Displaying publications 1 - 20 of 34 in total

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  1. Isolation of palm oil-utilising, polyhydroxyalkanoate (PHA)-producing bacteria by an enrichment technique
    Alias Z, Tan IK
    Bioresour Technol, 2005 Jul;96(11):1229-34.
    PMID: 15734309
    In early attempts to isolate palm oil-utilising bacteria from palm oil mill effluent (POME), diluted liquid samples of POME were spread on agar containing POME as primary nutrient. 45 purified colonies were screened for intracellular lipids by staining with Sudan Black B. Of these, 10 isolates were positively stained. The latter were grown in a nitrogen-limiting medium with palm olein (a triglyceride) or saponified palm olein (salts of fatty acids) as carbon source. None of the isolates grew in the palm olein medium but all grew well in the saponified palm olein medium. Of the latter however, only one isolate was positively stained with Nile Blue A, indicating the presence of PHA. This method did not successfully generate bacterial isolates which could metabolise palm olein to produce PHA. An enrichment technique was therefore developed whereby a selective medium was designed. The latter comprised minerals and palm olein (1% w/v) as sole carbon source to which POME (2.5% v/v) was added as the source of bacteria. The culture was incubated with shaking at 30 degrees C for 4 weeks. Out of seven isolates obtained from the selective medium, two isolates, FLP1 and FLP2, could utilise palm olein for growth and production of the homopolyester, poly(3-hydroxybutyrate). FLP1 is gram-negative and is identified (BIOLOG) to have 80% similarity to Burkholderia cepacia. When grown with propionate or valerate, FLP1 produced a copolyester, poly(3-hydroxybutyrate-co-3-hydroxyvalerate).
    Matched MeSH terms: Proteobacteria/isolation & purification*; Proteobacteria/metabolism*
  2. A novel medium for the isolation of N-acylhomoserine lactone-degrading bacteria
    Chan KG, Yin WF, Sam CK, Koh CL
    J Ind Microbiol Biotechnol, 2009 Feb;36(2):247-51.
    PMID: 18946694 DOI: 10.1007/s10295-008-0491-x
    A novel chemically defined medium, named KG medium, supplemented with N-3-oxo-hexanoylhomoserine lactone (3-oxo-C6-HSL), an acylhomoserine lactone (AHL) used as signalling molecules in Gram-negative bacterial cell-to-cell communication, as the sole source of carbon and nitrogen, was designed and successfully used for the enrichment and isolation of AHL-degrading bacteria. A 3-oxo-C6-HSL-degrading bacterium, 13sw7, was isolated from sewage after six enrichment transfers in the 3-oxo-C6-HSL-containing KG medium. On the basis of the almost complete 16S ribosomal DNA sequence, isolate 13sw7 was clustered with unculturable beta-proteobacteria. This study indicates that the AHL-containing KG medium is effective in isolating AHL-degrading bacteria, including those previously considered unculturable, from environmental sources. To the best of our knowledge, this is the first documentation of the isolation of an AHL-degrading proteobacterium from sewage.
    Matched MeSH terms: Proteobacteria/classification; Proteobacteria/genetics; Proteobacteria/growth & development; Proteobacteria/isolation & purification*
  3. Fulltext Analysis of Antarctic proteobacteria by PCR fingerprinting and screening for antimicrobial secondary metabolites
    Lee LH, Cheah YK, Nurul Syakima AM, Shiran MS, Tang YL, Lin HP, et al.
    Genet. Mol. Res., 2012;11(2):1627-41.
    PMID: 22782582 DOI: 10.4238/2012.June.15.12
    Fifty-seven proteobacterium species were successfully isolated from soils of Barrientos Island of the Antarctic using 11 different isolation media. Analysis of 16S rDNA sequencing of these isolates showed that they belonged to eight different genera, namely Bradyrhizobium, Sphingomonas, Methylobacterium, Caulobacter, Paracoccus, Ralstonia, Rhizobium, and Staphylococcus. All isolates were studied for capability of producing antimicrobial and antifungal secondary metabolites using high-throughput screening models. Approximately 23 (13/57) and 2% (1/57) of isolates inhibited growth of Candida albicans ATCC 10231(T) and Staphylococcus aureus ATCC 51650(T), respectively. These results indicated that proteobacterium species isolates from Antarctic could serve as potential source of useful bioactive metabolites. Enterobacterial repetitive intergenic consensus (ERIC)-PCR fingerprinting produced nine clusters and 13 single isolates, with a high D value of 0.9248. RAPD fingerprinting produced six clusters and 13 single isolates, with a relatively low D value of 0.7776. ERIC-PCR analysis proved to have better discrimination capability than RAPD analysis and generated better clustering for all proteobacterium species isolates. We conclude that ERIC-PCR is a robust, reliable and rapid molecular typing method for discriminating different genera of proteobacteria.
