Microorganisms

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26 pages, 2311 KiB

Open AccessArticle

Analysis of Bacterial Communities around the Adventdalen Landfill Site in Svalbard

by Hermi Amores-Arrocha, Alex K. B. Asamoah-Asare, Joyce Opio, Alex Martin, Lewis Cuthbertson, Hannah R. Bradford, Maria-Luisa Avila-Jimenez and David A. Pearce

Microorganisms 2023, 11(4), 1093; https://doi.org/10.3390/microorganisms11041093 - 21 Apr 2023

Cited by 1 | Viewed by 2469

Abstract

Ecosystems are often resilient enough to fully recover following a natural disturbance, or to transform into a new equilibrium favourable to the surrounding flora and fauna. However, at a local level, whether this transformation will be beneficial or not depends strongly on the [...] Read more.

Ecosystems are often resilient enough to fully recover following a natural disturbance, or to transform into a new equilibrium favourable to the surrounding flora and fauna. However, at a local level, whether this transformation will be beneficial or not depends strongly on the level of disturbance and the available mechanisms for recovery. The Arctic, however, provides a potentially extreme environment for microbial growth and this is reflected in the microbial biodiversity, the in-situ growth rates, the biogeochemical cycling and its sensitivity to environmental change. In this study, we evaluated the current microbial biodiversity and environmental conditions around the landfill site in Adventdalen, Svalbard to identify differences across bacterial communities that might promote or accelerate naturally occurring environmental recovery. Landfill sites can induce changes in the local environment through the input of exogenous chemicals (both organic and inorganic) and microorganisms. Leachate can flow with run-off from the primary location of the landfill site due to rain, snow or ice melt and spread material into soils surrounding the site. In this study we found a strong effect of the landfill site on the bacterial diversity in the local landscape. Intervention is highly desirable to enhance the environment and improve the restoration by subtly altering the conditions at the site (such as the pH or drainage courses) and by encouraging specific groups of naturally occurring indigenous microorganisms to bioremediate the site. Full article

(This article belongs to the Special Issue Polar Microbes)

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16 pages, 2853 KiB

Open AccessArticle

A Tale of Two Seasons: Distinct Seasonal Viral Communities in a Thermokarst Lake

by Valérie Langlois, Catherine Girard, Warwick F. Vincent and Alexander I. Culley

Microorganisms 2023, 11(2), 428; https://doi.org/10.3390/microorganisms11020428 - 8 Feb 2023

Cited by 2 | Viewed by 2735

Abstract

Thermokarst lakes are important features of subarctic landscapes and are a substantial source of greenhouse gases, although the extent of gas produced varies seasonally. Microbial communities are responsible for the production of methane and CO₂ but the “top down” forces that influence [...] Read more.

Thermokarst lakes are important features of subarctic landscapes and are a substantial source of greenhouse gases, although the extent of gas produced varies seasonally. Microbial communities are responsible for the production of methane and CO₂ but the “top down” forces that influence microbial dynamics (i.e., grazers and viruses) and how they vary temporally within these lakes are still poorly understood. The aim of this study was to examine viral diversity over time to elucidate the seasonal structure of the viral communities in thermokarst lakes. We produced virus-enriched metagenomes from a subarctic peatland thermokarst lake in the summer and winter over three years. The vast majority of vOTUs assigned to viral families belonged to Caudovirales (Caudoviricetes), notably the morphological groups myovirus, siphovirus and podovirus. We identified two distinct communities: a dynamic, seasonal community in the oxygenated surface layer during the summer and a stable community found in the anoxic water layer at the bottom of the lake in summer and throughout much of the water column in winter. Comparison with other permafrost and northern lake metagenomes highlighted the distinct composition of viral communities in this permafrost thaw lake ecosystem. Full article

(This article belongs to the Special Issue Polar Microbes)

