Enhancement of microbial 2,4,6-trinitrotoluene transformation with increased toxicity by exogenous nutrient amendment.

Science.gov (United States)

Liang, Shih-Hsiung; Hsu, Duen-Wei; Lin, Chia-Ying; Kao, Chih-Ming; Huang, Da-Ji; Chien, Chih-Ching; Chen, Ssu-Ching; Tsai, Isheng Jason; Chen, Chien-Cheng

2017-04-01

In this study, the bacterial strain Citrobacter youngae strain E4 was isolated from 2,4,6-trinitrotoluene (TNT)-contaminated soil and used to assess the capacity of TNT transformation with/without exogenous nutrient amendments. C. youngae E4 poorly degraded TNT without an exogenous amino nitrogen source, whereas the addition of an amino nitrogen source considerably increased the efficacy of TNT transformation in a dose-dependent manner. The enhanced TNT transformation of C. youngae E4 was mediated by increased cell growth and up-regulation of TNT nitroreductases, including NemA, NfsA and NfsB. This result indicates that the increase in TNT transformation by C. youngae E4 via nitrogen nutrient stimulation is a cometabolism process. Consistently, TNT transformation was effectively enhanced when C. youngae E4 was subjected to a TNT-contaminated soil slurry in the presence of an exogenous amino nitrogen amendment. Thus, effective enhancement of TNT transformation via the coordinated inoculation of the nutrient-responsive C. youngae E4 and an exogenous nitrogen amendment might be applicable for the remediation of TNT-contaminated soil. Although the TNT transformation was significantly enhanced by C. youngae E4 in concert with biostimulation, the 96-h LC50 value of the TNT transformation product mixture on the aquatic invertebrate Tigriopus japonicas was higher than the LC50 value of TNT alone. Our results suggest that exogenous nutrient amendment can enhance microbial TNT transformation; however, additional detoxification processes may be needed due to the increased toxicity after reduced TNT transformation. Copyright © 2016 Elsevier Inc. All rights reserved.

Short- and long-term effects of nutrient enrichment on microbial exoenzyme activity in mangrove peat

KAUST Repository

Keuskamp, Joost A.

2015-02-01

© 2014 Elsevier Ltd. Mangroves receive increasing quantities of nutrients as a result of coastal development, which could lead to significant changes in carbon sequestration and soil subsidence. We hypothesised that mangrove-produced tannins induce a nitrogen (N) limitation on microbial decomposition even when plant growth is limited by phosphorus (P). As a result, increased N influx would lead to a net loss of sequestered carbon negating the ability to compensate for sea level rise in P-limited mangroves. To examine this, we quantified the short- and long-term effects of N and P enrichment on microbial biomass and decomposition-related enzyme activities in a Rhizophora mangle-dominated mangrove, which had been subjected to fertilisation treatments for a period of fifteen years. We compared microbial biomass, elemental stoichiometry and potential enzyme activity in dwarf and fringe-type R. mangle-dominated sites, where primary production is limited by P or N depending on the proximity to open water. Even in P-limited mangroves, microbial activity was N-limited as indicated by stoichiometry and an increase in enzymic activity upon N amendment. Nevertheless, microbial biomass increased upon field additions of P, indicating that the carbon supply played even a larger role. Furthermore, we found that P amendment suppressed phenol oxidase activity, while N amendment did not. The possible differential nutrient limitations of microbial decomposers versus primary producers implies that the direction of the effect of eutrophication on carbon sequestration is nutrient-specific. In addition, this study shows that phenol oxidase activities in this system decrease through P, possibly strengthening the enzymic latch effect of mangrove tannins. Furthermore, it is argued that the often used division between N-harvesting, P-harvesting, and carbon-harvesting exoenzymes needs to be reconsidered.

Chlorine stress mediates microbial surface attachment in drinking water systems.

Science.gov (United States)

Liu, Li; Le, Yang; Jin, Juliang; Zhou, Yuliang; Chen, Guowei

2015-03-01

Microbial attachment to drinking water pipe surfaces facilitates pathogen survival and deteriorates disinfection performance, directly threatening the safety of drinking water. Notwithstanding that the formation of biofilm has been studied for decades, the underlying mechanisms for the origins of microbial surface attachment in biofilm development in drinking water pipelines remain largely elusive. We combined experimental and mathematical methods to investigate the role of environmental stress-mediated cell motility on microbial surface attachment in chlorination-stressed drinking water distribution systems. Results show that at low levels of disinfectant (0.0-1.0 mg/L), the presence of chlorine promotes initiation of microbial surface attachment, while higher amounts of disinfectant (>1.0 mg/L) inhibit microbial attachment. The proposed mathematical model further demonstrates that chlorination stress (0.0-5.0 mg/L)-mediated microbial cell motility regulates the frequency of cell-wall collision and thereby controls initial microbial surface attachment. The results reveal that transport processes and decay patterns of chlorine in drinking water pipelines regulate microbial cell motility and, thus, control initial surface cell attachment. It provides a mechanistic understanding of microbial attachment shaped by environmental disinfection stress and leads to new insights into microbial safety protocols in water distribution systems.

A microbial bioassay to estimate nutrient availability in organic fertilizers; field calibration:

International Nuclear Information System (INIS)

Salas, E.; Ramirez, C.

2001-01-01

A good correlation was recently shown between the increase in the microbial biomass (BM) in a mixture of soil/organic amendment and the growth of a test plant, sorghum, in the same substrate. This work reports the validation of the microbial assay as a potential guide to establish the fertilization rate for organic fertilizers such as compost under field conditions. A field trial was established with green pepper (Capsicum annum L.) and tomato (Lycopersicum esculentum L) as test plants. Treatments were soil alone or amended with 10% (W/W) of organic amendments of contrasting nutrient value, namely: chicken manure (CM), compost (C), bocashi (B), vermicompost (V) and coffe hulls (Br). A complete randomized block design with 4 replicates was used. The following variables were determined: plant dry weight (PSC) and fresh fruit weight (PFF) for green pepper, 97 days after showing; for tomato, plant dry weight (PST) was determined 32 days after showing. For the microbial biomass a complete randomized block design was also used, with 6 replicates, for the same mixtures. Microbial biomass was determined 2 days after amendment with glucose (0.8%) using the substrate- induce respiration assay. The organic amendments CM, C and B induced the highest values for BM as well as fro PSC, PFF and PST, which indicates a high nutrient availability for these organic amendments, whereas the organic amendments V and Br showed the lowest values (P [es

Seasonal variations and effects of nutrient applications on N and P and microbial biomass under two temperate heathland plants

DEFF Research Database (Denmark)

Nielsen, Pia Lund; Andresen, Louise Christoffersen; Michelsen, Anders

2009-01-01

. The microbial biomass on the other hand was positively related to soil water content in fertilized plots indicating that this was due to an indirect effect of enhanced nutrient availability. Microbial N and P pools were respectively 1000 and 100 times higher than the pool of inorganic N and P, and microbes...... this process. In this study the soil properties under two dominant heathland plants, the dwarf shrub Calluna vulgaris and the grass Deschampsia flexuosa, were investigated, with focus on nutrient content in the organic top soil and soil microbes during the main growing season and effects of nutrient amendments...... therefore may play an important role in regulating plant nutrient supply. Judged from responses of inorganic and microbial N and P concentrations to added N and P, N seemed to limit C. vulgaris and soil microbes below while P seemed to limit D. flexuosa and soil microbes below this species. There were lower...

Enhancement and inhibition of microbial activity in hydrocarbon- contaminated arctic soils: Implications for nutrient-amended bioremediation

Science.gov (United States)

Braddock, J.F.; Ruth, M.L.; Catterall, P.H.; Walworth, J.L.; McCarthy, K.A.

1997-01-01

Bioremediation is being used or proposed as a treatment option at many hydrocarbon-contaminated sites. One such site is a former bulk-fuel storage facility near Barrow, AK, where contamination persists after approximately 380 m3 of JP-5 was spilled in 1970. The soil at the site is primarily coarse sand with low organic carbon (soil from this site in laboratory microcosms and in mesocosms incubated for 6 weeks in the field. Nitrogen was the major limiting nutrient in this system, but microbial populations and activity were maximally enhanced by additions of both nitrogen and phosphorus. When nutrients were added to soil in the field at three levels of N:P (100:45, 200:90, and 300:135 mg/kg soil), the greatest stimulation in microbial activity occurred at the lowest, rather than the highest, level of nutrient addition. The total soil-water potentials ranged from -2 to -15 bar with increasing levels of fertilizer. Semivolatile hydrocarbon concentrations declined significantly only in the soils treated at the low fertilizer level. These results indicate that an understanding of nutrient effects at a specific site is essential for successful bioremediation.Bioremediation is being used or proposed as a treatment option at many hydrocarbon-contaminated sites. One such site is a former bulk-fuel storage facility near Barrow, AK, where contamination persists after approximately 380 m3 of JP-5 was spilled in 1970. The soil at the site is primarily coarse sand with low organic carbon (soil from this site in laboratory microcosms and in mesocosms incubated for 6 weeks in the field. Nitrogen was the major limiting nutrient in this system, but microbial populations and activity were maximally enhanced by additions of both nitrogen and phosphorus. When nutrients were added to soil in the field at three levels of N:P (100:45, 200:90, and 300:135 mg/kg soil), the greatest stimulation in microbial activity occurred at the lowest, rather than the highest, level of nutrient addition

Effects of nutrient enrichment on the decomposition of wood and associated microbial activity in streams

Science.gov (United States)

Vladislav Gulis; Amy D. Rosemond; Keller Suberkropp; Holly S. Weyers; Jonathan P. Benstead

2004-01-01

We determined the effects of nutrient enrichment on wood decomposition rates and microbial activity during a 3-year study in two headwater streams at Coweeta Hydrologic Laboratory, NC, U.S.A. After a 1-year pretreatment period, one of the streams was continuously enriched with inorganic nutrients (nitrogen and phosphorus) for 2 years while the other stream served as a...

Microbial exopolysaccharide-mediated synthesis and stabilization of metal nanoparticles.

Science.gov (United States)

Sathiyanarayanan, Ganesan; Dineshkumar, Krishnamoorthy; Yang, Yung-Hun

2017-11-01

Exopolysaccharides (EPSs) are structurally and functionally valuable biopolymer secreted by different prokaryotic and eukaryotic microorganisms in response to biotic/abiotic stresses and to survive in extreme environments. Microbial EPSs are fascinating in various industrial sectors due to their excellent material properties and less toxic, highly biodegradable, and biocompatible nature. Recently, microbial EPSs have been used as a potential template for the rapid synthesis of metallic nanoparticles and EPS-mediated metal reduction processes are emerging as simple, harmless, and environmentally benign green chemistry approaches. EPS-mediated synthesis of metal nanoparticles is a distinctive metabolism-independent bio-reduction process due to the formation of interfaces between metal cations and the polyanionic functional groups (i.e. hydroxyl, carboxyl and amino groups) of the EPS. In addition, the range of physicochemical features which facilitates the EPS as an efficient stabilizing or capping agents to protect the primary structure of the metal nanoparticles with an encapsulation film in order to separate the nanoparticle core from the mixture of composites. The EPS-capping also enables the further modification of metal nanoparticles with expected material properties for multifarious applications. The present review discusses the microbial EPS-mediated green synthesis/stabilization of metal nanoparticles, possible mechanisms involved in EPS-mediated metal reduction, and application prospects of EPS-based metal nanoparticles.

Humic substances-mediated microbial reductive dehalogenation of triclosan

Science.gov (United States)

Wang, L.; Xu, S.; Yang, Y.

2015-12-01

The role of natural organic matter in regulating the redox reactions as an electron shuttle has received lots of attention, because it can significantly affect the environmental degradation of contaminants and biogeochemical cycles of major elements. However, up to date, limited studies examined the role of natural organic matter in affecting the microbial dehalogenation of emergent organohalides, a critical detoxification process. In this study, we investigated the humic substance (HS)-mediated microbial dehalogenation of triclosan, a widely used antimicrobial agent. We found that the presence of HS stimulated the microbial degradation of triclosan by Shewanella putrefaciens CN-32. In the absence of HS, the triclosan was degraded gradually, achieving 8.6% residual at 8 days. With HS, the residual triclosan was below 2% after 4 days. Cl- was confirmed by ion chromatography analysis, but the dehalogenation processes and other byproducts warrant further investigations. The impact of HS on the degradation of triclosan was highly dependent on the concentration of HS. When the HS was below 15 mg/L, the degradation rate constant for triclosan increased with the organic carbon concentration. Beyond that point, the increased organic carbon concentration decreased the degradation of triclosan. Microbially pre-reduced HS abiotically reduced triclosan, testifying the electron shuttling processes. These results indicate that dissolved organic matter plays a dual role in regulating the degradation of triclosan: it mediates electron transport and inhibits the bioavailability through complexation. Such novel organic matter-mediated reactions for organohalides are important for evaluating the natural attenuation of emergent contaminants and designing cost-effective engineering treatment.

[Effect of microbial nutrient concentration on improvement of municipal sewage sludge dewaterability through bioleaching].

Science.gov (United States)

Song, Yong-wei; Liu, Fen-wu; Zhou, Li-xiang

2012-08-01

In this study, shaking flask batch experiments and practical engineering application tests were performed to investigate the effect of microbial nutrient concentration on the dewaterability of municipal sewage sludge with 2%, 3%, 4% and 5% solid contents via bioleaching. Meanwhile, the changes of pH value and the utilization efficiency of microbial nutrients during bioleaching were analyzed in this study. The results showed that the pH value decreased gradually at the beginning and then maintained a stable state in the treatments with different solid contents, and the nutrients were completely used up by the microorganisms after 2 days of bioleaching. It was found that the SRF of 2%, 3%, 4%, 5% sludges decreased quickly and then rose gradually with the extension of bioleaching time. In addition, the higher solid content the greater the increase. It was determined that the optimum microbial nutrient dosage for sludge with solid content of 2%, 3%, 4% and 5% were 3.0 g x L(-1), 4.5 g x L(-1), 8.3 g x L(-1) and 12.8 g x L(-1) respectively. At this point, the lowest SRF of sludge with each solid content were 0.61 x 10(12) m x kg(-1), 1.22 x 10(12) m x kg(-1), 3.09 x 10(12) m x kg(-1) and 4.83 x 10(12) m x kg(-1), respectively. Through the engineering application, it was showed that diluting the solid content of sewage sludge from 5% to 3% before bioleaching was feasible. It could not only improve the dewaterability of bioleached sewage sludge (the SRF declined from 3.29 x 10(12) m x kg(-1) to 1.10 x 10(12) m x kg(-1)), but also shorten the sludge nutrient time (shortened from 4 days to 2.35 days) and reduce the operation costs. Therefore, the results of this study have important significance for the engineering application of bioleaching of municipal sewage sludge with high solid content.

Agroforestry systems, nutrients in litter and microbial activity in soils cultivated with coffee at high altitude

Directory of Open Access Journals (Sweden)

Krystal de Alcantara Notaro

2014-04-01

Full Text Available Agroforestry systems are an alternative option for sustainable production management. These systems contain trees that absorb nutrients from deeper layers of the soil and leaf litter that help improve the soil quality of the rough terrain in high altitude areas, which are areas extremely susceptible to environmental degradation. The aim of this study was to characterize the stock and nutrients in litter, soil activity and the population of microorganisms in coffee (Coffea arabica L. plantations under high altitude agroforestry systems in the semi-arid region of the state of Pernambuco, Brazil. Samples were collected from the surface litter together with soil samples taken at two depths (0-10 and 10-20 cm from areas each subject to one of the following four treatments: agroforestry system (AS, native forest (NF, biodynamic system (BS and coffee control (CT.The coffee plantation had been abandoned for nearly 15 years and, although there had been no management or harvesting, still contained productive coffee plants. The accumulation of litter and mean nutrient content of the litter, the soil nutrient content, microbial biomass carbon, total carbon, total nitrogen, C/N ratio, basal respiration, microbial quotient, metabolic quotient and microbial populations (total bacteria, fluorescent bacteria group, total fungi and Trichoderma spp. were all analyzed. The systems thatwere exposed to human intervention (A and BS differed in their chemical attributes and contained higher levels of nutrients when compared to NF and CT. BS for coffee production at high altitude can be used as a sustainable alternative in the high altitude zones of the semi-arid region in Brazil, which is an area that is highly susceptible to environmental degradation.

Microbial controls on metal mobility under the low nutrient fluxes found throughout the subsurface

International Nuclear Information System (INIS)

Boult, Stephen; Hand, Victoria L.; Vaughan, David J.

2006-01-01

Laboratory simulations and field studies of the shallow subsurface have shown that microbes and their extracellular products can influence the mobility of toxic metals from waste disposal sites. Modelling the transport of contaminants in groundwater may, therefore, require the input of microbial ecology data in addition to geochemical data, thus increasing the costs and the uncertainty of predictions. However, whether microbial effects on contaminant mobility occur extensively in the natural subsurface is unknown because the conditions under which they have been observed hitherto are generally unrepresentative of the average subsurface environment. Here, we show that microbial activity affects the mobility of a toxic trace metal (Cu) under the relatively low nutrient fluxes that dominate subsurface systems. More particularly, we show that under these low nutrient conditions, microbes and microbial products can immobilize metal but may themselves be subject to subsequent mobilization, thus complicating the pattern of metal storage and release. Our results show that the capability of microbes in the subsurface to change both the capacity of porous media to store metal, and the behaviour of metal that is released, is not restricted to the well researched environments close to sites of waste disposal. We anticipate our simulations will be a starting point for generating input data for transport models, and specifying the mechanism of metal remobilisation in environments more representative of the subsurface generally

Microbial community composition affects soil fungistasis.

Science.gov (United States)

de Boer, Wietse; Verheggen, Patrick; Klein Gunnewiek, Paulien J A; Kowalchuk, George A; van Veen, Johannes A

2003-02-01

Most soils inhibit fungal germination and growth to a certain extent, a phenomenon known as soil fungistasis. Previous observations have implicated microorganisms as the causal agents of fungistasis, with their action mediated either by available carbon limitation (nutrient deprivation hypothesis) or production of antifungal compounds (antibiosis hypothesis). To obtain evidence for either of these hypotheses, we measured soil respiration and microbial numbers (as indicators of nutrient stress) and bacterial community composition (as an indicator of potential differences in the composition of antifungal components) during the development of fungistasis. This was done for two fungistatic dune soils in which fungistasis was initially fully or partly relieved by partial sterilization treatment or nutrient addition. Fungistasis development was measured as restriction of the ability of the fungi Chaetomium globosum, Fusarium culmorum, Fusarium oxysporum, and Trichoderma harzianum to colonize soils. Fungistasis did not always reappear after soil treatments despite intense competition for carbon, suggesting that microbial community composition is important in the development of fungistasis. Both microbial community analysis and in vitro antagonism tests indicated that the presence of pseudomonads might be essential for the development of fungistasis. Overall, the results lend support to the antibiosis hypothesis.

Effects of adding bulking agent, inorganic nutrient and microbial inocula on biopile treatment for oil-field drilling waste.

Science.gov (United States)

Ma, Jie; Yang, Yongqi; Dai, Xiaoli; Chen, Yetong; Deng, Hanmei; Zhou, Huijun; Guo, Shaohui; Yan, Guangxu

2016-05-01

Contamination from oil-field drilling waste is a worldwide environmental problem. This study investigated the performance of four bench-scale biopiles in treating drilling waste: 1) direct biopile (DW), 2) biopile plus oil-degrading microbial consortium (DW + M), 3) biopile plus microbial consortium and bulking agents (saw dust) (DW + M + BA), 4) biopile plus microbial consortium, bulking agents, and inorganic nutrients (Urea and K2HPO4) (DW + M + BA + N). Ninety days of biopiling removed 41.0%, 44.0%, 55.7% and 87.4% of total petroleum hydrocarbon (TPH) in the pile "DW", "DW + M", "DW + M + BA", and "DW + M + BA + N" respectively. Addition of inorganic nutrient and bulking agents resulted in a 56.9% and 26.6% increase in TPH removal efficiency respectively. In contrast, inoculation of hydrocarbon-degrading microorganisms only slightly enhanced the contaminant removal (increased 7.3%). The biopile with stronger contaminant removal also had higher pile temperature and lower pile pH (e.g., in "DW + M + BA + N"). GC-MS analysis shows that biopiling significantly reduced the total number of detected contaminants and changed the chemical composition. Overall, this study shows that biopiling is an effective remediation technology for drilling waste. Adding inorganic nutrients and bulking agents can significantly improve biopile performance while addition of microbial inocula had minimal positive impacts on contaminant removal. Copyright © 2016 Elsevier Ltd. All rights reserved.

A critical review on the interaction of substrate nutrient balance and microbial community structure and function in anaerobic co-digestion.

Science.gov (United States)

Xu, Rong; Zhang, Kai; Liu, Pu; Khan, Aman; Xiong, Jian; Tian, Fake; Li, Xiangkai

2018-01-01

Anaerobic co-digestion generally results in a higher yield of biogas than mono-digestion, hence co-digestion has become a topic of general interest in recent studies of anaerobic digestion. Compared with mono-digestion, co-digestion utilizes multiple substrates. The balance of substrate nutrient in co-digestion comprises better adjustments of C/N ratio, pH, moisture, trace elements, and dilution of toxic substances. All of these changes could result in positive shifts in microbial community structure and function in the digestion processes and consequent augmentation of biogas production. Nevertheless, there have been few reviews on the interaction of nutrient and microbial community in co-digestions. The objective of this review is to investigate recent achievements and perspectives on the interaction of substrate nutrient balance and microbial community structure and function. This may provide valuable information on the optimization of combinations of substrates and prediction of bioreactor performance. Copyright © 2017 Elsevier Ltd. All rights reserved.

Short- and long-term effects of nutrient enrichment on microbial exoenzyme activity in mangrove peat

NARCIS (Netherlands)

Keuskamp, Joost; Feller, Ilka C; Laanbroek, Riks; Verhoeven, Jos; Hefting, Mariet

2014-01-01

Mangroves receive increasing quantities of nutrients as a result of coastal development, which could lead to significant changes in carbon sequestration and soil subsidence. We hypothesised that mangroveproduced tannins induce a nitrogen (N) limitation on microbial decomposition even when plant

Short- and long-term effects of nutrient enrichment on microbial exoenzyme activity in mangrove peat

NARCIS (Netherlands)

Keuskamp, Joost A.; Feller, Ilka C.; Laanbroek, Hendrikus J.; Verhoeven, Jos T.A.; Hefting, Mariet M.

2015-01-01

Abstract Mangroves receive increasing quantities of nutrients as a result of coastal development, which could lead to significant changes in carbon sequestration and soil subsidence. We hypothesised that mangrove-produced tannins induce a nitrogen (N) limitation on microbial decomposition even when

Short- and long-term effects of nutrient enrichment on microbial exoenzyme activity in mangrove peat

NARCIS (Netherlands)

Keuskamp, Joost|info:eu-repo/dai/nl/315031840; Feller, Ilka C; Laanbroek, Riks|info:eu-repo/dai/nl/070378282; Verhoeven, Jos|info:eu-repo/dai/nl/068425023; Hefting, Mariet|info:eu-repo/dai/nl/256197628

Mangroves receive increasing quantities of nutrients as a result of coastal development, which could lead to significant changes in carbon sequestration and soil subsidence. We hypothesised that mangroveproduced tannins induce a nitrogen (N) limitation on microbial decomposition even when plant

Closed nutrient recycling via microbial catabolism in an eco-engineered self regenerating mixed anaerobic microbiome for hydrogenotrophic methanogenesis.

Science.gov (United States)

Savvas, Savvas; Donnelly, Joanne; Patterson, Tim P; Dinsdale, Richard; Esteves, Sandra R

2017-03-01

A novel eco-engineered mixed anaerobic culture was successfully demonstrated for the first time to be capable of continuous regeneration in nutrient limiting conditions. Microbial catabolism has been found to support a closed system of nutrients able to enrich a culture of lithotrophic methanogens and provide microbial cell recycling. After enrichment, the hydrogenotrophic species was the dominating methanogens while a bacterial substratum was responsible for the redistribution of nutrients. q-PCR results indicated that 7% of the total population was responsible for the direct conversion of the gases. The efficiency of H 2 /CO 2 conversion to CH 4 reached 100% at a gassing rate of above 60v/v/d. The pH of the culture media was effectively sustained at optimal levels (pH 7-8) through a buffering system created by the dissolved CO 2 . The novel approach can reduce the process nutrient/metal requirement and enhance the environmental and financial performance of hydrogenotrophic methanogenesis for renewable energy storage. Copyright © 2016 Elsevier Ltd. All rights reserved.

Herbivory and eutrophication mediate grassland plant nutrient responses across a global climatic gradient

Science.gov (United States)

Anderson, T. Michael; Griffith, Daniel M.; Grace, James B.; Lind, Eric M.; Adler, Peter B.; Biederman, Lori A.; Blumenthal, Dana M.; Daleo, Pedro; Firn, Jennifer; Hagenah, Nicole; Harpole, W. Stanley; MacDougall, Andrew S.; McCulley, Rebecca L.; Prober, Suzanne M.; Risch, Anita C.; Sankaran, Mahesh; Schütz, Martin; Seabloom, Eric W.; Stevens, Carly J.; Sullivan, Lauren; Wragg, Peter; Borer, Elizabeth T.

2018-01-01

Plant stoichiometry, the relative concentration of elements, is a key regulator of ecosystem functioning and is also being altered by human activities. In this paper we sought to understand the global drivers of plant stoichiometry and compare the relative contribution of climatic vs. anthropogenic effects. We addressed this goal by measuring plant elemental (C, N, P and K) responses to eutrophication and vertebrate herbivore exclusion at eighteen sites on six continents. Across sites, climate and atmospheric N deposition emerged as strong predictors of plot‐level tissue nutrients, mediated by biomass and plant chemistry. Within sites, fertilization increased total plant nutrient pools, but results were contingent on soil fertility and the proportion of grass biomass relative to other functional types. Total plant nutrient pools diverged strongly in response to herbivore exclusion when fertilized; responses were largest in ungrazed plots at low rainfall, whereas herbivore grazing dampened the plant community nutrient responses to fertilization. Our study highlights (1) the importance of climate in determining plant nutrient concentrations mediated through effects on plant biomass, (2) that eutrophication affects grassland nutrient pools via both soil and atmospheric pathways and (3) that interactions among soils, herbivores and eutrophication drive plant nutrient responses at small scales, especially at water‐limited sites.

Cool tadpoles from Arctic environments waste fewer nutrients - high gross growth efficiencies lead to low consumer-mediated nutrient recycling in the North.

Science.gov (United States)

Liess, Antonia; Guo, Junwen; Lind, Martin I; Rowe, Owen

2015-11-01

Endothermic organisms can adapt to short growing seasons, low temperatures and nutrient limitation by developing high growth rates and high gross growth efficiencies (GGEs). Animals with high GGEs are better at assimilating limiting nutrients and thus should recycle (or lose) fewer nutrients. Longer guts in relation to body mass may facilitate higher GGE under resource limitation. Within the context of ecological stoichiometry theory, this study combines ecology with evolution by relating latitudinal life-history adaptations in GGE, mediated by gut length, to its ecosystem consequences, such as consumer-mediated nutrient recycling. In common garden experiments, we raised Rana temporaria tadpoles from two regions (Arctic/Boreal) under two temperature regimes (18/23 °C) crossed with two food quality treatments (high/low-nitrogen content). We measured tadpole GGEs, total nutrient loss (excretion + egestion) rates and gut length during ontogeny. In order to maintain their elemental balance, tadpoles fed low-nitrogen (N) food had lower N excretion rates and higher total phosphorous (P) loss rates than tadpoles fed high-quality food. In accordance with expectations, Arctic tadpoles had higher GGEs and lower N loss rates than their low-latitude conspecifics, especially when fed low-N food, but only in ambient temperature treatments. Arctic tadpoles also had relatively longer guts than Boreal tadpoles during early development. That temperature and food quality interacted with tadpole region of origin in affecting tadpole GGEs, nutrient loss rates and relative gut length, suggests evolved adaptation to temperature and resource differences. With future climate change, mean annual temperatures will increase. Additionally, species and genotypes will migrate north. This will change the functioning of Boreal and Arctic ecosystems by affecting consumer-mediated nutrient recycling and thus affect nutrient dynamics in general. Our study shows that evolved latitudinal adaption can

The role of aquatic fungi in transformations of organic matter mediated by nutrients

Science.gov (United States)

Cynthia J. Tant; Amy D. Rosemond; Andrew S. Mehring; Kevin A. Kuehn; John M. Davis

2015-01-01

1. We assessed the key role of aquatic fungi in modifying coarse particulate organic matter (CPOM) by affecting its breakdown rate, nutrient concentration and conversion to fine particulate organic matter (FPOM). Overall, we hypothesised that fungal-mediated conditioning and breakdown of CPOM would be accelerated when nutrient concentrations are increased and tested...

Overfishing and nutrient pollution interact with temperature to disrupt coral reefs down to microbial scales.

Science.gov (United States)

Zaneveld, Jesse R; Burkepile, Deron E; Shantz, Andrew A; Pritchard, Catharine E; McMinds, Ryan; Payet, Jérôme P; Welsh, Rory; Correa, Adrienne M S; Lemoine, Nathan P; Rosales, Stephanie; Fuchs, Corinne; Maynard, Jeffrey A; Thurber, Rebecca Vega

2016-06-07

Losses of corals worldwide emphasize the need to understand what drives reef decline. Stressors such as overfishing and nutrient pollution may reduce resilience of coral reefs by increasing coral-algal competition and reducing coral recruitment, growth and survivorship. Such effects may themselves develop via several mechanisms, including disruption of coral microbiomes. Here we report the results of a 3-year field experiment simulating overfishing and nutrient pollution. These stressors increase turf and macroalgal cover, destabilizing microbiomes, elevating putative pathogen loads, increasing disease more than twofold and increasing mortality up to eightfold. Above-average temperatures exacerbate these effects, further disrupting microbiomes of unhealthy corals and concentrating 80% of mortality in the warmest seasons. Surprisingly, nutrients also increase bacterial opportunism and mortality in corals bitten by parrotfish, turning normal trophic interactions deadly for corals. Thus, overfishing and nutrient pollution impact reefs down to microbial scales, killing corals by sensitizing them to predation, above-average temperatures and bacterial opportunism.

Microbial planktonic communities in the Red Sea: high levels of spatial and temporal variability shaped by nutrient availability and turbulence

KAUST Repository

Pearman, John K.; Ellis, Joanne; Irigoien, Xabier; Yellepeddi, Sarma B.; Jones, Burton; Carvalho, Susana

2017-01-01

The semi-enclosed nature of the Red Sea (20.2°N-38.5°N) makes it a natural laboratory to study the influence of environmental gradients on microbial communities. This study investigates the composition and structure of microbial prokaryotes and eukaryotes using molecular methods, targeting ribosomal RNA genes across different regions and seasons. The interaction between spatial and temporal scales results in different scenarios of turbulence and nutrient conditions allowing for testing of ecological theory that categorizes the response of the plankton community to these variations. The prokaryotic reads are mainly comprised of Cyanobacteria and Proteobacteria (Alpha and Gamma), with eukaryotic reads dominated by Dinophyceae and Syndiniophyceae. Periodic increases in the proportion of Mamiellophyceae and Bacillariophyceae reads were associated with alterations in the physical oceanography leading to nutrient increases either through the influx of Gulf of Aden Intermediate Water (south in the fall) or through water column mixing processes (north in the spring). We observed that in general dissimilarity amongst microbial communities increased when nutrient concentrations were higher, whereas richness (observed OTUs) was higher in scenarios of higher turbulence. Maximum abundance models showed the differential responses of dominant taxa to temperature giving an indication how taxa will respond as waters become warmer and more oligotrophic.

Microbial planktonic communities in the Red Sea: high levels of spatial and temporal variability shaped by nutrient availability and turbulence

KAUST Repository

Pearman, John K.

2017-07-20

The semi-enclosed nature of the Red Sea (20.2°N-38.5°N) makes it a natural laboratory to study the influence of environmental gradients on microbial communities. This study investigates the composition and structure of microbial prokaryotes and eukaryotes using molecular methods, targeting ribosomal RNA genes across different regions and seasons. The interaction between spatial and temporal scales results in different scenarios of turbulence and nutrient conditions allowing for testing of ecological theory that categorizes the response of the plankton community to these variations. The prokaryotic reads are mainly comprised of Cyanobacteria and Proteobacteria (Alpha and Gamma), with eukaryotic reads dominated by Dinophyceae and Syndiniophyceae. Periodic increases in the proportion of Mamiellophyceae and Bacillariophyceae reads were associated with alterations in the physical oceanography leading to nutrient increases either through the influx of Gulf of Aden Intermediate Water (south in the fall) or through water column mixing processes (north in the spring). We observed that in general dissimilarity amongst microbial communities increased when nutrient concentrations were higher, whereas richness (observed OTUs) was higher in scenarios of higher turbulence. Maximum abundance models showed the differential responses of dominant taxa to temperature giving an indication how taxa will respond as waters become warmer and more oligotrophic.

Stream microbial diversity responds to environmental changes: Review and synthesis of existing research

Directory of Open Access Journals (Sweden)

Lydia eZeglin

2015-05-01

Full Text Available The importance of microbial activity to ecosystem function in aquatic ecosystems is well established, but microbial diversity has been less frequently addressed. This review and synthesis of the hundreds of published studies on stream microbial diversity shows that factors known to drive ecosystem processes, such as nutrient availability, hydrology, metal contamination, contrasting land-use and temperature, also cause heterogeneity in bacterial diversity. Temporal heterogeneity in stream bacterial diversity was frequently observed, reflecting the dynamic nature of both stream ecosystems and microbial community composition. However, within-stream spatial differences in stream bacterial diversity were more commonly observed, driven specifically by different organic matter compartments. Bacterial phyla showed similar patterns in relative abundance with regard to compartment type across different streams. For example, surface water contained the highest relative abundance of Actinobacteria, while epilithon contained the highest relative abundance of Cyanobacteria and Bacteroidetes. This suggests that contrasting physical and/or nutritional habitats characterized by different stream organic matter compartment types may select for certain bacterial lineages. When comparing the prevalence of physicochemical effects on stream bacterial diversity, effects of changing metal concentrations were most, while effects of differences in nutrient concentrations were least frequently observed. This may indicate that although changing nutrient concentrations do tend to affect microbial diversity, other environmental factors are more likely to alter stream microbial diversity and function. The common observation of connections between ecosystem process drivers and microbial diversity suggests that microbial taxonomic turnover could mediate ecosystem-scale responses to changing environmental conditions, including both microbial habitat distribution and

Ecosystem and physiological scales of microbial responses to nutrients in a detritus-based stream: results of a 5-year continuous enrichment

Science.gov (United States)

Keller Suberkropp; Vladislav Gulis; Amy D. Rosemond; Jonathan Benstead

2010-01-01

Our study examined the response of leaf detritus–associated microorganisms (both bacteria and fungi) to a 5-yr continuous nutrient enrichment of a forested headwater stream. Leaf litter dominates detritus inputs to such streams and, on a system wide scale, serves as the key substrate for microbial colonization. We determined physiological responses as microbial biomass...

Nutrient Control of Yeast Gametogenesis Is Mediated by TORC1, PKA and Energy Availability.

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Hilla Weidberg

2016-06-01

Full Text Available Cell fate choices are tightly controlled by the interplay between intrinsic and extrinsic signals, and gene regulatory networks. In Saccharomyces cerevisiae, the decision to enter into gametogenesis or sporulation is dictated by mating type and nutrient availability. These signals regulate the expression of the master regulator of gametogenesis, IME1. Here we describe how nutrients control IME1 expression. We find that protein kinase A (PKA and target of rapamycin complex I (TORC1 signalling mediate nutrient regulation of IME1 expression. Inhibiting both pathways is sufficient to induce IME1 expression and complete sporulation in nutrient-rich conditions. Our ability to induce sporulation under nutrient rich conditions allowed us to show that respiration and fermentation are interchangeable energy sources for IME1 transcription. Furthermore, we find that TORC1 can both promote and inhibit gametogenesis. Down-regulation of TORC1 is required to activate IME1. However, complete inactivation of TORC1 inhibits IME1 induction, indicating that an intermediate level of TORC1 signalling is required for entry into sporulation. Finally, we show that the transcriptional repressor Tup1 binds and represses the IME1 promoter when nutrients are ample, but is released from the IME1 promoter when both PKA and TORC1 are inhibited. Collectively our data demonstrate that nutrient control of entry into sporulation is mediated by a combination of energy availability, TORC1 and PKA activities that converge on the IME1 promoter.

Stimulation of microbial nitrogen cycling in aquatic ecosystems by benthic macrofauna: mechanisms and environmental implications

OpenAIRE

P. Stief

2013-01-01

Invertebrate animals that live at the bottom of aquatic ecosystems (i.e., benthic macrofauna) are important mediators between nutrients in the water column and microbes in the benthos. The presence of benthic macrofauna stimulates microbial nutrient dynamics through different types of animal–microbe interactions, which potentially affect the trophic status of aquatic ecosystems. This review contrasts three types of animal–microbe interactions in the benthos of aquatic ecosystems: (i) e...

Role of EPS, Dispersant and Nutrients on the Microbial Response and MOS Formation in the Subarctic Northeast Atlantic

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Tony Gutierrez

2017-04-01

Full Text Available In this study we report the formation of marine oil snow (MOS, its associated microbial community, the factors influencing its formation, and the microbial response to crude oil in surface waters of the Faroe-Shetland Channel (FSC. The FSC is a subarctic region that is hydrodynamically complex located in the northeast Atlantic where oil extraction is currently occurring and where exploration is likely to expand into its deeper waters (>500 m. A major oil spill in this region may mirror the aftermath that ensued following the Deepwater Horizon (DWH blowout in the Gulf of Mexico, where the massive influx of Macondo crude oil triggered the formation of copious quantities of rapidly sinking MOS and successional blooms of opportunistic oil-degrading bacteria. In laboratory experiments, we simulated environmental conditions in sea surface waters of the FSC using water collected from this site during the winter of 2015. We demonstrated that the presence of dispersant triggers the formation of MOS, and that nutrient amendments magnify this. Illumina MiSeq sequencing revealed the enrichment on MOS of associated oil-degrading (Cycloclasticus, Thalassolituus, Marinobacter and EPS-producing (Halomonas, Pseudoalteromonas, Alteromonas bacteria, and included major representation by Psychrobacter and Cobetia with putative oil-degrading/EPS-producing qualities. The formation of marine snow, in the absence of crude oil and dispersant, in seawater amended with nutrients alone indicated that the de novo synthesis of bacterial EPS is a key factor in MOS formation, and the glycoprotein composition of the MOS aggregates confirmed that its amorphous biopolymeric matrix was of microbial (likely bacterial origin. The presence of dispersants and crude oil with/without nutrients resulted in distinct microbial responses marked by intermittent, and in some cases short-lived, blooms of opportunistic heterotrophs, principally obligate hydrocarbonoclastic (Alcanivorax

Inferred effects of cloud deposition on forest floor nutrient cycling and microbial properties along a short elevation gradient

International Nuclear Information System (INIS)

Lavoie, M.; Bradley, R.L.

2003-01-01

Higher cloud cover significantly decreases forest floor pH, decrease exchangeable cations, modifies mineral-N speciation and increases physiological stress within microbial communities. - Cloud water deposition often increases with elevation, and it is widely accepted that this cloud water increases acid loading to upland forest ecosystems. A study was undertaken in south-eastern Quebec to determine if a 250 m elevation gradient (i.e. 420-665 m), along a uniform sugar-maple stand on the slope of Mount Orford, corresponded to a pH gradient in the forest floor and to predictable changes in soil nutrient availability and microbial properties. Precipitation data from a nearby study, and a photographic survey, provided presumptive evidence that this elevation gradient corresponded to a strong gradient in cloud water deposition. Forest floor temperature did not differ significantly across elevations. Forest floor moisture content was significantly higher, whereas pH and exchangeable Ca and Mg were significantly lower, at the higher elevations. Average seasonal net nitrification rates, determined by long-term laboratory incubations, did not differ significantly across elevations, whereas average seasonal net ammonification rates were significantly higher at higher elevations. Basal respiration rates and microbial biomass did not differ significantly across elevations, but metabolic quotient was significantly higher at higher elevations indicating possible environmental stress on forest floor microbial communities due to cloud water deposition. Anaerobic N mineralisation rates were significantly higher at higher elevations suggesting that N-limited microbial communities frequently exposed to cloud cover can be important short-term sinks for atmospheric N, thereby contributing to increase the active-N fraction of forest floors. We conclude that, where no significant changes in vegetation or temperature occur, elevation gradients can still be used to understand the spatial

Dietary marker effects on fecal microbial ecology, fecal VFA, nutrient digestibility coefficients, and growth performance in finishing pigs.

Science.gov (United States)

Kerr, B J; Weber, T E; Ziemer, C J

2015-05-01

Use of indigestible markers such as Cr2O3, Fe2O3, and TiO2 are commonly used in animal studies to evaluate digesta rate of passage and nutrient digestibility. Yet, the potential impact of indigestible markers on fecal microbial ecology and subsequent VFA generation is not known. Two experiments utilizing a total of 72 individually fed finishing pigs were conducted to describe the impact of dietary markers on fecal microbial ecology, fecal ammonia and VFA concentrations, nutrient digestibility, and pig performance. All pigs were fed a common diet with no marker or with 0.5% Cr2O3, Fe2O3, or TiO2. In Exp. 1, after 33 d of feeding, fresh fecal samples were collected for evaluation of microbial ecology, fecal ammonia and VFA concentrations, and nutrient digestibility, along with measures of animal performance. No differences were noted in total microbes or bacterial counts in pig feces obtained from pigs fed the different dietary markers while Archaea counts were decreased (P = 0.07) in feces obtained from pigs fed the diet containing Fe2O 3compared to pigs fed the control diet. Feeding Cr2O3, Fe2O3, or TiO2 increased fecal bacterial richness (P = 0.03, 0.01, and 0.10; respectively) when compared to pigs fed diets containing no marker, but no dietary marker effects were noted on fecal microbial evenness or the Shannon-Wiener index. Analysis of denaturing gradient gel electrophoresis gels did not reveal band pattern alterations due to inclusion of dietary markers in pig diets. There was no effect of dietary marker on fecal DM, ammonia, or VFA concentrations. Pigs fed diets containing Cr2O3 had greater Ca, Cu, Fe, and P (P ≤ 0.02), but lower Ti ( P= 0.08) digestibility compared to pigs fed the control diet. Pigs fed diets containing Fe2O3 had greater Ca (P = 0.08) but lower Ti (P = 0.01) digestibility compared to pigs fed the control diet. Pigs fed diets containing TiO2 had greater Fe and Zn (P ≤ 0.09), but lower Ti ( P= 0.01) digestibility compared to pigs fed the

Electricity generation by Enterobacter cloacae SU-1 in mediator less microbial fuel cell

Energy Technology Data Exchange (ETDEWEB)

Samrot, Antony V.; Senthilkumar, P.; Pavankumar, K.; Akilandeswari, G.C. [Department of Biotechnology, Sathyabama University, Rajiv Gandhi Salai, Chennai, Tamilnadu (India); Rajalakshmi, N.; Dhathathreyan, K.S. [Center for Fuel Cell Technology ARCI, IITM Research Park, Phase I, 2nd Floor, 6 Kanagam Road, Tharamani, Chennai 600 113, Tamilnadu (India)

2010-08-15

We have investigated a Enterobacter cloacae SU-1, bacteria for mediator less microbial fuel cell with different carbon sources and is found to be more effective as the microorganism is able to transfer electrons directly (exo-electrogenic organism) via the cytochromes or the ubiquinone. These carriers of electrons are in form of stable reversible redox couples, not biologically degraded and not toxic to cell. The major advantage of mediator less microbial fuel cells emphasize that additives in the anolyte is not compatible with the purpose of water purification. The anode chamber with the bacteria is maintained under anaerobic conditions so that the bacteria will undergo anaerobic biochemical pathways like Glycolysis, TCA cycle, Electron Transport Chain (ETC) where electrons and protons are released. Here protons are released in TCA cycle and whereas electrons are released from ETC. The mediator less microbial fuel cell delivered an open circuit potential (OCP) of 0.93 V and power of 3 mW/sq cm. During power generation from the microbes, there was a drop in coulombic efficiency in terms of fluctuations during drawing power, as the carbon source is being utilized for the cell growth. (author)

Response of the soil microbial community and soil nutrient bioavailability to biomass harvesting and reserve tree retention in northern Minnesota aspen-dominated forests

Science.gov (United States)

Tera E. Lewandowski; Jodi A. Forrester; David J. Mladenoff; Anthony W. D' Amato; Brian J. Palik

2016-01-01

Intensive forest biomass harvesting, or the removal of harvesting slash (woody debris from tree branches and tops) for use as biofuel, has the potential to negatively affect the soil microbial community (SMC) due to loss of carbon and nutrient inputs from the slash, alteration of the soil microclimate, and increased nutrient leaching. These effects could result in...

Microbial community assembly and metabolic function during mammalian corpse decomposition

Energy Technology Data Exchange (ETDEWEB)

Metcalf, J. L.; Xu, Z. Z.; Weiss, S.; Lax, S.; Van Treuren, W.; Hyde, E. R.; Song, S. J.; Amir, A.; Larsen, P.; Sangwan, N.; Haarmann, D.; Humphrey, G. C.; Ackermann, G.; Thompson, L. R.; Lauber, C.; Bibat, A.; Nicholas, C.; Gebert, M. J.; Petrosino, J. F.; Reed, S. C.; Gilbert, J. A.; Lynne, A. M.; Bucheli, S. R.; Carter, D. O.; Knight, R.

2015-12-10

Vertebrate corpse decomposition provides an important stage in nutrient cycling in most terrestrial habitats, yet microbially mediated processes are poorly understood. Here we combine deep microbial community characterization, community-level metabolic reconstruction, and soil biogeochemical assessment to understand the principles governing microbial community assembly during decomposition of mouse and human corpses on different soil substrates. We find a suite of bacterial and fungal groups that contribute to nitrogen cycling and a reproducible network of decomposers that emerge on predictable time scales. Our results show that this decomposer community is derived primarily from bulk soil, but key decomposers are ubiquitous in low abundance. Soil type was not a dominant factor driving community development, and the process of decomposition is sufficiently reproducible to offer new opportunities for forensic investigations.

Microbial community assembly and metabolic function during mammalian corpse decomposition

Science.gov (United States)

Metcalf, Jessica L; Xu, Zhenjiang Zech; Weiss, Sophie; Lax, Simon; Van Treuren, Will; Hyde, Embriette R.; Song, Se Jin; Amir, Amnon; Larsen, Peter; Sangwan, Naseer; Haarmann, Daniel; Humphrey, Greg C; Ackermann, Gail; Thompson, Luke R; Lauber, Christian; Bibat, Alexander; Nicholas, Catherine; Gebert, Matthew J; Petrosino, Joseph F; Reed, Sasha C.; Gilbert, Jack A; Lynne, Aaron M; Bucheli, Sibyl R; Carter, David O; Knight, Rob

2016-01-01

Vertebrate corpse decomposition provides an important stage in nutrient cycling in most terrestrial habitats, yet microbially mediated processes are poorly understood. Here we combine deep microbial community characterization, community-level metabolic reconstruction, and soil biogeochemical assessment to understand the principles governing microbial community assembly during decomposition of mouse and human corpses on different soil substrates. We find a suite of bacterial and fungal groups that contribute to nitrogen cycling and a reproducible network of decomposers that emerge on predictable time scales. Our results show that this decomposer community is derived primarily from bulk soil, but key decomposers are ubiquitous in low abundance. Soil type was not a dominant factor driving community development, and the process of decomposition is sufficiently reproducible to offer new opportunities for forensic investigations.

Seasonal and scale-dependent variability in nutrient- and allelopathy-mediated macrophyte–phytoplankton interactions

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Lombardo P.

2013-08-01

Full Text Available macrophyte–phytoplankton interactions were investigated using a dual laboratory and field approach during a growing season, with responses quantified as changes in biomass. Short-term, close-range interactions in laboratory microcosms always led to mutual exclusion of macrophytes (Elodea canadensis or Ceratophyllum demersum and algae (Raphidocelis subcapitata, Fistulifera pelliculosa or cyanobacteria (Synechococcus leopoliensis, suggesting regulation by positive feedback mechanisms, progressively establishing and reinforcing a “stable state”. Laboratory results suggest that close-range regulation of R. subcapitata and F. pelliculosa by macrophytes was primarily via nutrient (N, P mediation. Sprig-produced allelochemicals may have contributed to inhibition of S. leopoliensis in C. demersum presence, while S. leopoliensis was apparently enhanced by nutrients leaked by subhealthy (discolored leaves; biomass loss E. canadensis. Seasonal changes in algal growth suppression were correlated with sprig growth. Marginal differences in in situ phytoplankton patterns inside and outside monospecific macrophyte stands suggest that the nutrient- and/or allelopathy-mediated close-range mechanisms observed in the laboratory did not propagate at the macrophyte-stand scale. Factors operating at a larger scale (e.g., lake trophic state, extent of submerged vegetation coverage appear to override in situ macrophyte–phytoplankton close-range interactions.

Rumen microbial variation and nutrient utilisation in mithun (Bos frontalis) under different feeding regimes.

Science.gov (United States)

Prakash, B; Saha, S K; Khate, K; Agarwal, N; Katole, S; Haque, N; Rajkhowa, C

2013-04-01

The aim of the study was to investigate the effect of feeding different diets on fermentation, enzyme activities and microbial population in the rumen fluid of mithun (Bos frontalis). In a randomized block design, 20 male mithun (6-8 months of age, 152 ± 12.6 kg body weight) were randomly divided into four experimental groups (n = 5/group) and fed experimental diets ad libitum for 180 days. The diet R1 contained tree foliages (TF), R2 comprised of 50% concentrate mixture (CM) and 50% TF, R3 contained 50% CM and 50% rice straw, and R4 contained 50% CM, 25% TF and 25% rice straw. Rumen liquor was collected at 0 and 180 days of the experiment for estimation of different ruminal parameters and a digestion trial was conducted at the end of the experiment. Rumen fluid was analysed for pH, ammonia nitrogen (NH3 -N), total-N, ruminal enzymes, short chain fatty acid (SCFA) and microbial profile. The relative quantification of ruminal microbes was carried out with real-time PCR using bacteria as the house keeping gene. The dry matter intake, nutrients digestibility, body weight gain, NH3 -N, total-N, carboxymethyl cellulase, avicelase, xylanase, amylase, protease and molar proportion of butyrate were (p ecology, nutrient utilization and thus better performance under stall fed system. © 2012 Blackwell Verlag GmbH.

Effect of long-term fertilization on humic redox mediators in multiple microbial redox reactions.

Science.gov (United States)

Guo, Peng; Zhang, Chunfang; Wang, Yi; Yu, Xinwei; Zhang, Zhichao; Zhang, Dongdong

2018-03-01

This study investigated the effects of different long-term fertilizations on humic substances (HSs), humic acids (HAs) and humins, functioning as redox mediators for various microbial redox biotransformations, including 2,2',4,4',5,5'- hexachlorobiphenyl (PCB 153 ) dechlorination, dissimilatory iron reduction, and nitrate reduction, and their electron-mediating natures. The redox activity of HSs for various microbial redox metabolisms was substantially enhanced by long-term application of organic fertilizer (pig manure). As a redox mediator, only humin extracted from soils with organic fertilizer amendment (OF-HM) maintained microbial PCB 153 dechlorination activity (1.03 μM PCB 153 removal), and corresponding HA (OF-HA) most effectively enhanced iron reduction and nitrate reduction by Shewanella putrefaciens. Electrochemical analysis confirmed the enhancement of their electron transfer capacity and redox properties. Fourier transform infrared analysis showed that C=C and C=O bonds, and carboxylic or phenolic groups in HSs might be the redox functional groups affected by fertilization. This research enhances our understanding of the influence of anthropogenic fertility on the biogeochemical cycling of elements and in situ remediation ability in agroecosystems through microorganisms' metabolisms. Copyright © 2017 Elsevier Ltd. All rights reserved.

Spring thaw ionic pulses boost nutrient availability and microbial growth in entombed Antarctic Dry Valley cryoconite holes.

Science.gov (United States)

Telling, Jon; Anesio, Alexandre M; Tranter, Martyn; Fountain, Andrew G; Nylen, Thomas; Hawkings, Jon; Singh, Virendra B; Kaur, Preeti; Musilova, Michaela; Wadham, Jemma L

2014-01-01

The seasonal melting of ice entombed cryoconite holes on McMurdo Dry Valley glaciers provides oases for life in the harsh environmental conditions of the polar desert where surface air temperatures only occasionally exceed 0°C during the Austral summer. Here we follow temporal changes in cryoconite hole biogeochemistry on Canada Glacier from fully frozen conditions through the initial stages of spring thaw toward fully melted holes. The cryoconite holes had a mean isolation age from the glacial drainage system of 3.4 years, with an increasing mass of aqueous nutrients (dissolved organic carbon, total nitrogen, total phosphorus) with longer isolation age. During the initial melt there was a mean nine times enrichment in dissolved chloride relative to mean concentrations of the initial frozen holes indicative of an ionic pulse, with similar mean nine times enrichments in nitrite, ammonium, and dissolved organic matter. Nitrate was enriched twelve times and dissolved organic nitrogen six times, suggesting net nitrification, while lower enrichments for dissolved organic phosphorus and phosphate were consistent with net microbial phosphorus uptake. Rates of bacterial production were significantly elevated during the ionic pulse, likely due to the increased nutrient availability. There was no concomitant increase in photosynthesis rates, with a net depletion of dissolved inorganic carbon suggesting inorganic carbon limitation. Potential nitrogen fixation was detected in fully melted holes where it could be an important source of nitrogen to support microbial growth, but not during the ionic pulse where nitrogen availability was higher. This study demonstrates that ionic pulses significantly alter the timing and magnitude of microbial activity within entombed cryoconite holes, and adds credence to hypotheses that ionic enrichments during freeze-thaw can elevate rates of microbial growth and activity in other icy habitats, such as ice veins and subglacial regelation zones.

Spring thaw ionic pulses boost nutrient availability and microbial growth in entombed Antarctic Dry Valley cryoconite holes

Directory of Open Access Journals (Sweden)

Jon eTelling

2014-12-01

Full Text Available The seasonal melting of ice entombed cryoconite holes on McMurdo Dry Valley glaciers provides oases for life in the harsh environmental conditions of the polar desert where surface air temperatures only occasionally exceed 0°C during the Austral summer. Here we follow temporal changes in cryoconite hole biogeochemistry on Canada Glacier from fully frozen conditions through the initial stages of spring thaw towards fully melted holes. The cryoconite holes had a mean isolation age from the glacial drainage system of 3.4 years, with an increasing mass of aqueous nutrients (dissolved organic carbon, total nitrogen, total phosphorus with longer isolation age. During the initial melt there was a mean nine times enrichment in dissolved chloride relative to mean concentrations of the initial frozen holes indicative of an ionic pulse, with similar mean nine times enrichments in nitrite, ammonium, and dissolved organic matter. Nitrate was enriched twelve times and dissolved organic nitrogen six times, suggesting net nitrification, while lower enrichments for dissolved organic phosphorus and phosphate were consistent with net microbial phosphorus uptake. Rates of bacterial production were significantly elevated during the ionic pulse, likely due to the increased nutrient availability. There was no concomitant increase in photosynthesis rates, with a net depletion of dissolved inorganic carbon suggesting inorganic carbon limitation. Potential nitrogen fixation was detected in fully melted holes where it could be an important source of nitrogen to support microbial growth, but not during the ionic pulse where nitrogen availability was higher. This study demonstrates that ionic pulses significantly alter the timing and magnitude of microbial activity within entombed cryoconite holes, and adds credence to hypotheses that ionic enrichments during freeze-thaw can elevate rates of microbial growth and activity in other icy habitats, such as ice veins and

Decoupling of microbial carbon, nitrogen, and phosphorus cycling in response to extreme temperature events

Science.gov (United States)

Mooshammer, Maria; Hofhansl, Florian; Frank, Alexander H.; Wanek, Wolfgang; Hämmerle, Ieda; Leitner, Sonja; Schnecker, Jörg; Wild, Birgit; Watzka, Margarete; Keiblinger, Katharina M.; Zechmeister-Boltenstern, Sophie; Richter, Andreas

2017-01-01

Predicted changes in the intensity and frequency of climate extremes urge a better mechanistic understanding of the stress response of microbially mediated carbon (C) and nutrient cycling processes. We analyzed the resistance and resilience of microbial C, nitrogen (N), and phosphorus (P) cycling processes and microbial community composition in decomposing plant litter to transient, but severe, temperature disturbances, namely, freeze-thaw and heat. Disturbances led temporarily to a more rapid cycling of C and N but caused a down-regulation of P cycling. In contrast to the fast recovery of the initially stimulated C and N processes, we found a slow recovery of P mineralization rates, which was not accompanied by significant changes in community composition. The functional and structural responses to the two distinct temperature disturbances were markedly similar, suggesting that direct negative physical effects and costs associated with the stress response were comparable. Moreover, the stress response of extracellular enzyme activities, but not that of intracellular microbial processes (for example, respiration or N mineralization), was dependent on the nutrient content of the resource through its effect on microbial physiology and community composition. Our laboratory study provides novel insights into the mechanisms of microbial functional stress responses that can serve as a basis for field studies and, in particular, illustrates the need for a closer integration of microbial C-N-P interactions into climate extremes research. PMID:28508070

Plant stimulation of soil microbial community succession: how sequential expression mediates soil carbon stabilization and turnover

Energy Technology Data Exchange (ETDEWEB)

Firestone, Mary [Univ. of California, Berkeley, CA (United States)

2015-03-31

It is now understood that most plant C is utilized or transformed by soil microorganisms en route to stabilization. Hence the composition of microbial communities that mediate decomposition and transformation of root C is critical, as are the metabolic capabilities of these communities. The change in composition and function of the C-transforming microbial communities over time in effect defines the biological component of soil C stabilization. Our research was designed to test 2 general hypotheses; the first two hypotheses are discussed first; H1: Root-exudate interactions with soil microbial populations results in the expression of enzymatic capacities for macromolecular, complex carbon decomposition; and H2: Microbial communities surrounding roots undergo taxonomic succession linked to functional gene activities as roots grow, mature, and decompose in soil. Over the term of the project we made significant progress in 1) quantifying the temporal pattern of root interactions with the soil decomposing community and 2) characterizing the role of root exudates in mediating these interactions.

Patterns of nutrient utilization. Implications for nitrogen metabolism

International Nuclear Information System (INIS)

Oldham, J.D.

1983-01-01

Nutrients react within both the rumen and the ruminant body, and the patterns of availability of different nutrients greatly influence their net utilization. In the rumen, microbial capture of N substrates, especially ammonia, depends on the degree of synchronization between rates of production of N substrates and of ATP to drive microbial protein synthesis. The form of dietary carbohydrate and of dietary N and the frequency of feeding can all affect the efficiency of microbial growth and digestion. The pattern of supply of nutrients to the body will also influence nutrient utilization. Disparities between diurnal patterns of supply of volatile fatty acids from the rumen and amino acids from the intestines will result in changes in balance of metabolic pathways. The balance between supply of glucogenic and lipogenic nutrients will influence efficiency of fattening. A major factor determining the pattern of utilization/metabolism of amino acids is the metabolic demand for protein synthesis, which varies with physiological state. (author)

New method for characterizing electron mediators in microbial systems using a thin-layer twin-working electrode cell.

Science.gov (United States)

Hassan, Md Mahamudul; Cheng, Ka Yu; Ho, Goen; Cord-Ruwisch, Ralf

2017-01-15

Microbial biofilms are significant ecosystems where the existence of redox gradients drive electron transfer often via soluble electron mediators. This study describes the use of two interfacing working electrodes (WEs) to simulate redox gradients within close proximity (250µm) for the detection and quantification of electron mediators. By using a common counter and reference electrode, the potentials of the two WEs were independently controlled to maintain a suitable "voltage window", which enabled simultaneous oxidation and reduction of electron mediators as evidenced by the concurrent anodic and cathodic currents, respectively. To validate the method, the electrochemical properties of different mediators (hexacyanoferrate, HCF, riboflavin, RF) were characterized by stepwise shifting the "voltage window" (ranging between 25 and 200mV) within a range of potentials after steady equilibrium current of both WEs was established. The resulting differences in electrical currents between the two WEs were recorded across a defined potential spectrum (between -1V and +0.5V vs. Ag/AgCl). Results indicated that the technique enabled identification (by the distinct peak locations at the potential scale) and quantification (by the peak of current) of the mediators for individual species as well as in an aqueous mixture. It enabled a precise determination of mid-potentials of the externally added mediators (HCF, RF) and mediators produced by pyocyanin-producing Pseudomonas aeruginosa (WACC 91) culture. The twin working electrode described is particularly suitable for studying mediator-dependent microbial electron transfer processes or simulating redox gradients as they exist in microbial biofilms. Copyright © 2016 Elsevier B.V. All rights reserved.

Microbially mediated mineral carbonation

Science.gov (United States)

Power, I. M.; Wilson, S. A.; Dipple, G. M.; Southam, G.

2010-12-01

Mineral carbonation involves silicate dissolution and carbonate precipitation, which are both natural processes that microorganisms are able to mediate in near surface environments (Ferris et al., 1994; Eq. 1). (Ca,Mg)SiO3 + 2H2CO3 + H2O → (Ca,Mg)CO3 + H2O + H4SiO4 + O2 (1) Cyanobacteria are photoautotrophs with cell surface characteristics and metabolic processes involving inorganic carbon that can induce carbonate precipitation. This occurs partly by concentrating cations within their net-negative cell envelope and through the alkalinization of their microenvironment (Thompson & Ferris, 1990). Regions with mafic and ultramafic bedrock, such as near Atlin, British Columbia, Canada, represent the best potential sources of feedstocks for mineral carbonation. The hydromagnesite playas near Atlin are a natural biogeochemical model for the carbonation of magnesium silicate minerals (Power et al., 2009). Field-based studies at Atlin and corroborating laboratory experiments demonstrate the ability of a microbial consortium dominated by filamentous cyanobacteria to induce the precipitation of carbonate minerals. Phototrophic microbes, such as cyanobacteria, have been proposed as a means for producing biodiesel and other value added products because of their efficiency as solar collectors and low requirement for valuable, cultivable land in comparison to crops (Dismukes et al., 2008). Carbonate precipitation and biomass production could be facilitated using specifically designed ponds to collect waters rich in dissolved cations (e.g., Mg2+ and Ca2+), which would allow for evapoconcentration and provide an appropriate environment for growth of cyanobacteria. Microbially mediated carbonate precipitation does not require large quantities of energy or chemicals needed for industrial systems that have been proposed for rapid carbon capture and storage via mineral carbonation (e.g., Lackner et al., 1995). Therefore, this biogeochemical approach may represent a readily

Fermented soybean meal improves the growth performance, nutrient digestibility, and microbial flora in piglets

Directory of Open Access Journals (Sweden)

Lin Yuan

2017-03-01

Full Text Available In order to increase nutritive values of soybean meal (SBM, 3 species of microbes were used to ferment SBM. Through a 3 × 3 orthogonal design and parameter measurements of soybean peptide and anti-nutritional factor contents in the fermented soybean meal (FSBM, it was estimated that the best microbial proportion of Bacillus subtilis, Hansenula anomala and Lactobacillus casei was 2:1:2 for SBM fermentation (P  0.05. However, newly-weaned piglets (d 28–38 fed 10% FSBM and different levels of plasma protein obtained higher average daily gain (ADG and feed conversion ratio (FCR, compared with those without FSBM but with 6% plasma protein (P < 0.05. Piglets (d 38–68 fed diets supplemented with FSBM and soybean protein concentrate (SBPC at 3.75% and 7.5% respectively increased nutrient digestibility, fecal enzyme activity and lactic acid bacteria counts, and decreased fecal Escherichia coli counts (P < 0.05, compared with the control. These data indicated that FSBM had positive effects on nutrient digestibility and fecal microflora for piglets.

Contrasting response to nutrient manipulation in Arctic mesocosms are reproduced by a minimum microbial food web model.

Science.gov (United States)

Larsen, Aud; Egge, Jorun K; Nejstgaard, Jens C; Di Capua, Iole; Thyrhaug, Runar; Bratbak, Gunnar; Thingstad, T Frede

2015-03-01

A minimum mathematical model of the marine pelagic microbial food web has previously shown to be able to reproduce central aspects of observed system response to different bottom-up manipulations in a mesocosm experiment Microbial Ecosystem Dynamics (MEDEA) in Danish waters. In this study, we apply this model to two mesocosm experiments (Polar Aquatic Microbial Ecology (PAME)-I and PAME-II) conducted at the Arctic location Kongsfjorden, Svalbard. The different responses of the microbial community to similar nutrient manipulation in the three mesocosm experiments may be described as diatom-dominated (MEDEA), bacteria-dominated (PAME-I), and flagellated-dominated (PAME-II). When allowing ciliates to be able to feed on small diatoms, the model describing the diatom-dominated MEDEA experiment give a bacteria-dominated response as observed in PAME I in which the diatom community comprised almost exclusively small-sized cells. Introducing a high initial mesozooplankton stock as observed in PAME-II, the model gives a flagellate-dominated response in accordance with the observed response also of this experiment. The ability of the model originally developed for temperate waters to reproduce population dynamics in a 10°C colder Arctic fjord, does not support the existence of important shifts in population balances over this temperature range. Rather, it suggests a quite resilient microbial food web when adapted to in situ temperature. The sensitivity of the model response to its mesozooplankton component suggests, however, that the seasonal vertical migration of Arctic copepods may be a strong forcing factor on Arctic microbial food webs.

Consistent nutrient storage and supply mediated by diverse fish communities in coral reef ecosystems.

Science.gov (United States)

Allgeier, Jacob E; Layman, Craig A; Mumby, Peter J; Rosemond, Amy D

2014-08-01

Corals thrive in low nutrient environments and the conservation of these globally imperiled ecosystems is largely dependent on mitigating the effects of anthropogenic nutrient enrichment. However, to better understand the implications of anthropogenic nutrients requires a heightened understanding of baseline nutrient dynamics within these ecosystems. Here, we provide a novel perspective on coral reef nutrient dynamics by examining the role of fish communities in the supply and storage of nitrogen (N) and phosphorus (P). We quantified fish-mediated nutrient storage and supply for 144 species and modeled these data onto 172 fish communities (71 729 individual fish), in four types of coral reefs, as well as seagrass and mangrove ecosystems, throughout the Northern Antilles. Fish communities supplied and stored large quantities of nutrients, with rates varying among ecosystem types. The size structure and diversity of the fish communities best predicted N and P supply and storage and N : P supply, suggesting that alterations to fish communities (e.g., overfishing) will have important implications for nutrient dynamics in these systems. The stoichiometric ratio (N : P) for storage in fish mass (~8 : 1) and supply (~20 : 1) was notably consistent across the four coral reef types (but not seagrass or mangrove ecosystems). Published nutrient enrichment studies on corals show that deviations from this N : P supply ratio may be associated with poor coral fitness, providing qualitative support for the hypothesis that corals and their symbionts may be adapted to specific ratios of nutrient supply. Consumer nutrient stoichiometry provides a baseline from which to better understand nutrient dynamics in coral reef and other coastal ecosystems, information that is greatly needed if we are to implement more effective measures to ensure the future health of the world's oceans. © 2014 John Wiley & Sons Ltd.

Nutrient and energy recovery from urine

NARCIS (Netherlands)

Kuntke, P.

2013-01-01

Keywords: urine, urine treatment, nutrient recovery, microbial fuel cells, energy production from urine, membrane capacitive deionization.