    Matched MeSH terms: Proteobacteria/classification; Proteobacteria/genetics*
  4. Fulltext Pandoraea sp. RB-44, a novel quorum sensing soil bacterium
    Han-Jen RE, Wai-Fong Y, Kok-Gan C
    Sensors (Basel), 2013 Oct 18;13(10):14121-32.
    PMID: 24145919 DOI: 10.3390/s131014121
    Proteobacteria are known to communicate via signaling molecules and this process is known as quorum sensing. The most commonly studied quorum sensing molecules are N-acylhomoserine lactones (AHLs) that consists of a homoserine lactone moiety and an N-acyl side chain with various chain lengths and degrees of saturation at the C-3 position. We have isolated a bacterium, RB-44, from a site which was formally a landfill dumping ground. Using matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry analysis, this isolate was identified as a Pandoraea sp.which was then screened for AHL production using biosensors which indicated its quorum sensing properties. To identify the AHL profile of Pandoraea sp. RB-44, we used high resolution tandem mass spectrometry confirming that this isolate produced N-octanoylhomoserine lactone (C8-HSL). To the best of our knowledge, this is the first report that showed quorum sensing activity exhibited by Pandoraea sp. Our data add Pandoraea sp. to the growing number of bacteria that possess QS systems.
    Matched MeSH terms: Proteobacteria/classification; Proteobacteria/isolation & purification*; Proteobacteria/physiology*
  5. High-temperature EBPR process: the performance, analysis of PAOs and GAOs and the fine-scale population study of Candidatus "Accumulibacter phosphatis"
    Ong YH, Chua ASM, Fukushima T, Ngoh GC, Shoji T, Michinaka A
    Water Res, 2014 Nov 01;64:102-112.
    PMID: 25046374 DOI: 10.1016/j.watres.2014.06.038
    The applicability of the enhanced biological phosphorus removal (EBPR) process for the removal of phosphorus in warm climates is uncertain due to frequent reports of EBPR deterioration at temperature higher than 25 °C. Nevertheless, a recent report on a stable and efficient EBPR process at 28 °C has inspired the present study to examine the performance of EBPR at 24 °C-32 °C, as well as the PAOs and GAOs involved, in greater detail. Two sequencing batch reactors (SBRs) were operated for EBPR in parallel at different temperatures, i.e., SBR-1 at 28 °C and SBR-2 first at 24 °C and subsequently at 32 °C. Both SBRs exhibited high phosphorus removal efficiencies at all three temperatures and produced effluents with phosphorus concentrations less than 1.0 mg/L during the steady state of reactor operation. Real-time quantitative polymerase chain reaction (qPCR) revealed Accumulibacter-PAOs comprised 64% of the total bacterial population at 24 °C, 43% at 28 °C and 19% at 32 °C. Based on fluorescent in situ hybridisation (FISH), the abundance of Competibacter-GAOs at both 24 °C and 28 °C was rather low (<10%), while it accounted for 40% of the total bacterial population at 32 °C. However, the smaller Accumulibacter population and larger population of Competibacter at 32 °C did not deteriorate the phosphorus removal performance. A polyphosphate kinase 1 (ppk1)-based qPCR analysis on all studied EBPR processes detected only Accumulibacter clade IIF. The Accumulibacter population shown by 16S rRNA and ppk1 was not significantly different. This finding confirmed the existence of single clade IIF in the processes and the specificity of the clade IIF primer sets designed in this study. Habitat filtering related to temperature could have contributed to the presence of a unique clade. The clade IIF was hypothesised to be able to perform the EBPR activity at high temperatures. The clade's robustness most likely helps it to fit the high-temperature EBPR sludge best and allows it not only to outcompete other Accumulibacter clades but coexist with GAOs without compromising EBPR activity.
