Bacterial diversity of autotrophic enriched cultures from remote, glacial Antarctic, Alpine and Andean aerosol, snow and soil samples

Abstract. Four different communities and one culture of autotrophic microbial assemblages were obtained by incubation of samples collected from high elevation snow in the Alps (Mt. Blanc area) and the Andes (Nevado Illimani summit, Bolivia), from Antarctic aerosol (French station Dumont d'Urville) and a maritime Antarctic soil (King George Island, South Shetlands, Uruguay Station Artigas), in a minimal mineral (oligotrophic) media. Molecular analysis of more than 200 16S rRNA gene sequences showed that all cultured cells belong to the Bacteria domain. Phylogenetic comparison with the currently available rDNA database allowed sequences belonging to Proteobacteria Alpha-, Beta- and Gamma-proteobacteria), Actinobacteria and Bacteroidetes phyla to be identified. The Andes snow culture was the richest in bacterial diversity (eight microorganisms identified) and the marine Antarctic soil the poorest (only one). Snow samples from Col du Midi (Alps) and the Andes shared the highest number of identified microorganisms (Agrobacterium, Limnobacter, Aquiflexus and two uncultured Alphaproteobacteria clones). These two sampling sites also shared four sequences with the Antarctic aerosol sample (Limnobacter, Pseudonocardia and an uncultured Alphaproteobacteriaclone). The only microorganism identified in the Antarctica soil (Brevundimonas sp.) was also detected in the Antarctic aerosol. Most of the identified microorganisms had been detected previously in cold environments, marine sediments soils and rocks. Air current dispersal is the best model to explain the presence of very specific microorganisms, like those identified in this work, in environments very distant and very different from each other.

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Diversity of bacteria producing pigmented colonies in aerosol, snow and soil samples from remote glacial areas (Antarctica, Alps and Andes)

Biogeosciences Discussions ◽

10.5194/bgd-5-1607-2008 ◽

2008 ◽

Vol 5 (2) ◽

pp. 1607-1630 ◽

Cited By ~ 8

Author(s):

E. González-Toril ◽

R. Amils ◽

R. J. Delmas ◽

J.-R. Petit ◽

J. Komárek ◽

...

Keyword(s):

Cultured Cells ◽

High Elevation ◽

Aerosol Sample ◽

Rrna Gene ◽

Antarctic Soil ◽

Maritime Antarctic ◽

The Andes ◽

The Alps ◽

The Antarctic ◽

Snow Samples

Abstract. Four different communities and one culture of pigmented microbial assemblages were obtained by incubation in mineral medium of samples collected from high elevation snow in the Alps (Mt. Blanc area) and the Andes (Nevado Illimani summit, Bolivia), from Antarctic aerosol (French station Dumont d'Urville) and a maritime Antarctic soil (King George Island, South Shetlands, Uruguay Station Artigas). Molecular analysis of more than 200 16S rRNA gene sequences showed that all cultured cells belong to the Bacteria domain. The phylogenetic comparison with the currently available rDNA database allowed the identification of sequences belonging to Proteobacteria (Alpha-, Beta- and Gamma-proteobacteria), Actinobacteria and Bacteroidetes phyla. The Andes snow culture was the richest in bacterial diversity (eight microorganisms identified) and the maritime Antarctic soil the poorest (only one). Snow samples from Col du midi (Alps) and the Andes shared the highest number of identified microorganisms (Agrobacterium, Limnobacter, Aquiflexus and two uncultured Alphaproteobacteria clones). These two sampling sites also shared four sequences with the Antarctic aerosol sample (Limnobacter, Pseudonocardia and an uncultured Alphaproteobacteria clone). The only microorganism identified in the maritime Antarctica soil (Brevundimonas sp.) was also detected in the Antarctic aerosol. The two snow samples from the Alps only shared one common microorganism. Most of the identified microorganisms have been detected previously in cold environments (Dietzia kujamenisi, Pseudonocardia Antarctica, Hydrogenophaga palleronii and Brebundimonas sp.), marine sediments (Aquiflexus balticus, Pseudomonas pseudoalkaligenes, Pseudomonas sp. and one uncultured Alphaproteobacteria), and soils and rocks (Pseudonocardia sp., Agrobactrium sp., Limnobacter sp. and two uncultured Alphaproteobacetria clones). Air current dispersal is the best model to explain the presence of very specific microorganisms, like those used in this work, in very distant environments. In addition these microorganisms have to be resistant to extreme conditions and able to grow in oligotrophic environments. Considering the habitats in which they have been identified, the presence of pigments must be related with their ability to resist high doses of radiation.

