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Chengbin Peng, Carlos M. Duarte, Daniel P. Costa, Christophe Guinet, Robert G. Harcourt, Mark A. Hindell, Clive R. McMahon, Monica Muelbert, Michele Thums, Ka-Chun Wong, Xiangliang Zhang |
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Title |
Deep Learning Resolves Representative Movement Patterns in a Marine Predator Species |
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2019 |
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Applied Sciences |
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9 |
Issue |
14 |
Pages |
2935 |
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Keywords |
marine animal movement analysis recurrent neural networks representative patterns |
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Abstract |
The analysis of animal movement from telemetry data provides insights into how and why animals move. While traditional approaches to such analysis mostly focus on predicting animal states during movement, we describe an approach that allows us to identify representative movement patterns of different animal groups. To do this, we propose a carefully designed recurrent neural network and combine it with telemetry data for automatic feature extraction and identification of non-predefined representative patterns. In the experiment, we consider a particular marine predator species, the southern elephant seal, as an example. With our approach, we identify that the male seals in our data set share similar movement patterns when they are close to land. We identify this pattern recurring in a number of distant locations, consistent with alternative approaches from previous research. |
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2076-3417 |
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yes |
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8772 |
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Francesco Enrichi, Dorthe Dahl-Jensen, Jørgen Peder Steffensen, Carlo Barbante |
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Title |
Theoretical and Experimental Analysis for Cleaning Ice Cores from EstisolTM 140 Drill Liquid |
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Journal |
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Year |
2021 |
Publication |
Applied Sciences |
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Volume |
11 |
Issue |
9 |
Pages |
3830 |
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Beyond EPICA drilling Estisol ice cores |
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To reconstruct climate history of the past 1.5 Million years, the project: Beyond EPICA Oldest Ice (BEOI) will drill about 2700 m of ice core in East Antarctica (2021–2025). As drilling fluid, an aliphatic ester fluid, EstisolTM 140, will be used. Newly drilled ice cores will be retrieved from the drill soaked in fluid, and this fluid should be removed from the cores. Most of it will be vacuum-cleaned off in a Fluid Extraction Device and wiped off with paper towels. Based on our experiences in Greenland deep ice coring, most of the residual fluid can be removed by storing the cores openly on shelves in a ventilated room. After a week of “drying”, the cores have a dry feel, handling them do not give “wet” gloves and they can easily be marked with lead pencils. This paper presents a theoretical investigation and some simple testing on the “drying” process. The rates of sublimation of ice and evaporation of fluid have been calculated at different temperatures. The calculations show that sublimation of the ice core should not occur, and that evaporation of fluid should be almost negligible. Our test results support these calculations, but also revealed significant fluid run-off and dripping, resulting in the removal of most of the fluid in a couple of days, independent of temperature and ventilation conditions. Finally, we discuss crucial factors that ensure optimal long-term ice core preservation in storage, such as temperature stability, defrosting cycles of freezers and open core storage versus storage of cores in insulated crates. |
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yes |
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8247 |
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Author |
Karl-Ludwig Klein |
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Title |
Radio Astronomical Tools for the Study of Solar Energetic Particles II.Time-Extended Acceleration at Subrelativistic and Relativistic Energies |
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Year |
2021 |
Publication |
Frontiers in Astronomy and Space Sciences |
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7 |
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93 |
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Solar energetic particle (SEP) events are commonly separated in two categories: numerous “impulsive” events of relatively short duration, and a few “gradual” events, where SEP-intensities may stay enhanced over several days at energies up to several tens of MeV. In some gradual events the SEP spectrum extends to relativistic energies (>1 GeV), over shorter durations. The two categories are strongly related to an idea developed in the 1960s based on radio observations: Type III bursts, which were addressed in a companion chapter, outline impulsive acceleration of electrons to subrelativistic energies, while the large and the relativistic SEP events were ascribed to a second acceleration process. At radio wavelengths, typical counterparts were bursts emitted by electrons accelerated at coronal shock waves (type II bursts) and by electron populations in large-scale closed coronal structures (type IV bursts). Both burst types are related to coronal mass ejections (CMEs). Type II bursts from metric to kilometric wavelengths tend to accompany large SEP events, which is widely considered as a confirmation that CME-driven shocks accelerate the SEPs. But type II bursts, especially those related to SEP events, are most often accompanied by type IV bursts, where the electrons are rather accelerated in the wake of the CME. Individual event studies suggest that although the CME shock is the most plausible accelerator of SEPs up to some yet unknown limiting energy, the relativistic SEP events show time structure that rather points to coronal acceleration related to type IV bursts. This chapter addresses the question what type II bursts tell us about coronal shock waves and how type II and type IV radio bursts are related with relativistic proton signatures as seen by particle detectors on the Earth and by their gamma-ray emission in the solar atmosphere, focusing on two relativistic SEP events, on 2005 Jan 20 and 2017 Sep 10. The importance of radio emissions as a complement to the upcoming SEP observations from close to the Sun is underlined. |
