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:email@example.comTel: +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.
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.
A study was conducted in none tilled coffee agroforestry fields of Eastern Uganda to understand the effects of application of inorganic fertilizers on soil nutrient loss in form of gas for mitigation of unsustainable agricultural practices. This study specifically i) assessed the effect of application of inorganic fertilizers on greenhouse gas emissions, ii) determined their effect on microbial carbon, nitrogen and phosphorus and iii) determined their effect on leaf litter decomposition under Albizzia-coffee growing systems of the Mount Elgon. Soil gas emissions were measured with the static chamber method for twelve months in a field experiment with five different fertilizer treatments. The effect of treatments was separated using ANOVA in Genstat discovery version 13. Microbial carbon, nitrogen and phosphorus was separated using Mann-Whitney U test. Results showed that annual emissions ranged from 19.6 to 26.1 (t C/ha/yr), 3.5 to 9 (Kg N/ha/yr) and 6.9 to 9.2 (Kg C/ha/yr) for carbon dioxide, nitrous oxide and methane respectively. Significant effects on soil emissions only occurred for nitrous oxide (P=0.017), microbial carbon (p=0.001) and microbial phosphorus (p<0.001) for the study period. The mixture of NPK fertilizers presented the lowest carbon dioxide loss and application of TSP presented the lowest nitrous oxide emission from soil. This study underscores the need for establishment of long-term experiments across several agro-ecological zones to confirm farmers’ perceptions of their soil fertility levels and ascertain the contribution of farm practices towards the retention of nutrients in the soil with minimal emission, to inform decisions of small holder farmers, policy and development partners for sustainable production.
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.
Around the world, water is considered a fundamental factor, and plays a role in public health and economic growth. Both the water development rates and the proportion of the population are directly related to water needs. Water quality regarding physiochemistry and microbiology is important in dietary needs. Drinking water is considered one of the most important food products. Therefore, the water should meet the recommended quality standards. So, it should be free of bacteria, parasites, all kinds of microorganisms, and chemical substances which are dangerous to human health. This research focused on five cities of the Alkalaa Municipal Community, which forms 43% of the inhabitants of this community, in the Bint Jbeil district south of Lebanon. The goal of this study is to determine the fundamental physicochemical and microbiological water properties of eight distinct sites, as well as the amount of pollution. These tests were carried out in accordance with World Health Organization criteria (WHO). The collected data were utilized to assess the level of pollution in the examined zone.
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.
In this paper we develop and test a rigorous modeling framework, based on Duhamel’s Theorem, for the unsteady one-dimensional transport and mixing of a solute across a flat sediment-water interface (SWI) and through the benthic biolayer of a turbulent stream. The modeling framework is novel in that it allows for depth-varying diffusivity profiles, accounts for the change in porosity across the SWI and captures the two-way coupling between evolving solute concentrations in both the overlying water column and interstitial fluids of the sediment bed. We apply this new modeling framework to an extensive set of previously published laboratory measurements of turbulent mixing across a flat sediment bed, with the goal of evaluating four diffusivity profiles (constant, exponentially declining, and two hybrid models that account for molecular diffusion and enhanced turbulent mixing in the surficial portion of the bed). The exponentially declining profile is superior (based on RMSE, coefficient of determination, AICc, and model parsimony) and its reference diffusivity scales with a dimensionless measure of stream turbulence and streambed permeability called the Permeability Reynolds Number, . The diffusivity’s dependence on changes abruptly at , reflecting different modes of mixing below (dispersion) and above (turbulent diffusion) this threshold value. The depth-scale over which the diffusivity exponentially decays is about equal to the thickness of the benthic biolayer (2 to 5 cm), implying that turbulent mixing, and specifically turbulent pumping, may play an outsized role in the biogeochemical processing of nutrients and other contaminants in stream and coastal sediments.
Most tree species predominantly associate with a single type of mycorrhizal fungi, which can differentially affect plant nutrient acquisition and biogeochemical cycling. Here, we address for the first time the impact of mycorrhizal distributions on global carbon and nutrient cycling. Using the state-of-the-art carbon-nitrogen economics within the Community Land Model version 5 (CLM5) we found Net Primary Productivity (NPP) increased throughout the 21st century by 20%; however, as soil nitrogen has progressively become limiting, the costs to NPP for nitrogen acquisition — i.e., to mycorrhizae — have increased at a faster rate by 60%. This suggests that nutrient acquisition will increasingly demand a higher portion of assimilated carbon to support the same productivity. Uncertainties in mycorrhizal distributions are non-trivial, however, with uncertainties in NPP by up to 345 Tg C yr-1, depending on which published distribution is used. Remote sensing capabilities for mycorrhizal detection show promise for refining these estimates further.
