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Journal articles on the topic 'Enriched microbial biomass'
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Holatko, Jiri, Tereza Hammerschmiedt, Antonin Kintl, Subhan Danish, Petr Skarpa, Oldrich Latal, Tivadar Baltazar, et al. "Effect of carbon-enriched digestate on the microbial soil activity." PLOS ONE 16, no. 7 (July 2, 2021): e0252262. http://dx.doi.org/10.1371/journal.pone.0252262.
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Objectives As a liquid organic fertilizer used in agriculture, digestate is rich in many nutrients (i.e. nitrogen, phosphorus, sulfur, calcium, potassium); their utilization may be however less efficient in soils poor in organic carbon (due to low carbon:nitrogen ratio). In order to solve the disadvantages, digestate enrichment with carbon-rich amendments biochar or humic acids (Humac) was tested. Methods Soil variants amended with enriched digestate: digestate + biochar, digestate + Humac, and digestate + combined biochar and humic acids—were compared to control with untreated digestate in their effect on total soil carbon and nitrogen, microbial biomass carbon, soil respiration and soil enzymatic activities in a pot experiment. Yield of the test crop lettuce was also determined for all variants. Results Soil respiration was the most significantly increased property, positively affected by digestate + Humac. Both digestate + biochar and digestate + Humac significantly increased microbial biomass carbon. Significant negative effect of digestate + biochar (compared to the control digestate) on particular enzyme activities was alleviated by the addition of humic acids. No significant differences among the tested variants were found in the above-ground and root plant biomass. Conclusions The tested organic supplements improved the digestate effect on some determined soil properties. We deduced from the results (carbon:nitrogen ratio, microbial biomass and activity) that the assimilation of nutrients by plants increased; however, the most desired positive effect on the yield of crop biomass was not demonstrated. We assume that the digestate enrichment with organic amendments may be more beneficial in a long time-scaled trial.
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Majone, M., M. Beccari, S. Di Gregorio, D. Dionisi, and G. Vallini. "Enrichment of activated sludge in a sequencing batch reactor for polyhydroxyalkanoate production." Water Science and Technology 54, no. 1 (July 1, 2006): 119–28. http://dx.doi.org/10.2166/wst.2006.379.
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The paper describes the start up of a process for the production of polyhydroxyalkanoates (PHAs) from activated sludge. The excess sludge from a wastewater treatment plant was inoculated in a lab-scale sequencing batch reactor (SBR) to be enriched under aerobic conditions through intermittent feeding with a mixture of organic acids. Enriching of activated sludge was monitored through the measurement of polymer concentrations either in the mixed liquor or in the microbial biomass. The bacterial population dynamics during the SBR start up was followed through denaturing gradient gel electrophoresis and the main species present at the steady state were identified. All the measured parameters significantly changed in the SBR during first two weeks after the inoculum was seeded into the reactor, they then stabilized. At the steady state, the SBR produced 2.6 gVSS l−1 d−1, with a PHA content of 11% (on a COD basis). The enriched microbial biomass was then transferred into a batch reactor where the bacterial polymer content was increased through a new feeding. In the final batch stage, maximum storage rate and maximum polymer content in the biomass were 405 mgCOD gCOD−1 h−1 and 44% (on a COD basis), respectively. The PHA storage from the enriched microbial biomass was about 20 times faster and the PHA content was about 4 times higher than that of the inoculated activated sludge. Observations by fluorescence microscopy showed that the majority of microorganisms in the enriched biomass could be stored. Among the numerically most representative genera in the enriched biomass, Thauera, Candidatus Meganema perideroedes, and Flavobacterium were identified.
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Carra, Maria Lidia, Vitória Teodoro Gonçalves, Tiago Palladino Delforno, Valéria Maia de Oliveira, and Ariovaldo José da Silva. "Evaluation of anaerobic and anoxic reactors installed in serial to treat fish tank effluent." Ambiente e Agua - An Interdisciplinary Journal of Applied Science 16, no. 3 (May 24, 2021): 1. http://dx.doi.org/10.4136/ambi-agua.2678.
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Effluent from a fish tank with Nile tilapia (Oreochromis niloticus) was treated in a system of two parallel fixed-bed anaerobic reactors followed by a suspended stirred, anoxic reactor for solids, organic matter and nitrogen removal. Microbial community structure was compared between the reactors and an enriched anammox culture originated from anaerobic sludge by using the PCR (Polymerase Chain Reaction) and DGGE (Denaturing Gradient Gel Electrophoresis) techniques. DGGE analysis revealed three large microbial clusters, namely, the biomass in the inoculum, the biomass growing in the reactors, and the enriched anammox culture. The similarity between the microbial community recovered from the anaerobic reactors and the anammox community was considered low (32.7%), suggesting differentiation of the bacterial community as a function of the selection of specific anammox groups. The last step in the anoxic reactor had worsened the effluent quality. The potential of organic matter and ammonia removal in a single anaerobic reactor was demonstrated.
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Rost, U., R. G. Joergensen, and K. Chander. "Effects of Zn enriched sewage sludge on microbial activities and biomass in soil." Soil Biology and Biochemistry 33, no. 4-5 (April 2001): 633–38. http://dx.doi.org/10.1016/s0038-0717(00)00207-8.
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Lee, Kang Hoon, Young Min Wie, and Yong-Soo Lee. "Characterization of 1,4-Dioxane Biodegradation by a Microbial Community." Water 12, no. 12 (December 1, 2020): 3372. http://dx.doi.org/10.3390/w12123372.
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In this study, a microbial community of bacteria was investigated for 1,4-dioxane(1,4-D) biodegradation. The enriched culture was investigated for 1,4-dioxane mineralization, co-metabolism of 1,4-dioxane and extra carbon sources, and characterized 1,4-dioxane biodegradation kinetics. The mineralization test indicates that the enriched culture was able to degrade 1,4-dioxane as the sole carbon and energy source. Interestingly, the distribution of 1,4-dioxane into the final biodegrading products were 36.9% into biomass, 58.3% completely mineralized to CO2, and about 4% escaped as VOC. The enriched culture has a high affinity with 1,4-dioxane during biodegradation. The kinetic coefficients of the Monod equation were qmax = 0.0063 mg 1,4-D/mg VSS/h, Ks = 9.42 mg/L, YT = 0.43 mg VSS/mg 1,4-dioxane and the decay rate was kd = 0.023 mg/mg/h. Tetrahydrofuran (THF) and ethylene glycol were both consumed together with 1,4-dioxane by the enriched culture; however, ethylene glycol did not show any influence on 1,4-dioxane biodegradation, while THF proved to be a competitive.
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Balota, Elcio L., Oswaldo Machineski, and Maria A. Matos. "Soil microbial biomass under different tillage and levels of applied pig slurry." Revista Brasileira de Engenharia Agrícola e Ambiental 16, no. 5 (May 2012): 487–95. http://dx.doi.org/10.1590/s1415-43662012000500004.
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ABSTRACT The objective of this work was to evaluate the changes in microbial biomass C, N and P due to the application of pig slurry under different soil tillage systems. The experiment was established in a clayey Oxisol, Eutrophic Red Latossol in Palotina, PR. Different quantities of pig slurry (0, 30, 60 and 120 m3 ha-1 year-1) were applied to the soil prior to the summer and winter crop season under conventional tillage (CT) and no tillage (NT), in three replicates. The area was cultivated with soybean (Glycine max L.) or maize (Zea mays L.) in the summer and wheat (Triticum sativum Lam.) or oat (Avena sativa L.) in the winter. The soil samples were collected in March and October of 1998 and 1999 at depths of 0-5, 5-10 and 10-20 cm. The soil tillage and pig slurry application influenced the microbial biomass C, N and P. The microbial biomass and the microbial activity presented high sensibility to detect changes in the soil due to tillage and the application of pig slurry. The soil microbial biomass and Cmic/Corg relation increased as the quantity of applied pig slurry increased. The metabolic quotient under CT increased with depth while under NT it decreased. The soil microbial biomass was enriched in N and P under NT and as the quantity of applied pig slurry increased.
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Tan, Wenbing, Renfei Li, Hanxia Yu, Xinyu Zhao, Qiuling Dang, Jie Jiang, Lei Wang, and Beidou Xi. "Prominent Conductor Mechanism-Induced Electron Transfer of Biochar Produced by Pyrolysis of Nickel-Enriched Biomass." Catalysts 8, no. 12 (November 22, 2018): 573. http://dx.doi.org/10.3390/catal8120573.
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Biochar is redox-active and can function as a sustainable electron shuttle in catalyzing relevant redox reactions. It plays a crucial role in environmental remediation. In this work, we used different-nickel (Ni)-level biochars produced by the pyrolysis of plant biomass with correspondingly different Ni levels as extracellular electron shuttles for microbial reduction of ferrihydrite by Shewanella oneidensis MR-1. A high Ni level of the precursor considerably enhanced the conductor mechanism of the produced biochar and thus enabled the biochar to catalyze increased microbial reductions of the Fe(III) mineral, but it did not promote the charging and discharging capacities of the produced biochar. This study can aid in the search for natural biomass with high Ni content to establish low-cost biochars with wide-ranging applications in catalyzing the redox-mediated reactions of pollutants.
