Forest Soil Samples Research Articles

Short-term effects of forest disturbances on soil nematode communities in European mountain spruce forests

The nematode communities in spruce forests were compared with the short-term effects of forest damage, caused by windstorm, wildfire and management practices of forest soils. Soil samples were collected in June and October from 2006 to 2008 in four different sites: (1) forest unaffected by the wind (REF); (2) storm-felled forest with salvaged timber (EXT); (3) modified forest affected by timber salvage (wood removal) and forest fire (FIR); and (4) storm-felled forest where timber had been left unsalvaged (NEX). Nematode analysis showed that the dominant species in all four investigated sites were Acrobeloides nanus and Eudorylaimus silvaticus. An increase of A. nanus (35% of the total nematode abundance) in the first year in the FIR site led to the highest total abundance of nematodes compared with other sites, where nematode abundance reached the same level in the third year. In the FIR site bacterial feeders appeared to be the most representative trophic group, although in the second and third year, after disturbance, the abundance of this trophic group gradually decreased. In the NEX site, the number of nematode species, population densities and Maturity Index were similar to that recorded for the FIR site. In EXT and NEX sites, the other dominant species was the plant parasitic nematode Paratylenchus microdorus. Analyses of nematodes extracted from different forest soil samples showed that the highest number of species and diversity index for species (H'spp) were in the REF site. Differences between the nematode fauna in REF and other localities were clearly depicted by cluster analysis. The greatest Structure Index and Enrichment Index values were also in REF. In the EXT site, the number of nematode species, their abundance, H'spp and Maturity Index were not significantly different from those recorded in the reference site.

Broad-spectrum In vitro antimicrobial activities of Streptomyces sp. strain BCNU 1001

Streptomyces sp. strain BCNU 1001 was isolated from forest soil samples. Cultural, morphological, and physiological characteristics as well as 16S rDNA analysis revealed that the isolate, BCNU 1001, belonged to the genus Streptomyces. The antimicrobial activity of the ethyl acetate extract was confirmed using the broth microdilution technique. The minimum inhibitory concentration (MIC) of the BCNU 1001 ethyl acetate extract was 0.25 mg/mL for Bacillus subtilis, Escherichia coli, and Pseudomonas aeruginosa, and 0.125 mg/mL for Micrococcus luteus, Staphylococcus aureus, and Pseudomonas fluorescens. The MIC of the BCNU 1001 ethyl acetate extract for Aspergillus niger, Candida albicans, and Saccharomyces cerevisiae was 0.5, 0.125, and 0.25 mg/mL, respectively. BCNU 1001 was also active against dermatophytic fungi such as Trichophyton mentagrophytes and T. rubrum. Furthermore, BCNU 1001 was also found to be effective against Methicillin-resistant Staphylococcus aureus (MRSA), and its ethyl acetate extract showed MIC = 0.5 mg/mL against MRSA. The most abundant antimicrobial compound was identified as a 2-hydroxybenzyl alcohol through analysis utilizing a nuclear magnetic resonance spectroscopy. This compound was seen to be very effective against some kinds of bacteria and fungi.

Cloning of transglutaminase gene from Streptomyces platensis YK-2 and its high expression in Streptomyces strains

The microbial transglutaminase (TGase) gene, stgA, was cloned from Streptomyces platensis YK-2, which was newly isolated from a forest soil sample collected in Daegu, Korea. The gene was expressed in several Streptomyces strains including the original strain as the host. The stgA consisted of an open reading frame of 1,257 bp encoding a putative signal peptide of 29 amino acids, a pro-domain of 57 amino acids, and a mature TGase of 332 amino acids, and also had the putative active site of TGase, YGCVG. For expression of the stgA gene, a high expression vector was constructed via the insertion of the entire stgA gene including its putative ribosomal binding site into pSET152ET, located immediately downstream of a strong constitutive ermE* promoter, and was introduced into several Streptomyces strains. The successful high expression and secretion of the correct StgA from streptomycetes were confirmed by electrophoretic sodium dodecyl sulfate polyacrylamide gel electrophoresis and N-terminal amino acid analysis.

