Indigenous Microbes Research Articles

The gut microbiome stability is altered by probiotic ingestion and improved by the continuous supplementation of galactooligosaccharide

ABSTRACT The stable gut microbiome plays a key role in sustaining host health, while the instability of gut microbiome also has been found to be a risk factor of various metabolic diseases. At the ecological and evolutionary scales, the inevitable competition between the ingested probiotic and indigenous gut microbiome can lead to an increase in the instability. It remains largely unclear if and how exogenous prebiotic can improve the overall gut microbiome stability in probiotic consumption. In this study, we used Lactobacillus plantarum HNU082 (Lp082) as a model probiotic to examine the impact of the continuous or pulsed supplementation of galactooligosaccharide (GOS) on the gut microbiome stability in mice using shotgun metagenomic sequencing. Only continuous GOS supplement promoted the growth of probiotic and decreased its single-nucleotide polymorphisms (SNPs) mutation under competitive conditions. Besides, persistent GOS supplementation increased the overall stability, reshaped the probiotic competitive interactions with Bacteroides species in the indigenous microbiome, which was also evident by over-abundance of carbohydrate-active enzymes (CAZymes) accordingly. Also, we identified a total of 793 SNPs arisen in probiotic administration in the indigenous microbiome. Over 90% of them derived from Bacteroides species, which involved genes encoding transposase, CAZymes, and membrane proteins. However, neither GOS supplementation here de-escalated the overall adaptive mutations within the indigenous microbes during probiotic intake. Collectively, our study demonstrated the beneficial effect of continuous prebiotic supplementation on the ecological and genetic stability of gut microbiomes.

Efficient biodegradation of DEHP by CM9 consortium and shifts in the bacterial community structure during bioremediation of contaminated soil

Di(2-ethylhexyl) phthalate (DEHP), the most extensively used plasticizer in plastic formulations, is categorized as a priority environmental contaminant with carcinogenic, teratogenic, and mutagenic toxicities. Many isolated microorganisms exhibit outstanding performance as pure cultures in the laboratory but are unable to cope with harsh environmental conditions in the field. In the present study, a microbial consortium (CM9) with efficient functionality was isolated from contaminated farmland soil. CM9 could consistently degrade 94.85% and 100.00% of DEHP (1000 mg/L) within 24 h and 72 h, respectively, a higher efficiency than those of other reported pure and mixed microorganism cultures. The degradation efficiencies of DEHP and di-n-butyl phthalate were significantly higher than those of dimethyl phthalate and diethyl phthalate (p < 0.05). The primary members of the CM9 consortium were identified as Rhodococcus, Niabella, Sphingopyxis, Achromobacter, Tahibacter, and Xenophilus. The degradation pathway was hypothesized to include both de-esterification and β-oxidation. In contaminated soil, bioaugmentation with CM9 and biochar markedly enhanced the DEHP removal rate to 87.53% within 42 d, compared to that observed by the indigenous microbes (49.31%) (p < 0.05). During simulated bioaugmentation, the dominant genera in the CM9 consortium changed significantly over time, indicating their high adaptability to soil conditions and contribution to DEHP degradation. Rhodococcus, Pigmentiphaga and Sphingopyxis sharply decreased, whereas Tahibacter, Terrimonas, Niabella, Unclassified_f_Caulobacteraceae, and Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium showed considerable increases. These results provide a theoretical framework for the development of in situ bioremediation of phthalate (PAE)-contaminated soil by composite microbial inocula.

