Hydrocarbon-Degrading Bacteria Alcanivorax and Marinobacter Associated With Microalgae Pavlova lutheri and Nannochloropsis oculata

© 2019, International Society for Microbial Ecology. Pectin is abundant in modern day diets, as it comprises the middle lamellae and one-third of the dry carbohydrate weight of fruit and vegetable cell walls. Currently there is no specialized model organism for studying pectin fermentation in the human colon, as our collective understanding is informed by versatile glycan-degrading bacteria rather than by specialist pectin degraders. Here we show that the genome of Monoglobus pectinilyticus possesses a highly specialized glycobiome for pectin degradation, unique amongst Firmicutes known to be in the human gut. Its genome encodes a simple set of metabolic pathways relevant to pectin sugar utilization, and its predicted glycobiome comprises an unusual distribution of carbohydrate-active enzymes (CAZymes) with numerous extracellular methyl/acetyl esterases and pectate lyases. We predict the M. pectinilyticus degradative process is facilitated by cell-surface S-layer homology (SLH) domain-containing proteins, which proteomics analysis shows are differentially expressed in response to pectin. Some of these abundant cell surface proteins of M. pectinilyticus share unique modular organizations rarely observed in human gut bacteria, featuring pectin-specific CAZyme domains and the cell wall-anchoring SLH motifs. We observed M. pectinilyticus degrades various pectins, RG-I, and galactan to produce polysaccharide degradation products (PDPs) which are presumably shared with other inhabitants of the human gut microbiome (HGM). This strain occupies a new ecological niche for a primary degrader specialized in foraging a habitually consumed plant glycan, thereby enriching our understanding of the diverse community profile of the HGM.

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Isolation and identification of novel geosmin-degrading bacteria

Frontiers in Bioscience ◽

10.2741/e290 ◽

2011 ◽

Vol E3 (3) ◽

pp. 830-833

Author(s):

Kazuya Shimizu

Keyword(s):

Isolation And Identification ◽

Degrading Bacteria

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MICROBIAL COMMUNITY DURING BIOREMEDIATION EXPERIMENTAL ON OIL SPILL IN COASTAL OF PARI ISLAND

Jurnal Ilmu dan Teknologi Kelautan Tropis ◽

10.29244/jitkt.v3i1.7838 ◽

2011 ◽

Vol 3 (1) ◽

Author(s):

Lies Indah Sutiknowati

Keyword(s):

Oil Spill ◽

Deoxyribonucleic Acid ◽

Denaturing Gradient Gel Electrophoresis ◽

Gas Chromatography Mass Spectrometry ◽

Oil Degradation ◽

Sequence Determination ◽

Blast Search ◽

Degrading Bacteria ◽

Gradient Gel Electrophoresis

There is an information how to identify hydrocarbon degrading bacteria for bioremediation of marine oil spill. We have Bioremediation treatment for degradation of oil spill on Pari island and need two kind of experiment there are tanks experiment (sampling 0 to 90 days) and semi enclosed system (sampling 0 to 150 days). Biostimulation with nutrients (N and P) was done to analyze biodegradation of hydrocarbon compounds. Experiment design using fertilizer Super IB and Linstar will stimulate bacteria can degrade oil, n-alkane, and alkane as poly aromatic hydrocarbon. The bacteria communities were monitored and analyzed by Denaturing Gradient Gel Electrophoresis (DGGE) and Clone Library; oil chemistry was analyzed by Gas Chromatography Mass Spectrometry (GCMS). DNA (deoxyribonucleic acid) was extracted from colonies of bacteria and sequence determination of the 16S rDNA was amplified by primers U515f and U1492r. Strains had been sequence and had similarity about 90-99% to their closest taxa by homology Blast search and few of them suspected as new species. The results showed that fertilizers gave a significant effect on alkane, PAH and oil degradation in tanks experiment but not in the field test. Dominant of the specific bacteria on this experiment were Alcanivorax, Marinobacter and Prosthecochloris. Keywords: Bioremediation, Biostimulation, DGGE, PAH, Pari Island

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Efektifitas Ekstrak Nannochloropsis oculata Terhadap Peningkatan Kepadatan Kolagen pada Proses Penyembuhan Alveolar Osteitis

DENTA ◽

10.30649/denta.v10i1.16 ◽

2016 ◽

Vol 10 (1) ◽

pp. 9

Author(s):

Ajeng Saghita Enggardini ◽

Syamsulina Revianti ◽

Noengki Prameswari

Keyword(s):