In conventional wastewater treatment plants large amounts of energy are required for the removal and recovery of nutrients (i.e. nitrogen and

Combined Effects of Nutrient and Pesticide Management on Soil Microbial Activity in Hybrid Rice Double Annual Cropping System

Institute of Scientific and Technical Information of China (English)

XIEXiao-mei; LIAOMin; LIUWei-ping; SusanneKLOSE

2004-01-01

Combined effects on soil microbial activity of nutrient and pesticide management in hybrid rice double annual cropping system were studied. Results of field experiment demonstrated significant changes in soil microbial biomass phospholipid contents,abundance of heterotrophic bacteria and proteolytic bacteria, electron transport system (ETS)/dehydrogenase activity, soil protein contents under different management practices and at various growth stages. Marked depletions in the soil microbial biomass phospholipid contents were found with the advancement of crop growth stages, while the incorporation of fertilizers and/or pesticides also induced slight changes, and the lowest microbial biomass phospholipid content was found with pesticides application alone. A decline in the bacterial abundance of heterotrophic bacteria and proteolytic bacteria was observed during the continuance of crop growth, while the lowest abundance of heterotrophic bacteria and proteolyrJc bacteria was found with pesticides application alone, which coincided with the decline of soil microbial biomass. A consistent increase in the electron transport svstem activit), was measured during the different crop growth stages of rice. The use of fertilizers (NPK) alone or combined with pesticides increased it, while a decline was noticed with pesticides application alone as compared with the control.The soil protein content was found to be relatively stable with fertilizers and/or pesticides application at various growth stages in both crops undertaken, but notable changes were detected at different growrh stages

Combined Effects of Nutrient and Pesticide Management on Soil Microbial Activity in Hybrid Rice Double Annual Cropping System

Institute of Scientific and Technical Information of China (English)

XIE Xiao-mei; LIAO Min; LIU Wei-ping; Susanne KLOSE

2004-01-01

Combined effects on soil microbial activity of nutrient and pesticide management in hybrid rice double annual cropping system were studied. Results of field experiment demonstrated significant changes in soil microbial biomass phospholipid contents,abundance of heterotrophic bacteria and proteolytic bacteria, electron transport system (ETS)/dehydrogenase activity, soil protein contents under different management practices and at various growth stages. Marked depletions in the soil microbial biomass phospholipid contents were found with the advancement of crop growth stages, while the incorporation of fertilizers and/or pesticides also induced slight changes, and the lowest microbial biomass phospholipid content was found with pesticides application alone. A decline in the bacterial abundance of heterotrophic bacteria and proteolytic bacteria was observed during the continuance of crop growth, while the lowest abundance of heterotrophic bacteria and proteolytic bacteria was found with pesticides application alone, which coincided with the decline of soil microbial biomass. A consistent increase in the electron transport system activity was measured during the different crop growth stages of rice. The use of fertilizers (NPK) alone or combined with pesticides increased it, while a decline was noticed with pesticides application alone as compared with the control.The soil protein content was found to be relatively stable with fertilizers and/or pesticides application at various growth stages in both crops undertaken, but notable changes were detected at different growth stages.

Insights into the Microbial and Viral Dynamics of a Coastal Downwelling-Upwelling Transition.

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Gustavo Bueno Gregoracci

Full Text Available Although previous studies have described opposing states in upwelling regions, i.e., the rise of cold nutrient-rich waters and prevalence of surface warm nutrient-poor waters, few have addressed the transition from one state to the other. This study aimed to describe the microbial and viral structure during this transition and was able to obtain the taxonomic and metabolic compositions as well as physical-chemical data. This integrated approach allowed for a better understanding of the dynamics of the downwelling upwelling transition, suggesting that a wealth of metabolic processes and ecological interactions are occurring in the minute fractions of the plankton (femto, pico, nano. These processes and interactions included evidence of microbial predominance during downwelling (with nitrogen recycling and aerobic anoxygenic photosynthesis, different viral predation pressures over primary production in different states (cyanobacteria vs eukaryotes, and a predominance of diatoms and selected bacterial and archaeal groups during upwelling (with the occurrence of a wealth of nitrogen metabolism involving ammonia. Thus, the results provided insights into which microbes, viruses and microbial-mediated processes are probably important in the functioning of upwelling systems.

Increased resiliency and activity of microbial mediated carbon cycling enzymes in diversified bioenergy cropping systems

Science.gov (United States)

Upton, R.; Bach, E.; Hofmockel, K. S.

2017-12-01

Microbes are mediators of soil carbon (C) and are influenced in membership and activity by nitrogen (N) fertilization and inter-annual abiotic factors. Microbial communities and their extracellular enzyme activities (EEA) are important parameters that influence ecosystem C cycling properties and are often included in microbial explicit C cycling models. In an effort to generate model relevant, empirical findings, we investigated how both microbial community structure and C degrading enzyme activity are influenced by inter-annual variability and N inputs in bioenergy crops. Our study was performed at the Comparison of Biofuel Systems field-site from 2011 to 2014, in three bioenergy cropping systems, continuous corn (CC) and two restored prairies, both fertilized (FP) and unfertilized (P). We hypothesized microbial community structure would diverge during the prairie restoration, leading to changes in C cycling enzymes over time. Using a sequencing approach (16S and ITS) we determined the bacterial and fungal community structure response to the cropping system, fertilization, and inter-annual variability. Additionally, we used EEA of β-glucosidase, cellobiohydrolase, and β-xylosidase to determine inter-annual and ecosystem impacts on microbial activity. Our results show cropping system was a main effect for microbial community structure, with corn diverging from both prairies to be less diverse. Inter-annual changes showed that a drought occurring in 2012 significantly impacted microbial community structure in both the P and CC, decreasing microbial richness. However, FP increased in microbial richness, suggesting the application of N increased resiliency to drought. Similarly, the only year in which C cycling enzymes were impacted by ecosystem was 2012, with FP supporting higher potential enzymatic activity then CC and P. The highest EEA across all ecosystems occurred in 2014, suggesting the continued root biomass and litter build-up in this no till system

Microbial properties and litter and soil nutrients after two prescribed fires in developing savannas in an upland Missouri Ozark Forest

Science.gov (United States)

Felix, Jr. Ponder; Mahasin Tadros; Edward F. Loewenstein

2009-01-01

On some landscapes periodic fire may be necessary to develop and maintain oak-dominated savannas. We studied the effects of two annual prescribed burns to determine their effect on microbial activity and soil and litter nutrients 1 year after the last burn. Surface litter and soil from the upper 0?5 cm soil layer in three developing savannas (oak-hickory, ...

Animal pee in the sea: consumer-mediated nutrient dynamics in the world's changing oceans.

Science.gov (United States)

Allgeier, Jacob E; Burkepile, Deron E; Layman, Craig A

2017-06-01

Humans have drastically altered the abundance of animals in marine ecosystems via exploitation. Reduced abundance can destabilize food webs, leading to cascading indirect effects that dramatically reorganize community structure and shift ecosystem function. However, the additional implications of these top-down changes for biogeochemical cycles via consumer-mediated nutrient dynamics (CND) are often overlooked in marine systems, particularly in coastal areas. Here, we review research that underscores the importance of this bottom-up control at local, regional, and global scales in coastal marine ecosystems, and the potential implications of anthropogenic change to fundamentally alter these processes. We focus attention on the two primary ways consumers affect nutrient dynamics, with emphasis on implications for the nutrient capacity of ecosystems: (1) the storage and retention of nutrients in biomass, and (2) the supply of nutrients via excretion and egestion. Nutrient storage in consumer biomass may be especially important in many marine ecosystems because consumers, as opposed to producers, often dominate organismal biomass. As for nutrient supply, we emphasize how consumers enhance primary production through both press and pulse dynamics. Looking forward, we explore the importance of CDN for improving theory (e.g., ecological stoichiometry, metabolic theory, and biodiversity-ecosystem function relationships), all in the context of global environmental change. Increasing research focus on CND will likely transform our perspectives on how consumers affect the functioning of marine ecosystems. © 2017 John Wiley & Sons Ltd.

Post-fire spatial patterns of soil nitrogen mineralization and microbial abundance.

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Erica A H Smithwick

Full Text Available Stand-replacing fires influence soil nitrogen availability and microbial community composition, which may in turn mediate post-fire successional dynamics and nutrient cycling. However, fires create patchiness at both local and landscape scales and do not result in consistent patterns of ecological dynamics. The objectives of this study were to (1 quantify the spatial structure of microbial communities in forest stands recently affected by stand-replacing fire and (2 determine whether microbial variables aid predictions of in situ net nitrogen mineralization rates in recently burned stands. The study was conducted in lodgepole pine (Pinus contorta var. latifolia and Engelmann spruce/subalpine fir (Picea engelmannii/Abies lasiocarpa forest stands that burned during summer 2000 in Greater Yellowstone (Wyoming, USA. Using a fully probabilistic spatial process model and Bayesian kriging, the spatial structure of microbial lipid abundance and fungi-to-bacteria ratios were found to be spatially structured within plots two years following fire (for most plots, autocorrelation range varied from 1.5 to 10.5 m. Congruence of spatial patterns among microbial variables, in situ net N mineralization, and cover variables was evident. Stepwise regression resulted in significant models of in situ net N mineralization and included variables describing fungal and bacterial abundance, although explained variance was low (R²<0.29. Unraveling complex spatial patterns of nutrient cycling and the biotic factors that regulate it remains challenging but is critical for explaining post-fire ecosystem function, especially in Greater Yellowstone, which is projected to experience increased fire frequencies by mid 21(st Century.

Composting of waste paint sludge containing melamine resin as affected by nutrients and gypsum addition and microbial inoculation

International Nuclear Information System (INIS)

Tian Yongqiang; Chen Liming; Gao Lihong; Michel, Frederick C.; Wan Caixia; Li Yebo; Dick, Warren A.

2012-01-01

Melamine formaldehyde resins have hard and durable properties and are found in many products, including automobile paints. These resins contain high concentrations of nitrogen and, if properly composted, can yield valuable products. We evaluated the effects of starter compost, nutrients, gypsum and microbial inoculation on composting of paint sludge containing melamine resin. A bench-scale composting experiment was conducted at 55 °C for 91 days and then at 30 °C for an additional 56 days. After 91 days, the composts were inoculated with a mixed population of melamine-degrading microorganisms. Melamine resin degradation after the entire 147 days of composting varied between 73 and 95% for the treatments with inoculation of microorganisms compared to 55–74% for the treatments without inoculation. Degradation was also enhanced by nutrients and gypsum additions. Our results infer that large scale composting of melamine resins in paint sludge is possible. - Highlights: ► Melamine resin in waste paint sludges could be efficiently composted at bench scale. ► Melamine resin degradation after 147 days of composting was 73–95% complete. ► Nutrients, gypsum and melamine-degrading microorganisms increased composting rate. ► Melamine degradation products first increased and then decreased in the compost. ► Final compost was enriched in nitrogen and other essential plant nutrients. - Melamine resin in waste paint sludges was efficiently composted at bench scale, with finished composts having low levels of heavy metals and enriched in plant nutrients.

Sponge-microbe associations survive high nutrients and temperatures.

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Rachel Simister

Full Text Available Coral reefs are under considerable pressure from global stressors such as elevated sea surface temperature and ocean acidification, as well as local factors including eutrophication and poor water quality. Marine sponges are diverse, abundant and ecologically important components of coral reefs in both coastal and offshore environments. Due to their exceptionally high filtration rates, sponges also form a crucial coupling point between benthic and pelagic habitats. Sponges harbor extensive microbial communities, with many microbial phylotypes found exclusively in sponges and thought to contribute to the health and survival of their hosts. Manipulative experiments were undertaken to ascertain the impact of elevated nutrients and seawater temperature on health and microbial community dynamics in the Great Barrier Reef sponge Rhopaloeides odorabile. R. odorabile exposed to elevated nutrient levels including 10 µmol/L total nitrogen at 31°C appeared visually similar to those maintained under ambient seawater conditions after 7 days. The symbiotic microbial community, analyzed by 16S rRNA gene pyrotag sequencing, was highly conserved for the duration of the experiment at both phylum and operational taxonomic unit (OTU (97% sequence similarity levels with 19 bacterial phyla and 1743 OTUs identified across all samples. Additionally, elevated nutrients and temperatures did not alter the archaeal associations in R. odorabile, with sequencing of 16S rRNA gene libraries revealing similar Thaumarchaeota diversity and denaturing gradient gel electrophoresis (DGGE revealing consistent amoA gene patterns, across all experimental treatments. A conserved eukaryotic community was also identified across all nutrient and temperature treatments by DGGE. The highly stable microbial associations indicate that R. odorabile symbionts are capable of withstanding short-term exposure to elevated nutrient concentrations and sub-lethal temperatures.

Recipient-Biased Competition for an Intracellularly Generated Cross-Fed Nutrient Is Required for Coexistence of Microbial Mutualists.

Science.gov (United States)

McCully, Alexandra L; LaSarre, Breah; McKinlay, James B

2017-11-28

Many mutualistic microbial relationships are based on nutrient cross-feeding. Traditionally, cross-feeding is viewed as being unidirectional, from the producer to the recipient. This is likely true when a producer's waste, such as a fermentation product, has value only for a recipient. However, in some cases the cross-fed nutrient holds value for both the producer and the recipient. In such cases, there is potential for nutrient reacquisition by producer cells in a population, leading to competition against recipients. Here, we investigated the consequences of interpartner competition for cross-fed nutrients on mutualism dynamics by using an anaerobic coculture pairing fermentative Escherichia coli and phototrophic Rhodopseudomonas palustris In this coculture, E. coli excretes waste organic acids that provide a carbon source for R. palustris In return, R. palustris cross-feeds E. coli ammonium (NH 4 + ), a compound that both species value. To explore the potential for interpartner competition, we first used a kinetic model to simulate cocultures with varied affinities for NH 4 + in each species. The model predicted that interpartner competition for NH 4 + could profoundly impact population dynamics. We then experimentally tested the predictions by culturing mutants lacking NH 4 + transporters in both NH 4 + competition assays and mutualistic cocultures. Both theoretical and experimental results indicated that the recipient must have a competitive advantage in acquiring cross-fed NH 4 + to sustain the mutualism. This recipient-biased competitive advantage is predicted to be crucial, particularly when the communally valuable nutrient is generated intracellularly. Thus, the very metabolites that form the basis for mutualistic cross-feeding can also be subject to competition between mutualistic partners. IMPORTANCE Mutualistic relationships, particularly those based on nutrient cross-feeding, promote stability of diverse ecosystems and drive global biogeochemical

Microbial ecology of phototrophic biofilms

NARCIS (Netherlands)

Roeselers, G.

2007-01-01

Biofilms are layered structures of microbial cells and an extracellular matrix of polymeric substances, associated with surfaces and interfaces. Biofilms trap nutrients for growth of the enclosed microbial community and help prevent detachment of cells from surfaces in flowing systems. Phototrophic

Effect of Carbohydrate Source and Cottonseed Meal Level in the Concentrate on Feed Intake, Nutrient Digestibility, Rumen Fermentation and Microbial Protein Synthesis in Swamp Buffaloes

Directory of Open Access Journals (Sweden)

M. Wanapat

2013-07-01

Full Text Available The objective of this study was to investigate the effect of carbohydrate source and cottonseed meal level in the concentrate on feed intake, nutrient digestibility, rumen fermentation and microbial protein synthesis in swamp buffaloes. Four, 4-yr old rumen fistulated swamp buffaloes were randomly assigned to receive four dietary treatments according to a 2×2 factorial arrangement in a 4×4 Latin square design. Factor A was carbohydrate source; cassava chip (CC and CC+rice bran at a ratio 3:1 (CR3:1, and factor B was level of cottonseed meal (CM; 109 g CP/kg (LCM and 328 g CP/kg (HCM in isonitrogenous diets (490 g CP/kg. Buffaloes received urea-treated rice straw ad libitum and supplemented with 5 g concentrate/kg BW. It was found that carbohydrate source did not affect feed intake, nutrient intake, digested nutrients, nutrient digestibility, ammonia nitrogen concentration, fungi and bacterial populations, or microbial protein synthesis (p>0.05. Ruminal pH at 6 h after feeding and the population of protozoa at 4 h after feeding were higher when buffalo were fed with CC than in the CR3:1 treatment (p0.05. Based on this experiment, concentrate with a low level of cottonseed meal could be fed with cassava chips as an energy source in swamp buffalo receiving rice straw.

Eddy Mediated Nutrient Pattern in the North Eastern Arabian Sea

Science.gov (United States)

Thachaparambil, M.; Moolakkal Antony, R.; B R, S.; V N, S.; N, C.; M, S.

2016-02-01

A Cold Core Eddy (CCE) mediated nutrient pattern in the North Eastern Arabian Sea (NEAS) is explained based on in situ measurments during March 2013 onboard FORV Sagar Sampada which was not reported earlier in the area. Samples for physical, chemical and biological parameters were collected in 5 stations along the diameter of the eddy and following standard protocols. The core of the CCE is identified at 21°20.38'N; 66°30.68'E with a diameter of 120Km. Earlier studies explaining the process and the forcing mechanism of the particular eddy records that, the eddy is short term (1-3 months) and is regular during the season. Surface waters were well oxygenated (>4.8 ml L-1) in the core. Surface value of nutrients viz., Nitrate, Nitrite, Silicate and phosphate in the core regions was 0.9µM, 0.01 µM, 0.5 µM and 0.7 µM respectively indicating upwelling in the core. Spring intermonsoon (SIM) is generally termed as a transition period between the active winter and summer seasons and as per earlier studies, high biological production and the regularly occurring Noctilica bloom is supported by the nutrient loading due to convective mixing during winter as well as regenerated production. However, present observations shows that, nutrient pumping due to the upwelling associated with the CCE also contributes for sustaining high biological production and are evident in the Chl a and mesozooplankton biovolume which records values of 4.35mg/m3 and 1.09ml/m3 respectively in the core. An intense Noctiluca blooms observed in the western flank of the eddy (Chl a 13.25 mg/m3; cell density 5.8×106 cells/litre), where Nitrate concentration records 1.04µM explains the role of such mesoscale processes in the sustenance of the HAB events. While eastern flank of the CCE showed typical open ocean condition of the season showing Nitrate 0.08µM; Chl a 0.23mg/m3; and phytoplankton cell density as 421 cells/litre. Keywords: Cold core eddy, nutrients, NEAS, SIM, biological production

Elemental economy: microbial strategies for optimizing growth in the face of nutrient limitation.

Science.gov (United States)

Merchant, Sabeeha S; Helmann, John D

2012-01-01

Microorganisms play a dominant role in the biogeochemical cycling of nutrients. They are rightly praised for their facility for fixing both carbon and nitrogen into organic matter, and microbial driven processes have tangibly altered the chemical composition of the biosphere and its surrounding atmosphere. Despite their prodigious capacity for molecular transformations, microorganisms are powerless in the face of the immutability of the elements. Limitations for specific elements, either fleeting or persisting over eons, have left an indelible trace on microbial genomes, physiology, and their very atomic composition. We here review the impact of elemental limitation on microbes, with a focus on selected genetic model systems and representative microbes from the ocean ecosystem. Evolutionary adaptations that enhance growth in the face of persistent or recurrent elemental limitations are evident from genome and proteome analyses. These range from the extreme (such as dispensing with a requirement for a hard to obtain element) to the extremely subtle (changes in protein amino acid sequences that slightly, but significantly, reduce cellular carbon, nitrogen, or sulfur demand). One near-universal adaptation is the development of sophisticated acclimation programs by which cells adjust their chemical composition in response to a changing environment. When specific elements become limiting, acclimation typically begins with an increased commitment to acquisition and a concomitant mobilization of stored resources. If elemental limitation persists, the cell implements austerity measures including elemental sparing and elemental recycling. Insights into these fundamental cellular properties have emerged from studies at many different levels, including ecology, biological oceanography, biogeochemistry, molecular genetics, genomics, and microbial physiology. Here, we present a synthesis of these diverse studies and attempt to discern some overarching themes. Copyright © 2012

Volatile-mediated suppression of plant pathogens is related to soil properties and microbial community composition

NARCIS (Netherlands)

Van Agtmaal, M.; Straathof, A.L.; Termorshuizen, Aad J; Lievens, Bart; Hoffland, Ellis; De Boer, W.

2018-01-01

There is increasing evidence that the soil microbial community produces a suite of volatile organic compounds that suppress plant pathogens. However, it remains unknown which soil properties and management practices influence volatile-mediated pathogen suppression. The aim of this study was to

Volatile-mediated suppression of plant pathogens is related to soil properties and microbial community composition

NARCIS (Netherlands)

Agtmaal, van Maaike; Straathof, Angela L.; Termorshuizen, Aad; Lievens, Bart; Hoffland, Ellis; Boer, de Wietse

2018-01-01

There is increasing evidence that the soil microbial community produces a suite of volatile organic compounds that suppress plant pathogens. However, it remains unknown which soil properties and management practices influence volatile-mediated pathogen suppression. The aim of this study was to

Soil Biogeochemical and Microbial Feedbacks along a Snowmelt-Dominated Hillslope-to-Floodplain Transect in Colorado.

Science.gov (United States)

Sorensen, P.; Beller, H. R.; Bill, M.; Bouskill, N.; Brodie, E.; Chakraborty, R.; Conrad, M. E.; Karaoz, U.; Polussa, A.; Steltzer, H.; Wang, S.; Williams, K. H.; Wilmer, C.; Wu, Y.

2017-12-01

Nitrogen export from mountainous watersheds is a product of multiple interactions among hydrological processes and soil-microbial-plant feedbacks along the continuum from terrestrial to aquatic environments. In snow-dominated systems, like the East River Watershed (CO), seasonal processes such as snowmelt exert significant influence on the annual hydrologic cycle and may also link spatially distinct catchment subsystems, such as hillslope and adjoining riparian floodplains. Further, snowmelt is occurring earlier each year and this is predicted to result in a temporal asynchrony between historically coupled microbial nutrient release and plant nutrient demand in spring, with the potential to increase N export from the East River Watershed. Here we summarize biogeochemical data collected along a hillslope-to-riparian floodplain transect at the East River site. Starting in Fall 2016, we sampled soils at 3 depths and measured dissolved pools of soil nutrients (e.g., NH4+, NO3-, DOC, P), microbial biomass CN, and microbial community composition over a seasonal time course, through periods of snow accumulation, snowmelt, and plant senescence. Soil moisture content in the top 5 cm of floodplain soils was nearly 4X greater across sampling dates, coinciding with 2X greater microbial biomass C, larger extractable pools of NH4+, and smaller pools of NO3- in floodplain vs. hillslope soils. These results suggest that microbially mediated redox processes played an important role in N cycling along the transect. Hillslope vs. floodplain location also appeared to be a key factor that differentiated soil microbial communities (e.g., a more important factor than seasonality or soil depth or type). Snow accumulation and snowmelt exerted substantial influence on soil biogeochemistry. For example, microbial biomass accumulation increased about 2X beneath the winter snowpack. Snowmelt resulted in a precipitous crash in the microbial population, with 2.5X reductions in floodplain and 2X

Role of microbial inoculation and industrial by-product phosphogypsum in growth and nutrient uptake of maize (Zea mays L.) grown in calcareous soil.

Science.gov (United States)

Al-Enazy, Abdul-Aziz R; Al-Oud, Saud S; Al-Barakah, Fahad N; Usman, Adel Ra

2017-08-01

Alkaline soils with high calcium carbonate and low organic matter are deficient in plant nutrient availability. Use of organic and bio-fertilizers has been suggested to improve their properties. Therefore, a greenhouse experiment was conducted to evaluate the integrative role of phosphogypsum (PG; added at 0.0, 10, 30, and 50 g PG kg -1 ), cow manure (CM; added at 50 g kg -1 ) and mixed microbial inoculation (Incl.; Azotobacter chroococcum, and phosphate-solubilizing bacteria Bacillus megaterium var. phosphaticum and Pseudomonas fluorescens) on growth and nutrients (N, P, K, Fe, Mn, Zn and Cu) uptake of maize (Zea mays L.) in calcareous soil. Treatment effects on soil chemical and biological properties and the Cd and Pb availability to maize plants were also investigated. Applying PG decreased soil pH. The soil available P increased when soil was inoculated and/or treated with CM, especially with PG. The total microbial count and dehydrogenase activity were enhanced with PG+CM+Incl. Inoculated soils treated with PG showed significant increases in NPK uptake and maize plant growth. However, the most investigated treatments showed significant decreases in shoot micronutrients. Cd and Pb were not detected in maize shoots. Applying PG with microbial inoculation improved macronutrient uptake and plant growth. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Conservation tillage, optimal water and organic nutrient supply enhance soil microbial activities during wheat (Triticum Aestivum L.) cultivation

Science.gov (United States)

Sharma, Pankaj; Singh, Geeta; Singh, Rana P.

2011-01-01

The field experiments were conducted on sandy loam soil at New Delhi, during 2007 and 2008 to investigate the effect of conservation tillage, irrigation regimes (sub-optimal, optimal and supra-optimal water regimes), and integrated nutrient management (INM) practices on soil biological parameters in wheat cultivation. The conservation tillage soils has shown significant (pbiofertilizer+25% Green Manure) has been used in combination with the conservation tillage and the optimum water supply. Study demonstrated that microbial activity could be regulated by tillage, water and nitrogen management in the soil in a sustainable manner. PMID:24031665

Nutrient controls on biocomplexity of mangrove ecosystems

Science.gov (United States)

McKee, Karen L.

2004-01-01

Mangrove forests are important coastal ecosystems that provide a variety of ecological and societal services. These intertidal, tree-dominated communities along tropical coastlines are often described as “simple systems,” compared to other tropical forests with larger numbers of plant species and multiple understory strata; however, mangrove ecosystems have complex trophic structures, and organisms exhibit unique physiological, morphological, and behavioral adaptations to environmental conditions characteristic of the land-sea interface. Biogeochemical functioning of mangrove forests is also controlled by interactions among the microbial, plant, and animal communities and feedback linkages mediated by hydrology and other forcing functions. Scientists with the U.S. Geological Survey (USGS) at the National Wetlands Research Center are working to understand more fully the impact of nutrient variability on these delicate and important ecosystems.

Microbial activity in the marine deep biosphere: progress and prospects.

Science.gov (United States)

Orcutt, Beth N; Larowe, Douglas E; Biddle, Jennifer F; Colwell, Frederick S; Glazer, Brian T; Reese, Brandi Kiel; Kirkpatrick, John B; Lapham, Laura L; Mills, Heath J; Sylvan, Jason B; Wankel, Scott D; Wheat, C Geoff

2013-01-01

The vast marine deep biosphere consists of microbial habitats within sediment, pore waters, upper basaltic crust and the fluids that circulate throughout it. A wide range of temperature, pressure, pH, and electron donor and acceptor conditions exists-all of which can combine to affect carbon and nutrient cycling and result in gradients on spatial scales ranging from millimeters to kilometers. Diverse and mostly uncharacterized microorganisms live in these habitats, and potentially play a role in mediating global scale biogeochemical processes. Quantifying the rates at which microbial activity in the subsurface occurs is a challenging endeavor, yet developing an understanding of these rates is essential to determine the impact of subsurface life on Earth's global biogeochemical cycles, and for understanding how microorganisms in these "extreme" environments survive (or even thrive). Here, we synthesize recent advances and discoveries pertaining to microbial activity in the marine deep subsurface, and we highlight topics about which there is still little understanding and suggest potential paths forward to address them. This publication is the result of a workshop held in August 2012 by the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) "theme team" on microbial activity (www.darkenergybiosphere.org).

Sub-soil microbial activity under rotational cotton crops in Australia

Science.gov (United States)

Polain, Katherine; Knox, Oliver; Wilson, Brian; Pereg, Lily

2016-04-01

Soil microbial communities contribute significantly to soil organic matter formation, stabilisation and destabilisation, through nutrient cycling and biodegradation. The majority of soil microbial research examines the processes occurring in the top 0 cm to 30 cm of the soil, where organic nutrients are easily accessible. In soils such as Vertosols, the high clay content causes swelling and cracking. When soil cracking is coupled with rain or an irrigation event, a flush of organic nutrients can move down the soil profile, becoming available for subsoil microbial community use and potentially making a significant contribution to nutrient cycling and biodegradation in soils. At present, the mechanisms and rates of soil nutrient turnover (such as carbon and nitrogen) at depth under cotton rotations are mostly speculative and the process-response relationships remain unclear, although they are undoubtedly underpinned by microbial activity. Our research aims to determine the contribution and role of soil microbiota to the accumulation, cycling and mineralisation of carbon and nitrogen through the whole root profile under continuous cotton (Gossypium hirsutum) and cotton-maize rotations in regional New South Wales, Australia. Through seasonal work, we have established both baseline and potential microbial activity rates from 0 cm to 100 cm down the Vertosol profile, using respiration and colourimetric methods. Further whole soil profile analyses will include determination of microbial biomass and isotopic carbon signatures using phospholipid fatty acid (PLFA) methodology, identification of microbial communities (sequencing) and novel experiments to investigate potential rates of nitrogen mineralisation and quantification of associated genes. Our preliminary observations and the hypotheses tested in this three-year study will be presented.

Groundwater shapes sediment biogeochemistry and microbial diversity in a submerged Great Lake sinkhole.

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Kinsman-Costello, L E; Sheik, C S; Sheldon, N D; Allen Burton, G; Costello, D M; Marcus, D; Uyl, P A Den; Dick, G J

2017-03-01

For a large part of earth's history, cyanobacterial mats thrived in low-oxygen conditions, yet our understanding of their ecological functioning is limited. Extant cyanobacterial mats provide windows into the putative functioning of ancient ecosystems, and they continue to mediate biogeochemical transformations and nutrient transport across the sediment-water interface in modern ecosystems. The structure and function of benthic mats are shaped by biogeochemical processes in underlying sediments. A modern cyanobacterial mat system in a submerged sinkhole of Lake Huron (LH) provides a unique opportunity to explore such sediment-mat interactions. In the Middle Island Sinkhole (MIS), seeping groundwater establishes a low-oxygen, sulfidic environment in which a microbial mat dominated by Phormidium and Planktothrix that is capable of both anoxygenic and oxygenic photosynthesis, as well as chemosynthesis, thrives. We explored the coupled microbial community composition and biogeochemical functioning of organic-rich, sulfidic sediments underlying the surface mat. Microbial communities were diverse and vertically stratified to 12 cm sediment depth. In contrast to previous studies, which used low-throughput or shotgun metagenomic approaches, our high-throughput 16S rRNA gene sequencing approach revealed extensive diversity. This diversity was present within microbial groups, including putative sulfate-reducing taxa of Deltaproteobacteria, some of which exhibited differential abundance patterns in the mats and with depth in the underlying sediments. The biological and geochemical conditions in the MIS were distinctly different from those in typical LH sediments of comparable depth. We found evidence for active cycling of sulfur, methane, and nutrients leading to high concentrations of sulfide, ammonium, and phosphorus in sediments underlying cyanobacterial mats. Indicators of nutrient availability were significantly related to MIS microbial community composition, while LH

Predicting the profile of nutrients available for absorption: from nutrient requirement to animal response and environmental impact.

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Dijkstra, J; Kebreab, E; Mills, J A N; Pellikaan, W F; López, S; Bannink, A; France, J

2007-02-01

Current feed evaluation systems for dairy cattle aim to match nutrient requirements with nutrient intake at pre-defined production levels. These systems were not developed to address, and are not suitable to predict, the responses to dietary changes in terms of production level and product composition, excretion of nutrients to the environment, and nutrition related disorders. The change from a requirement to a response system to meet the needs of various stakeholders requires prediction of the profile of absorbed nutrients and its subsequent utilisation for various purposes. This contribution examines the challenges to predicting the profile of nutrients available for absorption in dairy cattle and provides guidelines for further improved prediction with regard to animal production responses and environmental pollution.The profile of nutrients available for absorption comprises volatile fatty acids, long-chain fatty acids, amino acids and glucose. Thus the importance of processes in the reticulo-rumen is obvious. Much research into rumen fermentation is aimed at determination of substrate degradation rates. Quantitative knowledge on rates of passage of nutrients out of the rumen is rather limited compared with that on degradation rates, and thus should be an important theme in future research. Current systems largely ignore microbial metabolic variation, and extant mechanistic models of rumen fermentation give only limited attention to explicit representation of microbial metabolic activity. Recent molecular techniques indicate that knowledge on the presence and activity of various microbial species is far from complete. Such techniques may give a wealth of information, but to include such findings in systems predicting the nutrient profile requires close collaboration between molecular scientists and mathematical modellers on interpreting and evaluating quantitative data. Protozoal metabolism is of particular interest here given the paucity of quantitative data

Biological wastewater treatment. II Nutrient elimination; Tratamiento biologico de aguas residuales. II Eliminacion de nutrientes

Energy Technology Data Exchange (ETDEWEB)

Arnaiz, C.; Isac, L.; Lebrato, J. [Universidad de Sevilla (Spain)

2000-07-01

Most biological wastewater processes are designed for carbonaceous compounds removal. In some cases, nutrient removal is required. In this work, biodiversity and microbial interactions of nitrogen and phosphorus removal are described. (Author) 12 refs.

Biochar Based Microbial Fuel Cell for Enhanced Wastewater Treatment and Nutrient Recovery

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Tyler M. Huggins

2016-02-01

Full Text Available Waste-wood derived biochar was evaluated for the first time as both an anode and cathode material, simultaneously, in an overflow style microbial fuel cell (MFC using actual industrial wastewater. Results show that the average chemical oxygen demand (COD removal was 95% with a reduction rate of 0.53 kg·COD·m−1·d−1 in closed operation mode. The ammonia and phosphorous reductions from wastewater was 73% and 88%, respectively. Stable power production was observed with a peak power density measured at 6 W/m3. Preliminary contributions of physical, biological, and electrochemical COD removals were evaluated, and the results show such combined mechanisms give BC an advantage for MFC applications. Nutrient recovery data showed high levels of macronutrients adsorbed onto the spent biochar electrodes, and phosphorus concentration increased from 0.16 g·kg−1 in raw BC to up to 1.9 g·kg−1 in the cathode. These findings highlight the use of biochar as electrodes in MFCs to facilitate simultaneous wastewater treatment and power production with additional agronomic benefits.

The Microbial Database for Danish wastewater treatment plants with nutrient removal (MiDas-DK) – a tool for understanding activated sludge population dynamics and community stability

DEFF Research Database (Denmark)

Mielczarek, Artur Tomasz; Saunders, Aaron Marc; Larsen, Poul

2013-01-01

Since 2006 more than 50 Danish full-scale wastewater treatment plants with nutrient removal have been investigated in a project called ‘The Microbial Database for Danish Activated Sludge Wastewater Treatment Plants with Nutrient Removal (MiDas-DK)’. Comprehensive sets of samples have been collected......, analyzed and associated with extensive operational data from the plants. The community composition was analyzed by quantitative fluorescence in situ hybridization (FISH) supported by 16S rRNA amplicon sequencing and deep metagenomics. MiDas-DK has been a powerful tool to study the complex activated sludge...

Microbial community responses to soil tillage and crop rotation in a corn/soybean agroecosystem.

Science.gov (United States)

Smith, Chris R; Blair, Peter L; Boyd, Charlie; Cody, Brianne; Hazel, Alexander; Hedrick, Ashley; Kathuria, Hitesh; Khurana, Parul; Kramer, Brent; Muterspaw, Kristin; Peck, Charles; Sells, Emily; Skinner, Jessica; Tegeler, Cara; Wolfe, Zoe

2016-11-01

The acreage planted in corn and soybean crops is vast, and these crops contribute substantially to the world economy. The agricultural practices employed for farming these crops have major effects on ecosystem health at a worldwide scale. The microbial communities living in agricultural soils significantly contribute to nutrient uptake and cycling and can have both positive and negative impacts on the crops growing with them. In this study, we examined the impact of the crop planted and soil tillage on nutrient levels, microbial communities, and the biochemical pathways present in the soil. We found that farming practice, that is conventional tillage versus no-till, had a much greater impact on nearly everything measured compared to the crop planted. No-till fields tended to have higher nutrient levels and distinct microbial communities. Moreover, no-till fields had more DNA sequences associated with key nitrogen cycle processes, suggesting that the microbial communities were more active in cycling nitrogen. Our results indicate that tilling of agricultural soil may magnify the degree of nutrient waste and runoff by altering nutrient cycles through changes to microbial communities. Currently, a minority of acreage is maintained without tillage despite clear benefits to soil nutrient levels, and a decrease in nutrient runoff-both of which have ecosystem-level effects and both direct and indirect effects on humans and other organisms.

Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir.

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Freedman, Adam J E; Tan, BoonFei; Thompson, Janelle R

2017-06-01

Microorganisms catalyze carbon cycling and biogeochemical reactions in the deep subsurface and thus may be expected to influence the fate of injected supercritical (sc) CO 2 following geological carbon sequestration (GCS). We hypothesized that natural subsurface scCO 2 reservoirs, which serve as analogs for the long-term fate of sequestered scCO 2 , harbor a 'deep carbonated biosphere' with carbon cycling potential. We sampled subsurface fluids from scCO 2 -water separators at a natural scCO 2 reservoir at McElmo Dome, Colorado for analysis of 16S rRNA gene diversity and metagenome content. Sequence annotations indicated dominance of Sulfurospirillum, Rhizobium, Desulfovibrio and four members of the Clostridiales family. Genomes extracted from metagenomes using homology and compositional approaches revealed diverse mechanisms for growth and nutrient cycling, including pathways for CO 2 and N 2 fixation, anaerobic respiration, sulfur oxidation, fermentation and potential for metabolic syntrophy. Differences in biogeochemical potential between two production well communities were consistent with differences in fluid chemical profiles, suggesting a potential link between microbial activity and geochemistry. The existence of a microbial ecosystem associated with the McElmo Dome scCO 2 reservoir indicates that potential impacts of the deep biosphere on CO 2 fate and transport should be taken into consideration as a component of GCS planning and modelling. © 2017 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Controlling Salmonella infection in weanling pigs through water delivery of direct-fed microbials or organic acids: Part II. Effects on intestinal histology and active nutrient transport

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The objective of this study was to evaluate the effects of water-delivered direct-fed microbials (DFM) or organic acids on intestinal morphology and active nutrient absorption in weanling pigs following deliberate Salmonella infection. Pigs (n = 88) were weaned at 19 ± 2 d of age and assigned to one...

Mechanistic Understanding of Microbial Plugging for Improved Sweep Efficiency

Energy Technology Data Exchange (ETDEWEB)

Steven Bryant; Larry Britton

2008-09-30

Microbial plugging has been proposed as an effective low cost method of permeability reduction. Yet there is a dearth of information on the fundamental processes of microbial growth in porous media, and there are no suitable data to model the process of microbial plugging as it relates to sweep efficiency. To optimize the field implementation, better mechanistic and volumetric understanding of biofilm growth within a porous medium is needed. In particular, the engineering design hinges upon a quantitative relationship between amount of nutrient consumption, amount of growth, and degree of permeability reduction. In this project experiments were conducted to obtain new data to elucidate this relationship. Experiments in heterogeneous (layered) beadpacks showed that microbes could grow preferentially in the high permeability layer. Ultimately this caused flow to be equally divided between high and low permeability layers, precisely the behavior needed for MEOR. Remarkably, classical models of microbial nutrient uptake in batch experiments do not explain the nutrient consumption by the same microbes in flow experiments. We propose a simple extension of classical kinetics to account for the self-limiting consumption of nutrient observed in our experiments, and we outline a modeling approach based on architecture and behavior of biofilms. Such a model would account for the changing trend of nutrient consumption by bacteria with the increasing biomass and the onset of biofilm formation. However no existing model can explain the microbial preference for growth in high permeability regions, nor is there any obvious extension of the model for this observation. An attractive conjecture is that quorum sensing is involved in the heterogeneous bead packs.

Microbial activity in the marine deep biosphere: Progress and prospects

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Beth N Orcutt

2013-07-01

Full Text Available The vast marine deep biosphere consists of microbial habitats within sediment, pore waters, upper basaltic crust and the fluids that circulate throughout it. A wide range of temperature, pressure, pH, and electron donor and acceptor conditions exists – all of which can combine to affect carbon and nutrient cycling and result in gradients on spatial scales ranging from millimeters to kilometers. Diverse and mostly uncharacterized microorganisms live in these habitats, and potentially play a role in mediating global scale biogeochemical processes. Quantifying the rates at which microbial activity in the subsurface occurs is a challenging endeavor, yet developing an understanding of these rates is essential to determine the impact of subsurface life on Earth's global biogeochemical cycles, and for understanding how microorganisms in these "extreme" environments survive (or even thrive. Here, we synthesize recent advances and discoveries pertaining to microbial activity in the marine deep subsurface, and we highlight topics about which there is still little understanding and suggest potential paths forward to address them. This publication is the result of a workshop held in August 2012 by the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI "theme team" on microbial activity (www.darkenergybiosphere.org.

Microbial activity in the marine deep biosphere: progress and prospects

Science.gov (United States)

Orcutt, Beth N.; LaRowe, Douglas E.; Biddle, Jennifer F.; Colwell, Frederick S.; Glazer, Brian T.; Reese, Brandi Kiel; Kirkpatrick, John B.; Lapham, Laura L.; Mills, Heath J.; Sylvan, Jason B.; Wankel, Scott D.; Wheat, C. Geoff

2013-01-01

The vast marine deep biosphere consists of microbial habitats within sediment, pore waters, upper basaltic crust and the fluids that circulate throughout it. A wide range of temperature, pressure, pH, and electron donor and acceptor conditions exists—all of which can combine to affect carbon and nutrient cycling and result in gradients on spatial scales ranging from millimeters to kilometers. Diverse and mostly uncharacterized microorganisms live in these habitats, and potentially play a role in mediating global scale biogeochemical processes. Quantifying the rates at which microbial activity in the subsurface occurs is a challenging endeavor, yet developing an understanding of these rates is essential to determine the impact of subsurface life on Earth's global biogeochemical cycles, and for understanding how microorganisms in these “extreme” environments survive (or even thrive). Here, we synthesize recent advances and discoveries pertaining to microbial activity in the marine deep subsurface, and we highlight topics about which there is still little understanding and suggest potential paths forward to address them. This publication is the result of a workshop held in August 2012 by the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) “theme team” on microbial activity (www.darkenergybiosphere.org). PMID:23874326

Fungi benefit from two decades of increased nutrient availability in tundra heath soil.

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Rinnan, Riikka; Michelsen, Anders; Bååth, Erland

2013-01-01

If microbial degradation of carbon substrates in arctic soil is stimulated by climatic warming, this would be a significant positive feedback on global change. With data from a climate change experiment in Northern Sweden we show that warming and enhanced soil nutrient availability, which is a predicted long-term consequence of climatic warming and mimicked by fertilization, both increase soil microbial biomass. However, while fertilization increased the relative abundance of fungi, warming caused only a minimal shift in the microbial community composition based on the phospholipid fatty acid (PLFA) and neutral lipid fatty acid (NLFA) profiles. The function of the microbial community was also differently affected, as indicated by stable isotope probing of PLFA and NLFA. We demonstrate that two decades of fertilization have favored fungi relative to bacteria, and increased the turnover of complex organic compounds such as vanillin, while warming has had no such effects. Furthermore, the NLFA-to-PLFA ratio for (13)C-incorporation from acetate increased in warmed plots but not in fertilized ones. Thus, fertilization cannot be used as a proxy for effects on warming in arctic tundra soils. Furthermore, the different functional responses suggest that the biomass increase found in both fertilized and warmed plots was mediated via different mechanisms.

Organic nitrogen rearranges both structure and activity of the soil-borne microbial seedbank.

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Leite, Márcio F A; Pan, Yao; Bloem, Jaap; Berge, Hein Ten; Kuramae, Eiko E

2017-02-15

Use of organic amendments is a valuable strategy for crop production. However, it remains unclear how organic amendments shape both soil microbial community structure and activity, and how these changes impact nutrient mineralization rates. We evaluated the effect of various organic amendments, which range in Carbon/Nitrogen (C/N) ratio and degradability, on the soil microbiome in a mesocosm study at 32, 69 and 132 days. Soil samples were collected to determine community structure (assessed by 16S and 18S rRNA gene sequences), microbial biomass (fungi and bacteria), microbial activity (leucine incorporation and active hyphal length), and carbon and nitrogen mineralization rates. We considered the microbial soil DNA as the microbial seedbank. High C/N ratio favored fungal presence, while low C/N favored dominance of bacterial populations. Our results suggest that organic amendments shape the soil microbial community structure through a feedback mechanism by which microbial activity responds to changing organic inputs and rearranges composition of the microbial seedbank. We hypothesize that the microbial seedbank composition responds to changing organic inputs according to the resistance and resilience of individual species, while changes in microbial activity may result in increases or decreases in availability of various soil nutrients that affect plant nutrient uptake.

Modulation of neonatal microbial recognition: TLR-mediated innate immune responses are specifically and differentially modulated by human milk.

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LeBouder, Emmanuel; Rey-Nores, Julia E; Raby, Anne-Catherine; Affolter, Michael; Vidal, Karine; Thornton, Catherine A; Labéta, Mario O

2006-03-15

The mechanisms controlling innate microbial recognition in the neonatal gut are still to be fully understood. We have sought specific regulatory mechanisms operating in human breast milk relating to TLR-mediated microbial recognition. In this study, we report a specific and differential modulatory effect of early samples (days 1-5) of breast milk on ligand-induced cell stimulation via TLRs. Although a negative modulation was exerted on TLR2 and TLR3-mediated responses, those via TLR4 and TLR5 were enhanced. This effect was observed in human adult and fetal intestinal epithelial cell lines, monocytes, dendritic cells, and PBMC as well as neonatal blood. In the latter case, milk compensated for the low capacity of neonatal plasma to support responses to LPS. Cell stimulation via the IL-1R or TNFR was not modulated by milk. This, together with the differential effect on TLR activation, suggested that the primary effect of milk is exerted upstream of signaling proximal to TLR ligand recognition. The analysis of TLR4-mediated gene expression, used as a model system, showed that milk modulated TLR-related genes differently, including those coding for signal intermediates and regulators. A proteinaceous milk component of > or =80 kDa was found to be responsible for the effect on TLR4. Notably, infant milk formulations did not reproduce the modulatory activity of breast milk. Together, these findings reveal an unrecognized function of human milk, namely, its capacity to influence neonatal microbial recognition by modulating TLR-mediated responses specifically and differentially. This in turn suggests the existence of novel mechanisms regulating TLR activation.

AMP-activated protein kinase (AMPK mediates nutrient regulation of thioredoxin-interacting protein (TXNIP in pancreatic beta-cells.

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Maayan Shaked

Full Text Available Thioredoxin-interacting protein (TXNIP regulates critical biological processes including inflammation, stress and apoptosis. TXNIP is upregulated by glucose and is a critical mediator of hyperglycemia-induced beta-cell apoptosis in diabetes. In contrast, the saturated long-chain fatty acid palmitate, although toxic to the beta-cell, inhibits TXNIP expression. The mechanisms involved in the opposing effects of glucose and fatty acids on TXNIP expression are unknown. We found that both palmitate and oleate inhibited TXNIP in a rat beta-cell line and islets. Palmitate inhibition of TXNIP was independent of fatty acid beta-oxidation or esterification. AMP-activated protein kinase (AMPK has an important role in cellular energy sensing and control of metabolic homeostasis; therefore we investigated its involvement in nutrient regulation of TXNIP. As expected, glucose inhibited whereas palmitate stimulated AMPK. Pharmacologic activators of AMPK mimicked fatty acids by inhibiting TXNIP. AMPK knockdown increased TXNIP expression in presence of high glucose with and without palmitate, indicating that nutrient (glucose and fatty acids effects on TXNIP are mediated in part via modulation of AMPK activity. TXNIP is transcriptionally regulated by carbohydrate response element-binding protein (ChREBP. Palmitate inhibited glucose-stimulated ChREBP nuclear entry and recruitment to the Txnip promoter, thereby inhibiting Txnip transcription. We conclude that AMPK is an important regulator of Txnip transcription via modulation of ChREBP activity. The divergent effects of glucose and fatty acids on TXNIP expression result in part from their opposing effects on AMPK activity. In light of the important role of TXNIP in beta-cell apoptosis, its inhibition by fatty acids can be regarded as an adaptive/protective response to glucolipotoxicity. The finding that AMPK mediates nutrient regulation of TXNIP may have important implications for the pathophysiology and treatment

Reduced Nutrient Excretion and Environmental Microbial Load with the Addition of a Combination of Enzymes and Direct-Fed Microbials to the Diet of Broiler Chickens

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MFFM Praes

2016-03-01

Full Text Available Abstract This study evaluated the effects of the dietary inclusion of an enzyme blend and a direct-fed microbials in broiler diets on litter production and quality. In total, 900 Cobb 500(r broiler chicks were distributed according to a completely randomized design into 4 treatments and 9 replicates of 25 birds each. Broilers were reared from 1 to 42 days of age. The treatments consisted of the following diets: NC: negative control; DFM: NC + 500 ppm of direct-fed microbials product (DFM, containing Bacillus subtilis and Bacillus licheniformis; ENZ: diet formulated with an enzyme blend (20 ppm phytase, 200 ppm protease and 200 ppm of xylanase; DFM+E: ENZ + DFM. Birds and litter were weighed at the start and end of the rearing period, for litter production and waste ratio (Rw determination. Litter samples were analyzed for dry matter (DM content, total and thermotolerant coliform counts, nutrient composition (nitrogen (N, phosphorous (P and potassium (K, and fiber fraction (neutral detergent fiber (NDF, acid detergent fiber (ADF and lignin. The dietary inclusion of the evaluated additivesdid not influence litter production or Rw; however, ADF (%, NDF (kg and kg/kg DM litter, and total and thermotolerant coliform counts were reduced, and N content increased in the litter. The diets containing enzymes (ENZ and DFM+E reduced litter P content. The addition of exogenous enzymes and their combination with a DFM based on Bacillus spp .Did not affect waste production, and reduced litter microbial load, and the contents of P and insoluble fiber in the litter.

Wastewater treatment plant effluent introduces recoverable shifts in microbial community composition in urban streams

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Ledford, S. H.; Price, J. R.; Ryan, M. O.; Toran, L.; Sales, C. M.

2017-12-01

New technologies are allowing for intense scrutiny of the impact of land use on microbial communities in stream networks. We used a combination of analytical chemistry, real-time polymerase chain reaction (qPCR) and targeted amplicon sequencing for a preliminary study on the impact of wastewater treatment plant effluent discharge on urban streams. Samples were collected on two dates above and below treatment plants on the Wissahickon Creek, and its tributary, Sandy Run, in Montgomery County, PA, USA. As expected, effluent was observed to be a significant source of nutrients and human and non-specific fecal associated taxa. There was an observed increase in the alpha diversity at locations immediately below effluent outflows, which contributed many taxa involved in wastewater treatment processes and nutrient cycling to the stream's microbial community. Unexpectedly, modeling of microbial community shifts along the stream was not controlled by concentrations of measured nutrients. Furthermore, partial recovery, in the form of decreasing abundances of bacteria and nutrients associated with wastewater treatment plant processes, nutrient cycling bacteria, and taxa associated with fecal and sewage sources, was observed between effluent sources. Antecedent moisture conditions impacted overall microbial community diversity, with higher diversity occurring after rainfall. These findings hint at resilience in stream microbial communities to recover from wastewater treatment plant effluent and are vital to understanding the impacts of urbanization on microbial stream communities.

The role microbial sulfate reduction in the direct mediation of sedimentary authigenic carbonate precipitation

Science.gov (United States)

Turchyn, A. V.; Walker, K.; Sun, X.

2016-12-01

The majority of modern deep marine sediments are bathed in water that is undersaturated with respect to calcium carbonate. However, within marine sediments changing chemical conditions, driven largely by the microbial oxidation of organic carbon in the absence of oxygen, lead to supersaturated conditions and drive calcium carbonate precipitation. This sedimentary calcium carbonate is often called `authigenic carbonate', and is found in the form of cements and disseminated crystals within the marine sedimentary pile. As this precipitation of this calcium carbonate is microbially mediated, identifying authigenic carbonate within the geological record and understanding what information its geochemical and/or isotopic signature may hold is key for understanding its importance and what information it may contain past life. However, the modern controls on authigenic carbonate precipitation remain enigmatic because the myriad of microbially mediated reactions occurring within sediments both directly and indirectly impact the proton balance. In this submission we present data from 25 ocean sediment cores spanning the globe where we explore the deviation from the stoichiometrically predicted relationships among alkalinity, calcium and sulfate concentrations. In theory for every mol of organic carbon reduced by sulfate, two mol of alkalinity is produced, and to precipitate subsurface calcium carbonate one mol of calcium is used to consume two mol of alkalinity. We use this data with a model to explore changes in carbonate saturation state with depth below the seafloor. Alkalinity changes in the subsurface are poorly correlated with changes in calcium concentrations, however calcium concentrations are directly and tightly coupled to changes in sulfate concentrations in all studied sites. This suggests a direct role for sulfate reducing bacteria in the precipitation of subsurface carbonate cements.

Far-UVC light: A new tool to control the spread of airborne-mediated microbial diseases.

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Welch, David; Buonanno, Manuela; Grilj, Veljko; Shuryak, Igor; Crickmore, Connor; Bigelow, Alan W; Randers-Pehrson, Gerhard; Johnson, Gary W; Brenner, David J

2018-02-09

Airborne-mediated microbial diseases such as influenza and tuberculosis represent major public health challenges. A direct approach to prevent airborne transmission is inactivation of airborne pathogens, and the airborne antimicrobial potential of UVC ultraviolet light has long been established; however, its widespread use in public settings is limited because conventional UVC light sources are both carcinogenic and cataractogenic. By contrast, we have previously shown that far-UVC light (207-222 nm) efficiently inactivates bacteria without harm to exposed mammalian skin. This is because, due to its strong absorbance in biological materials, far-UVC light cannot penetrate even the outer (non living) layers of human skin or eye; however, because bacteria and viruses are of micrometer or smaller dimensions, far-UVC can penetrate and inactivate them. We show for the first time that far-UVC efficiently inactivates airborne aerosolized viruses, with a very low dose of 2 mJ/cm 2 of 222-nm light inactivating >95% of aerosolized H1N1 influenza virus. Continuous very low dose-rate far-UVC light in indoor public locations is a promising, safe and inexpensive tool to reduce the spread of airborne-mediated microbial diseases.

Developing and using artificial soils to analyze soil microbial processes

Science.gov (United States)

Gao, X.; Cheng, H. Y.; Boynton, L.; Masiello, C. A.; Silberg, J. J.

2017-12-01

Microbial diversity and function in soils are governed by soil characteristics such as mineral composition, particles size and aggregations, soil organic matter (SOM), and availability of nutrients and H2O. The spatial and temporal heterogeneity of soils creates a range of niches (hotspots) differing in the availability of O2, H2O, and nutrients, which shapes microbial activities at scales ranging from nanometer to landscape. Synthetic biologists often examine microbial response trigged by their environment conditions in nutrient-rich aqueous media using single strain microbes. While these studies provided useful insight in the role of soil microbes in important soil biogeochemical processes (e.g., C cycling, N cycling, etc.), the results obtained from the over-simplified model systems are often not applicable natural soil systems. On the contrary, soil microbiologists examine microbial processes in natural soils using longer incubation time. However, due to its physical, chemical and biological complexity of natural soils, it is often difficult to examine soil characteristics independently and understand how each characteristic influences soil microbial activities and their corresponding soil functioning. Therefore, it is necessary to bridge the gap and develop a model matrix to exclude unpredictable influences from the environment while still reliably mimicking real environmental conditions. The objective of this study is to design a range of ecologically-relevant artificial soils with varying texture (particle size distribution), structure, mineralogy, SOM content, and nutrient heterogeneity. We thoroughly characterize the artificial soils for pH, active surface area and surface morphology, cation exchange capacity (CEC), and water retention curve. We demonstrate the effectiveness of the artificial soils as useful matrix for microbial processes, such as microbial growth and horizontal gene transfer (HGT), using the gas-reporting biosensors recently developed in

Microbial brokers of insect-plant interactions revisited.

Science.gov (United States)

Douglas, Angela E

2013-07-01

Recent advances in sequencing methods have transformed the field of microbial ecology, making it possible to determine the composition and functional capabilities of uncultured microorganisms. These technologies have been instrumental in the recognition that resident microorganisms can have profound effects on the phenotype and fitness of their animal hosts by modulating the animal signaling networks that regulate growth, development, behavior, etc. Against this backdrop, this review assesses the impact of microorganisms on insect-plant interactions, in the context of the hypothesis that microorganisms are biochemical brokers of plant utilization by insects. There is now overwhelming evidence for a microbial role in insect utilization of certain plant diets with an extremely low or unbalanced nutrient content. Specifically, microorganisms enable insect utilization of plant sap by synthesizing essential amino acids. They also can broker insect utilization of plant products of extremely high lignocellulose content, by enzymatic breakdown of complex plant polysaccharides, nitrogen fixation, and sterol synthesis. However, the experimental evidence for microbial-mediated detoxification of plant allelochemicals is limited. The significance of microorganisms as brokers of plant utilization by insects is predicted to vary, possibly widely, as a result of potentially complex interactions between the composition of the microbiota and the diet and insect developmental age or genotype. For every insect species feeding on plant material, the role of resident microbiota as biochemical brokers of plant utilization is a testable hypothesis.

The impact of dissolved inorganic nitrogen and phosphorous on responses of microbial plankton to the Texas City "Y" oil spill in Galveston Bay, Texas (USA).

Science.gov (United States)

Williams, Alicia K; Bacosa, Hernando P; Quigg, Antonietta

2017-08-15

Ongoing bioremediation research seeks to promote naturally occurring microbial polycyclic aromatic hydrocarbon (PAH) degradation during and after oil spill events. However, complex relationships among functionally different microbial groups, nutrients and PAHs remain unconstrained. We conducted a surface water survey and corresponding nutrient amendment bioassays following the Texas City "Y" oil spill in Galveston Bay, Texas. Resident microbial groups, defined as either heterotrophic or autotrophic were enumerated by flow cytometry. Heterotrophic abundance was increased by oil regardless of nutrient concentrations. Contrastingly, autotrophic abundance was inhibited by oil, but this reaction was less severe when nutrient concentrations were higher. Several PAH compounds were reduced in nutrient amended treatments relative to controls suggesting nutrient enhanced microbial PAH processing. These findings provide a first-look at nutrient limitation during microbial oil processing in Galveston Bay, an important step in understanding if nutrient additions would be a useful bioremediation strategy in this and other estuarine systems. Copyright © 2017. Published by Elsevier Ltd.

Dredging effects on selected nutrient concentrations and ecoenzymatic activity in two drainage ditch sediments in the lower Mississippi River Valley

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Matt Moore

2017-09-01

Full Text Available Agricultural drainage ditches are conduits between production acreage and receiving aquatic systems. Often overlooked for their mitigation capabilities, agricultural drainage ditches provide an important role for nutrient transformation via microbial metabolism. Variations in ecoenzyme activities have been used to elucidate microbial metabolism and resource demand of microbial communities to better understand the relationship between altered nutrient ratios and microbial activity in aquatic ecosystems. Two agricultural drainage ditches, one in the northeast portion of the Arkansas Delta and the other in the lower Mississippi Delta, were monitored for a year. Sediment samples were collected prior to each ditch being dredged (cleaned, and subsequent post-dredging samples occurred as soon as access was available. Seasonal samples were then collected throughout a year to examine effects of dredging on selected nutrient concentrations and ecoenzymatic activity recovery in drainage ditch sediments. Phosphorus concentrations in sediments after dredging decreased 33–66%, depending on ditch and phosphorus extraction methodology. Additionally, ecoenzymatic activity was significantly decreased in most sediment samples after dredging. Fluorescein diacetate hydrolysis activity, an estimate of total microbial activity, decreased 56–67% after dredging in one of the two ditches. Many sample sites also had significant phosphorus and ecoenzymatic activity differences between the post-dredge samples and the year-long follow-up samples. Results indicate microbial metabolism in dredged drainage ditches may take up to a year or more to recover to pre-dredged levels. Likewise, while sediment nutrient concentrations may be decreased through dredging and removal, runoff and erosion events over time tend to quickly replenish nutrient concentrations in replaced sediments. Understanding nutrient dynamics and microbial metabolism within agricultural drainage ditches is

The role of microbial communities in phosphorus cycling during litter decomposition in a tropical forest

Science.gov (United States)

Lloret Sevilla, E.; Brodie, E.; Bouskill, N.; Hao, Z.

2016-12-01

Phosphorus is an essential nutrient with a reduced availability in tropical forests. In these ecosystems, P is recycled highly efficiently through resorption and mineralization and P immobilization in the microbial biomass prevents its loss through occlusion in the soil mineral fraction. To improve models of ecosystem response to global change, further studies of the above and belowground plant and microbial traits related to P availability and uptake, are required. In tropical forests, high temperature and rainfall lead to some of the highest rates of litter decomposition on earth. Litter decomposition is a complex process mediated by a range of trophic groups: meso and microfauna initiate litter turnover through litter fragmentation facilitating colonization by fungi, and bacteria mediate the mineralization of organic matter and release of nutrients. To determine the important functional traits of these players in the efficient cycling of P in soils with low P availability, we are performing a leaf litter decomposition experiment in a humid tropical forest in Puerto Rico. Nylon litterbags with three mesh sizes (2mm, 20 μm and 0.45 μm) containing litter with different chemistry (tabonuco and palm) will be deployed on soil surface and sampled 6 times throughout 12 months. The use of different mesh sizes will allow us to identify the leading roles in litter turnover by physical allowance and/or exclusion of the decomposers. The 2 mm bags allow meso and microfauna, roots, fungi and bacteria. 20 μm bags will exclude fauna and roots and 0.45 μm only allow some bacteria. We hypothesize that fungi will dominate over bacteria in earlier stages of the decomposition with a higher production of extracellular hydrolytic enzymes. On the other hand, bacterial biomass is expected to increase with time. Qualitative changes in both fungal and bacterial communities along the decomposition process are also expected leading to changes in enzyme activity. We also postulate an

Soil plus root respiration and microbial biomass following water, nitrogen, and phosphorus application at a high arctic semi desert

DEFF Research Database (Denmark)

Illeris, Lotte; Michelsen, Anders; Jonasson, Sven Evert

2003-01-01

CO2 emmision, Decomposition, Microbial biomass carbon, Soil organic matter, Tundra, Water and nutrient limitation......CO2 emmision, Decomposition, Microbial biomass carbon, Soil organic matter, Tundra, Water and nutrient limitation...

The Role of Soil Organic Matter, Nutrients, and Microbial Community Structure on the Performance of Microbial Fuel Cells

Science.gov (United States)

Rooney-Varga, J. N.; Dunaj, S. J.; Vallino, J. J.; Hines, M. E.; Gay, M.; Kobyljanec, C.

2011-12-01

Microbial fuel cells (MFCs) offer the potential for generating electricity, mitigating greenhouse gas emissions, and bioremediating pollutants through utilization of a plentiful, natural, and renewable resource: soil organic carbon. In the current study, we analyzed microbial community structure, MFC performance, and soil characteristics in different microhabitats (bulk soil, anode, and cathode) within MFCs constructed from agricultural or forest soils in order to determine how soil type and microbial dynamics influence MFC performance. MFCs were constructed with soils from agricultural and hardwood forest sites at Harvard Forest (Petersham, MA). The bulk soil characteristics were analyzed, including polyphenols, short chain fatty acids, total organic C and N, abiotic macronutrients, N and P mineralization rates, CO2 respiration rates, and MFC power output. Microbial community structure of the anodes, cathodes, and bulk soils was determined with molecular fingerprinting methods, which included terminal restriction length polymorphism (T-RFLP) analysis and 16S rRNA gene sequencing analysis. Our results indicated that MFCs constructed from agricultural soil had power output about 17 times that of forest soil-based MFCs and respiration rates about 10 times higher than forest soil MFCs. Agricultural soil MFCs had lower C:N ratios, polyphenol content, and acetate concentrations than forest soil MFCs, suggesting that active agricultural MFC microbial communities were supported by higher quality organic carbon. Microbial community profile data indicate that the microbial communities at the anode of the high power MFCs were less diverse than in low power MFCs and were dominated by Deltaproteobacteria, Geobacter, and, to a lesser extent, Clostridia, while low-power MFC anode communities were dominated by Clostridia. These data suggest that the presence of organic carbon substrate (acetate) was not the major limiting factor in selecting for highly electrogenic microbial

Influence of Silver nanoparticles on nutrient removal and microbial communities in SBR process after long-term exposure

Energy Technology Data Exchange (ETDEWEB)

Zhang, Zhaohan [State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, No73, Huanghe Road, Nangang District, Harbin 150090 (China); Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, No 43, Songfa Street, Daoli District, Harbin 150001 (China); Gao, Peng, E-mail: hitzzh@hit.edu.cn [State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, No73, Huanghe Road, Nangang District, Harbin 150090 (China); Li, Moqing; Cheng, Jiaqi [State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, No73, Huanghe Road, Nangang District, Harbin 150090 (China); Liu, Wei [Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, No 43, Songfa Street, Daoli District, Harbin 150001 (China); Feng, Yujie, E-mail: yujief@hit.edu.cn [State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, No73, Huanghe Road, Nangang District, Harbin 150090 (China)

2016-11-01

The widespread utilization of silver nanoparticles (AgNPs) in industrial and commercial products inevitably raises the release into wastewater that might cause potential negative impacts on sewage treatment system. In this paper, long-term exposure experiments at four levels were conducted to determine whether AgNPs caused adverse impacts on nutrient removals in sequencing batch reactors (SBRs) and changes of microbial community structure. Compared with the control reactor (without AgNPs), carbon, nitrogen and phosphorus removal in presence of 0.1 mg/L AgNPs was no difference. However, presence of 1.0 and 10 mg/L AgNPs decreased the average removal efficiencies of COD from 95.4% to 85.2% and 68.3%, ammonia nitrogen from 98.8% to 71.2% and 49%, SOP from 97.6% to 75.5% and 54.1%, respectively. It was found that AgNPs could accumulate in sludge with the distribution coefficients of 39.2–114 L/g, inhibit the protein and polysaccharide production in EPS, reduce the SOUR of sludge, and greatly increase LDH release from microbial cells. The illumina high-throughput sequencing results indicated that AgNPs concentration changed the structures of bacterial communities, associating with the effects of AgNPs on reactor performance. Sequence analyses showed that Proteobacteria, Bacteroidetes and Acidobacteria were the dominant phyla. It was notable that AgNPs addition reduced the contents of several nitrifying bacteria at genera level in sludge, leading to the lower removal of nitrogen. - Highlights: • More than 1.0 mg/L AgNPs evidently reduce COD, NH{sub 4}{sup +}-N and SOP removal in SBR process. • AgNPs decrease the protein and polysaccharide contents of EPS. • AgNPs increase LDH release for 1.46–2.41 times. • AgNPs are apt to accumulate on surface and even into microbial cells. • AgNPs levels affect microbial community structure and composition.

Influence of Silver nanoparticles on nutrient removal and microbial communities in SBR process after long-term exposure

International Nuclear Information System (INIS)

Zhang, Zhaohan; Gao, Peng; Li, Moqing; Cheng, Jiaqi; Liu, Wei; Feng, Yujie

2016-01-01

The widespread utilization of silver nanoparticles (AgNPs) in industrial and commercial products inevitably raises the release into wastewater that might cause potential negative impacts on sewage treatment system. In this paper, long-term exposure experiments at four levels were conducted to determine whether AgNPs caused adverse impacts on nutrient removals in sequencing batch reactors (SBRs) and changes of microbial community structure. Compared with the control reactor (without AgNPs), carbon, nitrogen and phosphorus removal in presence of 0.1 mg/L AgNPs was no difference. However, presence of 1.0 and 10 mg/L AgNPs decreased the average removal efficiencies of COD from 95.4% to 85.2% and 68.3%, ammonia nitrogen from 98.8% to 71.2% and 49%, SOP from 97.6% to 75.5% and 54.1%, respectively. It was found that AgNPs could accumulate in sludge with the distribution coefficients of 39.2–114 L/g, inhibit the protein and polysaccharide production in EPS, reduce the SOUR of sludge, and greatly increase LDH release from microbial cells. The illumina high-throughput sequencing results indicated that AgNPs concentration changed the structures of bacterial communities, associating with the effects of AgNPs on reactor performance. Sequence analyses showed that Proteobacteria, Bacteroidetes and Acidobacteria were the dominant phyla. It was notable that AgNPs addition reduced the contents of several nitrifying bacteria at genera level in sludge, leading to the lower removal of nitrogen. - Highlights: • More than 1.0 mg/L AgNPs evidently reduce COD, NH_4"+-N and SOP removal in SBR process. • AgNPs decrease the protein and polysaccharide contents of EPS. • AgNPs increase LDH release for 1.46–2.41 times. • AgNPs are apt to accumulate on surface and even into microbial cells. • AgNPs levels affect microbial community structure and composition.

The Microbial Database for Danish wastewater treatment plants with nutrient removal (MiDas-DK) - a tool for understanding activated sludge population dynamics and community stability.

Science.gov (United States)

Mielczarek, A T; Saunders, A M; Larsen, P; Albertsen, M; Stevenson, M; Nielsen, J L; Nielsen, P H

2013-01-01

Since 2006 more than 50 Danish full-scale wastewater treatment plants with nutrient removal have been investigated in a project called 'The Microbial Database for Danish Activated Sludge Wastewater Treatment Plants with Nutrient Removal (MiDas-DK)'. Comprehensive sets of samples have been collected, analyzed and associated with extensive operational data from the plants. The community composition was analyzed by quantitative fluorescence in situ hybridization (FISH) supported by 16S rRNA amplicon sequencing and deep metagenomics. MiDas-DK has been a powerful tool to study the complex activated sludge ecosystems, and, besides many scientific articles on fundamental issues on mixed communities encompassing nitrifiers, denitrifiers, bacteria involved in P-removal, hydrolysis, fermentation, and foaming, the project has provided results that can be used to optimize the operation of full-scale plants and carry out trouble-shooting. A core microbial community has been defined comprising the majority of microorganisms present in the plants. Time series have been established, providing an overview of temporal variations in the different plants. Interestingly, although most microorganisms were present in all plants, there seemed to be plant-specific factors that controlled the population composition thereby keeping it unique in each plant over time. Statistical analyses of FISH and operational data revealed some correlations, but less than expected. MiDas-DK (www.midasdk.dk) will continue over the next years and we hope the approach can inspire others to make similar projects in other parts of the world to get a more comprehensive understanding of microbial communities in wastewater engineering.

