A novel alkane monooxygenase evolved from a broken piece of ribonucleotide reductase in Geobacillus kaustophilus HTA426 isolated from Mariana Trench

We have accidentally found that a thermophilic Geobacillus kaustophilus HTA426 is capable of degrading alkanes although it has no alkane oxygenating enzyme genes. Our experimental results revealed that a putative ribonucleotide reductase small subunit GkR2loxI (GK2771) gene encodes a novel heterodinuclear Mn-Fe alkane monooxygenase/hydroxylase. GkR2loxI protein can perform two-electron oxidations similar to homonuclear diiron bacterial multicomponent soluble methane monooxygenases. This finding not only answers a long-standing question about the substrate of the R2lox protein clade, but also expands our understanding of the vast diversity and new evolutionary lineage of the bacterial alkane monooxygenase/hydroxylase family.

Actinomycetospora lemnae sp. nov., A Novel Actinobacterium Isolated from Lemna aequinoctialis Able to Enhance Duckweed Growth

Duckweed-associated actinobacteria are co-existing microbes that affect duckweed growth and adaptation. In this study, we aimed to report a novel actinobacterium species and explore its ability to enhance duckweed growth. Strain DW7H6T was isolated from duckweed, Lemna aequinoctialis. Phylogenetic analysis based on its 16S rRNA gene sequence revealed that the strain was most closely related to Actinomycetospora straminea IY07-55T (99.0%), Actinomycetospora chibensis TT04-21T (98.9%), Actinomycetospora lutea TT00-04T (98.8%) and Actinomycetospora callitridis CAP 335T (98.4%). Chemotaxonomic and morphological characteristics of strain DW7H6T were consistent with members of the genus Actinomycetospora, while average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) between the draft genomes of this strain and its closely related type strains were below the proposed threshold values used for species discrimination. Based on chemotaxonomic, phylogenetic, phenotypic, and genomic evidence obtained, we describe a novel Actinomycetospora species, for which the name Actinomycetospora lemnae sp. nov. is proposed. The type strain is DW7H6T (TBRC 15165T, NBRC 115294T). Additionally, the duckweed-associated actinobacterium strain DW7H6T was able to enhance duckweed growth when compared to the control, in which the number of fronds and biomass dry weight were increased by up to 1.4 and 1.3 fold, respectively. Moreover, several plant-associated gene features in the genome of strain DW7H6T potentially involved in plant-microbe interactions were identified.

Duckweed-associated bacteria as plant growth-promotor to enhance growth of Spirodela polyrhiza in wastewater effluent from a poultry farm

Duckweed has been highlighted as an invaluable resource because of its abilities to remove nitrogen and phosphorus from wastewater coupling with the production of high starch/protein-containing plant biomass. Duckweed recruits microbes and particularly forms a stable "core" bacterial microbiota, which greatly reduces the colonization efficiency of plant growth-promoting bacteria (PGPB). In this study, natural duckweeds were enriched in a sterilized-partially treated wastewater effluent from a poultry farm. After 24 days of cultivation, the duckweed-associated bacteria (DAB) were isolated and evaluated for their plant growth-promoting (PGP) potentials by co-cultivation with axenic Spirodela polyrhiza. Ten species were found in more than one location and could be considered candidates for the stable "core" DAB. Among them, all isolates of Acinetobacter soli, Acidovorax kalamii, Brevundimonas vesicularis, Pseudomonas toyotomiensis, and Shinella curvata increased duckweed growth in Hoagland medium. The highest PGP ability was observed in Sh. curvata W12-8 (with EPG value of 208.72%), followed by Paracoccus marcusii W7-16 (171.31%), Novosphingobium subterraneum W5-13 (156.96%), and Ac. kalamii W7-18 (156.96%). However, the highest growth promotion in the wastewater was observed when co-cultured with W7-16, which was able to increase biomass dry weight and root length of duckweed by 3.17 and 2.26 folds, respectively.