Microcosm experiments using microbial mats can be useful at times to understand mineral precipitation induced by microorganisms and their extracellular polymeric substances (EPS). Currently, the existing knowledge limits our ability to elucidate the interactions between microbes, which form communities as microbial mats, and minerals that precipitate in natural environments (e.g., lagoons, rivers, springs, soils). Much of the prior research did not consider entire microbial communities, despite recent evidence that microorganisms interact in a community-based way. This is especially relevant in extreme environments where the entire microbial communities are not yet known despite their relevance to biosignatures exploration on other planets. Here, we grew microbial mats on natural substrates in the laboratory to monitor changes in mat texture and mineral paragenesis. Several analytical techniques were used to compare mineral paragenesis in association with and without microbes. This paragenesis included major phases of chemical sedimentary deposits, such as gypsum, calcium carbonate, and some silicates, whose formation is traditionally linked to evaporative processes but was not in these experiments. In addition, some of the phases only precipitated within microbial mat samples and there were differences in mineral fabrics between mat samples and abiotic controls.
Minerals are information-rich materials that offer researchers a glimpse into the evolution of planetary bodies. Thus it is important to extract, analyze, and interpret this abundance of information in order to improve our understanding of the planetary bodies in our solar system and the role our planet’s geosphere played in the origin and evolution of life. Over the past decades, data-driven efforts in mineralogy have seen a gradual increase. The development and application of data science and analytics methods to mineralogy, while extremely promising, has also been somewhat ad-hoc in nature. In order to systematize and synthesize the direction of these efforts, we introduce the concept of “Mineral Informatics”. Mineral Informatics is the next frontier for researchers working with mineral data. In this paper, we present our vision for Mineral Informatics, the X-Informatics underpinnings that led to its conception, the needs, challenges, opportunities, and future directions. The intention of this paper is not to create a new specific field or a sub-field as a separate silo, but to document the needs of researchers studying minerals in various contexts and fields of study, to demonstrate how the systemization and increased access to mineralogical data will increase cross- and interdisciplinary studies, and how data science and informatics methods are a key next step in integrative mineralogical studies.
The community of Kotzebue, located on the coast of Kotzebue Sound, which is northeast of the Bering Straits adjacent to the Chukchi Sea, is reliant on the waters around Kotzebue Sound for food and economy. There have been reports of cyanobacterial blooms in these waters around Kotzebue but they have not been systematically studied yet, because the region is sparsely populated with few in-situ observations. Cyanobacteria often form surface blooms in freshwater and coastal ecosystems which can be detected using remote sensing techniques. Cyanobacteria are found to have low nutritional value and many species of cyanobacteria produce cyanotoxins, and thus can be harmful to aquatic life and cause public health hazards. In addition, consumption of decaying cyanobacterial blooms by microbes depletes oxygen level which can lead to hypoxia, adversely impacting the benthic community. As the Arctic is warming twice as fast as the rest of the planet due to climate change, thawing permafrost is releasing nutrients that might be enhancing cyanobacterial blooms in the coastal, marine and lacustrine waters of Alaska. In this study, we used remote sensing to study phytoplankton biomass, turbidity and cyanobacterial blooms between mid-June to end of September each year from 2013 to 2019 when the waters around Kotzebue are ice-free. Using images from Landsat-8 and Sentinel-2, processed using ACOLITE software, we investigated spatial and temporal changes in water quality parameters such as turbidity and chlorophyll concentration between June and September. We used a combination of true-color images and fai (floating algal index) to detect cyanobacterial blooms. There were about two scenes from Sentinel-2 and about one scene from Landsat-8, for a total of about three scenes every week between June and September. Of these, only 49% of the images were cloud-free. Of the cloud-free images, 29% were found to have a cyanobacterial bloom between August and September for an average of two to four scenes every year. Most of the cyanobacterial blooms were detected in Kobuk Lake near Kotzebue, and nearby sites in Hotham Inlet and Selawik Lake. In 2013, 68% of the images were cloudy which was the highest in the observed years and no cyanobacterial blooms were detected.
Studies on the molecular mechanisms of microbial adaptation in chaotropic and low water activity (aw) environments are poorly understood. Chaotropic environments are characterized as salt rich, MgCl2 and CaCl2, which lowers the availability of water for biological processes. PATRIC, an integrated genomic browsing tool containing vast libraries of sequenced genomes, can help us identify unique genetic markers in chaophilic and xerophilic microbes. Halophilic microbes are characterized as obligate hypersaline with the ability to tolerate exposure to chaotropic agents. Microbes with the greatest tolerance in these extreme environments must have advanced adaptive methods. Halobacterium salinarum and Haloquadratum walsbyi are chaotolerant and well adapted to low water activity. Haloquadratum walsbyi is unique among the halophilics as having the highest tolerance for chaotropes and its square shape. Performing comparative genomics using fully sequenced halophilic archaea such as Halobacterium salinarum NRC-1, a model halophile, and Haloquadratum walsbyi C23, we were able to identify genes that confer adaptation to chaotropic and low aw environments, as well as individual adaptations that may be responsible for the varying levels of tolerance in chaotropic environments . Characterizing genes associated with chaotolerance and low aw adaptations can help elucidate the cellular functions that make these microbes unique. Chaotropic brines may be used as analogs to study the origin of life and the possibility of suitable environments hosting extremophilic microbes on other planets like the Martian brines and the icy moons of Europa; therefore, studying the microbiome of chaotropic environments are essential in the field of astrobiology.