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Bacterial diversity within the planktonic community of an artesian water supply

Canadian Journal of Microbiology ◽

10.1139/w05-108 ◽

2006 ◽

Vol 52 (3) ◽

pp. 246-259 ◽

Cited By ~ 9

Author(s):

Christopher L Ball ◽

Ronald L Crawford

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Water Supply ◽

Bacterial Diversity ◽

Cultured Cells ◽

Denaturing Gradient Gel Electrophoresis ◽

Enrichment Culture ◽

Rrna Gene ◽

Artesian Water ◽

Planktonic Community

Culture and molecular methods were used to describe the planktonic bacterial diversity of an artesian water supply in rural Latah County, Idaho, within the drainage of a small perennial stream, Thorn Creek. The surrounding depth to groundwater at this location is thought to be significant (>100 m), and this transitional zone (basalt–granite) of the Palouse aquifer system is little studied. The water produced by this artesian source is consistent even in years of drought and is of high quality, both mineralogically and microbiologically. A culture-based analysis using 30 media types and four incubation temperatures demonstrated that several metabolic types were present in the water. 16S rRNA gene fragments amplified from the DNA of pooled cultured cells and from the DNA extracted from 1 L of the source water were compared using denaturing gradient gel electrophoresis. The results indicated that the two DNA samples did not have similar 16S rRNA gene compositions and that several uncultured phyla were present in the community DNA sample. These results indicated that large-scale culturing did not accurately represent the structure planktonic community. 16S rRNA gene sequences from 17 different genera were obtained from the community DNA sample; the most abundant were similar to Rhodoferax, Rhodobacter, and Polaromonas species. Sequences related to the Proteo bacteria, Bacteroidetes/Chlorobi, Firmicutes, and Acidobacterium/Fibrobacter divisions were also detected.Key words: artesian spring, bacterial diversity, DGGE, 16S rRNA, enrichment culture.

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Marine diatoms in ice cores from the Antarctic Peninsula and Ellsworth Land, Antarctica – species diversity and regional variability

10.5194/tc-2021-160 ◽

2021 ◽

Author(s):

Dieter R. Tetzner ◽

Elizabeth R. Thomas ◽

Claire S. Allen

Keyword(s):

Antarctic Peninsula ◽

Temporal Distribution ◽

Ice Cores ◽

High Elevation ◽

Polar Regions ◽

Regional Variability ◽

Marine Diatoms ◽

The Andes ◽

Glacier Ice ◽

The Antarctic

Abstract. The presence of marine microfossils (diatoms) in glacier ice and ice cores has been documented from numerous sites in Antarctica, Greenland, as well as from sites in the Andes and the Altai mountains, and attributed to entrainment and transport by winds. However, their presence and diversity in snow and ice, especially in polar regions, is not well documented and still poorly understood. Here we present the first data to resolve the regional and temporal distribution of diatoms in ice cores, spanning a 20 year period across four sites in the southern Antarctic Peninsula and Ellsworth Land, Antarctica. We assess the regional variability in diatom composition and abundance at annual and sub-annual resolution across all four sites. These data corroborate the dominance of contemporary marine diatoms in Antarctic Peninsula ice cores, reveal that the timing and amount of diatoms deposited vary between low and high elevation sites and support existing evidence that marine diatoms have the potential to yield a novel wind paleoenvironmental proxy for ice cores in the southern Antarctic Peninsula and Ellsworth Land.

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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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Marisediminicola antarctica gen. nov., sp. nov., an actinobacterium isolated from the Antarctic

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.018754-0 ◽

2010 ◽

Vol 60 (11) ◽

pp. 2535-2539 ◽

Cited By ~ 36

Author(s):

Hui-Rong Li ◽

Yong Yu ◽

Wei Luo ◽

Yin-Xin Zeng

Keyword(s):

