Article
Biotechnology & Applied Microbiology
Dimitry Y. Sorokin, Michail M. Yakimov, Enzo Messina, Alexander Y. Merkel, Michel Koenen, Nicole J. Bale, Jaap S. Sinninghe Damste
Summary: Nine new strains of neutrophilic haloarchaea were isolated from hypersaline lakes in Siberia and Russia, showing various metabolic pathways including anaerobic sulfur respiration. These strains exhibit unique physiological properties and can utilize different electron acceptors and donors for growth.
SYSTEMATIC AND APPLIED MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Dimitry Y. Sorokin, Michail Yakimov, Enzo Messina, Alexander Y. Merkel, Michel Koenen, Nicole J. Bale, Jaap S. Sinninghe Damste
Summary: A pure culture of alkaliphilic haloarchaeon strain AArc-ST capable of anaerobic growth by carbohydratedependent sulfur respiration was obtained from hypersaline lakes in southwestern Siberia. According to phylogenetic analysis, AArc-ST formed a new genus level branch most related to the genus Natronoarchaeum in the order Halobacteriales. The strain is facultatively anaerobic with strictly respiratory metabolism growing either by anaerobic respiration with elemental sulfur and thiosulfate as the electron acceptors or by aerobic respiration at microoxic conditions. Thiosulfate is reduced partially to sulfide and sulfite. It is a first sulfur-reducing alkaliphilic haloarchaeon utilizing sugars, starch and glycerol as substrates for anaerobic growth. It is extremely halophilic (optimum at 3.5 M total Na+) and obligately alkaliphilic (optimum at pH 9.5). The dominant polar lipids include PG and PGP-Me with the archaeol (C20-C20) or extended archaeol (C20-C25) cores. The dominant respiratory lipoquinone is MK8:8. On the basis of unique physiological properties and results of phylogenetic analysis, the soda lake isolate is suggested to be classified into a novel genus and species Natranaeroarchaeum sulfidigenes gen. nov., sp. nov. (=JCM 34033T = UNIQEM U1000T). Furthermore, on the bases of phylogenomic reconstruction, a new family Natronoarchaeaceae fam. nov. is proposed within the order Halobacteriales incorporating Natranaeroarchaeum and three related genera: Natronoarchaeum, Salinarchaeum and Halostella.
SYSTEMATIC AND APPLIED MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Dimitry Y. Sorokin, Alexander G. Elcheninov, Alexander Y. Merkel, Nicole J. Bale, Jaap Sininghe-Damste, Ilya Kublanov
Summary: Two strains of neutrophilic haloaloarchaea were enriched from hypersaline lakes in southwestern Siberia using specific substrates. These strains exhibit unique physiological properties and are classified as a novel species.
SYSTEMATIC AND APPLIED MICROBIOLOGY
(2023)
Article
Microbiology
D. Y. Sorokin
Summary: This study enriched for GB-utilizing bacteria and archaea from sediments of hypersaline soda lakes in southwestern Siberia. Gamma-proteobacterial strains and sulfur-reducing haloarchaea were isolated under different conditions, demonstrating their ability to utilize various methylated compounds for growth.
Review
Microbiology
Boglarka Somogyi, Tamas Felfoldi, Emil Boros, Attila Szabo, Lajos Voros
Summary: The extreme environmental conditions of diverse saline inland waters favor high abundance and contribution to phytoplankton biomass by picophytoplankton. Differences in picophytoplankton abundances exist among different saline water types, with higher abundances in hypersaline lakes compared to humic soda lakes and the highest numbers in turbid soda lakes. Despite the extreme conditions, the diversity of picophytoplankton remains remarkable.
Article
Biochemistry & Molecular Biology
Dimitry Y. Sorokin, Pawel Roman, Tatjana Kolganova
Summary: The study showed that haloarchaea can utilize methionine sulfoxide and tetramethylene sulfoxide for anaerobic respiration, expanding our understanding of their energy metabolism pathways.
Article
Biotechnology & Applied Microbiology
Mohamed Ibrahim Abo-Alkasem, Dina A. Maany, Mostafa A. El-Abd, Abdelnasser S. S. Ibrahim
Summary: Strain NRC-R is a highly efficient Cr(VI)-reducing haloalkaliphilic bacterium that can grow and effectively reduce Cr(VI) under a wide range of conditions. It exhibits tolerance to different heavy metals and oxyanions and can utilize various electron donors for Cr(VI) reduction. The Cr(VI) reduction by strain NRC-R is achieved through direct enzymatic reduction.