    Matched MeSH terms: Proteobacteria/isolation & purification*; Proteobacteria/metabolism
  6. Fulltext Inhibiting N-acyl-homoserine lactone synthesis and quenching Pseudomonas quinolone quorum sensing to attenuate virulence
    Chan KG, Liu YC, Chang CY
    Front Microbiol, 2015;6:1173.
    PMID: 26539190 DOI: 10.3389/fmicb.2015.01173
    Bacteria sense their own population size, tune the expression of responding genes, and behave accordingly to environmental stimuli by secreting signaling molecules. This phenomenon is termed as quorum sensing (QS). By exogenously manipulating the signal transduction bacterial population behaviors could be controlled, which may be done through quorum quenching (QQ). QS related regulatory networks have been proven their involvement in regulating many virulence determinants in pathogenic bacteria in the course of infections. Interfering with QS signaling system could be a novel strategy against bacterial infections and therefore requires more understanding of their fundamental mechanisms. Here we review the development of studies specifically on the inhibition of production of N-acyl-homoserine lactone (AHL), a common proteobacterial QS signal. The opportunistic pathogen, Pseudomonas aeruginosa, equips the alkylquinolone (AQ)-mediated QS which also plays crucial roles in its pathogenicity. The studies in QQ targeting on AQ are also discussed.
    Matched MeSH terms: Proteobacteria
  7. Fulltext Whole genome sequencing enables the characterization of BurI, a LuxI homologue of Burkholderia cepacia strain GG4
    How KY, Hong KW, Chan KG
    PeerJ, 2015;3:e1117.
    PMID: 26290785 DOI: 10.7717/peerj.1117
    Quorum sensing is a mechanism for regulating proteobacterial gene expression in response to changes in cell population. In proteobacteria, N-acyl homoserine lactone (AHL) appears to be the most widely used signalling molecules in mediating, among others, the production of extracellular virulence factors for survival. In this work, the genome of B. cepacia strain GG4, a plasmid-free strain capable of AHL synthesis was explored. In silico analysis of the 6.6 Mb complete genome revealed the presence of a LuxI homologue which correspond to Type I quorum sensing. Here, we report the molecular cloning and characterization of this LuxI homologue, designated as BurI. This 609 bp gene was cloned and overexpressed in Escherichia coli BL21(DE3). The purified protein was approximately 25 kDa and is highly similar to several autoinducer proteins of the LuxI family among Burkholderia species. To verify the AHL synthesis activity of this protein, high resolution liquid chromatography-mass spectrometry analysis revealed the production of 3-oxo-hexanoylhomoserine lactone, N-octanoylhomoserine lactone and 3-hydroxy-octanoylhomoserine lactone from induced E. coli BL21 harboring the recombinant BurI. Our data show, for the first time, the cloning and characterization of the LuxI homologue from B. cepacia strain GG4 and confirmation of its AHL synthesis activity.
    Matched MeSH terms: Proteobacteria
  8. Fulltext Unravelling the genome of long chain N-acylhomoserine lactone-producing Acinetobacter sp. strain GG2 and identification of its quorum sensing synthase gene
    How KY, Hong KW, Sam CK, Koh CL, Yin WF, Chan KG
    Front Microbiol, 2015;6:240.
    PMID: 25926817 DOI: 10.3389/fmicb.2015.00240
    Myriad proteobacteria use N-acyl homoserine lactone (AHL) molecules as quorum sensing (QS) signals to regulate different physiological functions, including virulence, antibiotic production, and biofilm formation. Many of these proteobacteria possess LuxI/LuxR system as the QS mechanism. Recently, we reported the 3.89 Mb genome of Acinetobacter sp. strain GG2. In this work, the genome of this long chain AHL-producing bacterium was unravelled which led to the molecular characterization of luxI homologue, designated as aciI. This 552 bp gene was cloned and overexpressed in Escherichia coli BL21(DE3). The purified protein was ∼20.5 kDa and is highly similar to several autoinducer proteins of LuxI family among Acinetobacter species. To verify the AHL synthesis activity of this protein, high-resolution liquid chromatography-mass spectrometry analysis revealed the production of 3-oxo-dodecanoyl-homoserine lactone and 3-hydroxy-dodecanoyl-homoserine lactone from induced E. coli harboring the recombinant AciI. Our data show for the first time, the cloning and characterization of the luxI homologue from Acinetobacter sp. strain GG2, and confirmation of its AHLs production. These data are of great significance as the annotated genome of strain GG2 has provided a valuable insight in the study of autoinducer molecules and its roles in QS mechanism of the bacterium.