Nannochloropsis Oculata ◽

Control Group ◽

Control Group Design ◽

Group Design ◽

Post Test ◽

Alveolar Osteitis

Latar Belakang: Alveolar osteitis merupakan salah satu komplikasi pasca pencabutan gigi. Kondisi ini biasanya menjadi masalah pasca pencabutan yang menyebabkan rasa nyeri dan menghambat penyembuhan soket. Ekstrak Nannochloropsis oculata mengandung alkaloid, carotenoid, flavonoid, terpenoid dan tocopherol yang dapat mempercepat proses penyembuhan luka. Tujuan: Mengetahui efektivitas ekstrak Nannochloropsis oculata terhadap peningkatan kepadatan kolagen pada proses penyembuhan alveolar osteitis. Bahan dan Metode: Rancangan penelitian ini adalah post test only control group design, dengan menggunakan 64 tikus Wistar jantan dibagi menjadi 2 kelompok besar, yaitu pemberian irigasi dan dressing. Pada masing-masing kelompok terdapat kelompok kontrol negatif (irigasi PBS atau dressing PBS), kelompok kontrol positif (irigasi Saline 0,9% atau dressing Alvogyl) dan kelompok perlakuan (irigasi atau dressing ekstrak Nannochloropsis oculata 2,5% dan 5%). Kemudian kepadatan kolagen diukur pada hari ke 3 dan ke 7 setelah perlakuan. Kepadatan kolagen yang diukur pada soket pasca pencabutan gigi. Setelah dilakukan treatment pada hari ke 3 dan ke 7, semua tikus dikorbankan lalu kepadatan kolagen diukur melalui preparat histopatologi anatomi dengan pengecatan Masson’s Trichom dan pembesaran 100x, kemudian dilakukan perhitungan kepadatan kolagen. Data yang diperoleh dianalisis Kruskal-Wallis dan Mann-Whitney. Hasil: Terdapat perbedaan kepadatan kolagen yang signifikan antara kelompok perlakuan irigasi (0,045), tetapi tidak terdapat perbedaan yang signifikan antara kelompok perlakuan dressing (0,243). Metode dressing lebih efektif dalam meningkatkan kepadatan kolagen jika dibandingkan dengan kelompok irigasi (0,026). Simpulan: Pemberian dressing ekstrak Nannochloropsis oculata konsentrasi 5% paling efektif dalam meningkatkan kepadatan kolagen pada proses penyembuhan alveolar osteitis pada hari ke 7.

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STUDY AND CHARACTERIZATION GROWTH OF FOUR MICROALGAE SPECIES AND TEST ANTIMICROBIAL ACTIVITY

Jurnal Zarah ◽

10.31629/zarah.v6i2.625 ◽

2018 ◽

Vol 6 (2) ◽

pp. 53-58

Author(s):

Marniati Salim

Keyword(s):

Dunaliella Salina ◽

Methanol Extract ◽

Sea Water ◽

Basal Medium ◽

Nannochloropsis Oculata ◽

Inhibitory Zone ◽

Antimicrobial Sensitivity ◽

Sensitivity Tests ◽

Microalgae Biomass ◽

Chaetoceros Calcitrans

Abstract In this study to the growth characteristics of microalgae (Dunaliella salina, Nannochloropsis oculata, Tetrasel mis chuii & Chaetoceros calcitrans), in different mediums, namely Bold’s Basal Medium (BBM) and BBM modification of sea water. The results obtained from microalgae (N.oculata, T.chuii, C.calcitrans) are better grown on BBM media while microlaga D.salina grows well on BBM modification of sea water. Microalgae biomass is extracted by maceration method in hexane and methanol solvents. Test bacteria used gram positive (Staphylococcus aureus) and gram negative (Escherichia coli). Inhibitory zone diameter results were compared with antimicrobial sensitivity tests according to Clinical and Laboratory Standards Institute (CLSI). From the results of microalgae hexane and methanol extract antibacterial activity tests (D.salina, N.oculata, T.chuii, C.calcitrans) showed that the extract was not too sensitive to inhibit bacterial growth. Keywords: microalgae, medium, antimicrobial

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Isolation, morphometry, and culture of Colurella sp. (Rotifera: Ploimida)

AQUATIC SCIENCE & MANAGEMENT ◽

10.35800/jasm.1.2.2013.7276 ◽

2013 ◽

Vol 1 (2) ◽

pp. 143

Author(s):

Petrus P Letsoin ◽

Henneke Pangkey ◽

Julius Sampekalo ◽

Inneke F.M Rumengan ◽

Stenly Wullur ◽

...

Keyword(s):

