A novel species is proposed for a high-affinity methanotrophic representative of the genus
. Strain FS
was isolated from a weakly acidic (pH 5.3) mixed forest soil of the southern Moscow area. Cells ...of FS
are aerobic, Gram-negative, non-motile, curved coccoids or short rods that contain an intracytoplasmic membrane system typical of type-II methanotrophs. Only methane and methanol are used as carbon sources. FS
grew at a temperature range of 4-37 °C (optimum 25-30 °C) and a pH range of 4.5 to 7.5 (optimum pH 6.0-6.5). The major fatty acids were C
ω8
, C
ω7
and C
; the major quinone as Q-8. FS
displays 16S rRNA gene sequences similarity to other taxonomically recognized members of the genus
with
CSC1
(99.6 % similarity) and
SV97
(99.3 % similarity) as its closest relatives. The genome comprises 3.85 Mbp and has a DNA G+C content of 62.6 mol%. Genomic analyses and DNA-DNA relatedness with genome-sequenced members of the genus
demonstrated that FS
could be separated from its closest relatives. FS
possesses two particulate methane monooxygenases (pMMO): low-affinity pMMO1 and high-affinity pMMO2. In laboratory experiments, it was demonstrated that FS
might oxidize methane at atmospheric concentration. The genome contained various genes for nitrogen fixation, polyhydroxybutyrate synthesis, antibiotic resistance and detoxification of arsenic, cyanide and mercury. On the basis of genotypic, phenotypic and chemotaxonomic characteristics, it is proposed that the isolate represents a novel species,
sp. nov. The type strain is FS
(=KCTC 82935
=VKM B-3535
).
Nitrogen-fixing bacterial strain, designated B2
, was isolated from methane-oxidation enrichment originating from a Sphagnum-dominated raised peatland in Tver region, Russia, and its phenotypic, ...chemotaxonomic and genomic characteristics were investigated. Cells of isolate were Gram-negative, aerobic, rod or spiral-shaped, with motility provided by a single polar flagellum in liquid media and peritrichous flagella on solid media. Strain was able to grow at 15-40 °C, pH 5.5-8.5 and tolerated NaCl to 2.0 % (w/v). Strain B2
gave positive amplification for dinitrogen reductase (nifH gene) and acetylene reduction activity was recorded up to 1250 nmol ethylene h
(mg protein)
. Analysis of 16S rRNA showed that B2
represents a member of the genus Azospirillum and had the highest sequence similarity with A. humicireducens SgZ-5
(97.92 %). The predominant quinone system was ubiquinone Q-10 and the major fatty acids were C18 : 1ω7, C16 : 1ω7 and C16 : 0. The strain was facultative methylotrophic and used methanol and formate for the growth. Genome sequencing revealed a genome size of 8.0 Mbp and a G+C content of 67.8 mol%. The mxaFI genes encoding methanol dehydrogenase were absent, but a homologous xoxF gene was detected. The genes encoding enzymes involved in the biosynthesis of tetrahydromethanopterin (H4MPT) (formaldehyde oxidation) and NAD-linked formate dehydrogenase (fdsABG) were identified. Pairwise determined whole genome average nucleotide identity (gANI) values confirmed that strain B2
represents a novel species, for which we propose the name Azospirillum palustre sp. nov. with the type strain B2
(VKM B-3233
, КСТС 62613
).
