The development and succession of microbial communities in 90-day Bioregenerative Life Support Experiment in the Lunar Palace 1

NASA Astrophysics Data System (ADS)

Sun, Yi; Liu, Hong; Fu, Yuming; Liu, Bojie; Su, Qiang; Xie, Beizhen; Qin, Youcai; Dong, Chen; Liu, Guanghui

Lunar Palace 1, as an integrative experiment facility for permanent astrobase life-support artificial closed ecosystem, is an artificial ecosystem which consists of plant cultivation, animal breeding and waste treatment units. It has been used to carry out a 90-day bioregenerative life support experiment with three crew members. Apparently, it’s hard to prevent the growth of microorganisms in such closed ecosystem for their strong adaptive capacity. Original microorganisms in the cabin, microbes in the course of loads delivery and the autologous microorganism by crew members and animals themselves are all the main source of the interior microorganisms, which may grow and regenerate in air, water and plants. Therefore, if these microorganisms could not be effectively monitored and controlled, it may cause microbial contamination and even lead to the unsteadiness of the whole closed ecosystem. In this study, the development and succession of the microbial communities of air, water system, plant system, and key facilities surfaces in Lunar Palace 1 were continuously monitored and analyzed by using plate counting method and molecular biological method during the 90-day experiment. The results were quite useful for the controlling of internal microorganisms and the safe operation of the whole system, and could also reveal the succession rules of microorganisms in an artificial closed ecosystem.

Soil mineral composition matters: response of microbial communities to phenanthrene and plant litter addition in long-term matured artificial soils.

PubMed

Babin, Doreen; Vogel, Cordula; Zühlke, Sebastian; Schloter, Michael; Pronk, Geertje Johanna; Heister, Katja; Spiteller, Michael; Kögel-Knabner, Ingrid; Smalla, Kornelia

2014-01-01

The fate of polycyclic aromatic hydrocarbons (PAHs) in soil is determined by a suite of biotic and abiotic factors, and disentangling their role in the complex soil interaction network remains challenging. Here, we investigate the influence of soil composition on the microbial community structure and its response to the spiked model PAH compound phenanthrene and plant litter. We used long-term matured artificial soils differing in type of clay mineral (illite, montmorillonite) and presence of charcoal or ferrihydrite. The soils received an identical soil microbial fraction and were incubated for more than two years with two sterile manure additions. The matured artificial soils and a natural soil were subjected to the following spiking treatments: (I) phenanthrene, (II) litter, (III) litter + phenanthrene, (IV) unspiked control. Total community DNA was extracted from soil sampled on the day of spiking, 7, 21, and 63 days after spiking. Bacterial 16S rRNA gene and fungal internal transcribed spacer amplicons were quantified by qPCR and subjected to denaturing gradient gel electrophoresis (DGGE). DGGE analysis revealed that the bacterial community composition, which was strongly shaped by clay minerals after more than two years of incubation, changed in response to spiked phenanthrene and added litter. DGGE and qPCR showed that soil composition significantly influenced the microbial response to spiking. While fungal communities responded only in presence of litter to phenanthrene spiking, the response of the bacterial communities to phenanthrene was less pronounced when litter was present. Interestingly, microbial communities in all artificial soils were more strongly affected by spiking than in the natural soil, which might indicate the importance of higher microbial diversity to compensate perturbations. This study showed the influence of soil composition on the microbiota and their response to phenanthrene and litter, which may increase our understanding of complex interactions in soils for bioremediation applications.

Soil Mineral Composition Matters: Response of Microbial Communities to Phenanthrene and Plant Litter Addition in Long-Term Matured Artificial Soils

PubMed Central

Babin, Doreen; Vogel, Cordula; Zühlke, Sebastian; Schloter, Michael; Pronk, Geertje Johanna; Heister, Katja; Spiteller, Michael; Kögel-Knabner, Ingrid; Smalla, Kornelia

2014-01-01

The fate of polycyclic aromatic hydrocarbons (PAHs) in soil is determined by a suite of biotic and abiotic factors, and disentangling their role in the complex soil interaction network remains challenging. Here, we investigate the influence of soil composition on the microbial community structure and its response to the spiked model PAH compound phenanthrene and plant litter. We used long-term matured artificial soils differing in type of clay mineral (illite, montmorillonite) and presence of charcoal or ferrihydrite. The soils received an identical soil microbial fraction and were incubated for more than two years with two sterile manure additions. The matured artificial soils and a natural soil were subjected to the following spiking treatments: (I) phenanthrene, (II) litter, (III) litter + phenanthrene, (IV) unspiked control. Total community DNA was extracted from soil sampled on the day of spiking, 7, 21, and 63 days after spiking. Bacterial 16S rRNA gene and fungal internal transcribed spacer amplicons were quantified by qPCR and subjected to denaturing gradient gel electrophoresis (DGGE). DGGE analysis revealed that the bacterial community composition, which was strongly shaped by clay minerals after more than two years of incubation, changed in response to spiked phenanthrene and added litter. DGGE and qPCR showed that soil composition significantly influenced the microbial response to spiking. While fungal communities responded only in presence of litter to phenanthrene spiking, the response of the bacterial communities to phenanthrene was less pronounced when litter was present. Interestingly, microbial communities in all artificial soils were more strongly affected by spiking than in the natural soil, which might indicate the importance of higher microbial diversity to compensate perturbations. This study showed the influence of soil composition on the microbiota and their response to phenanthrene and litter, which may increase our understanding of complex interactions in soils for bioremediation applications. PMID:25222697

The Role of Microbial Processes in the Oxidation and Removal of Ammonia from Drinking Water

EPA Science Inventory

The purpose of this study was two-fold: (1) to monitor and evaluate nitrification in a full-scale iron removal filtration plant with biologically active granular media filters located in Ohio, and (2) to determine how to most efficiently regain nitrification following filter rebe...

Decreased plant productivity resulting from plant group removal experiment constrains soil microbial functional diversity.

PubMed

Zhang, Ximei; Johnston, Eric R; Barberán, Albert; Ren, Yi; Lü, Xiaotao; Han, Xingguo

2017-10-01

Anthropogenic environmental changes are accelerating the rate of biodiversity loss on Earth. Plant diversity loss is predicted to reduce soil microbial diversity primarily due to the decreased variety of carbon/energy resources. However, this intuitive hypothesis is supported by sparse empirical evidence, and most underlying mechanisms remain underexplored or obscure altogether. We constructed four diversity gradients (0-3) in a five-year plant functional group removal experiment in a steppe ecosystem in Inner Mongolia, China, and quantified microbial taxonomic and functional diversity with shotgun metagenome sequencing. The treatments had little effect on microbial taxonomic diversity, but were found to decrease functional gene diversity. However, the observed decrease in functional gene diversity was more attributable to a loss in plant productivity, rather than to the loss of any individual plant functional group per se. Reduced productivity limited fresh plant resources supplied to microorganisms, and thus, intensified the pressure of ecological filtering, favoring genes responsible for energy production/conversion, material transport/metabolism and amino acid recycling, and accordingly disfavored many genes with other functions. Furthermore, microbial respiration was correlated with the variation in functional composition but not taxonomic composition. Overall, the amount of carbon/energy resources driving microbial gene diversity was identified to be the critical linkage between above- and belowground communities, contrary to the traditional framework of linking plant clade/taxonomic diversity to microbial taxonomic diversity. © 2017 John Wiley & Sons Ltd.

Contaminants of emerging concern affect Trichoplusia ni growth and development on artificial diets and a key host plant

PubMed Central

Rothman, Jason A.; Dudley, Stacia L.; Jones, Michael B.; McFrederick, Quinn S.; Gan, Jay; Trumble, John T.

2017-01-01

Many countries are utilizing reclaimed wastewater for agriculture because drought, rising temperatures, and expanding human populations are increasing water demands. Unfortunately, wastewater often contains biologically active, pseudopersistent pharmaceuticals, even after treatment. Runoff from farms and output from wastewater treatment plants also contribute high concentrations of pharmaceuticals to the environment. This study assessed the effects of common pharmaceuticals on an agricultural pest, Trichoplusia ni (Lepidoptera: Noctuidae). Larvae were reared on artificial diets spiked with contaminants of emerging concern (CECs) at environmentally relevant concentrations. Trichoplusia ni showed increased developmental time and mortality when reared on artificial diets containing antibiotics, hormones, or a mixture of contaminants. Mortality was also increased when T. ni were reared on tomatoes grown hydroponically with the same concentrations of antibiotics. The antibiotic-treated plants translocated ciprofloxacin through their tissues to roots, shoots, and leaves. Microbial communities of T. ni changed substantially between developmental stages and when exposed to CECs in their diets. Our results suggest that use of reclaimed wastewater for irrigation of crops can affect the developmental biology and microbial communities of an insect of agricultural importance. PMID:29087336

Microbial ecology of the closed artificial ecosystem MELiSSA (Micro-Ecological Life Support System Alternative): reinventing and compartmentalizing the Earth's food and oxygen regeneration system for long-haul space exploration missions.

PubMed

Hendrickx, Larissa; De Wever, Heleen; Hermans, Veronik; Mastroleo, Felice; Morin, Nicolas; Wilmotte, Annick; Janssen, Paul; Mergeay, Max

2006-01-01

MELiSSA is a bioregenerative life support system designed by the European Space Agency (ESA) for the complete recycling of gas, liquid and solid wastes during long distance space exploration. The system uses the combined activity of different living organisms: microbial cultures in bioreactors, a plant compartment and a human crew. In this minireview, the development of a short-cut ecological system for the biotransformation of organic waste is discussed from a microorganism's perspective. The artificial ecological model--still in full development--that is inspired by Earth's own geomicrobiological ecosystem serves as an ideal study object on microbial ecology and will become an indispensable travel companion in manned space exploration.

Artificial Surfaces in Phyllosphere Microbiology.

PubMed

Doan, Hung K; Leveau, Johan H J

2015-08-01

The study of microorganisms that reside on plant leaf surfaces, or phyllosphere microbiology, greatly benefits from the availability of artificial surfaces that mimic in one or more ways the complexity of foliage as a microbial habitat. These leaf surface proxies range from very simple, such as nutrient agars that can reveal the metabolic versatility or antagonistic properties of leaf-associated microorganisms, to the very complex, such as silicon-based casts that replicate leaf surface topography down to nanometer resolution. In this review, we summarize the various uses of artificial surfaces in experimental phyllosphere microbiology and discuss how these have advanced our understanding of the biology of leaf-associated microorganisms and the habitat they live in. We also provide an outlook into future uses of artificial leaf surfaces, foretelling a greater role for microfluidics to introduce biological and chemical gradients into artificial leaf environments, stressing the importance of artificial surfaces to generate quantitative data that support computational models of microbial life on real leaves, and rethinking the leaf surface ('phyllosphere') as a habitat that features two intimately connected but very different compartments, i.e., the leaf surface landscape ('phylloplane') and the leaf surface waterscape ('phyllotelma').

Drag Enhancement of Microbial Slime Films on Rotating Discs.

DTIC Science & Technology

1981-03-27

barnacle and algal growth , had also occurred (7). Laboratory culture eliminated these contaminants. The bacteria were grown in artificial seawater (Instant...attachment and growth under flow conditions , using an aquarium power filter pump (12). Films grown in this manner were sufficiently adherent to plastic...the large and easily visible organisms, such as barnacles, bryozoa, and tubeworms do not prevent attachment and growth of micro-organisms, which may

Bacterial carbon utilization in vertical subsurface flow constructed wetlands.

PubMed

Tietz, Alexandra; Langergraber, Günter; Watzinger, Andrea; Haberl, Raimund; Kirschner, Alexander K T

2008-03-01

Subsurface vertical flow constructed wetlands with intermittent loading are considered as state of the art and can comply with stringent effluent requirements. It is usually assumed that microbial activity in the filter body of constructed wetlands, responsible for the removal of carbon and nitrogen, relies mainly on bacterially mediated transformations. However, little quantitative information is available on the distribution of bacterial biomass and production in the "black-box" constructed wetland. The spatial distribution of bacterial carbon utilization, based on bacterial (14)C-leucine incorporation measurements, was investigated for the filter body of planted and unplanted indoor pilot-scale constructed wetlands, as well as for a planted outdoor constructed wetland. A simple mass-balance approach was applied to explain the bacterially catalysed organic matter degradation in this system by comparing estimated bacterial carbon utilization rates with simultaneously measured carbon reduction values. The pilot-scale constructed wetlands proved to be a suitable model system for investigating microbial carbon utilization in constructed wetlands. Under an ideal operating mode, the bulk of bacterial productivity occurred within the first 10cm of the filter body. Plants seemed to have no significant influence on productivity and biomass of bacteria, as well as on wastewater total organic carbon removal.

PAH dissipation in spiked soil: impacts of bioavailability, microbial activity, and trees.

PubMed

Mueller, Kevin E; Shann, Jodi R

2006-08-01

While trees have demonstrated potential in phytoremediation of several organic contaminants, little is known regarding their ability to impact the common soil contaminant PAHs. Several species of native North American trees were planted in soil artificially contaminated with three PAHs. Plant biomass, PAH dissipation, and microbial mineralization were monitored over the course of one year and environmental conditions were allowed to follow typical seasonal patterns. PAH dissipation and mineralization were not affected by planting. Extensive and rapid loss of PAHs was observed and attributed to high bioavailability and microbial activity in all treatments. The rate of this loss may have masked any significant planting effects. Anthracene was found to be more recalcitrant than pyrene or phenanthrene. Parallel soil aging studies indicated that sequestration to soil components was minimal. Contrary to common inferences in literature, amendment with decaying fine roots inhibited PAH degradation by the soil microbial community. Seasonal variation in environmental factors and rhizosphere dynamics may have also reduced or negated the effect of planting and should be taken into account in future phytoremediation trials. The unique root traits of trees may pose a challenge to traditional thought regarding PAH dissipation in the rhizosphere of plants.

Biohybrid Control of General Linear Systems Using the Adaptive Filter Model of Cerebellum.

PubMed

Wilson, Emma D; Assaf, Tareq; Pearson, Martin J; Rossiter, Jonathan M; Dean, Paul; Anderson, Sean R; Porrill, John

2015-01-01

The adaptive filter model of the cerebellar microcircuit has been successfully applied to biological motor control problems, such as the vestibulo-ocular reflex (VOR), and to sensory processing problems, such as the adaptive cancelation of reafferent noise. It has also been successfully applied to problems in robotics, such as adaptive camera stabilization and sensor noise cancelation. In previous applications to inverse control problems, the algorithm was applied to the velocity control of a plant dominated by viscous and elastic elements. Naive application of the adaptive filter model to the displacement (as opposed to velocity) control of this plant results in unstable learning and control. To be more generally useful in engineering problems, it is essential to remove this restriction to enable the stable control of plants of any order. We address this problem here by developing a biohybrid model reference adaptive control (MRAC) scheme, which stabilizes the control algorithm for strictly proper plants. We evaluate the performance of this novel cerebellar-inspired algorithm with MRAC scheme in the experimental control of a dielectric electroactive polymer, a class of artificial muscle. The results show that the augmented cerebellar algorithm is able to accurately control the displacement response of the artificial muscle. The proposed solution not only greatly extends the practical applicability of the cerebellar-inspired algorithm, but may also shed light on cerebellar involvement in a wider range of biological control tasks.

Comparison between mixed liquors of two side-stream membrane bioreactors treating wastewaters from waste management plants with high and low solids anaerobic digestion.

PubMed

Zuriaga-Agustí, E; Mendoza-Roca, J A; Bes-Piá, A; Alonso-Molina, J L; Fernández-Giménez, E; Álvarez-Requena, C; Muñagorri-Mañueco, F; Ortiz-Villalobos, G

2016-09-01

In the last years, biological treatment plants for the previously separated organic fraction from municipal solid wastes (OFMSW) have gained importance. In these processes a liquid effluent (liquid fraction from the digestate and leachate from composting piles), which has to be treated previously to its discharge, is produced. In this paper, the characteristics of the mixed liquor from two full-scale membrane bioreactors treating the effluents of two OFMSW treatment plants have been evaluated in view to study their influence on membrane fouling in terms of filterability. For that, the mixed liquor samples have been ultrafiltrated in an UF laboratory plant. Besides, the effect of the influent characteristics to MBRs and the values of the chemical and physical parameters of the mixed liquors on the filterability have been studied. Results showed that the filterability of the mixed liquor was strongly influenced by the soluble microbial products in the mixed liquors and the influent characteristics to MBR. Permeate flux of MBR mixed liquor treating the most polluted wastewater was considerable the lowest (around 20 L/m(2) h for some samples), what was explained by viscosity and soluble microbial products concentration higher than those measured in other MBR mixed liquor. Copyright © 2016 Elsevier Ltd. All rights reserved.

Contrasting diets reveal metabolic plasticity in the tree-killing beetle, Anoplophora glabripennis (Cerambycidae: Lamiinae)

NASA Astrophysics Data System (ADS)

Mason, Charles J.; Scully, Erin D.; Geib, Scott M.; Hoover, Kelli

2016-09-01

Wood-feeding insects encounter challenging diets containing low protein quantities, recalcitrant carbohydrate sources, and plant defensive compounds. The Asian longhorned beetle (Anoplophora glabripennis) is a wood-feeding insect that attacks and kills a diversity of hardwood tree species. We compared gene expression of midguts collected from larvae feeding in a preferred tree, sugar maple, to those consuming a nutrient-rich artificial diet, to identify genes putatively involved in host plant utilization. Anoplophora glabripennis larvae exhibited differential expression of ~3600 genes in response to different diets. Genes with predicted capacity for plant and microbial carbohydrate usage, detoxification, nutrient recycling, and immune-related genes relevant for facilitating interactions with microbial symbionts were upregulated in wood-feeding larvae compared to larvae feeding in artificial diet. Upregulation of genes involved in protein degradation and synthesis was also observed, suggesting that proteins incur more rapid turnover in insects consuming wood. Additionally, wood-feeding individuals exhibited elevated expression of several mitochondrial cytochrome C oxidase genes, suggesting increased aerobic respiration compared to diet-fed larvae. These results indicate that A. glabripennis modulates digestive and basal gene expression when larvae are feeding in a nutrient-poor, yet suitable host plant compared to a tractable and nutrient-rich diet that is free of plant defensive compounds.

Preferential flow in the vadose zone and interface dynamics: Impact of microbial exudates

NASA Astrophysics Data System (ADS)

Li, Biting; Pales, Ashley R.; Clifford, Heather M.; Kupis, Shyla; Hennessy, Sarah; Liang, Wei-Zhen; Moysey, Stephen; Powell, Brian; Finneran, Kevin T.; Darnault, Christophe J. G.

2018-03-01

In the hydrological cycle, the infiltration process is a critical component in the distribution of water into the soil and in the groundwater system. The nonlinear dynamics of the soil infiltration process yield preferential flow which affects the water distribution in soil. Preferential flow is influenced by the interactions between water, soil, plants, and microorganisms. Although the relationship among the plant roots, their rhizodeposits and water transport in soil has been the subject of extensive study, the effect of microbial exudates has been studied in only a few cases. Here the authors investigated the influence of two artificial microbial exudates-catechol and riboflavin-on the infiltration process, particularly unstable fingered flow, one form of preferential flow. Flow experiments investigating the effects of types and concentrations of microbial exudates on unstable fingered flow were conducted in a two-dimensional tank that was filled with ASTM

The Cacti Microbiome: Interplay between Habitat-Filtering and Host-Specificity

DOE PAGES

Fonseca-García, Citlali; Coleman-Derr, Devin; Garrido, Etzel; ...

2016-02-12

Cactaceae represents one of the most species-rich families of succulent plants native to arid and semi-arid ecosystems, yet the associations Cacti establish with microorganisms and the rules governing microbial community assembly remain poorly understood. We analyzed the composition, diversity, and factors influencing above- and below-ground bacterial, archaeal, and fungal communities associated with two native and sympatric Cacti species: Myrtillocactus geometrizans and Opuntia robusta. Phylogenetic profiling showed that the composition and assembly of microbial communities associated with Cacti were primarily influenced by the plant compartment; plant species, site, and season played only a minor role. Remarkably, bacterial, and archaeal diversity wasmore » higher in the phyllosphere than in the rhizosphere of Cacti, while the opposite was true for fungi. Semi-arid soils exhibited the highest levels of microbial diversity whereas the stem endosphere the lowest. Despite their taxonomic distance, M. geometrizans and O. robusta shared most microbial taxa in all analyzed compartments. Influence of the plant host did only play a larger role in the fungal communities of the stem endosphere. These results suggest that fungi establish specific interactions with their host plant inside the stem, whereas microbial communities in the other plant compartments may play similar functional roles in these two species. Biochemical and molecular characterization of seed-borne bacteria of Cacti supports the idea that these microbial symbionts may be vertically inherited and could promote plant growth and drought tolerance for the fitness of the Cacti holobiont. We envision this knowledge will help improve and sustain agriculture in arid and semi-arid regions of the world.« less

The Cacti Microbiome: Interplay between Habitat-Filtering and Host-Specificity

PubMed Central

Fonseca-García, Citlali; Coleman-Derr, Devin; Garrido, Etzel; Visel, Axel; Tringe, Susannah G.; Partida-Martínez, Laila P.

2016-01-01

Cactaceae represents one of the most species-rich families of succulent plants native to arid and semi-arid ecosystems, yet the associations Cacti establish with microorganisms and the rules governing microbial community assembly remain poorly understood. We analyzed the composition, diversity, and factors influencing above- and below-ground bacterial, archaeal, and fungal communities associated with two native and sympatric Cacti species: Myrtillocactus geometrizans and Opuntia robusta. Phylogenetic profiling showed that the composition and assembly of microbial communities associated with Cacti were primarily influenced by the plant compartment; plant species, site, and season played only a minor role. Remarkably, bacterial, and archaeal diversity was higher in the phyllosphere than in the rhizosphere of Cacti, while the opposite was true for fungi. Semi-arid soils exhibited the highest levels of microbial diversity whereas the stem endosphere the lowest. Despite their taxonomic distance, M. geometrizans and O. robusta shared most microbial taxa in all analyzed compartments. Influence of the plant host did only play a larger role in the fungal communities of the stem endosphere. These results suggest that fungi establish specific interactions with their host plant inside the stem, whereas microbial communities in the other plant compartments may play similar functional roles in these two species. Biochemical and molecular characterization of seed-borne bacteria of Cacti supports the idea that these microbial symbionts may be vertically inherited and could promote plant growth and drought tolerance for the fitness of the Cacti holobiont. We envision this knowledge will help improve and sustain agriculture in arid and semi-arid regions of the world. PMID:26904020

UV filters for lighting of plants

DOE Office of Scientific and Technical Information (OSTI.GOV)

Doehring, T.; Koefferlein, M.; Thiel, S.

1994-12-31

Different filter glasses are available which provide absorption properties suitable for gradual changes of the spectral UV-B illumination of artificial lighting. Using a distinct set of lamps and filter glasses an acceptable simulation of the UV-B part of natural global radiation can be achieved. The ageing of these and other filter materials under the extreme UV radiation in the lamphouse of a solar simulator is presently unavoidable. This instability can be dealt with only by a precise spectral monitoring and by replacing the filters accordingly. For this reason attempts would be useful to develop real ozone filters which can replacemore » glass filters. In any case chamber experiments require a careful selection of the filter material used and must be accompanied by a continuous UV-B monitoring.« less

The function of advanced treatment process in a drinking water treatment plant with organic matter-polluted source water.

PubMed

Lin, Huirong; Zhang, Shuting; Zhang, Shenghua; Lin, Wenfang; Yu, Xin

2017-04-01

To understand the relationship between chemical and microbial treatment at each treatment step, as well as the relationship between microbial community structure in biofilms in biofilters and their ecological functions, a drinking water plant with severe organic matter-polluted source water was investigated. The bacterial community dynamics of two drinking water supply systems (traditional and advanced treatment processes) in this plant were studied from the source to the product water. Analysis by 454 pyrosequencing was conducted to characterize the bacterial diversity in each step of the treatment processes. The bacterial communities in these two treatment processes were highly diverse. Proteobacteria, which mainly consisted of beta-proteobacteria, was the dominant phylum. The two treatment processes used in the plant could effectively remove organic pollutants and microbial polution, especially the advanced treatment process. Significant differences in the detection of the major groups were observed in the product water samples in the treatment processes. The treatment processes, particularly the biological pretreatment and O 3 -biological activated carbon in the advanced treatment process, highly influenced the microbial community composition and the water quality. Some opportunistic pathogens were found in the water. Nitrogen-relative microorganisms found in the biofilm of filters may perform an important function on the microbial community composition and water quality improvement.

Aquatic Plants and Wastewater Treatment (an Overview)

NASA Technical Reports Server (NTRS)

Wolverton, B. C.

1986-01-01

The technology for using water hyacinth to upgrade domestic sewage effluent from lagoons and other wastewater treatment facilities to secondary and advanced secondary standards has been sufficiently developed to be used where the climate is warm year round. The technology of using emergent plants such as bulrush combined with duckweed is also sufficiently developed to make this a viable wastewater treatment alternative. This system is suited for both temperate and semi-tropical areas found throughout most of the U.S. The newest technology in artificial marsh wastewater treatment involves the use of emergent plant roots in conjunction with high surface area rock filters. Smaller land areas are required for these systems because of the increased concentration of microorganisms associated with the rock and plant root surfaces. Approximately 75 percent less land area is required for the plant-rock system than is required for a strict artificial wetland to achieve the same level of treatment.

Soil biota effects on clonal growth and flowering in the forest herb Stachys sylvatica

NASA Astrophysics Data System (ADS)

de la Peña, Eduardo; Bonte, Dries

2011-03-01

The composition of a soil community can vary drastically at extremely short distances. Therefore, plants from any given population can be expected to experience strong differences in belowground biotic interactions. Although it is well recognized that the soil biota plays a significant role in the structure and dynamics of plant communities, plastic responses in growth strategies as a function of soil biotic interactions have received little attention. In this study, we question whether the biotic soil context from two forest associated contrasting environments (the forest understory and the hedgerows) determines the balance between clonal growth and flowering of the perennial Stachys sylvatica. Using artificial soils, we compared the growth responses of this species following inoculation with the mycorrhizal and microbial community extracted either from rhizospheric soil of the forest understory or from the hedgerows. The microbial context had a strong effect on plant functional traits, determining the production of runners and inflorescences. Plants inoculated with the hedgerow community had a greater biomass, larger number of runners, and lower resource investment in flower production than was seen in plants inoculated with the understory microbial community. The obtained results illustrate that belowground biotic interactions are essential to understand basic plastic growth responses determinant for plant establishment and survival. The interactions with microbial communities from two contrasting habitats resulted in two different, and presumably adaptive, growth strategies that were optimal for the conditions prevalent in the environments compared; and they are as such an essential factor to understand plant-plant, plant-animal interactions and the dispersal capacities of clonal plants.

Poly iron sulfate flocculant as an effective additive for improving the performance of microbial fuel cells.

PubMed

Miyahara, Morio; Sakamoto, Akihiro; Kouzuma, Atsushi; Watanabe, Kazuya

2016-12-01

Laboratory microbial fuel cells were supplied with artificial wastewater and used to examine how supplementation with poly iron sulfate, an inorganic polymer flocculant widely used in wastewater-treatment plants, affects electricity generation and anode microbiomes. It is shown that poly iron sulfate substantially increases electric outputs from microbial fuel cells. Microbiological analyses show that iron and sulfate separately affect anode microbiomes, and the increase in power output is associated with the increases in bacteria affiliated with the families Geobacteraceae and/or Desulfuromonadaceae. We suggest that poly iron sulfate is an effective additive for increasing the electric output from microbial fuel cells. Other utilities of poly iron sulfate in microbial fuel cells are also discussed. Copyright © 2016 Elsevier Ltd. All rights reserved.

Ecological filtering and plant traits variation across quarry geomorphological surfaces: implication for restoration.

PubMed

Gilardelli, Federica; Sgorbati, Sergio; Armiraglio, Stefano; Citterio, Sandra; Gentili, Rodolfo

2015-05-01

Revegetation patterns after quarry abandonment have been widely studied from several ecological points of view, but a trait-based approach is still lacking. The aim of this study was to characterise the plant species assemblages and the associated functional traits filtered on different geomorphological surfaces in abandoned limestone quarry areas: artificial cliffs, embankments, and platforms. We then verified if species with certain traits were better able to overcome the dispersal and environmental filters necessary for establishment. To this aim, we analyzed 113 vegetation plots and collected data on 25 morphological, ecological, and dispersal traits to detect species adaptaions across these man-made environments. As a case study, we investigated the extraction basin of Botticino (Lombardy, Italy), the second largest in Italy. The results obtained by SIMPER and CCA analyses showed that rockiness, stoniness, slope, elevation, and time of surfaces are the main filters that varied across quarries and affected plant assemblages at the macro-scale level. Across the three geomorphological surfaces (meso-scale) of quarries, more specific abiotic filters selecting species were found. In turn, traits differentiation according to the three main geomorphological surfaces of quarry emphasized that further filters acting at the micro-scale imply differences in dispersal mechanisms and resource availability. This work highlighted the utility to study species assemblages and environmental filters to address quarry restoration according to the type of geomorphological surface. The investigation of some traits (chorological form, life forms, seed dispersal,s and plant height) can furnish some interesting indications for practice individuating further abiotic filters acting at the micro-scale.

Microbial Community Profiles in Wastewaters from Onsite Wastewater Treatment Systems Technology

PubMed Central

Jałowiecki, Łukasz; Chojniak, Joanna Małgorzata; Dorgeloh, Elmar; Hegedusova, Berta; Ejhed, Helene; Magnér, Jörgen; Płaza, Grażyna Anna

2016-01-01

The aim of the study was to determine the potential of community-level physiological profiles (CLPPs) methodology as an assay for characterization of the metabolic diversity of wastewater samples and to link the metabolic diversity patterns to efficiency of select onsite biological wastewater facilities. Metabolic fingerprints obtained from the selected samples were used to understand functional diversity implied by the carbon substrate shifts. Three different biological facilities of onsite wastewater treatment were evaluated: fixed bed reactor (technology A), trickling filter/biofilter system (technology B), and aerated filter system (the fluidized bed reactor, technology C). High similarities of the microbial community functional structures were found among the samples from the three onsite wastewater treatment plants (WWTPs), as shown by the diversity indices. Principal components analysis (PCA) showed that the diversity and CLPPs of microbial communities depended on the working efficiency of the wastewater treatment technologies. This study provided an overall picture of microbial community functional structures of investigated samples in WWTPs and discerned the linkages between microbial communities and technologies of onsite WWTPs used. The results obtained confirmed that metabolic profiles could be used to monitor treatment processes as valuable biological indicators of onsite wastewater treatment technologies efficiency. This is the first step toward understanding relations of technology types with microbial community patterns in raw and treated wastewaters. PMID:26807728

Microbial As(III) Oxidation in Water Treatment Plant Filters

EPA Science Inventory

Arsenic exists in two oxidation states in water - arsenite [As(III)] and arsenate [As(V)]. As(III) is relatively mobile in water and difficult to remove by arsenic-removal treatment processes. Source waters that contain As(III) must add a strong oxidant such as free chlorine or p...

In situ microbial filter used for bioremediation

DOEpatents

Carman, M. Leslie; Taylor, Robert T.

2000-01-01

An improved method for in situ microbial filter bioremediation having increasingly operational longevity of an in situ microbial filter emplaced into an aquifer. A method for generating a microbial filter of sufficient catalytic density and thickness, which has increased replenishment interval, improved bacteria attachment and detachment characteristics and the endogenous stability under in situ conditions. A system for in situ field water remediation.

Ammonium removal pathways and microbial community in GAC-sand dual media filter in drinking water treatment.

PubMed

Feng, Shuo; Xie, Shuguang; Zhang, Xiaojian; Yang, Zhiyu; Ding, Wei; Liao, Xiaobin; Liu, Yuanyuan; Chen, Chao

2012-01-01

A GAC-sand dual media filter (GSF) was devised as an alternative solution for drinking water treatment plant to tackle the raw water polluted by ammonium in place of expensive ozone-GAC processes or bio-pretreatments. The ammonium removal pathways and microbial community in the GSFs were investigated. The concentrations of ammonium, nitrite and nitrate nitrogen were monitored along the filter. Total inorganic nitrogen (TIN) loss occurred during the filtration. For 1 mg ammonium removal, the TIN loss was as high as 0.35 mg, DO consumption was 3.06 mg, and alkalinity consumption was 5.55 mg. It was assumed that both nitrification and denitrification processes occur in the filters to fit the TIN loss and low DO consumption. During the filtration, nitritation, nitrification and nitritation-anaerobic ammonium oxidation processes probably occur, while traditional nitrification and denitrification and simultaneous nitrification and denitrification processes may occur. In the GSFs, Nitrosomonas and Nitrospira are likely to be involved in nitrification processes, while Novosphingobium, Comamonadaceae and Oxalobacteraceae may be involved in denitrification processes.

Hydrodynamics of microbial filter feeding

PubMed Central

Asadzadeh, Seyed Saeed; Dölger, Julia; Walther, Jens H.; Andersen, Anders

2017-01-01

Microbial filter feeders are an important group of grazers, significant to the microbial loop, aquatic food webs, and biogeochemical cycling. Our understanding of microbial filter feeding is poor, and, importantly, it is unknown what force microbial filter feeders must generate to process adequate amounts of water. Also, the trade-off in the filter spacing remains unexplored, despite its simple formulation: A filter too coarse will allow suitably sized prey to pass unintercepted, whereas a filter too fine will cause strong flow resistance. We quantify the feeding flow of the filter-feeding choanoflagellate Diaphanoeca grandis using particle tracking, and demonstrate that the current understanding of microbial filter feeding is inconsistent with computational fluid dynamics (CFD) and analytical estimates. Both approaches underestimate observed filtration rates by more than an order of magnitude; the beating flagellum is simply unable to draw enough water through the fine filter. We find similar discrepancies for other choanoflagellate species, highlighting an apparent paradox. Our observations motivate us to suggest a radically different filtration mechanism that requires a flagellar vane (sheet), something notoriously difficult to visualize but sporadically observed in the related choanocytes (sponges). A CFD model with a flagellar vane correctly predicts the filtration rate of D. grandis, and using a simple model we can account for the filtration rates of other microbial filter feeders. We finally predict how optimum filter mesh size increases with cell size in microbial filter feeders, a prediction that accords very well with observations. We expect our results to be of significance for small-scale biophysics and trait-based ecological modeling. PMID:28808016

Hydrodynamics of microbial filter feeding.

PubMed

Nielsen, Lasse Tor; Asadzadeh, Seyed Saeed; Dölger, Julia; Walther, Jens H; Kiørboe, Thomas; Andersen, Anders

2017-08-29

Microbial filter feeders are an important group of grazers, significant to the microbial loop, aquatic food webs, and biogeochemical cycling. Our understanding of microbial filter feeding is poor, and, importantly, it is unknown what force microbial filter feeders must generate to process adequate amounts of water. Also, the trade-off in the filter spacing remains unexplored, despite its simple formulation: A filter too coarse will allow suitably sized prey to pass unintercepted, whereas a filter too fine will cause strong flow resistance. We quantify the feeding flow of the filter-feeding choanoflagellate Diaphanoeca grandis using particle tracking, and demonstrate that the current understanding of microbial filter feeding is inconsistent with computational fluid dynamics (CFD) and analytical estimates. Both approaches underestimate observed filtration rates by more than an order of magnitude; the beating flagellum is simply unable to draw enough water through the fine filter. We find similar discrepancies for other choanoflagellate species, highlighting an apparent paradox. Our observations motivate us to suggest a radically different filtration mechanism that requires a flagellar vane (sheet), something notoriously difficult to visualize but sporadically observed in the related choanocytes (sponges). A CFD model with a flagellar vane correctly predicts the filtration rate of D. grandis , and using a simple model we can account for the filtration rates of other microbial filter feeders. We finally predict how optimum filter mesh size increases with cell size in microbial filter feeders, a prediction that accords very well with observations. We expect our results to be of significance for small-scale biophysics and trait-based ecological modeling.

Aerial Photography: Use in Detecting Simulated Insect Defoliation in Corn

NASA Technical Reports Server (NTRS)

Chiang, H. C.; Latham, R.; Meyer, M. P.

1973-01-01

Artificial defoliation in corn was used to explore the usefulness of aerial photography in detecting crop insect infestations. Defoliation on the top of plants was easily detected, while that on the base was less so. Aero infrared film with Wratten 89B filter gave the best results, and morning flights at the scale of 1:15840 are recommended. Row direction, plant growth stage, and time elapse since defoliation were not important factors.

System for enhanced longevity of in situ microbial filter used for bioremediation

DOEpatents

Carman, M. Leslie; Taylor, Robert T.

2000-01-01

An improved method for in situ microbial filter bioremediation having increasingly operational longevity of an in situ microbial filter emplaced into an aquifer. A method for generating a microbial filter of sufficient catalytic density and thickness, which has increased replenishment interval, improved bacteria attachment and detachment characteristics and the endogenous stability under in situ conditions. A system for in situ field water remediation.

Method for enhanced longevity of in situ microbial filter used for bioremediation

DOEpatents

Carman, M. Leslie; Taylor, Robert T.

1999-01-01

An improved method for in situ microbial filter bioremediation having increasingly operational longevity of an in situ microbial filter emplaced into an aquifer. A method for generating a microbial filter of sufficient catalytic density and thickness, which has increased replenishment interval, improved bacteria attachment and detachment characteristics and the endogenous stability under in situ conditions. A system for in situ field water remediation.

Plant Host Species and Geographic Distance Affect the Structure of Aboveground Fungal Symbiont Communities, and Environmental Filtering Affects Belowground Communities in a Coastal Dune Ecosystem.

PubMed

David, Aaron S; Seabloom, Eric W; May, Georgiana

2016-05-01

Microbial symbionts inhabit tissues of all plants and animals. Their community composition depends largely on two ecological processes: (1) filtering by abiotic conditions and host species determining the environments that symbionts are able to colonize and (2) dispersal-limitation determining the pool of symbionts available to colonize a given host and community spatial structure. In plants, the above- and belowground tissues represent such distinct habitats for symbionts that we expect different effects of filtering and spatial structuring on their symbiont communities. In this study, we characterized above- and belowground communities of fungal endophytes--fungi living asymptomatically within plants--to understand the contributions of filtering and spatial structure to endophyte community composition. We used a culture-based approach to characterize endophytes growing in leaves and roots of three species of coastal beachgrasses in dunes of the USA Pacific Northwest. For leaves, endophyte isolation frequency and OTU richness depended primarily on plant host species. In comparison, for roots, both isolation frequency and OTU richness increased from the nutrient-poor front of the dune to the higher-nutrient backdune. Endophyte community composition in leaves exhibited a distance-decay relationship across the region. In a laboratory assay, faster growth rates and lower spore production were more often associated with leaf- than root-inhabiting endophytes. Overall, our results reveal a greater importance of biotic filtering by host species and dispersal-limitation over regional geographic distances for aboveground leaf endophyte communities and stronger effects of abiotic environmental filtering and locally patchy distributions for belowground root endophyte communities.

Microbial pesticide removal in rapid sand filters for drinking water treatment--potential and kinetics.

PubMed

Hedegaard, Mathilde J; Albrechtsen, Hans-Jørgen

2014-01-01

Filter sand samples, taken from aerobic rapid sand filters used for treating groundwater at three Danish waterworks, were investigated for their pesticide removal potential and to assess the kinetics of the removal process. Microcosms were set up with filter sand, treated water, and the pesticides or metabolites mecoprop (MCPP), bentazone, glyphosate and p-nitrophenol were applied in initial concentrations of 0.03-2.4 μg/L. In all the investigated waterworks the concentration of pesticides in the water decreased - MCPP decreased to 42-85%, bentazone to 15-35%, glyphosate to 7-14% and p-nitrophenol 1-3% - from the initial concentration over a period of 6-13 days. Mineralisation of three out of four investigated pesticides was observed at Sjælsø waterworks Plant II - up to 43% of the initial glyphosate was mineralised within six days. At Sjælsø waterworks Plant II the removal kinetics of bentazone revealed that less than 30 min was needed to remove 50% of the bentazone at all the tested initial concentrations (0.1-2.4 μg/L). Increased oxygen availability led to greater and faster removal of bentazone in the microcosms. After 1 h, bentazone removal (an initial bentazone concentration of 0.1 μg/L) increased from 0.21%/g filter sand to 0.75%/g filter sand, when oxygen availability was increased from 0.28 mg O2/g filter sand to 1.09 mg O2/g filter sand. Bentazone was initially cleaved in the removal process. A metabolite, which contained the carbonyl group, was removed rapidly from the water phase and slowly mineralised after 24 h, while a metabolite which contained the benzene-ring was still present in the water phase. However, the microbial removal of this metabolite was initiated over seven days. Copyright © 2013 Elsevier Ltd. All rights reserved.

Plant-microbe interactions as drivers of ecosystem functions relevant for the biodegradation of organic contaminants.

PubMed

Fester, Thomas; Giebler, Julia; Wick, Lukas Y; Schlosser, Dietmar; Kästner, Matthias

2014-06-01

The plant organism and associated microbial communities can be seen as a sunlight driven hotspot for the turnover of organic chemicals. In such environments the fate of a chemical will not only depend on its intrinsic structural stability toward (bio-)chemical reactions and its bioavailability but also on the functional effectiveness and stability of natural microbial communities as main drivers of natural attenuation of chemicals. Recent research demonstrates that interactions between plants and microorganisms are crucial for the biotransformation of organic chemicals, for various processes affecting the bioavailability of such compounds, and for the stability of the affected ecosystem. Practical bioremediation approaches, therefore, should encompass integrated measures targeting functional vegetation as well as functional microbial communities. Good examples for a successful practical approach are constructed wetlands, where an artificial, simplified ecosystem is used for the detoxification of organic contaminants. While such systems have considerable practical success, they are often treated as a black box and a sound mechanistic understanding of functional resilience and of the 'reactive power' of such plant-microbe ecosystems is poor. This situation has to change, if progress in the application of bioremediation is to be made. Copyright © 2014 Elsevier Ltd. All rights reserved.

Replicating the microbial community and water quality performance of full-scale slow sand filters in laboratory-scale filters.

PubMed

Haig, Sarah-Jane; Quince, Christopher; Davies, Robert L; Dorea, Caetano C; Collins, Gavin

2014-09-15

Previous laboratory-scale studies to characterise the functional microbial ecology of slow sand filters have suffered from methodological limitations that could compromise their relevance to full-scale systems. Therefore, to ascertain if laboratory-scale slow sand filters (L-SSFs) can replicate the microbial community and water quality production of industrially operated full-scale slow sand filters (I-SSFs), eight cylindrical L-SSFs were constructed and were used to treat water from the same source as the I-SSFs. Half of the L-SSFs sand beds were composed of sterilized sand (sterile) from the industrial filters and the other half with sand taken directly from the same industrial filter (non-sterile). All filters were operated for 10 weeks, with the microbial community and water quality parameters sampled and analysed weekly. To characterize the microbial community phyla-specific qPCR assays and 454 pyrosequencing of the 16S rRNA gene were used in conjunction with an array of statistical techniques. The results demonstrate that it is possible to mimic both the water quality production and the structure of the microbial community of full-scale filters in the laboratory - at all levels of taxonomic classification except OTU - thus allowing comparison of LSSF experiments with full-scale units. Further, it was found that the sand type composing the filter bed (non-sterile or sterile), the water quality produced, the age of the filters and the depth of sand samples were all significant factors in explaining observed differences in the structure of the microbial consortia. This study is the first to the authors' knowledge that demonstrates that scaled-down slow sand filters can accurately reproduce the water quality and microbial consortia of full-scale slow sand filters. Copyright © 2014 Elsevier Ltd. All rights reserved.

[Characteristics of microbial community and operation efficiency in biofilter process for drinking water purification].

PubMed

Xiang, Hong; Lü, Xi-Wu; Yang, Fei; Yin, Li-Hong; Zhu, Guang-Can

2011-04-01

In order to explore characteristics of microbial community and operation efficiency in biofilter (biologically-enhanced active filter and biological activated carbon filter) process for drinking water purification, Biolog and polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) techniques were applied to analyze the metabolic function and structure of microbial community developing in biofilters. Water quality parameters, such as NH; -N, NO; -N, permanganate index, UV254 and BDOC etc, were determined in inflow and outflow of biofilters for investigation of operation efficiency of the biofilters. The results show that metabolic capacity of microbial community of the raw water is reduced after the biofilters, which reflect that metabolically active microbial communities in the raw water can be intercepted by biofilters. After 6 months operation of biofilters, the metabolic profiles of microbial communities are similar between two kinds of biologically-enhanced active filters, and utilization of carbon sources of microbial communities in the two filters are 73.4% and 75.5%, respectively. The metabolic profiles of microbial communities in two biological activated carbon filters showed significant difference. The carbon source utilization rate of microbial community in granule-activated carbon filter is 79.6%, which is obviously higher than 53.8% of the rate in the columnar activated carbon filter (p < 0.01). The analysis results of PCR-SSCP indicate that microbial communities in each biofilter are variety, but the structure of dominant microorganisms is similar among different biofilters. The results also show that the packing materials had little effect on the structure and metabolic function of microbial community in biologically-enhanced active filters, and the difference between two biofilters for the water purification efficiency was not significant (p > 0.05). However, in biological activated carbon filters, granule-activated carbon is conducive to microbial growth and reproduction, and the microbial communities in the biofilter present high metabolic activities, and the removal efficiency for NH4(+)-N, permanganate index and BDOC is better than the columnar activated carbon filter(p < 0.05). The results also suggest that operation efficiency of biofilter is related to the metabolic capacity of microbial community in biofilter.

Combined air and water pollution control system

NASA Technical Reports Server (NTRS)

Wolverton, Billy C. (Inventor); Jarrell, Lamont (Inventor)

1990-01-01

A bioaquatic air pollution control system for controlling both water and atmospheric pollution is disclosed. The pollution control system includes an exhaust for directing polluted gases out of a furnace and a fluid circulating system which circulates fluid, such as waste water, from a source, past the furnace where the fluid flow entrains the pollutants from the furnace. The combined fluid and pollutants are then directed through a rock/plant/microbial filtering system. A suction pump pumps the treated waste water from the filter system past the exhaust to again entrain more pollutants from the furnace where they are combined with the fluid (waste water) and directed to the filter system.

Microbial Glucuronoyl Esterases: 10 Years after Discovery

PubMed Central

2016-01-01

A carbohydrate esterase called glucuronoyl esterase (GE) was discovered 10 years ago in a cellulolytic system of the wood-rotting fungus Schizophyllum commune. Genes coding for GEs were subsequently found in a number of microbial genomes, and a new family of carbohydrate esterases (CE15) has been established. The multidomain structures of GEs, together with their catalytic properties on artificial substrates and positive effect on enzymatic saccharification of plant biomass, led to the view that the esterases evolved for hydrolysis of the ester linkages between 4-O-methyl-d-glucuronic acid of plant glucuronoxylans and lignin alcohols, one of the crosslinks in the plant cell walls. This idea of the function of GEs is further supported by the effects of cloning of fungal GEs in plants and by very recently reported evidence for changes in the size of isolated lignin-carbohydrate complexes due to uronic acid de-esterification. These facts make GEs interesting candidates for biotechnological applications in plant biomass processing and genetic modification of plants. This article is a brief summary of current knowledge of these relatively recent and unexplored esterases. PMID:27694239

Effects of antimicrobial treatment on fiberglass-acrylic filters.

PubMed

Cecchini, C; Verdenelli, M C; Orpianesi, C; Dadea, G M; Cresci, A

2004-01-01

The aims of the present study were to: (i) analyse a group of antimicrobial agents and to select the most active against test microbial strains; (ii) test the effect of the antimicrobial treatment on air filters in order to reduce microbial colonization. Different kinds of antimicrobial agents were analysed to assess their compatibility with the production process of air filter media. The minimal inhibitory concentration for each antimicrobial agent was determined against a defined list of microbial strains, and an antimicrobial activity assay of filter prototypes was developed to determine the most active agent among the compatible antimicrobials. Then, the most active was chosen and added directly to the filter during the production process. The microbial colonization of treated and untreated filter media was assessed at different working times for different incubation times by stereomicroscope and scanning electron microscope analysis. Some of the antimicrobial agents analysed were more active against microbial test strains and compatible with the production process of the filter media. Filter sections analysis of treated filter media showed a significantly lower microbial colonization than those untreated, a reduction of species both in density and varieties and of the presence of bacteria and fungal hyphae with reproductive structures. This study demonstrated the ability of antimicrobial treatments to inhibit the growth of micro-organisms in filter media and subsequently to increase indoor air quality (IAQ), highlighting the value of adding antimicrobials to filter media. To make a contribution to solving the problem of microbial contamination of air filters, by demonstrating the efficacy of incorporating antimicrobial agents in the filter media to improve IAQ and health.

Abiotic Nitrous Oxide Production in Natural and Artificial Seawater

NASA Astrophysics Data System (ADS)

Ochoa, H.; Stanton, C. L.; Cavazos, A. R.; Ostrom, N. E.; Glass, J. B.

2014-12-01

The ocean contributes approximately one third of global sources of nitrous oxide (N2O) to the atmosphere. While nitrification is thought to be the dominant pathway for marine N2O production, mechanisms remain unresolved. Previous studies have carried the implicit assumption that marine N2O originates directly from enzymatic sources. However, abiotic production of N2O is possible via chemical reactions between nitrogenous intermediates and redox active trace metals in seawater. In this study, we investigated N2O production and isotopic composition in treatments with and without added hydroxylamine (NH2OH) and nitric oxide (NO), intermediates in microbial oxidation of ammonia to nitrite, and Fe(III). Addition of substrates to sterile artificial seawater was compared with filtered and unfiltered seawater from Sapelo Island, coastal Georgia, USA. N2O production was observed immediately after addition of Fe(III) in the presence of NH2OH at pH 8 in sterile artificial seawater. Highest N2O production was observed in the presence of Fe(III), NO, and NH2OH. The isotopomer site preference of abiotically produced N2O was consistent with previous studies (31 ± 2 ‰). Higher abiotic N2O production was observed in sterile artificial seawater (salinity: 35 ppt) than filtered Sapelo Island seawater (salinity: 25 ppt) whereas diluted sterile artificial seawater (18 ppt) showed lowest N2O production, suggesting that higher salinity promotes enhanced abiotic N2O production. Addition of Fe(III) to unfiltered Sapelo Island seawater stimulated N2O production. The presence of ammonia-oxidizing archaea (AOA), which lack known N2O producing enzymes, in Sapelo Island seawater was confirmed by successful amplification of the archaeal amoA gene, whereas ammonia-oxidizing bacteria (AOB), which contain N2O-producing enzymes were undetected. Given the few Fe-containing proteins present in AOA, it is likely that Fe(III) addition promoted N2O production via an abiotic vs. enzymatic N2O mechanism. Overall, this study suggests that abiotic N2O production may be occurring in marine environments where microbial ammonia oxidation occurs in the presence of elevated Fe and/or other redox-active metals, such as coastal areas, oxygen minimum zones, and near the sediment-water interface.

Global-Scale Structure of the Eelgrass Microbiome.

PubMed

Fahimipour, Ashkaan K; Kardish, Melissa R; Lang, Jenna M; Green, Jessica L; Eisen, Jonathan A; Stachowicz, John J

2017-06-15

Plant-associated microorganisms are essential for their hosts' survival and performance. Yet, most plant microbiome studies to date have focused on terrestrial species sampled across relatively small spatial scales. Here, we report the results of a global-scale analysis of microbial communities associated with leaf and root surfaces of the marine eelgrass Zostera marina throughout its range in the Northern Hemisphere. By contrasting host microbiomes with those of surrounding seawater and sediment, we uncovered the structure, composition, and variability of microbial communities associated with eelgrass. We also investigated hypotheses about the assembly of the eelgrass microbiome using a metabolic modeling approach. Our results reveal leaf communities displaying high variability and spatial turnover that mirror their adjacent coastal seawater microbiomes. By contrast, roots showed relatively low compositional turnover and were distinct from surrounding sediment communities, a result driven by the enrichment of predicted sulfur-oxidizing bacterial taxa on root surfaces. Predictions from metabolic modeling of enriched taxa were consistent with a habitat-filtering community assembly mechanism whereby similarity in resource use drives taxonomic cooccurrence patterns on belowground, but not aboveground, host tissues. Our work provides evidence for a core eelgrass root microbiome with putative functional roles and highlights potentially disparate processes influencing microbial community assembly on different plant compartments. IMPORTANCE Plants depend critically on their associated microbiome, yet the structure of microbial communities found on marine plants remains poorly understood in comparison to that for terrestrial species. Seagrasses are the only flowering plants that live entirely in marine environments. The return of terrestrial seagrass ancestors to oceans is among the most extreme habitat shifts documented in plants, making them an ideal testbed for the study of microbial symbioses with plants that experience relatively harsh abiotic conditions. In this study, we report the results of a global sampling effort to extensively characterize the structure of microbial communities associated with the widespread seagrass species Zostera marina , or eelgrass, across its geographic range. Our results reveal major differences in the structure and composition of above- versus belowground microbial communities on eelgrass surfaces, as well as their relationships with the environment and host. Copyright © 2017 Fahimipour et al.

Method for enhanced longevity of in situ microbial filter used for bioremediation

DOEpatents

Carman, M.L.; Taylor, R.T.