Production, partitioning and stoichiometry of organic matter under variable nutrient supply during mesocosm experiments in the tropical Pacific and Atlantic Ocean

Directory of Open Access Journals (Sweden)

J. M. S. Franz

2012-11-01

Full Text Available Oxygen-deficient waters in the ocean, generally referred to as oxygen minimum zones (OMZ, are expected to expand as a consequence of global climate change. Poor oxygenation is promoting microbial loss of inorganic nitrogen (N and increasing release of sediment-bound phosphate (P into the water column. These intermediate water masses, nutrient-loaded but with an N deficit relative to the canonical N:P Redfield ratio of 16:1, are transported via coastal upwelling into the euphotic zone. To test the impact of nutrient supply and nutrient stoichiometry on production, partitioning and elemental composition of dissolved (DOC, DON, DOP and particulate (POC, PON, POP organic matter, three nutrient enrichment experiments were conducted with natural microbial communities in shipboard mesocosms, during research cruises in the tropical waters of the southeast Pacific and the northeast Atlantic. Maximum accumulation of POC and PON was observed under high N supply conditions, indicating that primary production was controlled by N availability. The stoichiometry of microbial biomass was unaffected by nutrient N:P supply during exponential growth under nutrient saturation, while it was highly variable under conditions of nutrient limitation and closely correlated to the N:P supply ratio, although PON:POP of accumulated biomass generally exceeded the supply ratio. Microbial N:P composition was constrained by a general lower limit of 5:1. Channelling of assimilated P into DOP appears to be the mechanism responsible for the consistent offset of cellular stoichiometry relative to inorganic nutrient supply and nutrient drawdown, as DOP build-up was observed to intensify under decreasing N:P supply. Low nutrient N:P conditions in coastal upwelling areas overlying O₂-deficient waters seem to represent a net source for DOP, which may stimulate growth of diazotrophic phytoplankton. These results demonstrate that microbial nutrient assimilation and

Toward Understanding, Managing, and Protecting Microbial Ecosystems

Science.gov (United States)

Bodelier, Paul L. E.

2011-01-01

Microbial communities are at the very basis of life on earth, catalyzing biogeochemical reactions driving global nutrient cycles. However, unlike for plants and animals, microbial diversity is not on the biodiversity–conservation agenda. The latter, however, would imply that microbial diversity is not under any threat by anthropogenic disturbance or climate change. This maybe a misconception caused by the rudimentary knowledge we have concerning microbial diversity and its role in ecosystem functioning. This perspective paper identifies major areas with knowledge gaps within the field of environmental microbiology that preclude a comprehension of microbial ecosystems on the level we have for plants and animals. Opportunities and challenges are pointed out to open the microbial black box and to go from descriptive to predictive microbial ecology. PMID:21747797

Towards understanding, managing and protecting microbial ecosystems

Directory of Open Access Journals (Sweden)

Paul eBodelier

2011-04-01

Full Text Available Microbial communities are at the very basis of life on earth, catalysing biogeochemical reactions driving global nutrient cycles. However, unlike for plants and animals, microbial diversity is not on the biodiversity conservation agenda. The latter, however, would imply that microbial diversity is not under any threat by anthropogenic disturbance or climate change. This maybe a misconception caused by the rudimentary knowledge we have concerning microbial diversity and its role in ecosystem functioning. This perspective paper indentifies major areas with knowledge gaps within the field of environmental microbiology that preclude a comprehension of microbial ecosystems on the level we have for plants and animals. Opportunities and challenges are pointed out to open the microbial black box and to go from descriptive to predictive microbial ecology.

Toward understanding, managing, and protecting microbial ecosystems.

Science.gov (United States)

Bodelier, Paul L E

2011-01-01

Microbial communities are at the very basis of life on earth, catalyzing biogeochemical reactions driving global nutrient cycles. However, unlike for plants and animals, microbial diversity is not on the biodiversity-conservation agenda. The latter, however, would imply that microbial diversity is not under any threat by anthropogenic disturbance or climate change. This maybe a misconception caused by the rudimentary knowledge we have concerning microbial diversity and its role in ecosystem functioning. This perspective paper identifies major areas with knowledge gaps within the field of environmental microbiology that preclude a comprehension of microbial ecosystems on the level we have for plants and animals. Opportunities and challenges are pointed out to open the microbial black box and to go from descriptive to predictive microbial ecology.

How agricultural management shapes soil microbial communities: patterns emerging from genetic and genomic studies

Science.gov (United States)

Daly, Amanda; Grandy, A. Stuart

2016-04-01

Agriculture is a predominant land use and thus a large influence on global carbon (C) and nitrogen (N) balances, climate, and human health. If we are to produce food, fiber, and fuel sustainably we must maximize agricultural yield while minimizing negative environmental consequences, goals towards which we have made great strides through agronomic advances. However, most agronomic strategies have been designed with a view of soil as a black box, largely ignoring the way management is mediated by soil biota. Because soil microbes play a central role in many of the processes that deliver nutrients to crops and support their health and productivity, agricultural management strategies targeted to exploit or support microbial activity should deliver additional benefits. To do this we must determine how microbial community structure and function are shaped by agricultural practices, but until recently our characterizations of soil microbial communities in agricultural soils have been largely limited to broad taxonomic classes due to methodological constraints. With advances in high-throughput genetic and genomic sequencing techniques, better taxonomic resolution now enables us to determine how agricultural management affects specific microbes and, in turn, nutrient cycling outcomes. Here we unite findings from published research that includes genetic or genomic data about microbial community structure (e.g. 454, Illumina, clone libraries, qPCR) in soils under agricultural management regimes that differ in type and extent of tillage, cropping selections and rotations, inclusion of cover crops, organic amendments, and/or synthetic fertilizer application. We delineate patterns linking agricultural management to microbial diversity, biomass, C- and N-content, and abundance of microbial taxa; furthermore, where available, we compare patterns in microbial communities to patterns in soil extracellular enzyme activities, catabolic profiles, inorganic nitrogen pools, and nitrogen

Basaltic substrate composition affects microbial community development and acts as a source of nutrients in the deep biosphere

Science.gov (United States)

Bailey, B.; Sudek, L.; Templeton, A.; Staudigel, H.; Tebo, B.; Moyer, C.; Davis, R.

2006-12-01

Studies of the oceanic crust over the past decade have revealed that in spite of the oligotrophic nature of this environment, a diverse biosphere is present in the upper 1 km of basaltic crust. The key energy source in this setting may be the high content of transistion metals (Fe, Mn) found in the basaltic glass, but in order to discover the role of Fe and Mn in the deep biosphere, we must first determine which microbes are present and how they attain the necessary metabolites for proliferation. Our work contributes to both questions through the use of molecular microbiology techniques and the exposure of specifically designed substrates on the ocean floor. Loihi Seamount off the southeast coast of the Big Island of Hawai'i provides a unique laboratory for the study of distribution and population of microbial communities associated with iron rich environments on the ocean floor. Iron oxide flocculent material (floc) dominates the direct and diffuse hydrothermal venting areas on Loihi which makes it a prime target for understanding the role of iron in biological systems in the deep biosphere. We collected iron oxide floc and basaltic glass from pillow basalts around several hydrothermal vents on the crater rim, within the pit crater Pele's Pit, and from deep off of the southern rift zone of Loihi using the HURL PISCES IV/V submersibles. We also deployed basaltic glass sand amended with various nutrients (phosphate, oxidized and reduced iron, manganese) and recovered them in subsequent years to determine how substrate composition affects community structure. We extracted DNA from both rock and iron flocs and used t-RFLP to obtain a genetic fingerprint of the microbial communities associated with each substrate. From olivine and tholeiitic basalt enrichments, it appears that substrate composition strongly influences microbial colonization and subsequent community development even when deployed in the same conditions. Culturing efforts have yielded several iron

Microbial biofilm formation and its consequences for the CELSS program

Science.gov (United States)

Mitchell, R.

1994-01-01

A major goal of the Controlled Ecology Life Support System (CELSS) program is to provide reliable and efficient life support systems for long-duration space flights. A principal focus of the program is on the growth of higher plants in growth chambers. These crops should be grown without the risk of damage from microbial contamination. While it is unlikely that plant pathogens will pose a risk, there are serious hazards associated with microorganisms carried in the nutrient delivery systems and in the atmosphere of the growth chamber. Our experience in surface microbiology showed that colonization of surfaces with microorganisms is extremely rapid even when the inoculum is small. After initial colonization extensive biofilms accumulate on moist surfaces. These microbial films metabolize actively and slough off continuously to the air and water. During plant growth in the CELSS program, microbial biofilms have the potential to foul sensors and to plug nutrient delivery systems. In addition both metabolic products of microbial growth and degradation products of materials being considered for use as nutrient reservoirs and for delivery are likely sources of chemicals known to adversly affect plant growth.

Community Structure and Activity of a Highly Dynamic and Nutrient-Limited Hypersaline Microbial Mat in Um Alhool Sabkha, Qatar

KAUST Repository

Al-Thani, Roda

2014-03-21

The Um Alhool area in Qatar is a dynamic evaporative ecosystem that receives seawater from below as it is surrounded by sand dunes. We investigated the chemical composition, the microbial activity and biodiversity of the four main layers (L1–L4) in the photosynthetic mats. Chlorophyll a (Chl a) concentration and distribution (measured by HPLC and hyperspectral imaging, respectively), the phycocyanin distribution (scanned with hyperspectral imaging), oxygenic photosynthesis (determined by microsensor), and the abundance of photosynthetic microorganisms (from 16S and 18S rRNA sequencing) decreased with depth in the euphotic layer (L1). Incident irradiance exponentially attenuated in the same zone reaching 1% at 1.7-mm depth. Proteobacteria dominated all layers of the mat (24%–42% of the identified bacteria). Anoxygenic photosynthetic bacteria (dominated by Chloroflexus) were most abundant in the third red layer of the mat (L3), evidenced by the spectral signature of Bacteriochlorophyll as well as by sequencing. The deep, black layer (L4) was dominated by sulfate reducing bacteria belonging to the Deltaproteobacteria, which were responsible for high sulfate reduction rates (measured using 35S tracer). Members of Halobacteria were the dominant Archaea in all layers of the mat (92%–97%), whereas Nematodes were the main Eukaryotes (up to 87%). Primary productivity rates of Um Alhool mat were similar to those of other hypersaline microbial mats. However, sulfate reduction rates were relatively low, indicating that oxygenic respiration contributes more to organic material degradation than sulfate reduction, because of bioturbation. Although Um Alhool hypersaline mat is a nutrient-limited ecosystem, it is interestingly dynamic and phylogenetically highly diverse. All its components work in a highly efficient and synchronized way to compensate for the lack of nutrient supply provided during regular inundation periods.

Chitosan matrices modified with carbon nanotubes for use in mediated microbial biosensing

International Nuclear Information System (INIS)

Demirkol, D.O.; Timur, S.

2011-01-01

We describe a microbial sensor based on Pseudomonas fluorescens cells that was prepared by modifying graphite electrodes with chitosan and carbon nanotubes. Chronoamperometry was performed at +0.3 V in the presence of hexacyanoferrate as a mediator and revealed a good response to glucose which is linear in the 1.0 to 5.0 mM concentration range. Linearity was defined by the equation of y = 102.120x-13.279 (R2 = 0.998) (y shows current density as nA. cm-2 and x shows glucose concentration in mM). The effect of the CNTs on the response was compared to that of electrodes made without CNTs. (author)

Metagenomic Insights Into the Microbial Community and Nutrient Cycling in the Western Subarctic Pacific Ocean.

Science.gov (United States)

Li, Yingdong; Jing, Hongmei; Xia, Xiaomin; Cheung, Shunyan; Suzuki, Koji; Liu, Hongbin

2018-01-01

The composition and metabolic functions of prokaryotic communities in the western subarctic Pacific (WSP), where strong mixing of waters from the Sea of Okhotsk and the East Kamchatka Current result in transfer to the Oyashio Current, were investigated using a shotgun metagenome sequencing approach. Functional metabolic genes related to nutrient cycling of nitrogen, sulfur, carbohydrates, iron and amino acids were differently distributed between the surface and deep waters of the WSP. Genes related to nitrogen metabolism were mainly found in deep waters, where Thaumarchaeaota, Sphingomonadales , and Pseudomonadales were closely associated and performing important roles in ammonia oxidation, assimilatory nitrate reduction, and dissimilatory nitrate reduction processes, respectively. In addition, orders affiliated to Spingobacteria and Alphaproteobacteria were crucial for sulfate reduction and abundant at 3000 m, whereas orders affiliated to Gammaproteobacteria , which harbored the most sulfate reduction genes, were abundant at 1000 m. Additionally, when compared with the East Kamchatka Current, the prokaryotes in the Oyashio Current were likely to consume more energy for synthesizing cellular components. Also, genes encoding iron transport and siderophore biosynthesis proteins were in low abundance, indicating that the iron was not a limiting factor in the Oyashio current. In contrast, in the East Kamchatka Current, prokaryotes were more likely to directly utilize the amino acids and absorb iron from the environment. Overall, our data indicated that the transformation from the East Kamchatka Current to the Oyashio Current reshapes not only the composition of microbial community, but also the function of the metabolic processes. These results extended our knowledge of the microbial composition and potential metabolism in the WSP.

Metagenomic Insights Into the Microbial Community and Nutrient Cycling in the Western Subarctic Pacific Ocean

Science.gov (United States)

Li, Yingdong; Jing, Hongmei; Xia, Xiaomin; Cheung, Shunyan; Suzuki, Koji; Liu, Hongbin

2018-01-01

The composition and metabolic functions of prokaryotic communities in the western subarctic Pacific (WSP), where strong mixing of waters from the Sea of Okhotsk and the East Kamchatka Current result in transfer to the Oyashio Current, were investigated using a shotgun metagenome sequencing approach. Functional metabolic genes related to nutrient cycling of nitrogen, sulfur, carbohydrates, iron and amino acids were differently distributed between the surface and deep waters of the WSP. Genes related to nitrogen metabolism were mainly found in deep waters, where Thaumarchaeaota, Sphingomonadales, and Pseudomonadales were closely associated and performing important roles in ammonia oxidation, assimilatory nitrate reduction, and dissimilatory nitrate reduction processes, respectively. In addition, orders affiliated to Spingobacteria and Alphaproteobacteria were crucial for sulfate reduction and abundant at 3000 m, whereas orders affiliated to Gammaproteobacteria, which harbored the most sulfate reduction genes, were abundant at 1000 m. Additionally, when compared with the East Kamchatka Current, the prokaryotes in the Oyashio Current were likely to consume more energy for synthesizing cellular components. Also, genes encoding iron transport and siderophore biosynthesis proteins were in low abundance, indicating that the iron was not a limiting factor in the Oyashio current. In contrast, in the East Kamchatka Current, prokaryotes were more likely to directly utilize the amino acids and absorb iron from the environment. Overall, our data indicated that the transformation from the East Kamchatka Current to the Oyashio Current reshapes not only the composition of microbial community, but also the function of the metabolic processes. These results extended our knowledge of the microbial composition and potential metabolism in the WSP. PMID:29670596

Studies on potential effects of fumaric acid on rumen microbial fermentation, methane production and microbial community.

Science.gov (United States)

Riede, Susanne; Boguhn, Jeannette; Breves, Gerhard

2013-01-01

The greenhouse gas methane (CH4) contributes substantially to global climate change. As a potential approach to decrease ruminal methanogenesis, the effects of different dosages of fumaric acid (FA) on ruminal microbial metabolism and on the microbial community (archaea, bacteria) were studied using a rumen simulation technique (RUSITEC). FA acts as alternative hydrogen acceptor diverting 2H from methanogenesis of archaea towards propionate formation of bacteria. Three identical trials were conducted with 12 fermentation vessels over a period of 14 days. In each trial, four fermentation vessels were assigned to one of the three treatment groups differing in FA dosage: low fumaric acid (LFA), high fumaric acid (HFA) and without FA (control). FA was continuously infused with the buffer. Grass silage and concentrate served as substrate. FA led to decreases in pH and to higher production rates of total short chain fatty acids (SCFA) mediated by increases in propionate for LFA of 1.69 mmol d(-1) and in propionate and acetate production for HFA of 4.49 and 1.10 mmol d(-1), respectively. Concentrations of NH3-N, microbial crude protein synthesis, their efficiency, degradation of crude nutrients and detergent fibre fraction were unchanged. Total gas and CH4 production were not affected by FA. Effects of FA on structure of microbial community by means of single strand conformation polymorphism (SSCP) analyses could not be detected. Given the observed increase in propionate production and the unaffected CH4 production it can be supposed that the availability of reduction equivalents like 2H was not limited by the addition of FA in this study. It has to be concluded from the present study that the application of FA is not an appropriate approach to decrease the ruminal CH4 production.

Microbial Metabolism in Serpentinite Fluids

Science.gov (United States)

Crespo-Medina, M.; Brazelton, W. J.; Twing, K. I.; Kubo, M.; Hoehler, T. M.; Schrenk, M. O.

2013-12-01

Serpentinization is the process in which ultramafic rocks, characteristic of the upper mantle, react with water liberating mantle carbon and reducing power to potenially support chemosynthetic microbial communities. These communities may be important mediators of carbon and energy exchange between the deep Earth and the surface biosphere. Our work focuses on the Coast Range Ophiolite Microbial Observatory (CROMO) in Northern California where subsurface fluids are accessible through a series of wells. Preliminary analyses indicate that the highly basic fluids (pH 9-12) have low microbial diversity, but there is limited knowledge about the metabolic capabilities of these communties. Metagenomic data from similar serpentine environments [1] have identified Betaproteobacteria belonging to the order Burkholderiales and Gram-positive bacteria from the order Clostridiales as key components of the serpentine microbiome. In an effort to better characterize the microbial community, metabolism, and geochemistry at CROMO, fluids from two representative wells (N08B and CSWold) were sampled during recent field campaigns. Geochemical characterization of the fluids includes measurements of dissolved gases (H2, CO, CH4), dissolved inorganic and organic carbon, volatile fatty acids, and nutrients. The wells selected can be differentiated in that N08B had higher pH (10-11), lower dissolved oxygen, and cell counts ranging from 105-106 cells mL-1 of fluid, with an abundance of the betaproteobacterium Hydrogenophaga. In contrast, fluids from CSWold have slightly lower pH (9-9.5), DO, and conductivity, as well as higher TDN and TDP. CSWold fluid is also characterized for having lower cell counts (~103 cells mL-1) and an abundance of Dethiobacter, a taxon within the phylum Clostridiales. Microcosm experiments were conducted with the purpose of monitoring carbon fixation, methanotrophy and metabolism of small organic compounds, such as acetate and formate, while tracing changes in fluid

Soil microbial community structure and diversity are largely influenced by soil pH and nutrient quality in 78-year-old tree plantations

Science.gov (United States)

Zhou, Xiaoqi; Guo, Zhiying; Chen, Chengrong; Jia, Zhongjun

2017-04-01

Forest plantations have been recognised as a key strategy management tool for stocking carbon (C) in soils, thereby contributing to climate warming mitigation. However, long-term ecological consequences of anthropogenic forest plantations on the community structure and diversity of soil microorganisms and the underlying mechanisms in determining these patterns are poorly understood. In this study, we selected 78-year-old tree plantations that included three coniferous tree species (i.e. slash pine, hoop pine and kauri pine) and a eucalypt species in subtropical Australia. We investigated the patterns of community structure, and the diversity of soil bacteria and eukaryotes by using high-throughput sequencing of 16S rRNA and 18S rRNA genes. We also measured the potential methane oxidation capacity under different tree species. The results showed that slash pine and Eucalyptus significantly increased the dominant taxa of bacterial Acidobacteria and the dominant taxa of eukaryotic Ascomycota, and formed clusters of soil bacterial and eukaryotic communities, which were clearly different from the clusters under hoop pine and kauri pine. Soil pH and nutrient quality indicators such as C : nitrogen (N) and extractable organic C : extractable organic N were key factors in determining the patterns of soil bacterial and eukaryotic communities between the different tree species treatments. Slash pine and Eucalyptus had significantly lower soil bacterial and eukaryotic operational taxonomical unit numbers and lower diversity indices than kauri pine and hoop pine. A key factor limitation hypothesis was introduced, which gives a reasonable explanation for lower diversity indices under slash pine and Eucalyptus. In addition, slash pine and Eucalyptus had a higher soil methane oxidation capacity than the other tree species. These results suggest that significant changes in soil microbial communities may occur in response to chronic disturbance by tree plantations, and highlight

Effects of different sources of protein on digestive characteristics, microbial efficiency, and nutrient flow in dairy goats

Directory of Open Access Journals (Sweden)

Nivea Regina de Oliveira Felisberto

2011-10-01

Full Text Available Diets formulated with protein sources presenting different resistance to ruminal degradation were compared by evaluating ruminal parameters, production and microbial efficiency and nutrients flow to the omasum in goats. Eight rumen cannulated non-lactating, non-pregnant goats were distributed in a 4 × 4 Latin square design with two replicates. Treatments consisted of four diets where different sources of plant protein accounted for the major protein source named soybean meal, source of higher ruminal degradability, and three other sources of higher resistance of degradation: roasted soybean, corn gluten meal, and cottonseed cake. Amounts of rumen protein were similar among rations; however, flows of dry matter, protein and non-fiber carbohydrate to omasum were higher for diets with protein source with reduced rumen degradation rate. Higher values of rumen ammonia were obtained by using ration with soybean meal as major source of protein. Higher values of pH were obtained for rations with roasted soybean e cottonseed cake. Regarding kinetic of transit, similar values were found among rations. Diets with protein sources presenting reduced ruminal degradation increase nutrients flow to the omasum in goats and alter digestive parameters such as pH and ammonia without compromising bacteria growth and efficiency, which grants their use for dairy goats with similar efficiency to rations using more degradable sources of protein.

Modelling the competition of planktonic and sessile aerobic heterotrophs for complementary nutrients in biofilm reactor.

Science.gov (United States)

Lu, T; Saikaly, P E; Oerther, D B

2007-01-01

A comprehensive, simplified microbial biofilm model was developed to evaluate the impact of bioreactor operating parameters on changes in microbial population abundance. Biofilm simulations were conducted using three special cases: fully penetrated, internal mass transfer resistance and external mass transfer resistance. The results of model simulations showed that for certain operating conditions, competition for growth limiting nutrients generated oscillations in the abundance of planktonic and sessile microbial populations. These oscillations resulted in the violation of the competitive exclusion principle where the number of microbial populations was greater than the number of growth limiting nutrients. However, the operating conditions which impacted microbial community diversity were different for the three special cases. Comparing the results of model simulations for dispersed-growth, biofilms and bioflocs showed that oscillations and microbial community diversity were a function of competition as well as other key features of the ecosystem. The significance of the current study is that it is the first to examine competition as a mechanism for controlling microbial community diversity in biofilm reactors.

Review on Periphyton as Mediator of Nutrient Transfer in Aquatic Ecosystems

Directory of Open Access Journals (Sweden)

Surjya K. Saikia

2011-12-01

Full Text Available In the studies of aquatic ecology, periphyton has been uncared for despite its vital role in nutrient uptake and transfer to the upper trophic organisms. Being the component of food chain as attached organism it takes part in nutrient cycling in the ecosystem like that of suspended planktonic counterparts. The present review, with an aim to understand the role of periphyton in nutrient transfer from benthic environment to upper trophic level, focuses many aspects of periphyton-nutrient relationship based on available literatures. It also attempts to redefine periphyton, as a part of biofilm, harboring nutrient components like protein, fat and carbohydrate preferably in its extracellular polymeric substance (EPS, cyanobacteria, diatom and other algal communities. In addition to physical processes, nutrient uptake by periphyton is catalyzed by enzymes like Nitrogen Reductase and Alkaline Phosphatase from the environment. This uptake and transfer is further regulated by periphytic C: nutrient (N or P stoichiometry, colonization time, distribution of periphyton cover on sediments and macrophytes, macronutrient concentration, grazing, sloughing, temperature, and advective transport. The Carbon (C sources of periphyton are mainly dissolve organic matter and photosynthetic C that enters into higher trophic levels through predation and transfers as C-rich nutrient components. Despite of emerging interests on utilizing periphyton as nutrient transfer tool in aquatic ecosystem, the major challenges ahead for modern aquatic biologists lies on determining nutrient uptake and transfer rate of periphyton, periphytic growth and simulating nutrient models of periphyton to figure a complete energy cycle in aquatic ecosystem.

Impact of organic carbon and nutrients mobilized during chemical oxidation on subsequent bioremediation of a diesel-contaminated soil.

Science.gov (United States)

Sutton, Nora B; Grotenhuis, Tim; Rijnaarts, Huub H M

2014-02-01

Remediation with in situ chemical oxidation (ISCO) impacts soil organic matter (SOM) and the microbial community, with deleterious effects on the latter being a major hurdle to coupling ISCO with in situ bioremediation (ISB). We investigate treatment of a diesel-contaminated soil with Fenton's reagent and modified Fenton's reagent coupled with a subsequent bioremediation phase of 187d, both with and without nutrient amendment. Chemical oxidation mobilized SOM into the liquid phase, producing dissolved organic carbon (DOC) concentrations 8-16 times higher than the untreated field sample. Higher aqueous concentrations of nitrogen and phosphorous species were also observed following oxidation; NH4(+) increased 14-172 times. During the bioremediation phase, dissolved carbon and nutrient species were utilized for microbial growth-yielding DOC concentrations similar to field sample levels within 56d of incubation. In the absence of nutrient amendment, the highest microbial respiration rates were correlated with higher availability of nitrogen and phosphorus species mobilized by oxidation. Significant diesel degradation was only observed following nutrient amendment, implying that nutrients mobilized by chemical oxidation can increase microbial activity but are insufficient for bioremediation. While all bioremediation occurred in the first 28d of incubation in the biotic control microcosm with nutrient amendment, biodegradation continued throughout 187d of incubation following chemical oxidation, suggesting that chemical treatment also affects the desorption of organic contaminants from SOM. Overall, results indicate that biodegradation of DOC, as an alternative substrate to diesel, and biological utilization of mobilized nutrients have implications for the success of coupled ISCO and ISB treatments. Copyright © 2013 Elsevier Ltd. All rights reserved.

An Exogenous Surfactant-Producing Bacillus subtilis Facilitates Indigenous Microbial Enhanced Oil Recovery.

Science.gov (United States)

Gao, Peike; Li, Guoqiang; Li, Yanshu; Li, Yan; Tian, Huimei; Wang, Yansen; Zhou, Jiefang; Ma, Ting

2016-01-01

This study used an exogenous lipopeptide-producing Bacillus subtilis to strengthen the indigenous microbial enhanced oil recovery (IMEOR) process in a water-flooded reservoir in the laboratory. The microbial processes and driving mechanisms were investigated in terms of the changes in oil properties and the interplay between the exogenous B. subtilis and indigenous microbial populations. The exogenous B. subtilis is a lipopeptide producer, with a short growth cycle and no oil-degrading ability. The B. subtilis facilitates the IMEOR process through improving oil emulsification and accelerating microbial growth with oil as the carbon source. Microbial community studies using quantitative PCR and high-throughput sequencing revealed that the exogenous B. subtilis could live together with reservoir microbial populations, and did not exert an observable inhibitory effect on the indigenous microbial populations during nutrient stimulation. Core-flooding tests showed that the combined exogenous and indigenous microbial flooding increased oil displacement efficiency by 16.71%, compared with 7.59% in the control where only nutrients were added, demonstrating the application potential in enhanced oil recovery in water-flooded reservoirs, in particular, for reservoirs where IMEOR treatment cannot effectively improve oil recovery.

Perspective for Aquaponic Systems: "Omic" Technologies for Microbial Community Analysis.

Science.gov (United States)

Munguia-Fragozo, Perla; Alatorre-Jacome, Oscar; Rico-Garcia, Enrique; Torres-Pacheco, Irineo; Cruz-Hernandez, Andres; Ocampo-Velazquez, Rosalia V; Garcia-Trejo, Juan F; Guevara-Gonzalez, Ramon G

2015-01-01

Aquaponics is the combined production of aquaculture and hydroponics, connected by a water recirculation system. In this productive system, the microbial community is responsible for carrying out the nutrient dynamics between the components. The nutrimental transformations mainly consist in the transformation of chemical species from toxic compounds into available nutrients. In this particular field, the microbial research, the "Omic" technologies will allow a broader scope of studies about a current microbial profile inside aquaponics community, even in those species that currently are unculturable. This approach can also be useful to understand complex interactions of living components in the system. Until now, the analog studies were made to set up the microbial characterization on recirculation aquaculture systems (RAS). However, microbial community composition of aquaponics is still unknown. "Omic" technologies like metagenomic can help to reveal taxonomic diversity. The perspectives are also to begin the first attempts to sketch the functional diversity inside aquaponic systems and its ecological relationships. The knowledge of the emergent properties inside the microbial community, as well as the understanding of the biosynthesis pathways, can derive in future biotechnological applications. Thus, the aim of this review is to show potential applications of current "Omic" tools to characterize the microbial community in aquaponic systems.

Metagenomic Insights Into the Microbial Community and Nutrient Cycling in the Western Subarctic Pacific Ocean

Directory of Open Access Journals (Sweden)

Yingdong Li

2018-04-01

Full Text Available The composition and metabolic functions of prokaryotic communities in the western subarctic Pacific (WSP, where strong mixing of waters from the Sea of Okhotsk and the East Kamchatka Current result in transfer to the Oyashio Current, were investigated using a shotgun metagenome sequencing approach. Functional metabolic genes related to nutrient cycling of nitrogen, sulfur, carbohydrates, iron and amino acids were differently distributed between the surface and deep waters of the WSP. Genes related to nitrogen metabolism were mainly found in deep waters, where Thaumarchaeaota, Sphingomonadales, and Pseudomonadales were closely associated and performing important roles in ammonia oxidation, assimilatory nitrate reduction, and dissimilatory nitrate reduction processes, respectively. In addition, orders affiliated to Spingobacteria and Alphaproteobacteria were crucial for sulfate reduction and abundant at 3000 m, whereas orders affiliated to Gammaproteobacteria, which harbored the most sulfate reduction genes, were abundant at 1000 m. Additionally, when compared with the East Kamchatka Current, the prokaryotes in the Oyashio Current were likely to consume more energy for synthesizing cellular components. Also, genes encoding iron transport and siderophore biosynthesis proteins were in low abundance, indicating that the iron was not a limiting factor in the Oyashio current. In contrast, in the East Kamchatka Current, prokaryotes were more likely to directly utilize the amino acids and absorb iron from the environment. Overall, our data indicated that the transformation from the East Kamchatka Current to the Oyashio Current reshapes not only the composition of microbial community, but also the function of the metabolic processes. These results extended our knowledge of the microbial composition and potential metabolism in the WSP.

Strategies to Optimize Microbially-Mediated Mitigation of Greenhouse Gas Emissions from Landfill Cover Soils

Energy Technology Data Exchange (ETDEWEB)

Jeremy Semrau; Sung-Woo Lee; Jeongdae Im; Sukhwan Yoon; Michael Barcelona

2010-09-30

The overall objective of this project, 'Strategies to Optimize Microbially-Mediated Mitigation of Greenhouse Gas Emissions from Landfill Cover Soils' was to develop effective, efficient, and economic methodologies by which microbial production of nitrous oxide can be minimized while also maximizing microbial consumption of methane in landfill cover soils. A combination of laboratory and field site experiments found that the addition of nitrogen and phenylacetylene stimulated in situ methane oxidation while minimizing nitrous oxide production. Molecular analyses also indicated that methane-oxidizing bacteria may play a significant role in not only removing methane, but in nitrous oxide production as well, although the contribution of ammonia-oxidizing archaea to nitrous oxide production can not be excluded at this time. Future efforts to control both methane and nitrous oxide emissions from landfills as well as from other environments (e.g., agricultural soils) should consider these issues. Finally, a methanotrophic biofiltration system was designed and modeled for the promotion of methanotrophic activity in local methane 'hotspots' such as landfills. Model results as well as economic analyses of these biofilters indicate that the use of methanotrophic biofilters for controlling methane emissions is technically feasible, and provided either the costs of biofilter construction and operation are reduced or the value of CO{sub 2} credits is increased, can also be economically attractive.

Sorption of radioiodide in an acidic, nutrient-poor boreal bog: insights into the microbial impact

International Nuclear Information System (INIS)

Lusa, M.; Bomberg, M.; Aromaa, H.; Knuutinen, J.; Lehto, J.

2015-01-01

Batch sorption experiments were conducted to evaluate the sorption behaviour of iodide and the microbial impact on iodide sorption in the surface moss, subsurface peat, gyttja, and clay layers of a nutrient-poor boreal bog. The batch distribution coefficient (K d ) values of iodide decreased as a function of sampling depth. The highest K d values, 4800 L/Kg dry weight (DW) (geometric mean), were observed in the fresh surface moss and the lowest in the bottom clay (geometric mean 90 mL/g DW). In the surface moss, peat and gyttja layers, which have a high organic matter content (on average 97%), maximum sorption was observed at a pH between ∼4 and 5 and in the clay layer at pH 2. The K d values were significantly lower in sterilized samples, being 20-fold lower than the values found for the unsterilized samples. In addition, the recolonization of sterilized samples with a microbial population from the fresh samples restored the sorption capacity of surface moss, peat and gyttja samples, indicating that the decrease in the sorption was due to the destruction of microbes and supporting the hypothesis that microbes are necessary for the incorporation of iodide into the organic matter. Anoxic conditions reduced the sorption of iodide in fresh, untreated samples, similarly to the effect of sterilization, which supports the hypothesis that iodide is oxidized into I 2 /HIO before incorporation into the organic matter. Furthermore, the K d values positively correlated with peroxidase activity in surface moss, subsurface peat and gyttja layers at +20 °C, and with the bacterial cell counts obtained from plate count agar at +4 °C. Our results demonstrate the importance of viable microbes for the sorption of iodide in the bog environment, having a high organic matter content and a low pH. - Highlights: • Sorption of iodide is highest on the surface Sphagnum layer of the bog. • Sterilization of peat decreases the sorption of iodide. • Anoxic conditions decrease

What is microbial community ecology?

Science.gov (United States)

Konopka, Allan

2009-11-01

The activities of complex communities of microbes affect biogeochemical transformations in natural, managed and engineered ecosystems. Meaningfully defining what constitutes a community of interacting microbial populations is not trivial, but is important for rigorous progress in the field. Important elements of research in microbial community ecology include the analysis of functional pathways for nutrient resource and energy flows, mechanistic understanding of interactions between microbial populations and their environment, and the emergent properties of the complex community. Some emergent properties mirror those analyzed by community ecologists who study plants and animals: biological diversity, functional redundancy and system stability. However, because microbes possess mechanisms for the horizontal transfer of genetic information, the metagenome may also be considered as a community property.

Microbial processes in coastal pollution

International Nuclear Information System (INIS)

Capone, D.G.; Bauer, J.E.

1992-01-01

In this chapter, the authors describe the nature and range of some of the interactions that can occur between the microbiota and environmental contaminants in coastal areas. The implications of such interactions are also discussed. Pollutant types include inorganic nutrients, heavy metals, bulk organics, organic contaminants, pathogenic microorganisms and microbial pollutants. Both the effects of pollutants such as petroleum hydrocarbons on natural microbial populations and the mitigation of contaminant effects by complexation and biodegradation are considered. Finally, several areas of emerging concerns are presented that involve a confluence of biogeochemistry, microbial ecology and applied and public health microbiology. These concerns range in relevance from local/regional to oceanic/global scales. 308 ref

Ocean acidification impacts bacteria-phytoplankton coupling at low-nutrient conditions

Science.gov (United States)

Hornick, Thomas; Bach, Lennart T.; Crawfurd, Katharine J.; Spilling, Kristian; Achterberg, Eric P.; Woodhouse, Jason N.; Schulz, Kai G.; Brussaard, Corina P. D.; Riebesell, Ulf; Grossart, Hans-Peter

2017-01-01

The oceans absorb about a quarter of the annually produced anthropogenic atmospheric carbon dioxide (CO2), resulting in a decrease in surface water pH, a process termed ocean acidification (OA). Surprisingly little is known about how OA affects the physiology of heterotrophic bacteria or the coupling of heterotrophic bacteria to phytoplankton when nutrients are limited. Previous experiments were, for the most part, undertaken during productive phases or following nutrient additions designed to stimulate algal blooms. Therefore, we performed an in situ large-volume mesocosm ( ˜ 55 m3) experiment in the Baltic Sea by simulating different fugacities of CO2 (fCO2) extending from present to future conditions. The study was conducted in July-August after the nominal spring bloom, in order to maintain low-nutrient conditions throughout the experiment. This resulted in phytoplankton communities dominated by small-sized functional groups (picophytoplankton). There was no consistent fCO2-induced effect on bacterial protein production (BPP), cell-specific BPP (csBPP) or biovolumes (BVs) of either free-living (FL) or particle-associated (PA) heterotrophic bacteria, when considered as individual components (univariate analyses). Permutational Multivariate Analysis of Variance (PERMANOVA) revealed a significant effect of the fCO2 treatment on entire assemblages of dissolved and particulate nutrients, metabolic parameters and the bacteria-phytoplankton community. However, distance-based linear modelling only identified fCO2 as a factor explaining the variability observed amongst the microbial community composition, but not for explaining variability within the metabolic parameters. This suggests that fCO2 impacts on microbial metabolic parameters occurred indirectly through varying physicochemical parameters and microbial species composition. Cluster analyses examining the co-occurrence of different functional groups of bacteria and phytoplankton further revealed a separation of

Acid-deposition research program. Volume 2. Effects of acid-forming emissions on soil microorganisms and microbially-mediated processes

Energy Technology Data Exchange (ETDEWEB)

Visser, S.; Danielson, R.M.; Parr, J.F.

1987-02-01

The interactions of soil physical, chemical, and biological processes are ultimately expressed in a soil's fertility and its capacity for plant production. Consequently, much of the research conducted to date regarding the impact of acid-forming pollutants on soil properties has been geared towards possible effects on plant productivity. This trend continues in this paper where the effects of acidic deposition on microbial communities are reviewed in relation to potential impact on plant growth. The objectives of the review are to discuss: (1) The effects of acid-forming emissions (primarily S-containing pollutants) on microbial community structure with emphasis on qualitative and quantitative aspects; (2) The effects of acidic deposition on microbially mediated processes (i.e., community functions); (3) Acidification effects of pollutants on symbiotic and disease-causing microorganisms. The symbionts discussed include ectomycorrhizal fungi, vesicular-arbuscular mycorrhizal fungi, and N/sub 2/-fixing bacteria, particularly Rhizobium, while the disease-causing microorganisms will include those responsible for foliage, stem, and root diseases.

Microbially-mediated method for synthesis of non-oxide semiconductor nanoparticles

Energy Technology Data Exchange (ETDEWEB)

Phelps, Tommy J.; Lauf, Robert J.; Moon, Ji-Won; Rondinone, Adam Justin; Love, Lonnie J.; Duty, Chad Edward; Madden, Andrew Stephen; Li, Yiliang; Ivanov, Ilia N.; Rawn, Claudia Jeanette

2017-09-19

The invention is directed to a method for producing non-oxide semiconductor nanoparticles, the method comprising: (a) subjecting a combination of reaction components to conditions conducive to microbially-mediated formation of non-oxide semiconductor nanoparticles, wherein said combination of reaction components comprises i) anaerobic microbes, ii) a culture medium suitable for sustaining said anaerobic microbes, iii) a metal component comprising at least one type of metal ion, iv) a non-metal component comprising at least one non-metal selected from the group consisting of S, Se, Te, and As, and v) one or more electron donors that provide donatable electrons to said anaerobic microbes during consumption of the electron donor by said anaerobic microbes; and (b) isolating said non-oxide semiconductor nanoparticles, which contain at least one of said metal ions and at least one of said non-metals. The invention is also directed to non-oxide semiconductor nanoparticle compositions produced as above and having distinctive properties.

Microbially-mediated method for synthesis of non-oxide semiconductor nanoparticles

Science.gov (United States)

Phelps, Tommy J.; Lauf, Robert J.; Moon, Ji Won; Rondinone, Adam J.; Love, Lonnie J.; Duty, Chad Edward; Madden, Andrew Stephen; Li, Yiliang; Ivanov, Ilia N.; Rawn, Claudia Jeanette

2014-06-24

The invention is directed to a method for producing non-oxide semiconductor nanoparticles, the method comprising: (a) subjecting a combination of reaction components to conditions conducive to microbially-mediated formation of non-oxide semiconductor nanoparticles, wherein said combination of reaction components comprises i) anaerobic microbes, ii) a culture medium suitable for sustaining said anaerobic microbes, iii) a metal component comprising at least one type of metal ion, iv) a non-metal component containing at least one non-metal selected from the group consisting of S, Se, Te, and As, and v) one or more electron donors that provide donatable electrons to said anaerobic microbes during consumption of the electron donor by said anaerobic microbes; and (b) isolating said non-oxide semiconductor nanoparticles, which contain at least one of said metal ions and at least one of said non-metals. The invention is also directed to non-oxide semiconductor nanoparticle compositions produced as above and having distinctive properties.

Nutrient uplift in a cyclonic eddy increases diversity, primary productivity and iron demand of microbial communities relative to a western boundary current

Directory of Open Access Journals (Sweden)

Martina A. Doblin

2016-04-01

Full Text Available The intensification of western boundary currents in the global ocean will potentially influence meso-scale eddy generation, and redistribute microbes and their associated ecological and biogeochemical functions. To understand eddy-induced changes in microbial community composition as well as how they control growth, we targeted the East Australian Current (EAC region to sample microbes in a cyclonic (cold-core eddy (CCE and the adjacent EAC. Phototrophic and diazotrophic microbes were more diverse (2–10 times greater Shannon index in the CCE relative to the EAC, and the cell size distribution in the CCE was dominated (67% by larger micro-plankton $(\\geq 20\\lrm{\\mu }\\mathrm{m}$ ≥ 20 μ m , as opposed to pico- and nano-sized cells in the EAC. Nutrient addition experiments determined that nitrogen was the principal nutrient limiting growth in the EAC, while iron was a secondary limiting nutrient in the CCE. Among the diazotrophic community, heterotrophic NifH gene sequences dominated in the EAC and were attributable to members of the gamma-, beta-, and delta-proteobacteria, while the CCE contained both phototrophic and heterotrophic diazotrophs, including Trichodesmium, UCYN-A and gamma-proteobacteria. Daily sampling of incubation bottles following nutrient amendment captured a cascade of effects at the cellular, population and community level, indicating taxon-specific differences in the speed of response of microbes to nutrient supply. Nitrogen addition to the CCE community increased picoeukaryote chlorophyll a quotas within 24 h, suggesting that nutrient uplift by eddies causes a ‘greening’ effect as well as an increase in phytoplankton biomass. After three days in both the EAC and CCE, diatoms increased in abundance with macronutrient (N, P, Si and iron amendment, whereas haptophytes and phototrophic dinoflagellates declined. Our results indicate that cyclonic eddies increase delivery of nitrogen to the upper ocean to potentially

Perspective for Aquaponic Systems: “Omic” Technologies for Microbial Community Analysis

Directory of Open Access Journals (Sweden)

Perla Munguia-Fragozo

2015-01-01

Full Text Available Aquaponics is the combined production of aquaculture and hydroponics, connected by a water recirculation system. In this productive system, the microbial community is responsible for carrying out the nutrient dynamics between the components. The nutrimental transformations mainly consist in the transformation of chemical species from toxic compounds into available nutrients. In this particular field, the microbial research, the “Omic” technologies will allow a broader scope of studies about a current microbial profile inside aquaponics community, even in those species that currently are unculturable. This approach can also be useful to understand complex interactions of living components in the system. Until now, the analog studies were made to set up the microbial characterization on recirculation aquaculture systems (RAS. However, microbial community composition of aquaponics is still unknown. “Omic” technologies like metagenomic can help to reveal taxonomic diversity. The perspectives are also to begin the first attempts to sketch the functional diversity inside aquaponic systems and its ecological relationships. The knowledge of the emergent properties inside the microbial community, as well as the understanding of the biosynthesis pathways, can derive in future biotechnological applications. Thus, the aim of this review is to show potential applications of current “Omic” tools to characterize the microbial community in aquaponic systems.

Perspective for Aquaponic Systems: “Omic” Technologies for Microbial Community Analysis

Science.gov (United States)

Munguia-Fragozo, Perla; Alatorre-Jacome, Oscar; Rico-Garcia, Enrique; Cruz-Hernandez, Andres; Ocampo-Velazquez, Rosalia V.; Garcia-Trejo, Juan F.; Guevara-Gonzalez, Ramon G.

2015-01-01

Aquaponics is the combined production of aquaculture and hydroponics, connected by a water recirculation system. In this productive system, the microbial community is responsible for carrying out the nutrient dynamics between the components. The nutrimental transformations mainly consist in the transformation of chemical species from toxic compounds into available nutrients. In this particular field, the microbial research, the “Omic” technologies will allow a broader scope of studies about a current microbial profile inside aquaponics community, even in those species that currently are unculturable. This approach can also be useful to understand complex interactions of living components in the system. Until now, the analog studies were made to set up the microbial characterization on recirculation aquaculture systems (RAS). However, microbial community composition of aquaponics is still unknown. “Omic” technologies like metagenomic can help to reveal taxonomic diversity. The perspectives are also to begin the first attempts to sketch the functional diversity inside aquaponic systems and its ecological relationships. The knowledge of the emergent properties inside the microbial community, as well as the understanding of the biosynthesis pathways, can derive in future biotechnological applications. Thus, the aim of this review is to show potential applications of current “Omic” tools to characterize the microbial community in aquaponic systems. PMID:26509157

Environmental controls on microbial communities in continental serpentinite fluids

Directory of Open Access Journals (Sweden)

Melitza eCrespo-Medina

2014-11-01

Full Text Available Geochemical reactions associated with serpentinization alter the composition of dissolved organic compounds in circulating fluids and potentially liberate mantle-derived carbon and reducing power to support subsurface microbial communities. Previous studies have identified Betaproteobacteria from the order Burkholderiales and bacteria from the order Clostridiales as key components of the serpentinite–hosted microbiome, however there is limited knowledge of their metabolic capabilities or growth characteristics. In an effort to better characterize microbial communities, their metabolism, and factors limiting their activities, microcosm experiments were designed with fluids collected from several monitoring wells at the Coast Range Ophiolite Microbial Observatory (CROMO in northern California during expeditions in March and August 2013. The incubations were initiated with a hydrogen atmosphere and a variety of carbon sources (carbon dioxide, methane, acetate and formate, with and without the addition of nutrients and electron acceptors. Growth was monitored by direct microscopic counts; DNA yield and community composition was assessed at the end of the three month incubation. For the most part, results indicate that bacterial growth was favored by the addition of acetate and methane, and that the addition of nutrients and electron acceptors had no significant effect on microbial growth, suggesting no nutrient- or oxidant-limitation. However the addition of sulfur amendments led to different community compositions. The dominant organisms at the end of the incubations were closely related to Dethiobacter sp. and to the family Comamonadaceae, which are also prominent in culture-independent gene sequencing surveys. These experiments provide one of first insights into the biogeochemical dynamics of the serpentinite subsurface environment and will facilitate experiments to trace microbial activities in serpentinizing ecosystems.

Changes in microbial and nutrient composition associated with rumen content compost incubation.

Science.gov (United States)

Shrestha, Karuna; Shrestha, Pramod; Adetutu, Eric M; Walsh, Kerry B; Harrower, Keith M; Ball, Andrew S; Midmore, David J

2011-02-01

Physico-chemical and microbiological investigations were carried out on rumen content material composted for nine months, fresh vermicasts (obtained after passing the same compost through the guts of a mixture of three species of earthworms: Eisenia fetida, Lumbricus rubellus and Perionyx excavates) and microbially enhanced extracts derived from rumen compost, vermicast and vermicast leachate incubated for up to 48 h. Compared to composted rumen contents, vermicast was only improved in terms of microbial biomass C, while vermicast leached extract was significantly higher in NH(4)(+)-N,PO(4)(-)-P, humic acid, bacterial counts and total microbial activity compared to rumen compost extract. Although no difference between treatments was observed in genetic diversity as indicated by DGGE analysis, community level functional diversity of vermicast leached extract (Biolog™) was higher than that of composted rumen contents, vermicast and rumen compost extract indicating an enhancement of microbial activity rather than diversity due to liquid incubation. Copyright © 2010 Elsevier Ltd. All rights reserved.

Periphytic biofilms: A promising nutrient utilization regulator in wetlands.

Science.gov (United States)

Wu, Yonghong; Liu, Junzhuo; Rene, Eldon R

2018-01-01

Low nutrient utilization efficiency in agricultural ecosystems is the main cause of nonpoint source (NPS) pollution. Therefore, novel approaches should be explored to improve nutrient utilization in these ecosystems. Periphytic biofilms composed of microalgae, bacteria and other microbial organisms are ubiquitous and form a 'third phase' in artificial wetlands such as paddy fields. Periphytic biofilms play critical roles in nutrient transformation between the overlying water and soil/sediment, however, their contributions to nutrient utilization improvement and NPS pollution control have been largely underestimated. This mini review summarizes the contributions of periphytic biofilms to nutrient transformation processes, including assimilating and storing bioavailable nitrogen and phosphorus, fixing nitrogen, and activating occluded phosphorus. Future research should focus on augmenting the nitrogen fixing, phosphate solubilizing and phosphatase producing microorganisms in periphytic biofilms to improve nutrient utilization and thereby reduce NPS pollution production in artificial and natural wetland ecosystems. Copyright © 2017 Elsevier Ltd. All rights reserved.

Does microbial biomass affect pelagic ecosystem efficiency? An experimental study.

Science.gov (United States)

Wehr, J D; Le, J; Campbell, L

1994-01-01

Bacteria and other microorganisms in the pelagic zone participate in the recycling of organic matter and nutrients within the water column. The microbial loop is thought to enhance ecosystem efficiency through rapid recycling and reduced sinking rates, thus reducing the loss of nutrients contained in organisms remaining within the photic zone. We conducted experiments with lake communities in 5400-liter mesocosms, and measured the flux of materials and nutrients out of the water column. A factorial design manipulated 8 nutrient treatments: 4 phosphorus levels × 2 nitrogen levels. Total sedimentation rates were greatest in high-N mesocosms; within N-surplus communities, [Symbol: see text]1 µM P resulted in 50% increase in total particulate losses. P additions without added N had small effects on nutrient losses from the photic zone; +2 µM P tanks received 334 mg P per tank, yet after 14 days lost only 69 mg more particulate-P than did control communities. Nutrient treatments resulted in marked differences in phytoplankton biomass (twofold N effect, fivefold P effect in +N mesocosms only), bacterioplankton densities (twofold N-effect, twofold P effects in -N and +N mesocosms), and the relative importance of autotrophic picoplankton (maximum in high NY mesocosms). Multiple regression analysis found that of 8 plankton and water chemistry variables, the ratio of autotrophic picoplankton to total phytoplankton (measured as chlorophyll α) explained the largest portion of the total variation in sedimentation loss rates (65% of P-flux, 57% of N-flux, 26% of total flux). In each case, systems with greater relative importance of autotrophic picoplankton had significantly reduced loss rates. In contrast, greater numbers of planktonic bacteria were associated with increased sedimentation rates and lower system efficiency. We suggest that different microbial components may have contrasting effects on the presumed enhanced efficiency provided by the microbial loop.

Emergence of nutrient limitation in tropical dry forests: hypotheses from simulation models

Science.gov (United States)

Medvigy, D.; Waring, B. G.; Xu, X.; Trierweiler, A.; Werden, L. K.; Wang, G.; Zhu, Q.; Powers, J. S.

2017-12-01

It is unclear to what extent tropical dry forest productivity may be limited by nutrients. Direct assessment of nutrient limitation through fertilization experiments has been rare, and paradigms pertaining to other ecosystems may not extend to tropical dry forests. For example, because dry tropical forests have a lower water supply than moist tropical forests, dry forests can have lower decomposition rates, higher soil carbon and nitrogen concentrations, and a more open nitrogen cycle than moist forests. We used a mechanistic, numerical model to generate hypotheses about nutrient limitation in tropical dry forests. The model dynamically couples ED2 (vegetation dynamics), MEND (biogeochemistry), and N-COM (plant-microbe competition for nutrients). Here, the MEND-component of the model has been extended to include nitrogen (N) and phosphorus (P) cycles. We focus on simulation of sixteen 25m x 25m plots in Costa Rica where a fertilization experiment has been underway since 2015. Baseline simulations are characterized by both nitrogen and phosphorus limitation of vegetation. Fertilization with N and P increased vegetation biomass, with N fertilization having a somewhat stronger effect. Nutrient limitation was also sensitive to climate and was more pronounced during drought periods. Overflow respiration was identified as a key process that mitigated nutrient limitation. These results suggest that, despite often having richer soils than tropical moist forests, tropical dry forests can also become nutrient-limited. If the climate becomes drier in the next century, as is expected for Central America, drier soils may decrease microbial activity and exacerbate nutrient limitation. The importance of overflow respiration underscores the need for appropriate treatment of microbial dynamics in ecosystem models. Ongoing and new nutrient fertilization experiments will present opportunities for testing whether, and how, nutrient limitation may indeed be emerging in tropical dry

Strong linkage between active microbial communities and microbial carbon usage in a deglaciated terrain of the High Arctic

Science.gov (United States)

Kim, M.; Gyeong, H. R.; Lee, Y. K.

2017-12-01

Soil microorganisms play pivotal roles in ecosystem development and carbon cycling in newly exposed glacier forelands. However, little is known about carbon utilization pattern by metabolically active microbes over the course of ecosystem succession in these nutrient-poor environments. We investigated RNA-based microbial community dynamics and its relation to microbial carbon usage along the chronosequence of a High Arctic glacier foreland. Among microbial taxa surveyed (bacteria, archaea and fungi), bacteria are among the most metabolically active taxa with a dominance of Cyanobacteria and Actinobacteria. There was a strong association between microbial carbon usage and active Actinobacterial communities, suggesting that member of Actinobacteria are actively involved in organic carbon degradation in glacier forelands. Both bacterial community and microbial carbon usage are converged towards later stage of succession, indicating that the composition of soil organic carbon plays important roles in structuring bacterial decomposer communities during ecosystem development.

Reactive Transport Modeling of Microbe-mediated Fe (II) Oxidation for Enhanced Oil Recovery

Science.gov (United States)

Surasani, V.; Li, L.

2011-12-01

Microbially Enhanced Oil Recovery (MEOR) aims to improve the recovery of entrapped heavy oil in depleted reservoirs using microbe-based technology. Reservoir ecosystems often contain diverse microbial communities those can interact with subsurface fluids and minerals through a network of nutrients and energy fluxes. Microbe-mediated reactions products include gases, biosurfactants, biopolymers those can alter the properties of oil and interfacial interactions between oil, brine, and rocks. In addition, the produced biomass and mineral precipitates can change the reservoir permeability profile and increase sweeping efficiency. Under subsurface conditions, the injection of nitrate and Fe (II) as the electron acceptor and donor allows bacteria to grow. The reaction products include minerals such as Fe(OH)3 and nitrogen containing gases. These reaction products can have large impact on oil and reservoir properties and can enhance the recovery of trapped oil. This work aims to understand the Fe(II) oxidation by nitrate under conditions relevant to MEOR. Reactive transport modeling is used to simulate the fluid flow, transport, and reactions involved in this process. Here we developed a complex reactive network for microbial mediated nitrate-dependent Fe (II) oxidation that involves both thermodynamic controlled aqueous reactions and kinetic controlled Fe (II) mineral reaction. Reactive transport modeling is used to understand and quantify the coupling between flow, transport, and reaction processes. Our results identify key parameter controls those are important for the alteration of permeability profile under field conditions.

Activation of CO2-reducing methanogens in oil reservoir after addition of nutrient.

Science.gov (United States)

Yang, Guang-Chao; Zhou, Lei; Mbadinga, Serge Maurice; You, Jing; Yang, Hua-Zhen; Liu, Jin-Feng; Yang, Shi-Zhong; Gu, Ji-Dong; Mu, Bo-Zhong

2016-12-01

Nutrient addition as part of microbial enhanced oil recovery (MEOR) operations have important implications for more energy recovery from oil reservoirs, but very little is known about the in situ response of microorganisms after intervention. An analysis of two genes as biomarkers, mcrA encoding the key enzyme in methanogenesis and fthfs encoding the key enzyme in acetogenesis, was conducted during nutrient addition in oil reservoir. Clone library data showed that dominant mcrA sequences changed from acetoclastic (Methanosaetaceae) to CO 2 -reducing methanogens (Methanomicrobiales and Methanobacteriales), and the authentic acetogens affiliated to Firmicutes decreased after the intervention. Principal coordinates analysis (PCoA) and Jackknife environment clusters revealed evidence on the shift of the microbial community structure among the samples. Quantitative analysis of methanogens via qPCR showed that Methanobacteriales and Methanomicrobiales increased after nutrient addition, while acetoclastic methanogens (Methanosaetaceae) changed slightly. Nutrient treatment activated native CO 2 -reducing methanogens in oil reservoir. The high frequency of Methanobacteriales and Methanomicrobiales (CO 2 -reducers) after nutrient addition in this petroleum system suggested that CO 2 -reducing methanogenesis was involved in methane production. The nutrient addition could promote the methane production. The results will likely improve strategies of utilizing microorganisms in subsurface environments. Copyright © 2016 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

The effect of resource quantity and resource stoichiometry on microbial carbon-use-efficiency

Science.gov (United States)

Kleiblinger, K.M.; Hall, E.K.; Wanek, W.; Szukics, U.; Hämmerle, I.; Ellersdorfer, G.; Böck, S.; Strauss, J.; Sterflinger, K.; Richter, A.; Zechmeister-Boltenstern, S.

2010-01-01

The carbon-use-efficiency (CUE) of microorganisms is an important parameter in determining ecosystem-level carbon (C) cycling; however, little is known about how variance in resources affects microbial CUE. To elucidate how resource quantity and resource stoichiometry affect microbial CUE, we cultured four microorganisms - two fungi (Aspergillus nidulans and Trichoderma harzianum) and two bacteria (Pectobacterium carotovorum and Verrucomicrobium spinosum) - under 12 unique C, nitrogen (N) and phosphorus (P) ratios. Whereas the CUE of A. nidulans was strongly affected by C, bacterial CUE was more strongly affected by mineral nutrients (N and P). Specifically, CUE in P. carotovorum was positively correlated with P, while CUE of V. spinosum primarily depended on N. This resulted in a positive relationship between fungal CUE and resource C : nutrient stoichiometry and a negative relationship between bacterial CUE and resource C : nutrient stoichiometry. The difference in the direction of the relationship between CUE and C : nutrient for fungi vs. bacteria was consistent with differences in biomass stoichiometry and suggested that fungi have a higher C demand than bacteria. These results suggest that the links between biomass stoichiometry, resource demand and CUE may provide a mechanism for commonly observed temporal and spatial patterns in microbial community structure and function in natural habitats.

Microbially mediated barite dissolution in anoxic brines

International Nuclear Information System (INIS)

Ouyang, Bingjie; Akob, Denise M.; Dunlap, Darren; Renock, Devon

2017-01-01

Fluids injected into shale formations during hydraulic fracturing of black shale return with extraordinarily high total-dissolved-solids (TDS) and high concentrations of barium (Ba) and radium (Ra). Barite, BaSO_4, has been implicated as a possible source of Ba as well as a problematic mineral scale that forms on internal well surfaces, often in close association with radiobarite, (Ba,Ra)SO_4. The dissolution of barite by abiotic processes is well quantified. However, the identification of microbial communities in flowback and produced water necessitates the need to understand barite dissolution in the presence of bacteria. Therefore, we evaluated the rates and mechanisms of abiotic and microbially-mediated barite dissolution under anoxic and hypersaline conditions in the laboratory. Barite dissolution experiments were conducted with bacterial enrichment cultures established from produced water from Marcellus Shale wells located in northcentral Pennsylvania. These cultures were dominated by anaerobic halophilic bacteria from the genus Halanaerobium. Dissolved Ba was determined by ICP-OES and barite surfaces were investigated by SEM and AFM. Our results reveal that: 1) higher amounts of barium (up to ∼5 × ) are released from barite in the presence of Halanaerobium cultures compared to brine controls after 30 days of reaction, 2) etch pits that develop on the barite (001) surface in the presence of Halanaerobium exhibit a morphology that is distinct from those that form during control experiments without bacteria, 3) etch pits that develop in the presence of Halanaerobium exhibit a morphology that is similar to the morphology of etch pits formed in the presence of strong organic chelators, EDTA and DTPA, and 4) experiments using dialysis membranes to separate barite from bacteria suggest that direct contact between the two is not required in order to promote dissolution. These results suggest that Halanaerobium increase the rate of barite dissolution in anoxic

Electricity generation and nutrients removal from high-strength liquid manure by air-cathode microbial fuel cells.

Science.gov (United States)

Lin, Hongjian; Wu, Xiao; Nelson, Chad; Miller, Curtis; Zhu, Jun

2016-01-01

Air-cathode microbial fuel cells (MFCs) are widely tested to recover electrical energy from waste streams containing organic matter. When high-strength wastewater, such as liquid animal manure, is used as a medium, inhibition on anode and cathode catalysts potentially impairs the effectiveness of MFC performance in power generation and pollutant removal. This study evaluated possible inhibitive effects of liquid swine manure components on MFC power generation, improved liquid manure-fed MFCs performance by pretreatment (dilution and selective adsorption), and modeled the kinetics of organic matter and nutrients removal kinetics. Parameters monitored included pH, conductivity, chemical oxygen demand (COD), volatile fatty acids (VFAs), total ammoniacal nitrogen (TAN), nitrite, nitrate, and phosphate concentrations. The removals of VFA and TAN were efficient, indicated by the short half-life times of 4.99 and 7.84 d, respectively. The mechanism for phosphate decrease was principally the salt precipitation on cathode, but the removal was incomplete after 42-d operation. MFC with an external resistor of 2.2 kΩ and fed with swine wastewater generated relatively small power (28.2 μW), energy efficiency (0.37%) and Coulombic efficiency (1.5%). Dilution of swine wastewater dramatically improved the power generation as the inhibitory effect was decreased. Zeolite and granular activated carbon were effective in the selective adsorption of ammonia or organic matter in swine wastewater, and so substantially improved the power generation, energy efficiency, and Coulombic efficiency. A smaller external resistor in the circuit was also observed to promote the organic matter degradation and thus to shorten the treatment time. Overall, air-cathode MFCs are promising for generating electrical power from livestock wastewater and meanwhile reducing the level of organic matter and nutrients.

Microbial ecosystem constructed in water for successful organic hydroponics

OpenAIRE

Makoto Shinohara; Hiromi Ohmori; Yoichi Uehara

2008-01-01

Conventional hydroponics systems generally use only chemical fertilisers, not organic ones, since there are no microbial ecosystems present in such systems to mineralise organic compounds to inorganic nutrients. Addition of organic compounds to the hydroponic solution generally has phytotoxic effects and causes poor plant growth. We developed a novel hydroponic culture method using organic fertiliser. A microbial ecosystem was constructed in hydroponic solution by regulating the amounts of or...

Carbon and nitrogen assimilation in deep subseafloor microbial cells

OpenAIRE

Morono, Yuki; Terada, Takeshi; Nishizawa, Manabu; Ito, Motoo; Hillion, François; Takahata, Naoto; Sano, Yuji; Inagaki, Fumio

2011-01-01

Remarkable numbers of microbial cells have been observed in global shallow to deep subseafloor sediments. Accumulating evidence indicates that deep and ancient sediments harbor living microbial life, where the flux of nutrients and energy are extremely low. However, their physiology and energy requirements remain largely unknown. We used stable isotope tracer incubation and nanometer-scale secondary ion MS to investigate the dynamics of carbon and nitrogen assimilation activities in individua...

Effect of soil carbohydrates on nutrient availability in natural forests and cultivated lands in Sri Lanka

Science.gov (United States)

Ratnayake, R. R.; Seneviratne, G.; Kulasooriya, S. A.

2013-05-01

Carbohydrates supply carbon sources for microbial activities that contribute to mineral nutrient production in soil. Their role on soil nutrient availability has not yet been properly elucidated. This was studied in forests and cultivated lands in Sri Lanka. Soil organic matter (SOM) fractions affecting carbohydrate availability were also determined. Soil litter contributed to sugars of plant origin (SPO) in croplands. The negative relationship found between clay bound organic matter (CBO) and glucose indicates higher SOM fixation in clay that lower its availability in cultivated lands. In forests, negative relationships between litter and sugars of microbial origin (SMO) showed that litter fuelled microbes to produce sugars. Fucose and glucose increased the availability of Cu, Zn and Mn in forests. Xylose increased Ca availability in cultivated lands. Arabinose, the main carbon source of soil respiration reduced the P availability. This study showed soil carbohydrates and their relationships with mineral nutrients could provide vital information on the availability of limiting nutrients in tropical ecosystems.

Microbial activity in Alaskan taiga soils contaminated by crude oil in 1976

International Nuclear Information System (INIS)

Monroe, E.M.; Lindstrom, J.E.; Brown, E.J.; Raddock, J.F.

1995-01-01

Biodegradation, often measured via microbial activity, includes destruction of environmental pollutants by living microorganisms and is dependent upon many physical and chemical factors. Effects of mineral nutrients and organic matter on biodegradation of Prudhoe Bay crude oil were investigated at a nineteen-year-old oil spill site in Alaskan taiga. Microcosms of two different soil types from the spill site; one undeveloped soil with forest litter and detritus (O horizon) and one more developed with lower organic content (A horizon), were treated with various nitrogen and phosphorus amendments, and incubated for up to six weeks. Each microcosm was sampled periodically and assayed for hydrocarbon mineralization potential using radiorespirometry, for total carbon dioxide respired using gas chromatography, and for numbers of hydrocarbon-degrading bacteria and heterotrophic bacteria using most probable number counting techniques. Organic matter in the O horizon soil along with combinations of mineral nutrients were found to stimulate microbial activity. No combination of mineral nutrient additions to the A horizon soil stimulated any of the parameters above those measured in control microcosms. The results of this study indicate that adding mineral nutrients and tilling the O horizon into the A horizon of subarctic soils contaminated with crude oil, would stimulate microbial activity, and therefore the biodegradation potential, ultimately increasing the rate of destruction of crude oil in these soils

Microbial Impacts to the Near-Field Environment Geochemistry (MING): A Model for Estimating Microbial Communities in Repository Drifts at Yucca Mountain

International Nuclear Information System (INIS)

Jolley, D.M.; Ehrhorn, T.F.; Horn, J.

2002-01-01

Geochemical and microbiological modeling was performed to evaluate the potential quantities and impact of microorganisms on the geochemistry of the area adjacent to and within nuclear waste packages in the proposed repository drifts at Yucca Mountain, Nevada. The microbial growth results from the introduction of water, ground support, and waste package materials into the deep unsaturated rock. The simulations, which spanned one million years, were accomplished using a newly developed computer code, Microbial Impacts to the Near-Field Environment Geochemistry (MING). MING uses environmental thresholds for limiting microbial growth to temperatures below 120 C and above relative humidities of 90 percent in repository drifts. Once these thresholds are met, MING expands upon a mass balance and thermodynamic approach proposed by McKinley and others (1997), by using kinetic rates to supply constituents from design materials and constituent fluxes including solubilized rock components into the drift, to perform two separate mass-balance calculations as a function of time. The first (nutrient limit) assesses the available nutrients (C, N, P and S) and calculates how many microorganisms can be produced based on a microorganism stoichiometry of C 160 (H 280 O 80 )N 30 P 2 S. The second (energy limit) calculates the energy available from optimally combined redox couples for the temperature, and pH at that time. This optimization maximizes those reactions that produce > 15kJ/mol (limit on useable energy) using an iterative linear optimization technique. The final available energy value is converted to microbial mass at a rate of 1 kg of biomass (dry weight) for every 64 MJ of energy. These two values (nutrient limit and energy limit) are then compared and the smaller value represents the number of microorganisms that can be produced over a specified time. MING can also be adapted to investigate other problems of interest as the model can be used in saturated and unsaturated

Microbial Transformations of Actinides and Fission Products in Radioactive Waste

Energy Technology Data Exchange (ETDEWEB)

Francis, A. J. [Pohang Univ. Science and Technology, Pohang (Korea, Republic of)

2011-07-01

The environmental factors that can affect microbial growth and activity include moisture, temperature, ph, Eh, availability of organic and inorganic nutrients, and radiation. The microbial activity in a specific repository is influenced by the ambient environment of the repository, and the materials to be emplaced. For example, a repository in unsaturated igneous rock formations such as volcanic tuff rocks at Yucca Mountain is generally expected to be oxidizing; a repository in a hydrologically expected to be oxidizing; a repository in a hydrologically saturated zone, especially in sedimentary rocks, could be reducing. Sedimentary rocks contain a certain amount of organic matter, which may stimulate microbial activities and, thus maintain the repository and its surrounding areas at reducing conditions. Although the impacts of microbial activity on high-level nuclear waste and the long-term performance of the repository have not fully investigated, little microbial activity is expected in the near-field because of the radiation, lack of nutrients and the harsh conditions. However in the far-field microbial effects could be significant. Much of our understanding of the microbial effects on radionuclides stems from studies conducted with selected transuranic elements and fission products and limited studies with low-level radioactive wastes. Significant aerobic- and anaerobic-microbial activity is expected to occur in the waste because of the presence of electron donors and acceptors. The actinides initially may be present as soluble- or insoluble-forms but, after disposal, may be converted from one to the other by microorganisms. The direct enzymatic or indirect non-enzymatic actions of microbes could alter the speciation, solubility, and sorption properties of the actinides, thereby increasing or decreasing their concentrations in solution.

