The structure and diversity of microbiomes of glacial cryoconites (North Caucasus Region)

2021 ◽  
Author(s):  
Ekaterina Ivanova ◽  
Grigory Gladkov ◽  
Anastasiia Kimeklis ◽  
Arina Kichko ◽  
Evgeny Andronov ◽  
...  
Keyword(s):  
Microbial Biomass ◽  
Microbial Consortia ◽  
Biogenic Elements ◽  
Biomass Estimation ◽  
Taxonomic Structure ◽  
Rrna Gene ◽  
North Caucasus ◽  
Vegetative Cover ◽  
Glacier Surface ◽  
Amino Acid Synthesis

<p>Studying the diversity and abundance of cryoconite biota is relevant due to global climate warming, since organo-mineral particles in their composition have a significant impact on the ice albedo decrease and, thus, increase the rate of glacier melting. Since cryoconites are "hot spots" for biota development and the only loci where soil-like bodies can form on glaciers, they contribute significantly to the cycles of biogenic elements of ice and oligotrophic ecosystems.</p><p>Samples were collected from cryoconites from the Garabashi (GBg_c) and Shkhelda (SHKg_c) glaciers as well as from moraine (Garabashi); nearby soils (Chernozem, Forest-meadow, and organo-accumulative soil) were used as controls.</p><p>GBg_c samples were characterized by potentially higher values of microbial biomass (abundance of 16 S rRNA gene copies and ITS), with maximal values in samples taken from the cracked glacier. In contrast, minimal abundance values of the studied taxonomic markers in SHKg_c were determined. The values for the samples of nearby soils occupied an intermediate position. These results may be partially explained by different colors of cryoconites, determined by differences in their biochemical composition and origin: the GBg_c were represented by "black dust", with low values of albedo and, accordingly, higher values of temperature and moisture, apparently, more favorable for microbial activity compared to the "gray" dust of the SHKg_c.</p><p>Taxonomic structure analysis revealed a specific pattern of GBg_c samples– an oligotrophic psychrophilic community with a pronounced cyanobacterial dominance was detected. Despite significant differences between cryoconites and nearby moraine in the presence of major autotrophic representatives (cyanobacteria Tychonema, Phormidesmis), the heterotrophic component is similar and is represented by a very specific set of soil microorganisms of Bacteroides, Shingomonas, Burkholderiales groups, apparently, due to the flushing out of part of the microbiome from the autotrophic microbial consortia of the glacier, explaining, as well, the grouping of these samples in the Bray-Curtis NMDS ordination. No autotrophic microbiota predominance was detected in SHKg_c, these microbiomes were typical for soils without vegetative cover, as well as without biofilms on the surface (Verrucromicrobia, Sphingomonacia, Bacteroides). A low number of phylotypes was detected for the community of the GBg_c and Сhernozem. Moreover, the alpha-diversity indices were inversely proportional to the results of microbial biomass estimation, which can be explained by greater "homogeneity" (and, apparently, narrower functional specialization) of more numerous communities.</p><p>The metabolic profile of cryoconites (according to Picrust2) is characterized by the predominance of aerobic metabolic enzymes (cytochrome c) and proteins (amino acid synthesis), indicating a potentially high level of metabolic activity of the cryoconite microbial community. These results can be explained by the reparative needs of microbial cells under the conditions of oxygenic stress and extremely low temperatures. In contrast to the control soils (especially, Chernozem), relatively low levels of the catalytic pathway and carbon exchange were determined for the cryoconites’ metabolic pathways, possibly associated with both low available carbon stocks and supply of the glacier surface, as compared to soils with higher stocks of available forms of mineral nutrition.</p><p>The work is supported by RFBR  project No 19-05-50107. </p>

Unravelling a microbial synergy to boost caproate production via carboxylates chain elongation with ethanol

2019 ◽  
Vol 26 (2) ◽  
pp. 63-71
Author(s):  
Ling Leng ◽  
Ying Wang ◽  
Peixian Yang ◽  
Takashi Narihiro ◽  
Masaru Konishi Nobu ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Volatile Fatty Acids ◽  
Microbial Consortia ◽  
Chain Elongation ◽  
Desulfovibrio Vulgaris ◽  
Rrna Gene ◽  
Selective Enrichment ◽  
Microbial Network ◽  
Cost Efficient ◽  
Rrna Gene Sequencing

