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

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.

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First record of the endophytic bacteria of Deschampsia antarctica Ė. Desv. from two distant localities of the maritime Antarctic

Czech Polar Reports ◽

10.5817/cpr2021-1-10 ◽

2021 ◽

Vol 11 (1) ◽

pp. 134-153

Author(s):

Olga Podolich ◽

Ievgeniia Prekrasna ◽

Ivan Parnikoza ◽

Tamara Voznyuk ◽

Ganna Zubova ◽

...

Keyword(s):

Endophytic Bacteria ◽

Bacterial Species ◽

Vascular Plant ◽

South Shetland Islands ◽

Deschampsia Antarctica ◽

Rrna Gene ◽

King George Island ◽

Maritime Antarctic ◽

Organic Input

Endophytic bacteria, recognized for their beneficial effects on plant development and adaptation, can facilitate the survival of Antarctic plants in severe environments. Here we studied endophytes of the vascular plant Deschampsia antarctica Ė. Desv. from two distantly located regions in the maritime Antarctic: King George Island (South Shetland Islands) and Galindez Island (Argentine Islands). Bacterial group-specific PCR indicated presence of Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Firmicutes, Cytophaga-Flavobacteria and Actinobacteria in root and leaf endosphere of D. antarctica sampled at four distinct sites of both locations. The diversity of endophytic bacteria was significantly higher in the leaves compared to the roots in plants from Galindez Island. Similarly, the diversity of endophytes was higher in the leaves rather than roots of plants from the King George Island. Twelve bacterial species were isolated from roots of D. antarctica of Galindez Island (the Karpaty Ridge and the Meteo Point) and identified by sequencing the 16S rRNA gene. Isolates were dominated by the Pseudomonas genus, followed by the genera Bacillus and Micrococcus. The vast majority of the isolates exhibited cellulase and pectinase activities, however, Bacillus spp. expressed neither of them, suggesting lack of genetic flow of these traits in endophytic bacilli in the maritime Antarctic. Pseudomonas sp. IMBG305 promoted an increase in the leaf number in most of the treated plant genotypes when compared with non-inoculated plants, and a rapid vegetation period of D. antarctica cultured in vitro, albeit the length of leaves in the treated plants was significantly lower, and flavonoid content leveled off in all treated plants. D. antarctica is known to develop diverse ecotypes with regard to ecological conditions, such as organic input, moisture or wind exposition. The D. antarctica phenotype could be extended further through the endophyte colonization, since phenotypic changes were observed in the inoculated D. antarcticaplants grown in vitro in our study. Herewith, endophytes can contribute to plant phenotypic plasticity, potentially beneficial for adaptation of D. antarctica.

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Pseudomonas fildesensis sp. nov., a psychrotolerant bacterium isolated from Antarctic soil of King George Island, South Shetland Islands

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.004165 ◽

2020 ◽

Vol 70 (5) ◽

pp. 3255-3263 ◽

Cited By ~ 4

Author(s):

Maria S. Pavlov ◽

Felipe Lira ◽

José Luis Martinez ◽

Jorge Olivares-Pacheco ◽

Sergio H. Marshall

Keyword(s):