Sequence Similarity ◽

Phylogenetic Analyses ◽

Intertidal Sediment ◽

Rrna Gene ◽

Optimum Growth ◽

Temperature Range ◽

Zhongshan Station ◽

Diamino Acid ◽

Ph Range ◽

The Antarctic

Strain ZS314T was isolated from a sandy intertidal sediment sample collected from the coastal area off the Chinese Antarctic Zhongshan Station, east Antarctica (6 ° 22′ 13″ S 7 ° 21′ 41″ E). The cells were Gram-positive, motile, short rods. The temperature range for growth was 0–26 °C and the pH for growth ranged from 5 to 10, with optimum growth occurring within the temperature range 18–23 °C and pH range 6.0–8.0. Growth occurred in the presence of 0–6 % (w/v) NaCl, with optimum growth occurring in the presence of 2–4 % (w/v) NaCl. Strain ZS314T had MK-10 as the major menaquinone and anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0 as major fatty acids. The cell-wall peptidoglycan type was B2β with ornithine as the diagnostic diamino acid. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The genomic DNA G+C content was approximately 67 mol%. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that strain ZS314T represents a new lineage in the family Microbacteriaceae. On the basis of the phylogenetic analyses and phenotypic characteristics, a new genus, namely Marisediminicola gen. nov., is proposed, harbouring the novel species Marisediminicola antarctica sp. nov. with the type strain ZS314T (=DSM 22350T =CCTCC AB 209077T).

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Spatial and Temporal Variation in Microbial Diversity and Community Structure in a Contaminated Mangrove Wetland

Applied Sciences ◽

10.3390/app10175850 ◽

2020 ◽

Vol 10 (17) ◽

pp. 5850

Author(s):

Jiaojiao Ma ◽

Ting Zhou ◽

Chunyu Xu ◽

Dawen Shen ◽

Songjun Xu ◽

...

Keyword(s):

Community Structure ◽

Spatial Variation ◽

Temporal Variation ◽

Bacterial Diversity ◽

Diversity Index ◽

Total Carbon ◽

Spatial And Temporal Variation ◽

Rrna Gene ◽

Mangrove Wetland ◽

Mangrove Soils

Field and laboratory investigations were conducted to characterize bacterial diversity and community structure in a badly contaminated mangrove wetland adjacent to the metropolitan area of a megacity in subtropical China. Next-generation sequencing technique was used for sequencing the V4–V5 region of the 16s rRNA gene on the Illumina system. Collectively, Proteobacteria, Chloroflexi, Planctomycetes, Actinobacteria and Bacteroidetes were the predominant phyla identified in the investigated soils. A significant spatial variation in bacterial diversity and community structure was observed for the investigated mangrove soils. Heavy metal pollution played a key role in reducing the bacterial diversity. The spatial variation in soil-borne heavy metals shaped the spatial variation in bacterial diversity and community structure in the study area. Other environmental factors such as total carbon and total nitrogen in the soils that are affected by seasonal change in temperature could also influence the bacterial abundance, diversity and community structure though the temporal variation was relatively weaker, as compared to spatial variation. The bacterial diversity index was lower in the investigated site than in the comparable reference site with less contaminated status. The community structure in mangrove soils at the current study site was, to a remarkable extent, different from those in the tropical mangrove wetlands around the world.

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Relationship between dental and periodontal health status and the salivary microbiome: bacterial diversity, co-occurrence networks and predictive models

Scientific Reports ◽

10.1038/s41598-020-79875-x ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

M. Relvas ◽

A. Regueira-Iglesias ◽

C. Balsa-Castro ◽

F. Salazar ◽

J. J. Pacheco ◽

...

Keyword(s):

Oral Health ◽

Periodontal Disease ◽

Bacterial Diversity ◽

Predictive Models ◽

Oral Disease ◽

Rrna Gene ◽

Convenience Sample ◽

Core Microbiome ◽

Rdna Sequencing ◽

The Impact

AbstractThe present study used 16S rRNA gene amplicon sequencing to assess the impact on salivary microbiome of different grades of dental and periodontal disease and the combination of both (hereinafter referred to as oral disease), in terms of bacterial diversity, co-occurrence network patterns and predictive models. Our scale of overall oral health was used to produce a convenience sample of 81 patients from 270 who were initially recruited. Saliva samples were collected from each participant. Sequencing was performed in Illumina MiSeq with 2 × 300 bp reads, while the raw reads were processed according to the Mothur pipeline. The statistical analysis of the 16S rDNA sequencing data at the species level was conducted using the phyloseq, DESeq2, Microbiome, SpiecEasi, igraph, MixOmics packages. The simultaneous presence of dental and periodontal pathology has a potentiating effect on the richness and diversity of the salivary microbiota. The structure of the bacterial community in oral health differs from that present in dental, periodontal or oral disease, especially in high grades. Supragingival dental parameters influence the microbiota’s abundance more than subgingival periodontal parameters, with the former making a greater contribution to the impact that oral health has on the salivary microbiome. The possible keystone OTUs are different in the oral health and disease, and even these vary between dental and periodontal disease: half of them belongs to the core microbiome and are independent of the abundance parameters. The salivary microbiome, involving a considerable number of OTUs, shows an excellent discriminatory potential for distinguishing different grades of dental, periodontal or oral disease; considering the number of predictive OTUs, the best model is that which predicts the combined dental and periodontal status.

