Ilya V. Kublanov
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24 records found
1
phylogenomic analysis placed the isolates into a separate lineage of the new genus level within the family Natrialbaceae of the class Halobacteria. The strains are moderate alkaliphiles, extremely halophilic, and aerobic saccharolytics. In addition to the three beta-mannan forms, they can also grow with cellulose, xylan, and xyloglucan. Functional genome analysis of two representative strains demonstrated the presence of several genes coding for extracellular endo-beta-1,4-mannanase from the GH5_7 and 5_8 subfamilies and the GH26 family of glycosyl hydrolases. Furthermore, a large spectrum of genes encoding other glycoside hydrolases that were potentially involved in the hydrolysis of cellulose and xylan were also identified in the genomes. A comparative genomics analysis also showed the presence of similar endo-beta-1,4-mannanase homologs in the cellulotrophic genera Natronobiforma and Halococcoides. Based on the unique physiological properties and the results of phylogenomic analysis, the novel mannan-utilizing halolarchaea are proposed to be classified into a new genus and species Natronoglomus mannanivorans gen. nov., sp. nov. with the type strain AArc-m2/3/4 (=JCM 34861=UQM 41565). ...
phylogenomic analysis placed the isolates into a separate lineage of the new genus level within the family Natrialbaceae of the class Halobacteria. The strains are moderate alkaliphiles, extremely halophilic, and aerobic saccharolytics. In addition to the three beta-mannan forms, they can also grow with cellulose, xylan, and xyloglucan. Functional genome analysis of two representative strains demonstrated the presence of several genes coding for extracellular endo-beta-1,4-mannanase from the GH5_7 and 5_8 subfamilies and the GH26 family of glycosyl hydrolases. Furthermore, a large spectrum of genes encoding other glycoside hydrolases that were potentially involved in the hydrolysis of cellulose and xylan were also identified in the genomes. A comparative genomics analysis also showed the presence of similar endo-beta-1,4-mannanase homologs in the cellulotrophic genera Natronobiforma and Halococcoides. Based on the unique physiological properties and the results of phylogenomic analysis, the novel mannan-utilizing halolarchaea are proposed to be classified into a new genus and species Natronoglomus mannanivorans gen. nov., sp. nov. with the type strain AArc-m2/3/4 (=JCM 34861=UQM 41565).
phylogenomic analysis, and represent a distant novel species group in the genus Halapricum of the family Haloarculaceae.
The main phenotypic property of the novel isolates is the ability to hydrolyze and grow with the polysaccharides curdlan and pachyman. Such potential has, to date, not been seen in any other haloarchaea in pure cultures. The strains are obligately aerobic saccharolytics. Apart from the insoluble β-1,3-glucans, they utilized soluble α-glucans (starch, pullulan and glycogen) and a limited number of sugars. The major ether-bound polar phospholipids include PGP-Me and PG. The glyco- and sulfolipids were absent. The major respiratory menaquinone is MK-8:8. On the basis of their unique physiological properties and the results of phylogenomic analysis, the isolates are suggested to be classified into a novel species Halapricum hydrolyticum sp. nov. (type strain HArc-curdl5-1T = DSM 114193T = UQM 41587T). ...
phylogenomic analysis, and represent a distant novel species group in the genus Halapricum of the family Haloarculaceae.
The main phenotypic property of the novel isolates is the ability to hydrolyze and grow with the polysaccharides curdlan and pachyman. Such potential has, to date, not been seen in any other haloarchaea in pure cultures. The strains are obligately aerobic saccharolytics. Apart from the insoluble β-1,3-glucans, they utilized soluble α-glucans (starch, pullulan and glycogen) and a limited number of sugars. The major ether-bound polar phospholipids include PGP-Me and PG. The glyco- and sulfolipids were absent. The major respiratory menaquinone is MK-8:8. On the basis of their unique physiological properties and the results of phylogenomic analysis, the isolates are suggested to be classified into a novel species Halapricum hydrolyticum sp. nov. (type strain HArc-curdl5-1T = DSM 114193T = UQM 41587T).
The authors regret that there is a mistake in the strain collection number: instead of UQ 51487 it should be UQM 51487 in the protologue Table 3 of their paper. The corrected protologue Table is presented below.