    Matched MeSH terms: Proteobacteria
  9. Fulltext Diversity of thermophiles in a Malaysian hot spring determined using 16S rRNA and shotgun metagenome sequencing
    Chan CS, Chan KG, Tay YL, Chua YH, Goh KM
    Front Microbiol, 2015;6:177.
    PMID: 25798135 DOI: 10.3389/fmicb.2015.00177
    The Sungai Klah (SK) hot spring is the second hottest geothermal spring in Malaysia. This hot spring is a shallow, 150-m-long, fast-flowing stream, with temperatures varying from 50 to 110°C and a pH range of 7.0-9.0. Hidden within a wooded area, the SK hot spring is continually fed by plant litter, resulting in a relatively high degree of total organic content (TOC). In this study, a sample taken from the middle of the stream was analyzed at the 16S rRNA V3-V4 region by amplicon metagenome sequencing. Over 35 phyla were detected by analyzing the 16S rRNA data. Firmicutes and Proteobacteria represented approximately 57% of the microbiome. Approximately 70% of the detected thermophiles were strict anaerobes; however, Hydrogenobacter spp., obligate chemolithotrophic thermophiles, represented one of the major taxa. Several thermophilic photosynthetic microorganisms and acidothermophiles were also detected. Most of the phyla identified by 16S rRNA were also found using the shotgun metagenome approaches. The carbon, sulfur, and nitrogen metabolism within the SK hot spring community were evaluated by shotgun metagenome sequencing, and the data revealed diversity in terms of metabolic activity and dynamics. This hot spring has a rich diversified phylogenetic community partly due to its natural environment (plant litter, high TOC, and a shallow stream) and geochemical parameters (broad temperature and pH range). It is speculated that symbiotic relationships occur between the members of the community.
    Matched MeSH terms: Proteobacteria
  10. Fulltext Contrasting soil bacterial community structure between the phyla Acidobacteria and Proteobacteria in tropical Southeast Asian and temperate Japanese forests
    Miyashita NT
    Genes Genet Syst, 2015;90(2):61-77.
    PMID: 26399766 DOI: 10.1266/ggs.90.61
    Soil bacterial community structures of six dominant phyla (Acidobacteria, Proteobacteria, Verrucomicrobia, Planctomycetes, Bacteroidetes and Actinobacteria) and unclassified bacteria detected in tropical Sarawakian and temperate Japanese forests were compared based on 16S rRNA gene sequence variation. The class composition in each phylum was similar among the studied forests; however, significant heterogeneities of class frequencies were detected. Acidobacteria and Proteobacteria were the most dominant phyla in all six forests, but differed in the level of bacterial species diversity, pattern of species occurrence and association pattern of species composition with physicochemical properties in soil. Species diversity among Acidobacteria was approximately half that among Proteobacteria, based on the number of clusters and the Chao1 index, even though a similar number of sequence reads were obtained for these two phyla. In contrast, species diversity within Planctomycetes and Bacteroidetes was nearly as high as within Acidobacteria, despite many fewer sequence reads. The density of species (the number of sequence reads per cluster) correlated negatively with species diversity, and species density within Acidobacteria was approximately twice that within Proteobacteria. Although the percentage of forest-specific species was high for all bacterial groups, sampling site-specific species varied among bacterial groups, indicating limited inter-forest migration and differential movement of bacteria in forest soil. For five of the seven bacterial groups, including Acidobacteria, soil pH appeared to strongly influence species composition, but this association was not observed for Proteobacterial species. Topology of UPGMA trees and pattern of NMDS plots among the forests differed among the bacterial groups, suggesting that each bacterial group has adapted and evolved independently in each forest.