Biocalcifying Potential of Ureolytic Bacteria Isolated from Soil for Biocementation and Material Crack Repair

Microbially induced calcium carbonate precipitation (MICP) has been highlighted for its application in civil engineering, and in the environmental and geotechnical fields. Ureolytic activity is one of the most promising bacterial mechanisms in terms of inducing calcium carbonate formation. In this study, four bacterial isolates with high-yield urease production capabilities were obtained from two-step screening using a high-buffered urea medium. The highest urease activity and calcium carbonate formation was observed in Lysinibacillus fusiformis 5.1 with 4.40 × 103 unit/L of urease and 24.15 mg/mL of calcium carbonate, followed by Lysinibacillus xylanilyticus 4.3 with 3.93 × 103 unit/L of urease and 22.85 mg/mL of calcium carbonate. The microstructure of the precipitated crystalline calcium carbonate was observed using scanning electron microscopy. X-ray diffraction analysis confirmed that the main polymorph of the calcium carbonate particle obtained from both isolates was calcite. Examination of the material-crack filling in mortar specimens showed that calcite layers had formed along the crack edges and inside after 10 days, and gradually filled the cracks up to the upper surface. These results showed that these two isolates presented robust characteristics of potential MICP-inducing bacteria for civil engineering and material engineering applications.

Indigenous bacteria, an excellent reservoir of functional plant growth promoters for enhancing duckweed biomass yield on site

The advantages of aquatic biomass production using wastewater as a cost-free fertilizer have recently been highlighted. Here, we report a successful study in which duckweed, Lemna gibba, biomass production in a food factory effluent containing low nitrogen and high salts was enhanced by employing customized plant growth-promoting bacteria (PGPB). Two common PGPB strains previously obtained from natural pond water, Acinetobacter calcoaceticus P23 and Pseudomonas fulva Ps6, hardly promoted the growth of duckweed; on the contrary, they inhibited its growth in treated factory wastewater, far different water conditions. Then, we asked if some indigenous wastewater bacteria could promote the growth of duckweed. We found that Chryseobacterium strains, a group of bacteria with limited nitrogen metabolism, were dominantly selected as effective PGPB. Moreover, we demonstrated that nitrogen limitation is the crucial environmental factor that induces the plant growth-inhibiting behavior of A. calcoaceticus P23 through competition for mineral nutrients with the host duckweed. This study uncovered points to be considered in PGPB technology to achieve efficient production of duckweed biomass in a factory effluent with unbalanced content of mineral nutrients.

Savitreea pentosicarens gen. nov., sp. nov., a yeast species in the family Saccharomycetaceae isolated from a grease trap

Two strains (DMKU-GTCP10-8 and CLIB 1740) representing a novel anamorphic yeast species were isolated from a grease sample collected from a grease trap in Thailand and from an unidentified fungus collected in French Guiana, respectively. On the basis of phylogenetic analysis based on the combined D1/D2 domain of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region, Lachancea fermentati CBS 707^T was the closely related species with 12.8 % sequence divergence (70 nucleotide substitutions and three gaps in 571 nucleotides) and 28.1 % sequence divergence (93 nucleotide substitutions and 90 gaps in 651 nucleotides) in the D1/D2 domain of the LSU rRNA gene and the ITS region, respectively. Phylogenetic analysis based on the concatenated sequences of the five genes including the small subunit rRNA gene, the D1/D2 domain of the LSU rRNA gene, the ITS region, translation elongation factor-1 alpha (TEF1) and RNA polymerase II subunit 2 (RPB2) genes confirmed that the two strains (DMKU-GTCP10-8 and CLIB 1740) were well-separated from other described yeast genera in Saccharomycetaceae. Hence, Savitreea pentosicarens gen. nov., sp. nov. is proposed to accommodate these two strains as members of the family Saccharomycetaceae. The holotype is S. pentosicarens DMKU-GTCP10-8^T (ex-type strain TBRC 12159=PYCC 8490; MycoBank number 835044).