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19 pages, 2760 KiB

Open AccessArticle

Dark Diazotrophy during the Late Summer in Surface Waters of Chile Bay, West Antarctic Peninsula

by María E. Alcamán-Arias, Jerónimo Cifuentes-Anticevic, Wilson Castillo-Inaipil, Laura Farías, Cynthia Sanhueza, Beatriz Fernández-Gómez, Josefa Verdugo, Leslie Abarzua, Christina Ridley, Javier Tamayo-Leiva and Beatriz Díez

Microorganisms 2022, 10(6), 1140; https://doi.org/10.3390/microorganisms10061140 - 31 May 2022

Cited by 1 | Viewed by 2787

Abstract

Although crucial for the addition of new nitrogen in marine ecosystems, dinitrogen (N₂) fixation remains an understudied process, especially under dark conditions and in polar coastal areas, such as the West Antarctic Peninsula (WAP). New measurements of light and dark N [...] Read more.

Although crucial for the addition of new nitrogen in marine ecosystems, dinitrogen (N₂) fixation remains an understudied process, especially under dark conditions and in polar coastal areas, such as the West Antarctic Peninsula (WAP). New measurements of light and dark N₂ fixation rates in parallel with carbon (C) fixation rates, as well as analysis of the genetic marker nifH for diazotrophic organisms, were conducted during the late summer in the coastal waters of Chile Bay, South Shetland Islands, WAP. During six late summers (February 2013 to 2019), Chile Bay was characterized by high NO₃⁻ concentrations (~20 µM) and an NH₄⁺ content that remained stable near 0.5 µM. The N:P ratio was approximately 14.1, thus close to that of the Redfield ratio (16:1). The presence of Cluster I and Cluster III nifH gene sequences closely related to Alpha-, Delta- and, to a lesser extent, Gammaproteobacteria, suggests that chemosynthetic and heterotrophic bacteria are primarily responsible for N₂ fixation in the bay. Photosynthetic carbon assimilation ranged from 51.18 to 1471 nmol C L⁻¹ d⁻¹, while dark chemosynthesis ranged from 9.24 to 805 nmol C L⁻¹ d⁻¹. N₂ fixation rates were higher under dark conditions (up to 45.40 nmol N L⁻¹ d⁻¹) than under light conditions (up to 7.70 nmol N L⁻¹ d⁻¹), possibly contributing more than 37% to new nitrogen-based production (≥2.5 g N m⁻² y⁻¹). Of all the environmental factors measured, only PO₄^3- exhibited a significant correlation with C and N₂ rates, being negatively correlated (p < 0.05) with dark chemosynthesis and N₂ fixation under the light condition, revealing the importance of the N:P ratio for these processes in Chile Bay. This significant contribution of N₂ fixation expands the ubiquity and biological potential of these marine chemosynthetic diazotrophs. As such, this process should be considered along with the entire N cycle when further reviewing highly productive Antarctic coastal waters and the diazotrophic potential of the global marine ecosystem. Full article

(This article belongs to the Special Issue Polar Microbes)

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17 pages, 2491 KiB

Open AccessArticle

Phytoplankton Surveys in the Arctic Fram Strait Demonstrate the Tiny Eukaryotic Alga Micromonas and Other Picoprasinophytes Contribute to Deep Sea Export

by Charles Bachy, Lisa Sudek, Chang Jae Choi, Charlotte A. Eckmann, Eva-Maria Nöthig, Katja Metfies and Alexandra Z. Worden

Microorganisms 2022, 10(5), 961; https://doi.org/10.3390/microorganisms10050961 - 3 May 2022

Cited by 12 | Viewed by 2868

Abstract

Critical questions exist regarding the abundance and, especially, the export of picophytoplankton (≤2 µm diameter) in the Arctic. These organisms can dominate chlorophyll concentrations in Arctic regions, which are subject to rapid change. The picoeukaryotic prasinophyte Micromonas grows in polar environments and appears [...] Read more.

