Actinomycetes in the rhizosphere of semidesert soils of Mongolia

The population density of actinomycetes in the desert-steppe soil, rhizosphere, and the above-ground parts of plants varies from tens to hundreds of thousands of colony-forming units (CFU) per gram of substrate. The actinomycetal complexes of the brown desert-steppe soil without plant roots are more diverse in their taxonomic composition than the actinomycetal complexes in the rhizosphere and the aboveground parts of plants. Additionally to representatives of the Streptomyces and Micromonospora genera, actinomycetes from the Nocardia, Saccharopolyspora, Thermomonospora, and Actinomadura genera were identified in the soil. The population density of actinomycetes in the rhizosphere and in the soil reached hundreds of thousand CFU/g; it considerably exceeded the population density of actinomycetes in the aboveground parts of plants. The maximum population density of actinomycetes was determined in the rhizosphere of Asparagus gobicus, Salsola pestifera, and Cleistogenes songorica.     

Actinomycetal complex of light sierozem on the Kopet-Dag piedmont plain

The population density of actinomycetes in the samples of light sierozem from the Kopet Dag piedmont plain (75 km from Ashkhabad, Turkmenistan) reaches hundreds of thousand CFU/g soil. The actinomycetal complex is represented by two genera: Streptomyces and Micromonospora. Representatives of the Streptomyces genus predominate and comprise 73 to 87% of the actinomycetal complex. In one sample, representatives of the Micromonospora genus predominated in the complex (75%). The Streptomyces genus in the studied soil samples is represented by the species from several sections and series: the species of section Helvolo-Flavus series Helvolus represent the dominant component of the streptomycetal complex; their portion is up to 77% of all isolated actinomycetes. The species of other sections and series are much less abundant. Thus, the percentage of the Cinereus Achromogenes section in the actinomycetal complex does not exceed 28%; representatives of the Albus section Albus series, Roseus section Lavendulae-Roseus series, and Imperfectus section belong to rare species; they have been isolated not from all the studied samples of light sierozem, and their portion does not exceed 10% of the actinomycetal complex.     

Ecological and Taxonomic Features of Actinomycetal Complexes in Soils of the Lake Elton Basin

In the sor (playa) solonchaks of chloride and sulfate–chloride salinity (the content of readily soluble salts is 0.9–1.0%) in the delta of the Khara River discharging into Lake Elton, the number of mycelial actinobacteria (actinomycetes) is low ((2–3) × 10³ CFU/g of soil). At a distance from the water’s edge, these soils are substituted for the light chestnut ones, for which an elevated number of actinomycetes (an order of magnitude higher than in the sor solonchaks) and a wider generic spectrum are characteristic. The actinomycetal complex is included the Streptomyces and Micromonospora genera, whereas in the sor solonchaks around the lake, representatives of Micromonospora were not found.     

Biosynthetic potential of actinomycetes in brown forest soil on the eastern coast of the aegean sea

The taxonomic and functional structures of the actinomycetal complex in the litter and upper horizon of the brown forest soil was studied in a Pinus brutia var. pendulifolia forest on the eastern coast of the Aegean Sea. The complex of actinomycetes included representatives of the Streptomyces and Micromonospora genera and oligosporus forms. Streptomycetes predominated (73.8%) in the soil, and micromonospores (66.7%) were dominants in the litter. Thirty isolates of ten Streptomyces species from five series and three sections prevailed. In the upper soil horizon, species of the Helvolo-Flavus Helvolus section predominated (48%); the S. felleus species occurred most frequently. Among the isolated cultures, the S. globisporus and S. sindenensis species capable to produce antitumor antibiotics were found. The testing of the antimicrobial activity of the natural isolates showed that five strains inhibit the growth of pathogenic Fusarium sp., Alternaria sp., Acremonium sp., and Bipolaris sorokiniana fungi. When testing the effect of streptomycetes on the production of cellulases, a high-efficient strain belonging to the S. noboritoensis species was revealed. All the streptomycetes isolated from the brown forest soil produced auxins at the rate of 7.8 to 19.7 μg of indole acetic acid/mL of the liquid medium in the presence of 200 mg/L of tryptophan. Twelve isolates of streptomycetes were transferred to the collection of biotechnologically promising cultures for studying their properties.     

