Publications by authors named "Svetlana N Dedysh"

92 Publications

Complete Genome Sequence of Paludibaculum fermentans P105, a Facultatively Anaerobic Acidobacterium Capable of Dissimilatory Fe(III) Reduction.

Microbiol Resour Announc 2021 Jan 7;10(1). Epub 2021 Jan 7.

Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia.

P105 is a facultatively anaerobic heterotroph of the phylum which is capable of dissimilatory Fe(III) reduction. This bacterium is a common inhabitant of wetlands and groundwater bodies. The finished genome of strain P105 is 9.53 Mb in size and contains multiple genes coding for membrane-bound multiheme cytochromes.
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http://dx.doi.org/10.1128/MRA.01313-20DOI Listing
January 2021

Methane-Oxidizing Communities in Lichen-Dominated Forested Tundra Are Composed Exclusively of High-Affinity USCα Methanotrophs.

Microorganisms 2020 Dec 21;8(12). Epub 2020 Dec 21.

Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33/2, Moscow 119071, Russia.

Upland soils of tundra function as a constant sink for atmospheric CH but the identity of methane oxidizers in these soils remains poorly understood. Methane uptake rates of -0.4 to -0.6 mg CH-C m day were determined by the static chamber method in a mildly acidic upland soil of the lichen-dominated forested tundra, North Siberia, Russia. The maximal CH oxidation activity was localized in an organic surface soil layer underlying the lichen cover. Molecular identification of methanotrophic bacteria based on retrieval of the gene revealed Upland Soil Cluster Alpha (USCα) as the only detectable methanotroph group. Quantification of these gene fragments by means of specific qPCR assay detected ~10 gene copies g dry soil. The diversity was represented by seven closely related phylotypes; the most abundant phylotype displayed 97.5% identity to of Methyloaffinis lahnbergensis. Further analysis of prokaryote diversity in this soil did not reveal 16S rRNA gene fragments from well-studied methanotrophs of the order and the family . The largest group of reads (~4% of all bacterial 16S rRNA gene fragments) that could potentially belong to methanotrophs was classified as uncultivated bacteria. These reads displayed 96-100 and 95-98% sequence similarity to 16S rRNA gene of Methyloaffinis lahnbergensis and " MG08, respectively, and were represented by eight species-level operational taxonomic units (OTUs), two of which were highly abundant. These identification results characterize subarctic upland soils, which are exposed to atmospheric methane concentrations only, as a unique habitat colonized mostly by USCα methanotrophs.
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http://dx.doi.org/10.3390/microorganisms8122047DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7766663PMC
December 2020

Wide distribution of Phycisphaera-like planctomycetes from WD2101 soil group in peatlands and genome analysis of the first cultivated representative.

Environ Microbiol 2021 Mar 22;23(3):1510-1526. Epub 2020 Dec 22.

Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia.

Phycisphaera-like WD2101 'soil group' is one of the as-yet-uncultivated phylogenetic clades within the phylum Planctomycetes. Members of this clade are commonly detected in various terrestrial habitats. This study shows that WD2101 represented one of the major planctomycete groups in 10 boreal peatlands, comprising up to 76% and 36% of all Planctomycetes-affiliated 16S rRNA gene reads in raised bogs and eutrophic fens respectively. These types of peatlands displayed clearly distinct intra-group diversity of WD2101-affiliated planctomycetes. The first isolate of this enigmatic planctomycete group, strain M1803, was obtained from a humic lake surrounded by Sphagnum peat bogs. Strain M1803 displayed 89.2% 16S rRNA gene similarity to Tepidisphaera mucosa and was represented by motile cocci that divided by binary fission and grew under micro-oxic conditions. The complete 7.19 Mb genome of strain M1803 contained an array of genes encoding Planctomycetal type bacterial microcompartment organelle likely involved in l-rhamnose metabolism, suggesting participation of M1803-like planctomycetes in polysaccharide degradation in peatlands. The corresponding cellular microcompartments were revealed in ultrathin cell sections. Strain M1803 was classified as a novel genus and species, Humisphaera borealis gen. nov., sp. nov., affiliated with the formerly recognized WD2101 'soil group'.
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http://dx.doi.org/10.1111/1462-2920.15360DOI Listing
March 2021

Frigoriglobus tundricola gen. nov., sp. nov., a psychrotolerant cellulolytic planctomycete of the family Gemmataceae from a littoral tundra wetland.

Syst Appl Microbiol 2020 Sep 30;43(5):126129. Epub 2020 Jul 30.

Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia. Electronic address:

Planctomycetes of the family Gemmataceae are characterized by large genome sizes and cosmopolitan distribution in freshwater and terrestrial environments but their ecological functions remain poorly understood. In this study, we characterized a novel representative of this family, strain PL17, which was isolated from a littoral tundra wetland and was capable of growth on xylan and cellulose. Cells of this isolate were represented by pink-pigmented spheres that multiplied by budding and occurred singly or in short chains and aggregates. Strain PL17 was obligately aerobic, mildly acidophilic chemoorganotrophic bacterium, which displayed good tolerance of low temperatures. The major fatty acids were C, C, and βOH-C; the major polar lipid was trimethylornithine. The genome of strain PL17 consisted of a 9.83 Mb chromosome and a 24.69kb plasmid. The G+C contents of the chromosomal and plasmid DNA were 67.4 and 62.3mol%, respectively. Over 8900 potential protein-coding genes were identified in the genome including a putative cellulase that contains a domain from the GH5 family of glycoside hydrolases. The genome of strain PL17 contained one linked and one unlinked rRNA operons with 16S rRNA gene sequences displaying 94.5% similarity to that in Gemmata obscuriglobus UQM2246. Based on the results of comparative phenotypic, chemotaxonomic and phylogenomic analyses, we propose to classify strain PL17 (= CECT 9407=VKM B-3467) as representing a novel genus and species of the family Gemmataceae, Frigoriglobus tundricola gen. nov., sp. nov.
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http://dx.doi.org/10.1016/j.syapm.2020.126129DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7534041PMC
September 2020

Pan-Genome-Based Analysis as a Framework for Demarcating Two Closely Related Methanotroph Genera and .

