Specificity of the chitinolytic microbial complex of soils incubated at different temperatures

The structural and functional specificity of the chitinolytic microbial complex changes dramatically depending on the incubation temperature of soil microcosms. It was shown that the highest rates of chitin degradation occurred in desert soils at high temperatures (50°C); in the moderate and northern zones, these rates peaked at lower temperatures (5°C). The role of prokaryotes as the main chitin degraders in soils incubated at high temperatures, with fungi more actively participating in chitin decomposition at low temperatures, was shown for the first time. Fluorescent in situ hybridization (FISH) revealed the predominance of actinomycetes in the metabolically active chitinolytic prokaryotic complex of desert soils (high temperatures); in the soils of the northern latitudes (low temperatures), proteobacteria prevailed. The relationship between the taxonomic position of the dominant members of the chitinolytic complex of soil microorganisms, isolated in pure cultures with the dominant phylogenetic groups and the sequence types obtained by using molecular biological techniques (FISH) was revealed.     

Comparative analysis of the functional activity and composition of hydrolytic microbial complexes from the lower Volga barrow and modern chestnut soils

The structure and specific characteristics of the hydrolytic microbial complexes from chestnut paleosols buried under the barrows of different ages (～4500 and ～3500 years) was compared with their modern analogue in microcosm experiments. Potential activity of the hydrolytic complex of the microbial community of the barrow paleosols was found to be higher than in the modern soil complex. The share of metabolically active cells revealed by FISH after the introduction of a growth-stimulating polysaccharide into the paleosol microcosm was 50% of the whole prokaryotic cell number. The paleosol community exhibited a more pronounced response to addition of the substrate than the modern soil community. The differences in the phylogenetic taxonomic structure of the prokaryotic metabolically active hydrolytic complex in the buried and modern soils were revealed. The hydrolytic complex of modern soil was more diverse, while the dominant hydrolytic organisms revealed in paleosols were unicellular and mycelial Actinobacteria, as well as Proteobacteria.     

Description of the phylogenetic structure of hydrolytic prokaryotic complex in the soils

With the help of the molecular-biological method of cell hybridization in situ (FISH), the abundance of a physiologically active hydrolytic prokaryotic complex in chernozem and gley-podzolic soils is determined. The total proportion of metabolically active cells, which were detected by hybridization with universal probes as representatives of the domains Bacteria and Archaea, in samples of the studied soil, was from 38% for chernozem up to 78% for gley-podzolic soil of the total number of cells. The differences in the structure of chitinolytic and pectinolytic prokaryotic soil complexes are detected. Along with the high abundance of Actinobacteria and Firmicutes in the soils with chitin, an increase in phylogenetic groups such as Alphaproteobacteria and Bacteroidetes is observed.     

Characterization of the structure of the prokaryotic complex of Antarctic permafrost by molecular genetic techniques

A prokaryotic mesophilic organotrophic community responsible for 10% of the total microbial number determined by epifluorescence microscopy was reactivated in the samples of Antarctic permafrost retrieved from the environment favoring long-term preservation of microbial communities (7500 years). No culturable forms were obtained without resuscitation procedures (CFU = 0). Proteobacteria, Actinobacteria, and Firmicutes were the dominant microbial groups in the complex. Initiation of the reactivated microbial complex by addition of chitin (0.1% wt/vol) resulted in an increased share of metabolically active biomass (up to 50%) due to the functional domination of chitinolytics caused by the target resource. Thus, sequential application of resuscitation procedures and initiation of a specific physiological group (in this case, chitinolytics) to a permafrost-preserved microbial community made it possible to reveal a prokaryotic complex capable of reversion of metabolic activity (FISH data), to determine its phylogenetic structure by metagenomic analysis, and to isolate a pure culture of the dominant microorganism with high chitinolytic activity.     