Psychrotolerant actinomycetes on plant substrates of tundra and taiga ecosystems

Studies of tundra flowering plants and mosses on the Тaymyr Peninsula have determined the presence of thousands and tens of thousands of colony formation units of psychrotolerant actinomycetes in 1 g of vegetation substrate, which is smaller than the amount of mesophilic forms by one to two orders of magnitude. Incubation of plants at 5°C has shown very small taxonomical variety of actinomycetes. The actinomycete complex is represented by species of the genus Streptomyces, belonging to the sections and series Albus Albus and Cinereus Achromogenes, and by the genus Micromonospora.     

Changes in the structure of the rhizosphere complex of actinomycetes in the ontogenesis of winter rye

Changes in the taxonomic structure of actinomycetes in the rhizosphere of winter rye (Secale cereale L.) growing on acid soddy-podzolic soil were studied. During the first stages of ontogenesis of winter rye, the rhizosphere complex of mycelial prokaryotes was characterized by a relatively level generic structure (with respect to the indices of abundance and frequency of particular genera), low values of the species diversity, and low domination frequency of the species from the Streptomyces genus. The numbers and species diversity of the streptomycetes increased during the further growth of the winter rye, so that streptomycetes became a dominant group in the complex of the rhizosphere actinomycetes. According to the two-way ANOVA, the population density of the Micromonospora and the Streptosporangium genera in the rhizosphere was mainly dictated by the winter rye variety, whereas the population density of the streptomycetes depended on the particular stage of the winter rye development. The differences between the actinomycetal complexes characteristic of different varieties of winter rye at the early stages of its development was leveled by the end of the winter rye growth.     

Influence of moisture on the vital activity of actinomycetes in a cultivated low-moor peat soil

It was found that the actinomycetal complex of a cultivated low-moor peat soil is characterized by a high population density and diversity of actinomycetes; representatives of eleven genera were isolated from this soil: Streptomyces, Micromonospora, Actinomadura, Saccharopolyspora, Microbispora, Microtetraspora, Streptosporangium, Nocardioides, Saccharomonospora, Kibdelosporangium, and Thermomonospora. Some genera were isolated from the soil under all the studied levels of soil moisture. The so-called rare (rarely occurring) genera (Saccharomonospora, Kibdelosporangium, and Thermomonospora) were isolated upon the low level of soil moisture, which ensured an absence of competition from the more abundant actinomycetes. Spores of all the studied actinomycetes could germinate under the low moisture level (a _w = 0.67). The level of moisture a _w = 0.98 was found to be optimal for the development of the actinomycetes. The complete cycle of the development of all the actinomycetes up to spore formation occurring was only observed under the high moisture level (a _w = 0.98).     

Aerobic and microaerophilic actinomycetes of typical agropeat and peat soils

A high number (from tens of thousands to millions of CFU/g of soil) of actinomycetes and a high diversity of genera were found in typical peat and agropeat soils. Agricultural use increases the number and diversity of the actinomycete complexes of the peat soils. In the peat soils, the actinomycete complex is represented by eight genera: Streptomyces, Micromonospora, Streptosporangium, Actinomadura, Microbispora, Saccharopolyspora, Saccharomonospora, and Microtetraspora. A considerable share of sporangial forms in the actinomycete complex of the peat soils not characteristic of the zonal soils was revealed. The number of actinomycetes that develop under aerobic conditions is smaller by 10–100 times than that of aerobic forms in the peat soils. Among the soil actinomycetes of the genera Streptomyces, Micromonospora, Streptosporangium, Actinomadura, Microbispora, and Microtetraspora, the microaerophilic forms were found; among the Saccharopolyspora and Saccharomonospora, no microaerophilic representatives were revealed.     