Fractionation of Sb and As in soil and sludge samples using different continuous-flow extraction techniques

The fractionation of Sb and As in soil and sludge samples had been comparably studied using two continuous-flow systems: a microcolumn (MC) and a rotating coiled column (RCC). The leachants were applied in correspondence with a five-step sequential extraction scheme addressing water-soluble, non-specifically sorbed, specifically sorbed, and bound to amorphous and crystalline Fe/Al oxide fractions of Sb and As. Inductively coupled plasma atomic emission spectroscopy was applied to determine antimony, arsenic, and major elements in the effluent and in the residual fractions after their digestion. Resemblances and discrepancies of the two methods were evaluated by the fractionation of Sb and As in forest soil, river sludge, and dumped waste (soil) samples. For the forest soil sample, which is very poor in organic matter, RCC and MC extractions yielded similar quantitative values of As and Sb contents in individual leachable fractions. However, for the river sludge sample with a moderate concentration of C (org) (3.3 %), the results obtained by both continuous-flow methods are in satisfactory agreement. RCC extraction enabled water-soluble and non-specifically sorbed As fractions to be recovered, whereas after MC leaching, these environmentally relevant forms of As were not detected. For the soil rich in organic matter (C(org) = 11.5 %), the discrepancy between the data of RCC and MC fractionations is significant. RCC extraction provides about six times higher recoveries of As and Sb bound to amorphous Fe/Al oxides. More efficient leaching of As and Sb in RCC may be attributed to the migration of organic-rich particles with low density inside the column that might enhance the mixing of the solid and liquid phases.

Soil acidity and mobile aluminum status in pseudogley soils in Cacak-Kraljevo basin

Soil acidity and aluminum toxicity are considered most damaging soil conditions affecting the growth of most crops. This paper reviews the results of tests of pH, exchangeable acidity and mobile aluminum (Al) concentration in profiles of pseudogley soils from Cacak-Kraljevo basin. For that purpose, 102 soil pits were dug in 2009 in several sites around Cacak- Kraljevo basin. The tests encompassed 54 field, 28 meadow, and 20 forest soil samples. Samples of soil in the disturbed state were taken from the Ah and Eg horizons (102 samples), from the B1tg horizon in 39 field, 24 meadow and 15 forest pits (a total of 78 samples) and from the B2tg horizon in 14 field, 11 meadow, and 4 forest pits (a total of 29 samples). Mean pH values (1M KCl) of the tested soil profiles were 4.28, 3.90 and 3.80 for the Ah, Eg and B1tg horizons, respectively. Soil pH of forest samples was lower than those in meadow and arable land samples (mean values of 4.06, 3.97 and 3.85 for arable land, meadow and forest samples, respectively). Soil acidification was especially intensive in deep horizons, as 27% (Ah), 77% (Eg) and 87% (B1tg) soil samples had the pH value below 4.0. Mean values of total exchangeable acidity (TEA) were 1.55, 2.33 and 3.40 meq 100 g-1 for the Ah, Eg and B1tg horizons, respectively. The TEA values in forest soils were considerably higher (3.39 meq 100 g-1) than those in arable soils and meadow soils (1.96 and 1.93, respectively). Mean mobile Al contents of tested soil samples were 11.02, 19.58 and 28.33 mg Al 100 g-1 for the Ah, Eg and B1tg horizons, respectively. According to the pH and TEA values, mobile Al was considerably higher in the forest soils (the mean value of 26.08 mg Al 100 g-1) than in the arable soils and meadow soils (the mean values of 16.85 and 16.00 mg Al 100 g-1, respectively). The Eg and B1tg horizons of the forest soil had especially high mobile Al contents (the mean values of 28.50 and 32.95 mg Al 100 g-1, respectively). High levels of mobile Al were especially frequent in the forest soils, with 35% (Ah), 85.0% (Eg) and 93.3% (B1tg) of the tested samples ranging above 10 mg Al 100 g-1.