Chain elongation of volatile fatty acids for medium chain fatty acids production (e.g. caproate) is an attractive approach to treat wastewater anaerobically and recover resource simultaneously. Undefined microbial consortia can be tailored to achieve chain elongation process with selective enrichment from anaerobic digestion sludge, which has advantages over pure culture approach for cost-efficient application. Whilst the metabolic pathway of the dominant caproate producer, Clostridium kluyveri, has been annotated, the role of other coexisting abundant microbiomes remained unclear. To this end, an ethanol-acetate fermentation inoculated with fresh digestion sludge at optimal conditions was conducted. Also, physiological study, thermodynamics and 16 S rRNA gene sequencing to elucidate the biological process by linking the system performance and dominant microbiomes were integrated. Results revealed a possible synergistic network in which C. kluyveri and three co-dominant species, Desulfovibrio vulgaris, Fusobacterium varium and Acetoanaerobium sticklandii coexisted. D. vulgaris and A. sticklandii (F. varium) were likely to boost the carboxylates chain elongation by stimulating ethanol oxidation and butyrate production through a syntrophic partnership with hydrogen (H2) serving as an electron messenger. This study unveils a synergistic microbial network to boost caproate production in mixed culture carboxylates chain elongation.

Gut microbiome of the emerald ash borer, Agrilus planipennis Fairmaire, and its relationship with insect population density

2020 ◽  
Vol 96 (8) ◽  
Author(s):  
Judith Mogouong ◽  
Philippe Constant ◽  
Robert Lavallée ◽  
Claude Guertin
Keyword(s):  
Population Density ◽  
Gut Microbiome ◽  
Emerald Ash Borer ◽  
Agrilus Planipennis ◽  
Economic Damage ◽  
Taxonomic Structure ◽  
Rrna Gene ◽  
Local Conditions ◽  
Β Diversity ◽  
Α Diversity

ABSTRACT The gut microbial communities of beetles play crucial roles in their adaptive capacities. Environmental factors such as temperature or nutrition naturally affect the insect microbiome, but a shift in local conditions like the population density on a host tree could also lead to changes in the microbiota. The emerald ash borer (EAB), Agrilus planipennis Fairmaire, is an exotic wood borer that causes environmental and economic damage to ash trees in North America. This study aimed to describe the taxonomic structure of the EAB gut microbiome and explore its potential relationship with borer population size. The number of EAB adults collected per tree through a 75 km transect from an epicenter allowed the creation of distinct classes of population density. The Gammaproteobacteria and Ascomycota predominated in bacterial and fungal communities respectively, as determined by sequencing of the bacterial 16S rRNA gene and the fungal internal transcribed spacer ITS2. Species richness and diversity of the bacterial community showed significant dependence on population density. Moreover, α-diversity and β-diversity analysis revealed some indicator amplicon sequence variants suggesting that the plasticity of the gut microbiome could be related to the EAB population density in host trees.

scholarly journals Djankuat glacier station in the North Caucasus, Russia: a database of glaciological, hydrological, and meteorological observations and stable isotope sampling results during 2007–2017

2019 ◽  
Vol 11 (3) ◽  
pp. 1463-1481 ◽  
Author(s):  
Ekaterina P. Rets ◽  
Viktor V. Popovnin ◽  
Pavel A. Toropov ◽  
Andrew M. Smirnov ◽  
Igor V. Tokarev ◽  
...  
Keyword(s):  
Wind Speed ◽  
Precipitation Amount ◽  
Turbulent Fluxes ◽  
Water Runoff ◽  
North Caucasus ◽  
Time Step ◽  
Glacier Surface ◽  
The North ◽  
Meteorological Observations ◽  
The Impact

Abstract. This study presents a dataset on long-term multidisciplinary glaciological, hydrological, and meteorological observations and isotope sampling in a sparsely monitored alpine zone of the North Caucasus in the Djankuat research basin. The Djankuat glacier, which is the largest in the basin, was chosen as representative of the central North Caucasus during the International Hydrological Decade and is one of 30 “reference” glaciers in the world that have annual mass balance series longer than 50 years (Zemp et al., 2009). The dataset features a comprehensive set of observations from 2007 to 2017 and contains yearly measurements of snow depth and density; measurements of dynamics of snow and ice melting; measurements of water runoff, conductivity, turbidity, temperature, δ18O, δD at the main gauging station (844 samples in total) with an hourly or sub-daily time step depending on the parameter; data on δ18O and δ2H sampling of liquid precipitation, snow, ice, firn, and groundwater in different parts of the watershed taken regularly during melting season (485 samples in total); measurements of precipitation amount, air temperature, relative humidity, shortwave incoming and reflected radiation, longwave downward and upward radiation, atmospheric pressure, and wind speed and direction – measured at several automatic weather stations within the basin with 15 min to 1 h time steps; gradient meteorological measurements to estimate turbulent fluxes of heat and moisture, measuring three components of wind speed at a frequency of 10 Hz to estimate the impulse of turbulent fluxes of sensible and latent heat over the glacier surface by the eddy covariance method. Data were collected during the ablation period (June–September). The observations were halted in winter. The dataset is available from PANGAEA (https://doi.org/10.1594/PANGAEA.894807, Rets et al., 2018a) and will be further updated. The dataset can be useful for developing and verifying hydrological, glaciological, and meteorological models for alpine areas, to study the impact of climate change on hydrology of mountain regions using isotopic and hydrochemical approaches in hydrology. As the dataset includes the measurements of hydrometeorological and glaciological variables during the catastrophic proglacial lake outburst in the neighboring Bashkara valley in September 2017, it is a valuable contribution to study lake outbursts.

