminants develop in the basin water. Aside from laboratory testing for water quality, contamination can be seen through direct observations, odors, watercolors, and patterns. The purpose of this study is to assess the level of pollution in the Ras El-Ain basin. This basin has been progressively subjected to a variety of quality degradation characteristics. This includes the most important physiochemical properties. As a result, the physicochemical and microbiological water characteristics of five selected samples from each basin were tested. These tests were performed in accordance with European Standard Methods and World Health Organization guidelines (WHO). The effect of pollutant disposal in the Ras El-Ain basin was studied using multivariate approaches. The obtained results were used to evaluate the pollution degree in various regions of the basin.
1. This study combines two approaches to explore the utility of Monod growth kinetics to predict competition outcomes between freshwater cyanobacteria and chlorophytes at low iron Fe. Fe threshold concentrations (FeT) below which growth ceases, and growth affinities (slope of Fe concentration vs growth rate near FeT) were estimated for three large-bodied cyanobacteria (two N-fixers and Microcystis) and two chlorophytes in batch cultures. 2. Mean FeT for N-replete cyanobacteria, N-deplete (when N-fixing) cyanobacteria and chlorophytes were 0.076, 0.736 and 0.245 nmol L-1 , respectively. Mean affinities were 0.937, 0.597 and 0.412 L nmol-1 d-1 , respectively. Assuming that the mean affinities are representative of their groups, affinities predict that N-replete cyanobacteria are more efficient at acquiring Fe than chlorophytes and should dominate when Fe is low but greater than their FeT. 3. A second study evaluated the competitive abilities of a pico-cyanobacterium and a third chlorophyte in dual species, serial dilution culture. The pico-cyanobacterium was dominant at 50 nmol L-1 total Fe (which limited both taxa) and 500 nmol L-1 total Fe. At 0.5 nmol L-1 total Fe, a stressful concentration below FeT during most of the incubation, growth rates and cell densities were extremely low but neither had washed out after several months. 4. These results show that Monod kinetics can successfully predict competition outcomes in laboratory settings at low Fe. While important, Monod kinetics are only one mechanism governing competition between cyanobacteria and eukaryotes in natural systems. Observed deviations from Monod predictions can be partially explained with known mechanisms.
Moisture recycling via evapotranspiration (ET) is often invoked as a mechanism for the high deuterium excess signals observed in continental precipitation (dP). However, a global-scale analysis of precipitation monitoring station isotope data shows that metrics of ET contributions to precipitation (van der Ent et al., 2014) explain little dp variability on seasonal timescales. This occurs despite the fact that ET contributions increase by ~50% in continental locations such as the Eurasian interior from wet to dry seasons. To explain this apparent paradox, we hypothesize that the effects of ET on dP are dampened during dry seasons due to contributions from isotopically-evolved residual water storage that act to lower the d-excess of ET fluxes (dET), in combination with changes in transpiration fraction (T/ET). To test this hypothesis, we develop a parsimonious two-season (wet, dry) model for dET incorporating residual water storage and ET partitioning effects. We find that in environments with limited water storage, such as shallow-rooted grasslands, dry season dET is lower than wet season dET despite lower relative humidity. As global average ratios of annual water storage to precipitation are relatively low (Guntner et al., 2007), these dynamics may be widespread over continents. In environments where water storage is not limiting, such as groundwater-dependent ecosystems, dry season dET is still likely lower; however, this effect arises instead due to higher seasonal T/ET when energy-driven plant water use is enhanced and surface evaporation is relatively limited by water availability. Together, these analyses also indicate multiple mechanisms by which dET may be lower than dp during the same season, challenging the view that moisture recycling feedback increases the dp in continental interiors. This work demonstrates the potential complexity of seasonal dp dynamics and cautions against simple interpretations of dP as a process tracer for moisture recycling. References: Guntner et al., 2007. Water Resour. Res., 43, W05416. van der Ent et al., 2014. Earth Syst. Dynam., 5, 471–489.
Mangrove forests are among the most productive ecosystems in the world. These tropical and subtropical coastal forests provide a wide array of ecosystem services, including the ability to sequester and store large amounts of ‘blue carbon’. Given rising concerns over anthropogenic carbon dioxide (CO2) emissions, mangrove forests have been increasingly recognized for their potential in climate change mitigation programs. However, their productivity differs considerably across environments, making it difficult to estimate carbon sequestration potentials at regional scales. Additionally, most research has focused in humid and tropical latitudes, with limited studies in arid and semi-arid regions. A semi-arid mangrove forest in Magdalena Bay, Baja California Sur, Mexico was studied to quantify the average net ecosystem exchange (NEE), determine the annual carbon (C) budget and the environmental controls driving those fluxes. Measurements were taken during 2012-2013 using the eddy covariance technique, with a daily mean NEE of -2.25 +/- 0.4 g C m-2 d-1 and annual carbon uptake of 894 g C m-2 y-1. Daily variations in NEE were primarily regulated by light, but air temperature and vapor pressure deficit were strong seasonal drivers. Our research demonstrates that despite the harsh and arid climate, the mangroves of Magdalena Bay were nearly as productive as mangroves found in tropical and subtropical climates. These results broaden understanding of the ecosystem services of one of the largest mangrove ecosystems in the Baja California peninsula, and highlight the potential role of arid mangrove ecosystems for C accounting, management and mitigation plans for the region.
The rise of high-throughput phenotyping (HTP) has led to a dramatic increase in the ability to rapidly – and accurately – phenotype various organisms including plants. However, methods for efficiently managing, processing, analyzing, and sharing HTP data have not caught up to this new-found ability to collect big data which in turn introduces a whole host of new challenges. To address these, we have architected and implemented a multi-faceted infrastructure of webservices to further unify and automate the entire data collection process. We have integrated CyVerse and Slack into our IoHTP, two commonly used tools within plant science labs. CyVerse is a cloud-based data storage & management solution and Slack allows for bilateral instant-message communication with the HTP machines to keep researchers in touch with their autonomous experiments. Next, we are also developing our own website for administering jobs remotely to any number of (possibly geographically distributed) HTP machines. This innovative open-source approach has the potential to further advance high-throughput phenotyping worldwide by allowing interdisciplinary experts, namely in the plant and computer sciences, to collaborate more effectively and efficiently.
Nitrogen inputs can be an important cost consideration for farmers in terms of economic profit as well as environmental impact. Elucidating genetic regions that are associated with plant phenotype response to nitrogen stress can help in facilitating breeding approaches that can mitigate these costs. A diverse population of 272 maize lines was planted at a field site in Champaign, IL in two consecutive years in reduced nitrogen conditions. 302 phenotypes were recorded including: seed ionomic content, root structural traits derived from 2-dimensional images as well as a 3-dimensional representation generated from x-ray computed tomography (XRT) scans, root traits extrapolated from mini-rhizotron systems, drone images across the growing season and end of season agronomic traits such as biomass and yield. BLUP models were fit to obtain estimates of single year genotypic values as well as across years values both of which took into account year specific spatial variation. Individual years and combined years BLUP values were used as response variables in genome wide association studies (GWAS) to identify loci significantly associated with each set of values. Significant associations were identified for all phenotype categories.