Wickerhamiella osmotolerans sp. nov. and Wickerhamiella tropicalis sp. nov., novel ascomycetous yeast in the family Wickerhamiellaceae

Seven yeast strains, DMKU VGT1-14T, DMKU VGT1-19T, DMKU-JMGT1-28, DMKU-JMGT1-32, DMKU VGT2-06, DMKU VGT2-19 and DMKU VGT6-14, were isolated from a grease trap in Thailand and two strains, SJ-1 and SN-102 were isolated from the sea surface microlayer in Taiwan. On the basis of phenotypic characteristics and sequence analysis of the D1/D2 region of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region, these strains represented two novel yeast species of the genus Wickerhamiella. In terms of pairwise sequence similarity, four strains, DMKU VGT1-14, DMKU-JMGT1-32, DMKU VGT6-14 and SN-102, were closely related to Wickerhamiella infanticola NRRL Y-17858T but differed by 13 nucleotide substitutions with one gap (2.46 %) in the D1/D2 domain of the LSU rRNA gene and 15 nucleotide substitutions with 23 gaps (4.2 %) in the ITS region. The strains DMKU VGT1-19T, DMKU-JMGT1-28, DMKU VGT2-06, DMKU VGT2-19 and SJ-1, differed from the type strain of the most closely related species, Wickerhamiella sorbophila NRRL Y-7921T, by nine nucleotide substitutions with one gap (1.66 %) in the D1/D2 domain of the LSU rRNA gene and nine nucleotide substitutions with 17 gaps (2.52%) in the ITS region. Hence, the names Wickerhamiella osmotolerans sp. nov. and Wickerhamiella tropicalis sp. nov. are proposed to accommodate these species in the genus Wickerhamiella. The holotypes are W. osmotolerans DMKU VGT1-14T (ex-type strain TBRC 11425=PYCC 8359=CGMCC 2.6179; Mycobank number 833394) and W. tropicalis DMKU VGT1-19T (ex-type strain TBRC 11426=PYCC 8360=CGMCC 2.6180; Mycobank number 833393).

Grease Waste as a Reservoir of Lipase-Producing Yeast and Description of Limtongella siamensis gen. nov., sp. nov

A total of 175 yeast isolates were obtained from grease samples. Based on the D1/D2 region of the large subunit (LSU) ribosomal RNA (rRNA) gene analysis, 150 yeast isolates were identified as belonging to 36 described yeast species, whereas 25 isolates required more analysis. Among the described species, Rhodotorula mucilaginosa was the only Basidiomycetous yeast, whereas 149 isolates were identified as belonging to 35 described species of 15 genera in the phylum Ascomycota, and Candida tropicalis was the most abundant species. A study of lipase production indicated that strain DMKU-JMGT1-45 showed volumetric activity of 38.89 ± 9.62 and 155.56 ± 14.70 U/mL when grown in yeast extract malt extract (YM) and YM supplemented with 1% olive oil, respectively. In addition, this strain intracellularly accumulated lipid, of which the fatty acid profile revealed the major fatty acids to be 39.9% oleic acid (C18:1), 27.61% palmitoleic acid (C16:1) and 14.97% palmitic acid (C16:0). A phylogenetic analysis of the combined multi-locus gene sequences showed that the strains DMKU-JMGT1-45^T and DMKU-JMGT4-14 formed a well-separated lineage and could not be assigned to any of the currently recognized genera of the Saccharomycetales. Limtongella siamensis gen. nov., sp. nov. is therefore proposed to accommodate these two strains as members of the order Saccharomycetales.

Limtongozyma siamensis gen. nov., sp. nov., a yeast species in the Saccharomycetales and reassignment of Candida cylindracea to the genus Limtongozyma

Two yeast strains, DMKU-WBL1-3 and DMKU GT3-16, were obtained from grease samples collected from grease traps at the Kasetsart University canteen, Thailand. Pairwise sequence analysis indicated that the strains were closely related to Candida cylindracea NRRL Y-17506^T, but differed by 11 and 35 nucleotide substitutions in the D1/D2 domain of the large subunit (LSU) rRNA gene and the ITS region, respectively. Based on sequence divergences, the novel species was distinguished from C. cylindracea. The results of phylogenetic analysis based on the concatenated sequences from small subunit rRNA, ITS region and LSU rRNA genes showed that the two strains and C. cylindracea NRRL Y-17506^T formed a distinct lineage related to the genus Babjeviella. A novel genus, Limtongozyma, is proposed to accommodate these clade members. Hence, Candida cylindracea NRRL Y-17506^T is transferred to this genus and assigned as the type species of the genus. The holotype of Limtongozyma siamensis is DMKU-WBL1-3.