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Effects of Simulated Nitrogen Deposition on the Bacterial Community of Urban Green Spaces

Applied Sciences ◽

10.3390/app11030918 ◽

2021 ◽

Vol 11 (3) ◽

pp. 918

Author(s):

Lingzi Mo ◽

Augusto Zanella ◽

Xiaohua Chen ◽

Bin Peng ◽

Jiahui Lin ◽

...

Keyword(s):

Bacterial Community ◽

Bacterial Diversity ◽

Negative Impact ◽

Bacterial Community Composition ◽

N Deposition ◽

Soil Bacterial Community ◽

Rrna Gene ◽

Soil Dna ◽

Urban Green ◽

Soil Bacterial

Continuing nitrogen (N) deposition has a wide-ranging impact on terrestrial ecosystems. To test the hypothesis that, under N deposition, bacterial communities could suffer a negative impact, and in a relatively short timeframe, an experiment was carried out for a year in an urban area featuring a cover of Bermuda grass (Cynodon dactylon) and simulating environmental N deposition. NH4NO3 was added as external N source, with four dosages (N0 = 0 kg N ha−2 y−1, N1 = 50 kg N ha−2 y−1, N2 = 100 kg N ha−2 y−1, N3 = 150 kg N ha−2 y−1). We analyzed the bacterial community composition after soil DNA extraction through the pyrosequencing of the 16S rRNA gene amplicons. N deposition resulted in soil bacterial community changes at a clear dosage-dependent rate. Soil bacterial diversity and evenness showed a clear trend of time-dependent decline under repeated N application. Ammonium nitrogen enrichment, either directly or in relation to pH decrease, resulted in the main environmental factor related to the shift of taxa proportions within the urban green space soil bacterial community and qualified as a putative important driver of bacterial diversity abatement. Such an impact on soil life induced by N deposition may pose a serious threat to urban soil ecosystem stability and surrounding areas.

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A new species of smooth-skinned Spinomantis frog (Anura: Mantellidae) from south-eastern Madagascar

Zootaxa ◽

10.11646/zootaxa.4317.2.12 ◽

2017 ◽

Vol 4317 (2) ◽

pp. 379

Author(s):

MIGUEL VENCES ◽

JÖRN KÖHLER ◽

FRANK GLAW

Keyword(s):

National Park ◽

Type Specimen ◽

High Elevation ◽

Type Locality ◽

Colour Pattern ◽

Molecular Evidence ◽

Rrna Gene ◽

Reciprocal Monophyly ◽

South Eastern ◽

Candidate Species

We present molecular evidence for the presence of two species morphologically similar to Spinomantis bertini in Andohahela National Park, south-eastern Madagascar, differing by 5.5−6.3% pairwise DNA sequence divergences in the mitochondrial 16S rRNA gene. One of these was observed at higher elevations of ca. 1650 m above sea level, whereas the other was found at lower elevations of ca. 715 m a.s.l., close to the type locality of S. bertini (Isaka-Ivondro), and in one other location (Andreoky, ca. 1050 a.s.l.). We herein assign these low- to mid-elevation specimens to S. bertini based on their occurrence near the type locality and general agreement in colour pattern with the type specimen of Gephyromantis bertini Guibé, 1947. The high-elevation form is described as Spinomantis beckei sp. nov. based on its molecular divergence and reciprocal monophyly with respect to S. bertini, lower expression of greenish dorsal colour and less distinct frenal stripe. Based on a comparison of published call descriptions for S. bertini and our recordings of S. beckei, we hypothesize that S. bertini has a lower note repetition rate in advertisement calls. Molecular data suggest that the S. bertini species complex is more diverse than previously recognized, with at least two more candidate species identified: S. sp. Ca7 from Ranomafana National Park, and a newly identified candidate species S. sp. Ca12 from Pic d’Ivohibe Special Reserve.

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