Indigenous Microbial Biostimulation for Microbial Enhanced Oil Recovery through Oil Degradation with Variation in Nutrent Concentrations

Oil production in Indonesia has been declining since 2002, and this decline is incompatible with the high oil consumption in Indonesia. As such oil production in Indonesia should be improved. Biostimulation in microbial enhanced oil recovery involves environmental modification to stimulate microbial growth within a reservoir by adding limiting nutrients. Variation in C, N, and P concentrations injected to reservoirs can induce different responses from indigenous microbes and increase oil recovery. In this study, molasses, urea and diammonium phosphate were used as nutrients injected to a reservoir for biostimulation. Biological, physical and chemical characteristics after biostimulation were observed and bacterial growth was monitored up to 42 days. The physical characteristics observed were pH, oil viscosity, and interfacial tension. Gas chromatography mass spectrometry was performed to determine the chemical characteristics of oil. Results showed that the addition of nutrients at various concentrations yielded different production patterns of metabolites. The addition of urea and diammonium phosphate induced biosurfactants overproduction and increase hydrocarbon degradation of by bacteria. Therefore, hydrocarbons were degraded for the first 14 days, and polymerized again on days 14 to 42.

Inoculation With a Microbe Isolated From the Negev Desert Enhances Corn Growth.

Corn (Zea mays L.) is not only an important food source, but also has numerous uses, including for biofuels, fillers for cosmetics, glues, and so on. The amount of corn grown in the U.S. has significantly increased since the 1960’s and with it, the demand for synthetic fertilizers and pesticides/fungicides to enhance its production. However, the downside of the continuous use of these products, especially N and P fertilizers, has been an increase in N2O emissions and other greenhouse gases into the atmosphere as well as run-off into waterways that fuel pollution and algal blooms. These approaches to agriculture, especially if exacerbated by climate change, will result in decreased soil health as well as human health. We searched for microbes from arid, native environments that are not being used for agriculture because we reasoned that indigenous microbes from such soils could promote plant growth and help restore degraded soils. Employing cultivation-dependent methods to isolate bacteria from the Negev Desert in Israel, we tested the effects of several microbial isolates on corn in both greenhouse and small field studies. One strain, Dietzia cinnamea 55, originally identified as Planomicrobium chinense, significantly enhanced corn growth over the uninoculated control in both greenhouse and outside garden experiments. We sequenced and analyzed the genome of this bacterial species to elucidate some of the mechanisms whereby D. cinnamea 55 promoted plant growth. In addition, to ensure the biosafety of this previously unknown plant growth promoting bacterial (PGPB) strain as a potential bioinoculant, we tested the survival and growth of Caenorhabditis elegans and Galleria mellonella (two animal virulence tests) as well as plants in response to D. cinnamea 55 inoculation. We also looked for genes for potential virulence determinants as well as for growth promotion.

Is the Arrhenius-correction of biodegradation rates, as recommended through REACH guidance, fit for environmentally relevant conditions? An example from petroleum biodegradation in environmental systems

Biodegradation is a major determinant of chemical persistence in the environment and an important consideration for PBT and environmental risk assessments. It is influenced by several environmental factors including temperature and microbial community structure. According to REACH guidance, a temperature correction based on the Arrhenius equation is recommended for chemical persistence data not performed at the recommended EU mean surface water temperature. Such corrections, however, can lead to overly conservative P/vP assessments. In this paper, the relevance of this temperature correction is assessed for petroleum hydrocarbons, using measured surface water (marine and freshwater) degradation half-time (DT50) and degradation half-life (HL) data compiled from relevant literature. Stringent screening criteria were used to specifically select data from biodegradation tests containing indigenous microbes and conducted at temperatures close to their ambient sampling temperature. As a result, ten independent studies were identified, with 993 data points covering 326 hydrocarbon constituents. These data were derived from tests conducted with natural seawater, or freshwater, at temperatures ranging from 5 to 21 °C. Regressions were performed on the full hydrocarbon dataset and on several individual hydrocarbons. The results were compared to the trend as predicted by the Arrhenius equation and using the activation energy (Ea) as recommend in the REACH Guidance. The comparison shows that the correction recommended in REACH Guidance over predicts the effect of temperature on hydrocarbon biodegradation. These results contrast with temperature manipulated inocula where the test temperature is different from the ambient sampling temperature. In these manipulated systems, the effect of temperature follows the Arrhenius equation more closely. In addition, a more striking effect of temperature on the lag phase was observed with longer lag phases more apparent at lower temperatures. This indicates that the effect of temperature may indeed be even lower when considering hydrocarbon biodegradation without the initial lag phase.