1999-03-30

An improved method is disclosed for in situ microbial filter bioremediation having increasingly operational longevity of an in situ microbial filter emplaced into an aquifer. A method is presented for generating a microbial filter of sufficient catalytic density and thickness, which has increased replenishment interval, improved bacteria attachment and detachment characteristics and the endogenous stability under in situ conditions. A system is also disclosed for in situ field water remediation. 31 figs.

Controlled Microbial Cenoses in Closed Spaces

NASA Astrophysics Data System (ADS)

Somova, Lydia; Mikheeva, Galina

Controlled microbial cenoses have good prospects in closed spaces: for air treatment in LSS and cellars industrial premises; for sewage treatment in LSS; for increase of productivity and protect of plants from infections in LSS. Possible methods of formation of microbiocenoses are: selection, autoselection, artificial formation taking into account their biochemical properties and metabolic interactions. Experimental microbiocenoses, has been produced on the basis of natural association of microorganisms by long cultivation on specially developed medium. Dominating groups are bacteria of genera: Lactobacillus, Streptococcus, Leuconostoc, Bidobac-terium, Rhodopseudomonas and yeast of genera: Kluyveromyces, Saccharomyces and Torulop-sis. Microbiocenoses do not contain pathogenic and conditionally pathogenic microorganisms, they possess opposing and probiotic properties. Different examples of microbial cenoses actions are to be presented in the paper.

Isolation and identification of culturable bacteria, capable of heterotrophic growth, from rapid sand filters of drinking water treatment plants.

PubMed

Vandermaesen, Johanna; Lievens, Bart; Springael, Dirk

The microbial community in sand filters (SFs) of drinking water treatment plants (DWTPs) likely contributes to SF functionalities, such as organic carbon removal through heterotrophic metabolism. However, the dynamics and functionality of the SF microbiome and microbial communities in oligotrophic freshwater environments in general, are poorly understood. Therefore, the availability of bacterial strains from these oligotrophic environments is of great interest, but such organisms are currently underrepresented in culture collections. Focusing on heterotrophic carbon metabolism, bacteria were isolated from SFs using conventional media and media that contained SF extracts to mimic the SF environment. The majority of isolates belonged to Betaproteobacteria, more specifically to the families Comamonadaceae (genera Acidovorax, Curvibacter, Hydrogenophaga, Simplicispira, Paucibacter, Pelomonas, Piscinibacter and Rhodoferax) and Oxalobacteraceae (Undibacterium). Additionally, members of Alphaproteobacteria (Mesorhizobium), Gammaproteobacteria (Aeromonas and Perlucidibaca) and Actinobacteria (Rhodococcus and Brachybacterium) were isolated. Several of those genera have only rarely been described, but appear typical inhabitants of oligotrophic freshwater environments. In this regard, the Comamonadaceae isolates are of particular interest. Our study shows that bacteria representative of oligotrophic environments can be isolated using simple isolation procedures. The isolates provide a microbial framework for extending our knowledge of the taxonomy, physiology and functionality of oligotrophic freshwater microbiomes and their interactions with possible invaders. Copyright © 2017 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Plant Volatile Genomics: Recent Developments and Putative Applications in Agriculture.

PubMed

Paul, Ishita; Bhadoria, Pratapbhanu Singh; Mitra, Adinpunya

2016-01-01

The review of patents reveals that investigation of plant volatiles and their biosynthetic pathways is a relatively new field in plant biochemistry. The diversity of structure and function of these volatiles is gradually being understood. However, the great diversity of volatile biochemicals plants emit through different parts plays numerous roles in stress resistance and other ecological interactions. From an agronomic point of view, regulation volatile production in crop plants may lead to desirable changes in plant defence, pollinator attraction and post-harvest qualities. In several crop species, genetic manipulation or metabolic channelling have led to altered emission I aroma profiles. This short review summarizes some recent cases of artificial manipulation of volatile profile in planta or in transformed microbial systems.

21 CFR 878.5040 - Suction lipoplasty system.

Code of Federal Regulations, 2010 CFR

2010-04-01

.... The device consists of a powered suction pump (containing a microbial filter on the exhaust and a microbial in-line filter in the connecting tubing between the collection bottle and the safety trap), collection bottle, cannula, and connecting tube. The microbial filters, tubing, collection bottle, and...

21 CFR 878.5040 - Suction lipoplasty system.

Code of Federal Regulations, 2011 CFR

2011-04-01

.... The device consists of a powered suction pump (containing a microbial filter on the exhaust and a microbial in-line filter in the connecting tubing between the collection bottle and the safety trap), collection bottle, cannula, and connecting tube. The microbial filters, tubing, collection bottle, and...

Bacterial Shifts in Nutrient Solutions Flowing Through Biofilters Used in Tomato Soilless Culture.

PubMed

Renault, David; Déniel, Franck; Vallance, Jessica; Bruez, Emilie; Godon, Jean-Jacques; Rey, Patrice

2017-11-25

In soilless culture, slow filtration is used to eliminate plant pathogenic microorganisms from nutrient solutions. The present study focused on the characterization and the potential functions of microbial communities colonizing the nutrient solutions recycled on slow filters during a whole cultivation season of 7 months in a tomato growing system. Bacterial microflora colonizing the solutions before and after they flew through the columns were studied. Two filters were amended with Pseudomonas putida (P-filter) or Bacillus cereus strains (B-filter), and a third filter was a control (C-filter). Biological activation of filter unit through bacterial amendment enhanced very significantly filter efficacy against plant potential pathogens Pythium spp. and Fusarium oxysporum. However, numerous bacteria (10 3 -10 4  CFU/mL) were detected in the effluent solutions. The community-level physiological profiling indicated a temporal shift of bacterial microflora, and the metabolism of nutrient solutions originally oriented towards carbohydrates progressively shifted towards degradation of amino acids and carboxylic acids over the 7-month period of experiment. Single-strand conformation polymorphism fingerprinting profiles showed that a shift between bacterial communities colonizing influent and effluent solutions of slow filters occurred. In comparison with influent, 16S rDNA sequencing revealed that phylotype diversity was low in the effluent of P- and C-filters, but no reduction was observed in the effluent of the B-filter. Suppressive potential of solutions filtered on a natural filter (C-filter), where the proportion of Proteobacteria (α- and β-) increased, whereas the proportion of uncultured candidate phyla rose in P- and B-filters, is discussed.

Microbial Contamination of Ice Machines Is Mediated by Activated Charcoal Filtration Systems in a City Hospital.

PubMed

Yorioka, Katsuhiro; Oie, Shigeharu; Hayashi, Koji; Kimoto, Hiroo; Furukawa, Hiroyuki

2016-06-01

Although microbial contamination of ice machines has been reported, no previous study has addressed microbial contamination of ice produced by machines equipped with activated charcoal (AC) filters in hospitals. The aim of this study was to provide clinical data for evaluating AC filters to prevent microbial contamination of ice. We compared microbial contamination in ice samples produced by machines with (n = 20) and without an AC filter (n = 40) in Shunan City Shinnanyo Municipal Hospital. All samples from the ice machine equipped with an AC filter contained 10-116 CFUs/g of glucose nonfermenting gram-negative bacteria such as Pseudomonas aeruginosa and Chryseobacterium meningosepticum. No microorganisms were detected in samples from ice machines without AC filters. After the AC filter was removed from the ice machine that tested positive for Gram-negative bacteria, the ice was resampled (n = 20). Analysis found no contaminants. Ice machines equipped with AC filters pose a serious risk factor for ice contamination. New filter-use guidelines and regulations on bacterial detection limits to prevent contamination of ice in healthcare facilities are necessary.

Short-term microbial dynamics in a drinking water plant treating groundwater with occasional high microbial loads.

PubMed

Besmer, Michael D; Hammes, Frederik

2016-12-15

Short-term fluctuations in bacterial concentrations in drinking water systems, occurring on time scales of hours-to-weeks, are essentially unexplored due to a lack of microbial monitoring tools that allow high frequency measurements. Here, we applied fully automated online flow cytometry to measure the total cell concentrations (TCC) in both raw water (karstic groundwater) and treated water (flocculation - ultrafiltration (UF) - ozonation - granular active carbon (GAC) filtration) during a period of 70 days at high temporal resolution (n > 4000 for both water types). We detected and characterized in considerable detail aperiodic fluctuations in the raw water following regional precipitation, with TCC increasing up to 50-fold from a dry weather baseline of approximately 120 cells μl -1 to an event peak of > 5000 cells μl -1 . Moreover, we observed the buffering of the treatment plant against these fluctuations, but in addition we recorded a completely unexpected periodic fluctuation of TCC in the treated water after GAC filtration. We concluded that the latter was the result of fluctuating water abstraction from the treatment plant reservoir by two connected water utilities, which resulted in variations in water throughput in the plant. This in turn influenced bacterial detachment and dilution in the GAC filter. This study provides strong evidence of multiple different microbial dynamics occurring in a drinking water treatment system. Given numerous possible sources of natural and operational fluctuations in raw water and drinking water treatment plants, such microbial fluctuations should be expected in many systems. The high-frequency monitoring approach presented herein can improve the understanding and eventual mitigation of such fluctuations. Copyright © 2016 Elsevier Ltd. All rights reserved.

A computational fluid dynamics simulation of the hypersonic flight of the Pegasus(TM) vehicle using an artificial viscosity model and a nonlinear filtering method. M.S. Thesis

NASA Technical Reports Server (NTRS)

Mendoza, John Cadiz

1995-01-01

The computational fluid dynamics code, PARC3D, is tested to see if its use of non-physical artificial dissipation affects the accuracy of its results. This is accomplished by simulating a shock-laminar boundary layer interaction and several hypersonic flight conditions of the Pegasus(TM) launch vehicle using full artificial dissipation, low artificial dissipation, and the Engquist filter. Before the filter is applied to the PARC3D code, it is validated in one-dimensional and two-dimensional form in a MacCormack scheme against the Riemann and convergent duct problem. For this explicit scheme, the filter shows great improvements in accuracy and computational time as opposed to the nonfiltered solutions. However, for the implicit PARC3D code it is found that the best estimate of the Pegasus experimental heat fluxes and surface pressures is the simulation utilizing low artificial dissipation and no filter. The filter does improve accuracy over the artificially dissipative case but at a computational expense greater than that achieved by the low artificial dissipation case which has no computational time penalty and shows better results. For the shock-boundary layer simulation, the filter does well in terms of accuracy for a strong impingement shock but not as well for weaker shock strengths. Furthermore, for the latter problem the filter reduces the required computational time to convergence by 18.7 percent.

Composition and Variability of Biofouling Organisms in Seawater Reverse Osmosis Desalination Plants ▿ †

PubMed Central

Zhang, Minglu; Jiang, Sunny; Tanuwidjaja, Dian; Voutchkov, Nikolay; Hoek, Eric M. V.; Cai, Baoli

2011-01-01

Seawater reverse osmosis (SWRO) membrane biofouling remains a common challenge in the desalination industry, but the marine bacterial community that causes membrane fouling is poorly understood. Microbial communities at different stages of treatment processes (intake, cartridge filtration, and SWRO) of a desalination pilot plant were examined by both culture-based and culture-independent approaches. Bacterial isolates were identified to match the genera Shewanella, Alteromonas, Vibrio, and Cellulophaga based on 16S rRNA gene sequencing analysis. The 16S rRNA gene clone library of the SWRO membrane biofilm showed that a filamentous bacterium, Leucothrix mucor, which belongs to the gammaproteobacteria, accounted for nearly 30% of the clone library, while the rest of the microorganisms (61.2% of the total clones) were related to the alphaproteobacteria. 16S rRNA gene terminal restriction fragment length polymorphism (T-RFLP) analysis indicated that bacteria colonizing the SWRO membrane represented a subportion of microbes in the source seawater; however, they were quite different from those colonizing the cartridge filter. The examination of five SWRO membranes from desalination plants located in different parts of the world showed that although the bacterial communities from the membranes were not identical to each other, some dominant bacteria were commonly observed. In contrast, bacterial communities in source seawater were significantly different based on location and season. Microbial profiles from 14 cartridge filters collected from different plants also revealed spatial trends. PMID:21551282

Performance of conventional multi-barrier drinking water treatment plants for the removal of four artificial sweeteners.

PubMed

Scheurer, Marco; Storck, Florian R; Brauch, Heinz-J; Lange, Frank T

2010-06-01

Due to incomplete removal of artificial sweeteners in wastewater treatment plants some of these compounds end up in receiving surface waters, which are used for drinking water production. The sum of removal efficiency of single treatment steps in multi-barrier treatment systems affects the concentrations of these compounds in the provided drinking water. This is the first systematic study revealing the effectiveness of single treatment steps in laboratory experiments and in waterworks. Six full-scale waterworks using surface water influenced raw water were sampled up to ten times to study the fate of acesulfame, saccharin, cyclamate and sucralose. For the most important treatment technologies the results were confirmed by laboratory batch experiments. Saccharin and cyclamate proved to play a minor role for drinking water treatment plants as they were eliminated by nearly 100% in all waterworks with biologically active treatment units like river bank filtration (RBF) or artificial groundwater recharge. Acesulfame and sucralose were not biodegraded during RBF and their suitability as wastewater tracers under aerobic conditions was confirmed. Sucralose proved to be persistent against ozone and its transformation was < 20% in lab and field investigations. Remaining traces were completely removed by subsequent granular activated carbon (GAC) filters. Acesulfame readily reacts with ozone (pseudo first-order rate constant k = 1.3 x 10(-3) s(-1) at 1 mg L(-1) ozone concentration). However, the applied ozone concentrations and contact times under typical waterworks conditions only led to an incomplete removal (18-60%) in the ozonation step. Acesulfame was efficiently removed by subsequent GAC filters with a low throughput of less than 30 m(3) kg(-1), but removal strongly depended on the GAC preload. Thus, acesulfame was detected up to 0.76 microg L(-1) in finished water. 2010 Elsevier Ltd. All rights reserved.

Nutrient Considerations for Plants Grown Under Space Flight Conditions

NASA Technical Reports Server (NTRS)

Levine, Howard G.; Krikorian, Abraham D.

2006-01-01

We present here results on the analysis of 100 mL medium samples extracted from sterilized foam (Smithers-Oasis, Kent OH) used to support the growth of both dicotyledonous (Haplopappus gracilis, n=75) and monocotyledonous (Hemerocallis cv Autumn Blaze, n=25) aseptic plants in NASA's Plant Growth Unit (PGU) during the 5-day CHROMEX-01 Space Shuttle flight (March 1989, STS-29). At recovery, the medium remaining within each of the five floral foam blocks (for both the space flight and ground control experiments) was extracted under vacuum, filtered and subjected to elemental analyses. Concentration levels of some elements remained the same, while some decreased and others increased. A unique aspect of this experiment was that all plants were either aseptic tissue culture generated plantlets or sterile seedling clones, and the design of the PGU facilitated the maintenance of asepsis throughout the mission (confirmed by postflight microbial sampling). This permitted the elimination of microbial considerations in the interpretation of the data. The significance of these findings for growing plants in altered gravity environments are discussed.

The Metagenome of Utricularia gibba's Traps: Into the Microbial Input to a Carnivorous Plant

PubMed Central

Alcaraz, Luis David; Martínez-Sánchez, Shamayim; Torres, Ignacio; Ibarra-Laclette, Enrique; Herrera-Estrella, Luis

2016-01-01

The genome and transcriptome sequences of the aquatic, rootless, and carnivorous plant Utricularia gibba L. (Lentibulariaceae), were recently determined. Traps are necessary for U. gibba because they help the plant to survive in nutrient-deprived environments. The U. gibba's traps (Ugt) are specialized structures that have been proposed to selectively filter microbial inhabitants. To determine whether the traps indeed have a microbiome that differs, in composition or abundance, from the microbiome in the surrounding environment, we used whole-genome shotgun (WGS) metagenomics to describe both the taxonomic and functional diversity of the Ugt microbiome. We collected U. gibba plants from their natural habitat and directly sequenced the metagenome of the Ugt microbiome and its surrounding water. The total predicted number of species in the Ugt was more than 1,100. Using pan-genome fragment recruitment analysis, we were able to identify to the species level of some key Ugt players, such as Pseudomonas monteilii. Functional analysis of the Ugt metagenome suggests that the trap microbiome plays an important role in nutrient scavenging and assimilation while complementing the hydrolytic functions of the plant. PMID:26859489

Gut microbial adaptation to dietary consumption of fructose, artificial sweeteners and sugar alcohols: implications for host-microbe interactions contributing to obesity.

PubMed

Payne, A N; Chassard, C; Lacroix, C

2012-09-01

The Western diet, comprised of highly refined carbohydrates and fat but reduced complex plant polysaccharides, has been attributed to the prevalence of obesity. A concomitant rise in the consumption of fructose and sugar substitutes such as sugar alcohols, artificial sweeteners, even rare sugars, has mirrored this trend, as both probable contributor and solution to the epidemic. Acknowledgement of the gut microbiota as a factor involved in obesity has sparked much controversy as to the cause and consequence of this relationship. Dietary intakes are a known modulator of gut microbial phylogeny and metabolic activity, frequently exploited to stimulate beneficial bacteria, promoting health benefits. Comparably little research exists on the impact of 'unconscious' dietary modulation on the resident commensal community mediated by increased fructose and sugar substitute consumption. This review highlights mechanisms of potential host and gut microbial fructose and sugar substitute metabolism. Evidence is presented suggesting these sugar compounds, particularly fructose, condition the microbiota, resulting in acquisition of a westernized microbiome with altered metabolic capacity. Disturbances in host-microbe interactions resulting from fructose consumption are also explored. © 2012 The Authors. obesity reviews © 2012 International Association for the Study of Obesity.

Ecology, Microbial

DOE Office of Scientific and Technical Information (OSTI.GOV)

Konopka, Allan

2009-05-15

Microbial ecology is a relatively young discipline within the field of microbiology. Its modern history spans just the past 60 years, and the field is defined by its emphasis on understanding the interactions of microbes with their environment, rather than their behavior under artificial laboratory conditions. Because microbes are ubiquitous, microbial ecologists study a broad diversity of habitats that range from aquatic to terrestrial to plant- or animal-associated. This has made it a challenge to identify unifying principles within the field. One approach is to recognize that although the activity of microbes in nature have effects at the macroscale, theymore » interact with their physical, chemical and biological milieu at a scale of micrometers. At this scale, several different microbial ecosystems can be defined, based upon association with particles, the presence of environmental gradients and the continuous availability of water. Principles applicable to microbial ecology reflect not only their population ecology and physiological ecology, but also their broad versatility and quantitative importance in the biosphere as biogeochemical catalysts and capacity for rapid physiological and evolutionary responses.« less

Comparison of aerobically-treated and untreated crop residue as a source of recycled nutrients in a recirculating hydroponic system

NASA Technical Reports Server (NTRS)

Mackowiak, C. L.; Garland, J. L.; Strayer, R. F.; Finger, B. W.; Wheeler, R. M.

1996-01-01

This study compared the growth of potato plants on nutrients recycled from inedible potato biomass. Plants were grown for 105 days in recirculating, thin-film hydroponic systems containing four separate nutrient solution treatments: (1) modified half-strength Hoagland's (control), 2) liquid effluent from a bioreactor containing inedible potato biomass, 3) filtered (0.2 micrometer) effluent, and 4) the water soluble fraction of inedible potato biomass (leachate). Approximately 50% of the total nutrient requirement in treatments 2-4 were provided (recycled) from the potato biomass. Leachate had an inhibitory effect on leaf conductance, photosynthetic rate, and growth (50% reduction in plant height and 60% reduction in tuber yield). Plants grown on bioreactor effluent (filtered or unfiltered) were similar to the control plants. These results indicated that rapidly degraded, water soluble organic material contained in the inedible biomass, i.e., material in leachate, brought about phytotoxicity in the hydroponic culture of potato. Recalcitrant, water soluble organic material accumulated in all nutrient recycling treatments (650% increase after 105 days), but no increase in rhizosphere microbial numbers was observed.

Microbial survey of a full-scale, biologically active filter for treatment of drinking water.

PubMed

White, Colin P; Debry, Ronald W; Lytle, Darren A

2012-09-01

The microbial community of a full-scale, biologically active drinking water filter was surveyed using molecular techniques. Nitrosomonas, Nitrospira, Sphingomonadales, and Rhizobiales dominated the clone libraries. The results elucidate the microbial ecology of biological filters and demonstrate that biological treatment of drinking water should be considered a viable alternative to physicochemical methods.

Characterization of the microbial community structure and nitrosamine-reducing isolates in drinking water biofilters.

PubMed

Wang, Wanfeng; Guo, Yanling; Yang, Qingxiang; Huang, Yao; Zhu, Chunyou; Fan, Jing; Pan, Feng

2015-07-15

Two biofilters were constructed using biological activated carbon (BAC) and nitrosamine-containing water from two drinking water treatment plants. The microbiome of each biofilter was characterized by 454 high-throughput pyrosequencing, and one nitrosamine-reducing bacterium was isolated. The results showed that nitrosamines changed the relative abundance at both the phylum and class levels, and the new genera were observed in the microbial communities of the two BAC filters after cultivation. As such, the genus Rhodococcus, which includes many nitrosamine-reducing strains reported in previous studies, was only detected in the BAC2 filter after cultivation. These findings indicate that nitrosamines can significantly affect the genus level in the microbial communities. Furthermore, the isolated bacterial culture Rhodococcus cercidiphylli A41 AS-1 exhibited the ability to reduce five nitrosamines (N-nitrosodimethylamine, N-nitrosodiethylamine, N-nitrosodi-n-propylamine, N-nitrosopyrrolidine, and N-nitrosodi-n-butylamine) with removal ratios that ranged from 38.1% to 85.4%. The isolate exhibited a better biodegradation ability with nitrosamine as the carbon source when compared with nitrosamine as the nitrogen source. This study increases our understanding of the microbial community in drinking water biofilters with trace quantities of nitrosamines, and provides information on the metabolism of nitrosamine-reducing bacteria. Copyright © 2015. Published by Elsevier B.V.

Animal protein production modules in biological life support systems: Novel combined aquaculture techniques based on the closed equilibrated biological aquatic system (C.E.B.A.S.)

NASA Astrophysics Data System (ADS)

Blüm, V.; Andriske, M.; Kreuzberg, K.; Schreibman, M. P.

Based on the experiences made with the Closed Equilibrated Biological Aquatic System (C.E.B.A.S.) which was primarily deveoloped for long-term and multi-generation experiments with aquatic animals and plants in a space station highly effective fresh water recycling modules were elaborated utilizing a combination of ammonia oxidizing bacteria filters and higher plants. These exhibit a high effectivity to eliminate phosphate and anorganic nitrogen compounds and arc. in addidition. able to contribute to the oxygen supply of the aquatic animals. The C.E.B.A.S. filter system is able to keep a closed artificial aquatic ecosystem containing teleost fishes and water snails biologically stable for several month and to eliminate waste products deriving from degraded dead fishes without a decrease of the oxygen concentration down to less than 3.5 mg/l at 25 °C. More advanced C.E.B.A.S. filter systems, the BIOCURE filters, were also developed for utilization in semiintensive and intensive aquaculture systems for fishes. In fact such combined animal-plant aquaculture systems represent highly effective productions sites for human food if proper plant and fish species are selected The present papers elucidates ways to novel aquaculture systems in which herbivorous fishes are raised by feeding them with plant biomass produced in the BIOCURE filters and presents the scheme of a modification which utilizes a plant species suitable also for human nutrition. Special attention is paid to the benefits of closed aquaculture system modules which may be integrated into bioregenerative life support systems of a higher complexity for, e. g.. lunar or planetary bases including some psychologiccal aspects of the introduction of animal protein production into plant-based life support systems. Moreover, the basic reproductive biological problems of aquatic animal breeding under reduced gravity are explained leading to a disposition of essential research programs in this context.

Application of Pulsed Electrical Fields for Advanced Cooling and Water Recovery in Coal-Fired Power Plant

DOE Office of Scientific and Technical Information (OSTI.GOV)

Young Cho; Alexander Fridman

2009-04-02

The overall objective of the present work was to develop technologies to reduce freshwater consumption in a cooling tower of coal-based power plant so that one could significantly reduce the need of make-up water. The specific goal was to develop a scale prevention technology based an integrated system of physical water treatment (PWT) and a novel filtration method so that one could reduce the need for the water blowdown, which accounts approximately 30% of water loss in a cooling tower. The present study investigated if a pulsed spark discharge in water could be used to remove deposits from the filtermore » membrane. The test setup included a circulating water loop and a pulsed power system. The present experiments used artificially hardened water with hardness of 1,000 mg/L of CaCO{sub 3} made from a mixture of calcium chloride (CaCl{sub 2}) and sodium carbonate (Na{sub 2}CO{sub 3}) in order to produce calcium carbonate deposits on the filter membrane. Spark discharge in water was found to produce strong shockwaves in water, and the efficiency of the spark discharge in cleaning filter surface was evaluated by measuring the pressure drop across the filter over time. Results showed that the pressure drop could be reduced to the value corresponding to the initial clean state and after that the filter could be maintained at the initial state almost indefinitely, confirming the validity of the present concept of pulsed spark discharge in water to clean dirty filter. The present study also investigated the effect of a plasma-assisted self-cleaning filter on the performance of physical water treatment (PWT) solenoid coil for the mitigation of mineral fouling in a concentric counterflow heat exchanger. The self-cleaning filter utilized shockwaves produced by pulse-spark discharges in water to continuously remove scale deposits from the surface of the filter, thus keeping the pressure drop across the filter at a relatively low value. Artificial hard water was used in the present fouling experiments for three different cases: no treatment, PWT coil only, and PWT coil plus self-cleaning filter. Fouling resistances decreased by 59-72% for the combined case of PWT coil plus filter compared with the values for no-treatment cases. SEM photographs showed much smaller particle sizes for the combined case of PWT coil plus filter as larger particles were continuously removed from circulating water by the filter. The x-ray diffraction data showed calcite crystal structures for all three cases.« less

Spatially Oscillating Activity and Microbial Succession of Mercury-Reducing Biofilms in a Technical-Scale Bioremediation System

PubMed Central

von Canstein, Harald; Li, Ying; Leonhäuser, Johannes; Haase, Elke; Felske, Andreas; Deckwer, Wolf-Dieter; Wagner-Döbler, Irene

2002-01-01

Mercury-contaminated chemical wastewater of a mercury cell chloralkali plant was cleaned on site by a technical-scale bioremediation system. Microbial mercury reduction of soluble Hg(II) to precipitating Hg(0) decreased the mercury load of the wastewater during its flow through the bioremediation system by up to 99%. The system consisted of a packed-bed bioreactor, where most of the wastewater's mercury load was retained, and an activated carbon filter, where residual mercury was removed from the bioreactor effluent by both physical adsorption and biological reduction. In response to the oscillation of the mercury concentration in the bioreactor inflow, the zone of maximum mercury reduction oscillated regularly between the lower and the upper bioreactor horizons or the carbon filter. At low mercury concentrations, maximum mercury reduction occurred near the inflow at the bottom of the bioreactor. At high concentrations, the zone of maximum activity moved to the upper horizons. The composition of the bioreactor and carbon filter biofilms was investigated by 16S-23S ribosomal DNA intergenic spacer polymorphism analysis. Analysis of spatial biofilm variation showed an increasing microbial diversity along a gradient of decreasing mercury concentrations. Temporal analysis of the bioreactor community revealed a stable abundance of two prevalent strains and a succession of several invading mercury-resistant strains which was driven by the selection pressure of high mercury concentrations. In the activated carbon filter, a lower selection pressure permitted a steady increase in diversity during 240 days of operation and the establishment of one mercury-sensitive invader. PMID:11916716

Activation of Actuating Hydrogels with WS2 Nanosheets for Biomimetic Cellular Structures and Steerable Prompt Deformation.

PubMed

Zong, Lu; Li, Xiankai; Han, Xiangsheng; Lv, Lili; Li, Mingjie; You, Jun; Wu, Xiaochen; Li, Chaoxu

2017-09-20

Macroscopic soft actuation is intrinsic to living organisms in nature, including slow deformation (e.g., contraction, bending, twisting, and curling) of plants motivated by microscopic swelling and shrinking of cells, and rapid motion of animals (e.g., deformation of jellyfish) motivated by cooperative nanoscale movement of motor proteins. These actuation behaviors, with an exceptional combination of tunable speed and programmable deformation direction, inspire us to design artificial soft actuators for broad applications in artificial muscles, nanofabrication, chemical valves, microlenses, soft robotics, etc. However, so far artificial soft actuators have been typically produced on the basis of poly(N-isopropylacrylamide) (PNiPAM), whose deformation is motived by volumetric shrinkage and swelling in analogue to plant cells, and exhibits sluggish actuation kinetics. In this study, alginate-exfoliated WS 2 nanosheets were incorporated into ice-template-polymerized PNiPAM hydrogels with the cellular microstructures which mimic plant cells, yet the prompt steerable actuation of animals. Because of the nanosheet-reinforced pore walls formed in situ in freezing polymerization and reasonable hierarchical water channels, this cellular hybrid hydrogel achieves super deformation speed (on the order of magnitude of 10° s), controllable deformation direction, and high near-infrared light responsiveness, offering an unprecedented platform of artificial muscles for various soft robotics and devices (e.g., rotator, microvalve, aquatic swimmer, and water-lifting filter).

Microbial Survey of a Full-Scale, Biologically Active Filter for Treatment of Drinking Water

PubMed Central

DeBry, Ronald W.; Lytle, Darren A.

2012-01-01

The microbial community of a full-scale, biologically active drinking water filter was surveyed using molecular techniques. Nitrosomonas, Nitrospira, Sphingomonadales, and Rhizobiales dominated the clone libraries. The results elucidate the microbial ecology of biological filters and demonstrate that biological treatment of drinking water should be considered a viable alternative to physicochemical methods. PMID:22752177

Laboratory method used for bioremediation

DOEpatents

Carman, M. Leslie; Taylor, Robert T.

2000-01-01

An improved method for in situ microbial filter bioremediation having increasingly operational longevity of an in situ microbial filter emplaced into an aquifer. A method for generating a microbial filter of sufficient catalytic density and thickness, which has increased replenishment interval, improved bacteria attachment and detachment characteristics and the endogenous stability under in situ conditions. A system for in situ field water remediation.

Photodegradation at day, microbial decomposition at night - decomposition in arid lands

NASA Astrophysics Data System (ADS)

Gliksman, Daniel; Gruenzweig, Jose

2014-05-01

Our current knowledge of decomposition in dry seasons and its role in carbon turnover is fragmentary. So far, decomposition during dry seasons was mostly attributed to abiotic mechanisms, mainly photochemical and thermal degradation, while the contribution of microorganisms to the decay process was excluded. We asked whether microbial decomposition occurs during the dry season and explored its interaction with photochemical degradation under Mediterranean climate. We conducted a litter bag experiment with local plant litter and manipulated litter exposure to radiation using radiation filters. We found notable rates of CO2 fluxes from litter which were related to microbial activity mainly during night-time throughout the dry season. This activity was correlated with litter moisture content and high levels of air humidity and dew. Day-time CO2 fluxes were related to solar radiation, and radiation manipulation suggested photodegradation as the underlying mechanism. In addition, a decline in microbial activity was followed by a reduction in photodegradation-related CO2 fluxes. The levels of microbial decomposition and photodegradation in the dry season were likely the factors influencing carbon mineralization during the subsequent wet season. This study showed that microbial decomposition can be a dominant contributor to CO2 emissions and mass loss in the dry season and it suggests a regulating effect of microbial activity on photodegradation. Microbial decomposition is an important contributor to the dry season decomposition and impacts the annual litter turn-over rates in dry regions. Global warming may lead to reduced moisture availability and dew deposition, which may greatly influence not only microbial decomposition of plant litter, but also photodegradation.

Bacterial community structure and variation in a full-scale seawater desalination plant for drinking water production.

PubMed

Belila, A; El-Chakhtoura, J; Otaibi, N; Muyzer, G; Gonzalez-Gil, G; Saikaly, P E; van Loosdrecht, M C M; Vrouwenvelder, J S

2016-05-01

Microbial processes inevitably play a role in membrane-based desalination plants, mainly recognized as membrane biofouling. We assessed the bacterial community structure and diversity during different treatment steps in a full-scale seawater desalination plant producing 40,000 m(3)/d of drinking water. Water samples were taken over the full treatment train consisting of chlorination, spruce media and cartridge filters, de-chlorination, first and second pass reverse osmosis (RO) membranes and final chlorine dosage for drinking water distribution. The water samples were analyzed for water quality parameters (total bacterial cell number, total organic carbon, conductivity, pH, etc.) and microbial community composition by 16S rRNA gene pyrosequencing. The planktonic microbial community was dominated by Proteobacteria (48.6%) followed by Bacteroidetes (15%), Firmicutes (9.3%) and Cyanobacteria (4.9%). During the pretreatment step, the spruce media filter did not impact the bacterial community composition dominated by Proteobacteria. In contrast, the RO and final chlorination treatment steps reduced the Proteobacterial relative abundance in the produced water where Firmicutes constituted the most dominant bacterial group. Shannon and Chao1 diversity indices showed that bacterial species richness and diversity decreased during the seawater desalination process. The two-stage RO filtration strongly reduced the water conductivity (>99%), TOC concentration (98.5%) and total bacterial cell number (>99%), albeit some bacterial DNA was found in the water after RO filtration. About 0.25% of the total bacterial operational taxonomic units (OTUs) were present in all stages of the desalination plant: the seawater, the RO permeates and the chlorinated drinking water, suggesting that these bacterial strains can survive in different environments such as high/low salt concentration and with/without residual disinfectant. These bacterial strains were not caused by contamination during water sample filtration or from DNA extraction protocols. Control measurements for sample contamination are important for clean water studies. Copyright © 2016 Elsevier Ltd. All rights reserved.

Artificial intelligence applied to process signal analysis

NASA Technical Reports Server (NTRS)

Corsberg, Dan

1988-01-01

Many space station processes are highly complex systems subject to sudden, major transients. In any complex process control system, a critical aspect of the human/machine interface is the analysis and display of process information. Human operators can be overwhelmed by large clusters of alarms that inhibit their ability to diagnose and respond to a disturbance. Using artificial intelligence techniques and a knowledge base approach to this problem, the power of the computer can be used to filter and analyze plant sensor data. This will provide operators with a better description of the process state. Once a process state is recognized, automatic action could be initiated and proper system response monitored.

Biorefining of by-product streams from sunflower-based biodiesel production plants for integrated synthesis of microbial oil and value-added co-products.

PubMed

Leiva-Candia, D E; Tsakona, S; Kopsahelis, N; García, I L; Papanikolaou, S; Dorado, M P; Koutinas, A A

2015-08-01

This study focuses on the valorisation of crude glycerol and sunflower meal (SFM) from conventional biodiesel production plants for the separation of value-added co-products (antioxidant-rich extracts and protein isolate) and for enhancing biodiesel production through microbial oil synthesis. Microbial oil production was evaluated using three oleaginous yeast strains (Rhodosporidium toruloides, Lipomyces starkeyi and Cryptococcus curvatus) cultivated on crude glycerol and nutrient-rich hydrolysates derived from either whole SFM or SFM fractions that remained after separation of value-added co-products. Fed-batch bioreactor cultures with R. toruloides led to the production of 37.4gL(-1) of total dry weight with a microbial oil content of 51.3% (ww(-1)) when a biorefinery concept based on SFM fractionation was employed. The estimated biodiesel properties conformed with the limits set by the EN 14214 and ASTM D 6751 standards. The estimated cold filter plugging point (7.3-8.6°C) of the lipids produced by R. toruloides is closer to that of biodiesel derived from palm oil. Copyright © 2015 Elsevier Ltd. All rights reserved.

Bacterial community structure in the drinking water microbiome is governed by filtration processes.

PubMed

Pinto, Ameet J; Xi, Chuanwu; Raskin, Lutgarde

2012-08-21

The bacterial community structure of a drinking water microbiome was characterized over three seasons using 16S rRNA gene based pyrosequencing of samples obtained from source water (a mix of a groundwater and a surface water), different points in a drinking water plant operated to treat this source water, and in the associated drinking water distribution system. Even though the source water was shown to seed the drinking water microbiome, treatment process operations limit the source water's influence on the distribution system bacterial community. Rather, in this plant, filtration by dual media rapid sand filters played a primary role in shaping the distribution system bacterial community over seasonal time scales as the filters harbored a stable bacterial community that seeded the water treatment processes past filtration. Bacterial taxa that colonized the filter and sloughed off in the filter effluent were able to persist in the distribution system despite disinfection of finished water by chloramination and filter backwashing with chloraminated backwash water. Thus, filter colonization presents a possible ecological survival strategy for bacterial communities in drinking water systems, which presents an opportunity to control the drinking water microbiome by manipulating the filter microbial community. Grouping bacterial taxa based on their association with the filter helped to elucidate relationships between the abundance of bacterial groups and water quality parameters and showed that pH was the strongest regulator of the bacterial community in the sampled drinking water system.

C.R.O.P. - Combined Regenerative Organic food Production: Employing the benefits of natural communities

NASA Astrophysics Data System (ADS)

Bornemann, Gerhild; Hauslage, Jens; Hemmersbach, Ruth; Hendrik Anken, Ralf; Moeller, Ralf; Wasser, Kai; Tonat, Tim

The reutilization of nutrients bound in organic wastes for food crop cultivation is a central topic of BLSS (Bioregenerative Life Support System) research. The conversion of organic wastes into inorganic compounds utilizable by plants proceeds stepwise and each step is carried out by specific microorganisms with varying environmental demands. In BLSS design different steps are often allocated to different treatment units. Each unit is inoculated with selected microbial cultures and provides optimal growth conditions for these. The compartmented set-up is also often used in public wastewater treatment. But as wastewaters usually carry their decomposers with them, specified inoculates are only applied in special cases. Due to the highly variable composition of wastewater, diverse communities of microorganisms are found in treatment plants enabling these to cope with the unpredictable substrate. Although in isolated space habitats, microorganisms necessary for degradation will also be present on wastes and in wastewaters, their diversity will be limited to those species introduced into the system until launch. Therefore, it is crucial to establish a stable microbial community in the waste processing system that is capable to degrade all kinds of wastes, including micropollutants like pharmaceutical residues, before launch. The C.R.O.P. project aims at combining the utilization of liquid and solid organic wastes with soilless plant cultivation. The envisioned waste processing system is a trickling filter designed to join all required functions in one compartment thus reducing size and weight. To achieve this, the filter medium provides habitats with differing conditions so that a diverse microbial community grows as biofilm on its surface. We assume that, once established, such a quasi-natural community makes the system multifunctional with regard to the substrates that can be degraded, and stable with regard to invasion of undesirable microorganisms. Our current research focuses on the characterisation of the system’s capability to degrade different substrates like urine and plant wastes and the usability of the filtrate as fertilizer. Molecular analyses revealed a variety of different microorganisms in the filters. Future research will address the question how to introduce specialised microorganisms into the system to enable it to degrade micropollutants, and the question how to maintain these during periods of absence of their substrate.

Direct Comparison of Phosphate Uptake by Adnate and Loosely Attached Microalgae within an Intact Biofilm Matrix

PubMed Central

Burkholder, JoAnn M.; Wetzel, Robert G.; Klomparens, Karen L.

1990-01-01

We report a direct comparison of phosphate uptake by adnate and loosely attached microalgae in an intact biofilm matrix, with resolution at the level of individual cells. Track scanning electron microscope autoradiography enabled assay of [33P]phosphate uptake from the overlying water by adnate algae left undisturbed on mature leaves of the macrophyte Potamogeton illinoensis or on artificial plant mimics. The epiphyte communities developed in either phosphate-poor or moderately phosphate-enriched water, and they were assayed on both natural and artificial plants. All adnate taxa examined from both natural and artificial plants in both habitats took up significantly less radiolabel when assayed beneath the overlying matrix than when they were exposed to the water upon removal of the overstory material. Track scanning electron microscope autoradiography and track light microscope autoradiography were intercalibrated to enable comparison of [33P]phosphate uptake by adnate and loosely attached components of the epiphyte matrix. Loosely attached cells on substrata from both habitats took up significantly more radiolabel than did underlying adnate cells, indicating that access to phosphate supplies from the water depended on the position of microbial cells in the matrix. In this short-term assay, the adnate microalgae were relatively isolated from the water column nutrient source. Images PMID:16348296

DRINKING WATER TURBIDITY AND EMERGENCY DEPARTMENT VISITS FOR GASTROINTESTINAL ILLNESS IN ATLANTA, 1993 – 2004

PubMed Central

Tinker, Sarah C.; Moe, Christine L.; Klein, Mitchel; Flanders, W. Dana; Uber, Jim; Amirtharajah, Appiah; Singer, Philip; Tolbert, Paige E.

2013-01-01

Background The extent to which drinking water turbidity measurements indicate the risk of gastrointestinal illness is not well-understood. Despite major advances in drinking water treatment and delivery, infectious disease can still be transmitted through drinking water in the U.S., and it is important to have reliable indicators of microbial water quality to inform public health decisions. The objective of our study was to assess the relationship between gastrointestinal illness, quantified through emergency department visits, and drinking water quality, quantified as raw water and filtered water turbidity measured at the treatment plant. Methods We examined the relationship between turbidity levels of raw and filtered surface water measured at eight major drinking water treatment plants in the metropolitan area of Atlanta, Georgia, and over 240 000 emergency department visits for gastrointestinal illness during 1993–2004 among the population served by these plants. We fit Poisson time-series statistical regression models that included turbidity in a 21-day distributed lag and that controlled for meteorological factors and long-term time trends. Results For filtered water turbidity, the results were consistent with no association with emergency department visits for gastrointestinal illness. We observed a modest association between raw water turbidity and emergency department visits for gastrointestinal illness. This association was not observed for all treatment plants in plant-specific analyses. Conclusions Our results suggest that source water quality may contribute modestly to endemic gastrointestinal illness in the study area. The association between turbidity and emergency department visits for gastrointestinal illness was only observed when raw water turbidity was considered; filtered water turbidity may not serve as a reliable indicator of modest pathogen risk at all treatment plants. PMID:18941478

DOE Office of Scientific and Technical Information (OSTI.GOV)

Konopka, Allan

Microbial ecology is a relatively young discipline within the field of microbiology. Its modern history spans just the past 60 years, and the field is defined by its emphasis on understanding the interactions of microbes with their environment, rather than their behavior under artificial laboratory conditions. Because microbes are ubiquitous, microbial ecologists study a broad diversity of habitats that range from aquatic to terrestrial to plant- or animal-associated. This has made it a challenge to identify unifying principles within the field. One approach is to recognize that although the activity of microbes in nature have effects at the macroscale, theymore » interact with their physical, chemical and biological milieu at a scale of micrometers. At this scale, several different microbial ecosystems can be defined, based upon association with particles, the presence of environmental gradients and the continuous availability of water. Principles applicable to microbial ecology reflect not only their population ecology and physiological ecology, but also their broad versatility and quantitative importance in the biosphere as biogeochemical catalysts and capacity for rapid physiological and evolutionary responses.« less

Chattering-Free Sliding Mode Control with Unmodeled Dynamics

NASA Technical Reports Server (NTRS)

Krupp, Don; Shtessel, Yuri B.

1999-01-01

Sliding mode control systems are valued for their robust accommodation of uncertainties and their ability to reject disturbances. In this paper, a design methodology is proposed to eliminate the chattering phenomenon affecting sliding mode controlled plants with input unmodeled actuator dynamics of second order or greater. The proposed controller design is based on the relative degrees of the plant and the unmodeled actuator dynamics and the ranges of the uncertainties of the plant and actuator. The controller utilizes the pass filter characteristics of the physical actuating device to provide a smoothing effect on the discontinuous control signal rather than introducing any artificial dynamics into the controller design thus eliminating chattering in the system's output response.

Drinking water turbidity and emergency department visits for gastrointestinal illness in Atlanta, 1993-2004.

PubMed

Tinker, Sarah C; Moe, Christine L; Klein, Mitchel; Flanders, W Dana; Uber, Jim; Amirtharajah, Appiah; Singer, Philip; Tolbert, Paige E

2010-01-01

The extent to which drinking water turbidity measurements indicate the risk of gastrointestinal illness is not well understood. Despite major advances in drinking water treatment and delivery, infectious disease can still be transmitted through drinking water in the United States, and it is important to have reliable indicators of microbial water quality to inform public health decisions. The objective of our study was to assess the relationship between gastrointestinal illness, quantified through emergency department visits, and drinking water quality, quantified as raw water and filtered water turbidity measured at the treatment plant. We examined the relationship between turbidity levels of raw and filtered surface water measured at eight major drinking water treatment plants in the metropolitan area of Atlanta, Georgia, and over 240,000 emergency department visits for gastrointestinal illness during 1993-2004 among the population served by these plants. We fit Poisson time-series statistical regression models that included turbidity in a 21-day distributed lag and that controlled for meteorological factors and long-term time trends. For filtered water turbidity, the results were consistent with no association with emergency department visits for gastrointestinal illness. We observed a modest association between raw water turbidity and emergency department visits for gastrointestinal illness. Our results suggest that source water quality may contribute modestly to endemic gastrointestinal illness in the study area. The association between turbidity and emergency department visits for gastrointestinal illness was only observed when raw water turbidity was considered; filtered water turbidity may not serve as a reliable indicator of modest pathogen risk at all treatment plants.

Microbiome Selection Could Spur Next-Generation Plant Breeding Strategies.

PubMed

Gopal, Murali; Gupta, Alka

2016-01-01

" No plant is an island too …" Plants, though sessile, have developed a unique strategy to counter biotic and abiotic stresses by symbiotically co-evolving with microorganisms and tapping into their genome for this purpose. Soil is the bank of microbial diversity from which a plant selectively sources its microbiome to suit its needs. Besides soil, seeds, which carry the genetic blueprint of plants during trans-generational propagation, are home to diverse microbiota that acts as the principal source of microbial inoculum in crop cultivation. Overall, a plant is ensconced both on the outside and inside with a diverse assemblage of microbiota. Together, the plant genome and the genes of the microbiota that the plant harbors in different plant tissues, i.e., the 'plant microbiome,' form the holobiome which is now considered as unit of selection: 'the holobiont.' The 'plant microbiome' not only helps plants to remain fit but also offers critical genetic variability, hitherto, not employed in the breeding strategy by plant breeders, who traditionally have exploited the genetic variability of the host for developing high yielding or disease tolerant or drought resistant varieties. This fresh knowledge of the microbiome, particularly of the rhizosphere, offering genetic variability to plants, opens up new horizons for breeding that could usher in cultivation of next-generation crops depending less on inorganic inputs, resistant to insect pest and diseases and resilient to climatic perturbations. We surmise, from ever increasing evidences, that plants and their microbial symbionts need to be co-propagated as life-long partners in future strategies for plant breeding. In this perspective, we propose bottom-up approach to co-propagate the co-evolved, the plant along with the target microbiome, through - (i) reciprocal soil transplantation method, or (ii) artificial ecosystem selection method of synthetic microbiome inocula, or (iii) by exploration of microRNA transfer method - for realizing this next-generation plant breeding approach. Our aim, thus, is to bring closer the information accrued through the advanced nucleotide sequencing and bioinformatics in conjunction with conventional culture-dependent isolation method for practical application in plant breeding and overall agriculture.

A Synthetic Community System for Probing Microbial Interactions Driven by Exometabolites

PubMed Central

Chodkowski, John L.

2017-01-01

ABSTRACT Though most microorganisms live within a community, we have modest knowledge about microbial interactions and their implications for community properties and ecosystem functions. To advance understanding of microbial interactions, we describe a straightforward synthetic community system that can be used to interrogate exometabolite interactions among microorganisms. The filter plate system (also known as the Transwell system) physically separates microbial populations, but allows for chemical interactions via a shared medium reservoir. Exometabolites, including small molecules, extracellular enzymes, and antibiotics, are assayed from the reservoir using sensitive mass spectrometry. Community member outcomes, such as growth, productivity, and gene regulation, can be determined using flow cytometry, biomass measurements, and transcript analyses, respectively. The synthetic community design allows for determination of the consequences of microbiome diversity for emergent community properties and for functional changes over time or after perturbation. Because it is versatile, scalable, and accessible, this synthetic community system has the potential to practically advance knowledge of microbial interactions that occur within both natural and artificial communities. IMPORTANCE Understanding microbial interactions is a fundamental objective in microbiology and ecology. The synthetic community system described here can set into motion a range of research to investigate how the diversity of a microbiome and interactions among its members impact its function, where function can be measured as exometabolites. The system allows for community exometabolite profiling to be coupled with genome mining, transcript analysis, and measurements of member productivity and population size. It can also facilitate discovery of natural products that are only produced within microbial consortia. Thus, this synthetic community system has utility to address fundamental questions about a diversity of possible microbial interactions that occur in both natural and engineered ecosystems. Author Video: An author video summary of this article is available. PMID:29152587

The chastity of amoebae: re-evaluating evidence for sex in amoeboid organisms

PubMed Central

Lahr, Daniel J. G.; Parfrey, Laura Wegener; Mitchell, Edward A. D.; Katz, Laura A.; Lara, Enrique

2011-01-01

Amoebae are generally assumed to be asexual. We argue that this view is a relict of early classification schemes that lumped all amoebae together inside the ‘lower’ protozoa, separated from the ‘higher’ plants, animals and fungi. This artificial classification allowed microbial eukaryotes, including amoebae, to be dismissed as primitive, and implied that the biological rules and theories developed for macro-organisms need not apply to microbes. Eukaryotic diversity is made up of 70+ lineages, most of which are microbial. Plants, animals and fungi are nested among these microbial lineages. Thus, theories on the prevalence and maintenance of sex developed for macro-organisms should in fact apply to microbial eukaryotes, though the theories may need to be refined and generalized (e.g. to account for the variation in sexual strategies and prevalence of facultative sex in natural populations of many microbial eukaryotes). We use a revised phylogenetic framework to assess evidence for sex in several amoeboid lineages that are traditionally considered asexual, and we interpret this evidence in light of theories on the evolution of sex developed for macro-organisms. We emphasize that the limited data available for many lineages coupled with natural variation in microbial life cycles overestimate the extent of asexuality. Mapping sexuality onto the eukaryotic tree of life demonstrates that the majority of amoeboid lineages are, contrary to popular belief, anciently sexual, and that most asexual groups have probably arisen recently and independently. Additionally, several unusual genomic traits are prevalent in amoeboid lineages, including cyclic polyploidy, which may serve as alternative mechanisms to minimize the deleterious effects of asexuality. PMID:21429931

Treatment of high ethanol concentration wastewater by biological sand filters: enhanced COD removal and bacterial community dynamics.

PubMed

Rodriguez-Caballero, A; Ramond, J-B; Welz, P J; Cowan, D A; Odlare, M; Burton, S G

2012-10-30

Winery wastewater is characterized by its high chemical oxygen demand (COD), seasonal occurrence and variable composition, including periodic high ethanol concentrations. In addition, winery wastewater may contain insufficient inorganic nutrients for optimal biodegradation of organic constituents. Two pilot-scale biological sand filters (BSFs) were used to treat artificial wastewater: the first was amended with ethanol and the second with ethanol, inorganic nitrogen (N) and phosphorus (P). A number of biochemical parameters involved in the removal of pollutants through BSF systems were monitored, including effluent chemistry and bacterial community structures. The nutrient supplemented BSF showed efficient COD, N and P removal. Comparison of the COD removal efficiencies of the two BSFs showed that N and P addition enhanced COD removal efficiency by up to 16%. Molecular fingerprinting of BSF sediment samples using denaturing gradient gel electrophoresis (DGGE) showed that amendment with high concentrations of ethanol destabilized the microbial community structure, but that nutrient supplementation countered this effect. Copyright © 2012 Elsevier Ltd. All rights reserved.

Responses of bacterial community structure and denitrifying bacteria in biofilm to submerged macrophytes and nitrate

NASA Astrophysics Data System (ADS)

Zhang, Songhe; Pang, Si; Wang, Peifang; Wang, Chao; Guo, Chuan; Addo, Felix Gyawu; Li, Yi

2016-10-01

Submerged macrophytes play important roles in constructed wetlands and natural water bodies, as these organisms remove nutrients and provide large surfaces for biofilms, which are beneficial for nitrogen removal, particularly from submerged macrophyte-dominated water columns. However, information on the responses of biofilms to submerged macrophytes and nitrogen molecules is limited. In the present study, bacterial community structure and denitrifiers were investigated in biofilms on the leaves of four submerged macrophytes and artificial plants exposed to two nitrate concentrations. The biofilm cells were evenly distributed on artificial plants but appeared in microcolonies on the surfaces of submerged macrophytes. Proteobacteria was the most abundant phylum in all samples, accounting for 27.3-64.8% of the high-quality bacterial reads, followed by Chloroflexi (3.7-25.4%), Firmicutes (3.0-20.1%), Acidobacteria (2.7-15.7%), Actinobacteria (2.2-8.7%), Bacteroidetes (0.5-9.7%), and Verrucomicrobia (2.4-5.2%). Cluster analysis showed that bacterial community structure can be significantly different on macrophytes versus from those on artificial plants. Redundancy analysis showed that electrical conductivity and nitrate concentration were positively correlated with Shannon index and operational taxonomic unit (OTU) richness (log10 transformed) but somewhat negatively correlated with microbial density. The relative abundances of five denitrifying genes were positively correlated with nitrate concentration and electrical conductivity but negatively correlated with dissolved oxygen.

Methodology for modeling the microbial contamination of air filters.