Glomalin related soil protein, carbon, nitrogen and soil aggregate stability as affected by land use variation in the humid forest zone of south Cameroon

Arbuscular mycorhizal fungi (AMF) produce a glycoprotein (glomalin) which play an important role in the maintenance of soil structure and fertility. On the other hand, it can be used to evaluate the impact of agricultural practices on soil quality across many land use systems. We assessed land use impact on glomalin related soil proteins (GRSPs), soil quality and aggregation in the humid forest zone in southern Cameroon. Forest, short fallow and field crop production soil samples were used to determine GRSPs, carbon (C), nitrogen (N) and water stable aggregate (WSA1–2mm). Results showed that GRSPs significantly decreased from the forest to fallow and the field crop production systems. The easily extractable GRSP (EEGRSP) was 30% and 39% less under fallow and field crop production respectively, relative to the forest soils. Similarly, total GRSP (TGRSP) was 17% and 46% less under fallow and field crop production respectively, relative to the forest soils. C, N, and organic matter (OM) did not change significantly within the land use systems. The WSA1–2mm was 20% less under fallow, and 33% less under field crop production relative to the forest system. However, AMF spores augmented from forest to fallow and field crop production system. There was a positive correlation between GRSPs (EEGRSP, TGRSP) and AM fungal spore density suggesting the possible implication of these fungi to the production of the GRSP in this zone. There was also a positive correlation between C, N and EEGRSP, suggesting the implication of GRSP in stocking soil C and N in this zone. Likewise, a positive correlation between OM and TGRSP was found meaning the implication of GRSPs to OM pools in the soil of this zone. WSA1–2mm was also correlated with TGRSP, C and OM, suggesting the possible coactions of GRSP, OM to the formation of WSA1–2mm, and thereby promoting the build up of soil structure. These results highlight the view that GRSP can be used as an indicator of soil quality in this region and should be considered as a criteria when define agricultural management strategies. AM fungal and GRSP might be useful to monitor soil degradation in this zone.

RESEARCH AND ASSESSMENT OF FOREST SOIL PROPERTIES IN SOUTH-EASTERN LITHUANIA / PIETRYČIŲ LIETUVOS MIŠKO DIRVOŽEMIO SAVYBIŲ TYRIMAI IR VERTINIMAS

Along with chemical research on the Scots pine (Pinus sylvestris L.) growing in the South – Eastern part of Lithuania, the analysis of soil properties was given close attention. The analysed forest soil samples were collected in the spring and summer seasons of 2011. Before sampling, a grid of the area covering 10×10 km including all biggest forest areas of the territory was made. In total, 42 composite forest soil samples were examined. The conducted analysis measured soil moisture, pH and the content of total organic carbon. The assessment of these parameters and performed statistical analysis has disclosed that the content of total organic carbon positively and significantly correlates with pH and the content of soil moisture. Additionally, it has been determined that the content of total organic carbon tends to increase when pH of soil is close to neutral and a total value of soil moisture does not reach 0,61%. Santrauka Tiriant Pietryčių Lietuvos paprastosiose pušyse (Pinus sylvestris L.) susikaupusių metalų kiekius, daug dėmesio buvo skiriama dirvožemio savybių analizei. Straipsnyje aptariami miško dirvožemio ėminiai, imti 2011 m. pavasarį ir vasarą. Prieš atliekant lauko tyrimus buvo sudarytas 10 ×10 km dydžio ėminių ėmimo tinklelis, apimantis didžiausius Pietryčių Lietuvos miškų masyvus. Iš viso ištirti 42 sudėtiniai miško dirvožemio ėminiai. Buvo nustatomas dirvožemio drėgnis, pH ir bendrosios organinės anglies kiekis. Įvertinus šiuos parametrus ir atlikus statistinę analizę nustatyta, kad dirvožemio bendrosios organinės anglies kiekis priklauso nuo dirvožemio pH ir drėgnio. Taip pat įvertinus organinės anglies kiekio priklausomybę nuo abiejų minėtųjų parametrų, pastebėta tendencija, kad bendrosios organinės anglies kiekis gali siekti net 30–50 mg/kg (vidutinė koncentracija Pietryčių Lietuvoje yra 6–10 mg/kg), dirvožemio pH vertė – 6–8, o dirvožemio drėgnis mažesnis nei 0,6 %.