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Qiu, Tian Lei, Xiao Hong Sun, Xu Ming Wang, Mei Lin Han, Lei Cheng, and Yu Deng. "Bioaugmentation for Biomass Production at Low Temperature Using Enriched Psychroactive Methanogenic Consortia." Advanced Materials Research 183-185 (January 2011): 1472–75. http://dx.doi.org/10.4028/www.scientific.net/amr.183-185.1472.
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Biogas fermentation is always limited or affected at low temperature conditions, one of key factors may be physiological adaption of methanogenic communities to low temperature. Howerer, biogas process could be stimulated and enhanced with addition of enriched consortia. Here, six psychroactive methanogenic consortiums were enriched as additives, and consortium E-1 was found to be most effective at 150C. The total biogas production addition with E-1 improved 39.3 % and 17.0% from pig manure and cow manure, respectively, when decreasing from 210C to 150C, which is a potential microbial addition for biogas fermentation at low temperature.
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Chander, K., P. C. Brookes, and S. A. Harding. "Microbial biomass dynamics following addition of metal-enriched sewage sludges to a sandy loam." Soil Biology and Biochemistry 27, no. 11 (November 1995): 1409–21. http://dx.doi.org/10.1016/0038-0717(95)00074-o.
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Bååth, E., M. Díaz-Raviña, and L. R. Bakken. "Microbial Biomass, Community Structure and Metal Tolerance of a Naturally Pb-Enriched Forest Soil." Microbial Ecology 50, no. 4 (November 2005): 496–505. http://dx.doi.org/10.1007/s00248-005-0008-3.
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Faseleh Jahromi, Mohammad, Juan Boo Liang, Rosfarizan Mohamad, Yong Meng Goh, Parisa Shokryazdan, and Yin Wan Ho. "Lovastatin-Enriched Rice Straw Enhances Biomass Quality and Suppresses Ruminal Methanogenesis." BioMed Research International 2013 (2013): 1–13. http://dx.doi.org/10.1155/2013/397934.
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The primary objective of this study was to test the hypothesis that solid state fermentation (SSF) of agro-biomass (using rice straw as model); besides, breaking down its lignocellulose content to improve its nutritive values also produces lovastatin which could be used to suppress methanogenesis in the rumen ecosystem. Fermented rice straw (FRS) containing lovastatin after fermentation withAspergillus terreuswas used as substrate for growth study of rumen microorganisms usingin vitrogas production method. In the first experiment, the extract from the FRS (FRSE) which contained lovastatin was evaluated for its efficacy for reduction in methane (CH4) production, microbial population, and activity in the rumen fluid. FRSE reduced total gas and CH4productions (P<0.01). It also reduced (P<0.01) total methanogens population and increased the cellulolytic bacteria includingRuminococcus albus,Fibrobacter succinogenes(P<0.01), andRuminococcus flavefaciens(P<0.05). Similarly, FRS reduced total gas and CH4productions, methanogens population, but increasedin vitrodry mater digestibility compared to the non-fermented rice straw. Lovastatin in the FRSE and the FRS significantly increased the expression of HMG-CoA reductase gene that produces HMG-CoA reductase, a key enzyme for cell membrane production in methanogenic Archaea.
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Ainalidou, Aggeliki, Foteini Bouzoukla, Urania Menkissoglu-Spiroudi, Despoina Vokou, and Katerina Karamanoli. "Impacts of Decaying Aromatic Plants on the Soil Microbial Community and on Tomato Seedling Growth and Metabolism: Suppression or Stimulation?" Plants 10, no. 9 (September 6, 2021): 1848. http://dx.doi.org/10.3390/plants10091848.
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This study provides insight into changes in the features of tomato seedlings growing in soils enriched with spearmint, peppermint, or rosemary leaves and into changes in the microbial communities of these soils used as seedbeds; an organic amendment was also applied as a positive control. While the soil microbial community flourished in the presence of all three aromatic plants, tomato growth was inhibited or stimulated depending on the plant that was used. More specifically, phospholipid fatty acid (PLFA) analysis showed an increase in the total microbial biomass and in the biomass of all the groups examined, except for actinobacteria, and changes in the microbial community structure, with Gram-negative bacteria and fungi being favoured in the mint treatments, in which the microbial biomass was maximized. Seedlings from the rosemary treatment were entirely inhibited; they were at the open-cotyledon stage throughout the experiment. Seedlings from the mint treatments were the heaviest, longest, and had the highest chlorophyll content and photosynthetic yield. Metabolomic analysis showed metabolism enhancement associated with both growth and priming in seedlings from the mint treatments and disruption of metabolic pathways in those from the rosemary treatment. There is a great potential for applying these aromatic plants as soil amendments and as either biostimulants of plant growth or as herbicides.
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Balota, Elcio Liborio, and Pedro Antonio Martins Auler. "Soil microbial biomass under different management and tillage systems of permanent intercropped cover species in an orange orchard." Revista Brasileira de Ciência do Solo 35, no. 6 (December 2011): 1873–83. http://dx.doi.org/10.1590/s0100-06832011000600004.
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To mitigate soil erosion and enhance soil fertility in orange plantations, the permanent protection of the inter-rows by cover species has been suggested. The objective of this study was to evaluate alterations in the microbial biomass, due to different soil tillage systems and intercropped cover species between rows of orange trees. The soil of the experimental area previously used as pasture (Brachiaria humidicola) was an Ultisol (Typic Paleudult) originating from Caiuá sandstone in the northwestern part of the State of Paraná, Brazil. Two soil tillage systems were evaluated: conventional tillage (CT) in the entire area and strip tillage (ST) (strip width 2 m), in combination with different ground cover management systems. The citrus cultivar 'Pera' orange (Citrus sinensis) grafted onto 'Rangpur' lime rootstock was used. Soil samples were collected after five years of treatment from a depth of 0-15 cm, under the tree canopy and in the inter-row, in the following treatments: (1) CT and an annual cover crop with the leguminous species Calopogonium mucunoides; (2) CT and a perennial cover crop with the leguminous peanut Arachis pintoi; (3) CT and an evergreen cover crop with Bahiagrass Paspalum notatum; (4) CT and a cover crop with spontaneous Brachiaria humidicola grass vegetation; and (5) ST and maintenance of the remaining grass (pasture) of Brachiaria humidicola. Soil tillage and the different cover species influenced the microbial biomass, both under the tree canopy and in the inter-row. The cultivation of brachiaria increased C and N in the microbial biomass, while bahiagrass increased P in the microbial biomass. The soil microbial biomass was enriched in N and P by the presence of ground cover species and according to the soil P content. The grass species increased C, N and P in the soil microbial biomass from the inter-row more than leguminous species.
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Mungkarndee, P., S. M. Rao Bhamidimarri, A. J. Mawson, and R. Chong. "Influence of changing microbial sludge characteristics on the degradation of an inhibitory compound." Water Science and Technology 31, no. 9 (May 1, 1995): 55–60. http://dx.doi.org/10.2166/wst.1995.0344.
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The biodegradation of 2,4-dichlorophenoxyacetic acid (2,4-D) by a mixed microbial consortium enriched from soil was investigated. The specific oxygen uptake rate (SOUR) as a measure of biomass was found to be inappropriate as the characteristics and composition of the mixed culture were found to change significantly as the operating conditions changed. Both SOUR and biomass measurements revealed an expected substrate inhibition pattern up to around 1000 mg/L 2,4-D in batch incubation trials. The maximum growth rate was recorded at a substrate concentration of around 300 mg/L when the biomass was measured by gravimetrically, although maximum oxygen uptake activity was at a substrate concentration of 500 mg/L. The continuous experiments showed that 2,4-D can be degraded at inlet concentrations of up to 6362 mg/L resulting in >99.5% degradation. The flocculation characteristics of the biomass were found to change as the substrate concentration changed and a microscopic examination confirmed that the changes in SOUR and specific substrate utilisation rate (SSUR) in the continuous system were due to changes in microbial culture characteristics.
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Wang, Yong, Xiongsheng Liu, Fengfan Chen, Ronglin Huang, Xiaojun Deng, and Yi Jiang. "Seasonal dynamics of soil microbial biomass C and N of Keteleeria fortunei var. cyclolepis forests with different ages." Journal of Forestry Research 31, no. 6 (October 23, 2019): 2377–84. http://dx.doi.org/10.1007/s11676-019-01058-w.
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Abstract Soil microbial biomass is an important indicator to measure the dynamic changes of soil carbon pool. It is of great significance to understand the dynamics of soil microbial biomass in plantation for rational management and cultivation of plantation. In order to explore the temporal dynamics and influencing factors of soil microbial biomass of Keteleeria fortunei var. cyclolepis at different stand ages, the plantation of different ages (young forest, 5 years; middle-aged forest, 22 years; mature forest, 40 years) at the Guangxi Daguishan forest station of China were studied to examine the seasonal variation of their microbial biomass carbon (MBC) and microbial biomass nitrogen (MBN) by chloroform fumigation extraction method. It was found that among the forests of different age, MBC and MBN differed significantly in the 0–10 cm soil layer, and MBN differed significantly in the 10–20 cm soil layer, but there was no significant difference in MBC for the 10–20 cm soil layer or in either MBC or MBN for the 20–40 cm soil layer. With increasing maturity of the forest, MBC gradually decreased in the 0–10 cm soil layer and increased firstly and then decreased in the 10–20 cm and 20–40 cm soil layers, and MBN increased firstly and then decreased in all three soil layers. As the soil depth increased, both MBC and MBN gradually decreased for all three forests. The MBC and MBN basically had the same seasonal variation in all three soil layers of all three forests, i.e., high in the summer and low in the winter. Correlation analysis showed that MBC was significantly positively correlated with soil organic matter, total nitrogen, and soil moisture, whereas MBN was significantly positively correlated with soil total nitrogen. It showed that soil moisture content was the main factor determining the variation of soil microbial biomass by Redundancy analysis. The results showed that the soil properties changed continuously as the young forest grew into the middle-aged forest, which increased soil microbial biomass and enriched the soil nutrients. However, the soil microbial biomass declined as the middle-age forest continued to grow, and the soil nutrients were reduced in the mature forest.
