scholarly journals Rhizobial isolates in active layer samples of permafrost soil of Spitsbergen, Arctic

2021 ◽  
Vol 66 (1) ◽  
Author(s):  
Denis Karlov ◽  
Anna Sazanova ◽  
Irina Kuznetsova ◽  
Nina Tikhomirova ◽  
Zhanna Popova ◽  
...  
Keyword(s):  
16S Rrna ◽  
Active Layer ◽  
Plant Roots ◽  
Permafrost Soil ◽  
Two Samples ◽  
Murmansk Region ◽  
Legume Plants ◽  
Sym Genes ◽  
Number Of Bacteria ◽  
Rhizobial Isolates

Twenty-nine strains were isolated from two samples of the permafrost active layer of the Spitsbergen archipelago. The estimated number of bacteria ranged from 4.0⋅104 to 1.7⋅107 CFU∙g-1. As a result of sequencing of the 16S rRNA (rrs) genes, the isolates were assigned to 13 genera belonging to the phyla Actinobacteria, Proteobacteria (classes α, β, and γ), Bacteroidetes, and Firmicutes. Six isolates belonged to the rhizobial genus Mesorhizobium (order Rhizobiales). A plant nodulation assay with seedlings of legume plants Astragalus norvegicus, A. frigidus, A. subpolaris and Oxytropis sordida, originated from Khibiny (Murmansk region, Russia) and inoculated with Mesorhizobium isolates, showed the inability of these strains to form nodules on plant roots. Symbiotic (sym) genes nodC and nodD were not detected in Mesorhizobium strains either.

scholarly journals Effects of freezing on soil temperature, freezing front propagation and moisture redistribution in peat: laboratory investigations

2012 ◽  
Vol 16 (2) ◽  
pp. 501-515 ◽  
Author(s):  
R. M. Nagare ◽  
R. A. Schincariol ◽  
W. L. Quinton ◽  
M. Hayashi
Keyword(s):  
Water Content ◽  
Active Layer ◽  
Water Movement ◽  
Peat Soil ◽  
Soil Column ◽  
Initial Period ◽  
Soil Freezing ◽  
Permafrost Soil ◽  
Freezing Front ◽  
Discontinuous Permafrost

Abstract. There are not many studies that report water movement in freezing peat. Soil column studies under controlled laboratory settings can help isolate and understand the effects of different factors controlling freezing of the active layer in organic covered permafrost terrain. In this study, four peat Mesocosms were subjected to temperature gradients by bringing the Mesocosm tops in contact with sub-zero air temperature while maintaining a continuously frozen layer at the bottom (proxy permafrost). Soil water movement towards the freezing front (from warmer to colder regions) was inferred from soil freezing curves, liquid water content time series and from the total water content of frozen core samples collected at the end of freezing cycle. A substantial amount of water, enough to raise the upper surface of frozen saturated soil within 15 cm of the soil surface at the end of freezing period appeared to have moved upwards during freezing. Diffusion under moisture gradients and effects of temperature on soil matric potential, at least in the initial period, appear to drive such movement as seen from analysis of freezing curves. Freezing front (separation front between soil zones containing and free of ice) propagation is controlled by latent heat for a long time during freezing. A simple conceptual model describing freezing of an organic active layer initially resembling a variable moisture landscape is proposed based upon the results of this study. The results of this study will help in understanding, and ultimately forecasting, the hydrologic response of wetland-dominated terrain underlain by discontinuous permafrost.

Soil aggregate-based nucleic acid analyses of the impact of maize roots and their root hairs on the structural diversity of microbial communities

2021 ◽  
Author(s):  
Christoph Tebbe ◽  
Damini Damini ◽  
Damien Finn ◽  
Nataliya Bilyera ◽  
Minh Ganther ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Root Hair ◽  
Soil Aggregates ◽  
Root Hairs ◽  
Soil Samples ◽  
Plant Roots ◽  
Bulk Soil ◽  
Rrna Gene ◽  
The Impact