Effect of Fermented Supplementation on Growth Performance, Nutrient Digestibility, Blood Characteristics, Fecal Microbial and Fecal Noxious Gas Content in Growing Pigs

Directory of Open Access Journals (Sweden)

L. Yan

2012-12-01

Full Text Available A total of 96 growing pigs ((Landrace×Yorkshire×Duroc; BW = 26.58±1.41 kg were used in a 6-wk feeding trail to evaluate the effects of fermented chlorella (FC supplementation on growth performance, nutrient digestibility, blood characteristics, fecal microbial and fecal noxious gas content in growing pigs. Pigs were randomly allotted into 1 of 4 dietary treatments with 6 replicate pens (2 barrows and 2 gilts per treatment. Dietary treatments were: i negative control (NC, basal diet (without antibiotics; ii positive control (PC, NC+0.05% tylosin; iii (fermented chlorella 01 FC01, NC+0.1% FC, and iv fermented chlorella 02 (FC02, NC+0.2% FC. In this study, feeding pigs PC or FC01 diets led to a higher average daily gain (ADG and dry matter (DM digestibility than those fed NC diet (p0.05 was observed on the body weight, average daily feed intake (ADFI, gain:feed (G:F ratio, the apparent total tract digestibility of N and energy throughout the experiment. The inclusion of PC or FC did not affect the blood characteristics (p>0.05. Moreover, dietary FC treatment led to a higher (p<0.05 lactobacillus concentration and lower E. coli concentration than the NC treatment, whereas the antibiotic supplementation only decreased the E. coli concentration. Pigs fed FC or PC diet had reduced (p<0.05 fecal NH3 and H2S content compared with those fed NC diet. In conclusion, our results indicated that the inclusion of FC01 treatment could improve the growth performance, nutrient digestibility, fecal microbial shedding (lower E. coli and higher lactobacillus, and decrease the fecal noxious gas emission in growing pigs when compared with the group fed the basal diet. In conclusion, dietary FC could be considered as a good source of supplementation in growing pigs because of its growth promoting effect.

CO2 and nutrient-driven changes across multiple levels of organization in Zostera noltii ecosystems

Science.gov (United States)

Martínez-Crego, B.; Olivé, I.; Santos, R.

2014-12-01

Increasing evidence emphasizes that the effects of human impacts on ecosystems must be investigated using designs that incorporate the responses across levels of biological organization as well as the effects of multiple stressors. Here we implemented a mesocosm experiment to investigate how the individual and interactive effects of CO2 enrichment and eutrophication scale-up from changes in primary producers at the individual (biochemistry) or population level (production, reproduction, and/or abundance) to higher levels of community (macroalgae abundance, herbivory, and global metabolism), and ecosystem organization (detritus release and carbon sink capacity). The responses of Zostera noltii seagrass meadows growing in low- and high-nutrient field conditions were compared. In both meadows, the expected CO2 benefits on Z. noltii leaf production were suppressed by epiphyte overgrowth, with no direct CO2 effect on plant biochemistry or population-level traits. Multi-level meadow response to nutrients was faster and stronger than to CO2. Nutrient enrichment promoted the nutritional quality of Z. noltii (high N, low C : N and phenolics), the growth of epiphytic pennate diatoms and purple bacteria, and shoot mortality. In the low-nutrient meadow, individual effects of CO2 and nutrients separately resulted in reduced carbon storage in the sediment, probably due to enhanced microbial degradation of more labile organic matter. These changes, however, had no effect on herbivory or on community metabolism. Interestingly, individual effects of CO2 or nutrient addition on epiphytes, shoot mortality, and carbon storage were attenuated when nutrients and CO2 acted simultaneously. This suggests CO2-induced benefits on eutrophic meadows. In the high-nutrient meadow, a striking shoot decline caused by amphipod overgrazing masked the response to CO2 and nutrient additions. Our results reveal that under future scenarios of CO2, the responses of seagrass ecosystems will be complex and

Effect of -based Direct-fed Microbial on Performance, Nutrient Utilization, Intestinal Morphology and Cecal Microflora in Broiler Chickens

Directory of Open Access Journals (Sweden)

Xinjian Lei

2015-02-01

Full Text Available The present study was conducted to evaluate the effect of the dietary supplementation of Bacillus amyloliquefaciens-based direct-fed microbial (DFM on growth performance, nutrient utilization, intestinal morphology and cecal microflora in broiler chickens. A total of two hundred and eighty eight 1-d-old Arbor Acres male broilers were randomly allocated to one of four experimental treatments in a completely randomized design. Each treatment was fed to eight replicate cages, with nine birds per cage. Dietary treatments were composed of an antibiotic-free basal diet (control, and the basal diet supplemented with either 15 mg/kg of virginiamycin as antibiotic growth promoter (AGP, 30 mg/kg of Bacillus amyloliquefaciens-based DFM (DFM 30 or 60 mg/kg of Bacillus amyloliquefaciens-based DFM (DFM 60. Experimental diets were fed in two phases: starter (d 1 to 21 and finisher (d 22 to 42. Growth performance, nutrient utilization, morphological parameters of the small intestine and cecal microbial populations were measured at the end of the starter (d 21 and finisher (d 42 phases. During the starter phase, DFM and virginiamycin supplementation improved the feed conversion ratio (FCR; p<0.01 compared with the control group. For the finisher phase and the overall experiment (d 1 to 42 broilers fed diets with the DFM had better body weight gain (BWG and FCR than that of control (p<0.05. Supplementation of virginiamycin and DFM significantly increased the total tract apparent digestibility of crude protein (CP, dry matter (DM and gross energy during both starter and finisher phases (p<0.05 compared with the control group. On d 21, villus height, crypt depth and villus height to crypt depth ratio of duodenum, jejunum, and ileum were significantly increased for the birds fed with the DFM diets as compared with the control group (p<0.05. The DFM 30, DFM 60, and AGP groups decreased the Escherichia coli population in cecum at d 21 and d 42 compared with control

Multivariate analyses in soil microbial ecology : a new paradigm

OpenAIRE

Thioulouse, J.; Prin, Y.; Duponnois, Robin

2012-01-01

Mycorrhizal symbiosis is a key component of a sustainable soil-plant system, governing the cycles of major plant nutrients and vegetation cover. The mycorrhizosphere includes plants roots, the mycorrhizal fungi, and a complex microbial compartment. A large number of methods have been used to characterize the genetic and functional diversity of these soil microbial communities. We present here a review of the multivariate data analysis methods that have been used in 16 research articles publis...

Molecular and risk-based approach to nutrient development for a proposed sub-surface biogasification field trial in a biogenic gas field

Energy Technology Data Exchange (ETDEWEB)

Lambo, Adewale J.; Strapoc, Dariusz; Pittenger, Michelle; Huizinga, Bradley [ConocoPhillips (Canada); Wood, Ladonna; Ashby, Matt [Taxon Biosciences (Canada)

2011-07-01

This paper presents the molecular and risk-based approach to nutrient development for a proposed sub-surface biogasification field trial in a biogenic gas field. From field sampling, variability was seen in water chemistry and environmental parameters across the field; DNA yield also varied across the field and showed distinct spatial variation. The composition of microbial populations and relative distribution of archaea populations in the Cooks Inlet water is represented using pie and bar charts. The nutrient recipe was developed using known information on nutrient requirements of mathematically correlated microbial associations. The process of on-site nutrient injection is explained. Some of the mitigation plans for the risks involved during the process include, among others, limiting biofilm prevalence and avoiding bio-plugging and bio-corrosion. Biofilm is likely to develop in the injection line but less likely in nutrient mixing due to the high nutrient concentration. From the study, it can be concluded that community composition correlates with field geochemical parameters and methane pathways.

Salmon-mediated nutrient flux in selected streams of the Columbia River basin, USA

Science.gov (United States)

Kohler, Andre E.; Kusnierz, Paul C.; Copeland, Timothy; Venditti, David A.; Denny, Lytle; Gable, Josh; Lewis, Bert; Kinzer, Ryan; Barnett, Bruce; Wipfli, Mark S.

2013-01-01

Salmon provide an important resource subsidy and linkage between marine and land-based ecosystems. This flow of energy and nutrients is not uni-directional (i.e., upstream only); in addition to passive nutrient export via stream flow, juvenile emigrants actively export nutrients from freshwater environments. In some cases, nutrient export can exceed import. We evaluated nutrient fluxes in streams across central Idaho, USA using Chinook salmon (Oncorhynchus tshawytscha) adult escapement and juvenile production data from 1998 to 2008. We found in the majority of stream-years evaluated, adults imported more nutrients than progeny exported; however, in 3% of the years, juveniles exported more nutrients than their parents imported. On average, juvenile emigrants exported 22 ± 3% of the nitrogen and 30 ± 4% of the phosphorus their parents imported. This relationship was density dependent and nonlinear; during periods of low adult abundance juveniles were larger and exported up to 194% and 268% of parental nitrogen and phosphorus inputs, respectively. We highlight minimum escapement thresholds that appear to 1) maintain consistently positive net nutrient flux and 2) reduce the average proportional rate of export across study streams. Our results suggest a state-shift occurs when adult spawner abundance falls below a threshold to a point where the probability of juvenile nutrient exports exceeding adult imports becomes increasingly likely.

A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems.

Science.gov (United States)

Budinich, Marko; Bourdon, Jérémie; Larhlimi, Abdelhalim; Eveillard, Damien

2017-01-01

Interplay within microbial communities impacts ecosystems on several scales, and elucidation of the consequent effects is a difficult task in ecology. In particular, the integration of genome-scale data within quantitative models of microbial ecosystems remains elusive. This study advocates the use of constraint-based modeling to build predictive models from recent high-resolution -omics datasets. Following recent studies that have demonstrated the accuracy of constraint-based models (CBMs) for simulating single-strain metabolic networks, we sought to study microbial ecosystems as a combination of single-strain metabolic networks that exchange nutrients. This study presents two multi-objective extensions of CBMs for modeling communities: multi-objective flux balance analysis (MO-FBA) and multi-objective flux variability analysis (MO-FVA). Both methods were applied to a hot spring mat model ecosystem. As a result, multiple trade-offs between nutrients and growth rates, as well as thermodynamically favorable relative abundances at community level, were emphasized. We expect this approach to be used for integrating genomic information in microbial ecosystems. Following models will provide insights about behaviors (including diversity) that take place at the ecosystem scale.

Does canine inflammatory bowel disease influence gut microbial profile and host metabolism?

OpenAIRE

Xu, Jia; Verbrugghe, Adronie; Louren?o, Marta; Janssens, Geert P. J.; Liu, Daisy J. X.; Van de Wiele, Tom; Eeckhaut, Venessa; Van Immerseel, Filip; Van de Maele, Isabel; Niu, Yufeng; Bosch, Guido; Junius, Greet; Wuyts, Brigitte; Hesta, Myriam

2016-01-01

Background Inflammatory bowel disease (IBD) refers to a diverse group of chronic gastrointestinal diseases, and gut microbial dysbiosis has been proposed as a modulating factor in its pathogenesis. Several studies have investigated the gut microbial ecology of dogs with IBD but it is yet unclear if this microbial profile can alter the nutrient metabolism of the host. The aim of the present study was to characterize the faecal bacterial profile and functionality as well as to determine host me...

Short-term incorporation of organic manures and biofertilizers influences biochemical and microbial characteristics of soils under an annual crop [Turmeric (Curcuma longa L.)].

Science.gov (United States)

Dinesh, R; Srinivasan, V; Hamza, S; Manjusha, A

2010-06-01

The study was conducted to determine whether short-term incorporation of organic manures and biofertilizers influence biochemical and microbial variables reflecting soil quality. For the study, soils were collected from a field experiment conducted on turmeric (Curcuma longa L.) involving organic nutrient management (ONM), chemical nutrient management (CNM) and integrated nutrient management (INM). The findings revealed that application of organic manures and biofertilizers (ONM and INM) positively influenced microbial biomass C, N mineralization, soil respiration and enzymes activities. Contrarily, greater metabolic quotient levels in CNM indicated a stressed soil microbial community. Principal component analysis indicated the strong relationship between microbial activity and the availability of labile and easily mineralizable organic matter. The findings imply that even short-term incorporation of organic manures and biofertilizers promoted soil microbial and enzyme activities and these parameters are sensitive enough to detect changes in soil quality due to short-term incorporation of biological fertilizers. (c) 2010 Elsevier Ltd. All rights reserved.

Short-Term Effects of Drying-Rewetting and Long-Term Effects of Nutrient Loading on Periphyton N:P Stoichiometry

Directory of Open Access Journals (Sweden)

Andres D. Sola

2018-01-01

Full Text Available Nitrogen (N and phosphorus (P concentrations and N:P ratios critically influence periphyton productivity and nutrient cycling in aquatic ecosystems. In coastal wetlands, variations in hydrology and water source (fresh or marine influence nutrient availability, but short-term effects of drying and rewetting and long-term effects of nutrient exposure on periphyton nutrient retention are uncertain. An outdoor microcosm experiment simulated short-term exposure to variation in drying-rewetting frequency on periphyton mat nutrient retention. A 13-year dataset from freshwater marshes of the Florida Everglades was examined for the effect of long-term proximity to different N and P sources on mat-forming periphyton nutrient standing stocks and stoichiometry. Field sites were selected from one drainage with shorter hydroperiod and higher connectivity to freshwater anthropogenic nutrient supplies (Taylor Slough/Panhandle, TS/Ph and another drainage with longer hydroperiod and higher connectivity to marine nutrient supplies (Shark River Slough, SRS. Total P, but not total N, increased in periphyton mats exposed to both low and high drying-rewetting frequency with respect to the control mats in our experimental microcosm. In SRS, N:P ratios slightly decreased downstream due to marine nutrient supplies, while TS/Ph increased. Mats exposed to short-term drying-rewetting had higher nutrient retention, similar to nutrient standing stocks from long-term field data. Periphyton mat microbial communities may undergo community shifts upon drying-rewetting and chronic exposure to nutrient loads. Additional work on microbial species composition may further explain how periphyton communities interact with drying-rewetting dynamics to influence nutrient cycling and retention in wetlands.

Effects of simulated acid rain on microbial characteristics in a lateritic red soil.

Science.gov (United States)

Xu, Hua-qin; Zhang, Jia-en; Ouyang, Ying; Lin, Ling; Quan, Guo-ming; Zhao, Ben-liang; Yu, Jia-yu

2015-11-01

A laboratory experiment was performed to examine the impact of simulated acid rain (SAR) on nutrient leaching, microbial biomass, and microbial activities in a lateritic red soil in South China. The soil column leaching experiment was conducted over a 60-day period with the following six SAR pH treatments (levels): 2.5, 3.0, 3.5, 4.0, 4.5, and 5.0 and one control treatment (pH = 7). Compared with the control treatment, the concentrations of soil organic matter, total nitrogen, total phosphorus, total potassium, soil microbial biomass carbon (MBC), soil microbial biomass nitrogen (MBN), and average well color density (AWCD) in the Ecoplates were all significantly decreased by leaching with SAR at different pH levels. The decrease in MBC and MBN indicated that acid rain reduced the soil microbial population, while the decrease in AWCD revealed that acid rain had a negative effect on soil bacterial metabolic function. Soil basal respiration increased gradually from pH 4.0 to 7.0 but decreased dramatically from pH 2.5 to 3.0. The decrease in soil nutrient was the major reason for the change of soil microbial functions. A principal component analysis showed that the major carbon sources used by the bacteria were carbohydrates and carboxylic acids.

Corals and Their Microbiomes Are Differentially Affected by Exposure to Elevated Nutrients and a Natural Thermal Anomaly

Directory of Open Access Journals (Sweden)

Lu Wang

2018-03-01

Full Text Available Nutrient pollution can increase the prevalence and severity of coral disease and bleaching in ambient temperature conditions or during experimental thermal challenge. However, there have been few opportunities to study the effects of nutrient pollution during natural thermal anomalies. Here we present results from an experiment conducted during the 2014 bleaching event in the Florida Keys, USA, that exposed Agaricia sp. (Undaria and Siderastrea siderea corals to 3 types of elevated nutrients: nitrogen alone, phosphorous alone, and the combination of nitrogen and phosphorus. Overall, bleaching prevalence and severity was high regardless of treatment, but nitrogen enrichment alone both prolonged bleaching and increased coral mortality in Agaricia corals. At the same time, the elevated temperatures increased the prevalence of Dark Spot Syndrome (DSS, a disease typically associated with cold temperatures in Siderastrea siderea corals. However, nutrient exposure alone did not increase the prevalence or severity of disease, suggesting that thermal stress overwhelms the effects of nutrient pollution on this disease during such an extreme thermal event. Analysis of 78 Siderastrea siderea microbial metagenomes also showed that the thermal event was correlated with significant shifts in the composition and function of the associated microbiomes, and corals with DSS had microbiomes distinct from apparently healthy corals. In particular, we identified shifts in viral, archaeal, and fungal families. These shifts were likely driven by the extreme temperatures or other environmental co-variates occurring during the 2014 bleaching event. However, no microbial taxa were correlated with signs of DSS. Furthermore, although nutrient exposure did not affect microbial alpha diversity, it did significantly affect microbiome beta-diversity, an effect that was independent of time. These results suggest that strong thermal anomalies and local nutrient pollution both

Gold nanoparticles produced in situ mediate bioelectricity and hydrogen production in a microbial fuel cell by quantized capacitance charging.

Science.gov (United States)

Kalathil, Shafeer; Lee, Jintae; Cho, Moo Hwan

2013-02-01

Oppan quantized style: By adding a gold precursor at its cathode, a microbial fuel cell (MFC) is demonstrated to form gold nanoparticles that can be used to simultaneously produce bioelectricity and hydrogen. By exploiting the quantized capacitance charging effect, the gold nanoparticles mediate the production of hydrogen without requiring an external power supply, while the MFC produces a stable power density. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Models of microbiome evolution incorporating host and microbial selection.

Science.gov (United States)

Zeng, Qinglong; Wu, Steven; Sukumaran, Jeet; Rodrigo, Allen

2017-09-25

Numerous empirical studies suggest that hosts and microbes exert reciprocal selective effects on their ecological partners. Nonetheless, we still lack an explicit framework to model the dynamics of both hosts and microbes under selection. In a previous study, we developed an agent-based forward-time computational framework to simulate the neutral evolution of host-associated microbial communities in a constant-sized, unstructured population of hosts. These neutral models allowed offspring to sample microbes randomly from parents and/or from the environment. Additionally, the environmental pool of available microbes was constituted by fixed and persistent microbial OTUs and by contributions from host individuals in the preceding generation. In this paper, we extend our neutral models to allow selection to operate on both hosts and microbes. We do this by constructing a phenome for each microbial OTU consisting of a sample of traits that influence host and microbial fitnesses independently. Microbial traits can influence the fitness of hosts ("host selection") and the fitness of microbes ("trait-mediated microbial selection"). Additionally, the fitness effects of traits on microbes can be modified by their hosts ("host-mediated microbial selection"). We simulate the effects of these three types of selection, individually or in combination, on microbiome diversities and the fitnesses of hosts and microbes over several thousand generations of hosts. We show that microbiome diversity is strongly influenced by selection acting on microbes. Selection acting on hosts only influences microbiome diversity when there is near-complete direct or indirect parental contribution to the microbiomes of offspring. Unsurprisingly, microbial fitness increases under microbial selection. Interestingly, when host selection operates, host fitness only increases under two conditions: (1) when there is a strong parental contribution to microbial communities or (2) in the absence of a strong

Growth Mechanism of Microbial Colonies

Science.gov (United States)

Zhu, Minhui; Martini, K. Michael; Kim, Neil H.; Sherer, Nicholas; Lee, Jia Gloria; Kuhlman, Thomas; Goldenfeld, Nigel

Experiments on nutrient-limited E. coli colonies, growing on agar gel from single cells reveal a power-law distribution of sizes, both during the growth process and in the final stage when growth has ceased. We developed a Python simulation to study the growth mechanism of the bacterial population and thus understand the broad details of the experimental findings. The simulation takes into account nutrient uptake, metabolic function, growth and cell division. Bacteria are modeled in two dimensions as hard circle-capped cylinders with steric interactions and elastic stress dependent growth characteristics. Nutrient is able to diffuse within and between the colonies. The mechanism of microbial colony growth involves reproduction of cells within the colonies and the merging of different colonies. We report results on the dynamic scaling laws and final state size distribution, that capture in semi-quantitative detail the trends observed in experiment. Supported by NSF Grant 0822613.

Graded substitution of grains with bakery by-products modulates ruminal fermentation, nutrient degradation, and microbial community composition in vitro.

Science.gov (United States)

Humer, E; Aditya, S; Kaltenegger, A; Klevenhusen, F; Petri, R M; Zebeli, Q

2018-04-01

A new segment of feed industry based on bakery by-products (BBP) has emerged. Yet, information is lacking regarding the effects of inclusion of BBP in ruminant diets on ruminal fermentation and microbiota. Therefore, the aim of this study was to evaluate the effect of the gradual replacement of grains by BBP on ruminal fermentation, nutrient degradation, and microbial community composition using the rumen-simulation technique. All diets consisted of hay and concentrate mixture with a ratio of 42:58 (dry matter basis), but differed in the concentrate composition with either 45% cereal grains or BBP, whereby 15, 30, or 45% of BBP were used in place of cereal grains. The inclusion of increasing levels of BBP in the diet linearly enhanced ruminal degradation of starch from 84% (control) to 96% (45% BBP), while decreasing degradation of crude protein and fiber. The formation of methane was lowered in the 45% BBP diet compared with all other diets. Whereas the ammonia concentration was similar in the control and 15% BBP, a significant decrease was found in 30% BBP (-23%) and 45% BBP (-33%). Also, BBP feeding shifted fermentation profile toward propionate at the expense of acetate. Moreover, isobutyrate linearly decreased with increasing BBP inclusion. Bacterial 16S rRNA Illumina MiSeq (Microsynth AG, Balach, Switzerland) sequencing revealed a decreased microbial diversity for the 45% BBP diet. Furthermore, the replacement of cereal grains with BBP went along with an increased abundance of the genera Prevotella, Roseburia, and Megasphaera, while decreasing Butyrivibrio and several OTU belonging to Ruminococcaceae. In conclusion, the inclusion of BBP at up to 30% of the dry matter had no detrimental effects on pH, fiber degradability, and microbial diversity, and enhanced propionate production. However, a higher replacement level (45%) impaired ruminal fermentation traits and fiber degradation and is not recommended. Copyright © 2018 American Dairy Science Association

Phosphorus uptake by decomposing leaf detritus: effect of microbial biomass and activity

Energy Technology Data Exchange (ETDEWEB)

Mulholland, P J; Elwood, J W; Newbold, J D; Webster, J R; Ferren, L A; Perkins, R E

1984-12-01

The dominant energy source in small woodland streams is the allochthonous input of leaves. Utilization of this energy source by stream biota establishes the patterns of secondary productivity and nutrient uptake in these ecosystems. Although leaf inputs support much of the production of macroinvertebrates and higher consumers in streams, microbes are the critical link between these organisms and the leaf resource, much of which is undigestible by higher organisms. A number of studies have indicated that stream macroinvertebrates preferentially select leaves with greater levels of microbial activity. Rates of microbial activity associated with decomposing leaves were shown to be dependent on the supply of P in one woodland stream. In other streams, leaf decomposition has been shown to be nutrient limited as well. Thus, as in many other ecosystems, maintenance of high levels of production in streams is dependent on retention and efficient recycling of nutrients. Uptake of P by microbes colonizing leaves is an important mechanism for nutrient retention in small woodland streams. In these systems, numerous debris collections efficiently retard downstream movement of particulate materials, especially decomposing leaves. Uptake of dissolved, easily transportable forms of P by microbes attached to decomposing leaves increases P retention in streams. The more rapid the rate of P uptake onto decomposing leaves for a given P supply, the shorter the P uptake length and the more times an atom of P is utilized within a given stream reach. In this study the authors examined the temporal patterns of P uptake during the early stages of leaf decomposition in streams. Patterns of P uptake were compared to patterns of other measurements of microbial activity to identify the effect of microbial succession or conditioning of leaves on P uptake. 22 references, 1 figure, 2 tables.

Out of sight - Profiling soil characteristics, nutrients and microbial communities affected by organic amendments down to one meter in a long-term maize cultivation experiment

Science.gov (United States)

Lehtinen, Taru; Mikkonen, Anu; Zavattaro, Laura; Grignani, Carlo; Baumgarten, Andreas; Spiegel, Heide

2016-04-01

Soil characteristics, nutrients and microbial activity in the deeper soil layers are topics not of-ten covered in agricultural studies since the main interest lies within the most active topsoils and deep soils are more time-consuming to sample. Studies have shown that deep soil does matter, although biogeochemical cycles are not fully understood yet. The main aim of this study is to investigate the soil organic matter dynamics, nutrients and microbial community composition in the first meter of the soil profiles in the long-term maize cropping system ex-periment Tetto Frati, in the vicinity of the Po River in Northern Italy. The trial site lies on a deep, calcareous, free-draining soil with a loamy texture. The following treatments have been applied since 1992: 1) maize for silage with 250 kg mineral N ha-1 (crop residue removal, CRR), 2) maize for grain with 250 kg mineral N ha-1 (crop residue incorporation, CRI), 3) maize for silage with 250 kg bovine slurry N ha-1 (SLU), 4) maize for silage with 250 kg farm yard manure N ha-1 (FYM). Soil characteristics (pH, carbonate content, soil organic carbon (SOC), aggregate stability (WSA)), and nutrients (total nitrogen (Nt), CAL-extractable phos-phorous (P) and potassium (K), potential N mineralisation) were investigated. Bacteri-al community composition was investigated with Ion PGM high-throughput sequencing at the depth of 8000 sequences per sample. Soil pH was moderately alkaline in all soil samples, in-creasing with increasing soil depth, as the carbonate content increased. SOC was significantly higher in the treatments with organic amendments (CRI, SLU and FYM) compared to CRR in 0-25 cm (11.1, 11.6, 14.7 vs. 9.8 g kg-1, respectively), but not in the deeper soil. At 50-75 cm soil depth FYM treatment revealed higher WSA compared to CRR, as well as higher CAL-extractable K (25 and 15 mg kg-1, respectively) and potential N mineralisation (11.30 and 8.78 mg N kg-1 7d-1, respectively). At 75-100 cm soil depth, SLU and

Functional ecology of soil microbial communities along a glacier forefield in Tierra del Fuego (Chile).

Science.gov (United States)

Fernández-Martínez, Miguel A; Pointing, Stephen B; Pérez-Ortega, Sergio; Arróniz-Crespo, María; Green, T G Allan; Rozzi, Ricardo; Sancho, Leopoldo G; de Los Ríos, Asunción

2016-09-01

A previously established chronosequence from Pia Glacier forefield in Tierra del Fuego (Chile) containing soils of different ages (from bare soils to forest ones) is analyzed. We used this chronosequence as framework to postulate that microbial successional development would be accompanied by changes in functionality. To test this, the GeoChip functional microarray was used to identify diversity of genes involved in microbial carbon and nitrogen metabolism, as well as other genes related to microbial stress response and biotic interactions. Changes in putative functionality generally reflected succession-related taxonomic composition of soil microbiota. Major shifts in carbon fixation and catabolism were observed, as well as major changes in nitrogen metabolism. At initial microbial dominated succession stages, microorganisms could be mainly involved in pathways that help to increase nutrient availability, while more complex microbial transformations such as denitrification and methanogenesis, and later degradation of complex organic substrates, could be more prevalent at vegetated successional states. Shifts in virus populations broadly reflected changes in microbial diversity. Conversely, stress response pathways appeared relatively well conserved for communities along the entire chronosequence. We conclude that nutrient utilization is likely the major driver of microbial succession in these soils. [Int Microbiol 19(3):161-173 (2016)]. Copyright© by the Spanish Society for Microbiology and Institute for Catalan Studies.

Contaminant immobilization via microbial activity

International Nuclear Information System (INIS)

1991-11-01

The aim of this study was to search the literature to identify biological techniques that could be applied to the restoration of contaminated groundwaters near uranium milling sites. Through bioremediation it was hypothesized that the hazardous heavy metals could be immobilized in a stable, low-solubility form, thereby halting their progress in the migrating groundwater. Three basic mechanisms were examined: reduction of heavy metals by microbially produced hydrogen sulfide; direct microbial mediated reduction; and biosorption

Investigation of nutrient feeding strategies in a countercurrent mixed-acid multi-staged fermentation: experimental data.

Science.gov (United States)

Smith, Aaron Douglas; Lockman, Nur Ain; Holtzapple, Mark T

2011-06-01

Nutrients are essential for microbial growth and metabolism in mixed-culture acid fermentations. Understanding the influence of nutrient feeding strategies on fermentation performance is necessary for optimization. For a four-bottle fermentation train, five nutrient contacting patterns (single-point nutrient addition to fermentors F1, F2, F3, and F4 and multi-point parallel addition) were investigated. Compared to the traditional nutrient contacting method (all nutrients fed to F1), the near-optimal feeding strategies improved exit yield, culture yield, process yield, exit acetate-equivalent yield, conversion, and total acid productivity by approximately 31%, 39%, 46%, 31%, 100%, and 19%, respectively. There was no statistical improvement in total acid concentration. The traditional nutrient feeding strategy had the highest selectivity and acetate-equivalent selectivity. Total acid productivity depends on carbon-nitrogen ratio.

Above- and belowground linkages in Sphagnum peatland: climate warming affects plant-microbial interactions.

Science.gov (United States)

Jassey, Vincent E J; Chiapusio, Geneviève; Binet, Philippe; Buttler, Alexandre; Laggoun-Défarge, Fatima; Delarue, Frédéric; Bernard, Nadine; Mitchell, Edward A D; Toussaint, Marie-Laure; Francez, André-Jean; Gilbert, Daniel

2013-03-01

Peatlands contain approximately one third of all soil organic carbon (SOC). Warming can alter above- and belowground linkages that regulate soil organic carbon dynamics and C-balance in peatlands. Here we examine the multiyear impact of in situ experimental warming on the microbial food web, vegetation, and their feedbacks with soil chemistry. We provide evidence of both positive and negative impacts of warming on specific microbial functional groups, leading to destabilization of the microbial food web. We observed a strong reduction (70%) in the biomass of top-predators (testate amoebae) in warmed plots. Such a loss caused a shortening of microbial food chains, which in turn stimulated microbial activity, leading to slight increases in levels of nutrients and labile C in water. We further show that warming altered the regulatory role of Sphagnum-polyphenols on microbial community structure with a potential inhibition of top predators. In addition, warming caused a decrease in Sphagnum cover and an increase in vascular plant cover. Using structural equation modelling, we show that changes in the microbial food web affected the relationships between plants, soil water chemistry, and microbial communities. These results suggest that warming will destabilize C and nutrient recycling of peatlands via changes in above- and belowground linkages, and therefore, the microbial food web associated with mosses will feedback positively to global warming by destabilizing the carbon cycle. This study confirms that microbial food webs thus constitute a key element in the functioning of peatland ecosystems. Their study can help understand how mosses, as ecosystem engineers, tightly regulate biogeochemical cycling and climate feedback in peatlands. © 2012 Blackwell Publishing Ltd.

Nematodes enhance plant growth and nutrient uptake under C and N-rich conditions

Science.gov (United States)

Gebremikael, Mesfin T.; Steel, Hanne; Buchan, David; Bert, Wim; de Neve, Stefaan

2016-09-01

The role of soil fauna in crucial ecosystem services such as nutrient cycling remains poorly quantified, mainly because of the overly reductionistic approach adopted in most experimental studies. Given that increasing nitrogen inputs in various ecosystems influence the structure and functioning of soil microbes and the activity of fauna, we aimed to quantify the role of the entire soil nematode community in nutrient mineralization in an experimental set-up emulating nutrient-rich field conditions and accounting for crucial interactions amongst the soil microbial communities and plants. To this end, we reconstructed a complex soil foodweb in mesocosms that comprised largely undisturbed native microflora and the entire nematode community added into defaunated soil, planted with Lolium perenne as a model plant, and amended with fresh grass-clover residues. We determined N and P availability and plant uptake, plant biomass and abundance and structure of the microbial and nematode communities during a three-month incubation. The presence of nematodes significantly increased plant biomass production (+9%), net N (+25%) and net P (+23%) availability compared to their absence, demonstrating that nematodes link below- and above-ground processes, primarily through increasing nutrient availability. The experimental set-up presented allows to realistically quantify the crucial ecosystem services provided by the soil biota.

Microbial Inoculants and Their Impact on Soil Microbial Communities: A Review

Directory of Open Access Journals (Sweden)

Darine Trabelsi

2013-01-01

Full Text Available The knowledge of the survival of inoculated fungal and bacterial strains in field and the effects of their release on the indigenous microbial communities has been of great interest since the practical use of selected natural or genetically modified microorganisms has been developed. Soil inoculation or seed bacterization may lead to changes in the structure of the indigenous microbial communities, which is important with regard to the safety of introduction of microbes into the environment. Many reports indicate that application of microbial inoculants can influence, at least temporarily, the resident microbial communities. However, the major concern remains regarding how the impact on taxonomic groups can be related to effects on functional capabilities of the soil microbial communities. These changes could be the result of direct effects resulting from trophic competitions and antagonistic/synergic interactions with the resident microbial populations, or indirect effects mediated by enhanced root growth and exudation. Combination of inoculants will not necessarily produce an additive or synergic effect, but rather a competitive process. The extent of the inoculation impact on the subsequent crops in relation to the buffering capacity of the plant-soil-biota is still not well documented and should be the focus of future research.

Aerobic Granular Sludge: Effect of Salt and Insights into Microbial Ecology

KAUST Repository

Wang, Zhongwei

2017-12-01

Aerobic granular sludge (AGS) technology is a next-generation technology for the biological treatment of wastewater. The advantages of AGS in terms of small footprint, low operation and capital cost and high effluent quality makes it a strong candidate for replacing conventional biological wastewater treatment based on activated sludge (CAS) process, and potentially become the standard for biological wastewater treatment in the future. Saline wastewater is generated from many industrial processes as well as from the use of sea water as a secondary quality water for non-potable use such as toilet flushing to mitigate shortage of fresh water in some coastal cities. Salt is known to inhibit biological wastewater treatment processes in terms of organic and nutrient removal. In the first part of my dissertation, I conducted three lab-scale experiments to 1) evaluate the effect of salt on granulation and nutrient removal in AGS (330 days); 2) develop engineering strategies to mitigate the adverse effect of salt on nutrient removal of AGS (164 days); and 3) compare the effect of salt on the stoichiometry and kinetics of different phosphate accumulating organisms (PAO) clades (PAOI and PAOII) and to determine the effect of potassium and sodium ions on the activities of different PAO clades (225 days). Like other artificial microbial ecosystems (e.g. CAS plant and anaerobic digester), a firm understanding of the microbial ecology of AGS system is essential for process design and optimization. The second part of my dissertation reported the first microbial ecology study of a full-scale AGS plant with the aim of addressing the role of regional (i.e. immigration) versus local factors in shaping the microbial community assembly of different-sized microbial aggregates in AGS. The microbial communities in a full-scale AGS plant in Garmerwolde, The Netherlands, was characterized periodically over 180 days using Illumina sequencing of 16S ribosomal RNA amplicons of the V3-V4

In Situ Ecophysiology of Microbial Biofilm Communities Analyzed by CMEIAS Computer-Assisted Microscopy at Single-Cell Resolution

Directory of Open Access Journals (Sweden)

Youssef G. Yanni

2013-06-01

Full Text Available This paper describes the utility of CMEIAS (Center for Microbial Ecology Image Analysis System computer-assisted microscopy to extract data from accurately segmented images that provide 63 different insights into the ecophysiology of microbial populations and communities within biofilms and other habitats. Topics include quantitative assessments of: (i morphological diversity as an indicator of impacts that substratum physicochemistries have on biofilm community structure and dominance-rarity relationships among populations; (ii morphotype-specific distributions of biovolume body size that relate microbial allometric scaling, metabolic activity and growth physiology; (iii fractal geometry of optimal cellular positioning for efficient utilization of allocated nutrient resources; (iv morphotype-specific stress responses to starvation, environmental disturbance and bacteriovory predation; (v patterns of spatial distribution indicating positive and negative cell–cell interactions affecting their colonization behavior; and (vi significant methodological improvements to increase the accuracy of color-discriminated ecophysiology, e.g., differentiation of cell viability based on cell membrane integrity, cellular respiratory activity, phylogenetically differentiated substrate utilization, and N-acyl homoserine lactone-mediated cell–cell communication by bacteria while colonizing plant roots. The intensity of these ecophysiological attributes commonly varies at the individual cell level, emphasizing the importance of analyzing them at single-cell resolution and the proper spatial scale at which they occur in situ.

Peran Information Conciousness dan Nutrient Information dalam Meningkatkan Kinerja Individual

Directory of Open Access Journals (Sweden)

Niken Wahyu Wilujeng

2014-12-01

Full Text Available The objective of this research is to analyze nutrient information and information consciousness as factors that influence employee’s performance and job satisfication as intervening variable for finance employee in Brawijaya University. By employing Partial Least Square technique, it was indicated that nutrient information and information consciousness have positive effect to job satisfication, while job satisfication can also fully mediate nutrient information and information consciousness to employee’s performance. This research also indicated that information consciousness and nutrient information are factors that influence finance employee’s performance through intelectual emphasis.

Microbial Impacts to the Near-Field Environment Geochemistry (MING): A Model for Estimating Microbial Communities in Repository Drifts at Yucca Mountain

Energy Technology Data Exchange (ETDEWEB)

D.M. Jolley; T.F. Ehrhorn; J. Horn

2002-03-19

Geochemical and microbiological modeling was performed to evaluate the potential quantities and impact of microorganisms on the geochemistry of the area adjacent to and within nuclear waste packages in the proposed repository drifts at Yucca Mountain, Nevada. The microbial growth results from the introduction of water, ground support, and waste package materials into the deep unsaturated rock. The simulations, which spanned one million years, were accomplished using a newly developed computer code, Microbial Impacts to the Near-Field Environment Geochemistry (MING). MING uses environmental thresholds for limiting microbial growth to temperatures below 120 C and above relative humidities of 90 percent in repository drifts. Once these thresholds are met, MING expands upon a mass balance and thermodynamic approach proposed by McKinley and others (1997), by using kinetic rates to supply constituents from design materials and constituent fluxes including solubilized rock components into the drift, to perform two separate mass-balance calculations as a function of time. The first (nutrient limit) assesses the available nutrients (C, N, P and S) and calculates how many microorganisms can be produced based on a microorganism stoichiometry of C{sub 160}(H{sub 280}O{sub 80})N{sub 30}P{sub 2}S. The second (energy limit) calculates the energy available from optimally combined redox couples for the temperature, and pH at that time. This optimization maximizes those reactions that produce > 15kJ/mol (limit on useable energy) using an iterative linear optimization technique. The final available energy value is converted to microbial mass at a rate of 1 kg of biomass (dry weight) for every 64 MJ of energy. These two values (nutrient limit and energy limit) are then compared and the smaller value represents the number of microorganisms that can be produced over a specified time. MING can also be adapted to investigate other problems of interest as the model can be used in saturated

Neuronal regulation of homeostasis by nutrient sensing.

Science.gov (United States)

Lam, Tony K T

2010-04-01

In type 2 diabetes and obesity, the homeostatic control of glucose and energy balance is impaired, leading to hyperglycemia and hyperphagia. Recent studies indicate that nutrient-sensing mechanisms in the body activate negative-feedback systems to regulate energy and glucose homeostasis through a neuronal network. Direct metabolic signaling within the intestine activates gut-brain and gut-brain-liver axes to regulate energy and glucose homeostasis, respectively. In parallel, direct metabolism of nutrients within the hypothalamus regulates food intake and blood glucose levels. These findings highlight the importance of the central nervous system in mediating the ability of nutrient sensing to maintain homeostasis. Futhermore, they provide a physiological and neuronal framework by which enhancing or restoring nutrient sensing in the intestine and the brain could normalize energy and glucose homeostasis in diabetes and obesity.

The effect of concentrating of whitewater to the microbial growth in papermachine; Paperikoneen kiertovesien konsentroitumisen vaikutus mikrobien kasvuun - MPKT 03

Energy Technology Data Exchange (ETDEWEB)

Yloestalo, T. [Helsinki Univ. of Technology, Otaniemi (Finland)

1998-12-31

The closing of the whitewater cycle increases the amount of nutrients available for the micro-organisms living in a papermachine. The microbial flora in papermachines can vary significantly. The type and concentration of nutrients and the operating conditions of the papermachine (for example pH and temperature) affect the type of microbes that may live there. Strong microbial contamination has negative impact to the quality of the products and the operation of the papermachine. In this project microbes isolated from papermachines are cultivated in different concentrations of whitewater and with different pH and temperature values. The cultivations of microbes and modeling of the microbial growth are used for finding out how the closing of the whitewater cycle affects the microbial growth in papermachines. (orig.)

The effect of concentrating of whitewater to the microbial growth in papermachine; Paperikoneen kiertovesien konsentroitumisen vaikutus mikrobien kasvuun - MPKT 03

Energy Technology Data Exchange (ETDEWEB)

Yloestalo, T [Helsinki Univ. of Technology, Otaniemi (Finland)

1999-12-31

The closing of the whitewater cycle increases the amount of nutrients available for the micro-organisms living in a papermachine. The microbial flora in papermachines can vary significantly. The type and concentration of nutrients and the operating conditions of the papermachine (for example pH and temperature) affect the type of microbes that may live there. Strong microbial contamination has negative impact to the quality of the products and the operation of the papermachine. In this project microbes isolated from papermachines are cultivated in different concentrations of whitewater and with different pH and temperature values. The cultivations of microbes and modeling of the microbial growth are used for finding out how the closing of the whitewater cycle affects the microbial growth in papermachines. (orig.)

ANALYSIS OF AQUATIC MICROBIAL COMMUNITIES IMPACTED BY LARGE POULTRY FORMS

Science.gov (United States)

Microbial communities often respond more rapidly and extensively to environmental change than communities of higher organisms. Thus, characterizing shifts in the structure of native bacterial communities as a response to changes in nutrients, antimicrobials, and invading pathogen...

A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems.

Directory of Open Access Journals (Sweden)

Marko Budinich

Full Text Available Interplay within microbial communities impacts ecosystems on several scales, and elucidation of the consequent effects is a difficult task in ecology. In particular, the integration of genome-scale data within quantitative models of microbial ecosystems remains elusive. This study advocates the use of constraint-based modeling to build predictive models from recent high-resolution -omics datasets. Following recent studies that have demonstrated the accuracy of constraint-based models (CBMs for simulating single-strain metabolic networks, we sought to study microbial ecosystems as a combination of single-strain metabolic networks that exchange nutrients. This study presents two multi-objective extensions of CBMs for modeling communities: multi-objective flux balance analysis (MO-FBA and multi-objective flux variability analysis (MO-FVA. Both methods were applied to a hot spring mat model ecosystem. As a result, multiple trade-offs between nutrients and growth rates, as well as thermodynamically favorable relative abundances at community level, were emphasized. We expect this approach to be used for integrating genomic information in microbial ecosystems. Following models will provide insights about behaviors (including diversity that take place at the ecosystem scale.

Microbial enhanced oil recovery and compositions therefor

Science.gov (United States)

Bryant, Rebecca S.

1990-01-01

A method is provided for microbial enhanced oil recovery, wherein a combination of microorganisms is empirically formulated based on survivability under reservoir conditions and oil recovery efficiency, such that injection of the microbial combination may be made, in the presence of essentially only nutrient solution, directly into an injection well of an oil bearing reservoir having oil present at waterflood residual oil saturation concentration. The microbial combination is capable of displacing residual oil from reservoir rock, which oil may be recovered by waterflooding without causing plugging of the reservoir rock. Further, the microorganisms are capable of being transported through the pores of the reservoir rock between said injection well and associated production wells, during waterflooding, which results in a larger area of the reservoir being covered by the oil-mobilizing microorganisms.

Numerical modelling of biophysicochemical effects on multispecies reactive transport in porous media involving Pseudomonas putida for potential microbial enhanced oil recovery application.

Science.gov (United States)

Sivasankar, P; Rajesh Kanna, A; Suresh Kumar, G; Gummadi, Sathyanarayana N

2016-07-01

pH and resident time of injected slug plays a critical role in characterizing the reservoir for potential microbial enhanced oil recovery (MEOR) application. To investigate MEOR processes, a multispecies (microbes-nutrients) reactive transport model in porous media was developed by coupling kinetic and transport model. The present work differs from earlier works by explicitly determining parametric values required for kinetic model by experimental investigations using Pseudomonas putida at different pH conditions and subsequently performing sensitivity analysis of pH, resident time and water saturation on concentrations of microbes, nutrients and biosurfactant within reservoir. The results suggest that nutrient utilization and biosurfactant production are found to be maximum at pH 8 and 7.5 respectively. It is also found that the sucrose and biosurfactant concentrations are highly sensitive to pH rather than reservoir microbial concentration, while at larger resident time and water saturation, the microbial and nutrient concentrations were lesser due to enhanced dispersion. Copyright © 2016 Elsevier Ltd. All rights reserved.

Microbial community dynamics in the forefield of glaciers.

Science.gov (United States)

Bradley, James A; Singarayer, Joy S; Anesio, Alexandre M

2014-11-22

Retreating ice fronts (as a result of a warming climate) expose large expanses of deglaciated forefield, which become colonized by microbes and plants. There has been increasing interest in characterizing the biogeochemical development of these ecosystems using a chronosequence approach. Prior to the establishment of plants, microbes use autochthonously produced and allochthonously delivered nutrients for growth. The microbial community composition is largely made up of heterotrophic microbes (both bacteria and fungi), autotrophic microbes and nitrogen-fixing diazotrophs. Microbial activity is thought to be responsible for the initial build-up of labile nutrient pools, facilitating the growth of higher order plant life in developed soils. However, it is unclear to what extent these ecosystems rely on external sources of nutrients such as ancient carbon pools and periodic nitrogen deposition. Furthermore, the seasonal variation of chronosequence dynamics and the effect of winter are largely unexplored. Modelling this ecosystem will provide a quantitative evaluation of the key processes and could guide the focus of future research. Year-round datasets combined with novel metagenomic techniques will help answer some of the pressing questions in this relatively new but rapidly expanding field, which is of growing interest in the context of future large-scale ice retreat.

Reduction of nutrients, microbes, and personal care products in domestic wastewater by a benchtop electrocoagulation unit

Science.gov (United States)

Symonds, E. M.; Cook, M. M.; McQuaig, S. M.; Ulrich, R. M.; Schenck, R. O.; Lukasik, J. O.; van Vleet, E. S.; Breitbart, M.

2015-03-01

To preserve environmental and human health, improved treatment processes are needed to reduce nutrients, microbes, and emerging chemical contaminants from domestic wastewater prior to discharge into the environment. Electrocoagulation (EC) treatment is increasingly used to treat industrial wastewater; however, this technology has not yet been thoroughly assessed for its potential to reduce concentrations of nutrients, a variety of microbial surrogates, and personal care products found in domestic wastewater. This investigation's objective was to determine the efficiency of a benchtop EC unit with aluminum sacrificial electrodes to reduce concentrations of the aforementioned biological and chemical pollutants from raw and tertiary-treated domestic wastewater. EC treatment resulted in significant reductions (p < 0.05, α = 0.05) in phosphate, all microbial surrogates, and several personal care products from raw and tertiary-treated domestic wastewater. When wastewater was augmented with microbial surrogates representing bacterial, viral, and protozoan pathogens to measure the extent of reduction, EC treatment resulted in up to 7-log10 reduction of microbial surrogates. Future pilot and full-scale investigations are needed to optimize EC treatment for the following: reducing nitrogen species, personal care products, and energy consumption; elucidating the mechanisms behind microbial reductions; and performing life cycle analyses to determine the appropriateness of implementation.

Context-dependent effects of nutrient loading on the coral-algal mutualism.

Science.gov (United States)

Shantz, Andrew A; Burkepile, Deron E

2014-07-01

Human-mediated increases in nutrient availability alter patterns of primary production, impact species diversity, and threaten ecosystem function. Nutrients can also alter community structure by disrupting the relationships between nutrient-sharing mutualists that form the foundation of communities. Given their oligotrophic nature and the dependence of reef-building corals on symbiotic relationships, coral reefs may be particularly vulnerable to excess nutrients. However, individual studies suggest complex, even contradictory, relationships among nutrient availability, coral physiology, and coral growth. Here, we used meta-analysis to establish general patterns of the impact of nitrogen (N) and phosphorus (P) on coral growth and photobiology. Overall, we found that over a wide range of concentrations, N reduced coral calcification 11%, on average, but enhanced metrics of coral photobiology, such as photosynthetic rate. In contrast, P enrichment increased average calcification rates by 9%, likely through direct impacts on the calcification process, but minimally impacted coral photobiology. There were few synergistic impacts of combined N and P on corals, as the nutrients impact corals via different pathways. Additionally, the response of corals to increasing nutrient availability was context dependent, varying with coral taxa and morphology, enrichment source, and nutrient identity. For example, naturally occurring enrichment from fish excretion increased coral growth, while human-mediated enrichment tended to decrease coral growth. Understanding the nuances of the relationship between nutrients and corals may allow for more targeted remediation strategies and suggest how other global change drivers such as overfishing and climate change will shape how nutrient availability impacts corals.

Effect of Fermentation Methods on Chemical and Microbial ...

African Journals Online (AJOL)

Mung flours were fermented using spontaneous and backslopping methods for 72 h and microbial analysis over a period of 72 h fermentation was carried out. The samples were subjected to biochemical test, anti-nutrient and selected mineral and vitamin contents evaluation using standard methods. There was a gradual ...

Direct evidence for microbial-derived soil organic matter formation and its ecophysiological controls

Science.gov (United States)

Kallenbach, Cynthia M.; Frey, Serita D.; Grandy, A. Stuart

2016-11-01

Soil organic matter (SOM) and the carbon and nutrients therein drive fundamental submicron- to global-scale biogeochemical processes and influence carbon-climate feedbacks. Consensus is emerging that microbial materials are an important constituent of stable SOM, and new conceptual and quantitative SOM models are rapidly incorporating this view. However, direct evidence demonstrating that microbial residues account for the chemistry, stability and abundance of SOM is still lacking. Further, emerging models emphasize the stabilization of microbial-derived SOM by abiotic mechanisms, while the effects of microbial physiology on microbial residue production remain unclear. Here we provide the first direct evidence that soil microbes produce chemically diverse, stable SOM. We show that SOM accumulation is driven by distinct microbial communities more so than clay mineralogy, where microbial-derived SOM accumulation is greatest in soils with higher fungal abundances and more efficient microbial biomass production.

Seasonality and vertical structure of microbial communities in an ocean gyre.

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Treusch, Alexander H; Vergin, Kevin L; Finlay, Liam A; Donatz, Michael G; Burton, Robert M; Carlson, Craig A; Giovannoni, Stephen J

2009-10-01

Vertical, seasonal and geographical patterns in ocean microbial communities have been observed in many studies, but the resolution of community dynamics has been limited by the scope of data sets, which are seldom up to the task of illuminating the highly structured and rhythmic patterns of change found in ocean ecosystems. We studied vertical and temporal patterns in the microbial community composition in a set of 412 samples collected from the upper 300 m of the water column in the northwestern Sargasso Sea, on cruises between 1991 and 2004. The region sampled spans the extent of deep winter mixing and the transition between the euphotic and the upper mesopelagic zones, where most carbon fixation and reoxidation occurs. A bioinformatic pipeline was developed to de-noise, normalize and align terminal restriction fragment length polymorphism (T-RFLP) data from three restriction enzymes and link T-RFLP peaks to microbial clades. Non-metric multidimensional scaling statistics resolved three microbial communities with distinctive composition during seasonal stratification: a surface community in the region of lowest nutrients, a deep chlorophyll maximum community and an upper mesopelagic community. A fourth microbial community was associated with annual spring blooms of eukaryotic phytoplankton that occur in the northwestern Sargasso Sea as a consequence of winter convective mixing that entrains nutrients to the surface. Many bacterial clades bloomed in seasonal patterns that shifted with the progression of stratification. These richly detailed patterns of community change suggest that highly specialized adaptations and interactions govern the success of microbial populations in the oligotrophic ocean.

Microbial biomass and activity in litter during the initial development of pure and mixed plantations of Eucalyptus grandis and Acacia mangium

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Daniel Bini

2013-02-01

Full Text Available Studies on microbial activity and biomass in forestry plantations often overlook the role of litter, typically focusing instead on soil nutrient contents to explain plant and microorganism development. However, since the litter is a significant source of recycled nutrients that affect nutrient dynamics in the soil, litter composition may be more strongly correlated with forest growth and development than soil nutrient contents. This study aimed to test this hypothesis by examining correlations between soil C, N, and P; litter C, N, P, lignin content, and polyphenol content; and microbial biomass and activity in pure and mixed second-rotation plantations of Eucalyptus grandis and Acacia mangium before and after senescent leaf drop. The numbers of cultivable fungi and bacteria were also estimated. All properties were correlated with litter C, N, P, lignin and polyphenols, and with soil C and N. We found higher microbial activity (CO2 evolution in litter than in soil. In the E. grandis monoculture before senescent leaf drop, microbial biomass C was 46 % higher in litter than in soil. After leaf drop, this difference decreased to 16 %. In A. mangium plantations, however, microbial biomass C was lower in litter than in soil both before and after leaf drop. Microbial biomass N of litter was approximately 94 % greater than that of the soil in summer and winter in all plantations. The number of cultivable fungi and bacteria increased after leaf drop, especially so in the litter. Fungi were also more abundant in the E. grandis litter. In general, the A. mangium monoculture was associated with higher levels of litter lignin and N, especially after leaf drop. In contrast, the polyphenol and C levels in E. grandis monoculture litter were higher after leaf drop. These properties were negatively correlated with total soil C and N. Litter in the mixed stands had lower C:N and C:P ratios and higher N, P, and C levels in the microbial biomass. This suggests more

Gastrointestinal microbial ecology and its health benefits in Dogs

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K.B. Kore

2010-06-01

Full Text Available Gastrointestinal microbial balance is the most important prerequisite for normal functions of digestive system, physiological and immunological homeostasis in dogs as well as in other animals. It helps in prevention of pathogenic colonization, provides energy through SCFA by nutrient breakdown, and improves mineral-vitamin supply to host, augment host immune status. Hence, it is imperative to explore the potential means to improve the gastrointestinal microbial diversity which in turns boost up dog health. [Vet. World 2010; 3(3.000: 140-141

Effects of a specific blend of essential oils on apparent nutrient digestion, rumen fermentation and rumen microbial populations in sheep fed a 50:50 alfalfa hay:concentrate diet

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N. Khateri

2017-03-01

Full Text Available Objective An experiment was conducted to investigate the effects of a specific mixture of essential oils (MEO, containing thyme, clove and cinnamon EO, on rumen microbial fermentation, nutrient apparent digestibility and blood metabolites in fistulated sheep. Methods Six sheep fitted with ruminal fistulas were used in a repeated measurement design with two 24-d periods to investigate the effect of adding MEO at 0 (control, 0.8, and 1.6 mL/d on apparent nutrient digestibility, rumen fermentation characteristics, rumen microbial population and blood chemical metabolites. Animals were fed with a 50:50 alfalfa hay:concentrate diet. Results Ruminal pH, total volatile fatty acids (VFA concentration, molar proportion of individual VFA, acetate: propionate ratio and methane production were not affected with MEO. Relative to the control, Small peptides plus amino acid nitrogen and large peptides nitrogen concentration in rumen fluid were not affected with MEO supplementation; while, rumen fluid ammonia nitrogen concentration at 0 and 6 h after morning feeding in sheep fed with 1.6 mL/d of MEO was lower (p<0.05 compared to the control and 0.8 mL/d of MEO. At 0 h after morning feeding, ammonia nitrogen concentration was higher (p<0.05 in sheep fed 0.8 mL/d of MEO relative to 1.6 mL/d and control diet. Ruminal protozoa and hyper ammonia producing (HAP bacteria counts were not affected by addition of MEO in the diet. Relative to the control, no changes were observed in the red and white blood cells, hemoglobin, hematocrit, glucose, beta-hydroxybutyric acid, cholesterol, total protein, albumin, blood urea nitrogen and aspartate aminotransferase and alanine aminotransferase concentration. Apparent total tract digestibility of dry matter, crude proten, organic matter, and neutral detergent fiber were not influenced by MEO supplementation. Conclusion The results of the present study suggested that supplementation of MEO may have limited effects on apparent

Targeted quantification of functional enzyme dynamics in environmental samples for microbially mediated biogeochemical processes: Targeted quantification of functional enzyme dynamics

Energy Technology Data Exchange (ETDEWEB)

Li, Minjing [School of Environmental Studies, China University of Geosciences, Wuhan 430074 People' s Republic of China; Gao, Yuqian [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Qian, Wei-Jun [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Shi, Liang [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Liu, Yuanyuan [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Nelson, William C. [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Nicora, Carrie D. [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Resch, Charles T. [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Thompson, Christopher [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Yan, Sen [School of Environmental Studies, China University of Geosciences, Wuhan 430074 People' s Republic of China; Fredrickson, James K. [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Zachara, John M. [Pacific Northwest National Laboratory, Richland, WA 99354 USA; Liu, Chongxuan [Pacific Northwest National Laboratory, Richland, WA 99354 USA; School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055 People' s Republic of China

2017-07-13

Microbially mediated biogeochemical processes are catalyzed by enzymes that control the transformation of carbon, nitrogen, and other elements in environment. The dynamic linkage between enzymes and biogeochemical species transformation has, however, rarely been investigated because of the lack of analytical approaches to efficiently and reliably quantify enzymes and their dynamics in soils and sediments. Herein, we developed a signature peptide-based technique for sensitively quantifying dissimilatory and assimilatory enzymes using nitrate-reducing enzymes in a hyporheic zone sediment as an example. Moreover, the measured changes in enzyme concentration were found to correlate with the nitrate reduction rate in a way different from that inferred from biogeochemical models based on biomass or functional genes as surrogates for functional enzymes. This phenomenon has important implications for understanding and modeling the dynamics of microbial community functions and biogeochemical processes in environments. Our results also demonstrate the importance of enzyme quantification for the identification and interrogation of those biogeochemical processes with low metabolite concentrations as a result of faster enzyme-catalyzed consumption of metabolites than their production. The dynamic enzyme behaviors provide a basis for the development of enzyme-based models to describe the relationship between the microbial community and biogeochemical processes.

Microbial and chemical characterization of underwater fresh water springs in the Dead Sea.

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Danny Ionescu

Full Text Available Due to its extreme salinity and high Mg concentration the Dead Sea is characterized by a very low density of cells most of which are Archaea. We discovered several underwater fresh to brackish water springs in the Dead Sea harboring dense microbial communities. We provide the first characterization of these communities, discuss their possible origin, hydrochemical environment, energetic resources and the putative biogeochemical pathways they are mediating. Pyrosequencing of the 16S rRNA gene and community fingerprinting methods showed that the spring community originates from the Dead Sea sediments and not from the aquifer. Furthermore, it suggested that there is a dense Archaeal community in the shoreline pore water of the lake. Sequences of bacterial sulfate reducers, nitrifiers iron oxidizers and iron reducers were identified as well. Analysis of white and green biofilms suggested that sulfide oxidation through chemolitotrophy and phototrophy is highly significant. Hyperspectral analysis showed a tight association between abundant green sulfur bacteria and cyanobacteria in the green biofilms. Together, our findings show that the Dead Sea floor harbors diverse microbial communities, part of which is not known from other hypersaline environments. Analysis of the water's chemistry shows evidence of microbial activity along the path and suggests that the springs supply nitrogen, phosphorus and organic matter to the microbial communities in the Dead Sea. The underwater springs are a newly recognized water source for the Dead Sea. Their input of microorganisms and nutrients needs to be considered in the assessment of possible impact of dilution events of the lake surface waters, such as those that will occur in the future due to the intended establishment of the Red Sea-Dead Sea water conduit.

Increased microbial functional diversity under long-term organic and integrated fertilization in a paddy soil.

Science.gov (United States)

Ding, Long-Jun; Su, Jian-Qiang; Sun, Guo-Xin; Wu, Jin-Shui; Wei, Wen-Xue

2018-02-01

Microbes play key roles in diverse biogeochemical processes including nutrient cycling. However, responses of soil microbial community and functional genes to long-term integrated fertilization (chemical combined with organic fertilization) remain unclear. Here, we used pyrosequencing and a microarray-based GeoChip to explore the shifts of microbial community and functional genes in a paddy soil which received over 21-year fertilization with various regimes, including control (no fertilizer), rice straw (R), rice straw plus chemical fertilizer nitrogen (NR), N and phosphorus (NPR), NP and potassium (NPKR), and reduced rice straw plus reduced NPK (L-NPKR). Significant shifts of the overall soil bacterial composition only occurred in the NPKR and L-NPKR treatments, with enrichment of certain groups including Bradyrhizobiaceae and Rhodospirillaceae families that benefit higher productivity. All fertilization treatments significantly altered the soil microbial functional structure with increased diversity and abundances of genes for carbon and nitrogen cycling, in which NPKR and L-NPKR exhibited the strongest effect, while R exhibited the least. Functional gene structure and abundance were significantly correlated with corresponding soil enzymatic activities and rice yield, respectively, suggesting that the structural shift of the microbial functional community under fertilization might promote soil nutrient turnover and thereby affect yield. Overall, this study indicates that the combined application of rice straw and balanced chemical fertilizers was more pronounced in shifting the bacterial composition and improving the functional diversity toward higher productivity, providing a microbial point of view on applying a cost-effective integrated fertilization regime with rice straw plus reduced chemical fertilizers for sustainable nutrient management.

A microbial trigger for gelled polymers

Energy Technology Data Exchange (ETDEWEB)

Bailey, S.; Bryant, R.; Zhu, T.

1995-12-31

A process using a microbially gelled biopolymer was developed and used to modify permeability in coreflood experiments. Alkaline-soluble curdlan biopolymer was mixed with microbial nutrients and acid-producing alkaliphilic bacteria, and injected into Berea sandstone cores. Concurrent bottle tests with the polymer solution were incubated beside the core. Polymer in the bottle tests formed rigid gel in 2-5 days at 27{degree}C. After 7 days incubation, 25-35 psi fluid pressure was required to begin flow through the cores. Permeability of the cores was decreased from 852 md to 2.99 md and from 904 md to 4.86 md, respectively, giving residual resistance factors of 334 and 186.

[Engineering issues of microbial ecology in space agriculture].

Science.gov (United States)

Yamashita, Masamichi; Ishikawa, Yoji; Oshima, Tairo

2005-03-01

Closure of the materials recycle loop for water-foods-oxygen is the primary purpose of space agriculture on Mars and Moon. A microbial ecological system takes a part of agriculture to process our metabolic excreta and inedible biomass and convert them to nutrients and soil substrate for cultivating plants. If we extend the purpose of space agriculture to the creation and control of a healthy and pleasant living environment, we should realize that our human body should not be sterilized but exposed to the appropriate microbial environment. We are proposing a use of hyper-thermophilic aerobic composting microbial ecology in space agriculture. Japan has a broad historical and cultural background on this subject. There had been agriculture that drove a closed loop of materials between consuming cities and farming villages in vicinity. Recent environmental problems regarding garbage collection and processing in towns have motivated home electronics companies to innovate "garbage composting" machines with bacterial technology. Based on those matured technology, together with new insights on microbiology and microbial ecology, we have been developing a conceptual design of space agriculture on Moon and Mars. There are several issues to be answered in order to prove effectiveness of the use of microbial systems in space. 1) Can the recycled nutrients, processed by the hyper-thermal aerobic composting microbial ecology, be formed in the physical and chemical state or configuration, with which plants can uptake those nutrients? A possibility of removing any major components of fertilizer from its recycle loop is another item to be evaluated. 2) What are the merits of forming soil microbial ecology around the root system of plants? This might be the most crucial question. Recent researches exhibit various mutually beneficial relationships among soil microbiota and plants, and symbiotic ecology in composting bacteria. It is essential to understand those features, and define

Nutrient amendment does not increase mineralisation of sequestered carbon during incubation of a nitrogen limited mangrove soil

KAUST Repository

Keuskamp, Joost A.

2013-02-01

Mangrove forests are sites of intense carbon and nutrient cycling, which result in soil carbon sequestration on a global scale. Currently, mangrove forests receive increasing quantities of exogenous nutrients due to coastal development. The present paper quantifies the effects of nutrient loading on microbial growth rates and the mineralisation of soil organic carbon (SOC) in two mangrove soils contrasting in carbon content. An increase in SOC mineralisation rates would lead to the loss of historically sequestered carbon and an enhanced CO2 release from these mangrove soils.In an incubation experiment we enriched soils from Avicennia and Rhizophora mangrove forests bordering the Red Sea with different combinations of nitrogen, phosphorus and glucose to mimic the effects of wastewater influx. We measured microbial growth rates as well as carbon mineralisation rates in the natural situation and after enrichment. The results show that microbial growth is energy limited in both soils, with nitrogen as a secondary limitation. Nitrogen amendment increased the rate at which labile organic carbon was decomposed, while it decreased SOC mineralisation rates. Such an inhibitory effect on SOC mineralisation was not found for phosphorus enrichment.Our data confirm the negative effect of nitrogen enrichment on the mineralisation of recalcitrant carbon compounds found in other systems. Based on our results it is not to be expected that nutrient enrichment by itself will cause degradation of historically sequestered soil organic carbon in nitrogen limited mangrove forests. © 2012 Elsevier Ltd.

Seasonality in ocean microbial communities.

Science.gov (United States)

Giovannoni, Stephen J; Vergin, Kevin L

2012-02-10

Ocean warming occurs every year in seasonal cycles that can help us to understand long-term responses of plankton to climate change. Rhythmic seasonal patterns of microbial community turnover are revealed when high-resolution measurements of microbial plankton diversity are applied to samples collected in lengthy time series. Seasonal cycles in microbial plankton are complex, but the expansion of fixed ocean stations monitoring long-term change and the development of automated instrumentation are providing the time-series data needed to understand how these cycles vary across broad geographical scales. By accumulating data and using predictive modeling, we gain insights into changes that will occur as the ocean surface continues to warm and as the extent and duration of ocean stratification increase. These developments will enable marine scientists to predict changes in geochemical cycles mediated by microbial communities and to gauge their broader impacts.

Visualizing Microbial Biogeochemistry: NanoSIMS and Stable Isotope Probing (Invited)

Science.gov (United States)

Pett-Ridge, J.; Weber, P. K.

2009-12-01

Linking phylogenetic information to function in microbial communities is a key challenge for microbial ecology. Isotope-labeling experiments provide a useful means to investigate the ecophysiology of microbial populations and cells in the environment and allow measurement of nutrient transfers between cell types, symbionts and consortia. The combination of Nano-Secondary Ion Mass Spectrometry (NanoSIMS) analysis, in situ labeling and high resolution microscopy allows isotopic analysis to be linked to phylogeny and morphology and holds great promise for fine-scale studies of microbial systems. In NanoSIMS analysis, samples are sputtered with an energetic primary beam (Cs+, O-) liberating secondary ions that are separated by the mass spectrometer and detected in a suite of electron multipliers. Five isotopic species may be analyzed concurrently with spatial resolution as fine as 50nm. A high sensitivity isotope ratio ‘map’ can then be generated for the analyzed area. NanoSIMS images of 13C, 15N and Mo (a nitrogenase co-factor) localization in diazotrophic cyanobacteria show how cells differentially allocate resources within filaments and allow calculation of nutrient uptake rates on a cell by cell basis. Images of AM fungal hyphae-root and cyanobacteria-rhizobia associations indicate the mobilization and sharing (stealing?) of newly fixed C and N. In a related technique, “El-FISH”, stable isotope labeled biomass is probed with oligonucleotide-elemental labels and then imaged by NanoSIMS. In microbial consortia and cyanobacterial mats, this technique helps link microbial structure and function simultaneously even in systems with unknown and uncultivated microbes. Finally, the combination of re-engineered universal 16S oligonucleotide microarrays with NanoSIMS analyses may allow microbial identity to be linked to functional roles in complex systems such as mats and cellulose degrading hindgut communities. These newly developed methods provide correlated

Mechanistic links between gut microbial community dynamics, microbial functions and metabolic health

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Ha, Connie WY; Lam, Yan Y; Holmes, Andrew J

2014-01-01

Gut microbes comprise a high density, biologically active community that lies at the interface of an animal with its nutritional environment. Consequently their activity profoundly influences many aspects of the physiology and metabolism of the host animal. A range of microbial structural components and metabolites directly interact with host intestinal cells and tissues to influence nutrient uptake and epithelial health. Endocrine, neuronal and lymphoid cells in the gut also integrate signals from these microbial factors to influence systemic responses. Dysregulation of these host-microbe interactions is now recognised as a major risk factor in the development of metabolic dysfunction. This is a two-way process and understanding the factors that tip host-microbiome homeostasis over to dysbiosis requires greater appreciation of the host feedbacks that contribute to regulation of microbial community composition. To date, numerous studies have employed taxonomic profiling approaches to explore the links between microbial composition and host outcomes (especially obesity and its comorbidities), but inconsistent host-microbe associations have been reported. Available data indicates multiple factors have contributed to discrepancies between studies. These include the high level of functional redundancy in host-microbiome interactions combined with individual variation in microbiome composition; differences in study design, diet composition and host system between studies; and inherent limitations to the resolution of rRNA-based community profiling. Accounting for these factors allows for recognition of the common microbial and host factors driving community composition and development of dysbiosis on high fat diets. New therapeutic intervention options are now emerging. PMID:25469018

Mangrove microbial diversity and the impact of trophic contamination.

