Four anaerobic-aerobic sequencing batch reactors were operated with either acetate or glucose as the main carbon sources under phosphorus poor or rich conditions. Limited phosphate loading may suppress the development of polyphosphate accumulating organisms (PAOs) leading to establishment of microbial communities without polyphosphate accumulation. These microbial communities were dominated by glycogen accumulating organisms (GAOs). PAO communities were established under the P rich loading conditions. Both PAO and GAO sludges clearly show that acetate absorption was accompanied by glycolysis with subsequent accumulation of PHAs. Glucose was anaerobically converted to PHAs and glycogen. Glycolysis in PHA synthesis was indicated by the presence of a PHA component polymer, 3-hydroxyvalerate (3HV). It is suspected that synthesis of 3HV is via formation of the intermediate metabolite Propionyl-CoA which consumes reducing power and enables microorganisms to maintain intracellular reduction oxidation potential. When glucose was injected, acetate and propionate were detected in the bulk solution suggesting that fermentation may have taken place. Respiratory quinone analyses and fluorescent in situ hybridization with an RNA targeted oligonucleotide probe revealed that there was no significant difference in microbial communities among the sludges tested.

The bacterial community structure in soil of a tropical rainforest in East Kalimantan, Indonesia, where forest fires occurred in 1997-1998, was analysed by denaturing gradient gel electrophoresis (DGGE) with soil samples collected from the area in 2001 and 2002. The study sites were composed of a control forest area without fire damage, a lightlyburned forest area, and a heavily-burned forest area. DGGE band patterns showed that there were many common bacterial taxa across the areas although the vegetation is not the same. In addition, it was indicated that a change of vegetation in burned areas brought the change in bacterial community structure during [2001][2002]. It was also indicated that, depending on a perspective, community structure of soil bacteria in post-fire non-climax forest several years after fire can be more heterogeneous compared with that in unburned climax forest. The dominant soil bacteria in the field of the present study were Acidobacteria, Actinobaceria, and Alphaproteobacteria based on the DNA sequences of DGGE bands, although they were not dominant among the culturable bacteria from the same soil samples.

A mesophilic, Gram-stain-positive, spore-forming bacterium that formed branched mycelia was isolated from paddy soil in Gunung Salak (Mount Salak), West Java, Indonesia. This strain, designated S-27T, grew at temperatures between 20 and 37 °C; the optimum growth temperature was 25 to 30 °C, and no growth was observed at 15 or 45 °C. The pH range for growth was pH 3.5 to 8.6; the optimum pH was 6.0, and no growth was observed at pH 3.0 or 9.2. Strain S-27T was able to hydrolyse polysaccharides such as starch, cellulose and xylan. The G+C content of the DNA of strain S-27T was 55.7 mol%. The major fatty acids were iso-C17 : 0 and C16 : 1 2-OH, and the major menaquinone was MK-9 (H2). The cell wall of strain S-27T contained d-glutamic acid, glycine, l-alanine, d-alanine, l-ornithine and β-alanine in a molar ratio of 1.0 : 1.6 : 1.4 : 0.6 : 0.9 : 1.1. The polar lipids consisted of phosphatidylglycerol, phosphatidylinositol and two glycolipids. The major cell-wall sugar was arabinose. Detailed phylogenetic analysis based on 16S rRNA gene sequences indicated that strain S-27T belongs to the order Ktedonobacterales and is most closely related to Ktedonobacter racemifer SOSP1-21T (89.6 % sequence identity). On the basis of its chemotaxonomic and phenotypic features and phylogenetic position, we concluded that strain S-27T represents a novel genus and species, for which we propose the name Dictyobacter aurantiacus gen. nov., sp. nov. The type strain of Dictyobacter aurantiacus is strain S-27T (=NBRC 109595T=InaCC B312T). Emendation of the description of the genus Thermosporothrix is also provided.

International audienceThe main purpose of the study was to isolate strains of bacteria capable of degrading hydrocarbons from contaminated mangroves and to investigate the ability of the isolated bacteria to degrade total petroleum hydrocarbons (TPH) in a microcosm model of an oily sludge. The potential use of these bacteria strains as environmental clean-up agents was tested by culturing them with six different polyaromatic hydrocarbon (PAH) compounds (phenothiazine, fluorene, fluoranthene, dibenzothiophene, phenanthrene, and pyrene). Six viable and culturable bacteria were isolated, and the 16S rDNA sequence for each was amplified using the primers 9F and 1510R. Sequence results were compared using the National Center for Biotechnology Information (NCBI) BLAST program and, combined with phenotypic and phylogenetic data, were used to identify three strains that belonged to the Bacillus genus and were most closely related (9899%) to Bacillus aquimaris, Bacillus megaterium, and Bacillus pumilus. The other three strains were closely related (98100%) to Flexibacteraceae bacterium, Halobacilus trueperi, and Rhodobacteraceae bacterium. Two isolates, BA-PZN and BM-PFFP, which were related to Bacillus aquimaris and Bacillus megaterium, respectively, were further characterized and showed great potential for the removal of more complex hydrocarbon compounds in the oily microcosm model