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Pandey, Ashok, and Carlos R. Soccol. "Bioconversion of biomass: a case study of ligno-cellulosics bioconversions in solid state fermentation." Brazilian Archives of Biology and Technology 41, no. 4 (August 1998): 379–90. http://dx.doi.org/10.1590/s1516-89131998000400001.
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Lignocellulosic residues obtained from crops cultivation form useful sources to be used as substrate for bioconversion processes. Sugarcane bagasse, which is a complex substrate obtained from the processing of sugar cane, is an important biomass among such sources. Due to its abundant availability, it can serve as an ideal substrate for microbial processes for the production of value added products. This paper reviews recent developments on biological processes developed on production of various products in solid state fermentation using sugarcane bagasse as the substrate and describes production of protein enriched feed, enzymes, amino acid, organic acids and compounds of pharmaceutical importance, etc. through microbial means.
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Mandal, Tej Narayan. "Restoration in soil and plant properties in landslide damaged forest ecosystem." Nepalese Journal of Biosciences 2 (January 24, 2013): 40–45. http://dx.doi.org/10.3126/njbs.v2i0.7488.
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The pattern of natural restoration in soil and plant components was studied in five landslide-damaged (1-58-year-old) sites in the tropical moist sal (Shorea robusta) forest ecosystem of Nepal Himalaya .Rate of restoration in soil properties was faster in the early successional stages (1-15 year) than late stages while plant biomass recovered rapidly after 15-year age. Based on the recovery in ecosystem properties; the 58- year-old landslide damaged site demonstrated the re-establishment of an ecosystem showing closer affinity with the mature sal forest. On the basis of best fit power function models it was concluded that the estimated times for the 58-year old site to reach the level of undisturbed matured sal forest would be about 30-35 years for microbial biomass (C and N) and plant biomass and about 100-150 year for soil organic Carbon and total N. Higher accumulation of soil microbial biomass, plant biomass and high N-mineralization rate at late successional stages indicated the re-establishment of an ecosystem with enriched soil and restitution of nutrient cycling during the course of ecosystem restoration DOI: http://dx.doi.org/10.3126/njbs.v2i0.7488 Nepalese Journal of Biosciences 2 : 40-45 (2012)
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Moridi, Ameneh, Mehdi Zarei, Ali Akbar Moosavi, and Abdolmajid Ronaghi. "Effect of Liquid Organic Fertilizers and Soil Moisture Status on Some Biological and Physical Properties of Soil." Polish Journal of Soil Science 54, no. 1 (June 29, 2021): 41. http://dx.doi.org/10.17951/pjss.2021.54.1.41-58.
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<p>This study was conducted to evaluate the effects of liquid organic fertilizers (LOFs) and soil moisture status on some biological and physical properties of postharvest soil of maize cultivation. For this purpose, a factorial greenhouse experiment was performed based on the completely randomized design with three replications. Treatments consisted of five levels of LOFs (control, vermicompost tea, vermiwash, plant growth-promoting rhizobacteria [PGPR] enriched vermicompost tea and PGPR enriched vermiwash) and three levels of soil moisture status (field capacity [FC], 0.8 FC and 0.6 FC). The results showed LOFs caused an increase of soil biological properties (soil microbial respiration, soil microbial biomass, dehydrogenase activity and the number of aerobic heterotrophic bacteria) and the improvement of soil physical condition. LOFs increased aggregate stability, hydrophobicity and total porosity, while decreased bulk density and soil penetration resistance. Increasing water stress levels reduced soil biological activity and made soil physical properties more unfavorable. In general, LOFs improved soil conditions by enhancing soil physical and biological properties and decreased the negative effects of water stress. In addition, results showed that LOFs enriched with PGPR could be more effective than non-enriched ones.</p>
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Ermakov, V. V., T. V. Guseva, Yu V. Kovalsky, and V. I. Panfilov. "Applied aspects of the geochemical ecology of microorganisms used for solving ecobiotechnological tasks." Biotekhnologiya 36, no. 6 (2020): 107–14. http://dx.doi.org/10.21519/0234-2758-2020-36-6-107-114.
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The article presents a new view on opportunities on using microorganisms for achieving a wide range of biotechnological and environmental objectives. Examples of recent innovations in applying bio-products based on living cells of microorganisms for remediating oil polluted soils and enhancing soil fertility are given. The significance of microbiological solutions with regards of achieving objectives of the National Project "Environment/Ecology" is underlined. Perspectives and effectiveness of technologies applying microbial biomass enriched in microelements for correcting microelementoses and preventing biogeochemical endemic diseases is demonstrated. biogeochemistry, biotechnology, geochemical ecology, microelementosis, effectiveness of application, microbial bio-products.
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M, D. Meena, and R. Biswas D. "Effect of rock phosphate enriched compost and chemical fertilizers on microbial biomass phosphorus and phosphorus fractions." African Journal of Microbiology Research 9, no. 23 (June 10, 2015): 1519–26. http://dx.doi.org/10.5897/ajmr2014.6957.
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de Lima Brossi, Maria Julia, Diego Javier Jiménez, Larisa Cortes-Tolalpa, and Jan Dirk van Elsas. "Soil-Derived Microbial Consortia Enriched with Different Plant Biomass Reveal Distinct Players Acting in Lignocellulose Degradation." Microbial Ecology 71, no. 3 (October 20, 2015): 616–27. http://dx.doi.org/10.1007/s00248-015-0683-7.
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Singh, K. M., Bhaskar Reddy, Dishita Patel, A. K. Patel, Nidhi Parmar, Anand Patel, J. B. Patel, and C. G. Joshi. "High Potential Source for Biomass Degradation Enzyme Discovery and Environmental Aspects Revealed through Metagenomics of Indian Buffalo Rumen." BioMed Research International 2014 (2014): 1–10. http://dx.doi.org/10.1155/2014/267189.
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The complex microbiomes of the rumen functions as an effective system for plant cell wall degradation, and biomass utilization provide genetic resource for degrading microbial enzymes that could be used in the production of biofuel. Therefore the buffalo rumen microbiota was surveyed using shot gun sequencing. This metagenomic sequencing generated 3.9 GB of sequences and data were assembled into 137270 contiguous sequences (contigs). We identified potential 2614 contigs encoding biomass degrading enzymes including glycoside hydrolases (GH: 1943 contigs), carbohydrate binding module (CBM: 23 contigs), glycosyl transferase (GT: 373 contigs), carbohydrate esterases (CE: 259 contigs), and polysaccharide lyases (PE: 16 contigs). The hierarchical clustering of buffalo metagenomes demonstrated the similarities and dissimilarity in microbial community structures and functional capacity. This demonstrates that buffalo rumen microbiome was considerably enriched in functional genes involved in polysaccharide degradation with great prospects to obtain new molecules that may be applied in the biofuel industry.
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Ishii, Shun'ichi, Kazuya Watanabe, Soichi Yabuki, Bruce E. Logan, and Yuji Sekiguchi. "Comparison of Electrode Reduction Activities of Geobacter sulfurreducens and an Enriched Consortium in an Air-Cathode Microbial Fuel Cell." Applied and Environmental Microbiology 74, no. 23 (October 3, 2008): 7348–55. http://dx.doi.org/10.1128/aem.01639-08.
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ABSTRACT An electricity-generating bacterium, Geobacter sulfurreducens PCA, was inoculated into a single-chamber, air-cathode microbial fuel cell (MFC) in order to determine the maximum electron transfer rate from bacteria to the anode. To create anodic reaction-limiting conditions, where electron transfer from bacteria to the anode is the rate-limiting step, anodes with electrogenic biofilms were reduced in size and tests were conducted using anodes of six different sizes. The smallest anode (7 cm2, or 1.5 times larger than the cathode) achieved an anodic reaction-limiting condition as a result of a limited mass of bacteria on the electrode. Under these conditions, the limiting current density reached a maximum of 1,530 mA/m2, and power density reached a maximum of 461 mW/m2. Per-biomass efficiency of the electron transfer rate was constant at 32 fmol cell−1 day−1 (178 μmol g of protein−1 min−1), a rate comparable to that with solid iron as the electron acceptor but lower than rates achieved with fumarate or soluble iron. In comparison, an enriched electricity-generating consortium reached 374 μmol g of protein−1 min−1 under the same conditions, suggesting that the consortium had a much greater capacity for electrode reduction. These results demonstrate that per-biomass electrode reduction rates (calculated by current density and biomass density on the anode) can be used to help make better comparisons of electrogenic activity in MFCs.
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Ginige, Maneesha P., Philip Hugenholtz, Holger Daims, Michael Wagner, Jürg Keller, and Linda L. Blackall. "Use of Stable-Isotope Probing, Full-Cycle rRNA Analysis, and Fluorescence In Situ Hybridization-Microautoradiography To Study a Methanol-Fed Denitrifying Microbial Community." Applied and Environmental Microbiology 70, no. 1 (January 2004): 588–96. http://dx.doi.org/10.1128/aem.70.1.588-596.2004.