Science.gov (United States)

Bouchez, Agnès; Pascault, Noémie; Chardon, Cècile; Bouvy, Marc; Cecchi, Philippe; Lambs, Luc; Herteman, Mélanie; Fromard, François; Got, Patrice; Leboulanger, Christophe

2013-01-15

Mangroves are threatened ecosystems that provide numerous ecosystem services, especially through their wide biodiversity, and their bioremediation capacity is a challenging question in tropical areas. In a mangrove in Mayotte, we studied the potential role of microbial biofilm communities in removing nutrient loads from pre-treated wastewater. Microbial community samples were collected from tree roots, sediments, water, and from a colonization device, and their structure and dynamics were compared in two areas: one exposed to sewage and the other not. The samples from the colonization devices accurately reflected the natural communities in terms of diversity. Communities in the zone exposed to sewage were characterized by more green algae and diatoms, higher bacteria densities, as well as different compositions. In the area exposed to sewage, the higher cell densities associated with specific diversity patterns highlighted adapted communities that may play a significant role in the fate of nutrients. Copyright © 2012 Elsevier Ltd. All rights reserved.

Nutritional responses to soil drying and rewetting cycles under partial root-zone drying irrigation

DEFF Research Database (Denmark)

Wang, Yaosheng; Jensen, Christian Richardt; Liu, Fulai

2017-01-01

signaling that regulates stomatal aperture. PRI induced soil DRW cycles and more soil water dynamics in the root zone enhance soil nutrient mineralization process and thus increase the bioavailability of soil nutrients, resulting in improved nitrogen (N) and phosphorus (P) uptake, in which soil microbial...... processes play a key role. Studies investigating how soil DRW cycles and water dynamics under PRI on nutrient transport in soil solution, soil microbe mediated P transformation, interactions between phytohormones and nutrient uptake, root morphological and architectural traits for nutrient acquisition......Abstract Repeated soil drying and rewetting (DRW) cycles occur in rainfed and irrigated agriculture. The intensity and frequency of DRW cycles regulate both microbial physiology and soil physical processes, hereby affecting the mineralization and immobilization of soil nutrients...

Temporal Changes in the Spatial Variability of Soil Nutrients

Energy Technology Data Exchange (ETDEWEB)

Hoskinson, Reed Louis; Hess, John Richard; Alessi, Randolph Samuel

1999-07-01

This paper reports the temporal changes in the spatial variability of soil nutrient concentrations across a field during the growing season, over a four-year period. This study is part of the Site-Specific Technologies for Agriculture (SST4Ag) precision farming research project at the INEEL. Uniform fertilization did not produce a uniform increase in fertility. During the growing season, several of the nutrients and micronutrients showed increases in concentration although no additional fertilization had occurred. Potato plant uptake did not explain all of these changes. Some soil micronutrient concentrations increased above levels considered detrimental to potatoes, but the plants did not show the effects in reduced yield. All the nutrients measured changed between the last sampling in the fall and the first sampling the next spring prior to fertilization. The soil microbial community may play a major role in the temporal changes in the spatial variability of soil nutrient concentrations. These temporal changes suggest potential impact when determining fertilizer recommendations, and when evaluating the results of spatially varying fertilizer application.

Microbial Indicators of Soil Quality under Different Land Use Systems in Subtropical Soils

Science.gov (United States)

Maharjan, M.

2016-12-01

Land-use change from native forest to intensive agricultural systems can negatively impact numerous soil parameters. Understanding the effects of forest ecosystem transformations on markers of long-term soil health is particularly important in rapidly developing regions such as Nepal, where unprecedented levels of agriculturally-driven deforestation have occurred in recent decades. However, the effects of widespread land use changes on soil quality in this region have yet to be properly characterized. Microbial indicators (soil microbial biomass, metabolic quotient and enzymes activities) are particularly suited to assessing the consequences of such ecosystem disturbances, as microbial communities are especially sensitive to environmental change. Thus, the aim of this study was to assess the effect of land use system; i.e. forest, organic and conventional farming, on soil quality in Chitwan, Nepal using markers of microbial community size and activity. Total organic C and N contents were higher in organic farming compared with conventional farming and forest, suggesting higher nutrient retention and soil preservation with organic farming practices compared to conventional. These differences in soil composition were reflected in the health of the soil microbial communities: Organic farm soil exhibited higher microbial biomass C, elevated β-glucosidase and chitinase activities, and a lower metabolic quotient relative to other soils, indicating a larger, more active, and less stressed microbial community, respectively. These results collectively demonstrate that application of organic fertilizers and organic residues positively influence nutrient availability, with subsequent improvements in soil quality and productivity. Furthermore, the sensitivity of microbial indicators to different management practices demonstrated in this study supports their use as effective markers of ecosystem disturbance in subtropical soils.

Spatial heterogeneity of physicochemical properties explains differences in microbial composition in arid soils from Cuatro Cienegas, Mexico

Directory of Open Access Journals (Sweden)

Silvia Pajares

2016-09-01

Full Text Available Arid ecosystems are characterized by high spatial heterogeneity, and the variation among vegetation patches is a clear example. Soil biotic and abiotic factors associated with these patches have also been well documented as highly heterogeneous in space. Given the low vegetation cover and little precipitation in arid ecosystems, soil microorganisms are the main drivers of nutrient cycling. Nonetheless, little is known about the spatial distribution of microorganisms and the relationship that their diversity holds with nutrients and other physicochemical gradients in arid soils. In this study, we evaluated the spatial variability of soil microbial diversity and chemical parameters (nutrients and ion content at local scale (meters occurring in a gypsum-based desert soil, to gain knowledge on what soil abiotic factors control the distribution of microbes in arid ecosystems. We analyzed 32 soil samples within a 64 m2 plot and: (a characterized microbial diversity using T-RFLPs of the bacterial 16S rRNA gene, (b determined soil chemical parameters, and (c identified relationships between microbial diversity and chemical properties. Overall, we found a strong correlation between microbial composition heterogeneity and spatial variation of cations (Ca2, K+ and anions (HCO ${}_{3}^{-}$ 3 − , Cl−, SO ${}_{4}^{2-}$ 4 2 − content in this small plot. Our results could be attributable to spatial differences of soil saline content, favoring the patchy emergence of salt and soil microbial communities.

Impact of an indigenous microbial enhanced oil recovery field trial on microbial community structure in a high pour-point oil reservoir

Energy Technology Data Exchange (ETDEWEB)

Zhang, Fan; Zhang, Xiao-Tao; Hou, Du-Jie [China Univ. of Geosciences, Beijing (China). The Key Lab. of Marine Reservoir Evolution and Hydrocarbon Accumulation Mechanism; She, Yue-Hui [Yangtze Univ., Jingzhou, Hubei (China). College of Chemistry and Environmental Engineering; Huazhong Univ. of Science and Technology, Wuhan (China). College of Life Science and Technology; Li, Hua-Min [Beijing Bioscience Research Center (China); Shu, Fu-Chang; Wang, Zheng-Liang [Yangtze Univ., Jingzhou, Hubei (China). College of Chemistry and Environmental Engineering; Yu, Long-Jiang [Huazhong Univ. of Science and Technology, Wuhan (China). College of Life Science and Technology

2012-08-15

Based on preliminary investigation of microbial populations in a high pour-point oil reservoir, an indigenous microbial enhanced oil recovery (MEOR) field trial was carried out. The purpose of the study is to reveal the impact of the indigenous MEOR process on microbial community structure in the oil reservoir using 16Sr DNA clone library technique. The detailed monitoring results showed significant response of microbial communities during the field trial and large discrepancies of stimulated microorganisms in the laboratory and in the natural oil reservoir. More specifically, after nutrients injection, the original dominant populations of Petrobacter and Alishewanella in the production wells almost disappeared. The expected desirable population of Pseudomonas aeruginosa, determined by enrichment experiments in laboratory, was stimulated successfully in two wells of the five monitored wells. Unexpectedly, another potential population of Pseudomonas pseudoalcaligenes which were not detected in the enrichment culture in laboratory was stimulated in the other three monitored production wells. In this study, monitoring of microbial community displayed a comprehensive alteration of microbial populations during the field trial to remedy the deficiency of culture-dependent monitoring methods. The results would help to develop and apply more MEOR processes. (orig.)

Impact of an indigenous microbial enhanced oil recovery field trial on microbial community structure in a high pour-point oil reservoir.

Science.gov (United States)

Zhang, Fan; She, Yue-Hui; Li, Hua-Min; Zhang, Xiao-Tao; Shu, Fu-Chang; Wang, Zheng-Liang; Yu, Long-Jiang; Hou, Du-Jie

2012-08-01

Based on preliminary investigation of microbial populations in a high pour-point oil reservoir, an indigenous microbial enhanced oil recovery (MEOR) field trial was carried out. The purpose of the study is to reveal the impact of the indigenous MEOR process on microbial community structure in the oil reservoir using 16Sr DNA clone library technique. The detailed monitoring results showed significant response of microbial communities during the field trial and large discrepancies of stimulated microorganisms in the laboratory and in the natural oil reservoir. More specifically, after nutrients injection, the original dominant populations of Petrobacter and Alishewanella in the production wells almost disappeared. The expected desirable population of Pseudomonas aeruginosa, determined by enrichment experiments in laboratory, was stimulated successfully in two wells of the five monitored wells. Unexpectedly, another potential population of Pseudomonas pseudoalcaligenes which were not detected in the enrichment culture in laboratory was stimulated in the other three monitored production wells. In this study, monitoring of microbial community displayed a comprehensive alteration of microbial populations during the field trial to remedy the deficiency of culture-dependent monitoring methods. The results would help to develop and apply more MEOR processes.

Secreted pitfall-trap fluid of carnivorous Nepenthes plants is unsuitable for microbial growth.

Science.gov (United States)

Buch, Franziska; Rott, Matthias; Rottloff, Sandy; Paetz, Christian; Hilke, Ines; Raessler, Michael; Mithöfer, Axel

2013-03-01

Carnivorous plants of the genus Nepenthes possess modified leaves that form pitfall traps in order to capture prey, mainly arthropods, to make additional nutrients available for the plant. These pitchers contain a digestive fluid due to the presence of hydrolytic enzymes. In this study, the composition of the digestive fluid was further analysed with regard to mineral nutrients and low molecular-weight compounds. A potential contribution of microbes to the composition of pitcher fluid was investigated. Fluids from closed pitchers were harvested and analysed for mineral nutrients using analytical techniques based on ion-chromatography and inductively coupled plasma-optical emission spectroscopy. Secondary metabolites were identified by a combination of LC-MS and NMR. The presence of bacteria in the pitcher fluid was investigated by PCR of 16S-rRNA genes. Growth analyses of bacteria and yeast were performed in vitro with harvested pitcher fluid and in vivo within pitchers with injected microbes. The pitcher fluid from closed pitchers was found to be primarily an approx. 25-mm KCl solution, which is free of bacteria and unsuitable for microbial growth probably due to the lack of essential mineral nutrients such as phosphate and inorganic nitrogen. The fluid also contained antimicrobial naphthoquinones, plumbagin and 7-methyl-juglone, and defensive proteins such as the thaumatin-like protein. Challenging with bacteria or yeast caused bactericide as well as fungistatic properties in the fluid. Our results reveal that Nepenthes pitcher fluids represent a dynamic system that is able to react to the presence of microbes. The secreted liquid of closed and freshly opened Nepenthes pitchers is exclusively plant-derived. It is unsuitable to serve as an environment for microbial growth. Thus, Nepenthes plants can avoid and control, at least to some extent, the microbial colonization of their pitfall traps and, thereby, reduce the need to vie with microbes for the prey

Representing Microbial Dormancy in Soil Decomposition Models Improves Model Performance and Reveals Key Ecosystem Controls on Microbial Activity

Science.gov (United States)

He, Y.; Yang, J.; Zhuang, Q.; Wang, G.; Liu, Y.

2014-12-01

Climate feedbacks from soils can result from environmental change and subsequent responses of plant and microbial communities and nutrient cycling. Explicit consideration of microbial life history traits and strategy may be necessary to predict climate feedbacks due to microbial physiology and community changes and their associated effect on carbon cycling. In this study, we developed an explicit microbial-enzyme decomposition model and examined model performance with and without representation of dormancy at six temperate forest sites with observed soil efflux ranged from 4 to 10 years across different forest types. We then extrapolated the model to all temperate forests in the Northern Hemisphere (25-50°N) to investigate spatial controls on microbial and soil C dynamics. Both models captured the observed soil heterotrophic respiration (RH), yet no-dormancy model consistently exhibited large seasonal amplitude and overestimation in microbial biomass. Spatially, the total RH from temperate forests based on dormancy model amounts to 6.88PgC/yr, and 7.99PgC/yr based on no-dormancy model. However, no-dormancy model notably overestimated the ratio of microbial biomass to SOC. Spatial correlation analysis revealed key controls of soil C:N ratio on the active proportion of microbial biomass, whereas local dormancy is primarily controlled by soil moisture and temperature, indicating scale-dependent environmental and biotic controls on microbial and SOC dynamics. These developments should provide essential support to modeling future soil carbon dynamics and enhance the avenue for collaboration between empirical soil experiment and modeling in the sense that more microbial physiological measurements are needed to better constrain and evaluate the models.

Fungi benefit from two decades of increased nutrient availability in tundra heath soil

DEFF Research Database (Denmark)

Rinnan, Riikka; Michelsen, Anders; Bååth, Erland

2013-01-01

is a predicted long-term consequence of climatic warming and mimicked by fertilization, both increase soil microbial biomass. However, while fertilization increased the relative abundance of fungi, warming caused only a minimal shift in the microbial community composition based on the phospholipid fatty acid......If microbial degradation of carbon substrates in arctic soil is stimulated by climatic warming, this would be a significant positive feedback on global change. With data from a climate change experiment in Northern Sweden we show that warming and enhanced soil nutrient availability, which...... (PLFA) and neutral lipid fatty acid (NLFA) profiles. The function of the microbial community was also differently affected, as indicated by stable isotope probing of PLFA and NLFA. We demonstrate that two decades of fertilization have favored fungi relative to bacteria, and increased the turnover...

Richness, biomass, and nutrient content of a wetland macrophyte community affect soil nitrogen cycling in a diversity-ecosystem functioning experiment

Science.gov (United States)

Korol, Alicia R.; Ahn, Changwoo; Noe, Gregory

2016-01-01

The development of soil nitrogen (N) cycling in created wetlands promotes the maturation of multiple biogeochemical cycles necessary for ecosystem functioning. This development proceeds from gradual changes in soil physicochemical properties and influential characteristics of the plant community, such as competitive behavior, phenology, productivity, and nutrient composition. In the context of a 2-year diversity experiment in freshwater mesocosms (0, 1, 2, 3, or 4 richness levels), we assessed the direct and indirect impacts of three plant community characteristics – species richness, total biomass, and tissue N concentration – on three processes in the soil N cycle – soil net ammonification, net nitrification, and denitrification potentials. Species richness had a positive effect on net ammonification potential (NAP) through higher redox potentials and likely faster microbial respiration. All NAP rates were negative, however, due to immobilization and high rates of ammonium removal. Net nitrification was inhibited at higher species richness without mediation from the measured soil properties. Higher species richness also inhibited denitrification potential through increased redox potential and decreased nitrification. Both lower biomass and/or higher tissue ratios of carbon to nitrogen, characteristics indicative of the two annual plants, were shown to have stimulatory effects on all three soil N processes. The two mediating physicochemical links between the young macrophyte community and microbial N processes were soil redox potential and temperature. Our results suggest that early-successional annual plant communities play an important role in the development of ecosystem N multifunctionality in newly created wetland soils.

Nitrogen cycling processes and microbial community composition in bed sediments in the Yukon River at Pilot Station

Science.gov (United States)

Repert, Deborah A.; Underwood, Jennifer C.; Smith, Richard L.; Song, Bongkeun

2014-01-01

Information on the contribution of nitrogen (N)-cycling processes in bed sediments to river nutrient fluxes in large northern latitude river systems is limited. This study examined the relationship between N-cycling processes in bed sediments and N speciation and loading in the Yukon River near its mouth at the Bering Sea. We conducted laboratory bioassays to measure N-cycling processes in sediment samples collected over distinct water cycle seasons. In conjunction, the microbial community composition in the bed sediments using genes involved in N-cycling (narG, napA, nosZ, and amoA) and 16S rRNA gene pyrosequences was examined. Temporal variation was observed in net N mineralization, nitrate uptake, and denitrification rate potentials and correlated strongly with sediment carbon (C) and extractable N content and microbial community composition rather than with river water nutrient concentrations. The C content of the bed sediment was notably impacted by the spring flood, ranging from 1.1% in the midst of an ice-jam to 0.1% immediately after ice-out, suggesting a buildup of organic material (OM) prior to scouring of the bed sediments during ice break up. The dominant members of the microbial community that explained differences in N-processing rates belonged to the genera Crenothrix,Flavobacterium, and the family of Comamonadaceae. Our results suggest that biogeochemical processing rates in the bed sediments appear to be more coupled to hydrology, nutrient availability in the sediments, and microbial community composition rather than river nutrient concentrations at Pilot Station.

Effect of methyl-β-cyclodextrin on gene expression in microbial conversion of phytosterol.

Science.gov (United States)

Shtratnikova, Victoria Y; Schelkunov, Mikhail I; Dovbnya, Dmitry V; Bragin, Eugeny Y; Donova, Marina V

2017-06-01

Modified β-cyclodextrins are widely used for the enhancement of microbial conversions of lipophilic compounds such as steroids. Multiple mechanisms of cyclodextrin-mediated enhancement of phytosterol bioconversion by mycobacteria had previously been shown to include steroid solubilization, alterations in the cell wall permeability for both steroids and nutrients, facilitation of protein leaking, and activity suppression of some steroid-transforming enzymes.In this work, we studied whether cyclodextrins might affect expression of the genes involved in the steroid catabolic pathway. Phytosterol bioconversion with 9α-hydroxy-androst-4-ene-3,17-dione accumulation by Mycobacterium sp. VKM Ac-1817D in the presence of methylated β-cyclodextrin (MCD) was investigated. RNA sequencing of the whole transcriptomes in different combinations of phytosterol and MCD showed a similar expression level of the steroid catabolism genes related to the KstR-regulon and was responsible for side chain and initial steps of steroid core oxidation; whereas, induction levels of the genes related to the KstR2-regulon were attenuated in the presence of MCD in this strain. The data were attenuated with quantitative real-time PCR.The results contribute to the understanding of cyclodextrin effects on microbial steroid conversion and provide a basis for the use of cyclodextrins as expression enhancers for studies of sterol catabolism in actinobacteria.

Microbial mitigation-exacerbation continuum: a novel framework for microbiome effects on hosts in the face of stress.

Science.gov (United States)

David, Aaron S; Thapa-Magar, Khum B; Afkhami, Michelle E

2018-03-01

A key challenge to understanding microbiomes and their role in ecological processes is contextualizing their effects on host organisms, particularly when faced with environmental stress. One influential theory, the Stress Gradient Hypothesis, might predict that the frequency of positive interactions increases with stressful conditions such that microbial taxa would mitigate harmful effects on host performance. Yet, equally plausible is that microbial taxa could exacerbate these effects. Here, we introduce the Mitigation-Exacerbation Continuum as a novel framework to conceptualize microbial mediation of stress. We (1) use this continuum to quantify microbial mediation of stress for six plant species and (2) test the association between these continuum values and natural species' abundance. We factorially manipulated a common stress (allelopathy) and the presence of soil microbes to quantify microbial effects in benign and stressed environments for two critical early life-history metrics, seed germination and seedling biomass. Although we found evidence of both mitigation and exacerbation among the six species, exacerbation was more common. Across species, the degree of microbial-mediated effects on germination explained >80% of the variation of natural field abundances. Our results suggest a critical role of soil microbes in mediating plant stress responses, and a potential microbial mechanism underlying species abundance. © 2018 by the Ecological Society of America.

Proposal for a method to estimate nutrient shock effects in bacteria

Directory of Open Access Journals (Sweden)

Azevedo Nuno F

2012-08-01

Full Text Available Abstract Background Plating methods are still the golden standard in microbiology; however, some studies have shown that these techniques can underestimate the microbial concentrations and diversity. A nutrient shock is one of the mechanisms proposed to explain this phenomenon. In this study, a tentative method to assess nutrient shock effects was tested. Findings To estimate the extent of nutrient shock effects, two strains isolated from tap water (Sphingomonas capsulata and Methylobacterium sp. and two culture collection strains (E. coli CECT 434 and Pseudomonas fluorescens ATCC 13525 were exposed both to low and high nutrient conditions for different times and then placed in low nutrient medium (R2A and rich nutrient medium (TSA. The average improvement (A.I. of recovery between R2A and TSA for the different times was calculated to more simply assess the difference obtained in culturability between each medium. As expected, A.I. was higher when cells were plated after the exposition to water than when they were recovered from high-nutrient medium showing the existence of a nutrient shock for the diverse bacteria used. S. capsulata was the species most affected by this phenomenon. Conclusions This work provides a method to consistently determine the extent of nutrient shock effects on different microorganisms and hence quantify the ability of each species to deal with sudden increases in substrate concentration.

Microbial ecology of a crude oil contaminated aquifer

Science.gov (United States)

Bekins, B.A.; Cozzarelli, I.M.; Warren, E.; Godsy, E.M.

2002-01-01

Detailed microbial analyses of a glacial outwash aquifer contaminated by crude oil provide insights into the pattern of microbial succession from iron reducing to methanogenic in the anaerobic portion of the contaminant plume. We analysed sediments from this area for populations of aerobes, iron reducers, fermenters and methanogens, using the most probable number method. On the basis of the microbial data the anaerobic area can be divided into distinct physiological zones dominated by either iron-reducers or a consortium of fermenters and methanogens. Chemistry and permeability data show that methanogenic conditions develop first in areas of high hydrocarbon flux. Thus, we find methanogens both in high permeability horizons and also where separate-phase crude oil is present in either the saturated or unsaturated zone. Microbial numbers peak at the top of the separate-phase oil suggesting that growth is most rapid in locations with access to both hydrocarbons and nutrients infiltrating from the surface.

Effects of Hurricane-Felled Tree Trunks on Soil Carbon, Nitrogen, Microbial Biomass, and Root Length in a Wet Tropical Forest

Directory of Open Access Journals (Sweden)

D. Jean Lodge

2016-11-01

Full Text Available Decaying coarse woody debris can affect the underlying soil either by augmenting nutrients that can be exploited by tree roots, or by diminishing nutrient availability through stimulation of microbial nutrient immobilization. We analyzed C, N, microbial biomass C and root length in closely paired soil samples taken under versus 20–50 cm away from large trunks of two species felled by Hugo (1989 and Georges (1998 three times during wet and dry seasons over the two years following the study conducted by Georges. Soil microbial biomass, % C and % N were significantly higher under than away from logs felled by both hurricanes (i.e., 1989 and 1998, at all sampling times and at both depths (0–10 and 10–20 cm. Frass from wood boring beetles may contribute to early effects. Root length was greater away from logs during the dry season, and under logs in the wet season. Root length was correlated with microbial biomass C, soil N and soil moisture (R = 0.36, 0.18, and 0.27, respectively; all p values < 0.05. Microbial biomass C varied significantly among seasons but differences between positions (under vs. away were only suggestive. Microbial C was correlated with soil N (R = 0.35. Surface soil on the upslope side of the logs had significantly more N and microbial biomass, likely from accumulation of leaf litter above the logs on steep slopes. We conclude that decaying wood can provide ephemeral resources that are exploited by tree roots during some seasons.

Changes in microbial water quality in RAS following altered feed loading

DEFF Research Database (Denmark)

Rojas-Tirado, Paula Andrea; Pedersen, Per Bovbjerg; Vadstein, Olav

2018-01-01

and inorganic nutrients available for microbial growth in RAS. How these nutrient inputs affect and regulate bacteria in RAS water is, however, unclear. To investigate this relationship and the associated water quality dynamics, the effects of altered feed loading on microbial water quality in RAS was studied....... The study included six independent, identical pilot-scale RAS, each with a total volume of 1.7 m3 (make-up water: 80 L/day) stocked with juvenile rainbow trout (Oncorhynchus mykiss). All systems had been operating with constant and identical feed loading of 3.13 kg feed/m3 make-up water for a period......Intensive recirculating aquaculture systems (RAS) with its hyper-eutrophic water offer ideal conditions for bacterial growth, abundance and activity, potentially affecting fish and system performance. Feed composition and feed loading in particular will have significant impact on organic...

Microbial processes at the beds of glaciers and ice sheets: a look at life below the Whillans Ice Stream

Science.gov (United States)

Mikucki, J.; Campen, R.; Vancleave, S.; Scherer, R. P.; Coenen, J. J.; Powell, R. D.; Tulaczyk, S. M.

2017-12-01

Groundwater, saturated sediments and hundreds of subglacial lakes exist below the ice sheets of Antarctica. The few Antarctic subglacial environments sampled to date all contain viable microorganisms. This is a significant finding because microbes are known to be key in mediating biogeochemical cycles. In sediments, microbial metabolic activity can also result in byproducts or direct interactions with sediment particles that influence the physical and geochemical characteristics of the matrix they inhabit. Subglacial Lake Whillans (SLW), a fresh water lake under the Whillans Ice Stream that drains into the Ross Sea at its grounding zone, was recently sampled as part of the NSF-funded Whillans Ice Stream Subglacial Access Research Drilling (WISSARD) project. Sediments from both SLW and its grounding zone contain microbial taxa related to iron, sulfur, nitrogen and methane oxidizers. In addition to molecular data, biogeochemical measurements and culture based experiments on Whillans sediments support the notion that the system is chemosynthetic with energy derived in part by cycling inorganic compounds. Etch pitting and mineral precipitates on fossil sponge spicules suggest that spicules may also provide microbial nutrients in these environments. Perhaps the most widespread microbial process that affects sediment structure and mineral weathering is the production of extra polymeric substances (EPS). Several phylogenetic groups detected in Whillans sediments are known to produce EPS and we have observed its production in pure cultures enriched directly from these sediments. Our data sheds light on how microbial life persists below the Antarctic Ice Sheet despite extended isolation in icy darkness, and how these microbes may be shaping their environment.

Fermentation of cereals - Influence on digestibility of nutrients in growing pigs

DEFF Research Database (Denmark)

Jørgensen, Henry; Sholly, Danielle; Pedersen, Anni Øyan

2010-01-01

) at a ratio of 1:2.75 (wt/wt). Four experimental diets consisting of either dry or fermented barley or wheat, supplemented with a protein mixture (not fermented) were formulated to contain recommended levels of nutrients. Eight pigs from two litters were surgically fitted with a T-cannula anterior to the ileo......-cecal junction and fed one of the four experimental diets according to a repeated 4 × 4 Latin-square design. The fermentation process was followed by measuring the changes in the major nutrients, microbial composition and organic acid concentrations. Fermentation caused a reduced concentration of carbohydrates...

Microbial control of the dark end of the biological pump

NARCIS (Netherlands)

Herndl, G.J.; Reinthaler, T.

2013-01-01

A fraction of the carbon captured by phytoplankton in the sunlit surface ocean sinks to depth as dead organic matter and faecal material. The microbial breakdown of this material in the subsurface ocean generates carbon dioxide. Collectively, this microbially mediated flux of carbon from the

Microbes mediate carbon and nitrogen retention in shallow photic sediments

Science.gov (United States)

Hardison, A.; Anderson, I.; Canuel, E. A.; Tobias, C.; Veuger, B.

2009-12-01

Sediments in shallow coastal bays are sites of intense biogeochemical cycling facilitated by a complex microbial consortium. Unlike deeper coastal environments, much of the benthos is illuminated by sunlight in these bays. As a result, benthic autotrophs such as benthic microalgae (BMA) and macroalgae play an integral role in nutrient cycling. Investigating pathways of carbon (C) and nitrogen (N) flow through individual compartments within the sediment microbial community has previously proved challenging due to methodological difficulties. However, it is now possible using stable isotopes and microbial biomarkers such as fatty acids and amino acids to track C and N flow through individual microbial pools. We investigated the uptake and retention of C and N by bacteria and BMA in a shallow subtidal system. Using bulk and compound specific isotopic analysis, we traced the pathways of dissolved inorganic 13C and 15N under various treatments: 1) in ambient light or dark, 2) from porewater or water column sources, and 3) in the presence or absence of bloom forming nuisance macroalgae. Excess 13C and 15N in THAAs and excess 13C in total PLFAs showed a strong dependence on light. Enrichment of these pools represents uptake by the microbial community, which can include both autotrophic and heterotrophic components. Higher excess 13C in benthic microalgal fatty acids (C20, C22 PUFAs) provides evidence that benthic microalgae were fixing 13C. Aditionally, the ratio of excess 13C in branched fatty acids to microbial fatty acids (BAR) and excess 13C and 15N in D-Ala to L-Ala (D/L-Ala) were low, suggesting dominance by benthic microalgae over bacteria to total label incorporation. Our results support uptake and retention of C and N by the sediment microbial community and indicate a tight coupling between BMA and bacteria in shallow illuminated systems. This uptake is diminished in the presence of macroalgae, likely due to shading and/or nutrient competition. Therefore

Live Cell Discovery of Microbial Vitamin Transport and Enzyme-Cofactor Interactions

Energy Technology Data Exchange (ETDEWEB)

Anderson, Lindsey N.; Koech, Phillip K.; Plymale, Andrew E.; Landorf, Elizabeth V.; Konopka, Allan; Collart, Frank; Lipton, Mary S.; Romine, Margaret F.; Wright, Aaron T.

2016-02-02

The rapid completion of microbial genomes is inducing a conundrum in functional gene discovery. Novel methods are critically needed to shorten the gap between characterizing a microbial genome and experimentally validating bioinformatically-predicted functions. Of particular importance are transport mechanisms, used to shuttle nutrients and metabolites across cell mem-branes, such as B vitamins, which are indispensable to metabolic reactions crucial to the survival of diverse microbes ranging from members of environmental microbial communities to human pathogens. Methods to accurately assign function and specificity for a wide range of experimentally unidentified and/or predicted membrane-embedded transport proteins, and characterization of intra-cellular enzyme-cofactor/nutrient associations are needed to enable a significantly improved understanding of microbial biochemis-try and physiology, how microbes associate with others, and how they sense and respond to environmental perturbations. Chemical probes derived from B vitamins B1, B2, and B7 have allowed us to experimentally address the aforementioned needs by identifying B vitamin transporters and intracellular protein-cofactor associations through live cell labeling of the filamentous anoxygenic pho-toheterotroph, Chloroflexus aurantiacus J-10-fl, known for both B vitamin biosynthesis and environmental salvage. Our probes provide a unique opportunity to directly link cellular activity and protein function back to ecosystem and/or host dynamics by iden-tifying B vitamin transport and disposition mechanisms required for survival.

Microbial activity during a coastal phytoplankton bloom on the Western Antarctic Peninsula in late summer.

Science.gov (United States)

Alcamán-Arias, María E; Farías, Laura; Verdugo, Josefa; Alarcón-Schumacher, Tomás; Díez, Beatriz

2018-05-01

Phytoplankton biomass during the austral summer is influenced by freezing and melting cycles as well as oceanographic processes that enable nutrient redistribution in the West Antarctic Peninsula (WAP). Microbial functional capabilities, metagenomic and metatranscriptomic activities as well as inorganic 13C- and 15N-assimilation rates were studied in the surface waters of Chile Bay during two contrasting summer periods in 2014. Concentrations of Chlorophyll a (Chla) varied from 0.3 mg m-3 in February to a maximum of 2.5 mg m-3 in March, together with a decrease in nutrients; however, nutrients were never depleted. The microbial community composition remained similar throughout both sampling periods; however, microbial abundance and activity changed with Chla levels. An increased biomass of Bacillariophyta, Haptophyceae and Cryptophyceae was observed along with night-grazing activity of Dinophyceae and ciliates (Alveolates). During high Chla conditions, HCO3- uptake rates during daytime incubations increased 5-fold (>2516 nmol C L-1 d-1), and increased photosynthetic transcript numbers that were mainly associated with cryptophytes; meanwhile night time NO3- (>706 nmol N L-1 d-1) and NH4+ (41.7 nmol N L-1 d-1) uptake rates were 2- and 3-fold higher, respectively, due to activity from Alpha-/Gammaproteobacteria and Bacteroidetes (Flavobacteriia). Due to a projected acceleration in climate change in the WAP, this information is valuable for predicting the composition and functional changes in Antarctic microbial communities.

The potential for microbial life in a Canadian high-level nuclear fuel waste disposal vault

International Nuclear Information System (INIS)

Stroes-Gascoyne, S.

1989-12-01

Recent studies have concluded that microbial contamination of a nuclear fuel waste disposal vault is inevitable. Factors that will affect the development of substantial population of micro-organisms include: physiological tolerance of microbes; fluid movement in a vault; availability of nutrients; and availability of energy sources. It is difficult to resolve whether microbial growth will either positively or negatively affect the performance of a vault. One of the necessary steps towards ultimately answering this question is to assess the potential for microbial growth in a disposal vault, based on a nutrient and energy budget. This report gives a quantitative (but conservative) inventory of nutrients and potential energy sources present in a Canadian nuclear fuel waste vault, which hypothetically could support the growth of micro-organisms. Maximum population densities are calculated based on these inventories and assuming that all conditions for microbial growth are optimal, although this will certainly not be the case. Laboratory studies under the vault-relevant conditions are being performed to put realistic boundaries on the calculated numbers. Initial results from these studies, combined with data from a natural analogue site indicate that the calculated population densities could be overestimated by four to five orders of magnitude. Limited data show no effect of the presence of microbes on the transport of Tc, I, and Sr in backfill sand columns. Additional work is needed to address transport effects on buffer and backfill clay columns

Microbial biomass and nutrient dynamics during decomposition of cover crop mixtures

NARCIS (Netherlands)

Drost, S.M.

2016-01-01

Sustainable agriculture is needed to reduce losses of soil organic matter (SOM) and to ensure crop production with a minimum of negative impact on the environment. Cover crops, planted in the fallow season, are commonly used to improve soil functions, such as soil structure, nutrient cycling,

An overview of electron acceptors in microbial fuel cells

DEFF Research Database (Denmark)

Ucar, Deniz; Zhang, Yifeng; Angelidaki, Irini

2017-01-01

Microbial fuel cells (MFC) have recently received increasing attention due to their promising potential in sustainable wastewater treatment and contaminant removal. In general, contaminants can be removed either as an electron donor via microbial catalyzed oxidization at the anode or removed at t...... acceptors (e.g., nitrate, iron, copper, perchlorate) and mediators....

Periodontitis: from microbial immune subversion to systemic inflammation

Science.gov (United States)

Hajishengallis, George

2014-01-01

Periodontitis is a dysbiotic inflammatory disease with an adverse impact on systemic health. Recent studies have provided insights into the emergence and persistence of dysbiotic oral microbial communities, which can mediate inflammatory pathology at local as well as distant sites. This Review discusses mechanisms of microbial immune subversion that tip the balance from homeostasis to disease in oral or extraoral sites. PMID:25534621

Quality or quantity: is nutrient transfer driven more by symbiont identity and productivity than by symbiont abundance?

Science.gov (United States)

Freeman, Christopher J; Thacker, Robert W; Baker, David M; Fogel, Marilyn L

2013-06-01

By forming symbiotic interactions with microbes, many animals and plants gain access to the products of novel metabolic pathways. We investigated the transfer of symbiont-derived carbon and nitrogen to the sponges Aplysina cauliformis, Aplysina fulva, Chondrilla caribensis, Neopetrosia subtriangularis and Xestospongia bocatorensis, all of which host abundant microbial populations, and Niphates erecta, which hosts a sparse symbiont community. We incubated sponges in light and dark bottles containing seawater spiked with (13)C- and (15)N-enriched inorganic compounds and then measured (13)C and (15)N enrichment in the microbial (nutrient assimilation) and sponge (nutrient transfer) fractions. Surprisingly, although most sponges hosting abundant microbial communities were more enriched in (13)C than N. erecta, only N. subtriangularis was more enriched in (15)N than N. erecta. Although photosymbiont abundance varied substantially across species, (13)C and (15)N enrichment was not significantly correlated with photosymbiont abundance. Enrichment was significantly correlated with the ratio of gross productivity to respiration (P:R), which varied across host species and symbiont phylotype. Because irradiance impacts P:R ratios, we also incubated A. cauliformis in (13)C-enriched seawater under different irradiances to determine whether symbiont carbon fixation and transfer are dependent on irradiance. Carbon fixation and transfer to the sponge host occurred in all treatments, but was greatest at higher irradiances and was significantly correlated with P:R ratios. Taken together, these results demonstrate that nutrient transfer from microbial symbionts to host sponges is influenced more by host-symbiont identities and P:R ratios than by symbiont abundance.

Effect of nutrient enrichment on the source and composition of sediment organic carbon in tropical seagrass beds in the South China Sea

International Nuclear Information System (INIS)

Liu, Songlin; Jiang, Zhijian; Zhang, Jingping; Wu, Yunchao; Lian, Zhonglian; Huang, Xiaoping

2016-01-01

To assess the effect of nutrient enrichment on the source and composition of sediment organic carbon (SOC) beneath Thalassia hemprichii and Enhalus acoroides in tropical seagrass beds, Xincun Bay, South China Sea, intertidal sediment, primary producers, and seawater samples were collected. No significant differences on sediment δ 13 C, SOC, and microbial biomass carbon (MBC) were observed between T. hemprichii and E. acoroides. SOC was mainly of autochthonous origin, while the contribution of seagrass to SOC was less than that of suspended particulate organic matter, macroalgae and epiphytes. High nutrient concentrations contributed substantially to SOC of seagrass, macroalgae, and epiphytes. The SOC, MBC, and MBC/SOC ratio in the nearest transect to fish farming were the highest. This suggested a more labile composition of SOC and shorter turnover times in higher nutrient regions. Therefore, the research indicates that nutrient enrichment could enhance plant-derived contributions to SOC and microbial use efficiency. - Highlights: • Response of sources and composition of SOC to nutrient enrichment was observed. • Similar SOC sources and composition were observed in the two seagrass communities. • Nutrient enrichment enhanced seagrass and macroalgae and epiphytes contribution to SOC. • High nutrient concentration stimulated the MBC and the MBC/SOC ratio.

Mineralogic control on abundance and diversity of surface-adherent microbial communities

Science.gov (United States)

Mauck, Brena S.; Roberts, Jennifer A.

2007-01-01

In this study, we investigated the role of mineral-bound P and Fe in defining microbial abundance and diversity in a carbon-rich groundwater. Field colonization experiments of initially sterile mineral surfaces were combined with community structure characterization of the attached microbial population. Silicate minerals containing varying concentrations of P (∼1000 ppm P) and Fe (∼4 wt % Fe 2 O3), goethite (FeOOH), and apatite [Ca5(PO4)3(OH)] were incubated for 14 months in three biogeochemically distinct zones within a petroleum-contaminated aquifer. Phospholipid fatty acid analysis of incubated mineral surfaces and groundwater was used as a measure of microbial community structure and biomass. Microbial biomass on minerals exhibited distinct trends as a function of mineralogy depending on the environment of incubation. In the carbon-rich, aerobic groundwater attached biomass did not correlate to the P- or Fe- content of the mineral. In the methanogenic groundwater, however, biomass was most abundant on P-containing minerals. Similarly, in the Fe-reducing groundwater a correlation between Fe-content and biomass was observed. The community structure of the mineral-adherent microbial population was compared to the native groundwater community. These two populations were significantly different regardless of mineralogy, suggesting differentiation of the planktonic community through attachment, growth, and death of colonizing cells. Biomarkers specific for dissimilatory Fe-reducing bacteria native to the aquifer were identified only on Fe-containing minerals in the Fe-reducing groundwater. These results demonstrate that the trace nutrient content of minerals affects both the abundance and diversity of surface-adherent microbial communities. This behavior may be a means to access limiting nutrients from the mineral, creating a niche for a particular microbial population. These results suggest that heterogeneity of microbial populations and their associated

Nitrogen fertilization decouples roots and microbes: Reductions in belowground carbon allocation limit microbial activity

Science.gov (United States)

Carrara, J.; Walter, C. A.; Govindarajulu, R.; Hawkins, J.; Brzostek, E. R.

2017-12-01

Nitrogen (N) deposition has enhanced the ability of trees to capture atmospheric carbon (C). The effect of elevated N on belowground C cycling, however, is variable and response mechanisms are largely unknown. Recent research has highlighted distinct differences between ectomycorrhizal (ECM) and arbuscular mycorrhizal (AM) trees in the strength of root-microbial interactions. In particular, ECM trees send more C to rhizosphere microbes to stimulate enzyme activity and nutrient mobilization than AM trees, which primarily rely on saprotrophic microbes to mobilize N. As such, we hypothesized that N fertilization would weaken root-microbial interactions and soil decomposition in ECM stands more than in AM stands. To test this hypothesis, we measured root-microbial interactions in ECM and AM plots in two long-term N fertilization studies, the Fernow Experimental Forest, WV and Bear Brook Watershed, ME. We found that N fertilization led to declines in plant C allocation belowground to fine root biomass, branching, and root exudation in ECM stands to a greater extent than in AM stands. As ECM roots are tightly coupled to the soil microbiome through energy and nutrient exchange, reductions in belowground C allocation were mirrored by shifts in microbial community composition and reductions in fungal gene expression. These shifts were accompanied by larger reductions in fungal-derived lignolytic and hydrolytic enzyme activity in ECM stands than in AM stands. In contrast, as the AM soil microbiome is less reliant on trees for C and are more adapted to high inorganic nutrient environments, the soil metagenome and transcriptome were more resilient to decreases in belowground C allocation. Collectively, our results indicate the N fertilization decoupled root-microbial interactions by reducing belowground carbon allocation in ECM stands. Thus, N fertilization may reduce soil turnover and increase soil C storage to a greater extent in forests dominated by ECM than AM trees.

Nutrient enrichment induces dormancy and decreases diversity of active bacteria in salt marsh sediments

Science.gov (United States)

Kearns, Patrick J.; Angell, John H.; Howard, Evan M.; Deegan, Linda A.; Stanley, Rachel H. R.; Bowen, Jennifer L.

2016-09-01

Microorganisms control key biogeochemical pathways, thus changes in microbial diversity, community structure and activity can affect ecosystem response to environmental drivers. Understanding factors that control the proportion of active microbes in the environment and how they vary when perturbed is critical to anticipating ecosystem response to global change. Increasing supplies of anthropogenic nitrogen to ecosystems globally makes it imperative that we understand how nutrient supply alters active microbial communities. Here we show that nitrogen additions to salt marshes cause a shift in the active microbial community despite no change in the total community. The active community shift causes the proportion of dormant microbial taxa to double, from 45 to 90%, and induces diversity loss in the active portion of the community. Our results suggest that perturbations to salt marshes can drastically alter active microbial communities, however these communities may remain resilient by protecting total diversity through increased dormancy.

Microbially-Mediated Precipitation of Calcium Carbonate Nanoparticles.

Science.gov (United States)

Kang, Ser Ku; Roh, Yul

2016-02-01

The objective of this study was to investigate the biomineralization of carbonate minerals using microorganisms (Wu Do-1) enriched from rhodoliths. A 16S rRNA sequence analysis showed that Wu Do-1 mainly contained Proteus mirabilis. The pH decreased from 6.5 to 5.3 over the first 4 days of incubation due to microbial oxidation of organic acids, after which it increased to 7.8 over the remaining incubation period. XRD analysis showed that the precipitates were Mg-rich cal- cite (MgxCa(1-x)CO3), whereas no precipitates were formed without the addition of Wu Do-1 in D-1 medium. SEM-EDS analyses showed that the Mg-rich calcite had a rhombohedron shape and consisted of Ca, Si and Mg with an extracelluar polymeric substance (EPS). In addition, TEM-EDS analyses revealed they were hexagon in shape, 500-700 nm in size, and composed of Ca, Mg, C, and O. These results indicated that Wu Do-1 induced precipitation of Mg-rich calcite on the cell walls and EPS via the accumulation of Ca and/or Mg ions. Therefore, microbial precipitation of carbonate nanoparticles may play an important role in metal and carbon biogeochemistry, as well as in carbon sequestration in natural environments.

Effect of nutrient enrichment on the source and composition of sediment organic carbon in tropical seagrass beds in the South China Sea.

Science.gov (United States)

Liu, Songlin; Jiang, Zhijian; Zhang, Jingping; Wu, Yunchao; Lian, Zhonglian; Huang, Xiaoping

2016-09-15

To assess the effect of nutrient enrichment on the source and composition of sediment organic carbon (SOC) beneath Thalassia hemprichii and Enhalus acoroides in tropical seagrass beds, Xincun Bay, South China Sea, intertidal sediment, primary producers, and seawater samples were collected. No significant differences on sediment δ(13)C, SOC, and microbial biomass carbon (MBC) were observed between T. hemprichii and E. acoroides. SOC was mainly of autochthonous origin, while the contribution of seagrass to SOC was less than that of suspended particulate organic matter, macroalgae and epiphytes. High nutrient concentrations contributed substantially to SOC of seagrass, macroalgae, and epiphytes. The SOC, MBC, and MBC/SOC ratio in the nearest transect to fish farming were the highest. This suggested a more labile composition of SOC and shorter turnover times in higher nutrient regions. Therefore, the research indicates that nutrient enrichment could enhance plant-derived contributions to SOC and microbial use efficiency. Copyright © 2016 Elsevier Ltd. All rights reserved.

Biotic interactions reduce microbial carbon use efficiency

Science.gov (United States)

Bradford, M.; Maynard, D. S.

2017-12-01

The efficiency by which microbes decompose organic matter governs the amount of carbon that is retained in microbial biomass versus lost to the atmosphere as respiration. This carbon use efficiency (CUE) is affected by various abiotic conditions, such as temperature and nutrient availability. In biogeochemical model simulations, CUE is a key variable regulating how much soil carbon is stored or lost from ecosystems under simulated global changes, such as climate warming. Theoretically, the physiological costs of biotic interactions such as competition should likewise alter CUE, yet the direction and magnitude of these costs are untested. Here we conduct a microcosm experiment to quantify how competitive interactions among saprotrophic fungi alter growth, respiration, and CUE. Free-living decomposer fungi representing a broad range of traits and phylogenies were grown alone, in pairwise competition, and in multi-species (up to 15) communities. By combing culturing and stable carbon isotope approaches, we could resolve the amount of carbon substrate allocated to fungal biomass versus respiration, and so estimate CUE. By then comparing individual performance to community-level outcomes, we show that species interactions induce consistent declines in CUE, regardless of abiotic conditions. Pairwise competition lowers CUE by as much as 25%, with the magnitude of these costs equal to or greater than the observed variation across abiotic conditions. However, depending on the competitive network structure, increasing species richness led to consistent gains or declines in CUE. Our results suggest that the extent to which microbial-mediated carbon fluxes respond to environmental change may be influenced strongly by competitive interactions. As such, knowledge of abiotic conditions and community composition is necessary to confidently project CUE and hence ecosystem carbon dynamics.

Compatible Rhizosphere-Competent Microbial Consortium Adds Value to the Nutritional Quality in Edible Parts of Chickpea.

Science.gov (United States)

Yadav, Sudheer K; Singh, Surendra; Singh, Harikesh B; Sarma, Birinchi K

2017-08-02

Chickpea is used as a high-energy and protein source in diets of humans and livestock. Moreover, chickpea straw can be used as alternative of forage in ruminant diets. The present study evaluates the effect of beneficial microbial inoculation on enhancing the nutritional values in edible parts of chickpea. Two rhizosphere-competent compatible microbes (Pseudomonas fluorescens OKC and Trichoderma asperellum T42) were selected and applied to seeds either individually or in consortium before sowing. Chickpea seeds treated with the microbes showed enhanced plant growth [88.93% shoot length at 60 days after sowing (DAS)] and biomass accumulation (21.37% at 120 DAS). Notably, the uptake of mineral nutrients, viz., N (90.27, 91.45, and 142.64%), P (14.13, 58.73, and 56.84%), K (20.5, 9.23, and 35.98%), Na (91.98, 101.66, and 36.46%), Ca (16.61, 29.46, and 16%), and organic carbon (28.54, 17.09, and 18.54%), was found in the seed, foliage, and pericarp of the chickpea plants, respectively. Additionally, nutritional quality, viz., total phenolic (59.7, 2.8, and 17.25%), protein (9.78, 18.53, and 7.68%), carbohydrate content (26.22, 30.21, and 26.63%), total flavonoid content (3.11, 9.15, and 7.81%), and reducing power (112.98, 75.42, and 111.75%), was also found in the seed, foliage, and pericarp of the chickpea plants. Most importantly, the microbial-consortium-treated plants showed the maximum increase of nutrient accumulation and enhancement in nutritional quality in all edible parts of chickpea. Nutritional partitioning in different edible parts of chickpea was also evident in the microbial treatments compared to their uninoculated ones. The results thus clearly demonstrated microbe-mediated enhancement in the dietary value of the edible parts of chickpea because seeds are consumed by humans, whereas pericarp and foliage (straw) are used as an alternative of forage and roughage in ruminant diets.

Microbial ecology of bacterially mediated PCB biodegradation

International Nuclear Information System (INIS)

Pettigrew, C.A. Jr.

1989-01-01

The roles of plasmid mediated and consortia mediated polychlorinated biphenyl (PCB) biodegradation by bacterial populations isolated from PCB contaminated freshwater sediments were investigated. PCB degrading bacteria were isolated by DNA:DNA colony hybridization, batch enrichments, and chemostat enrichment. Analysis of substrate removal and metabolite production were done using chlorinated biphenyl spray plates, reverse phase high pressure liquid chromatography, Cl - detection, and 14 C-labeled substrate mineralization methods. A bacterial consortium, designated LPS10, involved in a concerted metabolic attack on chlorinated biphenyls, was shown to mineralize 4-chlorobiphenyl (4CB) and 4,4'-dichlorobiphenyl (4,4' CB). The LPS10 consortium was isolated by both batch and chemostat enrichment using 4CB and biphenyl (BP) as sole carbon source and was found to have tree bacterial isolates that predominated; these included: Pseudomonas, testosteroni LPS10A which mediated the breakdown of 4CB and 4,4' CB to the putative meta-cleavage product and subsequently to 4-chlorobenzoic acid (4CBA), an isolate tentatively identified as an Arthrobacter sp. LPS10B which mediated 4CBA degradation, and Pseudomonas putida by A LPS10C whose role in the consortium has not been determined

Linking Soil Microbial Ecology to Ecosystem Functioning in Integrated Crop-Livestock Systems

Science.gov (United States)

Enhanced soil stability, nutrient cycling and C sequestration potential are important ecosystem functions driven by soil microbial processes and are directly influenced by agricultural management. Integrated crop-livestock agroecosystems (ICL) can enhance these functions via high-residue returning c...

Effects of phosphorus and nitrogen additions on tropical soil microbial activity in the context of experimental warming

Science.gov (United States)

Foley, M.; Nottingham, A.; Turner, B. L.

2017-12-01

Soil warming is generally predicted to increase microbial mineralization rates and accelerate soil C losses which could establish a positive feedback to climatic warming. Tropical rain forests account for a third of global soil C, yet the responseto of tropical soil C a warming climate remains poorly understood. Despite predictions of soil C losses, decomposition of soil organic matter (SOM) in tropical soils may be constrained by several factors including microbial nutrient deficiencies. We performed an incubation experiment in conjunction with an in-situ soil warming experiment in a lowland tropical forest on Barro Colorado Island, Panama, to measure microbial response to two key nutrient additions in shallow (0-10cm) and deep (50-100 cm) soils. We compared the response of lowland tropical soils to montane tropical soils, predicting that lowland soils would display the strongest response to phosphorus additions. Soils were treated with either carbon alone (C), nitrogen (CN), phosphorus (CP) or nitrogen and phosphorus combined (CNP). Carbon dioxide (CO2) production was measured by NaOH capture and titrimetric analysis for 10 days. Cumulative CO2 production in montane soils increased significantly with all additions, suggesting these soils are characterized by a general microbial nutrient deficiency. The cumulative amount of C respired in deep soils from the lowland site increased significantly with CP and CNP additions, suggesting that microbial processes in deep lowland tropical soils are phosphorus-limited. These results support the current understanding that lowland tropical forests are growing on highly weathered, phosphorus-deplete soils, and provide novel insight that deep tropical SOM may be stabilized by a lack of biologically-available phosphorus. Further, this data suggests tropical soil C losses under elevated temperature may be limited by a strong microbial phosphorus deficiency.

Bentonite. Geotechnical barrier and source for microbial life

International Nuclear Information System (INIS)

Matschiavelli, Nicole; Kluge, Sindy; Cherkouk, Andrea; Steglich, Jennifer

2017-01-01

Due to their properties, namely a high swelling capacity and a low hydraulic conductivity, Bentonites fulfil as geotechnical barrier a sealing and buffering function in the nuclear waste repository. Depending on the mineral composition Bentonites contain many suitable electron-donors and -acceptors, enabling potential microbial life. For the potential repository of highly radioactive waste the microbial mediated transformation of Bentonite could influence its properties as a barrier material. Microcosms were set up containing Bentonite and anaerobic synthetic Opalinus-clay-pore water solution under an N_2/CO_2-atmosphere to elucidate the microbial potential within selected Bentonites. Substrates like acetate and lactate were supplemented to stimulate potential microbial activity. First results show that bentonites represent a source for microbial life, demonstrated by the consumption of lactate and the formation of pyruvate. Furthermore, microbial iron-reduction was determined, which plays a crucial role in Betonite-transformation.

Bentonite. Geotechnical barrier and source for microbial life

Energy Technology Data Exchange (ETDEWEB)

Matschiavelli, Nicole; Kluge, Sindy; Cherkouk, Andrea [Helmholtz-Zentrum Dresden-Rossendorf e.V., Dresden (Germany). HZDR Young Investigator Group; Steglich, Jennifer

2017-06-01

Due to their properties, namely a high swelling capacity and a low hydraulic conductivity, Bentonites fulfil as geotechnical barrier a sealing and buffering function in the nuclear waste repository. Depending on the mineral composition Bentonites contain many suitable electron-donors and -acceptors, enabling potential microbial life. For the potential repository of highly radioactive waste the microbial mediated transformation of Bentonite could influence its properties as a barrier material. Microcosms were set up containing Bentonite and anaerobic synthetic Opalinus-clay-pore water solution under an N{sub 2}/CO{sub 2}-atmosphere to elucidate the microbial potential within selected Bentonites. Substrates like acetate and lactate were supplemented to stimulate potential microbial activity. First results show that bentonites represent a source for microbial life, demonstrated by the consumption of lactate and the formation of pyruvate. Furthermore, microbial iron-reduction was determined, which plays a crucial role in Betonite-transformation.

The Study of Microbial Environmental Processes Related to the Natural Attenuation of Uranium at the Rifle Site using Systems-level Biology

Energy Technology Data Exchange (ETDEWEB)

Methe, Barbara [J. Craig Venter Inst. (JCVI), Rockville, MD (United States); Lipton, Mary [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Mahadevan, Krishna [Univ. of Toronto, ON (Canada)

2016-08-31

Microbes exist in communities in the environment where they are fundamental drivers of global carbon, nutrient and metal cycles. In subsurface environments, they possess significant metabolic potential to affect these global cycles including the transformation of radionuclides. This study examined the influence of microbial communities in sediment zones undergoing biogeochemical cycling of carbon, nutrients and metals including natural attenuation of uranium. This study examined the relationship of both the microbiota (taxonomy) and their metabolic capacity (function) in driving carbon, nutrient and metal cycles including uranium reduction at the Department of Energy (DOE) Rifle Integrated Field Research Challenge (RIFRC). Objectives of this project were: 1) to apply systems-level biology through application of ‘metaomics’ approaches (collective analyses of whole microbial community DNA, RNA and protein) to the study of microbial environmental processes and their relationship to C, N and metals including the influence of microbial communities on uranium contaminant mobility in subsurface settings undergoing natural attenuation, 2) improve methodologies for data generation using metaomics (collectively metagenomics, metatranscriptomics and proteomics) technologies and analysis and interpretation of that data and 3) use the data generated from these studies towards microbial community-scale metabolic modeling. The strategy for examining these subsurface microbial communities was to generate sequence reads from microbial community DNA (metagenomics or whole genome shotgun sequencing (WGS)) and RNA (metatranscriptomcs or RNAseq) and protein information using proteomics. Results were analyzed independently and through computational modeling. Overall, the community model generated information on the microbial community structure that was observed using metaomic approaches at RIFRC sites and thus provides an important framework for continued community modeling

Seasonal and interannual dynamics of soil microbial biomass and available nitrogen in an alpine meadow in the eastern part of Qinghai-Tibet Plateau, China

Science.gov (United States)

Xu, Bo; Wang, Jinniu; Wu, Ning; Wu, Yan; Shi, Fusun

2018-01-01

Soil microbial activity varies seasonally in frozen alpine soils during cold seasons and plays a crucial role in available N pool accumulation in soil. The intra- and interannual patterns of microbial and nutrient dynamics reflect the influences of changing weather factors, and thus provide important insights into the biogeochemical cycles and ecological functions of ecosystems. We documented the seasonal and interannual dynamics of soil microbial and available N in an alpine meadow in the eastern part of Qinghai-Tibet Plateau, China, between April 2011 and October 2013. Soil was collected in the middle of each month and analyzed for water content, microbial biomass C (MBC) and N (MBN), dissolved organic C and N, and inorganic N. Soil microbial community composition was measured by the dilution-plate method. Fungi and actinomycetes dominated the microbial community during the nongrowing seasons, and the proportion of bacteria increased considerably during the early growing seasons. Trends of consistently increasing MBC and available N pools were observed during the nongrowing seasons. MBC sharply declined during soil thaw and was accompanied by a peak in available N pool. Induced by changes in soil temperatures, significant shifts in the structures and functions of microbial communities were observed during the winter-spring transition and largely contributed to microbial reduction. The divergent seasonal dynamics of different N forms showed a complementary nutrient supply pattern during the growing season. Similarities between the interannual dynamics of microbial biomass and available N pools were observed, and soil temperature and water conditions were the primary environmental factors driving interannual fluctuations. Owing to the changes in climate, seasonal soil microbial activities and nutrient supply patterns are expected to change further, and these changes may have crucial implications for the productivity and biodiversity of alpine ecosystems.

Microbial community functional change during vertebrate carrion decomposition.

Directory of Open Access Journals (Sweden)

Jennifer L Pechal

Full Text Available Microorganisms play a critical role in the decomposition of organic matter, which contributes to energy and nutrient transformation in every ecosystem. Yet, little is known about the functional activity of epinecrotic microbial communities associated with carrion. The objective of this study was to provide a description of the carrion associated microbial community functional activity using differential carbon source use throughout decomposition over seasons, between years and when microbial communities were isolated from eukaryotic colonizers (e.g., necrophagous insects. Additionally, microbial communities were identified at the phyletic level using high throughput sequencing during a single study. We hypothesized that carrion microbial community functional profiles would change over the duration of decomposition, and that this change would depend on season, year and presence of necrophagous insect colonization. Biolog EcoPlates™ were used to measure the variation in epinecrotic microbial community function by the differential use of 29 carbon sources throughout vertebrate carrion decomposition. Pyrosequencing was used to describe the bacterial community composition in one experiment to identify key phyla associated with community functional changes. Overall, microbial functional activity increased throughout decomposition in spring, summer and winter while it decreased in autumn. Additionally, microbial functional activity was higher in 2011 when necrophagous arthropod colonizer effects were tested. There were inconsistent trends in the microbial function of communities isolated from remains colonized by necrophagous insects between 2010 and 2011, suggesting a greater need for a mechanistic understanding of the process. These data indicate that functional analyses can be implemented in carrion studies and will be important in understanding the influence of microbial communities on an essential ecosystem process, carrion decomposition.

A role for N-acetylglucosamine as a nutrient sensor and mediator of insulin resistance.

Science.gov (United States)

Wells, L; Vosseller, K; Hart, G W

2003-02-01

The ability to regulate energy balance at both the cellular and whole body level is an essential process of life. As western society has shifted to a higher caloric diet and more sedentary lifestyle, the incidence of type 2 diabetes (non-insulin-dependent diabetes mellitus) has increased to epidemic proportions. Thus, type 2 diabetes has been described as a disease of 'chronic overnutrition'. There are abundant data to support the relationship between nutrient availability and insulin action. However, there have been multiple hypotheses and debates as to the mechanism by which nutrient availability modulates insulin signaling and how excess nutrients lead to insulin resistance. One well-established pathway for nutrient sensing is the hexosamine biosynthetic pathway (HSP), which produces the acetylated aminosugar nucleotide uridine 5'-diphospho-N-acetylglucosamine (UDP-Glc-NAc) as its end product. Since UDP-GlcNAc is the donor substrate for modification of nucleocytoplasmic proteins at serine and threonine residues with N-acetylglucosamine (O-GlcNAc), the possibility of this posttranslational modification serving as the nutrient sensor has been proposed. We have recently directly tested this model in adipocytes by examining the effect of elevated levels of O-GlcNAc on insulin-stimulated glucose uptake. In this review, we summarize the existing work that implicates the HSP and O-GlcNAc modification as nutrient sensors and regulators of insulin signaling.

Microbial Community Structure of an Alluvial Aquifer Treated to Encourage Microbial Induced Calcite Precipitation

Science.gov (United States)

Ohan, J.; Saneiyan, S.; Lee, J.; Ntarlagiannis, D.; Burns, S.; Colwell, F. S.

2017-12-01

An oligotrophic aquifer in the Colorado River floodplain (Rifle, CO) was treated with molasses and urea to encourage microbial induced calcite precipitation (MICP). This would stabilize the soil mass by reducing porosity and strengthening the mineral fabric. Over the course of a 15-day treatment period, microbial biomass was collected from monitoring well groundwater for DNA extraction and sequencing. Bromide, a conservative tracer, was co-injected and subsequently detected in downgradient wells, confirming effective nutrient delivery. Conductivity increased during the injection regime and an overall decrease in pH was observed. Groundwater chemistry showed a marked increase in ammonia, suggesting urea hydrolysis - a process catalyzed by the enzyme urease - the primary enzyme implicated in MICP. Additionally, soluble iron was detected, suggesting a general increase in microbial activity; possibly as iron-reducing bacteria changed insoluble ferric oxide to soluble ferrous hydroxide in the anoxic aquifer. DNA sequencing of the 16S rRNA gene confirmed the presence of iron reducing bacteria, including Shewanella and Desulfuromonadales. Generally, a decrease in microbial community diversity was observed when pre-injection community taxa were compared with post-injection community taxa. Phyla indicative of anoxic aquifers were represented in accordance with previous literature at the Rifle site. Linear discriminant analysis showed significant differences in representative phyla over the course of the injection series. Geophysical monitoring of the site further suggested changes that could be due to MICP. Induced polarization increased the phase shift in the primary treated area, in agreement with laboratory experiments. Cross-hole seismic testing confirmed that the shear wave velocities increased in the treated soil mass, implying the soil matrix became more stable. Future investigations will help elucidate the viability and efficacy of MICP treatment in changing

Application of biocathode in microbial fuel cells: cell performance and microbial community

Energy Technology Data Exchange (ETDEWEB)

Guo-Wei, Chen [Pusan National Univ. (Korea). Dept. of Environmental Engineering; Hefei Univ. of Technology (China). School of Civil Engineering; Choi, Soo-Jung; Lee, Tae-Ho; Lee, Gil-Young; Cha, Jae-Hwan; Kim, Chang-Won [Pusan National Univ. (Korea). Dept. of Environmental Engineering

2008-06-15

Instead of the utilization of artificial redox mediators or other catalysts, a biocathode has been applied in a two-chamber microbial fuel cell in this study, and the cell performance and microbial community were analyzed. After a 2-month startup, the microorganisms of each compartment in microbial fuel cell were well developed, and the output of microbial fuel cell increased and became stable gradually, in terms of electricity generation. At 20 ml/min flow rate of the cathodic influent, the maximum power density reached 19.53 W/m{sup 3}, while the corresponding current and cell voltage were 15.36 mA and 223 mV at an external resistor of 14.9 {omega}, respectively. With the development of microorganisms in both compartments, the internal resistance decreased from initial 40.2 to 14.0 {omega}, too. Microbial community analysis demonstrated that five major groups of the clones were categorized among those 26 clone types derived from the cathode microorganisms. Betaproteobacteria was the most abundant division with 50.0% (37 of 74) of the sequenced clones in the cathode compartment, followed by 21.6% (16 of 74) Bacteroidetes, 9.5% (7 of 74) Alphaproteobacteria, 8.1% (6 of 74) Chlorobi, 4.1% (3 of 74) Deltaproteobacteria, 4.1% (3 of 74) Actinobacteria, and 2.6% (2 of 74) Gammaproteobacteria. (orig.)

Gammarus-Microbial Interactions: A Review

Directory of Open Access Journals (Sweden)

Daniel Nelson

2011-01-01

Full Text Available Gammarus spp. are typically classified as shredders under the functional feeding group classification. In the wild and in the laboratory, Gammarus spp. will often shred leaves, breaking them down into finer organic matter fractions. However, leaf litter is a poor quality food source (i.e., high C : N and C : P ratios and very little leaf material is assimilated by shredders. In freshwater habitats leaf litter is colonized rapidly (within ∼1-2 weeks by aquatic fungi and bacteria, making the leaves more palatable and nutritious to consumers. Several studies have shown that Gammarus spp. show preference for conditioned leaves over nonconditioned leaves and certain fungal species to others. Furthermore, Gammarus spp. show increased survival and growth rates when fed conditioned leaves compared to non-conditioned leaves. Thus, Gammarus spp. appear to rely on the microbial biofilm associated with leaf detritus as a source of carbon and/or essential nutrients. Also, Gammarus spp. can have both positive and negative effects on the microbial communities on which they fed, making them an important component of the microbial loop in aquatic ecosystems.

Board-invited review: Rumen microbiology: leading the way in microbial ecology.

Science.gov (United States)

Krause, D O; Nagaraja, T G; Wright, A D G; Callaway, T R

2013-01-01

Robert Hungate, considered the father of rumen microbiology, was the first to initiate a systematic exploration of the microbial ecosystem of the rumen, but he was not alone. The techniques he developed to isolate and identify cellulose-digesting bacteria from the rumen have had a major impact not only in delineating the complex ecosystem of the rumen but also in clinical microbiology and in the exploration of a number of other anaerobic ecosystems, including the human hindgut. Rumen microbiology has pioneered our understanding of much of microbial ecology and has broadened our knowledge of ecology in general, as well as improved the ability to feed ruminants more efficiently. The discovery of anaerobic fungi as a component of the ruminal flora disproved the central dogma in microbiology that all fungi are aerobic organisms. Further novel interactions between bacterial species such as nutrient cross feeding and interspecies H2 transfer were first described in ruminal microorganisms. The complexity and diversity present in the rumen make it an ideal testing ground for microbial theories (e.g., the effects of nutrient limitation and excess) and techniques (such as 16S rRNA), which have rewarded the investigators that have used this easily accessed ecosystem to understand larger truths. Our understanding of characteristics of the ruminal microbial population has opened new avenues of microbial ecology, such as the existence of hyperammonia-producing bacteria and how they can be used to improve N efficiency in ruminants. In this review, we examine some of the contributions to science that were first made in the rumen, which have not been recognized in a broader sense.

Trait-mediated diversification in nematode predator–prey systems

NARCIS (Netherlands)

Mulder, C.; Helder, J.; Vervoort, M.T.W.; Vonk, J.A.

2011-01-01

Nematodes are presumably the most numerous Metazoans in terrestrial habitats. They are represented at all trophic levels and are known to respond to nutrient limitation, prey availability, and microbial resources. Predatory nematodes reside at the highest trophic level, and as such their feeding

Microbial community composition affects soil fungistasis

NARCIS (Netherlands)

De Boer, W.; Verheggen, P.; Klein Gunnewiek, P.J.A.; Kowalchuk, G.A.; Van Veen, J.A.