A novel, aerobic nitrogen-fixing methylotrophic bacterium, strain 29k
, was enriched and isolated from sludge generated during wastewater treatment at a paper mill in Baikal, Russian Federation. ...Cells were Gram-stain-variable. The cell wall was of the negative Gram-type. Cells were curved oval rod-shaped, 0.5-0.7×1.7-3.4 µm and formed yellow-coloured colonies. Cells tended to be pleomorphic if grown on media containing succinate or coccoid if grown in the presence of methyl alcohol as the sole carbon source. Cells were non-motile, non-spore-forming and contained retractile (polyphosphate) and lipid (poly-β-hydroxybutyrate) bodies. The major respiratory quinone was ubiquinone Q-10 and the predominant cellular fatty acids were C
ω7, C
cyclo and C
. The genomic DNA G+C content was 67.95 mol%. Strain 29k
was able to grow at 4-37 °C (optimum, 30 °C), at pH 6.0-8.5 (optimum, pH 6.5-7.0) and at salinities of 0-0.5% (w/v) NaCl (optimum, 0% NaCl). Catalase and oxidase were positive. Strain 29k
could grow chemolithoautotrophically in mineral media under an atmosphere of H
, O
and CO
as well as chemoorganoheterotrophically on methanol, ethanol, n-propanol, n-butanol and various organic acids. The carbohydrate utilization spectrum is limited by glucose and raffinose. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the newly isolated strain was a member of the genus
with
7c
(99.9% similarity) and
7d
(99.4 % similarity) as closest relatives among species with validly published names. The average nucleotide identity and digital DNA-DNA hybridization values of 92.7 and 44.9%, respectively, of the 29k
to the genome of the most closely related species,
7c
, were below the species cutoffs. Based on genotypic, phenotypic and chemotaxonomic characteristics, it is proposed that the isolate represents a novel species,
sp. nov. The type strain is 29k
(=KCTC 72777
=VKM B-3453
).
The green blowfly, Lucilia sericata (Meigen) (Diptera: Calliphoridae), is a cosmopolitan species of great medical, veterinary, and forensic importance. In addition, their larvae are among the most ...promising agents for the bioconversion of low‐quality biomass, such as organic waste, into sustainable and nutritionally valuable proteins for farmed fish and poultry. Despite the considerable medical and economic importance, the current literature provides limited information about microbiota associated with larvae. The present study aims to fill this knowledge gap. Freshly harvested L. sericata larvae (maggots) grown on fish wastes were investigated by conventional and molecular approaches to evaluate culturable microbial numbers and unculturable microbial diversity associated with the larval cuticle (external samples) and the internal body. In total 200 bacterial isolates were obtained; 46% of the strains originated from external samples and 58% originated from internal body samples produced extracellular protease enzymes, which may be involved in the digestion of proteins during larval feeding. In total 12 predominant bacteria with high proteolytic activity were further identified by morphological, physiological, biochemical, and molecular tools. Proteolytic bacteria in internal samples included Proteus, Providencia, Micrococcus, Deinococcus, whereas in external samples Providencia, Pseudomonas, and Acinetobacter were found. 16S rRNA clone library analysis revealed that the majority of internal bacteria (35%) were taxonomically assigned as Xanthomonadaceae (Schineria, Xylella, Ignnatzchineria), 28% Morganellaceae (Proteus, Providencia, Serratia), and 14% Enterobacteriaceae (Vagococcus, Serratia). Less abundant were bacteria of the genera Clostridium (3%), Erypelothrix (3%), and Oceanispherum (2%). This knowledge will be useful for biotechnological application of L. sericata.
The green blowfly, Lucilia sericata (Diptera: Calliphoridae), is a cosmopolitan species of great medical, veterinary, and forensic importance. In addition, their larvae are among the most promising agents for the bioconversion of wastes into nutritionally valuable proteins for farmed fish and poultry. Information about the safety of the edible insects as far as the diversity and activity of microorganisms providing them with the essential nutrients is scarce. Our study provides knowledge about the microbial communities associated with green blowflies.