Biodegradation of insensitive munition formulations IMX101 and IMX104 in surface soils

The biodegradation potential of insensitive munition melt cast formulations IMX101 and IMX104 was investigated in two unamended training range soils under aerobic and anaerobic growth conditions. Changes in community profiles in soil microcosms were monitored via high-throughput 16S rRNA sequencing over the course of the experiments to infer key microbial phylotypes that may be linked to IMX degradation. Complete anaerobic biotransformation occurred for IMX101 and IMX104 constituents 2,4-dinitroanisole (DNAN) and 3-nitro-1,2,4-triazol-5-one during the 30-day incubation period with Camp Shelby (CS) soil. By comparison, soil from Umatilla chemical depot demonstrated incomplete DNAN degradation with reduced transformation rates for both IMX101 and IMX104. Aerobic soil microcosms for both soils demonstrated reduced transformation rates compared to anaerobic degradation for all IMX constituents with DNAN the most susceptible to biotransformation by CS soil. Overall, IMX constituents hexahydro-1,3,5-trinitro-1,3,5-triazine and 1-nitroguanidine did not undergo significant transformation. In CS soil, organisms that have been associated with explosives degradation, namely members of the Burkholderiaceae, Bacillaceae, and Paenibacillaceae phylotypes increased significantly in anaerobic treatments whereas Sphingomonadaceae increased significantly in aerobic treatments. Collectively, these data may be used to populate fate and transport models to provide more accurate estimates for assessing environmental costs associated with release of IMX101 and IMX104.     

Thermophilic chitinolytic microorganisms of brown semidesert soil

In brown semidesert soil, thermophilic prokaryotic organisms identified as Streptomyces roseolilacinus and Silanimonas lenta were shown to play the main role in chitin transformation at 50°C. The phylogenetic positions of the isolated dominant chitinolytic microorganisms were determined on the basis of 16S rRNA gene sequencing. The consumption of chitin as a source of carbon and nitrogen by both the bacterium and the actinomycete was evident from considerable biomass accumulation, high emission of carbon dioxide, and presence in the medium of the chitinase exoenzyme.     

Isolation of Chitin-Specific Wheat Oxidoreductases

Anionic peroxidase (pI ～ 3.5) and oxalate oxidase (pI ～ 7.0) were isolated from wheat seedlings using chitin. The strength of binding of enzymes with chitin depended on the degree of its acetylation and the ionic strength of the buffer. It was assumed that the acetyl groups of chitin are involved in sorption of enzymes on this biopolymer. The ability of anionic peroxidase and oxalate oxidase for sorption on chitin allows this biopolymer to be used for isolation of these proteins from plants. Coadsorption of anionic peroxidase and oxalate oxidase on chitin suggests that these enzymes cooperate to ensure a defensive response of wheat against chitin-containing pathogens.     

Water availability determines physiognomic gradient in an area of low-fertility soils under Cerrado vegetation

Soil is one of the environmental elements to influence Cerrado vegetation. Aluminum toxicity of Cerrado soils is well known, but the importance of water availability is still to be understood, especially in Cerrado under wetter climates. We studied the association between Cerrado physiognomies (cerrado sensu stricto and cerradão) and morphological, chemical, physical, and physical–hydrical soil attributes at southwestern São Paulo State, Brazil. Characterization of soil morphology, classification and sample collection for particle-size distribution, and chemical and water-retention analyses were carried out in 15 permanent plots, where vegetation was characterized floristically and structurally. Simple correlation and canonical correspondence analyses were performed with soil data. Classification of soils (U.S. Soil Taxonomy) with very low clay contents was not able to separate soils under cerradão—forestry physiognomy—from those under cerrado sensu stricto—savannic physiognomy, even though it tends to distinguish soils under greater biomass from those under lower biomass physiognomies. High soil acidity of all studied soils and increased at the sites with greater contents of organic matter, mainly with the cerradão physiognomy, precluded Al toxicity as a cause of the physiognomic gradient within Cerrado. Clay content, microporosity, and residual and saturation moisture were the most significant soil attributes to correlate directly with the cerradão physiognomy, indicating that water availability is the main factor explaining the physiognomic gradient of Cerrado vegetation in a local scale, where climate and soil fertility do not vary spatially.     