Body Size ◽

Marine Fish ◽

Fish Larvae ◽

Nannochloropsis Oculata ◽

Tropical Fish ◽

Sampling Location ◽

Larval Rearing ◽

Brachionus Rotundiformis ◽

Marine Fish Larvae ◽

Significant Difference

The rotifer Brachionus rotundiformis (total body length 240.59±10.24 μm, lorica length 175.28±9.18 μm, and lorica width 124.28±7.76μm) is commonly used as starter food in the larval rearing of marine fish. But, larvae of some marine tropical fish species required starter food with body size smaller than B. rotundiformis. The present study was aimed to isolate minute rotifers from nature and to assess the possibility of culturing these rotifers. Sampling of rotifers was conducted in an estuary of Mangket (Kema-Minut), using plankton net (mesh size 40 µm). A trial of culturing the rotifers was conducted at salinities of 10, 20 and 30 ppt by using a microalga, Nannochloropsis oculata. A species of rotifer identified as Colurella sp. (family Lepadellidae) was successfully isolated from the sampling location. Body size of Colurella sp. was extremely small (Total length 123.22±5.45 μm, lorica length 95.96±3.81 μm, and lorica width 53.57±3.11 μm), which were smaller than Brachionus rotundiformis SS-type as a conventional starter food for marine fish larvae. Results of culturing the minute rotifer Colurella sp. showed that the species grew well at salinities of 10, 20 and 30 ppt with no significant difference among treatments (ANOVA, p>0.05), indicating a potential use of minute rotifer Colurellasp. as starter food for marine fish larvae. Rotifera Branchionus rotundiformis (ukuran tubuh: panjang total 240,59±10,24 μm, panjang lorika 175,28±9,18 μm, dan lebar lorika 124,28±7,76μm) sering digunakan sebagai pakan awal pemeliharaan larva ikan laut. Namun, larva beberapa spesis ikan laut tropis membutuhkan pakan awal berukuran tubuh lebih kecil dari Branchionus rotundiformis. Penelitian ini bertujuan untuk mendapatkan minute rotifer dari alam (berukuran tubuh lebih kecil dari B. rotundiformis) dan menguji kemungkinan pemeliharaannya. Sampling rotifer dilakukan di perairan estuari Desa Mangket (Kema-Minut), menggunakan plankton net (ukuran mata jaring 40 µm). Uji coba pemeliharaan dilakukan pada salinitas (10, 20, dan 30 ppt) dengan menggunakan Nannochloropsis oculata. Satu spesies minute rotifer yang teridentifikasi sebagai Colurella sp. (family Lepadellidae) berhasil diisolasi dari lokasi sampling. Colurella sp. memiliki ukuran tubuh sangat kecil (panjang total [PT] 123,22±5,45 µm, panjang lorika [PL] 95,96±3,81 µm, dan lebar lorik [LL] 53,57±3,11 µm) yang mana lebih kecil dari Branchionus rotundiformis tipe-SS sebagai pakan awal larva ikan laut. Hasil uji coba pemeliharaan minute rotifer Colurella sp. menunjukkan bahwa spesis ini dapat tumbuh pada salinitas 10, 20, dan 30 ppt dengan perbedaan kepadatan populasi yang tidak signifikan antar perlakuan (Uji ANOVA, p > 0.05) mengindikasikan potensi pemanfaatan minute rotifer Colurella sp. sebagai pakan awal larva ikan laut.

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Effect of Low Temperature on Hexadecane Biodegradation by Oil-Degrading Bacteria Rhodoccocus sp. X5 Capable of Producing Glycolipid Biosurfactants

Biotekhnologiya ◽

10.21519/0234-2758-2017-33-6-49-56 ◽

2017 ◽

Vol 33 (6) ◽

pp. 49-56

Author(s):

T.M. Luong ◽

◽

I.A. Nechaeva ◽

O.N. Ponamoreva ◽

H.G. Vu ◽

...

Keyword(s):

Low Temperature ◽

Degrading Bacteria

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Biodegradation of organophosphorus Pollutants by Soil Bacteria: Biochemical Aspects and Unsolved Problems

Biotekhnologiya ◽

10.21519/0234-2758-2020-36-4-126-135 ◽

2020 ◽

Vol 36 (4) ◽

pp. 126-135

Author(s):

T.V. Shushkova ◽

D.O. Epiktetov ◽

S.V. Tarlachkov ◽

I.T. Ermakova ◽

A.A. Leontievskii

Keyword(s):

Genome Sequencing ◽

Soil Bacteria ◽

Activity Regulation ◽

Bacterial Isolates ◽

Bacterial Strains ◽

Russian Science ◽

Degrading Bacteria ◽

Phosphorus Source ◽

Glyphosate Herbicide ◽

Enzymatic Pathways

The degradation of persistent organophosphorus pollutants have been studied in 6 soil bacterial isolates and in 3 bacterial strains adapted for utilization of glyphosate herbicide (GP) under laboratory conditions. Significant differences in the uptake of organophosphonates were found in taxonomically close strains possessing similar enzymatic pathways of catabolism of these compounds, which indicates the existence of unknown mechanisms of activity regulation of these enzymes. The effect of adaptation for GP utilization as a sole phosphorus source on assimilation rates of several other phosphonates was observed in studied bacteria. The newly found efficient stains provided up to 56% of GP decomposition after application to the soil in the laboratory. The unresolved problems of microbial GP metabolism and the trends for further research on the creation of reliable biologicals capable of decomposing organophosphonates in the environment are discussed. organophosphonates, glyphosate, biodegradation, bioremediation, C-P lyase, phosphonatase, degrading bacteria Investigation of phosphonatase and genome sequencing were supported by Russian Science Foundation Grant no. 18-074-00021.

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