<p>The deposition of energy rich carbon sources released by plant roots during their growth fuels microbially driven ecosystem processes in soil, but there is a lack of understanding how microorganisms interact and collaborate. The objective of this research was therefore to characterize microbial networks as they assemble under the influence of plant roots. To identify the specific importance of root hairs, we compared the impact of a maize wild-type to a root-air defective mutant (rth3; (1).</p><p>The microbial community structure was analyzed by qPCR and 16S rRNA gene amplicon sequencing from soil DNA. In order to increase the probability of detecting truly interacting microbial partners as a basis for network analyses, we first evaluated a new protocol to obtain DNA from as little as 1 mg instead of the usual 250 mg soil samples, thereby approaching the aggregate level (2). While the diversity of bacterial 16S rRNA gene amplicons of 250-mg samples taken from the same soil was not distinct, DNA analyses from individual aggregates clearly differed from each other underlining that soil aggregates represent distinct microbial habitats.</p><p>Soil column experiments with maize grown in a loam soil (3) revealed distinct communities between rhizosphere and bulk soil. The community composition of individual aggregates showed more differences in bulk soil compared to rhizosphere. Less elaborated networks were seen in bulk soil and a profound effect of root hairs could be unravelled. Null model testing demonstrated that Actinobacteria were equally important for network connectivity independent of the root hair mutation, but for networks of the wildtype, Acidobacteria were essential for synergistic interactions and overall network structure. In contrast, Proteobacteria and Firmicutes connectivity became more important. The observed differences in community composition and interactions suggests carbon cycling, and perhaps other microbially-driven functions, are markedly affected by the presence of root hairs.</p><p>Utilizing maize root soil microcosms for studying soil zymography in the rhizosphere allowed to obtain soil samples from regions with distinct specific enzyme activities. In order to enhance the detection of actively metabolizing bacterial community members, we studied rRNA sequences and compared it to rRNA gene sequences from the same samples. Currently the data are under analysis.</p><p>References</p><p>(1) Wen, T-J, Schnable PS (1994) Analyses of mutants of three genes that influence root hair development in Zea mays (Gramineae) suggest that root hairs are dispensable. Am. J. Bot. 81, 833–842.</p><p>(2) Szoboszlay M, Tebbe CC (2020) Hidden heterogeneity and co-occurrence networks of soil prokaryotic communities revealed at the scale of individual soil aggregates. Microbiol. Open, e1144. DOI: 10.1002/mbo3.1144</p><p>(3) Vetterlein D et al. (2020) Experimental platforms for the investigation of spatiotemporal patterns in the rhizosphere – laboratory and field scale. J. Plant Nutr. Soil Sci., 000, 1–16 DOI: 10.1002/jpln.202000079</p>

Evidence for Iron- and Sulfur-Oxidizing Bacteria and Archaea in a Currently Active Lignite Mining Area of Lusatia (Eastern Germany)

2009 ◽  
Vol 71-73 ◽  
pp. 97-100 ◽  
Author(s):  
H.M. Siebert ◽  
Thore Rohwerder ◽  
Wolfgang Sand ◽  
M. Strzodka ◽  
K.P. Stahmann
Keyword(s):  
16S Rrna ◽  
Mining Area ◽  
16S Rrna Genes ◽  
Open Pit ◽  
Rrna Genes ◽  
Published Data ◽  
Lignite Mining ◽  
Two Samples ◽  
Pure Cultures ◽  
Sulfur Oxidizing

The largest lignite mining area in Europe is located 150 km southeast of Berlin. Acidic lakes exist in this area, known to be caused by marcasite oxidation. Thirty-two samples from the open-pit brown coal-mine Jaenschwalde were analyzed for microorganisms. Cell numbers determined after separation from sand particles revealed concentrations of 102 to 107 microorganisms per g sample. In samples exposed to the air within an hour, up to 4x107 cells were counted. Measurement of metabolic activity by microcalorimetry showed for such samples up to 50 µW per g sand, whereas in heap samples (with low moisture) low or even no activity was measurable. DNA extraction was successful for 28 samples. In 26 samples microbial 16S rRNA genes were amplified by PCR. Acidithiobacillus ferrooxidans and At. thiooxidans specific amplificates were detected by nested PCR in 23 and 10 cases, respectively. A specific signal indicating Leptospirillum ferrooxidans was obtained with nine samples. Random samples were sequenced and showed 96 to 99 % identity with published data of all three species. Surprisingly, in four samples archaeal 16S rRNA genes were amplified by PCR. Sequencing of two samples showed 99 % identity with unidentified or uncultured archaea found in NCBI-databases. Molecular biology results for At. ferrooxidans as well as for At. thiooxidans were supported by successful isolations of pure cultures in 23 cases. Cultivation of the archaea failed so far. These data indicate that iron- and sulfur-oxidizing microorganisms occur at these sites in large numbers. If in addition the evidence for archaea can become verified, a screening for hot spots as the sites of their occurrence would become interesting.