scholarly journals Impact of Oral Fidaxomicin Administration on the Intestinal Microbiota and Susceptibility to Clostridium difficile Colonization in Mice

2018 ◽  
Vol 62 (5) ◽  
Author(s):  
N. J. Ajami ◽  
J. L. Cope ◽  
M. C. Wong ◽  
J. F. Petrosino ◽  
L. Chesnel
Keyword(s):  
Clostridium Difficile ◽  
Gut Microbiota ◽  
16S Rrna Gene Sequencing ◽  
Taxonomic Structure ◽  
Rrna Gene ◽  
Colonization Resistance ◽  
Content Type ◽  
Rrna Gene Sequencing ◽  
Hospital Acquired ◽  
Predetermined Time

ABSTRACT Clostridium difficile infection (CDI), a common cause of hospital-acquired infections, typically occurs after disruption of the normal gut microbiome by broad-spectrum antibiotics. Fidaxomicin is a narrow-spectrum antibiotic that demonstrates a reduced impact on the normal gut microbiota and is approved for the treatment of CDI. To further explore the benefits of this property, we used a murine model to examine the effects of fidaxomicin versus vancomycin on gut microbiota and susceptibility to C. difficile colonization while tracking microbiota recovery over time. Mice were exposed to fidaxomicin or vancomycin by oral gavage for 3 days and subsequently challenged with C. difficile spores at predetermined time points up to 21 days postexposure to antibiotics. Fecal samples were subsequently collected for analysis. Twenty-four hours postchallenge, mice were euthanized and the colon contents harvested. The microbiota was characterized using 16S rRNA gene sequencing. All fidaxomicin-exposed mice (except for one at day 8) were resistant to C. difficile colonization. However, 9 of 15 vancomycin-exposed mice were susceptible to C. difficile colonization until day 12. All vancomycin-exposed mice recovered colonization resistance by day 16. Bacterial diversity was similar prior to antibiotic exposure in both arms and decreased substantially after exposure. A shift in taxonomic structure and composition occurred after both exposures; however, the shift was greater in vancomycin-exposed than in fidaxomicin-exposed mice. In summary, compared with vancomycin, fidaxomicin exposure had less impact on microbiota composition, promoted faster microbial recovery, and had less impact on the loss of C. difficile colonization resistance.

scholarly journals Effect of oral consumption of capsules containing Lactobacillus paracasei LPC-S01 on the vaginal microbiota of healthy adult women: a randomized, placebo-controlled, double-blind crossover study

2020 ◽  
Vol 96 (6) ◽  
Author(s):  
Ranjan Koirala ◽  
Giorgio Gargari ◽  
Stefania Arioli ◽  
Valentina Taverniti ◽  
Walter Fiore ◽  
...  
Keyword(s):  
Daily Intake ◽  
Vaginal Microbiota ◽  
Lactobacillus Paracasei ◽  
Gardnerella Vaginalis ◽  
Taxonomic Structure ◽  
Rrna Gene ◽  
Vaginal Mucosa ◽  
Adult Women ◽  
Oral Consumption ◽  
Vaginal Swabs

ABSTRACT Oral consumption of probiotics is practical and can be an effective solution to preserve vaginal eubiosis. Here, we studied the ability of orally administered Lactobacillus paracasei LPC-S01 (DSM 26760) to affect the composition of the vaginal microbiota and colonize the vaginal mucosa in nondiseased adult women. A total of 40 volunteers took oral probiotic (24 billion CFU) or placebo capsules daily for 4 weeks, and after a 4-week washout, they switched to placebo or probiotic capsules according to the crossover design. A total of 23 volunteers completed the study according to the protocol. Before and after capsule ingestion, vaginal swabs were collected for qPCR quantification to detect L. paracasei LPC-S01 and for 16S rRNA gene sequencing. Vaginal swabs were grouped according to their bacterial taxonomic structure into nine community state types (CSTs), four of which were dominated by lactobacilli. Lactobacillus paracasei LPC-S01 was detected in the vagina of two participants. Statistical modeling (including linear mixed-effects model analysis) demonstrated that daily intake of probiotic capsules reduced the relative abundance of Gardnerella spp. Quantitative PCR with Gardnerella vaginalis primers confirmed this result. Considering the pathogenic nature of G. vaginalis, these results suggest a potential positive effect of this probiotic capsule on the vaginal microbial ecosystem.