16S Rrna ◽

Type Species ◽

Bacterial Species ◽

Housekeeping Genes ◽

South Shetland Islands ◽

Rrna Gene ◽

King George Island ◽

Content Type ◽

Link Type ◽

Pseudomonas Veronii

The strain KG01T was isolated from a soil sample from King George Island, Antarctica. Cells of KG01T are rod-shaped and motile by means of multiple polar flagella. The absence of arginine dihydrolase activity could be a key feature to readily distinguish KG01T from its closest phylogenetic relative species. The main fatty acids of the strain include summed feature 3 (C16 : 1 ω7c and/or C15 : 0 iso 2-OH), C16 : 0 and C18 : 1 ω7c. Phylogenetic analysis based on the 16S rRNA gene sequence and on a multilocus sequence analysis (MLSA) using housekeeping genes (16S rRNA, rpoB, rpoD, gyrB) were carried out. These analyses allowed us to include the strain within the Pseudomonas fluorescens group, presenting the highest similarity of multilocus sequence with Pseudomonas veronii LMG 17761T (96.67 %). The genome of KG01T was sequenced and in silico compared with genomes of the most closely related species of the P. fluore scens group. The average nucleotide identity (ANIb) and average amino acid identity (AAI) values of the species phylogenetically closest to KG01T were less than 95–96 %, threshold currently accepted to define strain as belonging to a bacterial species, the highest scores being those to Pseudomonas veronii LMG 17761T (87.98 %) and Pseudomonas marginalis ICMP 3553T (91.90 %). Therefore, the phenotypic and genotypic analyses results, allow us to propose that KG01T represents a member of a novel species of the genus Pseudomonas , for which the name Pseudomonas fildesensis is proposed, and KG01T (=CECT 9084T;=DSM 102036T) is established as the type strain .

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Transition of Bacterial Diversity and Composition in Tongue Microbiota during the First Two Years of Life

mSphere ◽

10.1128/msphere.00187-19 ◽

2019 ◽

Vol 4 (3) ◽

Cited By ~ 1

Author(s):

Shinya Kageyama ◽

Mikari Asakawa ◽

Toru Takeshita ◽

Yukari Ihara ◽

Shunsuke Kanno ◽

...

Keyword(s):

Oral Cavity ◽

Bacterial Diversity ◽

Bacterial Species ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Oral Microbiota ◽

Bacterial Composition ◽

Content Type ◽

Operational Taxonomic Units ◽

Rrna Gene Sequencing

ABSTRACTNewborns are constantly exposed to various microbes from birth; hence, diverse commensal bacteria colonize the oral cavity. However, how or when these bacteria construct a complex and stable ecosystem remains unclear. This prospective cohort study examined the temporal changes in bacterial diversity and composition in tongue microbiota during infancy. We longitudinally collected a total of 464 tongue swab samples from 8 infants (age of <6 months at baseline) for approximately 2 years. We also collected samples from 32 children (aged 0 to 2 years) and 73 adults (aged 20 to 29 years) cross-sectionally as control groups. Bacterial diversities and compositions were determined by 16S rRNA gene sequencing. The tongue bacterial diversity in infancy, measured as the number of observed operational taxonomic units (OTUs), rapidly increased and nearly reached the same level as that in adults by around 80 weeks. The overall tongue bacterial composition in the transitional phase, 80 to 120 weeks, was more similar to that of adults than to that of the early exponential phase (EEP), 10 to 29 weeks, according to analysis of similarities. Dominant OTUs in the EEP corresponding toStreptococcus perorisandStreptococcus lactariusexponentially decreased immediately after EEP, around 30 to 49 weeks, whereas several OTUs corresponding toGranulicatella adiacens,Actinomyces odontolyticus, andFusobacterium periodonticumreciprocally increased during the same period. These results suggest that a drastic compositional shift of tongue microbiota occurs before the age of 1 year, and then bacterial diversity and overall bacterial composition reach levels comparable to those in adults by the age of 2 years.IMPORTANCEEvaluating the development of oral microbiota during infancy is important for understanding the subsequent colonization of bacterial species and the process of formation of mature microbiota in the oral cavity. We examined tongue microbiota longitudinally collected from 8 infants and found that drastic compositional shifts in tongue microbiota occur before the age of 1 year, and then bacterial diversity and overall bacterial composition reach levels comparable to those in adults by the age of 2 years. These results may be helpful for preventing the development of various diseases associated with oral microbiota throughout life.