Microorganisms 2020 May 20;8(5). Epub 2020 May 20.

Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia.

The and are two of the five genera that were included in the first taxonomic framework of methanotrophic bacteria created half a century ago. Members of both genera are widely distributed in various environments and play a key role in reducing methane fluxes from soils and wetlands. The original separation of these methanotrophs in two distinct genera was based mainly on their differences in cell morphology. Further comparative studies that explored various single-gene-based phylogenies suggested the monophyletic nature of each of these genera. Current availability of genome sequences from members of the / clade opens the possibility for in-depth comparison of the genomic potentials of these methanotrophs. Here, we report the finished genome sequence of heyeri H2 and compare it to 23 currently available genomes of and species. The phylogenomic analysis confirmed that members of these genera form two separate clades. The / pan-genome core comprised 1,173 genes, with the accessory genome containing 4,941 and 11,192 genes in the shell and the cloud, respectively. Major differences between the genome-encoded environmental traits of these methanotrophs include a variety of enzymes for methane oxidation and dinitrogen fixation as well as genomic determinants for cell motility and photosynthesis.
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http://dx.doi.org/10.3390/microorganisms8050768DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7285482PMC
May 2020

Closely Located but Totally Distinct: Highly Contrasting Prokaryotic Diversity Patterns in Raised Bogs and Eutrophic Fens.

Microorganisms 2020 Mar 29;8(4). Epub 2020 Mar 29.

Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia.

Large areas in Northern Russia are covered by extensive mires, which represent a complex mosaic of ombrotrophic raised bogs, minerotrophic and eutrophic fens, all in a close proximity to each other. In this paper, we compared microbial diversity patterns in the surface peat layers of the neighbouring raised bogs and eutrophic fens that are located within two geographically remote mire sites in Vologda region using 16S rRNA gene sequencing. Regardless of location, the microbial communities in raised bogs were highly similar to each other but were clearly distinct from those in eutrophic fens. Bogs were dominated by the (30%-40% of total 16S rRNA gene reads), which belong to the orders and . Other bog-specific bacteria included the -like group WD2101 and the families and of the , orders and of the and a particular group of alphaproteobacteria within the . In contrast, fens hosted -affiliated , - and -affiliated , , uncultivated group OM190 of the and several groups of betaproteobacteria. The were detected in both types of wetlands but their relative abundance was higher in fens. A number of key parameters that define the distribution of particular bacterial groups in mires were identified.
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http://dx.doi.org/10.3390/microorganisms8040484DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7232223PMC
March 2020

Linking ecology and systematics of acidobacteria: Distinct habitat preferences of the Acidobacteriia and Blastocatellia in tundra soils.

PLoS One 2020 17;15(3):e0230157. Epub 2020 Mar 17.

Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia.

The Acidobacteria is one of the major bacterial phyla in soils and peatlands. The currently explored diversity within this phylum is assigned to 15 class-level units, five of which contain described members. The ecologically relevant traits of acidobacteria from different classes remain poorly understood. Here, we compared the patterns of acidobacterial diversity in sandy soils of tundra, along a gradient of increasing vegetation-unfixed aeolian sand, semi-fixed surfaces with mosses and lichens, and mature soil under fully developed plant cover. The Acidobacteria-affiliated 16S rRNA gene sequences retrieved from these soils comprised 11 to 33% of total bacterial reads and belonged mostly to members of the classes Acidobacteriia and Blastocatellia, which displayed opposite habitat preferences. The relative abundance of the Blastocatellia was maximal in unfixed sands and declined in soils of vegetated plots, showing positive correlation with soil pH and negative correlation with carbon and nitrogen availability. An opposite tendency was characteristic for the Acidobacteriia. Most Blastocatellia-affiliated reads belonged to as-yet-undescribed members of the family Arenimicrobiaceae, which appears to be characteristic for dry, depleted in organic matter soil habitats. The pool of Acidobacteriia-affiliated sequences, apart from Acidobacteriaceae- and Bryobacteraceae-related reads, had a large proportion of sequences from as-yet-undescribed families, which seem to specialize in degrading plant-derived organic matter. This analysis reveals sandy soils of tundra as a source of novel acidobacterial diversity and provides an insight into the ecological preferences of different taxonomic groups within this phylum.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0230157PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7077872PMC
June 2020

Lacipirellula parvula gen. nov., sp. nov., representing a lineage of planctomycetes widespread in low-oxygen habitats, description of the family Lacipirellulaceae fam. nov. and proposal of the orders Pirellulales ord. nov., Gemmatales ord. nov. and Isosphaerales ord. nov.

Syst Appl Microbiol 2020 Jan 19;43(1):126050. Epub 2019 Dec 19.

Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia.

Pirellula-like planctomycetes are ubiquitous aquatic bacteria, which are often detected in anoxic or micro-oxic habitats. By contrast, the taxonomically described representatives of these bacteria, with very few exceptions, are strict aerobes. Here, we report the isolation and characterization of the facultatively anaerobic planctomycete, strain PX69, which was isolated from a boreal lake. Its 16S rRNA gene sequence is affiliated with the Pirellula-related Pir4 clade, which is dominated by environmental sequences retrieved from a variety of low-oxygen habitats. Strain PX69 was represented by ellipsoidal cells that multiplied by budding and grew on sugars, some polysaccharides and glycerol. Anaerobic growth occurred by means of fermentation. Strain PX69 grew at pH 5.5-7.5 and at temperatures between 10 and 30°C. The major fatty acids were C18:1ω9c, C16:0 and C16:1ω7c; the major intact polar lipid was dimethylphosphatidylethanolamine. The complete genome of strain PX69 was 6.92Mb in size; DNA G+C content was 61.7mol%. Among characterized planctomycetes, the highest 16S rRNA gene similarity (90.4%) was observed with 'Bythopirellula goksoyri' Pr1d, a planctomycete from deep-sea sediments. We propose to classify PX69 as a novel genus and species, Lacipirellula parvula gen. nov., sp. nov.; the type strain is strain PX69 (=KCTC 72398=CECT 9826=VKM B-3335). This genus is placed in a novel family, Lacipirellulaceae fam. nov., which belongs to the order Pirellulales ord. nov. Based on the results of comparative genome analysis, we also suggest establishment of the orders Gemmatales ord. nov. and Isosphaerales ord. nov. as well as an emendation of the order Planctomycetales.
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http://dx.doi.org/10.1016/j.syapm.2019.126050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6995999PMC
January 2020

Thriving in Wetlands: Ecophysiology of the Spiral-Shaped Methanotroph as Revealed by the Complete Genome Sequence.