Two heterotrophic bacteroidetes strains were isolated as satellites from autotrophic enrichments inoculated with samples from hypersaline soda lakes in southwestern Siberia. Strain Z-1702 T is an obligate anaerobic fermentative saccharolytic bacterium from an iron-reducing enrichment culture, while Ca. Cyclonatronum proteinivorum Omega T is an obligate aerobic proteolytic microorganism from a cyanobacterial enrichment. Cells of isolated bacteria are characterized by highly variable morphology. Both strains are chloride-independent moderate salt-tolerant obligate alkaliphiles and mesophiles. Strain Z-1702 T ferments glucose, maltose, fructose, mannose, sorbose, galactose, cellobiose, N-acetyl-glucosamine and alpha-glucans, including starch, glycogen, dextrin, and pullulan. Strain Omega T is strictly proteolytic utilizing a range of proteins and peptones. The main polar lipid fatty acid in both strains is iso-C 15:0, while other major components are various C 16 and C 17 isomers. According to pairwise sequence alignments using BLAST Gracilimonas was the nearest cultured relative to both strains (<90% of 16S rRNA gene sequence identity). Phylogenetic analysis placed strain Z-1702 T and strain Omega T as two different genera in a deep-branching clade of the new family level within the order Balneolales with genus. Based on physiological characteristics and phylogenetic position of strain Z-1702 T it was proposed to represent a novel genus and species Natronogracilivirga saccharolityca gen. nov., sp. nov. (= DSMZ 109061 T =JCM 32930 T =VKM B 3262 T). Furthermore, phylogenetic and phenotypic parameters of N. saccharolityca and C. proteinivorum gen. nov., sp. nov., strain Omega T (=JCM 31662 T, =UNIQEM U979 T), make it possible to include them into a new family with a proposed designation Cyclonatronaceae fam. nov.
Cellulose metabolism in halo(natrono)archaea
A comparative genomics study
a dominant group of aerobic heterotrophic prokaryotic communities in
salt-saturated habitats, such as salt lakes and solar salterns. Most of the
pure cultures of haloarchaea were enriched, isolated, and cultivated on
rich soluble substrates such as amino acids, peptides or simple sugars.
So far, the evidences on the capability of haloarchaea to use different
polysaccharides as growth substrates remained scarce. However, it is
becoming increasingly obvious that these archaea can also actively participate
in mineralization of complex biopolymers, in particular cellulose and chitin–
two dominant biomass polysaccharides on the planet. Here we used an
array of commercially available homo- and heteropolysaccharides to enrich
hydrolytic haloarchaea from hypersaline salt lakes with neutral pH and from
alkaline soda lakes. This resulted in isolation of a range of halo- and natronoarchaea, respectively, belonging to already described taxa as well as several new genus-level lineages. In some cases, the isolates enriched with different polysaccharides happened to be closely related, thus representing generalistic ecotype, while the others were narrow specialists. In general, soda lakes yielded a broader range of polysaccharide-utilizing specialists in comparison to neutral salt lakes. The results demonstrated a significant diversity of halo(natrono)archaea with a previously unrecognized potential for utilization
of a broad range of natural polysaccharides in hypersaline habitats. ...
a dominant group of aerobic heterotrophic prokaryotic communities in
salt-saturated habitats, such as salt lakes and solar salterns. Most of the
pure cultures of haloarchaea were enriched, isolated, and cultivated on
rich soluble substrates such as amino acids, peptides or simple sugars.
So far, the evidences on the capability of haloarchaea to use different
polysaccharides as growth substrates remained scarce. However, it is
becoming increasingly obvious that these archaea can also actively participate
in mineralization of complex biopolymers, in particular cellulose and chitin–
two dominant biomass polysaccharides on the planet. Here we used an
array of commercially available homo- and heteropolysaccharides to enrich
hydrolytic haloarchaea from hypersaline salt lakes with neutral pH and from
alkaline soda lakes. This resulted in isolation of a range of halo- and natronoarchaea, respectively, belonging to already described taxa as well as several new genus-level lineages. In some cases, the isolates enriched with different polysaccharides happened to be closely related, thus representing generalistic ecotype, while the others were narrow specialists. In general, soda lakes yielded a broader range of polysaccharide-utilizing specialists in comparison to neutral salt lakes. The results demonstrated a significant diversity of halo(natrono)archaea with a previously unrecognized potential for utilization
of a broad range of natural polysaccharides in hypersaline habitats.