Article
Biotechnology & Applied Microbiology
Dimitry Y. Sorokin, Alexander G. Elcheninov, Tatjana Khizhniak, Michel Koenen, Nicole J. Bale, Jaap S. Sinninghe Damste, Ilya V. Kublanov
Summary: This study isolated and classified several alkaliphilic haloaloarchaea from hypersaline soda lakes in southwestern Siberia. These archaea can grow using various starch-like substrates and exhibit moderate alkaliphilic and low Mg-demanding properties.
SYSTEMATIC AND APPLIED MICROBIOLOGY
(2022)
Article
Engineering, Multidisciplinary
Elham F. Mohamed, Gamal Awad, Abdelnasser S. S. Ibrahim
Summary: This study tested the performance of a novel haloalkaliphilic bacterium in the biodegradation of indoor formaldehyde gas. The results showed that the immobilized strain was able to efficiently remove formaldehyde gas, even at high concentrations, suggesting its potential application in air pollutant control and bioremediation.
RESULTS IN ENGINEERING
(2023)
Article
Biotechnology & Applied Microbiology
Tatjana N. Zhilina, Dimitry Y. Sorokin, Stepan V. Toshchakov, Ilya V. Kublanov, Daria G. Zavarzina
Summary: Two heterotrophic bacteroidetes strains were isolated from hypersaline soda lakes in southwestern Siberia. Strain Z-1702T is an obligate anaerobic fermentative saccharolytic bacterium, while Ca. Cyclonatronum proteinivorum OmegaT is an obligate aerobic proteolytic microorganism. Both strains have highly variable morphology and are chloride-independent moderate salt-tolerant obligate alkaliphiles and mesophiles.
SYSTEMATIC AND APPLIED MICROBIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Mohamed Ibrahim Abo-Alkasem, Mostafa A. El-Abd, Dina A. Maany, Abdelnasser S. S. Ibrahim
Summary: We reported a novel haloalkaliphilic bacterial strain NRC-Y with remarkable hexavalent chromium reduction efficiency and studied its detoxification mechanism.
EGYPTIAN JOURNAL OF CHEMISTRY
(2023)
Article
Biotechnology & Applied Microbiology
Marco A. Distaso, Tatyana N. Chernikova, Rafael Bargiela, Cristina Coscolin, Peter Stogios, Jose L. Gonzalez-Alfonso, Sofia Lemak, Anna N. Khusnutdinova, Francisco J. Plou, Elena Evdokimova, Alexei Savchenko, Evgenii A. Lunev, Michail M. Yakimov, Olga V. Golyshina, Manuel Ferrer, Alexander F. Yakunin, Peter N. Golyshin
Summary: In this study, three novel thermotolerant carboxylesterases (IS10, IS11, and IS12) were identified from high-temperature enrichment cultures. These enzymes exhibited high catalytic activity towards polyester plastics and mycotoxin T-2, indicating their potential applications in various industries.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Marco Distaso, Isabel Cea-Rama, Cristina Coscolin, Tatyana N. N. Chernikova, Hai Tran, Manuel Ferrer, Julia Sanz-Aparicio, Peter N. N. Golyshin
Summary: Metagenomics was used to build a metagenomic library and screen for a novel esterase from the Sorghum bicolor rhizosphere. The esterase EH0 showed a broad substrate specificity and a unique structural feature. This research provides new insights into the relationship between enzyme structure and function.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Environmental Sciences
Filippo Dell'Anno, Leonardo Joaquim van Zyl, Marla Trindade, Emanuela Buschi, Antonio Cannavacciuolo, Milva Pepi, Clementina Sansone, Christophe Brunet, Adrianna Ianora, Donatella de Pascale, Peter N. Golyshin, Antonio Dell'Anno, Eugenio Rastelli
Summary: Petroleum hydrocarbons and heavy metals are widespread contaminants in marine ecosystems, and microbial-based bioremediation shows promise as an effective and sustainable solution. In this study, we enriched the microbiome of heavily polluted sediments and isolated two novel bacterial strains that exhibited high degradation of PAHs and removal of HMs, with the best results observed for naphthalene, pyrene, and lead. The genetic repertoire of these strains may be further utilized for bioremediation of marine environments contaminated with PAHs and HMs.