Critical questions exist regarding the abundance and, especially, the export of picophytoplankton (≤2 µm diameter) in the Arctic. These organisms can dominate chlorophyll concentrations in Arctic regions, which are subject to rapid change. The picoeukaryotic prasinophyte Micromonas grows in polar environments and appears to constitute a large, but variable, proportion of the phytoplankton in these waters. Here, we analyze 81 samples from the upper 100 m of the water column from the Fram Strait collected over multiple years (2009–2015). We also analyze sediment trap samples to examine picophytoplankton contributions to export, using both 18S rRNA gene qPCR and V1-V2 16S rRNA Illumina amplicon sequencing to assess the Micromonas abundance within the broader diversity of photosynthetic eukaryotes based on the phylogenetic placement of plastid-derived 16S amplicons. The material sequenced from the sediment traps in July and September 2010 showed that 11.2 ± 12.4% of plastid-derived amplicons are from picoplanktonic prasinophyte algae and other green lineage (Viridiplantae) members. In the traps, Micromonas dominated (83.6 ± 21.3%) in terms of the overall relative abundance of Viridiplantae amplicons, specifically the species Micromonas polaris. Temporal variations in Micromonas abundances quantified by qPCR were also observed, with higher abundances in the late-July traps and deeper traps. In the photic zone samples, four prasinophyte classes were detected in the amplicon data, with Micromonas again being the dominant prasinophyte, based on the relative abundance (89.4 ± 8.0%), but with two species (M. polaris and M. commoda-like) present. The quantitative PCR assessments showed that the photic zone samples with higher Micromonas abundances (>1000 gene copies per mL) had significantly lower standing stocks of phosphate and nitrate, and a shallower average depth (20 m) than those with fewer Micromonas. This study shows that despite their size, prasinophyte picophytoplankton are exported to the deep sea, and that Micromonas is particularly important within this size fraction in Arctic marine ecosystems. Full article

(This article belongs to the Special Issue Polar Microbes)

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15 pages, 1702 KiB

Open AccessArticle

Use of Stress Signals of Their Attached Bacteria to Monitor Sympagic Algae Preservation in Canadian Arctic Sediments

by Rémi Amiraux, Bonin Patricia, Burot Christopher and Rontani Jean-François

Microorganisms 2021, 9(12), 2626; https://doi.org/10.3390/microorganisms9122626 - 20 Dec 2021

Cited by 4 | Viewed by 2883

Abstract

Based on the strong aggregation of sympagic (ice-associated) algae and the high mortality or inactivity of bacteria attached to them, it was previously hypothesized that sympagic algae should be significant contributors to the export of carbon to Arctic sediments. In the present work, [...] Read more.

Based on the strong aggregation of sympagic (ice-associated) algae and the high mortality or inactivity of bacteria attached to them, it was previously hypothesized that sympagic algae should be significant contributors to the export of carbon to Arctic sediments. In the present work, the lipid content of 30 sediment samples collected in the Canadian Arctic was investigated to test this hypothesis. The detection of high proportions of trans vaccenic fatty acid (resulting from cis-trans isomerase (CTI) activity of bacteria under hypersaline conditions) and 10S-hydroxyhexadec-8(trans)-enoic acid (resulting from 10S-DOX bacterial detoxification activity in the presence of deleterious free palmitoleic acid) confirmed: (i) the strong contribution of sympagic material to some Arctic sediments, and (ii) the impaired physiological status of its associated bacterial communities. Unlike terrestrial material, sympagic algae that had escaped zooplanktonic grazing appeared relatively preserved from biotic degradation in Arctic sediments. The expected reduction in sea ice cover resulting from global warming should cause a shift in the relative contributions of ice-associated vs. pelagic algae to the seafloor, and thus to a strong modification of the carbon cycle. Full article

(This article belongs to the Special Issue Polar Microbes)