Yeast communities of primary and secondary peat swamp forests in southern Thailand

Khanthuli peat swamp forest (PSF) is one of a few fertile peat swamp forests that remain in Thailand. It is composed of primary PSF and some areas which have been degraded to secondary PSF due to drought, wildfires and land conversion, which have resulted in a decrease in peat layers and change in the species of the plant community. In this study, diversity of yeasts in peat from both primary and secondary PSF areas of the Khanthuli PSF was determined based on culture-dependent approaches, using dilution plate and enrichment techniques. A total of 66 yeast isolates were identified by the analysis of sequence similarity of the D1/D2 region of the large subunit rRNA gene or the combined analysis of sequence of the D1/D2 region and internal transcribed spacer region and confirmed by phylogenetic analysis of the D1/D2 region to belong to 22 known yeast species and six potential new species in the genera Candida (Kurtzmaniella, Lodderomyces, Ogataea, Pichia and Yamadazyma clades), Clavispora, Cyberlindnera, Galactomyces, Hanseniaspora, Metschnikowia, Saturnispora, Schwanniomyces, Cryptotrichosporon, Pichia, Curvibasidium, Papiliotrema, Rhodotorula, and Saitozyma. The most prevalent yeasts in the primary PSF were Cyberlindnera subsufficiens and Galactomyces candidus, while Saitozyma podzolica was the most frequently found in peat from the secondary PSF. Common yeast species in both, primary and secondary PSF, were Cy. subsufficiens, G. candidus and Rhodotorula mucilaginosa.

Papiliotrema phichitensis f.a., sp. nov., a novel yeast species isolated from sugarcane leaf in Thailand

Strain DMKU-SP105^T representing a novel yeast species was isolated from the external surface of a sugarcane leaf (Saccharum officinarum L.) collected from a sugarcane plantation field in Phichit province, Thailand. On the basis of sequence analysis of the D1/D2 region of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region, the strain DMKU-SP105^T differed by 7-16 substitutions in the D1/D2 region of LSU rRNA gene and 6-22 substitutions in the ITS region from a group of related species, Papiliotrema aspenensis, Papiliotrema odontotermitis, Papiliotrema rajasthanensis and Papiliotrema laurentii. A phylogenetic analysis based on the concatenated sequences of ITS region and the D1/D2 region of the LSU rRNA gene indicated that strain DMKU-SP105^T belongs to the laurentii clade of Papiliotrema in the Tremellales and is distinct from other related species in the clade. It therefore represents a novel species of the genus Papiliotrema although the formation of basidiospores was not observed. The name Papiliotrema phichitensis f.a., sp. nov. is proposed. The type is DMKU-SP105^T (= CBS 13390^T = BCC 61187^T = NBRC 109699^T).

Isolation and characterization of a thermotolerant ammonia-oxidizing bacterium Nitrosomonas sp. JPCCT2 from a thermal power station

A thermotolerant ammonia-oxidizing bacterium strain JPCCT2 was isolated from activated sludge in a thermal power station. Cells of JPCCT2 are short non-motile rods or ellipsoidal. Molecular phylogenetic analysis of 16S rRNA gene sequences demonstrated that JPCCT2 belongs to the genus Nitrosomonas with the highest similarity to Nitrosomonas nitrosa Nm90 (100%), Nitrosomonas sp. Nm148 (99.7%), and Nitrosomonas communis Nm2 (97.7%). However, G+C content of JPCCT2 DNA was 49.1 mol% and clearly different from N. nitrosa Nm90, 47.9%. JPCCT2 was capable of growing at temperatures up to 48°C, while N. nitrosa Nm90 and N. communis Nm2 could not grow at 42°C. Moreover, JPCCT2 grew similarly at concentrations of carbonate 0 and 5 gL⁻¹. This is the first report that Nitrosomonas bacterium is capable of growing at temperatures higher than 37°C.