Microorganisms 2019 Dec 11;7(12). Epub 2019 Dec 11.

Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia.

Methylospira mobilis is a recently described spiral-shaped, micro-aerobic methanotroph, which inhabits northern freshwater wetlands and sediments. Due to difficulties of cultivation, it could not be obtained in a pure culture for a long time. Here, we report on the successful isolation of strain Shm1, the first axenic culture of this unique methanotroph. The complete genome sequence obtained for strain Shm1 was 4.7 Mb in size and contained over 4800 potential protein-coding genes. The array of genes encoding C metabolic capabilities in strain Shm1 was highly similar to that in the closely related non-motile, moderately thermophilic methanotroph Methylococcus capsulatus Bath. The genomes of both methanotrophs encoded both low- and high-affinity oxidases, which allow their survival in a wide range of oxygen concentrations. The repertoire of signal transduction systems encoded in the genome of strain Shm1, however, by far exceeded that in Methylococcus capsulatus Bath but was comparable to those in other motile gammaproteobacterial methanotrophs. The complete set of motility genes, the presence of both the molybdenum-iron and vanadium-iron nitrogenases, as well as a large number of insertion sequences were also among the features, which define environmental adaptation of to water-saturated, micro-oxic, heterogeneous habitats depleted in available nitrogen.
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http://dx.doi.org/10.3390/microorganisms7120683DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6956133PMC
December 2019

gen. nov., sp. nov., a novel freshwater planctomycete with a giant genome from the family .

Int J Syst Evol Microbiol 2020 Feb;70(2):1240-1249

Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia.

The family accommodates aerobic, chemoorganotrophic planctomycetes, which inhabit various freshwater ecosystems, wetlands and soils. Here, we describe a novel member of this family, strain PX52, which was isolated from a boreal eutrophic lake in Northern Russia. This isolate formed pink-pigmented colonies and was represented by spherical cells that occurred singly, in pairs or aggregates and multiplied by budding. Daughter cells were highly motile. PX52 was an obligate aerobic chemoorganotroph, which utilized various sugars and some heteropolysaccharides. Growth occurred at pH 5.0-7.5 (optimum pH 6.5) and at temperatures between 10 and 30 °C (optimum 20-25 °C). The major fatty acids were Cɷ7c, C and βOH-C; the major intact polar lipid was trimethylornithine, and the quinone was MK-6. The complete genome of PX52 was 9.38 Mb in size and contained nearly 8000 potential protein-coding genes. Among those were genes encoding a wide repertoire of carbohydrate-active enzymes (CAZymes) including 33 glycoside hydrolases (GH) and 87 glycosyltransferases (GT) affiliated with 17 and 12 CAZy families, respectively. DNA G+C content was 65.6 mol%. PX52 displayed only 86.0-89.8 % 16S rRNA gene sequence similarity to taxonomically described planctomycetes and differed from them by a number of phenotypic characteristics and by fatty acid composition. We, therefore, propose to classify it as representing a novel genus and species, gen. nov., sp. nov. The type strain is strain PX52 (=KCTC 72397=VKM B-3275).
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http://dx.doi.org/10.1099/ijsem.0.003904DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7397252PMC
February 2020

100-year-old enigma solved: identification, genomic characterization and biogeography of the yet uncultured Planctomyces bekefii.

Environ Microbiol 2020 01 11;22(1):198-211. Epub 2019 Nov 11.

Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German, Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.

The first representative of the phylum Planctomycetes, Planctomyces bekefii, was described nearly one century ago. This morphologically conspicuous freshwater bacterium is a rare example of as-yet-uncultivated prokaryotes with validly published names and unknown identity. We report the results of molecular identification of this elusive bacterium, which was detected in a eutrophic boreal lake in Northern Russia. By using high-performance cell sorting, P. bekefii-like cell rosettes were selectively enriched from lake water. The retrieved 16S rRNA gene sequence was nearly identical to those in dozens of metagenomes assembled from freshwater lakes during cyanobacterial blooms and was phylogenetically placed within a large group of environmental sequences originating from various freshwater habitats worldwide. In contrast, 16S rRNA gene sequence similarity to all currently described members of the order Planctomycetales was only 83%-92%. The metagenome assembled for P. bekefii reached 43% genome coverage and showed the potential for degradation of peptides, pectins, and sulfated polysaccharides. Tracing the seasonal dynamics of P. bekefii by Illumina paired-end sequencing of 16S rRNA gene fragments and by fluorescence in situ hybridization revealed that these bacteria only transiently surpass the detection limit, with a characteristic population peak of up to 10 cells ml following cyanobacterial blooms.
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http://dx.doi.org/10.1111/1462-2920.14838DOI Listing
January 2020

Draft Genome Sequence of Methylocystis heyeri H2, a Methanotroph with Habitat-Specific Adaptations, Isolated from a Peatland Ecosystem.

Microbiol Resour Announc 2019 Jul 18;8(29). Epub 2019 Jul 18.

Winogradsky Institute of Microbiology, Research Center of Biotechnology RAS, Moscow, Russia.

H2 is an aerobic facultative methanotroph which was isolated from an acidic peat bog lake and is a common inhabitant of peatland ecosystems. This bacterium possesses two particulate methane monooxygenases with low and high affinity to methane and a number of genomic adaptations to acidic conditions.
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http://dx.doi.org/10.1128/MRA.00454-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6639610PMC
July 2019

Strain C50C1 Is a Novel Type Ib Gammaproteobacterial Methanotroph Adapted to Freshwater Environments.

mSphere 2019 06 5;4(3). Epub 2019 Jun 5.