PubMed

Joe, Yun Haeng; Yoon, Ki Young; Hwang, Jungho

2014-01-01

In this paper, we propose a theoretical model to simulate microbial growth on contaminated air filters and entrainment of bioaerosols from the filters to an indoor environment. Air filter filtration and antimicrobial efficiencies, and effects of dust particles on these efficiencies, were evaluated. The number of bioaerosols downstream of the filter could be characterized according to three phases: initial, transitional, and stationary. In the initial phase, the number was determined by filtration efficiency, the concentration of dust particles entering the filter, and the flow rate. During the transitional phase, the number of bioaerosols gradually increased up to the stationary phase, at which point no further increase was observed. The antimicrobial efficiency and flow rate were the dominant parameters affecting the number of bioaerosols downstream of the filter in the transitional and stationary phase, respectively. It was found that the nutrient fraction of dust particles entering the filter caused a significant change in the number of bioaerosols in both the transitional and stationary phases. The proposed model would be a solution for predicting the air filter life cycle in terms of microbiological activity by simulating the microbial contamination of the filter.

Effects of discharge fluctuation and the addition of fine sediment on stream fish and macroinvertebrates below a water-filtration facility

NASA Astrophysics Data System (ADS)

Erman, Don C.; Ligon, Franklin K.

1988-01-01

A small, coastal stream in the San Francisco Bay area of California, USA, received the discharges from a drinking-water filtration plant. Two types of discharges were present. Discharges from filter backwashing were 3 4 times base stream flow, occurred 10 60 times per day, contained fine sediments, and each lasted about 10 min. The other discharge was a large, steady flow of relatively sediment-free water from occasional overflow of the delivery aqueduct which generally lasted several hours a day. Samples of invertebrates from natural substrates had significantly fewer taxa and lower density at the two stations below the backwash than at the two above. However, when stable artificial substrates were used, there were no significant differences among all four stations. The aqueduct apparently had no effect because the. invertebrate community at the station upstream of the backwash but downstream of the aqueduct was statistically similar to the station above the aqueduct. To test for acute toxicity, we exposed additional artificial substrates to short-term simulated backwash conditions. These exposures had no effect on invertebrate density or drift. Three-spine stickleback ( Gasterosteus aculeatus) populations were also significantly reduced at the two downstream stations and were made up mostly of larger, adult fish. Prickly sculpins ( Cottus asper), restricted to the most downstream station, were emaciated and had poor growth, probably as a result of scarce benthic food organisms. Artificial redds with eggs of rainbow trout ( Salmo gairdneri) had significantly lower survival at two stations below the plant backwash (30.7% and 41.8%) than at the one above it (61.4%). Hatchery rainbow trout held in cages below the treatment plant from 7 to 37 days survived and continued to feed. Thus, the major effect of the water treatment plant on fish and invertebrates probably was not from acute toxicity in the discharges or the occasionally large discharge of clean water from the aqueduct, but was from the fluctuating backwash flows containing fine sediment that displaced small fish downstream and created unstable benthic substrates for invertebrates. The filter plant that we studied is a direct-feed type (that is, no sedimentation before filtration). These generally require greater frequencies of backwashing than do conventional plants and may therefore have greater biological impacts. Direct-feed plants are becoming increasingly popular throughout the world, for the most part because they are cheaper to build and operate. But if the associated biological problems are mitigated, then the cost savings of direct-feed compared to conventional plants may be lost.

Food-mediated modulation of immunity in a phytophagous insect: An effect of nutrition rather than parasitic contamination.

PubMed

Vogelweith, Fanny; Moreau, Jérôme; Thiéry, Denis; Moret, Yannick

2015-06-01

Inherent to the cost of immunity, the immune system itself can exhibit tradeoffs between its arms. Phytophagous insects face a wide range of microbial and eukaryotic parasites, each activating different immune pathways that could compromise the activity of the others. Feeding larvae are primarily exposed to microbes, which growth is controlled by antibiotic secondary metabolites produced by the host plant. The resulting variation in abundance of microbes on plants is expected to differentially stimulate the insect antimicrobial immune defenses. Under the above tradeoff hypothesis, stimulation of the insect antimicrobial defenses is expected to compromise immune activity against eukaryote parasites. In the European grape berry moth, Eupoecilia ambiguella, immune effectors directed towards microbes are negatively correlated to those directed towards eukaryotic parasites among host plants. Here, we hypothesize this relationship is caused by a variable control of the microbial community among host plants by their antibiotic metabolites. To test this hypothesis, we first quantified antimicrobial activity in berries of several grape varieties. We then measured immune defenses of E. ambiguella larvae raised on artificial diets in which we mimicked levels of antimicrobial activity of grape berries using tetracycline to control the abundance of growing microbes. Another group of larvae was raised on artificial diets made of berry extracts only to control for the effect of nutrition. We found that controlling microbe abundance with tetracycline in diets did not explain variation in the immune function whereas the presence of berry extracts did. This suggests that variation in immune defenses of E. ambiguella among grape varieties is caused by nutritional difference among host plants rather than microbe abundance. Further study of the effects of berry compounds on larval immune parameters will be needed to explain the observed tradeoff among immune system components. Copyright © 2015 Elsevier Ltd. All rights reserved.

Production of dehydrogingerdione derivatives in Escherichia coli by exploiting a curcuminoid synthase from Oryza sativa and a β-oxidation pathway from Saccharomyces cerevisiae.

PubMed

Katsuyama, Yohei; Ohnishi, Yasuo; Horinouchi, Sueharu

2010-09-24

Gingerol derivatives are bioactive compounds isolated from the rhizome of ginger. They possess various beneficial activities, such as anticancer and hepatoprotective activities, and are therefore attractive targets of bioengineering. However, the microbial production of gingerol derivatives has not yet been established, primarily because the biosynthetic pathway of gingerol is unknown. Here, we report the production of several dehydrogingerdione (a gingerol derivative) analogues from a recombinant Escherichia coli strain that has an "artificial" biosynthesis pathway for dehydrogingerdione that was not based on the original biosynthesis pathway of gingerol derivatives in plants. The system consists of a 4-coumarate:CoA ligase from Lithospermum erythrorhizon, a fatty acid CoA ligase from Oryza sativa, a β-oxidation system from Saccharomyces cerevisiae, and a curcuminoid synthase from O. sativa. To our knowledge, this is the first report of the microbial production of a plant metabolite the biosynthetic pathway of which has not yet been identified.

Stanols as a tool to track the origin of microbial contamination of oysters, Crassostrea gigas, in shellfish areas.

NASA Astrophysics Data System (ADS)

Harrault, Loïc; Jardé, Emilie; Jeanneau, Laurent; Petitjean, Patrice

2013-04-01

Runoff of cattle manures (cows, pigs, sheeps) or discharge of effluent from wastewater treatment plants (WWTP) into aquatic ecosystems can lead to microbiological contamination of waters and living organisms. In coastal ecosystems and particularly in shellfish harvesting areas, the presence of pathogen microorganisms in waters induces fecal contamination of filter feeding bivalves (oysters, mussels, scallops…), therefore leading to human health risks associated to the consumption of these contaminated organisms. Watershed management plans that aim at limiting these risks require the development of tools able to identify fecal contamination sources. The fecal indicator bacteria used in the regulations to determine fecal contamination are not source specific since they are found in the feces of most warm-blooded animals. Thus, microbiological biomarkers have been developed in association with chemical biomarkers as Microbial Source Tracking (MST) methods. Fecal stanols, by-products of sterols obtained by human and animal microbial gut flora, are found in considerable amounts in feces with different relative proportions depending on their animal or human source. Recently, in association with microbiological biomarkers, the stanol fingerprint of contaminated waters has been successfully used to determine the main source of fecal contamination (cow, pig or human sources) in rural watersheds (Brittany, France). Up to now, the use of the stanol fingerprint to track the fecal contamination in shellfish tissues, especially bivalves, has been limited to the analysis of coprostanol, a stanol commonly associated to human contamination. Therefore, whether the stanol fingerprint can be used as a MST method in bivalves or not is still unknown. The first aim of this study was to compare several organic extraction procedures of stanols in the oyster Crassostrea gigas to determine a reliable method for stanol fingerprint analysis in bivalves. Solvent extraction and purification steps have been carried out with attention as they are critical for stanol quantification. Secondly, the evolution of the stanol fingerprint of oysters with time was evaluated during 6 days by artificially contaminating microcosms with two concentrations of a WWTP effluent. In the microcosms, the fingerprint of stanols as a chemical biomarkers of fecal (human) contamination was compared to counts of Escherichia coli, a commonly used microbial indicator. In association with microbial markers, the method developed from the two previous steps will be applied at the watershed scale in order to identify sources of fecal contamination in Brittany and Normandy (France).

Microbial resource management of one-stage partial nitritation/anammox.

PubMed

Vlaeminck, S E; De Clippeleir, H; Verstraete, W

2012-05-01

About 30 full-scale partial nitritation/anammox plants are established, treating mostly sewage sludge reject water, landfill leachate or food processing digestate. Although two-stage and one-stage processes each have their advantages, the one-stage configuration is mostly applied, termed here as oxygen-limited autotrophic nitrification/denitrification (OLAND), and is the focus of this review. The OLAND application domain is gradually expanding, with technical-scale plants on source-separated domestic wastewater, pre-treated manure and sewage, and liquors from organic waste bioenergy plants. A 'microbial resource management' (MRM) OLAND framework was elaborated, showing how the OLAND engineer/operator (1: input) can design/steer the microbial community (2: biocatalyst) to obtain optimal functionality (3: output). In the physicochemical toolbox (1), design guidelines are provided, as well as advantages of different reactor technologies. Particularly the desirable aeration regime, feeding regime and shear forces are not clear yet. The development of OLAND trickling filters, membrane bioreactors and systems with immobilized biomass is awaited. The biocatalyst box (2) considers 'Who': biodiversity and its dynamic patterns, 'What': physiology, and 'Where': architecture creating substrate gradients. Particularly community dynamics and extracellular polymeric substances (EPS) still require insights. Performant OLAND (3) comprises fast start-up (storage possibility; fast growth of anammox bacteria), process stability (endured biomass retention; stress resilience), reasonable overall costs, high nitrogen removal efficiency and a low environmental footprint. Three important OLAND challenges are elaborated in detailed frameworks, demonstrating how to maximize nitrogen removal efficiency, minimize NO and N(2)O emissions and obtain through OLAND a plant-wide net energy gain from sewage treatment. © 2012 The Authors. Microbial Biotechnology © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

Bespoke microbiome therapy to manage plant diseases.

PubMed

Gopal, Murali; Gupta, Alka; Thomas, George V

2013-01-01

Information gathered with advanced nucleotide sequencing technologies, small molecule detection systems and computational biology is revealing that a community of microbes and their genes, now termed "the microbiome," located in gut and rhizosphere, is responsible for maintaining the health of human beings and plants, respectively. Within the complete microbiome a "core-microbiome" exists that plays the pivotal role in well being of humans and plants. Recent studies in medicine have shown that an artificial mixture of bacteria representing the core gut microbiome of healthy person when transferred into gut of diseased person results in re-establishment of normal microflora in the latter leading to alleviation from diseased condition. In agriculture, though not exactly in similar manner as in medicine, success in plant disease management has been achieved through transfer of microbiome by mixing disease suppressive soils with disease conducive soils. A study more similar to artificial gut microbiome transfer in medical field has been recently reported in agriculture, in which transfer of microbiome via soil solutions (filtered and unfiltered) has shown ability to alleviate drought stress in Arabidopsis thaliana. However, the exact practice of transferring artificially cultivated core-microbiome as in medicine has not thus far been attempted in plant disease management. Nonetheless, as the gut and rhizosphere microbiome are known to share many common traits, there exists a good scope for accomplishing similar studies in agriculture. Based upon the information drawn from all recent works in microbiome studies of gut and rhizosphere, we propose that tailor-made core-microbiome transfer therapy can be a success in agriculture too and it could become a viable strategy for management of plant diseases in future.

Community analysis of plant biomass-degrading microorganisms from Obsidian Pool, Yellowstone National Park.

PubMed

Vishnivetskaya, Tatiana A; Hamilton-Brehm, Scott D; Podar, Mircea; Mosher, Jennifer J; Palumbo, Anthony V; Phelps, Tommy J; Keller, Martin; Elkins, James G

2015-02-01

The conversion of lignocellulosic biomass into biofuels can potentially be improved by employing robust microorganisms and enzymes that efficiently deconstruct plant polysaccharides at elevated temperatures. Many of the geothermal features of Yellowstone National Park (YNP) are surrounded by vegetation providing a source of allochthonic material to support heterotrophic microbial communities adapted to utilize plant biomass as a primary carbon and energy source. In this study, a well-known hot spring environment, Obsidian Pool (OBP), was examined for potential biomass-active microorganisms using cultivation-independent and enrichment techniques. Analysis of 33,684 archaeal and 43,784 bacterial quality-filtered 16S rRNA gene pyrosequences revealed that archaeal diversity in the main pool was higher than bacterial; however, in the vegetated area, overall bacterial diversity was significantly higher. Of notable interest was a flooded depression adjacent to OBP supporting a stand of Juncus tweedyi, a heat-tolerant rush commonly found growing near geothermal features in YNP. The microbial community from heated sediments surrounding the plants was enriched in members of the Firmicutes including potentially (hemi)cellulolytic bacteria from the genera Clostridium, Anaerobacter, Caloramator, Caldicellulosiruptor, and Thermoanaerobacter. Enrichment cultures containing model and real biomass substrates were established at a wide range of temperatures (55-85 °C). Microbial activity was observed up to 80 °C on all substrates including Avicel, xylan, switchgrass, and Populus sp. Independent of substrate, Caloramator was enriched at lower (<65 °C) temperatures while highly active cellulolytic bacteria Caldicellulosiruptor were dominant at high (>65 °C) temperatures.

Microbiological monitoring in geothermal plants and a cold storage

NASA Astrophysics Data System (ADS)

Alawi, Mashal; Lerm, Stephanie; Vieth, Andrea; Vetter, Alexandra; Miethling-Graff, Rona; Seibt, Andrea; Wolfgramm, Markus; Würdemann, Hilke

2010-05-01

Enhanced process understanding of engineered geothermal systems is mandatory to optimize plant reliability and economy. In the scope of the research project 'AquiScreen' we investigated geothermally used groundwater systems under microbial, geochemical, mineralogical and petrological aspects. Geothermal systems located in the North German Basin and the Molasse Basin were analyzed by sampling of fluids and solid phases. The investigated sites were characterized by different temperatures, salinities and potential microbial substrates. The microbial population was analyzed by the use of genetic fingerprinting techniques based on PCR-amplified 16S rRNA genes. Sequencing of dominant bands of fingerprints from different sites and the subsequent comparison on public databases enables a correlation to metabolic classes and provides information about the biochemical processes. In all investigated geothermal plants covering a temperature range from 45° to 120° C microorganisms were found. Phylogenetic gene analyses indicate a broad diversity of microorganisms adapted to the specific conditions in the engineered system. Beside characterized bacteria like Thermus scotoductus, Siderooxidans lithoautotrophicus and the archaeon Methanothermobacter thermoautotrophicus a high number of so far uncultivated microorganisms was detected. As it is known that -in addition to abiotic factors- microbes like sulfate-reducing bacteria (SRB) are involved in the processes of corrosion and scaling in plant components we identified SRB by specific analyses of dissimilatoric sulfite reductase genes. The SRB detected are closely related to thermotolerant and thermophilic species of Desulfotomaculum, Thermodesulfovibrio and Thermodesulfobacterium, respectively. Overall, the detection of microbes known to be involved in biocorrosion and examined precipitation products like iron sulfides are indicating that microorganisms play an important role for the understanding of processes in engineered geothermal systems. Furthermore, an observed reduction of the filter operation times in a cold storage could be traced back to an enhanced growth of a filamentous iron-oxidizing bacterium related to Thiotrix. The further identificaton of crucial process parameters that are influencing microbial activities will help developing appropriate counter measures against microbial induced clogging and corrosion.

A bitter aftertaste: unintended effects of artificial sweeteners on the gut microbiome

PubMed Central

Bokulich, Nicholas A.; Blaser, Martin J.

2015-01-01

Intestinal microbial communities regulate a range of host physiological functions, from energy harvest and glucose homeostasis to immune development and regulation. Suez and colleagues (2014) recently demonstrated that artificial sweeteners alter gut microbial communities, leading to glucose intolerance in both mice and humans. PMID:25440050

Unconventional processes for food regeneration in space - An overview

NASA Technical Reports Server (NTRS)

Stokes, B. O.; Petersen, G. R.; Schubert, W. W.; Mueller, W. A.

1981-01-01

Alternatives to conventional plant agriculture for the regeneration of food during space missions of extended duration are examined. The options considered, which may be used in combination with conventional agriculture, include the production of food from plant wastes, the chemical synthesis of food from carbon dioxide and other simple molecules or the substitution of edible chemicals, and the use of microrganisms for food and oxygen regeneration, with suitable processing. A comparison of solar energy conversion efficiencies is presented for nonphotosynthetic bacteria grown on hydrogen and algal systems photosynthetically, and it is shown that hydrogen bacteria are potentially more attractive than photosynthetic algae using artificial light. Weight-volume requirements for the conventional plant, algae and hydrogen bacteria systems are also compared to demonstrate the advantages of microbial systems.

Methodology for Modeling the Microbial Contamination of Air Filters

PubMed Central

Joe, Yun Haeng; Yoon, Ki Young; Hwang, Jungho

2014-01-01

In this paper, we propose a theoretical model to simulate microbial growth on contaminated air filters and entrainment of bioaerosols from the filters to an indoor environment. Air filter filtration and antimicrobial efficiencies, and effects of dust particles on these efficiencies, were evaluated. The number of bioaerosols downstream of the filter could be characterized according to three phases: initial, transitional, and stationary. In the initial phase, the number was determined by filtration efficiency, the concentration of dust particles entering the filter, and the flow rate. During the transitional phase, the number of bioaerosols gradually increased up to the stationary phase, at which point no further increase was observed. The antimicrobial efficiency and flow rate were the dominant parameters affecting the number of bioaerosols downstream of the filter in the transitional and stationary phase, respectively. It was found that the nutrient fraction of dust particles entering the filter caused a significant change in the number of bioaerosols in both the transitional and stationary phases. The proposed model would be a solution for predicting the air filter life cycle in terms of microbiological activity by simulating the microbial contamination of the filter. PMID:24523908

Study of methanogenesis during bioutilization of plant residuals

NASA Astrophysics Data System (ADS)

Ilyin, V. K.; Korniushenkova, I. N.; Starkova, L. V.; Lauriniavichius, K. S.

2005-02-01

The waste management strategy for the future should meet the benefits of human safety, respect principles of planet ecology, and compatibility with other habitability systems. For these purposes waste management technologies relevant to application of the biodegradation properties of bacteria are of great value. Biological treatment method is based on the biodegradation of organic substances by various microorganisms. The objectives of our study were: to evaluate the effectiveness of microbial biodegradation of vegetable non-edible residual, using artificial inoculum, and to study the peculiarities of biogas, and possibilities of optimizing or reducing the share of methane. The diminution rate of organic gained 76% from initial mass within 9 days of fermentation. The biogas production achieved 46 l/kg of substrate. The microbial studies of biodegradation process revealed the following peculiarities: (i) gradual quantitative increase of Lactobacillus sp. (from 103 to 105 colony-forming units (CFU) per ml); (ii) activation of Clostridia sp. (from 102 to 10 4 CFU/ml); and (iii) elimination of aerobic conventional pathogens (Enterobacteriaceae, Protea sp., Staphylococci). Chromatography analysis revealed the constant presence of carbon dioxide (up to 90.9%). The methane content measures revealed traces 0.1-0.4%. However, when we optimized the methane production in "boiling layer" using methanogenic granules, the amount of methane in biogas reached 80-90%. Based on the results obtained the artificial inoculum was created which was capable of initiating biodegradation of vegetable wastes. This inoculum consisted of active sludge adapted to wastes mixed with excretea of insects which consume plant wastes. Using this inoculum the biodegradation process takes less time than that using active sludge. Regulation of methane concentration from traces to 90% may be achieved by adding methane reactor to the plant digester.

Associations between Ectomycorrhizal Fungi and Bacterial Needle Endophytes in Pinus radiata: Implications for Biotic Selection of Microbial Communities

PubMed Central

Rúa, Megan A.; Wilson, Emily C.; Steele, Sarah; Munters, Arielle R.; Hoeksema, Jason D.; Frank, Anna C.

2016-01-01

Studies of the ecological and evolutionary relationships between plants and their associated microbes have long been focused on single microbes, or single microbial guilds, but in reality, plants associate with a diverse array of microbes from a varied set of guilds. As such, multitrophic interactions among plant-associated microbes from multiple guilds represent an area of developing research, and can reveal how complex microbial communities are structured around plants. Interactions between coniferous plants and their associated microbes provide a good model system for such studies, as conifers host a suite of microorganisms including mutualistic ectomycorrhizal (ECM) fungi and foliar bacterial endophytes. To investigate the potential role ECM fungi play in structuring foliar bacterial endophyte communities, we sampled three isolated, native populations of Monterey pine (Pinus radiata), and used constrained analysis of principal coordinates to relate the community matrices of the ECM fungi and bacterial endophytes. Our results suggest that ECM fungi may be important factors for explaining variation in bacterial endophyte communities but this effect is influenced by population and environmental characteristics, emphasizing the potential importance of other factors — biotic or abiotic — in determining the composition of bacterial communities. We also classified ECM fungi into categories based on known fungal traits associated with substrate exploration and nutrient mobilization strategies since variation in these traits allows the fungi to acquire nutrients across a wide range of abiotic conditions and may influence the outcome of multi-species interactions. Across populations and environmental factors, none of the traits associated with fungal foraging strategy types significantly structured bacterial assemblages, suggesting these ECM fungal traits are not important for understanding endophyte-ECM interactions. Overall, our results suggest that both biotic species interactions and environmental filtering are important for structuring microbial communities but emphasize the need for more research into these interactions. PMID:27065966

Hydrological modelling in a drinking water catchment area as a means of evaluating pathogen risk reduction

NASA Astrophysics Data System (ADS)

Bergion, Viktor; Sokolova, Ekaterina; Åström, Johan; Lindhe, Andreas; Sörén, Kaisa; Rosén, Lars

2017-01-01

Waterborne outbreaks of gastrointestinal diseases are of great concern to drinking water producers and can give rise to substantial costs to the society. The World Health Organisation promotes an approach where the emphasis is on mitigating risks close to the contamination source. In order to handle microbial risks efficiently, there is a need for systematic risk management. In this paper we present a framework for microbial risk management of drinking water systems. The framework incorporates cost-benefit analysis as a decision support method. The hydrological Soil and Water Assessment Tool (SWAT) model, which was set up for the Stäket catchment area in Sweden, was used to simulate the effects of four different mitigation measures on microbial concentrations. The modelling results showed that the two mitigation measures that resulted in a significant (p < 0.05) reduction of Cryptosporidium spp. and Escherichia coli concentrations were a vegetative filter strip linked to cropland and improved treatment (by one Log10 unit) at the wastewater treatment plants. The mitigation measure with a vegetative filter strip linked to grazing areas resulted in a significant reduction of Cryptosporidium spp., but not of E. coli concentrations. The mitigation measure with enhancing the removal efficiency of all on-site wastewater treatment systems (total removal of 2 Log10 units) did not achieve any significant reduction of E. coli or Cryptosporidium spp. concentrations. The SWAT model was useful when characterising the effect of different mitigation measures on microbial concentrations. Hydrological modelling implemented within an appropriate risk management framework is a key decision support element as it identifies the most efficient alternative for microbial risk reduction.

Microbial Communities Shaped by Treatment Processes in a Drinking Water Treatment Plant and Their Contribution and Threat to Drinking Water Safety.

PubMed

Li, Qi; Yu, Shuili; Li, Lei; Liu, Guicai; Gu, Zhengyang; Liu, Minmin; Liu, Zhiyuan; Ye, Yubing; Xia, Qing; Ren, Liumo

2017-01-01

Bacteria play an important role in water purification in drinking water treatment systems. On one hand, bacteria present in the untreated water may help in its purification through biodegradation of the contaminants. On the other hand, some bacteria may be human pathogens and pose a threat to consumers. The present study investigated bacterial communities using Illumina MiSeq sequencing of 16S rRNA genes and their functions were predicted using PICRUSt in a treatment system, including the biofilms on sand filters and biological activated carbon (BAC) filters, in 4 months. In addition, quantitative analyses of specific bacterial populations were performed by real-time quantitative polymerase chain reaction (qPCR). The bacterial community composition of post-ozonation effluent, BAC effluent and disinfected water varied with sampling time. However, the bacterial community structures at other treatment steps were relatively stable, despite great variations of source water quality, resulting in stable treatment performance. Illumina MiSeq sequencing illustrated that Proteobacteria was dominant bacterial phylum. Chlorine disinfection significantly influenced the microbial community structure, while other treatment processes were synergetic. Bacterial communities in water and biofilms were distinct, and distinctions of bacterial communities also existed between different biofilms. By contrast, the functional composition of biofilms on different filters were similar. Some functional genes related to pollutant degradation were found widely distributed throughout the treatment processes. The distributions of Mycobacterium spp. and Legionella spp. in water and biofilms were revealed by real-time quantitative polymerase chain reaction (qPCR). Most bacteria, including potential pathogens, could be effectively removed by chlorine disinfection. However, some bacteria presented great resistance to chlorine. qPCRs showed that Mycobacterium spp. could not be effectively removed by chlorine. These resistant bacteria and, especially potential pathogens should receive more attention. Redundancy analysis (RDA) showed that turbidity, ammonia nitrogen and total organic carbon (TOC) exerted significant effects on community profiles. Overall, this study provides insight into variations of microbial communities in the treatment processes and aids the optimization of drinking water treatment plant design and operation for public health.

Microbial Communities Shaped by Treatment Processes in a Drinking Water Treatment Plant and Their Contribution and Threat to Drinking Water Safety

PubMed Central

Li, Qi; Yu, Shuili; Li, Lei; Liu, Guicai; Gu, Zhengyang; Liu, Minmin; Liu, Zhiyuan; Ye, Yubing; Xia, Qing; Ren, Liumo

2017-01-01

Bacteria play an important role in water purification in drinking water treatment systems. On one hand, bacteria present in the untreated water may help in its purification through biodegradation of the contaminants. On the other hand, some bacteria may be human pathogens and pose a threat to consumers. The present study investigated bacterial communities using Illumina MiSeq sequencing of 16S rRNA genes and their functions were predicted using PICRUSt in a treatment system, including the biofilms on sand filters and biological activated carbon (BAC) filters, in 4 months. In addition, quantitative analyses of specific bacterial populations were performed by real-time quantitative polymerase chain reaction (qPCR). The bacterial community composition of post-ozonation effluent, BAC effluent and disinfected water varied with sampling time. However, the bacterial community structures at other treatment steps were relatively stable, despite great variations of source water quality, resulting in stable treatment performance. Illumina MiSeq sequencing illustrated that Proteobacteria was dominant bacterial phylum. Chlorine disinfection significantly influenced the microbial community structure, while other treatment processes were synergetic. Bacterial communities in water and biofilms were distinct, and distinctions of bacterial communities also existed between different biofilms. By contrast, the functional composition of biofilms on different filters were similar. Some functional genes related to pollutant degradation were found widely distributed throughout the treatment processes. The distributions of Mycobacterium spp. and Legionella spp. in water and biofilms were revealed by real-time quantitative polymerase chain reaction (qPCR). Most bacteria, including potential pathogens, could be effectively removed by chlorine disinfection. However, some bacteria presented great resistance to chlorine. qPCRs showed that Mycobacterium spp. could not be effectively removed by chlorine. These resistant bacteria and, especially potential pathogens should receive more attention. Redundancy analysis (RDA) showed that turbidity, ammonia nitrogen and total organic carbon (TOC) exerted significant effects on community profiles. Overall, this study provides insight into variations of microbial communities in the treatment processes and aids the optimization of drinking water treatment plant design and operation for public health. PMID:29312177

Developing and using artificial soils to analyze soil microbial processes

NASA Astrophysics Data System (ADS)

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 our lab.

Different types of stainless steel used in equipment in meat plants do not affect the initial microbial transfer, including pathogens, from pork skin.

PubMed

Larivière-Gauthier, Guillaume; Quessy, Sylvain; Fournaise, Sylvain; Letellier, Ann; Fravalo, Philippe

2015-07-01

This study describes and measures the impact of different compositions and finishes of stainless steel used in equipment in the meat industry on the transfer of natural flora and selected pathogens from artificially contaminated pork skin. It is known that the adhesion to surfaces of Listeria monocytogenes and Salmonella, 2 pathogens frequently found in contaminated pork meat, depends on the nature and roughness of the surface. Our results show no statistically significant differences in microbial transfer regardless of the types of stainless steel considered, with the highest measured transfer difference being 0.18 log colony-forming units (CFUs)/800 cm(2). Moreover, no differences in total microbial community were observed after transfer on the 5 types of stainless steel using single-strand conformation polymorphism (SSCP). It was concluded that the different characteristics of the stainless steel tested did not affect the initial bacterial transfer in this study.

The most frequently encountered volatile contaminants of essential oils and plant extracts introduced during the isolation procedure: fast and easy profiling.

PubMed

Radulović, Niko S; Blagojević, Polina D

2012-01-01

Unfortunately, contaminants of synthetic/artificial origin are sometimes identified as major constituents of essential oils or plant extracts and considered to be biologically active native plant metabolites. To explore the possibility of early recognition and to create a list of some of the most common semi-volatile contaminants of essential oils and plant extracts. Detailed GC and GC-MS analyses of the evaporation residues of six commercially available diethyl ethers and of a plastic bag hydrodistillate were performed. Average mass scans of the total ion chromatogram profiles of the analysed samples were performed. Almost 200 different compounds, subdivided into two groups, were identified in the analysed samples: (i) compounds that could be only of a synthetic/artificial origin, such as butylated hydroxytoluene and o-phthalic acid esters, i.e. requiring exclusion from the list of identified plant constituents; (ii) compounds possibly of synthetic and/or natural plant origin, i.e. compounds derived from the fatty acid metabolism or products of anaerobic intracellular/microbial fermentation. Average mass scans of the total ion chromatogram profiles provide meaningful and convenient information on uncovering important solvent-derived contamination. A database of the most common semi-volatile contaminants of essential oils and plant extracts has been generated that provides information on the likelihood of rejection or acceptance of contaminants as possible plant constituents. The suggested average mass scan approach enables fast and easy profiling of solvents, allowing even inexperienced researchers to pinpoint contaminants. Copyright © 2011 John Wiley & Sons, Ltd.

Phytochrome, plant growth and flowering

NASA Technical Reports Server (NTRS)

King, R. W.; Bagnall, D. J.

1994-01-01

Attempts to use artificially lit cabinets to grow plants identical to those growing in sunlight have provided compelling evidence of the importance of light quality for plant growth. Changing the balance of red (R) to far-red (FR) radiation, but with a fixed photosynthetic input can shift the phytochrome photoequilibrium in a plant and generate large differences in plant growth. With FR enrichment the plants elongate, and may produce more leaf area and dry matter. Similar morphogenic responses are also obtained when light quality is altered only briefly (15-30 min) at the end-of-the-day. Conversely, for plants grown in natural conditions the response of plant form to selective spectral filtering has again shown that red and far-red wavebands are important as found by Kasperbauer and coworkers. Also, where photosynthetic photon flux densities (PPFD) of sunlight have been held constant, the removal of far-red alone alters plant growth. With FR depletion plants grown in sunlight are small, more branched and darker green. Here we examine the implications for plant growth and flowering when the far-red composition of incident radiation in plant growth chambers is manipulated.

A bitter aftertaste: unintended effects of artificial sweeteners on the gut microbiome.

PubMed

Bokulich, Nicholas A; Blaser, Martin J

2014-11-04

Intestinal microbial communities regulate a range of host physiological functions, from energy harvest and glucose homeostasis to immune development and regulation. Suez et al. (2014) recently demonstrated that artificial sweeteners alter gut microbial communities, leading to glucose intolerance in both mice and humans. Copyright © 2014 Elsevier Inc. All rights reserved.

Microbial Nitrogen Cycle Hotspots in the Plant-Bed/Ditch System of a Constructed Wetland with N2O Mitigation.

PubMed

Wang, Shanyun; Wang, Weidong; Liu, Lu; Zhuang, Linjie; Zhao, Siyan; Su, Yu; Li, Yixiao; Wang, Mengzi; Wang, Cheng; Xu, Liya; Zhu, Guibing

2018-05-24

Artificial microbial nitrogen (N) cycle hotspots in the plant-bed/ditch system were developed and investigated based on intact core and slurry assays measurement using isotopic tracing technology, quantitative PCR and high-throughput sequencing. By increasing hydraulic retention time and periodically fluctuating water level in heterogeneous riparian zones, hotspots of anammox, nitrification, denitrification, ammonium (NH 4 + ) oxidation, nitrite (NO 2 - ) oxidation, nitrate (NO 3 - ) reduction and DNRA were all stimulated at the interface sediments, with the abundance and activity being about 1-3 orders of magnitude higher than those in nonhotspots. Isotopic pairing experiments revealed that in microbial hotspots, nitrite sources were higher than the sinks, and both NH 4 + oxidation (55.8%) and NO 3 - reduction (44.2%) provided nitrite for anammox, which accounted for 43.0% of N-loss and 44.4% of NH 4 + removal in riparian zones but did not involve nitrous oxide (N 2 O) emission risks. High-throughput analysis identified that bacterial quorum sensing mediated this anammox hotspot with B.fulgida dominating the anammox community, but it was B. anammoxidans and Jettenia sp. that contributed more to anammox activity. In the nonhotspot zones, the NO 2 - source (NO 3 - reduction dominated) was lower than the sink, limiting the effects on anammox. The in situ N 2 O flux measurement showed that the microbial hotspot had a 27.1% reduced N 2 O emission flux compared with the nonhotspot zones.

Community analysis of plant biomass-degrading microorganisms from Obsidian Pool, Yellowstone National Park

DOE PAGES

Vishnivetskaya, Tatiana A.; Hamilton-Brehm, Scott D.; Podar, Mircea; ...

2014-10-16

The conversion of lignocellulosic biomass into biofuels can potentially be improved by employing robust microorganisms and enzymes that efficiently deconstruct plant polysaccharides at elevated temperatures. Many of the geothermal features of Yellowstone National Park (YNP) are surrounded by vegetation providing a source of allochthonic material to support heterotrophic microbial communities adapted to utilize plant biomass as a primary carbon and energy source. In this paper, a well-known hot spring environment, Obsidian Pool (OBP), was examined for potential biomass-active microorganisms using cultivation-independent and enrichment techniques. Analysis of 33,684 archaeal and 43,784 bacterial quality-filtered 16S rRNA gene pyrosequences revealed that archaeal diversitymore » in the main pool was higher than bacterial; however, in the vegetated area, overall bacterial diversity was significantly higher. Of notable interest was a flooded depression adjacent to OBP supporting a stand of Juncus tweedyi, a heat-tolerant rush commonly found growing near geothermal features in YNP. The microbial community from heated sediments surrounding the plants was enriched in members of the Firmicutes including potentially (hemi)cellulolytic bacteria from the genera Clostridium, Anaerobacter, Caloramator, Caldicellulosiruptor, and Thermoanaerobacter. Enrichment cultures containing model and real biomass substrates were established at a wide range of temperatures (55–85 °C). Microbial activity was observed up to 80 °C on all substrates including Avicel, xylan, switchgrass, and Populus sp. Finally, independent of substrate, Caloramator was enriched at lower (<65 °C) temperatures while highly active cellulolytic bacteria Caldicellulosiruptor were dominant at high (>65 °C) temperatures.« less

Community analysis of plant biomass-degrading microorganisms from Obsidian Pool, Yellowstone National Park

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vishnivetskaya, Tatiana A.; Hamilton-Brehm, Scott D.; Podar, Mircea

The conversion of lignocellulosic biomass into biofuels can potentially be improved by employing robust microorganisms and enzymes that efficiently deconstruct plant polysaccharides at elevated temperatures. Many of the geothermal features of Yellowstone National Park (YNP) are surrounded by vegetation providing a source of allochthonic material to support heterotrophic microbial communities adapted to utilize plant biomass as a primary carbon and energy source. In this paper, a well-known hot spring environment, Obsidian Pool (OBP), was examined for potential biomass-active microorganisms using cultivation-independent and enrichment techniques. Analysis of 33,684 archaeal and 43,784 bacterial quality-filtered 16S rRNA gene pyrosequences revealed that archaeal diversitymore » in the main pool was higher than bacterial; however, in the vegetated area, overall bacterial diversity was significantly higher. Of notable interest was a flooded depression adjacent to OBP supporting a stand of Juncus tweedyi, a heat-tolerant rush commonly found growing near geothermal features in YNP. The microbial community from heated sediments surrounding the plants was enriched in members of the Firmicutes including potentially (hemi)cellulolytic bacteria from the genera Clostridium, Anaerobacter, Caloramator, Caldicellulosiruptor, and Thermoanaerobacter. Enrichment cultures containing model and real biomass substrates were established at a wide range of temperatures (55–85 °C). Microbial activity was observed up to 80 °C on all substrates including Avicel, xylan, switchgrass, and Populus sp. Finally, independent of substrate, Caloramator was enriched at lower (<65 °C) temperatures while highly active cellulolytic bacteria Caldicellulosiruptor were dominant at high (>65 °C) temperatures.« less

Variables Influencing Extraction of Nucleic Acids from Microbial Plankton (Viruses, Bacteria, and Protists) Collected on Nanoporous Aluminum Oxide Filters

PubMed Central

Mueller, Jaclyn A.; Culley, Alexander I.

2014-01-01

Anodic aluminum oxide (AAO) filters have high porosity and can be manufactured with a pore size that is small enough to quantitatively capture viruses. These properties make the filters potentially useful for harvesting total microbial communities from water samples for molecular analyses, but their performance for nucleic acid extraction has not been systematically or quantitatively evaluated. In this study, we characterized the flux of water through commercially produced nanoporous (0.02 μm) AAO filters (Anotop; Whatman) and used isolates (a virus, a bacterium, and a protist) and natural seawater samples to test variables that we expected would influence the efficiency with which nucleic acids are recovered from the filters. Extraction chemistry had a significant effect on DNA yield, and back flushing the filters during extraction was found to improve yields of high-molecular-weight DNA. Using the back-flush protocol, the mass of DNA recovered from microorganisms collected on AAO filters was ≥100% of that extracted from pellets of cells and viruses and 94% ± 9% of that obtained by direct extraction of a liquid bacterial culture. The latter is a minimum estimate of the relative recovery of microbial DNA, since liquid cultures include dissolved nucleic acids that are retained inefficiently by the filter. In conclusion, we demonstrate that nucleic acids can be extracted from microorganisms on AAO filters with an efficiency similar to that achievable by direct extraction of microbes in suspension or in pellets. These filters are therefore a convenient means by which to harvest total microbial communities from multiple aqueous samples in parallel for subsequent molecular analyses. PMID:24747903

Isolation of pathogenic Naegleria from artificially heated waters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tyndall, R L; Willaert, E; Stevens, A R

1977-01-01

Investigations were undertaken to determine whether heated waters facilitate the proliferation of free-living amoeba that cause primary amoebic meningoencephalitis. Water samples were taken close to the discharges of power plants situated on lakes or rivers in Florida and Texas and from cooling towers in Tennessee. The water temperatures ranged from 29 to 42/sup 0/C. Water samples were also taken from several lakes in Florida and Texas without associated power plants. The water temperatures of these ranged from 30/sup 0/ to 34/sup 0/C. Twenty-five-250-ml samples were filtered through membranes. Samples taken from the control lakes and cooling towers showed no growthmore » of pathogenic amoeba, whereas growth was obtained from 2 of the 8 lakes and rivers in Florida and from 1 of the 7 man-made lakes in Texas that were artificially heated. The amoebae were identified as belonging to the genus Naegleria from their trophozoite and cyst structure, ability to grow at 45/sup 0/C, to transform into flagellates, and to produce primary amebic meningoencephalitis (PAME) in mice after intranasal instillation. Their identification as N. fowleri was confirmed by indirect immunofluorescent analysis with antiserum produced against N. fowleri. These findings indicate that artificial heating of waters may facilitate the growth of pathogenic free living amoeba.« less

Internal Porosity of Mineral Coating Supports Microbial Activity in Rapid Sand Filters for Groundwater Treatment

PubMed Central

Gülay, Arda; Tatari, Karolina; Musovic, Sanin; Mateiu, Ramona V.; Albrechtsen, Hans-Jørgen

2014-01-01

A mineral coating develops on the filter grain surface when groundwater is treated via rapid sand filtration in drinking water production. The coating changes the physical and chemical properties of the filter material, but little is known about its effect on the activity, colonization, diversity, and abundance of microbiota. This study reveals that a mineral coating can positively affect the colonization and activity of microbial communities in rapid sand filters. To understand this effect, we investigated the abundance, spatial distribution, colonization, and diversity of all and of nitrifying prokaryotes in filter material with various degrees of mineral coating. We also examined the physical and chemical characteristics of the mineral coating. The amount of mineral coating correlated positively with the internal porosity, the packed bulk density, and the biologically available surface area of the filter material. The volumetric NH4+ removal rate also increased with the degree of mineral coating. Consistently, bacterial 16S rRNA and amoA abundances positively correlated with increased mineral coating levels. Microbial colonization could be visualized mainly within the outer periphery (60.6 ± 35.6 μm) of the mineral coating, which had a thickness of up to 600 ± 51 μm. Environmental scanning electron microscopic (E-SEM) observations suggested an extracellular polymeric substance-rich matrix and submicron-sized bacterial cells. Nitrifier diversity profiles were similar irrespective of the degree of mineral coating, as indicated by pyrosequencing analysis. Overall, our results demonstrate that mineral coating positively affects microbial colonization and activity in rapid sand filters, most likely due to increased volumetric cell abundances facilitated by the large surface area of internal mineral porosity accessible for microbial colonization. PMID:25192987

Microbial Communities as Experimental Units

PubMed Central

DAY, MITCH D.; BECK, DANIEL; FOSTER, JAMES A.

2011-01-01

Artificial ecosystem selection is an experimental technique that treats microbial communities as though they were discrete units by applying selection on community-level properties. Highly diverse microbial communities associated with humans and other organisms can have significant impacts on the health of the host. It is difficult to find correlations between microbial community composition and community-associated diseases, in part because it may be impossible to define a universal and robust species concept for microbes. Microbial communities are composed of potentially thousands of unique populations that evolved in intimate contact, so it is appropriate in many situations to view the community as the unit of analysis. This perspective is supported by recent discoveries using metagenomics and pangenomics. Artificial ecosystem selection experiments can be costly, but they bring the logical rigor of biological model systems to the emerging field of microbial community analysis. PMID:21731083

Spectral transmittance of intraocular lenses under natural and artificial illumination: criteria analysis for choosing a suitable filter.

PubMed

Artigas, Jose M; Felipe, Adelina; Navea, Amparo; Artigas, Cristina; García-Domene, Maria C

2011-01-01

To compare the spectral transmission of different intraocular lenses (IOLs) with either ultraviolet (UV) or blue-light filters, and to analyze the performance of these filters with artificial light sources as well as sunlight. Experimental study. The spectral transmission curve of 10 IOLs was measured using a PerkinElmer Lambda 800 UV/VIS spectrometer (Waltham, MA). Different filtering simulations were performed using the D65 standard illuminant as daylight and standard incandescent lamp and fluorescent bulb illuminants. Spectral transmittance of the IOLs. All the IOLs studied provide good UVC (200-280 nm) and UVB (280-315 nm) protection, except for one that presented an appreciable window at 270 nm. Nevertheless, both natural and artificial sources have practically no emission under 300 nm. In the UVA (315-380 nm) range the curves of the different IOLs manifested different degrees of absorption. Not all the UV filters incorporated in different IOLs protect equally. The filters that provide greater photoprotection against UV radiation, even blue light, are yellow and orange. Then, yellow and orange IOL filters may be best suited for cases requiring special retinal protection. The filters that favor better photoreception of visible light (380-780 nm) are those that transmit this radiation close to 100%. Artificial illumination practically does not emit in the UV range, but its levels of illumination are very low when compared with solar light. A possible balance between photoprotection and photoreception could be a sharp cutoff filter with the cutoff wavelength near 400 nm and a maximum transmittance around 100%. Copyright © 2011 American Academy of Ophthalmology. Published by Elsevier Inc. All rights reserved.

Comparative analysis of the gastrointestinal microbial communities of bar-headed goose (Anser indicus) in different breeding patterns by high-throughput sequencing.

PubMed

Wang, Wen; Cao, Jian; Li, Ji-Rong; Yang, Fang; Li, Zhuo; Li, Lai-Xing

2016-01-01

The bar-headed goose is currently one of the most popular species for rare birds breeding in China. However, bar-headed geese in captivity display a reduced reproductive rate. The gut microbiome has been shown to influence host factors such as nutrient and energy metabolism, immune homeostasis and reproduction. It is therefore of great scientific and agriculture value to analyze the microbial communities associated with bar-headed geese in order to improve their reproductive rate. Here we describe the first comparative study of the gut microbial communities of bar-headed geese in three different breeding pattern groups by 16SrRNA sequences using the Illumina MiSeq platform. The results showed that Firmicutes predominated (58.33%) among wild bar-headed geese followed by Proteobacteria (30.67%), Actinobacteria (7.33%) and Bacteroidetes (3.33%). In semi-artificial breeding group, Firmicutes was also the most abundant bacteria (62.00%), followed by Bacteroidetes (28.67%), Proteobacteria (4.20%), Actinobacteria (3.27%) and Fusobacteria (1.51%). The microbial communities of artificial breeding group were dominated by Firmicutes (60.67%), Fusobacteria (29.67%) and Proteobacteria (9.33%). Wild bar-headed geese had a significant higher relative abundance of Proteobacteria and Actinobacteria, while semi-artificial breeding bar-headed geese had significantly more Bacteroidetes. The semi-artificial breeding group had the highest microbial community diversity and richness, followed by wild group, and then the artificial breeding group. The marked differences of genus level group-specific microbes create a baseline for future bar-headed goose microbiology research. Copyright © 2015 Elsevier GmbH. All rights reserved.

Where the bugs are: analyzing distributions of bacterial phyla by descriptor keyword search in the nucleotide database.

PubMed

Squartini, Andrea

2011-07-26

The associations between bacteria and environment underlie their preferential interactions with given physical or chemical conditions. Microbial ecology aims at extracting conserved patterns of occurrence of bacterial taxa in relation to defined habitats and contexts. In the present report the NCBI nucleotide sequence database is used as dataset to extract information relative to the distribution of each of the 24 phyla of the bacteria superkingdom and of the Archaea. Over two and a half million records are filtered in their cross-association with each of 48 sets of keywords, defined to cover natural or artificial habitats, interactions with plant, animal or human hosts, and physical-chemical conditions. The results are processed showing: (a) how the different descriptors enrich or deplete the proportions at which the phyla occur in the total database; (b) in which order of abundance do the different keywords score for each phylum (preferred habitats or conditions), and to which extent are phyla clustered to few descriptors (specific) or spread across many (cosmopolitan); (c) which keywords individuate the communities ranking highest for diversity and evenness. A number of cues emerge from the results, contributing to sharpen the picture on the functional systematic diversity of prokaryotes. Suggestions are given for a future automated service dedicated to refining and updating such kind of analyses via public bioinformatic engines.

Integrated Artificial Intelligence Approaches for Disease Diagnostics.

PubMed

Vashistha, Rajat; Chhabra, Deepak; Shukla, Pratyoosh

2018-06-01

Mechanocomputational techniques in conjunction with artificial intelligence (AI) are revolutionizing the interpretations of the crucial information from the medical data and converting it into optimized and organized information for diagnostics. It is possible due to valuable perfection in artificial intelligence, computer aided diagnostics, virtual assistant, robotic surgery, augmented reality and genome editing (based on AI) technologies. Such techniques are serving as the products for diagnosing emerging microbial or non microbial diseases. This article represents a combinatory approach of using such approaches and providing therapeutic solutions towards utilizing these techniques in disease diagnostics.

The use of controlled microbial cenoses in producers' link to increase steady functioning of artificial ecosystems

NASA Astrophysics Data System (ADS)

Somova, Lydia; Mikheeva, Galina; Somova, Lydia

The life support systems (LSS) for long-term missions are to use cycling-recycling systems, including biological recycling. Simple ecosystems include 3 links: producers (plants), consumers (man, animals) and reducers (microorganisms). Microorganisms are substantial component of every link of LSS. Higher plants are the traditional regenerator of air and producer of food. They should be used in many successive generations of their reproduction in LSS. Controlled microbiocenoses can increase productivity of producer's link and protect plants from infections. The goal of this work was development of methodological bases of formation of stable, controlled microbiocenoses, intended for increase of productivity of plants and for obtaining ecologically pure production of plants. Main results of our investigations: 1. Experimental microbiocenoses, has been produced in view of the developed methodology on the basis of natural association of microorganisms by long cultivation on specially developed medium. Dominating groups are bacteria of genera: Lactobacillus, Streptococcus, Leuconostoc, Bifidobacterium, Rhodopseudomonas and yeast of genera: Kluyveromyces, Saccharomyces, Torulopsis. 2. Optimal parameters of microbiocenosis cultivation (t, pH, light exposure, biogenic elements concentrations) were experimentally established. Conditions of cultivation on which domination of different groups of microbiocenosis have been found. 3. It was shown, that processing of seeds of wheat, oats, bulbs and plants Allium cepa L. (an onions) with microbial association raised energy of germination of seeds and bulbs and promoted the increase (on 20-30 %) of growth green biomass and root system of plants in comparison with the control. This work is supported by grant, Yenissey , 07-04-96806

Density and distribution of nitrifying guilds in rapid sand filters for drinking water production: Dominance of Nitrospira spp.

PubMed

Tatari, Karolina; Musovic, Sanin; Gülay, Arda; Dechesne, Arnaud; Albrechtsen, Hans-Jørgen; Smets, Barth F

2017-12-15

We investigated the density and distribution of total bacteria, canonical Ammonia Oxidizing Bacteria (AOB) (Nitrosomonas plus Nitrosospira), Ammonia Oxidizing Archaea (AOA), as well as Nitrobacter and Nitrospira in rapid sand filters used for groundwater treatment. To investigate the spatial distribution of these guilds, filter material was sampled at four drinking water treatment plants (DWTPs) in parallel filters of the pre- and after-filtration stages at different locations and depths. The target guilds were quantified by qPCR targeting 16S rRNA and amoA genes. Total bacterial densities (ignoring 16S rRNA gene copy number variation) were high and ranged from 10 9 to 10 10 per gram (10 15 to 10 16 per m 3 ) of filter material. All examined guilds, except AOA, were stratified at only one of the four DWTPs. Densities varied spatially within filter (intra-filter variation) at two of the DWTPs and in parallel filters (inter-filter variation) at one of the DWTPs. Variation analysis revealed random sampling as the most efficient strategy to yield accurate mean density estimates, with collection of at least 7 samples suggested to obtain an acceptable (below half order of magnitude) density precision. Nitrospira was consistently the most dominant guild (5-10% of total community), and was generally up to 4 orders of magnitude more abundant than Nitrobacter and up to 2 orders of magnitude more abundant than canonical AOBs. These results, supplemented with further analysis of the previously reported diversity of Nitrospira in the studied DWTPs based on 16S rRNA and nxrB gene phylogeny (Gülay et al., 2016; Palomo et al., 2016), indicate that the high Nitrospira abundance is due to their comammox (complete ammonia oxidation) physiology. AOA densities were lower than AOB densities, except in the highly stratified filters, where they were of similar abundance. In conclusion, rapid sand filters are microbially dense, with varying degrees of spatial heterogeneity, which requires replicate sampling for a sufficiently precise determination of total microbial community and specific population densities. A consistently high Nitrospira to bacterial and archaeal AOB density ratio suggests that non-canonical pathways for nitrification may dominate the examined RSFs. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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) and long-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 undergroundmore » 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.« less

Clay minerals and metal oxides strongly influence the structure of alkane-degrading microbial communities during soil maturation.

PubMed

Steinbach, Annelie; Schulz, Stefanie; Giebler, Julia; Schulz, Stephan; Pronk, Geertje J; Kögel-Knabner, Ingrid; Harms, Hauke; Wick, Lukas Y; Schloter, Michael

2015-07-01

Clay minerals, charcoal and metal oxides are essential parts of the soil matrix and strongly influence the formation of biogeochemical interfaces in soil. We investigated the role of these parental materials for the development of functional microbial guilds using the example of alkane-degrading bacteria harbouring the alkane monooxygenase gene (alkB) in artificial mixtures composed of different minerals and charcoal, sterile manure and a microbial inoculum extracted from an agricultural soil. We followed changes in abundance and community structure of alkane-degrading microbial communities after 3 and 12 months of soil maturation and in response to a subsequent 2-week plant litter addition. During maturation we observed an overall increasing divergence in community composition. The impact of metal oxides on alkane-degrading community structure increased during soil maturation, whereas the charcoal impact decreased from 3 to 12 months. Among the clay minerals illite influenced the community structure of alkB-harbouring bacteria significantly, but not montmorillonite. The litter application induced strong community shifts in soils, maturated for 12 months, towards functional guilds typical for younger maturation stages pointing to a resilience of the alkane-degradation function potentially fostered by an extant 'seed bank'.