Analytical pyrolysis of humic substances from a Latosol (Typic Hapludox) under different land uses in Minas Gerais, Brazil

Humic acid (HA) and fulvic acid (FA) fractions isolated from a humic red-yellow Latosol (Typic Hapludox) under different land uses (forest, pasture, coffee) were studied by pyrolysis-gas chromatography–mass spectrometry (Py-GC/MS). Humic substances were extracted from soxhlet lipid free soil samples and the pyrolysis experiments consisted of a thermal desorption at sub-pyrolysis temperature (280 °C) followed by a flash pyrolysis (600 °C) on the same sample. Thermal desorption of HA and FA released mainly carbohydrate-derived compounds, N-compounds and series of alkanes. In surface samples most lignin- and carbohydrate-derived compounds are found weakly bounded to the HA structure indicating recent lignocellulosic contribution. In deeper dark soil layers the release of carbohydrate-derived moieties and N-compounds could indicate active biosynthesis by soil biota producing secondary biopolymers like chitin. Major compounds released after pyrolysis of HA were phenol and other benzene derivatives, whereas for FA aromatic and polyaromatic, N-containing and furan derivatives prevailed. In terms of land use the soils under pasture, FA became more aromatic and enriched in carbohydrate-derived compounds and the presence of p-vinylguaiacol in the HA could indicate the contribution of lignin from grasses. In contrast, the coffee culture seems to favor the formation of FA with a more polyaromatic and phenolic structure. Most N-bearing compounds in HA and FA extracted from forest soil samples were released by desorption, indicating comparatively weaker bonds in their structure. This could be explained as a more recent contribution and/or comparatively rapid cycling of these organic substances in natural environments. With respect to the general dynamic of organic matter (OM) in the studied Oxisol, our results are compatible with the occurrence of a high biological activity associated with fast humification processes and the migration of oxidized OM, probably with soil cations as vectors.

Synthesis of (−)-β-caryophyllene oxide via regio- and stereoselective endocyclic epoxidation of β-caryophyllene with Nemania aenea SF 10099-1 in a liquid–liquid interface bioreactor (L–L IBR)

Nemania aenea SF 10099-1, a basidiomycete isolated from a forest soil sample, regio- and stereoselectively epoxidized β-caryophyllene (Car) to (-)-β-caryophyllene oxide (Car-Ox) in a liquid-liquid interface bioreactor (L-L IBR) consisted of a liquid medium (a bottom phase), a fungus-ballooned microsphere (MS) mat (a middle phase), and an organic phase containing Car (a top phase). The cultivation conditions, such as carbon and nitrogen sources, kind of MS, initial medium pH and Car concentration, were optimized in the L-L IBR system. The best carbon and nitrogen sources were xylose and tryptone, respectively. The most suitable polyacrylonitrile MS was MMF-DE-1 (former MFL-80SDE; non-coated type). Although the strain could not grow below pH 5.5, the endocyclic epoxidation of Car efficiently proceeded at a wide range of initial medium pH (6.0 to 9.0). The bioconversion system exhibited an excellent alleviation effect toward substrate and product inhibitions. While Car could be added into an organic phase (KF-96L-1CS, dimethyl silicone oil) at 50% (w/v), the accumulation of Car-Ox reached over 30g/l in spite of these strong microbial toxicities. Moreover, the epoxidation reaction smoothly proceeded in a novel L-L IBR system, a multistory L-L IBR systems, consisted of 5 stacked reactor units. The optical rotation of Car-Ox produced was (-) and the enantiomeric excesses of (-)-β-Car-Ox purified by 1st and 2nd recrystallization from methanol reached 97.51 and 99.33%, respectively.