Candida saraburiensis sp. nov. and Candida prachuapensis sp. nov., xylose-utilizing yeast species isolated in Thailand

Four strains of two novel xylose-utilizing yeast species were obtained from samples collected in Thailand from decaying corncobs (strains KU-Xs13T and KU-Xs18), a decaying grass (KU-Xs20) and estuarine water from a mangrove forest (WB15T). On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics and sequence analysis of the D1/D2 domain of the large subunit rRNA gene, the four strains were found to represent two novel species of the genus Candida in the Candida albicans/Lodderomyces elongisporus clade. Three strains (KU-Xs13T, KU-Xs18 and KU-Xs20) were assigned as a single novel species, which was named Candida saraburiensis sp. nov. The type strain is KU-Xs13T (=CBS 11696T=NBRC 106721T=BCC 39601T). Strain WB15T represented another novel species of the genus Candida that was named Candida prachuapensis sp. nov. The type strain is WB15T (=CBS 11024T=NBRC 104881T=BCC 29904T).

Candida xylanilytica sp. nov., a xylan-degrading yeast species isolated from Thailand

Xylan is a major component of hemicellulose, which constitutes about 40 % of plant biomass. Hydrolysis of xylan into simple sugars is one of the important steps in the conversion of lignocellulosic material to value-added products. During an investigation of cellulose- and xylan-degrading yeasts, two yeast strains that were able to use cellulose and xylan as sole carbon source were found to represent a phylogenetically distinct species in the Spathaspora clade. The closest species in terms of pairwise sequence similarity in the D1/D2 domain of the LSU rRNA gene was Candida subhashii. The novel species can be distinguished from the other species in the Spathaspora clade based on the ability to assimilate methanol and raffinose, growth in medium containing 60 % glucose, and growth at 42 °C. It ferments glucose but not other carbohydrates. The name Candida xylanilytica sp. nov. is proposed for this species. The type strain is KU-Xn11(T) ( = NBRC 106499(T)  = BCC 34694(T)  = CBS 11761(T)).

Candida siamensis sp. nov., an anamorphic yeast species in the Saturnispora clade isolated in Thailand

Three strains of a novel anamorphic yeast species were isolated from natural samples collected in Thailand, including strain EF10 isolated from sediment in a mangrove forest, strain ST-473 from rotten wood, and strain ST-479 from a wild mushroom (Hygrophorus sp.). Analysis of the D1/D2 domains of the large-subunit rRNA gene sequence revealed that the sequence of strain EF10 differed from the other two strains (ST-473 and ST-479), which had identical sequences, by only one nucleotide (nt) substitution in 535 nt. The closest species in terms of pairwise sequence similarity was Saturnispora mendoncae, with 32 nt substitutions and seven gaps in 535 nt. Phylogenetic analysis demonstrated that the three strains form a cluster with S. mendoncae and the other eight species in the Saturnispora clade. Phenotypic characteristics of the three strains were the same including proliferation by multilateral budding, absence of ascospores and negative diazonium blue B and urease reactions. The major ubiquinone was Q-7. On this basis, the three strains were assigned to a single novel species of the genus Candida, for which the name Candida siamensis sp. nov. is proposed. The type strain is EF10(T) (=BCC 29901(T)=NBRC 104878(T)=CBS 11022(T)).

A mobile unit: an effective service for cervical cancer screening among rural Thai women

BACKGROUND

We carried out a systematic screening programme using a mobile unit with the purpose of increasing use of Papanicolaou (Pap) smear screening among rural Thai women. The mobile unit campaign was carried out initially between January and February 1993 and then in 1996 in all the 54 rural villages in Mae Sot District, Tak Province, northern Thailand.

METHODS

To evaluate the effect of the programme on changes in knowledge and use of screening, we compared the results of three interview surveys of women, 18-65 years old, in villages selected by systematic sampling for each survey; first in 1991 (before the operation of the programme), secondly in 1994 (one year after the first screening campaign), and last in 1997 (one year after the second campaign). This report also compares data on Pap smears taken by the mobile unit with other existing screening services in the study area.

RESULTS

A total of 1603, 1369, and 1576 women respectively, participated in each survey. The proportion of women reported knowing of the Pap smear test increased from 20.8% in 1991 to 57.3% in 1994 and to 75.5% in 1997. The proportion of women who had ever had a Pap smear increased from 19.9% in 1991 to 58.1% in 1994 and to 70.1% by 1997. Screening by the mobile unit accounted for 85.2% of all cervical intraepithelial neoplasia (CIN) III and all invasive cancers identified among the Pap smears taken by screening services in the area between 1992 and 1996. The rate of CIN III was 3.5/1000 smears in this screening programme, which was 5.2 and 2.0 times higher than the rates in the maternal and child health/family planning clinic and the annual one-week mass screening campaign respectively.