The interface between rivers and groundwater is a key driver for the turnover of reactive nitrogen compounds, that cause eutrophication of rivers and endanger drinking-water production from groundwater. Molecular-biological data and omics tools have been used to characterize microorganisms responsible for the turnover of nitrogen compounds. While transcripts of functional genes and enzymes are used as measures of microbial activity it is not yet clear how they quantitatively relate to actual turnover rates under variable environmental conditions. We developed a reactive-transport model for denitrification that simultaneously predicts the distributions of functional-gene transcripts, enzymes and reaction rates. Applying the model, we evaluate the response of transcripts and enzymes at the river–groundwater interface to stable and dynamic hydrogeochemical regimes. While functional-gene transcripts respond to short-term (diurnal) fluctuations of substrate availability and oxygen concentrations, enzyme concentrations are stable over such time scales. The presence of functional-gene transcripts and enzymes globally coincides with the zones of active denitrification. However, transcript and enzyme concentrations do not directly translate into denitrification rates in a quantitative way because of non-linear effects and hysteresis caused by variable substrate availability and oxygen inhibition. Based on our simulations, we suggest that molecular-biological data should be combined with aqueous chemical data, which can typically be obtained at higher spatial and temporal resolution, to parameterize and calibrate reactive-transport models.
This study deals with the riverbed of the Columbia river in the vicinity of the Hanford 300 Area study site in eastern Washington, where fluctuations in river stage take place both naturally (i.e. seasonally) and in conjunction with hydroelectric power dam operations. These fluctuations create conditions conducive to the influx and transport of fine-grained POM (a biological colloid originating from the river water and/or in situ periphyton production), within near-surface riverbed sediments. Although a great deal is known about dissolved organic matter (DOM) transport and metabolism in hyporheic zone sediments, there is a paucity of quantitative information on POM dynamics and its influence on hyporheic zone biogeochemistry (e.g. dissolved oxygen dynamics). We have developed a hydrobiogeochemical model capable of simulating the transport and metabolism of POM and its impact on dissolved oxygen (DO) distribution within the riverbed as influenced by periodic changes in river stage and fluid flow rate and direction. The model was employed as a tool to interpret the results of in situ measurements of POM intrusion into the riverbed made using “POM traps” emplaced within the upper 20 cm of the riverbed, as well as real-time in situ dissolved oxygen concentrations determined with a novel optical sensor buried directly in the riverbed at 20 cm depth. The simulations reproduced the accumulation of fresh POM within the upper few 5 cm of the riverbed observed in field POM trap deployments. Once sufficient surface POM accumulation takes place, an underlying zone of DO depletion develops as a consequence of variation in the rate of fluid exchange and POM/DOM degradation. The model predicted cyclic, hydrologically-driven variations in near-surface DO that are consistent with the results of the in situ DO probe deployments together with parallel measurements of fluid conductivity and hydrologic pressure. Our results suggest a complex interplay between fluid flow rate/direction and DO distribution that has important implication for riverbed biogeochemical dynamics at a variety of scales, as influenced by hydrological variability as well as the relative intensity of POM input and the availability of oxygen and other electron acceptors for microbial metabolism.
Water-mediated linkages that connect landscape components are collectively referred to as hydrologic connectivity. In river-floodplain systems, quantifying hydrologic connectivity enables descriptions of hydrologic function that emerge from complex, heterogeneous interactions of underlying geomorphic, climatic and biologic controls. Here, we measure hydrologic connectivity using field indicators and develop a continuous connectivity metric that represents a vector strength between a source along the North St Vrain river to ten surface water target sites within the river-floodplain system. To measure this connectivity strength, we analyzed hydrometric, injected conservative tracers, and natural occurring geochemical and microbial indicators across streamflows in 2018. We developed empirical models of hydrologic connectivity as a function of river stage to predict daily connectivity strength across multiple floodplain sites for five years between May and September of 2016-2020. Three sites were either consistently connected or disconnected to the river, while seven varied across time in their hydrologic connectivity strength. Of the sites with variable connectivity, some disconnected very quickly and others had a prolonged disconnection phase. By scaling site dynamics to the system scale, we found across-system hydrologic connectivity always increased with streamflow while across-system variance in hydrologic connectivity peaked at intermediate streamflow. At sites with intermittent connections to the river, river stage disconnection thresholds were variable (308 to 650 mm) and their connectivity dynamics were sensitive to inter-annual variation in streamflows, suggesting that future connectivity behavior under climate change will depend on how flow durations change across a range of flow states.