Clay minerals and metal oxides strongly influence the structure of alkane-degrading microbial communities during soil maturation

PubMed Central

Steinbach, Annelie; Schulz, Stefanie; Giebler, Julia; Schulz, Stephan; Pronk, Geertje J; Kögel-Knabner, Ingrid; Harms, Hauke; Wick, Lukas Y; Schloter, Michael

2015-01-01

Clay minerals, charcoal and metal oxides are essential parts of the soil matrix and strongly influence the formation of biogeochemical interfaces in soil. We investigated the role of these parental materials for the development of functional microbial guilds using the example of alkane-degrading bacteria harbouring the alkane monooxygenase gene (alkB) in artificial mixtures composed of different minerals and charcoal, sterile manure and a microbial inoculum extracted from an agricultural soil. We followed changes in abundance and community structure of alkane-degrading microbial communities after 3 and 12 months of soil maturation and in response to a subsequent 2-week plant litter addition. During maturation we observed an overall increasing divergence in community composition. The impact of metal oxides on alkane-degrading community structure increased during soil maturation, whereas the charcoal impact decreased from 3 to 12 months. Among the clay minerals illite influenced the community structure of alkB-harbouring bacteria significantly, but not montmorillonite. The litter application induced strong community shifts in soils, maturated for 12 months, towards functional guilds typical for younger maturation stages pointing to a resilience of the alkane-degradation function potentially fostered by an extant ‘seed bank'. PMID:25535940

The Dust at Altitude Recovery Technology (DART) System was Developed to Recover Plant, Human, and Animal Pathogens in Asian and African Dust Storms over North America

NASA Astrophysics Data System (ADS)

Schuerger, A. C.; Tench, B.; Nehr, A.; Emmons, T.; Valbuena, F.; Palaia, J.; Sugars, C.

2014-12-01

Dust emanates year-round from Africa and Asia and impacts air quality in North America. Asian dust plumes deliver up to 64 million tonnes of dust over the NW of the USA, and African dust storms deliver over 50 million tonnes of dust over Florida each year. Several recent studies have demonstrated that human and plant pathogens from Asian [1] African [2] aerosols can be transported to N. America in naturally occurring dust storms. What is unknown is whether these 'presumptive pathogens' impact human, plant, or animal health in the USA. In order to initiate a long-term monitoring program of pathogens in Asian and African dust plumes, we have developed a dust collection system called DART (Dust at Altitude Recovery Technology) (figure). The DART dust sampler can be mounted on a F104 Starfighter jet (figure) and a T6 Texan propeller driven airplane (not shown), and was test flown over FL in Dec. 2013 on the F104 and on the T6 in the summer of 2014. The DART system utilizes a high-volume pump to pass air through 6 separate filtration units where both aerosols and microbial cells are captured. The filtration systems exhibit flow rates from 25-142 L/min depending on the pore size and brand of filters used. Flow rates are directly correlated to increased air speed, and are inversely correlated to increased altitude. Filtration units can be turned on and off individually as required for specific science flight objectives. The DART dust sampler has performed nominally up to 7600 m, 0.92 Mach, and 3.5 +G's. During initial test flights in Dec. 2013, 5 of 8 genera of fungi recovered from the lower atmosphere over FL contained plant pathogens including species in the genera: Acremonium, Aspergillus, Cladosporium, Curvularia, and Fusarium. Numbers of recovered fungi, but not bacteria, increased significantly when 5 or 10 µm filters were used in the DART system compared to filter pore sizes ≤ 1.2 µm. Future sampling programs for both Asian and African dust events will be discussed. References: [1] Smith, D. J., et al., 2012. Microbial Ecology 64,973-985. [2] Griffin, D. W. 2007, Clinical Microbiology Reviews 20, 459-477.

Phytochrome, plant growth and flowering

DOE Office of Scientific and Technical Information (OSTI.GOV)

King, R.W.; Bagnall, D.J.

1994-12-31

Attempts to use artificially lit cabinets to grow plants identical to those growing in sunlight have provided compelling evidence of the importance of light quality for plant growth. Changing the balance of red (R) to far-red (FR) radiation, but with a fixed photosynthetic input can shift the phytochrome photoequilibrium in a plant and generate large differences in plant growth. With FR enrichment the plants elongate, and may produce more leaf area and dry matter. Similar morphogenic responses are also obtained when light quality is altered only briefly (15-30 min) at the end-of-the-day. Conversely, for plants grown in natural conditions themore » response of plant form to selective spectral filtering has again shown that red and far-red wavebands are important as found by Kasperbauer and coworkers. Also, where photosynthetic photon flux densities (PPFD) of sunlight have been held constant, the removal of far-red alone alters plant growth. As shown for chrysanthemum, with FR depletion plants grown in sunlight are small, more branched and darker green. We examine the implications for plant growth and flowering when the far-red composition of incident radiation in plant growth chambers is manipulated.« less

Evaluating potential spectral impacts of various artificial lights on melatonin suppression, photosynthesis, and star visibility.

PubMed

Aubé, Martin; Roby, Johanne; Kocifaj, Miroslav

2013-01-01

Artificial light at night can be harmful to the environment, and interferes with fauna and flora, star visibility, and human health. To estimate the relative impact of a lighting device, its radiant power, angular photometry and detailed spectral power distribution have to be considered. In this paper we focus on the spectral power distribution. While specific spectral characteristics can be considered harmful during the night, they can be considered advantageous during the day. As an example, while blue-rich Metal Halide lamps can be problematic for human health, star visibility and vegetation photosynthesis during the night, they can be highly appropriate during the day for plant growth and light therapy. In this paper we propose three new indices to characterize lamp spectra. These indices have been designed to allow a quick estimation of the potential impact of a lamp spectrum on melatonin suppression, photosynthesis, and star visibility. We used these new indices to compare various lighting technologies objectively. We also considered the transformation of such indices according to the propagation of light into the atmosphere as a function of distance to the observer. Among other results, we found that low pressure sodium, phosphor-converted amber light emitting diodes (LED) and LED 2700 K lamps filtered with the new Ledtech's Equilib filter showed a lower or equivalent potential impact on melatonin suppression and star visibility in comparison to high pressure sodium lamps. Low pressure sodium, LED 5000 K-filtered and LED 2700 K-filtered lamps had a lower impact on photosynthesis than did high pressure sodium lamps. Finally, we propose these indices as new standards for the lighting industry to be used in characterizing their lighting technologies. We hope that their use will favor the design of new environmentally and health-friendly lighting technologies.

Evaluating Potential Spectral Impacts of Various Artificial Lights on Melatonin Suppression, Photosynthesis, and Star Visibility

PubMed Central

Aubé, Martin; Roby, Johanne; Kocifaj, Miroslav

2013-01-01

Artificial light at night can be harmful to the environment, and interferes with fauna and flora, star visibility, and human health. To estimate the relative impact of a lighting device, its radiant power, angular photometry and detailed spectral power distribution have to be considered. In this paper we focus on the spectral power distribution. While specific spectral characteristics can be considered harmful during the night, they can be considered advantageous during the day. As an example, while blue-rich Metal Halide lamps can be problematic for human health, star visibility and vegetation photosynthesis during the night, they can be highly appropriate during the day for plant growth and light therapy. In this paper we propose three new indices to characterize lamp spectra. These indices have been designed to allow a quick estimation of the potential impact of a lamp spectrum on melatonin suppression, photosynthesis, and star visibility. We used these new indices to compare various lighting technologies objectively. We also considered the transformation of such indices according to the propagation of light into the atmosphere as a function of distance to the observer. Among other results, we found that low pressure sodium, phosphor-converted amber light emitting diodes (LED) and LED 2700 K lamps filtered with the new Ledtech’s Equilib filter showed a lower or equivalent potential impact on melatonin suppression and star visibility in comparison to high pressure sodium lamps. Low pressure sodium, LED 5000 K-filtered and LED 2700 K-filtered lamps had a lower impact on photosynthesis than did high pressure sodium lamps. Finally, we propose these indices as new standards for the lighting industry to be used in characterizing their lighting technologies. We hope that their use will favor the design of new environmentally and health-friendly lighting technologies. PMID:23861808

Effectiveness of a full-scale horizontal slow sand filter for controlling phytopathogens in recirculating hydroponics: From microbial isolation to full microbiome assessment.

PubMed

Prenafeta-Boldú, Francesc X; Trillas, Isabel; Viñas, Marc; Guivernau, Miriam; Cáceres, Rafaela; Marfà, Oriol

2017-12-01

The microbial disinfestation efficiency of an innovative horizontal-flow slow sand filter (HSSF) for treating nutrient solution spent from an experimental closed-loop nursery was evaluated by means of a combination of culture-dependent and independent molecular techniques. A dense inoculum of the fungal plant pathogen Fusarium oxysporum f.sp. lycopersici was applied in the fertigation system (10 6 cells per mL). Indigenous and introduced populations of eubacteria and fungi were assessed in the nutrient solution, the HSSF influent/effluent, and a sand bed transect by isolation on selective media, as well as by quantitative qPCR and next-generation sequencing (NGS) on target ribosomal genes. The HSSF effectively reduced viable Fusarium propagules and fungal gene content with an efficiency consistently above 99.9% (5 orders of magnitude down). On the other hand, Fusarium cells accumulated in the sand bed, indicating that physical entrapment was the main removal mechanism. The viability of retained Fusarium cells tended to decrease in time, so that treatment efficiency might be enhanced by antagonistic species from the genera Bacillus, Pseudomonas, and Trichoderma, also identified in the sand bed. Indigenous bacterial populations from the HSSF effluent were reduced by 87.2% and 99.9% in terms of colony forming units and gene counts, respectively, when compared to the influent. Furthermore, microbial populations from the HSSF effluent were different from those observed in the sand bed and the influent. In summary, the HSSF microbial disinfestation efficiency is comparable to that reported for other more intensive and costly methodologies, while allowing a significant recovery of water and nutrients. Copyright © 2017 Elsevier B.V. All rights reserved.

Influence of the Natural Microbial Flora on the Acid Tolerance Response of Listeria monocytogenes in a Model System of Fresh Meat Decontamination Fluids

PubMed Central

Samelis, John; Sofos, John N.; Kendall, Patricia A.; Smith, Gary C.

2001-01-01

Depending on its composition and metabolic activity, the natural flora that may be established in a meat plant environment can affect the survival, growth, and acid tolerance response (ATR) of bacterial pathogens present in the same niche. To investigate this hypothesis, changes in populations and ATR of inoculated (105 CFU/ml) Listeria monocytogenes were evaluated at 35°C in water (10 or 85°C) or acidic (2% lactic or acetic acid) washings of beef with or without prior filter sterilization. The model experiments were performed at 35°C rather than lower (≤15°C) temperatures to maximize the response of inoculated L. monocytogenes in the washings with or without competitive flora. Acid solution washings were free (<1.0 log CFU/ml) of natural flora before inoculation (day 0), and no microbial growth occurred during storage (35°C, 8 days). Inoculated L. monocytogenes died off (negative enrichment) in acid washings within 24 h. In nonacid (water) washings, the pathogen increased (approximately 1.0 to 2.0 log CFU/ml), irrespective of natural flora, which, when present, predominated (>8.0 log CFU/ml) by day 1. The pH of inoculated water washings decreased or increased depending on absence or presence of natural flora, respectively. These microbial and pH changes modulated the ATR of L. monocytogenes at 35°C. In filter-sterilized water washings, inoculated L. monocytogenes increased its ATR by at least 1.0 log CFU/ml from days 1 to 8, while in unfiltered water washings the pathogen was acid tolerant at day 1 (0.3 to 1.4 log CFU/ml reduction) and became acid sensitive (3.0 to >5.0 log CFU/ml reduction) at day 8. These results suggest that the predominant gram-negative flora of an aerobic fresh meat plant environment may sensitize bacterial pathogens to acid. PMID:11375145

Microbial community in a full-scale drinking water biosand filter.

PubMed

Feng, Shuo; Chen, Chao; Wang, Qingfeng; Yang, Zhiyu; Zhang, Xiaojian; Xie, Shuguang

2013-04-01

To remove turbidity and minimize microbiological risks, rapid sand filtration is one of main drinking water treatment processes in the world. However, after a long-term operation, sand particles will be colonized by microorganisms which can remove biodegradable organic matters and nitrogen compounds. In this study, 16S rRNA gene clone library analysis was applied to characterize the microbial community in a full-scale biosand filter used for drinking water treatment. The results indicate that phylum Nitrospirae and class Alphaproteobacteria were the dominant bacterial groups in the biosand sample collected from the upper filter layer. The dominance of Sphingomonas species might pose a microbiological risk. This work could provide some new insights into microbial community in drinking water biofilter.

Robust crop and weed segmentation under uncontrolled outdoor illumination.

PubMed

Jeon, Hong Y; Tian, Lei F; Zhu, Heping

2011-01-01

An image processing algorithm for detecting individual weeds was developed and evaluated. Weed detection processes included were normalized excessive green conversion, statistical threshold value estimation, adaptive image segmentation, median filter, morphological feature calculation and Artificial Neural Network (ANN). The developed algorithm was validated for its ability to identify and detect weeds and crop plants under uncontrolled outdoor illuminations. A machine vision implementing field robot captured field images under outdoor illuminations and the image processing algorithm automatically processed them without manual adjustment. The errors of the algorithm, when processing 666 field images, ranged from 2.1 to 2.9%. The ANN correctly detected 72.6% of crop plants from the identified plants, and considered the rest as weeds. However, the ANN identification rates for crop plants were improved up to 95.1% by addressing the error sources in the algorithm. The developed weed detection and image processing algorithm provides a novel method to identify plants against soil background under the uncontrolled outdoor illuminations, and to differentiate weeds from crop plants. Thus, the proposed new machine vision and processing algorithm may be useful for outdoor applications including plant specific direct applications (PSDA).

Environmental Filtering Process Has More Important Roles than Dispersal Limitation in Shaping Large-Scale Prokaryotic Beta Diversity Patterns of Grassland Soils.

PubMed

Cao, Peng; Wang, Jun-Tao; Hu, Hang-Wei; Zheng, Yuan-Ming; Ge, Yuan; Shen, Ju-Pei; He, Ji-Zheng

2016-07-01

Despite the utmost importance of microorganisms in maintaining ecosystem functioning and their ubiquitous distribution, our knowledge of the large-scale pattern of microbial diversity is limited, particularly in grassland soils. In this study, the microbial communities of 99 soil samples spanning over 3000 km across grassland ecosystems in northern China were investigated using high-throughput sequencing to analyze the beta diversity pattern and the underlying ecological processes. The microbial communities were dominated by Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, and Planctomycetes across all the soil samples. Spearman's correlation analysis indicated that climatic factors and soil pH were significantly correlated with the dominant microbial taxa, while soil microbial richness was positively linked to annual precipitation. The environmental divergence-dissimilarity relationship was significantly positive, suggesting the importance of environmental filtering processes in shaping soil microbial communities. Structural equation modeling found that the deterministic process played a more important role than the stochastic process on the pattern of soil microbial beta diversity, which supported the predictions of niche theory. Partial mantel test analysis have showed that the contribution of independent environmental variables has a significant effect on beta diversity, while independent spatial distance has no such relationship, confirming that the deterministic process was dominant in structuring soil microbial communities. Overall, environmental filtering process has more important roles than dispersal limitation in shaping microbial beta diversity patterns in the grassland soils.

A comparison of hand washing techniques to remove Escherichia coli and caliciviruses under natural or artificial fingernails.

PubMed

Lin, Chia-Min; Wu, Fone-Mao; Kim, Hoi-Kyung; Doyle, Michael P; Michael, Barry S; Williams, L Keoki

2003-12-01

Compared with other parts of the hand, the area beneath fingernails harbors the most microorganisms and is most difficult to clean. Artificial fingernails, which are usually long and polished, reportedly harbor higher microbial populations than natural nails. Hence, the efficacy of different hand washing methods for removing microbes from natural and artificial fingernails was evaluated. Strains of nonpathogenic Escherichia coli JM109 and feline calicivirus (FCV) strain F9 were used as bacterial and viral indicators, respectively. Volunteers with artificial or natural nails were artificially contaminated with ground beef containing E. coli JM109 or artificial feces containing FCV. Volunteers washed their hands with tap water, regular liquid soap, antibacterial liquid soap, alcohol-based hand sanitizer gel, regular liquid soap followed by alcohol gel, or regular liquid soap plus a nailbrush. The greatest reduction of inoculated microbial populations was obtained by washing with liquid soap plus a nailbrush, and the least reduction was obtained by rubbing hands with alcohol gel. Lower but not significantly different (P > 0.05) reductions of E. coli and FCV counts were obtained from beneath artificial than from natural fingernails. However, significantly (P < or = 0.05) higher E. coli and FCV counts were recovered from hands with artificial nails than from natural nails before and after hand washing. In addition, microbial cell numbers were correlated with fingernail length, with greater numbers beneath fingernails with longer nails. These results indicate that best practices for fingernail sanitation of food handlers are to maintain short fingernails and scrub fingernails with soap and a nailbrush when washing hands.

Mecoprop (MCPP) removal in full-scale rapid sand filters at a groundwater-based waterworks.

PubMed

Hedegaard, Mathilde J; Arvin, Erik; Corfitzen, Charlotte B; Albrechtsen, Hans-Jørgen

2014-11-15

Contamination by the herbicide mecoprop (MCPP) was detected in groundwater abstraction wells at Kerteminde Waterworks in concentrations up to 0.08μg/L. MCPP was removed to below detection limit in a simple treatment line where anaerobic groundwater was aerated and subsequently filtered by primary and secondary rapid sand filters. Water quality parameters were measured throughout the waterworks, and they behaved as designed for. MCPP was removed in secondary rapid sand filters--removal was the greatest in the sand filters in the filter line with the highest contact time (63 min). In these secondary sand filters, MCPP concentration decreased from 0.037 μg/L to below the detection limit of 0.01 μg/L. MCPP was removed continuously at different filter depths (0.80 m). Additionally, biodegradation, mineralisation and adsorption were investigated in the laboratory in order to elucidate removal mechanisms in the full-scale system. Therefore, microcosms were set up with filter sand, water and (14)C-labelled MCPP at an initial concentration of 0.2 μg/L. After 24 h, 79-86% of the initial concentration of MCPP was removed. Sorption removed 11-15%, while the remaining part was removed by microbial processes, leading to a complete mineralisation of 13-18%. Microbial removal in the filter sand was similar at different depths of the rapid sand filter, while the amount of MCPP which adsorbed to the filter sand after 48 h decreased with depth from 21% of the initial MCPP in the top layer to 7% in the bottom layer. It was concluded that MCPP was removed in secondary rapid sand filters at Kerteminde Waterworks, to which both adsorption and microbial degradation contributed. Copyright © 2014 Elsevier B.V. All rights reserved.

Automatic Keyword Identification by Artificial Neural Networks Compared to Manual Identification by Users of Filtering Systems.

ERIC Educational Resources Information Center

Boger, Zvi; Kuflik, Tsvi; Shoval, Peretz; Shapira, Bracha

2001-01-01

Discussion of information filtering (IF) and information retrieval focuses on the use of an artificial neural network (ANN) as an alternative method for both IF and term selection and compares its effectiveness to that of traditional methods. Results show that the ANN relevance prediction out-performs the prediction of an IF system. (Author/LRW)

Presence, infectivity, and stability of enteric viruses in seawater: Relationship to marine water quality in the Florida Keys

USGS Publications Warehouse

Wetz, J.J.; Lipp, E.K.; Griffin, Dale W.; Lukasik, J.; Wait, D.; Sobsey, M.D.; Scott, T.M.; Rose, J.B.

2004-01-01

Concerns about the presence of enteric viruses in the surface waters of the Florida Keys prompted analyses of virus stability and persistence in these waters. In an in vitro study we evaluated the survival of poliovirus and stability of viral RNA in filtered natural seawater (FSW), unfiltered natural seawater (USW), artificial seawater (ASW) and DI water. This study compared cell culture infectivity with direct reverse transcription-polymerase chain reaction analysis. Attenuated poliovirus was seeded in the above water types and incubated in the dark at 22 and 30??C for 60 days. At 22??C, enhanced poliovirus survival and enhanced detection of viral RNA was observed in the seeded DI water control, artificial seawater and FSW samples. Detection of viruses in unfiltered seawater decreased rapidly at both temperatures by both methods of detection, suggesting that in the natural environment detection of enteroviral RNA may indicate a recent contamination event. In addition, in situ sampling in the Florida Keys during the late winter of 2000 revealed the presence of infectious enteroviruses at two sites and no sites exceeded recommended levels of microbial water quality indicators (enterococci or fecal coliform bacteria). ?? 2003 Elsevier Ltd. All rights reserved.

Microbial resource management of one‐stage partial nitritation/anammox

PubMed Central

Vlaeminck, S. E.; De Clippeleir, H.; Verstraete, W.

2012-01-01

Summary About 30 full‐scale partial nitritation/anammox plants are established, treating mostly sewage sludge reject water, landfill leachate or food processing digestate. Although two‐stage and one‐stage processes each have their advantages, the one‐stage configuration is mostly applied, termed here as oxygen‐limited autotrophic nitrification/denitrification (OLAND), and is the focus of this review. The OLAND application domain is gradually expanding, with technical‐scale plants on source‐separated domestic wastewater, pre‐treated manure and sewage, and liquors from organic waste bioenergy plants. A ‘microbial resource management’ (MRM) OLAND framework was elaborated, showing how the OLAND engineer/operator (1: input) can design/steer the microbial community (2: biocatalyst) to obtain optimal functionality (3: output). In the physicochemical toolbox (1), design guidelines are provided, as well as advantages of different reactor technologies. Particularly the desirable aeration regime, feeding regime and shear forces are not clear yet. The development of OLAND trickling filters, membrane bioreactors and systems with immobilized biomass is awaited. The biocatalyst box (2) considers ‘Who’: biodiversity and its dynamic patterns, ‘What’: physiology, and ‘Where’: architecture creating substrate gradients. Particularly community dynamics and extracellular polymeric substances (EPS) still require insights. Performant OLAND (3) comprises fast start‐up (storage possibility; fast growth of anammox bacteria), process stability (endured biomass retention; stress resilience), reasonable overall costs, high nitrogen removal efficiency and a low environmental footprint. Three important OLAND challenges are elaborated in detailed frameworks, demonstrating how to maximize nitrogen removal efficiency, minimize NO and N2O emissions and obtain through OLAND a plant‐wide net energy gain from sewage treatment. PMID:22452819

Reduction of bacteria and somatic coliphages in constructed wetlands for the treatment of combined sewer overflow (retention soil filters).

PubMed

Ruppelt, Jan P; Tondera, Katharina; Schreiber, Christiane; Kistemann, Thomas; Pinnekamp, Johannes

2018-05-01

Combined sewer overflows (CSOs) introduce numerous pathogens from fecal contamination, such as bacteria and viruses, into surface waters, thus endangering human health. In Germany, retention soil filters (RSFs) treat CSOs at sensitive discharge points and can contribute to reducing these hygienically relevant microorganisms. In this study, we evaluated the extent of how dry period, series connection and filter layer thickness influence the reduction efficiency of RSFs for Escherichia coli (E. coli), intestinal enterococci (I. E.) and somatic coliphages. To accomplish this, we had four pilot scale RSFs built on a test field at the wastewater treatment plant Aachen-Soers. While two filters were replicates, the other two filters were installed in a series connection. Moreover, one filter had a thinner filtration layer than the other three. Between April 2015 and December 2016, the RSFs were loaded in 37 trials with pre-conditioned CSO after dry periods ranging from 4 to 40 days. During 17 trials, samples for microbial analysis were taken and analyzed. The series connection of two filters showed that the removal increases when two systems with a filter layer of the same height are operated in series. Since the microorganisms are exposed twice to the environmental conditions on the filter surface and in the upper filter layers, there is a greater chance for abiotic adsorption increase. The same effect could be shown when filters with different depths were compared: the removal efficiency increases as filter thickness increases. This study provides new evidence that regardless of seasonal effects and dry period, RSFs can improve hygienic situation significantly. Copyright © 2018 Elsevier GmbH. All rights reserved.

Effect of filtered wood smoke treatment on chemical and microbial changes in mahi mahi fillets.

PubMed

Kristinsson, Hordur G; Danyali, Nineveh; Ua-Angkoon, Siriporn

2007-01-01

A study was performed to investigate the effect of filtered wood smoke processing on quality and safety of mahi mahi compared to no treatment. Skinless mahi mahi fillet portions were either treated with filtered smoke (FS) or left untreated for 24 h, followed by either (a) aerobic storage at 4 degrees C for 8 d or (b) freezing for 30 d (-25 degrees C) followed by thawing and aerobic storage at 4 degrees C for 8 d. Results show that treating mahi mahi fillets with FS increased (P < 0.05) a* values (redness) of the muscle and stabilized it during frozen storage. The redness did, however, decay (P < 0.05) rapidly on cold storage for both defrosted and fresh filtered-smoke-treated products, and reached initial (presmoking) redness levels in 2 d. The FS process overall significantly (P < 0.05) improved microbial stability of the product. Stability toward lipid oxidation was also significantly (P < 0.05) increased for the FS products compared to untreated products, particularly after defrosting. Sensory studies supported the microbial and lipid oxidation findings, showing that products treated with FS were better accepted and had increased (P < 0.05) shelf life over the untreated products. The shelf life was, however, compromised when microbial levels increased; that is, the process did not mask microbial spoilage; the spoilage did become evident in the sensory trials.

A Structural and Content-Based Analysis for Web Filtering.

ERIC Educational Resources Information Center

Lee, P. Y.; Hui, S. C.; Fong, A. C. M.

2003-01-01

Presents an analysis of the distinguishing features of pornographic Web pages so that effective filtering techniques can be developed. Surveys the existing techniques for Web content filtering and describes the implementation of a Web content filtering system that uses an artificial neural network. (Author/LRW)

Biotic and Abiotic Properties Mediating Plant Diversity Effects on Soil Microbial Communities in an Experimental Grassland

PubMed Central

Lange, Markus; Habekost, Maike; Eisenhauer, Nico; Roscher, Christiane; Bessler, Holger; Engels, Christof; Oelmann, Yvonne; Scheu, Stefan; Wilcke, Wolfgang; Schulze, Ernst-Detlef; Gleixner, Gerd

2014-01-01

Plant diversity drives changes in the soil microbial community which may result in alterations in ecosystem functions. However, the governing factors between the composition of soil microbial communities and plant diversity are not well understood. We investigated the impact of plant diversity (plant species richness and functional group richness) and plant functional group identity on soil microbial biomass and soil microbial community structure in experimental grassland ecosystems. Total microbial biomass and community structure were determined by phospholipid fatty acid (PLFA) analysis. The diversity gradient covered 1, 2, 4, 8, 16 and 60 plant species and 1, 2, 3 and 4 plant functional groups (grasses, legumes, small herbs and tall herbs). In May 2007, soil samples were taken from experimental plots and from nearby fields and meadows. Beside soil texture, plant species richness was the main driver of soil microbial biomass. Structural equation modeling revealed that the positive plant diversity effect was mainly mediated by higher leaf area index resulting in higher soil moisture in the top soil layer. The fungal-to-bacterial biomass ratio was positively affected by plant functional group richness and negatively by the presence of legumes. Bacteria were more closely related to abiotic differences caused by plant diversity, while fungi were more affected by plant-derived organic matter inputs. We found diverse plant communities promoted faster transition of soil microbial communities typical for arable land towards grassland communities. Although some mechanisms underlying the plant diversity effect on soil microorganisms could be identified, future studies have to determine plant traits shaping soil microbial community structure. We suspect differences in root traits among different plant communities, such as root turnover rates and chemical composition of root exudates, to structure soil microbial communities. PMID:24816860

Microbial diversity and metabolic networks in acid mine drainage habitats

PubMed Central

Méndez-García, Celia; Peláez, Ana I.; Mesa, Victoria; Sánchez, Jesús; Golyshina, Olga V.; Ferrer, Manuel

2015-01-01

Acid mine drainage (AMD) emplacements are low-complexity natural systems. Low-pH conditions appear to be the main factor underlying the limited diversity of the microbial populations thriving in these environments, although temperature, ionic composition, total organic carbon, and dissolved oxygen are also considered to significantly influence their microbial life. This natural reduction in diversity driven by extreme conditions was reflected in several studies on the microbial populations inhabiting the various micro-environments present in such ecosystems. Early studies based on the physiology of the autochthonous microbiota and the growing success of omics-based methodologies have enabled a better understanding of microbial ecology and function in low-pH mine outflows; however, complementary omics-derived data should be included to completely describe their microbial ecology. Furthermore, recent updates on the distribution of eukaryotes and archaea recovered through sterile filtering (herein referred to as filterable fraction) in these environments demand their inclusion in the microbial characterization of AMD systems. In this review, we present a complete overview of the bacterial, archaeal (including filterable fraction), and eukaryotic diversity in these ecosystems, and include a thorough depiction of the metabolism and element cycling in AMD habitats. We also review different metabolic network structures at the organismal level, which is necessary to disentangle the role of each member of the AMD communities described thus far. PMID:26074887

An improved method to set significance thresholds for β diversity testing in microbial community comparisons.

PubMed

Gülay, Arda; Smets, Barth F

2015-09-01

Exploring the variation in microbial community diversity between locations (β diversity) is a central topic in microbial ecology. Currently, there is no consensus on how to set the significance threshold for β diversity. Here, we describe and quantify the technical components of β diversity, including those associated with the process of subsampling. These components exist for any proposed β diversity measurement procedure. Further, we introduce a strategy to set significance thresholds for β diversity of any group of microbial samples using rarefaction, invoking the notion of a meta-community. The proposed technique was applied to several in silico generated operational taxonomic unit (OTU) libraries and experimental 16S rRNA pyrosequencing libraries. The latter represented microbial communities from different biological rapid sand filters at a full-scale waterworks. We observe that β diversity, after subsampling, is inflated by intra-sample differences; this inflation is avoided in the proposed method. In addition, microbial community evenness (Gini > 0.08) strongly affects all β diversity estimations due to bias associated with rarefaction. Where published methods to test β significance often fail, the proposed meta-community-based estimator is more successful at rejecting insignificant β diversity values. Applying our approach, we reveal the heterogeneous microbial structure of biological rapid sand filters both within and across filters. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Metal oxides, clay minerals and charcoal determine the composition of microbial communities in matured artificial soils and their response to phenanthrene.

PubMed

Babin, Doreen; Ding, Guo-Chun; Pronk, Geertje Johanna; Heister, Katja; Kögel-Knabner, Ingrid; Smalla, Kornelia

2013-10-01

Microbial communities in soil reside in a highly heterogeneous habitat where diverse mineral surfaces, complex organic matter and microorganisms interact with each other. This study aimed to elucidate the long-term effect of the soil mineral composition and charcoal on the microbial community composition established in matured artificial soils and their response to phenanthrene. One year after adding sterile manure to different artificial soils and inoculating microorganisms from a Cambisol, the matured soils were spiked with phenanthrene or not and incubated for another 70 days. 16S rRNA gene and internal transcribed spacer fragments amplified from total community DNA were analyzed by denaturing gradient gel electrophoresis. Metal oxides and clay minerals and to a lesser extent charcoal influenced the microbial community composition. Changes in the bacterial community composition in response to phenanthrene differed depending on the mineral composition and presence of charcoal, while no shifts in the fungal community composition were observed. The abundance of ring-hydroxylating dioxygenase genes was increased in phenanthrene-spiked soils except for charcoal-containing soils. Here we show that the formation of biogeochemical interfaces in soil is an ongoing process and that different properties present in artificial soils influenced the bacterial response to the phenanthrene spike. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Expanding Upon the MEMS Framework: How Temperature Impacts Organo-Mineral Interactions

NASA Astrophysics Data System (ADS)

Smith, K.; Waring, B. G.

2017-12-01

Microbial substrate use efficiency (SUE; the fraction of substrate carbon (C) incorporated into biomass vs. respired) affects the development of soil organic matter (SOM). An emerging theoretical model (the Microbial Efficiency-Matrix Stabilization (MEMS) framework) posits that microbial SUE acts as a filter for plant litter inputs, whereby a larger proportion of microbial products are synthesized from labile (and not recalcitrant) plant substrates. Thus, SOM stability depends on both the efficiency of microbial anabolism as well as the degree to which microbial products stabilize within the mineral soil matrix. In this study, we performed a laboratory microcosm experiment using diverse soils collected in Utah to test how substrate complexity, soil mineralogy, and temperature interact to control SOM formation. Prior to microcosm setup, we first removed organic C from our field soils by washing with concentrated hypochlorite solution. Microcosms were then assembled by mixing C-free soil with one of three substrates (glucose, cellulose, and lignin), and placed in incubators set to different temperatures (18°, 28°, and 38°C). Respiration rates were then estimated by periodically sampling headspace CO2 concentrations in each microcosm. Prior to C removal, we found that field soils exhibited distinct properties ranging from clay-rich vertisols (55:27:18, sand:silt:clay; 1.1% C), to loamy-sand entisols (85:11:4; 0.3% C), and organic-rich mollisols (79:17:4; 1.7% C). In the incubation experiment, consistent with enzyme kinetics theory, respiration rates increased as a function of incubation temperature (p < 0.0001), and that the temperature response of respiration was dependent on substrate (p < 0.0001), with the lignin treatment exhibiting the greatest temperature sensitivity. While respiration was significantly lower in the mollisol treatment (p < 0.0001), other soil effects (including interactions with temperature and substrate) were less clear. Together these results build upon the MEMS framework by highlighting the importance of organo-mineral interactions and temperature as controls on soil C cycling.

Characterization of microbial communities and fungal metabolites on field grown strawberries from organic and conventional production.

PubMed

Jensen, Birgit; Knudsen, Inge M B; Andersen, Birgitte; Nielsen, Kristian Fog; Thrane, Ulf; Jensen, Dan Funck; Larsen, John

2013-01-01

The background levels of culturable indigenous microbial communities (microbiotas) on strawberries were examined in a field survey with four conventional and four organic growers with different production practise and geographic distribution. The microbiota on apparently healthy strawberries was complex including potential plant pathogens, opportunistic human pathogens, plant disease biocontrol agents and mycotoxin producers. The latter group was dominated by Penicillium spp. and Aspergillus niger was also isolated. As expected, bacteria were the most abundant and diverse group of the strawberry microbiota followed by yeasts and filamentous fungi. No obvious correlation between grower practice and the strawberry microbiota was observed. Differences between microbiotas on strawberries from conventional systems with up to 10 fungicide spray treatments and organic production systems were insignificant. Mycotoxins were not detected in mature strawberries from any of the eight different growers neither in additional samples of low quality berries. However, isolates of Penicillium expansum and A. niger produced high amounts of mycotoxins when incubated on strawberries at 25°C. Penicillium polonicum produced cyclopenol, cyclopenin, and viridicatin on the artificially infected berries, while Alternaria arborescens produced tenuazonic acid, Alternaria tenuissima produced altertoxin I and altenuene, and Trichoderma spp. produced several peptaibols. In conclusion, native strawberry microbiotas are highly diverse both in terms of taxonomic groups and functional traits that are important in relation to plant and human health. Copyright © 2012 Elsevier B.V. All rights reserved.

Integrated Metagenomic and Physiochemical Analyses to Evaluate the Potential Role of Microbes in the Sand Filter of a Drinking Water Treatment System

PubMed Central

Bai, Yaohui; Liu, Ruiping; Liang, Jinsong; Qu, Jiuhui

2013-01-01

While sand filters are widely used to treat drinking water, the role of sand filter associated microorganisms in water purification has not been extensively studied. In the current investigation, we integrated molecular (based on metagenomic) and physicochemical analyses to elucidate microbial community composition and function in a common sand filter used to treat groundwater for potable consumption. The results revealed that the biofilm developed rapidly within 2 days (reaching ∼1011 prokaryotes per gram) in the sand filter along with abiotic and biotic particulates accumulated in the interstitial spaces. Bacteria (up to 90%) dominated the biofilm microbial community, with Alphaproteobacteria being the most common class. Thaumarchaeota was the sole phylum of Archaea, which might be involved in ammonia oxidation. Function annotation of metagenomic datasets revealed a number of aromatic degradation pathway genes, such as aromatic oxygenase and dehydrogenase genes, in the biofilm, suggesting a significant role for microbes in the breakdown of aromatic compounds in groundwater. Simultaneous nitrification and denitrification pathways were confirmed as the primary routes of nitrogen removal. Dissolved heavy metals in groundwater, e.g. Mn2+ and As3+, might be biologically oxidized to insoluble or easily adsorbed compounds and deposited in the sand filter. Our study demonstrated that the role of the microbial community in the sand filter treatment system are critical to effective water purification in drinking water. PMID:23593378

Microbial community characterization of ozone-biofiltration systems in drinking water and potable reuse applications.

PubMed

Gerrity, Daniel; Arnold, Mayara; Dickenson, Eric; Moser, Duane; Sackett, Joshua D; Wert, Eric C

2018-05-15

Microbial community structure in the ozone-biofiltration systems of two drinking water and two wastewater treatment facilities was characterized using 16S rRNA gene sequencing. Collectively, these datasets enabled comparisons by facility, water type (drinking water, wastewater), pre-oxidation (ozonation, chlorination), media type (anthracite, activated carbon), media depth, and backwash dynamics. Proteobacteria was the most abundant phylum in drinking water filters, whereas Bacteroidetes, Chloroflexi, Firmicutes, and Planctomycetes were differentially abundant in wastewater filters. A positive correlation was observed between media depth and relative abundance of Cyanobacteria in drinking water filters, but there was only a slight increase in one alpha diversity metric with depth in the wastewater filters. Media type had a significant effect on beta but not alpha diversity in drinking water and wastewater filters. Pre-ozonation caused a significant decrease in alpha diversity in the wastewater filters, but the effect on beta diversity was not statistically significant. An evaluation of backwash dynamics resulted in two notable observations: (1) endosymbionts such as Neochlamydia and Legionella increased in relative abundance following backwashing and (2) nitrogen-fixing Bradyrhizobium dominated the microbial community in wastewater filters operated with infrequent backwashing. Bradyrhizobium is known to generate extracellular polymeric substances (EPS), which may adversely impact biofilter performance and effluent water quality. These findings have important implications for public health and the operation and resiliency of biofiltration systems. Copyright © 2018 Elsevier Ltd. All rights reserved.

Integrated metagenomic and physiochemical analyses to evaluate the potential role of microbes in the sand filter of a drinking water treatment system.

PubMed

Bai, Yaohui; Liu, Ruiping; Liang, Jinsong; Qu, Jiuhui

2013-01-01

While sand filters are widely used to treat drinking water, the role of sand filter associated microorganisms in water purification has not been extensively studied. In the current investigation, we integrated molecular (based on metagenomic) and physicochemical analyses to elucidate microbial community composition and function in a common sand filter used to treat groundwater for potable consumption. The results revealed that the biofilm developed rapidly within 2 days (reaching ≈ 10(11) prokaryotes per gram) in the sand filter along with abiotic and biotic particulates accumulated in the interstitial spaces. Bacteria (up to 90%) dominated the biofilm microbial community, with Alphaproteobacteria being the most common class. Thaumarchaeota was the sole phylum of Archaea, which might be involved in ammonia oxidation. Function annotation of metagenomic datasets revealed a number of aromatic degradation pathway genes, such as aromatic oxygenase and dehydrogenase genes, in the biofilm, suggesting a significant role for microbes in the breakdown of aromatic compounds in groundwater. Simultaneous nitrification and denitrification pathways were confirmed as the primary routes of nitrogen removal. Dissolved heavy metals in groundwater, e.g. Mn(2+) and As(3+), might be biologically oxidized to insoluble or easily adsorbed compounds and deposited in the sand filter. Our study demonstrated that the role of the microbial community in the sand filter treatment system are critical to effective water purification in drinking water.

Effects of plant diversity on microbial nitrogen and phosphorus dynamics in soil

NASA Astrophysics Data System (ADS)

Prommer, Judith; Braun, Judith; Daly, Amanda; Gorka, Stefan; Hu, Yuntao; Kaiser, Christina; Martin, Victoria; Meyerhofer, Werner; Walker, Tom W. N.; Wanek, Wolfgang; Wasner, Daniel; Wiesenbauer, Julia; Zezula, David; Zheng, Qing; Richter, Andreas

2017-04-01

There is a general consensus that plant diversity affects many ecosystem functions. One example of such an effect is the enhanced aboveground and belowground plant biomass production with increasing species richness, with implications for carbon and nutrient distribution in soil. The Jena Experiment (http://www.the-jena-experiment.de/), a grassland biodiversity experiment established in 2002 in Germany, comprises different levels of plant species richness and different numbers of plant functional groups. It provides the opportunity to examine how changes in biodiversity impact on microbially-mediated nutrient cycling processes. We here report on plant diversity and plant functional composition effects on growth and nitrogen and phosphorus transformation rates, including nitrogen use efficiency, of microbial communities. Microbial growth rates and microbial biomass were positively affected by increasing plant species richness. Amino acid and ammonium concentrations in soil were also positively affected by plant species richness, while phosphate concentrations in contrast were negatively affected. The cycling of organic N in soils (estimated as gross protein depolymerization rates) increased about threefold with plant diversity, while gross N and P mineralization were not significantly affected by either species or functional richness. Microbial nitrogen use efficiency did not respond to different levels of plant diversity but was very high (0.96 and 0.98) across all levels of plant species richness, demonstrating a low N availability for microbes. Taken together this indicates that soil microbial communities were able to meet the well-documented increase in plant N content with species richness, and also the higher N demand of the microbial community by increasing the recycling of organic N such as proteins. In fact, the microbial community even overcompensated the increased plant and microbial N demand, as evidenced by increased levels of free amino acids and ammonium in the soil solution at higher species richness. A possible explanation for increased organic nitrogen transformation rates is the increased microbial biomass, which has previously been related to higher quantity and variety of plant derived compounds that are available to the microbial communities at higher plant diversity. Given that this explanation is right, it is interesting to note that the additional (plant-derived) microbial biomass at higher species richness, did not translate in higher soil P mineralization rates or phosphate availability.

Teaching learning based optimization-functional link artificial neural network filter for mixed noise reduction from magnetic resonance image.

PubMed

Kumar, M; Mishra, S K

2017-01-01

The clinical magnetic resonance imaging (MRI) images may get corrupted due to the presence of the mixture of different types of noises such as Rician, Gaussian, impulse, etc. Most of the available filtering algorithms are noise specific, linear, and non-adaptive. There is a need to develop a nonlinear adaptive filter that adapts itself according to the requirement and effectively applied for suppression of mixed noise from different MRI images. In view of this, a novel nonlinear neural network based adaptive filter i.e. functional link artificial neural network (FLANN) whose weights are trained by a recently developed derivative free meta-heuristic technique i.e. teaching learning based optimization (TLBO) is proposed and implemented. The performance of the proposed filter is compared with five other adaptive filters and analyzed by considering quantitative metrics and evaluating the nonparametric statistical test. The convergence curve and computational time are also included for investigating the efficiency of the proposed as well as competitive filters. The simulation outcomes of proposed filter outperform the other adaptive filters. The proposed filter can be hybridized with other evolutionary technique and utilized for removing different noise and artifacts from others medical images more competently.

Variations of soil microbial community structures beneath broadleaved forest trees in temperate and subtropical climate zones

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Sihang; Zhang, Yuguang; Cong, Jing

Global warming has shifted climate zones poleward or upward. Furthermore, understanding the responses and mechanism of microbial community structure and functions relevant to natural climate zone succession is challenged by the high complexity of microbial communities. Here, we examined soil microbial community in three broadleaved forests located in the Wulu Mountain (WLM, temperate climate), Funiu Mountain (FNM, at the border of temperate and subtropical climate zones), or Shennongjia Mountain (SNJ, subtropical climate). Although plant species richness decreased with latitudes, the microbial taxonomic α-diversity increased with latitudes, concomitant with increases in soil total and available nitrogen and phosphorus contents. Phylogenetic NRImore » (Net Relatedness Index) values increased from 0.718 in temperate zone (WLM) to 1.042 in subtropical zone (SNJ), showing a shift from over dispersion to clustering likely caused by environmental filtering such as low pH and nutrients. Similarly, taxonomybased association networks of subtropical forest samples were larger and tighter, suggesting clustering. In contrast, functional α-diversity was similar among three forests, but functional gene networks of the FNM forest significantly (P < 0.050) differed from the others. A significant correlation (R = 0.616, P < 0.001) between taxonomic and functional β-diversity was observed only in the FNM forest, suggesting low functional redundancy at the border of climate zones. Using a strategy of space-fortime substitution, we predict that poleward climate range shift will lead to decreased microbial taxonomic α-diversities in broadleaved forest.« less

Variations of soil microbial community structures beneath broadleaved forest trees in temperate and subtropical climate zones

DOE PAGES

Yang, Sihang; Zhang, Yuguang; Cong, Jing; ...

2017-02-10

Global warming has shifted climate zones poleward or upward. Furthermore, understanding the responses and mechanism of microbial community structure and functions relevant to natural climate zone succession is challenged by the high complexity of microbial communities. Here, we examined soil microbial community in three broadleaved forests located in the Wulu Mountain (WLM, temperate climate), Funiu Mountain (FNM, at the border of temperate and subtropical climate zones), or Shennongjia Mountain (SNJ, subtropical climate). Although plant species richness decreased with latitudes, the microbial taxonomic α-diversity increased with latitudes, concomitant with increases in soil total and available nitrogen and phosphorus contents. Phylogenetic NRImore » (Net Relatedness Index) values increased from 0.718 in temperate zone (WLM) to 1.042 in subtropical zone (SNJ), showing a shift from over dispersion to clustering likely caused by environmental filtering such as low pH and nutrients. Similarly, taxonomybased association networks of subtropical forest samples were larger and tighter, suggesting clustering. In contrast, functional α-diversity was similar among three forests, but functional gene networks of the FNM forest significantly (P < 0.050) differed from the others. A significant correlation (R = 0.616, P < 0.001) between taxonomic and functional β-diversity was observed only in the FNM forest, suggesting low functional redundancy at the border of climate zones. Using a strategy of space-fortime substitution, we predict that poleward climate range shift will lead to decreased microbial taxonomic α-diversities in broadleaved forest.« less

Optimizing Fungal DNA Extraction Methods from Aerosol Filters

NASA Astrophysics Data System (ADS)

Jimenez, G.; Mescioglu, E.; Paytan, A.

2016-12-01

Fungi and fungal spores can be picked up from terrestrial ecosystems, transported long distances, and deposited into marine ecosystems. It is important to study dust-borne fungal communities, because they can stay viable and effect the ambient microbial populations, which are key players in biogeochemical cycles. One of the challenges of studying dust-borne fungal populations is that aerosol samples contain low biomass, making extracting good quality DNA very difficult. The aim of this project was to increase DNA yield by optimizing DNA extraction methods. We tested aerosol samples collected from Haifa, Israel (polycarbonate filter), Monterey Bay, CA (quartz filter) and Bermuda (quartz filter). Using the Qiagen DNeasy Plant Kit, we tested the effect of altering bead beating times and incubation times, adding three freeze and thaw steps, initially washing the filters with buffers for various lengths of time before using the kit, and adding a step with 30 minutes of sonication in 65C water. Adding three freeze/thaw steps, adding a sonication step, washing with a phosphate buffered saline overnight, and increasing incubation time to two hours, in that order, resulted in the highest increase in DNA for samples from Israel (polycarbonate). DNA yield of samples from Monterey (quart filter) increased about 5 times when washing with buffers overnight (phosphate buffered saline and potassium phophate buffer), adding a sonication step, and adding three freeze and thaw steps. Samples collected in Bermuda (quartz filter) had the highest increase in DNA yield from increasing incubation to 2 hours, increasing bead beating time to 6 minutes, and washing with buffers overnight (phosphate buffered saline and potassium phophate buffer). Our results show that DNA yield can be increased by altering various steps of the Qiagen DNeasy Plant Kit protocol, but different types of filters collected at different sites respond differently to alterations. These results can be used as preliminary results to continue developing fungi DNA extraction methods. Developing these methods will be important as dust storms are predicted to increase due to increased draughts and anthropogenic activity, and the fungal communities of these dust-storms are currently relatively understudied.

How do microorganisms influence trace element uptake by plants? Screening in an agar model rhizosphere.

NASA Astrophysics Data System (ADS)

Marchetti, M.; Robinson, B. H.; Evangelou, M. W. H.; Vachey, A.; Schwitzguebel, J. P.; Bernier-Latmani, R.; Schulin, R.

2009-04-01

Trace elements (TE) are essential for humans and plants, but they may be toxic if their concentration is too high. For this reason, the management of TE in soils is very important. In some cases it may be necessary to increase the uptake of nutrients or TE by plants, for example in a biofortification perspective. Conversely, in some other cases TE uptake by plants should be decreased, for instance to avoid heavy metals entering the food chain via edible crops. Microorganisms living in the rhizosphere affect trace element (TE) uptake by plants. However, due to the complexity of this space and the variety of microorganisms that occur there, it is difficult to isolate the effect of any particular strain. To overcome this hurdle, we developed a system in which we grew plants under sterile conditions in agar and inoculated their rhizosphere with a single, well-defined microbial strain. For many years, agar has been used as a growth substrate for microorganisms and plant tissues. It is cheap, easy to use, and can be autoclaved to ensure its sterility. Because of its widespread use, an experiment conducted using this substrate can be reproduced under the same conditions in any laboratory. In contrast to soil, there is little interaction between the trace elements and the agar matrix. There are many studies investigating the influence of microorganisms on TE uptake by plants. However, so far only a small variety of microorganisms has been tested on few plant species. Therefore, the first objective of our research was to develop a method to rapidly screen a large variety of microorganisms on various plant species. Once this goal was achieved, we sought to study the effect of single, well-defined microbial strains on TE uptake by sunflower and wheat. The substrate for plants growth was a 10% agar solution prepared with modified Hoagland's solution and a TE solution containing 1 mg/kg Pb and molar equivalents of Cu, Ni and Zn. The agar solution was autoclaved and poured into sterile, transparent plastic boxes, whose lid was equipped with a filter allowing gas exchanges without contamination by external microorganisms. The seed surface was sterilised and the plants grew one week in agar before their rhizosphere was inoculated with LB broth containing a pure bacterial strain or agar plugs colonized by fungal hyphae. We tested 14 strains, with 5 replicates per treatment and a control where the system was inoculated with sterile LB broth. The plants grew for 2 weeks in a climate chamber and their shoots were analysed for their TEs by ICP-OES. Samples of agar and roots were collected to confirm microbial colonization of the rhizosphere, respectively sterile conditions in the control treatments. Concerning the method development, the plants grew without visible toxicity in all the boxes, and the analysis of root and agar samples indicated that the controls were sterile and the strains inoculated were growing along the roots. More than 90% of the TE and nutrients added to the system were in the liquid fraction of the agar medium, thus available for root uptake. The screening showed that the microorganisms in general decreased TE uptake by wheat and sunflower, although some of them had an opposite effect on the plants. However, with the same plant species, the microorganisms had a consistent effect on all TE tested, i.e. a given single strain caused the same effect (increase or decrease of TE uptake) on all TE tested. In sunflower, 3 microorganisms (Paenibacillus polymyxa, Pythium ultimum and Rhizoctonia solani) decreased Cu and Zn uptake by 50% compared to the control treatment. These three species are common soil microorganisms. All three are known to exude auxin, a phytohormone. This hormone can modify root morphology and physiology and thus may affect TE uptake by plants. R. solani and P. ultimum are root pathogens. Their effect was opposite to what we expected. If roots are damaged, TE should have flooded into the plant and accumulate in the tissues, but this was not the case. One explanation could be the biosorption of TE by these microorganisms, reducing the uptake by plant. Conversely to sunflower, none of the microorganisms tested showed a significant effect on TE uptake by wheat. With our research, we created an agar system allowing the screening of several microbial strains for their effect on plant TE uptake. Future work will involve screening of several other strains in a wide range of conditions in agar. A method validation with a pot experiment is also needed, as some interactions in this artificial rhizosphere may be different from those that would take place in soil. We will also pursue the investigation of two interesting mechanisms revealed by the screening: the effect of pathogens and phytohormone-exuding microorganisms on TE uptake by plants.