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227 |
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2296-987X |
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yes |
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7777 |
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Karl-Ludwig Klein |
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Title |
Radio Astronomical Tools for the Study of Solar Energetic Particles I. Correlations and Diagnostics of Impulsive Acceleration and Particle Propagation |
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Year |
2021 |
Publication |
Frontiers in Astronomy and Space Sciences |
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Volume |
7 |
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Pages |
105 |
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Abstract |
Solar energetic particles (SEPs) are sporadically ejected from the Sun during flares and coronal mass ejections. They are of major astrophysical interest, because the proximity of the Sun allows for detailed multi-messenger studies. They affect space weather due to interactions with electronics, with the Earth’s atmosphere, and with humans if they leave the protective shield of the magnetosphere of the Earth. Since early studies in the 1950s, starting with particle detectors on the ground, SEP events have been related to radio bursts. Two subjects are addressed in this chapter: attempts to establish quantitative correlations between SEPs and microwave bursts produced by gyro synchrotron radiation of mildly relativistic electrons, and the information derived from type III radio bursts on impulsive processes of particle acceleration and the coronal and interplanetary propagation. Type III radio bursts produced by electron beams on open magnetic field lines have a wide range of applications, including the identification of acceleration regions, the identification of confined particle acceleration with coronal signatures, but no SEPs, and the paths that the electrons, and energetic charged particles in general, take to travel from the low corona to the Heliosphere in case they escape. Simple scenarios of coronal particle acceleration are confirmed in relatively simple and short events. But the comparison with particle transport models shows that longer and delayed acceleration episodes exist especially in large SEP events. They will be discussed in a companion chapter. |
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227 |
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2296-987X |
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yes |
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6775 |
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Lorène Julia Marchand, Françoise Hennion, Michèle Tarayre, Marie-Claire Martin, Benoit Renaud Martins, Cécile Monard |
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Title |
Fellfields of the Kerguelen Islands harbour specific soil microbiomes and rhizomicrobiomes of an endemic plant facing necrosis |
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2022 |
Publication |
Frontiers in Soil Science |
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2 |
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Polar regions are characterized by rocky terrains with sparse vegetation and oligotrophic soils, i.e. “fellfields”. In such ecosystems, microbial communities should be essential for soil-plant functioning but their diversity is poorly explored. The sub-Antarctic Kerguelen Islands fellfields are characterized by an endemic long-lived cushion plant, Lyallia kerguelensis which rhizosphere may be a shelter for microbes in this harsh environment. Cushions are affected by necrosis and we expect the rhizomicrobiome composition to be related to plant necrosis. We analysed bacterial and fungal communities in bulk- and rhizospheric soils from L. kerguelensis in five different fellfields across the Kerguelen Islands using 16S rRNA and ITS1 metabarcoding. We found that soil microbial communities were composed of both restricted and cosmopolitan taxa. While all sites were dominated by the same bacterial taxa (Chloroflexi, Actinobacteria, α-Proteobacteria and Acidobacteria), the relative abundance of the main fungal phyla (Ascomycota, Basidiomycota, Mortierellomycota and Rozellomycota) highly differed between sites. L. kerguelensis rhizomicrobiome was at least as diverse as the bulk soil, making the rhizosphere a possible reservoir of microbial diversity. It was composed of the same main bacterial phyla than detected in the bulk soil while the composition of the rhizosphere fungal communities was specific to each plant. No common microorganisms were identified regarding cushion necrosis extent across plants and sites, but several microbial putative functions were shared, suggesting a possible shift in soil functioning with cushion necrosis increase. Our study brings new information on the diversity and composition of the microbial communities of fellfield soils in a sub-Antarctic Island and the rhizomicrobiome of a characteristic endemic cushion plant. |
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1116 |
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2673-8619 |
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yes |
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8492 |
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Author |