Several pure cultures of alkaliphilic haloaloarchaea were enriched and isolated from hypersaline soda lakes in southwestern Siberia using amylopectin and fructans as substrates. Phylogenomic analysis placed the isolates into two distinct groups within the class Halobacteria. Four isolates forming group 1 were closely related to a recently described Natranaeroarchaeum sulfidigenes and the other three strains forming group 2 represent a novel genus-level phylogenetic lineage. All isolates are saccharolytic archaea growing with various starch-like alpha-glucans including soluble starch, amylopectin, dextrin, glycogen, pullulane and cyclodextrin. In addition, group 1 can use levan while group 2 – inulin (plant storage beta-fructans). Group 1 strains can also grow anaerobically with either glucose or maltose using elemental sulfur as the electron acceptor. Both groups are moderately alkaliphilic with a pH range for growth from 7.2 to 9.3 (optimum between 8.0–8.8) and low Mg-demanding extreme halophiles growing optimally at 4 M total Na+. The major respiratory menaquinone is MK-8:8 and the core biphytanyl lipids are dominated by archaeol (C20-C20) and a less abundant extended archaeol (C20-C25) with PG and PGP-Me as polar groups. The four isolates of group 1 are suggested to be classified into a new species as Natranaeroarchaeum aerophilus sp. nov. (type strain AArc-St1-1T = JCM 32519T = UQM 41458T). The three isolates of group 2 are proposed to form a new genus and species for which the name Natronocalculus amylovorans gen. nov., sp. nov. is suggested (type strain AArc-St2T = JCM 32475T = UQM 41459T).
A haloalkaliphilic hydrolytic actinobacterium, strain ACPA22T, was enriched and isolated in pure culture from saline alkaline soil (soda solonchak) in northeastern Mongolia. The isolate was facultatively alkaliphilic, growing at pH 6.5–10.5 (optimum at 7.3–9.0) and highly salt-tolerant, tolerating up to 3 M total Na+ as carbonates. The hydrolytic nature of ACPA22T was confirmed by two different growth-dependent methods and by the presence of multiple glycosidase-encoding genes in the genome. The 16S rRNA gene-based phylogenetic analysis demonstrated that strain ACPA22T formed a deep-branching lineage within the family Glycomycetaceae, with the highest sequence similarity value to Glycomyces buryatensis 18T (92.1%) and Salininema pro-teolyticum Miq-4T (91.8%). The average amino acid identity values (56.1–61.5%) between ACPA22T and other Glycomycetaceae members with available genomes did not exceed the threshold reported for different genera. The cell wall of ACPA22T contained meso-diaminopimelic acid, glycine, glutamic acid and alanine in a molar ratio, characteristic of the peptidoglycan type A1γ'. The whole-cell sugars included mannose, galactose, arabinose, ribose and xylose. The major menaquinones were MK-10(Н4) and MK-11(Н4). The identified polar lipids were represented by phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylg-lycerol, phosphatidylinositol and phosphatidylinositol mannosides. In addition, the strain had a few unidentified characteristic polar lipids, including an amine-containing phospholipid with chromatographic mobility similar to that of phosphatidylinositol. The polar lipid fatty acids were dominated by anteiso-C17:0 and iso-C16:0. The genome included a chromosome of 3.94 Mbp (G+C content 61.5 mol%) encoding 3285 proteins and two plasmids of 59.8 and 14.8 kBp. Based on the data obtained in this study, a new genus and species, Natronoglycomyces albus gen. nov., sp. nov, is proposed with the type strain ACPA22T (=DSM 106290T=VKM Ac-2771T).