Actinomycetes of rare genera in plain chestnut soils of Mongolia

The population and taxonomy of actinomycetes in chestnut soils of Mongolian plains were studied. The actinomycetes identified belong to the genera Streptomyces, Micromonospora, Saccharopolyspotra, Streptosporangium, and Microbiospora. In the composition of Streptomyces, the species of sections Cinereus, Helvo-Flavus, Albus, and Imperfectus were present. The species of Imperfectus section predominated in the Streptomyces complex and amounted to 88.2%.     

Chemical composition of soils in the areas of volcanic ashfalls around active volcanoes in Kamchatka

The geochemical features of volcanic soils (Andosols) in the northern soil province of Kamchatka are identified. The background regional concentrations (Cb_r) of most of chemical elements in the studied soils are lower than their average concentrations in soils of the world and in the European volcanic soils. Only Na, Ca, and Mg are present in elevated concentrations in all the studied soils in the north of Kamchatka. Regional background concentrations of elements are exceeded by 1.6 times in the area of active ashfalls of the Tolbachik volcano and by 1.3 times in the area of active ashfalls of the Shiveluch volcano. The concentrations of mobile forms of elements in these areas exceed their regional background concentrations by 2.1 and 2.6 times, respectively.     

A comparative analysis of microbiomes in natural and anthropogenically disturbed soils of northwestern Kazakhstan

The goal of this study was to determine the relationships between the structure of the soil microbiome and the agroecological state of soils by the example of natural undisturbed (steppe areas) and anthropogenically disturbed (pastures, croplands, fallows) areas in the territory of northwestern Kazakhstan. The highest abundance of proteobacteria was found in the anthropogenically disturbed of fallows and in undisturbed soils; in other cases, actinobacteria and representatives of the Firmicutes phylum predominated. Different kinds of anthropogenic impacts resulted in the decrease in the portions of bacteria from the Acidobacteria, Gemmatimonadetes, and Firmicutes phyla. In the disturbed soils, the portions of bacteria from the Erysipelothrix, Mycobacterium, Methylibium, Skermanella, Ralstonia, Lactococcus, Bdellovibrio, Candidatus nitrososphaera, Catellatospora, Cellulomonas, Stenotrophomonas, and Steroidobacter genera increased. Bacteria of the Erysipelothrix and Methylibium genera occurred only in the undisturbed soils. The anthropogenically disturbed and undisturbed soils differed significantly in the taxonomic structure of their microbiomes forming two separate clusters, which confirms the efficiency of using the data on the structure of soil microbiomes when assessing the agroecological status of soils.     

Soil actinomycetes in the National Forest Park in northeastern China

The taxonomic and functional structure of actinomycete complexes in the litters and upper horizons of the soils under an artificial coniferous–broad-leaved forest located around the town of Chanchun (Tszilin province, PRС). The complex of actinomycetes included representatives of the Streptomyces, Micromonospora, Streptosporangium, and Streptoverticillium genera and oligosporous forms. In the actinomycete complexes, streptomycetes prevailed in the abundance (61–95%) and frequency of occurrence (100%). In the parcels of Korean pine (Pinus koraiensis) and Mongolian oak (Quercus mongolica), streptomycetes of 19 species from 8 series and 4 sections were isolated. The most representative, as in European forest biomes, was the Cinereus Achromogenes series. A distinguishing feature of the streptomycete complex in the biomes studied was the high participation of species from the Imperfectus series. The verification of the functional activity of natural isolates made it possible to reveal strains with high antagonistic and cellulolytic abilities. A high similarity of actinomycete complexes was found in Eurasian forest ecosystems remote from each other, probably due to the similarity of plant polymers decomposable by actinomycetes.     