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Microbial biomass and basal respiration of selected Sub-Antarctic and Antarctic soils in the areas of some Russian polar stations

Solid Earth ◽

10.5194/se-5-705-2014 ◽

2014 ◽

Vol 5 (2) ◽

pp. 705-712 ◽

Cited By ~ 16

Author(s):

E. Abakumov ◽

N. Mukhametova

Keyword(s):

Microbial Biomass ◽

Organic Carbon ◽

Total Organic Carbon ◽

Carbon Content ◽

Metabolic Activity ◽

Basal Respiration ◽

South Shetland Islands ◽

Organic Layer ◽

King George Island ◽

Antarctic Soils

Abstract. Antarctica is a unique place for soil, biological, and ecological investigations. Soils of Antarctica have been studied intensively during the last century, when different national Antarctic expeditions visited the sixth continent with the aim of investigating nature and the environment. Antarctic investigations are comprised of field surveys mainly in the terrestrial landscapes, where the polar stations of different countries are situated. That is why the main and most detailed soil surveys were conducted in the McMurdo Valleys, Transantarctic Mountains, South Shetland Islands, Larsemann Hills and the Schirmacher Oasis. Our investigations were conducted during the 53rd and 55th Russian Antarctic expeditions in the base of soil pits, and samples were collected in Sub-Antarctic and Antarctic regions. Sub-Antarctic or maritime landscapes are considered to be very different from Antarctic landscapes due to differing climatic and geogenic conditions. Soils of diverse zonal landscapes were studied with the aim of assessing the microbial biomass level, basal respiration rates and metabolic activity of microbial communities. This investigation shows that Antarctic soils are quite diverse in profile organization and carbon content. In general, Sub-Antarctic soils are characterized by more developed humus (sod) organo-mineral horizons as well as by an upper organic layer. The most developed organic layers were revealed in peat soils of King George Island, where its thickness reach, in some cases, was 80 cm. These soils as well as soils formed under guano are characterized by the highest amount of total organic carbon (TOC), between 7.22 and 33.70%. Coastal and continental Antarctic soils exhibit less developed Leptosols, Gleysols, Regolith and rare Ornhitosol, with TOC levels between 0.37 and 4.67%. The metabolic ratios and basal respiration were higher in Sub-Antarctic soils than in Antarctic ones, which can be interpreted as a result of higher amounts of fresh organic remnants in organic and organo-mineral horizons. The soils of King George Island also have higher portions of microbial biomass (max 1.54 mg g−1) compared to coastal (max 0.26 mg g−1) and continental (max 0.22 mg g−1) Antarctic soils. Sub-Antarctic soils differ from Antarctic ones mainly by having increased organic layer thickness and total organic carbon content, higher microbial biomass carbon content, basal respiration, and metabolic activity levels.

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Restoration of soil microbiome in various soil horizons after crown and surface wildfires.

Ecological genetics ◽

10.17816/ecogen17641 ◽

2020 ◽

Author(s):

Grigory V. Gladkov ◽

Ekaterina Chebykina ◽

Elizaveta Evdokimova ◽

Ekaterina Ivanova ◽

Anastasiia Kimeklis ◽

...

Keyword(s):

16S Rrna Gene Sequencing ◽

Taxonomic Composition ◽

Soil Microbiome ◽

Soil Restoration ◽

Rrna Gene ◽

Crown Fire ◽

Soil Horizons ◽

Rrna Gene Sequencing ◽

And Shifts ◽

The City

Fires have a strong effect on soil microbiome, and the mechanisms of soil restoration after fires are currently not well understood.Thisstudy describes the characteristics of microbial communities in the Psamment Entisol soils of pine forests in the city of Togliatti after forest crown and surface fires.Geochemistry, soil respiration and microbial community structure via 16S rRNA gene sequencing were studied in different soil horizons. Both crown and surface fires resulted in the variations of microbial diversity and shifts in taxonomic composition. There is a tendency to an increase in the proportion of representatives from phylaActinobacteria and Gemmatimonadetes for soil samples recovering after fires. An increase in the proportion of bacteria (Micrococcaceae, Blastocatellaceae) associated with the degradation of substances formed after combustionalsohas been shown. The research has shown that the crown fire has a smaller effect on the soil microbiome than thesurfacefire,the largest changes in the microbiome structure were found in the intermediate horizon.At the same time, differences in the structure of the soil microbiome between horizons are intensified after exposure to the soil of asurfacefire.