Modulation of microbial consortia enriched from different polluted environments during petroleum biodegradation

Environmental microbial communities are key players in the bioremediation of hydrocarbon pollutants. Here we assessed changes in bacterial abundance and diversity during the degradation of Tunisian Zarzatine oil by four indigenous bacterial consortia enriched from a petroleum station soil, a refinery reservoir soil, a harbor sediment and seawater. The four consortia were found to efficiently degrade up to 92.0% of total petroleum hydrocarbons after 2 months of incubation. Illumina 16S rRNA gene sequencing revealed that the consortia enriched from soil and sediments were dominated by species belonging to Pseudomonas and Acinetobacter genera, while in the seawater-derived consortia Dietzia, Fusobacterium and Mycoplana emerged as dominant genera. We identified a number of species whose relative abundances bloomed from small to high percentages: Dietzia daqingensis in the seawater microcosms, and three OTUs classified as Acinetobacter venetianus in all two soils and sediment derived microcosms. Functional analyses on degrading genes were conducted by comparing PCR results of the degrading genes alkB, ndoB, cat23, xylA and nidA1 with inferences obtained by PICRUSt analysis of 16S amplicon data: the two data sets were partly in agreement and suggest a relationship between the catabolic genes detected and the rate of biodegradation obtained. The work provides detailed insights about the modulation of bacterial communities involved in petroleum biodegradation and can provide useful information for in situ bioremediation of oil-related pollution.     

Ecotypic response to ultramafic soils by some plant species of northwestern United States

Soils high in magnesium derived from ultramafic rocks (serpentine, peridotite, and dunite) in northwestern United States support endemic as well as wide-ranging but edaphically indifferent(bodenvag) species. The latter occur widely on diverse rock formations of the region. Severalbodenvag species are shown to respond ecotypically to ultramafic soils. Of 18 species tested, all but three are differentiated into strains either tolerant or intolerant of ultramafic soils. Tests for edaphic preferences were conducted with seedlings and mature transplants on ultramafic soils. Growth performances were determined in greenhouse pot tests, outdoor soil bins, and by transplants in the wild. Herbaceous perennials (e.g.,Achillea millefolium, Fragaria virginiana, Prunella vulgaris, Rumex acetosella) gave the clearest ecotypic differences. Woody species either showed only slight ecotypic response(Spiraea douglasii var.menziesii andGaultheria shallon) or delayed the expression of their genotypic adaptability(Pinus contorta). Where ultramafic abut non-ultramafic soils, those populations ofbodenvag species that grow in non-ultramafic habitats can have a significant proportion of individuals tolerant to ferromagnesian soils (e.g.,Achillea millefolium). This suggests gene flow between populations of contrasting edaphic sites and possibly preadaptedness for the ultramafic habitat. Strains of two introduced weeds(Prunella vulgaris andRumex acetosella) have become ecotypically tolerant to ultramafic soils, probably within the last 75 years.     

Thermotolerant and thermophilic actinomycetes from soils of Mongolia desert steppe zone

In the actinomycete complexes of Mongolian desert soils, thermotolerant and thermophilic actinomycetes were found in high abundance, exceeding that of the mesophilic forms. Among the thermotolerant members of the order Actinomycetales, Streptomyces, Micromonospora, Actinomadura, and Streptosporangium species were most widespread in desert soils. Experiments with soil microcosms demonstrated that thermophilic actinomycetes in desert soils grew, developed, and formed mycelia of the length comparable to that of the mesophilic forms of actinomycetes. Molecular biological investigation of the samples of desert steppe soils by denaturing gradient gel electrophoresis (DGGE) and fluorescent in situ hybridization (FISH) revealed members of the phylum Actinobacteria. FISH analysis revealed that the biomass of the metabolically active mycelial actinobacteria in the prokaryotic community of Mongolian desert soils exceeded that of the unicellular Actinobacteria.     