CONCLUSIONS

The use of a mobile unit may be an effective screening programme in rural areas where existing screening activities cannot effectively reach the female population at risk.

Screening assessment of persons 40-59 years of age in rural Thailand by a mobile health unit

This paper reports a screening survey using a mobile unit to determine the prevalence of chronic disorders among persons aged 40-59 years in rural Thailand. A total of 4,812 persons from all the 54 rural villages in Mae Sot District, Tak Province, northern Thailand, were interviewed and examined in 1995. A higher proportion (59.3%) of men were current tobacco smokers than among women (40.4%). A higher proportion (69.6%) of men were current alcohol drinkers compared with women (38.6%). Cutting/piercing was the most frequently reported injury, followed by falls. About half (47.9%) of the persons surveyed had a body mass index (BMI) between 20 and 24.9 and only 2.6 per cent had a BMI of 30 or over. The overall prevalence rates of hypertension and diabetes in the persons surveyed were 13.3 per cent and 2.4 per cent respectively. Of the persons screened, 28.8 per cent had borderline-high blood cholesterol (200-239 mg/dl) and 12.9 per cent had high blood cholesterol (> or = 240 mg/dl). About 61 per cent of hypertensive persons, 92 per cent of diabetic persons, and nearly all of those with dyslipidaemia were first detected during this screening programme. Five women with breast cancer and 22 with benign breast disorders were also identified during the survey. A screening programme using a mobile unit may be useful in identifying treatable disorders in rural areas, where existing screening services cannot effectively cover the population at risk.

Effect of motorcycle rider education on changes in risk behaviours and motorcycle-related injuries in rural Thailand

A community-based programme for motorcycle rider education was provided for motorcyclists in all villages of 3 randomly selected subdistricts in Mae Sot District, Tak Province, northern Thailand, between January and March 1995. To determine the extent of changes in risk-taking behaviours, we conducted an interview survey of motorcyclists in 3 villages selected by systematic sampling from the 3 intervention subdistricts and in 3 control (without intervention) villages for comparison in March 1997, 2 years after the programme. Motorcyclists in the intervention villages (69.7%) were significantly more likely to have valid licences than those in the control villages (46.5%). The proportion of motorcyclists who always or often wore helmets was significantly greater in the intervention sample (46.0%) than in the control sample (20.5%). In 1994, the annual incidence rate of motorcycle-related injuries was slightly higher in the intervention areas than in the control areas Following the education programme, the injury rates for 1995 and 1996 were significantly lower in the intervention than in the control population. The annual number and rate of fatal motorcycle injuries decreased after the intervention although there was no significant difference between the two populations. Motorcycle rider education may be a promising intervention for prevention of motorcycle-related injuries in rural areas where road safety measures, particularly enforcement activities, are commonly limited.

Screening assessment of the elderly in rural Thailand by a mobile unit

Using a mobile health unit, we conducted a survey to determine the prevalence of social and medical problems among an elderly population in rural Thailand. 3302 persons aged 60 years and older from 54 villages in Mae Sot District, Tak Province, northern Thailand, were interviewed and examined between November 1993 and April 1994. About 4% of those surveyed lived alone and most of them preferred to remain with their relatives and neighbours in the community. The proportion of current tobacco smokers was slightly higher in men (55.5%) than in women (51.4%). Men also had a higher proportion of current alcohol drinkers (20.3%) than women (5.3%). About 80% of the elderly reported having used medication within one month before the interview. Falls were the most common cause of reported injury, followed by cutting/piercing. The proportion of the elderly who had difficulty with activities of daily living was higher for women than men and increased with age. Meal preparation was the most common activity needing help. About 58% of hypertensive persons and 75% of those with diabetes were first detected during the survey. Some persons with treatable disorders such as senile cataract and dyslipidaemia were also detected by the screening programme. Geriatric screening assessment using mobile units may be helpful in uncovering treatable conditions among the elderly in rural areas.