Fusarium species isolated from forest soil samples

Fusarium species isolated from forest soil samples

Geochemical position of Pb, Zn and Cd in soils near the Olkusz mine/smelter, South Poland: effects of land use, type of contamination and distance from pollution source

The soils adjacent to an area of historical mining, ore processing and smelting activities reflects the historical background and a mixing of recent contamination sources. The main anthropogenic sources of metals can be connected with historical and recent mine wastes, direct atmospheric deposition from mining and smelting processes and dust particles originating from open tailings ponds. Contaminated agriculture and forest soil samples with mining and smelting related pollutants were collected at different distances from the source of emission in the Pb-Zn-Ag mining area near Olkusz, Upper Silesia to (a) compare the chemical speciation of metals in agriculture and forest soils situated at the same distance from the point source of pollution (paired sampling design), (b) to evaluate the relationship between the distance from the polluter and the retention of the metals in the soil, (c) to describe mineralogy transformation of anthropogenic soil particles in the soils, and (d) to assess the effect of deposited fly ash vs. dumped mining/smelting waste on the mobility and bioavailability of metals in the soil. Forest soils are much more affected with smelting processes than agriculture soils. However, agriculture soils suffer from the downward metal migration more than the forest soils. The maximum concentrations of Pb, Zn, and Cd were detected in a forest soil profile near the smelter and reached about 25 g kg(- 1), 20 g kg(- 1) and 200 mg kg(- 1) for Pb, Zn and Cd, respectively. The metal pollutants from smelting processes are less stable under slightly alkaline soil pH then acidic due to the metal carbonates precipitation. Metal mobility ranges in the studied forest soils are as follows: Pb > Zn ≈ Cd for relatively circum-neutral soil pH (near the smelter), Cd > Zn > Pb for acidic soils (further from the smelter). Under relatively comparable pH conditions, the main soil properties influencing metal migration are total organic carbon and cation exchange capacity. The mobilization of Pb, Zn and Cd in soils depends on the persistence of the metal-containing particles in the atmosphere; the longer the time, the more abundant the stable forms. The dumped mining/smelting waste is less risk of easily mobilizable metal forms, however, downward metal migration especially due to the periodical leaching of the waste was observed.

Chryseobacterium vietnamense sp. nov., isolated from forest soil

A Gram-reaction-negative bacterial strain, designated GIMN1.005T, was isolated from a forest soil sample in Vietnam. The isolate was yellow-pigmented, strictly aerobic, and unable to grow below 5 °C or above 37 °C and in the presence of more than 2.0 % NaCl. Cells were non-motile, non-gliding and non-spore-forming. The yellow pigment was of the flexirubin type, non-diffusible and non-fluorescent. Analysis of 16S rRNA gene sequences showed that strain GIMN1.005T occupied a distinct lineage within the genus Chryseobacterium, with sequence similarity values of 98.6, 98.5 and 98.3 % to Chryseobacterium aquifrigidense KCTC 12894T, Chryseobacterium jejuense KACC 12501T and Chryseobacterium indologenes GIFU 1347T, respectively. The level of DNA-DNA relatedness between strain GIMN1.005T and C. jejuense KACC 12501T was <30 %. The DNA G+C content of strain GIMN1.005T was 42.1 mol%. The predominant cellular fatty acids were iso-C15:0, iso-C17:0 3-OH and summed feature 3 (C16:1ω7c and/or C16:1ω6c); menaquinone 6 (MK-6) was the sole respiratory quinone. On the basis of phenotypic properties and phylogenetic distinctiveness, strain GIMN1.005T is considered to represent a novel species of the genus Chryseobacterium, for which the name Chryseobacterium vietnamense sp. nov. is proposed. The type strain is GIMN1.005T (=CCTCC M 209230T=NRRL B-59550T).

Description of Sinomonas soli sp. nov., reclassification of Arthrobacter echigonensis and Arthrobacter albidus (Ding et al. 2009) as Sinomonas echigonensis comb. nov. and Sinomonas albida comb. nov., respectively, and emended description of the genus Sinomonas