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ABSTRACT A denitrifying microbial consortium was enriched in an anoxically operated, methanol-fed sequencing batch reactor (SBR) fed with a mineral salts medium containing methanol as the sole carbon source and nitrate as the electron acceptor. The SBR was inoculated with sludge from a biological nutrient removal activated sludge plant exhibiting good denitrification. The SBR denitrification rate improved from less than 0.02 mg of NO3 −-N mg of mixed-liquor volatile suspended solids (MLVSS)−1 h−1 to a steady-state value of 0.06 mg of NO3 −-N mg of MLVSS−1 h−1 over a 7-month operational period. At this time, the enriched microbial community was subjected to stable-isotope probing (SIP) with [13C]methanol to biomark the DNA of the denitrifiers. The extracted [13C]DNA and [12C]DNA from the SIP experiment were separately subjected to full-cycle rRNA analysis. The dominant 16S rRNA gene phylotype (group A clones) in the [13C]DNA clone library was closely related to those of the obligate methylotrophs Methylobacillus and Methylophilus in the order Methylophilales of the Betaproteobacteria (96 to 97% sequence identities), while the most abundant clone groups in the [12C]DNA clone library mostly belonged to the family Saprospiraceae in the Bacteroidetes phylum. Oligonucleotide probes for use in fluorescence in situ hybridization (FISH) were designed to specifically target the group A clones and Methylophilales (probes DEN67 and MET1216, respectively) and the Saprospiraceae clones (probe SAP553). Application of these probes to the SBR biomass over the enrichment period demonstrated a strong correlation between the level of SBR denitrification and relative abundance of DEN67-targeted bacteria in the SBR community. By contrast, there was no correlation between the denitrification rate and the relative abundances of the well-known denitrifying genera Hyphomicrobium and Paracoccus or the Saprospiraceae clones visualized by FISH in the SBR biomass. FISH combined with microautoradiography independently confirmed that the DEN67-targeted cells were the dominant bacterial group capable of anoxic [14C]methanol uptake in the enriched biomass. The well-known denitrification lag period in the methanol-fed SBR was shown to coincide with a lag phase in growth of the DEN67-targeted denitrifying population. We conclude that Methylophilales bacteria are the dominant denitrifiers in our SBR system and likely are important denitrifiers in full-scale methanol-fed denitrifying sludges.
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Flury, Sabine, and Mark O. Gessner. "Experimentally Simulated Global Warming and Nitrogen Enrichment Effects on Microbial Litter Decomposers in a Marsh." Applied and Environmental Microbiology 77, no. 3 (December 10, 2010): 803–9. http://dx.doi.org/10.1128/aem.01527-10.
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ABSTRACTAtmospheric warming and increased nitrogen deposition can lead to changes of microbial communities with possible consequences for biogeochemical processes. We used an enclosure facility in a freshwater marsh to assess the effects on microbes associated with decomposing plant litter under conditions of simulated climate warming and pulsed nitrogen supply. Standard batches of litter were placed in coarse-mesh and fine-mesh bags and submerged in a series of heated, nitrogen-enriched, and control enclosures. They were retrieved later and analyzed for a range of microbial parameters. Fingerprinting profiles obtained by denaturing gradient gel electrophoresis (DGGE) indicated that simulated global warming induced a shift in bacterial community structure. In addition, warming reduced fungal biomass, whereas bacterial biomass was unaffected. The mesh size of the litter bags and sampling date also had an influence on bacterial community structure, with the apparent number of dominant genotypes increasing from spring to summer. Microbial respiration was unaffected by any treatment, and nitrogen enrichment had no clear effect on any of the microbial parameters considered. Overall, these results suggest that microbes associated with decomposing plant litter in nutrient-rich freshwater marshes are resistant to extra nitrogen supplies but are likely to respond to temperature increases projected for this century.
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Yan, Yixin, Dafang Fu, and Jiayuan Shi. "Screening and Immobilizing the Denitrifying Microbes in Sediment for Bioremediation." Water 11, no. 3 (March 25, 2019): 614. http://dx.doi.org/10.3390/w11030614.
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In this study, immobilized microbial beads were proposed as a solution for excessive nitrogen concentration of the river sediment. The predominant denitrifying microbes were screened from the river sediment. The optimized production of immobilized microbial beads and long-term nitrogen removal efficiency were investigated. 16S rRNA gene sequencing analysis showed that denitrifying bacteria such as Pseudomonas, Alcaligenes, Proteiniclasticum, Achromobacter and Methylobacillus were dominant microflora in the enriched microbial agent, which accounted for 94.43% of the total microbes. Pseudomonas belongs to Gammaproteo bacteria, accounting for 49.22% and functioned as the most predominant denitrifying bacteria. The material concentration of 8% polyvinyl alcohol, 0.5% sodium alginate and 12.5% microbial biomass were found to be the optimal immobilizing conditions. The NH4+-N and total nitrogen (TN) removal rates in sediment with dosing immobilized microbial beads were estimated as 68.1% and 67.8%, respectively, when compared to the dosing liquid microbial agent were 50.5% and 49.3%. Meanwhile, the NH4+-N and TN removal rates in overlying water went up from 53.14% to 59.69% and from 68.03% to 78.13%, respectively, by using immobilized microbial beads.
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Billah, Motsim, Matiullah Khan, Asghari Bano, Sobia Nisa, Ahmad Hussain, Khadim Muhammad Dawar, Asia Munir, and Naeem Khan. "Rock Phosphate-Enriched Compost in Combination with Rhizobacteria; A Cost-Effective Source for Better Soil Health and Wheat (Triticum aestivum) Productivity." Agronomy 10, no. 9 (September 14, 2020): 1390. http://dx.doi.org/10.3390/agronomy10091390.
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Organic materials from various sources have been commonly adopted as soil amendments to improve crop productivity. Phosphorus deficiency and fixation in alkaline calcareous soils drives a reduction in crop production. A two-year field experiment was conducted to evaluate the impact of rock phosphate enriched composts and chemical fertilizers both individually and in combination with plant growth promoting rhizobacteria (PGPR) on wheat productivity and soil chemical and biological and biochemical properties. The present study demonstrates significant increments in crop agronomic and physiological parameters with Pseudomonas sp. inoculated RPEC1 (rock phosphate + poultry litter + Pseudomonas sp.) over the un-inoculated untreated control. However, among all other treatments i.e., RPEC2 (rock phosphate + poultry litter solubilized with Proteus sp.), RPC (rock phosphate + poultry litter), HDP (half dose inorganic P from Single Super Phosphate-SSP 18% P2O5) and SPLC (poultry litter only); RPEC1 remained the best by showing increases in soil chemical properties (available phosphorus, nitrate nitrogen, extractable potassium), biochemical properties (alkaline phosphatase activity) and biological properties (microbial biomass carbon and microbial biomass phosphorus). Economic analysis in terms of Value Cost Ratio (VCR) showed that the seed inoculation with Pseudomonas sp. in combination with RPEC1 gave maximum VCR (3.23:1) followed by RPEC2 (2.61:1), FDP (2.37:1), HDP (2.05:1) and SPLC (2.03:1). It is concluded that inoculated rock phosphate (RP) enriched compost (RPEC1) can be a substitute to costly chemical fertilizers and seed inoculation with Pseudomonas sp. may further increase the efficiency of composts.
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Esperschütz, J., A. Pérez-de-Mora, K. Schreiner, G. Welzl, F. Buegger, J. Zeyer, F. Hagedorn, J. C. Munch, and M. Schloter. "Microbial food web dynamics along a soil chronosequence of a glacier forefield." Biogeosciences Discussions 8, no. 1 (February 10, 2011): 1275–308. http://dx.doi.org/10.5194/bgd-8-1275-2011.
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Abstract. Microbial food webs are critical for efficient nutrient turnover providing the basis for functional and stable ecosystems. However, the successional development of such microbial food webs and their role in "young" ecosystems is unclear. Due to a continuous glacier retreat since the middle of the 19th century, glacier forefields have expanded offering an excellent opportunity to study food web development at differently developed soils. In the present study, litter degradation and the corresponding C fluxes into microbial communities were investigated along the forefield of the Damma glacier (Switzerland). 13C-enriched litter of the pioneering plant Leucanthemopsis alpina (L.) Heywood was incorporated into the soil at sites that have been free from ice for approximately 10, 60, 100 and more than 700 years. The structure and function of microbial communities were identified by 13C analysis of phospholipid fatty acids (PLFA) and phospholipid ether lipids (PLEL). Results showed increasing microbial diversity and biomass, and enhanced proliferation of bacterial groups as ecosystem development progressed. Initially, litter decomposition proceeded faster at the more developed sites, but at the end of the experiment loss of litter mass was similar at all sites, once the more easily-degradable litter fraction was processed. As a result incorporation of 13C into microbial biomass was more evident during the first weeks of litter decomposition. 13C enrichments of both PLEL and PUFA biomarkers following litter incorporation were observed at all sites, suggesting similar microbial foodwebs at all stages of soil development. Nonetheless, the contribution of bacteria and actinomycetes to litter turnover became more pronounced as soil age increased in detriment of archaea, fungi and protozoa, more prominent in recently deglaciated terrain.