The removal of arsenic species from aqueous solution by indigenous microbes: Batch bioadsorption and artificial neural network model

Arsenic contamination of groundwater is a problem that affects millions of people across the world. Biological treatment of arsenic using microorganisms is an interesting alternative to conventional methods because it is most efficient, low cost and eco-friendly. In this study, three different bacterial species were isolated from arsenic laden tailing dam sludge at gold mining and the 16S rRNA sequencing data exposed their affiliation to three different genera, Bacillus thuringiensis strain WS3, Pseudomonas stutzeri strain WS9 and Micrococcus yunnanensis strain WS11. Considering the advantage of the different structures of these bacterial cell walls in adsorption, attempts were made to use individual and mixed dried biomass of these strains to achieve highest As (III) and As (V) removal under different conditions. Mixed dried biomass of WS3, WS9 and WS11 were found to be efficient in the removal of As (III) and As (V) up to 95% and 98%, respectively. Optimal conditions for arsenic removal were found; 8 and 6 h of contact time for As (III) and As (V), respectively, 7.5 (ppm) As (III) and 9 (ppm) As (V) concentration at 37 °C, pH 7, and 0.60 mg/ml of biomass dosage. In comparison of estimated coefficient of determination (R2), Langmuir isotherm model provided the best fit to the experimental data while the adsorption kinetic model followed the pseudo-second-order. FESEM–EDX analysis established diverse cell morphological changes with significant amounts of arsenic adsorbed onto the biomass compared to original biomass. FTIR analysis showed the involvement of hydroxyl, thiol, amide and amine functional groups in arsenic removal. Comparisons between actual and model adsorption results show that the artificial neural network model can predict adsorption efficiency with high accuracy (R2 > 0.98). Consequently, mixed dried biomass of WS3, WS9 and WS11 are strongly recommended for bio-treatment of toxic arsenic from the environment.

Biodegradation of artisanally refined diesel and the influence of organic wastes on oil-polluted soil remediation

The increasing rate of oil-pollution in the Niger Delta due to artisanal crude oil refining has led to the destruction of farmlands/aquaculture and loss of biodiversity. The aim of this study was to determine the effect of poultry waste, granite dust and palm bunch ash on the rate of hydrocarbon degradation. Oil-polluted soil was obtained from an artisanal refining site in the Niger Delta and amended with various combinations (granite dust + poultry waste + palm bunch ash (1:2:1), granite dust only, poultry waste only) of the wastes. Chemical parameters monitored for 70 days included total petroleum hydrocarbons (TPH), polycyclic aromatic hydrocarbons (PAHs), nitrate, phosphorus, potassium and the soil pH. The degradative potentials of the isolated indigenous bacterial species were determined using redox indicator 2,6-dichlorophenolindophenol (DCPIP). Bacterial classification was determined using 16S rRNA gene as molecular marker. Initial TPH (16,388.88 mg/kg) and PAHs (8,579.26 mg/kg) exceeded Department of Petroleum Resources’ intervention limits of 5000 mg/kg and 40 mg/kg for TPH and PAHs respectively. The rate of hydrocarbon removal was significantly higher in the treatment amended with the combined waste materials (0.04 d-1) than the treatments amended with a single waste (0.02 d-1). TPH in the combined waste treatment reduced from 16,000 mg/kg to 533.85 mg/kg on day 70 while pH increased from 6.1 to between 6.8 and 7.1 in all treatments following amendment with nutrients. Observed increases in hydrocarbon utilizing bacterial counts significantly correlated with pH (R = 0.82; p = 0.04), phosphate (R = 0.93; p = 0.006) and TPH (R= -0.88; p = 0.02) reduction. The degradation studies revealed that the artisanally refined diesel was less biodegradable with the genera Lysinibacillus and Providencia demonstrating the strongest biodegradation potential. This study would be relevant for designing engineered remedial strategies for the clean-up of hydrocarbon spills related to artisanal refining as the extant indigenous microbes in this region are mostly hydrocarbon degraders.