A novel actinomycete strain, designated CW 59T, was isolated from a polluted forest soil sample in Anhui Province, China. Cells were strictly aerobic, non-motile, bent rods. The strain grew optimally at 30-37 °C and pH 6.0-8.0. The major fatty acids were ai-C15:0 (34.7 %), i-C15:0 (11.6 %) and ai-C17:0 (14.9 %); the predominant respiratory quinone was MK-9(H2), with MK-8(H2) present as a minor component. The polar lipid composition of strain CW 59T consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, two glycolipids and phosphatidylmonomethylethanolamine (minor component). The whole-cell sugars contained galactose, mannose, ribose and glucose; the major amino acids of the cell-wall were lysine, alanine and glutamic acid. The genomic DNA G+C content was 66.9 mol%. Phylogenetic analysis showed that CW 59T belonged to the genus Sinomonas and grouped with members of the species Sinomonas atrocyanea, Sinomonas flava, Arthrobacter echigonensis and Arthrobacter albidus. 16S rRNA gene sequence similarities of CW 59T to S. atrocyanea DSM 20127T, S. flava CW 108T, A. echigonensis LC10T and A. albidus LC13T were 99.5, 99.3, 98.2 and 98.0 %, respectively. DNA-DNA hybridization of the isolate showed relatedness values of 58.3 % (DSM 20127T), 41.8 % (CW 108T), 21.6 % (LC10T) and 25.5 % (LC13T) with its four closest neighbours. The taxonomic relationships of strains LC10T and LC13T with the genus Sinomonas were further clarified by means of a direct experimental comparison; results showed that strains LC10T and LC13T showed the same major fatty acid, polar lipid, cell-wall amino acid, whole-cell sugar and respiratory quinone compositions as members of the genus Sinomonas. Based on phenotypic, chemotaxonomic and phylogenetic analysis, it is proposed that: strain CW 59T represents a novel species of the genus Sinomonas, Sinomonas soli sp. nov., with CW 59T (=CCTCC AB 207193T=KCTC 19389T) as the type strain; and the type strains of A. echigonensis and A. albidus should be reclassified as Sinomonas echigonensis comb. nov. and Sinomonas albida comb. nov., respectively. An emended description of the genus Sinomonas is given.

Description of Belnapia rosea sp. nov. and emended description of the genus Belnapia Reddy et al. 2006

A novel alphaproteobacterial strain, designated CPCC 100156(T), was isolated from a forest soil sample collected from Hainan Island, South China, and subjected to taxonomic investigation using a polyphasic approach. The pink- to rosy-coloured colonies on TSA and YM agar were smooth and moist. Good growth occurred at 28-32 °C and at pH 7.0-7.5. The respiratory quinone was ubiquinone-9. The polar lipids consisted of phosphatidylcholine (PC), hydroxyphosphatidylethanolamine (OH-PE), phosphatidylglycerol (PG), diphosphatidylglycerol (DPG) and two unidentified aminolipids (AL1, AL2), with a minor amount of ninhydrin-positive phosphoglycolipid. (NPG). The major cellular fatty acids were summed feature 8 (C(18:1)ω7c /C(18:1)ω6c) (49.5%), summed feature 3 (C(16:1)ω7c/C(16:1)ω6c) (22.5%), and C(16:0) (14.0%). The G+C content of the genomic DNA was 70.3 mol%. The organism showed 16S rRNA gene sequence similarity of 97.37% with Belnapia moabensis DSM 16746(T). Phylogenetic analyses based on 16S rRNA gene sequences showed that the isolate belonged to the family Acetobacteraceae and consistently formed a robust cluster with Belnapia moabensis DSM 16746(T) in the phylogenetic tree. The DNA-DNA hybridization value between the new isolate and Belnapia moabensis DSM 16746(T) was 45.6%. On the basis of the taxonomic evidence, it is proposed that strain CPCC 100156(T) represents a novel species, for which the name Belnapia rosea sp. nov. is proposed. The type strain is CPCC 100156(T) (=DSM 23312(T)=CGMCC 1.10758(T)). The description of the genus Belnapia is emended accordingly.

The endoglucanase from Bacillus subtilis BEC-1 bears halo-tolerant, acidophilic and dithiothreitol-stimulated enzyme activity

A Bacillus subtilis strain BEC-1 demonstrating high carboxymethylcellulose-degrading activity was isolated from the forest soil sample. In order to characterize the biochemical specialty of its cellulase, the endoglucanase gene egl173 was cloned from this strain and was expressed in Escherichia coli. The gene encoded a protein of 499 amino acids with a molecular weight of 64 kDa. The purified Egl173 could hydrolyze both soluble and insoluble celluloses with distinct activities. This enzyme showed the highest enzyme activity at pH 4, maintained at least 85% activity in the pH range of 3–7, displayed maximum activity at 60°C and was highly stable between 30 and 60°C. It was found that this endoglucanase was increasedly active and retained its high stability after incubation with 5 M NaCl or 3 M KCl for 24 h. Furthermore, after incubation with 10 mM of dithiothreitol, the enzyme activity was significantly enhanced (125% of the control level). In the presence of diverse metal ions (except mercury and manganese cations), organic solvents, surfactants (except SDS) and chelating agent, this enzyme kept more than 85% active. This halo-tolerant, acidophilic and highly stable endoglucanase is prospectively to be exploited as the advanced enzymatic product for diverse industrial applications.