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Esperschütz, J., A. Pérez-de-Mora, K. Schreiner, G. Welzl, F. Buegger, J. Zeyer, F. Hagedorn, J. C. Munch, and M. Schloter. "Microbial food web dynamics along a soil chronosequence of a glacier forefield." Biogeosciences 8, no. 11 (November 11, 2011): 3283–94. http://dx.doi.org/10.5194/bg-8-3283-2011.
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Abstract. Microbial food webs are critical for efficient nutrient turnover providing the basis for functional and stable ecosystems. However, the successional development of such microbial food webs and their role in "young" ecosystems is unclear. Due to a continuous glacier retreat since the middle of the 19th century, glacier forefields have expanded offering an excellent opportunity to study food web dynamics in soils at different developmental stages. In the present study, litter degradation and the corresponding C fluxes into microbial communities were investigated along the forefield of the Damma glacier (Switzerland). 13C-enriched litter of the pioneering plant Leucanthemopsis alpina (L.) Heywood was incorporated into the soil at sites that have been free from ice for approximately 10, 60, 100 and more than 700 years. The structure and function of microbial communities were identified by 13C analysis of phospholipid fatty acids (PLFA) and phospholipid ether lipids (PLEL). Results showed increasing microbial diversity and biomass, and enhanced proliferation of bacterial groups as ecosystem development progressed. Initially, litter decomposition proceeded faster at the more developed sites, but at the end of the experiment loss of litter mass was similar at all sites, once the more easily-degradable litter fraction was processed. As a result incorporation of 13C into microbial biomass was more evident during the first weeks of litter decomposition. 13C enrichments of both PLEL and PLFA biomarkers following litter incorporation were observed at all sites, suggesting similar microbial foodwebs at all stages of soil development. Nonetheless, the contribution of bacteria, especially actinomycetes to litter turnover became more pronounced as soil age increased in detriment of archaea, fungi and protozoa, more prominent in recently deglaciated terrain.
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Morrison, Jessica M., Chelsea L. Murphy, Kristina Baker, Richard M. Zamor, Steve J. Nikolai, Shawn Wilder, Mostafa S. Elshahed, and Noha H. Youssef. "Microbial communities mediating algal detritus turnover under anaerobic conditions." PeerJ 5 (January 10, 2017): e2803. http://dx.doi.org/10.7717/peerj.2803.
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BackgroundAlgae encompass a wide array of photosynthetic organisms that are ubiquitously distributed in aquatic and terrestrial habitats. Algal species often bloom in aquatic ecosystems, providing a significant autochthonous carbon input to the deeper anoxic layers in stratified water bodies. In addition, various algal species have been touted as promising candidates for anaerobic biogas production from biomass. Surprisingly, in spite of its ecological and economic relevance, the microbial community involved in algal detritus turnover under anaerobic conditions remains largely unexplored.ResultsHere, we characterized the microbial communities mediating the degradation ofChlorella vulgaris(Chlorophyta),Charasp. strain IWP1 (Charophyceae), and kelpAscophyllum nodosum(phylum Phaeophyceae), using sediments from an anaerobic spring (Zodlteone spring, OK; ZDT), sludge from a secondary digester in a local wastewater treatment plant (Stillwater, OK; WWT), and deeper anoxic layers from a seasonally stratified lake (Grand Lake O’ the Cherokees, OK; GL) as inoculum sources. Within all enrichments, the majority of algal biomass was metabolized within 13–16 weeks, and the process was accompanied by an increase in cell numbers and a decrease in community diversity. Community surveys based on the V4 region of the 16S rRNA gene identified different lineages belonging to the phyla Bacteroidetes, Proteobacteria (alpha, delta, gamma, and epsilon classes), Spirochaetes, and Firmicutes that were selectively abundant under various substrate and inoculum conditions. Within all kelp enrichments, the microbial communities structures at the conclusion of the experiment were highly similar regardless of the enrichment source, and were dominated by the genusClostridium, or familyVeillonellaceaewithin the Firmicutes. In all other enrichments the final microbial community was dependent on the inoculum source, rather than the type of algae utilized as substrate. Lineages enriched included the uncultured groups VadinBC27 and WCHB1-69 within the Bacteroidetes, genusSpirochaetaand the uncultured group SHA-4 within Spirochaetes,Ruminococcaceae,Lachnospiraceae,Yongiibacter,Geosporobacter, andAcidaminobacterwithin the Firmicutes, and generaKluyvera,Pantoea,EdwardsiellaandAeromonas,andButtiauxellawithin the Gamma-Proteobaceteria order Enterobacteriales.ConclusionsOur results represent the first systematic survey of microbial communities mediating turnover of algal biomass under anaerobic conditions, and highlights the diversity of lineages putatively involved in the degradation process.
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Ferretti, Giacomo, Barbara Faccini, Livia Vittori Antisari, Dario Di Giuseppe, and Massimo Coltorti. "15N Natural Abundance, Nitrogen and Carbon Pools in Soil-Sorghum System Amended with Natural and NH4+-Enriched Zeolitites." Applied Sciences 9, no. 21 (October 25, 2019): 4524. http://dx.doi.org/10.3390/app9214524.
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The use of rocks containing high amounts of natural zeolites (zeolitites) as soil amendment has been found as a valuable method for increasing agriculture sustainability. However, the potentialities and the effects of zeolitites on the biogeochemical cycles of nitrogen (N) and carbon (C) have still not been clearly addressed in the literature. The objective of this study was therefore to investigate the N and C pools and 15N distribution in an agricultural soil amended with both natural and NH4+-enriched zeolitites with the aim of understanding their effects on the soil-plant system, during sorghum cultivation, under fertilization reductions. Zeolitites were applied to an agricultural soil both at natural state (5 and 15 kg m−2) and in an enriched state with NH4+ ions from pig slurry (7 kg m−2). Both zeolitites at natural and enriched state increased soil cation exchange capacity and affected microbial biomass, causing an initial decrease of microbial C and N and then a possible increase of fungal population. N-NO3− content was lower in natural zeolitite treatments, that lead to a lower NO3− availability for denitrifying bacteria. Zeolitites slightly affected the fixed N-NH4+ pool. δ15N turnover indicated that N from NH4+-enriched zeolitites remained in the soil until the growing season and that fertilizers partially substituted the fixed pool. Leaf δ15N content indicated that plants assimilated N from NH4+-enriched zeolitites and evidenced a higher fertilization recovery in natural zeolitite treatments. Organic C tended to be higher in all zeolitite treatment rhizospheres. In soils amended with zeolitites at natural state (at both application rates) sorghum yield was similar (+3.7%) to that obtained in the control while it was higher (+13.9%) in the plot amended with NH4+-enriched zeolitites.
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Lerch, Thomas Z., Marie-France Dignac, Enrique Barriuso, and André Mariotti. "Effect of Glucose on the Fatty Acid Composition of Cupriavidus necator JMP134 during 2,4-Dichlorophenoxyacetic Acid Degradation: Implications for Lipid-Based Stable Isotope Probing Methods." Applied and Environmental Microbiology 77, no. 20 (August 19, 2011): 7296–306. http://dx.doi.org/10.1128/aem.06438-11.
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ABSTRACTCombining lipid biomarker profiling with stable isotope probing (SIP) is a powerful technique for studying specific microbial populations responsible for the degradation of organic pollutants in various natural environments. However, the presence of other easily degradable substrates may induce significant physiological changes by altering both the rate of incorporation of the target compound into the biomass and the microbial lipid profiles. In order to test this hypothesis,Cupriavidus necatorJMP134, a 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacterium, was incubated with [13C]2,4-D, [13C]glucose, or mixtures of both substrates alternatively labeled with13C.C. necatorJMP134 exhibited a preferential use of 2,4-D over glucose. The isotopic analysis showed that glucose had only a small effect on the incorporation of the acetic chain of 2,4-D into the biomass (at days 2 and 3) and no effect on that of the benzenic ring. The addition of glucose did change the fatty acid methyl ester (FAME) composition. However, the overall FAME isotopic signature reflected that of the entire biomass. Compound-specific individual isotopic analyses of FAME composition showed that the13C-enriched FAME profiles were slightly or not affected when tracing the 2,4-D acetic chain or 2,4-D benzenic ring, respectively. This batch study is a necessary step for validating the use of lipid-based SIP methods in complex environments.
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Luyima, Deogratius, Michael Egyir, Yeo-Uk Yun, Seong-Jin Park, and Taek-Keun Oh. "Nutrient Dynamics in Sandy Soil and Leaf Lettuce Following the Application of Urea and Urea-Hydrogen Peroxide Impregnated Co-Pyrolyzed Animal Manure and Bone Meal." Agronomy 11, no. 8 (August 20, 2021): 1664. http://dx.doi.org/10.3390/agronomy11081664.