Effects of Plant Diversity, Functional Group Composition, and Fertilization on Soil Microbial Properties in Experimental Grassland

PubMed Central

Strecker, Tanja; Barnard, Romain L.; Niklaus, Pascal A.; Scherer-Lorenzen, Michael; Weigelt, Alexandra; Scheu, Stefan; Eisenhauer, Nico

2015-01-01

Background Loss of biodiversity and increased nutrient inputs are two of the most crucial anthropogenic factors driving ecosystem change. Although both received considerable attention in previous studies, information on their interactive effects on ecosystem functioning is scarce. In particular, little is known on how soil biota and their functions are affected by combined changes in plant diversity and fertilization. Methodology/Principal Findings We investigated the effects of plant diversity, functional community composition, and fertilization on the biomass and respiration of soil microbial communities in a long-term biodiversity experiment in semi-natural grassland (Jena Experiment). Plant species richness enhanced microbial basal respiration and microbial biomass, but did not significantly affect microbial specific respiration. In contrast, the presence of legumes and fertilization significantly decreased microbial specific respiration, without altering microbial biomass. The effect of legumes was superimposed by fertilization as indicated by a significant interaction between the presence of legumes and fertilization. Further, changes in microbial stoichiometry (C-to-N ratio) and specific respiration suggest the presence of legumes to reduce N limitation of soil microorganisms and to modify microbial C use efficiency. Conclusions/Significance Our study highlights the role of plant species and functional group diversity as well as interactions between plant community composition and fertilizer application for soil microbial functions. Our results suggest soil microbial stoichiometry to be a powerful indicator of microbial functioning under N limited conditions. Although our results support the notion that plant diversity and fertilizer application independently affect microbial functioning, legume effects on microbial N limitation were superimposed by fertilization, indicating significant interactions between the functional composition of plant communities and nutrient inputs for soil processes. PMID:25938580

Environmental Regulation of Microbial Community Structure

NASA Technical Reports Server (NTRS)

Bebout, Leslie; DesMarais, D.; Heyenga, G.; Nelson, F.; DeVincenzi, D. (Technical Monitor)

2002-01-01

Most naturally occurring microbes live in complex microbial communities consisting of thousands of phylotypes of microorganisms living in close proximity. Each of these draws nutrients from the environment and releases metabolic waste products, which may in turn serve as substrates for other microbial groups. Gross environmental changes, such as irradiance level, hydrodynamic flow regime, temperature or water chemistry can directly affect the productivity of some community members, which in turn will affect other dependent microbial populations and rate processes. As a first step towards the development of "standard" natural communities of microorganisms for a variety of potential NASA applications, we are measuring biogeochemical cycling in artificially structured communities of microorganisms, created using natural microbial mat communities as inoculum. The responses of these artificially assembled communities of microorganisms to controlled shifts in ecosystem incubation conditions is being determined. This research requires close linking of environmental monitoring, with community composition in a closed and controlled incubation setting. We are developing new incubation chamber designs to allow for this integrated approach to examine the interplay between environmental conditions, microbial community composition and biogeochemical processes.

40 CFR 141.715 - Microbial toolbox options for meeting Cryptosporidium treatment requirements.

Code of Federal Regulations, 2010 CFR

2010-07-01

... filter performance 0.5-log credit for combined filter effluent turbidity less than or equal to 0.15 NTU...) Individual filter performance 0.5-log credit (in addition to 0.5-log combined filter performance credit) if individual filter effluent turbidity is less than or equal to 0.15 NTU in at least 95 percent of samples each...

40 CFR 141.715 - Microbial toolbox options for meeting Cryptosporidium treatment requirements.

Code of Federal Regulations, 2011 CFR

2011-07-01

... filter performance 0.5-log credit for combined filter effluent turbidity less than or equal to 0.15 NTU...) Individual filter performance 0.5-log credit (in addition to 0.5-log combined filter performance credit) if individual filter effluent turbidity is less than or equal to 0.15 NTU in at least 95 percent of samples each...

40 CFR 141.715 - Microbial toolbox options for meeting Cryptosporidium treatment requirements.

Code of Federal Regulations, 2012 CFR

2012-07-01

... filter performance 0.5-log credit for combined filter effluent turbidity less than or equal to 0.15 NTU...) Individual filter performance 0.5-log credit (in addition to 0.5-log combined filter performance credit) if individual filter effluent turbidity is less than or equal to 0.15 NTU in at least 95 percent of samples each...

Differences in Intertidal Microbial Assemblages on Urban Structures and Natural Rocky Reef

PubMed Central

Tan, Elisa L.-Y.; Mayer-Pinto, Mariana; Johnston, Emma L.; Dafforn, Katherine A.

2015-01-01

Global seascapes are increasingly modified to support high levels of human activity in the coastal zone. Modifications include the addition of defense structures and boating infrastructure, such as seawalls and marinas that replace natural habitats. Artificial structures support different macrofaunal communities to those found on natural rocky shores; however, little is known about differences in microbial community structure or function in urban seascapes. Understanding how artificial constructions in marine environments influence microbial communities is important as these assemblages contribute to many basic ecological processes. In this study, the bacterial communities of intertidal biofilms were compared between artificial structures (seawalls) and natural habitats (rocky shores) within Sydney Harbour. Plots were cleared on each type of habitat at eight locations. After 3 weeks the newly formed biofilm was sampled and the 16S rRNA gene sequenced using the Illumina Miseq platform. To account for differences in orientation and substrate material between seawalls and rocky shores that might have influenced our survey, we also deployed recruitment blocks next to the habitats at all locations for 3 weeks and then sampled and sequenced their microbial communities. Intertidal bacterial community structure sampled from plots differed between seawalls and rocky shores, but when substrate material, age and orientation were kept constant (with recruitment blocks) then bacterial communities were similar in composition and structure among habitats. This suggests that changes in bacterial communities on seawalls are not related to environmental differences between locations, but may be related to other intrinsic factors that differ between the habitats such as orientation, complexity, or predation. This is one of the first comparisons of intertidal microbial communities on natural and artificial surfaces and illustrates substantial ecological differences with potential consequences for biofilm function and the recruitment of macrofauna. PMID:26635747

Maintenance of CO2 level in a BLSS by controlling solid waste treatment unit

NASA Astrophysics Data System (ADS)

Dong, Yingying; Li, Leyuan; Liu, Hong; Fu, Yuming; Xie, Beizhen; Hu, Dawei; Liu, Dianlei; Dong, Chen; Liu, Guanghui

A bioregenerative life support system (BLSS) is an artificial closed ecosystem for providing basic human life support for long-duration, far-distance space explorations such as lunar bases. In such a system, the circulation of gases is one of the main factor for realizing a higher closure degree. O2 produced by higher plants goes to humans, as well as microorganisms for the treatment of inedible plant biomass and human wastes; CO2 produced by the crew and microorganisms is provided for plant growth. During this process, an excessively high CO2 level will depress plant growth and may be harmful to human health; and if the CO2 level is too low, plant growth will also be affected. Thus, keeping the balance between CO2 and O2 levels is a crucial problem. In this study, a high-efficiency, controllable solid waste treatment unit is constructed, which adopts microbial fermentation of the mixture of inedible biomass and human wastes. CO2 production during the fermentation process is controlled by adjusting fermentation temperature, aeration rate, moisture, etc., so as to meet the CO2 requirement of plants

Plant diversity drives soil microbial biomass carbon in grasslands irrespective of global environmental change factors.

PubMed

Thakur, Madhav Prakash; Milcu, Alexandru; Manning, Pete; Niklaus, Pascal A; Roscher, Christiane; Power, Sally; Reich, Peter B; Scheu, Stefan; Tilman, David; Ai, Fuxun; Guo, Hongyan; Ji, Rong; Pierce, Sarah; Ramirez, Nathaly Guerrero; Richter, Annabell Nicola; Steinauer, Katja; Strecker, Tanja; Vogel, Anja; Eisenhauer, Nico

2015-11-01

Soil microbial biomass is a key determinant of carbon dynamics in the soil. Several studies have shown that soil microbial biomass significantly increases with plant species diversity, but it remains unclear whether plant species diversity can also stabilize soil microbial biomass in a changing environment. This question is particularly relevant as many global environmental change (GEC) factors, such as drought and nutrient enrichment, have been shown to reduce soil microbial biomass. Experiments with orthogonal manipulations of plant diversity and GEC factors can provide insights whether plant diversity can attenuate such detrimental effects on soil microbial biomass. Here, we present the analysis of 12 different studies with 14 unique orthogonal plant diversity × GEC manipulations in grasslands, where plant diversity and at least one GEC factor (elevated CO2 , nutrient enrichment, drought, earthworm presence, or warming) were manipulated. Our results show that higher plant diversity significantly enhances soil microbial biomass with the strongest effects in long-term field experiments. In contrast, GEC factors had inconsistent effects with only drought having a significant negative effect. Importantly, we report consistent non-significant effects for all 14 interactions between plant diversity and GEC factors, which indicates a limited potential of plant diversity to attenuate the effects of GEC factors on soil microbial biomass. We highlight that plant diversity is a major determinant of soil microbial biomass in experimental grasslands that can influence soil carbon dynamics irrespective of GEC. © 2015 John Wiley & Sons Ltd.

Artificial Neural Networks and Instructional Technology.

ERIC Educational Resources Information Center

Carlson, Patricia A.

1991-01-01

Artificial neural networks (ANN), part of artificial intelligence, are discussed. Such networks are fed sample cases (training sets), learn how to recognize patterns in the sample data, and use this experience in handling new cases. Two cognitive roles for ANNs (intelligent filters and spreading, associative memories) are examined. Prototypes…

Robust Crop and Weed Segmentation under Uncontrolled Outdoor Illumination

PubMed Central

Jeon, Hong Y.; Tian, Lei F.; Zhu, Heping

2011-01-01

An image processing algorithm for detecting individual weeds was developed and evaluated. Weed detection processes included were normalized excessive green conversion, statistical threshold value estimation, adaptive image segmentation, median filter, morphological feature calculation and Artificial Neural Network (ANN). The developed algorithm was validated for its ability to identify and detect weeds and crop plants under uncontrolled outdoor illuminations. A machine vision implementing field robot captured field images under outdoor illuminations and the image processing algorithm automatically processed them without manual adjustment. The errors of the algorithm, when processing 666 field images, ranged from 2.1 to 2.9%. The ANN correctly detected 72.6% of crop plants from the identified plants, and considered the rest as weeds. However, the ANN identification rates for crop plants were improved up to 95.1% by addressing the error sources in the algorithm. The developed weed detection and image processing algorithm provides a novel method to identify plants against soil background under the uncontrolled outdoor illuminations, and to differentiate weeds from crop plants. Thus, the proposed new machine vision and processing algorithm may be useful for outdoor applications including plant specific direct applications (PSDA). PMID:22163954

Microbial ice nucleators are scavenged from the atmosphere during artificial rain events

NASA Astrophysics Data System (ADS)

Hanlon, Regina; Powers, Craig; Failor, Kevin; Vinatzer, Boris; Schmale, David

2016-04-01

Some microorganisms associated with rain may catalyze the nucleation of ice crystals at significantly warmer temperatures than would normally be required for ice formation, suggesting that they may play an important role in the onset of precipitation. Rain samples collected near the surface of the earth contain an array of microbial ice nucleators, but the little is known about their source(s) and life history. We conducted a series of field experiments to test the hypothesis that microbial ice nucleators are scavenged from the atmosphere by rainfall. Thirty three artificial rain events were conducted over four months (Nov 2014, Dec 2014, April 2015, and June 2015) off the side of the Smart Road Bridge in Blacksburg, VA, USA. In each event, sterile water was dispensed over the side of the bridge and recovered in sterile containers following gravitational settling from the bridge to an open fallow agricultural field below (a distance of ~55m). Microbes scavenged from the artificial rain events were cultured on six different types of agar media (R2A, TSA, CA; +/-cycloheximide), and the ice nucleation activity was examined for colonies cultured from the different media types. Mean CFUs scavenged by artificial rain ranged from 2 to 267 CFUs/mL. Microbial ice nucleators were cultured from 94% (31/33) of the simulated rain events, and represented 1.4% (121/8871) of the total number of colonies assayed. This percentage is similar to the percentage of culturable microbial ice nucleators occurring in about half of the natural rain events studied in Blacksburg, VA. Sequence-assisted identification of the repeatable microbial ice nucleators that were scavenged from the atmosphere showed a number of unique prokaryotic and eukaryotic taxa. This work expands our knowledge of the scavenging properties of rainfall, and suggests that at least some ice nucleators in natural precipitation events may have been scrubbed from the atmosphere during rainfall, and thus are not likely to be involved in the onset of precipitation.

Fabrication of artificially stacked ultrathin ZnS/MgF2 multilayer dielectric optical filters.

PubMed

Kedawat, Garima; Srivastava, Subodh; Jain, Vipin Kumar; Kumar, Pawan; Kataria, Vanjula; Agrawal, Yogyata; Gupta, Bipin Kumar; Vijay, Yogesh K

2013-06-12

We report a design and fabrication strategy for creating an artificially stacked multilayered optical filters using a thermal evaporation technique. We have selectively chosen a zinc sulphide (ZnS) lattice for the high refractive index (n = 2.35) layer and a magnesium fluoride (MgF2) lattice as the low refractive index (n = 1.38) layer. Furthermore, the microstructures of the ZnS/MgF2 multilayer films are also investigated through TEM and HRTEM imaging. The fabricated filters consist of high and low refractive 7 and 13 alternating layers, which exhibit a reflectance of 89.60% and 99%, respectively. The optical microcavity achieved an average transmittance of 85.13% within the visible range. The obtained results suggest that these filters could be an exceptional choice for next-generation antireflection coatings, high-reflection mirrors, and polarized interference filters.

Seasonal dynamics of microbial community composition and function in oak canopy and open grassland soils

USGS Publications Warehouse

Waldrop, M.P.; Firestone, M.K.

2006-01-01

Soil microbial communities are closely associated with aboveground plant communities, with multiple potential drivers of this relationship. Plants can affect available soil carbon, temperature, and water content, which each have the potential to affect microbial community composition and function. These same variables change seasonally, and thus plant control on microbial community composition may be modulated or overshadowed by annual climatic patterns. We examined microbial community composition, C cycling processes, and environmental data in California annual grassland soils from beneath oak canopies and in open grassland areas to distinguish factors controlling microbial community composition and function seasonally and in association with the two plant overstory communities. Every 3 months for up to 2 years, we monitored microbial community composition using phospholipid fatty acid (PLFA) analysis, microbial biomass, respiration rates, microbial enzyme activities, and the activity of microbial groups using isotope labeling of PLFA biomarkers (13C-PLFA) . Distinct microbial communities were associated with oak canopy soils and open grassland soils and microbial communities displayed seasonal patterns from year to year. The effects of plant species and seasonal climate on microbial community composition were similar in magnitude. In this Mediterranean ecosystem, plant control of microbial community composition was primarily due to effects on soil water content, whereas the changes in microbial community composition seasonally appeared to be due, in large part, to soil temperature. Available soil carbon was not a significant control on microbial community composition. Microbial community composition (PLFA) and 13C-PLFA ordination values were strongly related to intra-annual variability in soil enzyme activities and soil respiration, but microbial biomass was not. In this Mediterranean climate, soil microclimate appeared to be the master variable controlling microbial community composition and function. ?? 2006 Springer Science+Business Media, Inc.

Functional microbial community response to nutrient pulses by artificial groundwater recharge practice in surface soils and subsoils.

PubMed

Schütz, Kirsten; Kandeler, Ellen; Nagel, Peter; Scheu, Stefan; Ruess, Liliane

2010-06-01

Subsurface microorganisms are essential constituents of the soil purification processes associated with groundwater quality. In particular, soil enzyme activity determines the biodegradation of organic compounds passing through the soil profile. Transects from surface soil to a depth of 3.5 m were investigated for microbial and chemical soil characteristics at two groundwater recharge sites and one control site. The functional diversity of the microbial community was analyzed via the activity of eight enzymes. Acid phosphomonoesterase was dominant across sites and depths, followed by L-leucine aminopeptidase and beta-glucosidase. Structural [e.g. phospholipid fatty acid (PLFA) pattern] and functional microbial diversities were linked to each other at the nonwatered site, whereas amendment with nutrients (DOC, NO(3)(-)) by flooding uncoupled this relationship. Microbial biomass did not differ between sites, whereas microbial respiration was the highest at the watered sites. Hence, excess nutrients available due to artificial groundwater recharge could not compensate for the limitation by others (e.g. phosphorus as assigned by acid phosphomonoesterase activity). Instead, at a similar microbial biomass, waste respiration via overflow metabolism occurred. In summary, ample supply of carbon by flooding led to a separation of decomposition and microbial growth, which may play an important role in regulating purification processes during groundwater recharge.

Mechanisms Controlling the Plant Diversity Effect on Soil Microbial Community Composition and Soil Microbial Diversity

NASA Astrophysics Data System (ADS)

Mellado Vázquez, P. G.; Lange, M.; Griffiths, R.; Malik, A.; Ravenek, J.; Strecker, T.; Eisenhauer, N.; Gleixner, G.

2015-12-01

Soil microorganisms are the main drivers of soil organic matter cycling. Organic matter input by living plants is the major energy and matter source for soil microorganisms, higher organic matter inputs are found in highly diverse plant communities. It is therefore relevant to understand how plant diversity alters the soil microbial community and soil organic matter. In a general sense, microbial biomass and microbial diversity increase with increasing plant diversity, however the mechanisms driving these interactions are not fully explored. Working with soils from a long-term biodiversity experiment (The Jena Experiment), we investigated how changes in the soil microbial dynamics related to plant diversity were explained by biotic and abiotic factors. Microbial biomass quantification and differentiation of bacterial and fungal groups was done by phospholipid fatty acid (PLFA) analysis; terminal-restriction fragment length polymorphism was used to determine the bacterial diversity. Gram negative (G-) bacteria predominated in high plant diversity; Gram positive (G+) bacteria were more abundant in low plant diversity and saprotrophic fungi were independent from plant diversity. The separation between G- and G+ bacteria in relation to plant diversity was governed by a difference in carbon-input related factors (e.g. root biomass and soil moisture) between plant diversity levels. Moreover, the bacterial diversity increased with plant diversity and the evenness of the PLFA markers decreased. Our results showed that higher plant diversity favors carbon-input related factors and this in turn favors the development of microbial communities specialized in utilizing new carbon inputs (i.e. G- bacteria), which are contributing to the export of new C from plants to soils.

Biofilms in lab and nature: a molecular geneticist's voyage to microbial ecology.

PubMed

Kolter, Roberto

2010-03-01

This article reviews the latest findings on how extracellular signaling controls cell fate determination during the process of biofilm formation by Bacillus subtilis in the artificial setting of the laboratory. To complement molecular genetic approaches, surface-associated communities in settings as diverse as the pitcher plant Sarracenia purpurea and the human lung were investigated. The study of the pitcher plant revealed that the presence or absence of a mosquito larva in the pitcher plant controlled bacterial diversity in the ecosystem inside the pitcher plant. Through the analysis of the respiratory tract microbiota of humans suffering from cystic fibrosis (CF) a correlation between lung function and bacterial community diversity was found. Those that had lungs in good condition had also more diverse communities, whereas patients harboring Pseudomonas aeruginosa-the predominant CF pathogen-in their lungs had less diverse communities. Further studies focused on interspecies and intraspecies relationships at the molecular level in search for signaling molecules that would promote biofilm formation. Two molecules were found that induced biofilm formation in B. subtilis: nystatin-released by other species-and surfactin-released by B. subtilis itself. This is a role not previously known for two molecules that were known for other activities-nystatin as an antifungal and surfactin as a surfactant. In addition, surfactin was found to also trigger cannibalism under starvation. This could be a strategy to maintain the population because the cells destroyed serve as nutrients for the rest. The path that led the author to the study of microbial biofilms is also described.

Growth rates of rhizosphere microorganisms depend on competitive abilities of plants for nitrogen

NASA Astrophysics Data System (ADS)

Blagodatskaya, Evgenia; Littschwager, Johanna; Lauerer, Marianna; Kuzyakov, Yakov

2010-05-01

Rhizosphere - one of the most important ‘hot spots' in soil - is characterized not only by accelerated turnover of microbial biomass and nutrients but also by strong intra- and inter-specific competition. Intra-specific competition occurs between individual plants of the same species, while inter-specific competition can occur both at population level (plant species-specific, microbial species-specific interactions) and at community level (plant - microbial interactions). Such plant - microbial interactions are mainly governed by competition for available N sources, since N is one of the main growth limiting nutrients in natural ecosystems. Functional structure and activity of microbial community in rhizosphere is not uniform and is dependent on quantity and quality of root exudates which are plant specific. It is still unclear how microbial growth and turnover in the rhizosphere are dependent on the features and competitive abilities of plants for N. Depending on C and N availability, acceleration and even retardation of microbial activity and carbon mineralization can be expected in the rhizosphere of plants with high competitive abilities for N. We hypothesized slower microbial growth rates in the rhizosphere of plants with smaller roots, as they usually produce less exudates compared to plants with small shoot-to-root ratio. As the first hypothesis is based solely on C availability, we also expected the greater effect of N availability on microbial growth in rhizosphere of plants with smaller root mass. These hypothesis were tested for two plant species of strawberry: Fragaria vesca L. (native species), and Duchesnea indica (Andrews) Focke (an invasive plant in central Europe) growing in intraspecific and interspecific competition. Microbial biomass and the kinetic parameters of microbial growth in the rhizosphere were estimated by dynamics of CO2 emission from the soil amended with glucose and nutrients. Specific growth rate (µ) of soil microorganisms was estimated by fitting the parameters of the equation: CO2(t) = A + B × exp(µ×t), to the measured CO2 production rate (CO2(t)) after glucose addition, where A is the initial respiration rate uncoupled from ATP production, B the initial rate of the growing fraction of total respiration coupled with ATP generation and cell growth, and t time. Our study revealed the linkage between growth strategies of rhizosphere microorganisms and different adaptation strategies of F. vesca and D. indica to N limitation. Plant - strong competitor for N (D. indica) did not change root mass under N limitation causing the deficit of N in the rhizosphere and altering the structure of rhizosphere microbial community. Benefiting of slow growing microorganisms with K-strategy under N limiting conditions was indicated by strong decrease in specific microbial growth rates in the rhizosphere of D. indica. Root mass of the plant with weak competitive abilities for N (F. vesca) increased under lack of N to compensate the lack of nutrients. The increase in root mass and possible increase in amount of root exudates coincided with no structural changes in microbial community in rhizosphere of F. vesca. By intraspecific competition at low N level a 2.4-fold slower microbial specific growth rates were observed under D. indica (0.09 h-1) characterized by smaller root biomass and lower N content in roots compared with F. vesca. The generation time of actively growing microbial biomass was for the 6 hours longer in rhizosphere of D. indica than under F. vesca (10.7 to 4.6 h, respectively). Thus, under N limitation the strong competition for N between plant and microorganisms decreased microbial growth rates and carbon turnover in rhizosphere. By interspecific competition of both plants at low N level, microbial growth rates were similar to those for D. indica indicating that plant with stronger competitive abilities for N controls microbial community in the rhizosphere. At high N availability the root biomass did not differ significantly between both plants. This resulted in similar microbial growth rates for intra- and interspecific plant competition. Since high N level smoothed the differences between plant species in root and microbial biomass as well as in microbial growth rates, we conclude that competitive abilities of plant species were responsible for microbial growth in rhizosphere only under N imitation. As it is common that fine root proliferation and root exudation decrease at high N level, N addition smoothed the differences in microbial growth independently on plant competitive abilities.

Leakage of soluble microbial products from biological activated carbon filtration in drinking water treatment plants and its influence on health risks.

PubMed

Hong, Shen; Xian-Chun, Tang; Nan-Xiang, Wu; Hong-Bin, Chen

2018-07-01

The application of ozone-biological activated carbon (O 3 -BAC) as an advanced treatment method in drinking water treatment plants (DWTPs) can help to remove organic micropollutants and further decrease the dissolved organic carbon (DOC) level in finished water. With the increase attention to microbial safety of drinking water, a pre-positioned O 3 -BAC followed by a sand filter has been implanted into DWTP located in Shanghai, China to increase the biostability of effluents. The results showed that BAC had high removal efficiencies of UV 254 , DOC and disinfection by-product formation potential (DBPFP). The removal efficiencies between pre- and post-positioned BAC filtrations were similar. Based on the analyses of fluorescence excitation-emission matrix spectrophotometry (FEEM), the generation and leakage of soluble microbial products (SMPs) were found in both two BAC filtrations on account of the increased fluorescence intensities and fluorescence regional integration (FRI) distribution of protein-like organics, as well as the enhanced biological index (BIX). The leakage of SMPs produced by metabolism of microbes during BAC process resulted in increased DBPFP yield and carcinogenic factor per unit of DOC (CF/DOC). Although BAC filtration reduced the DBPFP and CF, there still was high health risk of effluents for the production of SMPs. Therefore, the health risks for SMPs generated by BAC filtration in drinking water advanced treatment process should be addressed, especially with that at high temperature. Copyright © 2018 Elsevier Ltd. All rights reserved.

Differential responses of soil bacteria, fungi, archaea and protists to plant species richness and plant functional group identity.

PubMed

Dassen, Sigrid; Cortois, Roeland; Martens, Henk; de Hollander, Mattias; Kowalchuk, George A; van der Putten, Wim H; De Deyn, Gerlinde B

2017-08-01

Plants are known to influence belowground microbial community structure along their roots, but the impacts of plant species richness and plant functional group (FG) identity on microbial communities in the bulk soil are still not well understood. Here, we used 454-pyrosequencing to analyse the soil microbial community composition in a long-term biodiversity experiment at Jena, Germany. We examined responses of bacteria, fungi, archaea, and protists to plant species richness (communities varying from 1 to 60 sown species) and plant FG identity (grasses, legumes, small herbs, tall herbs) in bulk soil. We hypothesized that plant species richness and FG identity would alter microbial community composition and have a positive impact on microbial species richness. Plant species richness had a marginal positive effect on the richness of fungi, but we observed no such effect on bacteria, archaea and protists. Plant species richness also did not have a large impact on microbial community composition. Rather, abiotic soil properties partially explained the community composition of bacteria, fungi, arbuscular mycorrhizal fungi (AMF), archaea and protists. Plant FG richness did not impact microbial community composition; however, plant FG identity was more effective. Bacterial richness was highest in legume plots and lowest in small herb plots, and AMF and archaeal community composition in legume plant communities was distinct from that in communities composed of other plant FGs. We conclude that soil microbial community composition in bulk soil is influenced more by changes in plant FG composition and abiotic soil properties, than by changes in plant species richness per se. © 2017 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

Size really does matter: effects of filter fractionation on microbial community structure in a model oxygen minimum zone.

NASA Astrophysics Data System (ADS)

Torres Beltran, M.

2016-02-01

The Scientific Committee on Oceanographic Research (SCOR) Working Group 144 "Microbial Community Responses to Ocean Deoxygenation" workshop held in Vancouver, British Columbia in July 2014 had the primary objective of kick-starting the establishment of a minimal core of technologies, techniques and standard operating procedures (SOPs) to enable compatible process rate and multi-molecular data (DNA, RNA and protein) collection in marine oxygen minimum zones (OMZs) and other oxygen starved waters. Experimental activities conducted in Saanich Inlet, a seasonally anoxic fjord on Vancouver Island British Columbia, were designed to compare and cross-calibrate in situ sampling devices (McLane PPS system) with conventional bottle sampling and incubation methods. Bottle effects on microbial community composition, and activity were tested using different filter combinations and sample volumes to compare PPS/IPS (0.4 µm) versus Sterivex (0.22 µm) filtration methods with and without prefilters (2.7 µm). Resulting biomass was processed for small subunit ribosomal RNA gene sequencing across all three domains of life on the 454 platform followed by downstream community structure analyses. Significant community shifts occurred within and between filter fractions for in situ versus on-ship processed samples. For instance, the relative abundance of several bacterial phyla including Bacteroidetes, Delta and Gammaproteobacteria decreased five-fold on-ship when compared to in situ filtration. Similarly, experimental mesocosms showed similar community structure and activity to in situ filtered samples indicating the need to cross-calibrate incubations to constrain bottle effects. In addition, alpha and beta diversity significantly changed as function of filter size and volume, as well as the operational taxonomic units identified using indicator species analysis for each filter size. Our results provide statistical support that microbial community structure is systematically biased by filter fraction methods and highlight the need for establishing compatible techniques among researchers that facilitate comparative and reproducible science for the whole community.

The soil microbial community composition and soil microbial carbon uptake are more affected by soil type than by different vegetation types (C3 and C4 plants) and seasonal changes

NASA Astrophysics Data System (ADS)

Griselle Mellado Vazquez, Perla; Lange, Markus; Gleixner, Gerd

2016-04-01

This study investigates the influence of different vegetation types (C3 and C4 plants), soil type and seasonal changes on the soil microbial biomass, soil microbial community composition and soil microbial carbon (C) uptake. We collected soil samples in winter (non-growing season) and summer (growing season) in 2012 from an experimental site cropping C3 and C4 plants for 6 years on two different soil types (sandy and clayey). The amount of phospholipid fatty acids (PLFAs) and their compound-specific δ13C values were used to determined microbial biomass and the flow of C from plants to soil microorganisms, respectively. Higher microbial biomass was found in the growing season. The microbial community composition was mainly explained by soil type. Higher amounts of SOC were driving the predominance of G+ bacteria, actinobacteria and cyclic G- bacteria in sandy soils, whereas root biomass was significantly related to the increased proportions of G- bacteria in clayey soils. Plant-derived C in G- bacteria increased significantly in clayey soils in the growing season. This increase was positively and significantly driven by root biomass. Moreover, changes in plant-derived C among microbial groups pointed to specific capabilities of different microbial groups to decompose distinct sources of C. We concluded that soil texture and favorable growth conditions driven by rhizosphere interactions are the most important factors controlling the soil microbial community. Our results demonstrate that a change of C3 plants vs. C4 plants has only a minor effect on the soil microbial community. Thus, such experiments are well suited to investigate soil organic matter dynamics as they allow to trace the C flow from plants into the soil microbial community without changing the community abundance and composition.

Biotechnological Aspects of Microbial Extracellular Electron Transfer

PubMed Central

Kato, Souichiro

2015-01-01

Extracellular electron transfer (EET) is a type of microbial respiration that enables electron transfer between microbial cells and extracellular solid materials, including naturally-occurring metal compounds and artificial electrodes. Microorganisms harboring EET abilities have received considerable attention for their various biotechnological applications, in addition to their contribution to global energy and material cycles. In this review, current knowledge on microbial EET and its application to diverse biotechnologies, including the bioremediation of toxic metals, recovery of useful metals, biocorrosion, and microbial electrochemical systems (microbial fuel cells and microbial electrosynthesis), were introduced. Two potential biotechnologies based on microbial EET, namely the electrochemical control of microbial metabolism and electrochemical stimulation of microbial symbiotic reactions (electric syntrophy), were also discussed. PMID:26004795

Status, Antimicrobial Mechanism, and Regulation of Natural Preservatives in Livestock Food Systems.

PubMed

Lee, Na-Kyoung; Paik, Hyun-Dong

2016-01-01

This review discusses the status, antimicrobial mechanisms, application, and regulation of natural preservatives in livestock food systems. Conventional preservatives are synthetic chemical substances including nitrates/nitrites, sulfites, sodium benzoate, propyl gallate, and potassium sorbate. The use of artificial preservatives is being reconsidered because of concerns relating to headache, allergies, and cancer. As the demand for biopreservation in food systems has increased, new natural antimicrobial compounds of various origins are being developed, including plant-derived products (polyphenolics, essential oils, plant antimicrobial peptides (pAMPs)), animal-derived products (lysozymes, lactoperoxidase, lactoferrin, ovotransferrin, antimicrobial peptide (AMP), chitosan and others), and microbial metabolites (nisin, natamycin, pullulan, ε-polylysine, organic acid, and others). These natural preservatives act by inhibiting microbial cell walls/membranes, DNA/RNA replication and transcription, protein synthesis, and metabolism. Natural preservatives have been recognized for their safety; however, these substances can influence color, smell, and toxicity in large amounts while being effective as a food preservative. Therefore, to evaluate the safety and toxicity of natural preservatives, various trials including combinations of other substances or different food preservation systems, and capsulation have been performed. Natamycin and nisin are currently the only natural preservatives being regulated, and other natural preservatives will have to be legally regulated before their widespread use.

Status, Antimicrobial Mechanism, and Regulation of Natural Preservatives in Livestock Food Systems

PubMed Central

Lee, Na-Kyoung; Paik, Hyun-Dong

2016-01-01

This review discusses the status, antimicrobial mechanisms, application, and regulation of natural preservatives in livestock food systems. Conventional preservatives are synthetic chemical substances including nitrates/nitrites, sulfites, sodium benzoate, propyl gallate, and potassium sorbate. The use of artificial preservatives is being reconsidered because of concerns relating to headache, allergies, and cancer. As the demand for biopreservation in food systems has increased, new natural antimicrobial compounds of various origins are being developed, including plant-derived products (polyphenolics, essential oils, plant antimicrobial peptides (pAMPs)), animal-derived products (lysozymes, lactoperoxidase, lactoferrin, ovotransferrin, antimicrobial peptide (AMP), chitosan and others), and microbial metabolites (nisin, natamycin, pullulan, ε-polylysine, organic acid, and others). These natural preservatives act by inhibiting microbial cell walls/membranes, DNA/RNA replication and transcription, protein synthesis, and metabolism. Natural preservatives have been recognized for their safety; however, these substances can influence color, smell, and toxicity in large amounts while being effective as a food preservative. Therefore, to evaluate the safety and toxicity of natural preservatives, various trials including combinations of other substances or different food preservation systems, and capsulation have been performed. Natamycin and nisin are currently the only natural preservatives being regulated, and other natural preservatives will have to be legally regulated before their widespread use. PMID:27621697

The Evolution of Stomach Acidity and Its Relevance to the Human Microbiome

PubMed Central

Beasley, DeAnna E.; Koltz, Amanda M.; Lambert, Joanna E.; Fierer, Noah; Dunn, Rob R.

2015-01-01

Gastric acidity is likely a key factor shaping the diversity and composition of microbial communities found in the vertebrate gut. We conducted a systematic review to test the hypothesis that a key role of the vertebrate stomach is to maintain the gut microbial community by filtering out novel microbial taxa before they pass into the intestines. We propose that species feeding either on carrion or on organisms that are close phylogenetic relatives should require the most restrictive filter (measured as high stomach acidity) as protection from foreign microbes. Conversely, species feeding on a lower trophic level or on food that is distantly related to them (e.g. herbivores) should require the least restrictive filter, as the risk of pathogen exposure is lower. Comparisons of stomach acidity across trophic groups in mammal and bird taxa show that scavengers and carnivores have significantly higher stomach acidities compared to herbivores or carnivores feeding on phylogenetically distant prey such as insects or fish. In addition, we find when stomach acidity varies within species either naturally (with age) or in treatments such as bariatric surgery, the effects on gut bacterial pathogens and communities are in line with our hypothesis that the stomach acts as an ecological filter. Together these results highlight the importance of including measurements of gastric pH when investigating gut microbial dynamics within and across species. PMID:26222383

The Evolution of Stomach Acidity and Its Relevance to the Human Microbiome.

PubMed

Beasley, DeAnna E; Koltz, Amanda M; Lambert, Joanna E; Fierer, Noah; Dunn, Rob R

2015-01-01

Gastric acidity is likely a key factor shaping the diversity and composition of microbial communities found in the vertebrate gut. We conducted a systematic review to test the hypothesis that a key role of the vertebrate stomach is to maintain the gut microbial community by filtering out novel microbial taxa before they pass into the intestines. We propose that species feeding either on carrion or on organisms that are close phylogenetic relatives should require the most restrictive filter (measured as high stomach acidity) as protection from foreign microbes. Conversely, species feeding on a lower trophic level or on food that is distantly related to them (e.g. herbivores) should require the least restrictive filter, as the risk of pathogen exposure is lower. Comparisons of stomach acidity across trophic groups in mammal and bird taxa show that scavengers and carnivores have significantly higher stomach acidities compared to herbivores or carnivores feeding on phylogenetically distant prey such as insects or fish. In addition, we find when stomach acidity varies within species either naturally (with age) or in treatments such as bariatric surgery, the effects on gut bacterial pathogens and communities are in line with our hypothesis that the stomach acts as an ecological filter. Together these results highlight the importance of including measurements of gastric pH when investigating gut microbial dynamics within and across species.

Plants regulate the effects of experimental warming on the soil microbial community in an alpine scrub ecosystem.

PubMed

Ma, Zhiliang; Zhao, Wenqiang; Zhao, Chunzhang; Wang, Dong; Liu, Mei; Li, Dandan; Liu, Qing

2018-01-01

Information on how soil microbial communities respond to warming is still scarce for alpine scrub ecosystems. We conducted a field experiment with two plant treatments (plant removal or undisturbed) subjected to warmed or unwarmed conditions to examine the effects of warming and plant removal on soil microbial community structures during the growing season in a Sibiraea angustata scrubland of the eastern Qinghai-Tibetan Plateau. The results indicate that experimental warming significantly influenced soil microbial biomass carbon (MBC) and microbial biomass nitrogen (MBN), but the warming effects were dependent on the plant treatments and sampling seasons. In the plant-removal plots, warming did not affect most of the microbial variables, while in the undisturbed plots, warming significantly increased the abundances of actinomycete and Gram-positive bacterial groups during the mid-growing season (July), but it did not affect the fungi groups. Plant removal significantly reduced fungal abundance throughout the growing season and significantly altered the soil microbial community structure in July. The interaction between warming and plant removal significantly influenced the soil MBC and MBN and the abundances of total microbes, bacteria and actinomycete throughout the growing season. Experimental warming significantly reduced the abundance of rare taxa, while the interaction between warming and plant removal tended to have strong effects on the abundant taxa. These findings suggest that the responses of soil microbial communities to warming are regulated by plant communities. These results provide new insights into how soil microbial community structure responds to climatic warming in alpine scrub ecosystems.

Plants regulate the effects of experimental warming on the soil microbial community in an alpine scrub ecosystem

PubMed Central

Ma, Zhiliang; Zhao, Wenqiang; Zhao, Chunzhang; Wang, Dong; Liu, Mei; Li, Dandan

2018-01-01

Information on how soil microbial communities respond to warming is still scarce for alpine scrub ecosystems. We conducted a field experiment with two plant treatments (plant removal or undisturbed) subjected to warmed or unwarmed conditions to examine the effects of warming and plant removal on soil microbial community structures during the growing season in a Sibiraea angustata scrubland of the eastern Qinghai–Tibetan Plateau. The results indicate that experimental warming significantly influenced soil microbial biomass carbon (MBC) and microbial biomass nitrogen (MBN), but the warming effects were dependent on the plant treatments and sampling seasons. In the plant-removal plots, warming did not affect most of the microbial variables, while in the undisturbed plots, warming significantly increased the abundances of actinomycete and Gram-positive bacterial groups during the mid-growing season (July), but it did not affect the fungi groups. Plant removal significantly reduced fungal abundance throughout the growing season and significantly altered the soil microbial community structure in July. The interaction between warming and plant removal significantly influenced the soil MBC and MBN and the abundances of total microbes, bacteria and actinomycete throughout the growing season. Experimental warming significantly reduced the abundance of rare taxa, while the interaction between warming and plant removal tended to have strong effects on the abundant taxa. These findings suggest that the responses of soil microbial communities to warming are regulated by plant communities. These results provide new insights into how soil microbial community structure responds to climatic warming in alpine scrub ecosystems. PMID:29668711

An Integrated Insight into the Relationship between Soil Microbial Community and Tobacco Bacterial Wilt Disease

PubMed Central

Yang, Hongwu; Li, Juan; Xiao, Yunhua; Gu, Yabing; Liu, Hongwei; Liang, Yili; Liu, Xueduan; Hu, Jin; Meng, Delong; Yin, Huaqun

2017-01-01

The soil microbial communities play an important role in plant health, however, the relationship between the below-ground microbiome and above-ground plant health remains unclear. To reveal such a relationship, we analyzed soil microbial communities through sequencing of 16S rRNA gene amplicons from 15 different tobacco fields with different levels of wilt disease in the central south part of China. We found that plant health was related to the soil microbial diversity as plants may benefit from the diverse microbial communities. Also, those 15 fields were grouped into ‘healthy’ and ‘infected’ samples based upon soil microbial community composition analyses such as unweighted paired-group method with arithmetic means (UPGMA) and principle component analysis, and furthermore, molecular ecological network analysis indicated that some potential plant-beneficial microbial groups, e.g., Bacillus and Actinobacteria could act as network key taxa, thus reducing the chance of plant soil-borne pathogen invasion. In addition, we propose that a more complex soil ecology network may help suppress tobacco wilt, which was also consistent with highly diversity and composition with plant-beneficial microbial groups. This study provides new insights into our understanding the relationship between the soil microbiome and plant health. PMID:29163453

Nectar microbes can reduce secondary metabolites in nectar and alter effects on nectar consumption by pollinators.

PubMed

Vannette, Rachel L; Fukami, Tadashi

2016-06-01

Secondary metabolites that are present in floral nectar have been hypothesized to enhance specificity in plant-pollinator mutualism by reducing larceny by non-pollinators, including microorganisms that colonize nectar. However, few studies have tested this hypothesis. Using synthetic nectar, we conducted laboratory and field experiments to examine the effects of five chemical compounds found in nectar on the growth and metabolism of nectar-colonizing yeasts and bacteria, and the interactive effects of these compounds and nectar microbes on the consumption of nectar by pollinators. In most cases, focal compounds inhibited microbial growth, but the extent of these effects depended on compound identity, concentration, and microbial species. Moreover, most compounds did not substantially decrease sugar metabolism by microbes, and microbes reduced the concentration of some compounds in nectar. Using artificial flowers in the field, we also found that the common nectar yeast Metschnikowia reukaufii altered nectar consumption by small floral visitors, but only in nectar containing catalpol. This effect was likely mediated by a mechanism independent of catalpol metabolism. Despite strong compound-specific effects on microbial growth, our results suggest that the secondary metabolites tested here are unlikely to be an effective general defense mechanism for preserving nectar sugars for pollinators. Instead, our results indicate that microbial colonization of nectar could reduce the concentration of secondary compounds in nectar and, in some cases, reduce deterrence to pollinators.

Native soils with their microbiotas elicit a state of alert in tomato plants.

PubMed

Chialva, Matteo; Salvioli di Fossalunga, Alessandra; Daghino, Stefania; Ghignone, Stefano; Bagnaresi, Paolo; Chiapello, Marco; Novero, Mara; Spadaro, Davide; Perotto, Silvia; Bonfante, Paola

2018-02-09

Several studies have investigated soil microbial biodiversity, but understanding of the mechanisms underlying plant responses to soil microbiota remains in its infancy. Here, we focused on tomato (Solanum lycopersicum), testing the hypothesis that plants grown on native soils display different responses to soil microbiotas. Using transcriptomics, proteomics, and biochemistry, we describe the responses of two tomato genotypes (susceptible or resistant to Fusarium oxysporum f. sp. lycopersici) grown on an artificial growth substrate and two native soils (conducive and suppressive to Fusarium). Native soils affected tomato responses by modulating pathways involved in responses to oxidative stress, phenol biosynthesis, lignin deposition, and innate immunity, particularly in the suppressive soil. In tomato plants grown on steam-disinfected soils, total phenols and lignin decreased significantly. The inoculation of a mycorrhizal fungus partly rescued this response locally and systemically. Plants inoculated with the fungal pathogen showed reduced disease symptoms in the resistant genotype in both soils, but the susceptible genotype was partially protected from the pathogen only when grown on the suppressive soil. The 'state of alert' detected in tomatoes reveals novel mechanisms operating in plants in native soils and the soil microbiota appears to be one of the drivers of these plant responses. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

Soil Microbial Properties and Plant Growth Responses to Carbon and Water Addition in a Temperate Steppe: The Importance of Nutrient Availability

PubMed Central

Guo, Chengyuan; Wang, Renzhong; Xiao, Chunwang

2012-01-01

Background Global climatic change is generally expected to stimulate net primary production, and consequently increase soil carbon (C) input. The enhanced C input together with potentially increased precipitation may affect soil microbial processes and plant growth. Methodology/Principal Findings To examine the effects of C and water additions on soil microbial properties and plant growth, we conducted an experiment lasting two years in a temperate steppe of northeastern China. We found that soil C and water additions significantly affected microbial properties and stimulated plant growth. Carbon addition significantly increased soil microbial biomass and activity but had a limited effect on microbial community structure. Water addition significantly increased soil microbial activity in the first year but the response to water decreased in the second year. The water-induced changes of microbial activity could be ascribed to decreased soil nitrogen (N) availability and to the shift in soil microbial community structure. However, no water effect on soil microbial activity was visible under C addition during the two years, likely because C addition alleviated nutrient limitation of soil microbes. In addition, C and water additions interacted to affect plant functional group composition. Water addition significantly increased the ratio of grass to forb biomass in C addition plots but showed only minor effects under ambient C levels. Our results suggest that soil microbial activity and plant growth are limited by nutrient (C and N) and water availability, and highlight the importance of nutrient availability in modulating the responses of soil microbes and plants to potentially increased precipitation in the temperate steppe. Conclusions/Significance Increased soil C input and precipitation would show significant effects on soil microbial properties and plant growth in the temperate steppe. These findings will improve our understanding of the responses of soil microbes and plants to the indirect and direct climate change effects. PMID:22496905

Plant rhizosphere species-specific stoichiometry and regulation of extracellular enzyme and microbial community structure

NASA Astrophysics Data System (ADS)

Bell, C. W.; Calderon, F.; Pendall, E.; Wallenstein, M. D.

2012-12-01

Plant communities affect the activity and composition of soil microbial communities through alteration of the soil environment during root growth; substrate availability through root exudation; nutrient availability through plant uptake; and moisture regimes through transpiration. As a result, positive feedbacks in soil properties can result from alterations in microbial community composition and function in the rhizosphere zone. At the ecosystem-scale, many properties of soil microbial communities can vary between forest stands dominated by different species, including community composition and stoichiometry. However, the influence of smaller individual plants on grassland soils and microbial communities is less well documented. There is evidence to suggest that some plants can modify their soil environment in a manner that favors their persistence. For example, when Bromus tectorum plants invade, soil microbial communities tend to have higher N mineralization rates (in the rhizosphere zone) relative to native plants. If tight linkages between individual plant species and microbial communities inhabiting the rhizosphere exist, we hypothesized that any differences among plant species specific rhizosphere zones could be observed by shifts in: 1) soil -rhizosphere microbial community structure, 2) enzymatic C:N:P acquisition activities, 3) alterations in the soil C chemistry composition in the rhizosphere, and 4) plant - soil - microbial C:N:P elemental stoichiometry. We selected and grew 4 different C3 grasses species including three species native to the Shortgrass Steppe region (Pascopyrum smithii, Koeleria macrantha, and Vulpia octoflora) and one exotic invasive plant species (B. tectorum) in root-boxes that are designed to allow for easy access to the rhizosphere. The field soil was homogenized using a 4mm sieve and mixed 1:1 with sterile sand and seeded as monocultures (24 replicate root - boxes for each species). Plant and soil samples (along with no - plant control soil samples) were collected on day 28, 78, and 148 (N = 4 /sample period/species). Microbial community structure was quantified using the barcoded pyrosequencing protocols. We measured the potential activity of seven hydrolytic soil enzymes to represent the degradation of C, N, and P-rich substrates. Soil microbial C:N biomass responses to specific plant rhizospheres (MBC and MBN) were measured using the chloroform fumigation extraction method followed by DOC & N analysis. Fourier Transform Infrared Spectroscopy was used to assess differences in plant and soil C chemistry. We found that species specific rhizospheres are characteristic of very different soil chemical, edaphic, and microbial properties. These plant species act as gateways that introduce variability into soil C, N, and P ecosystem functional dynamics directly facilitated by rhizosphere - microbe associations. Our results suggest that nutrient stoichiometry within plant species' rhizospheres is a useful tool for identifying intra-ecosystem functional patterns. By identifying what and how specific species rhizospheres differ among the overall plant community, we can better predict how below-ground microbial community function and subsequent ecosystem processes can be influenced by alterations in plant community shifts based on the rhizosphere effects.

[Succession pattern of artificial vegetation community and its ecological mechanism in an arid desert region].

PubMed

Xu, Cailin; Li, Zizhen

2003-09-01

Focusing on the artificial vegetation protection system of the Shapotou section of Baotou-Lanzhou railway in the arid desert region of China, this paper examined the dynamics of dominant plant species and the succession pattern of artificial plant community in the process of establishing and developing regional artificial vegetation. It also studied the driving force and the ecologically intrinsic mechanism of the community succession. The results demonstrated that the species composition of the artificial vegetation dramatically changed after 40 years of succession, from original artificial plant community of shrub and semi-shrub to artificial-natural desert plant community with annual herb dominated. During the process of succession, the importance values of artificial shrubs, such as Caragana korshinskii and Hedysarum scoparius, decreased and gradually retreated from the artificial plant community, while the naturally multiplied annual herb, such as Eragrostis poaeoides, Bassia dasyphylla, Salsola ruthenica, Chloris virgata and etc., were presented one after another and gradually became dominant. Besides, Artemisia ordosica always played a key role in the community due to its ability of naturally sowing and self-replacement. This type of succession pattern was closely related to the shortage of precipitation resource in this region and the formation of soil crust which inhibited the reproduction of shrub and perennial herb with deep root systems. This study provided a theoretical ground for realizing persistent development of artificial plant community.

Biofilm formation and microbial community analysis of the simulated river bioreactor for contaminated source water remediation.

PubMed

Xu, Xiang-Yang; Feng, Li-Juan; Zhu, Liang; Xu, Jing; Ding, Wei; Qi, Han-Ying

2012-06-01

The start-up pattern of biofilm remediation system affects the biofilm characteristics and operating performances. The objective of this study was to evaluate the performances of the contaminated source water remediation systems with different start-up patterns in view of the pollutants removal performances and microbial community succession. The operating performances of four lab-scale simulated river biofilm reactors were examined which employed different start-up methods (natural enrichment and artificial enhancement via discharging sediment with influent velocity gradient increase) and different bio-fillers (Elastic filler and AquaMats® ecobase). At the same time, the microbial communities of the bioreactors in different phases were analyzed by polymerase chain reaction, denaturing gradient gel electrophoresis, and sequencing. The pollutants removal performances became stable in the four reactors after 2 months' operation, with ammonia nitrogen and permanganate index (COD(Mn)) removal efficiencies of 84.41-94.21% and 69.66-76.60%, respectively. The biomass of mature biofilm was higher in the bioreactors by artificial enhancement than that by natural enrichment. Microbial community analysis indicated that elastic filler could enrich mature biofilm faster than AquaMats®. The heterotrophic bacteria diversity of biofilm decreased by artificial enhancement, which favored the ammonia-oxidizing bacteria (AOB) developing on the bio-fillers. Furthermore, Nitrosomonas- and Nitrosospira-like AOB coexisted in the biofilm, and Pseudomonas sp., Sphaerotilus sp., Janthinobacterium sp., Corynebacterium aurimucosum were dominant in the oligotrophic niche. Artificial enhancement via the combination of sediment discharging and influent velocity gradient increasing could enhance the biofilm formation and autotrophic AOB enrichment in oligotrophic niche.

Generation of soluble microbial products by bio-activated carbon filter during drinking water advanced treatment and its influence on spectral characteristics.

PubMed

Shen, Hong; Chen, Xin; Zhang, Dong; Chen, Hong-Bin

2016-11-01

In order to improve our understanding of bio-activated carbon (BAC) filter, the water quality of influent and effluent treated with BAC in a drinking water treatment plant (DWTP) of Shanghai during 2015 was valued. Combining the results from UV254, SUVA254, dissolved organic carbon (DOC) and scanning electron microscopic (SEM), it is found that performance of BAC treatment will be affected by characteristics of activated carbon (AC), which is relevant to the type of activated carbon (including shape and operating time) in this study. Fluorescence excitation-emission matrix (FEEM) shows that the humification index (HIX) and index of recent autochthonous contribution (BIX) is a reliable indicator to descript the variation of dissolved organic matter (DOM) during BAC process. The pattern of variation in BIX and HIX implies that soluble microbial products (SMPs) are formed and humic-like substances are removed during BAC treatment, which is also confirmed by the change of peaks of FEEM in BAC effluent. Large, positive correlations between SUVA254 and disinfection by-products formation potential yield (DBPFP yield) demonstrate that UV-absorbing DOM is directly related to the generation of DBPs. Poor correlations of HIX with DBPFP suggest that non-humic substances with UV-absorbing properties play an important role in the generation of DBPs in water with low SUVA254. Finally, strong but negative correlations between BIX and DBPFP suggest that vigorous microbial metabolism of BAC results in a decrease in DBPFP. However, the DBPFP yield will be enhanced for the generation of SMPs by BAC, especially in summer. Copyright © 2016 Elsevier B.V. All rights reserved.

Short- and long-term influence of stand density on soil microbial communities in ponderosa pine forests

Treesearch

Steven T. Overby

2009-01-01

Soil microbial communities process plant detritus and returns nutrients needed for plant growth. Increased knowledge of this intimate linkage between plant and soil microbial communities will provide a better understanding of ecosystem response to changing abiotic and biotic conditions. This dissertation consists of three studies to determine soil microbial community...

Machine learning for the meta-analyses of microbial pathogens' volatile signatures.

PubMed

Palma, Susana I C J; Traguedo, Ana P; Porteira, Ana R; Frias, Maria J; Gamboa, Hugo; Roque, Ana C A

2018-02-20

Non-invasive and fast diagnostic tools based on volatolomics hold great promise in the control of infectious diseases. However, the tools to identify microbial volatile organic compounds (VOCs) discriminating between human pathogens are still missing. Artificial intelligence is increasingly recognised as an essential tool in health sciences. Machine learning algorithms based in support vector machines and features selection tools were here applied to find sets of microbial VOCs with pathogen-discrimination power. Studies reporting VOCs emitted by human microbial pathogens published between 1977 and 2016 were used as source data. A set of 18 VOCs is sufficient to predict the identity of 11 microbial pathogens with high accuracy (77%), and precision (62-100%). There is one set of VOCs associated with each of the 11 pathogens which can predict the presence of that pathogen in a sample with high accuracy and precision (86-90%). The implemented pathogen classification methodology supports future database updates to include new pathogen-VOC data, which will enrich the classifiers. The sets of VOCs identified potentiate the improvement of the selectivity of non-invasive infection diagnostics using artificial olfaction devices.