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15 pages, 1736 KiB

Open AccessArticle

Effects of UV Radiation on the Chlorophyte Micromonas polaris Host–Virus Interactions and MpoV-45T Virus Infectivity

by Charlotte Eich, Sven B. E. H. Pont and Corina P. D. Brussaard

Microorganisms 2021, 9(12), 2429; https://doi.org/10.3390/microorganisms9122429 - 25 Nov 2021

Cited by 4 | Viewed by 2594

Abstract

Polar seas are under threat of enhanced UV-radiation as well as increasing shipping activities. Considering the ecological importance of marine viruses, it is timely to study the impact of UV-AB on Arctic phytoplankton host–virus interactions and also test the efficacy of ballast water [...] Read more.

Polar seas are under threat of enhanced UV-radiation as well as increasing shipping activities. Considering the ecological importance of marine viruses, it is timely to study the impact of UV-AB on Arctic phytoplankton host–virus interactions and also test the efficacy of ballast water (BW) UV-C treatment on virus infectivity. This study examined the effects of: (i) ecologically relevant doses of UV-AB radiation on Micromonas polaris RCC2258 and its virus MpoV-45T, and (ii) UV-C radiation (doses 25–800 mJ cm⁻²) on MpoV-45T and other temperate algal viruses. Total UV-AB exposure was 6, 12, 28 and 48 h (during the light periods, over 72 h total). Strongest reduction in algal growth and photosynthetic efficiency occurred for 28 and 48 h UV-AB treatments, and consequently the virus production rates and burst sizes were reduced by more than half (compared with PAR-only controls). For the shorter UV-AB exposed cultures, negative effects by UV (especially Fv/Fm) were overcome without impacting virus proliferation. To obtain the BW desired log⁻⁴ reduction in virus infectivity, a UV-C dose of at least 400 mJ cm⁻² was needed for MpoV-45T and the temperate algal viruses. This is higher than the commonly used dose of 300 mJ cm⁻² in BW treatment. Full article

(This article belongs to the Special Issue Polar Microbes)

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21 pages, 4170 KiB

Open AccessArticle

How Microbial Food Web Interactions Shape the Arctic Ocean Bacterial Community Revealed by Size Fractionation Experiments

by Oliver Müller, Lena Seuthe, Bernadette Pree, Gunnar Bratbak, Aud Larsen and Maria Lund Paulsen

Microorganisms 2021, 9(11), 2378; https://doi.org/10.3390/microorganisms9112378 - 17 Nov 2021

Cited by 3 | Viewed by 3307

Abstract

In the Arctic, seasonal changes are substantial, and as a result, the marine bacterial community composition and functions differ greatly between the dark winter and light-intensive summer. While light availability is, overall, the external driver of the seasonal changes, several internal biological interactions [...] Read more.

In the Arctic, seasonal changes are substantial, and as a result, the marine bacterial community composition and functions differ greatly between the dark winter and light-intensive summer. While light availability is, overall, the external driver of the seasonal changes, several internal biological interactions structure the bacterial community during shorter timescales. These include specific phytoplankton–bacteria associations, viral infections and other top-down controls. Here, we uncover these microbial interactions and their effects on the bacterial community composition during a full annual cycle by manipulating the microbial food web using size fractionation. The most profound community changes were detected during the spring, with ‘mutualistic phytoplankton’—Gammaproteobacteria interactions dominating in the pre-bloom phase and ‘substrate-dependent phytoplankton’—Flavobacteria interactions during blooming conditions. Bacterivores had an overall limited effect on the bacterial community composition most of the year. However, in the late summer, grazing was the main factor shaping the community composition and transferring carbon to higher trophic levels. Identifying these small-scale interactions improves our understanding of the Arctic marine microbial food web and its dynamics. Full article

(This article belongs to the Special Issue Polar Microbes)

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14 pages, 1206 KiB

Open AccessArticle

Microbial Communities Present in Hydrothermal Sediments from Deception Island, Antarctica

by Javier Vicente, Miguel de Celis, Alejandro Alonso, Domingo Marquina and Antonio Santos

Microorganisms 2021, 9(8), 1631; https://doi.org/10.3390/microorganisms9081631 - 30 Jul 2021

Cited by 5 | Viewed by 2612

Abstract

Deception Island is a geothermal location in Antarctica that presents active fumaroles, which confers unique characteristics to this habitat. Several studies about microbial communities in Antarctica have been carried out, nevertheless, Antarctic microbiota is still partially unknown. Here we present a multidisciplinary study [...] Read more.