An extremely halophilic euryarchaeon, strain HArcel1T, was enriched and isolated in pure culture from the surface brines and sediments of hypersaline athalassic lakes in the Kulunda Steppe (Altai region, Russia) using amorphous cellulose as the growth substrate. The colonies of HArcel1T are pale-orange, and form large zones of cellulose hydrolysis around them. The cells are non-motile cocci of variable size with a thin monolayer cell wall. The isolate is an obligate aerobic heterotroph capable of growth with only three substrates: various forms of insoluble cellulose, xylan and cellobiose. Strain HArcel1T is an extremely halophilic neutrophile, growing within the salinity range from 2.5 to 5 M NaCl (optimum at 3.5-4 M). The core archaeal lipids are dominated by C20-C20 and C25-C20 dialkyl glycerol ethers, in approximately 6:1 proportion. The 16S rRNA and rpoB' gene analysis indicated that HArcel1T forms a separate lineage within the family Haloarculaceae, order Halobacteriales, with the genera Halorhabdus and Halopricus as closest relatives. On the basis of the unique phenotypic properties and distinct phylogeny of the 16S rRNA and rpoB' genes, it is suggested that strain HArcel1T is classified into a new genus and species Halococcoides cellulosivorans gen. nov., sp. nov. (JCM 31941T=UNIQEM U975T).
Two groups of alkaliphilic haloarchaea from hypersaline alkaline lakes in Central Asia, Egypt and North America were enriched and isolated in pure culture using chitin as growth substrate. These cultures, termed AArcht, were divided into two groups: group 1 which includes eleven isolates from highly alkaline soda lakes and group 2 which contains a single isolate obtained from the alkaline hypersaline Searles Lake. The colonies of chitin-utilizing natronoarchaea were red-pigmented and surrounded by large zones of chitin hydrolysis. The free cells of both groups were mostly flat nonmotile rods, while the cells that attached to chitin or formed colonies on chitin plates were mostly coccoid. The isolates are obligate aerobic saccharolytic archaea utilizing chitin and chitosane (less actively) as the only sugar polymers as well as a few hexoses as their carbon and energy source. Both groups are extremely halophilic, growing optimally at 3.5–4 M total Na+, but they differ in their pH profiles: the main group 1 isolates are obligately alkaliphilic, while the single group 2 strain (AArcht-SlT) is alkalitolerant. The core archaeal lipids in both groups are dominated by C20–C20 and C20–C25 dialkyl glycerol ethers (DGE) in approximately equal proportion. Phylogenetic analysis indicated that the isolates form an independent genus-level lineage within the family Natrialbaceae with 3 species-level subgroups. The available genomes of the closest cultured relatives of the AArcht strains, belonging to the genera Natrialba and Halopiger, do not encode any chitinase-related genes. On the basis of their unique phenotypic properties and distinct phylogeny, we suggest that the obligate alkaliphilic AArcht isolates (group 1) with an identical phenotype are classified into a new genus and species Natrarchaeobius chitinivorans gen. nov., sp. nov., with strain AArcht4T as the type strain (JCM 32476T = UNIQEM U966T), while the facultatively alkaliphilic strain AArcht-SlT (group 2) — as a new species Natrarchaeobius halalkaliphilus sp. nov. (JCM 32477T = UNIQEM U969T).
n. Natronobiforma the dimorphic natronoarchaeon. The genus Natronobiforma, classified within the family Natrialbaceae, order Natrialbales, in the class
Halobacteria, currently consists of a single species, Natronobiforma cellulositropha. It is a moderately alkaliphilic, obligately aerobic, extreme halophile, forming pink colonies with large clearance zones on plates
containing amorphous cellulose. The cells are pleomorphic flat motile rods or nonmotile coccoid cells. Multiple strains classified within this genus were isolated
from alkaline hypersaline lakes in different locations. They grow optimally on insoluble native celluloses. Xylan, β-mannan, cellobiose, and maltose can also be used as carbon and energy sources. Other organic compounds used by most members of the Halobacteria do not support growth. DNA G+C content (mol%): 65.4–65.5 (genome sequences).