ENVIRONMENTAL POLLUTION
(2023)
Article
Food Science & Technology
Darya A. A. Golovkina, Elena V. V. Zhurishkina, Olga N. N. Ayrapetyan, Artem E. E. Komissarov, Anastasiya S. S. Krylova, Elizaveta N. N. Vinogradova, Stepan V. V. Toshchakov, Filipp K. K. Ermilov, Artak M. M. Barsegyan, Anna A. A. Kulminskaya, Irina M. M. Lapina
Summary: Kombucha tea was fermented with the SCOBY culture of green tea broth and the addition of Fucus vesiculosus algae extract, Cetraria islandica lichen extract and their mixture. The presence of yeast Zygosaccharomyces bailii and bacteria Komagataeibacter cocois was detected in the samples with herbal extracts. The kombucha with herbal additives showed a decrease in yeast fraction compared to the control, but the polyphenols content and antioxidant activity were comparable. The algae extract enhanced the sucrose and organic acids content in the kombucha, while the fructose and glucose content were lower in samples with algae and the mixture of extracts. The samples with algae extract had the highest organoleptic indicators, while the control samples had slightly higher taste and aftertaste indicators. These findings suggest the potential of algae and lichens as functional supplements for non-alcoholic fermented beverages.
Article
Biochemistry & Molecular Biology
Dmitry I. Karetnikov, Gennady V. Vasiliev, Stepan V. Toshchakov, Nikolay A. Shmakov, Mikhail A. Genaev, Mikhail A. Nesterov, Salmaz M. Ibragimova, Daniil A. Rybakov, Tatjana A. Gavrilenko, Elena A. Salina, Maxim V. Patrushev, Alex V. Kochetov, Dmitry A. Afonnikov
Summary: By comparing the genomic sequences of potato cultivars from Russia and South America, we found that the Russian potatoes have a more homogeneous genome with smaller copy number variations and deletion size compared to the South American ones. We identified genes related to immune/abiotic stress response, transport, tuberization, and photoperiod control. Additionally, we discovered a novel gene similar to Arabidopsis poly(ADP-ribose) glycohydrolase (PARG) that may play a role in circadian rhythm control and contribute to the acclimatization processes of Russian potato cultivars.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Ramona Marasco, Marco Fusi, Cristina Coscolin, Alan Barozzi, David Almendral, Rafael Bargiela, Christina Gohlke Nee Nutschel, Christopher Pfleger, Jonas Dittrich, Holger Gohlke, Ruth Matesanz, Sergio Sanchez-Carrillo, Francesca Mapelli, Tatyana N. Chernikova, Peter N. Golyshin, Manuel Ferrer, Daniele Daffonchio
Summary: Temperature has a significant impact on the adaptation and composition of microbiomes, and their enzymes play a crucial role in the thermal response. This study demonstrates that enzyme thermal properties not only explain microbial thermal plasticity but are also finely tuned by the thermal variability of the environment. The findings highlight the importance of temperature-driven enzyme selection in shaping microbiome thermal plasticity and emphasize the need to consider thermal variability in addition to mean annual temperature in understanding microbial community response to temperature.
NATURE COMMUNICATIONS
(2023)
Article
Biotechnology & Applied Microbiology
Violetta La Cono, Enzo Messina, Oleg Reva, Francesco Smedile, Gina La Spada, Francesca Crisafi, Laura Marturano, Noa Miguez, Manuel Ferrer, Elena A. A. Selivanova, Olga V. V. Golyshina, Peter N. N. Golyshin, Manfred Rohde, Mart Krupovic, Alexander Y. Y. Merkel, Dimitry Y. Y. Sorokin, John E. E. Hallsworth, Michail M. M. Yakimov
Summary: Climate change and other environmental factors are creating or modifying microbial habitats, which can affect the degradation of polysaccharides in saline environments. This study investigated the relationship between nanohaloarchaea and haloarchaea in xylan-degrading communities in hypersaline environments. The findings suggest that nanohaloarchaea act as ectosymbionts of Haloferax, which scavenges oligosaccharides produced by xylan-hydrolysing Halorhabdus. The study also demonstrated that nanohaloarchaea can be easily isolated in co-cultures and discussed the implications of xylan degradation in biotechnology and sustainable development goals.