Deception Island is a geothermal location in Antarctica that presents active fumaroles, which confers unique characteristics to this habitat. Several studies about microbial communities in Antarctica have been carried out, nevertheless, Antarctic microbiota is still partially unknown. Here we present a multidisciplinary study about sediments obtained by deposition during 4 years in which several approaches have been considered for their characterization. First, a physicochemical characterization, using ionic chromatography and mass spectrometry for the determination of most abundant ions (chloride and sulphate) and elements (mainly silicon), was conducted. In addition, the total microbial community was studied using a metataxonomical approach, revealing a bacterial community dominated by Proteobacteria and Thaumarchaeota as the main archaeal genera and a fungal community mainly composed by Aspergillaceae. Culture-dependent studies showed low microbial diversity, only achieving the isolation of Bacillus-related species, some of them thermophilic, and the isolation of common fungi of Aspergillus or Penicillium spp. Furthermore, diatoms were detected in the sediment and characterized attending to their morphological characteristics using scanning electron microscopy. The study reveals a high influence of the physicochemical conditions in the microbial populations and their distribution, offering valuable data on the interaction between the island and water microbiota. Full article

(This article belongs to the Special Issue Polar Microbes)

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19 pages, 2494 KiB

Open AccessArticle

Bacterial Communities Associated with Poa annua Roots in Central European (Poland) and Antarctic Settings (King George Island)

by Anna Znój, Jakub Grzesiak, Jan Gawor, Robert Gromadka and Katarzyna J. Chwedorzewska

Microorganisms 2021, 9(4), 811; https://doi.org/10.3390/microorganisms9040811 - 12 Apr 2021

Cited by 13 | Viewed by 3051

Abstract

Poa annua (annual bluegrass) is one of the most ubiquitous grass species in the world. In isolated regions of maritime Antarctica, it has become an invasive organism threatening native tundra communities. In this study, we have explored and compared the rhizosphere and root-endosphere [...] Read more.

Poa annua (annual bluegrass) is one of the most ubiquitous grass species in the world. In isolated regions of maritime Antarctica, it has become an invasive organism threatening native tundra communities. In this study, we have explored and compared the rhizosphere and root-endosphere dwelling microbial community of P. annua specimens of maritime Antarctic and Central European origin in terms of bacterial phylogenetic diversity and microbial metabolic activity with a geochemical soil background. Our results show that the rhizospheric bacterial community was unique for each sampling site, yet the endosphere communities were similar to each other. However, key plant-associated bacterial taxa such as the Rhizobiaceae family were poorly represented in Antarctic samples, probably due to high salinity and heavy metal concentrations in the soil. Metabolic activity in the Antarctic material was considerably lower than in Central European samples. Antarctic root endosphere showed unusually high numbers of certain opportunistic bacterial groups, which proliferated due to low competition conditions. Thirteen bacterial families were recognized in this study to form a core microbiome of the P. annua root endosphere. The most numerous were the Flavobacteriaceae, suspected to be major contributors to the ecological success of annual bluegrass, especially in harsh, Antarctic conditions. Full article

(This article belongs to the Special Issue Polar Microbes)

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12 pages, 1895 KiB

Open AccessArticle

Shift from Carbon Flow through the Microbial Loop to the Viral Shunt in Coastal Antarctic Waters during Austral Summer

by Claire Evans, Joost Brandsma, Michael P. Meredith, David N. Thomas, Hugh J. Venables, David W. Pond and Corina P. D. Brussaard

Microorganisms 2021, 9(2), 460; https://doi.org/10.3390/microorganisms9020460 - 23 Feb 2021

Cited by 14 | Viewed by 5128

Abstract

The relative flow of carbon through the viral shunt and the microbial loop is a pivotal factor controlling the contribution of secondary production to the food web and to rates of nutrient remineralization and respiration. The current study examines the significance of these [...] Read more.