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There is a paucity of data regarding the effect of nutrient-enriched biochar amendments on nutrient dynamics in both soil and crops. This is important because unlike pristine biochar, nutrient-enriched biochar is applied to the soil in minute quantities as large amounts may led to over application of the nutrients loaded in it. The current study examined the effects of both phosphorus- and nitrogen-enriched biochars on the dynamics of both macro and micronutrients in the sandy soil and leaf lettuce grown thereon. The phosphorus enrichment followed co-pyrolysis of animal manure (cow dung) with 25% and 50% bone meal (w/w), while the nitrogen enrichment was achieved by soaking the co-pyrolyzed biochar into urea and urea-hydrogen peroxide. The performances of the nutrient-enriched biochar were compared with the conventional amendment of urea and triple superphosphate (TSP) in the production of leaf lettuce over a period of two seasons in a pot experiment. The nutrient-enriched biochar amendments resulted into higher microbial biomass carbon and carbon to nitrogen ratios than the conventional amendment. The conventional amendment caused more phosphorus, potassium, and magnesium accumulations in the leaf lettuce than the nutrient-enriched biochar amendments. The nutrient-enriched biochar amendments led to more accumulations of nitrogen, calcium, and micronutrient elements in the leaf lettuce and availabilities of all the nutrient elements in the soil and thus, nutrient-enriched biochar acted as a reservoir that could provide nutrients to the growing lettuce beyond a single growing season.
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Gaind, Sunita, and Alok Kumar Pandey. "Microbial Biomass, P-Nutrition, and Enzymatic Activities of Wheat Soil in Response to Phosphorus Enriched Organic and Inorganic Manures." Journal of Environmental Science and Health, Part B 41, no. 2 (March 1, 2006): 177–87. http://dx.doi.org/10.1080/03601230500365044.
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Pearson, Ann, Kimberly S. Kraunz, Alex L. Sessions, Anne E. Dekas, William D. Leavitt, and Katrina J. Edwards. "Quantifying Microbial Utilization of Petroleum Hydrocarbons in Salt Marsh Sediments by Using the 13C Content of Bacterial rRNA." Applied and Environmental Microbiology 74, no. 4 (December 14, 2007): 1157–66. http://dx.doi.org/10.1128/aem.01014-07.
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ABSTRACT Natural remediation of oil spills is catalyzed by complex microbial consortia. Here we took a whole-community approach to investigate bacterial incorporation of petroleum hydrocarbons from a simulated oil spill. We utilized the natural difference in carbon isotopic abundance between a salt marsh ecosystem supported by the 13C-enriched C4 grass Spartina alterniflora and 13C-depleted petroleum to monitor changes in the 13C content of biomass. Magnetic bead capture methods for selective recovery of bacterial RNA were used to monitor the 13C content of bacterial biomass during a 2-week experiment. The data show that by the end of the experiment, up to 26% of bacterial biomass was derived from consumption of the freshly spilled oil. The results contrast with the inertness of a nearby relict spill, which occurred in 1969 in West Falmouth, MA. Sequences of 16S rRNA genes from our experimental samples also were consistent with previous reports suggesting the importance of Gamma- and Deltaproteobacteria and Firmicutes in the remineralization of hydrocarbons. The magnetic bead capture approach makes it possible to quantify uptake of petroleum hydrocarbons by microbes in situ. Although employed here at the domain level, RNA capture procedures can be highly specific. The same strategy could be used with genus-level specificity, something which is not currently possible using the 13C content of biomarker lipids.
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de Nardi, I. R., M. B. A. Varesche, M. Zaiat, and E. Foresti. "Anaerobic degradation of BTEX in a packed-bed reactor." Water Science and Technology 45, no. 10 (May 1, 2002): 175–80. http://dx.doi.org/10.2166/wst.2002.0323.
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A bench-scale horizontal-flow anaerobic immobilized biomass (HAIB) reactor was assayed aiming to verify its performance in degrading benzene, toluene, ethylbenzene and xylene (BTEX). A 138-ml HAIB reactor filled with polyurethane foam matrices containing immobilized anaerobic biomass was initially fed with synthetic substrate containing protein, carbohydrates and lipids. Thereafter, BTEX degradation was evaluated in the presence of the co-solvents ethanol and lineal alkylbenzene sulphonate (LAS), in two sequential experiments. The inlet BTEX concentration ranged from 1.3 to 27.0 mg/L of each compound and outlet concentrations were lower than 0.1 mg BTEX/L for both the experiments with ethanol and LAS. An active enriched microbial consortium was observed in the reactor, containing BTEX-degraders, and also acetogenic, acetotrophic and hydrogenotrophic microorganisms. The results from the most probable number (MPN) tests indicated a decrease in the number of methanogenic archae, while the number of anaerobic microorganisms in the biofilm was maintained during the experimental period. Methanogenic archae were found to represent less than 0.5 % of the total anaerobic organisms in the biomass inside the reactor.
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Gulis, Vladislav, Keller Suberkropp, and Amy D. Rosemond. "Comparison of Fungal Activities on Wood and Leaf Litter in Unaltered and Nutrient-Enriched Headwater Streams." Applied and Environmental Microbiology 74, no. 4 (December 14, 2007): 1094–101. http://dx.doi.org/10.1128/aem.01903-07.
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ABSTRACT Fungi are the dominant organisms decomposing leaf litter in streams and mediating energy transfer to other trophic levels. However, less is known about their role in decomposing submerged wood. This study provides the first estimates of fungal production on wood and compares the importance of fungi in the decomposition of submerged wood versus that of leaves at the ecosystem scale. We determined fungal biomass (ergosterol) and activity associated with randomly collected small wood (<40 mm diameter) and leaves in two southern Appalachian streams (reference and nutrient enriched) over an annual cycle. Fungal production (from rates of radiolabeled acetate incorporation into ergosterol) and microbial respiration on wood (per gram of detrital C) were about an order of magnitude lower than those on leaves. Microbial activity (per gram of C) was significantly higher in the nutrient-enriched stream. Despite a standing crop of wood two to three times higher than that of leaves in both streams, fungal production on an areal basis was lower on wood than on leaves (4.3 and 15.8 g C m−2 year−1 in the reference stream; 5.5 and 33.1 g C m−2 year−1 in the enriched stream). However, since the annual input of wood was five times lower than that of leaves, the proportion of organic matter input directly assimilated by fungi was comparable for these substrates (15.4 [wood] and 11.3% [leaves] in the reference stream; 20.0 [wood] and 20.2% [leaves] in the enriched stream). Despite a significantly lower fungal activity on wood than on leaves (per gram of detrital C), fungi can be equally important in processing both leaves and wood in streams.
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Tuominen, Tapani, and Heikki Rosenqvist. "Annual variations in the microflora of some varieties of Finnish malting barley." Agricultural and Food Science 4, no. 4 (December 1, 1995): 407–18. http://dx.doi.org/10.23986/afsci.72618.
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Three major Finnish malting barley varieties were studied for annual variations in the incidence of seed-derived fungi, bacteria and actinomycetes. In 1990-1992, 114 characterized fungal, 59 uncharacterized bacterial and 12 uncharacterized actinomycetal isolates were extracted from samples of seed intended for use in malting. When the yield of the plant hormone, indole-3-acetic acid (lAA), from enriched microbial cultures was weighed against the microbial biomass and the endogenous lAA concentration of the barley harvests, it was concluded that potential exists for bacterial lAA production in biologically significant amounts, given some minor annual variations. As expected from the average rainfall and temperature during the growing season, microbial counts in all cultivars were highest in 1992. Most of the fungal species found were of saphrophytic character, and field fungi were dominant in the samples. On the whole, microbial counts and spectra in all samples confirmed that each harvest of all cultivars was of good vigour and well suited for malting purposes. Strains of plant pathogenic character included species of Septoria nodorum (Berk) Berk, Drechlera teres (Sacc) Subraim & Jain, D. sorokiniana (Sacc) Subram & Jain and D. graminea (Rab.) Shoem. A consistent difference was noted in the microbial infection severities of the cultivars.
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Saw, Nay Min Min Thaw, Pipob Suwanchaikasem, Rogelio Zuniga-Montanez, Guanglei Qiu, Ezequiel M. Marzinelli, Stefan Wuertz, and Rohan B. H. Williams. "Influence of Extraction Solvent on Nontargeted Metabolomics Analysis of Enrichment Reactor Cultures Performing Enhanced Biological Phosphorus Removal (EBPR)." Metabolites 11, no. 5 (April 26, 2021): 269. http://dx.doi.org/10.3390/metabo11050269.
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Metabolome profiling is becoming more commonly used in the study of complex microbial communities and microbiomes; however, to date, little information is available concerning appropriate extraction procedures. We studied the influence of different extraction solvent mixtures on untargeted metabolomics analysis of two continuous culture enrichment communities performing enhanced biological phosphate removal (EBPR), with each enrichment targeting distinct populations of polyphosphate-accumulating organisms (PAOs). We employed one non-polar solvent and up to four polar solvents for extracting metabolites from biomass. In one of the reactor microbial communities, we surveyed both intracellular and extracellular metabolites using the same set of solvents. All samples were analysed using ultra-performance liquid chromatography mass spectrometry (UPLC-MS). UPLC-MS data obtained from polar and non-polar solvents were analysed separately and evaluated using extent of repeatability, overall extraction capacity and the extent of differential abundance between physiological states. Despite both reactors demonstrating the same bioprocess phenotype, the most appropriate extraction method was biomass specific, with methanol: water (50:50 v/v) and methanol: chloroform: water (40:40:20 v/v/v) being chosen as the most appropriate for each of the two different bioreactors, respectively. Our approach provides new data on the influence of solvent choice on the untargeted surveys of the metabolome of PAO enriched EBPR communities and suggests that metabolome extraction methods need to be carefully tailored to the specific complex microbial community under study.
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Buragohain, Smrita, Banashree Sarma, Dhruba J. Nath, Nirmali Gogoi, Ram S. Meena, and Rattan Lal. "Effect of 10 years of biofertiliser use on soil quality and rice yield on an Inceptisol in Assam, India." Soil Research 56, no. 1 (2018): 49. http://dx.doi.org/10.1071/sr17001.