The impacts of deglaciation and human activity on the taxonomic structure of prokaryotic communities in Antarctic soils on King George Island

2018 ◽  
Vol 30 (5) ◽  
pp. 278-288 ◽  
Author(s):  
E.V. Pershina ◽  
E.A. Ivanova ◽  
E.V. Abakumov ◽  
E.E. Andronov
Keyword(s):  
Bacterial Species ◽  
Taxonomic Composition ◽  
South Shetland Islands ◽  
Soil Microbiome ◽  
Taxonomic Structure ◽  
Rrna Gene ◽  
King George Island ◽  
Antarctic Soils ◽  
Operational Taxonomic Units ◽  
Taxonomic Analysis

AbstractThe soil microbiome was investigated at environmentally distinct locations on King George Island in the South Shetland Islands (Antarctic Peninsula) using 16 S rRNA gene pyrosequencing. The taxonomic composition of the soil prokaryotes (bacteria and archaea) was evaluated at three sites representing human-disturbed soils (Bellingshausen Station) and soils undergoing different stages of deglaciation (fresh and old moraines located near Ecology Glacier). The taxonomic analysis revealed 20 bacterial and archaeal phyla, among which Proteobacteria (29.6%), Actinobacteria (25.3%), Bacteroidetes (15.8%), Cyanobacteria (11.2%), Acidobacteria (4.9%) and Verrucomicrobia (4.5%) comprised most of the microbiome. In a beta-diversity analysis, the samples formed separate clusters. The Bellingshausen Station samples were characterized by an increased amount ofNostocsp. andJanibactersp. Although the deglaciation history had less of an effect on the soil microbiome, the early stages of deglaciation (Sample 1) had a higher proportion of bacteria belonging to the families Xanthomonadaceae, Sphingomonadaceae and Nocardioidaceae, whereas the older moraines (Sample 2) were enriched with Chthoniobacteriacae and N1423WL. Solirubrobacteriales, Gaiellaceae and Chitinophagaceae bacteria were present in both stages of deglaciation, characterized by genus-level differences. Taxonomic analysis of the abundant operational taxonomic units (OTUs) revealed both endemic (Marisediminicola antarctica,Hymenobacter glaciei) and cosmopolitan bacterial species in the microbiomes.

scholarly journals Ability of Trichoderma hamatum Isolated from Plastics-Polluted Environments to Attack Petroleum-Based, Synthetic Polymer Films

Processes ◽  
2020 ◽  
Vol 8 (4) ◽  
pp. 467
Author(s):  
Kateřina Malachová ◽  
Čeněk Novotný ◽  
Grażyna Adamus ◽  
Nadia Lotti ◽  
Zuzana Rybková ◽  
...  
Keyword(s):  
Functional Groups ◽  
Polymer Surface ◽  
Microbial Consortia ◽  
Low Density Polyethylene ◽  
High Temperature Treatment ◽  
Rrna Gene ◽  
Its Sequencing ◽  
Low Density ◽  
Bacterial Strains ◽  
Trichoderma Hamatum

Microorganisms colonizing plastic waste material collected in composting-, landfill-, and anaerobic digestion plants were isolated to obtain novel strains maximally adapted to the degradation of plastics due to long-term contact with plastic polymers. Twenty-six bacterial strains were isolated and identified by the 16 S rRNA method, and eighteen strains of yeasts and fungi using 18 S rRNA and the internal transcribed spacer ITS sequencing of the 18 S rRNA gene. In selected strains, the ability to degrade linear low-density polyethylene (LLDPE), low-density polyethylene (LDPE), polystyrene (PS), and polyvinyl chloride (PVC) was tested in aerobic liquid-medium cultures. An oxidative, two-step pretreatment of LLDPE and LDPE using γ- or UV-irradiation followed by a high-temperature treatment was carried out, and the pretreated plastics were also included in the degradation experiments. The respective weight losses after biodegradation by Trichoderma hamatum were: virgin and γ/T90-pretreated LLDPE (2.2 ± 1.2 and 3.9 ± 0.5%), virgin and UV/T60-pretreated LDPE (0.5 ± 0.4 and 1.3 ± 0.4%), and virgin PS (0.9 ± 0.4%). The Fourier transform infrared spectroscopy (FTIR) analysis showed that during the treatment of pretreated LLDPE, T. hamatum attacked low molecular weight LLDPE oligomers, reducing the functional groups (carbonyl C = O), which was paralleled by a slight increase of the molar mass of pretreated LLDPE and a decrease of the dispersity index, as demonstrated by gel permeation chromatography (GPC). Thermogravimetric analysis (TGA) highlighted the formation of functional groups on LLDPE due to polymer pretreatment that favored fungal attack at the polymer surface. The results provide insight into microbial consortia that spontaneously colonize the surface of plastics in various environments and their capability to attack plastic polymers.

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