2003-01-01

Most soils inhibit fungal germination and growth to a certain extent, a phenomenon known as soil fungistasis. Previous observations have implicated microorganisms as the causal agents of fungistasis, with their action mediated either by available carbon limitation (nutrient deprivation hypothesis)

Effects of microbial processes on gas generation under expected WIPP repository conditions: Annual report through 1992

International Nuclear Information System (INIS)

Francis, A.J.; Gillow, J.B.

1993-09-01

Microbial processes involved in gas generation from degradation of the organic constituents of transuranic waste under conditions expected at the Waste Isolation Pilot Plant (WIPP) repository are being investigated at Brookhaven National Laboratory. These laboratory studies are part of the Sandia National Laboratories -- WIPP Gas Generation Program. Gas generation due to microbial degradation of representative cellulosic waste was investigated in short-term ( 6 months) experiments by incubating representative paper (filter paper, paper towels, and tissue) in WIPP brine under initially aerobic (air) and anaerobic (nitrogen) conditions. Samples from the WIPP surficial environment and underground workings harbor gas-producing halophilic microorganisms, the activities of which were studied in short-term experiments. The microorganisms metabolized a variety of organic compounds including cellulose under aerobic, anaerobic, and denitrifying conditions. In long-term experiments, the effects of added nutrients (trace amounts of ammonium nitrate, phosphate, and yeast extract), no nutrients, and nutrients plus excess nitrate on gas production from cellulose degradation

Microbial Community Dynamics in Soil Depth Profiles Over 120,000 Years of Ecosystem Development

Directory of Open Access Journals (Sweden)

Stephanie Turner

2017-05-01

Full Text Available Along a long-term ecosystem development gradient, soil nutrient contents and mineralogical properties change, therefore probably altering soil microbial communities. However, knowledge about the dynamics of soil microbial communities during long-term ecosystem development including progressive and retrogressive stages is limited, especially in mineral soils. Therefore, microbial abundances (quantitative PCR and community composition (pyrosequencing as well as their controlling soil properties were investigated in soil depth profiles along the 120,000 years old Franz Josef chronosequence (New Zealand. Additionally, in a microcosm incubation experiment the effects of particular soil properties, i.e., soil age, soil organic matter fraction (mineral-associated vs. particulate, O2 status, and carbon and phosphorus additions, on microbial abundances (quantitative PCR and community patterns (T-RFLP were analyzed. The archaeal to bacterial abundance ratio not only increased with soil depth but also with soil age along the chronosequence, coinciding with mineralogical changes and increasing phosphorus limitation. Results of the incubation experiment indicated that archaeal abundances were less impacted by the tested soil parameters compared to Bacteria suggesting that Archaea may better cope with mineral-induced substrate restrictions in subsoils and older soils. Instead, archaeal communities showed a soil age-related compositional shift with the Bathyarchaeota, that were frequently detected in nutrient-poor, low-energy environments, being dominant at the oldest site. However, bacterial communities remained stable with ongoing soil development. In contrast to the abundances, the archaeal compositional shift was associated with the mineralogical gradient. Our study revealed, that archaeal and bacterial communities in whole soil profiles are differently affected by long-term soil development with archaeal communities probably being better adapted to

Trichoderma Biofertilizer Links to Altered Soil Chemistry, Altered Microbial Communities, and Improved Grassland Biomass

Directory of Open Access Journals (Sweden)

Fengge Zhang

2018-04-01

Full Text Available In grasslands, forage and livestock production results in soil nutrient deficits as grasslands typically receive no nutrient inputs, leading to a loss of grassland biomass. The application of mature compost has been shown to effectively increase grassland nutrient availability. However, research on fertilization regime influence and potential microbial ecological regulation mechanisms are rarely conducted in grassland soil. We conducted a two-year experiment in meadow steppe grasslands, focusing on above- and belowground consequences of organic or Trichoderma biofertilizer applications and potential soil microbial ecological mechanisms underlying soil chemistry and microbial community responses. Grassland biomass significantly (p = 0.019 increased following amendment with 9,000 kg ha−1 of Trichoderma biofertilizer (composted cattle manure + inoculum compared with other assessed organic or biofertilizer rates, except for BOF3000 (fertilized with 3,000 kg ha−1 biofertilizer. This rate of Trichoderma biofertilizer treatment increased soil antifungal compounds that may suppress pathogenic fungi, potentially partially responsible for improved grassland biomass. Nonmetric multidimensional scaling (NMDS revealed soil chemistry and fungal communities were all separated by different fertilization regime. Trichoderma biofertilizer (9,000 kg ha−1 increased relative abundances of Archaeorhizomyces and Trichoderma while decreasing Ophiosphaerella. Trichoderma can improve grassland biomass, while Ophiosphaerella has the opposite effect as it may secrete metabolites causing grass necrosis. Correlations between soil properties and microbial genera showed plant-available phosphorus may influence grassland biomass by increasing Archaeorhizomyces and Trichoderma while reducing Ophiosphaerella. According to our structural equation modeling (SEM, Trichoderma abundance was the primary contributor to aboveground grassland biomass. Our results suggest Trichoderma

Trichoderma Biofertilizer Links to Altered Soil Chemistry, Altered Microbial Communities, and Improved Grassland Biomass.

Science.gov (United States)

Zhang, Fengge; Huo, Yunqian; Cobb, Adam B; Luo, Gongwen; Zhou, Jiqiong; Yang, Gaowen; Wilson, Gail W T; Zhang, Yingjun

2018-01-01

In grasslands, forage and livestock production results in soil nutrient deficits as grasslands typically receive no nutrient inputs, leading to a loss of grassland biomass. The application of mature compost has been shown to effectively increase grassland nutrient availability. However, research on fertilization regime influence and potential microbial ecological regulation mechanisms are rarely conducted in grassland soil. We conducted a two-year experiment in meadow steppe grasslands, focusing on above- and belowground consequences of organic or Trichoderma biofertilizer applications and potential soil microbial ecological mechanisms underlying soil chemistry and microbial community responses. Grassland biomass significantly ( p = 0.019) increased following amendment with 9,000 kg ha -1 of Trichoderma biofertilizer (composted cattle manure + inoculum) compared with other assessed organic or biofertilizer rates, except for BOF3000 (fertilized with 3,000 kg ha -1 biofertilizer). This rate of Trichoderma biofertilizer treatment increased soil antifungal compounds that may suppress pathogenic fungi, potentially partially responsible for improved grassland biomass. Nonmetric multidimensional scaling (NMDS) revealed soil chemistry and fungal communities were all separated by different fertilization regime. Trichoderma biofertilizer (9,000 kg ha -1 ) increased relative abundances of Archaeorhizomyces and Trichoderma while decreasing Ophiosphaerella . Trichoderma can improve grassland biomass, while Ophiosphaerella has the opposite effect as it may secrete metabolites causing grass necrosis. Correlations between soil properties and microbial genera showed plant-available phosphorus may influence grassland biomass by increasing Archaeorhizomyces and Trichoderma while reducing Ophiosphaerella . According to our structural equation modeling (SEM), Trichoderma abundance was the primary contributor to aboveground grassland biomass. Our results suggest Trichoderma

The response of soil carbon storage and microbially mediated carbon turnover to simulated climatic disturbance in a northern peatland forest. Revisiting the concept of soil organic matter recalcitrance

Energy Technology Data Exchange (ETDEWEB)

Kostka, Joel [Georgia Inst. of Technology, Atlanta, GA (United States)

2015-09-14

closely paralleled the chemical evolution of peat, with large shifts in microbial populations occurring in the biogeochemical hotspot, the mesotelm, where the highest rates of decomposition were detected. Stable isotope geochemistry and potential rates of methane production paralleled vertical changes in methanogen community composition to indicate a predominance of acetoclastic methanogenesis mediated by the Methanosarcinales in the mesotelm, while hydrogen-utilizing methanogens dominated in the deeper catotelm. Evidence pointed to the availability of phosphorus as well as nitrogen limiting the microbially-mediated turnover of organic carbon at MEF. Prior to initiation of the experimental treatments, our study provided key baseline data for the SPRUCE site on the vertical stratification of peat decomposition, key enzymatic pathways, and microbial taxa containing these pathways. The sensitivity of soil carbon turnover to climate change is strongly linked to recalcitrant carbon stocks and the temperature sensitivity of decomposition is thought to increase with increasing molecular complexity of carbon substrates. This project delivered results on how climate change perturbations impact the microbially-mediated turnover of recalcitrant organic matter in peatland forest soils, both under controlled conditions in the laboratory and at the ecosystem-scale in the field. This project revisited the concept of “recalcitrance” in the regulation of soil carbon turnover using a combination of natural abundance radiocarbon and optical spectroscopic measurements on bulk DOM, and high resolution molecular characterization of DOM. The project elucidated how organic matter reactivity and decomposition will respond to climate change in a both a qualitative (organic matter lability) and quantitiative (increased rates) manner. An Aromaticity Index was developed to represent a more direct and accurate parameter for modeling of DOM reactivity in peatlands. The abundance and community

A role for programmed cell death in the microbial loop.

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Mónica V Orellana

Full Text Available The microbial loop is the conventional model by which nutrients and minerals are recycled in aquatic eco-systems. Biochemical pathways in different organisms become metabolically inter-connected such that nutrients are utilized, processed, released and re-utilized by others. The result is that unrelated individuals end up impacting each others' fitness directly through their metabolic activities. This study focused on the impact of programmed cell death (PCD on a population's growth as well as its role in the exchange of carbon between two naturally co-occurring halophilic organisms. Flow cytometric, biochemical, ¹⁴C radioisotope tracing assays, and global transcriptomic analyses show that organic algal photosynthate released by Dunalliela salina cells undergoing PCD complements the nutritional needs of other non-PCD D. salina cells. This occurs in vitro in a carbon limited environment and enhances the growth of the population. In addition, a co-occurring heterotroph Halobacterium salinarum re-mineralizes the carbon providing elemental nutrients for the mixoheterotrophic chlorophyte. The significance of this is uncertain and the archaeon can also subsist entirely on the lysate of apoptotic algae. PCD is now well established in unicellular organisms; however its ecological relevance has been difficult to decipher. In this study we found that PCD in D. salina causes the release of organic nutrients such as glycerol, which can be used by others in the population as well as a co-occurring halophilic archaeon. H. salinarum also re-mineralizes the dissolved material promoting algal growth. PCD in D. salina was the mechanism for the flow of dissolved photosynthate between unrelated organisms. Ironically, programmed death plays a central role in an organism's own population growth and in the exchange of nutrients in the microbial loop.

Insights into environmental controls on microbial communities in a continental serpentinite aquifer using a microcosm-based approach.

Science.gov (United States)

Crespo-Medina, Melitza; Twing, Katrina I; Kubo, Michael D Y; Hoehler, Tori M; Cardace, Dawn; McCollom, Tom; Schrenk, Matthew O

2014-01-01

Geochemical reactions associated with serpentinization alter the composition of dissolved organic compounds in circulating fluids and potentially liberate mantle-derived carbon and reducing power to support subsurface microbial communities. Previous studies have identified Betaproteobacteria from the order Burkholderiales and bacteria from the order Clostridiales as key components of the serpentinite-hosted microbiome, however there is limited knowledge of their metabolic capabilities or growth characteristics. In an effort to better characterize microbial communities, their metabolism, and factors limiting their activities, microcosm experiments were designed with fluids collected from several monitoring wells at the Coast Range Ophiolite Microbial Observatory (CROMO) in northern California during expeditions in March and August 2013. The incubations were initiated with a hydrogen atmosphere and a variety of carbon sources (carbon dioxide, methane, acetate, and formate), with and without the addition of nutrients and electron acceptors. Growth was monitored by direct microscopic counts; DNA yield and community composition was assessed at the end of the 3 month incubation. For the most part, results indicate that bacterial growth was favored by the addition of acetate and methane, and that the addition of nutrients and electron acceptors had no significant effect on microbial growth, suggesting no nutrient- or oxidant-limitation. However, the addition of sulfur amendments led to different community compositions. The dominant organisms at the end of the incubations were closely related to Dethiobacter sp. and to the family Comamonadaceae, which are also prominent in culture-independent gene sequencing surveys. These experiments provide one of first insights into the biogeochemical dynamics of the serpentinite subsurface environment and will facilitate experiments to trace microbial activities in serpentinizing ecosystems.

Mangrove succession enriches the sediment microbial community in South China.

Science.gov (United States)

Chen, Quan; Zhao, Qian; Li, Jing; Jian, Shuguang; Ren, Hai

2016-06-06

Sediment microorganisms help create and maintain mangrove ecosystems. Although the changes in vegetation during mangrove forest succession have been well studied, the changes in the sediment microbial community during mangrove succession are poorly understood. To investigate the changes in the sediment microbial community during succession of mangroves at Zhanjiang, South China, we used phospholipid fatty acid (PLFA) analysis and the following chronosequence from primary to climax community: unvegetated shoal; Avicennia marina community; Aegiceras corniculatum community; and Bruguiera gymnorrhiza + Rhizophora stylosa community. The PLFA concentrations of all sediment microbial groups (total microorganisms, fungi, gram-positive bacteria, gram-negative bacteria, and actinomycetes) increased significantly with each stage of mangrove succession. Microbial PLFA concentrations in the sediment were significantly lower in the wet season than in the dry season. Regression and ordination analyses indicated that the changes in the microbial community with mangrove succession were mainly associated with properties of the aboveground vegetation (mainly plant height) and the sediment (mainly sediment organic matter and total nitrogen). The changes in the sediment microbial community can probably be explained by increases in nutrients and microhabitat heterogeneity during mangrove succession.

Effect of tree species and soil properties on nutrient immobilization in the forest floor

DEFF Research Database (Denmark)

Raulund-Rasmussen, Karsten; Vejre, Henrik

1995-01-01

of ammonium, nitrate and phosphate in the soil solution was much higher at the loamy site under all species showing a stronger microbial activity. It is therefore hypothesized that the differences in accumulation rates were, at least partly, caused by differences in the mineralization regimes. Strong root...... infiltration in the forest floors at the sandy site compared to almost none at the loamy site, is probably responsible for the differences in mineralization rate due to competition between the organic matter decomposers and the tree-roots/mycorrhiza for nutrients. Author Keywords: EFFECTS OF ROOTS; NUTRIENT...

The effect of glyphosate application on soil microbial activities in ...

African Journals Online (AJOL)

In this study, glyphosate effects as N, P and C nutrient sources on microbial population and the effect of different concentration of it on dehydrogenease activity and soil respiration were investigated. The results show that in a soil with a long historical use of glyphosate (soil 1), the hetrotrophic bacterial population was ...

Lake nutrient stoichiometry is less predictable than nutrient concentrations at regional and sub-continental scales.

Science.gov (United States)

Collins, Sarah M; Oliver, Samantha K; Lapierre, Jean-Francois; Stanley, Emily H; Jones, John R; Wagner, Tyler; Soranno, Patricia A

2017-07-01

. Our results suggest ecological context mediates controls on lake nutrients and stoichiometry. Predicting stoichiometry was generally more difficult than predicting nutrient concentrations, but human activity may decouple N and P, leading to better prediction of N:P stoichiometry in regions with high anthropogenic activity. © 2017 by the Ecological Society of America.

Research and Application of Marine Microbial Enzymes: Status and Prospects

Science.gov (United States)

Zhang, Chen; Kim, Se-Kwon

2010-01-01

Over billions of years, the ocean has been regarded as the origin of life on Earth. The ocean includes the largest range of habitats, hosting the most life-forms. Competition amongst microorganisms for space and nutrients in the marine environment is a powerful selective force, which has led to evolution. The evolution prompted the marine microorganisms to generate multifarious enzyme systems to adapt to the complicated marine environments. Therefore, marine microbial enzymes can offer novel biocatalysts with extraordinary properties. This review deals with the research and development work investigating the occurrence and bioprocessing of marine microbial enzymes. PMID:20631875

Studies about behavior of microbial degradation of organic compounds

International Nuclear Information System (INIS)

Ohtsuka, Makiko

2003-02-01

Some of TRU waste include organic compounds, thus these organic compounds might be nutrients for microbial growth at disposal site. This disposal system might be exposed to high alkali condition by cement compounds as engineering barrier material. In the former experimental studies, it has been supposed that microbial exist under pH = 12 and the microbial activity acclimated to high alkali condition are able to degrade asphalt under anaerobic condition. Microbes are called extremophile that exist in cruel habitat as high alkali or reductive condition. We know less information about the activity of extremophile, though any recent studies reveal them. In this study, the first investigation is metabolic pathway as microbial activity, the second is microbial degradation of aromatic compounds in anaerobic condition, and the third is microbial activity under high alkali. Microbial metabolic pathway consist of two systems that fulfill their function each other. One system is to generate energy for microbial activities and the other is to convert substances for syntheses of organisms' structure materials. As these systems are based on redox reaction between substances, it is made chart of the microbial activity region using pH, Eh, and depth as parameter, There is much report that microbe is able to degrade aromatic compounds under aerobic or molecular O 2 utilizing condition. For degradation of aromatic compounds in anaerobic condition, supplying electron acceptor is required. Co-metabolism and microbial consortia has important role, too. Alcalophile has individual transporting system depending Na + and acidic compounds contained in cell wall. Generating energy is key for survival and growth under high alkali condition. Co-metabolism and microbial consortia are effective for microbial degradation of aromatic compounds under high alkali and reductive condition, and utilizable electron acceptor and degradable organic compounds are required for keeping microbial activity and

Effects of Biochar Blends on Microbial Community Composition in Two Coastal Plain Soils

Directory of Open Access Journals (Sweden)

Thomas F. Ducey

2015-11-01

Full Text Available The amendment of soil with biochar has been demonstrated to have an effect not only on the soil physicochemical properties, but also on soil microbial community composition and activity. Previous reports have demonstrated significant impacts on soil microbial community structure. These impacts are modulated not only by the biochar composition, but also on the soil’s physicochemical characteristics. This indicates that soil characteristics must be considered prior to biochar amendment. A significant portion of the soils of the southeastern coastal plain are severely degraded and, therefore, candidates for biochar amendment to strengthen soil fertility. In this study we focused on two common soil series in the southeastern coastal plain, utilizing feedstocks endemic to the area. We chose feedstocks in four ratios (100% pine chip; 80:20 mixture of pine chip to poultry litter; 50:50 mixture of pine chip to poultry litter; 100% poultry litter prior to pyrolysis and soil amendment as a biochar product. Soil was analyzed for bioavailable nutrients via Mehlich-1 extractions, as well as microbial community composition using phospholipid fatty acid analysis (PLFA. Our results demonstrated significant shifts in microbial community composition in response to biochar amendment, the effects of which were greatest with 100% poultry litter biochar. Strong relationships between PLFAs and several Mehlich-1 extractable nutrients (Al, Cu, Fe, and P were observed.

Microbial community diversity and physical-chemical features of the Southwestern Atlantic Ocean

NARCIS (Netherlands)

Alves Junior, Nelson; Meirelles, Pedro Milet; de Oliveira Santos, Eidy; Dutilh, Bas; Silva, Genivaldo G Z; Paranhos, Rodolfo; Cabral, Anderson S; Rezende, Carlos; Iida, Tetsuya; de Moura, Rodrigo L; Kruger, Ricardo Henrique; Pereira, Renato C; Valle, Rogério; Sawabe, Tomoo; Thompson, Cristiane; Thompson, Fabiano

2014-01-01

Microbial oceanography studies have demonstrated the central role of microbes in functioning and nutrient cycling of the global ocean. Most of these former studies including at Southwestern Atlantic Ocean (SAO) focused on surface seawater and benthic organisms (e.g., coral reefs and sponges). This

Microbial Communities in Danish Wastewater Treatment Plants with Nutrient Removal

DEFF Research Database (Denmark)

Mielczarek, Artur Tomasz

Activated sludge treatment plants are the most used wastewater treatment systems worldwide for biological nutrient removal from wastewater. Nevertheless, the treatment systems have been for many years operated as so called “black-box”, where specific process parameters were adjusted without...... that plants with return sludge Side-Stream Hydrolysis (SSH) instead of the normal anaerobic process tank tended to have significantly fewer unwanted GAOs in contrast to many plants with traditional mainstream anaerobic tank and thus it was proposed that this system might be an effective strategy of control...

Effects of atrazine, metolachlor, carbaryl and chlorothalonil on benthic microbes and their nutrient dynamics.

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Daniel Elias

Full Text Available Atrazine, metolachlor, carbaryl, and chlorothalonil are detected in streams throughout the U.S. at concentrations that may have adverse effects on benthic microbes. Sediment samples were exposed to these pesticides to quantify responses of ammonium, nitrate, and phosphate uptake by the benthic microbial community. Control uptake rates of sediments had net remineralization of nitrate (-1.58 NO3 µg gdm⁻¹ h⁻¹, and net assimilation of phosphate (1.34 PO4 µg gdm⁻¹ h⁻¹ and ammonium (0.03 NH4 µg gdm⁻¹ h⁻¹. Metolachlor decreased ammonium and phosphate uptake. Chlorothalonil decreased nitrate remineralization and phosphate uptake. Nitrate, ammonium, and phosphate uptake rates are more pronounced in the presence of these pesticides due to microbial adaptations to toxicants. Our interpretation of pesticide availability based on their water/solid affinities supports no effects for atrazine and carbaryl, decreasing nitrate remineralization, and phosphate assimilation in response to chlorothalonil. Further, decreased ammonium and phosphate uptake in response to metolachlor is likely due to affinity. Because atrazine target autotrophs, and carbaryl synaptic activity, effects on benthic microbes were not hypothesized, consistent with results. Metolachlor and chlorothalonil (non-specific modes of action had significant effects on sediment microbial nutrient dynamics. Thus, pesticides with a higher affinity to sediments and/or broad modes of action are likely to affect sediment microbes' nutrient dynamics than pesticides dissolved in water or specific modes of action. Predicted nutrient uptake rates were calculated at mean and peak concentrations of metolachlor and chlorothalonil in freshwaters using polynomial equations generated in this experiment. We concluded that in natural ecosystems, peak chlorothalonil and metolachlor concentrations could affect phosphate and ammonium by decreasing net assimilation, and nitrate uptake rates by

Microbial biomass carbon and enzyme activities of urban soils in Beijing.

Science.gov (United States)

Wang, Meie; Markert, Bernd; Shen, Wenming; Chen, Weiping; Peng, Chi; Ouyang, Zhiyun

2011-07-01

To promote rational and sustainable use of soil resources and to maintain the urban soil quality, it is essential to assess urban ecosystem health. In this study, the microbiological properties of urban soils in Beijing and their spatial distribution patterns across the city were evaluated based on measurements of microbial biomass carbon and urease and invertase activities of the soils for the purpose of assessing the urban ecosystem health of Beijing. Grid sampling design, normal Kriging technique, and the multiple comparisons among different land use types were used in soil sampling and data treatment. The inherent chemical characteristics of urban soils in Beijing, e.g., soil pH, electronic conductivity, heavy metal contents, total N, P and K contents, and soil organic matter contents were detected. The size and diversity of microbial community and the extent of microbial activity in Beijing urban soils were measured as the microbial biomass carbon content and the ratio of microbial biomass carbon content to total soil organic carbon. The microbial community health measured in terms of microbial biomass carbon, urease, and invertase activities varied with the organic substrate and nutrient contents of the soils and were not adversely affected by the presence of heavy metals at p urban soils influenced the nature and activities of the microbial communities.

Nutrient-mediated architectural plasticity of a predatory trap.

Directory of Open Access Journals (Sweden)

Sean J Blamires

Full Text Available BACKGROUND: Nutrients such as protein may be actively sought by foraging animals. Many predators exhibit foraging plasticity, but how their foraging strategies are affected when faced with nutrient deprivation is largely unknown. In spiders, the assimilation of protein into silk may be in conflict with somatic processes so we predicted web building to be affected under protein depletion. METHODOLOGY/PRINCIPAL FINDINGS: To assess the influence of protein intake on foraging plasticity we fed the orb-web spiders Argiope aemula and Cyclosa mulmeinensis high, low or no protein solutions over 10 days and allowed them to build webs. We compared post-feeding web architectural components and major ampullate (MA silk amino acid compositions. We found that the number of radii in webs increased in both species when fed high protein solutions. Mesh size increased in A. aemula when fed a high protein solution. MA silk proline and alanine compositions varied in each species with contrasting variations in alanine between the two species. Glycine compositions only varied in C. mulmeinensis silk. No spiders significantly lost or gained mass on any feeding treatment, so they did not sacrifice somatic maintenance for amino acid investment in silk. CONCLUSIONS/SIGNIFICANCE: Our results show that the amount of protein taken in significantly affects the foraging decisions of trap-building predators, such as orb web spiders. Nevertheless, the subtle differences found between species in the association between protein intake, the amino acids invested in silk and web architectural plasticity show that the influence of protein deprivation on specific foraging strategies differs among different spiders.

Nutrient-mediated architectural plasticity of a predatory trap.

Science.gov (United States)

Blamires, Sean J; Tso, I-Min

2013-01-01

Nutrients such as protein may be actively sought by foraging animals. Many predators exhibit foraging plasticity, but how their foraging strategies are affected when faced with nutrient deprivation is largely unknown. In spiders, the assimilation of protein into silk may be in conflict with somatic processes so we predicted web building to be affected under protein depletion. To assess the influence of protein intake on foraging plasticity we fed the orb-web spiders Argiope aemula and Cyclosa mulmeinensis high, low or no protein solutions over 10 days and allowed them to build webs. We compared post-feeding web architectural components and major ampullate (MA) silk amino acid compositions. We found that the number of radii in webs increased in both species when fed high protein solutions. Mesh size increased in A. aemula when fed a high protein solution. MA silk proline and alanine compositions varied in each species with contrasting variations in alanine between the two species. Glycine compositions only varied in C. mulmeinensis silk. No spiders significantly lost or gained mass on any feeding treatment, so they did not sacrifice somatic maintenance for amino acid investment in silk. Our results show that the amount of protein taken in significantly affects the foraging decisions of trap-building predators, such as orb web spiders. Nevertheless, the subtle differences found between species in the association between protein intake, the amino acids invested in silk and web architectural plasticity show that the influence of protein deprivation on specific foraging strategies differs among different spiders.

Poorly known microbial taxa dominate the microbiome of permafrost thaw ponds.

Science.gov (United States)

Wurzbacher, Christian; Nilsson, R Henrik; Rautio, Milla; Peura, Sari

2017-08-01

In the transition zone of the shifting permafrost border, thaw ponds emerge as hotspots of microbial activity, processing the ancient carbon freed from the permafrost. We analyzed the microbial succession across a gradient of recently emerged to older ponds using three molecular markers: one universal, one bacterial and one fungal. Age was a major modulator of the microbial community of the thaw ponds. Surprisingly, typical freshwater taxa comprised only a small fraction of the community. Instead, thaw ponds of all age classes were dominated by enigmatic bacterial and fungal phyla. Our results on permafrost thaw ponds lead to a revised perception of the thaw pond ecosystem and their microbes, with potential implications for carbon and nutrient cycling in this increasingly important class of freshwaters.

Seasonal variability in the persistence of dissolved environmental DNA (eDNA in a marine system: The role of microbial nutrient limitation.

Directory of Open Access Journals (Sweden)

Ian Salter

be linked to the metabolic response of microbial communities to nutrient limitation. Future studies should consider the effect of natural environmental gradients on the seasonal persistence of eDNA, which will be of particular relevance for time-series biomonitoring programs.

Stable, geochemically mediated biospheres in the Deep Mine Microbial Observatory, SD, USA

Science.gov (United States)

Osburn, M. R.; Casar, C. P.; Kruger, B.; Flynn, T. M.

2017-12-01

The terrestrial subsurface is a vast reservoir of life, hosting diverse microbial ecosystems with varying levels of connectivity to surface inputs. Understanding long term ecosystem dynamics within the subsurface biosphere is very challenging due to limitations in accessibility, sample availability, and slow microbial growth rates. The establishment of the Deep Mine Microbial Observatory (DeMMO) at the Sanford Underground Research Facility, SD, USA has allowed for bimonthly sampling for nearly two years at six sites spanning 250 to 1500 m below the surface. Here we present a time-resolved analysis of the geomicrobiology of the six DeMMO sites, which have been created from legacy mine boreholes modified to allow for controlled sampling. Our interdisciplinary approach includes analysis of passively draining fracture fluid for aqueous and gas geochemistry, DNA sequencing, microscopy, and isotopic measurements of organic and inorganic substrates. Fluid geochemistry varies significantly between sites, but is relatively stable over time for a given site, even through significant external perturbations such as drilling and installation of permanent sampling devices into the boreholes. The fluid-hosted microbial diversity follows these trends, with consistent populations present at each site through time, even through drilling events. For instance, the shallowest site (DeMMO 1) consistently hosts >30% uncharacterized phyla and >25% Omnitrophica whereas the deepest site (DeMMO 6) is dominated by Firmicutes and Bacterioidetes. Microbial diversity appears to respond to the availability of energy sources such as organic carbon, sulfate, sulfide, hydrogen, and iron. Carbon isotopic measurements reveal closed system behavior with significant recycling of organic carbon into the DIC pool. Together these observations suggest DeMMO hosts isolated subsurface microbial populations adapted to local geochemistry that are stable on yearlong timescales.

The Impacts of Soil Fertility and Salinity on Soil Nitrogen Dynamics Mediated by the Soil Microbial Community Beneath the Halophytic Shrub Tamarisk.

Science.gov (United States)

Iwaoka, Chikae; Imada, Shogo; Taniguchi, Takeshi; Du, Sheng; Yamanaka, Norikazu; Tateno, Ryunosuke

2018-05-01

Nitrogen (N) is one of the most common limiting nutrients for primary production in terrestrial ecosystems. Soil microbes transform organic N into inorganic N, which is available to plants, but soil microbe activity in drylands is sometimes critically suppressed by environmental factors, such as low soil substrate availability or high salinity. Tamarisk (Tamarix spp.) is a halophytic shrub species that is widely distributed in the drylands of China; it produces litter enriched in nutrients and salts that are thought to increase soil fertility and salinity under its crown. To elucidate the effects of tamarisks on the soil microbial community, and thus N dynamics, by creating "islands of fertility" and "islands of salinity," we collected soil samples from under tamarisk crowns and adjacent barren areas at three habitats in the summer and fall. We analyzed soil physicochemical properties, inorganic N dynamics, and prokaryotic community abundance and composition. In soils sampled beneath tamarisks, the N mineralization rate was significantly higher, and the prokaryotic community structure was significantly different, from soils sampled in barren areas, irrespective of site and season. Tamarisks provided suitable nutrient conditions for one of the important decomposers in the area, Verrucomicrobia, by creating "islands of fertility," but provided unsuitable salinity conditions for other important decomposers, Flavobacteria, Gammaproteobacteria, and Deltaproteobacteria, by mitigating salt accumulation. However, the quantity of these decomposers tended to be higher beneath tamarisks, because they were relatively unaffected by the small salinity gradient created by the tamarisks, which may explain the higher N mineralization rate beneath tamarisks.

Microbial population changes during bioremediation of an experimental oil spill

International Nuclear Information System (INIS)

Venosa, A.D.; Stephen, J.R.; Macnaughton, S.J.; Chang, Y.; White, D.C.

2000-01-01

Three crude oil bioremediation techniques were tested in a field experiment in Delaware, United States to determine the progress of natural and accelerated attenuation during a controlled oil spill. The four treatments studied were: no oil control, oil alone, oil plus nutrients, and oil plus nutrients plus an indigenous inoculum. During the first 14 weeks, microbial numbers were high but were steadily declining with no major differences among treatments. However, after the 14 week period, phospholipid fatty acid (PLFA) results showed that the communities shifted from being composed mostly of eukaryotes to gram-negative bacteria. The dominant species diversity changed and increased significantly over 14 weeks. Nutrient addition and the addition of the indigenous inoculum altered the nature of this change. Gas chromatography/mass spectrometry analyses of the oil analytes detected major differences in rates of biodegradation between the amended and unamended natural attenuation plots, but not between the nutrient and inoculum plots. 11 refs., 3 figs

Genome-Enabled Modeling of Biogeochemical Processes Predicts Metabolic Dependencies that Connect the Relative Fitness of Microbial Functional Guilds

Science.gov (United States)

Brodie, E.; King, E.; Molins, S.; Karaoz, U.; Steefel, C. I.; Banfield, J. F.; Beller, H. R.; Anantharaman, K.; Ligocki, T. J.; Trebotich, D.

2015-12-01

Pore-scale processes mediated by microorganisms underlie a range of critical ecosystem services, regulating carbon stability, nutrient flux, and the purification of water. Advances in cultivation-independent approaches now provide us with the ability to reconstruct thousands of genomes from microbial populations from which functional roles may be assigned. With this capability to reveal microbial metabolic potential, the next step is to put these microbes back where they belong to interact with their natural environment, i.e. the pore scale. At this scale, microorganisms communicate, cooperate and compete across their fitness landscapes with communities emerging that feedback on the physical and chemical properties of their environment, ultimately altering the fitness landscape and selecting for new microbial communities with new properties and so on. We have developed a trait-based model of microbial activity that simulates coupled functional guilds that are parameterized with unique combinations of traits that govern fitness under dynamic conditions. Using a reactive transport framework, we simulate the thermodynamics of coupled electron donor-acceptor reactions to predict energy available for cellular maintenance, respiration, biomass development, and enzyme production. From metagenomics, we directly estimate some trait values related to growth and identify the linkage of key traits associated with respiration and fermentation, macromolecule depolymerizing enzymes, and other key functions such as nitrogen fixation. Our simulations were carried out to explore abiotic controls on community emergence such as seasonally fluctuating water table regimes across floodplain organic matter hotspots. Simulations and metagenomic/metatranscriptomic observations highlighted the many dependencies connecting the relative fitness of functional guilds and the importance of chemolithoautotrophic lifestyles. Using an X-Ray microCT-derived soil microaggregate physical model combined

An Examination of Sex Differences in Relation to the Eating Habits and Nutrient Intakes of University Students

Science.gov (United States)

Li, Kin-Kit; Concepcion, Rebecca Y.; Lee, Hyo; Cardinal, Bradley J.; Ebbeck, Vicki; Woekel, Erica; Readdy, R. Tucker

2012-01-01

Objectives: To examine sex differences in eating habits and nutrient intakes and explore whether eating habits mediate the effects of sex on nutrient intakes and whether sex moderates the effects of eating habits on nutrient intakes. Methods: Cross-sectional survey of eating habits and food-intake frequency in a convenience sample of college…

Microbial N and P mining regulates the effect of N deposition on soil organic matter turnover

Science.gov (United States)

Meyer, Nele; Welp, Gerhard; Rodionov, Andrei; Borchard, Nils; Martius, Christopher; Amelung, Wulf

2017-04-01

Nitrogen (N) deposition to soils has become a global issue during the last decades. Its effect on mineralization of soil organic carbon (SOC), however, is still debated. Common theories based on Liebig's law predict higher SOC mineralization rates in nutrient-rich than in nutrient-poor soils. Contrastingly, the concept of microbial N mining predicts lower mineralization rates after N deposition. The latter is explained by ceased decomposition of recalcitrant soil organic matter (SOM) as the need of microbes to acquire N from this pool decreases. As N deposition might shift the nutrient balance towards relative phosphorus (P) deficiency, it is also necessary to consider P mining in this context. Due to limited knowledge about microbial nutrient mining, any predictions of N deposition effects are difficult. This study aims at elucidating the preconditions under which microbial nutrient mining occurs in soil. We hypothesized that the occurrence of N and P mining is controlled by the current nutrient status of the soil. Likewise, soils might respond differently to N additions. To investigate this hypothesis, we conducted substrate-induced respiration measurements on soils with pronounced gradients of N and P availability. We used topsoil samples taken repeatedly from a site which was up to 7 years under bare fallow (Selhausen, Germany) and up to 4 m deep tropical forest soils (Kalimantan, Indonesia). Additional nutrient manipulations (glucose, glucose+N, glucose+P, glucose+N+P additions) were conducted to study the effect of nutrient additions. Samples were incubated for one month. We further conducted 13C labeling experiments to trace the sources of CO2 (sugar vs. SOM derived CO2) for further hints on nutrient mining. Mineralization of glucose was limited by a lack of available N in the bare fallow soil but microbes were able to slowly acquire N from previously unavailable pools. This resulted in a slightly higher release of native SOM-derived CO2 compared to N

Variation of power generation at different buffer types and conductivities in single chamber microbial fuel cells

KAUST Repository

Nam, Joo-Youn; Kim, Hyun-Woo; Lim, Kyeong-Ho; Shin, Hang-Sik; Logan, Bruce E.

2010-01-01

Microbial fuel cells (MFCs) are operated with solutions containing various chemical species required for the growth of electrochemically active microorganisms including nutrients and vitamins, substrates, and chemical buffers. Many different buffers

Local geology determines responses of stream producers and fungal decomposers to nutrient enrichment: A field experiment.

Science.gov (United States)

Mykrä, Heikki; Sarremejane, Romain; Laamanen, Tiina; Karjalainen, Satu Maaria; Markkola, Annamari; Lehtinen, Sirkku; Lehosmaa, Kaisa; Muotka, Timo

2018-04-16

We examined how short-term (19 days) nutrient enrichment influences stream fungal and diatom communities, and rates of leaf decomposition and algal biomass accrual. We conducted a field experiment using slow-releasing nutrient pellets to increase nitrate (NO 3 -N) and phosphate (PO 4 -P) concentrations in a riffle section of six naturally acidic (naturally low pH due to catchment geology) and six circumneutral streams. Nutrient enrichment increased microbial decomposition rate on average by 14%, but the effect was significant only in naturally acidic streams. Nutrient enrichment also decreased richness and increased compositional variability of fungal communities in naturally acidic streams. Algal biomass increased in both stream types, but algal growth was overall very low. Diatom richness increased in response to nutrient addition by, but only in circumneutral streams. Our results suggest that primary producers and decomposers are differentially affected by nutrient enrichment and that their responses to excess nutrients are context dependent, with a potentially stronger response of detrital processes and fungal communities in naturally acidic streams than in less selective environments.

A global analysis of soil microbial biomass carbon, nitrogen and phosphorus in terrestrial ecosystems

Energy Technology Data Exchange (ETDEWEB)

Xu, Xiaofeng [ORNL; Thornton, Peter E [ORNL; Post, Wilfred M [ORNL

2013-01-01

Soil microbes play a pivotal role in regulating land-atmosphere interactions; the soil microbial biomass carbon (C), nitrogen (N), phosphorus (P) and C:N:P stoichiometry are important regulators for soil biogeochemical processes; however, the current knowledge on magnitude, stoichiometry, storage, and spatial distribution of global soil microbial biomass C, N, and P is limited. In this study, 3087 pairs of data points were retrieved from 281 published papers and further used to summarize the magnitudes and stoichiometries of C, N, and P in soils and soil microbial biomass at global- and biome-levels. Finally, global stock and spatial distribution of microbial biomass C and N in 0-30 cm and 0-100 cm soil profiles were estimated. The results show that C, N, and P in soils and soil microbial biomass vary substantially across biomes; the fractions of soil nutrient C, N, and P in soil microbial biomass are 1.6% in a 95% confidence interval of (1.5%-1.6%), 2.9% in a 95% confidence interval of (2.8%-3.0%), and 4.4% in a 95% confidence interval of (3.9%-5.0%), respectively. The best estimates of C:N:P stoichiometries for soil nutrients and soil microbial biomass are 153:11:1, and 47:6:1, respectively, at global scale, and they vary in a wide range among biomes. Vertical distribution of soil microbial biomass follows the distribution of roots up to 1 m depth. The global stock of soil microbial biomass C and N were estimated to be 15.2 Pg C and 2.3 Pg N in the 0-30 cm soil profiles, and 21.2 Pg C and 3.2 Pg N in the 0-100 cm soil profiles. We did not estimate P in soil microbial biomass due to data shortage and insignificant correlation with soil total P and climate variables. The spatial patterns of soil microbial biomass C and N were consistent with those of soil organic C and total N, i.e. high density in northern high latitude, and low density in low latitudes and southern hemisphere.

Microbial biofilm growth on irradiated, spent nuclear fuel cladding

International Nuclear Information System (INIS)

Bruhn, D.F.; Frank, S.M.; Roberto, F.F.; Pinhero, P.J.; Johnson, S.G.

2009-01-01

A fundamental criticism regarding the potential for microbial influenced corrosion in spent nuclear fuel cladding or storage containers concerns whether the required microorganisms can, in fact, survive radiation fields inherent in these materials. This study was performed to unequivocally answer this critique by addressing the potential for biofilm formation, the precursor to microbial-influenced corrosion, in radiation fields representative of spent nuclear fuel storage environments. This study involved the formation of a microbial biofilm on irradiated spent nuclear fuel cladding within a hot cell environment. This was accomplished by introducing 22 species of bacteria, in nutrient-rich media, to test vessels containing irradiated cladding sections and that was then surrounded by radioactive source material. The overall dose rate exceeded 2 Gy/h gamma/beta radiation with the total dose received by some of the bacteria reaching 5 x 10 3 Gy. This study provides evidence for the formation of biofilms on spent-fuel materials, and the implication of microbial influenced corrosion in the storage and permanent deposition of spent nuclear fuel in repository environments

Organic nitrogen rearranges both structure and activity of the soil-borne microbial seedbank

NARCIS (Netherlands)

Leite, Márcio F.A.; Pan, Yao; Bloem, Jaap; Berge, ten Hein; Kuramae, Eiko E.

2017-01-01

Use of organic amendments is a valuable strategy for crop production. However, it remains unclear how organic amendments shape both soil microbial community structure and activity, and how these changes impact nutrient mineralization rates. We evaluated the effect of various organic amendments,

Organic nitrogen rearranges both structure and activity of the soil-borne microbial seedbank

NARCIS (Netherlands)

Leite, M.F.A.; Pan, Y.; Bloem, J.; ten Berge, H.; Kuramae, E.E.

2017-01-01

Use of organic amendments is a valuable strategy for crop production. However, it remains unclear how organic amendments shape both soil microbial community structure and activity, and how these changes impact nutrient mineralization rates. We evaluated the effect of various organic amendments,

Strain- and Substrate-Dependent Redox Mediator and Electricity Production by Pseudomonas aeruginosa.

Science.gov (United States)

Bosire, Erick M; Blank, Lars M; Rosenbaum, Miriam A

2016-08-15

Pseudomonas aeruginosa is an important, thriving member of microbial communities of microbial bioelectrochemical systems (BES) through the production of versatile phenazine redox mediators. Pure culture experiments with a model strain revealed synergistic interactions of P. aeruginosa with fermenting microorganisms whereby the synergism was mediated through the shared fermentation product 2,3-butanediol. Our work here shows that the behavior and efficiency of P. aeruginosa in mediated current production is strongly dependent on the strain of P. aeruginosa We compared levels of phenazine production by the previously investigated model strain P. aeruginosa PA14, the alternative model strain P. aeruginosa PAO1, and the BES isolate Pseudomonas sp. strain KRP1 with glucose and the fermentation products 2,3-butanediol and ethanol as carbon substrates. We found significant differences in substrate-dependent phenazine production and resulting anodic current generation for the three strains, with the BES isolate KRP1 being overall the best current producer and showing the highest electrochemical activity with glucose as a substrate (19 μA cm(-2) with ∼150 μg ml(-1) phenazine carboxylic acid as a redox mediator). Surprisingly, P. aeruginosa PAO1 showed very low phenazine production and electrochemical activity under all tested conditions. Microbial fuel cells and other microbial bioelectrochemical systems hold great promise for environmental technologies such as wastewater treatment and bioremediation. While there is much emphasis on the development of materials and devices to realize such systems, the investigation and a deeper understanding of the underlying microbiology and ecology are lagging behind. Physiological investigations focus on microorganisms exhibiting direct electron transfer in pure culture systems. Meanwhile, mediated electron transfer with natural redox compounds produced by, for example, Pseudomonas aeruginosa might enable an entire microbial

Shifts in microbial communities and soil nutrients along a fire chronosequence in Alaskan boreal forest

Science.gov (United States)

Treseder, K. K.; Mack, M. C.; Cross, A.

2002-12-01

Fires are important pathways of carbon loss from boreal forests, while microbial communities form equally important mechanisms for carbon accumulation between fires. We used a chronosequence in Alaska to examine shifts in microbial abundance and community composition in the several decades following severe fire, and then related these responses to soil characteristics in the same sites. The sites are located in upland forests near Delta Junction, Alaska, and represent stages at 3-, 15-, 45-, and over 100-yr following fire. Plant communities shift from herbaceous species in the youngest site, to deciduous shrubs and trees (e.g. Populus tremuloides and Salix) in the intermediate sites, to black spruce (Picea mariana) forest in the oldest site. Soil organic matter accumulated 2.8-fold over time. Potential mineralization was highest in the intermediate-aged sites, as was nitrification and standing pools of inorganic nitrogen. In contrast, inorganic phosphorus pools were highest immediately following fire, and then decreased nine-fold with age. As measured with BiologTM plates, bacterial diversity and abundance were greatest in the oldest sites. Plant roots in the intermediate-aged sites displayed higher colonization by ecto- and arbuscular mycorrhizal fungi than those in the youngest and oldest sites. Likewise, glomalin, a glycoprotein produced by arbuscular mycorrhizal fungi, was most abundant in the 14-yr old site. Glomalin is believed to contribute to the formation of water-stable aggregates in the soil. However, water stable aggregates were most abundant in the younger sites and did not follow the pattern of glomalin or arbuscular mycorrhizal abundance. Our results indicate that fire may maintain landscape-level diversity of microbial functional groups, and that carbon sequestration in microbial tissues (e.g. glomalin and fungal biomass) may be greatest in areas that have burned several decades earlier. Changes in soil structure may not be directly attributable to

Physical Factors Correlate to Microbial Community Structure and Nitrogen Cycling Gene Abundance in a Nitrate Fed Eutrophic Lagoon.

Science.gov (United States)

Highton, Matthew P; Roosa, Stéphanie; Crawshaw, Josie; Schallenberg, Marc; Morales, Sergio E

2016-01-01

Nitrogenous run-off from farmed pastures contributes to the eutrophication of Lake Ellesmere, a large shallow lagoon/lake on the east coast of New Zealand. Tributaries periodically deliver high loads of nitrate to the lake which likely affect microbial communities therein. We hypothesized that a nutrient gradient would form from the potential sources (tributaries) creating a disturbance resulting in changes in microbial community structure. To test this we first determined the existence of such a gradient but found only a weak nitrogen (TN) and phosphorous gradient (DRP). Changes in microbial communities were determined by measuring functional potential (quantification of nitrogen cycling genes via nifH , nirS , nosZI , and nosZII using qPCR), potential activity (via denitrification enzyme activity), as well as using changes in total community (via 16S rRNA gene amplicon sequencing). Our results demonstrated that changes in microbial communities at a phylogenetic (relative abundance) and functional level (proportion of the microbial community carrying nifH and nosZI genes) were most strongly associated with physical gradients (e.g., lake depth, sediment grain size, sediment porosity) and not nutrient concentrations. Low nitrate influx at the time of sampling is proposed as a factor contributing to the observed patterns.

Physical factors correlate to microbial community structure and nitrogen cycling gene abundance in a nitrate fed eutrophic lagoon

Directory of Open Access Journals (Sweden)

Matthew Paul Highton

2016-10-01

Full Text Available Nitrogenous run-off from farmed pastures contributes to the eutrophication of Lake Ellesmere, a large shallow lagoon/lake on the east coast of New Zealand. Tributaries periodically deliver high loads of nitrate to the lake which likely affect microbial communities therein. We hypothesized that a nutrient gradient would form from the potential sources (tributaries creating a disturbance resulting in changes in microbial community structure. To test this we first determined the existence of such a gradient but found only a weak nitrogen (TN and phosphorous gradient (DRP. Changes in microbial communities were determined by measuring functional potential (quantification of nitrogen cycling genes via nifH, nirS, nosZI and nosZII using qPCR, potential activity (via denitrification enzyme activity, as well as using changes in total community (via 16S rRNA gene amplicon sequencing. Our results demonstrated that changes in microbial communities at a phylogenetic (relative abundance and functional level (proportion of the microbial community carrying nifH and nosZI genes were most strongly associated with physical gradients (e.g. lake depth, sediment grain size, sediment porosity and not nutrient concentrations. Low nitrate influx at the time of sampling is proposed as a factor contributing to the observed patterns.

Biologically mediated dissolution of volcanic glass in seawater

NARCIS (Netherlands)

Staudigel, H; Yayanos, A; Chastain, R; Davies, G.T.; Verdurmen, E.A Th; Schiffmann, P; Bourcier, R; de Baar, H.J.W.

1998-01-01

We studied the effects of biological mediation on the dissolution of basaltic glass in seawater. Experiments with typical seawater microbial populations were contrasted with a sterile control, and reactions were monitored chemically and isotopically. Biologically mediated experiments produce twice

Nontronite and Montmorillonite as Nutrient Sources for Life on Mars

Science.gov (United States)

Craig, P. I.; Mickol, R. L.; Archer, P. D.; Kral, T. A.

2017-01-01

Clay minerals have been identified on Mars' oldest (Noachian) terrain and their presence suggests long-term water-rock interactions. The most commonly identified clay minerals on Mars to date are nontronite (Fe-smectite) and montmorillonite (Al-smectite) [1], both of which contain variable amounts of water both adsorbed on their surface and within their structural layers. Over Mars' history, these clay miner-al-water assemblages may have served as nutrient sources for microbial life.

Dopamine alleviates nutrient deficiency-induced stress in Malus hupehensis.

Science.gov (United States)

Liang, Bowen; Li, Cuiying; Ma, Changqing; Wei, Zhiwei; Wang, Qian; Huang, Dong; Chen, Qi; Li, Chao; Ma, Fengwang

2017-10-01

Dopamine mediates many physiological processes in plants. We investigated its role in regulating growth, root system architecture, nutrient uptake, and responses to nutrient deficiencies in Malus hupehensis Rehd. Under a nutrient deficiency, plants showed significant reductions in growth, chlorophyll concentrations, and net photosynthesis, along with disruptions in nutrient uptake, transport, and distribution. However, pretreatment with 100 μM dopamine markedly alleviated such inhibitions. Supplementation with that compound enabled plants to maintain their photosynthetic capacity and development of the root system while promoting the uptake of N, P, K, Ca, Mg, Fe, Mn, Cu, Zn, and B, altering the way in which those nutrients were partitioned throughout the plant. The addition of dopamine up-regulated genes for antioxidant enzymes involved in the ascorbate-glutathione cycle (MdcAPX, MdcGR, MdMDHAR, MdDHAR-1, and MdDHAR-2) but down-regulated genes for senescence (SAG12, PAO, and MdHXK). These results indicate that exogenous dopamine has an important antioxidant and anti-senescence effect that might be helpful for improving nutrient uptake. Our findings demonstrate that dopamine offers new opportunities for its use in agriculture, especially when addressing the problem of nutrient deficiencies. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

An investigation of nutrient-dependent mRNA translation in Drosophila larvae

Directory of Open Access Journals (Sweden)

Sabarish Nagarajan

2014-10-01

Full Text Available The larval period of the Drosophila life cycle is characterized by immense growth. In nutrient rich conditions, larvae increase in mass approximately two hundred-fold in five days. However, upon nutrient deprivation, growth is arrested. The prevailing view is that dietary amino acids drive this larval growth by activating the conserved insulin/PI3 kinase and Target of rapamycin (TOR pathways and promoting anabolic metabolism. One key anabolic process is protein synthesis. However, few studies have attempted to measure mRNA translation during larval development or examine the signaling requirements for nutrient-dependent regulation. Our work addresses this issue. Using polysome analyses, we observed that starvation rapidly (within thirty minutes decreased larval mRNA translation, with a maximal decrease at 6–18 hours. By analyzing individual genes, we observed that nutrient-deprivation led to a general reduction in mRNA translation, regardless of any starvation-mediated changes (increase or decrease in total transcript levels. Although sugars and amino acids are key regulators of translation in animal cells and are the major macronutrients in the larval diet, we found that they alone were not sufficient to maintain mRNA translation in larvae. The insulin/PI3 kinase and TOR pathways are widely proposed as the main link between nutrients and mRNA translation in animal cells. However, we found that genetic activation of PI3K and TOR signaling, or regulation of two effectors – 4EBP and S6K – could not prevent the starvation-mediated translation inhibition. Similarly, we showed that the nutrient stress-activated eIF2α kinases, GCN2 and PERK, were not required for starvation-induced inhibition of translation in larvae. These findings indicate that nutrient control of mRNA translation in larvae is more complex than simply amino acid activation of insulin and TOR signaling.

Insight into litter decomposition driven by nutrient demands of symbiosis system through the hypha bridge of arbuscular mycorrhizal fungi.

Science.gov (United States)

Kong, Xiangshi; Jia, Yanyan; Song, Fuqiang; Tian, Kai; Lin, Hong; Bei, Zhanlin; Jia, Xiuqin; Yao, Bei; Guo, Peng; Tian, Xingjun

2018-02-01

Arbuscular mycorrhizal fungi (AMF) play an important role in litter decomposition. This study investigated how soil nutrient level affected the process. Results showed that AMF colonization had no significant effect on litter decomposition under normal soil nutrient conditions. However, litter decomposition was accelerated significantly under lower nutrient conditions. Soil microbial biomass in decomposition system was significantly increased. Especially, in moderate lower nutrient treatment (condition of half-normal soil nutrient), litters exhibited the highest decomposition rate, AMF hypha revealed the greatest density, and enzymes (especially nitrate reductase) showed the highest activities as well. Meanwhile, the immobilization of nitrogen (N) in the decomposing litter remarkably decreased. Our results suggested that the roles AMF played in ecosystem were largely affected by soil nutrient levels. At normal soil nutrient level, AMF exhibited limited effects in promoting decomposition. When soil nutrient level decreased, the promoting effect of AMF on litter decomposition began to appear, especially on N mobilization. However, under extremely low nutrient conditions, AMF showed less influence on decomposition and may even compete with decomposer microorganisms for nutrients.

Reconstructing the Genetic Potential of the Microbially-Mediated Nitrogen Cycle in a Salt Marsh Ecosystem.

Science.gov (United States)

Dini-Andreote, Francisco; Brossi, Maria Julia de L; van Elsas, Jan Dirk; Salles, Joana F

2016-01-01

Coastal ecosystems are considered buffer zones for the discharge of land-derived nutrients without accounting for potential negative side effects. Hence, there is an urgent need to better understand the ecological assembly and dynamics of the microorganisms that are involved in nitrogen (N) cycling in such systems. Here, we employed two complementary methodological approaches (i.e., shotgun metagenomics and quantitative PCR) to examine the distribution and abundance of selected microbial genes involved in N transformations. We used soil samples collected along a well-established pristine salt marsh soil chronosequence that spans over a century of ecosystem development at the island of Schiermonnikoog, The Netherlands. Across the examined soil successional stages, the structure of the populations of genes involved in N cycling processes was strongly related to (shifts in the) soil nitrogen levels (i.e., [Formula: see text], [Formula: see text]), salinity and pH (explaining 73.8% of the total variation, R (2) = 0.71). Quantification of the genes used as proxies for N fixation, nitrification and denitrification revealed clear successional signatures that corroborated the taxonomic assignments obtained by metagenomics. Notably, we found strong evidence for niche partitioning, as revealed by the abundance and distribution of marker genes for nitrification (ammonia-oxidizing bacteria and archaea) and denitrification (nitrite reductase nirK, nirS and nitrous oxide reductase nosZ clades I and II). This was supported by a distinct correlation between these genes and soil physico-chemical properties, such as soil physical structure, pH, salinity, organic matter, total N, [Formula: see text], [Formula: see text] and [Formula: see text], across four seasonal samplings. Overall, this study sheds light on the successional trajectories of microbial N cycle genes along a naturally developing salt marsh ecosystem. The data obtained serve as a foundation to guide the formulation of

Microbial activity in bentonite buffers. Literature study

Energy Technology Data Exchange (ETDEWEB)

Ratto, M.; Itavaara, M.

2012-07-01

The proposed disposal concept for high-level radioactive wastes involves storing the wastes underground in copper-iron containers embedded in buffer material of compacted bentonite. Hydrogen sulphide production by sulphate-reducing prokaryotes is a potential mechanism that could cause corrosion of waste containers in repository conditions. The prevailing conditions in compacted bentonite buffer will be harsh. The swelling pressure is 7-8 MPa, the amount of free water is low and the average pore and pore throat diameters are small. This literature study aims to assess the potential of microbial activity in bentonite buffers. Literature on the environmental limits of microbial life in extreme conditions and the occurrence of sulphatereducing prokaryotes in extreme environments is reviewed briefly and the results of published studies characterizing microbes and microbial processes in repository conditions or in relevant subsurface environments are presented. The presence of bacteria, including SRBs, has been confirmed in deep groundwater and bentonite-based materials. Sulphate reducers have been detected in various high-pressure environments, and sulphate-reduction based on hydrogen as an energy source is considered a major microbial process in deep subsurface environments. In bentonite, microbial activity is strongly suppressed, mainly due to the low amount of free water and small pores, which limit the transport of microbes and nutrients. Spore-forming bacteria have been shown to survive in compacted bentonite as dormant spores, and they are able to resume a metabolically active state after decompaction. Thus, microbial sulphide production may increase in repository conditions if the dry density of the bentonite buffer is locally reduced. (orig.)

Assessing marine microbial induced corrosion at Santa Catalina Island, California

Directory of Open Access Journals (Sweden)

Gustavo Antonio Ramírez

2016-10-01

Full Text Available High iron and eutrophic conditions are reported as environmental factors leading to accelerated low-water corrosion, an enhanced form of near-shore microbial-induced corrosion. To explore this hypothesis, we deployed flow-through colonization systems in laboratory-based aquarium tanks under a continuous flow of surface seawater from Santa Catalina Island, California, USA, for periods of two and six months. Substrates consisted of mild steel – a major constituent of maritime infrastructure – and the naturally occurring iron sulfide mineral pyrite. Four conditions were tested: free-venting high-flux conditions; a stagnant condition; an active flow-through condition with seawater slowly pumped over the substrates; and an enrichment condition where the slow pumping of seawater was supplemented with nutrient rich medium. Electron microscopy analyses of the two-month high flux incubations document coating of substrates with twisted stalks, resembling iron oxyhydroxide bioprecipitates made by marine neutrophilic Fe-oxidizing bacteria. Six-month incubations exhibit increased biofilm and substrate corrosion in the active flow and nutrient enriched conditions relative to the stagnant condition. A scarcity of twisted stalks was observed for all six month slow-flow conditions compared to the high-flux condition, which may be attributable to oxygen concentrations in the slow-flux conditions being prohibitively low for sustained growth of stalk-producing bacteria. All substrates developed microbial communities reflective of the original seawater input, as based on 16S rRNA gene sequencing. Deltaproteobacteria sequences increased in relative abundance in the active flow and nutrient enrichment conditions, whereas Gammaproteobacteria sequences were relatively more abundant in the stagnant condition. These results indicate that i high-flux incubations with higher oxygen availability favor the development of biofilms with twisted stalks resembling those of

Factors limiting microbial growth and activity at a proposed high-level nuclear repository, Yucca Mountain, Nevada

International Nuclear Information System (INIS)

Kieft, T.L.; Kovacik, W.P. Jr.; Ringelberg, D.B.; White, D.C.; Haldeman, D.L.; Amy, P.S.; Hersman, L.E.

1997-01-01

As part of the characterization of Yucca Mountain, Nev., as a potential repository for high-level nuclear waste, volcanic tuff was analyzed for microbial abundance and activity. Tuff was collected aseptically from nine sites along a tunnel in Yucca Mountain. Microbial abundance was generally low: direct microscopic cell counts were near detection limits at all sites (3.2 X 10(1) to 2.0 X 10(5) cells g-1 [dry weight]); plate counts of aerobic heterotrophs ranged from 1.0 X 10(1) to 3.2 X 10(3) CFU g-1 (dry weight). Phospholipid fatty acid concentrations (0.1 to 3.7 pmol g-1) also indicated low microbial biomasses: diglyceride fatty acid concentrations, indicative of dead cells, were in a similar range (0.2 to 2.3 pmol g-1). Potential microbial activity was quantified as 14CO2 production in microcosms containing radiolabeled substrates (glucose, acetate, and glutamic acid); amendments with water and nutrient solutions (N and P) were used to test factors potentially limiting this activity. Similarly, the potential for microbial growth and the factors limiting growth were determined by performing plate counts before and after incubating volcanic tuff samples for 24 h under various conditions: ambient moisture, water-amended, and amended with various nutrient solutions (N, P, and organic C). A high potential for microbial activity was demonstrated by high rates of substrate mineralization (as much as 70% of added organic C in 3 weeks). Water was the major limiting factor to growth and microbial activity, while amendments with N and P resulted in little further stimulation. Organic C amendments stimulated growth more than water alone

Early microbial contact, the breast milk microbiome and child health.

Science.gov (United States)

Rautava, S

2016-02-01

The significance of contact with microbes in early life for subsequent health has been the subject of intense research during the last 2 decades. Disturbances in the establishment of the indigenous intestinal microbiome caused by cesarean section delivery or antibiotic exposure in early life have been linked to the risk of immune-mediated and inflammatory conditions such as atopic disorders, inflammatory bowel disease and obesity later in life. Distinct microbial populations have recently been discovered at maternal sites including the amniotic cavity and breast milk, as well as meconium, which have previously been thought to be sterile. Our understanding of the impact of fetal microbial contact on health outcomes is still rudimentary. Breast milk is known to modulate immune and metabolic programming. The breast milk microbiome is hypothesized to guide infant gut colonization and is affected by maternal health status and mode of delivery. Immunomodulatory factors in breast milk interact with the maternal and infant gut microbiome and may mediate some of the health benefits associated with breastfeeding. The intimate connection between the mother and the fetus or the infant is a potential target for microbial therapeutic interventions aiming to support healthy microbial contact and protect against disease.

Initial studies to assess microbial impacts on nuclear waste disposal

International Nuclear Information System (INIS)

Horn, J.M.; Meike, A.; McCright, R.D.; Economides, B.

1996-01-01

The impacts of the native and introduced bacteria on the performance of geologic nuclear waste disposal facilities should be evaluated because these bacteria could promote corrosion of repository components and alteration of chemical and hydrological properties of the surrounding engineered and rock barriers. As a first step towards investigating these potentialities, native and introduced bacteria obtained from post-construction Yucca Mountain (YM) rock were isolated under varying conditions, including elevated temperature, low nutrient availability, and the absence of available oxygen. Individual isolates are being screened for activities associated with microbially induced corrosion of metals (MIC). Preliminary determination of growth rates of whole YM microbial communities under varying conditions was also undertaken

The Abundance and Activity of Nitrate-Reducing Microbial Populations in Estuarine Sediments

Science.gov (United States)

Cardarelli, E.; Francis, C. A.

2014-12-01

Estuaries are productive ecosystems that ameliorate nutrient and metal contaminants from surficial water supplies. At the intersection of terrestrial and aquatic environments, estuarine sediments host major microbially-mediated geochemical transformations. These include denitrification (the conversion of nitrate to nitrous oxide and/or dinitrogen) and dissimilatory nitrate reduction to ammonium (DNRA). Denitrification has historically been seen as the predominant nitrate attenuation process and functions as an effective sink for nitrate. DNRA has previously been believed to be a minor nitrate reduction process and transforms nitrate within the ecosystem to ammonium, a more biologically available N species. Recent studies have compared the two processes in coastal environments and determined fluctuating environmental conditions may suppress denitrification, supporting an increased role for DNRA in the N cycle. Nitrate availability and salinity are factors thought to influence the membership of the microbial communities present, and the nitrate reduction process that predominates. The aim of this study is to investigate how nitrate concentration and salinity alter the transcript abundances of N cycling functional gene markers for denitrification (nirK, nirS) and DNRA (nrfA) in estuarine sediments at the mouth of the hypernutrified Old Salinas River, CA. Short-term whole core incubations amended with artificial freshwater/artificial seawater (2 psu, 35 psu) and with varying NO3- concentrations (200mM, 2000mM) were conducted to assess the activity as well as the abundance of the nitrate-reducing microbial populations present. Gene expression of nirK, nirS, and nrfA at the conclusion of the incubations was quantified using reverse transcription quantitative polymerase chain reaction (RT-qPCR). High abundances of nirK, nirS, and nrfA under particular conditions coupled with the resulting geochemical data ultimately provides insight onto how the aforementioned factors

Rumen microbial growth estimation using in vitro radiophosphorous incorporation technique

International Nuclear Information System (INIS)

Bueno, Ives Claudio da Silva; Machado, Mariana de Carvalho; Cabral Filho, Sergio Lucio Salomon; Gobbo, Sarita Priscila; Vitti, Dorinha Miriam Silber Schmidt; Abdalla, Adibe Luiz

2002-01-01

Rumen microorganisms are able to transform low biological value nitrogen of feed stuff into high quality protein. To determine how much microbial protein that process forms, radiomarkers can be used. Radiophosphorous has been used to mark microbial protein, as element P is present in all rumen microorganisms (as phospholipids) and the P:N ratio of rumen biomass is quite constant. The aim of this work was to estimate microbial synthesis from feedstuff commonly used in ruminant nutrition in Brazil. Tested feeds were fresh alfalfa, raw sugarcane bagasse, rice hulls, rice meal, soybean meal, wheat meal, Tifton hay, leucaena, dehydrated citrus pulp, wet brewers' grains and cottonseed meal. 32 P-labelled phosphate solution was used as marker for microbial protein. Results showed the diversity of feeds by distinct quantities of nitrogen incorporated into microbial mass. Low nutrient availability feeds (sugarcane bagasse and rice hulls) promoted the lowest values of incorporated nitrogen. Nitrogen incorporation showed positive relationship (r=0.56; P=0.06) with the rate of degradation and negative relationship (r=-0.59; P<0.05) with fiber content of feeds. The results highlight that easier fermentable feeds (higher rates of degradation) and/or with lower fiber contents promote a more efficient microbial growth and better performance for the host animal. (author)

Rumen microbial growth estimation using in vitro radiophosphorous incorporation technique

Energy Technology Data Exchange (ETDEWEB)

Bueno, Ives Claudio da Silva; Machado, Mariana de Carvalho; Cabral Filho, Sergio Lucio Salomon; Gobbo, Sarita Priscila; Vitti, Dorinha Miriam Silber Schmidt; Abdalla, Adibe Luiz [Centro de Energia Nuclear na Agricultura (CENA), Piracicaba, SP (Brazil)

2002-07-01

Rumen microorganisms are able to transform low biological value nitrogen of feed stuff into high quality protein. To determine how much microbial protein that process forms, radiomarkers can be used. Radiophosphorous has been used to mark microbial protein, as element P is present in all rumen microorganisms (as phospholipids) and the P:N ratio of rumen biomass is quite constant. The aim of this work was to estimate microbial synthesis from feedstuff commonly used in ruminant nutrition in Brazil. Tested feeds were fresh alfalfa, raw sugarcane bagasse, rice hulls, rice meal, soybean meal, wheat meal, Tifton hay, leucaena, dehydrated citrus pulp, wet brewers' grains and cottonseed meal. {sup 32} P-labelled phosphate solution was used as marker for microbial protein. Results showed the diversity of feeds by distinct quantities of nitrogen incorporated into microbial mass. Low nutrient availability feeds (sugarcane bagasse and rice hulls) promoted the lowest values of incorporated nitrogen. Nitrogen incorporation showed positive relationship (r=0.56; P=0.06) with the rate of degradation and negative relationship (r=-0.59; P<0.05) with fiber content of feeds. The results highlight that easier fermentable feeds (higher rates of degradation) and/or with lower fiber contents promote a more efficient microbial growth and better performance for the host animal. (author)

Changes in the Nutrient Composition of Brewery Spent Grain ...

African Journals Online (AJOL)

BSN

animal feed production. Feed costs are ... industry. Agro-industrial by-products are in abundance in Nigeria (Iyayi, 2004). One of such ... a significant part of costs for the breweries. Today .... exothermic reactions mediated by microbial enzymes. This increase in temperature was ... digestibility, carcass traits and economic.

Plant nutrient mobilization in temperate heathland responds to elevated CO2, temperature and drought

DEFF Research Database (Denmark)

Andresen, Louise C.; Michelsen, Anders; Jonasson, Sven

2010-01-01

Temperate terrestrial ecosystems are currently exposed to increased atmospheric CO2 and progressive climatic changes with increased temperature and periodical drought. We here present results from a field experiment, where the effects of these three main climate change related factors...... decreased in response to drought. These complex changes in availability and release of nutrients from soil organic matter turnover and mineralization in response to elevated CO2 and climate change may influence the future plant carbon sequestration and species composition at temperate heathlands....... in Deschampsia soil, and microbial immobilization of N and P decreased in warmed Calluna soil. Warming tended to increase microbial N and P in Calluna but not in Deschampsia soil in fall, and more microbial C was accumulated under drought in Calluna soil. The effects of warming were often counteracted or erased...