Complete chloroplast DNA sequences of Georgian indigenous polyploid wheats (<Emphasis Type="Italic">Triticum</Emphasis> spp.) and B plasmon evolution

Three types of plasmon (A, B and G) are present for genus Triticum. Plasmon B is detected in polyploid species - Triticum turgidum L. and Triticum aestivum L. By now, 21 complete sequences of chloroplast DNA of the genus Triticum is published by different authors. Many inaccuracies can be detected in the sequenced chloroplast DNAs. Therefore, we found it necessary to study of plasmon B evolution to use only those sequences obtained by our method in our laboratory. Complete nucleotide sequences of chloroplast DNA of 11 representatives of Georgian wheat polyploid species were determined. Chloroplast DNA sequencing was performed on an Illumina MiSeq platform. Chloroplast DNA molecules were assembled using the SOAPdenovo computer program. Using T. aestivum L. subsp. macha var. palaeocolchicum as a reference, 5 SNPs were identified in chloroplast DNA of Georgian indigenous polyploid wheats. 38 and 56 bp inversions were observed in paleocolchicum subspecies. The phylogeny tree shows that subspecies macha, durum, carthlicum and palaeocolchicum occupy different positions. According the simplified scheme based on SNP and indel data the ancestral, female parent of all studied polyploid wheats is an unknown X predecesor, from which four lines were formed.     

Algological and Mycological Characterization of Soils under Pine and Birch Forests in the Pasvik Reserve

The structure of algological and mycological complexes in Al–Fe-humus podzols (Albic Podzols) under pine and birch forests of the Pasvik Reserve is characterized. The number of micromycetes is higher in more acid soils of the pine forest, while the species diversity is greater under the birch forest. The genus Penicillium includes the largest number of species. The greatest abundance and occurrence frequency are typical for Penicillium spinulosum, P. glabrum, and Trichoderma viride in pine forest and for Umbelopsis isabellina, Mucor sp., Mortierella alpinа, P. glabrum, Aspergillus ustus, Trichoderma viride, and T. koningii in birch forest. Cyanobacteria–algal cenoses of the investigated soils are predominated by green algae. Soils under birch forest are distinguished by a greater diversity of algal groups due to the presence of diatoms and xanthophytes. Species of frequent occurrence are represented by Pseudococcomyxa simplex and Parietochloris alveolaris in soils of the pine forest and by Tetracystis cf. aplanospora, Halochlorella rubescens, Pseudococcomyxa simplex, Fottea stichococcoides, Klebsormidium flaccidum, Hantzschia amphioxys, Microcoleus vaginatus, and Aphanocapsa sp. in soils under birch forest     

Genotyping-by-sequencing reveals the origin of the Tunisian relatives of cultivated carrot (<Emphasis Type="Italic">Daucus carota</Emphasis>)

Tunisia, other countries in northwestern Africa, and the Iberian Peninsula, represent a center of diversity of Daucus. The genus traditionally has included about 20–25 species worldwide, but a recent molecular study redefined and expanded Daucus to include representatives from nine other genera. By this classification, Daucus now contains about 40 species, with some of them having winged fruits in addition to its traditionally recognized spiny fruits. The taxonomy of Daucus in Tunisia has recently been studied with morphological data, concluding that D. carota subsp. capillifolius is a subspecies that co-occurs and crosses with subsp. carota. The present study extends these findings with additional data from Genotyping-by-Sequencing (GBS) from 33 Tunisian accessions of D. carota (93 individuals with two to three replicates per accession), including the first collections of subsp. gummifer from Tunisia. Placed in the context of additional GBS data, D. carota subsp. gummifer has separate origins from other collections of subsp. carota in Tunisia and/or immediately adjacent areas to the north in Italy or its surrounding islands. Our results add support to the utility of large SNP datasets for species-level phylogenetic studies in Daucus.     

The structural-functional organization of thermotolerant complexes of actinomycetes in desert and volcanic soils

It has been found that the number of thermotolerant actinomycetes in strongly heated soils of deserts and volcanic regions is comparable to or exceeds the number of mesophilic actinomycetes. Among the latter group, streptomyces usually predominate; among thermotolerant actinomycetes, representatives of the Micromonospora, Streptosporangium, Actinomadura, Saccharopolyspora, Microtetraspora, and Microbispora genera are identified. Thermotolerant actinomycetes display the full cycle of their development in these soils. The method of fluorescent in situ hybridization has made it possible to determine that mycelial forms predominate among the metabolically active representatives of Actinobacteria; their portion increases with the rise in the temperature of soil incubation.     