Evidence for extensive anaerobic dechlorination and transformation of the pesticide chlordecone (C10Cl10O) by indigenous microbes in microcosms from Guadeloupe soil.

The historic use of chlordecone (C10Cl10O) as a pesticide to control banana weevil infestations has resulted in pollution of large land areas in the French West Indies. Although currently banned, chlordecone persists because it adsorbs strongly to soil and its complex bis-homocubane structure is stable, particularly under aerobic conditions. Abiotic chemical transformation catalyzed by reduced vitamin B12 has been shown to break down chlordecone by opening the cage structure to produce C9 polychloroindenes. More recently these C9 polychloroindenes were also observed as products of anaerobic microbiological transformation. To investigate the anaerobic biotransformation of chlordecone by microbes native to the French West Indies, microcosms were constructed anaerobically from chlordecone impacted Guadeloupe soil and sludge to mimic natural attenuation and eletron donor-stimulated reductive dechlorination. Original microcosms and transfers were incubated over a period of 8 years, during which they were repeatedly amended with chlordecone and electron donor (ethanol and acetone). Using LC-MS, chlordecone and degradation products were detected in all the biologically active microcosms. Observed products included monohydro-, dihydro- and trihydrochlordecone derivatives (C10Cl10-nO2Hn; n = 1,2,3), as well as “open cage” C9 polychloroindene compounds (C9Cl5-nH3+n n = 0,1,2) and C10 carboxylated polychloroindene derivatives (C10Cl4-nO2H4+n, n = 0–3). Products with as many as 9 chlorine atoms removed were detected. These products were not observed in sterile (poisoned) microcosms. Chlordecone concentrations decreased in active microcosms as concentrations of products increased, indicating that anaerobic dechlorination processes have occurred. The data enabled a crude estimation of partitioning coefficients between soil and water, showing that carboxylated intermediates sorb poorly and as a consequence may be flushed away, while polychlorinated indenes sorb strongly to soil. Microbial community analysis in microcosms revealed enrichment of anaerobic fermenting and acetogenic microbes possibly involved in anaerobic chlordecone biotransformation. It thus should be possible to stimuilate anaerobic dechlorination through donor amendment to contaminated soils, particularly as some metabolites (in particular pentachloroindene) were already detected in field samples as a result of intrinsic processes. Extensive dechlorination in the microcosms, with evidence for up to 9 Cl atoms removed from the parent molecule is game-changing, giving hope to the possibility of using bioremediation to reduce the impact of CLD contamination.

Electrolytic groundwater circulation well for trichloroethylene degradation in a simulated aquifer

An in situ groundwater remediation process, termed EGCW, was developed in this study by integrating in-well groundwater electrolysis into groundwater circulation well. Groundwater circulation carries electrolytically generated O2 and H2 into the impacted aquifer for in situ biodegradation of contaminants. In a two-dimensional tank filled with field sandy sediments, simulated trichloroethylene (TCE)-contaminated groundwater was circulated between an injection well with electrodes inside and a pumping well. Results from a 50-day EGCW experiment show that in-well electrolysis oxygenated most region near the injection well, and 10 mg/L TCE was mainly biodegraded aerobically to about 2.7 mg/L (73% removal) by the indigenous microbes. Aerobic TCE degradation was enhanced by the pulsed addition of acetate. Together with the proofs of stable carbon isotope fractionation (enrichment factor: −0.57‰–−1.53‰) and microbial community variation after EGCW treatment, aerobic cometabolism was proposed to be the most likely mechanism for TCE degradation. It is interesting to find that the intrinsic organic carbon in aquifer matrix could fuel the aerobic TCE degradation, particularly at low TCE concentrations. EGCW treatment is advantageous in terms of supplying appropriate dosages of electron acceptor (O2) and donor (H2) for in situ bioremediation because groundwater electrolysis and circulation are expedient and controllable.