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Litter decomposition in terrestrial ecosystems has a major role in the biogeochemical cycling of biogenic elements, but initial stages of this process in temperate forest ecosystems remain poorly ...understood. Soil organic matter in forest ecosystems is highly sensitive to temperature rise, which makes it the most vulnerable under global warming. This article assesses the influence of aspen leaf and twig litter on the activity and quantitative characteristics of microbial communities of soils in conditions modelling climate warming. The experiments were performed with samples of grey forest soil, one of the most representative soil types of Europian Russia, from forest biocenosis in the Moscow region. Incubation of soil samples, in which crushed leaves and twigs were added at the rate of 0.5% by weight, was carried out at constant temperature of 5°C, 15°C and 25°C for 28 days. CO₂ emission, organic carbon and microbial biomass content, and number of ribosomal genes of bacteria, archaea and fungi were evaluated. The optimal temperature for decomposition of the plant litter was found to be 15°C, and both decrease and increase led to a reduction in the intensity of the degradation process. In the temperature range 5°C–15°C, application of plant residues led to significant increase in temperature sensitivity of the soil respiration process, and temperature coefficient Q
10 increased from 1.75 to 3.44–3.54. At high temperatures, addition of litter stimulated the decomposition of soil organic matter. No significant changes in microbial biomass, bacteria and fungi numbers were observed. The obtained results contribute to understanding the dynamics of soil carbon and can be used in predictive models of plant litter and soil organic matter dynamics in forest biocenoses of Eurasia under climate change.
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Here, we report the genomic sequences of the novel
Azospirillum
sp. strains B21 and Sh1, isolated from raised bogs, along with the genome sequences of
Azospirillum lipoferum
59b
T
, the type species ...of the genus, and
Azospirillum oryzae
COC8
T
, which were analyzed to get more knowledge about the genus
Azospirillum
.
ABSTRACT
Here, we report the genomic sequences of the novel
Azospirillum
sp. strains B21 and Sh1, isolated from raised bogs, along with the genome sequences of
Azospirillum lipoferum
59b
T
, the type species of the genus, and
Azospirillum oryzae
COC8
T
, which were analyzed to get more knowledge about the genus
Azospirillum
.
sp. strain B2 is a soil bacterium which was originally isolated from the Sosvyatskoe raised
bog in Russia. Here, we present the approximately 8-Mb draft genome sequence of
sp. B2, with the aim of ...providing insight into the genomic basis of its ecological success in peatland settings.
1 Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-let Octyabrya 7/2, 117811 Moscow, Russia
2 Bioengineering Center, Russian Academy of Sciences, Moscow, Russia
3 ...Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
Correspondence Dimitry Yu. Sorokin soroc{at}inmi.host.ru
Strain MS 6 T was obtained from a microoxic enrichment with a soda soil sample from north-eastern Mongolia in nitrogen-free alkaline medium at pH 10. The isolate had clostridia-like motile cells and formed ellipsoid endospores. It was able to fix dinitrogen gas growing on nitrogen-free alkaline medium. Strain MS 6 T was a strictly fermentative bacterium without a respiratory chain, although it had a high catalase activity and tolerated aerobic conditions. It was an obligate alkaliphile with a pH range for growth between 7.5 and 10.6 (optimum at 9.0–9.5). Growth and nitrogen fixation at pH 10 were possible at a total salt content of up to 1.2 M Na + (optimum at 0.2–0.3 M). The dominant cellular fatty acids included C 16 : 0 , C 16 : 1 7, anteiso-C 15 : 0 and C 14 : 0 . The dominant isoprenoid quinone was MK-7. The cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. 16S rRNA gene sequencing identified strain MS 6 T as a member of the genus Bacillus . Its closest relative was Bacillus arseniciselenatis E1H T . The key functional nitrogenase gene nifH was detected in both strain MS 6 T and its close relative and these strains formed a novel lineage in the nifH gene family. On the basis of these phenotypic and genetic comparisons, strain MS 6 T is proposed to represent a novel species of the genus Bacillus , Bacillus alkalidiazotrophicus sp. nov. with the type strain MS 6 T (=NCCB 100213 T =UNIQEM U377 T ).