PCR Analysis of Nasal Polyps, Chronic Sinusitis, and Hypertrophied Turbinates for DNA Encoding Bacterial 16S rRNA

2002 ◽  
Vol 16 (3) ◽  
pp. 169-173 ◽  
Author(s):  
Gerald A Bucholtz ◽  
Sherry A. Salzman ◽  
Fernando B. Bersalona ◽  
Timothy R. Boyle ◽  
Victor S. Ejercito ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Nasal Polyps ◽  
Chronic Sinusitis ◽  
Consensus Sequence ◽  
Rrna Gene ◽  
Dna Encoding ◽  
Bacterial Dna ◽  
Two Samples ◽  
The 16S Rrna Gene

Background Nasal polyps are considered to result from chronic inflammation, but the initial or persisting stimulus for the inflammation is not known. A variety of bacteria and fungi have been cultured from nasal polyps, but ∼35% have sterile cultures. Previously, Mycoplasma pneumoniae–specific DNA was detected in human nasal polyps using polymerase chain reaction (PCR) techniques, suggesting M. pneumoniae as a causative agent in the etiology of nasal polyps. Methods In this study, we tested for the presence of bacterial DNA in nasal polyps resected from 40 patients, in nasal mucosa membrane from 9 patients undergoing turbinectomy for hypertrophy, and in sinus mucosa membrane from 6 patients undergoing endoscopic surgery for chronic sinusitis. Tissue DNA was extracted and analyzed by PCR using M. pneumoniae specific primers for DNA that encode the 16S rRNA gene in 41 specimens (31 polyps, 6 turbinates, and 4 sinus), and by consensus sequence-based PCR using broad range primers for most eubacterial DNA encoding the 16S rRNA gene in 38 specimens (26 polyps, 7 turbinates, and 5 sinuses). Results Only two samples were positive for bacterial DNA encoding 16S rRNA: Streptococcus sp. DNA was isolated from one polyp specimen and Pseudomonas aeruginosa DNA was isolated in one maxillary sinusitis specimen. No evidence of M. pneumoniae–specific DNA encoding 16S rRNA was found in any of the tissues. Conclusions This study suggests that chronic bacterial infection is not a major component of nasal polyp etiology.

Verification of clinical samples, positive in AMPLICOR Neisseria gonorrhoeae polymerase chain reaction, by 16S rRNA and gyrA compared with culture

2005 ◽  
Vol 16 (6) ◽  
pp. 415-419 ◽  
Author(s):  
Åsa Airell ◽  
Emma Lindbäck ◽  
Ferda Ataker ◽  
Kirsti Jalakas Pörnull ◽  
Bengt Wretlind
Keyword(s):  
Polymerase Chain Reaction ◽  
16S Rrna ◽  
Neisseria Gonorrhoeae ◽  
False Negative ◽  
Clinical Samples ◽  
Rrna Gene ◽  
Chain Reaction ◽  
Gyra Gene ◽  
Two Samples ◽  
Polymerase Chain

We compared 956 samples for AMPLICOR Neisseria gonorrhoeae polymerase chain reaction (PCR) (Roche) with species verification using the 16S rRNA gene to verification using gyrA gene. Control was the culture method. The gyrA verification uses pyrosequencing of the quinolone resistance-determining region of gyrA. Of 52 samples with optical density ≥0.2 in PCR, 27 were negative in culture, two samples from pharynx were false negative in culture and four samples from pharynx were false positives in verification with 16S rRNA. Twenty-five samples showed growth of gonococci, 18 of the corresponding PCR samples were verified by both methods; three urine samples were positive only in gyrA ; and one pharynx specimen was positive only in 16S rRNA. Three samples were lost. We conclude that AMPLICOR N. gonorrhoeae PCR with verification in gyrA gene can be considered as a diagnostic tool in populations with low prevalence of gonorrhoea and that pharynx specimens should not be analysed by PCR.

scholarly journals Nonlinear thermal and moisture dynamics of high Arctic wetland polygons following permafrost disturbance