Diversity of fungal community associated with cacao (Theobromae cacao L.) top clones from Sulawesi, Indonesia

Cocoa (Theobroma cacao L.), one of the most significant smallholder commodities in Indonesia, is mainly planted in the Sulawesi island of Indonesia. The new paradigm approach for improving plant health is the use of indigenous microbes which associates with cocoa tree. One of microbial communities is endophytic fungi. The research aimed to identify of fungal endophyte of cocoa top clones Sulawesi. A total of 27 isolates of fungi was isolated from two clones and three areas; 11 isolates from East Luwu area (MCC-02 Clone was six; Sulawesi-2 (S-2) was five), seven isolates from North Luwu area (MCC-02 clone was four; Sulawesi-2 (S-2) was three), Nine isolates from Bantaeng area (MCC-02 was three; Sulawesi-2 (S-2) was six). The isolates belonged to genera Penicillium (two isolates), Aspergillus (five isolates), Geotrichum (two isolates), Sordaria, Lasiodiplodia, Myrothecium, Monilia, Colletotrichum, dan and five isolates that have not been identified as not showing conidia on media of PDA. The result revealed that fungi associated with cacao was diverse and every clone and cocoa producing area shows different diversity of fungi. The endophytic fungi were potential to be biological control for controlling cacao diseases.

Microbially-mediated de-watering and consolidation (“Biodensification”) of oil sands mature fine tailings, amended with agri-business by-products

Oil sands surface mining operations in northeastern, Alberta, Canada produce enormous volumes of fluid fine tailings, an aqueous suspension of fine clays, sand, unrecovered bitumen, and diluent hydrocarbons. The tailings are deposited and retained on-site in large settling basins where the colloidal solids sediment and consolidate very slowly by gravity and pore water collects at the surface for re-use. Tailings ‘biodensification’, mediated by indigenous microbes that produce methane and/or carbon dioxide, is a phenomenon observed in situ and in vitro whereby tailings with active anaerobic microbial communities consolidate and de-water faster than predicted by gravitational (self-weighted) consolidation alone. To exploit this phenomenon, we used organic amendments to stimulate endogenous anaerobic tailings microorganisms. Tailings from three different operators were amended with agri-business by-products, placed in 100-mL microcosms and 1.5-L settling columns, and monitored for methanogenesis, pore water recovery, and solids densification. Several amendments increased methane production and accelerated biodensification compared to unamended and negative controls. Hydrolyzed canola, blood meal, bone meal and glycerol generally accelerated biodensification, stimulated methane production and supported growth of methanogens and fermentative microbes. Amendment altered the chemistry of the tailings, generally decreasing pH, increasing conductivity and magnesium, potassium, sodium, and bicarbonate concentrations. Biodensification is a potential engineered technology for accelerating water recovery and reducing the volume of stored oil sands tailings.

Bioremediation of oil-contaminated soil by combination of soil conditioner and microorganism

Oil hydrocarbons are widespread pollutants in soil which pose serious threats to ecological environment. Thus, this study carried out the bioremediation of oil-contaminated soil by using the efficient petroleum-degrading bacteria and soil conditioner, to investigate the changes of physicochemical properties of contaminated soil during bioremediation, reveal the relationship among the exogenous degradation strains and indigenous microbe, and finally illuminate the effects of soil conditioner and microbe on the bioremediation of oil-contaminated soil. A PAH-degrading strain named Stenotrophomonas maltophilia was used in this study, which was isolated from an e-waste dismantling area. The soil conditioner in this present study was developed previously by using agricultural wastes, which was in a powdered form and rich in N, P, and K. The simulated experiments were conducted under the control environmental conditions of greenhouse, to study the effects of inoculation and soil conditioner on bioremediation of oil-contaminated soil. Then, the physicochemical properties of soil and the degradation rates of oil were measured at different set times to evaluate the bioremediation effect. Adding 1% soil conditioner could significantly improve the soil conditions and offer microorganism enough N, P, and K, which would promote microbial growth and played a key role on bioremediation of oil-contaminated soil. Although in polluted soil, the microorganism could maintain metabolic activity and use the petroleum as carbon source. The soil indigenous microbe was more easily to adapt to the contaminated surrounding. However, when both of them co-existed in soil, they would restrain each other, and go against the oil decomposition. Thus, making two types of microorganisms work to achieve synergy was the key to gain much better remediation effect. Because the indigenous microbe was good at decomposing low molecular compounds and saturated hydrocarbons, while the oil-degrading strains can effectively decompose high molecular weight aromatics. The soil nutrient and microorganism, including the exogenous oil-degrading strains and the soil indigenous microbe, had an important effect on degradation of petroleum. The addition of soil conditioner, presence of indigenous microbe, and inoculation of oil-degrading strains all were conducive to bioremediation of oil-contaminated site, but the key was to control the proportion and relationship of the three.