Department of Microbiology, IWWR, Radboud University, Nijmegen, the Netherlands.

Methane-oxidizing microorganisms perform an important role in reducing emissions of the greenhouse gas methane to the atmosphere. To date, known bacterial methanotrophs belong to the , , and NC10 phyla. Within the phylum, they can be divided into type Ia, type Ib, and type II methanotrophs. Type Ia and type II are well represented by isolates. Contrastingly, the vast majority of type Ib methanotrophs have not been able to be cultivated so far. Here, we compared the distributions of type Ib lineages in different environments. Whereas the cultivated type Ib methanotrophs ( and ) are found in landfill and upland soils, lineages that are not represented by isolates are mostly dominant in freshwater environments, such as paddy fields and lake sediments. Thus, we observed a clear niche differentiation within type Ib methanotrophs. Our subsequent isolation attempts resulted in obtaining a pure culture of a novel type Ib methanotroph, tentatively named "" C50C1. Strain C50C1 was further characterized to be an obligate methanotroph, containing Cω9c as the major membrane phospholipid fatty acid, which has not been found in other methanotrophs. Genome analysis of strain C50C1 showed the presence of two operon copies and XoxF5-type methanol dehydrogenase in addition to MxaFI. The genome also contained genes involved in nitrogen and sulfur cycling, but it remains to be demonstrated if and how these help this type Ib methanotroph to adapt to fluctuating environmental conditions in freshwater ecosystems. Most of the methane produced on our planet gets naturally oxidized by a group of methanotrophic microorganisms before it reaches the atmosphere. These microorganisms are able to oxidize methane, both aerobically and anaerobically, and use it as their sole energy source. Although methanotrophs have been studied for more than a century, there are still many unknown and uncultivated groups prevalent in various ecosystems. This study focused on the diversity and adaptation of aerobic methane-oxidizing bacteria in different environments by comparing their phenotypic and genotypic properties. We used lab-scale microcosms to create a countergradient of oxygen and methane for preenrichment, followed by classical isolation techniques to obtain methane-oxidizing bacteria from a freshwater environment. This resulted in the discovery and isolation of a novel methanotroph with interesting physiological and genomic properties that could possibly make this bacterium able to cope with fluctuating environmental conditions.
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http://dx.doi.org/10.1128/mSphere.00631-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6553558PMC
June 2019

Complete Genome Sequence of the Aerobic Facultative Methanotroph Methylocella tundrae Strain T4.

Microbiol Resour Announc 2019 May 16;8(20). Epub 2019 May 16.

School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom.

T4 is a facultative aerobic methanotroph which was isolated from an acidic tundra wetland and possesses only a soluble methane monooxygenase. The complete genome, which includes two megaplasmids, was sequenced using a combination of Illumina and Nanopore technologies. One of the megaplasmids carries a propane monooxygenase gene cluster.
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http://dx.doi.org/10.1128/MRA.00286-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6522787PMC
May 2019

Fatty Acid and Hopanoid Adaption to Cold in the Methanotroph .

Front Microbiol 2019 5;10:589. Epub 2019 Apr 5.

Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, and Utrecht University, Texel, Netherlands.

Three strains of aerobic psychrotolerant methanotrophic bacteria , isolated from geographically remote low-temperature environments in Northern Russia, were grown at three different growth temperatures, 20, 10 and 4°C and were found to be capable of oxidizing methane at all temperatures. The three strains adapted their membranes to decreasing growth temperature by increasing the percent of unsaturated fatty acid (FAs), both for the bulk and intact polar lipid (IPL)-bound FAs. Furthermore, the ratio of βOH-C to -C increased as growth temperature decreased. The IPL head group composition did not change as an adaption to temperature. The most notable hopanoid temperature adaptation of was an increase in unsaturated hopanols with decreasing temperature. As the growth temperature decreased from 20 to 4°C, the percent of unsaturated bulk-FAs increased from 79 to 89 % while the total percent of unsaturated hopanoids increased from 27 to 49 %. While increased FA unsaturation in response to decreased temperature is a commonly observed response in order to maintain the liquid-crystalline character of bacterial membranes, hopanoid unsaturation upon cold exposition has not previously been described. In order to investigate the mechanisms of both FA and hopanoid cold-adaption in we identified genes in the genome of that potentially code for FA and hopanoid desaturases. The unsaturation of hopanoids represents a novel membrane adaption to maintain homeostasis upon cold adaptation.
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http://dx.doi.org/10.3389/fmicb.2019.00589DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6460317PMC
April 2019

Widespread soil bacterium that oxidizes atmospheric methane.

Proc Natl Acad Sci U S A 2019 04 8;116(17):8515-8524. Epub 2019 Apr 8.

Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, 9037 Tromsoe, Norway;

The global atmospheric level of methane (CH), the second most important greenhouse gas, is currently increasing by ∼10 million tons per year. Microbial oxidation in unsaturated soils is the only known biological process that removes CH from the atmosphere, but so far, bacteria that can grow on atmospheric CH have eluded all cultivation efforts. In this study, we have isolated a pure culture of a bacterium, strain MG08 that grows on air at atmospheric concentrations of CH [1.86 parts per million volume (p.p.m.v.)]. This organism, named , is globally distributed in soils and closely related to uncultured members of the upland soil cluster α. CH oxidation experiments and C-single cell isotope analyses demonstrated that it oxidizes atmospheric CH aerobically and assimilates carbon from both CH and CO Its estimated specific affinity for CH (a) is the highest for any cultivated methanotroph. However, growth on ambient air was also confirmed for and , close relatives with a lower specific affinity for CH, suggesting that the ability to utilize atmospheric CH for growth is more widespread than previously believed. The closed genome of MG08 encodes a single particulate methane monooxygenase, the serine cycle for assimilation of carbon from CH and CO, and CO fixation via the recently postulated reductive glycine pathway. It also fixes dinitrogen and expresses the genes for a high-affinity hydrogenase and carbon monoxide dehydrogenase, suggesting that atmospheric CH oxidizers harvest additional energy from oxidation of the atmospheric trace gases carbon monoxide (0.2 p.p.m.v.) and hydrogen (0.5 p.p.m.v.).
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http://dx.doi.org/10.1073/pnas.1817812116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6486757PMC
April 2019

Granulicella sibirica sp. nov., a psychrotolerant acidobacterium isolated from an organic soil layer in forested tundra, West Siberia.