New processes of microbial transformation of nitrogen in soils as a source of greenhouse gases

DNA isolation from soil samples and amplification of fragment of a key gene of nitrification, archaeal and bacterial amoA, revealed presence of the product in all investigated soil samples. Characteristics of ammonia-oxidizing microbial communities in agrocenoses and undisturbed soil were determined. Bacteria were predominant in agrocenoses (at circum-neurtal pH), whereas the share of representatives of domain Archaea (phylum Thaumarchaeota) increased in prokaryotic ammonia-oxidizing complexes of undisturbed forest ecosystems (at low pH). It was demonstrated that the contribution of taumarhaea in nitrous oxide emission from gray forest soil may reach 20–25%.     

Potentialities of Six Plant Species on Phytoremediation Attempts of Fuel Oil-Contaminated Soils

A field experiment investigating the phytoremediation potential of six plant species—Goosegrass (Eleusine indica), Bermuda grass (Cynodon dactylon), Sessile joyweed (Alternanthera sessilis), Benghal dayflower (Commelina benghalensis), Lovanga (Cleome ciliata), and Chinese violet (Asystasia gangetica)—on soil contaminated with fuel oil (82.5 ml/kg of soil) have been conducted from March to August 2016. The experiments consider three modalities—Tn: unpolluted planted soils, To: unplanted polluted soils, and Tp: polluted planted soil—randomized arranged. Only three (E. indica, C. dactylon, and A. sessilis) of the six species survived while the others died 1 month after the beginning of experimentations. The relative growth indexes showed a strong similarity between the growth parameters of E. indica and C. dactylon, each on polluted and control soils, unlike A. sessilis. Total petroleum hydrocarbons (TPHs) removal efficiency were 82.56, 80.69, and 77% on soil planted with E. indica, C. dactylon, and A. sessilis, respectively; and 57.25% on non-planted soil. According to the bioconcentration and translocation factors, E. indica and A. sessilis are involved on rhizodegradation and phytoextraction of hydrocarbons whereas C. dactylon is only involved into rhizodegradation. Overall, E. indica and C. dactylon out-yielded A. sessilis in the phytoremediation capacity of fuel oil-contaminated soils.     

Molecular phylogenetics and systematics of Trigonella L. (Fabaceae) based on nuclear ribosomal ITS and chloroplast trnL intron sequences

The genus Trigonella includes the widely cultivated T. foenum-graecum and a number of other medicinal and aromatic plant species distributed around the Mediterranean region. Sectional delimitation of Trigonella species is still based on morphology and interspecific relationships within the genus are not yet sufficiently resolved. Phylogenetic relationships in 22 species representing 11 of the 12 sections recognized within the genus Trigonella were analyzed using nuclear ITS and plastid trnL-F DNA sequences. Within nuclear ITS region, ITS-II was found to evolve faster compared to ITS-I. Maximal phylogenetic resolution and support was obtained in the combined analysis of the two selected regions. Trees resulting from maximum parsimony as well as Bayesian inference of combined data provided evidence for Trigonella being monophyletic with high support but did not agree with the traditional subgeneric division. Phylogenetic reconstructions indicated three major lineages supported by apomorphies in inflorescence and stipule. The phylogram supported the sectional delimitation of sections Cylindricae, Vérae, Samaroideae, Pectinatae, Erosae and Callicerates. There is strong support to combine monotypic sections Pectinatae and Erosae into one. However, species belonging to section Foenum-graecum and Falcatulae clustered in different subclades, contrary to their current classification. Inflorescence type appears to be a useful character with taxonomic potential for phenetic implications at subgeneric and sectional level within the genus. Moreover, some legume and seed characteristics, considered important in existing taxonomy, appear to have arisen more than once in Trigonella and are homoplastic.