Type species: Natronobiforma cellulositropha Sorokin et al. 2019, VL187. ...
n. Natronobiforma the dimorphic natronoarchaeon. The genus Natronobiforma, classified within the family Natrialbaceae, order Natrialbales, in the class
Halobacteria, currently consists of a single species, Natronobiforma cellulositropha. It is a moderately alkaliphilic, obligately aerobic, extreme halophile, forming pink colonies with large clearance zones on plates
containing amorphous cellulose. The cells are pleomorphic flat motile rods or nonmotile coccoid cells. Multiple strains classified within this genus were isolated
from alkaline hypersaline lakes in different locations. They grow optimally on insoluble native celluloses. Xylan, β-mannan, cellobiose, and maltose can also be used as carbon and energy sources. Other organic compounds used by most members of the Halobacteria do not support growth. DNA G+C content (mol%): 65.4–65.5 (genome sequences).
Type species: Natronobiforma cellulositropha Sorokin et al. 2019, VL187.
Protologue Table 4 describing properties of Natrachaeobius chitinivorans gen. nov., sp. nov., and Natrarchaeobius haloalkaliphilus sp. nov. has been amended with an extra line designating Natrarchaeobius chitinivoransas the type species of the genus Natrarchaeobius, in accordance to the Rule 20a of the ICNPA.
This is a corrigendum to the protologue Table 3 describing properties of Natronobiforma cellulositropha gen. nov sp. nov. 1. The species name “cellulotropha” was corrected to “cellulositropha” in the (SPNA), (SPEP) and TITL lines.2. The author name “Damstéd” in the (AUT) was corrected to “Damsté”.3. The word “neutral” in the (GETY/SPTY) was corrected to “neut”.4. Some of the relevant values have been added to both genus and species columns.
Novel hydrolases from hot and other extreme environments showing appropriate performance and/or novel functionalities and new approaches for their systematic screening are of great interest for developing new processes, for improving safety, health and environment issues. Existing processes could benefit as well from their properties. The workflow, based on the HotZyme project, describes a multitude of technologies and their integration from discovery to application, providing new tools for discovering, identifying and characterizing more novel thermostable hydrolases with desired functions from hot terrestrial and marine environments. To this end, hot springs worldwide were mined, resulting in hundreds of environmental samples and thousands of enrichment cultures growing on polymeric substrates of industrial interest. Using high-throughput sequencing and bioinformatics, 15 hot spring metagenomes, as well as several sequenced isolate genomes and transcriptomes were obtained. To facilitate the discovery of novel hydrolases, the annotation platform Anastasia and a whole-cell bioreporter-based functional screening method were developed. Sequence-based screening and functional screening together resulted in about 100 potentially new hydrolases of which more than a dozen have been characterized comprehensively from a biochemical and structural perspective. The characterized hydrolases include thermostable carboxylesterases, enol lactonases, quorum sensing lactonases, gluconolactonases, epoxide hydrolases, and cellulases. Apart from these novel thermostable hydrolases, the project generated an enormous amount of samples and data, thereby allowing the future discovery of even more novel enzymes.
Stable development of a heterotrophic bacterial satellite with a peculiar cell morphology has been observed in several enrichment cultures of haloalkaliphilic benthic filamentous cyanobacteria from a hypersaline soda lake in Kulunda Steppe (Altai, Russia). The organism was isolated in pure culture (strain Omega) using sonicated cyanobacterial cells as substrate and it was identified as a deep phylogenetic lineage within the recently proposed phylum Balneolaeota. It is an obligately aerobic heterotroph utilizing proteins and peptides for growth. The cell morphology significantly varied from semicircles to long filaments depending on the growth conditions. The cultures are red-orange colored due to a presence of carotenoids. The isolate is an obligate alkaliphile with a pH range for growth from 8.5 to 10.5 (optimum at 9.5-10) and moderately salt-tolerant with a range from 0.3 to 3 M total Na+ (optimum at 1 M). The genome analysis of strain Omega demonstrated a presence of gene, encoding a proteorhodopsin forming a separate branch in the sodium-translocating proteorhodopsin family. Experiments with washed cells of Omega confirmed light-dependent sodium export. A possible physiological role of the sodium proteorhodopsin in strain Omega is discussed. Phylogenomic analysis demostrated that strain Omega forms an deep, independent branch of a new genus and family level within a recently established phylum Balneolaeota.
