The paper deals with the phylogenetic and functional microbial diversity in the samples of umbric luvisol contaminated and uncontaminated with hydrocarbons and of urban stratozem. High-throughput ...sequencing of the V3–V4 region of the 16S rRNA gene revealed predomination of bacteria of the phyla
Proteobacteria
,
Actinobacteria
, and
Acidobacteria
in the studied soil samples. Bacteria of the genera
Sphingomonas
,
Bradyrhizobium
, and
Pseudolabrys
in the samples of umbric luvisol and bacteria of the genera
Brevundimonas
,
Stenotrophomonas
, and
Streptomyces
in urbostratozem had the greatest potential functional activity in conversion of nitrogen compounds, degradation of chloroalkanes, chloroalkenes, and benzoate. Strains of
Stenotrophomonas maltophilia
, which degraded oil, petroleum products, and polycyclic aromatic hydrocarbons (PAHs, phenanthrene, anthracene, and pyrene) were isolated from oil-contaminated soils. Under microcosm conditions, microorganisms of umbric luvisol efficiently degraded various components of naphthenic-methane and methane-naphthenic oil. While the content of aromatic components in naphthenic-methane oil degraded by the soil microbial community and by the community enriched with
S. maltophilia
strain P420c was almost the same, in the variant with bioaugmentation the degradation process of these components proceeded 14 days faster. The enrichment of soil with specific degraders of PAHs and aromatic compounds may be appropriate for the soils of northern regions with a low duration of the summer period, which are polluted with oil with a high content of aromatic and asphalt-resinous compounds.
—
In this work, we investigated the phylogenetic diversity and potential functional activity of microorganisms in the samples of hydrocarbon-contaminated Arctic soils. High-throughput sequencing of ...the V4 region of the 16S rRNA gene revealed predominance of bacterial sequences of the phyla
Proteobacteria
and
Actinobacteria
in the libraries from contaminated soils. Relative abundance of bacterial sequences of the phyla
Acidobacteria
,
Chloroflexi
, and
Gemmatimonadetes
was lower in the libraries of contaminated soil samples compared to the samples not contaminated with hydrocarbons. The 16S rRNA gene sequences of potential oil degraders of the genera
Alkanindiges
,
Aquabacterium
,
Polaromonas
,
Pseudomonas
, and
Sphingomonas
were revealed. The number of cultivated hydrocarbon-oxidizing bacteria (HOB) in soil samples, determined at 5 and 15°C, varied from 10
4
to 10
6
cells/g of soil. Thirteen pure HOB cultures were isolated, belonging to the genera
Arthrobacter
,
Bacillus
,
Brevibacillus
,
Janthinobacterium
,
Paenibacillus
,
Pseudomonas
,
Rhodococcus
, and
Sphingomonas
, which were capable of growing with hydrocarbons and decrease the surface tension of the medium. The information obtained expands the existing understanding of the composition and physiological characteristics of microbial communities in Arctic soils.
For the first time, a comparative analysis of 8 strains of the genus Shewanella isolated from various natural sources is carried out according to the level of the reducing activity of Ag+ to ...silver-containing nanoparticles (NPs). The characteristics of biogenic NPs in terms of shape, size, crystal-lattice parameters, hydrodynamic diameter, ζ potential, and optical characteristics are obtained using scanning transmission electron microscopy, dynamic light scattering, spectrophotometry, atomic emission spectroscopy, and assessment of the biocidal activity against various types of microorganisms, including the studied strains of the genus Shewanella. It is found that the shape of the NPs is close to spherical, the sizes vary from 2 to 30 nm, the samples are polydisperse colloidal systems. Analysis of crystal lattices of the NPs confirms the presence of AgNPs, as well as Ag2O2NPs and Ag3O4NPs in some samples. The results of atomic emission spectroscopy on the quantitative analysis of the content of Ag in the nanomaterial samples are obtained, on the basis of which strains with a high ability to form a Ag-containing nanomaterial are identified. The high sensitivity of gram-positive bacteria to AgNPs is established. Different levels of resistance of 8 strains of the genus Shewanella to the action of biogenic AgNPs are demonstrated. The results indicate the metabolic diversity of strains of the genus Shewanella isolated from various natural sources. The analysis of strains of the genus Shewanella according to the level of the reducing activity is relevant for the development of an effective technology for the “green” synthesis of biogenic NPs.