Int J Syst Evol Microbiol 2019 Apr 18;69(4):1195-1201. Epub 2019 Feb 18.

Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia.

An isolate of strictly aerobic, pale-pink pigmented bacteria, strain AF10, was obtained from an organic soil layer in forested tundra, Nadym region, West Siberia. Cells of strain AF10 were Gram-negative, non-motile rods that produced an amorphous extracellular polysaccharide-like substance and formed large cell aggregates in old cultures. These bacteria were chemoorganotrophic, mildly acidophilic and psychrotolerant, and grew between pH 3.5 and 7.0 (optimum, pH 4.5-5.0) and at temperatures between 2 and 30 °C. The preferred growth substrates were sugars and some polysaccharides. The major fatty acids were iso-C15 : 0, C16 : 0, C16 : 1∆9 c and 13,16-dimethyl octacosanedioic acid. The genome of strain AF10 was 6.14 Mbp in size and encoded a wide repertoire of carbohydrate active enzymes. The genomic DNA G+C content was 59.8 mol%. Phylogenetic analysis indicated that strain AF10 is a member of the genus Granulicella, family Acidobacteriaceae, but displays 94.4-98.0 % 16S rRNA gene sequence similarity to currently described members of this genus. On the basis of phenotypic, chemotaxonomic, phylogenetic and genomic analyses, we propose to classify this bacterium as representing a novel species of the genus Granulicella, Granulicellasibirica sp. nov. Strain AF10 (=DSM 104461=VKM B-3276) is the type strain.
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http://dx.doi.org/10.1099/ijsem.0.003290DOI Listing
April 2019

Hydrolytic Capabilities as a Key to Environmental Success: Chitinolytic and Cellulolytic From Acidic Sub-arctic Soils and Boreal Peatlands.

Front Microbiol 2018 19;9:2775. Epub 2018 Nov 19.

Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia.

Members of the are among the most efficient colonizers of acidic terrestrial habitats but the key traits underlying their environmental fitness remain to be understood. We analyzed indigenous assemblages of in a lichen-covered acidic (pH 4.1) soil of forested tundra dominated by uncultivated members of subdivision 1. An isolate of these bacteria with cells occurring within saccular chambers, strain SBC82, was obtained. The genome of strain SBC82 consists of a 7.11-Mb chromosome and four megaplasmids, and encodes a wide repertoire of enzymes involved in degradation of chitin, cellulose, and xylan. Among those, four secreted chitinases affiliated with the glycoside hydrolase family GH18 were identified. Strain SBC82 utilized amorphous chitin as a source of carbon and nitrogen; the respective enzyme activities were detected in tests with synthetic substrates. Chitinolytic capability was also confirmed for another phylogenetically related acidobacterium isolated from a peat bog, strain CCO287. As revealed by metatranscriptomic analysis of chitin-amended peat, 16S rRNA reads from these acidobacteria increased in response to chitin availability. Strains SBC82 and CCO287 were assigned to a novel genus and species, gen. nov., sp. nov. Members of this genus colonize acidic soils and peatlands and specialize in degrading complex polysaccharides.
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http://dx.doi.org/10.3389/fmicb.2018.02775DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6252331PMC
November 2018

Planctomycetes in boreal and subarctic wetlands: diversity patterns and potential ecological functions.

FEMS Microbiol Ecol 2019 02;95(2)

Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Leninsky prospect 33-2, Russia.

Members of the phylum Planctomycetes are common inhabitants of boreal Sphagnum peat bogs and lichen-dominated tundra wetlands. These bacteria colonize both oxic and anoxic peat layers and reach the population size of 107 cells per gram of wet peat. The 16S rRNA gene sequences from planctomycetes comprise 5%-22% of total 16S rRNA gene reads retrieved from peat samples. Most abundant peat-inhabiting planctomycetes affiliate with the families Isosphaeraceae and Gemmataceae, and with as-yet-uncultured Phycisphaera-related group WD2101. The use of metatranscriptomics to assess the functional role of planctomycetes in peatlands suggested the presence of versatile hydrolytic capabilities in these bacteria. This evidence was further confirmed by the analysis of genome-encoded capabilities of isolates from wetlands. Large (up to 12 Mbp) genomes of planctomycetes encode wide repertoires of carbohydrate-active enzymes including many unclassified putative glycoside hydrolases, which suggests the presence of extremely high glycolytic potential in these bacteria. Experimental tests confirmed their ability to grow on xylan, pectin, starch, lichenan, cellulose, chitin and polysaccharides of microbial origin. These results provide an insight into the ecological roles of peat-inhabiting planctomycetes and suggest their participation in degradation of plant-derived polymers, exoskeletons of peat-inhabiting arthropods as well as exopolysaccharides produced by other bacteria.
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http://dx.doi.org/10.1093/femsec/fiy227DOI Listing
February 2019

Refining the taxonomic structure of the phylum Acidobacteria.

Int J Syst Evol Microbiol 2018 Dec 16;68(12):3796-3806. Epub 2018 Oct 16.

2​Microbial Physiology Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.