2015 ◽  
Vol 12 (14) ◽  
pp. 11797-11831 ◽  
Author(s):  
E. Godin ◽  
D. Fortier ◽  
E. Lévesque
Keyword(s):  
Active Layer ◽  
Arid Region ◽  
High Arctic ◽  
Permafrost Soil ◽  
Active Layer Thickness ◽  
Green House Gas ◽  
Heterogeneous Nature ◽  
Thaw Depth ◽  
Moisture Dynamics ◽  
Permafrost Regions

Abstract. Low-centre polygonal terrain developing within gentle sloping surfaces and lowlands in the high Arctic have a potential to retain snowmelt water in their bowl-shaped centre and as such are considered high latitude wetlands. Such wetlands in the continuous permafrost regions have an important ecological role in an otherwise generally arid region. In the valley of the glacier C-79 on Bylot Island (Nunavut, Canada), thermal erosion gullies are rapidly eroding the permafrost along ice wedges affecting the integrity of the polygons by breaching and collapsing the surrounding rims. While intact polygons were characterized by a relative homogeneity (topography, snow cover, maximum active layer thaw depth, ground moisture content, vegetation cover), eroded polygons had a non-linear response for the same elements following their perturbation. The heterogeneous nature of disturbed terrains impacts active layer thickness, ground ice aggradation in the upper portion of permafrost, soil moisture and vegetation dynamics, carbon storage and terrestrial green-house gas emissions.

The morphological characteristic strain KPABG LID-610023 of Chroococcus s.l. group (Cyanoprokaryota)

2021 ◽  
pp. 108-113
Author(s):  
Denis A. Davydov ◽  
Sergei S. Shalygin ◽  
Anna A. Vilnet ◽  
Vera V. Redkina
Keyword(s):  
New Species ◽  
16S Rrna ◽  
Barents Sea ◽  
Genetic Difference ◽  
Nucleotide Composition ◽  
Nucleotide Sequences ◽  
Rrna Gene ◽  
Murmansk Region ◽  
Established Species ◽  
A New Species

The Chroococcus-like strain was collected from anthropogenic meadow on the Barents Sea coast (Murmansk Region, Russia). It was studied by light microscope, the nucleotide sequences of 16S rRNA and ITS were obtained. Based on 16S rRNA phylogenetic analysis, the strain KPABG LID-610023 was placed in the clade of Inacoccus in spite of morphological and molecular differences from one already established species: Inacoccus carmineus. Morphologically the tested strain did not show colored hyaline envelopes, and nanocytes were absent. The nucleotide sequences of 16S rRNA gene clearly demonstrated a genetic difference, separating it from Inacoccus carmineus. In addition, we compared ITS sequences of KPABG LID-610023 strain and Inacoccus carmineus and found that nucleotide composition, length, and secondary structures of D1–D1' and Box-B were different. These results suggest that the strain KPABG LID-610023 appear to be a new species of the genus Inacoccus. Possibly this new species is a cryptic taxon due to its morphological similarity with Chroococcus pallidus Näg.

scholarly journals Temporal and spatial variation in Anaplasma phagocytophilum infection in Swedish moose (Alces alces)

2013 ◽  
Vol 142 (6) ◽  
pp. 1205-1213 ◽  
Author(s):  
J. MALMSTEN ◽  
D. GAVIER WIDÉN ◽  
G. RYDEVIK ◽  
L. YON ◽  
M. R. HUTCHINGS ◽  
...  
Keyword(s):  
16S Rrna ◽  
Spatial Variation ◽  
Anaplasma Phagocytophilum ◽  
Alces Alces ◽  
Sequence Similarity ◽  
Serum Samples ◽  
Temporal And Spatial Variation ◽  
Granulocytic Anaplasmosis ◽  
Two Samples ◽  
Temporal And Spatial

SUMMARYThe occurrence of Anaplasma phagocytophilum was investigated in spleen and serum samples from Swedish moose (Alces alces) in southern Sweden (island and mainland). Samples were analysed for presence of A. phagocytophilum DNA by real-time PCR (n = 263), and for Anaplasma antibodies with ELISA serology (n = 234). All serum samples had antibodies against A. phagocytophilum. The mean DNA-based prevalence was 26·3%, and significant (P < 0·01) temporal, and spatial variation was found. Island moose had significantly (P < 0·001) higher prevalence of A. phagocytophilum DNA than moose from the mainland areas. Two samples were sequenced to determine genetic variation in the 16S rRNA and groESL genes. Genetic sequence similarity with the human granulocytic anaplasmosis agent, equine granulocytic ehrlichiosis agent, and different wildlife-associated A. phagocytophilum variants were observed in the 16S rRNA and groESL genes. Our study shows that moose are exposed to A. phagocytophilum in Sweden, and represent a potential wildlife reservoir of the pathogen.

