Temperature as an autoecological factor of chitinolytic microbial complex formation in soils

The dynamics of carbon dioxide emission from soil was studied during chitinolytic succession induced by humidification and chitin introduction at different temperatures (5, 27, and 50°C) using gas chromatography. The abundance and biomass of the chitinolytic bacterial and actinomycete complex in soil were evaluated by luminescent microscopy. Active development of the chitinolytic microbial complexes was observed at all studied temperatures. The most active growth of chitinolytic microorganisms was observed at high temperature during early succession and at low temperature during late succession. High and low temperatures provided for active development of the chitinolytic microbial complex in soils confined to warm climatic zones (brown desert-steppe soil) and soils of temporary zones (gray forest soil). Actinomycetes demonstrated the most active growth among chitinolytic microorganisms in the studied soil samples both at low and high temperatures.     

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.     

Chitinolytic actinobacteria isolated from an Algerian semi-arid soil: development of an antifungal chitinase-dependent assay and GH18 chitinase gene identification

The purpose of this study was to explore the microbial potential of a semi-arid sandy soil from south-central Algeria in order to isolate new chitinolytic actinobacteria. This soil is subjected to high temperatures (up to 43 °C) and has low nutrient content. Strains were isolated by plating soil suspensions on Bennett and Colloidal Chitin (CCM) medium. An initial clustering of isolates was made through BOX-PCR genetic profiling. Next, a 16S rRNA gene sequencing of representative isolates was realized. We also identified optimum physicochemical conditions for chitinolytic activity. A rapid in vitro assay based on glucose catabolic repression was developed to select isolates having a chitinase-dependent antifungal activity against two phytopathogenic fungi. Gene identification of glycosyl hydrolase family 18 (GH18) permitted us to assess the divergence of chitinase genes. Forty isolates were obtained from the semi-arid sandy soil. The molecular identification permitted us to assign them to Streptomyces or Micromonospora genera with seven possibly new bacterial species. For chitinolytic activity, 100% of isolates were able to grow and degrade colloidal chitin at pH 7 and at a temperature ranging from 30 to 40 °C. We also observed that Micromonospora strains had atypical activity patterns, with a strong chitinase activity maintained at high temperature. Finally, three strains presented an interesting chitinolytic potential to reduce fungal growth with new GH18 sequences. This study presents a new rapid method to detect antifungal chitinase-dependent activity that allowed to identify potentially new species of actinobacteria and new GH18 gene sequences.     

Microbial transformation of chitin in soil under anaerobic conditions

Anaerobic chitinolytic complex was studied in three soil types: chernozem, gray forest soil, and chestnut soil. The abundance and biomass of anaerobic chitinolytic microbial complex of fungi, bacteria, and actinomycetes were evaluated by luminescent microscopy. The dynamics of methane emission from soil during chitinolytic succession was studied by gas chromatography. All three studied microbial groups proved to participate in chitin transformation in soil under anaerobic conditions. The highest biomass growth was observed among prokaryotes, particularly actinomycetes, whose biomass doubled. The increase in methane emission during chitinolytic succession was most pronounced in soils with low organic matter content.     

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.     

The importance of amino sugar turnover to C and N cycling in organic horizons of old-growth Douglas-fir forest soils colonized by ectomycorrhizal mats

Amino sugar dynamics represent an important but under-investigated component of the carbon (C) and nitrogen (N) cycles in old-growth Douglas-fir forest soils. Because fungal biomass is high in these soils, particularly in areas colonized by rhizomorphic ectomycorrhizal fungal mats, organic matter derived from chitinous cell wall material (or the monomeric building block of chitin, N-acetylglucosamine (NAG)) could be a significant source of C or N to the soil microbiota, and thus an important driver of microbial C and N processing. This paper reports the results of incubation experiments initiated to measure chitin degradation, NAG utilization, and the contribution of these substrates to soil respiration and N mineralization rates in mat-colonized and non-mat soil organic horizons. Amendments of chitin and NAG stimulated respiration, N mineralization, and biomass accumulation in mat and non-mat soils, and responses to NAG amendment were stronger than to chitin amendment. NAG-induced respiration was consistently two-fold higher in mat soils than non-mat soils, but induced N mineralization was similar between the two soil patch types. Assimilation of both C and N into microbial biomass was apparent, biomass C:N ratio decreased in all treatments, and microbial N use efficiency (treatment means 0.25 ± 0.06–0.50 ± 0.05) was greater than C use efficiency (treatment means 0.12 ± 0.04–0.32 ± 0.02). NAGase enzyme response was non-linear and showed the same pattern in chitin and NAG amendments. Responses to NAG and chitin amendment differed between mat and non-mat soils, indicating different mechanisms driving NAG and chitin utilization or differences in saprotrophic community composition between the two soil patch types. Net chitin and NAG processing rates were 0.08–3.4 times the basal respiration rates and 0.07–14 times the ambient net N mineralization rates, high enough for the turnover of total soil amino sugars to potentially occur in days to weeks. The results support the hypotheses that amino sugars are important microbial C and N sources and drivers of C and N cycling in these soils.     