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Urinary TMAO Levels Are Associated with the Taxonomic Composition of the Gut Microbiota and with the Choline TMA-Lyase Gene (cutC) Harbored by Enterobacteriaceae

Nutrients ◽

10.3390/nu12010062 ◽

2019 ◽

Vol 12 (1) ◽

pp. 62 ◽

Cited By ~ 6

Author(s):

Alessandro Dalla Via ◽

Giorgio Gargari ◽

Valentina Taverniti ◽

Greta Rondini ◽

Ilaria Velardi ◽

...

Keyword(s):

Gut Microbiota ◽

Method Development ◽

Ultra Performance Liquid Chromatography ◽

Taxonomic Composition ◽

Gene Profiling ◽

Rrna Gene ◽

Operational Taxonomic Units ◽

Two Factors ◽

Polymerase Chain ◽

Dietary Choline

Gut microbiota metabolization of dietary choline may promote atherosclerosis through trimethylamine (TMA), which is rapidly absorbed and converted in the liver to proatherogenic trimethylamine-N-oxide (TMAO). The aim of this study was to verify whether TMAO urinary levels may be associated with the fecal relative abundance of specific bacterial taxa and the bacterial choline TMA-lyase gene cutC. The analysis of sequences available in GenBank grouped the cutC gene into two main clusters, cut-Dd and cut-Kp. A quantitative real-time polymerase chain reaction (qPCR) protocol was developed to quantify cutC and was used with DNA isolated from three fecal samples collected weekly over the course of three consecutive weeks from 16 healthy adults. The same DNA was used for 16S rRNA gene profiling. Concomitantly, urine was used to quantify TMAO by ultra-performance liquid chromatography coupled with tandem mass spectrometry (UPLC-MS/MS). All samples were positive for cutC and TMAO. Correlation analysis showed that the cut-Kp gene cluster was significantly associated with Enterobacteriaceae. Linear mixed models revealed that urinary TMAO levels may be predicted by fecal cut-Kp and by 23 operational taxonomic units (OTUs). Most of the OTUs significantly associated with TMAO were also significantly associated with cut-Kp, confirming the possible relationship between these two factors. In conclusion, this preliminary method-development study suggests the existence of a relationship between TMAO excreted in urine, specific fecal bacterial OTUs, and a cutC subgroup ascribable to the choline-TMA conversion enzymes of Enterobacteriaceae.

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Soil microbiome in chronosequence of spoil heaps of Kursk Magnetic Anomaly

Biological Communications ◽

10.21638/spbu03.2019.306 ◽

2019 ◽

Vol 64 (3) ◽

Cited By ~ 1

Author(s):

Ekaterina Ivanova ◽

Elizaveta Pershina ◽

Dina Karpova ◽

Olga Rogova ◽

Evgeny Abakumov ◽

...

Keyword(s):

Magnetic Anomaly ◽

Soil Formation ◽

Variable Region ◽

Active Role ◽

Taxonomic Diversity ◽

Taxonomic Composition ◽

Soil Microbiome ◽

Rrna Gene ◽

Kursk Magnetic Anomaly ◽

Mining Areas

The physicochemical parameters, vegetation and biodiversity of microbiomes inhabiting 10-, 35- and 50-year-old embryonic soils (technozems) formed in the mining areas of the Kursk Magnetic Anomaly (Russia) were analyzed in the current study. Analysis of taxonomic diversity was carried out by 454-pyrosequencing of the V4 variable region of the 16S rRNA gene. All points of the chronosequence were characterized by microbiomes reliably differing in taxonomic composition. The older the dump, the higher the proportion of bacteria from the phyla Actinobacteria (mostly representatives of the Solirubrobacteriaceae family), Chloroflexi and Acidobacteria in the community. In 10-year-old dumps, bacteria from the phyla Proteobacteria, Gemmatimonadetes and Bacteroides prevailed. The most pronounced changes in the community structure at the early and middle stages of microbiological succession were demonstrated by bacteria from the genus Delftia, which may indicate their active role in the processes of soil formation in this ecosystem.