Modeling the Sustainability of a Ceramic Water Filter Intervention

PubMed Central

Mellor, Jonathan; Abebe, Lydia; Ehdaie, Beeta; Dillingham, Rebecca; Smith, James

2014-01-01

Ceramic water filters (CWFs) are a point-of-use water treatment technology that has shown promise in preventing early childhood diarrhea (ECD) in resource-limited settings. Despite this promise, some researchers have questioned their ability to reduce ECD incidences over the long term since most effectiveness trials conducted to date are less than one year in duration limiting their ability to assess long-term sustainability factors. Most trials also suffer from lack of blinding making them potentially biased. This study uses an agent-based model (ABM) to explore factors related to the long-term sustainability of CWFs in preventing ECD and was based on a three year longitudinal field study. Factors such as filter user compliance, microbial removal effectiveness, filter cleaning and compliance declines were explored. Modeled results indicate that broadly defined human behaviors like compliance and declining microbial effectiveness due to improper maintenance are primary drivers of the outcome metrics of household drinking water quality and ECD rates. The model predicts that a ceramic filter intervention can reduce ECD incidence amongst under two year old children by 41.3%. However, after three years, the average filter is almost entirely ineffective at reducing ECD incidence due to declining filter microbial removal effectiveness resulting from improper maintenance. The model predicts very low ECD rates are possible if compliance rates are 80-90%, filter log reduction efficiency is 3 or greater and there are minimal long-term compliance declines. Cleaning filters at least once every 4 months makes it more likely to achieve very low ECD rates as does the availability of replacement filters for purchase. These results help to understand the heterogeneity seen in previous intervention-control trials and reemphasize the need for researchers to accurately measure confounding variables and ensure that field trials are at least 2-3 years in duration. In summary, the CWF can be a highly effective tool in the fight against ECD, but every effort should be made by implementing agencies to ensure consistent use and maintenance. PMID:24355289

Effect of Diethylene Glycol Monomethyl Ether (DiEGME) and Triethylene Glycol Monomethyl Ether (TriEGME) on Microbial Contaminants in Aviation Fuel

DTIC Science & Technology

2010-03-01

still be effective at controlling microbial growth. DiEGME and TriEGME’s ability to inhibit biofilm growth is also demonstrated. TriEGME is shown to...MO) with DiEGME or TriEGME added as appropriate. Fuel was filtered with a 0.45µm hydrophobic cellulose nitrate filter (Nalge Nunc, Rochester, NY... biofilm formation. However, no numerical standards have been universally accepted which define a particular colony count level as problematic (27). This

Artificial Soil With Build-In Plant Nutrients

NASA Technical Reports Server (NTRS)

Ming, Douglas W.; Allen, Earl; Henninger, Donald; Golden, D. C.

1995-01-01

Nutrients contained in sandlike material. Artificial soil provides nutrients to plants during several growing seasons without need to add fertilizer or nutrient solution. When watered, artificial soil slowly releases all materials a plant needs to grow. Developed as medium for growing crops in space. Also used to grow plants on Earth under controlled conditions or even to augment natural soil.

The Power Plant Operating Data Based on Real-time Digital Filtration Technology

NASA Astrophysics Data System (ADS)

Zhao, Ning; Chen, Ya-mi; Wang, Hui-jie

2018-03-01

Real-time monitoring of the data of the thermal power plant was the basis of accurate analyzing thermal economy and accurate reconstruction of the operating state. Due to noise interference was inevitable; we need real-time monitoring data filtering to get accurate information of the units and equipment operating data of the thermal power plant. Real-time filtering algorithm couldn’t be used to correct the current data with future data. Compared with traditional filtering algorithm, there were a lot of constraints. First-order lag filtering method and weighted recursive average filtering method could be used for real-time filtering. This paper analyzes the characteristics of the two filtering methods and applications for real-time processing of the positive spin simulation data, and the thermal power plant operating data. The analysis was revealed that the weighted recursive average filtering method applied to the simulation and real-time plant data filtering achieved very good results.

Microbial Community Analysis in the Roots of Aquatic Plants and Isolation of Novel Microbes Including an Organism of the Candidate Phylum OP10

PubMed Central

Tanaka, Yasuhiro; Tamaki, Hideyuki; Matsuzawa, Hiroaki; Nigaya, Masahiro; Mori, Kazuhiro; Kamagata, Yoichi

2012-01-01

A number of molecular ecological studies have revealed complex and unique microbial communities in various terrestrial plant roots; however, little is known about the microbial communities of aquatic plant roots in spite of their potential use for water quality improvement in aquatic environments (e.g. floating treatment wetland system). Here, we report the microbial communities inhabiting the roots of emerged plants, reed (Phragmites australis) and Japanese loosestrife (Lythrum anceps), collected from a floating treatment wetland in a pond by both culture-independent and culture-dependent approaches. Culture-independent analysis based on 16S rRNA gene sequences revealed that the microbial compositions between the two aquatic plant roots were clearly different (e.g. the predominant microbe was Betaproteobacteria for reed and Alphaproteobacteria for Japanese loosestrife). In comparisons of microbial communities between the plant roots and pond water taken from near the plants, the microbial diversity in the plant roots (e.g. 4.40–4.26 Shannon-Weiner index) were higher than that of pond water (e.g. 3.15 Shannon-Weiner index). Furthermore, the plant roots harbored 2.5–3.5 times more phylogenetically novel clone phylotypes than pond water. The culture-dependent approach also revealed differences in the microbial composition and diversity among the two plant roots and pond water. More importantly, compared to pond water, we succeeded in isolating approximately two times more novel isolate phylotypes, including a bacterium of candidate phylum OP10 (recently named Armatimonadetes) from the plant roots. These findings suggest that aquatic plants roots are significant sources for a variety of novel organisms. PMID:22791047

The EmulSiv filter removes microbial contamination from propofol but is not a substitute for aseptic technique.

PubMed

Hall, Wendy C E; Jolly, Donald T; Hrazdil, Jiri; Galbraith, John C; Greacen, Maria; Clanachan, Alexander S

2003-01-01

To evaluate the ability of the EmulSiv filter (EF) to remove extrinsic microbial contaminants from propofol. Aliquots of Staphylococcus aureus (S. aureus), Candida albicans (C. albicans), Klebsiella pneumoniae (K. pneumoniae), Moraxella osloensis (M. osloensis), Enterobacter agglomerans (E. agglomerans), Escherichia coli (E. coli), Serratia marcescens (S. marcescens), Moraxella catarrhalis (M. catarrhalis), Haemophilus influenzae (H. influenzae) and Campylobacter jejuni (C. jejuni) were inoculated into vials containing 20 mL of sterile propofol. The unfiltered inoculated propofol solutions served as controls. Ten millilitres and 20 mL samples of the inoculated propofol were filtered through the EF. All solutions were then subplated onto three culture plates using a precision 1 micro L calibrated platinum loop and incubated. The number of colony forming units (CFU) were counted. Data were analyzed using a one-sample t test, and a P value of less than 0.05 was selected as the level of statistical significance. The EF was able to completely remove CFU of S. aureus, C. albicans, K. pneumoniae, M. osloensis, E. agglomerans, E. coli, S. marcescens, and M. catarrhalis (P < 0.05). A small number of H. influenzae CFU were able to evade filtration in both the 10 mL and 20 mL samples. C. jejuni CFU were able to evade filtration in only the 10 mL sample. The EF removes the majority of microbial contaminates from propofol with the exception of H. influenzae and C. jejuni. Although the EF is capable of removing most of the microbial contamination produced by H. influenzae and C. jejuni, a few CFU are capable of evading filtration. Consequently, even the use of a filter capable of removing microbial contaminants is not a substitute for meticulous aseptic technique and prompt administration when propofol is used.

Soil microbial communities alter leaf chemistry and influence allelopathic potential among coexisting plant species.

PubMed

Meiners, Scott J; Phipps, Kelsey K; Pendergast, Thomas H; Canam, Thomas; Carson, Walter P

2017-04-01

While both plant-soil feedbacks and allelochemical interactions are key drivers of plant community dynamics, the potential for these two drivers to interact with each other remains largely unexplored. If soil microbes influence allelochemical production, this would represent a novel dimension of heterogeneity in plant-soil feedbacks. To explore the linkage between soil microbial communities and plant chemistry, we experimentally generated soil microbial communities and evaluated their impact on leaf chemical composition and allelopathic potential. Four native perennial old-field species (two each of Aster and Solidago) were grown in pairwise combination with each species' soil microbial community as well as a sterilized inoculum. We demonstrated unequivocally that variation in soil microbial communities altered leaf chemical fingerprints for all focal plant species and also changed their allelopathic potential. Soil microbes reduced allelopathic potential in bioassays by increasing germination 25-54% relative to sterile control soils in all four species. Plants grown with their own microbial communities had the lowest allelopathic potential, suggesting that allelochemical production may be lessened when growing with microbes from conspecifics. The allelopathic potential of plants grown in congener and confamilial soils was indistinguishable from each other, indicating an equivalent response to all non-conspecific microbial communities within these closely related genera. Our results clearly demonstrated that soil microbial communities cause changes in leaf tissue chemistry that altered their allelopathic properties. These findings represent a new mechanism of plant-soil feedbacks that may structure perennial plant communities over very small spatial scales that must be explored in much more detail.

Artificial Structural Color Pixels: A Review

PubMed Central

Zhao, Yuqian; Zhao, Yong; Hu, Sheng; Lv, Jiangtao; Ying, Yu; Gervinskas, Gediminas; Si, Guangyuan

2017-01-01

Inspired by natural photonic structures (Morpho butterfly, for instance), researchers have demonstrated varying artificial color display devices using different designs. Photonic-crystal/plasmonic color filters have drawn increasing attention most recently. In this review article, we show the developing trend of artificial structural color pixels from photonic crystals to plasmonic nanostructures. Such devices normally utilize the distinctive optical features of photonic/plasmon resonance, resulting in high compatibility with current display and imaging technologies. Moreover, dynamical color filtering devices are highly desirable because tunable optical components are critical for developing new optical platforms which can be integrated or combined with other existing imaging and display techniques. Thus, extensive promising potential applications have been triggered and enabled including more abundant functionalities in integrated optics and nanophotonics. PMID:28805736

Behaviour and biodegradation of sulfonamides (p-TSA, o-TSA, BSA) during drinking water treatment.

PubMed

Richter, Doreen; Massmann, Gudrun; Dünnbier, Uwe

2008-04-01

Three sulfonamides -para-toluenesulfonamide (p-TSA), ortho-toluenesulfonamide (o-TSA) and benzenesulfonamide (BSA) - have recently been detected in groundwater within a catchment area of one drinking water treatment plant (DWTP), which is located downstream of a former sewage farm. The degradation pathways of p-TSA, o-TSA and BSA were investigated during drinking water treatment with incubation experiments and an experimental filter. Incubation experiments showed that p-TSA is removed during the treatment by microbiological processes. Removal of p-TSA is performed by adapted microorganisms only present in polluted groundwater. The elimination in an experimental filter of 1.6m length applying filtration velocities from 2 to 6 m h(-1) was approximately 93% of p-TSA. The microbial degradation rates in the incubation experiment were approximately 0.029 microg l(-1) h(-1) (zero order reaction). In the experimental filter, the reaction rate constants were around 0.0063 s(-1) for all filtration velocities (1st order reaction). Drinking water treatment does not reduce the concentration of o-TSA and BSA under conditions encountered in Berlin. p-TSA, o-TSA and BSA were only measured in the low microg l(-1) concentrations range in the purified water.

Modelling the removal of p-TSA (para-toluenesulfonamide) during rapid sand filtration used for drinking water treatment.

PubMed

Meffe, Raffaella; Kohfahl, Claus; Holzbecher, Ekkehard; Massmann, Gudrun; Richter, Doreen; Dünnbier, Uwe; Pekdeger, Asaf

2010-01-01

A finite element model was set-up to determine degradation rate constants for p-TSA during rapid sand filtration (RSF). Data used for the model originated from a column experiment carried out in the filter hall of a drinking water treatment plant in Berlin (Germany). Aerated abstracted groundwater was passed through a 1.6m long column-shaped experimental sand filter applying infiltration rates from 2 to 6mh(-1). Model results were fitted to measured profiles and breakthrough curves of p-TSA for different infiltration rates using both first-order reaction kinetics and Michaelis-Menten kinetics. Both approaches showed that degradation rates varied both in space and time. Higher degradation rates were observed in the upper part of the column, probably related to higher microbial activity in this zone. Measured and simulated breakthrough curves revealed an adaption phase with lower degradation rates after infiltration rates were changed, followed by an adapted phase with more elevated degradation rates. Irrespective of the mathematical approach and the infiltration rate, degradation rates were very high, probably owing to the fact that filter sands have been in operation for decades, receiving high p-TSA concentrations with the raw water.

Nutrient gradients in a granular activated carbon biofilter drives bacterial community organization and dynamics.

PubMed

Boon, Nico; Pycke, Benny F G; Marzorati, Massimo; Hammes, Frederik

2011-12-01

The quality of drinking water is ensured by hygienic barriers and filtration steps, such as ozonation and granular activated carbon (GAC) filtration. Apart from adsorption, GAC filtration involves microbial processes that remove biodegradable organic carbon from the ozonated ground or surface water and ensures biological stability of the treated water. In this study, microbial community dynamics in were monitored during the start-up and maturation of an undisturbed pilot-scale GAC filter at 4 depths (10, 45, 80 and 115 cm) over a period of 6 months. New ecological tools, based on 16S rRNA gene-DGGE, were correlated to filter performance and microbial activity and showed that the microbial gradients developing in the filter was of importance. At 10 cm from the top, receiving the freshly ozonated water with the highest concentration of nutrients, the microbial community dynamics were minimal and the species richness remained low. However, the GAC samples at 80-115 cm showed a 2-3 times higher species richness than the 10-45 cm samples. The highest biomass densities were observed at 45-80 cm, which corresponded with maximum removal of dissolved and assimilable organic carbon. Furthermore, the start-up period was clearly distinguishable using the Lorenz analysis, as after 80 days, the microbial community shifted to an apparent steady-state condition with increased evenness. This study showed that GAC biofilter performance is not necessarily correlated to biomass concentration, but rather that an elevated functionality can be the result of increased microbial community richness, evenness and dynamics. Copyright © 2011 Elsevier Ltd. All rights reserved.

Filter forensics: microbiota recovery from residential HVAC filters.

PubMed

Maestre, Juan P; Jennings, Wiley; Wylie, Dennis; Horner, Sharon D; Siegel, Jeffrey; Kinney, Kerry A

2018-01-30

Establishing reliable methods for assessing the microbiome within the built environment is critical for understanding the impact of biological exposures on human health. High-throughput DNA sequencing of dust samples provides valuable insights into the microbiome present in human-occupied spaces. However, the effect that different sampling methods have on the microbial community recovered from dust samples is not well understood across sample types. Heating, ventilation, and air conditioning (HVAC) filters hold promise as long-term, spatially integrated, high volume samplers to characterize the airborne microbiome in homes and other climate-controlled spaces. In this study, the effect that dust recovery method (i.e., cut and elution, swabbing, or vacuuming) has on the microbial community structure, membership, and repeatability inferred by Illumina sequencing was evaluated. The results indicate that vacuum samples captured higher quantities of total, bacterial, and fungal DNA than swab or cut samples. Repeated swab and vacuum samples collected from the same filter were less variable than cut samples with respect to both quantitative DNA recovery and bacterial community structure. Vacuum samples captured substantially greater bacterial diversity than the other methods, whereas fungal diversity was similar across all three methods. Vacuum and swab samples of HVAC filter dust were repeatable and generally superior to cut samples. Nevertheless, the contribution of environmental and human sources to the bacterial and fungal communities recovered via each sampling method was generally consistent across the methods investigated. Dust recovery methodologies have been shown to affect the recovery, repeatability, structure, and membership of microbial communities recovered from dust samples in the built environment. The results of this study are directly applicable to indoor microbiota studies utilizing the filter forensics approach. More broadly, this study provides a better understanding of the microbial community variability attributable to sampling methodology and helps inform interpretation of data collected from other types of dust samples collected from indoor environments.

An evaluation of the infection control potential of a UV clinical podiatry unit.

PubMed

Humphreys, Paul N; Davies, Chris S; Rout, Simon

2014-02-28

Infection control is a key issue in podiatry as it is in all forms of clinical practice. Airborne contamination may be particularly important in podiatry due to the generation of particulates during treatment. Consequently, technologies that prevent contamination in podiatry settings may have a useful role. The aims of this investigation were twofold, firstly to determine the ability of a UV cabinet to protect instruments from airborne contamination and secondly to determine its ability to remove microbes from contaminated surfaces and instruments. A UV instrument cabinet was installed in a University podiatry suite. Impact samplers and standard microbiological techniques were used to determine the nature and extent of microbial airborne contamination. Sterile filters were used to determine the ability of the UV cabinet to protect exposed surfaces. Artificially contaminated instruments were used to determine the ability of the cabinet to remove microbial contamination. Airborne bacterial contamination was dominated by Gram positive cocci including Staphylococcus aureus. Airborne fungal levels were much lower than those observed for bacteria. The UV cabinet significantly reduced (p < 0.05) the observed levels of airborne contamination. When challenged with contaminated instruments the cabinet was able to reduce microbial levels by between 60% to 100% with more complex instruments e.g. clippers, remaining contaminated. Bacterial airborne contamination is a potential infection risk in podiatry settings due to the presence of S. aureus. The use of a UV instrument cabinet can reduce the risk of contamination by airborne microbes. The UV cabinet tested was unable to decontaminate instruments and as such could pose an infection risk if misused.

An evaluation of the infection control potential of a UV clinical podiatry unit

PubMed Central

2014-01-01

Background Infection control is a key issue in podiatry as it is in all forms of clinical practice. Airborne contamination may be particularly important in podiatry due to the generation of particulates during treatment. Consequently, technologies that prevent contamination in podiatry settings may have a useful role. The aims of this investigation were twofold, firstly to determine the ability of a UV cabinet to protect instruments from airborne contamination and secondly to determine its ability to remove microbes from contaminated surfaces and instruments. Method A UV instrument cabinet was installed in a University podiatry suite. Impact samplers and standard microbiological techniques were used to determine the nature and extent of microbial airborne contamination. Sterile filters were used to determine the ability of the UV cabinet to protect exposed surfaces. Artificially contaminated instruments were used to determine the ability of the cabinet to remove microbial contamination. Results Airborne bacterial contamination was dominated by Gram positive cocci including Staphylococcus aureus. Airborne fungal levels were much lower than those observed for bacteria. The UV cabinet significantly reduced (p < 0.05) the observed levels of airborne contamination. When challenged with contaminated instruments the cabinet was able to reduce microbial levels by between 60% to 100% with more complex instruments e.g. clippers, remaining contaminated. Conclusions Bacterial airborne contamination is a potential infection risk in podiatry settings due to the presence of S. aureus. The use of a UV instrument cabinet can reduce the risk of contamination by airborne microbes. The UV cabinet tested was unable to decontaminate instruments and as such could pose an infection risk if misused. PMID:24576315

Study of quadrature FIR filters for extraction of low-frequency instantaneous information in biophysical signals

NASA Astrophysics Data System (ADS)

Arce-Guevara, Valdemar E.; Alba-Cadena, Alfonso; Mendez, Martín O.

Quadrature bandpass filters take a real-valued signal and output an analytic signal from which the instantaneous amplitude and phase can be computed. For this reason, they represent a useful tool to extract time-varying, narrow-band information from electrophysiological signals such as electroencephalogram (EEG) or electrocardiogram. One of the defining characteristics of quadrature filters is its null response to negative frequencies. However, when the frequency band of interest is close to 0 Hz, a careless filter design could let through negative frequencies, producing distortions in the amplitude and phase of the output. In this work, three types of quadrature filters (Ideal, Gabor and Sinusoidal) have been evaluated using both artificial and real EEG signals. For the artificial signals, the performance of each filter was measured in terms of the distortion in amplitude and phase, and sensitivity to noise and bandwidth selection. For the real EEG signals, a qualitative evaluation of the dynamics of the synchronization between two EEG channels was performed. The results suggest that, while all filters under study behave similarly under noise, they differ in terms of their sensitivity to bandwidth choice. In this study, the Sinusoidal filter showed clear advantages for the estimation of low-frequency EEG synchronization.

Contribution of above- and below-ground plant traits to the structure and function of grassland soil microbial communities

PubMed Central

Legay, N.; Baxendale, C.; Grigulis, K.; Krainer, U.; Kastl, E.; Schloter, M.; Bardgett, R. D.; Arnoldi, C.; Bahn, M.; Dumont, M.; Poly, F.; Pommier, T.; Clément, J. C.; Lavorel, S.

2014-01-01

Background and Aims Abiotic properties of soil are known to be major drivers of the microbial community within it. Our understanding of how soil microbial properties are related to the functional structure and diversity of plant communities, however, is limited and largely restricted to above-ground plant traits, with the role of below-ground traits being poorly understood. This study investigated the relative contributions of soil abiotic properties and plant traits, both above-ground and below-ground, to variations in microbial processes involved in grassland nitrogen turnover. Methods In mountain grasslands distributed across three European sites, a correlative approach was used to examine the role of a large range of plant functional traits and soil abiotic factors on microbial variables, including gene abundance of nitrifiers and denitrifiers and their potential activities. Key Results Direct effects of soil abiotic parameters were found to have the most significant influence on the microbial groups investigated. Indirect pathways via plant functional traits contributed substantially to explaining the relative abundance of fungi and bacteria and gene abundances of the investigated microbial communities, while they explained little of the variance in microbial activities. Gene abundances of nitrifiers and denitrifiers were most strongly related to below-ground plant traits, suggesting that they were the most relevant traits for explaining variation in community structure and abundances of soil microbes involved in nitrification and denitrification. Conclusions The results suggest that consideration of plant traits, and especially below-ground traits, increases our ability to describe variation in the abundances and the functional characteristics of microbial communities in grassland soils. PMID:25122656

Changes in River Organic Matter Through Time.

NASA Astrophysics Data System (ADS)

Hudson, N.; Baker, A.; Ward, D.

2006-12-01

Samples of river water from central England were collected during the summer base-flow period. They were analysed for BOD and filtered at 1.2μm and 0.1μm increments to obtain i) the colloidal and dissolved, and ii) dissolved filter sterilized fractions. Each filtered fraction was plated up for microbiological cell counts and the agar plates and water samples were stored under a range of environmental conditions (4° C dark, 11° C light/ dark, 11° C dark, and 20° C dark) for 26 days. Absorbance, fluorescence, pH, conductivity and total organic carbon (TOC) were measured and colony forming units (CFU) counted on days 1, 2, 3, 4, 5, 12, 19 and 26. The fluorescence intensity was recorded for 5 commonly studied regions: protein like fluorescence, indicative of microbial activity, represented by the fluorescent amino acids tyrosine and tryptophan (which has two clear fluorescence regions) and humic and fulvic acids derived from the break down of terrestrial and aquatic plant material. Humic and fulvic-like fluorescence increased in all samples under all storage conditions suggesting that peaks A and C probably include a microbial element, either a product of the living community or as dead cell material in all fraction sizes including <0.1μm. Tryptophan and tyrosine-like fluorescence intensities demonstrated less clear trends which may be reflective of the intrinsic variation in natural samples. Tryptophan-like fluorescence generally decreased or showed minimal change, except in samples exposed to light in which an increase was observed in line with algal growth. A decrease in intensity may relate to the use of the tryptophan-like material as a microbial substrate. The increase in tryptophan-like fluorescence intensity suggests that this fluorescent material is being produced, either by algae, or bacterial activity associated with algal growth. It may also occur as a result of changing water chemistry causing a change in molecular conformation, and resulting fluorescence, as an increase in pH was also observed in these samples. This work illustrates the dynamic character of river organic matter within a timescale and under conditions that are representative of the natural system.

Microbial monitoring by molecular tools of an upflow anaerobic filter treating abattoir wastewaters.

PubMed

Gannoun, Hana; Khelifi, Eltaief; Omri, Ilhem; Jabari, Linda; Fardeau, Marie-Laure; Bouallagui, Hassib; Godon, Jean-Jacques; Hamdi, Moktar

2013-08-01

The performance of anaerobic digestion of abattoir wastewaters (AW) in an upflow anaerobic filter (UAF) was investigated under mesophilic (37°C) and thermophilic (55°C) conditions. The effects of increasing temperature on the performance of the UAF and on the dynamics of the microbial community of the anaerobic sludge were studied. The results showed that chemical oxygen demand (COD) removal efficiency of 90% was achieved for organic loading rates (OLRs) up to 4.5g CODL(-1)d(-1) in mesophilic conditions, while in thermophilic conditions, the highest OLRs of 9 g CODL(-1)d(-1) led to the efficiency of 72%. The use of molecular and microbiological methods to recover microbial populations involved in this process showed that fermentative bacteria were the prominent members of the sludge microbial community. Three novel strains were identified as Macellibacteroides fermentans, Desulfotomaculum peckii and Defluviitalea saccharophila. Copyright © 2013 Elsevier Ltd. All rights reserved.

Natural Air Purifier

NASA Technical Reports Server (NTRS)

1993-01-01

NASA environmental research has led to a plant-based air filtering system. Dr. B.C. Wolverton, a former NASA engineer who developed a biological filtering system for space life support, served as a consultant to Terra Firma Environmental. The company is marketing the BioFilter, a natural air purifier that combines activated carbon and other filter media with living plants and microorganisms. The filter material traps and holds indoor pollutants; plant roots and microorganisms then convert the pollutants into food for the plant. Most non-flowering house plants will work. After pollutants have been removed, the cleansed air is returned to the room through slits in the planter. Terra Firma is currently developing a filter that will also disinfect the air.

A Mechanistic Study of Plant and Microbial Controls over R* for Nitrogen in an Annual Grassland

PubMed Central

Levine, Jonathan M.; HilleRisLambers, Janneke

2014-01-01

Differences in species' abilities to capture resources can drive competitive hierarchies, successional dynamics, community diversity, and invasions. To investigate mechanisms of resource competition within a nitrogen (N) limited California grassland community, we established a manipulative experiment using an R* framework. R* theory holds that better competitors within a N limited community should better depress available N in monoculture plots and obtain higher abundance in mixture plots. We asked whether (1) plant uptake or (2) plant species influences on microbial dynamics were the primary drivers of available soil N levels in this system where N structures plant communities. To disentangle the relative roles of plant uptake and microbially-mediated processes in resource competition, we quantified soil N dynamics as well as N pools in plant and microbial biomass in monoculture plots of 11 native or exotic annual grassland plants over one growing season. We found a negative correlation between plant N content and soil dissolved inorganic nitrogen (DIN, our measure of R*), suggesting that plant uptake drives R*. In contrast, we found no relationship between microbial biomass N or potential net N mineralization and DIN. We conclude that while plant-microbial interactions may have altered the overall quantity of N that plants take up, the relationship between species' abundance and available N in monoculture was largely driven by plant N uptake in this first year of growth. PMID:25170943

Spatial variation in edaphic characteristics is a stronger control than nitrogen inputs in regulating soil microbial effects on a desert grass

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chung, Y. Anny; Sinsabaugh, Robert L.; Kuske, Cheryl Rae

Increased atmospheric nitrogen (N) deposition can have wide-ranging effects on plant community structure and ecosystem function, some of which may be indirectly mediated by soil microbial responses to an altered biogeochemical environment. In this study, soils from a field N fertilization experiment that spanned a soil texture gradient were used as inocula in the greenhouse to assess the indirect effects of soil microbial communities on growth of a desert grass. Plant performance and interaction with soil microbiota were evaluated via plant above- and belowground biomass, leaf N concentration, and root fungal colonization. Nitrogen fertilization in the field increased the benefitsmore » of soil microbial inoculation to plant leaf N concentration, but did not alter the effect of soil microbes on plant growth. Plant-microbe interaction outcomes differed most strongly among sites with different soil textures, where the soil microbial community from the sandiest site was most beneficial to host plant growth. In conclusion, the findings of this study suggest that in a desert grassland, increases in atmospheric N deposition may exert a more subtle influence on plant-microbe interactions by altering plant nutrient status, whereas edaphic factors can alter the whole-plant growth response to soil microbial associates.« less

Spatial variation in edaphic characteristics is a stronger control than nitrogen inputs in regulating soil microbial effects on a desert grass

DOE PAGES

Chung, Y. Anny; Sinsabaugh, Robert L.; Kuske, Cheryl Rae; ...

2017-03-22

Increased atmospheric nitrogen (N) deposition can have wide-ranging effects on plant community structure and ecosystem function, some of which may be indirectly mediated by soil microbial responses to an altered biogeochemical environment. In this study, soils from a field N fertilization experiment that spanned a soil texture gradient were used as inocula in the greenhouse to assess the indirect effects of soil microbial communities on growth of a desert grass. Plant performance and interaction with soil microbiota were evaluated via plant above- and belowground biomass, leaf N concentration, and root fungal colonization. Nitrogen fertilization in the field increased the benefitsmore » of soil microbial inoculation to plant leaf N concentration, but did not alter the effect of soil microbes on plant growth. Plant-microbe interaction outcomes differed most strongly among sites with different soil textures, where the soil microbial community from the sandiest site was most beneficial to host plant growth. In conclusion, the findings of this study suggest that in a desert grassland, increases in atmospheric N deposition may exert a more subtle influence on plant-microbe interactions by altering plant nutrient status, whereas edaphic factors can alter the whole-plant growth response to soil microbial associates.« less

Spatial variation in edaphic characteristics is a stronger control than nitrogen inputs in regulating soil microbial effects on a desert grass

USGS Publications Warehouse

Chung, Y. Anny; Sinsabaugh, Robert L; Kuske, Cheryl R.; Reed, Sasha C.; Rudgers, Jennifer A.

2017-01-01

Increased atmospheric nitrogen (N) deposition can have wide-ranging effects on plant community structure and ecosystem function, some of which may be indirectly mediated by soil microbial responses to an altered biogeochemical environment. In this study, soils from a field N fertilization experiment that spanned a soil texture gradient were used as inocula in the greenhouse to assess the indirect effects of soil microbial communities on growth of a desert grass. Plant performance and interaction with soil microbiota were evaluated via plant above- and belowground biomass, leaf N concentration, and root fungal colonization. Nitrogen fertilization in the field increased the benefits of soil microbial inoculation to plant leaf N concentration, but did not alter the effect of soil microbes on plant growth. Plant-microbe interaction outcomes differed most strongly among sites with different soil textures, where the soil microbial community from the sandiest site was most beneficial to host plant growth. The findings of this study suggest that in a desert grassland, increases in atmospheric N deposition may exert a more subtle influence on plant-microbe interactions by altering plant nutrient status, whereas edaphic factors can alter the whole-plant growth response to soil microbial associates.

Interplay Between Innate Immunity and the Plant Microbiota.

PubMed

Hacquard, Stéphane; Spaepen, Stijn; Garrido-Oter, Ruben; Schulze-Lefert, Paul

2017-08-04

The innate immune system of plants recognizes microbial pathogens and terminates their growth. However, recent findings suggest that at least one layer of this system is also engaged in cooperative plant-microbe interactions and influences host colonization by beneficial microbial communities. This immune layer involves sensing of microbe-associated molecular patterns (MAMPs) by pattern recognition receptors (PRRs) that initiate quantitative immune responses to control host-microbial load, whereas diversification of MAMPs and PRRs emerges as a mechanism that locally sculpts microbial assemblages in plant populations. This suggests a more complex microbial management role of the innate immune system for controlled accommodation of beneficial microbes and in pathogen elimination. The finding that similar molecular strategies are deployed by symbionts and pathogens to dampen immune responses is consistent with this hypothesis but implies different selective pressures on the immune system due to contrasting outcomes on plant fitness. The reciprocal interplay between microbiota and the immune system likely plays a critical role in shaping beneficial plant-microbiota combinations and maintaining microbial homeostasis.

Optical restoration of images blurred by atmospheric turbulence using optimum filter theory.

PubMed

Horner, J L

1970-01-01

The results of optimum filtering from communications theory have been applied to an image restoration problem. Photographic film imagery, degraded by long-term artificial atmospheric turbulence, has been restored by spatial filters placed in the Fourier transform plane. The time-averaged point spread function was measured and used in designing the filters. Both the simple inverse filter and the optimum least-mean-square filters were used in the restoration experiments. The superiority of the latter is conclusively demonstrated. An optical analog processor was used for the restoration.

System Identification for Nonlinear Control Using Neural Networks

NASA Technical Reports Server (NTRS)

Stengel, Robert F.; Linse, Dennis J.

1990-01-01

An approach to incorporating artificial neural networks in nonlinear, adaptive control systems is described. The controller contains three principal elements: a nonlinear inverse dynamic control law whose coefficients depend on a comprehensive model of the plant, a neural network that models system dynamics, and a state estimator whose outputs drive the control law and train the neural network. Attention is focused on the system identification task, which combines an extended Kalman filter with generalized spline function approximation. Continual learning is possible during normal operation, without taking the system off line for specialized training. Nonlinear inverse dynamic control requires smooth derivatives as well as function estimates, imposing stringent goals on the approximating technique.

Estimation of biotransformation and sorption of emerging organic compounds (EOCs) during artificial recharge through a reactive barrier.

NASA Astrophysics Data System (ADS)

Valhondo, C.; Martinez-Landa, L.; Carrera, J.; Hidalgo, J. J.; Ayora, C.

2016-12-01

The reuse of lesser quality water such as effluents from wastewater treatment plants or effluent-receiving water bodies has been promoted due to the water shortages affecting many regions of the world. Artificial recharge through infiltration basins is known to improve several water quality parameters including the attenuation of emerging organic compounds (EOCs). Many of these contaminants exhibit redox dependent biotransformation because the redox state is one of the factors controlling microbial community development. Together with biotransformation, sorption also affects the behavior of EOCs in their passage through the soil. We studied EOCs attenuation in an infiltration system is located in Sant Vicenç dells Horts on the Llobregat delta (Barcelona, Spain), where the local water agency has an artificial recharge pilot project . The Llobregat river water used for the artificial recharge is affected by treatment plant effluents which contain EOCs. A reactive barrier consisting of vegetable compost, clay, and iron oxide was installed in the bottom of the infiltration basin to enhance biotransformation and sorption of EOCs. The barrier releases dissolved organic carbon, which favors the development of a broad range of redox environments, and supplies neutral, cationic, and anionic surfaces to favor sorption of different types of contaminants. Results were excellent, but quantitative evaluation of the EOCs attenuation requires knowledge of the residence time distribution of infiltrated water. A tracer test was performed by adding tracers to the infiltration water and interpreting the breakthrough curves at diverse monitoring points with a 2D multilayer numerical model. The calibrated model quantify degradation, as a first order law, and sorption through a linear distribution coefficient for ten selected EOCs. Results indicate higher degradation rates and sorption coefficients in the reactive barrier than in the rest of the aquifer for nine and eight of the ten studied EOCs, respectively, which demonstrates the efficiency of the reactive barrier to enhance the removal of EOCs.

Root hairs increase root exudation and rhizosphere extension

NASA Astrophysics Data System (ADS)

Holz, Maire; Zarebandanadkouki, Mohsen; Kuzyakov, Yakov; Carmintati, Andrea

2017-04-01

Plant roots employ various mechanisms to increase their access to limited soil resources. An example of such strategies is the production of root hairs. Root hairs extend the root surface and therefore increase the access to nutrients. Additionally, carbon release from root hairs might facilitate nutrient uptake by spreading of carbon in the rhizosphere and enhancing microbial activity. The aim of this study was to test: i) how root hairs change the allocation of carbon in the soil-plant system; ii) whether root hairs exude carbon into the soil and iii) how differences in C release between plants with and without root hairs affect rhizosphere extension. We grew barley plants with and without root hairs (wild type: WT, bald root barley: brb) in rhizoboxes filled with a sandy soil. Root elongation was monitored over time. After 4 weeks of growth, plants were labelled with 14CO2. A filter paper was placed on the soil surface before labelling and was removed after 36 h. 14C imaging of the soil surface and of the filter paper was used to quantify the allocation of 14C into the roots and the exudation of 14C, respectively. Plants were sampled destructively one day after labeling to quantify 14C in the plant-soil system. 14CO2 release from soil over time (17 d) was quantified by trapping CO2 in NaOH with an additional subset of plants. WT and brb plants had a similar aboveground biomass and allocated similar amounts of 14C into shoots (170 KBq for WT; 152 KBq for brb) and roots one day after labelling. Biomass of root, rhizosphere soil as well as root elongation were lower for brb compared to the wild type. WT plants transported more C from the shoots to the roots (22.8% for WT; 13.8% for brb) and from the root into the rhizosphere (8.8% for WT 3.5% for brb). Yet lower amounts of 14CO2 were released from soil over time for WT. Radial and longitudinal rhizosphere extension was increased for WT compared to brb (4.7 vs. 2.6 mm; 5.6 vs. 3.1 cm). The total exudation which was estimated based on the grey values of the filter paper images was 1.6 times higher for WT compared to brb. After one month, brb plants performed as good as WT plants, presumably because nutrients and water were not limiting for young plants. Under nutrient limiting conditions higher C release as well as increased longitudinal and radial rhizosphere extension for WT may maintain higher nutrient accessibility compared to root hair free plants.

Composition and stability of bacterial communities associated with granular activated carbon and anthracite filters in a pilot scale municipal drinking water treatment facility.

PubMed

Shirey, T B; Thacker, R W; Olson, J B

2012-06-01

Granular activated carbon (GAC) is an alternative filter substrate for municipal water treatment as it provides a high surface area suitable for microbial colonization. The resulting microbial growth promotes biodegradation of organic materials and other contaminants from influent waters. Here, the community structure of the bacteria associated with three GAC and two anthracite filters was examined over 12 months to monitor changes in community composition. Nearly complete 16S rRNA genes were polymerase chain reaction amplified for terminal restriction fragment length polymorphism (T-RFLP) analyses. The identity of commonly occurring peaks was determined through the construction of five representative 16S rRNA clone libraries. Based on sequence analysis, the bacterial communities associated with both anthracite and GAC filters appear to be composed of environmentally derived bacteria, with no known human pathogens. Analysis of similarity tests revealed that significant differences in bacterial community structure occurred over time, with filter substrate playing an important role in determining community composition. GAC filters exhibited the greatest degree of bacterial community variability over the sampling period, while anthracite filters showed a lower degree of variability and less change in community composition. Thus, GAC may be a suitable biologically active filter substrate for the treatment of municipal drinking water.

The Effect of Diethylene Glycol Monomethyl Ether (DiEGME) on Microbial Contamination of Jet Fuel: A Minimum Concentration Study

DTIC Science & Technology

2010-03-01

added as appropriate. Fuel was filtered with a 0.45µm hydrophobic cellulose nitrate filter (Nalge Nunc, Rochester, NY) prior to use in the test setup...it may not be clear from the images above, biofilms were also present in all 0% test setups. In fuel systems, a biofilm is a microbial growth...formation that typically appears as a sheen, pellicule, or mat that forms between the fuel and water layers or on the interior sides of a tank. Biofilms

Planting increases the abundance and structure complexity of soil core functional genes relevant to carbon and nitrogen cycling

PubMed Central

Wang, Feng; Liang, Yuting; Jiang, Yuji; Yang, Yunfeng; Xue, Kai; Xiong, Jinbo; Zhou, Jizhong; Sun, Bo

2015-01-01

Plants have an important impact on soil microbial communities and their functions. However, how plants determine the microbial composition and network interactions is still poorly understood. During a four-year field experiment, we investigated the functional gene composition of three types of soils (Phaeozem, Cambisols and Acrisol) under maize planting and bare fallow regimes located in cold temperate, warm temperate and subtropical regions, respectively. The core genes were identified using high-throughput functional gene microarray (GeoChip 3.0), and functional molecular ecological networks (fMENs) were subsequently developed with the random matrix theory (RMT)-based conceptual framework. Our results demonstrated that planting significantly (P < 0.05) increased the gene alpha-diversity in terms of richness and Shannon – Simpson’s indexes for all three types of soils and 83.5% of microbial alpha-diversity can be explained by the plant factor. Moreover, planting had significant impacts on the microbial community structure and the network interactions of the microbial communities. The calculated network complexity was higher under maize planting than under bare fallow regimes. The increase of the functional genes led to an increase in both soil respiration and nitrification potential with maize planting, indicating that changes in the soil microbial communities and network interactions influenced ecological functioning. PMID:26396042

Transcriptome changes in artificial dosing of rumen content in neonatal calves

USDA-ARS?s Scientific Manuscript database

In mammals, microbial colonization in the digestive tract (GIT) occurs right after birth by the main bacteria groups. Numerous human and mouse studies have reported the importance of early gut microbial inhabitants on host health. However, few attempts have been undertaken to understand the role of ...

Plant diversity does not buffer drought effects on early-stage litter mass loss rates and microbial properties.

PubMed

Vogel, Anja; Eisenhauer, Nico; Weigelt, Alexandra; Scherer-Lorenzen, Michael

2013-09-01

Human activities are decreasing biodiversity and changing the climate worldwide. Both global change drivers have been shown to affect ecosystem functioning, but they may also act in concert in a non-additive way. We studied early-stage litter mass loss rates and soil microbial properties (basal respiration and microbial biomass) during the summer season in response to plant species richness and summer drought in a large grassland biodiversity experiment, the Jena Experiment, Germany. In line with our expectations, decreasing plant diversity and summer drought decreased litter mass loss rates and soil microbial properties. In contrast to our hypotheses, however, this was only true for mass loss of standard litter (wheat straw) used in all plots, and not for plant community-specific litter mass loss. We found no interactive effects between global change drivers, that is, drought reduced litter mass loss rates and soil microbial properties irrespective of plant diversity. High mass loss rates of plant community-specific litter and low responsiveness to drought relative to the standard litter indicate that soil microbial communities were adapted to decomposing community-specific plant litter material including lower susceptibility to dry conditions during summer months. Moreover, higher microbial enzymatic diversity at high plant diversity may have caused elevated mass loss of standard litter. Our results indicate that plant diversity loss and summer drought independently impede soil processes. However, soil decomposer communities may be highly adapted to decomposing plant community-specific litter material, even in situations of environmental stress. Results of standard litter mass loss moreover suggest that decomposer communities under diverse plant communities are able to cope with a greater variety of plant inputs possibly making them less responsive to biotic changes. © 2013 John Wiley & Sons Ltd.

The role of biotic interactions in plant community assembly: What is the community species pool?

NASA Astrophysics Data System (ADS)

Švamberková, Eva; Vítová, Alena; Lepš, Jan

2017-11-01

Differences in plant species composition between a community and its species pool are considered to reflect the effect of community filters. If we define the species pool as a set of species able to reach a site and form a viable population in a given abiotic environment (i.e. to pass the dispersal and abiotic filter), the difference in species composition should correspond to the effect of biotic interactions. However, most of the operational definitions of the species pool are based on co-occurrence patterns and thus also reflect the effect of biotic relationships, including definitions based on functional plant traits, Ellenberg indicator values or Beals index. We conducted two seed introduction experiments in an oligotrophic wet meadow with the aim of demonstrating that many species excluded, according to the above definitions, from a species pool are in fact able to establish there successfully if competition is removed. In sowing experiments, we studied the establishment and survival of species after the removal of competition (i.e. in artificial gaps) and in intact vegetation. We also investigated inter-annual variability of seed germination and seedling establishment and competitive exclusion of sown species. The investigated species also included those from very different habitats (i.e. species with very low corresponding Beals index or Ellenberg indicator values that were different from the target community weighted mean). Many of these species were able to grow in the focal wet meadow if competition was removed, but they did not establish and survive in the intact community. These species are thus not limited by abiotic conditions, but by the biotic filter. We also recorded a great inter-annual variability in seed germination and seedling establishment. Competitive exclusion of species with different ecological requirements could be quite fast (one and half seasons) in some species, but some non-resident species were able to survive several seasons; the resident species were able to persist in competition. Comparison of realized vegetation composition with the corresponding species pool greatly underestimates the potential impact of the biotic filter if the delimitation of the species pool is based on the realized niches of species and co-occurrence patterns.

Can soil microbial diversity influence plant metabolites and life history traits of a rhizophagous insect? A demonstration in oilseed rape.

PubMed

Lachaise, Tom; Ourry, Morgane; Lebreton, Lionel; Guillerm-Erckelboudt, Anne-Yvonne; Linglin, Juliette; Paty, Chrystelle; Chaminade, Valérie; Marnet, Nathalie; Aubert, Julie; Poinsot, Denis; Cortesero, Anne-Marie; Mougel, Christophe

2017-12-01

Interactions between plants and phytophagous insects play an important part in shaping the biochemical composition of plants. Reciprocally plant metabolites can influence major life history traits in these insects and largely contribute to their fitness. Plant rhizospheric microorganisms are an important biotic factor modulating plant metabolites and adaptation to stress. While plant-insects or plant-microorganisms interactions and their consequences on the plant metabolite signature are well-documented, the impact of soil microbial communities on plant defenses against phytophagous insects remains poorly known. In this study, we used oilseed rape (Brassica napus) and the cabbage root fly (Delia radicum) as biological models to tackle this question. Even though D. radicum is a belowground herbivore as a larva, its adult life history traits depend on aboveground signals. We therefore tested whether soil microbial diversity influenced emergence rate and fitness but also fly oviposition behavior, and tried to link possible effects to modifications in leaf and root metabolites. Through a removal-recolonization experiment, 3 soil microbial modalities ("high," "medium," "low") were established and assessed through amplicon sequencing of 16S and 18S ribosomal RNA genes. The "medium" modality in the rhizosphere significantly improved insect development traits. Plant-microorganism interactions were marginally associated to modulations of root metabolites profiles, which could partly explain these results. We highlighted the potential role of plant-microbial interaction in plant defenses against Delia radicum. Rhizospheric microbial communities must be taken into account when analyzing plant defenses against herbivores, being either below or aboveground. © 2017 Institute of Zoology, Chinese Academy of Sciences.

Potential sources of microbial colonizers in an initial soil ecosystem after retreat of an alpine glacier

PubMed Central

Rime, Thomas; Hartmann, Martin; Frey, Beat

2016-01-01

Rapid disintegration of alpine glaciers has led to the formation of new terrain consisting of mineral debris colonized by microorganisms. Despite the importance of microbial pioneers in triggering the formation of terrestrial ecosystems, their sources (endogenous versus exogenous) and identities remain elusive. We used 454-pyrosequencing to characterize the bacterial and fungal communities in endogenous glacier habitats (ice, sub-, supraglacial sediments and glacier stream leaving the glacier forefront) and in atmospheric deposition (snow, rain and aeolian dust). We compared these microbial communities with those occurring in recently deglaciated barren soils before and after snow melt (snow-covered soil and barren soil). Atmospheric bacteria and fungi were dominated by plant-epiphytic organisms and differed from endogenous glacier habitats and soils indicating that atmospheric input of microorganisms is not a major source of microbial pioneers in newly formed soils. We found, however, that bacterial communities in newly exposed soils resembled those of endogenous habitats, which suggests that bacterial pioneers originating from sub- and supraglacial sediments contributed to the colonization of newly exposed soils. Conversely, fungal communities differed between habitats suggesting a lower dispersal capability than bacteria. Yeasts putatively adapted to cold habitats characteristic of snow and supraglacial sediments were similar, despite the fact that these habitats were not spatially connected. These findings suggest that environmental filtering selects particular fungi in cold habitats. Atmospheric deposition provided important sources of dissolved organic C, nitrate and ammonium. Overall, microbial colonizers triggering soil development in alpine environments mainly originate from endogenous glacier habitats, whereas atmospheric deposition contributes to the establishment of microbial communities by providing sources of C and N. PMID:26771926

Potential sources of microbial colonizers in an initial soil ecosystem after retreat of an alpine glacier.

PubMed

Rime, Thomas; Hartmann, Martin; Frey, Beat

2016-07-01

Rapid disintegration of alpine glaciers has led to the formation of new terrain consisting of mineral debris colonized by microorganisms. Despite the importance of microbial pioneers in triggering the formation of terrestrial ecosystems, their sources (endogenous versus exogenous) and identities remain elusive. We used 454-pyrosequencing to characterize the bacterial and fungal communities in endogenous glacier habitats (ice, sub-, supraglacial sediments and glacier stream leaving the glacier forefront) and in atmospheric deposition (snow, rain and aeolian dust). We compared these microbial communities with those occurring in recently deglaciated barren soils before and after snow melt (snow-covered soil and barren soil). Atmospheric bacteria and fungi were dominated by plant-epiphytic organisms and differed from endogenous glacier habitats and soils indicating that atmospheric input of microorganisms is not a major source of microbial pioneers in newly formed soils. We found, however, that bacterial communities in newly exposed soils resembled those of endogenous habitats, which suggests that bacterial pioneers originating from sub- and supraglacial sediments contributed to the colonization of newly exposed soils. Conversely, fungal communities differed between habitats suggesting a lower dispersal capability than bacteria. Yeasts putatively adapted to cold habitats characteristic of snow and supraglacial sediments were similar, despite the fact that these habitats were not spatially connected. These findings suggest that environmental filtering selects particular fungi in cold habitats. Atmospheric deposition provided important sources of dissolved organic C, nitrate and ammonium. Overall, microbial colonizers triggering soil development in alpine environments mainly originate from endogenous glacier habitats, whereas atmospheric deposition contributes to the establishment of microbial communities by providing sources of C and N.

Chemical Oxygen Demand abatement in sewage using Micro-Aeration Enhanced Ecological Floating Bed

NASA Astrophysics Data System (ADS)

Shi, Hongle; Zhou, Gaofeng; Liu, Yiqing; Tan, Jiancong; Fu, Yongsheng

2018-02-01

The traditional ecological floating bed combined with micro-aeration system and artificial medium was developed for the removal of contaminants and remediation of surface water. This micro-aeration enhanced ecological floating bed (MAEEFB) consisted of aeration unit, microbial processing unit and aquatic plant unit. Batch experiments were conducted in different operating conditions on the removal of chemical oxygen demand (COD) in the sewage using MAEEFB. The removal rate of COD by MAEEFB, enhanced ecological floating bed (EEFB) and traditional ecological floating bed (TEFB) in the same reaction conditions was 59.2%, 56.9% and 30.6%, respectively, indicating that the combination of micro-aeration system and artificial medium could enhance the removal efficiency of COD in TEFB. In MAEEFB, the aeration intensity should be designed reasonablely considering both treatment efficiency and operation cost. Only increasing the specific surface area of the packing cannot effectively improve the purification efficiency of water. Factors like packing material, ability of intercepting organics and complicated extent of microorganisms attaching on the packing should also be considered.

Short-term parasite-infection alters already the biomass, activity and functional diversity of soil microbial communities

PubMed Central

Li, Jun-Min; Jin, Ze-Xin; Hagedorn, Frank; Li, Mai-He

2014-01-01

Native parasitic plants may be used to infect and control invasive plants. We established microcosms with invasive Mikania micrantha and native Coix lacryma-jobi growing in mixture on native soils, with M. micrantha being infected by parasitic Cuscuta campestris at four intensity levels for seven weeks to estimate the top-down effects of plant parasitism on the biomass and functional diversity of soil microbial communities. Parasitism significantly decreased root biomass and altered soil microbial communities. Soil microbial biomass decreased, but soil respiration increased at the two higher infection levels, indicating a strong stimulation of soil microbial metabolic activity (+180%). Moreover, a Biolog assay showed that the infection resulted in a significant change in the functional diversity indices of soil microbial communities. Pearson correlation analysis indicated that microbial biomass declined significantly with decreasing root biomass, particularly of the invasive M. micrantha. Also, the functional diversity indices of soil microbial communities were positively correlated with soil microbial biomass. Therefore, the negative effects on the biomass, activity and functional diversity of soil microbial community by the seven week long plant parasitism was very likely caused by decreased root biomass and root exudation of the invasive M. micrantha. PMID:25367357

Short-term parasite-infection alters already the biomass, activity and functional diversity of soil microbial communities

NASA Astrophysics Data System (ADS)

Li, Jun-Min; Jin, Ze-Xin; Hagedorn, Frank; Li, Mai-He

2014-11-01

Native parasitic plants may be used to infect and control invasive plants. We established microcosms with invasive Mikania micrantha and native Coix lacryma-jobi growing in mixture on native soils, with M. micrantha being infected by parasitic Cuscuta campestris at four intensity levels for seven weeks to estimate the top-down effects of plant parasitism on the biomass and functional diversity of soil microbial communities. Parasitism significantly decreased root biomass and altered soil microbial communities. Soil microbial biomass decreased, but soil respiration increased at the two higher infection levels, indicating a strong stimulation of soil microbial metabolic activity (+180%). Moreover, a Biolog assay showed that the infection resulted in a significant change in the functional diversity indices of soil microbial communities. Pearson correlation analysis indicated that microbial biomass declined significantly with decreasing root biomass, particularly of the invasive M. micrantha. Also, the functional diversity indices of soil microbial communities were positively correlated with soil microbial biomass. Therefore, the negative effects on the biomass, activity and functional diversity of soil microbial community by the seven week long plant parasitism was very likely caused by decreased root biomass and root exudation of the invasive M. micrantha.

Developing microbial inoculants for native Hawaiian trees

Treesearch

Kim H. Wilkinson

2002-01-01

We use certain microbial inoculants in the nursery as a part of supporting the objectives of accelerating rehabilitation of degraded land and ecosystem function, as well as reducing costs in establishment and maintenance of forest plantings. Microbial inoculants re-create natural partnerships between plants and some of the beneficial microorganisms that support plants...