Bioremediation of a petroleum‐contaminated cryic soil: Effects of phosphorus,nitrogen, and temperature

Bioremediation has been shown to be an effective means of treating petroleum‐contaminated soils in cold areas, although the conditions required to maximize bioremediation in cold region (cryic) soils are not well documented. A laboratory study was conducted to investigate the effects of nitrogen and phosphorus levels and temperature on petroleum bioremediation. A cryic entisol contaminated with diesel fuel was treated with nitrogen (0, 400, 800, or 1200 mg/kg of soil) and phosphorus (0, 60, 120, or 180 mg/kg of soil) and incubated at two temperatures (10 and 20°C). At 10°C, bioremediation rates were not affected by fertility treatments. At 20°C, reaction rates were increased by the addition of P, but unaffected by N. Regardless of fertility regime, the rate of diesel loss was much greater in soil incubated at 20°C than in soil incubated at 10°C.     

Phylogeny and Ecophysiology of Opportunistic “Snow Molds” from a Subalpine Forest Ecosystem

Mats of coenocytic “snow molds” are commonly observed covering the soil and litter of alpine and subalpine areas immediately following snow melt. Here, we describe the phylogenetic placement, growth rates, and metabolic potential of cold-adapted fungi from under-snow mats in the subalpine forests of Colorado. SSU rDNA sequencing revealed that these fungi belong to the zygomycete orders Mucorales and Mortierellales. All of the isolates could grow at temperatures observed under the snow at our sites (0°C and −2°C) but were unable to grow at temperatures above 25°C and were unable to grow anaerobically. Growth rates for these fungi were very high at −2°C, approximately an order of magnitude faster than previously studied cold-tolerant fungi from Antarctic soils. Given the rapid aerobic growth of these fungi at low temperatures, we propose that they are uniquely adapted to take advantage of the flush of nutrient that occurs at the soil–snow interface beneath late winter snow packs. In addition, extracellular enzyme production was relatively high for the Mucorales, but quite low for the Mortierellales, perhaps indicating some niche separation between these fungi beneath the late winter snow pack.     

Variations in soil culturable bacteria communities and biochemical characteristics in the Dongkemadi glacier forefield along a chronosequence

The variations in the soil culturable bacterial communities and biochemical parameters of early successional soils from a receding glacier in the Tanggula Mountain were investigated. We examined low organic carbon (C) and nitrogen (N) contents and enzymatic activity, correlated with fewer bacterial groups and numbers in the glacier forefield soils. The soil pH values decreased, but the soil water content, organic C and total N significantly increased, along the chronosequence. The soil C/N ratio decreased in the early development soils and increased in the late development soils and it did not correlate with the soil age since deglaciation. The activities of soil urease, sucrase, protease, polyphenol oxidase, catalase, and dehydrogenase increased along the chronosequence. The numbers of culturable bacteria in the soils increased as cultured at 25°C while decreased at 4°C from younger soils to older soils. Total numbers of culturable bacteria in the soils cultured at 25°C were significantly positively correlated to the soil total N, organic C, and soil water content, as well as the activities of soil urease, sucrase, dehydrogenase, catalase, and polyphenol oxidase. We have obtained 224 isolates from the glacier forefield soils. The isolates were clustered into 28 groups by amplified ribosomal DNA restriction analysis (ARDRA). Among them, 27 groups and 25 groups were obtained from the soils at 25°C and at 4°C incubation temperatures, respectively. These groups are affiliated with 18 genera that belong to six taxa, viz, Actinobacteria, Gammaproteobacteria, Bacteroidetes, Firmicutes, Alphaproteobacteria, and Betaproteobacteria. The dominant taxa were Actinobacteria, Gammaproteobacteria, and Bacteroidetes in all the samples. The abundance and the diversity of the genera isolated at 25°C incubation temperature were greater than that at 4°C.     