The phylum Acidobacteria was created in 1997 in order to accommodate a large number of 16S rRNA gene sequences retrieved from various environments in cultivation-independent studies. At present, 26 major sequence clades or subdivisions (SDs) are recognized within this phylum, but only seven of them (SDs 1, 3, 4, 6, 8, 10 and 23) are commonly addressed as containing taxonomically described representatives. Here, we examined the currently explored diversity within the Acidobacteria using the candidate taxonomic unit circumscription system. Based on this analysis, 26 subdivisions were assigned to 15 class-level units, five of which contain described members. These include three earlier established classes Acidobacteriia, Blastocatellia and Holophagae, as well as two as-yet-undescribed groups defined by SDs 6 and 23, which we propose to name Vicinamibacteria classis nov. and Thermoanaerobaculia classis nov., respectively. The former assignment of Thermotomaculum hydrothermale to SD10 was found to be incorrect. This bacterium, therefore, was placed in the family Thermotomaculaceae fam. nov., order Thermotomaculales ord. nov. within the class Holophagae. We also propose establishing a number of high-level taxa to accommodate described representatives of SDs 3, 4, 6 and 23. The family Bryobacteraceae of SD3 Acidobacteria is placed in the order Bryobacterales ord. nov. within the taxonomic range of the class Acidobacteriia. The order Vicinamibacteriales ord. nov. is proposed to accommodate the family Vicinamibacteriaceae of SD6 Acidobacteria. Finally, the family Thermoanaerobaculaceae fam. nov., the order Thermoanaerobaculales ord. nov. are proposed to accommodate the only described representative of SD23, Thermoanaerobaculum aquaticum.
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http://dx.doi.org/10.1099/ijsem.0.003062DOI Listing
December 2018

Draft Genome Sequence of Methylovulum psychrotolerans Sph1, an Obligate Methanotroph from Low-Temperature Environments.

Genome Announc 2018 Mar 15;6(11). Epub 2018 Mar 15.

Winogradsky Institute of Microbiology, Research Center of Biotechnology RAS, Moscow, Russia

Sph1 is an aerobic, obligate methanotroph, which was isolated from cold methane seeps in West Siberia. This bacterium possesses only a particulate methane monooxygenase and is widely distributed in low-temperature environments. Strain Sph1 has the genomic potential for biosynthesis of hopanoids required for the maintenance of intracytoplasmic membranes.
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http://dx.doi.org/10.1128/genomeA.01488-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5854766PMC
March 2018

sp. nov., a member of the family from lichen-dominated forested tundra.

Int J Syst Evol Microbiol 2018 Apr;68(4):1265-1270

Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia.

An isolate of aerobic, Gram-stain-negative, rod-shaped, non-motile and light-pink pigmented bacteria, designated SBC68, was obtained from slightly decomposed thalli of the lichen sp. collected from the forested tundra of north-western Siberia. Cells of this isolate occurred singly, in pairs or in rosettes. These bacteria were acidophilic (optimum growth at pH 4.3-5.6) and mesophilic (optimum growth at 20-30 °C) but were also capable of growth at low temperatures, down to 7 °C. The preferred growth substrates were sugars, some organic acids and lichenan. The major fatty acids were iso-C, Cω7, C, Cω7, and 13,16-dimethyl octacosanedioic acid. The only quinone was MK-8, and the G+C content of the DNA was 54.7 mol%. SBC68 represented a member of the family ; the closest taxonomically described relatives were DHF9 and TPB6028 (97.2 and 97.1 % 16S rRNA gene sequence similarity, respectively). In 16S rRNA gene-based trees, SBC68 clustered together with species of the genus . However, this isolate differed from all previously described species of the genus with respect to the pink pigmentation, formation of cell rosettes and substrate utilization pattern. On the basis of these data, strain SBC68 should be considered to represent a novel species of acidobacteria, for which the name sp. nov. is proposed. The type strain is SBC68 (=DSM 104462=VKM B-3208).
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http://dx.doi.org/10.1099/ijsem.0.002663DOI Listing
April 2018

Unusual Genomic Traits Suggest Methylocystis bryophila S285 to Be Well Adapted for Life in Peatlands.

Genome Biol Evol 2018 02;10(2):623-628

Research Group Methanotrophic Bacteria and Environmental Genomics/Transcriptomics, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.

The genus Methylocystis belongs to the class Alphaproteobacteria, the family Methylocystaceae, and encompasses aerobic methanotrophic bacteria with the serine pathway of carbon assimilation. All Methylocystis species are able to fix dinitrogen and several members of this genus are also capable of using acetate or ethanol in the absence of methane, which explains their wide distribution in various habitats. One additional trait that enables their survival in the environment is possession of two methane-oxidizing isozymes, the conventional particulate methane monooxygenase (pMMO) with low-affinity to substrate (pMMO1) and the high-affinity enzyme (pMMO2). Here, we report the finished genome sequence of Methylocystis bryophila S285, a pMMO2-possessing methanotroph from a Sphagnum-dominated wetland, and compare it to the genome of Methylocystis sp. strain SC2, which is the first methanotroph with confirmed high-affinity methane oxidation potential. The complete genome of Methylocystis bryophila S285 consists of a 4.53 Mb chromosome and one plasmid, 175 kb in size. The genome encodes two types of particulate MMO (pMMO1 and pMMO2), soluble MMO and, in addition, contains a pxmABC-like gene cluster similar to that present in some gammaproteobacterial methanotrophs. The full set of genes related to the serine pathway, the tricarboxylic acid cycle as well as the ethylmalonyl-CoA pathway is present. In contrast to most described methanotrophs including Methylocystis sp. strain SC2, two different types of nitrogenases, that is, molybdenum-iron and vanadium-iron types, are encoded in the genome of strain S285. This unique combination of genome-based traits makes Methylocystis bryophila well adapted to the fluctuation of carbon and nitrogen sources in wetlands.
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http://dx.doi.org/10.1093/gbe/evy025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5808792PMC
February 2018

Genome Analysis of Fimbriiglobus ruber SP5, a Planctomycete with Confirmed Chitinolytic Capability.

Appl Environ Microbiol 2018 04 19;84(7). Epub 2018 Mar 19.

Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia

Members of the bacterial order have often been observed in associations with Crustacea. The ability to degrade chitin, however, has never been reported for any of the cultured planctomycetes although utilization of -acetylglucosamine (GlcNAc) as a sole carbon and nitrogen source is well recognized for these bacteria. Here, we demonstrate the chitinolytic capability of a member of the family , SP5, which was isolated from a peat bog. As revealed by metatranscriptomic analysis of chitin-amended peat, the pool of 16S rRNA reads from increased in response to chitin availability. Strain SP5 displayed only weak growth on amorphous chitin as a sole source of carbon but grew well with chitin as a source of nitrogen. The genome of SP5 is 12.364 Mb in size and is the largest among all currently determined planctomycete genomes. It encodes several enzymes putatively involved in chitin degradation, including two chitinases affiliated with the glycoside hydrolase (GH) family GH18, GH20 family β--acetylglucosaminidase, and the complete set of enzymes required for utilization of GlcNAc. The gene encoding one of the predicted chitinases was expressed in , and the endochitinase activity of the recombinant enzyme was confirmed. The genome also contains genes required for the assembly of type IV pili, which may be used to adhere to chitin and possibly other biopolymers. The ability to use chitin as a source of nitrogen is of special importance for planctomycetes that inhabit N-depleted ombrotrophic wetlands. Planctomycetes represent an important part of the microbial community in -dominated peatlands, but their potential functions in these ecosystems remain poorly understood. This study reports the presence of chitinolytic potential in one of the recently described peat-inhabiting members of the family , SP5 This planctomycete uses chitin, a major constituent of fungal cell walls and exoskeletons of peat-inhabiting arthropods, as a source of nitrogen in N-depleted ombrotrophic -dominated peatlands. This study reports the chitin-degrading capability of representatives of the order .
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http://dx.doi.org/10.1128/AEM.02645-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5861812PMC
April 2018

Distinct diversity patterns of Planctomycetes associated with the freshwater macrophyte Nuphar lutea (L.) Smith.

Antonie Van Leeuwenhoek 2018 Jun 17;111(6):811-823. Epub 2017 Nov 17.

Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia, 119071.

Members of the phylum Planctomycetes were originally described as freshwater bacteria. Most recent studies, however, address planctomycete diversity in other environments colonized by these microorganisms, including marine and terrestrial ecosystems. This study was initiated in order to revisit the specific patterns of planctomycete diversity in freshwater habitats using cultivation-independent approaches. The specific focus was made on planctomycetes associated with Nuphar lutea (L.) Smith, an emergent macrophyte with floating leaves, which is widespread in the Holarctic. As revealed by Illumina pair-end sequencing of 16S rRNA gene fragments, the bacterial assemblages colonizing floating leaf blades of waterlilies sampled from two different boreal lakes displayed similar composition but were distinct from the planktonic bacterial communities. 16S rRNA gene fragments from the Planctomycetes comprised 0.1-1 and 1-2.2% of total 16S rRNA gene reads retrieved from water samples and plant leaves, respectively. Planktonic planctomycetes were mostly affiliated with the class Planctomycetaceae (77-97%), while members of the Phycisphaerae were less abundant (3-22%). The relative proportion of the latter group, however, increased by 13-45% on leaves of N. lutea. The Phycisphaera-related group WD2101, Pirellula-like planctomycetes, as well as Gemmata, Zavarzinella and Planctopirus species were the most abundant groups of planctomycetes associated with plant leaves, which may suggest their involvement in the degradation of plant-derived organic matter.
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http://dx.doi.org/10.1007/s10482-017-0986-4DOI Listing
June 2018

Metatranscriptomics reveals the hydrolytic potential of peat-inhabiting Planctomycetes.

Antonie Van Leeuwenhoek 2018 Jun 13;111(6):801-809. Epub 2017 Nov 13.

Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave, Moscow, 119071, Russia.

Members of the phylum Planctomycetes are common inhabitants of northern Sphagnum-dominated wetlands. Evidence is accumulating that, in these environments, some planctomycetes may be involved in degrading polymeric organic matter. The experimental data, however, remain scarce due to the low number of characterized representatives of this phylum. In a previous study, we used metatranscriptomics to assess the activity response of peat-inhabiting microorganisms to biopolymers abundantly present in native peat. The community responses to cellulose, xylan, pectin, and chitin availability were analysed relative to unamended controls. Here, we re-analysed these metatranscriptomes and retrieved a total of 1,602,783 rRNA and 35,522 mRNA sequences affiliated with the Planctomycetes. Each of the four polymers induced specific planctomycete responses. These were most pronounced on chitin. The two groups with increased 16S rRNA transcript pools were Gemmata- and Phycisphaera-like planctomycetes. Among uncultivated members of the Planctomycetaceae, two increased transcript pools were detected in pectin-amended samples and belonged to Pirellula-like bacteria. The analysis of taxonomically assigned mRNA reads confirmed the specific response of Gemmata-related planctomycetes to chitin amendment suggesting the presence of chitinolytic capabilities in these bacteria.
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http://dx.doi.org/10.1007/s10482-017-0973-9DOI Listing
June 2018

Tundrisphaera lichenicola gen. nov., sp. nov., a psychrotolerant representative of the family Isosphaeraceae from lichen-dominated tundra soils.

Int J Syst Evol Microbiol 2017 Sep 22;67(9):3583-3589. Epub 2017 Aug 22.

Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia.

Two strains of aerobic, budding, pink-pigmented bacteria, P12T and P515, were isolated from a lichen-dominated peatland and a forested tundra soil of north-western Siberia, respectively. Cells of these isolates were represented by non-motile spheres that occurred singly or were arranged in short chains and aggregates. While growing on solid media, cells of strains P12T and P515 attached to the surface by means of holdfast-like appendages. These isolates were mildly acidophilic (optimum growth at pH 5.5-6.0), psychrotolerant bacteria, which displayed tolerance of low temperatures (4-15 °C), grew optimally at 15-22 °C and did not grow at temperatures above 28 °C. The preferred growth substrates were sugars and some heteropolysaccharides. The major fatty acids were C18 : 1ω9c, C16 : 0 and C14 : 0. Trimethylornithine lipid was the major polar lipid. The only quinone was MK-6, and the G+C content of the DNA was 61.2-62.2 mol%. Strains P12T and P515 possessed identical 16S rRNA gene sequences, which affiliated them with the family Isosphaeraceae, order Planctomycetales, and these displayed the highest similarity (93-94 %) to 16S rRNA gene sequences from members of the genus Singulisphaera. However, the signature fatty acid of species of the genus Singulisphaera, i.e. C18 : 2ω6c,12c, was absent in cells of strains P12T and P515. They also differed from members of the genus Singulisphaera by substrate utilization pattern and a number of physiological characteristics. Based on these data, the novel isolates should be considered as representing a novel genus and species of planctomycetes, for which the name Tundrisphaera lichenicola gen. nov., sp. nov, is proposed. The type strain is P12T (=LMG 29571T=VKM B-3044T).
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http://dx.doi.org/10.1099/ijsem.0.002172DOI Listing
September 2017

Pheno- and Genotyping of Hopanoid Production in .