Indigenous Microbiota Protects against Inflammation-Induced Osteonecrosis

Medication-related osteonecrosis of the jaw (MRONJ) is a rare intraoral lesion that occurs in patients undergoing long-term and/or high-dose therapy with nitrogen-containing bisphosphonates, a RANKL inhibitor, antiangiogenic agents, or mTOR inhibitors. The presence of pathogenic bacteria is highly associated with advanced stages of MRONJ lesions; however, the exact role of indigenous microbes in MRONJ development is unknown. Here, we report that the normal oral flora in mice protects against inflammation-induced osteonecrosis. In mice that developed osteonecrosis following tooth extraction, there was increased bacterial infiltration when compared with healed controls. Antibiotic-mediated oral dysbiosis led to a local inhibition of bone resorption in the presence of ligature-induced periodontitis (LIP). There was no significant difference in empty lacunae, necrotic bone formation, osteoclast number, and surface area in antibiotic-treated as compared with conventionally colonized mice following extraction of healthy teeth after zoledronic acid infusions. However, extraction of LIP teeth led to increased empty lacunae, necrotic bone, and osteoclast surface area in antibiotic- and zoledronic acid–treated mice as compared with conventionally colonized mice. Our findings suggest that the presence of the indigenous microbiota protects against LIP-induced osteonecrosis.

The role of phosphorus in growing tomatoes in near water-saturated soil

High-yielding, waterlogged cultivations with considerable nitrogen input are widely practiced in Kyushu Island, Japan. Our objective was to determine the role of available phosphorus in relation to nitrogen and soil microorganisms on tomato growth in such systems. Tomato seedlings were grown in a pasteurized soil with ample KNO3 in addition to different amounts of sodium or potassium phosphates to assess effects of phosphorus on growth enhancement and water-use efficiency in the seedlings grown with copious soil water (>－0.7 kPa). Both monobasic and dibasic phosphates applied at 40 mM to near-saturated soil markedly promoted seedling growth when fertilized with 120 mM KNO3 or NH4Cl, but not in the soil without nitrogen. The final concentration of NO3－ near the soil surface was maximized in the nitrated soil with no added PO43－ but declined significantly when fertilized with any phosphates except Na2HPO4. No significant accumulation of NO3－ was detected in the water-saturated bottom soils regardless of soil fertilization with any plant minerals. Increased seedling growth was accompanied by lower dry root/shoot ratios and marked increases in evapotranspiration efficiency. Such positive effects of PO43－ were greater with NO3－ than NH4＋ but diminished with increased concentrations of Na＋ up to 160 mM. Nonetheless, growth promotions by ample NO3－ with PO43－ were nearly negated in the non-pasteurized soil. Apparently, the activities of indigenous soil microbes were more significant than soil nitrogen and phosphorus in limiting the growth potential of tomato plants in near-saturated soils.