Temperature responses of carbon mineralization in conifer forest soils from different regional climates incubated under standard laboratory conditions

¹⁴C‐labelled straw was mixed with soils collected from seven coniferous forests located on a climatic gradient in Western Europe ranging from boreal to Mediterranean conditions. The soils were incubated in the laboratory at 4°, 10°, 16°, 23° and 30 °C with constant moisture over 550 days. The temperature coefficient (Q₁₀) for straw carbon mineralization decreased with increasing incubation temperatures. This was a characteristic of all the soils with a difference of two Q₁₀ units between the 4–10° and the 23? 30 °C temperature ranges. It was also found that the magnitude of the temperature response function was related to the period of soil incubation. Initial temperature responses of microbial communities were different to those shown after a long period of laboratory incubation and may have reflected shifts in microbial species composition in response to changes in the temperature regime. The rapid exhaustion of the labile fractions of the decomposing material at higher temperatures could also lead to underestimation of the temperature sensitivity of soils unless estimated for carbon pools of similar qualities. Finally, the thermal optima for the organic soil horizons (Of and Oh) were lower than 30 °C even after 550 days of incubation. It was concluded that these responses could not be attributed to microbial physiological adaptations, but rather to the rates at which recalcitrant microbial secondary products were formed at higher temperatures. The implication of these variable temperature responses of soil materials is discussed in relation to modelling potential effects of global warming.     

Rates of net nitrogen mineralization in disturbed and undisturbed soils

Quantification of net nitrogen mineralization (NNM) in soils is indispensable in order to optimize N fertilization of crops. Two long-term laboratory incubation methods were applied to determine rates of net nitrogen mineralization (r_NNM) of soils from two sites of arable land (sandy loam soil, silty loam soil) at four temperature levels (2°C, 8°C, 14°C, 21°C). Since variability within replicates was small, the modified 12-week incubation method of Stanford and Smith (1972) using disturbed soils allowed to establish reliable Arrhenius functions with reasonable expenditure. The fit of the functions derived from the 5-month incubation of 23 undisturbed soil columns (4420 cm³) was worse. This was caused by greater variability and less differentiation between temperature levels. Results of both experiments could be described best by zero-order kinetics. Mean mineralization rates of disturbed samples were approximately twice as high than those of undisturbed samples. The suitability of both methods for the prediction of NNM at site conditions is discussed. Actual respiration (AR) at incubation temperatures and substrate induced respiration (SIR) were measured at the end of the incubation of undisturbed soil columns. The results presented reveal that soil microbial communities develop in a different manner during long-term incubation at different temperatures. This behavior offends the underlying assumption that soil microbes remain in steady-state during incubation and that rising rates are physiological reactions to temperature enhancement. Therefore soil microbial biomass (SMB) dynamics during the experiment has to be accounted for when rates of NNM and Arrhenius functions are established. R Merck Section editor     

The temperature responses of soil respiration in deserts: a seven desert synthesis

The temperature response of soil respiration in deserts is not well quantified. We evaluated the response of respiration to temperatures spanning 67°C from seven deserts across North America and Greenland. Deserts have similar respiration rates in dry soil at 20°C, and as expected, respiration rates are greater under wet conditions, rivaling rates observed for more mesic systems. However, deserts differ in their respiration rates under wet soil at 20°C and in the strength of the effect of current and antecedent soil moisture on the sensitivity and magnitude of respiration. Respiration increases with temperature below 30°C but declines for temperatures exceeding 35°C. Hot deserts have lower temperature sensitivity than cold deserts, and insensitive or negative temperature sensitivities were predicted under certain moisture conditions that differed among deserts. These results have implications for large-scale modeling efforts because we highlight the unique behavior of desert soil respiration relative to other systems. These behaviors include variable temperature responses and the importance of antecedent moisture conditions for soil respiration.     

Members of <Emphasis Type="Italic">Gammaproteobacteria</Emphasis> and <Emphasis Type="Italic">Bacilli</Emphasis> represent the culturable diversity of chitinolytic bacteria in chitin-enriched soils

Culturable chitinolytic bacterial diversity was studied in chitin-rich soils collected from two industries involved in chitin production. A total of 27 chitinolytic isolates were isolated among which only 10 showed zone of clearance ≥4 mm on colloidal chitin agar plate. Using morphological, biochemical and 16S rDNA analysis, isolates were identified as Bacillus, Paenibacillus, Stenotrophomonas and Pseudomonas. Molecular phylogenetic analysis revealed that Gammaproteobacteria and Bacilli were found to be the predominant classes in these chitin-enriched soils. Chitinolytic bacterial population densities were significantly high and showed a rather simple community composition dominated by genus Bacillus and Stenotrophomonas (74%). This is the first report on assessing the chitinolytic bacterial diversity of soils from industries involved in chitin production.     