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Abstract. Tropical peatlands from southeast Asia are undergoing extensive drainage, deforestation and degradation for agriculture and human settlement purposes. This is resulting in biomass loss and subsidence of peat from its oxidation. Molecular profiling approaches were used to understand the relative influences of different land-use patterns, hydrological and physicochemical parameters on the state of degraded tropical peatlands. As microbial communities play a critical role in biogeochemical cascades in the functioning of peatlands, we used microbial and metabolic profiles as surrogates of community structure and functions, respectively. Profiles were generated from 230 bacterial 16 S rDNA fragments and 145 metabolic markers of 46 samples from 10 sites, including those from above and below water table in a contiguous area of 48 km2 covering five land-use types. These were degraded forest, degraded land, oil palm plantation, mixed crop plantation and settlements. Bacterial profiles were most influenced by variations in water table and land-use patterns, followed by age of drainage and peat thickness in that order. Bacterial profiling revealed differences in sites, based on the duration and frequency of water table fluctuations and on oxygen availability. Mixed crop plantations had the most diverse bacterial and metabolic profiles. Metabolic profiling, being closely associated with biogeochemical functions, could distinguish communities not only based on land-use types but also their geographic locations, thus providing a finer resolution than bacterial profiles. Agricultural inputs, such as nitrates, were highly associated with bacterial community structure of oil palm plantations, whereas phosphates and dissolved organic carbon influenced those from mixed crop plantations and settlements. Our results provide a basis for adopting molecular marker-based approaches to classify peatlands and determine relative importance of factors that influence peat functioning. Our findings will be useful in peatland management by providing a basis to focus early efforts on hydrological interventions and improving sustainability of oil palm plantations by adopting mixed cropping practices to increase microbial diversity in the long term.

Latar belakang metanalisis ini adalah masih banyak guru/dosen masih belum mampu mengembangkan media pembelajaran yang efektif dan efisien khususnya untuk pendidikan biologi. Sehingga perlu dilakukan analisis artikel dari hasil-hasil penelitian terdahulu untuk memahami media yang tepat untuk pembelajaran biologi. Tujuan penelitian ini adalah untuk mengetahui: (1) jenis penelitian yang terkait dengan media pembelajaran biologi; (2) effect size media pembelajaran biologi berdasarkan tingkat Pendidikan; (3) effect size media pembelajaran biologi berdasarkan jenis media; (4) effect size media pembelajaran biologi berdasarkan materi yang digunakan sebagai konten pembelajaran. Metode yang digunakan dalam penelitian ini adalah meta analisis (Glass, 1981). Hasil penelitian menunjukkan bahwa: (1) jenis penelitian yang terkait dengan media pembelajaran biologi antara lain eksperimen, R & D, deskriptif kuantitatif dan deskriptif kualitatif; (2) effect size media pembelajaran biologi berdasarkan tingkat pendidikan terbaik pada SMP/MTs (1,00) masuk kategori tinggi; (3) effect size media pembelajaran biologi berdasarkan jenis media terbaik pada multimedia (1,00) masuk kategori effect size dengan pengaruh yang tinggi; (4) effect size media pembelajaran biologi berdasarkan materi terbaik pada Spermathopyta (2,00) masuk kategori effect size dengan pengaruh yang tinggi. Berdasarkan simpulan tersebut dapat disarankan untuk penelitian selanjutnya sebaiknya: (1) penelitian media pembelajaran dikembangkan dengan R & D dengan pengujian yang lebih lengkap dan lebih baik; (2) implementasi media pembelajaran terbaik diperoleh dari penelitian pada tingkat Pendidikan SMP/MTs, pada SMA dan PT dapat dilakukan analisis kebutuhan yang lebih mendalam agar media yang digunakan benar-benar efektif dan sesuai dengan psikologi dan kecenderungan pola belajarnya; dan (3) multimedia merupakan media pembelajaran yang paling efektif, multimedia selanjutnya dapat dikembangkan berupa multimedia yang daring, blended, atau berbasis android sehingga lebih mudah diakses oleh peserta didik

Defining appropriate null expectations for species distribution hypotheses is important because sampling bias and spatial autocorrelation can produce realistic, but ecologically meaningless, geographic patterns. Generating null species occurrences with similar spatial structure to observed data can help overcome these problems, but existing methods focus on single or pairs of species and do not incorporate between-species spatial structure that may occlude comparative biogeographic analyses. Here, we describe an algorithm for generating randomised species occurrence points that mimic the within- and between-species spatial structure of real datasets and implement it in a new R package - fauxcurrence. The algorithm can be implemented on any geographic domain for any number of species, limited only by computing power. To demonstrate its utility, we apply the algorithm to two common analysis-types: testing the fit of species distribution models (SDMs) and evaluating niche-overlap. The method works well on all tested datasets within reasonable timescales. We found that many SDMs, despite a good fit to the data, were not significantly better than null expectations and identified only two cases (out of a possible 32) of significantly higher niche divergence than expected by chance. The package is user-friendly, flexible and has many potential applications beyond those tested here, such as joint SDM evaluation and species co-occurrence analysis, spanning the areas of ecology, evolutionary biology and biogeography.