Subsurface microbial communities and degradative capacities during trichloroethylene bioremediation

International Nuclear Information System (INIS)

Pfiffner, S.M.; Ringelberg, D.B.; Hedrick, D.B.; Phelps, T.J.; Palumbo, A.V.

1995-01-01

Subsurface amendments of air, methane, and nutrients were investigated for the in situ stimulation of trichloroethylene- degrading microorganisms at the US DOE Savannah River Integrated Demonstration. Amendments were injected into a lower horizontal well coupled with vacuum extraction from the vadose zone horizontal well. The amendments were sequenced to give increasingly more aggressive treatments. Microbial populations and degradative capacities were monitored in groundwaters samples bimonthly

Divergent taxonomic and functional responses of microbial communities to field simulation of aeolian soil erosion and deposition.

Science.gov (United States)

Ma, Xingyu; Zhao, Cancan; Gao, Ying; Liu, Bin; Wang, Tengxu; Yuan, Tong; Hale, Lauren; Nostrand, Joy D Van; Wan, Shiqiang; Zhou, Jizhong; Yang, Yunfeng

2017-08-01

Aeolian soil erosion and deposition have worldwide impacts on agriculture, air quality and public health. However, ecosystem responses to soil erosion and deposition remain largely unclear in regard to microorganisms, which are the crucial drivers of biogeochemical cycles. Using integrated metagenomics technologies, we analysed microbial communities subjected to simulated soil erosion and deposition in a semiarid grassland of Inner Mongolia, China. As expected, soil total organic carbon and plant coverage were decreased by soil erosion, and soil dissolved organic carbon (DOC) was increased by soil deposition, demonstrating that field simulation was reliable. Soil microbial communities were altered (p soil erosion and deposition, with dramatic increase in Cyanobacteria related to increased stability in soil aggregates. amyA genes encoding α-amylases were specifically increased (p = .01) by soil deposition and positively correlated (p = .02) to DOC, which likely explained changes in DOC. Surprisingly, most of microbial functional genes associated with carbon, nitrogen, phosphorus and potassium cycling were decreased or unaltered by both erosion and deposition, probably arising from acceleration of organic matter mineralization. These divergent responses support the necessity to include microbial components in evaluating ecological consequences. Furthermore, Mantel tests showed strong, significant correlations between soil nutrients and functional structure but not taxonomic structure, demonstrating close relevance of microbial function traits to nutrient cycling. © 2017 John Wiley & Sons Ltd.

Nutrient, metal and microbial loss in surface runoff following treated sludge and dairy cattle slurry application to an Irish grassland soil

Energy Technology Data Exchange (ETDEWEB)

Peyton, D.P. [Teagasc, Environment Research Centre, Johnstown Castle, Co. Wexford (Ireland); Civil Engineering, National University of Ireland, Galway, Co. Galway (Ireland); Healy, M.G. [Civil Engineering, National University of Ireland, Galway, Co. Galway (Ireland); Fleming, G.T.A. [Microbiology, National University of Ireland, Galway, Co. Galway (Ireland); Grant, J. [Teagasc, Ashtown, Co. Dublin (Ireland); Wall, D. [Teagasc, Environment Research Centre, Johnstown Castle, Co. Wexford (Ireland); Morrison, L. [Earth and Ocean Sciences and Ryan Institute, National University of Ireland, Galway, Co. Galway (Ireland); Cormican, M. [School of Medicine, National University of Ireland, Galway, Co. Galway (Ireland); Fenton, O., E-mail: owen.fenton@teagasc.ie [Teagasc, Environment Research Centre, Johnstown Castle, Co. Wexford (Ireland)

2016-01-15

Treated municipal sewage sludge (“biosolids”) and dairy cattle slurry (DCS) may be applied to agricultural land as an organic fertiliser. This study investigates losses of nutrients in runoff water (nitrogen (N) and phosphorus (P)), metals (copper (Cu), nickel (Ni), lead (Pb), zinc (Zn), cadmium (Cd), chromium (Cr)), and microbial indicators of pollution (total and faecal coliforms) arising from the land application of four types of treated biosolids and DCS to field micro-plots at three time intervals (24, 48, 360 h) after application. Losses from biosolids-amended plots or DCS-amended plots followed a general trend of highest losses occurring during the first rainfall event and reduced losses in the subsequent events. However, with the exception of total and faecal coliforms and some metals (Ni, Cu), the greatest losses were from the DCS-amended plots. For example, average losses over the three rainfall events for dissolved reactive phosphorus and ammonium-nitrogen from DCS-amended plots were 5 and 11.2 mg L{sup −1}, respectively, which were in excess of the losses from the biosolids plots. When compared with slurry treatments, for the parameters monitored biosolids generally do not pose a greater risk in terms of losses along the runoff pathway. This finding has important policy implications, as it shows that concern related to the reuse of biosolids as a soil fertiliser, mainly related to contaminant losses upon land application, may be unfounded. - Highlights: • This study investigated surface runoff of contaminants from biosolids in field plots. • Contaminants investigated were nutrients, metals, microbes and trace elements. • Compared to slurry, biosolids do not pose a greater risk of contaminant losses. • Fears concerning contaminant losses from land applied biosolids may be unfounded.

Nutrient, metal and microbial loss in surface runoff following treated sludge and dairy cattle slurry application to an Irish grassland soil

International Nuclear Information System (INIS)

Peyton, D.P.; Healy, M.G.; Fleming, G.T.A.; Grant, J.; Wall, D.; Morrison, L.; Cormican, M.; Fenton, O.

2016-01-01

Treated municipal sewage sludge (“biosolids”) and dairy cattle slurry (DCS) may be applied to agricultural land as an organic fertiliser. This study investigates losses of nutrients in runoff water (nitrogen (N) and phosphorus (P)), metals (copper (Cu), nickel (Ni), lead (Pb), zinc (Zn), cadmium (Cd), chromium (Cr)), and microbial indicators of pollution (total and faecal coliforms) arising from the land application of four types of treated biosolids and DCS to field micro-plots at three time intervals (24, 48, 360 h) after application. Losses from biosolids-amended plots or DCS-amended plots followed a general trend of highest losses occurring during the first rainfall event and reduced losses in the subsequent events. However, with the exception of total and faecal coliforms and some metals (Ni, Cu), the greatest losses were from the DCS-amended plots. For example, average losses over the three rainfall events for dissolved reactive phosphorus and ammonium-nitrogen from DCS-amended plots were 5 and 11.2 mg L −1 , respectively, which were in excess of the losses from the biosolids plots. When compared with slurry treatments, for the parameters monitored biosolids generally do not pose a greater risk in terms of losses along the runoff pathway. This finding has important policy implications, as it shows that concern related to the reuse of biosolids as a soil fertiliser, mainly related to contaminant losses upon land application, may be unfounded. - Highlights: • This study investigated surface runoff of contaminants from biosolids in field plots. • Contaminants investigated were nutrients, metals, microbes and trace elements. • Compared to slurry, biosolids do not pose a greater risk of contaminant losses. • Fears concerning contaminant losses from land applied biosolids may be unfounded.

Microbial C:P stoichiometry is shaped by redox conditions along an elevation gradient in humid tropical rainforests

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Lin, Y.; Gross, A.; Silver, W. L.

2017-12-01

Elemental stoichiometry of microorganisms is intimately related to ecosystem carbon and nutrient fluxes and is ultimately controlled by the chemical (plant tissue, soil, redox) and physical (temperature, moisture, aeration) environment. Previous meta-analyses have shown that the C:P ratio of soil microbial biomass exhibits significant variations among and within biomes. Little is known about the underlying causes of this variability. We examined soil microbial C:P ratios along an elevation gradient in the Luquillo Experimental Forest in Puerto Rico. We analyzed soils from mixed forest paired with monodominant palm forest every 100 m from 300 m to 1000 m a.s.l.. Mean annual precipitation increased with increasing elevation, resulting in stronger reducing conditions and accumulation of soil Fe(II) at higher elevations. The mean value and variability of soil microbial C:P ratios generally increased with increasing elevation except at 1000 m. At high elevations (600-900 m), the average value of microbial C:P ratio (108±10:1) was significantly higher than the global average ( 55:1). We also found that soil organic P increased with increasing elevation, suggesting that an inhibition of organic P mineralization, not decreased soil P availability, may cause the high microbial C:P ratio. The soil microbial C:P ratio was positively correlated with soil HCl-extractable Fe(II), suggesting that reducing conditions may be responsible for the elevational changes observed. In a follow-up experiment, soils from mixed forests at four elevation levels (300, 500, 700, and 1000 m) were incubated under aerobic and anaerobic conditions for two weeks. We found that anaerobic incubation consistently increased the soil microbial C:P ratio relative to the aerobic incubation. Overall, our results indicate that redox conditions can shift the elemental composition of microbial biomass. The high microbial C:P ratios induced under anoxic conditions may reflect inhibition of microbial P

Microbial Growth and Carbon Use Efficiency in the Rhizosphere and Root-Free Soil

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Blagodatskaya, Evgenia; Blagodatsky, Sergey; Anderson, Traute-Heidi; Kuzyakov, Yakov

2014-01-01

Plant-microbial interactions alter C and N balance in the rhizosphere and affect the microbial carbon use efficiency (CUE)–the fundamental characteristic of microbial metabolism. Estimation of CUE in microbial hotspots with high dynamics of activity and changes of microbial physiological state from dormancy to activity is a challenge in soil microbiology. We analyzed respiratory activity, microbial DNA content and CUE by manipulation the C and nutrients availability in the soil under Beta vulgaris. All measurements were done in root-free and rhizosphere soil under steady-state conditions and during microbial growth induced by addition of glucose. Microorganisms in the rhizosphere and root-free soil differed in their CUE dynamics due to varying time delays between respiration burst and DNA increase. Constant CUE in an exponentially-growing microbial community in rhizosphere demonstrated the balanced growth. In contrast, the CUE in the root-free soil increased more than three times at the end of exponential growth and was 1.5 times higher than in the rhizosphere. Plants alter the dynamics of microbial CUE by balancing the catabolic and anabolic processes, which were decoupled in the root-free soil. The effects of N and C availability on CUE in rhizosphere and root-free soil are discussed. PMID:24722409

Evaluation of Kefir as a New Anodic Biocatalyst Consortium for Microbial Fuel Cell.

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Silveira, Gustavo; Schneedorf, José Maurício

2018-02-21

Kefir, a combined consortium of bacteria and yeast encapsulated by a polymeric matrix of exopolysaccharides, was used as anodic biocatalyst in a two-chamber microbial fuel cell (MFC). Fermentation was followed during 72 h and polarization curves were obtained from linear sweep voltammetry. The effect of methylene blue as charge-transfer mediator in the kefir metabolism was evaluated. UV/Vis spectrophotometry and cyclic voltammetry were applied to evaluate the redox state of the mediator and to characterize the electrochemical activity, whereas current interruption was used for internal resistance determination. Aiming to establish a relationship between the microbial development inside the anodic chamber with the generated power in the MFC, total titratable acidity, pH, viscosity, carbohydrate assimilation, and microbial counting were assayed. The kefir-based MFC demonstrated a maximum power density of 54 mW m -2 after 24 h fermentation, revealing the potential use of kefir as a biocatalyst for microbial fuel cells.

Microbial stability of worm castings and sugarcane filter mud compost blended with biochar

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Organic amendments such as worm castings and filter mud compost can provide nutrient rich substrates for enhanced plant growth. Physico-chemical and microbial stability of these substrates might be enhanced with the addition of biochar. A series of experiments was carried out to determine the stab...

Dormancy contributes to the maintenance of microbial diversity.

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Jones, Stuart E; Lennon, Jay T

2010-03-30

Dormancy is a bet-hedging strategy used by a variety of organisms to overcome unfavorable environmental conditions. By entering a reversible state of low metabolic activity, dormant individuals become members of a seed bank, which can determine community dynamics in future generations. Although microbiologists have documented dormancy in both clinical and natural settings, the importance of seed banks for the diversity and functioning of microbial communities remains untested. Here, we develop a theoretical model demonstrating that microbial communities are structured by environmental cues that trigger dormancy. A molecular survey of lake ecosystems revealed that dormancy plays a more important role in shaping bacterial communities than eukaryotic microbial communities. The proportion of dormant bacteria was relatively low in productive ecosystems but accounted for up to 40% of taxon richness in nutrient-poor systems. Our simulations and empirical data suggest that regional environmental cues and dormancy synchronize the composition of active communities across the landscape while decoupling active microbes from the total community at local scales. Furthermore, we observed that rare bacterial taxa were disproportionately active relative to common bacterial taxa, suggesting that microbial rank-abundance curves are more dynamic than previously considered. We propose that repeated transitions to and from the seed bank may help maintain the high levels of microbial biodiversity that are observed in nearly all ecosystems.

Multitrophic microbial interactions for eco- and agro-biotechnological processes: theory and practice.

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Saleem, Muhammad; Moe, Luke A

2014-10-01

Multitrophic level microbial loop interactions mediated by protist predators, bacteria, and viruses drive eco- and agro-biotechnological processes such as bioremediation, wastewater treatment, plant growth promotion, and ecosystem functioning. To what extent these microbial interactions are context-dependent in performing biotechnological and ecosystem processes remains largely unstudied. Theory-driven research may advance the understanding of eco-evolutionary processes underlying the patterns and functioning of microbial interactions for successful development of microbe-based biotechnologies for real world applications. This could also be a great avenue to test the validity or limitations of ecology theory for managing diverse microbial resources in an era of altering microbial niches, multitrophic interactions, and microbial diversity loss caused by climate and land use changes. Copyright © 2014 Elsevier Ltd. All rights reserved.

Evaluation of Biostimulation (Nutrients) in hydrocarbons contaminated soils by respirometry

International Nuclear Information System (INIS)

Garcia, Erika; Roldan, Fabio; Garzon, Laura

2011-01-01

The biostimulation process was evaluated in a hydrocarbon contaminated soil by respirometry after amendment with inorganic compound fertilizer (ICF) (N: P: K 28:12:7) and simple inorganic salts (SIS) (NH 4 NO 3 and K 2 HPO 4 ). The soil was contaminated with oily sludge (40.000 MgTPH/Kgdw). The oxygen uptake was measured using two respirometers (HACH 2173b and OXITOP PF 600) during thirteen days (n=3). Two treatments (ICF and SIS) and three controls (abiotic, reference substance and without nutrients) were evaluated during the study. Physicochemical (pH, nutrients, and TPH) and microbiological analysis (heterotrophic and hydrocarbon-utilizing microorganisms) were obtained at the beginning and at the end of each assay. Higher respiration rates were recorded in sis and without nutrient control. Results were 802.28 and 850.72- 1 d-1, MgO 2 kgps - 1d i n HACH, while in OXITOP were 936.65 and 502.05 MgO 2 Kgps respectively. These data indicate that amendment of nutrients stimulated microbial metabolism. ICF had lower respiration rates (188.18 and 139.87 MgO 2 kgps - 1d - 1 i n HACH and OXITOP, respectively) as well as counts; this could be attributed to ammonia toxicity.

Microbial drivers of spatial heterogeneity of nitrous oxide pulse dynamics following drought in an experimental tropical rainforest

Science.gov (United States)

Young, J. C.; Sengupta, A.; U'Ren, J.; Van Haren, J. L. M.; Meredith, L. K.

2017-12-01

Nitrous oxide (N2O) is a long-lived, potent greenhouse gas with increasing atmospheric concentrations. Soil microbes in agricultural and natural ecosystems are the dominant source of N2O, which involves complex interactions between N-cycling microbes, metabolisms, soil properties, and plants. Tropical rainforests are the largest natural source of N2O, however the microbial and environmental drivers are poorly understood as few studies have been performed in these environments. Thus, there is an urgent need for further research to fill in knowledge gaps regarding tropical N-cycling, and the response of soil microbial communities to changes in precipitation patterns, temperature, nitrogen deposition, and land use. To address this data gap, we performed a whole-forest drought in the tropical rainforest biome in Biosphere 2 (B2) and analyzed connections between soil microbes, forest heterogeneity, and N2O emissions. The B2 rainforest is the hottest tropical rainforest on Earth, and is an important model system for studying the response of tropical forests to warming with controlled experimentation. In this study, we measured microbial community abundance and diversity profiles (16S rRNA and ITS2 amplicon sequencing) along with their association with soil properties (e.g. pH, C, N) during the drought and rewetting at five locations (3 depths), including regions that have been previously characterized with high and low N2O drought pulse dynamics (van Haren et al., 2005). In this study, we present the spatial distribution of soil microbial communities within the rainforest at Biosphere 2 and their correlations with edaphic factors. In particular, we focus on microbial, soil, and plant factors that drive high and low N2O pulse zones. As in the past, we found that N2O emissions were highest in response to rewetting in a zone hypothesized to be rich in nutrients from a nearby sugar palm. We will characterize microbial indicator species and nitrogen cycling genes to better

Nutrient management for rice production

International Nuclear Information System (INIS)

Khan, A.R.; Chandra, D.; Nanda, P.; Singh, S.S.; Singh, S.R.; Ghorai, A.K.

2002-06-01

The nutrient removed by the crops far exceeds the amounts replenished through fertilizer, causing a much greater strain on the native soil reserves. The situation is further aggravated in countries like India, where sub-optimal fertilizer used by the farmers is a common phenomenon rather than an exception. The total consumption of nutrients of all crops in India, even though reached 15 million tons in 1997, remains much below the estimated nutrient removal of 25 million tons (Swarup and Goneshamurthy, 1998). The gap between nutrient removal supplied through fertilizer has widened further in 2000 to 34 million tons of plant nutrients from the soil against an estimated fertilizer availability of 18 million tons (Singh and Dwivedi, 1996). Nitrogen is the nutrient which limits the most the rice production worldwide. In Asia, where more than 90 percent of the world's rice is produced, about 60 percent of the N fertilizer consumed is used on rice (Stangel and De Dutta, 1985). Conjunctive use of organic material along with fertilizer has been proved an efficient source of nitrogen. Organic residue recycling is becoming an increasingly important aspect of environmentally sound sustainable agriculture. Returning residues like green manure to the soil is necessary for maintaining soil organic matter, which is important for favourable soil structure, soil water retention and soil microbial flora and fauna activities. Use of organic manures in conjunction or as an alternative to chemical fertilizer is receiving attention. Green manure, addition to some extent, helps not only in enhancing the yield but also in improving the physical and chemical nature of soils. The excessive application of chemical fertilizers made it imperative that a part of inorganic fertilizer may be substituted with the recycling of organic wastes. Organic manure has been recorded to enhance the efficiency and reduce the requirement of chemical fertilizers. Partial nitrogen substitution through organic

Transcriptional regulation of nutrient metabolism by PPARa,y and LXRa

NARCIS (Netherlands)

Patsouris, D.A.

2006-01-01

Peroxisome Proliferators Activated Receptors (PPARs) and Liver X Receptors (LXRs) are Nuclear Hormones Receptors that mediate the effect of nutrients on gene expression by acting as sensors for fatty acids and cholesterol-derived metabolites, respectively. In as much as metabolic diseases evolve by

Microbial functional diversity associated with plant litter decomposition along a climatic gradient.

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Sherman, Chen; Steinberger, Yosef

2012-08-01

Predicted changes in climate associated with increased greenhouse gas emissions can cause increases in global mean temperature and changes in precipitation regimes. These changes may affect key soil processes, e.g., microbial CO(2) evolution and biomass, mineralization rates, primary productivity, biodiversity, and litter decomposition, which play an important role in carbon and nutrient cycling in terrestrial ecosystems. Our study examined the changes in litter microbial communities and decomposition along a climatic gradient, ranging from arid desert to humid Mediterranean regions in Israel. Wheat straw litter bags were placed in arid, semi-arid, Mediterranean, and humid Mediterranean sites. Samples were collected seasonally over a 2-year period in order to evaluate mass loss, litter moisture, C/N ratio, bacterial colony-forming units (CFUs), microbial CO(2) evolution and biomass, microbial functional diversity, and catabolic profile. Decomposition rate was the highest during the first year of the study at the Mediterranean and arid sites. Community-level physiological profile and microbial biomass were the highest in summer, while bacterial CFUs were the highest in winter. Microbial functional diversity was found to be highest at the humid Mediterranean site, whereas substrate utilization increased at the arid site. Our results support the assumption that climatic factors control litter degradation and regulate microbial activity.

Microbial Gene Abundance and Expression Patterns across a River to Ocean Salinity Gradient.

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Caroline S Fortunato

Full Text Available Microbial communities mediate the biogeochemical cycles that drive ecosystems, and it is important to understand how these communities are affected by changing environmental conditions, especially in complex coastal zones. As fresh and marine waters mix in estuaries and river plumes, the salinity, temperature, and nutrient gradients that are generated strongly influence bacterioplankton community structure, yet, a parallel change in functional diversity has not been described. Metagenomic and metatranscriptomic analyses were conducted on five water samples spanning the salinity gradient of the Columbia River coastal margin, including river, estuary, plume, and ocean, in August 2010. Samples were pre-filtered through 3 μm filters and collected on 0.2 μm filters, thus results were focused on changes among free-living microbial communities. Results from metagenomic 16S rRNA sequences showed taxonomically distinct bacterial communities in river, estuary, and coastal ocean. Despite the strong salinity gradient observed over sampling locations (0 to 33, the functional gene profiles in the metagenomes were very similar from river to ocean with an average similarity of 82%. The metatranscriptomes, however, had an average similarity of 31%. Although differences were few among the metagenomes, we observed a change from river to ocean in the abundance of genes encoding for catabolic pathways, osmoregulators, and metal transporters. Additionally, genes specifying both bacterial oxygenic and anoxygenic photosynthesis were abundant and expressed in the estuary and plume. Denitrification genes were found throughout the Columbia River coastal margin, and most highly expressed in the estuary. Across a river to ocean gradient, the free-living microbial community followed three different patterns of diversity: 1 the taxonomy of the community changed strongly with salinity, 2 metabolic potential was highly similar across samples, with few differences in

Microbial Gene Abundance and Expression Patterns across a River to Ocean Salinity Gradient.

Science.gov (United States)

Fortunato, Caroline S; Crump, Byron C

2015-01-01

Microbial communities mediate the biogeochemical cycles that drive ecosystems, and it is important to understand how these communities are affected by changing environmental conditions, especially in complex coastal zones. As fresh and marine waters mix in estuaries and river plumes, the salinity, temperature, and nutrient gradients that are generated strongly influence bacterioplankton community structure, yet, a parallel change in functional diversity has not been described. Metagenomic and metatranscriptomic analyses were conducted on five water samples spanning the salinity gradient of the Columbia River coastal margin, including river, estuary, plume, and ocean, in August 2010. Samples were pre-filtered through 3 μm filters and collected on 0.2 μm filters, thus results were focused on changes among free-living microbial communities. Results from metagenomic 16S rRNA sequences showed taxonomically distinct bacterial communities in river, estuary, and coastal ocean. Despite the strong salinity gradient observed over sampling locations (0 to 33), the functional gene profiles in the metagenomes were very similar from river to ocean with an average similarity of 82%. The metatranscriptomes, however, had an average similarity of 31%. Although differences were few among the metagenomes, we observed a change from river to ocean in the abundance of genes encoding for catabolic pathways, osmoregulators, and metal transporters. Additionally, genes specifying both bacterial oxygenic and anoxygenic photosynthesis were abundant and expressed in the estuary and plume. Denitrification genes were found throughout the Columbia River coastal margin, and most highly expressed in the estuary. Across a river to ocean gradient, the free-living microbial community followed three different patterns of diversity: 1) the taxonomy of the community changed strongly with salinity, 2) metabolic potential was highly similar across samples, with few differences in functional gene abundance

Soil microbial diversity in the vicinity of desert shrubs.

Science.gov (United States)

Saul-Tcherkas, Vered; Unc, Adrian; Steinberger, Yosef

2013-04-01

Water and nutrient availability are the major limiting factors of biological activity in arid and semiarid ecosystems. Therefore, perennial plants have developed different ecophysiological adaptations to cope with harsh conditions. The chemical profile of the root exudates varies among plant species and this can induce variability in associated microbial populations. We examined the influence of two shrubs species, Artemisia sieberi and Noaea mucronata, on soil microbial diversity. Soil samples were collected monthly, from December 2006 to November 2007, near canopies of both shrubs (0-10-cm depth). Samples were used for abiotic tests and determination of soil bacterial diversity. No significant differences were found in the abiotic variables (soil moisture, total organic matter, and total soluble nitrogen (TSN)) between soil samples collected from under the two shrubs during the study period. No obvious differences in the Shannon-Weaver index, evenness values, or total phylogenetic distances were found for the soil microbial communities. However, detailed denaturing gradient gel electrophoresis (DGGE) clustering as well as taxonomic diversity analyses indicated clear shifts in the soil microbial community composition. These shifts were governed by seasonal variability in water availability and, significantly, by plant species type.

Enhanced conversion of newly-added maize straw to soil microbial biomass C under plastic film mulching and organic manure management

Science.gov (United States)

Jin, X.; Filley, T. R.

2017-12-01

Management of crop residues using plastic film mulching (PFM) has the potential to improve soil health by accelerating nutrient cycling and facilitating stable C pool production; however, a key aspect of this process—microbial immobilization of residue C—is poorly understood, especially under PFM when combined with different fertilization treatments. A 360-day in situ 13C-tracing technique was used to analyze the contribution and dynamics of microbial biomass C (MBC) to soil organic C (SOC) after 13C-labelled maize straw residue was applied to micro-plot topsoil in a cultivated maize (Zea mays L.) field under 27-year PFM and four fertilization treatments. Over the course of the experiment, MBC content was significantly (P<0.05) higher in treatments of manure (M) and manure plus nitrogen (MN) compared to the no-fertilization (CK) and nitrogen (N) treatments, regardless of PFM. Compared to no PFM controls, PFM enhanced the decomposition of maize straw during summer (Day 60) in the M and MN treatments, exhibiting increases of 93.0% and 28.6% in straw-derived 13C-MBC and 80.4% and 82.9% in 13C-MBC/13C-SOC, respectively. Overall, both PFM and organic manure treatments improved soil fertility through microbe-mediated incorporation of C derived from newly-added maize straw. Our results indicate that microbial growth and activity are affected by the utilization of different C sources and most dramatically during early seasonal transition.

Quorum sensing alters the microbial community of electrode-respiring bacteria and hydrogen scavengers toward improving hydrogen yield in microbial electrolysis cells

International Nuclear Information System (INIS)

Cai, Weiwei; Zhang, Zhaojing; Ren, Ge; Shen, Qiuxuan; Hou, Yanan; Ma, Anzhou; Deng, Ye; Wang, Aijie; Liu, Wenzong

2016-01-01

Highlights: • Enhanced hydrogen yield has been achieved with addition of AHL. • AHL regulated exoelectrogens resulting in electrochemical activity enhancement. • Microbial community shift in cathodic biofilm inhibited hydrogen loss. - Abstract: Quorum sensing has been widely applied to enhance the energy recovery of bioelectrochemical system as a sustainable pathway to enhance communication between cells and electrodes. However, how signalling molecules (acyl-homoserine lactones, AHLs) regulate the microbial community to improve hydrogen generation in microbial electrolysis cells (MECs) is not well understood, especially the subsequent influence on interspecies relationships among not only electrode-respiring bacteria but also hydrogen scavengers. Understanding AHL regulation in a complicated and actual biofilm system will be valuable for future applications of microbial electrochemical technology. Herein, we added short-chain AHLs (3OC6) to regulate the biofilm community on bio-electrodes in MECs. As a result, hydrogen yields were enhanced with AHL addition, increasing by 5.57%, 38.68%, and 81.82% with varied external voltages (0.8 V, 0.6 V, and 0.4 V, respectively). Accordingly, overall reactor performance was enhanced, including coulombic efficiency, electron recovery efficiency, and energy efficiency. Based on an electrochemical impedance spectra analysis, the structured biofilm under simple nutrient conditions (acetate) showed a lower internal resistance with AHL addition, indicating that the microbial communities were altered to enhance electron transfer between the biofilm and electrode. The change in the cathodic microbial structure with more electrochemically active bacteria and fewer hydrogen scavengers could contribute to a higher electron recovery and hydrogen yield with AHL addition. The regulation of the microbial community structure by AHLs represents a potential strategy to enhance electron transfer and hydrogen generation in

Microbial Enzymatic Degradation of Biodegradable Plastics.

Science.gov (United States)

Roohi; Bano, Kulsoom; Kuddus, Mohammed; Zaheer, Mohammed R; Zia, Qamar; Khan, Mohammed F; Ashraf, Ghulam Md; Gupta, Anamika; Aliev, Gjumrakch

2017-01-01

The renewable feedstock derived biodegradable plastics are important in various industries such as packaging, agricultural, paper coating, garbage bags and biomedical implants. The increasing water and waste pollution due to the available decomposition methods of plastic degradation have led to the emergence of biodegradable plastics and biological degradation with microbial (bacteria and fungi) extracellular enzymes. The microbes utilize biodegradable polymers as the substrate under starvation and in unavailability of microbial nutrients. Microbial enzymatic degradation is suitable from bioremediation point of view as no waste accumulation occurs. It is important to understand the microbial interaction and mechanism involved in the enzymatic degradation of biodegradable plastics under the influence of several environmental factors such as applied pH, thermo-stability, substrate molecular weight and/or complexity. To study the surface erosion of polymer film is another approach for hydrolytic degradation characteristion. The degradation of biopolymer is associated with the production of low molecular weight monomer and generation of carbon dioxide, methane and water molecule. This review reported the degradation study of various existing biodegradable plastics along with the potent degrading microbes (bacteria and fungi). Patents available on plastic biodegradation with biotechnological significance is also summarized in this paper. This paper assesses that new disposal technique should be adopted for the degradation of polymers and further research is required for the economical production of biodegradable plastics along with their enzymatic degradation. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Microbial diversity in different compartments of an aquaponics system.

Science.gov (United States)

Schmautz, Zala; Graber, Andreas; Jaenicke, Sebastian; Goesmann, Alexander; Junge, Ranka; Smits, Theo H M

2017-05-01

Aquaponics is a solution for sustainable production of fish and plants in a single semi-closed system, where nutrient-rich water from the aquaculture provides nutrients for plant growth. We examined the microbial communities within an experimental aquaponics system. Whereas the fish feces contained a separate community dominated by bacteria of the genus Cetobacterium, the samples from plant roots, biofilter, and periphyton were more similar to each other, while the communities were more diverse. Detailed examination of the data gave the first indications to functional groups of organisms in the different compartments of the aquaponic system. As other nitrifiers other than members of the genus Nitrospira were only present at low numbers, it was anticipated that Nitrospirae may perform the nitrification process in the biofilm.

Microbial ecology of coal mine refuse

Energy Technology Data Exchange (ETDEWEB)

Cameron, R. E.; Miller, R. M.

1977-01-01

Baseline microbial and ecological studies of samples obtained from two abandoned coal mine refuse sites in the State of Illinois indicate that the unfavorable nature of refuse materials can be a very limiting factor for survival and growth of organisms. Despite the ''foothold'' obtained by some microorganisms, especially acidophilic fungi and some acidotolerant algae, the refuse materials should be amended or ameliorated to raise the pH, provide needed nutrients, especially nitrogen, and provide biodegradable organic matter, both for physical and biological purposes. Finally, the role of microbial populations, responses, and interactions in acid mine wastes must be put into larger perspective. Acid mine drainage amounts to over 4 million tons per year of acidity from active and abandoned mines. Microorganisms appear to be significantly responsible for this problem, but they also can play a beneficial and significant role in the amelioration or alleviation of this detrimental effect as abandoned mines are reclaimed and returned to useful productivity.

Engineering chemical interactions in microbial communities.

Science.gov (United States)

Kenny, Douglas J; Balskus, Emily P

2018-03-05

Microbes living within host-associated microbial communities (microbiotas) rely on chemical communication to interact with surrounding organisms. These interactions serve many purposes, from supplying the multicellular host with nutrients to antagonizing invading pathogens, and breakdown of chemical signaling has potentially negative consequences for both the host and microbiota. Efforts to engineer microbes to take part in chemical interactions represent a promising strategy for modulating chemical signaling within these complex communities. In this review, we discuss prominent examples of chemical interactions found within host-associated microbial communities, with an emphasis on the plant-root microbiota and the intestinal microbiota of animals. We then highlight how an understanding of such interactions has guided efforts to engineer microbes to participate in chemical signaling in these habitats. We discuss engineering efforts in the context of chemical interactions that enable host colonization, promote host health, and exclude pathogens. Finally, we describe prominent challenges facing this field and propose new directions for future engineering efforts.

Does iron inhibit cryptoendolithic microbial communities?

Science.gov (United States)

Johnston, C. G.; Vestal, J. R.; Friedmann, E. I. (Principal Investigator)

1988-01-01

Photosynthetic activity of three cryptoendolithic microbial communities was studied under controlled conditions in the laboratory. In two of these communities, the dominant organisms were lichens, collected from Linnaeus Terrace and from Battleship Promontory. The third community, dominated by cyanobacteria, was collected from Battleship Promontory. Both sites are in the ice-free valleys of southern Victoria Land. Previous efforts have shown how physical conditions can influence metabolic activity in endolithic communities (Kappen and Friedmann 1983; Kappen, Friedmann, and Garty 1981; Vestal, Federle, and Friedmann 1984). Biological activity can also be strongly influenced by the chemical environment. Inorganic nutrients such as nitrate, ammonia, and phosphate are often limiting factors, so their effects on photosynthetic carbon-14 bicarbonate incorporation were investigated. Iron and manganese are two metals present in Linnaeus Terrace and Battleship Promontory sandstones, and their effects on photosynthesis were also studied. The results may add to our understanding of biogeochemical interactions within this unique microbial community.

Flow-through Column Experiments and Modeling of Microbially Mediated Cr(VI) Reduction at Hanford 100H

Science.gov (United States)

Yang, L.; Molins, S.; Beller, H. R.; Brodie, E. L.; Steefel, C.; Nico, P. S.; Han, R.

2010-12-01

Microbially mediated Cr(VI) reduction at the Hanford 100H area was investigated by flow-through column experiments. Three separate experiments were conducted to promote microbial activities associated with denitrification, iron and sulfate reduction, respectively. Replicate columns packed with natural sediments from the site under anaerobic environment were injected with 5mM Lactate as the electron donor and 5 μM Cr(VI) in all experiments. Sulfate and nitrate solutions were added to act as the main electron acceptors in the respective experiments, while iron columns relied on the indigenous sediment iron (and manganese) oxides as electron acceptors. Column effluent solutions were analyzed by IC and ICP-MS to monitor the microbial consumption/conversion of lactate and the associated Cr(VI) reduction. Biogeochemical reactive transport modeling was performed to gain further insights into the reaction mechanisms and Cr(VI) bioreduction rates. All experimental columns showed a reduction of the injected Cr(VI). Columns under denitrifying conditions showed the least Cr(VI) reduction at early stages (simulations indicated that biomass growth completely depleted influent ammonium, and called for an additional source of N to account for the measured reduction rates. Iron columns were the least active with undetectable consumption of the injected lactate, slowest cell growth, and the smallest change in Cr(VI) concentrations during the course of the experiment. In contrast, columns under sulfate-reducing/fermentative conditions exhibited the greatest Cr(VI) reduction capacity. Two sulfate columns evolved to complete lactate fermentation with acetate and propionate produced in the column effluent after 40 days of experiments. These fermenting columns showed a complete removal of injected Cr(VI), visible precipitation of sulfide minerals, and a significant increase in effluent Fe and Mn concentrations. Reactive transport simulations suggested that direct reduction of Cr(VI) by

Soils mediate the impact of fine woody debris on invasive and native grasses as whole trees are mechanically shredded into firebreaks in piñon-juniper woodlands

Science.gov (United States)

Aanderud, Zachary T.; Schoolmaster, Donald R.; Rigby, Deborah; Bybee, Jordon; Campbell, Tayte; Roundy, Bruce A.

2017-01-01

To stem wildfires, trees are being mechanically shredded into firebreaks with the resulting fine woody debris (FWD) potentially exerting immense control over soil and plants. We linked FWD-induced changes in microbial activity and nutrient availability to the frequency of Bromus tectorum and three native, perennial grasses across 31 piñon-juniper woodlands, UT, USA. Using a series of mixed models, we found that FWD increased the frequency of three of the four grasses by at least 12%. Deep, as opposed to shallow, soils mediated frequencies following FWD additions but only partially explained the variation in Bromus and Pseudoroegneria spicata. Although fertile areas associated with tree-islands elicited no response, FWD-induced increases in nitrogen mineralization in deep soils (15–17 cm) caused the frequency of the exotic and Pseudoroegneria to rise. Higher phosphorus availability in FWD-covered surface soils (0–2 cm) had no impact on grasses. FWD altered deep soil respiration, and deep and shallow microbial biomass structuring Pseudoroegneria frequencies, suggesting that microorganism themselves regulated Pseudoroegneria. The positive effects of FWD on grass frequencies intensified over time for natives but diminished for Bromus. Our results demonstrate that microorganisms in deeper soils helped mediate species-specific responses to disturbance both facilitating exotic invasion and promoting native establishment.

Recurrence and frequency of disturbance have cumulative effect on methanotrophic activity, abundance, and community structure.

NARCIS (Netherlands)

Ho, A.; van den Brink, E.; Reim, A.; Krause, S.; Bodelier, P.L.E.

2016-01-01

Alternate prolonged drought and heavy rainfall is predicted to intensify with global warming. Desiccation-rewetting events alter the soil quality and nutrient concentrations which drive microbial-mediated processes, including methane oxidation, a key biogeochemical process catalyzed by

Effect of Carbohydrate Sources and Levels of Cotton Seed Meal in Concentrate on Feed Intake, Nutrient Digestibility, Rumen Fermentation and Microbial Protein Synthesis in Young Dairy Bulls

Directory of Open Access Journals (Sweden)

M. Wanapat

2013-04-01

Full Text Available The objective of this study was to investigate the effect of levels of cottonseed meal with various carbohydrate sources in concentrate on feed intake, nutrient digestibility, rumen fermentation and microbial protein synthesis in dairy bulls. Four, 6 months old dairy bulls were randomly assigned to receive four dietary treatments according to a 2×2 factorial arrangement in a 4×4 Latin square design. Factor A was carbohydrate source; cassava chip (CC and cassava chip+rice bran in the ratio of 3:1 (CR3:1, and factor B was cotton seed meal levels in the concentrate; 109 g CP/kg (LCM and 328 g CP/kg (HCM at similar overall CP levels (490 g CP/kg. Bulls received urea-lime treated rice straw ad libitum and were supplemented with 10 g of concentrate/kg BW. It was found that carbohydrate source and level of cotton seed meal did not have significant effects on ruminal pH, ammonia nitrogen concentration, microbial protein synthesis or feed intake. Animals which received CC showed significantly higher BUN concentration, ruminal propionic acid and butyric acid proportions, while dry matter, organic matter digestibility, populations of total viable bacteria and proteolytic bacteria were lower than those in the CR3:1 treatment. The concentration of total volatile fatty acids was higher in HCM than LCM treatments, while the concentration of butyric acid was higher in LCM than HCM treatments. The population of proteolytic bacteria with the LCM treatments was higher than the HCM treatments; however other bacteria groups were similar among the different levels of cotton seed meal. Bulls which received LCM had higher protein digestibility than those receiving HCM. Therefore, using high levels of cassava chip and cotton seed meal might positively impact on energy and nitrogen balance for the microbial population in the rumen of the young dairy bull.

Effects of nutrient additions on ecosystem carbon cycle in a Puerto Rican tropical wet forest

Science.gov (United States)

YIQING LI; MING XU; XIAOMING ZOU

2006-01-01

Wet tropical forests play a critical role in global ecosystem carbon (C) cycle, but C allocation and the response of different C pools to nutrient addition in these forests remain poorly understood. We measured soil organic carbon (SOC), litterfall, root biomass, microbial biomass and soil physical and chemical properties in a wet tropical forest from May 1996 to July...

Eicosanoid-mediated immunity in insects

Science.gov (United States)

Eicosanoid is a collective term for oxygenated metabolites of C20 polyunsaturated fatty acids. As seen in mammals, eicosanoids play crucial roles in mediating various physiological processes, including immune responses, in insects. Upon microbial pathogen infection, non-self recognition signals are ...

An overview of field specific designs of microbial EOR

Energy Technology Data Exchange (ETDEWEB)

Robertson, E.P.; Bala, G.A.; Fox, S.L.; Jackson, J.D.; Thomas, C.P.

1995-12-01

The selection and design of a microbial enhanced oil recovery (MEOR) process for application in a specific field involves geological, reservoir, and biological characterization. Microbially mediated oil recovery mechanisms (biogenic gas, biopolymers, and biosurfactants) are defined by the types of microorganisms used. The engineering and biological character of a given reservoir must be understood to correctly select a microbial system to enhance oil recovery. The objective of this paper is to discuss the methods used to evaluate three fields with distinct characteristics and production problems for the applicability of MEOR technology. Reservoir characteristics and laboratory results indicated that MEOR would not be applicable in two of the three fields considered. The development of a microbial oil recovery process for the third field appeared promising. Development of a bacterial consortium capable of producing the desired metabolites was initiated and field isolates were characterized.

Influence of organic and inorganic sources of nutrients on the functional diversity of microbial communities in the vegetable cropping system of the Indo-Gangetic plains.

Science.gov (United States)

Manjunath, Mallappa; Kumar, Upendra; Yadava, Raj Bahadur; Rai, Awadhesh Bahadur; Singh, Bijendra

2018-05-31

The aim of the present study was to assess the effects of different organic and inorganic fertilizers on the functional diversity of soil microbial community under a vegetable production system. The Biolog ® Eco-plate technique and indices, such as average well-colour development (AWCD), McIntosh and Shannon diversity were employed to study the diversity of soil microorganisms. The AWCD, i.e. overall utilization of carbon sources, suggested that different organic treatments had a significant impact on the metabolic activity of soil microorganisms. After 120h, the highest AWCD values were observed in poultry manure (2.5 t·ha -1 )+vermicompost (3.5 t·ha -1 ) (0.63) and farm yard manure (FYM) (10 t·ha -1 )+vermicompost (3.5 t·ha -1 ) (0.61). After 72h, the highest value of the McIntosh diversity index was recorded in poultry manure (2.5 t·ha -1 )+vermicompost (3.5 t·ha -1 ) (3.87), followed by poultry manure (2.5 t·ha -1 )+vermicompost (3.5 t·ha -1 )+biofertilizers (Azotobacter 500 g·ha -1 applied as seed treatment) (3.12). In the case of the Shannon diversity index, the highest values were noticed in organic treatments; however, there was no significant differences between organic and inorganic treatments. Biplot analysis showed a clear differentiation of organic treatments from the inorganic control. The amino acids, phenolics and polymer utilizing microorganisms were dominant in organic treatments. Inorganic control recorded the lowest values of the microbial diversity indices. Through this study, we have identified the best combination of organic nutrients, i.e. poultry manure (2.5 t·ha -1 )+vermicompost (3.5 t·ha -1 ) for the stimulation of metabolically active soil microbial communities. Copyright © 2018 Académie des sciences. Published by Elsevier Masson SAS. All rights reserved.

Toward Understanding the Dynamics of Microbial Communities in an Estuarine System

KAUST Repository

Zhang, Weipeng; Bougouffa, Salim; Wang, Yong; Lee, On On; Yang, Jiangke; Chan, Colin; Song, Xingyu; Qian, Pei-Yuan

2014-01-01

Community assembly theories such as species sorting theory provide a framework for understanding the structures and dynamics of local communities. The effect of theoretical mechanisms can vary with the scales of observation and effects of specific environmental factors. Based on 16S rRNA gene tag pyrosequencing, different structures and temporal succession patterns were discovered between the surface sediments and bottom water microbial communities in the Pearl River Estuary (PRE). The microbial communities in the surface sediment samples were more diverse than those in the bottom water samples, and several genera were specific for the water or sediment communities. Moreover, water temperature was identified as the main variable driving community dynamics and the microbial communities in the sediment showed a greater temporal change. We speculate that nutrient-based species sorting and bacterial plasticity to the temperature contribute to the variations observed between sediment and water communities in the PRE. This study provides a more comprehensive understanding of the microbial community structures in a highly dynamic estuarine system and sheds light on the applicability of ecological theoretical mechanisms.

Toward understanding the dynamics of microbial communities in an estuarine system.

Directory of Open Access Journals (Sweden)

Weipeng Zhang

Full Text Available Community assembly theories such as species sorting theory provide a framework for understanding the structures and dynamics of local communities. The effect of theoretical mechanisms can vary with the scales of observation and effects of specific environmental factors. Based on 16S rRNA gene tag pyrosequencing, different structures and temporal succession patterns were discovered between the surface sediments and bottom water microbial communities in the Pearl River Estuary (PRE. The microbial communities in the surface sediment samples were more diverse than those in the bottom water samples, and several genera were specific for the water or sediment communities. Moreover, water temperature was identified as the main variable driving community dynamics and the microbial communities in the sediment showed a greater temporal change. We speculate that nutrient-based species sorting and bacterial plasticity to the temperature contribute to the variations observed between sediment and water communities in the PRE. This study provides a more comprehensive understanding of the microbial community structures in a highly dynamic estuarine system and sheds light on the applicability of ecological theoretical mechanisms.

Toward Understanding the Dynamics of Microbial Communities in an Estuarine System

KAUST Repository

Zhang, Weipeng

2014-04-14

Community assembly theories such as species sorting theory provide a framework for understanding the structures and dynamics of local communities. The effect of theoretical mechanisms can vary with the scales of observation and effects of specific environmental factors. Based on 16S rRNA gene tag pyrosequencing, different structures and temporal succession patterns were discovered between the surface sediments and bottom water microbial communities in the Pearl River Estuary (PRE). The microbial communities in the surface sediment samples were more diverse than those in the bottom water samples, and several genera were specific for the water or sediment communities. Moreover, water temperature was identified as the main variable driving community dynamics and the microbial communities in the sediment showed a greater temporal change. We speculate that nutrient-based species sorting and bacterial plasticity to the temperature contribute to the variations observed between sediment and water communities in the PRE. This study provides a more comprehensive understanding of the microbial community structures in a highly dynamic estuarine system and sheds light on the applicability of ecological theoretical mechanisms.

Microbial ecology of hot desert edaphic systems.

Science.gov (United States)

Makhalanyane, Thulani P; Valverde, Angel; Gunnigle, Eoin; Frossard, Aline; Ramond, Jean-Baptiste; Cowan, Don A

2015-03-01

A significant proportion of the Earth's surface is desert or in the process of desertification. The extreme environmental conditions that characterize these areas result in a surface that is essentially barren, with a limited range of higher plants and animals. Microbial communities are probably the dominant drivers of these systems, mediating key ecosystem processes. In this review, we examine the microbial communities of hot desert terrestrial biotopes (including soils, cryptic and refuge niches and plant-root-associated microbes) and the processes that govern their assembly. We also assess the possible effects of global climate change on hot desert microbial communities and the resulting feedback mechanisms. We conclude by discussing current gaps in our understanding of the microbiology of hot deserts and suggest fruitful avenues for future research. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

The role of diatom nanostructures in biasing diffusion to improve uptake in a patchy nutrient environment.

Directory of Open Access Journals (Sweden)

James G Mitchell

Full Text Available BACKGROUND: Diatoms are important single-celled autotrophs that dominate most lit aquatic environments and are distinguished by surficial frustules with intricate designs of unknown function. PRINCIPAL FINDINGS: We show that some frustule designs constrain diffusion to positively alter nutrient uptake. In nutrient gradients of 4 to 160 times over <5 cm, the screened-chambered morphology of Coscincodiscus sp. biases the nutrient diffusion towards the cell by at least 3.8 times the diffusion to the seawater. In contrast, the open-chambers of Thalassiosira eccentrica produce at least a 1.3 times diffusion advantage to the membrane over Coscincodiscus sp. when nutrients are homogeneous. SIGNIFICANCE: Diffusion constraint explains the success of particular diatom species at given times and the overall success of diatoms. The results help answer the unresolved question of how adjacent microplankton compete. Furthermore, diffusion constraint by supramembrane nanostructures to alter molecular diffusion suggests that microbes compete via supramembrane topology, a competitive mechanism not considered by the standard smooth-surface equations used for nutrient uptake nor in microbial ecology and cell physiology.

Microbial enhancement of compost extracts based on cattle rumen content compost - characterisation of a system.

Science.gov (United States)

Shrestha, Karuna; Shrestha, Pramod; Walsh, Kerry B; Harrower, Keith M; Midmore, David J

2011-09-01

Microbially enhanced compost extracts ('compost tea') are being used in commercial agriculture as a source of nutrients and for their perceived benefit to soil microbiology, including plant disease suppression. Rumen content material is a waste of cattle abattoirs, which can be value-added by conversion to compost and 'compost tea'. A system for compost extraction and microbial enhancement was characterised. Molasses amendment increased bacterial count 10-fold, while amendment based on molasses and 'fish and kelp hydrolysate' increased fungal count 10-fold. Compost extract incubated at 1:10 (w/v) dilution showed the highest microbial load, activity and humic/fulvic acid content compared to other dilutions. Aeration increased the extraction efficiency of soluble metabolites, and microbial growth rate, as did extraction of compost without the use of a constraining bag. A protocol of 1:10 dilution and aerated incubation with kelp and molasses amendments is recommended to optimise microbial load and fungal-to-bacterial ratio for this inoculum source. Copyright © 2011 Elsevier Ltd. All rights reserved.

Unlocking Ft: Modeling thermodynamic controls and isotope fractionation factors in nutrient limited environments

Science.gov (United States)

Druhan, J. L.; Giannetta, M.; Sanford, R. A.

2017-12-01

In recent years, reactive transport principles have expanded from early applications, largely based in contaminant hydrology, to a wide range of biologically mediated redox environments including marine sedimentary diagenesis, terrestrial metal ore deposits, soils, and critical zone weathering profiles. A common observation across this diversity of systems is that they often function under energetically limited conditions in comparison to those typical of contaminated aquifers subject to engineered remediation techniques. As a result, the kinetic rate expressions traditionally employed within reactive transport frameworks to simulate microbially mediated redox transformations have required modification. This was recognized in a series of seminal papers by Jin and Bethke (2005, 2007) in which the authors expanded upon a Monod rate law to include a thermodynamic potential factor `Ft' which exerts a limitation on the overall rate based on the thermodynamic driving force of the electron transfer reaction. This new rate expression is now commonly implemented within many of the major reactive transport software packages, though appropriate application has yet to be thoroughly demonstrated. Notably, the characteristically large partitioning of stable isotopes during microbially mediated reactions, which is extensively utilized to identify and quantify these redox transformations, has yet to be simulated under conditions in which the Ft term may be expected to exert a significant mass dependent influence. Here, we develop a series of simplified simulations for the microbially mediated reduction of sulfate based on the datasets reported by Jin and Bethke, and apply appropriate mass-bias within the Ft term to consider the extent to which the resulting isotopic fractionation is consistent with that observed in energetically limited systems. We show that the Ft term can exert a significant influence on the observed fractionation factor under common environmental conditions

The Biogeographic Pattern of Microbial Functional Genes along an Altitudinal Gradient of the Tibetan Pasture

Energy Technology Data Exchange (ETDEWEB)

Qi, Qi; Zhao, Mengxin; Wang, Shiping; Ma, Xingyu; Wang, Yuxuan; Gao, Ying; Lin, Qiaoyan; Li, Xiangzhen; Gu, Baohua; Li, Guoxue; Zhou, Jizhong; Yang, Yunfeng

2017-06-13

As the highest place of the world, the Tibetan plateau is a fragile ecosystem. Given the importance of microbial communities in driving soil nutrient cycling, it is of interest to document the microbial biogeographic pattern here. We adopted a microarray-based tool named GeoChip 4.0 to investigate grassland microbial functional genes along an elevation gradient from 3200 to 3800 m above sea level open to free grazing by local herdsmen and wild animals. Interestingly, microbial functional diversities increase with elevation, so does the relative abundances of genes associated with carbon degradation, nitrogen cycling, methane production, cold shock and oxygen limitation. The range of Shannon diversities (10.27–10.58) showed considerably smaller variation than what was previously observed at ungrazed sites nearby (9.95–10.65), suggesting the important role of livestock grazing on microbial diversities. Closer examination showed that the dissimilarity of microbial community at our study sites increased with elevations, revealing an elevation-decay relationship of microbial functional genes. Both microbial functional diversity and the number of unique genes increased with elevations. Furthermore, we detected a tight linkage of greenhouse gas (CO2) and relative abundances of carbon cycling genes. Our biogeographic study provides insights on microbial functional diversity and soil biogeochemical cycling in Tibetan pastures.

The Biogeographic Pattern of Microbial Functional Genes along an Altitudinal Gradient of the Tibetan Pasture

Directory of Open Access Journals (Sweden)

Qi Qi

2017-06-01

Full Text Available As the highest place of the world, the Tibetan plateau is a fragile ecosystem. Given the importance of microbial communities in driving soil nutrient cycling, it is of interest to document the microbial biogeographic pattern here. We adopted a microarray-based tool named GeoChip 4.0 to investigate grassland microbial functional genes along an elevation gradient from 3200 to 3800 m above sea level open to free grazing by local herdsmen and wild animals. Interestingly, microbial functional diversities increase with elevation, so does the relative abundances of genes associated with carbon degradation, nitrogen cycling, methane production, cold shock and oxygen limitation. The range of Shannon diversities (10.27–10.58 showed considerably smaller variation than what was previously observed at ungrazed sites nearby (9.95–10.65, suggesting the important role of livestock grazing on microbial diversities. Closer examination showed that the dissimilarity of microbial community at our study sites increased with elevations, revealing an elevation-decay relationship of microbial functional genes. Both microbial functional diversity and the number of unique genes increased with elevations. Furthermore, we detected a tight linkage of greenhouse gas (CO2 and relative abundances of carbon cycling genes. Our biogeographic study provides insights on microbial functional diversity and soil biogeochemical cycling in Tibetan pastures.

Importance of PGPR application and its effect on microbial activity in maize rhizosphere

Directory of Open Access Journals (Sweden)

Mrkovački Nastasija

2012-01-01

Full Text Available Microorganisms are involved in the formation of soil fertility, both potential and effective. They facilitate the processes of humification and dehumification and play a key role in the cycling of nutrients - macro and microelements. Rhizosphere is the soil in direct contact with plant roots and influenced by plant exudates. Root exudates of maize significantly affect the composition and abundance of microorganisms in the rhizosphere. Bio-fertilizers are microbial fertilizers composed of highly effective strains of bacteria, algae and fungi isolated from soil. Their application activates microbial processes that secure a better and steadier supply of plants with nitrogen, phosphorus, potassium and some micronutrients. The application of PGPR-containing biofertilizers reduces the need for expensive nitrogen fertilizers, facilitates phosphorus uptake by plants and affects the direction and dynamics of microbial processes.

Soil Microbial Activity Responses to Fire in a Semi-arid Savannah Ecosystem Pre- and Post-Monsoon Season

Science.gov (United States)

Jimenez, J. R.; Raub, H. D.; Jong, E. L.; Muscarella, C. R.; Smith, W. K.; Gallery, R. E.

2017-12-01

Extracellular enzyme activities (EEA) of soil microorganisms can act as important proxies for nutrient limitation and turnover in soil and provide insight into the biochemical requirements of microbes in terrestrial ecosystems. In semi-arid ecosystems, microbial activity is influenced by topography, disturbances such as fire, and seasonality from monsoon rains. Previous studies from forest ecosystems show that microbial communities shift to similar compositions after severe fires despite different initial conditions. In semi-arid ecosystems with high spatial heterogeniety, we ask does fire lead to patch intensification or patch homogenization and how do monsoon rains influence the successional trajectories of microbial responses? We analyzed microbial activity and soil biogeochemistry throughout the monsoon season in paired burned and unburned sites in the Santa Rita Experimental Range, AZ. Surface soil (5cm) from bare-ground patches, bole, canopy drip line, and nearby grass patches for 5 mesquite trees per site allowed tests of spatiotemporal responses to fire and monsoon rain. Microbial activity was low during the pre-monsoon season and did not differ between the burned and unburned sites. We found greater activity near mesquite trees that reflects soil water and nutrient availability. Fire increased soil alkalinity, though soils near mesquite trees were less affected. Soil water content was significantly higher in the burned sites post-monsoon, potentially reflecting greater hydrophobicity of burned soils. Considering the effects of fire in these semi-arid ecosystems is especially important in the context of the projected changing climate regime in this region. Assessing microbial community recovery pre-, during, and post-monsoon is important for testing predictions about whether successional pathways post-fire lead to recovery or novel trajectories of communities and ecosystem function.

Nutrients, Microglia Aging, and Brain Aging

Directory of Open Access Journals (Sweden)

Zhou Wu

2016-01-01

Full Text Available As the life expectancy continues to increase, the cognitive decline associated with Alzheimer’s disease (AD becomes a big major issue in the world. After cellular activation upon systemic inflammation, microglia, the resident immune cells in the brain, start to release proinflammatory mediators to trigger neuroinflammation. We have found that chronic systemic inflammatory challenges induce differential age-dependent microglial responses, which are in line with the impairment of learning and memory, even in middle-aged animals. We thus raise the concept of “microglia aging.” This concept is based on the fact that microglia are the key contributor to the acceleration of cognitive decline, which is the major sign of brain aging. On the other hand, inflammation induces oxidative stress and DNA damage, which leads to the overproduction of reactive oxygen species by the numerous types of cells, including macrophages and microglia. Oxidative stress-damaged cells successively produce larger amounts of inflammatory mediators to promote microglia aging. Nutrients are necessary for maintaining general health, including the health of brain. The intake of antioxidant nutrients reduces both systemic inflammation and neuroinflammation and thus reduces cognitive decline during aging. We herein review our microglia aging concept and discuss systemic inflammation and microglia aging. We propose that a nutritional approach to controlling microglia aging will open a new window for healthy brain aging.

Nutrients, Microglia Aging, and Brain Aging.

Science.gov (United States)

Wu, Zhou; Yu, Janchun; Zhu, Aiqin; Nakanishi, Hiroshi

2016-01-01

As the life expectancy continues to increase, the cognitive decline associated with Alzheimer's disease (AD) becomes a big major issue in the world. After cellular activation upon systemic inflammation, microglia, the resident immune cells in the brain, start to release proinflammatory mediators to trigger neuroinflammation. We have found that chronic systemic inflammatory challenges induce differential age-dependent microglial responses, which are in line with the impairment of learning and memory, even in middle-aged animals. We thus raise the concept of "microglia aging." This concept is based on the fact that microglia are the key contributor to the acceleration of cognitive decline, which is the major sign of brain aging. On the other hand, inflammation induces oxidative stress and DNA damage, which leads to the overproduction of reactive oxygen species by the numerous types of cells, including macrophages and microglia. Oxidative stress-damaged cells successively produce larger amounts of inflammatory mediators to promote microglia aging. Nutrients are necessary for maintaining general health, including the health of brain. The intake of antioxidant nutrients reduces both systemic inflammation and neuroinflammation and thus reduces cognitive decline during aging. We herein review our microglia aging concept and discuss systemic inflammation and microglia aging. We propose that a nutritional approach to controlling microglia aging will open a new window for healthy brain aging.

Microbial diversity in oiled and un-oiled shoreline sediments in the Norwegian Arctic

International Nuclear Information System (INIS)

Grossman, M.J.; Prince, R.C.; Garrett, R.M.; Garrett, K.K.; Bare, R.E.; O'Neil, K.R.; Sowlay, M.R.; Hinton, S.M.; Lee, K.; Sergy, G.A.; Guenette, C.C.

2000-01-01

Field trials were conducted at an oiled shoreline on the island of Spitsbergen to examine the effect of nutrient addition on the metabolic status, potential for aromatic hydrocarbon degradation, and the phylogenetic diversity of the microbial community in oiled Arctic shoreline sediments. IF-30 intermediate fuel grade oil was applied to the shoreline which was then divided into four plots. One was left untreated and two were tilled. Four applications of fertilizer were applied over a two-month period. Phospholipid fatty acid (PLFA), gene probe and 16S microbial community analysis suggested that bioremediation stimulated the metabolic activity, increased microbial biomass and genetic potential for aromatic hydrocarbon degradation, and increased the population of hydrocarbon degradation of an oiled Arctic shoreline microbial community. The results of this study are in agreement with the results from stimulation of oil biodegradation in temperate marine environments. It was concluded that biodegradation and fertilizer addition are feasible treatment methods for oil spills in Arctic regions. 31 refs., 3 tabs., 3 figs

Irradiation of microbial controlling on package tofu

International Nuclear Information System (INIS)

Gao Meixu; Li Shurong; Wang Li; Wang Shuo; Wang Ning

2009-01-01

The effects of irradiation on microbiological controlling, nutrient and sensory qualities of packaged tofu (bean curd) stored at commercial condition. Results showed that D 10 values of Listeria innocua and Samonella enteritidis inoculated in packaged tofu were 0.225 and 0.240kGy, respectively. Irradiation dose lower than 2.0kGy had no significant effects on content of crude protein and amino acid (p>0.05). γ-irradiation could decrease microbial in packaged tofu and 2.0kGy should be applied to ensure the hygienic quality of the products. (authors)

Manipulating soil microbial communities in extensive green roof substrates.

Science.gov (United States)

Molineux, Chloe J; Connop, Stuart P; Gange, Alan C

2014-09-15

There has been very little investigation into the soil microbial community on green roofs, yet this below ground habitat is vital for ecosystem functioning. Green roofs are often harsh environments that would greatly benefit from having a healthy microbial system, allowing efficient nutrient cycling and a degree of drought tolerance in dry summer months. To test if green roof microbial communities could be manipulated, we added mycorrhizal fungi and a microbial mixture ('compost tea') to green roof rootzones, composed mainly of crushed brick or crushed concrete. The study revealed that growing media type and depth play a vital role in the microbial ecology of green roofs. There are complex relationships between depth and type of substrate and the biomass of different microbial groups, with no clear pattern being observed. Following the addition of inoculants, bacterial groups tended to increase in biomass in shallower substrates, whereas fungal biomass change was dependent on depth and type of substrate. Increased fungal biomass was found in shallow plots containing more crushed concrete and deeper plots containing more crushed brick where compost tea (a live mixture of beneficial bacteria) was added, perhaps due to the presence of helper bacteria for arbuscular mycorrhizal fungi (AMF). Often there was not an additive affect of the microbial inoculations but instead an antagonistic interaction between the added AM fungi and the compost tea. This suggests that some species of microbes may not be compatible with others, as competition for limited resources occurs within the various substrates. The overall results suggest that microbial inoculations of green roof habitats are sustainable. They need only be done once for increased biomass to be found in subsequent years, indicating that this is a novel and viable method of enhancing roof community composition. Copyright © 2014 Elsevier B.V. All rights reserved.

Systematic review of nutrient intake and growth in children with multiple IgE-mediated food allergies.

Science.gov (United States)

Sova, Cassandra; Feuling, Mary Beth; Baumler, Megan; Gleason, Linda; Tam, Jonathan S; Zafra, Heidi; Goday, Praveen S

2013-12-01

Food allergies affect up to 8% of American children. The current recommended treatment for food allergies is strict elimination of the allergens from the diet. Dietary elimination of nutrient-dense foods may result in inadequate nutrient intake and impaired growth. The purpose of this review was to critically analyze available research on the effect of an elimination diet on nutrient intake and growth in children with multiple food allergies. A systematic review of the literature was conducted and a workgroup was established to critically analyze each relevant article. The findings were summarized and a conclusion was generated. Six studies were analyzed. One study found that children with food allergies are more likely to be malnourished than children without food allergies. Three studies found that children with multiple food allergies were shorter than children with 1 food allergy. Four studies assessed nutrient intake of children with multiple food allergies, but the inclusion and comparison criteria were different in each of the studies and the findings were conflicting. One study found that children with food allergies who did not receive nutrition counseling were more likely to have inadequate intake of calcium and vitamin D. Children with multiple food allergies have a higher risk of impaired growth and may have a higher risk of inadequate nutrient intake than children without food allergies. Until more research is available, we recommend monitoring of nutrition and growth of children with multiple food allergies to prevent possible nutrient deficiencies and to optimize growth.

Strength and stability of microbial plugs in porous media

Energy Technology Data Exchange (ETDEWEB)

Sarkar, A.K. [NIPER/BDM-Oklahoma, Inc., Bartlesville, OK (United States); Sharma, M.M.; Georgiou, G. [Univ. of Texas, Austin, TX (United States)

1995-12-31

Mobility reduction induced by the growth and metabolism of bacteria in high-permeability layers of heterogeneous reservoirs is an economically attractive technique to improve sweep efficiency. This paper describes an experimental study conducted in sandpacks using an injected bacterium to investigate the strength and stability of microbial plugs in porous media. Successful convective transport of bacteria is important for achieving sufficient initial bacteria distribution. The chemotactic and diffusive fluxes are probably not significant even under static conditions. Mobility reduction depends upon the initial cell concentrations and increase in cell mass. For single or multiple static or dynamic growth techniques, permeability reduction was approximately 70% of the original permeability. The stability of these microbial plugs to increases in pressure gradient and changes in cell physiology in a nutrient-depleted environment needs to be improved.

Skeletal nutrient vascular adaptation induced by external oscillatory intramedullary fluid pressure intervention

Directory of Open Access Journals (Sweden)

Qin Yi-Xian

2010-03-01

Full Text Available Abstract Background Interstitial fluid flow induced by loading has demonstrated to be an important mediator for regulating bone mass and morphology. It is shown that the fluid movement generated by the intramedullary pressure (ImP provides a source for pressure gradient in bone. Such dynamic ImP may alter the blood flow within nutrient vessel adjacent to bone and directly connected to the marrow cavity, further initiating nutrient vessel adaptation. It is hypothesized that oscillatory ImP can mediate the blood flow in the skeletal nutrient vessels and trigger vasculature remodeling. The objective of this study was then to evaluate the vasculature remodeling induced by dynamic ImP stimulation as a function of ImP frequency. Methods Using an avian model, dynamics physiological fluid ImP (70 mmHg, peak-peak was applied in the marrow cavity of the left ulna at either 3 Hz or 30 Hz, 10 minutes/day, 5 days/week for 3 or 4 weeks. The histomorphometric measurements of the principal nutrient arteries were done to quantify the arterial wall area, lumen area, wall thickness, and smooth muscle cell layer numbers for comparison. Results The preliminary results indicated that the acute cyclic ImP stimuli can significantly enlarge the nutrient arterial wall area up to 50%, wall thickness up to 20%, and smooth muscle cell layer numbers up to 37%. In addition, 3-week of acute stimulation was sufficient to alter the arterial structural properties, i.e., increase of arterial wall area, whereas 4-week of loading showed only minimal changes regardless of the loading frequency. Conclusions These data indicate a potential mechanism in the interrelationship between vasculature adaptation and applied ImP alteration. Acute ImP could possibly initiate the remodeling in the bone nutrient vasculature, which may ultimately alter blood supply to bone.

Incorporating the soil environment and microbial community into plant competition theory.

Science.gov (United States)

Ke, Po-Ju; Miki, Takeshi

2015-01-01

Plants affect microbial communities and abiotic properties of nearby soils, which in turn influence plant growth and interspecific interaction, forming a plant-soil feedback (PSF). PSF is a key determinant influencing plant population dynamics, community structure, and ecosystem functions. Despite accumulating evidence for the importance of PSF and development of specific PSF models, different models are not yet fully integrated. Here, we review the theoretical progress in understanding PSF. When first proposed, PSF was integrated with various mathematical frameworks to discuss its influence on plant competition. Recent theoretical models have advanced PSF research at different levels of ecological organizations by considering multiple species, applying spatially explicit simulations to examine how local-scale predictions apply to larger scales, and assessing the effect of PSF on plant temporal dynamics over the course of succession. We then review two foundational models for microbial- and litter-mediated PSF. We present a theoretical framework to illustrate that although the two models are typically presented separately, their behavior can be understood together by invasibility analysis. We conclude with suggestions for future directions in PSF theoretical studies, which include specifically addressing microbial diversity to integrate litter- and microbial-mediated PSF, and apply PSF to general coexistence theory through a trait-based approach.