Temperature Dependence of Methane Production in Tropical Rice Soils

Although CH 4 production is sensitive to temperature, it is not clear how temperature controls CH 4 production directly versus the production of organic substrates that methanogens convert into CH 4 . Therefore, this study was done to better understand how CH 4 production in rice paddy soil responded to temperature when the process was not limited by the availability of substrates. In a laboratory-incubation study using three Indian rice soils under flooded conditions, the effect of temperature on CH 4 production was examined. CH 4 production in acid sulphate, laterite, and alluvial soil samples under flooded conditions distinctly increased with increase in temperature from 15°C to 35°C. Laterite and acid sulphate soils produced distinctly less CH 4 than alluvial soils. CO 2 production increased with increase in temperature in all the soils. The readily mineralizable carbon C and Fe 2+ contents in soils were least at 15°C and highest at 35°C, irrespective of soil type. Likewise, a significant correlation existed between microbial population (methanogens and sulphate reducers) and CH 4 production. Comparing the temperature coefficients ( Q 10 ) for methane production within each soil type at low (15°C-25°C) and medium (25°C-35°C) temperature intervals revealed that these values were not uniform for both alluvial and laterite soils. But acid sulphate soil had Q 10 values that were near 2 at both temperature intervals. When these soil samples were amended with substrates (acetate, H 2 -CO 2 , and rice straw), there were stimulatory effects on methane production rates and consequently on the Q 10 values. The pattern of temperature coefficients was characteristic of the soil type and the nature of substrates used for amendment.     

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.     

Purification and characterization of a Bacillus circulans No. 4.1 chitinase expressed in Escherichia coli

Summary A DNA fragment encoding for 598 amino acids of chitinase protein from Bacillus circulans No. 4.1 was subcloned into pQE-30 expression vector and transformed into Escherichia coli M15 (pREP4). The molecular weight of the expressed protein was approximately 66 kDa. Enzymatic activity of the recombinant protein was assayed after purification using affinity chromatography on a nickel chelating resin. The enzyme hydrolyzed N-acetylchitooligosaccharides mainly to N-acetylchitobiose, and was active toward chitin, carboxymethyl-chitin, colloidal chitin, glycol chitin and 4-methylumbelliferyl-β-d-N, N′-diacetylchitobiose. The pH and temperature optima of the chitinase enzyme were 7.0 and 45 °C, respectively. This enzyme was stable in the pH range of 5.0–9.0 and at temperatures up to 50 °C. In addition, when cleaved by a proteolytic enzyme, the 20-kDa product could retain high chitinolytic activity.     

N2O emission rates in a California meadow soil are influenced by fertilizer level, soil moisture and the community structure of ammonia-oxidizing bacteria

The response of nitrous oxide (N₂O) emission rates and β‐proteobacterial ammonia‐oxidizing (AOB) communities to manipulations of temperature, soil moisture and nitrogenous fertilizer concentration were studied for 16–20 weeks in a multifactorial laboratory experiment using a California meadow soil. Interactions among these three environmental factors influenced the N₂O emission rates, and two patterns of N₂O emission rates due to nitrification (NitN₂O) were observed. First, in soils receiving low or moderate amounts of fertilizer, the rates decreased sharply in response to increasing soil moisture and temperature. Second, in soils receiving high amounts of fertilizer, the rates were influenced by an interaction between soil moisture and temperature, such that at 20 °C increasing soil moisture resulted in an increase in the rates, and at 30 °C the highest rate was observed at moderate soil moisture. We used path analysis to identify the interrelationships that best explain these two patterns. Path analysis revealed that in the high fertilizer (HF) treatment, the major path by which ammonia influenced NitN₂O rates was indirect through an influence on the abundance of one particular phylogenetic group (AOB ‘cluster 10’). In contrast, in the low and moderate fertilizer treatments soil moisture influenced the rates both directly (the major path) and indirectly through AOB community structure. Although terminal restriction fragment length polymorphism (T‐RFLP) analysis revealed shifts in the community structure of AOB in all treatments, the shifts at HF concentrations were particularly striking, with dominance by three different phylogenetic groups under different combinations of the three environmental factors. The high emission rates observed at the lowest soil moistures suggest that bacterial nitrifiers may use denitrification as a stress response.     