Microbial community and performance of slaughterhouse wastewater treatment filters.

PubMed

Stets, M I; Etto, R M; Galvão, C W; Ayub, R A; Cruz, L M; Steffens, M B R; Barana, A C

2014-06-16

The performance of anaerobic filter bioreactors (AFs) is influenced by the composition of the substrate, support medium, and the microbial species present in the sludge. In this study, the efficiency of a slaughterhouse effluent treatment using three AFs containing different support media was tested, and the microbial diversity was investigated by amplified ribosomal DNA restriction analysis and 16S rRNA gene sequencing. The physicochemical analysis of the AF systems tested suggested their feasibility, with rates of chemical oxygen demand removal of 72±8% in hydraulic retention times of 1 day. Analysis of pH, alkalinity, volatile acidity, total solids, total volatile solids, total Kjeldahl nitrogen, and the microbial community structures indicated high similarity among the three AFs. The composition of prokaryotic communities showed a prevalence of Proteobacteria (27.3%) and Bacteroidetes (18.4%) of the Bacteria domain and Methanomicrobiales (36.4%) and Methanosarcinales (35.3%) of the Archaea domain. Despite the high similarity of the microbial communities among the AFs, the reactor containing pieces of clay brick as a support medium presented the highest richness and diversity of bacterial and archaeal operational taxonomic units.

Microbial Life in Soil - Linking Biophysical Models with Observations

NASA Astrophysics Data System (ADS)

Or, Dani; Tecon, Robin; Ebrahimi, Ali; Kleyer, Hannah; Ilie, Olga; Wang, Gang

2015-04-01

Microbial life in soil occurs within fragmented aquatic habitats formed in complex pore spaces where motility is restricted to short hydration windows (e.g., following rainfall). The limited range of self-dispersion and physical confinement promote spatial association among trophically interdepended microbial species. Competition and preferences for different nutrient resources and byproducts and their diffusion require high level of spatial organization to sustain the functioning of multispecies communities. We report mechanistic modeling studies of competing multispecies microbial communities grown on hydrated surfaces and within artificial soil aggregates (represented by 3-D pore network). Results show how trophic dependencies and cell-level interactions within patchy diffusion fields promote spatial self-organization of motile microbial cells. The spontaneously forming patterns of segregated, yet coexisting species were robust to spatial heterogeneities and to temporal perturbations (hydration dynamics), and respond primarily to the type of trophic dependencies. Such spatially self-organized consortia may reflect ecological templates that optimize substrate utilization and could form the basic architecture for more permanent surface-attached microbial colonies. Hydration dynamics affect structure and spatial arrangement of aerobic and anaerobic microbial communities and their biogeochemical functions. Experiments with well-characterized artificial soil microbial assemblies grown on porous surfaces provide access to community dynamics during wetting and drying cycles detected through genetic fingerprinting. Experiments for visual observations of spatial associations of tagged bacterial species with known trophic dependencies on model porous surfaces are underway. Biophysical modeling provide a means for predicting hydration-mediated critical separation distances for activation of spatial self-organization. The study provides new modeling and observational tools that enable new mechanistic insights into how differences in substrate affinities among microbial species and soil micro-hydrological conditions may give rise to a remarkable spatial and functional order in an extremely heterogeneous soil microbial world

Microbial Life in Soil - Linking Biophysical Models with Observations

NASA Astrophysics Data System (ADS)

Or, D.; Tecon, R.; Ebrahimi, A.; Kleyer, H.; Ilie, O.; Wang, G.

2014-12-01

Microbial life in soil occurs within fragmented aquatic habitats in complex pore spaces where motility is restricted to short hydration windows (e.g., following rainfall). The limited range of self-dispersion and physical confinement promote spatial association among trophically interdepended microbial species. Competition and preferences for different nutrient resources and byproducts and their diffusion require high level of spatial organization to sustain the functioning of multispecies communities. We report mechanistic modeling studies of competing multispecies microbial communities grown on hydrated surfaces and within artificial soil aggregates (represented by 3-D pore network). Results show how trophic dependencies and cell-level interactions within patchy diffusion fields promote spatial self-organization of motile microbial cells. The spontaneously forming patterns of segregated, yet coexisting species were robust to spatial heterogeneities and to temporal perturbations (hydration dynamics), and respond primarily to the type of trophic dependencies. Such spatially self-organized consortia may reflect ecological templates that optimize substrate utilization and could form the basic architecture for more permanent surface-attached microbial colonies. Hydration dynamics affect structure and spatial arrangement of aerobic and anaerobic microbial communities and their biogeochemical functions. Experiments with well-characterized artificial soil microbial assemblies grown on porous surfaces provide access to community dynamics during wetting and drying cycles detected through genetic fingerprinting. Experiments for visual observations of spatial associations of tagged bacterial species with known trophic dependencies on model porous surfaces are underway. Biophysical modeling provide a means for predicting hydration-mediated critical separation distances for activation of spatial self-organization. The study provides new modeling and observational tools that enable new mechanistic insights into how differences in substrate affinities among microbial species and soil micro-hydrological conditions may give rise to a remarkable spatial and functional order in an extremely heterogeneous soil microbial world.

Modeling the sustainability of a ceramic water filter intervention.

PubMed

Mellor, Jonathan; Abebe, Lydia; Ehdaie, Beeta; Dillingham, Rebecca; Smith, James

2014-02-01

Ceramic water filters (CWFs) are a point-of-use water treatment technology that has shown promise in preventing early childhood diarrhea (ECD) in resource-limited settings. Despite this promise, some researchers have questioned their ability to reduce ECD incidences over the long term since most effectiveness trials conducted to date are less than one year in duration limiting their ability to assess long-term sustainability factors. Most trials also suffer from lack of blinding making them potentially biased. This study uses an agent-based model (ABM) to explore factors related to the long-term sustainability of CWFs in preventing ECD and was based on a three year longitudinal field study. Factors such as filter user compliance, microbial removal effectiveness, filter cleaning and compliance declines were explored. Modeled results indicate that broadly defined human behaviors like compliance and declining microbial effectiveness due to improper maintenance are primary drivers of the outcome metrics of household drinking water quality and ECD rates. The model predicts that a ceramic filter intervention can reduce ECD incidence amongst under two year old children by 41.3%. However, after three years, the average filter is almost entirely ineffective at reducing ECD incidence due to declining filter microbial removal effectiveness resulting from improper maintenance. The model predicts very low ECD rates are possible if compliance rates are 80-90%, filter log reduction efficiency is 3 or greater and there are minimal long-term compliance declines. Cleaning filters at least once every 4 months makes it more likely to achieve very low ECD rates as does the availability of replacement filters for purchase. These results help to understand the heterogeneity seen in previous intervention-control trials and reemphasize the need for researchers to accurately measure confounding variables and ensure that field trials are at least 2-3 years in duration. In summary, the CWF can be a highly effective tool in the fight against ECD, but every effort should be made by implementing agencies to ensure consistent use and maintenance. Copyright © 2013 Elsevier Ltd. All rights reserved.

Relating belowground microbial composition to the taxonomic, phylogenetic, and functional trait distributions of trees in a tropical forest.

PubMed

Barberán, Albert; McGuire, Krista L; Wolf, Jeffrey A; Jones, F Andrew; Wright, Stuart Joseph; Turner, Benjamin L; Essene, Adam; Hubbell, Stephen P; Faircloth, Brant C; Fierer, Noah

2015-12-01

The complexities of the relationships between plant and soil microbial communities remain unresolved. We determined the associations between plant aboveground and belowground (root) distributions and the communities of soil fungi and bacteria found across a diverse tropical forest plot. Soil microbial community composition was correlated with the taxonomic and phylogenetic structure of the aboveground plant assemblages even after controlling for differences in soil characteristics, but these relationships were stronger for fungi than for bacteria. In contrast to expectations, the species composition of roots in our soil core samples was a poor predictor of microbial community composition perhaps due to the patchy, ephemeral, and highly overlapping nature of fine root distributions. Our ability to predict soil microbial composition was not improved by incorporating information on plant functional traits suggesting that the most commonly measured plant traits are not particularly useful for predicting the plot-level variability in belowground microbial communities. © 2015 John Wiley & Sons Ltd/CNRS.

The first collection of spacecraft-associated microorganisms: a public source for extremotolerant microorganisms from spacecraft assembly clean rooms.

PubMed

Moissl-Eichinger, Christine; Rettberg, Petra; Pukall, Rüdiger

2012-11-01

For several reasons, spacecraft are constructed in so-called clean rooms. Particles could affect the function of spacecraft instruments, and for missions under planetary protection limitations, the biological contamination has to be restricted as much as possible. The proper maintenance of clean rooms includes, for instance, constant control of humidity and temperature, air filtering, and cleaning (disinfection) of the surfaces. The combination of these conditions creates an artificial, extreme biotope for microbial survival specialists: spore formers, autotrophs, multi-resistant, facultative, or even strictly anaerobic microorganisms have been detected in clean room habitats. Based on a diversity study of European and South-American spacecraft assembly clean rooms, the European Space Agency (ESA) has initialized and funded the creation of a public library of microbial isolates. Isolates from three different European clean rooms, as well as from the final assembly and launch facility in Kourou (French Guiana), have been phylogenetically analyzed and were lyophilized for long-term storage at the German Culture Collection facilities in Brunswick, Germany (Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen). The isolates were obtained by either following the standard protocol for the determination of bioburden on, and around, spacecraft or the use of alternative cultivation strategies. Currently, the database contains 298 bacterial strains. Fifty-nine strains are Gram-negative microorganisms, belonging to the α-, β- and γ-Proteobacteria. Representatives of the Gram-positive phyla Actinobacteria, Bacteroidetes/Chlorobi, and Firmicutes were subjected to the collection. Ninety-four isolates (21 different species) of the genus Bacillus were included in the ESA collection. This public collection of extremotolerant microbes, which are adapted to a complicated artificial biotope, provides a wonderful source for industry and research focused on very unusual properties of microbes. For ESA, this collection is an essential resource with which to evaluate the contamination potential of spacecraft-associated biology and validate new biological contamination control and reduction procedures.

Removal of helminth eggs by centralized and decentralized wastewater treatment plants in South Africa and Lesotho: health implications for direct and indirect exposure to the effluents.

PubMed

Amoah, Isaac Dennis; Reddy, Poovendhree; Seidu, Razak; Stenström, Thor Axel

2018-05-01

Wastewater may contain contaminants harmful to human health; hence, there is the need for treatment before discharge. Centralized wastewater treatment systems are the favored treatment options globally, but these are not necessarily superior in reduction of pathogens as compared to decentralized wastewater treatment systems (collectively called DEWATS). This study was therefore undertaken to assess the soil-transmitted helminth (STH) and Taenia sp. egg reduction efficiency of selected anaerobic baffled reactors and planted gravel filters compared to centralized wastewater treatment plants in South Africa and Lesotho. The risk of ascariasis with exposure to effluents from the centralized wastewater treatment plants was also assessed using the quantitative microbial risk assessment (QMRA) approach. Eggs of Ascaris spp., hookworm, Trichuris spp., Taenia spp., and Toxocara spp. were commonly detected in the untreated wastewater. The DEWATS plants removed between 95 and 100% of the STH and Taenia sp. eggs, with centralized plants removing between 67 and 100%. Helminth egg concentrations in the final effluents from the centralized wastewater treatment plants were consistently higher than those in the WHO recommended guideline (≤ 1 helminth egg/L) for agricultural use resulting in higher risk of ascariasis. Therefore, in conclusion, DEWATS plants may be more efficient in reducing the concentration of helminth eggs in wastewater, resulting in lower risks of STH infections upon exposure.

Forced-air warming blowers: An evaluation of filtration adequacy and airborne contamination emissions in the operating room.

PubMed

Albrecht, Mark; Gauthier, Robert L; Belani, Kumar; Litchy, Mark; Leaper, David

2011-05-01

Forced-air warming (FAW) is widely used to prevent hypothermia during surgical procedures. The airflow from these blowers is often vented near the operative site and should be free of contaminants to minimize the risk of surgical site infection. Popular FAW blowers contain a 0.2-μm rated intake filter to reduce these risks. However, there is little evidence that the efficiency of the intake filter is adequate to prevent airborne contamination emissions or protect the internal air path from microbial contamination buildup. Five new intake filters were obtained directly from the manufacturer (Bair Hugger 505, model 200708D; Arizant Healthcare, Eden Prairie, MN), and 5 model 200708C filters currently in hospital use were removed from FAW devices. The retention efficiency of these filters was assessed using a monodisperse sodium chloride aerosol. In the same hospitals, internal air path surface swabs and hose outlet particle counts were performed on 52 forced-air warming devices (all with the model 200708C filter) to assess internal microbial buildup and airborne contamination emissions. Intake filter retention efficiency at 0.2 μm was 93.8% for the 200708C filter and 61.3% at for the 200708D filter. The 200708D filter obtained directly from the manufacturer has a thinner filtration media than the 200708C filter in current hospital use, suggesting that the observed differences in retention efficiency were due to design changes. Fifty-eight percent of the FAW blowers evaluated were internally generating and emitting airborne contaminants, with microorganisms detected on the internal air path surfaces of 92.3% of these blowers. Isolates of Staphylococcus aureus, coagulase-negative Staphylococcus, and methicillin-resistant S aureus were detected in 13.5%, 3.9%, and 1.9% of FAW blowers, respectively. The design of popular FAW devices using the 200708C filter was found to be inadequate for preventing the internal buildup and emission of microbial contaminants into the operating room. Substandard intake filtration allowed airborne contaminants (both viable and nonviable) to penetrate the intake filter and reversibly attach to the internal surfaces within the FAW blowers. The reintroduction of these contaminants into the FAW blower air stream was detected and could contribute to the risk of cross-infection. Given the deficiencies identified with the 200708C intake filter, the introduction of a new filter (model 200708D) with substantially lower retention efficiency is of concern. Copyright © 2011 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Mosby, Inc. All rights reserved.

Biochar increases plant growth and alters microbial communities via regulating the moisture and temperature of green roof substrates.

PubMed

Chen, Haoming; Ma, Jinyi; Wei, Jiaxing; Gong, Xin; Yu, Xichen; Guo, Hui; Zhao, Yanwen

2018-09-01

Green roofs have increasingly been designed and applied to relieve environmental problems, such as water loss, air pollution as well as heat island effect. Substrate and vegetation are important components of green roofs providing ecosystem services and benefiting the urban development. Biochar made from sewage sludge could be potentially used as the substrate amendment for green roofs, however, the effects of biochar on substrate quality and plant performance in green roofs are still unclear. We evaluated the effects of adding sludge biochar (0, 5, 10, 15 and 20%, v/v) to natural soil planted with three types of plant species (ryegrass, Sedum lineare and cucumber) on soil properties, plant growth and microbial communities in both green roof and ground ecosystems. Our results showed that sludge biochar addition significantly increased substrate moisture, adjusted substrate temperature, altered microbial community structure and increased plant growth. The application rate of 10-15% sludge biochar on the green roof exerted the most significant effects on both microbial and plant biomass by 63.9-89.6% and 54.0-54.2% respectively. Path analysis showed that biochar addition had a strong effect on microbial biomass via changing the soil air-filled porosity, soil moisture and temperature, and promoted plant growth through the positive effects on microbial biomass. These results suggest that the applications of biochar at an appropriate rate can significantly alter plant growth and microbial community structure, and increase the ecological benefits of green roofs via exerting effects on the moisture, temperature and nutrients of roof substrates. Copyright © 2018 Elsevier B.V. All rights reserved.

Forest understory plant and soil microbial response to an experimentally induced drought and heat-pulse event: the importance of maintaining the continuum.

PubMed

von Rein, Isabell; Gessler, Arthur; Premke, Katrin; Keitel, Claudia; Ulrich, Andreas; Kayler, Zachary E

2016-08-01

Drought duration and intensity are expected to increase with global climate change. How changes in water availability and temperature affect the combined plant-soil-microorganism response remains uncertain. We excavated soil monoliths from a beech (Fagus sylvatica L.) forest, thus keeping the understory plant-microbe communities intact, imposed an extreme climate event, consisting of drought and/or a single heat-pulse event, and followed microbial community dynamics over a time period of 28 days. During the treatment, we labeled the canopy with (13) CO2 with the goal of (i) determining the strength of plant-microbe carbon linkages under control, drought, heat and heat-drought treatments and (ii) characterizing microbial groups that are tightly linked to the plant-soil carbon continuum based on (13) C-labeled PLFAs. Additionally, we used 16S rRNA sequencing of bacteria from the Ah horizon to determine the short-term changes in the active microbial community. The treatments did not sever within-plant transport over the experiment, and carbon sinks belowground were still active. Based on the relative distribution of labeled carbon to roots and microbial PLFAs, we determined that soil microbes appear to have a stronger carbon sink strength during environmental stress. High-throughput sequencing of the 16S rRNA revealed multiple trajectories in microbial community shifts within the different treatments. Heat in combination with drought had a clear negative effect on microbial diversity and resulted in a distinct shift in the microbial community structure that also corresponded to the lowest level of label found in the PLFAs. Hence, the strongest changes in microbial abundances occurred in the heat-drought treatment where plants were most severely affected. Our study suggests that many of the shifts in the microbial communities that we might expect from extreme environmental stress will result from the plant-soil-microbial dynamics rather than from direct effects of drought and heat on soil microbes alone. © 2016 John Wiley & Sons Ltd.

[Results of salad machine experiment within the MARS-500 project].

PubMed

Berkovich, Iu A; Erokhin, A N; Ziablova, N V; Krivobok, A S; Krivobok, N M; Smolianina, S O; Mukhamedieva, L N; Pakhomova, A A; Novikova, N D; Poddubko, S V; Korsak, I V

2012-01-01

The salad machine experiment was aimed to fulfill performance testing of a prototype of space conveyor-type cylindrical greenhouse PHYTOCYCLE-SL, to study growth and development of plants, and to evaluate microbial contamination of equipment in the closed manned environment. Crops of leaf cabbage Brassica chinensis L., cultivar Vesnianka were raised in the time interval between MARS-500 days 417 and 515. The greenhouse proved it serviceability demanding 17 min/(man x d) in the normal mode. Most likely that the slow growth rate and deviations in plant morphology were caused by the presence of volatile pollutants in the greenhouse compartment Accumulation of micromycetes was observed at the sites of humid surfaces contact with ambient air; reduction of the artificial soil area contacting with air decreased population of micromycetes in 40 times. Cabbage leafs were free of pathogenic microflora. These results of the experiment helped develop recommendations on how to work out some units and systems in projectable greenhouse VITACYCLE-T

Modeling E. Coli release and transport in a creek during artificial high-flow events

USDA-ARS?s Scientific Manuscript database

In-stream fate and transport of E. Coli, is a leading indicator of microbial contamination of natural waters, and so needs to be understood to eventually minimize surface water contamination by microbial organisms. The objective of this work was to simulate E. Coli release and transport from soil se...

Plant community influence on soil microbial response after a wildfire in Sierra Nevada National Park (Spain).

PubMed

Bárcenas-Moreno, Gema; García-Orenes, Fuensanta; Mataix-Solera, Jorge; Mataix-Beneyto, Jorge

2016-12-15

Plant community influence on microbial response after fire has been studied in a Sierra Nevada National Park area affected by a wildfire in 2005. Two different plant communities adapted to different altitudes were selected to analyse possible differences on soil microbial recolonisation process after fire, in oak forest and high mountain shrub communities. Microbial abundance, activity and community composition were monitored to evaluate medium-term changes. Microbial abundance was studied by mean of microbial biomass carbon and plate count methods; microbial activity was analysed by microbial respiration and bacterial growth while microbial community composition was determined by analysing phospholipid fatty acid pattern. Under unburnt conditions oak forest showed higher nutrient content, pH and microbial abundance and activity values than the high mountain shrubs community. Different parameters studied showed different trends with time, highlighting important changes in microbial community composition in high mountain shrubs from first sampling to the second one. Post-fire recolonisation process was different depending on plant community studied. Highlighting fungal response and microbial activity were stimulated in burnt high mountain shrubs community whilst it was negatively affected in oak forest. Fire induced changes in oak forest were almost neutralized 20months after the fire, while high mountain shrubs community still showed fire-induced changes at the end of the study. Copyright © 2016 Elsevier B.V. All rights reserved.

Microbially reduced graphene oxide shows efficient electricity ecovery from artificial dialysis wastewater.

PubMed

Goto, Yuko; Yoshida, Naoko

2017-07-11

Anodes are crucial in determining the electricity recovery of microbial fuel cells (MFCs). In this study, graphene oxide (GO) was used as an anodic material for electricity recovery from artificial dialysis wastewater (ADWW). Anaerobic incubation of ADWW with GO for 21 days produced a hydrogel complex containing embedded microbial cells and microbially reduced GO (rGO). The rGO complex recovered 540 to 810 μA/cm 3 of catalytic current from ADWW after 10 days of electrochemical cultivation at 200 mV (vs. Ag/AgCl), which was approximately thirty times higher than that recovered from graphite felt (GF), a representative anode in MFCs. High-throughput sequencing analysis of prokaryotic 16S rRNA genes revealed a predominance of the Geobacter genus (35% of all prokaryotic sequences identified), particularly in the rGO complex after 20 days of polarization. The superior electricity recovery of the rGO complex was attributable to enhanced direct electron transfer via a well-developed biofilm, while indirect electron transfer via an electron mediator occurred in culture using GF.

Electricity generation from an inorganic sulfur compound containing mining wastewater by acidophilic microorganisms.

PubMed

Ni, Gaofeng; Christel, Stephan; Roman, Pawel; Wong, Zhen Lim; Bijmans, Martijn F M; Dopson, Mark

2016-09-01

Sulfide mineral processing often produces large quantities of wastewaters containing acid-generating inorganic sulfur compounds. If released untreated, these wastewaters can cause catastrophic environmental damage. In this study, microbial fuel cells were inoculated with acidophilic microorganisms to investigate whether inorganic sulfur compound oxidation can generate an electrical current. Cyclic voltammetry suggested that acidophilic microorganisms mediated electron transfer to the anode, and that electricity generation was catalyzed by microorganisms. A cation exchange membrane microbial fuel cell, fed with artificial wastewater containing tetrathionate as electron donor, reached a maximum whole cell voltage of 72 ± 9 mV. Stepwise replacement of the artificial anolyte with real mining process wastewater had no adverse effect on bioelectrochemical performance and generated a maximum voltage of 105 ± 42 mV. 16S rRNA gene sequencing of the microbial consortia resulted in sequences that aligned within the genera Thermoplasma, Ferroplasma, Leptospirillum, Sulfobacillus and Acidithiobacillus. This study opens up possibilities to bioremediate mining wastewater using microbial fuel cell technology. Copyright © 2016 The Authors. Published by Elsevier Masson SAS.. All rights reserved.

Networks of soil biota in a secondary succession gradient: Is it biodiversity or network structure that determines soil function?

NASA Astrophysics Data System (ADS)

Morriën, Elly; Hannula, Emilia; Snoek, Basten; Hol, Gera; van Veen, Hans; van der Putten, Wim

2017-04-01

Land abandonment is considered an effective tool for restoring biodiversity and ecosystem functions. However, thus far little attention is given to the role of soil biodiversity. Here, we present results of a soil biodiversity development and ecosystem functioning from a chonosequence of ex-arable fields in The Netherlands. These fields are typically managed by low-intensive grazing while undergoing a transition from an arable system into a species-rich grassland. We manipulated soil biodiversity to be able to couple biodiversity loss to loss of soil functions. We hypothesized that biodiversity loss would lead to less N uptake by plants and slower C transfer to microbes. A greenhouse mesocosm experiment was performed in which sterilized soils from the chronosequence were re-inoculated with a dilution series of soil suspensions (filtered to include only bacteria, fungi and protozoa) to manipulate soil diversity. These mesocosms were planted with a community of plants that naturally occur in all of the grasslands along the chronosequence. We measured microbial community development with TRFLP and sequencing, plant C, N and biomass and using dual labelled 15N ammonium nitrate (15NH415NO3) and 13C in the form of 13CO2 fed to the plants to assess the short term fate, turnover and retention of recent plant assimilated carbon and nitrogen in soil. The faith of the C and N were followed by sequential sampling of aboveground and belowground plant tissues and soil bacterial and fungal PLFA and NLFA biomarkers. With the first method the role of microbial diversity and soil on plant carbon assimilation and nitrogen uptake was evaluated. This was further related to the amount of recently photosynthesized carbon plants allocated to different microbial groups in soils. Microbial end-communities were pyrosequenced to evaluate the end diversity. In this study we showed the effects of the loss of soil biodiversity to C and N cycling in plants and microbes. Next to this manipulative experiment we did a field sampling of intact soil cores within the same chronosequence of ex-arable fields. We identified bacteria and fungi by pyrosequencing, while archaea were identified using TRFLP. The protists, micro-fauna, nematodes, enchytraeids and earthworms were extracted and morphologically identified until high taxonomic levels, often species level. In total, around 15 000 species were identified from the soils. We created a Spearman-rank correlation matrix based on abundance data of species which we visualized in a network categorized as recent, mid-term and long-term abandoned fields as an overview of the soil community present. After stable isotope probing using similar methods the soil food web structure was resolved by identifying the microbes using phospholipid markers and identifying soil fauna by morphology into similar groups as for the network analysis, both combined with isotopic measurements. We show that structural changes in the food web topology also leads to functional changes in the soil food web which can act as a driving force during land use change after human disturbance.

Albumin Apheresis for Artificial Liver Support: In Vitro Testing of a Novel Filter.

PubMed

Piatek, Tomasz; Giebultowicz, Joanna; Rüth, Marieke; Lemke, Horst-Dieter; Bonn, Florian; Wroczynski, Piotr; Malkowski, Piotr; Rozga, Jacek

2018-05-16

Currently there is no direct therapy for liver failure. We have previously described selective plasma exchange therapy using a hemofilter permeable to substances that have a molecular mass of up to 100 kDa. The proof-of-concept studies and a Phase I study in patients with decompensated cirrhosis demonstrated that hemofiltration using an albumin-leaking membrane is safe and effective in removing target molecules, alleviating severe encephalopathy and improving blood chemistry. In this study a novel large-pore filter for similar clinical application is described. The performance of the filter was studied in vitro; it was found to effectively remove a wide spectrum of pathogenic factors implicated in the pathophysiology of hepatic failure, including protein bound toxins and defective forms of circulating albumin. Data on mass transport characteristics and functionality using various modes of filtration and dialysis provide rationale for clinical evaluation of the filter for artificial liver support using albumin apheresis. © 2018 International Society for Apheresis, Japanese Society for Apheresis, and Japanese Society for Dialysis Therapy.

Poisson filtering of laser ranging data

NASA Technical Reports Server (NTRS)

Ricklefs, Randall L.; Shelus, Peter J.

1993-01-01

The filtering of data in a high noise, low signal strength environment is a situation encountered routinely in lunar laser ranging (LLR) and, to a lesser extent, in artificial satellite laser ranging (SLR). The use of Poisson statistics as one of the tools for filtering LLR data is described first in a historical context. The more recent application of this statistical technique to noisy SLR data is also described.

Bioavailability of five hydrophobic organic compounds to earthworms from sterile and non-sterile artificial soils.

PubMed

Šmídová, Klára; Kim, Sooyeon; Hofman, Jakub

2017-07-01

Bioaccumulation factors (BAFs) of organic pollutants to soil biota, often required by risk assessment, are mostly obtained in non-sterile laboratory-contaminated artificial soils. However, microbial degradation has been indicated by many authors to influence the fate of hydrophobic organic compounds (HOCs) in soils. A question arises if the microbial community of peat which is used for artificial soil preparation affects the measured values of BAFs. In this study the effect of soil microorganisms on bioavailability of HOCs was studied and a portion of each soil was sterilized by gamma irradiation. Results indicated that the sterilization process significantly affected the fate of polycyclic aromatic hydrocarbons (PAHs; phenanthrene and pyrene) and increased bioavailability of these compounds to earthworms with BAFs several times higher in the sterile soils compared to their non-sterile variants. This suggests that sterilization of soils can be used as the "worst-case scenario" for laboratory tests of toxicity or bioaccumulation of biodegradable HOCs such as PAHs. It represents a situation of limited microbial degradation resulting in higher bioavailable fractions to other organisms (e.g. invertebrates). This may be the case in soils where microbial communities face stresses caused by contamination or land management. The bioavailability of chlorinated HOCs (lindane, 4,4'-DDT and PCB 153) was not affected by sterilization, as their BAFs were similar in the sterile and non-sterile soils during the experiment. Copyright © 2017 Elsevier Ltd. All rights reserved.

Rhizosphere effect of colonizer plant species on the development of soil microbial community during primary succession on postmining sites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Elhottova, D.; Kristufek, V.; Maly, S.

2009-07-01

The impact of pioneer plant species Tussilago farfara on structural, functional, and growth characterization of microbial community colonizing the spoil colliery substrate was studied in a laboratory microcosm experiment. Microcosms consisting of spoil substrate (0.7 dm{sup 3} of tertiary alkaline clay sediment from Sokolov brown-coal mine area) from a pioneer site (without vegetation, 5 years after heaping) were cultivated in a greenhouse with one plant of this species. Plant roots substantially increased microbial diversity and biomass after one season (7 months) of cultivation. Roots influenced the microbial community and had nearly twice the size, higher growth, and metabolic potential inmore » comparison to the control. The development of microbial specialists improves the plant nutrient status. Bacterial nitrogen (N{sub 2}) fixators (Bradyrhizobium japonicum, Rhizobium radiobacter) and arbuscular mycorrhizal fungi were confirmed in the rhizosphere of Tussilago farfara.« less

Biodegradation of Microcystins during Gravity-Driven Membrane (GDM) Ultrafiltration

PubMed Central

Kohler, Esther; Villiger, Jörg; Posch, Thomas; Derlon, Nicolas; Shabarova, Tanja; Morgenroth, Eberhard; Pernthaler, Jakob; Blom, Judith F.

2014-01-01

Gravity-driven membrane (GDM) ultrafiltration systems require little maintenance: they operate without electricity at ultra-low pressure in dead-end mode and without control of the biofilm formation. These systems are already in use for water purification in some regions of the world where adequate treatment and distribution of drinking water is not readily available. However, many water bodies worldwide exhibit harmful blooms of cyanobacteria that severely lower the water quality due to the production of toxic microcystins (MCs). We studied the performance of a GDM system during an artificial Microcystis aeruginosa bloom in lake water and its simulated collapse (i.e., the massive release of microcystins) over a period of 21 days. Presence of live or destroyed cyanobacterial cells in the feed water decreased the permeate flux in the Microcystis treatments considerably. At the same time, the microbial biofilms on the filter membranes could successfully reduce the amount of microcystins in the filtrate below the critical threshold concentration of 1 µg L−1 MC for human consumption in three out of four replicates after 15 days. We found pronounced differences in the composition of bacterial communities of the biofilms on the filter membranes. Bacterial genera that could be related to microcystin degradation substantially enriched in the biofilms amended with microcystin-containing cyanobacteria. In addition to bacteria previously characterized as microcystin degraders, members of other bacterial clades potentially involved in MC degradation could be identified. PMID:25369266

Metagenomic profiling of gut microbial communities in both wild and artificially reared Bar-headed goose (Anser indicus).

PubMed

Wang, Wen; Zheng, Sisi; Sharshov, Kirill; Sun, Hao; Yang, Fang; Wang, Xuelian; Li, Laixing; Xiao, Zhixiong

2017-04-01

Bar-headed goose (Anser indicus), a species endemic to Asia, has become one of the most popular species in recent years for rare bird breeding industries in several provinces of China. There has been no information on the gut metagenome configuration in both wild and artificially reared Bar-headed geese, even though the importance of gut microbiome in vertebrate nutrient and energy metabolism, immune homeostasis and reproduction is widely acknowledged. In this study, metagenomic methods have been used to describe the microbial community structure and composition of functional genes associated with both wild and artificially reared Bar-headed goose. Taxonomic analyses revealed that Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes were the four most abundant phyla in the gut of Bar-headed geese. Bacteroidetes were significantly abundant in the artificially reared group compared to wild group. Through functional profiling, we found that artificially reared Bar-headed geese had higher bacterial gene content related to carbohydrate transport and metabolism, energy metabolism and coenzyme transport, and metabolism. A comprehensive gene catalog of Bar-headed geese metagenome was built, and the metabolism of carbohydrate, amino acid, nucleotide, and energy were found to be the four most abundant categories. These results create a baseline for future Bar-headed goose microbiology research, and make an original contribution to the artificial rearing of this bird. © 2016 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

The impact of cotton growing practices on soil microbiology and its relation to plant and soil health

NASA Astrophysics Data System (ADS)

Pereg, Lily

2013-04-01

Crop production and agricultural practices heavily impact the soil microbial communities, which differ among varying types of soils and environmental conditions. Soil-borne microbial communities in cotton production systems, as in every other cropping system, consist of microbial populations that may either be pathogenic, beneficial or neutral with respect to the cotton crop. Crop production practices have major roles in determining the composition of microbial communities and function of microbial populations in soils. The structure and function of any given microbial community is determined by various factors, including those that are influenced by farming and those not controlled by farming activities. Examples of the latter are environmental conditions such as soil type, temperature, daylight length and UV radiation, air humidity, atmospheric pressure and some abiotic features of the soil. On the other hand, crop production practices may determine other abiotic soil properties, such as water content, density, oxygen levels, mineral and elemental nutrient levels and the load of other crop-related soil amendments. Moreover, crop production highly influences the biotic properties of the soil and has a major role in determining the fate of soil-borne microbial communities associated with the crop plant. Various microbial strains react differently to the presence of certain plants and plant exudates. Therefore, the type of plant and crop rotations are important factors determining microbial communities. In addition, practice management, e.g. soil cultivation versus crop stubble retention, have a major effect on the soil conditions and, thus, on microbial community structure and function. All of the above-mentioned factors can lead to preferential selection of certain microbial population over others. It may affect not only the composition of microbial communities (diversity and abundance of microbial members) but also the function of the community (the ability of different microbes to perform certain activities). Therefore, agricultural practices may determine the ability of beneficial microbes to realise their plant growth promoting potential or the pathogenic expression of others. This presentation will review the current knowledge about the impact of cotton growing practices on microbial communities and soil health in different environments as well as endeavour to identify gaps worthwhile exploring in future research for promoting plant growth in healthy soils.

Denitrifying and diazotrophic community responses to artificial warming in permafrost and tallgrass prairie soils

DOE PAGES

Penton, Christopher R.; St. Louis, Derek; Pham, Amanda; ...

2015-07-21

Increasing temperatures have been shown to impact soil biogeochemical processes, although the corresponding changes to the underlying microbial functional communities are not well understood. Alterations in the nitrogen (N) cycling functional component are particularly important as N availability can affect microbial decomposition rates of soil organic matter and influence plant productivity. To assess changes in the microbial component responsible for these changes, the composition of the N-fixing (nifH), and denitrifying (nirS, nirK, nosZ) soil microbial communities was assessed by targeted pyrosequencing of functional genes involved in N cycling in two major biomes where the experimental effect of climate warming ismore » under investigation, a tallgrass prairie in Oklahoma (OK) and the active layer above permafrost in Alaska (AK). Raw reads were processed for quality, translated with frameshift correction, and a total of 313,842 amino acid sequences were clustered and linked to a nearest neighbor using reference datasets. The number of OTUs recovered ranged from 231 (NifH) to 862 (NirK). The N functional microbial communities of the prairie, which had experienced a decade of experimental warming were the most affected with changes in the richness and/or overall structure of NifH, NirS, NirK and NosZ. In contrast, the AK permafrost communities, which had experienced only 1 year of warming, showed decreased richness and a structural change only with the nirK-harboring bacterial community. A highly divergent nirK-harboring bacterial community was identified in the permafrost soils, suggesting much novelty, while other N functional communities exhibited similar relatedness to the reference databases, regardless of site. Lastly, prairie and permafrost soils also harbored highly divergent communities due mostly to differing major populations.« less

Denitrifying and diazotrophic community responses to artificial warming in permafrost and tallgrass prairie soils

DOE Office of Scientific and Technical Information (OSTI.GOV)

Penton, Christopher R.; St. Louis, Derek; Pham, Amanda

Increasing temperatures have been shown to impact soil biogeochemical processes, although the corresponding changes to the underlying microbial functional communities are not well understood. Alterations in the nitrogen (N) cycling functional component are particularly important as N availability can affect microbial decomposition rates of soil organic matter and influence plant productivity. To assess changes in the microbial component responsible for these changes, the composition of the N-fixing (nifH), and denitrifying (nirS, nirK, nosZ) soil microbial communities was assessed by targeted pyrosequencing of functional genes involved in N cycling in two major biomes where the experimental effect of climate warming ismore » under investigation, a tallgrass prairie in Oklahoma (OK) and the active layer above permafrost in Alaska (AK). Raw reads were processed for quality, translated with frameshift correction, and a total of 313,842 amino acid sequences were clustered and linked to a nearest neighbor using reference datasets. The number of OTUs recovered ranged from 231 (NifH) to 862 (NirK). The N functional microbial communities of the prairie, which had experienced a decade of experimental warming were the most affected with changes in the richness and/or overall structure of NifH, NirS, NirK and NosZ. In contrast, the AK permafrost communities, which had experienced only 1 year of warming, showed decreased richness and a structural change only with the nirK-harboring bacterial community. A highly divergent nirK-harboring bacterial community was identified in the permafrost soils, suggesting much novelty, while other N functional communities exhibited similar relatedness to the reference databases, regardless of site. Lastly, prairie and permafrost soils also harbored highly divergent communities due mostly to differing major populations.« less

Artificial and Solar UV Radiation Induces Strand Breaks and Cyclobutane Pyrimidine Dimers in Bacillus subtilis Spore DNA

PubMed Central

Slieman, Tony A.; Nicholson, Wayne L.

2000-01-01

The loss of stratospheric ozone and the accompanying increase in solar UV flux have led to concerns regarding decreases in global microbial productivity. Central to understanding this process is determining the types and amounts of DNA damage in microbes caused by solar UV irradiation. While UV irradiation of dormant Bacillus subtilis endospores results mainly in formation of the “spore photoproduct” 5-thyminyl-5,6-dihydrothymine, genetic evidence indicates that an additional DNA photoproduct(s) may be formed in spores exposed to solar UV-B and UV-A radiation (Y. Xue and W. L. Nicholson, Appl. Environ. Microbiol. 62:2221–2227, 1996). We examined the occurrence of double-strand breaks, single-strand breaks, cyclobutane pyrimidine dimers, and apurinic-apyrimidinic sites in spore DNA under several UV irradiation conditions by using enzymatic probes and neutral or alkaline agarose gel electrophoresis. DNA from spores irradiated with artificial 254-nm UV-C radiation accumulated single-strand breaks, double-strand breaks, and cyclobutane pyrimidine dimers, while DNA from spores exposed to artificial UV-B radiation (wavelengths, 290 to 310 nm) accumulated only cyclobutane pyrimidine dimers. DNA from spores exposed to full-spectrum sunlight (UV-B and UV-A radiation) accumulated single-strand breaks, double-strand breaks, and cyclobutane pyrimidine dimers, whereas DNA from spores exposed to sunlight from which the UV-B component had been removed with a filter (“UV-A sunlight”) accumulated only single-strand breaks and double-strand breaks. Apurinic-apyrimidinic sites were not detected in spore DNA under any of the irradiation conditions used. Our data indicate that there is a complex spectrum of UV photoproducts in DNA of bacterial spores exposed to solar UV irradiation in the environment. PMID:10618224

Sources of Variation in the Gut Microbial Community of Lycaeides melissa Caterpillars.

PubMed

Chaturvedi, Samridhi; Rego, Alexandre; Lucas, Lauren K; Gompert, Zachariah

2017-09-12

Microbes can mediate insect-plant interactions and have been implicated in major evolutionary transitions to herbivory. Whether microbes also play a role in more modest host shifts or expansions in herbivorous insects is less clear. Here we evaluate the potential for gut microbial communities to constrain or facilitate host plant use in the Melissa blue butterfly (Lycaeides melissa). We conducted a larval rearing experiment where caterpillars from two populations were fed plant tissue from two hosts. We used 16S rRNA sequencing to quantify the relative effects of sample type (frass versus whole caterpillar), diet (plant species), butterfly population and development (caterpillar age) on the composition and diversity of the caterpillar gut microbial communities, and secondly, to test for a relationship between microbial community and larval performance. Gut microbial communities varied over time (that is, with caterpillar age) and differed between frass and whole caterpillar samples. Diet (host plant) and butterfly population had much more limited effects on microbial communities. We found no evidence that gut microbe community composition was associated with caterpillar weight, and thus, our results provide no support for the hypothesis that variation in microbial community affects performance in L. melissa.

The role of soil microbiology in soil health

USDA-ARS?s Scientific Manuscript database

Microbial diversity in the rhizosphere is enormous. The complex plant-associated microbial community, or second genome of the plant, is crucial for plant health and soil function. Microbes are active in decomposition, release mineralizable nutrients, synthesize plant growth regulators, degrade/inact...

Effect of plant harvesting on the performance of constructed wetlands during winter: radial oxygen loss and microbial characteristics.

PubMed

Wang, Qian; Xie, Huijun; Zhang, Jian; Liang, Shuang; Ngo, Huu Hao; Guo, Wenshan; Liu, Chen; Zhao, Congcong; Li, Hao

2015-05-01

The aboveground tissue of plants is important for providing roots with constant photosynthetic resources. However, the aboveground biomass is usually harvested before winter to maintain the permanent removal of nutrients. In this work, the effects of harvest on plants' involvement in oxygen input as well as in microbial abundance and activity were investigated in detail. Three series of constructed wetlands with integrated plants ("unharvested"), harvested plants ("harvested"), and fully cleared plants ("cleared") were set up. Better performance was found in the unharvested units, with the radial oxygen loss (ROL) rates ranging from 0.05 to 0.59 μmol O₂/h/plant, followed by the harvested units that had relatively lower ROL rates (0.01 to 0.52 μmol O₂/h/plant). The cleared units had the lowest removal efficiency, which had no rhizome resources from the plants. The microbial population and activity were highest in the unharvested units, followed by the harvested and cleared units. Results showed that bacterial abundances and enhanced microbial activity were ten times higher on root surfaces compared with sands. These results indicate that late autumn harvesting of the aboveground biomass exhibited negative effects on plant ROL as well as on the microbial population and activity during the following winter.

Sniffing on microbes: diverse roles of microbial volatile organic compounds in plant health.

PubMed

Bitas, Vasileios; Kim, Hye-Seon; Bennett, Joan W; Kang, Seogchan

2013-08-01

Secreted proteins and metabolites play diverse and critical roles in organismal and organism-environment interactions. Volatile organic compounds (VOC) can travel far from the point of production through the atmosphere, porous soils, and liquid, making them ideal info-chemicals for mediating both short- and long-distance intercellular and organismal interactions. Critical ecological roles for animal- and plant-derived VOC in directing animal behaviors and for VOC as a language for plant-to-plant communication and regulators of various physiological processes have been well documented. Similarly, microbial VOC appear to be involved in antagonism, mutualism, intra- and interspecies regulation of cellular and developmental processes, and modification of their surrounding environments. However, the available knowledge of how microbial VOC affect other organisms is very limited. Evidence supporting diverse roles of microbial VOC with the focus on their impact on plant health is reviewed here. Given the vast diversity of microbes in nature and the critical importance of microbial communities associated with plants for their ecology and fitness, systematic exploration of microbial VOC and characterization of their biological functions and ecological roles will likely uncover novel mechanisms for controlling diverse biological processes critical to plant health and will also offer tangible practical benefits in addressing agricultural and environmental problems.

Spectral filtering for plant production

DOE Office of Scientific and Technical Information (OSTI.GOV)

Young, R.E.; McMahon, M.J.; Rajapakse, N.C.

1994-12-31

Research to date suggests that spectral filtering can be an effective alternative to chemical growth regulators for altering plant development. If properly implemented, it can be nonchemical and environmentally friendly. The aqueous CuSO{sub 4}, and CuCl{sub 2} solutions in channelled plastic panels have been shown to be effective filters, but they can be highly toxic if the solutions contact plants. Some studies suggest that spectral filtration limited to short EOD intervals can also alter plant development. Future research should be directed toward confirmation of the influence of spectral filters and exposure times on a broader range of plant species andmore » cultivars. Efforts should also be made to identify non-noxious alternatives to aqueous copper solutions and/or to incorporate these chemicals permanently into plastic films and panels that can be used in greenhouse construction. It would also be informative to study the impacts of spectral filters on insect and microbal populations in plant growth facilities. The economic impacts of spectral filtering techniques should be assessed for each delivery methodology.« less

Optimized Extraction Method To Remove Humic Acid Interferences from Soil Samples Prior to Microbial Proteome Measurements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Qian, Chen; Hettich, Robert L.

The microbial composition and their activities in soil environments play a critical role in organic matter transformation and nutrient cycling, perhaps most specifically with respect to impact on plant growth but also more broadly to global impact on carbon and nitrogen-cycling. Liquid chromatography coupled to high performance mass spectrometry provides a powerful approach to characterize soil microbiomes; however, the limited microbial biomass and the presence of abundant interferences in soil samples present major challenges to soil proteome extraction and subsequent MS measurement. To address some of the major issues, we have designed and optimized an experimental method to enhance microbialmore » proteome extraction concomitant with minimizing the soil-borne humic substances co-extraction from soils. Among the range of interferences, humic substances are often the worst in terms of adversely impacting proteome extraction and mass spectrometry measurement. Our approach employs an in-situ detergent-based microbial lysis / TCA precipitation coupled with an additional acidification precipitation step at the peptide level which efficiently removes humic acids. By combing filtration and pH adjustment of the final peptide solution, the remaining humic acids can be differentially precipitated and removed with a membrane filter, thereby leaving much cleaner proteolytic peptide samples for MS measurement. As a result, this modified method is a reliable and straight-forward protein extraction method that efficiently removes soil-borne humic substances without inducing proteome sample loss or reducing or biasing protein identification in mass spectrometry.« less

Optimized Extraction Method To Remove Humic Acid Interferences from Soil Samples Prior to Microbial Proteome Measurements

DOE PAGES

Qian, Chen; Hettich, Robert L.

2017-05-24

The microbial composition and their activities in soil environments play a critical role in organic matter transformation and nutrient cycling, perhaps most specifically with respect to impact on plant growth but also more broadly to global impact on carbon and nitrogen-cycling. Liquid chromatography coupled to high performance mass spectrometry provides a powerful approach to characterize soil microbiomes; however, the limited microbial biomass and the presence of abundant interferences in soil samples present major challenges to soil proteome extraction and subsequent MS measurement. To address some of the major issues, we have designed and optimized an experimental method to enhance microbialmore » proteome extraction concomitant with minimizing the soil-borne humic substances co-extraction from soils. Among the range of interferences, humic substances are often the worst in terms of adversely impacting proteome extraction and mass spectrometry measurement. Our approach employs an in-situ detergent-based microbial lysis / TCA precipitation coupled with an additional acidification precipitation step at the peptide level which efficiently removes humic acids. By combing filtration and pH adjustment of the final peptide solution, the remaining humic acids can be differentially precipitated and removed with a membrane filter, thereby leaving much cleaner proteolytic peptide samples for MS measurement. As a result, this modified method is a reliable and straight-forward protein extraction method that efficiently removes soil-borne humic substances without inducing proteome sample loss or reducing or biasing protein identification in mass spectrometry.« less

Taxonomy and Classification Scheme for Artificial Space Objects

DTIC Science & Technology

2013-09-01

filter UVB and spectroscopic measurements) and albedo (including polarimetry ). Earliest classifications of asteroids [17] were based on the filter...similarities of the asteroid colors to K0 to K2V stars. The first more complete asteroid taxonomy was based on a synthesis of polarimetry , radiometry, and

Microbial community diversity in agroforestry and grass vegetative filter strips

USDA-ARS?s Scientific Manuscript database

Vegetative filter strips (VFS) have long been promoted as a soil conservation practice that yields many additional environmental benefits. Most previous studies have focused primarily on the role of vegetation and/or soil physical properties in these ecosystem services. Few studies have investigated...

The use of sewage sludge and horticultural waste to develop artificial soil for plant cultivation in Singapore.

PubMed

Stabnikova, O; Goh, W-K; Ding, H-B; Tay, J-H; Wang, J-Y

2005-06-01

Greenhouse pot experiments were performed with Ipomoea aquatica (Kang Kong) to evaluate artificial soil produced from poor fertility subsoil, horticultural compost, and sewage sludge. The addition of horticultural compost and sewage sludge to subsoil substantially improved plant growth, improved the physical properties of subsoil and enriched subsoil by essential nutrients for plants. The effect was enhanced when the two ingredients were added to subsoil together. The highest yield of biomass of I. aquatica was observed in artificial soil prepared by mixing subsoil with 4% (wet weight/wet weight) of horticultural compost and 2% (dry weight/wet weight) of sewage sludge. The contents of heavy metals in plants, grown in the artificial soil, were significantly lower than toxic levels. The artificial soil could be recommended for urban landscaping and gardening in Singapore.

Microbial Survey of a Full-Scale, Biologically Active Filter for Treatment of Drinking Water

EPA Science Inventory

Biological nitrification has been used as a reliable technology in wastewater treatment for decades. Implementing biological approaches to drinking water treatment has faced resistance in the United States due in part to the lack of understanding of microbial processes and conce...

Effects of elevated O₃ on microbes in the rhizosphere of mycorrhizal snap bean with different O₃ sensitivity.

PubMed

Wang, Shuguang; Wang, Fei; Diao, Xiaojun; He, Liansheng

2014-02-01

Elevated ozone (O₃) generally affects microbial biomass and community structure in rhizosphere, but these effects are unclear in mycorrhizal plants because arbuscular mycorrhizal (AM) fungi often benefit microbial growth in the rhizosphere. Here, we investigate the effects of elevated O₃ on microbial biomass and community structure in the rhizosphere of mycorrhizal snap bean (Phaseolus vulgaris L.) with different O₃ sensitivity (R123: O₃-tolerant plant; S156: O₃-sensitive plant) based on the phospholipid fatty acids (PLFAs) method. Compared with ambient O₃, elevated O₃ significantly decreased mycorrhizal colonization rates in the 2 genotypes, especially in S156 plants. The wet masses of shoot and root were decreased by elevated O₃ in the 2 genotypes independent of AM inoculation, but they were higher in the mycorrhizal plant than in the nonmycorrhizal plant independent of O₃ concentration. Elevated O₃ significantly decreased the relative proportion of specific fungal PLFAs in the nonmycorrhizal plant, but this effect disappeared in the mycorrhizal plant. The relative proportions of specific PLFAs of other microbial groups (Gram-positive, Gram-negative, and actinomycete) in the rhizosphere and all specific PLFAs in the hyphosphere were not affected by elevated O₃ independent of AM inoculation. In the rhizosphere of the 2 genotypes, microbial community structure was changed by AM inoculation and elevated O₃ as well as by their interaction; in the hyphosphere, however, microbial community structure was changed by elevated O₃ only in R123 plants. It is concluded that AM inoculation can offset negative effect of elevated O₃ on fungal biomass but seems to enhance shift of microbial community structure in rhizosphere under elevated O₃.

Using Plant Phylogenetic Relatedness as a Predictor for Plants' Control on Soil Microbial Communities and Nitrogen Cycling

NASA Astrophysics Data System (ADS)

Potter, T.; Bowman, W. D.

2016-12-01

Despite the known importance of soil microbes and their influence on soil processes, a mechanistic understanding is still needed to predict how plants and soil microbes interact at scales that are relevant to community and ecosystem-scale processes. Closely related plant species have similar traits aboveground, but we don't know whether this is also true for belowground traits that affect soil microbial community structure and function. Determining how tightly plant phylogeny and plant functional traits are linked to soil microbial communities is a useful approach for discovering plant-microbe associations that are generalizable across plant species (a limitation of studies that employ a single or few plant species). Using this approach, we conducted a greenhouse study with seven congeneric grasses (genus Poa) and their native soils to examine whether plants' influences on microbial community structure were consistent with plant phylogenetic relatedness and/or plant functional traits. Seeds of each Poa species were planted in native soil (from the seed source population) as well as a homogenized soil from all seven populations. Additionally, a nitrogen treatment was added to address how an environmental change (such as nitrogen deposition) alters plant-microbe associations. Rhizosphere community composition of bacteria and fungi was obtained via marker gene sequencing to compare community composition across plant species. Patterns in plant-microbe associations across plant species reveal plant control on nutrient cycling via plant species' influence on microbial community structure. These results determine if we are ready to generalize about plant-microbe interactions at the genus level, an important stepping-stone to applying knowledge of plant-microbe interactions to larger ecological scales.

Desert Perennial Shrubs Shape the Microbial-Community Miscellany in Laimosphere and Phyllosphere Space.

PubMed

Martirosyan, Varsik; Unc, Adrian; Miller, Gad; Doniger, Tirza; Wachtel, Chaim; Steinberger, Yosef

2016-10-01

Microbial function, composition, and distribution play a fundamental role in ecosystem ecology. The interaction between desert plants and their associated microbes is expected to greatly affect their response to changes in this harsh environment. Using comparative analyses, we studied the impact of three desert shrubs, Atriplex halimus (A), Artemisia herba-alba (AHA), and Hammada scoparia (HS), on soil- and leaf-associated microbial communities. DNA extracted from the leaf surface and soil samples collected beneath the shrubs were used to study associated microbial diversity using a sequencing survey of variable regions of bacterial 16S rRNA and fungal ribosomal internal transcribed spacer (ITS1). We found that the composition of bacterial and fungal orders is plant-type-specific, indicating that each plant type provides a suitable and unique microenvironment. The different adaptive ecophysiological properties of the three plant species and the differential effect on their associated microbial composition point to the role of adaptation in the shaping of microbial diversity. Overall, our findings suggest a link between plant ecophysiological adaptation as a "temporary host" and the biotic-community parameters in extreme xeric environments.