Identification of metolachlor mineralizing bacteria in aerobic and anaerobic soils using DNA-stable isotope probing

The influence of soil environmental factors such as aeration on the ecology of microorganisms involved in the mineralization and degradation of the popular soil-applied pre-emergent herbicide, metolachlor is unknown. To address this knowledge gap, we utilized DNA-based stable isotope probing (SIP) where soil microcosms were incubated aerobically or anaerobically and received herbicide treatments with unlabeled metolachlor or ¹³C-metolachlor. Mineralization of metolachlor was confirmed as noted from the evolution of ¹⁴CO₂ from ¹⁴C-metolachlor-treated microcosms and clearly demonstrated the efficient utilization of the herbicide as a carbon source. Terminal restriction fragment length polymorphisms (T-RFLP) bacterial community profiling performed on soil DNA extracts indicated that fragment 307 bp from aerobic soil and 212 bp from anaerobic soil were detected only in the herbicide-treated (both unlabeled metolachlor and ¹³C-metolachlor) soils when compared to the untreated control microcosms. T-RFLP profiles from the ultracentrifugation fractions illustrated that these individual fragments experienced an increase in relative abundance at a higher buoyant density (BD) in the labeled fractions when compared to the unlabeled herbicide amendment fractions. The shift in BD of individual T-RFLP fragments in the density-resolved fractions suggested the incorporation of ¹³C from labeled herbicide into the bacterial DNA and enabled the identification of organisms responsible for metolachlor uptake from the soil. Subsequent cloning and 16S rRNA gene sequencing of the ¹³C-enriched fractions implicated the role of organisms closely related to Bacillus spp. in aerobic mineralization and members of Acidobacteria phylum in anaerobic mineralization of metolachlor in soil.     

Vertical profiles of microbial communities in perfluoroalkyl substance-contaminated soils

Poly- and perfluoroalkyl compounds (PFASs) are ubiquitous in the environment, but their influences on microbial community remain poorly known. The present study investigated the depth-related changes of archaeal and bacterial communities in PFAS-contaminated soils. The abundance and structure of microbial community were characterized using quantitative PCR and high-throughput sequencing, respectively. Microbial abundance changed considerably with soil depth. The richness and diversity of both bacterial and archaeal communities increased with soil depth. At each depth, bacterial community was more abundant and had higher richness and diversity than archaeal community. The structure of either bacterial or archaeal community displayed distinct vertical variations. Moreover, a higher content of perfluorooctane sulfonate (PFOS) could have a negative impact on bacterial richness and diversity. The rise of soil organic carbon content could increase bacterial abundance but lower the richness and diversity of both bacterial and archaeal communities. In addition, Proteobacteria, Actinobacteria, Chloroflexi, Cyanobacteria, and Acidobacteria were the major bacterial groups, while Thaumarchaeota, Euryarchaeota, and unclassified Archaea dominated in soil archaeal communities. PFASs could influence soil microbial community.     

Microarthropod communities in anthropogenic urban soils. 2. Seasonal dynamics of microarthropod abundance in soils at roundabout junctions

The seasonal dynamics of microarthropods in anthropogenic soils was studied in the central lawns of roundabout junctions in the city of Vilnius. The microarthropod communities were found to suffer from the impact of automobile exhausts: their abundance was minimum at the curb and increased significantly at a distance of 10 m from it (at the center of a lawn), but it did not reach the values typical of the soil of the control plot. The dynamics of the microarthropod abundance in anthropogenically disturbed and control soils were similar, with the abundance of microarthropods increasing in the autumn-winter period (October–December). The microarthropod communities formed in the anthropogenic soils were unstable, with a high level of dominance of a few species. Oribatids Scutovertex minutus and Tectocepheus velatus, the gamasid mite Rhodacarus coronatus, and the springtail Brachystomella parvula proved to be well adapted to alkaline soils.     