—
The composition of microbial communities in rock samples, reservoir water, and enrichment cultures from subsurface horizons of an uranium deposit (Russia) was determined. The studied horizons were ...located in the zone of hindered water exchange at a depth of 513–544 m, characterized by moderate salinity (up to 15 g/L) of reservoir water and the presence of charry plant organic matter. The biodiversity of autochthonous subsurface prokaryotes was determined by high-throughput sequencing of the V4 region of the 16S rRNA gene. Bacterial phyla predominant in the rock samples were
Firmicutes
(24.2%),
Fusobacteriota
(23.0%),
Proteobacteria
(18.7%),
Actinobacteriota
(15.5%) and
Bacteroidota
(9.0%). The predominant bacterial phylum in the reservoir water was
Proteobacteria
(90.7%), including representatives of the genera
Methylophaga
,
Porphyrobacter
,
Roseovarius
,
Pseudomonas
, and
Methylococcus
. Sequencing of the internal transcribed spacer (ITS) revealed occurrence of lower fungi of the genera
Mucor
and
Thamnidium
(phylum
Mucoromycota
) and of the genus
Penicillium
(phylum
Ascomycota
) in the rock samples; members of these genera are known for their resistance to heavy metals and the ability to use complex organic substrates. The functional characteristics of bacterial communities of the rock and reservoir water samples, predicted by the iVicodak program and the KEGG database, showed that reservoir water bacteria had a higher potential ability to carry out the pathways of carbohydrate, nitrogen, and sulfur metabolism, degradation of xenobiotics, benzoate, polycyclic aromatic hydrocarbons and chlorinated organic compounds than the rock microbiota. Enrichment cultures of iron-reducing and sulfate-reducing bacteria and pure cultures of denitrifying bacteria of the genera
Bacillus
,
Paenibacillus
, and
Acinetobacter
were obtained. These results indicate the presence of a small but viable microbial community that can participate in the processes of transformations of carbon, nitrogen, sulfur, and metals in the subsurface horizon when water exchange is activated.
—
Underground natural gas storage facilities (UGS) have been recently proposed as sites to store “green” gas containing biogas, synthetic methane, and molecular hydrogen. The composition of the UGS ...microbial communities and the effect of H
2
on these communities are poorly understood. This work deals with determination of microbial diversity in the samples of reservoir water from the underground horizons of the Shchelkovo, Kasimov, and Kaluga UGS. Groundwater is an anaerobic habitat containing acetic and other lower fatty acids, methanol, and dissolved gases that may serve as substrates for microorganisms. Low abundance of cultivated aerobic organotrophic bacteria and anaerobic fermenting, sulfate-reducing, and methanogenic microorganisms in the studied samples was shown. High-throughput sequencing of the V4 region of the 16S rRNA gene revealed the presence of
Firmicutes
(2.4–53.6%),
Bacteroidetes
(1.0–39.7%),
Alphaproteobacteria
(0.9–9.6%),
Actinobacteria
(0.1–1.7%),
Desulfobacteria
(0.1–1.6%),
Verrucomicrobia
(0–3.4%), and
Planctomycetes
(0–1.3%) in the studied microbial communities. The share of archaeal sequences in the libraries did not exceed 1.5%. In the water sample from the Kaluga UGS, members of the genus
Marinobacter
predominated; methanogens of the genera
Methanosphaera
,
Methanolobus
, and
Methanobrevibacter
were found among the minor components. Methylotrophic bacteria of the genera
Methylococcus
and
Methylobacterium‒Methylorubrum
and anaerobic fermenting bacteria of the genus
Bacteroides
predominated in the reservoir water from the Shchelkovo and Kasimov UGSs. Using the iVikodak program, the potential ability of microbial communities to use methane, methanol, benzoate, and polycyclic aromatic hydrocarbons, as well as to participate in the transformations of sulfur and nitrogen compounds, was shown. In the underground communities, bacteria and archaea were found, potentially capable of using H
2
in their energy metabolism, including the processes of sulfate reduction, methanogenesis and acetogenesis. These results indicate that microbiological and geochemical monitoring is required during the operation of UGS, especially during the injection of hydrogen.