    Matched MeSH terms: Proteobacteria/classification; Proteobacteria/genetics*; Proteobacteria/isolation & purification
  11. Phototrophic purple bacteria as feed supplement on the growth, feed utilization and body compositions of Malaysian mahseer, tor tambroides juveniles
    Nor Hafizah Zakaria, Mohammad Mustafizur Rahman, Ahmed Jalal Khan Chowdhury, Zaima Azira Zainal Abidin
    Sains Malaysiana, 2016;45:135-140.
    The application of microbial techniques in aquaculture has been playing a vital role to increase the production yield by improving the nutritional values of the targeted fish. Phototrophic purple bacteria as single cell protein (SCP) appears to be a promising substitution for protein rich supplement for aquaculture feeds making them a promising growth enhancer in aquaculture industry. Two species of phototrophic purple bacteria, Marichromatium sp. and Rhodopseudomonas sp. were used in the commercial diet to compare the growth, survival rate and feed utilizationon for Tor tambroides juvenile. Purple bacteria were isolated from mangrove sediment and fish tank and mass cultured using 112 synthetic media under anaerobic light condition. Bacterial cells were included in the diets by mixing the fresh biomass with the crushed commercial pellet, re-pelleted and air-dried. The experimental diets were fed to the fingerlings twice per day for 10 weeks to satiation level. The results showed that there were trends of increased growth, better survival rate and improved feed conversion ratio when fed with diet 1 (Marichromatium sp.) compared with other diets. There was significant difference (p<0.05) between the sampling days. The specific growth rate and weight gain of the fish fed with diet 1 were 0.49 % and 4.92 g, respectively, compared to 0.42% and 4.11 g from the control. This study suggested that purple bacteria could be used in feed formulation as a supplement to promote growth and survival of freshwater fishes in Malaysia.
    Matched MeSH terms: Proteobacteria
  12. Isolation and identification of metabolites from the gram-negative proteobacteria of burkholderia cenocepacia and serratia marcescens
    Chan Kg, Yap Ac, Choo Ym
    Sains Malaysiana, 2016;45:1073-1077.
    Burkholderia cenocepacia and Serratia marcescens are Gram-negative proteobacteria commonly found in the natural
    environment and are also opportunistic pathogens that caused a number of human diseases. The fermentation culture of
    Burkholderia cenocepacia yielded three compounds, 4-(2-hydroxyethoxy)-phenol (1), Maculosin (2) and methyl myristate
    (3). Compound 2 was also isolated together with cyclo(L-Leu-L-Pro) (4) from Serratia marcescens. Compound 1 was
    isolated from a natural source for the first time and the first isolation of compounds 2-4 was also reported from both
    Burkholderia cenocepacia and Serratia marcescens.
    Matched MeSH terms: Proteobacteria
  13. Diversity of microbiota associated with symptomatic and non-symptomatic bacterial wilt-diseased banana plants determined using 16S rRNA metagenome sequencing
    Suhaimi NSM, Goh SY, Ajam N, Othman RY, Chan KG, Thong KL
    World J Microbiol Biotechnol, 2017 Aug 21;33(9):168.
    PMID: 28828756 DOI: 10.1007/s11274-017-2336-0
    Banana is one of the most important fruits cultivated in Malaysia, and it provides many health benefits. However, bacterial wilt disease, which attacks bananas, inflicts major losses on the banana industry in Malaysia. To understand the complex interactions of the microbiota of bacterial wilt-diseased banana plants, we first determined the bacterial communities residing in the pseudostems of infected (symptomatic) and diseased-free (non-symptomatic) banana plants. We characterized the associated microorganisms using the targeted 16S rRNA metagenomics sequencing on the Illumina MiSeq platform. Taxonomic classifications revealed 17 and nine known bacterial phyla in the tissues of non-symptomatic and symptomatic plants, respectively. Cyanobacteria and Proteobacteria (accounted for more than 99% of the 16S rRNA gene fragments) were the two most abundant phyla in both plants. The five major genera found in both plant samples were Ralstonia, Sphingomonas, Methylobacterium, Flavobacterium, and Pseudomonas. Ralstonia was more abundant in symptomatic plant (59% out of the entire genera) as compared to those in the non-symptomatic plant (only 36%). Our data revealed that 102 bacterial genera were only assigned to the non-symptomatic plant. Overall, this study indicated that more diverse and abundant microbiota were associated with the non-symptomatic bacterial wilt-diseased banana plant as compared to the symptomatic plant. The higher diversity of endophytic microbiota in the non-symptomatic banana plant could be an indication of pathogen suppression which delayed or prevented the disease expression. This comparative study of the microbiota in the two plant conditions might provide caveats for potential biological control strategies.