항균물질을 생산하는 토착 미생물 Paenibacillus sp. BCNU 5011의 특성화

Strain BCNU 5011 was isolated from forest soil samples collected in the Taebaek mountain in the Gangwon province, Korea. The biochemical, physiological and 16S rRNA sequence analysis strongly indicated that this isolate was most closely related to Paenibacillus polymyxa. A maximum production level of antimicrobial substances of Paenibacillus sp. BCNU 5011 was achieved under aerobic incubation at <TEX>$30^{\circ}C$</TEX> for 3 days in SST broth.Paenibacillus sp. BCNU 5011 showed a broad spectrum of activity against Gram positive and Gram negative bacteria, including methicllinresistant Staphylococcus aureus (MRSA). Paenibacillus sp. BCNU 5011 was also shown to inhibit the growth of different potential human pathogenic bacteria and fungi in vitro. Peptide extract showed better antimicrobial activity than solvent extracts. But active antimicrobial compounds might be included in both peptide extract and solvent extracts. Further separation, purification and identification of active principles leads project to develop antimicrobial agents and anti-MRSA agents.

Evaluation of pink-pigmented facultative methylotrophic bacteria for phosphate solubilization

Thirteen pink-pigmented facultative methylotrophic (PPFM) strains isolated from Adyar and Cooum rivers in Chennai and forest soil samples in Tamil Nadu, India, along with Methylobacterium extorquens, M. organophilum, M. gregans, and M. komagatae were screened for phosphate solubilization in plates. P-solubilization index of the PPFMs grown on NBRIP-BPB plates for 7days ranged from 1.1 to 2.7. The growth of PPFMs in tricalcium phosphate amended media was found directly proportional to the glucose concentration. Higher phosphate solubilization was observed in four strains MSF 32 (415mgl(-l)), MDW 80 (301mgl(-l)), M. komagatae (279mgl(-l)), and MSF 34 (202mgl(-l)), after 7days of incubation. A drop in the media pH from 6.6 to 3.4 was associated with an increase in titratable acidity. Acid phosphatase activity was more pronounced in the culture filtrate than alkaline phosphatase activity. Adherence of phosphate to densely grown bacterial surface was observed under scanning electron microscope after 7-day-old cultures. Biochemical characterization and screening for methanol dehydrogenase gene (mxaF) confirmed the strains as methylotrophs. The mxaF gene sequence from MSF 32 clustered towards M. lusitanum sp. with 99% similarity. This study forms the first detailed report on phosphate solubilization by the PPFMs.

Capillary electrophoresis characterisation of humic acids: application to diverse forest soil samples

Environmental contextAnalysis of soil organic matter is important for understanding turnover and stabilisation processes of organic carbon in soils. Capillary electrophoresis is used here to investigate humic acids from soils of diverse forest sites, and show that the patterns of signals are indicative of soil characteristics. The method provides useful information of soil types and complements the existing set of methods for humic acid characterisation. AbstractAnalyses of humic substances provide very useful information about turnover characteristics and stabilisation processes of soil organic matter in environmental soil samples. The present study investigates 113 samples of forest soils from three different layers (undecomposed litter (L), if present, mixed samples of F (intermediate decomposed) and H (highly decomposed) organic matter (FH) and upper mineral soil layers (Ah horizon) from 0 to 5 cm) by extracting humic acids (HAs) and recording electropherograms. Five signals of these electropherograms were evaluated and correlated with basic parameters from soil (organic carbon, Corg, and total nitrogen, Nt, and extraction yields of HAs) and HAs (total carbon, Ct, and Nt), and with signals from photometry, mid-infrared and fluorescence spectroscopy. The developed method was able to separate HAs from different soil layers by calculating a discriminant function based on the five evaluated electrophoretic signals. The dataset of this work opened the opportunity to correlate the observed electrophoretic signals with the other determined soil parameters and spectroscopic signals. This can be seen as a very important step in the direction to assignments of the obtained electrophoretic signals. Soil characteristics were reflected quite well by this method and, combined with the other approaches, it is suitable for applications in further studies.