MICROBIAL BIOTECHNOLOGY
(2023)
Article
Microbiology
Zorigto Namsaraev, Anna Bobrik, Aleksandra Kozlova, Anastasia Krylova, Anastasia Rudenko, Anastasia Mitina, Aleksandr Saburov, Maksim Patrushev, Olga Karnachuk, Stepan Toshchakov
Summary: Cryogenic soils are important carbon reservoirs, and their microbial diversity has a strong impact on CO2 emissions. Rising temperatures in the high Arctic can activate microbial processes and increase carbon input from these soils. Using high-throughput sequencing, the microbial community composition and diversity were studied in the soil of Barents Sea archipelagos. The study found that soil moisture and temperature were the main factors influencing the microbial community composition, and CO2 emission levels were influenced by local factors such as moisture, microclimate, and animal fecal input from reindeer.
Article
Chemistry, Medicinal
Anastasiia Yu. Ivanova, Ivan V. Shirokov, Stepan V. Toshchakov, Aleksandra D. Kozlova, Olga N. Obolenskaya, Sofia S. Mariasina, Vasily A. Ivlev, Ilya B. Gartseev, Oleg S. Medvedev
Summary: The main route of drug administration for Coenzyme Q10 (CoQ10) is oral administration, which has a bioavailability of about 2-3%. Prolonged use of CoQ10 can lead to higher concentrations in the intestine and impact the gut microbiota and biomarkers it produces. In a study on Wistar rats, oral administration of CoQ10 at a dose of 30 mg/kg/day for 21 days resulted in increased hydrogen concentration, total SCFA concentration, and relative abundance of certain bacterial groups, as well as decreased TMA levels and relative representation of Helicobacter. The antioxidant effect of orally administered CoQ10 may involve modification of the gut microbiota composition, increased hydrogen generation, and protection of the gut barrier function.
Article
Multidisciplinary Sciences
Javier Glez-Vaz, Arantza Azpilikueta, Maria C. Ochoa, Irene Olivera, Gabriel Gomis, Asunta Cirella, Carlos Luri-Rey, Maite alvarez, Jose. L. L. Perez-Gracia, Sergio Ciordia, Inaki Eguren-Santamaria, Raluca Alexandru, Pedro Berraondo, Carlos de Andrea, Alvaro Teijeira, Fernando Corrales, Juan. M. M. Zapata, Ignacio Melero
Summary: CD137 is a member of the TNFR family that mediates potent T cell costimulatory signals upon ligation by CD137L or agonist monoclonal antibodies (mAbs). The physical association between cIAP1/cIAP2 and the CD137 signaling complex is demonstrated. cIAPs are required for CD137 signaling towards NF-κB and MAPK pathways, and for the costimulation of human and mouse T lymphocytes.
Article
Biology
Zorigto Namsaraev, Aleksandra Kozlova, Fedor Tuzov, Anastasia Krylova, Anna Izotova, Ivan Makarov, Andrei Bezgreshnov, Anna Melnikova, Anna Trofimova, Denis Kuzmin, Maksim Patrushev, Stepan Toshchakov
Summary: The prokaryotic communities in the Barents Sea are strongly affected by climate change and influenced by microbiota from the Atlantic Ocean. This study identified two distinct types of communities and discussed their origin in terms of biogeography.
Article
Biology
Evgenii N. Frolov, Sergey N. Gavrilov, Stepan V. Toshchakov, Daria G. Zavarzina
Summary: The anaerobic oxidation of fatty acids and alcohols is carried out by syntrophic bacteria that oxidize these compounds and their syntrophic partners that consume the products. The only available method to study these microorganisms is through genomic and metabolic analysis of syntrophic cultures.
Article
Genetics & Heredity
Rafael Bargiela, Aleksei A. Korzhenkov, Owen A. McIntosh, Stepan V. Toshchakov, Mikhail M. Yakimov, Peter N. Golyshin, Olga V. Golyshina
Summary: This study analysed the metagenome-assembled genome of E-plasma, which provides the basis for their predominance in the Parys Mountain environmental microbiome, their global ubiquity, and points in the right direction for further cultivation attempts. The results suggest distinct evolutionary trajectories of organisms comprising the order Thermoplasmatales, which is important for understanding their evolution and lifestyle.
ENVIRONMENTAL MICROBIOME
(2023)