Influence of pathogen contamination on beef microbiota under different storage temperatures

Outbreaks of food poisoning due to the consumption of contaminated beef from fast-food chains are becoming more frequent. Pathogen contamination in beef influences its spoilage as well as the development of foodborne illness. Thus, the influence of pathogen contamination on beef microbiota should be analyzed to evaluate food safety. We analyzed the influence of pathogen contamination on the shift in microbiota and the interactions between the pathogen and indigenous microbes in beef stored under different conditions. Sixty beef samples were stored at 25 °C and 4 °C for 24 h, and the shifts in microbiota were analyzed using the MiSeq system. The influence of pathogen contamination on microbiota was analyzed by artificial contamination experiments with Escherichia coli FORC_044, which was isolated from the stool of a food poisoning patient in Korea. The bacterial amounts and the proportion of Escherichia were higher when the beef was stored at 25 °C. Artificially contaminated Escherichia positively correlated with the indigenous microbes such as Pseudomonas, Brochothrix, Staphylococcus, Rahnella, and Rhizobium as determined by co-occurrence network analyses. Carnobacterium, a potential spoilage microbe, was negatively correlated with other microbes. The predicted functions of altered microbiota showed that the pathways related to the process of spoilage including biosynthesis of acetic acid and lactic acid increased over time. The shift in pathways was more pronounced in contaminated beef stored at 25 °C. Carnobacterium, Lactobacillus, and Escherichia were the main genera contributing to the shift in the relative abundance of functional genes involved in the various spoilage pathways. Our results indicated that pathogen contamination could influence beef microbiota and mediate spoilage. This study extends our understanding of the beef microbiota and provides insights into the role of pathogen and storage conditions in meat spoilage.

The role of indigenous cellulolytic and amylolytic microbes in cassava pulp during the drying process

Cassava pulp is a solid waste resulted from the processing of cassava into tapioca. Cassava pulp is composed of cellulose and residual starch extract. In addition, cassava pulp contains undigested oligosaccharides. During the cassava pulp drying process, various indigenous microbes grow so that it affects the quality of dried cassava pulp. This study aimed to examine the role of indigenous cellulolytic and amylolytic microbes in cassava pulp during the drying process. Indigenous microbes were isolated from cassava pulp from 0 to 15 days using CMC and starch agar to obtain cellulolytic and amylolytic bacteria. Thirty-two types of cellulolytic bacteria and four types of amylolytic bacteria from cassava pulp were selected based on their cellulolytic and amylolytic index. The dominance of cellulolytic bacteria occurred during the drying process (15 days). The highest cellulolytic index obtained was 1.47 and the amylolytic index was 0.86. Selected isolates that had a high index value were then further tested for growth and cellulase enzyme activity. Cellulase produced by isolates of COC1 bacteria had the highest enzyme activity at the 15th hour, which was 0.06 U / mL. Cassava pulp which underwent a drying process for 15 days had crude fiber and carbohydrates changes.

SUMBANGAN MIKROBA PELARUF FOSFAT INDEGENUS TERHADAP PENINGKATAN PRODUKTIVITAS LAHAN PERTANIAN DI PROVINSI RIAU

ABSTRACT&#x0D; &#x0D; The obstacle to agricultural development in peatlands is the low nutrient content needed for plant growth. One effort that can be done to increase agricultural productivity in peatlands is a friendly environmental fertilization. This research aims to find out the role of indigenous phosphate solubilizing microbes in enhanced peat soil fertility in Kampar District in 2014 by using a Factorial Randomized Block Design with 3 replications. First factor was MPF inoculation (control; Burkholderia gladioli and penicillium aculeatum), and the second factor was Ameliorants (Control, Oil Palm Empty Fruit Bunch (TKKS) Compost, 4 kg TKKS compost/polybag and 25% recommended dosage, 4 kg TKKS compost/polybag and 50% recommended dosage, 4 kg TKKS compost/polybag and 75% recommended dosage, 4 kg TKKS compost/polybag and 100% P recommended dosage. Soil Nutrient analyses carried out at the laboratories of Vegetable Crops Research Institute Lembang. The parameters observed were: soil content of nutrients N, P, K, Ca, and Mg. The results showed that the indigenous phosphate solubilizing microbe increased the soil's nutrient content.