Abbreviations: NF, nitrogen fixation
Supplementary figures showing the cell morphology of strain MS 6 T grown anaerobically at 0.6 M Na + and pH 10 with glucose and two additional phylogenetic trees are available with the online version of this paper.
The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA and nifH gene sequences for Bacillus alkalidiazotrophicus sp. nov. MS 6 T are EU143680 and EU204959 , respectively. The GenBank/EMBL/DDBJ accession number for the nifH gene sequence of Bacillus arseniciselenatis E1H T determined in this study is EU204960 .
Background. By 2020, breast cancer (BC) has become the most frequent malignancy in the world. The most common type of BC is HR+/HER2-negative cancer,2540% of which harbors PIK3CA mutations that ...affect the catalytic subunit of the PI3K protein. PIK3CA alterations are actionable, as such neoplasms can be treated with a combination of fulvestrant and the PI3K inhibitor alpelisib. As PIK3CA mutations have an extremely versatile effect on the characteristics of a tumor cell, numerous associations of PIK3CA mutations and various clinico-pathological characteristics of BC can be traced.
Aim. Our aim was to clarify the information on the frequency and spectrum of PIK3CA mutations in Russian patients with HR+/HER2- advanced BC, and to study the association of PIK3CA mutations with clinical and pathological parameters of BC.
Materials and methods. Tissue samples from 694 patients with HR+/HER2- advanced BC (mixed population of primary metastatic and relapsed tumors) who received any line of anti-cancer treatment in Dec 2020 to June 2021 in Russian Federation were analyzed by high-resolution melting, allele-specific PCR, digital droplet PCR and Sanger sequencing (exons 7,9, and 20 of the PIK3CA gene). Mutation rates in different BC subgroups were compared using the Fishers exact test. The age at diagnosis in patients with different PIK3CA status was compared using the MannWhitney U-test. The relationship between the PIK3CA status and the degree of tumor differentiation was compared using the CochraneArmitage test for trends. Luminal A and B BC expression subtypes were distinguished with surrogate IHC markers according to St.-Gallen recommendations (2013).
Results. Mutations were identified in 220/694 (32%) BC patients. The three most frequent missense substitutions in the PIK3CA gene (p.E542K, p.E545K, and p.H1047R) accounted for 190/220 (86%) mutations. Associations of PIK3CA mutations with luminal A subtype of BC, low proliferation index, small size of the primary tumor, and absence of signs of hereditary cancer were revealed. Associations of mutations in the kinase domain of PIK3CA (p.H1047R) with late recurrence of locally advanced BC and with non-Slavic ethnic origin of patients were found.
Conclusion. PIK3CA mutation rate of 32% confirms high prevalence of mutation in Russian population, with some differences reflecting the ethnic origin of patients.
The potential methane consumption activity was examined in various plant communities of a boreal Sphagnum-dominated Bakchar bog of West Siberia. In aerobic laboratory incubations, the peat consumed ...methane with the maximal rates varied from 17 to 153 nmol CH4 h-1g-1.The highest oxidation took place in the peat from the cotton grass and dwarf shrub-cotton grass communities. The addition of different N-compounds inhibited CH4-uptake and was not a simple influence of shift in ionic balance ('salt effect'). The introduction of sodium chloride resulted in significantly weaker inhibition effect than the same amount of nitrite and nitrate salts. The inhibition occurred at NH4+-N concentrations exceeding 100 mg kg-1, which was more than 200 times higher native N-content in peat. Communities with high CE4-uptake activity were more sensitive to ammonium. The inhibition by ammonium was non-competitive. The inhibition by ammonium was mainly due to the toxic action of nitrite and/or nitrate produced by nitrifiers. A strong positive correlation was found between the potential nitrifying activity and inhibition of CH4-uptake in ammonium-treated peat (R2= 0.87). The oxidized N-compounds were more strong inhibitors than ammonium and their toxicity increased in the following range: NH4+ < NO2- < NO3-.
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