Six strains of extremely halophilic and alkaliphilic euryarchaea were enriched and isolated in pure culture from surface brines and sediments of hypersaline alkaline lakes in various geographical locations with various forms of insoluble cellulose as growth substrate. The cells are mostly flat motile rods with a thin monolayer cell wall while growing on cellobiose. In contrast, the cells growing with cellulose are mostly nonmotile cocci covered with a thick external EPS layer. The isolates, designated AArcel, are obligate aerobic heterotrophs with a narrow substrate spectrum. All strains can use insoluble celluloses, cellobiose, a few soluble glucans and xylan as their carbon and energy source. They are extreme halophiles, growing within the range from 2.5 to 4.8 M total Na+ (optimum at 4 M) and obligate alkaliphiles, with the pH range for growth from 7.5 to 9.9 (optimum at 8.5–9). The core archaeal lipids of strain AArcel5T were dominated by C20–C20 dialkyl glycerol ether (DGE) (i.e. archaeol) and C20–C25 DGE in nearly equal proportion. The 16S rRNA gene analysis indicated that all six isolates belong to a single genomic species mostly related to the genera Saliphagus-Natribaculum-Halovarius. Taking together a substantial phenotypic difference of the new isolates from the closest relatives and the phylogenetic distance, it is concluded that the AArcel group represents a novel genus-level branch within the family Natrialbaceae for which the name Natronobiforma cellulositropha gen. nov., sp. nov. is proposed with AArcel5T as the type strain (JCM 31939T = UNIQEM U972T).
Hypersaline anoxic habitats harbour numerous novel uncultured archaea whose metabolic and ecological roles remain to be elucidated. Until recently, it was believed that energy generation via dissimilatory reduction of sulfur compounds is not functional at salt saturation conditions. Recent discovery of the strictly anaerobic acetotrophic Halanaeroarchaeum compels to change both this assumption and the traditional view on haloarchaea as aerobic heterotrophs. Here we report on isolation and characterization of a novel group of strictly anaerobic lithoheterotrophic haloarchaea, which we propose to classify as a new genus Halodesulfurarchaeum. Members of this previously unknown physiological group are capable of utilising formate or hydrogen as electron donors and elemental sulfur, thiosulfate or dimethylsulfoxide as electron acceptors. Using genome-wide proteomic analysis we have detected the full set of enzymes required for anaerobic respiration and analysed their substrate-specific expression. Such advanced metabolic plasticity and type of respiration, never seen before in haloarchaea, empower the wide distribution of Halodesulfurarchaeum in hypersaline inland lakes, solar salterns, lagoons and deep submarine anoxic brines. The discovery of this novel functional group of sulfur-respiring haloarchaea strengthens the evidence of their possible role in biogeochemical sulfur cycling linked to the terminal anaerobic carbon mineralisation in so far overlooked hypersaline anoxic habitats.
Two proteolytic bacterial strains, BSker2Tand BSker3T, were enriched from sediments of hypersaline alkaline lakes in Kulunda Steppe (Altai, Russia) with chicken feathers as substrate, followed by pure culture isolation on hypersaline alkaline media with casein. The cells were non-motile, filamentous, flexible rods. The isolates were obligately aerobic heterotrophs utilizing proteins and peptides as growth substrates. Both were obligate alkaliphiles, but differed in their pH optimum for growth: pH 9.5-9.8 for Bsker2Tand pH 8.5-8.8 for BSker3T. The salt range for growth of both isolates was between 2 and 4.5 M total Na+ with an optimum at 2.5-3 M. No organic osmolytes were detected in cells of BSker2T, but they accumulated high intracellular concentrations of K+. The polar lipid fatty acids were dominated by unsaturated C16 and C18 species. The 16S rRNA gene phylogeny indicated that both strains belong to the recently proposed phylum Rhodothermaeota. BSker2Tforms a novel genus-level branch, while BSker3Trepresents a novel species-level member in the genus Longimonas. On the basis of distinct phenotypic and genotypic properties, strain BSker2T(=JCM 31342T=UNIQEM U1009T) is proposed to be classified as a representative of a novel genus and species, Natronotalea proteinilyticagen. nov., sp. nov., and strain BSker3T(=JCM 31343T=UNIQEM U1010T) as a representative of a novel species, Longimonas haloalkaliphila sp. nov.