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Microbial biomass and basal respiration in Sub-Antarctic and Antarctic soils in the areas of some Russian polar stations

Solid Earth Discussions ◽

10.5194/sed-6-869-2014 ◽

2014 ◽

Vol 6 (1) ◽

pp. 869-885

Author(s):

E. Abakumov ◽

N. Mukhametova

Keyword(s):

Microbial Biomass ◽

Organic Carbon ◽

Total Organic Carbon ◽

Carbon Content ◽

Metabolic Activity ◽

Basal Respiration ◽

South Shetland Islands ◽

King George Island ◽

Organic Layers ◽

Antarctic Soils

Abstract. Antarctica is the unique place for pedological investigations. Soils of Antarctica have been studied intensively during the last century. Antarctic logistic provides the possibility to scientists access the terrestrial landscapes mainly in the places of polar stations. That is why the main and most detailed pedological investigations were conducted in Mc Murdo Valleys, Transantarctic Mountains, South Shetland Islands, Larsemann hills and Schirmacher Oasis. Investigations were conducted during the 53rd and 55th Russian Antarctic expeditions on the base of soil pits and samples collected in Sub-Antarctic and Antarctic regions. Soils of diverse Antarctic landscapes were studied with aim to assess the microbial biomass level, basal respiration rates and metabolic activity of microbial communities. The investigation conducted shows that soils of Antarctic are quite different in profile organization and carbon content. In general, Sub-Antarctic soils are characterized by more developed humus (sod) organo-mineral horizons as well as the upper organic layer. The most developed organic layers were revealed in peat soils of King-George Island, where its thickness reach even 80 cm. These soils as well as soils under guano are characterized by the highest amount of total organic carbon (TOC) 7.22–33.70%. Coastal and continental soils of Antarctic are presented by less developed Leptosols, Gleysols, Regolith and rare Ornhitosol with TOC levels about 0.37–4.67%. The metabolic ratios and basal respiration were higher in Sub-Antarctic soils than in Antarctic ones which can be interpreted as result of higher amounts of fresh organic remnants in organic and organo-mineral horizons. Also the soils of King-George island have higher portion of microbial biomass (max 1.54 mg g−1) than coastal (max 0.26 mg g−1) and continental (max 0.22 mg g−1) Antarctic soils. Sub-Antarctic soils mainly differ from Antarctic ones in increased organic layers thickness and total organic carbon content, higher microbial biomass carbon content, basal respiration and metabolic activity levels.

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DIVERSITY OF CULTURABLE BACTERIAL MICROBIOTA OF THE Eisenia foetida DIGESTIVE TRACT

Revista Fitotecnia Mexicana ◽

10.35196/rfm.2018.3.255-264 ◽

2018 ◽

Vol 41 (3) ◽

pp. 255-264 ◽

Cited By ~ 1

Author(s):

J. Abraham Pérez-Pérez ◽

David Espinosa-Victoria ◽

Hilda V. Silva-Rojas ◽

Lucía López-Reyes

Keyword(s):