Tignat-Perrier, R., Vogel, T. M., Técher, N., Larose, C., and Dommergue, A. |
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Title |
Microorganisms Floating Through the Air |
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Year |
2022 |
Publication |
Frontiers for young minds |
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Would you believe us if we told you that, when you breathe in, you inhale thousands of microorganisms with every breath. Although this might sound scary, be assured that they are safe for your health. These airborne microorganisms, too small to see with the naked eye, consist of many different species. Who are they? Where do they come from? What do they do in the air? These are some of the questions that we answer in this article, although many questions about airborne microorganisms remain to be explored. |
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1028 |
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yes |
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8407 |
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Natasja Krog Noer, Mathias Hamann Sørensen, Hervé Colinet, David Renault, Simon Bahrndorff, Torsten Nygaard Kristensen |
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Title |
Rapid Adjustments in Thermal Tolerance and the Metabolome to Daily Environmental Changes – A Field Study on the Arctic Seed Bug Nysius groenlandicus |
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Year |
2022 |
Publication |
Frontiers in physiology |
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13 |
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Laboratory investigations on terrestrial model-species, typically of temperate origin, have demonstrated that terrestrial ectotherms can cope with daily temperature variations through rapid hardening responses. However, few studies have investigated this ability and its physiological basis in the field. Especially in polar regions, where the temporal and spatial temperature variations can be extreme, are hardening responses expected to be important. Here, we examined diurnal adjustments in heat and cold tolerance in the Greenlandic seed bug Nysius groenlandicus by collecting individuals for thermal assessment at different time points within and across days. We found a significant correlation between observed heat or cold tolerance and the ambient microhabitat temperatures at the time of capture, indicating that N. groenlandicus continuously and within short time-windows respond physiologically to thermal changes and/or other environmental variables in their microhabitats. Secondly, we assessed underlying metabolomic fingerprints using GC-MS metabolomics in a subset of individuals collected during days with either low or high temperature variation. Concentrations of metabolites, including sugars, polyols, and free amino acids varied significantly with time of collection. For instance, we detected elevated sugar levels in animals caught at the lowest daily field temperatures. Polyol concentrations were lower in individuals collected in the morning and evening and higher at midday and afternoon, possibly reflecting changes in temperature. Additionally, changes in concentrations of metabolites associated with energetic metabolism were observed across collection times. Our findings suggest that in these extreme polar environments hardening responses are marked and likely play a crucial role for coping with microhabitat temperature variation on a daily scale, and that metabolite levels are actively altered on a daily basis. |
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136 |
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1664-042X |
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yes |
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8479 |
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Author |
Guillaume Schwob, Nicolás I. Segovia, Claudio González-Wevar, Léa Cabrol, Julieta Orlando, Elie Poulin |
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Title |
Exploring the Microdiversity Within Marine Bacterial Taxa: Toward an Integrated Biogeography in the Southern Ocean |
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Year |
2021 |
Publication |
Frontiers in Microbiology |
Abbreviated Journal |
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Volume |
12 |
Issue |
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Pages |
1985 |
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Most of the microbial biogeographic patterns in the oceans have been depicted at the whole community level, leaving out finer taxonomic resolution (i.e., microdiversity) that is crucial to conduct intra-population phylogeographic study, as commonly done for macroorganisms. Here, we present a new approach to unravel the bacterial phylogeographic patterns combining community-wide survey by 16S rRNA gene metabarcoding and intra-species resolution through the oligotyping method, allowing robust estimations of genetic and phylogeographic indices, and migration parameters. As a proof-of-concept, we focused on the bacterial genus Spirochaeta across three distant biogeographic provinces of the Southern Ocean; maritime Antarctica, sub-Antarctic Islands, and Patagonia. Each targeted Spirochaeta operational taxonomic units were characterized by a substantial intrapopulation microdiversity, and significant genetic differentiation and phylogeographic structure among the three provinces. Gene flow estimations among Spirochaeta populations support the role of the Antarctic Polar Front as a biogeographic barrier to bacterial dispersal between Antarctic and sub-Antarctic provinces. Conversely, the Antarctic Circumpolar Current appears as the main driver of gene flow, connecting sub-Antarctic Islands with Patagonia and maritime Antarctica. Additionally, historical processes (drift and dispersal limitation) govern up to 86% of the spatial turnover among Spirochaeta populations. Overall, our approach bridges the gap between microbial and macrobial ecology by revealing strong congruency with macroorganisms distribution patterns at the populational level, shaped by the same oceanographic structures and ecological processes. |