Incorporating the soil environment and microbial community into plant competition theory

Science.gov (United States)

Ke, Po-Ju; Miki, Takeshi

2015-01-01

Plants affect microbial communities and abiotic properties of nearby soils, which in turn influence plant growth and interspecific interaction, forming a plant-soil feedback (PSF). PSF is a key determinant influencing plant population dynamics, community structure, and ecosystem functions. Despite accumulating evidence for the importance of PSF and development of specific PSF models, different models are not yet fully integrated. Here, we review the theoretical progress in understanding PSF. When first proposed, PSF was integrated with various mathematical frameworks to discuss its influence on plant competition. Recent theoretical models have advanced PSF research at different levels of ecological organizations by considering multiple species, applying spatially explicit simulations to examine how local-scale predictions apply to larger scales, and assessing the effect of PSF on plant temporal dynamics over the course of succession. We then review two foundational models for microbial- and litter-mediated PSF. We present a theoretical framework to illustrate that although the two models are typically presented separately, their behavior can be understood together by invasibility analysis. We conclude with suggestions for future directions in PSF theoretical studies, which include specifically addressing microbial diversity to integrate litter- and microbial-mediated PSF, and apply PSF to general coexistence theory through a trait-based approach. PMID:26500621

Incorporating the soil environment and microbial community into plant competition theory

Directory of Open Access Journals (Sweden)

Po-Ju eKe

2015-10-01

Full Text Available Plants affect microbial communities and abiotic properties of nearby soils, which in turn influence plant growth and interspecific interaction, forming a plant-soil feedback (PSF. PSF is a key determinant influencing plant population dynamics, community structure, and ecosystem functions. Despite accumulating evidence for the importance of PSF and development of specific PSF models, different models are not yet fully integrated. Here, we review the theoretical progress in understanding PSF. When first proposed, PSF was integrated with various mathematical frameworks to discuss its influence on plant competition. Recent theoretical models have advanced PSF research at different levels of ecological organizations by considering multiple species, applying spatially explicit simulations to examine how local-scale predictions apply to larger scales, and assessing the effect of PSF on plant temporal dynamics over the course of succession. We then review two foundational models for microbial- and litter-mediated PSF. We present a theoretical framework to illustrate that although the two models are typically presented separately, their behavior can be understood together by invasibility analysis. We conclude with suggestions for future directions in PSF theoretical studies, which include specifically addressing microbial diversity to integrate litter- and microbial-mediated PSF, and apply PSF to general coexistence theory through a trait-based approach.

Microbially induced corrosion of carbon steel in deep groundwater environment

Directory of Open Access Journals (Sweden)

Pauliina eRajala

2015-07-01

Full Text Available The metallic low and intermediate level radioactive waste generally consists of carbon steel and stainless steels. The corrosion rate of carbon steel in deep groundwater is typically low, unless the water is very acidic or microbial activity in the environment is high. Therefore, the assessment of microbially induced corrosion of carbon steel in deep bedrock environment has become important for evaluating the safety of disposal of radioactive waste. Here we studied the corrosion inducing ability of indigenous microbial community from a deep bedrock aquifer. Carbon steel coupons were exposed to anoxic groundwater from repository site 100 m depth (Olkiluoto, Finland for periods of three and eight months. The experiments were conducted at both in situ temperature and room temperature to investigate the response of microbial population to elevated temperature. Our results demonstrate that microorganisms from the deep bedrock aquifer benefit from carbon steel introduced to the nutrient poor anoxic deep groundwater environment. In the groundwater incubated with carbon steel the planktonic microbial community was more diverse and 100-fold more abundant compared to the environment without carbon steel. The betaproteobacteria were the most dominant bacterial class in all samples where carbon steel was present, whereas in groundwater incubated without carbon steel the microbial community had clearly less diversity. Microorganisms induced pitting corrosion and were found to cluster inside the corrosion pits. Temperature had an effect on the species composition of microbial community and also affected the corrosion deposits layer formed on the surface of carbon steel.

Next-generation sequencing (NGS) for assessment of microbial water quality: current progress, challenges, and future opportunities

OpenAIRE

BoonFei eTan; Charmaine Marie Ng; Jean Pierre Nshimyimana; Jean Pierre Nshimyimana; Lay-Leng eLoh; Lay-Leng eLoh; Karina Yew-Hoong Gin; Janelle Renee Thompson; Janelle Renee Thompson

2015-01-01

Water quality is an emergent property of a complex system comprised of interacting microbial populations and introduced microbial and chemical contaminants. Studies leveraging next-generation sequencing (NGS) technologies are providing new insights into the ecology of microbially mediated processes that influence fresh water quality such as algal blooms, contaminant biodegradation, and pathogen dissemination. In addition, sequencing methods targeting small subunit (SSU) rRNA hypervariable reg...

Microbial Biosynthesis of Silver Nanoparticles in Different Culture Media.

Science.gov (United States)

Luo, Ke; Jung, Samuel; Park, Kyu-Hwan; Kim, Young-Rok

2018-01-31

Microbial biosynthesis of metal nanoparticles has been extensively studied for the applications in biomedical sciences and engineering. However, the mechanism for their synthesis through microorganism is not completely understood. In this study, several culture media were investigated for their roles in the microbial biosynthesis of silver nanoparticles (AgNPs). The size and morphology of the synthesized AgNPs were analyzed by UV-vis spectroscopy, Fourier-transform-infrared (FT-IR), transmission electron microscopy (TEM), and dynamic light scattering (DLS). The results demonstrated that nutrient broth (NB) and Mueller-Hinton broth (MHB) among tested media effectively reduced silver ions to form AgNPs with different particle size and shape. Although the involved microorganism enhanced the reduction of silver ions, the size and shape of the particles were shown to mainly depend on the culture media. Our findings suggest that the growth media of bacterial culture play an important role in the synthesis of metallic nanoparticles with regard to their size and shape. We believe our findings would provide useful information for further exploration of microbial biosynthesis of AgNPs and their biomedical applications.

Rapid microbial respiration of oil from the Deepwater Horizon spill in offshore surface waters of the Gulf of Mexico

International Nuclear Information System (INIS)

Edwards, Bethanie R; Reddy, Christopher M; Carmichael, Catherine A; Longnecker, Krista; Van Mooy, Benjamin A S; Camilli, Richard

2011-01-01

The Deepwater Horizon oil spill was one of the largest oil spills in history, and the fate of this oil within the Gulf of Mexico ecosystem remains to be fully understood. The goal of this study-conducted in mid-June of 2010, approximately two months after the oil spill began-was to understand the key role that microbes would play in the degradation of the oil in the offshore oligotrophic surface waters near the Deepwater Horizon site. As the utilization of organic carbon by bacteria in the surface waters of the Gulf had been previously shown to be phosphorus limited, we hypothesized that bacteria would be unable to rapidly utilize the oil released from the Macondo well. Although phosphate was scarce throughout the sampling region and microbes exhibited enzymatic signs of phosphate stress within the oil slick, microbial respiration within the slick was enhanced by approximately a factor of five. An incubation experiment to determine hydrocarbon degradation rates confirmed that a large fraction of this enhanced respiration was supported by hydrocarbon degradation. Extrapolating our observations to the entire area of the slick suggests that microbes had the potential to degrade a large fraction of the oil as it arrived at the surface from the well. These observations decidedly refuted our hypothesis. However, a concomitant increase in microbial abundance or biomass was not observed in the slick, suggesting that microbial growth was nutrient limited; incubations amended with nutrients showed rapid increases in cell number and biomass, which supported this conclusion. Our study shows that the dynamic microbial community of the Gulf of Mexico supported remarkable rates of oil respiration, despite a dearth of dissolved nutrients.

Microbial effects

International Nuclear Information System (INIS)

Sharpe, V.J.

1985-10-01

The long term safety and integrity of radioactive waste disposal sites proposed for use by Ontario Hydro may be affected by the release of radioactive gases. Microbes mediate the primary pathways of waste degradation and hence an assessment of their potential to produce gaseous end products from the breakdown of low level waste was performed. Due to a number of unknown variables, assumptions were made regarding environmental and waste conditions that controlled microbial activity; however, it was concluded that 14 C and 3 H would be produced, albeit over a long time scale of about 1500 years for 14 C in the worst case situation

Microbial diversity in restored wetlands of San Francisco Bay

Energy Technology Data Exchange (ETDEWEB)

Theroux, Susanna [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.; Hartman, Wyatt [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.; He, Shaomei [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.; Univ. of Wisconsin, Madison, WI (United States); Tringe, Susannah [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.

2013-12-09

Wetland ecosystems may serve as either a source or a sink for atmospheric carbon and greenhouse gases. This delicate carbon balance is influenced by the activity of belowground microbial communities that return carbon dioxide and methane to the atmosphere. Wetland restoration efforts in the San Francisco Bay-Delta region may help to reverse land subsidence and possibly increase carbon storage in soils. However, the effects of wetland restoration on microbial communities, which mediate soil metabolic activity and carbon cycling, are poorly studied. In an effort to better understand the underlying factors which shape the balance of carbon flux in wetland soils, we targeted the microbial communities in a suite of restored and historic wetlands in the San Francisco Bay-Delta region. Using DNA and RNA sequencing, coupled with greenhouse gas monitoring, we profiled the diversity and metabolic potential of the wetland soil microbial communities along biogeochemical and wetland age gradients. Our results show relationships among geochemical gradients, availability of electron acceptors, and microbial community composition. Our study provides the first genomic glimpse into microbial populations in natural and restored wetlands of the San Francisco Bay-Delta region and provides a valuable benchmark for future studies.

Measurement and characteristics of microbial biomass in forest soils

International Nuclear Information System (INIS)

Vance, E.D.

1986-01-01

The soil microbial biomass is the primary agent responsible for the breakdown and mineralization of soil organic matter and plays a major role in regulating nutrient availability to plants. In this study, methods for measuring biomass in soil were compared and tested in forest soils ranging in pH from 3.2 to 7.2. A good relationship between biomass C measured using the chloroform fumigation-incubation method and soil ATP or microbial biomass C by direct microscopy was found in soils at or above pH 4.2. The fumigation-incubation method consistently underestimated biomass C in soils below pH 4.2, however. Hypotheses for the breakdown of the fumigation-incubation method in strongly acid soils were tested by using an alterative fumigant, measuring the proportion of added 14 C labelled fungi and bacteria decomposed in fumigated soils (k/sub C/), and by studying the effect of large, non-fumigated soil inocula on the flush of respiration following fumigation. These studies indicated that the failure of the method in strongly acid soils was due to inhibited decomposition of non-microbial soil organic matter by the microbial recolonizing population following fumigation. A modified method for measuring biomass C by fumigation-incubation in acid soils is proposed

An overview of field-specific designs of microbial EOR

Energy Technology Data Exchange (ETDEWEB)

Robertson, E.P.; Bala, G.A.; Fox, S.L.; Jackson, J.D.; Thomas, C.P. [Idaho National Engineering Lab., Idaho Falls, ID (United States)

1995-12-31

The selection and design of an MEOR process for application in a specific field involves geological, reservoir, and biological characterization. Microbially mediated oil recovery mechanisms (bigenic gas, biopolymers, and biosurfactants) are defined by the types of microorganisms used. The engineering and biological character of a given reservoir must be understood to correctly select a microbial system to enhance oil recovery. This paper discusses the methods used to evaluate three fields with distinct characteristics and production problems for the applicability of MEOR would not be applicable in two of the three fields considered. The development of a microbial oil recovery process for the third field appeared promising. Development of a bacterial consortium capable of producing the desired metabolites was initiated, and field isolates were characterized.

Microbial lipases: Production, properties and biotechnological applications

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Josana Maria Messias

2011-09-01

Full Text Available Lipases belong to the group of hydrolases that catalyze the hydrolysis of triacylglycerol lipids to free fatty acids and glycerol. They have significant potential biotechnological applications in catalyzing organic synthesis reactions in non-aqueous solvents using simplified procedures resulting in conversions of high yields. Lipase production has conventionally been performed by submerged fermentation; however, solid-state fermentation processes have been prominent when residues are used as substrates because they serve as low-cost nutrient sources. Microbial lipases can be used as additives in foods to modify and enhance organoleptic properties, as well as in detergents to hydrolyse fats in the treatment of oily effluents, and also have value for pharmaceutical, cosmetic, agrochemical, and oil chemical industries. More recently, they are used in transesterification reactions to convert plant seed oils into biodiesel. The objective of this work was to review the published literature on the production, properties and applications of microbial lipases, and its biotechnological role in producing biodiesel.

Extracellular Electron Uptake: Among Autotrophs and Mediated by Surfaces

DEFF Research Database (Denmark)

Tremblay, Pier-Luc; Angenent, Largus T.; Zhang, Tian

2017-01-01

Autotrophic microbes can acquire electrons from solid donors such as steel, other microbial cells, or electrodes. Based on this feature, bioprocesses are being developed for the microbial electrosynthesis (MES) of useful products from the greenhouse gas CO2. Extracellular electron-transfer mechan......Autotrophic microbes can acquire electrons from solid donors such as steel, other microbial cells, or electrodes. Based on this feature, bioprocesses are being developed for the microbial electrosynthesis (MES) of useful products from the greenhouse gas CO2. Extracellular electron......; or (iii) mediator-generating enzymes detached from cells. This review explores the interactions of autotrophs with solid electron donors and their importance in nature and for biosustainable technologies....

Bottom-up nutrient and top-down fish impacts on insect-mediated mercury flux from aquatic ecosystems.

Science.gov (United States)

Jones, Taylor A; Chumchal, Matthew M; Drenner, Ray W; Timmins, Gabrielle N; Nowlin, Weston H

2013-03-01

Methyl mercury (MeHg) is one of the most hazardous contaminants in the environment, adversely affecting the health of wildlife and humans. Recent studies have demonstrated that aquatic insects biotransport MeHg and other contaminants to terrestrial consumers, but the factors that regulate the flux of MeHg out of aquatic ecosystems via emergent insects have not been studied. The authors used experimental mesocosms to test the hypothesis that insect emergence and the associated flux of MeHg from aquatic to terrestrial ecosystems is affected by both bottom-up nutrient effects and top-down fish consumer effects. In the present study, nutrient addition led to an increase in MeHg flux primarily by enhancing the biomass of emerging insects whose tissues were contaminated with MeHg, whereas fish decreased MeHg flux primarily by reducing the biomass of emerging insects. Furthermore, the authors found that these factors are interdependent such that the effects of nutrients are more pronounced when fish are absent, and the effects of fish are more pronounced when nutrient concentrations are high. The present study is the first to demonstrate that the flux of MeHg from aquatic to terrestrial ecosystems is strongly enhanced by bottom-up nutrient effects and diminished by top-down consumer effects. Copyright © 2012 SETAC.

Aerobic carbon-cycle related microbial communities in boreal peatlands: responses to water-level drawdown

Energy Technology Data Exchange (ETDEWEB)

Peltoniemi, K

2010-07-01

Boreal peatlands represent a considerable portion of the global carbon (C) pool. Water-level drawdown (WLD) causes peatland drying and induces a vegetation change, which affects the decomposition of soil organic matter and the release of greenhouse gases (CO{sub 2} and CH{sub 4}). The objective of this thesis was to study the microbial communities related to the C cycle and their response to WLD in two boreal peatlands. Both sampling depth and site type had a strong impact on all microbial communities. In general, bacteria dominated the deeper layers of the nutrient-rich fen and the wettest surfaces of the nutrient-poor bog sites, whereas fungi seemed more abundant in the drier surfaces of the bog. WLD clearly affected the microbial communities but the effect was dependent on site type. The fungal and methane-oxidizing bacteria (MOB) community composition changed at all sites but the actinobacterial community response was apparent only in the fen after WLD. Microbial communities became more similar among sites after long-term WLD. Litter quality had a large impact on community composition, whereas the effects of site type and WLD were relatively minor. The decomposition rate of fresh organic matter was influenced slightly by actinobacteria, but not at all by fungi. Field respiration measurements in the northern fen indicated that WLD accelerates the decomposition of soil organic matter. In addition, a correlation between activity and certain fungal sequences indicated that community composition affects the decomposition of older organic matter in deeper peat layers. WLD had a negative impact on CH{sub 4} oxidation, especially in the oligotrophic fen. Fungal sequences were matched to taxa capable of utilizing a broad range of substrates. Most of the actinobacterial sequences could not be matched to characterized taxa in reference databases. This thesis represents the first investigation of microbial communities and their response to WLD among a variety of boreal

Metal-macrofauna interactions determine microbial community structure and function in copper contaminated sediments.

Science.gov (United States)

Mayor, Daniel J; Gray, Nia B; Elver-Evans, Joanna; Midwood, Andrew J; Thornton, Barry

2013-01-01

Copper is essential for healthy cellular functioning, but this heavy metal quickly becomes toxic when supply exceeds demand. Marine sediments receive widespread and increasing levels of copper contamination from antifouling paints owing to the 2008 global ban of organotin-based products. The toxicity of copper will increase in the coming years as seawater pH decreases and temperature increases. We used a factorial mesocosm experiment to investigate how increasing sediment copper concentrations and the presence of a cosmopolitan bioturbating amphipod, Corophium volutator, affected a range of ecosystem functions in a soft sediment microbial community. The effects of copper on benthic nutrient release, bacterial biomass, microbial community structure and the isotopic composition of individual microbial membrane [phospholipid] fatty acids (PLFAs) all differed in the presence of C. volutator. Our data consistently demonstrate that copper contamination of global waterways will have pervasive effects on the metabolic functioning of benthic communities that cannot be predicted from copper concentrations alone; impacts will depend upon the resident macrofauna and their capacity for bioturbation. This finding poses a major challenge for those attempting to manage the impacts of copper contamination on ecosystem services, e.g. carbon and nutrient cycling, across different habitats. Our work also highlights the paucity of information on the processes that result in isotopic fractionation in natural marine microbial communities. We conclude that the assimilative capacity of benthic microbes will become progressively impaired as copper concentrations increase. These effects will, to an extent, be mitigated by the presence of bioturbating animals and possibly other processes that increase the influx of oxygenated seawater into the sediments. Our findings support the move towards an ecosystem approach for environmental management.

Metal-macrofauna interactions determine microbial community structure and function in copper contaminated sediments.

Directory of Open Access Journals (Sweden)

Daniel J Mayor

Full Text Available Copper is essential for healthy cellular functioning, but this heavy metal quickly becomes toxic when supply exceeds demand. Marine sediments receive widespread and increasing levels of copper contamination from antifouling paints owing to the 2008 global ban of organotin-based products. The toxicity of copper will increase in the coming years as seawater pH decreases and temperature increases. We used a factorial mesocosm experiment to investigate how increasing sediment copper concentrations and the presence of a cosmopolitan bioturbating amphipod, Corophium volutator, affected a range of ecosystem functions in a soft sediment microbial community. The effects of copper on benthic nutrient release, bacterial biomass, microbial community structure and the isotopic composition of individual microbial membrane [phospholipid] fatty acids (PLFAs all differed in the presence of C. volutator. Our data consistently demonstrate that copper contamination of global waterways will have pervasive effects on the metabolic functioning of benthic communities that cannot be predicted from copper concentrations alone; impacts will depend upon the resident macrofauna and their capacity for bioturbation. This finding poses a major challenge for those attempting to manage the impacts of copper contamination on ecosystem services, e.g. carbon and nutrient cycling, across different habitats. Our work also highlights the paucity of information on the processes that result in isotopic fractionation in natural marine microbial communities. We conclude that the assimilative capacity of benthic microbes will become progressively impaired as copper concentrations increase. These effects will, to an extent, be mitigated by the presence of bioturbating animals and possibly other processes that increase the influx of oxygenated seawater into the sediments. Our findings support the move towards an ecosystem approach for environmental management.

Soil microbial community successional patterns during forest ecosystem restoration.

Science.gov (United States)

Banning, Natasha C; Gleeson, Deirdre B; Grigg, Andrew H; Grant, Carl D; Andersen, Gary L; Brodie, Eoin L; Murphy, D V

2011-09-01

Soil microbial community characterization is increasingly being used to determine the responses of soils to stress and disturbances and to assess ecosystem sustainability. However, there is little experimental evidence to indicate that predictable patterns in microbial community structure or composition occur during secondary succession or ecosystem restoration. This study utilized a chronosequence of developing jarrah (Eucalyptus marginata) forest ecosystems, rehabilitated after bauxite mining (up to 18 years old), to examine changes in soil bacterial and fungal community structures (by automated ribosomal intergenic spacer analysis [ARISA]) and changes in specific soil bacterial phyla by 16S rRNA gene microarray analysis. This study demonstrated that mining in these ecosystems significantly altered soil bacterial and fungal community structures. The hypothesis that the soil microbial community structures would become more similar to those of the surrounding nonmined forest with rehabilitation age was broadly supported by shifts in the bacterial but not the fungal community. Microarray analysis enabled the identification of clear successional trends in the bacterial community at the phylum level and supported the finding of an increase in similarity to nonmined forest soil with rehabilitation age. Changes in soil microbial community structure were significantly related to the size of the microbial biomass as well as numerous edaphic variables (including pH and C, N, and P nutrient concentrations). These findings suggest that soil bacterial community dynamics follow a pattern in developing ecosystems that may be predictable and can be conceptualized as providing an integrated assessment of numerous edaphic variables.

Mineral vs. organic amendments: microbial community structure, activity and abundance of agriculturally relevant microbes are driven by long-term fertilization strategies

Directory of Open Access Journals (Sweden)

Davide Francioli

2016-09-01

Full Text Available Soil management is fundamental to all agricultural systems and fertilization practices have contributed substantially to the impressive increases in food production. Despite the pivotal role of soil microorganisms in agro-ecosystems, we still have a limited understanding of the complex response of the soil microbiota to organic and mineral fertilization in the very long-term. Here we report the effects of different fertilization regimes (mineral, organic and combined mineral and organic fertilization, carried out for more than a century, on the structure and activity of the soil microbiome. Organic matter content, nutrient concentrations and microbial biomass carbon were significantly increased by mineral, and even more strongly by organic fertilization. Pyrosequencing revealed significant differences between the structures of bacterial and fungal soil communities associated to each fertilization regime. Organic fertilization increased bacterial diversity, and stimulated microbial groups (Firmicutes, Proteobacteria and Zygomycota that are known to prefer nutrient-rich environments, and that are involved in the degradation of complex organic compounds. In contrast, soils not receiving manure harbored distinct microbial communities enriched in oligotrophic organisms adapted to nutrient-limited environments, as Acidobacteria. The fertilization regime also affected the relative abundances of plant beneficial and detrimental microbial taxa, which may influence productivity and stability of the agroecosystem. As expected, the activity of microbial exoenzymes involved in carbon, nitrogen and phosphorous mineralization were enhanced by both types of fertilization. However, in contrast to comparable studies, the highest chitinase and phosphatase activities were observed in the solely mineral fertilized soil. Interestingly, these two enzymes showed also a particular high biomass-specific activities and a strong negative relation with soil pH. As many soil

Electron transfer mechanisms, new applications, and performance of biocathode microbial fuel cells

KAUST Repository

Huang, Liping; Regan, John M.; Quan, Xie

2011-01-01

Broad application of microbial fuel cells (MFCs) requires low cost and high operational sustainability. Microbial-cathode MFCs, or cathodes using only bacterial catalysts (biocathodes), can satisfy these demands and have gained considerable attention in recent years. Achievements with biocathodes over the past 3-4. years have been particularly impressive not only with respect to the biological aspects but also the system-wide considerations related to electrode materials and solution chemistry. The versatility of biocathodes enables us to use not only oxygen but also contaminants as possible electron acceptors, allowing nutrient removal and bioremediation in conjunction with electricity generation. Moreover, biocathodes create opportunities to convert electrical current into microbially generated reduced products. While many new experimental results with biocathodes have been reported, we are still in the infancy of their engineering development. This review highlights the opportunities, limits, and challenges of biocathodes. © 2010 Elsevier Ltd.

The Stoichiometry of Nutrient Release by Terrestrial Herbivores and Its Ecosystem Consequences

Directory of Open Access Journals (Sweden)

Judith Sitters

2017-04-01

Full Text Available It is widely recognized that the release of nutrients by herbivores via their waste products strongly impacts nutrient availability for autotrophs. The ratios of nitrogen (N and phosphorus (P recycled through herbivore release (i.e., waste N:P are mainly determined by the stoichiometric composition of the herbivore's food (food N:P and its body nutrient content (body N:P. Waste N:P can in turn impact autotroph nutrient limitation and productivity. Herbivore-driven nutrient recycling based on stoichiometric principles is dominated by theoretical and experimental research in freshwater systems, in particular interactions between algae and invertebrate herbivores. In terrestrial ecosystems, the impact of herbivores on nutrient cycling and availability is often limited to studying carbon (C:N and C:P ratios, while the role of terrestrial herbivores in mediating N:P ratios is also likely to influence herbivore-driven nutrient recycling. In this review, we use rules and predictions on the stoichiometry of nutrient release originating from algal-based aquatic systems to identify the factors that determine the stoichiometry of nutrient release by herbivores. We then explore how these rules can be used to understand the stoichiometry of nutrient release by terrestrial herbivores, ranging from invertebrates to mammals, and its impact on plant nutrient limitation and productivity. Future studies should focus on measuring both N and P when investigating herbivore-driven nutrient recycling in terrestrial ecosystems, while also taking the form of waste product (urine or feces and other pathways by which herbivores change nutrients into account, to be able to quantify the impact of waste stoichiometry on plant communities.

Switchgrass ecotypes alter microbial contribution to deep-soil C

Science.gov (United States)

Roosendaal, Damaris; Stewart, Catherine E.; Denef, Karolien; Follett, Ronald F.; Pruessner, Elizabeth; Comas, Louise H.; Varvel, Gary E.; Saathoff, Aaron; Palmer, Nathan; Sarath, Gautam; Jin, Virginia L.; Schmer, Marty; Soundararajan, Madhavan

2016-05-01

Switchgrass (Panicum virgatum L.) is a C4, perennial grass that is being developed as a bioenergy crop for the United States. While aboveground biomass production is well documented for switchgrass ecotypes (lowland, upland), little is known about the impact of plant belowground productivity on microbial communities down deep in the soil profiles. Microbial dynamics in deeper soils are likely to exert considerable control on ecosystem services, including C and nutrient cycles, due to their involvement in such processes as soil formation and ecosystem biogeochemistry. Differences in root biomass and rooting characteristics of switchgrass ecotypes could lead to distinct differences in belowground microbial biomass and microbial community composition. We quantified root abundance and root architecture and the associated microbial abundance, composition, and rhizodeposit C uptake for two switchgrass ecotypes using stable-isotope probing of microbial phospholipid fatty acids (PLFAs) after 13CO2 pulse-chase labeling. Kanlow, a lowland ecotype with thicker roots, had greater plant biomass above- and belowground (g m-2), greater root mass density (mg cm-3), and lower specific root length (m g-1) compared to Summer, an upland ecotype with finer root architecture. The relative abundance of bacterial biomarkers dominated microbial PLFA profiles for soils under both Kanlow and Summer (55.4 and 53.5 %, respectively; P = 0.0367), with differences attributable to a greater relative abundance of Gram-negative bacteria in soils under Kanlow (18.1 %) compared to soils under Summer (16.3 %; P = 0.0455). The two ecotypes also had distinctly different microbial communities process rhizodeposit C: greater relative atom % 13C excess in Gram-negative bacteria (44.1 ± 2.3 %) under the thicker roots of Kanlow and greater relative atom % 13C excess in saprotrophic fungi under the thinner roots of Summer (48.5 ± 2.2 %). For bioenergy production systems, variation between switchgrass

Biochar-enhanced composts reduce the potential leaching of nutrients and heavy metals and suppress plant-parasitic nematodes in excessively fertilized cucumber soils.

Science.gov (United States)

Cao, Yune; Gao, Yanming; Qi, Yanbin; Li, Jianshe

2018-03-01

Excessive fertilization is a common agricultural practice that has largely reduced soil nutrient retention capacity and led to nutrient leaching in China. To reduce nutrient leaching, in this study, we evaluated the application of biochar, compost, and biochar-compost on soil properties, leaching water quality, and cucumber plant growth in soils with different nutrient levels. In general, the concentrations of nutrients and heavy metals in leaching water were higher under high-nutrient conditions than under low-nutrient conditions. Both biochar and compost efficiently enhanced soil cation exchange capacity (CEC), water holding capacity (WHC), and microbial biomass carbon (MBC), nitrogen (MBN), and phosphorus (MBP), reduced the potential leaching of nutrients and heavy metals, and improved plant growth. The efficiency of biochar and compost in soil CEC, WHC, MBC, MBN, and MBP and plant growth was enhanced when applied jointly. In addition, biochar and biochar-enhanced compost efficiently suppressed plant-parasitic nematode infestation in a soil with high levels of both N and P. Our results suggest that biochar-enhanced compost can reduce the potential environmental risks in excessively fertilized vegetable soils.

Microbial Gas Generation Under Expected Waste Isolation Pilot Plant Repository Conditions: Final Report

International Nuclear Information System (INIS)

Gillow, J.B.; Francis, A.

2011-01-01

Gas generation from the microbial degradation of the organic constituents of transuranic (TRU) waste under conditions expected in the Waste Isolation Pilot Plant (WIPP) was investigated. The biodegradation of mixed cellulosic materials and electron-beam irradiated plastic and rubber materials (polyethylene, polyvinylchloride, hypalon, leaded hypalon, and neoprene) was examined. We evaluated the effects of environmental variables such as initial atmosphere (air or nitrogen), water content (humid (∼70% relative humidity, RH) and brine inundated), and nutrient amendments (nitogen phosphate, yeast extract, and excess nitrate) on microbial gas generation. Total gas production was determined by pressure measurement and carbon dioxide (CO 2 ) and methane (CH 4 ) were analyzed by gas chromatography; cellulose degradation products in solution were analyzed by high-performance liquid chromatography. Microbial populations in the samples were determined by direct microscopy and molecular analysis. The results of this work are summarized.

Microbial Nitrogen-Cycle Gene Abundance in Soil of Cropland Abandoned for Different Periods.

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Huhe

Full Text Available In Inner Mongolia, steppe grasslands face desertification or degradation because of human overuse and abandonment after inappropriate agricultural management. The soils in these abandoned croplands exist in heterogeneous environments characterized by widely fluctuating microbial growth. Quantitative polymerase chain reaction analysis of microbial genes encoding proteins involved in the nitrogen cycle was used to study Azotobacter species, nitrifiers, and denitrifiers in the soils from steppe grasslands and croplands abandoned for 2, 6, and 26 years. Except for nitrifying archaea and nitrous oxide-reducing bacteria, the relative genotypic abundance of microbial communities involved in nitrogen metabolism differed by approximately 2- to 10-fold between abandoned cropland and steppe grassland soils. Although nitrogen-cycle gene abundances varied with abandonment time, the abundance patterns of nitrogen-cycle genes separated distinctly into abandoned cropland versus light-grazing steppe grassland, despite the lack of any cultivation for over a quarter-century. Plant biomass and plant diversity exerted a significant effect on the abundance of microbial communities that mediate the nitrogen cycle (P < 0.002 and P < 0.03, respectively. The present study elucidates the ecology of bacteria that mediate the nitrogen cycle in recently abandoned croplands.

Soil Rhizosphere Microbial Communities and Enzyme Activities under Organic Farming in Alabama

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Zachary Senwo

2011-07-01

Full Text Available Evaluation of the soil rhizosphere has been limited by the lack of robust assessments that can explore the vast complex structure and diversity of soil microbial communities. Our objective was to combine fatty acid methyl ester (FAME and pyrosequencing techniques to evaluate soil microbial community structure and diversity. In addition, we evaluated biogeochemical functionality of the microbial communities via enzymatic activities of nutrient cycling. Samples were taken from a silt loam at 0–10 and 10–20 cm in an organic farm under lettuce (Lactuca sativa, potato (Solanum tuberosum, onion (Allium cepa L, broccoli (Brassica oleracea var. botrytis and Tall fescue pasture grass (Festuca arundinacea. Several FAMEs (a15:0, i15:0, i15:1, i16:0, a17:0, i17:0, 10Me17:0, cy17:0, 16:1ω5c and 18:1ω9c varied among the crop rhizospheres. FAME profiles of the soil microbial community under pasture showed a higher fungal:bacterial ratio compared to the soil under lettuce, potato, onion, and broccoli. Soil under potato showed higher sum of fungal FAME indicators compared to broccoli, onion and lettuce. Microbial biomass C and enzyme activities associated with pasture and potato were higher than the other rhizospheres. The lowest soil microbial biomass C and enzyme activities were found under onion. Pyrosequencing revealed significant differences regarding the maximum operational taxonomic units (OTU at 3% dissimilarity level (roughly corresponding to the bacterial species level at 0–10 cm (581.7–770.0 compared to 10–20 cm (563.3–727.7 soil depths. The lowest OTUs detected at 0–10 cm were under broccoli (581.7; whereas the lowest OTUs found at 10–20 cm were under potato (563.3. The predominant phyla (85% in this soil at both depths were Bacteroidetes (i.e., Flavobacteria, Sphingobacteria, and Proteobacteria. Flavobacteriaceae and Xanthomonadaceae were predominant under broccoli. Rhizobiaceae, Hyphomicrobiaceae, and Acidobacteriaceae were more

Comparison of seasonal soil microbial process in snow-covered temperate ecosystems of northern China.

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Xinyue Zhang

Full Text Available More than half of the earth's terrestrial surface currently experiences seasonal snow cover and soil frost. Winter compositional and functional investigations in soil microbial community are frequently conducted in alpine tundra and boreal forest ecosystems. However, little information on winter microbial biogeochemistry is known from seasonally snow-covered temperate ecosystems. As decomposer microbes may differ in their ability/strategy to efficiently use soil organic carbon (SOC within different phases of the year, understanding seasonal microbial process will increase our knowledge of biogeochemical cycling from the aspect of decomposition rates and corresponding nutrient dynamics. In this study, we measured soil microbial biomass, community composition and potential SOC mineralization rates in winter and summer, from six temperate ecosystems in northern China. Our results showed a clear pattern of increased microbial biomass C to nitrogen (N ratio in most winter soils. Concurrently, a shift in soil microbial community composition occurred with higher fungal to bacterial biomass ratio and gram negative (G- to gram positive (G+ bacterial biomass ratio in winter than in summer. Furthermore, potential SOC mineralization rate was higher in winter than in summer. Our study demonstrated a distinct transition of microbial community structure and function from winter to summer in temperate snow-covered ecosystems. Microbial N immobilization in winter may not be the major contributor for plant growth in the following spring.

Conditioning biomass for microbial growth

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Bodie, Elizabeth A; England, George

2015-03-31

The present invention relates to methods for improving the yield of microbial processes that use lignocellulose biomass as a nutrient source. The methods comprise conditioning a composition comprising lignocellulose biomass with an enzyme composition that comprises a phenol oxidizing enzyme. The conditioned composition can support a higher rate of growth of microorganisms in a process. In one embodiment, a laccase composition is used to condition lignocellulose biomass derived from non-woody plants, such as corn and sugar cane. The invention also encompasses methods for culturing microorganisms that are sensitive to inhibitory compounds in lignocellulose biomass. The invention further provides methods of making a product by culturing the production microorganisms in conditioned lignocellulose biomass.

Microbial population changes during bioremediation of an experimental oil spill

International Nuclear Information System (INIS)

MacNaughton, S.J.; Stephen, J.R.; Chang, Y.J.; Davis, G.A.; White, D.C.; Oak Ridge National Lab., TN

1999-01-01

Three crude oil bioremediation techniques were applied in a randomized block field experiment simulating a coastal oil spill. Four treatments (no oil control, oil alone, oil plus nutrients, and oil plus nutrients plus an indigenous inoculum) were applied. In situ microbial community structures were monitored by phospholipid fatty acid (PLFA) analysis and 16S rDNA PCR-denaturing gradient gel electrophoresis (DGGE) to (i) identify the bacterial community members responsible for the decontamination of the site and (ii) define an end point for the removal of the hydrocarbon substrate. The results of PLFA analysis demonstrated a community shift in all plots from primarily eukaryotic biomass to gram-negative bacterial biomass with time. PLFA profiles from the oiled plots suggested increased gram-negative biomass and adaptation to metabolic stress compared to unoiled controls. DGGE analysis of untreated control plots revealed a simple, dynamic dominant population structure throughout the experiment. This banding pattern disappeared in all oiled plots, indicating that the structure and diversity of the dominant bacterial community changed substantially. No consistent differences were detected between nutrient-amended and indigenous inoculum-treated plots, but both differed from the oil-only plots. Prominent bands were excised for sequence analysis and indicated that oil treatment encouraged the growth of gram-negative microorganisms within the α-proteobacteria and Flexibacter-Cytophaga-Bacteroides phylum. α-Proteobacteria were never detected in unoiled controls. PLFA analysis indicated that by week 14 the microbial community structures of the oiled plots were becoming similar to those of the unoiled controls from the same time point, but DGGE analysis suggested that major differences in the bacterial communities remained

Mineralogical controls on surface colonization by sulfur-metabolizing microbial communities

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Jones, A. A.; Bennett, P.

2012-12-01

When characterizing microbial diversity and the microbial ecosystem of the shallow subsurface the mineral matrix is generally assumed to be homogenous and unreactive. We report here experimental evidence that microorganisms colonize rock surfaces according to the rock's chemistry and the organism's metabolic requirements and tolerances. We investigated this phenomenon using laboratory biofilm reactors with both a pure culture of sulfur-oxidizing Thiothrix unzii and a mixed environmental sulfur-metabolizing community from Lower Kane, Cave, WY, USA. Reactors contained rock and mineral chips (calcite, albite, microcline, quartz, chert, Madison Limestone (ML), Madison Dolostone (MD), and basalt) amended with one of the two inoculants. Biomass of attached microorganisms on each mineral surface was quantified. The 16S rRNA of attached microbial communities were compared using Roche FLX and Titanium 454 next generation pyrosequencing. A primary controlling factor on taxonomy of attached microorganisms in both pure and mixed culture experiments was mineral buffering capacity. In mixed culture experiments acid-buffering carbonates were preferentially colonized by neutrophilic sulfur-oxidizing microorganisms (~18% to ~27% of microorganisms), while acidophilic sulfur-oxidizing microorganisms colonized non-buffering quartz exclusively (~46% of microorganisms). The nutrient content of the rock was a controlling factor on biomass accumulation, with neutrophilic organisms selecting between carbonate surfaces of equivalent buffer capacities according to the availability of phosphate. Dry biomass on ML was 17.8 ± 2.3 mg/cm2 and MD was 20.6 ± 6.8 mg/cm2; while nutrient poor calcite accumulated 2.4 ± 0.3 mg/cm2. Biomass accumulation was minimal on non-buffering nutrient-limited surfaces. These factors are countered by the competitive exclusion of some populations. A pure culture of T. unzii preferentially colonizes carbonates while a very closely related Thiothrix spp is excluded

Novel approaches to microbial enhancement of oil recovery.

Science.gov (United States)

Kryachko, Yuriy

2018-01-20

Microbially enhanced oil recovery (MEOR) was shown to be feasible in a number of laboratory experiments and field trials. However, it has not been widely used in the oil industry because necessary conditions cannot always be easily established in an oil reservoir. Novel approaches to MEOR, which are based on newly discovered biosurfactant-mediated MEOR-mechanisms, are discussed in this review. Particularly, the possibility of combining MEOR with chemical enhancement of oil recovery in heterogeneous oil reservoirs, which involves rock surface wettability shifts and emulsion inversions, is discussed. In wider (centimeter/millimeter-scale) rock pores, the activity of (bio)surfactants and microbial cells attached to oil may allow releasing trapped oil blobs through oil-in-water emulsification. After no more oil can be emulsified, the addition of alkali or surfactants, which turn rock surface oil-wet, may help release oil droplets trapped in narrow (micrometer-scale) pores through coalescence of the droplets and water-in-oil emulsification. Experiments demonstrating the possibility of (bio)surfactant-mediated enhancement of immiscible gas-driven oil recovery are also reviewed. Interestingly, very low (bio)surfactant concentrations were shown to be needed for enhancement of immiscible gas-driven oil recovery. Some possible side effects of MEOR, such as unintended bioplugging and microbially influenced corrosion (MIC), are discussed as well. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

Current state of knowledge in microbial degradation of polycyclic aromatic hydrocarbons (PAHs: a review

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Debajyoti Ghosal

2016-08-01

Full Text Available Polycyclic aromatic hydrocarbons (PAHs include a group of organic priority pollutants of critical environmental and public health concern due to their toxic, genotoxic, mutagenic and/or carcinogenic properties and their ubiquitous occurrence as well as recalcitrance. The increased awareness of their various adverse effects on ecosystem and human health has led to a dramatic increase in research aimed towards removing PAHs from the environment. PAHs may undergo adsorption, volatilization, photolysis, and chemical oxidation, although transformation by microorganisms is the major neutralization process of PAH-contaminated sites in an ecologically accepted manner. Microbial degradation of PAHs depends on various environmental conditions, such as nutrients, number and kind of the microorganisms, nature as well as chemical property of the PAH being degraded. A wide variety of bacterial, fungal and algal species have the potential to degrade/transform PAHs, among which bacteria and fungi mediated degradation has been studied most extensively. In last few decades microbial community analysis, biochemical pathway for PAHs degradation, gene organization, enzyme system, genetic regulation for PAH degradation have been explored in great detail. Although, xenobiotic-degrading microorganisms have incredible potential to restore contaminated environments inexpensively yet effectively, but new advancements are required to make such microbes effective and more powerful in removing those compounds, which were once thought to be recalcitrant. Recent analytical chemistry and genetic engineering tools might help to improve the efficiency of degradation of PAHs by microorganisms, and minimize uncertainties of successful bioremediation. However, appropriate implementation of the potential of naturally occurring microorganisms for field bioremediation could be considerably enhanced by optimizing certain factors such as bioavailability, adsorption and mass transfer of

Current State of Knowledge in Microbial Degradation of Polycyclic Aromatic Hydrocarbons (PAHs): A Review

Science.gov (United States)

Ghosal, Debajyoti; Ghosh, Shreya; Dutta, Tapan K.; Ahn, Youngho

2016-01-01

Polycyclic aromatic hydrocarbons (PAHs) include a group of organic priority pollutants of critical environmental and public health concern due to their toxic, genotoxic, mutagenic and/or carcinogenic properties and their ubiquitous occurrence as well as recalcitrance. The increased awareness of their various adverse effects on ecosystem and human health has led to a dramatic increase in research aimed toward removing PAHs from the environment. PAHs may undergo adsorption, volatilization, photolysis, and chemical oxidation, although transformation by microorganisms is the major neutralization process of PAH-contaminated sites in an ecologically accepted manner. Microbial degradation of PAHs depends on various environmental conditions, such as nutrients, number and kind of the microorganisms, nature as well as chemical property of the PAH being degraded. A wide variety of bacterial, fungal and algal species have the potential to degrade/transform PAHs, among which bacteria and fungi mediated degradation has been studied most extensively. In last few decades microbial community analysis, biochemical pathway for PAHs degradation, gene organization, enzyme system, genetic regulation for PAH degradation have been explored in great detail. Although, xenobiotic-degrading microorganisms have incredible potential to restore contaminated environments inexpensively yet effectively, but new advancements are required to make such microbes effective and more powerful in removing those compounds, which were once thought to be recalcitrant. Recent analytical chemistry and genetic engineering tools might help to improve the efficiency of degradation of PAHs by microorganisms, and minimize uncertainties of successful bioremediation. However, appropriate implementation of the potential of naturally occurring microorganisms for field bioremediation could be considerably enhanced by optimizing certain factors such as bioavailability, adsorption and mass transfer of PAHs. The main

Microbial bioenergetics of coral-algal interactions

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Ty N.F. Roach

2017-06-01

Full Text Available Human impacts are causing ecosystem phase shifts from coral- to algal-dominated reef systems on a global scale. As these ecosystems undergo transition, there is an increased incidence of coral-macroalgal interactions. Mounting evidence indicates that the outcome of these interaction events is, in part, governed by microbially mediated dynamics. The allocation of available energy through different trophic levels, including the microbial food web, determines the outcome of these interactions and ultimately shapes the benthic community structure. However, little is known about the underlying thermodynamic mechanisms involved in these trophic energy transfers. This study utilizes a novel combination of methods including calorimetry, flow cytometry, and optical oxygen measurements, to provide a bioenergetic analysis of coral-macroalgal interactions in a controlled aquarium setting. We demonstrate that the energetic demands of microbial communities at the coral-algal interaction interface are higher than in the communities associated with either of the macroorganisms alone. This was evident through higher microbial power output (energy use per unit time and lower oxygen concentrations at interaction zones compared to areas distal from the interface. Increases in microbial power output and lower oxygen concentrations were significantly correlated with the ratio of heterotrophic to autotrophic microbes but not the total microbial abundance. These results suggest that coral-algal interfaces harbor higher proportions of heterotrophic microbes that are optimizing maximal power output, as opposed to yield. This yield to power shift offers a possible thermodynamic mechanism underlying the transition from coral- to algal-dominated reef ecosystems currently being observed worldwide. As changes in the power output of an ecosystem are a significant indicator of the current state of the system, this analysis provides a novel and insightful means to quantify

Beaver-mediated lateral hydrologic connectivity, fluvial carbon and nutrient flux, and aquatic ecosystem metabolism

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Wegener, Pam; Covino, Tim; Wohl, Ellen

2017-06-01

River networks that drain mountain landscapes alternate between narrow and wide valley segments. Within the wide segments, beaver activity can facilitate the development and maintenance of complex, multithread planform. Because the narrow segments have limited ability to retain water, carbon, and nutrients, the wide, multithread segments are likely important locations of retention. We evaluated hydrologic dynamics, nutrient flux, and aquatic ecosystem metabolism along two adjacent segments of a river network in the Rocky Mountains, Colorado: (1) a wide, multithread segment with beaver activity; and, (2) an adjacent (directly upstream) narrow, single-thread segment without beaver activity. We used a mass balance approach to determine the water, carbon, and nutrient source-sink behavior of each river segment across a range of flows. While the single-thread segment was consistently a source of water, carbon, and nitrogen, the beaver impacted multithread segment exhibited variable source-sink dynamics as a function of flow. Specifically, the multithread segment was a sink for water, carbon, and nutrients during high flows, and subsequently became a source as flows decreased. Shifts in river-floodplain hydrologic connectivity across flows related to higher and more variable aquatic ecosystem metabolism rates along the multithread relative to the single-thread segment. Our data suggest that beaver activity in wide valleys can create a physically complex hydrologic environment that can enhance hydrologic and biogeochemical buffering, and promote high rates of aquatic ecosystem metabolism. Given the widespread removal of beaver, determining the cumulative effects of these changes is a critical next step in restoring function in altered river networks.

Formation of higher plant component microbial community in closed ecological system

Science.gov (United States)

Tirranen, L. S.

2001-07-01

Closed ecological systems (CES) place at the disposal of a researcher unique possibilities to study the role of microbial communities in individual components and of the entire system. The microbial community of the higher plant component has been found to form depending on specific conditions of the closed ecosystem: length of time the solution is reused, introduction of intrasystem waste water into the nutrient medium, effect of other component of the system, and system closure in terms of gas exchange. The higher plant component formed its own microbial complex different from that formed prior to closure. The microbial complex of vegetable polyculture is more diverse and stable than the monoculture of wheat. The composition of the components' microflora changed, species diversity decreased, individual species of bacteria and fungi whose numbers were not so great before the closure prevailed. Special attention should be paid to phytopathogenic and conditionally pathogenic species of microorganisms potentially hazardous to man or plants and the least controlled in CES. This situation can endanger creation of CES and make conjectural existence of preplanned components, man, specifically, and consequently, of CES as it is.

Integrated Field, Laboratory, and Modeling Studies to Determine the Effects of Linked Microbial and Physical Spatial Heterogeneity on Engineered Vadose Zone Bioremediation

Energy Technology Data Exchange (ETDEWEB)

Fred Brokman; John Selker; Mark Rockhold

2004-01-26

While numerous techniques exist for remediation of contaminant plumes in groundwater or near the soil surface, remediation methods in the deep vadose zone are less established due to complex transport dynamics and sparse microbial populations. There is a lack of knowledge on how physical and hydrologic features of the vadose zone control microbial growth and colonization in response to nutrient delivery during bioremediation. Yet pollution in the vadose zone poses a serious threat to the groundwater resources lying deeper in the sediment. While the contaminants may be slowly degraded by native microbial communities, microbial degradation rates rarely keep pace with the spread of the pollutant. It is crucial to increase indigenous microbial degradation in the vadose zone to combat groundwater contamination.

Integrated Field, Laboratory, and Modeling Studies to Determine the Effects of Linked Microbial and Physical Spatial Heterogeneity on Engineered Vadose Zone Bioremediation

Energy Technology Data Exchange (ETDEWEB)

Brockman, Fred J.; Selker, John S.; Rockhold, Mark L.

2004-10-31

Executive Summary - While numerous techniques exist for remediation of contaminant plumes in groundwater or near the soil surface, remediation methods in the deep vadose zone are less established due to complex transport dynamics and sparse microbial populations. There is a lack of knowledge on how physical and hydrologic features of the vadose zone control microbial growth and colonization in response to nutrient delivery during bioremediation. Yet pollution in the vadose zone poses a serious threat to the groundwater resources lying deeper in the sediment. While the contaminants may be slowly degraded by native microbial communities, microbial degradation rates rarely keep pace with the spread of the pollutant. It is crucial to increase indigenous microbial degradation in the vadose zone to combat groundwater contamination...

Nutrient-dependent/pheromone-controlled adaptive evolution: a model

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James Vaughn Kohl

2013-06-01

Full Text Available Background: The prenatal migration of gonadotropin-releasing hormone (GnRH neurosecretory neurons allows nutrients and human pheromones to alter GnRH pulsatility, which modulates the concurrent maturation of the neuroendocrine, reproductive, and central nervous systems, thus influencing the development of ingestive behavior, reproductive sexual behavior, and other behaviors. Methods: This model details how chemical ecology drives adaptive evolution via: (1 ecological niche construction, (2 social niche construction, (3 neurogenic niche construction, and (4 socio-cognitive niche construction. This model exemplifies the epigenetic effects of olfactory/pheromonal conditioning, which alters genetically predisposed, nutrient-dependent, hormone-driven mammalian behavior and choices for pheromones that control reproduction via their effects on luteinizing hormone (LH and systems biology. Results: Nutrients are metabolized to pheromones that condition behavior in the same way that food odors condition behavior associated with food preferences. The epigenetic effects of olfactory/pheromonal input calibrate and standardize molecular mechanisms for genetically predisposed receptor-mediated changes in intracellular signaling and stochastic gene expression in GnRH neurosecretory neurons of brain tissue. For example, glucose and pheromones alter the hypothalamic secretion of GnRH and LH. A form of GnRH associated with sexual orientation in yeasts links control of the feedback loops and developmental processes required for nutrient acquisition, movement, reproduction, and the diversification of species from microbes to man. Conclusion: An environmental drive evolved from that of nutrient ingestion in unicellular organisms to that of pheromone-controlled socialization in insects. In mammals, food odors and pheromones cause changes in hormones such as LH, which has developmental affects on pheromone-controlled sexual behavior in nutrient-dependent reproductively

Status of microbial diversity in agroforestry systems in Tamil Nadu, India.

Science.gov (United States)

Radhakrishnan, Srinivasan; Varadharajan, Mohan

2016-06-01

Soil is a complex and dynamic biological system. Agroforestry systems are considered to be an alternative land use option to help and prevent soil degradation, improve soil fertility, microbial diversity, and organic matter status. An increasing interest has emerged with respect to the importance of microbial diversity in soil habitats. The present study deals with the status of microbial diversity in agroforestry systems in Tamil Nadu. Eight soil samples were collected from different fields in agroforestry systems in Cuddalore, Villupuram, Tiruvanamalai, and Erode districts, Tamil Nadu. The number of microorganisms and physico-chemical parameters of soils were quantified. Among different microbial population, the bacterial population was recorded maximum (64%), followed by actinomycetes (23%) and fungi (13%) in different samples screened. It is interesting to note that the microbial population was positively correlated with the physico-chemical properties of different soil samples screened. Total bacterial count had positive correlation with soil organic carbon (C), moisture content, pH, nitrogen (N), and micronutrients such as Iron (Fe), copper (Cu), and zinc (Zn). Similarly, the total actinomycete count also showed positive correlations with bulk density, moisture content, pH, C, N, phosphorus (P), potassium (K), calcium (Ca), copper (Cu), magnesium (Mg), manganese (Mn), and zinc (Zn). It was also noticed that the soil organic matter, vegetation, and soil nutrients altered the microbial community under agroforestry systems. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Experimental drought induces short-term changes in soil functionality and microbial community structure after fire in a Mediterranean shrubland

Science.gov (United States)

Hinojosa, M. B.; Parra, A.; Laudicina, V. A.; Moreno, J. M.

2014-10-01

Fire is a major ecosystem driver, causing significant changes in soil nutrients and microbial community structure and functionality. Post-fire soil dynamics can vary depending on rainfall patterns, although variations in response to drought are poorly known. This is particularly important in areas with poor soils and limited rainfall, like arid and semiarid ones. Furthermore, climate change projections in many such areas anticipate reduced precipitation and longer drought, together with an increase in fire severity. The effects of experimental drought and fire were studied on soils in a Mediterranean Cistus-Erica shrubland in Central Spain. A replicated (n = 4) field experiment was carried out in which four levels of rainfall pattern were implemented by means of a rain-out shelters and irrigation system. The treatments were: environmental control (natural rainfall), historical control (long-term average rainfall, 2 months drought), moderate drought (25% reduction of historical control, 5 months drought) and severe drought (45% reduction, 7 months drought). After one growing season, the plots were burned with high fire intensity, except a set of unburned plots that served as control. Soils were collected seasonally during one year and variables related to soil nutrient availability and microbial community structure and functionality were studied. Burned soils increased nutrient availability (P, N, K) with respect to unburned ones, but drought reduced such an increase in P, while it further increased N and K. Such changes in available soil nutrients were short-lived. Drought caused a further decrease of enzyme activities, carbon mineralization rate and microbial biomass. Fire decreased the relative abundance of fungi and actinomycetes. However, fire and drought caused a further reduction in fungi, with bacteria becoming relatively more abundant. Arguably, increasing drought and fires due to climate change will likely shift soil recovery after fire.

Microbial hotspots and hot moments in soil

Science.gov (United States)

Kuzyakov, Yakov; Blagodatskaya, Evgenia

2015-04-01

increases in C stocks. Consequently, the intensification of fluxes is much stronger than the increase of pools. Maintenance of stoichiometric ratios by accelerated microbial growth in hotspots requires additional nutrients (e.g. N and P), causing their microbial mining from soil organic matter, i.e. priming effects. Consequently, priming effects are localized in microbial hotspots and are consequences of hot moments. Finally, we estimated the contribution of the hotspots to the whole soil profile and suggested that, irrespective of their volume, the hotspots are mainly responsible for the ecologically relevant processes in soil.

Short- and long-term effects of nutrient enrichment on microbial exoenzyme activity in mangrove peat

KAUST Repository

Keuskamp, Joost A.; Feller, Ilka C.; Laanbroek, Hendrikus J.; Verhoeven, Jos T.A.; Hefting, Mariet M.

2015-01-01

-limited mangroves. To examine this, we quantified the short- and long-term effects of N and P enrichment on microbial biomass and decomposition-related enzyme activities in a Rhizophora mangle-dominated mangrove, which had been subjected to fertilisation treatments

Extracellular Saccharide-Mediated Reduction of Au3+ to Gold Nanoparticles: New Insights for Heavy Metals Biomineralization on Microbial Surfaces.

Science.gov (United States)

Kang, Fuxing; Qu, Xiaolei; Alvarez, Pedro J J; Zhu, Dongqiang

2017-03-07

Biomineralization is a critical process controlling the biogeochemical cycling, fate, and potential environmental impacts of heavy metals. Despite the indispensability of extracellular polymeric substances (EPS) to microbial life and their ubiquity in soil and aquatic environments, the role played by EPS in the transformation and biomineralization of heavy metals is not well understood. Here, we used gold ion (Au 3+ ) as a model heavy metal ion to quantitatively assess the role of EPS in biomineralization and discern the responsible functional groups. Integrated spectroscopic analyses showed that Au 3+ was readily reduced to zerovalent gold nanoparticles (AuNPs, 2-15 nm in size) in aqueous suspension of Escherichia coli or dissolved EPS extracted from microbes. The majority of AuNPs (95.2%) was formed outside Escherichia coli cells, and the removal of EPS attached to cells pronouncedly suppressed Au 3+ reduction, reflecting the predominance of the extracellular matrix in Au 3+ reduction. XPS, UV-vis, and FTIR analyses corroborated that Au 3+ reduction was mediated by the hemiacetal groups (aldehyde equivalents) of reducing saccharides of EPS. Consistently, the kinetics of AuNP formation obeyed pseudo-second-order reaction kinetics with respect to the concentrations of Au 3+ and the hemiacetal groups in EPS, with minimal dependency on the source of microbial EPS. Our findings indicate a previously overlooked, universally significant contribution of EPS to the reduction, mineralization, and potential detoxification of metal species with high oxidation state.

Effect of Integrated Water-Nutrient Management Strategies on Soil Erosion Mediated Nutrient Loss and Crop Productivity in Cabo Verde Drylands

Science.gov (United States)

Baptista, Isaurinda; Ritsema, Coen; Geissen, Violette

2015-01-01

Soil erosion, runoff and related nutrient losses are a big risk for soil fertility in Cabo Verde drylands. In 2012, field trials were conducted in two agro-ecological zones to evaluate the effects of selected techniques of soil-water management combined with organic amendments (T1: compost/manure + soil surfactant; T2: compost/animal or green manure + pigeon-pea hedges + soil surfactant; T3: compost/animal or green manure + mulch + pigeon-pea hedges) on nitrogen (N) and phosphorus (P) losses in eroded soil and runoff and on crop yields. Three treatments and one control (traditional practice) were tested in field plots at three sites with a local maize variety and two types of beans. Runoff and eroded soil were collected after each erosive rain, quantified, and analysed for NO3-N and PO4-P concentrations. In all treatments runoff had higher concentrations of NO3-N (2.20-4.83 mg L-1) than of PO4-P (0.02-0.07 mg L-1), and the eroded soil had higher content of PO4-P (5.27-18.8 mg g-1) than of NO3-N (1.30-8.51 mg g-1). The control had significantly higher losses of both NO3-N (5.4, 4.4 and 19 kg ha-1) and PO4-P (0.2, 0.1 and 0.4 kg ha-1) than the other treatments. T3 reduced soil loss, runoff and nutrient losses to nearly a 100% while T1 and T2 reduced those losses from 43 to 88%. The losses of NO3-N and PO4-P were highly correlated with the amounts of runoff and eroded soil. Nutrient losses from the applied amendments were low (5.7% maximum), but the losses in the control could indicate long-term nutrient depletion in the soil (19 and 0.4 kg ha-1 of NO3-N and PO4-P, respectively). T1-T3 did not consistently increase crop yield or biomass in all three sites, but T1 increased both crop yield and biomass. We conclude that T3 (combining crop-residue mulch with organic amendment and runoff hedges) is the best treatment for steep slope areas but, the pigeon-pea hedges need to be managed for higher maize yield. T1 (combining organic amendment with soil surfactant) could be a

Effect of Integrated Water-Nutrient Management Strategies on Soil Erosion Mediated Nutrient Loss and Crop Productivity in Cabo Verde Drylands.

Science.gov (United States)

Baptista, Isaurinda; Ritsema, Coen; Geissen, Violette

2015-01-01

Soil erosion, runoff and related nutrient losses are a big risk for soil fertility in Cabo Verde drylands. In 2012, field trials were conducted in two agro-ecological zones to evaluate the effects of selected techniques of soil-water management combined with organic amendments (T1: compost/manure + soil surfactant; T2: compost/animal or green manure + pigeon-pea hedges + soil surfactant; T3: compost/animal or green manure + mulch + pigeon-pea hedges) on nitrogen (N) and phosphorus (P) losses in eroded soil and runoff and on crop yields. Three treatments and one control (traditional practice) were tested in field plots at three sites with a local maize variety and two types of beans. Runoff and eroded soil were collected after each erosive rain, quantified, and analysed for NO3-N and PO4-P concentrations. In all treatments runoff had higher concentrations of NO3-N (2.20-4.83 mg L-1) than of PO4-P (0.02-0.07 mg L-1), and the eroded soil had higher content of PO4-P (5.27-18.8 mg g-1) than of NO3-N (1.30-8.51 mg g-1). The control had significantly higher losses of both NO3-N (5.4, 4.4 and 19 kg ha-1) and PO4-P (0.2, 0.1 and 0.4 kg ha-1) than the other treatments. T3 reduced soil loss, runoff and nutrient losses to nearly a 100% while T1 and T2 reduced those losses from 43 to 88%. The losses of NO3-N and PO4-P were highly correlated with the amounts of runoff and eroded soil. Nutrient losses from the applied amendments were low (5.7% maximum), but the losses in the control could indicate long-term nutrient depletion in the soil (19 and 0.4 kg ha-1 of NO3-N and PO4-P, respectively). T1-T3 did not consistently increase crop yield or biomass in all three sites, but T1 increased both crop yield and biomass. We conclude that T3 (combining crop-residue mulch with organic amendment and runoff hedges) is the best treatment for steep slope areas but, the pigeon-pea hedges need to be managed for higher maize yield. T1 (combining organic amendment with soil surfactant) could be a

Performance of a novel baffled osmotic membrane bioreactor-microfiltration hybrid system under continuous operation for simultaneous nutrient removal and mitigation of brine discharge

KAUST Repository

Pathak, Nirenkumar; Chekli, Laura; Wang, Jin; Kim, Youngjin; Phuntsho, Sherub; Li, Sheng; Ghaffour, NorEddine; Leiknes, TorOve; Shon, Hokyong

2017-01-01

in an attempt to reduce the process footprint and energy costs associated with continuous aeration. The process performance was evaluated in terms of water flux, salinity build up in the bioreactor, organic and nutrient removal and microbial activity using

Changes in nutrient stoichiometry, elemental homeostasis and growth rate of aquatic litter-associated fungi in response to inorganic nutrient supply.

Science.gov (United States)

Gulis, Vladislav; Kuehn, Kevin A; Schoettle, Louie N; Leach, Desiree; Benstead, Jonathan P; Rosemond, Amy D

2017-12-01

Aquatic fungi mediate important energy and nutrient transfers in freshwater ecosystems, a role potentially altered by widespread eutrophication. We studied the effects of dissolved nitrogen (N) and phosphorus (P) concentrations and ratios on fungal stoichiometry, elemental homeostasis, nutrient uptake and growth rate in two experiments that used (1) liquid media and a relatively recalcitrant carbon (C) source and (2) fungi grown on leaf litter in microcosms. Two monospecific fungal cultures and a multi-species assemblage were assessed in each experiment. Combining a radioactive tracer to estimate fungal production (C accrual) with N and P uptake measurements provided an ecologically relevant estimate of mean fungal C:N:P of 107:9:1 in litter-associated fungi, similar to the 92:9:1 obtained from liquid cultures. Aquatic fungi were found to be relatively homeostatic with respect to their C:N ratio (~11:1), but non-homeostatic with respect to C:P and N:P. Dissolved N greatly affected fungal growth rate and production, with little effect on C:nutrient stoichiometry. Conversely, dissolved P did not affect fungal growth and production but controlled biomass C:P and N:P, probably via luxury P uptake and storage. The ability of fungi to immobilize and store excess P may alter nutrient flow through aquatic food webs and affect ecosystem functioning.

The role of autophagy in microbial infection and immunity

Directory of Open Access Journals (Sweden)

Desai M

2015-01-01

Full Text Available Mayura Desai,1 Rong Fang,2 Jiaren Sun11Department of Microbiology and Immunology, 2Department of Pathology, University of Texas Medical Branch at Galveston, Galveston, TX, USAAbstract: The autophagy pathway represents an evolutionarily conserved cell recycling process that is activated in response to nutrient deprivation and other stress signals. Over the years, it has been linked to an array of cellular functions. Equally, a wide range of cell-intrinsic, as well as extracellular, factors have been implicated in the induction of the autophagy pathway. Microbial infections represent one such factor that can not only activate autophagy through specific mechanisms but also manipulate the response to the invading microbe's advantage. Moreover, in many cases, particularly among viruses, the pathway has been shown to be intricately involved in the replication cycle of the pathogen. Conversely, autophagy also plays a role in combating the infection process, both through direct destruction of the pathogen and as one of the key mediating factors in the host defense mechanisms of innate and adaptive immunity. Further, the pathway also plays a role in controlling the pathogenesis of infectious diseases by regulating inflammation. In this review, we discuss various interactions between pathogens and the cellular autophagic response and summarize the immunological functions of the autophagy pathway.Keywords: autophagy, xenophagy, antiviral, antibacterial

Composition of Mediterranean fruit fly third instar larvae (Diptera: Tephritidae) and diet: Nutrient balance studies on amino acids, minerals and nutrient composition in fresh and spent mass rearing diets

International Nuclear Information System (INIS)

Chan, Harvey T. Jr.; Jang, Eric B.; Ako, Harry; Niino-Duponte, Ruth Y.; Carpenter, James R.

2000-01-01

Mass production of the Mediterranean fruit fly (Medfly) larvae, Ceratitis capitata Wiedemann, requires a rearing diet (Tanaka et al. 1969 1970) of which the nutrient requirements and digestibility have not been established. Setbacks in rearing productivity from the expected 100% yield to as low as 3% yield may occasionally be directly attributed to insecticide contamination or a variety of possible cause(s) (Kobayashi, 1993). These causes include inadequate nutrition, poor diet formulation, overcrowding of either microorganisms or Drosophila, or to the inherent processes of oxidative or microbial deterioration of nutrients. The purpose of this study was to establish the nutritional status of the Mediterranean fruit fly diet through a material balance study for changes in proximate composition (i.e., moisture, protein, fat, ash, carbohydrates), amino acids, minerals between fresh and spent diets, and in the fruit fly larvae themselves

Nutrient Addition Leads to a Weaker CO2 Sink and Higher CH4 Emissions through Vegetation-Microclimate Feedbacks at Mer Bleue Bog, Canada

Science.gov (United States)

Bubier, J. L.; Arnkil, S.; Humphreys, E.; Juutinen, S.; Larmola, T.; Moore, T. R.

2015-12-01

Atmospheric nitrogen (N) deposition has led to nutrient enrichment in wetlands globally, affecting plant community composition, carbon (C) cycling, and microbial dynamics. Nutrient-limited boreal bogs are long-term sinks of carbon dioxide (CO2), but sources of methane (CH4), an important greenhouse gas. We fertilized Mer Bleue Bog, a Sphagnum moss and evergreen shrub-dominated ombrotrophic bog near Ottawa, Ontario, for 10-15 years with N as NO3 and NH4 at 5, 10 and 20 times ambient N deposition (0.6-0.8 g N m-2 y-1), with and without phosphorus (P) and potassium (K). Treatments were applied to triplicate plots (3 x 3 m) from May - August 2000-2015 and control plots received distilled water. We measured net ecosystem CO2 exchange (NEE), ecosystem photosynthesis and respiration, and CH4 flux with climate-controlled chambers; leaf-level CO2 exchange and biochemistry; substrate-induced respiration, CH4 production and consumption potentials with laboratory incubations; plant species composition and abundance; and microclimate (peat temperature, moisture, light interception). After 15 years, we have found that NEE has decreased, and CH4 emissions have increased, in the highest nutrient treatments owing to changes in vegetation, microtopography, and peat characteristics. Vegetation changes include a loss of Sphagnum moss and introduction of new deciduous species. Simulated atmospheric N deposition has not benefitted the photosynthetic apparatus of the dominant evergreen shrubs, but resulted in higher foliar respiration, contributing to a weaker ecosystem CO2 sink. Loss of moss has led to wetter near-surface substrate, higher rates of decomposition and CH4 emission, and a shift in microbial communities. Thus, elevated atmospheric deposition of nutrients may endanger C storage in peatlands through a complex suite of feedbacks and interactions among vegetation, microclimate, and microbial communities.

Efecto del enriquecimiento con nutrientes en la degradación de clorpirifos, malatión y metil paratión Inorganic nutrients effect addition over the chlorpyrifos, malathion and methyl parathion degradation

Directory of Open Access Journals (Sweden)

S. A. Upegui

2011-01-01

Full Text Available Con el fin de evaluar el efecto del enriquecimiento con nutrientes (una sal de fósforo o un fertilizante comercial con N, P y K como alternativa para mejorar la capacidad de degradación de los microorganismos en una matriz sólida, contaminada con los pesticidas organofosforados: clorpirifos, malatión y metil paratión, se realizaron experimentos de cultivo bajo condiciones controladas de oscuridad, temperatura y humedad por 30 días. En todos los tratamientos hubo degradación de los pesticidas; sin embargo, en el tratamiento con fósforo los tiempos para degradar el clorpirifos y el metil paratión fueron mayores. La presencia de los pesticidas no generó efectos tóxicos detectables sobre la microflora en ninguno de los tratamientos evaluados. La actividad biológica de las matrices no presentó una relación directa con la capacidad de degradación.In order to evaluate the effect of inorganic nutrient addition (phosphorus or commercial fertilizer over the microbial degradation capacity present in a solid matrix contaminated with chlorpyrifos, malathion and methyl parathion, microcosms assays were held under controlled conditions of light, moisture and temperature for 30 days. Results showed that even though three treatments microorganisms were able to degrade the three organophosphorus pesticides, microorganisms of phosphorus-enrichment treatment were less efficient to degrade Chlorpyrifos and Methyl Parathion than microorganisms of Fertilizer-enrichment treatment. It was not observed a direct relation between mineralization and microbial pesticides degradation capacity. The microbial activity was not affected by the presence of organophosphorus pesticides.

Mitochondrial protein acetylation mediates nutrient sensing of mitochondrial protein synthesis and mitonuclear protein balance.