Front Microbiol 2017 8;8:968. Epub 2017 Jun 8.

Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Utrecht UniversityDen Burg, Netherlands.

Hopanoids are pentacyclic triterpenoid lipids synthesized by different bacterial groups. Methylated hopanoids were believed to be exclusively synthesized by cyanobacteria and aerobic methanotrophs until the genes encoding for the methylation at the C-2 and C-3 position (P and R) were found to be widespread in the bacterial domain, invalidating their use as specific biomarkers. These genes have been detected in the genome of the ". Koribacter versatilis," but our knowledge of the synthesis of hopanoids and the presence of genes of their biosynthetic pathway in other member of the is limited. We analyzed 38 different strains of seven subdivisions (SDs 1, 3, 4, 6, 8, 10, and 23) for the presence of C hopenes and C bacteriohopane polyols (BHPs) using the Rohmer reaction. BHPs and/or C hopenes were detected in all strains of SD1 and SD3 but not in SD4 (excepting ), 6, 8, 10, and 23. This is in good agreement with the presence of genes required for hopanoid biosynthesis in the 31 available whole genomes of cultivated . All genomes encode the enzymes involved in the non-mevalonate pathway ultimately leading to farnesyl diphosphate but only SD1 and 3 and encode all three enzymes required for the synthesis of squalene, its cyclization (), and addition and modification of the extended side chain (). In almost all strains, only tetrafunctionalized BHPs were detected; three strains contained variable relative abundances (up to 45%) of pentafunctionalized BHPs. Only ". K. versatilis" contained methylated hopanoids (i.e., 2,3-dimethyl bishomohopanol), although in low (<10%) amounts. These genes are not present in any other , consistent with the absence of methylated BHPs in the other examined strains. These data are in agreement with the scattered occurrence of methylated BHPs in other bacterial phyla such as the -, -, and and the , limiting their biomarker potential. Metagenomes of were also examined for the presence of genes required for hopanoid biosynthesis. The complete pathway for BHP biosynthesis was evident in SD2 and a group phylogenetically related to SD1 and SD3, in line with the limited occurrence of BHPs in acidobacterial cultures.
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http://dx.doi.org/10.3389/fmicb.2017.00968DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5462960PMC
June 2017

Draft Genome Sequence of NE2, an Obligate Methanotroph from Subarctic Soil.

Genome Announc 2017 Jun 15;5(24). Epub 2017 Jun 15.

UiT The Arctic University of Norway, Department of Arctic and Marine Biology, Tromsø, Norway.

NE2 is an aerobic, mildly acidophilic, obligate methanotroph. Similar to other species, it possesses only a particulate methane monooxygenase and is capable of atmospheric nitrogen fixation. The genome sequence of this typical inhabitant of subarctic wetlands and soils also contains genes indicative of aerobic anoxygenic photosynthesis.
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http://dx.doi.org/10.1128/genomeA.00504-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5473262PMC
June 2017

Comparative Genomics of Four Isosphaeraceae Planctomycetes: A Common Pool of Plasmids and Glycoside Hydrolase Genes Shared by PX4, IS1B, DSM 18658, and Strain SH-PL62.

Front Microbiol 2017 16;8:412. Epub 2017 Mar 16.

Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia.

The family Isosphaeraceae accommodates stalk-free planctomycetes with spherical cells, which can be assembled in short chains, long filaments, or aggregates. These bacteria inhabit a wide variety of terrestrial environments, among those the recently described PX4 that was isolated from acidic boreal wetlands. Here, we analyzed its finished genome in comparison to those of three other members of the Isosphaeraceae: IS1B, DSM 18658, and the uncharacterized planctomycete strain SH-PL62. The complete genome of PX4 consists of a 7.5 Mb chromosome and two plasmids, 112 and 43 kb in size. Annotation of the genome sequence revealed 5802 potential protein-coding genes of which 2775 could be functionally assigned. The genes encoding metabolic pathways common for chemo-organotrophic bacteria, such as glycolysis, citrate cycle, pentose-phosphate pathway, and oxidative phosphorylation were identified. Several genes involved in the synthesis of peptidoglycan as well as -methylated ornithine lipids were present in the genome of PX4. A total of 26 giant genes with a size >5 kb were detected. The genome encodes a wide repertoire of carbohydrate-active enzymes (CAZymes) including 44 glycoside hydrolases (GH) and 83 glycosyltransferases (GT) affiliated with 21 and 13 CAZy families, respectively. The most-represented families are GH5, GH13, GH57, GT2, GT4, and GT83. The experimentally determined carbohydrate utilization pattern agrees well with the genome-predicted capabilities. The CAZyme repertoire in PX4 is highly similar to that in the uncharacterized planctomycete SH-PL62 and DSM 18658, but different to that in the thermophile IS1B. The latter strain has a strongly reduced CAZyme content. In PX4, many of its CAZyme genes are organized in clusters. Contrary to most other members of the order Planctomycetales, all four analyzed Isosphaeraceae planctomycetes have plasmids in numbers varying from one to four. The plasmids from PX4 display synteny to plasmids from other family members, providing evidence for their common evolutionary origin.
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http://dx.doi.org/10.3389/fmicb.2017.00412DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5352709PMC
March 2017