Temperature impacts on anaerobic biotransformation of LNAPL and concurrent shifts in microbial community structure

Thermally-enhanced bioremediation is a promising treatment approach for petroleum contamination; however, studies examining temperature effects on anaerobic biodegradation in zones containing light non-aqueous phase liquids (LNAPLs) are lacking. Herein, laboratory microcosm studies were conducted for a former refinery to evaluate LNAPL transformation, sulfate reduction, and methane generation over a one-year period for temperatures ranging from 4 to 40 °C, and microbial community shifts were characterized. Temperatures of 22 and 30 °C significantly increased total biogas generation compared to lower (4 and 9 °C) and higher temperatures (35 and 40 °C; p < 0.1). Additionally, at 22 and 30 °C methane generation commenced ~6 months earlier than for 35 and 40 °C. Statistically significant biodegradation of benzene, toluene and xylenes was observed at elevated temperatures but not at lower temperatures (p < 0.1). Additionally, a novel differential chromatogram approach was developed to overcome challenges associated with resolving losses in complex mixtures of hydrocarbons, and application of this method revealed greater losses of hydrocarbons at 22 and 30 °C as compared to lower and higher temperatures. Finally, molecular biology assays revealed that the composition and activity of microbial communities shifted in a temperature-dependent manner. Collectively, results demonstrated that anaerobic biodegradation processes can be enhanced by increasing the temperature of LNAPL-containing soils, but biodegradation does not simply increase as temperature increases likely due to a lack of microorganisms that thrive at temperatures well above the historical high temperatures for a site. Rather, optimal degradation is achieved by holding soils at the high end of, or slightly higher than, their natural range.     

Comparing temperature sensitivity of bacterial growth in Antarctic marine water and soil

The western Antarctic Peninsula is an extreme low temperature environment that is warming rapidly due to global change. Little is known, however, on the temperature sensitivity of growth of microbial communities in Antarctic soils and in the surrounding oceanic waters. This is the first study that directly compares temperature adaptation of adjacent marine and terrestrial bacteria in a polar environment. The bacterial communities in the ocean were adapted to lower temperatures than those from nearby soil, with cardinal temperatures for growth in the ocean being the lowest so far reported for microbial communities. This was reflected in lower minimum (T_min) and optimum temperatures (T_opt) for growth in water (?17 and +20°C, respectively) than in soil (?11 and +27°C), with lower sensitivity to changes in temperature (Q₁₀; 0–10°C interval) in Antarctic water (2.7) than in soil (3.9). This is likely due to the more stable low temperature conditions of Antarctic waters than soils, and the fact that maximum in situ temperatures in water are lower than in soils, at least in summer. Importantly, the thermally stable environment of Antarctic marine water makes it feasible to create a single temperature response curve for bacterial communities. This would thus allow for calculations of temperature‐corrected growth rates, and thereby quantifying the influence of factors other than temperature on observed growth rates, as well as predicting the effects of future temperature increases on Antarctic marine bacteria.     

The Effect of Temperature and Aeration Rate on Bioremediation of Diesel-contaminated Soil in Solid-phase Bench-scale Bioreactors

Bioremediation of hydrocarbon (HC) contaminated soils is most effective in aerobic conditions. Despite the fact that mass transfer of oxygen is an important process parameter, the effect of this parameter on solid-phase bioremediation has received limited attention. In this study, the combined effect of temperature and aeration on the bioremediation of low organic content coarse-grained soils, freshly contaminated with diesel, was investigated in solid-phase bench-scale bioreactors. Total HC and carbon range soil concentrations, volatilization, and microbial activity were monitored throughout the six-month experiments at two temperatures (7 and 22°C) and at two aeration rates (13 and 45 mL·s^?1). Total HC removal reached between 48 and 83%. Generally, removal increased proportionally with temperature and aeration rates, and decreased proportionally with HC compounds molecular weight. Both biodegradation and volatilization played important roles in removal in all treatments. The high aeration rate enhanced microbial activity in soil. Enhancement was believed to be due to increased mass transfer of oxygen from the soil gas to the soil solution, where microbial activity occurs. However, high aeration also enhanced volatilization, especially at 22°C where 51% of HCs were lost to volatilization. High aeration rate enhanced biodegradation of compounds > nC15 without promoting their excessive volatilization.