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1044 |
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1664-302X |
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1664-302X |
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yes |
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6457 |
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Alexandra T. Holland, Benoît Bergk Pinto, Rose Layton, Christopher J. Williamson, Alexandre M. Anesio, Timothy M. Vogel, Catherine Larose, Martyn Tranter |
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Title |
Over Winter Microbial Processes in a Svalbard Snow Pack: An Experimental Approach |
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Year |
2020 |
Publication |
Frontiers in Microbiology |
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11 |
Issue |
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Pages |
1029 |
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Abstract |
Snow packs cover large expanses of Earth’s land surface, making them integral components of the cryosphere in terms of past climate and atmospheric proxies, surface albedo regulators, insulators for other Arctic environments and habitats for diverse microbial communities such as algae, bacteria and fungi. Yet, most of our current understanding of snow pack environments, specifically microbial activity and community interaction, is limited to the main microbial growing season during spring ablation. At present, little is known about microbial activity and its influence on nutrient cycling during the subfreezing temperatures and 24-h darkness of the polar winter. Here, we examined microbial dynamics in a simulated cold (−5°C), dark snow pack to determine polar winter season microbial activity and its dependence on critical nutrients. Snow collected from Ny-Ålesund, Svalbard was incubated in the dark over a 5-week period with four different nutrient additions, including glacial mineral particles, dissolved inorganic nitrogen (DIN), dissolved inorganic phosphorus (DIP) and a combined treatment of DIN plus DIP. Data indicate a consumption of dissolved inorganic nutrients, particularly DIN, by heterotrophic communities, suggesting a potential nitrogen limitation, contradictory to phosphorus limitations found in most aquatic environments. 16S amplicon sequencing also reveal a clear difference in microbial community composition in the particulate mineral treatment compared to dissolved nutrient treatments and controls, suggesting that certain species of heterotrophs living within the snow pack are more likely to associate with particulates. Particulate phosphorus analyses indicate a potential ability of heterotrophic communities to access particulate sources of phosphorous, possibly explaining the lack of phosphorus limitation. These findings have importance for understanding microbial activity during the polar winter season and its potential influences on the abundance and bioavailability of nutrients released to surface ice and downstream environments during the ablation season. |
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1192 |
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1664-302X |
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yes |
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7965 |
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Author |
Benoît Bergk Pinto, Lorrie Maccario, Aurélien Dommergue, Timothy M. Vogel, Catherine Larose |
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Title |
Do Organic Substrates Drive Microbial Community Interactions in Arctic Snow? |
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Journal |
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Year |
2019 |
Publication |
Frontiers in Microbiology |
Abbreviated Journal |
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Volume |
10 |
Issue |
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Pages |
2492 |
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Abstract |
The effect of nutrients on microbial interactions, including competition and collaboration, has mainly been studied in laboratories, but their potential application to complex ecosystems is unknown. Here, we examined the effect of changes in organic acids among other parameters on snow microbial communities in situ over 2 months. We compared snow bacterial communities from a low organic acid content period to that from a higher organic acid period. We hypothesized that an increase in organic acids would shift the dominant microbial interaction from collaboration to competition. To evaluate microbial interactions, we built taxonomic co-variance networks from OTUs obtained from 16S rRNA gene sequencing. In addition, we tracked marker genes of microbial cooperation (plasmid backbone genes) and competition (antibiotic resistance genes) across both sampling periods in metagenomes and metatranscriptomes. Our results showed a decrease in the average connectivity of the network during late spring compared to the early spring that we interpreted as a decrease of cooperation. This observation was strengthened by the significantly more abundant plasmid backbone genes in the metagenomes from the early spring. The modularity of the network from the late spring was also found to be higher than the one from the early spring, which is another possible indicator of increased competition. Antibiotic resistance genes were significantly more abundant in the late spring metagenomes. In addition, antibiotic resistance genes were also positively correlated to the organic acid concentration of the snow across both seasons. Snow organic acid content might be responsible for this change in bacterial interactions in the Arctic snow community. |
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1192 |
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1664-302X |
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yes |
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7966 |
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