    Matched MeSH terms: Proteobacteria/classification; Proteobacteria/genetics; Proteobacteria/isolation & purification
  14. Fulltext Geographical variation in soil bacterial community structure in tropical forests in Southeast Asia and temperate forests in Japan based on pyrosequencing analysis of 16S rRNA
    Ito N, Iwanaga H, Charles S, Diway B, Sabang J, Chong L, et al.
    Genes Genet Syst, 2017 Sep 12;92(1):1-20.
    PMID: 28003572 DOI: 10.1266/ggs.16-00013
    Geographical variation in soil bacterial community structure in 26 tropical forests in Southeast Asia (Malaysia, Indonesia and Singapore) and two temperate forests in Japan was investigated to elucidate the environmental factors and mechanisms that influence biogeography of soil bacterial diversity and composition. Despite substantial environmental differences, bacterial phyla were represented in similar proportions, with Acidobacteria and Proteobacteria the dominant phyla in all forests except one mangrove forest in Sarawak, although highly significant heterogeneity in frequency of individual phyla was detected among forests. In contrast, species diversity (α-diversity) differed to a much greater extent, being nearly six-fold higher in the mangrove forest (Chao1 index = 6,862) than in forests in Singapore and Sarawak (~1,250). In addition, natural mixed dipterocarp forests had lower species diversity than acacia and oil palm plantations, indicating that aboveground tree composition does not influence soil bacterial diversity. Shannon and Chao1 indices were correlated positively, implying that skewed operational taxonomic unit (OTU) distribution was associated with the abundance of overall and rare (singleton) OTUs. No OTUs were represented in all 28 forests, and forest-specific OTUs accounted for over 70% of all detected OTUs. Forests that were geographically adjacent and/or of the same forest type had similar bacterial species composition, and a positive correlation was detected between species divergence (β-diversity) and direct distance between forests. Both α- and β-diversities were correlated with soil pH. These results suggest that soil bacterial communities in different forests evolve largely independently of each other and that soil bacterial communities adapt to their local environment, modulated by bacterial dispersal (distance effect) and forest type. Therefore, we conclude that the biogeography of soil bacteria communities described here is non-random, reflecting the influences of contemporary environmental factors and evolutionary history.
    Matched MeSH terms: Proteobacteria/classification; Proteobacteria/genetics*
  15. Fulltext Exposure to environmental microbiota explains persistent abdominal pain and irritable bowel syndrome after a major flood
    Yusof N, Hamid N, Ma ZF, Lawenko RM, Wan Mohammad WMZ, Collins DA, et al.
    Gut Pathog, 2017;9:75.
    PMID: 29255490 DOI: 10.1186/s13099-017-0224-7
    Background: After an environmental disaster, the affected community is at increased risk for persistent abdominal pain but mechanisms are unclear. Therefore, our study aimed to determine association between abdominal pain and poor water, sanitation and hygiene (WaSH) practices, and if small intestinal bacterial overgrowth (SIBO) and/or gut dysbiosis explain IBS, impaired quality of life (QOL), anxiety and/or depression after a major flood.

    Results: New onset abdominal pain, IBS based on the Rome III criteria, WaSH practices, QOL, anxiety and/or depression, SIBO (hydrogen breath testing) and stools for metagenomic sequencing were assessed in flood victims. Of 211 participants, 37.9% (n = 80) had abdominal pain and 17% (n = 36) with IBS subtyped diarrhea and/or mixed type (n = 27 or 12.8%) being the most common. Poor WaSH practices and impaired quality of life during flood were significantly associated with IBS. Using linear discriminant analysis effect size method, gut dysbiosis was observed in those with anxiety (Bacteroidetes and Proteobacteria, effect size 4.8), abdominal pain (Fusobacteria, Staphylococcus, Megamonas and Plesiomonas, effect size 4.0) and IBS (Plesiomonas and Trabulsiella, effect size 3.0).