Yeast Communities of the Moscow City Soils

Yeast abundance and diversity were studied in the soils (topsoil) of Moscow city: urban soils under lawn vegetation and close to the areas of household waste disposal, as well as in zonal soddy-podzolic soils (retisols) in parks (Losiny Ostrov and Izmailovo). The numbers of soil yeasts were similar in all studied urban biocenoses (on average ~3.5 × 10³ CFU/g). From all studied soils, 54 yeast species were isolated. The highest yeast diversity was found in the soils adjacent to the areas of household waste storage. Soils from different urban sites were found to have different ratios of ascomycetous and basidiomycetous yeasts: basidiomycetes predominated in urban soils under lawn vegetation, while in the areas close to the waste disposal sites their share was considerably lower. The differences between the studied urban soils were also found in the structure of soil yeast complexes. In urban soils with high anthropogenic impact, the isolation frequency of clinically important yeast species (Candida parapsilosis, C. tropicalis, Diutina catenulata, and Pichia kudriavzevii) was as high as 35% of all studied samples, while its share in the community was 17%. The factors responsible for development of specific features of yeast communities in various urban soils are discussed in the paper.     

The composition of the chitinolytic microbial complex and its effect on chitin decomposition at various humidity levels

The dynamics of assimilation of chitin by soil microorganisms (primarily prokaryotes) as a source of carbon and nitrogen has been determined by gas chromatography and fluorescence microscopy. The highest rates of chitin decomposition in chernozem were detected at humidity levels corresponding to the pressure of soil moisture (P) of ?1.4 atm. The rate of microbial consumption of chitin is three times higher than that of the carbon of soil organic matter. Fluorescence microscopy revealed that an increase in the pressure of soil moisture from P = ?10 atm to P = ?0.7 atm resulted in a considerable increase in the proportion of the specific surface of mycelial bacteria (actinomycetes).     

Testacean communities in perturbed soils: the influence of the wandering albatross

On Île de la Possession (Crozet Archipelago, sub-Antarctica), the testate amoebae (Protozoa, Rhizopoda) fauna in soils around abandoned and occupied nests of the wandering albatross (Diomedea exulans) was investigated. A comparison with control samples, a cluster analysis and several ordination techniques indicated that the presence of the breeding albatrosses induced modifications in physico-chemical soil characteristics and in the soil inhabiting testacean fauna. Only 11 testate species occurred frequently in the soils in the albatross’ zone. Soils around occupied nests had significantly higher moisture values, less acid pH values, an increased specific conductance and elevated phosphate and ammonium concentrations. Highly influenced testacean communities were characterised by high abundances of Difflugiella oviformis and extremely high abundances of Trinema lineare, resulting in a very low diversity and evenness within these communities. The intermediary situation of one abandoned nest indicated that soils around abandoned nests evolve gradually back to undisturbed soils. Although an overall negative influence on the testacean diversity, a limited albatross’ influence may increase the living fraction within the testacean soil communities.     

Isolation and characterization of biosurfactant producing <Emphasis Type="Italic">Bacillus</Emphasis> sp. from diesel fuel-contaminated site

Among hydrocarbon pollutants, diesel oil is a complex mixture of alkanes and aromatic compounds which are often encountered as soil contaminants leaking from storage tanks and pipelines or as result of accidental spillage. One of the best ecofriendly approaches is to restore contaminated soil by using microorganisms able to degrade those toxic compounds in a bioremediation process. In the present study, nineteen bacteria were isolated by enrichment culture technique from diesel spilled soil collected from electric generator shed of NBAIM, Mau. All the isolates were subjected to screening for lipase production and twelve isolates were found to be positive for lipase. When the isolates were screened for biosurfactant production using CTAB-methylene blue agar plates, only one isolate viz. 2NBDSH3 was found positive which was found to be phylogenetically closely related with Bacillus flexus. Despite having low emulsification index, the bacterium could degrade 88.6% of diesel oil in soil. Biosurfactant from the isolate was extracted and characterized through infra-red spectroscopy which indicated its possible lipopeptide nature which was further supported by strong absorption in UV range in the UV-Vis spectrum. The results of the present study indicated that the isolate either does not produce any bioemulsifier or produces very low amount of emulsifier rather it produces a lipopeptide biosurfactant which helps in degradation of diesel oil by lowering the surface tension. The bacterium thus isolated and characterized can serve as a promising solution for ecofriendly remediation of bacterium diesel contaminated soils.