Several bills moving through Congress are likely to provide significant funding for expanding research and results in climate change solutions (CCS). This is also a priority of the Biden-Harris Administration. The National Science Foundation (NSF) will be expected to distribute and manage much of this funding through its grant processes. Effective solutions require both a continuation and expansion of research on climate change–to understand and thus plan for potential impacts locally to globally and to continually assess solutions against a changing climate–and rapid adoption and implementation of this science with society at all levels. NSF asked AGU to convene its community to help provide guidance and recommendations for enabling significant and impactful CCS outcomes by 1 June. AGU was asked in particular to address the following: 1. Identify the biggest, more important interdisciplinary/convergent challenges in climate change that can be addressed in the next 2 to 3 years 2. Create 2-year and 3-year roadmaps to address the identified challenges. Indicate partnerships required to deliver on the promise. 3. Provide ideas on the creation of an aggressive outreach/communications plan to inform the public and decision makers on the critical importance of geoscience. 4. Identify information, training, and other resources needed to embed a culture of innovation, entrepreneurialism, and translational research in the geosciences. Given the short time frame for this report, AGU reached out to key leaders, including Council members, members of several committees, journal editors, early career scientists, and also included additional stakeholders from sectors relevant to CCS, including community leaders, planners and architects, business leaders, NGO representatives, and others. Participants were provided a form to submit ideas, and also invited to two workshops. The first was aimed at ideation around broad efforts and activities needed for impactful CCS; the second was aimed at in depth development of several broad efforts at scale. Overall, about 125 people participated; 78 responded to the survey, 82 attended the first workshop, and 28 attended the more-focused second workshop (see contributor list). This report provides a high-level summary of these inputs and recommendations, focusing on guiding principles and several ideas that received broader support at the workshops and post-workshop review. These guiding principles and ideas cover a range of activities and were viewed as having high importance for realizing impactful CCS at the scale of funding anticipated. These cover the major areas of the charge, including research and solutions, education, communication, and training. The participants and full list of ideas and suggestions are provided as an appendix. Many contributed directly to this report; the listed authors are the steering committee.
Introduction: It has been proposed that the recently discovered superphylum of Asgard archaea may represent a historical link/bridge between the Archaea and Eukarya. The arrangement of genes in genomes is a window to understand how organisms are related. In particular, the translation machinery and the genes that encode the same have a long evolutionary history. In order to gain further insight into the evolutionary position of the Asgard archaea, the genome order of ribosomal protein coding genes was analyzed. The Asgard archaea were compared with non-Asgard archaeal and bacterial genomes. Results: A core of co-occurring 15 genes belonging to the segment of the S10 and spc cluster (which are characterized and established as operons in Bacteria), was identified as conserved in gene order, arrangement and genome location in Asgard archaea, non-Asgard archaea and Bacteria. This core occurs as a complete set in the genomes of Lokiarchaeota MK-D1 (Candidatus Prometheoarchaeum syntrophicum), and Candidatus Odinarchaeota archaeon LCB_4. The genome assemblies of the other Asgard genomes are incomplete and occur in multiple contigs (>50) and hence this cluster is found in sections across contigs, with a section often either ending or beginning a contig. The cluster organization is indicative of co-occurrence, if the genome was complete. A second smaller cluster comprising the homologs of the most conserved genes of the bacterial S10 operon/cluster namely, uS10-uL3-uL4-uL23-uL2 occurs independently on the Asgard genomes, separate from the rest, a feature shared by many non-Asgard archaea as well. Other clusters. A new cluster L7ae-infB was identified to co-occur with the minor S24e-S27ae cluster in the two complete Asgard genomes. The L7ae-infB cluster co-occurs with the S24e-S27ae cluster in some (non-Asgard) Crenarchaeota (Desulfurococcacea) and Euryarchaeota (Methanobacteriaceae), while it co-occurs with the (Alpha operon) L18e cluster in some (non-Asgard) Euryarchaeota (Halobacteriaceae). Overall, the organization of the most universal and highly conserved S10 and spc cluster in Asgard archaea resembles that of the non-Asgard Thaumarchaeota and the DPANN group. References: Wang J et al (2009) Archaea, 2(4), 241–251. Da Cunha V et al (2017) Plos Genetics 13(6), e1006810. Bowman J. C. et al. (2020) Chem Rev, 120(11), 4848-4878.