Bacterial Diversity ◽

Digestive Tract ◽

Bacterial Species ◽

Brain Heart Infusion ◽

Rrna Gene ◽

Eisenia Foetida ◽

Bacterial Isolates ◽

Bacterial Microbiota ◽

Decomposition Of Organic Matter ◽

Earthworm Gut

Bacteria are an unavoidable component of the natural earthworm diet; thus, bacterial diversity in the earthworm gut is directly linked to decomposition of organic matter and development of the surrounding plants. The aim of this research was to isolate and to identify biochemically and molecularly the culturable bacterial microbiota of the digestive tract of Eisenia foetida. Earthworms were sourced from Instituto de Reconversión Productiva y Bioenergética (IRBIO) and Colegio de Postgraduados (COLPOS), México. Bacterial isolation was carried out on plates of Brain Heart Infusion (BHI) culture medium. Fifty six and 44 bacterial isolates were obtained from IRBIO and COLPOS, respectively. The population was composed of 44 Gram-negative and 56 Gram-positive isolates. Over 50 % of the bacterial isolates were rod-shaped cells. The 16S rRNA gene was sequenced and nine genera were identified in worms from IRBIO (Bacillus, Paenibacillus, Solibacillus, Staphylococcus, Arthrobacter, Pantoea, Stenotrophomonas, Acinetobacter and Aeromonas) and six in worms from COLPOS (Bacillus, Paenibacillus, Stenotrophomonas, Staphylococcus, Acinetobacter and Aeromonas). Bacillus was the predominant genus, with eight and six species in the oligochaetes from IRBIO and COLPOS, respectively. The most represented bacteria in the worms from both sites were Bacillus sp. and B. subtilis. The predominance of Bacillus was probably due to spore formation, a reproductive strategy that ensures survival and dispersion in the soil and oligochaetes digestive tract. The gut of E. foetida not only harbored bacterial species of agronomic importance but also species potentially pathogenic for humans (Staphylococcus warneri, Pantoea agglomerans and Stentrophomonas sp.). The larger bacterial diversity in worms from IRBIO could be due to their feeding on cattle manure, which is a rich source of bacteria.

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Metagenomic, Metabolomic, and Functional Evaluation of Kimchi Broth Treated with Light-Emitting Diodes (LEDs)

Metabolites ◽

10.3390/metabo11080472 ◽

2021 ◽

Vol 11 (8) ◽

pp. 472

Author(s):

Yeong-Ji Oh ◽

Ye-Rin Park ◽

Jungil Hong ◽

Do-Yup Lee

Keyword(s):

Amplicon Sequencing ◽

Taxonomic Composition ◽

Metabolic Phenotype ◽

Rrna Gene ◽

Functional Evaluation ◽

Initial Condition ◽

Microbial Composition ◽

Light Emitting ◽

Blue Led ◽

Red Led

The light-emitting diode (LED) has been widely used in the food industry, and its application has been focused on microbial sterilization, specifically using blue-LED. The investigation has been recently extended to characterize the biotic and abiotic (photodynamic) effects of different wavelengths. Here, we investigated LED effects on kimchi fermentation. Kimchi broths were treated with three different colored-LEDs (red, green, and blue) or kept in the dark as a control. Multiomics was applied to evaluate the microbial taxonomic composition using 16S rRNA gene amplicon sequencing, and the metabolomic profiles were determined using liquid chromatography–Orbitrap mass spectrometry. Cell viability was tested to determine the potential cytotoxicity of the LED-treated kimchi broths. First, the amplicon sequencing data showed substantial changes in taxonomic composition at the family and genus levels according to incubation (initial condition vs. all other groups). The differences among the treated groups (red-LED (RLED), green-LED (GLED), blue-LED (BLED), and dark condition) were marginal. The relative abundance of Weissella was decreased in all treated groups compared to that of the initial condition, which coincided with the decreased composition of Lactobacillus. Compositional changes were relatively high in the GLED group. Subsequent metabolomic analysis indicated a unique metabolic phenotype instigated by different LED treatments, which led to the identification of the LED treatment-specific and common compounds (e.g., luteolin, 6-methylquinoline, 2-hydroxycinnamic acid, and 9-HODE). These results indicate that different LED wavelengths induce characteristic alterations in the microbial composition and metabolomic content, which may have applications in food processing and storage with the aim of improving nutritional quality and the safety of food.

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