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In the present study, field experiments were performed over 10 consecutive years (2006–15) to assess the effects of biofertiliser and enriched biocompost on soil quality, total organic carbon (TOC) and rice yields in an Inceptisol. Experiments were conducted in a randomised block design with four replicates and five treatments: unfertilised control (T1); recommended doses of inorganic fertiliser (T2); biofertiliser with reduced (50%) inorganic N and P fertilisers (T3); reduced (50%) inorganic N and P fertilisers with 1 t ha–1 enriched biocompost (T4); and reduced (75%) inorganic N and P fertilisers with 2 t ha–1 enriched biocompost (T5). T3 improved soil chemical and biological properties with enhanced soil quality index (40%), total P (23%), total K (42%) and fungal (38%) and bacterial (44%) colony counts. T5 significantly improved the carbon pool index (29%) and available nutrients (N, P and K at rates of 37%, 22% and 10% respectively) and increased soil pH (11%), resulting in a higher sustainable yield index (39%) of rice. Fraction 2 (labile carbon) of TOC, total P, available K, microbial biomass carbon and phosphate-solubilising bacteria were key indicators to assess the suitability of these fertilisers in rice cultivation in north-east India.
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Yanuka-Golub, Keren, Leah Reshef, Judith Rishpon, and Uri Gophna. "Specific Desulfuromonas Strains Can Determine Startup Times of Microbial Fuel Cells." Applied Sciences 10, no. 23 (November 30, 2020): 8570. http://dx.doi.org/10.3390/app10238570.
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Microbial fuel cells (MFCs) can generate electricity simultaneously with wastewater treatment. For MFCs to be considered a cost-effective treatment technology, they should quickly re-establish a stable electroactive microbial community in the case of system failure. In order to shorten startup times, temporal studies of anodic biofilm development are required, however, frequent sampling can reduce the functionality of the system due to electroactive biomass loss; therefore, on-line monitoring of the microbial community without interfering with the system’s stability is essential. Although all anodic biofilms were composed of Desulfuromonadaceae, MFCs differed in startup times. Generally, a Desulfuromonadaceae-dominated biofilm was associated with faster startup MFCs. A positive PCR product of a specific 16S rRNA gene PCR primer set for detecting the acetate-oxidizing, Eticyclidine (PCE)-dechlorinating Desulfuromonas group was associated with efficient MFCs in our samples. Therefore, this observation could serve as a biomarker for monitoring the formation of an efficient anodic biofilm. Additionally, we successfully enriched an electroactive consortium from an active anode, also resulting in a positive amplification of the specific primer set. Direct application of this enrichment to a clean MFC anode showed a substantial reduction of startup times from 18 to 3 days.
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Adams, Aaron S., Frank O. Aylward, Sandye M. Adams, Nadir Erbilgin, Brian H. Aukema, Cameron R. Currie, Garret Suen, and Kenneth F. Raffa. "Mountain Pine Beetles Colonizing Historical and Naïve Host Trees Are Associated with a Bacterial Community Highly Enriched in Genes Contributing to Terpene Metabolism." Applied and Environmental Microbiology 79, no. 11 (March 29, 2013): 3468–75. http://dx.doi.org/10.1128/aem.00068-13.
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ABSTRACTThe mountain pine beetle,Dendroctonus ponderosae, is a subcortical herbivore native to western North America that can kill healthy conifers by overcoming host tree defenses, which consist largely of high terpene concentrations. The mechanisms by which these beetles contend with toxic compounds are not well understood. Here, we explore a component of the hypothesis that beetle-associated bacterial symbionts contribute to the ability ofD. ponderosaeto overcome tree defenses by assisting with terpene detoxification. Such symbionts may facilitate host tree transitions during range expansions currently being driven by climate change. For example, this insect has recently breached the historical geophysical barrier of the Canadian Rocky Mountains, providing access to näive tree hosts and unprecedented connectivity to eastern forests. We use culture-independent techniques to describe the bacterial community associated withD. ponderosaebeetles and their galleries from their historical host,Pinus contorta, and their more recent host, hybridP. contorta-Pinus banksiana. We show that these communities are enriched with genes involved in terpene degradation compared with other plant biomass-processing microbial communities. These pine beetle microbial communities are dominated by members of the generaPseudomonas,Rahnella,Serratia, andBurkholderia, and the majority of genes involved in terpene degradation belong to these genera. Our work provides the first metagenome of bacterial communities associated with a bark beetle and is consistent with a potential microbial contribution to detoxification of tree defenses needed to survive the subcortical environment.
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Kostrzewska-Szlakowska, Iwona, and Bartosz Kiersztyn. "Microbial Biomass and Enzymatic Activity of the Surface Microlayer and Subsurface Water in Two Dystrophic Lakes." Polish Journal of Microbiology 66, no. 1 (March 30, 2017): 75–84. http://dx.doi.org/10.5604/17331331.1234995.
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Nutrient and organic matter concentration, microbial biomass and activities were studied at the surface microlayers (SML) and subsurface waters (SSW) in two small forest lakes of different water colour. The SML in polyhumic lake is more enriched with dissolved inorganic nitrogen (0.141 mg l–1) than that of oligohumic lake (0.124 mg l–1), the former also contains higher levels of total nitrogen (2.66 mg l–1). Higher activities of lipase (Vmax 2290 nmol l–1 h–1 in oligo- and 6098 in polyhumic) and glucosidase (Vmax 41 nmol l–1 h–1 in oligo- and 49 in polyhumic) were in the SMLs in both lakes. Phosphatase activity was higher in the oligohumic SML than in SSW (Vmax 632 vs. 339 nmol l–1 h–1) while in polyhumic lake was higher in SSW (Vmax 2258 nmol l–1 h–1 vs. 1908 nmol l–1 h–1). Aminopeptidase activity in the SSW in both lakes was higher than in SMLs (Vmax 2117 in oligo- and 1213 nmol l–1 h–1 in polyhumic). It seems that solar radiation does inhibit neuston microbial community as a whole because secondary production and the share of active bacteria in total bacteria number were higher in SSW. However, in the oligohumic lake the abundance of bacteria in the SML was always higher than in the SSW (4.07 vs. 2.69 × 106 cells ml–1) while in the polyhumic lake was roughly equal (4.48 vs. 4.33 × 106 cells ml–1) in both layers. Results may also suggest that surface communities are not supplemented by immigration from bulk communities. The SML of humic lakes may act as important sinks for allochthonous nutrient resources and may then generate considerable energy pools for microbial food webs.
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Zhang, Weiwei, Jigang Han, Haibing Wu, Qicheng Zhong, Wen Liu, Shanwen He, and Lang Zhang. "Diversity patterns and drivers of soil microbial communities in urban and suburban park soils of Shanghai, China." PeerJ 9 (April 15, 2021): e11231. http://dx.doi.org/10.7717/peerj.11231.
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Background The rapid expansion of urbanization leads to significant losses of soil ecological functions. Microbes directly participate in key soil processes and play crucial roles in maintaining soil functions. However, we still have a limited understanding of underlying mechanisms shaping microbial communities and the interactions among microbial taxa in park soils. Methods In this study, the community variations of bacteria and fungi in urban and suburban park soils were investigated in Shanghai, China. Real-time PCR and high-throughput Illumina sequencing were used to examine the microbial abundance and community composition, respectively. Results The results showed that soil molecular biomass and fungal abundance in urban park soils were significantly higher than those in suburban park soils, while no significant difference was observed in the bacterial abundance between urban and suburban park soils. The alpha diversity of soil microbes in urban and suburban park soils was similar to each other, except for Chao1 index of fungal communities. The results of similarity analysis (ANOSIM) revealed remarkable differences in the composition of bacterial and fungal communities between urban and suburban park soils. Specifically, park soils in urban areas were enriched with the phyla Methylomirabilota and Verrucomicrobiota, while the relative abundance of Gemmatimonadota was higher in suburban park soils. Moreover, the fungal class Eurotiomycetes was also enriched in urban park soils. Compared with suburban park soils, nodes and average paths of the bacterial and fungal networks were higher in urban park soils, but the number of module hubs and connectors of the bacterial networks and negative interactions among bacterial taxa were lower. Compared with suburban park soils, Acidobacteriota bacterium and Mortierellomycota fungus played more important roles in the ecological networks of urban park soils. Soil available zinc (Zn), available nitrogen (N), pH, and total potassium (K) significantly affected fungal community composition in park soils in Shanghai. Soil available Zn was also the most important factor affecting the bacterial community composition in this study. Conclusion There were significant differences in the soil molecular biomass, fungal abundance, and the community composition and co-occurrence relations of both soil bacterial and fungal communities between urban and suburban park soils. Soil available Zn played an important part in shaping the structures of both the bacterial and fungal communities in park soils in Shanghai.
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Wardle, D. A., and K. S. Nicholson. "Synergistic Effects of Grassland Plant Spcies on Soil Microbial Biomass and Activity: Implications for Ecosystem-Level Effects of Enriched Plant Diversity." Functional Ecology 10, no. 3 (June 1996): 410. http://dx.doi.org/10.2307/2390291.
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Hartland, Adam, Graham D. Fenwick, and Sarah J. Bury. "Tracing sewage-derived organic matter into a shallow groundwater food web using stable isotope and fluorescence signatures." Marine and Freshwater Research 62, no. 2 (2011): 119. http://dx.doi.org/10.1071/mf10110.