Directional culture of petroleum hydrocarbon degrading bacteria for enhancing crude oil recovery

An oxygen-constrained system of crude oil reservoir environment was constructed to stimulate the growth of indigenous microbes, such as petroleum hydrocarbon-degrading bacteria. Addition of nitrogen and phosphorus sources was investigated for the growth of petroleum hydrocarbon-degrading bacteria. The results show that nitrates and phosphates stimulated the growth of the bacteria and promoted the biodegradation of crude oil as the sole carbon source in this process. The minimum surface tension was 29.63 mN/m when the amounts of the nitrogen (NaNO3: NH42SO4 = 2:1) and phosphorus (KH2PO4: NaH2PO4 = 5:2) sources added were 0.8 wt% and 1.4 wt%, respectively. Furthermore, the dominant petroleum hydrocarbon-degrading bacteria were shifted from Arcobacter in production water to Pseudomonas after the first subculture and then to Bacillus after the sixth subculture. The heteroatom groups in the crude oil were biodegraded simultaneously with normal alkanes and alkyl cyclohexanes. Addition of the nutrients resulted in microbial growth, microbial community shift, and enhanced microbial degradation.

Degradation of Cypermethrin by Indigenous Bacteria from Contaminated Soil

Soil contamination by pesticides should be controlled by using soil microbes with the ability to degrade pesticide resi-dues. Microorganisms that have adapted to a particular pesticide could accelerate the degradation process. The present study aimed to select bacteria in soil that could potentially degrade cypermethrin residues. Experiments were carried out in a laboratory and employed soil samples collected from the districts of Demak, Magelang, and Brebes. Each soil sample was initially tested for the presence of bacteria and pesticide residues. Indigenous microbes capable of living in contaminated environments were adapted to cypermethryn and cultured in the laboratory. Experiment was carried out in several stages, namely, (1) isolation and identification of microbes that could degrade cypermethrin, (2) testing of the growth characteristics of isolates in cypermethrin, and (3) determination of cypermethrin residues in cultures. Three isolates, namely Pseudomonas alcaligenes, Bacillus amyloliquenfaciens, and Pseudomonas aeruginosa, were found to decrease cypermethrin residues by up to 95% with fast half-lives and good growth capability. The results demonstrate the potential applications of the isolates in biodegradation processes and remediation of cultivation fields.

Variation in soil microbial population and enzyme activities under faba bean as affected by pentachlorophenol

Pentachlorophenol (PCP) is a widely detectable toxic chemical with a detrimental effect on the functioning of ecosystems. A field trial was undertaken to study its effects on the activities, metabolic and genetic diversities, as well as soil bacterial and fungal community composition. The seeds of faba bean (Vicia faba L.) were either treated (PCP) or left untreated (Control) with pentachlorophenol before sowing. During the vegetative period, soil samples were taken three times from the rhizosphere in order to assess the influence of PCP on soil enzymatic activity, metabolic diversity (Biolog EcoPlate), community of ammonia-oxidizing archaea (DGGE and t-RFLP) and the fungal and bacterial microbiome (NGS). PCP treatment led to a considerable reduction in the activities of enzymes connected with the N cycle (protease and urease) and showed a significant negative correlation with them (r = −0.934 and − 0.716, respectively). Dehydrogenase and respiration activities were also reduced by PCP. In contrast to other enzymes analysed, PCP significantly increased acid phosphomonoesterase activity compared to the Control (r = 0.850). PCP also decreased the carbon utilization efficiency of indigenous microbes and caused the lower utilization of amines, amides and carboxylic acids. The amount of isolated DNA was lower in PCP-treated soil than in the Control. The technique of t-RFLP fingerprinting revealed the changes caused by contamination and new specific fragments were observed in PCP-contaminated soil. Additionally, pentachlorophenol changed more fungal than bacterial structures in the faba bean rhizosphere. For most of the analysis parameters, the effect of PCP was notable during the entire analysis period of faba bean growth (from 5‐6 leaves to pod formation). The results demonstrated the harmful effect of PCP on soil activity and changes in soil microorganism genetic diversity, which could result in the deterioration of the environment for soil function and processes as well as for plant growth.