    Conclusion: Disturbed gut microbiota because of environmentally-derived organisms may explain persistent abdominal pain and IBS after a major environmental disaster in the presence of poor WaSH practices.

    Matched MeSH terms: Proteobacteria
  16. Fulltext Effects of Physiochemical Factors on Prokaryotic Biodiversity in Malaysian Circumneutral Hot Springs
    Chan CS, Chan KG, Ee R, Hong KW, Urbieta MS, Donati ER, et al.
    Front Microbiol, 2017;8:1252.
    PMID: 28729863 DOI: 10.3389/fmicb.2017.01252
    Malaysia has a great number of hot springs, especially along the flank of the Banjaran Titiwangsa mountain range. Biological studies of the Malaysian hot springs are rare because of the lack of comprehensive information on their microbial communities. In this study, we report a cultivation-independent census to describe microbial communities in six hot springs. The Ulu Slim (US), Sungai Klah (SK), Dusun Tua (DT), Sungai Serai (SS), Semenyih (SE), and Ayer Hangat (AH) hot springs exhibit circumneutral pH with temperatures ranging from 43°C to 90°C. Genomic DNA was extracted from environmental samples and the V3-V4 hypervariable regions of 16S rRNA genes were amplified, sequenced, and analyzed. High-throughput sequencing analysis showed that microbial richness was high in all samples as indicated by the detection of 6,334-26,244 operational taxonomy units. In total, 59, 61, 72, 73, 65, and 52 bacterial phyla were identified in the US, SK, DT, SS, SE, and AH hot springs, respectively. Generally, Firmicutes and Proteobacteria dominated the bacterial communities in all hot springs. Archaeal communities mainly consisted of Crenarchaeota, Euryarchaeota, and Parvarchaeota. In beta diversity analysis, the hot spring microbial memberships were clustered primarily on the basis of temperature and salinity. Canonical correlation analysis to assess the relationship between the microbial communities and physicochemical variables revealed that diversity patterns were best explained by a combination of physicochemical variables, rather than by individual abiotic variables such as temperature and salinity.
    Matched MeSH terms: Proteobacteria
  17. Fulltext Cloning and Characterization of the Autoinducer Synthase Gene from Lipid-Degrading Bacterium Cedecea neteri
    Tan KH, How KY, Tan JY, Yin WF, Chan KG
    Front Microbiol, 2017;8:72.
    PMID: 28197135 DOI: 10.3389/fmicb.2017.00072
    The process of intercellular communication among bacteria, termed quorum sensing (QS), is mediated by small diffusible molecules known as the autoinducers. QS allows the population to react to the change of cell density in unison, in processes such as biofilm formation, plasmid conjugation, virulence, motility and root nodulation. In Gram-negative proteobacteria, N-acyl homoserine lactone (AHL) is the common "language" to coordinate gene expression. This signaling molecule is usually synthesized by LuxI-type proteins. We have previously discovered that a rare bacterium, Cedecea neteri, exhibits AHL-type QS activity. With information generated from genome sequencing, we have identified the luxIR gene pair responsible for AHL-type QS and named it cneIR. In this study, we have cloned and expressed the 636 bp luxI homolog in an Escherichia coli host for further characterization. Our findings show that E. coli harboring cneI produced the same AHL profile as the wild type C. neteri, with the synthesis of AHL known as N-butyryl-homoserine lactone. This 25 kDa LuxI homolog shares high similarity with other AHL synthases from closely related species. This work is the first documentation of molecular cloning and characterization of luxI homolog from C. neteri.
    Matched MeSH terms: Proteobacteria
  18. Microbial Community Structure in a Malaysian Tropical Peat Swamp Forest: The Influence of Tree Species and Depth
    Too CC, Keller A, Sickel W, Lee SM, Yule CM
    Front Microbiol, 2018;9:2859.