—The kinetics of Np(VI and V) reduction was studied in model underground water in the presence of bacteria, isolated from from deep-injection disposal of liquid radioactive wastes of Siberian ...Chemical Plant. Obtained data indicate a chemical instability of Np(VI) in the studied system. The reduction of neptunium (V) depended on its initial concentration and the presence of microorganisms. In microbiome samples, the reduction rate has significantly increased and neptunium-bearing particles more than 200 nm in size were formed. At neptunium concentrations less than 10
–7
М, the reduction rate constant did not depend on the radionuclide content (half-reaction period of 36–40 days). An increase of Np concentration to 10
–6
М led to a two-fold decrease of the reduction rate constant.
Biogenic sulfide production in oilfields results in lower quality of oil and gas and in corrosion of oil-producing equipment. Bactericidal agents are not used at the Karazhanbas oilfield ...(Kazakhstan), since sulfate concentrations in both injected and formation water are low or zero. However, increasing corrosion of steel equipment and sulfide release into formation water were observed in the course of the oilfield development. The goal of the present work was to reveal the potential agents of microbial corrosion and to investigate the possibility to suppress development of sulfidogens using nitrate. Environmental conditions and the composition of microbial communities in production and injection water were studied for the sites with different temperatures. High-throughput sequencing of the V3–V4 region of the 16S rRNA gene revealed predominance of thermophilic sulfate-reducing bacteria (genera
Thermodesulfobacterium
,
Thermodesulfovibrio, Desulfotomaculum, Thermodesulforhabdus, Desulfovirgula, Defluviitoga,
and
Desulfonauticus
) and archaea (genus
Archaeoglobus
) at the high-temperature horizon, as well as of thiosulfate-reducing (genera
Thermoanaerobacter
,
Anaerobaculum
, and
Coprothermobacter
) and syntrophic bacteria, while abundance of methanogens (genera
Methanolinea
and
Methanothermobacter
) was low
.
Communities from low-temperature horizons contained mesophilic methanogens (genera
Methanococcus
,
Methanobacterium
, and
Methanothrix
), thermophilic and mesophilic sulfate-reducing bacteria (genera
Desulfovibrio, Desulfomicrobium, Desulfosarcina, Desulfoglaeba, Desulfotignum,
and
Desulfocurvus
), syntrophic bacteria (genus
Smithella
)
,
and members of the genera
Marinobacter
,
Paracoccus, Alcaligenes, Arcobacter,
and
Halomonas
. Enrichment cultures of bacteria producing sulfide were obtained from formation water, as well as the cultures reducing nitrate to nitrite and suppressing growth of sulfate- and thiosulfate-reducing bacteria. These findings may indicate the possibility of using nitrate as a competitive inhibitor of sulfidogenesis in this oilfield. Corrosion-active hydrogen-utilizing methanogens and acetogens were also found, which implies the necessity for monitoring the oilfield microbial communities.