The relative flow of carbon through the viral shunt and the microbial loop is a pivotal factor controlling the contribution of secondary production to the food web and to rates of nutrient remineralization and respiration. The current study examines the significance of these processes in the coastal waters of the Antarctic during the productive austral summer months. Throughout the study a general trend towards lower bacterioplankton and heterotrophic nanoflagellate (HNF) abundances was observed, whereas virioplankton concentration increased. A corresponding decline of HNF grazing rates and shift towards viral production, indicative of viral infection, was measured. Carbon flow mediated by HNF grazing decreased by more than half from 5.7 µg C L⁻¹ day⁻¹ on average in December and January to 2.4 µg C L⁻¹ day⁻¹ in February. Conversely, carbon flow through the viral shunt increased substantially over the study from on average 0.9 µg C L⁻¹ day⁻¹ in December to 7.6 µg C L⁻¹ day⁻¹ in February. This study shows that functioning of the coastal Antarctic microbial community varied considerably over the productive summer months. In early summer, the system favors transfer of matter and energy to higher trophic levels via the microbial loop, however towards the end of summer carbon flow is redirected towards the viral shunt, causing a switch towards more recycling and therefore increased respiration and regeneration. Full article

(This article belongs to the Special Issue Polar Microbes)

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22 pages, 2221 KiB

Open AccessArticle

Enhanced Viral Activity in the Surface Microlayer of the Arctic and Antarctic Oceans

by Dolors Vaqué, Julia A. Boras, Jesús Maria Arrieta, Susana Agustí, Carlos M. Duarte and Maria Montserrat Sala

Microorganisms 2021, 9(2), 317; https://doi.org/10.3390/microorganisms9020317 - 4 Feb 2021

Cited by 9 | Viewed by 3261

Abstract

The ocean surface microlayer (SML), with physicochemical characteristics different from those of subsurface waters (SSW), results in dense and active viral and microbial communities that may favor virus–host interactions. Conversely, wind speed and/or UV radiation could adversely affect virus infection. Furthermore, in polar [...] Read more.

The ocean surface microlayer (SML), with physicochemical characteristics different from those of subsurface waters (SSW), results in dense and active viral and microbial communities that may favor virus–host interactions. Conversely, wind speed and/or UV radiation could adversely affect virus infection. Furthermore, in polar regions, organic and inorganic nutrient inputs from melting ice may increase microbial activity in the SML. Since the role of viruses in the microbial food web of the SML is poorly understood in polar oceans, we aimed to study the impact of viruses on prokaryotic communities in the SML and in the SSW in Arctic and Antarctic waters. We hypothesized that a higher viral activity in the SML than in the SSW in both polar systems would be observed. We measured viral and prokaryote abundances, virus-mediated mortality on prokaryotes, heterotrophic and phototrophic nanoflagellate abundance, and environmental factors. In both polar zones, we found small differences in environmental factors between the SML and the SSW. In contrast, despite the adverse effect of wind, viral and prokaryote abundances and virus-mediated mortality on prokaryotes were higher in the SML than in the SSW. As a consequence, the higher carbon flux released by lysed cells in the SML than in the SSW would increase the pool of dissolved organic carbon (DOC) and be rapidly used by other prokaryotes to grow (the viral shunt). Thus, our results suggest that viral activity greatly contributes to the functioning of the microbial food web in the SML, which could influence the biogeochemical cycles of the water column. Full article

(This article belongs to the Special Issue Polar Microbes)

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