scholarly journals Rumen Microbial Population Dynamics during Adaptation to a High-Grain Diet

2010 ◽  
Vol 76 (22) ◽  
pp. 7482-7490 ◽  
Author(s):  
S. C. Fernando ◽  
H. T. Purvis ◽  
F. Z. Najar ◽  
L. O. Sukharnikov ◽  
C. R. Krehbiel ◽  
...  
Keyword(s):  
Population Dynamics ◽  
Population Structure ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Population ◽  
Rflp Analysis ◽  
Rrna Gene ◽  
Gene Libraries ◽  
The 16S Rrna Gene ◽  
Number Of Bacteria

ABSTRACT High-grain adaptation programs are widely used with feedlot cattle to balance enhanced growth performance against the risk of acidosis. This adaptation to a high-grain diet from a high-forage diet is known to change the rumen microbial population structure and help establish a stable microbial population within the rumen. Therefore, to evaluate bacterial population dynamics during adaptation to a high-grain diet, 4 ruminally cannulated beef steers were adapted to a high-grain diet using a step-up diet regimen containing grain and hay at ratios of 20:80, 40:60, 60:40, and 80:20. The rumen bacterial populations were evaluated at each stage of the step-up diet after 1 week of adaptation, before the steers were transitioned to the next stage of the diet, using terminal restriction fragment length polymorphism (T-RFLP) analysis, 16S rRNA gene libraries, and quantitative real-time PCR. The T-RFLP analysis displayed a shift in the rumen microbial population structure during the final two stages of the step-up diet. The 16S rRNA gene libraries demonstrated two distinct rumen microbial populations in hay-fed and high-grain-fed animals and detected only 24 common operational taxonomic units out of 398 and 315, respectively. The 16S rRNA gene libraries of hay-fed animals contained a significantly higher number of bacteria belonging to the phylum Fibrobacteres, whereas the 16S rRNA gene libraries of grain-fed animals contained a significantly higher number of bacteria belonging to the phylum Bacteroidetes. Real-time PCR analysis detected significant fold increases in the Megasphaera elsdenii, Streptococcus bovis, Selenomonas ruminantium, and Prevotella bryantii populations during adaptation to the high-concentrate (high-grain) diet, whereas the Butyrivibrio fibrisolvens and Fibrobacter succinogenes populations gradually decreased as the animals were adapted to the high-concentrate diet. This study evaluates the rumen microbial population using several molecular approaches and presents a broader picture of the rumen microbial population structure during adaptation to a high-grain diet from a forage diet.

scholarly journals Molecular Evidence for the Broad Distribution of Anaerobic Ammonium-Oxidizing Bacteria in Freshwater and Marine Sediments

2006 ◽  
Vol 72 (10) ◽  
pp. 6829-6832 ◽  
Author(s):  
C. Ryan Penton ◽  
Allan H. Devol ◽  
James M. Tiedje
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Marine Sediments ◽  
Permafrost Soil ◽  
Anammox Bacteria ◽  
Molecular Evidence ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Primer Sets

ABSTRACT Previously available primer sets for detecting anaerobic ammonium-oxidizing (anammox) bacteria are inefficient, resulting in a very limited database of such sequences, which limits knowledge of their ecology. To overcome this limitation, we designed a new primer set that was 100% specific in the recovery of ∼700-bp 16S rRNA gene sequences with >96% homology to the “Candidatus Scalindua” group of anammox bacteria, and we detected this group at all sites studied, including a variety of freshwater and marine sediments and permafrost soil. A second primer set was designed that exhibited greater efficiency than previous primers in recovering full-length (1,380-bp) sequences related to “Ca. Scalindua,” “Candidatus Brocadia,” and “Candidatus Kuenenia.” This study provides evidence for the widespread distribution of anammox bacteria in that it detected closely related anammox 16S rRNA gene sequences in 11 geographically and biogeochemically diverse freshwater and marine sediments.

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