    PMID: 30564202 DOI: 10.3389/fmicb.2018.02859
    Tropical peat swamp forests sequester globally significant stores of carbon in deep layers of waterlogged, anoxic, acidic and nutrient-depleted peat. The roles of microbes in supporting these forests through the formation of peat, carbon sequestration and nutrient cycling are virtually unknown. This study investigated physicochemical peat properties and microbial diversity between three dominant tree species: Shorea uliginosa (Dipterocarpaceae), Koompassia malaccensis (legumes associated with nitrogen-fixing bacteria), Eleiodoxa conferta (palm) and depths (surface, 45 and 90 cm) using microbial 16S rRNA gene amplicon sequencing. Water pH, oxygen, nitrogen, phosphorus, total phenolic contents and C/N ratio differed significantly between depths, but not tree species. Depth also strongly influenced microbial diversity and composition, while both depth and tree species exhibited significant impact on the archaeal communities. Microbial diversity was highest at the surface, where fresh leaf litter accumulates, and nutrient supply is guaranteed. Nitrogen was the core parameter correlating to microbial communities, but the interactive effects from various environmental variables displayed significant correlation to relative abundance of major microbial groups. Proteobacteria was the dominant phylum and the most abundant genus, Rhodoplanes, might be involved in nitrogen fixation. The most abundant methanogens and methanotrophs affiliated, respectively, to families Methanomassiliicoccaceae and Methylocystaceae. Our results demonstrated diverse microbial communities and provide valuable insights on microbial ecology in these extreme ecosystems.
    Matched MeSH terms: Proteobacteria
  19. Bacterial diversity and community structure of banana rhizosphere in orang asli fields and commercial plantations
    Lee JYN, Tan IKP
    Sains Malaysiana, 2018;47:243-251.
    Bacteria play an important roles in the soil ecosystem and in the rhizosphere, they are intricately linked to nutrient content
    and its accessibility to plants, plant protection and sometimes pathogenicity. Banana grows well in the tropics and it is
    popularly grown in Orang Asli (OA) (indigenous people) settlements. Banana is also grown in commercial plantations.
    In traditional planting practices, the OA do not add pesticide nor fertilizer to their crops which are planted for selfsustenance
    mainly. On the other hand, fertilizer and pesticide are added to commercial banana plantations to maximise
    yield. Rhizosphere bacteria from the banana plant, Pisang Nipah, grown in OA fields and commercial plantations were
    identified by clone library construction of the 16S rRNA gene. This was to determine whether farming practices influenced
    the bacterial community in the banana plant rhizosphere. Acidobacteria, Proteobacteria and Actinobacteria were found in
    all the soil. Other common phyla found in some soil (but not all) were Nitrospirae, Firmicutes, Bacteroidetes, Chloroflexi,
    Verrumicrobia, Gemmatimonadetes and Cyanobacteria. The bacterial diversity was a little more diverse in the OA fields
    than the commercial plantations. The latter had higher contents of nitrogen, phosphorus and potassium. These could
    have exerted selective pressure to reduce the bacterial diversity in the commercial plantations.
    Matched MeSH terms: Proteobacteria
  20. Profiles of bacterial assemblages from microplastics of tropical coastal environments
    Curren E, Leong SCY
    Sci Total Environ, 2019 Mar 10;655:313-320.
    PMID: 30471599 DOI: 10.1016/j.scitotenv.2018.11.250
    Plastic waste is a global issue of an increasing concern in aquatic ecosystems. Microplastics form a large proportion of plastic pollution in marine environments. Although microplastics are prevalent, their distribution along the coasts of tropical regions is not well studied. Microplastic pieces (1-5 mm) were collected from two distinct regions along the coastlines of Singapore, from the northern coast in the Johor Strait and the southern coast in the Singapore Strait. Microplastics were present in concentrations ranging from 9.20-59.9 particles per kg of dry sand sediment. The majority of microplastics identified were foam particles (55%) and fragments (35%). Microplastics were significantly more abundant on heavily populated beaches compared to pristine beaches. High throughput sequencing was used to profile the communities of bacteria on the surfaces of microplastic particles. The structure of the microbial communities was primarily characterised by Proteobacteria and Bacteroidetes and were distinct across sites. Hydrocarbon-degrading genera such as Erythrobacter were dominant in areas with heavy shipping and pollution. Potential pathogenic genera such as Vibrio and Pseudomonas were also identified. This study highlights the diverse bacterial assemblages present on marine microplastic surfaces and the importance of understanding the bacterial plastisphere.
    Matched MeSH terms: Proteobacteria
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