Aquatic Microbial Habitats Within a Neotropical Rainforest: Bromeliads and pH-Associated Trends in Bacterial Diversity and Composition

Tank-forming bromeliads, suspended in the rainforest canopy, possess foliage arranged in compact rosettes capable of long-term retention of rainwater. This large and unique aquatic habitat is inhabited by microorganisms involved in the important decomposition of impounded material. Moreover, these communities are likely influenced by environmental factors such as pH, oxygen, and light. Bacterial community composition and diversity was determined for the tanks of several bromeliad species (Aechmea and Werauhia) from northern Costa Rica, which span a range of parameters, including tank morphology and pH. These were compared with a nearby forest soil sample, an artificial tank (amber bottle), and a commercially available species (Aechmea). Bacterial community diversity, as measured by 16S rRNA analysis and tRFLP, showed a significant positive correlation with tank pH. A majority of 16S rRNA bacterial phylotypes found in association with acidic bromeliad tanks of pH < 5.1 were affiliated with the Alphaproteobacteria, Acidobacteria, Planctomycetes, and Bacteroidetes, and were similar to those found in acidic peat bogs, yet distinct from the underlying soil community. In contrast, bromeliads with tank pH > 5.3, including the commercial bromeliad with the highest pH (6.7), were dominated by Betaproteobacteria, Firmicutes, and Bacteroidetes. To empirically determine the effect of pH on bacterial community, the tank pH of a specimen of Aechmea was depressed, in the field, from 6.5 to 4.5, for 62 days. The resulting community changed predictably with decreased abundance of Betaproteobacteria and Firmicutes and a concomitant increase in Alphaproteobacteria and Acidobacteria. Collectively, these results suggest that bromeliad tanks provide important habitats for a diverse microbial community, distinct from the surrounding environment, which are influenced greatly by acid-base conditions. Additionally, total organic carbon (∼46%) and nitrogen (∼2%) of bromeliad-impounded sediment was elevated relative to soil and gene surveys confirmed the presence of both chitinases and nitrogenases, suggesting that bromeliad tanks may provide important habitats for microbes involved in the biological cycling of carbon and nitrogen in tropical forests.

Nocardioides iriomotensis sp. nov., an actinobacterium isolated from forest soil

An actinomycete strain, designated IR27-S3(T), was isolated from a forest soil sample collected from Iriomote Island, Okinawa, Japan. Cells of the isolate were Gram-stain-positive, aerobic, non-sporulating, non-motile coccoids or short rods. The strain grew in the presence of 0-7 % (w/v) NaCl, at pH 6-8 and at 12-37 °C, with optimum growth at 30 °C. Chemotaxonomically, the strain contained LL-diaminopimelic acid as the diagnostic diamino acid and MK-8(H₄) as the predominant menaquinone. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unknown phospholipid. The major cellular fatty acids were iso-C₁₆:₀, C₁₇:₁ cis-9, C₁₅:₀ and iso-C₁₅:₀. The DNA G+C content was 73.7 mol%. On the basis of 16S rRNA gene sequence analysis, strain IR27-S3(T) was closely related to Nocardioides mesophilus MSL-22(T) (98.1 % 16S rRNA gene sequence similarity), Marmoricola bigeumensis MSL-05(T) (97.2 %) and Nocardioides jensenii DSM 20641(T) (96.5 %). On the basis of fatty acid analysis, phylogenetic analysis and phenotypic data, the isolate should be classified in a novel species of the genus Nocardioides, for which the name Nocardioides iriomotensis sp. nov. is proposed. The type strain is IR27-S3(T) ( = NBRC 105384(T) = KACC 14926(T)).