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Little is known about the feeding modes of groundwater invertebrates (stygofauna). Incorporation of sewage-derived organic matter (OM) into a shallow groundwater food web was studied using fluorescence and stable isotope signatures (δ13C and δ15N). Organic pollution was hypothesised to limit sensitive species’ abundances along the contamination gradient and isotope signatures of stygofauna consuming sewage-derived OM were expected to be enriched in δ15N. Stygofauna communities near a sewage treatment plant in New Zealand were sampled over 4 months and microbial biofilms were incubated in situ on native gravel for 1 month. As anticipated, OM stress-subsidy gradients altered stygofauna composition: the biomass of oligochaetes and Paraleptamphopus amphipods increased in OM-enriched groundwater (higher dissolved organic carbon (DOC) and tryptophan-like fluorescence), whereas other, probably less-tolerant taxa (e.g. ostracods, Dytiscidae) were absent. Isotopic signatures for stygofauna from polluted groundwater were consistent with assimilation of isotopically enriched sewage-N (δ15N values of 7–16‰), but highly depleted in δ13C relative to sewage. Negative 13C discriminations probably occur in Paraleptamphopus amphipods, and may also occur in oligochaetes and Dytiscidae, a finding with implications for the application of δ13C for determining food sources in groundwaters. Organic pollution of groundwaters may have serious repercussions for stygofauna community structure with potentially irreversible consequences.
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Jones, Elizabeth J. P., Mary A. Voytek, Margo D. Corum, and William H. Orem. "Stimulation of Methane Generation from Nonproductive Coal by Addition of Nutrients or a Microbial Consortium." Applied and Environmental Microbiology 76, no. 21 (September 3, 2010): 7013–22. http://dx.doi.org/10.1128/aem.00728-10.
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ABSTRACT Biogenic formation of methane from coal is of great interest as an underexploited source of clean energy. The goal of some coal bed producers is to extend coal bed methane productivity and to utilize hydrocarbon wastes such as coal slurry to generate new methane. However, the process and factors controlling the process, and thus ways to stimulate it, are poorly understood. Subbituminous coal from a nonproductive well in south Texas was stimulated to produce methane in microcosms when the native population was supplemented with nutrients (biostimulation) or when nutrients and a consortium of bacteria and methanogens enriched from wetland sediment were added (bioaugmentation). The native population enriched by nutrient addition included Pseudomonas spp., Veillonellaceae, and Methanosarcina barkeri. The bioaugmented microcosm generated methane more rapidly and to a higher concentration than the biostimulated microcosm. Dissolved organics, including long-chain fatty acids, single-ring aromatics, and long-chain alkanes accumulated in the first 39 days of the bioaugmented microcosm and were then degraded, accompanied by generation of methane. The bioaugmented microcosm was dominated by Geobacter sp., and most of the methane generation was associated with growth of Methanosaeta concilii. The ability of the bioaugmentation culture to produce methane from coal intermediates was confirmed in incubations of culture with representative organic compounds. This study indicates that methane production could be stimulated at the nonproductive field site and that low microbial biomass may be limiting in situ methane generation. In addition, the microcosm study suggests that the pathway for generating methane from coal involves complex microbial partnerships.
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Jia, Yangyang, David Wilkins, Hongyuan Lu, Mingwei Cai, and Patrick K. H. Lee. "Long-Term Enrichment on Cellulose or Xylan Causes Functional and Taxonomic Convergence of Microbial Communities from Anaerobic Digesters." Applied and Environmental Microbiology 82, no. 5 (December 28, 2015): 1519–29. http://dx.doi.org/10.1128/aem.03360-15.
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ABSTRACTCellulose and xylan are two major components of lignocellulosic biomass, which represents a potentially important energy source, as it is abundant and can be converted to methane by microbial action. However, it is recalcitrant to hydrolysis, and the establishment of a complete anaerobic digestion system requires a specific repertoire of microbial functions. In this study, we maintained 2-year enrichment cultures of anaerobic digestion sludge amended with cellulose or xylan to investigate whether a cellulose- or xylan-digesting microbial system could be assembled from sludge previously used to treat neither of them. While efficient methane-producing communities developed under mesophilic (35°C) incubation, they did not under thermophilic (55°C) conditions. Illumina amplicon sequencing results of the archaeal and bacterial 16S rRNA genes revealed that the mature cultures were much lower in richness than the inocula and were dominated by single archaeal (genusMethanobacterium) and bacterial (orderClostridiales) groups, although at finer taxonomic levels the bacteria were differentiated by substrates. Methanogenesis was primarily via the hydrogenotrophic pathway under all conditions, although the identity and growth requirements of syntrophic acetate-oxidizing bacteria were unclear. Incubation conditions (substrate and temperature) had a much greater effect than inoculum source in shaping the mature microbial community, although analysis based on unweighted UniFrac distance found that the inoculum still determined the pool from which microbes could be enriched. Overall, this study confirmed that anaerobic digestion sludge treating nonlignocellulosic material is a potential source of microbial cellulose- and xylan-digesting functions given appropriate enrichment conditions.
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DeRito, Christopher M., Graham M. Pumphrey, and Eugene L. Madsen. "Use of Field-Based Stable Isotope Probing To Identify Adapted Populations and Track Carbon Flow through a Phenol-Degrading Soil Microbial Community." Applied and Environmental Microbiology 71, no. 12 (December 2005): 7858–65. http://dx.doi.org/10.1128/aem.71.12.7858-7865.2005.
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ABSTRACT The goal of this field study was to provide insight into three distinct populations of microorganisms involved in in situ metabolism of phenol. Our approach measured 13CO2 respired from [13C]phenol and stable isotope probing (SIP) of soil DNA at an agricultural field site. Traditionally, SIP-based investigations have been subject to the uncertainties posed by carbon cross-feeding. By altering our field-based, substrate-dosing methodologies, experiments were designed to look beyond primary degraders to detect trophically related populations in the food chain. Using gas chromatography-mass spectrometry (GC/MS), it was shown that 13C-labeled biomass, derived from primary phenol degraders in soil, was a suitable growth substrate for other members of the soil microbial community. Next, three dosing regimes were designed to examine active members of the microbial community involved in phenol metabolism in situ: (i) 1 dose of [13C]phenol, (ii) 11 daily doses of unlabeled phenol followed by 1 dose of [13C]phenol, and (iii) 12 daily doses of [13C]phenol. GC/MS analysis demonstrated that prior exposure to phenol boosted 13CO2 evolution by a factor of 10. Furthermore, imaging of 13C-treated soil using secondary ion mass spectrometry (SIMS) verified that individual bacteria incorporated 13C into their biomass. PCR amplification and 16S rRNA gene sequencing of 13C-labeled soil DNA from the 3 dosing regimes revealed three distinct clone libraries: (i) unenriched, primary phenol degraders were most diverse, consisting of α-, β-, and γ-proteobacteria and high-G+C-content gram-positive bacteria, (ii) enriched primary phenol degraders were dominated by members of the genera Kocuria and Staphylococcus, and (iii) trophically related (carbon cross-feeders) were dominated by members of the genus Pseudomonas. These data show that SIP has the potential to document population shifts caused by substrate preexposure and to follow the flow of carbon through terrestrial microbial food chains.
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Grigs, Oskars, Emils Bolmanis, and Vytautas Galvanauskas. "Application of In-Situ and Soft-Sensors for Estimation of Recombinant P. pastoris GS115 Biomass Concentration: A Case Analysis of HBcAg (Mut+) and HBsAg (MutS) Production Processes under Varying Conditions." Sensors 21, no. 4 (February 10, 2021): 1268. http://dx.doi.org/10.3390/s21041268.
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Microbial biomass concentration is a key bioprocess parameter, estimated using various labor, operator and process cross-sensitive techniques, analyzed in a broad context and therefore the subject of correct interpretation. In this paper, the authors present the results of P. pastoris cell density estimation based on off-line (optical density, wet/dry cell weight concentration), in-situ (turbidity, permittivity), and soft-sensor (off-gas O2/CO2, alkali consumption) techniques. Cultivations were performed in a 5 L oxygen-enriched stirred tank bioreactor. The experimental plan determined varying aeration rates/levels, glycerol or methanol substrates, residual methanol levels, and temperature. In total, results from 13 up to 150 g (dry cell weight)/L cultivation runs were analyzed. Linear and exponential correlation models were identified for the turbidity sensor signal and dry cell weight concentration (DCW). Evaluated linear correlation between permittivity and DCW in the glycerol consumption phase (<60 g/L) and medium (for Mut+ strain) to significant (for MutS strain) linearity decline for methanol consumption phase. DCW and permittivity-based biomass estimates used for soft-sensor parameters identification. Dataset consisting from 4 Mut+ strain cultivation experiments used for estimation quality (expressed in NRMSE) comparison for turbidity-based (8%), permittivity-based (11%), O2 uptake-based (10%), CO2 production-based (13%), and alkali consumption-based (8%) biomass estimates. Additionally, the authors present a novel solution (algorithm) for uncommon in-situ turbidity and permittivity sensor signal shift (caused by the intensive stirrer rate change and antifoam agent addition) on-line identification and minimization. The sensor signal filtering method leads to about 5-fold and 2-fold minimized biomass estimate drifts for turbidity- and permittivity-based biomass estimates, respectively.