Functional and phylogenetic microbial diversity in formation waters of carbonate low-temperature bed 302 of the Romashkinskoe oil field was studied using microbiological, molecular and radioisotope ...techniques. Cultivable sulfate-reducing prokaryotes (103–106 cells ml−1) predominated in formation water and the process of sulfate reduction was paramount. The rate of sulfate reduction varied within the range 2.28–26.60 μg S2− l−1−day−1. The number of fermentative bacteria varied from 102 to 104 cells ml−1, of methanogens – from 10 to 104 cells ml−1. Methanogenesis was a minor process with the rate not exceeding 0.395 μg CH4 l−1 day−1. 16S rRNA gene clone libraries for Bacteria and Archaea were constructed on the basis of DNA extracted from formation water. From the bacterial clone library, 16S rRNA genes of aerobic organotrophs (genera Pseudomonas, Acinetobacter, ‘Brachymonas’ etc.), anaerobic organotrophs (genus Thauera, Bacteroidetes) and sulfate reducers (Desulfoglaeba, Desulfomicrobium, Desulfovibrio and Desulfobacterales) were retrieved. For the first time, the predominance of nucleotide sequences of the bacterium Desulfoglaeba alkanexedens known to grow on n-alkanes was revealed in the clone library from the carbonate oil reservoir. Archaeal sequences in the library of formation water were not attributable to any recognized methanogens. Both the sulfate-reducing bacterium D. alkanexedens and syntrophic assemblages could be involved in biodegradation of crude oil associated with sulfate reduction in the carbonate petroleum reservoir.
► Microorganisms of carbonate petroleum reservoir (Russia) were studied. ► Fermentative and sulfate-reducing bacteria were predominant cultivated groups. ► Sulfate reduction is a major process in produced water samples. ► 16S rRNA genes of Desulfoglaeba dominate in the clone library of water samples. ► Both sulfidogenic assemblages and sulfate-reducer Desulfoglaeba degrades oil in the oil field.
Decommissioned surface repositories of liquid radioactive waste remain a potential source of groundwater pollution. Establishment of biogeochemical barriers results in decreased migration of both ...radioactive and toxic macro-components of the waste. The article presents the results of studying the composition of the microbial community of groundwater sampled in the area of a surface repository for liquid radioactive waste. High-throughput sequencing of the 16S rRNA genes revealed the dominant and minor components of the community, among which were found bacteria of the genus
Shewanella
. Isolated pure cultures of
Shewanella putrefaciens
J1-6-2-2 and A-4-3 and
Shewanella xiamenensis
DCB2-1 were capable of reducing nitrate ions to dinitrogen, which resulted in a decrease in the redox potential of the medium and contributed to reduction and deposition of pertechnetate, uranyl, and chromate ions. In the presence of organic substrates the strains formed biofilms on a number of natural materials (vermiculite, pearlite, schungite, etc.) with high sorption characteristics for cesium, strontium, uranium, and technetium. Analysis of the genome of strain DCB2-1 revealed a cluster of genes homologous to those determining biofilm formation in the well-known strain
Shewanella oneidensis
MR-1. The isolated strains may be used for introduction into subsurface horizons and enrichment of the natural microbial community in order to create a biogeochemical barrier for purification of groundwater from nitrate ions and immobilization of radioactive waste components.
Ability to degrade crude oil
n
-alkanes was revealed in new strains of thermophilic bacilli isolated from petroleum reservoirs and a hot spring:
Geobacillus toebii
В-1024,
Geobacillus
sp. 1017, and
...Aeribacillus pallidus
8m3. The strains utilized С
10
–С
30
n
-alkanes (В-1024), С
10
, C
11
, and С
13
–С
19,22
n
-alkanes (1017), and C
11
–C
29
n
-alkanes (8m3). In all three strains, PCR amplification with specific degenerate oligonucleotide primers revealed the
alkB
gene encoding rubredoxin-dependent alkane monooxygenase. In strains В-1024 and 1017, fragments of the genes homologous to the
ladA
gene determining flavin-dependent alkane monooxygenase were also amplified. Nucleotide sequences of these genes were practically identical to those of the genes
ladA
α
B23
,
ladA
β
B23
, and
ladB
B23
, which were revealed previously in
Geobacillus thermoleovorans
strain B23. For the latter strain, activity of respective enzymes in the oxidation of long-chain
n
-alkanes has been shown. Thus, simultaneous presence of the
alkB
and
ladA
genes coding alkane monooxygenases responsible for oxidation of medium-chain and long-chain n-alkanes in thermophilic bacilli was revealed for the first time.