Use of in-field bioreactors demonstrate groundwater filtration influences planktonic bacterial community assembly, but not biofilm composition

DOE PAGES

Christensen, Geoffrey A.; Moon, Ji Won; Veach, Allison M.; ...

2018-03-20

Using in-field bioreactors, we investigated the influence of exogenous microorganisms in groundwater planktonic and biofilm microbial communities as part of the Integrated Field Research Challenge (IFRC). After an acclimation period with source groundwater, bioreactors received either filtered (0.22 μM filter) or unfiltered well groundwater in triplicate and communities were tracked routinely for 23 days after filtration was initiated. To address geochemical influences, the planktonic phase was assayed periodically for protein, organic acids, physico-/geochemical measurements and bacterial community (via 16S rRNA gene sequencing), while biofilms (i.e. microbial growth on sediment coupons) were targeted for bacterial community composition at the completion ofmore » the experiment (23 d). Based on Bray-Curtis distance, planktonic bacterial community composition varied temporally and between treatments (filtered, unfiltered bioreactors). Notably, filtration led to an increase in the dominant genus, Zoogloea relative abundance over time within the planktonic community, while remaining relatively constant when unfiltered. At day 23, biofilm communities were more taxonomically and phylogenetically diverse and substantially different from planktonic bacterial communities; however, the biofilm bacterial communities were similar regardless of filtration. These results suggest that although planktonic communities were sensitive to groundwater filtration, bacterial biofilm communities were stable and resistant to filtration. Bioreactors are useful tools in addressing questions pertaining to microbial community assembly and succession. These data provide a first step in understanding how an extrinsic factor, such as a groundwater inoculation and flux of microbial colonizers, impact how microbial communities assemble in environmental systems.« less

Use of in-field bioreactors demonstrate groundwater filtration influences planktonic bacterial community assembly, but not biofilm composition

PubMed Central

Moon, JiWon; Veach, Allison M.; Mosher, Jennifer J.; Wymore, Ann M.; van Nostrand, Joy D.; Zhou, Jizhong; Hazen, Terry C.; Arkin, Adam P.; Elias, Dwayne A.

2018-01-01

Using in-field bioreactors, we investigated the influence of exogenous microorganisms in groundwater planktonic and biofilm microbial communities as part of the Integrated Field Research Challenge (IFRC). After an acclimation period with source groundwater, bioreactors received either filtered (0.22 μM filter) or unfiltered well groundwater in triplicate and communities were tracked routinely for 23 days after filtration was initiated. To address geochemical influences, the planktonic phase was assayed periodically for protein, organic acids, physico-/geochemical measurements and bacterial community (via 16S rRNA gene sequencing), while biofilms (i.e. microbial growth on sediment coupons) were targeted for bacterial community composition at the completion of the experiment (23 d). Based on Bray-Curtis distance, planktonic bacterial community composition varied temporally and between treatments (filtered, unfiltered bioreactors). Notably, filtration led to an increase in the dominant genus, Zoogloea relative abundance over time within the planktonic community, while remaining relatively constant when unfiltered. At day 23, biofilm communities were more taxonomically and phylogenetically diverse and substantially different from planktonic bacterial communities; however, the biofilm bacterial communities were similar regardless of filtration. These results suggest that although planktonic communities were sensitive to groundwater filtration, bacterial biofilm communities were stable and resistant to filtration. Bioreactors are useful tools in addressing questions pertaining to microbial community assembly and succession. These data provide a first step in understanding how an extrinsic factor, such as a groundwater inoculation and flux of microbial colonizers, impact how microbial communities assemble in environmental systems. PMID:29558522

Use of in-field bioreactors demonstrate groundwater filtration influences planktonic bacterial community assembly, but not biofilm composition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Christensen, Geoffrey A.; Moon, Ji Won; Veach, Allison M.

Using in-field bioreactors, we investigated the influence of exogenous microorganisms in groundwater planktonic and biofilm microbial communities as part of the Integrated Field Research Challenge (IFRC). After an acclimation period with source groundwater, bioreactors received either filtered (0.22 μM filter) or unfiltered well groundwater in triplicate and communities were tracked routinely for 23 days after filtration was initiated. To address geochemical influences, the planktonic phase was assayed periodically for protein, organic acids, physico-/geochemical measurements and bacterial community (via 16S rRNA gene sequencing), while biofilms (i.e. microbial growth on sediment coupons) were targeted for bacterial community composition at the completion ofmore » the experiment (23 d). Based on Bray-Curtis distance, planktonic bacterial community composition varied temporally and between treatments (filtered, unfiltered bioreactors). Notably, filtration led to an increase in the dominant genus, Zoogloea relative abundance over time within the planktonic community, while remaining relatively constant when unfiltered. At day 23, biofilm communities were more taxonomically and phylogenetically diverse and substantially different from planktonic bacterial communities; however, the biofilm bacterial communities were similar regardless of filtration. These results suggest that although planktonic communities were sensitive to groundwater filtration, bacterial biofilm communities were stable and resistant to filtration. Bioreactors are useful tools in addressing questions pertaining to microbial community assembly and succession. These data provide a first step in understanding how an extrinsic factor, such as a groundwater inoculation and flux of microbial colonizers, impact how microbial communities assemble in environmental systems.« less

An Artificial Diet for Cottonwood and Imported Williow leaf Beetles (Coleoptera: Chrysomelidae) and Comparative Performance on Poplar Foliage1,2

Treesearch

Leah S. Bauer; Joann Meerschaert; Thomas O. Forrester

1989-01-01

An artificial diet was developed for labortory rearing of the cottonwood leaf beetle, Chrysomela scripta F., and the imported willow leaf beetle, Plagiodera versicolira (Laicharting). To reduce microbial contamination of the media, procedures were developed for the separating egg masses and sterilizing egg surfaces. Cottonwood leaf...

Isolating Flow-field Discontinuities while Preserving Monotonicity and High-order Accuracy on Cartesian Meshes

DTIC Science & Technology

2017-01-09

2017 Distribution A – Approved for public release; Distribution Unlimited. PA Clearance 17030 Introduction • Filtering schemes offer a less...dissipative alternative to the standard artificial dissipation operators when applied to high- order spatial/temporal schemes • Limiting Fact: Filters impart...systems require a preconditioned dual-time framework to be solved efficiently • Limiting Fact: Filtering cannot be applied only at the physical- time

Carbon and nitrogen limitation explain the contrasting responses of rhizospheric N-cycling microbial communities to maize inoculation by Azospirillum lipoferum CRT1

NASA Astrophysics Data System (ADS)

Florio, Alessandro; Pommier, Thomas; Gervaix, Jonathan; Bréfort, Caroline; Bérard, Annette; Le Roux, Xavier

2017-04-01

Introduction Maize inoculation with the plant-growth promoting rhizobacterium Azospirillum stimulates root growth and carbon, C, exudation, thereby enabling a better exploitation of soil and enhancing plant uptake of nitrogen, N. This can modulate the availability of N in the rhizosphere, by enhancing plant-microbe competition for N and modifying rhizosphere environmental variables important for N-cycling microbial communities, i.e. the amount of soil mineral N and oxygen availability. We tested the hypothesis that inoculation-induced stimulation of root N uptake and C exudation would enhance plant competition over microorganisms for N while increasing C availability for heterotrophs, thus leading to (i) a decrease of nitrifier abundance and activity, and (ii) a decrease or increase of denitrifier abundance and activity depending on the level of denitrifier limitation by N and C. Methods The extent of inoculation-induced changes in microbial activities (potential nitrification and denitrification), abundances and diversity of (de)nitrifiers as well as in root functional traits was assessed at 4 dates over two consecutive years in a multi-site field trial. Measurements were performed for the 6- and 12-leaves maize stages. In a second experiment, we artificially altered the level of denitrifier limitation by N and C in a greenhouse pot experiment by applying synthetic root exudates to inoculated and non-inoculated maize plants. Inoculation-induced response to nutrient limitation on microbial N-related activities and abundances was assessed for the 6-leaves stage maizeplants. Results Inoculation resulted in an idiosyncratic response of nitrification and nitrifier (AOA, AOB) abundance, which varied from one sampling date to another at a given site, and between sites and treatments at a given date. Modifications of water balance and soil moisture rather than increased plant-nitrifiers competition for soil NH4+ were the main drivers of nitrification. Conversely, inoculation-induced changes in denitrifier activity and abundance (nirK, nirS) were consistent across sites and ranged from -23% to +84% depending on sites. Particularly, in soils with high C limitation levels, inoculation increased nirS-denitrifier abundance and denitrification, likely by stimulating root C exudation. Conversely, in soils with lower C limitation, the stimulating effect of inoculation on root C exudation was less critical for denitrifiers whereas the increased competition between roots and denitrifiers for NO3- became prominent, thus resulting in slightly decreased nirS-denitrifier abundance and denitrification. Pot experiment results revealed that the inoculation effect on denitrification decreased with increased amount of root exudates-like amended to soil. Discussion Maize seed inoculation with the beneficial Azospirillum lipoferum CRT1 can be a sustainable, though soil-specific, agricultural practice providing both beneficial agronomic and environmental effects. Our findings may indicate that the crop seed inoculation practice would increase potential N2O losses from agricultural soils where denitrifiers are highly C-limited. However, our results also demonstrate that the responses of nitrite reducers and N2O reducers to inoculation are tightly coupled, and that inoculation thus does not necessarily represent a risk for increased N2O losses from C-limited soils. Finally, the nirS-denitrifier abundance to microbial basal respiration ratio could be successfully used as a proxy of gaseous-N losses through denitrification from the soil-plant system following inoculation.

Integrating plant-microbe interactions to understand soil C stabilization with the MIcrobial-MIneral Carbon Stabilization model (MIMICS)

NASA Astrophysics Data System (ADS)

Grandy, Stuart; Wieder, Will; Kallenbach, Cynthia; Tiemann, Lisa

2014-05-01

If soil organic matter is predominantly microbial biomass, plant inputs that build biomass should also increase SOM. This seems obvious, but the implications fundamentally change how we think about the relationships between plants, microbes and SOM. Plant residues that build microbial biomass are typically characterized by low C/N ratios and high lignin contents. However, plants with high lignin contents and high C/N ratios are believed to increase SOM, an entrenched idea that still strongly motivates agricultural soil management practices. Here we use a combination of meta-analysis with a new microbial-explicit soil biogeochemistry model to explore the relationships between plant litter chemistry, microbial communities, and SOM stabilization in different soil types. We use the MIcrobial-MIneral Carbon Stabilization (MIMICS) model, newly built upon the Community Land Model (CLM) platform, to enhance our understanding of biology in earth system processes. The turnover of litter and SOM in MIMICS are governed by the activity of r- and k-selected microbial groups and temperature sensitive Michaelis-Menten kinetics. Plant and microbial residues are stabilized short-term by chemical recalcitrance or long-term by physical protection. Fast-turnover litter inputs increase SOM by >10% depending on temperature in clay soils, and it's only in sandy soils devoid of physical protection mechanisms that recalcitrant inputs build SOM. These results challenge centuries of lay knowledge as well as conventional ideas of SOM formation, but are they realistic? To test this, we conducted a meta-analysis of the relationships between the chemistry of plant liter inputs and SOM concentrations. We find globally that the highest SOM concentrations are associated with plant inputs containing low C/N ratios. These results are confirmed by individual tracer studies pointing to greater stabilization of low C/N ratio inputs, particularly in clay soils. Our model and meta-analysis results suggest that current ideas about plant-microbe-SOM relationships are unraveling. If so, our reconsideration of the mechanisms stabilizing SOM will also challenge long-held views about how to optimize plant community management to increase SOM.

Veggie ISS Validation Test Results and Produce Consumption

NASA Technical Reports Server (NTRS)

Massa, Gioia; Hummerick, Mary; Spencer, LaShelle; Smith, Trent

2015-01-01

The Veggie vegetable production system flew to the International Space Station (ISS) in the spring of 2014. The first set of plants, Outredgeous red romaine lettuce, was grown, harvested, frozen, and returned to Earth in October. Ground control and flight plant tissue was sub-sectioned for microbial analysis, anthocyanin antioxidant phenolic analysis, and elemental analysis. Microbial analysis was also performed on samples swabbed on orbit from plants, Veggie bellows, and plant pillow surfaces, on water samples, and on samples of roots, media, and wick material from two returned plant pillows. Microbial levels of plants were comparable to ground controls, with some differences in community composition. The range in aerobic bacterial plate counts between individual plants was much greater in the ground controls than in flight plants. No pathogens were found. Anthocyanin concentrations were the same between ground and flight plants, while antioxidant and phenolic levels were slightly higher in flight plants. Elements varied, but key target elements for astronaut nutrition were similar between ground and flight plants. Aerobic plate counts of the flight plant pillow components were significantly higher than ground controls. Surface swab samples showed low microbial counts, with most below detection limits. Flight plant microbial levels were less than bacterial guidelines set for non-thermostabalized food and near or below those for fungi. These guidelines are not for fresh produce but are the closest approximate standards. Forward work includes the development of standards for space-grown produce. A produce consumption strategy for Veggie on ISS includes pre-flight assessments of all crops to down select candidates, wiping flight-grown plants with sanitizing food wipes, and regular Veggie hardware cleaning and microbial monitoring. Produce then could be consumed by astronauts, however some plant material would be reserved and returned for analysis. Implementation of this plan is a step toward developing pick-and-eat food production to supplement the packaged diet on ISS and for future exploration missions where plants could make up a larger portion of the diet. Supported by NASA Space Biology Program.

Soil and plant factors driving the community of soil-borne microorganisms across chronosequences of secondary succession of chalk grasslands with a neutral pH.

PubMed

Kuramae, Eiko; Gamper, Hannes; van Veen, Johannes; Kowalchuk, George

2011-08-01

Although soil pH has been shown to be an important factor driving microbial communities, relatively little is known about the other potentially important factors that shape soil-borne microbial community structure. This study examined plant and microbial communities across a series of neutral pH fields (pH=7.0-7.5) representing a chronosequence of secondary succession after former arable fields were taken out of production. These fields ranged from 17 to >66 years since the time of abandonment, and an adjacent arable field was included as a reference. Hierarchical clustering analysis, nonmetric multidimensional scaling and analysis of similarity of 52 different plant species showed that the plant community composition was significantly different in the different chronosequences, and that plant species richness and diversity increased with time since abandonment. The microbial community structure, as analyzed by phylogenetic microarrays (PhyloChips), was significantly different in arable field and the early succession stage, but no distinct microbial communities were observed for the intermediate and the late succession stages. The most determinant factors in shaping the soil-borne microbial communities were phosphorous and NH(4)(+). Plant community composition and diversity did not have a significant effect on the belowground microbial community structure or diversity. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Habitat Fragmentation can Modulate Drought Effects on the Plant-soil-microbial System in Mediterranean Holm Oak (Quercus ilex) Forests.

PubMed

Flores-Rentería, Dulce; Curiel Yuste, Jorge; Rincón, Ana; Brearley, Francis Q; García-Gil, Juan Carlos; Valladares, Fernando

2015-05-01

Ecological transformations derived from habitat fragmentation have led to increased threats to above-ground biodiversity. However, the impacts of forest fragmentation on soils and their microbial communities are not well understood. We examined the effects of contrasting fragment sizes on the structure and functioning of soil microbial communities from holm oak forest patches in two bioclimatically different regions of Spain. We used a microcosm approach to simulate the annual summer drought cycle and first autumn rainfall (rewetting), evaluating the functional response of a plant-soil-microbial system. Forest fragment size had a significant effect on physicochemical characteristics and microbial functioning of soils, although the diversity and structure of microbial communities were not affected. The response of our plant-soil-microbial systems to drought was strongly modulated by the bioclimatic conditions and the fragment size from where the soils were obtained. Decreasing fragment size modulated the effects of drought by improving local environmental conditions with higher water and nutrient availability. However, this modulation was stronger for plant-soil-microbial systems built with soils from the northern region (colder and wetter) than for those built with soils from the southern region (warmer and drier) suggesting that the responsiveness of the soil-plant-microbial system to habitat fragmentation was strongly dependent on both the physicochemical characteristics of soils and the historical adaptation of soil microbial communities to specific bioclimatic conditions. This interaction challenges our understanding of future global change scenarios in Mediterranean ecosystems involving drier conditions and increased frequency of forest fragmentation.

"Artificial But Better Than Nothing".

PubMed

Blaschke, Sarah; O'Callaghan, Clare C; Schofield, Penelope

2017-04-01

To investigate patient, staff, and carer responses to an environmental intervention in an oncology clinic waiting room and evaluate the acceptability of artificial plant materials. Design Postintervention: Cross-sectional survey study. Oncology outpatient clinic waiting room located in a metropolitan comprehensive cancer center in Australia. Observer ratings of perceived qualities and effects of lifelike (fake) plants while spending time in the waiting room. Convenience sample ( N = 143) consisted of 73 cancer patients, 13 staff, 52 carers, and 5 "others" aged between 24 and 89 years ( M = 56, SD = 14.5). Artificial plant arrangements, hanging installations, two movable green walls, and one rock garden on wheels placed throughout the outpatients' clinic waiting room. Eighty-one percent (115/142) of respondents noticed the green features when first entering the waiting room and 67% (90/134) noticed they were artificial. Eighty-one percent (115/142) indicated "like/like a lot" when reporting their first reaction to the green features. Forty-eight percent (68/143) were positively affected and 23% (33/143) were very positively affected. Eighty-one percent (110/135) agreed/strongly agreed that "The greenery brightens the waiting room," 62% (80/130) agreed/strongly agreed that they "prefer living plants," and 76% (101/133) agreed/strongly agreed that "'lifelike' plants are better than no plants." Comments included mostly positive appraisals and occasional adverse reactions to artificial plants. No significant differences were found between patients', staff, and carers' reactions. The environmental intervention positively impacted patients', staff, and carers' perceptions of the oncology waiting room environment. Patients, staff, and carers mostly accepted artificial plants as an alternative design solution to real plants.

Artificial neural network (ANN)-based prediction of depth filter loading capacity for filter sizing.

PubMed

Agarwal, Harshit; Rathore, Anurag S; Hadpe, Sandeep Ramesh; Alva, Solomon J

2016-11-01

This article presents an application of artificial neural network (ANN) modelling towards prediction of depth filter loading capacity for clarification of a monoclonal antibody (mAb) product during commercial manufacturing. The effect of operating parameters on filter loading capacity was evaluated based on the analysis of change in the differential pressure (DP) as a function of time. The proposed ANN model uses inlet stream properties (feed turbidity, feed cell count, feed cell viability), flux, and time to predict the corresponding DP. The ANN contained a single output layer with ten neurons in hidden layer and employed a sigmoidal activation function. This network was trained with 174 training points, 37 validation points, and 37 test points. Further, a pressure cut-off of 1.1 bar was used for sizing the filter area required under each operating condition. The modelling results showed that there was excellent agreement between the predicted and experimental data with a regression coefficient (R 2 ) of 0.98. The developed ANN model was used for performing variable depth filter sizing for different clarification lots. Monte-Carlo simulation was performed to estimate the cost savings by using different filter areas for different clarification lots rather than using the same filter area. A 10% saving in cost of goods was obtained for this operation. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:1436-1443, 2016. © 2016 American Institute of Chemical Engineers.

Context dependency and saturating effects of loss of rare soil microbes on plant productivity.

PubMed

Hol, W H Gera; de Boer, Wietse; de Hollander, Mattias; Kuramae, Eiko E; Meisner, Annelein; van der Putten, Wim H

2015-01-01

Land use intensification is associated with loss of biodiversity and altered ecosystem functioning. Until now most studies on the relationship between biodiversity and ecosystem functioning focused on random loss of species, while loss of rare species that usually are the first to disappear received less attention. Here we test if the effect of rare microbial species loss on plant productivity depends on the origin of the microbial soil community. Soils were sampled from three land use types at two farms. Microbial communities with increasing loss of rare species were created by inoculating sterilized soils with serially diluted soil suspensions. After 8 months of incubation, the effects of the different soil communities on abiotic soil properties, soil processes, microbial community composition, and plant productivity was measured. Dilution treatments resulted in increasing species loss, which was in relation to abundance of bacteria in the original field soil, without affecting most of the other soil parameters and processes. Microbial species loss affected plant biomass positively, negatively or not at all, depending on soil origin, but not on land use history. Even within fields the effects of dilution on plant biomass varied between replicates, suggesting heterogeneity in microbial community composition. The effects of medium and severe species loss on plant biomass were similar, pointing toward a saturating effect of species loss. We conclude that changes in the composition of the soil microbial community, including rare species loss, can affect plant productivity, depending on the composition of the initial microbial community. Future work on the relation between function and species loss effects should address this variation by including multiple sampling origins.

Empirical evidence that soil carbon formation from plant inputs is positively related to microbial growth

Treesearch

Mark A. Bradford; Ashley D. Keiser; Christian A. Davies; Calley A. Mersmann; Michael S. Strickland

2012-01-01

Plant-carbon inputs to soils in the form of dissolved sugars, organic acids and amino acids fuel much of heterotrophic microbial activity belowground. Initial residence times of these compounds in the soil solution are on the order of hours, with microbial uptake a primary removal mechanism. Through microbial biosynthesis, the dissolved compounds become dominant...

Evaluation of a membrane bioreactor system as post-treatment in waste water treatment for better removal of micropollutants.

PubMed

Arriaga, Sonia; de Jonge, Nadieh; Nielsen, Marc Lund; Andersen, Henrik Rasmus; Borregaard, Vibeke; Jewel, Kevin; Ternes, Thomas A; Nielsen, Jeppe Lund

2016-12-15

Organic micropollutants (OMPs) such as pharmaceuticals are persistent pollutants that are only partially degraded in waste water treatment plants (WWTPs). In this study, a membrane bioreactor (MBR) system was used as a polishing step on a full-scale WWTP, and its ability to remove micropollutants was examined together with the development and stability of the microbial community. Two stages of operation were studied during a period of 9 months, one with (S1) and one without (S2) the addition of exogenous OMPs. Ibuprofen and naproxen had the highest degradation rates with values of 248 μg/g VSS ·h and 71 μg/g VSS ·h, whereas diclofenac was a more persistent OMP (7.28 μg/g VSS ·h). Mineralization of 14 C-labeled OMPs in batch kinetic experiments indicates that higher removal rates (∼0.8 ng/mg T SS ·h) with a short lag phase can be obtained when artificial addition of organic micropollutants was performed. Similar microbial populations dominated S1 and S2, despite the independent operations. Hydrogenophaga, Nitrospira, p55-a5, the actinobacterial Tetrasphaera, Propionicimonas, Fodinicola, and Candidatus Microthrix were the most abundant groups in the polishing MBR. Finally, potential microbial candidates for ibuprofen and naproxen degradation are proposed. Copyright © 2016 Elsevier Ltd. All rights reserved.

Preparation of BAC libraries from marine microbial populations.

PubMed

Sabehi, Gazalah; Béjà, Oded

2013-01-01

A protocol is presented here for the construction of BAC (bacterial artificial chromosome) libraries from planktonic microbial communities collected in marine environments. The protocol describes the collection and preparation of the planktonic microbial cells, high molecular weight DNA purification from those cells, the preparation of the BAC vector, and the special ligation and electrotransformation procedures required for successful library preparation. With small modifications, this protocol can be applied to microbes collected from other environments. © 2013 Elsevier Inc. All rights reserved.

Description of the microbial ecology evaluation device, flight equipment, and ground transporter

NASA Technical Reports Server (NTRS)

Chassay, C. E.; Taylor, G. R.

1973-01-01

Exposure of test systems in space required the fabrication of specialized hardware termed a Microbial Ecology Evaluation Device that had individual test chambers and a complex optical filter system. The characteristics of this device and the manner in which it was deployed in space are described.

Influence of corn, switchgrass, and prairie cropping systems on soil microbial communities in the upper Midwest of the United States

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jesus, Ederson da C.; Liang, Chao; Quensen, John F.

Because soil microbes drive many of the processes underpinning ecosystem services provided by soils, understanding how cropping systems affect soil microbial communities is important for productive and sustainable management. We characterized and compared soil microbial communities under restored prairie and three potential cellulosic biomass crops (corn, switchgrass, and mixed prairie grasses) in two spatial experimental designs – side-by-side plots where plant communities were in their second year since establishment (i.e., intensive sites) and regionally distributed fields where plant communities had been in place for at least 10 years (i.e., extensive sites). We assessed microbial community structure and composition using lipidmore » analysis, pyrosequencing of rRNA genes (targeting fungi, bacteria, archaea, and lower eukaryotes), and targeted metagenomics of nifH genes. For the more recently established intensive sites, soil type was more important than plant community in determining microbial community structure, while plant community was the more important driver of soil microbial communities for the older extensive sites where microbial communities under corn were clearly differentiated from those under switchgrass and restored prairie. Here, bacterial and fungal biomasses, especially biomass of arbuscular mycorrhizal fungi, were higher under perennial grasses and restored prairie, suggesting a more active carbon pool and greater microbial processing potential, which should be beneficial for plant acquisition and ecosystem retention of carbon, water, and nutrients.« less

Influence of corn, switchgrass, and prairie cropping systems on soil microbial communities in the upper Midwest of the United States

DOE PAGES

Jesus, Ederson da C.; Liang, Chao; Quensen, John F.; ...

2015-06-28

Because soil microbes drive many of the processes underpinning ecosystem services provided by soils, understanding how cropping systems affect soil microbial communities is important for productive and sustainable management. We characterized and compared soil microbial communities under restored prairie and three potential cellulosic biomass crops (corn, switchgrass, and mixed prairie grasses) in two spatial experimental designs – side-by-side plots where plant communities were in their second year since establishment (i.e., intensive sites) and regionally distributed fields where plant communities had been in place for at least 10 years (i.e., extensive sites). We assessed microbial community structure and composition using lipidmore » analysis, pyrosequencing of rRNA genes (targeting fungi, bacteria, archaea, and lower eukaryotes), and targeted metagenomics of nifH genes. For the more recently established intensive sites, soil type was more important than plant community in determining microbial community structure, while plant community was the more important driver of soil microbial communities for the older extensive sites where microbial communities under corn were clearly differentiated from those under switchgrass and restored prairie. Here, bacterial and fungal biomasses, especially biomass of arbuscular mycorrhizal fungi, were higher under perennial grasses and restored prairie, suggesting a more active carbon pool and greater microbial processing potential, which should be beneficial for plant acquisition and ecosystem retention of carbon, water, and nutrients.« less

Microbial genome-enabled insights into plant-microorganism interactions.

PubMed

Guttman, David S; McHardy, Alice C; Schulze-Lefert, Paul

2014-12-01

Advances in genome-based studies on plant-associated microorganisms have transformed our understanding of many plant pathogens and are beginning to greatly widen our knowledge of plant interactions with mutualistic and commensal microorganisms. Pathogenomics has revealed how pathogenic microorganisms adapt to particular hosts, subvert innate immune responses and change host range, as well as how new pathogen species emerge. Similarly, culture-independent community profiling methods, coupled with metagenomic and metatranscriptomic studies, have provided the first insights into the emerging field of research on plant-associated microbial communities. Together, these approaches have the potential to bridge the gap between plant microbial ecology and plant pathology, which have traditionally been two distinct research fields.

11. DETAIL VIEW OF FILTER TANK IN FILTRATION PLANT (#1773), ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

11. DETAIL VIEW OF FILTER TANK IN FILTRATION PLANT (#1773), LOOKING NORTHWEST - Presidio Water Treatment Plant, Filtration Plant, East of Lobos Creek at Baker Beach, San Francisco, San Francisco County, CA

Examining responses of ecosystem carbon exchange to environmental changes using particle filtering mathod

NASA Astrophysics Data System (ADS)

Yokozawa, M.

2017-12-01

Attention has been paid to the agricultural field that could regulate ecosystem carbon exchange by water management and residual treatments. However, there have been less known about the dynamic responses of the ecosystem to environmental changes. In this study, focussing on paddy field, where CO2 emissions due to microbial decomposition of organic matter are suppressed and alternatively CH4 emitted under flooding condition during rice growth season and subsequently CO2 emission following the fallow season after harvest, the responses of ecosystem carbon exchange were examined. We conducted model data fusion analysis for examining the response of cropland-atmosphere carbon exchange to environmental variation. The used model consists of two sub models, paddy rice growth sub-model and soil decomposition sub-model. The crop growth sub-model mimics the rice plant growth processes including formation of reproductive organs as well as leaf expansion. The soil decomposition sub-model simulates the decomposition process of soil organic carbon. Assimilating the data on the time changes in CO2 flux measured by eddy covariance method, rice plant biomass, LAI and the final yield with the model, the parameters were calibrated using a stochastic optimization algorithm with a particle filter method. The particle filter method, which is one of the Monte Carlo filters, enable us to evaluating time changes in parameters based on the observed data until the time and to make prediction of the system. Iterative filtering and prediction with changing parameters and/or boundary condition enable us to obtain time changes in parameters governing the crop production as well as carbon exchange. In this study, we focused on the parameters related to crop production as well as soil carbon storage. As the results, the calibrated model with estimated parameters could accurately predict the NEE flux in the subsequent years. The temperature sensitivity, denoted by Q10s in the decomposition rate of soil organic carbon (SOC) were obtained as 1.4 for no cultivation period and 2.9 for cultivation period (submerged soil condition in flooding season). It suggests that the response of ecosystem carbon exchange differs due to SOC decomposition process which is sensitive to environmental variation during paddy rice cultivation period.

Soil microbial species loss affects plant biomass and survival of an introduced bacterial strain, but not inducible plant defences.

PubMed

Kurm, Viola; van der Putten, Wim H; Pineda, Ana; Hol, W H Gera

2018-02-12

Plant growth-promoting rhizobacteria (PGPR) strains can influence plant-insect interactions. However, little is known about the effect of changes in the soil bacterial community in general and especially the loss of rare soil microbes on these interactions. Here, the influence of rare soil microbe reduction on induced systemic resistance (ISR) in a wild ecotype of Arabidopsis thaliana against the aphid Myzus persicae was investigated. To create a gradient of microbial abundances, soil was inoculated with a serial dilution of a microbial community and responses of Arabidopsis plants that originated from the same site as the soil microbes were tested. Plant biomass, transcription of genes involved in plant defences, and insect performance were measured. In addition, the effects of the PGPR strain Pseudomonas fluorescens SS101 on plant and insect performance were tested under the influence of the various soil dilution treatments. Plant biomass showed a hump-shaped relationship with soil microbial community dilution, independent of aphid or Pseudomonas treatments. Both aphid infestation and inoculation with Pseudomonas reduced plant biomass, and led to downregulation of PR1 (salicylic acid-responsive gene) and CYP79B3 (involved in synthesis of glucosinolates). Aphid performance and gene transcription were unaffected by soil dilution. Neither the loss of rare microbial species, as caused by soil dilution, nor Pseudomonas affect the resistance of A. thaliana against M. persicae. However, both Pseudomonas survival and plant biomass respond to rare species loss. Thus, loss of rare soil microbial species can have a significant impact on both above- and below-ground organisms. © The Author(s) 2018. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Microbial activity promotes carbon storage in temperate soils

NASA Astrophysics Data System (ADS)

Lange, Markus; Eisenhauer, Nico; Sierra, Carlos; Gleixner, Gerd

2014-05-01

Soils are one of the most important carbon sink and sources. Soils contain up to 3/4 of all terrestrial carbon. Beside physical aspects of soil properties (e.g. soil moisture and texture) plants play an important role in carbon sequestration. The positive effect of plant diversity on carbon storage is already known, though the underlying mechanisms remain still unclear. In the frame of the Jena Experiment, a long term biodiversity experiment, we are able to identify these processes. Nine years after an land use change from an arable field to managed grassland the mean soil carbon concentrations increased towards the concentrations of permanent meadows. The increase was positively linked to a plant diversity gradient. High diverse plant communities produce more biomass, which in turn results in higher amounts of litter inputs. The plant litter is transferred to the soil organic matter by the soil microbial community. However, higher plant diversity also causes changes in micro-climatic condition. For instance, more diverse plant communities have a more dense vegetation structure, which reduced the evaporation of soils surface and thus, increases soil moisture in the top layer. Higher inputs and higher soil moisture lead to an enlarged respiration of the soil microbial community. Most interestingly, the carbon storage in the Jena Experiment was much more related to microbial respiration than to plant root inputs. Moreover, using radiocarbon, we found a significant younger carbon age in soils of more diverse plant communities than in soils of lower diversity, indicating that more fresh carbon is integrated into the carbon pool. Putting these findings together, we could show, that the positive link between plant diversity and carbon storage is due to a higher microbial decomposition of plant litter, pointing out that carbon storage in soils is a function of the microbial community.

Phyllosphere Microbiota Composition and Microbial Community Transplantation on Lettuce Plants Grown Indoors

PubMed Central

Williams, Thomas R.

2014-01-01

ABSTRACT The aerial surfaces of plants, or phyllosphere, are microbial habitats important to plant and human health. In order to accurately investigate microbial interactions in the phyllosphere under laboratory conditions, the composition of the phyllosphere microbiota should be representative of the diversity of microorganisms residing on plants in nature. We found that Romaine lettuce grown in the laboratory contained 10- to 100-fold lower numbers of bacteria than age-matched, field-grown lettuce. The bacterial diversity on laboratory-grown plants was also significantly lower and contained relatively higher proportions of Betaproteobacteria as opposed to the Gammaproteobacteria-enriched communities on field lettuce. Incubation of field-grown Romaine lettuce plants in environmental growth chambers for 2 weeks resulted in bacterial cell densities and taxa similar to those on plants in the field but with less diverse bacterial populations overall. In comparison, the inoculation of laboratory-grown Romaine lettuce plants with either freshly collected or cryopreserved microorganisms recovered from field lettuce resulted in the development of a field-like microbiota on the lettuce within 2 days of application. The survival of an inoculated strain of Escherichia coli O157:H7 was unchanged by microbial community transfer; however, the inoculation of E. coli O157:H7 onto those plants resulted in significant shifts in the abundance of certain taxa. This finding was strictly dependent on the presence of a field-associated as opposed to a laboratory-associated microbiota on the plants. Phyllosphere microbiota transplantation in the laboratory will be useful for elucidating microbial interactions on plants that are important to agriculture and microbial food safety. PMID:25118240

Spacelab J air filter debris analysis

NASA Technical Reports Server (NTRS)

Obenhuber, Donald C.

1993-01-01

Filter debris from the Spacelab module SLJ of STS-49 was analyzed for microbial contamination. Debris for cabin and avionics filters was collected by Kennedy Space Center personnel on 1 Oct. 1992, approximately 5 days postflight. The concentration of microorganisms found was similar to previous Spacelab missions averaging 7.4E+4 CFU/mL for avionics filter debris and 4.5E+6 CFU/mL for the cabin filter debris. A similar diversity of bacterial types was found in the two filters. Of the 13 different bacterial types identified from the cabin and avionics samples, 6 were common to both filters. The overall analysis of these samples as compared to those of previous missions shows no significant differences.

Microbial production of plant hormones: Opportunities and challenges.

PubMed

Shi, Tian-Qiong; Peng, Hui; Zeng, Si-Yu; Ji, Rong-Yu; Shi, Kun; Huang, He; Ji, Xiao-Jun

2017-03-04

Plant hormones are a class of organic substances which are synthesized during the plant metabolism. They have obvious physiological effect on plant growth at very low concentrations. Generally, plant hormones are mainly divided into 5 categories: auxins, cytokinins, ethylene, gibberellins (GAs) and abscisic acid (ABA). With the deepening of research, some novel plant hormones such as brassinosteroid and salicylates have been found and identified. The plant hormone products are mainly obtained through plant extraction, chemical synthesis as well as microbial fermentation. However, the extremely low yield in plants and relatively complex chemical structure limit the development of the former 2 approaches. Therefore, more attention has been paid into the microbial fermentative production. In this commentary, the developments and technological achievements of the 2 important plant hormones (GAs and ABA) have been discussed. The discovery, producing strains, fermentation technologies, and their accumulation mechanisms are first introduced. Furthermore, progresses in the industrial mass scale production are discussed. Finally, guidelines for future studies for GAs and ABA production are proposed in light of the current progress, challenges and trends in the field. With the widespread use of plant hormones in agriculture, we believe that the microbial production of plant hormones will have a bright future.

In Vitro propagation of Jasminum officinale L.: a woody ornamental vine yielding aromatic oil from flowers.

PubMed

Bhattacharya, Sabita; Bhattacharyya, Sanghamitra

2010-01-01

The growing demand for flower extracts in perfume trade can primarily be met by increasing flower production and multiplying planting material. The major commercial aromatic flower yielding plants including Jasminum officinale L., a member of the Family Oleaceae have drawn the attention of a large section of the concerned sectors leading to a thrust upon developing advanced propagation technologies for these floral crops, in addition to conventional nature-dependent agro-techniques. This chapter describes concisely and critically, a protocol developed for in vitro propagation of Jasminum officinale by shoot regeneration from existing as well as newly developed adventitious axillary buds via proper phytohormonal stimulation. To start with nodal segments as explants, March-April is the most ideal time of the year when planting material suitable for in vitro multiplication is abundantly available. Prior to inoculation of explants in the culture medium, special care is needed to reduce microbial contamination by spraying on selected spots of the donor plant with anti-microbial agents 24 h prior to collection; treatment with antiseptic solution after final cleaning and surface sterilization by treating explants with mercuric chloride. Inoculated explants are free from brown leaching from cut ends by two consecutive subcultures within 48 h in MS basal medium. Multiplication of shoots, average 4-5 at each node, takes place in MS medium containing 4.0 mg/L BAP, 0.1 mg/L NAA, and 40 g/L sucrose over a period of 8 weeks. For elongation of regenerated shoots, cultures are transferred to MS medium, supplemented with a single growth hormone, kinetin at 2.0 mg/L. Emergence and elongation of roots from shoot base is facilitated by placing on the notch of a filter paper bridge. The hardened in vitro propagated plants are able to grow normally in soil like other conventionally propagated Jasminum officinale.

Seawater quality and microbial communities at a desalination plant marine outfall. A field study at the Israeli Mediterranean coast.

PubMed

Drami, Dror; Yacobi, Yosef Z; Stambler, Noga; Kress, Nurit

2011-11-01

Global desalination quadrupled in the last 15 years and the relative importance of seawater desalination by reverse osmosis (SWRO) increased as well. While the technological aspects of SWRO plants are extensively described, studies on the environmental impact of brine discharge are lacking, in particular in situ marine environmental studies. The Ashqelon SWRO plant (333,000 m(3) d(-1) freshwater) discharges brine and backwash of the pre-treatment filters (containing ferric hydroxide coagulant) at the seashore, next to the cooling waters of a power plant. At the time of this study brine and cooling waters were discharged continuously and the backwash discharge was pulsed, with a frequency dependent on water quality at the intake. The effects of the discharges on water quality and neritic microbial community were identified, quantified and attributed to the different discharges. The mixed brine-cooling waters discharge increased salinity and temperature at the outfall, were positively buoyant, and dispersed at the surface up to 1340 m south of the outfall. Nutrient concentrations were higher at the outfall while phytoplankton densities were lower. Chlorophyll-a and picophytoplankton cell numbers were negatively correlated with salinity, but more significantly with temperature probably as a result of thermal pollution. The discharge of the pulsed backwash increased turbidity, suspended particulate matter and particulate iron and decreased phytoplankton growth efficiency at the outfall, effects that declined with distance from the outfall. The discharges clearly reduced primary production but we could not attribute the effect to a specific component of the discharge. Bacterial production was also affected but differently in the three surveys. The combined and possible synergistic effects of SWRO desalination along the Israeli shoreline should be taken into account when the three existing plants and additional ones are expected to produce 2 Mm(3) d(-1) freshwater by 2020. Copyright © 2011 Elsevier Ltd. All rights reserved.

[Influence of Submerged Plants on Microbial Community Structure in Sediment of Hongze Lake].

PubMed

Zhang, Ding-yu; Zhang, Ting-xi; Dong, Dan-ping; Li, De-fang; Wang, Guo-xiang

2016-05-15

Phospholipid fatty acids (PLFAs) method was applied to analyze the influence of submerged plants on sediment microbial community structure, in order to investigate the changes of sediment microbial community structure for different kinds of the submerged plants in different growth periods. Particularly, Potamogeton crispus L., Potamogeton pectinatus L and the mixed group were chosen as the typical submerged plants in Hongze Lake for investigation in this paper. The results indicated that the change of total PLFAs in different periods was significant, on the contrary, the PLFA change for different groups in the same period was insignificant. The values of G⁺ PLFA/G⁻ PLFA in the submerged plant group were also highly related to the different growth periods, which demonstrated that the root function of the submerged plant had a severe impact on the microbial community in sediment. Furthermore, some environmental factors, such as Temperature, pH, TOC and DO, were correlated to characteristic phospholipid of PLFAs in sediment, which means the environmental factors could also affect the microbial community structure.

Novel techniques and findings in the study of plant microbiota: search for plant probiotics.

PubMed

Berlec, Aleš

2012-09-01

Plants live in intimate relationships with numerous microorganisms present inside or outside plant tissues. The plant exterior provides two distinct ecosystems, the rhizosphere (below ground) and the phyllosphere (above ground), both populated by microbial communities. Most studies on plant microbiota deal with pathogens or mutualists. This review focuses on plant commensal bacteria, which could represent a rich source of bacteria beneficial to plants, alternatively termed plant probiotics. Plant commensal bacteria have been addressed only recently with culture-independent studies. These use next-generation sequencing, DNA microarray technologies and proteomics to decipher microbial community composition and function. Diverse bacterial populations are described in both rhizosphere and phyllosphere of different plants. The microorganisms can emerge from neighboring environmental ecosystems at random; however their survival is regulated by the plant. Influences from the environment, such as pesticides, farming practice and atmosphere, also affect the composition of microbial communities. Apart from community composition studies, some functional studies have also been performed. These include identification of broad-substrate surface receptors and methanol utilization enzymes by the proteomic approach, as well as identification of bacterial species that are important mediators of disease-suppressive soil phenomenon. Experience from more advanced human microbial studies could provide useful information and is discussed in the context of methodology and common trends. Administration of microbial mixtures of whole communities, rather than individual species, is highlighted and should be considered in future agricultural applications. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Factors Affecting Soil Microbial Community Structure in Tomato Cropping Systems

USDA-ARS?s Scientific Manuscript database

Soil and rhizosphere microbial communities in agroecosystems may be affected by soil, climate, plant species, and management. We identified some of the most important factors controlling microbial biomass and community structure in an agroecosystem utilizing tomato plants with the following nine tre...

Trophic interactions induce spatial self-organization of microbial consortia on rough surfaces.

PubMed

Wang, Gang; Or, Dani

2014-10-24

The spatial context of microbial interactions common in natural systems is largely absent in traditional pure culture-based microbiology. The understanding of how interdependent microbial communities assemble and coexist in limited spatial domains remains sketchy. A mechanistic model of cell-level interactions among multispecies microbial populations grown on hydrated rough surfaces facilitated systematic evaluation of how trophic dependencies shape spatial self-organization of microbial consortia in complex diffusion fields. The emerging patterns were persistent irrespective of initial conditions and resilient to spatial and temporal perturbations. Surprisingly, the hydration conditions conducive for self-assembly are extremely narrow and last only while microbial cells remain motile within thin aqueous films. The resulting self-organized microbial consortia patterns could represent optimal ecological templates for the architecture that underlie sessile microbial colonies on natural surfaces. Understanding microbial spatial self-organization offers new insights into mechanisms that sustain small-scale soil microbial diversity; and may guide the engineering of functional artificial microbial consortia.

The rhizosphere microbiota of plant invaders: an overview of recent advances in the microbiomics of invasive plants

PubMed Central

Coats, Vanessa C.; Rumpho, Mary E.

2014-01-01

Plants in terrestrial systems have evolved in direct association with microbes functioning as both agonists and antagonists of plant fitness and adaptability. As such, investigations that segregate plants and microbes provide only a limited scope of the biotic interactions that dictate plant community structure and composition in natural systems. Invasive plants provide an excellent working model to compare and contrast the effects of microbial communities associated with natural plant populations on plant fitness, adaptation, and fecundity. The last decade of DNA sequencing technology advancements opened the door to microbial community analysis, which has led to an increased awareness of the importance of an organism’s microbiome and the disease states associated with microbiome shifts. Employing microbiome analysis to study the symbiotic networks associated with invasive plants will help us to understand what microorganisms contribute to plant fitness in natural systems, how different soil microbial communities impact plant fitness and adaptability, specificity of host–microbe interactions in natural plant populations, and the selective pressures that dictate the structure of above-ground and below-ground biotic communities. This review discusses recent advances in invasive plant biology that have resulted from microbiome analyses as well as the microbial factors that direct plant fitness and adaptability in natural systems. PMID:25101069

Performance of Anaerobic Biotrickling Filter and Its Microbial Diversity for the Removal of Stripped Disinfection By-products

EPA Science Inventory

The objective of this research was to evaluate the biodegradation of chloroform by using biotrickling filter (BTF) and determining the dominant bacteria responsible for the degradation. The research was conducted in three phases under anaerobic condition, namely, in the presence ...

Identifying the role of plant-microbial interactions in driving Arctic carbon cycle changes using a 13C isotope tracer

NASA Astrophysics Data System (ADS)

Hough, M.; Tfaily, M. M.; Blazewicz, S.; Dorrepaal, E.; Crill, P. M.; Rich, V. I.; Saleska, S. R.

2017-12-01

Thawing arctic permafrost (which contains 30-50% of global soil carbon) is expected to drive substantial alterations to carbon (C) cycling that will accelerate climate change. As permafrost thaws, old C may decompose more rapidly and be released as methane (CH4) and carbon dioxide (CO2), but thawing soil can also increase plant productivity as perennial shrub communities transition to faster growing annual wetland plants. The effect of plant community changes on the C cycle is not yet well understood. It could mitigate C loss if C input rates are high enough, or it could increase contributions to CH4 emission (a more potent greenhouse gas than CO2) if it decomposes anaerobically. To investigate the influence of fresh plant litter inputs on peat organic material, microbial communities, and greenhouse gas emissions we traced 13C-enriched plant material from Eriophorum and Sphagnum plants added to arctic peat decomposition incubations into each of these components. High resolution FT-ICR mass spectrometry showed changes in the types of enriched compounds over time indicative of microbial processing. Density fractionation of microbial DNA showed enrichment of the microbial community indicating uptake of 13C-enriched compounds from the plant litter. CO2 and CH4 fluxes were highly 13C enriched and showed three distinct phases of flux after litter addition which were not seen in incubations with no litter added. Together, these lines of evidence indicate that fresh litter inputs may play an important role in structuring microbial decomposition. Future work will explore this influence through closer examination of organic matter and microbial community changes during decomposition.

Phosphorus cycling in natural and low input soil/plant systems: the role of soil microorganisms

NASA Astrophysics Data System (ADS)

Tamburini, F.; Bünemann, E. K.; Oberson, A.; Bernasconi, S. M.; Frossard, E.

2011-12-01

Availability of phosphorus (as orthophosphate, Pi) limits biological production in many terrestrial ecosystems. During the first phase of soil development, weathering of minerals and leaching of Pi are the processes controlling Pi concentrations in the soil solution, while in mature soils, Pi is made available by desorption of mineral Pi and mineralization of organic compounds. In agricultural soils additional Pi is supplied by fertilization, either with mineral P and/or organic inputs (animal manure or plant residues). Soil microorganisms (bacteria and fungi) mediate several processes, which are central to the availability of Pi to plants. They play a role in the initial release of Pi from the mineral phase, and through extracellular phosphatase enzymes, they decompose and mineralize organic compounds, releasing Pi. On the other hand, microbial immobilization and internal turnover of Pi can decrease the soil available Pi pool, competing in this way with plants. Using radio- and stable isotopic approaches, we show evidence from different soil/plant systems which points to the central role of the microbial activity. In the presented case studies, P contained in the soil microbial biomass is a larger pool than available Pi. In a soil chronosequence after deglaciation, stable isotopes of oxygen associated to phosphate showed that even in the youngest soils microbial activity highly impacted the isotopic signature of available Pi. These results suggested that microorganisms were rapidly taking up and cycling Pi, using it to sustain their community. Microbial P turnover time was faster in the young (about 20 days) than in older soils (about 120 days), reflecting a different functioning of the microbial community. Microbial community crashes, caused by drying/rewetting and freezing/thawing cycles, were most likely responsible for microbial P release to the available P pool. In grassland fertilization experiments with mineral NK and NPK amendments, microbial P turnover was faster in the P-free treatment. Laboratory incubation also showed a more rapid P uptake by microbial biomass in the NK than in the NPK treatment (37% and 6% of added 33P recovered in microbial P after 100 minutes in NK and NPK, respectively). The seasonal microbial P flux in both treatments was 1.5-4 times larger than the annual plant P uptake. In field studies carried out on highly weathered low P soils in Colombia, the comparison between grass-legume and grass-only pastures showed that the presence of legumes had an impact on the overall biological activity. In fact, microbial biomass and phosphatase activity were significantly larger in grass-legume pastures than in the legume-free experiments. Larger release of Pi from the organic P pool improved P availability to plants and pointed at a modified C:N:P stoichiometry along pathways of the nutrient cycle in the soil/plant system. All these data are evidence of a highly dynamic microbial P pool, which controls Pi concentration and, hence, availability for plants in natural and low input agricultural ecosystems.

Functional characterization of cinnamyl alcohol dehydrogenase and caffeic acid O-methyltransferase in Brachypodium distachyon

PubMed Central

2013-01-01

Background Lignin is a significant barrier in the conversion of plant biomass to bioethanol. Cinnamyl alcohol dehydrogenase (CAD) and caffeic acid O-methyltransferase (COMT) catalyze key steps in the pathway of lignin monomer biosynthesis. Brown midrib mutants in Zea mays and Sorghum bicolor with impaired CAD or COMT activity have attracted considerable agronomic interest for their altered lignin composition and improved digestibility. Here, we identified and functionally characterized candidate genes encoding CAD and COMT enzymes in the grass model species Brachypodium distachyon with the aim of improving crops for efficient biofuel production. Results We developed transgenic plants overexpressing artificial microRNA designed to silence BdCAD1 or BdCOMT4. Both transgenes caused altered flowering time and increased stem count and weight. Downregulation of BdCAD1 caused a leaf brown midrib phenotype, the first time this phenotype has been observed in a C3 plant. While acetyl bromide soluble lignin measurements were equivalent in BdCAD1 downregulated and control plants, histochemical staining and thioacidolysis indicated a decrease in lignin syringyl units and reduced syringyl/guaiacyl ratio in the transgenic plants. BdCOMT4 downregulated plants exhibited a reduction in total lignin content and decreased Maule staining of syringyl units in stem. Ethanol yield by microbial fermentation was enhanced in amiR-cad1-8 plants. Conclusion These results have elucidated two key genes in the lignin biosynthetic pathway in B. distachyon that, when perturbed, may result in greater stem biomass yield and bioconversion efficiency. PMID:23902793

An overview of challenges in modeling heat and mass transfer for living on Mars.

PubMed

Yamashita, Masamichi; Ishikawa, Yoji; Kitaya, Yoshiaki; Goto, Eiji; Arai, Mayumi; Hashimoto, Hirofumi; Tomita-Yokotani, Kaori; Hirafuji, Masayuki; Omori, Katsunori; Shiraishi, Atsushi; Tani, Akira; Toki, Kyoichiro; Yokota, Hiroki; Fujita, Osamu

2006-09-01

Engineering a life-support system for living on Mars requires the modeling of heat and mass transfer. This report describes the analysis of heat and mass transfer phenomena in a greenhouse dome, which is being designed as a pressurized life-support system for agricultural production on Mars. In this Martian greenhouse, solar energy will be converted into chemical energy in plant biomass. Agricultural products will be harvested for food and plant cultivation, and waste materials will be processed in a composting microbial ecosystem. Transpired water from plants will be condensed and recycled. In our thermal design and analysis for the Martian greenhouse, we addressed the question of whether temperature and pressure would be maintained in the appropriate range for humans as well as plants. Energy flow and material circulation should be controlled to provide an artificial ecological system on Mars. In our analysis, we assumed that the greenhouse would be maintained at a subatmospheric pressure under 1/3-G gravitational force with 1/2 solar light intensity on Earth. Convection of atmospheric gases will be induced inside the greenhouse, primarily by heating from sunlight. Microclimate (thermal and gas species structure) could be generated locally around plant bodies, which would affect gas transport. Potential effects of those environmental factors are discussed on the phenomena including plant growth and plant physiology and focusing on transport processes. Fire safety is a crucial issue and we evaluate its impact on the total gas pressure in the greenhouse dome.

Divergence in plant and microbial allocation strategies explains continental patterns in microbial allocation and biogeochemical fluxes.

PubMed

Averill, Colin

2014-10-01

Allocation trade-offs shape ecological and biogeochemical phenomena at local to global scale. Plant allocation strategies drive major changes in ecosystem carbon cycling. Microbial allocation to enzymes that decompose carbon vs. organic nutrients may similarly affect ecosystem carbon cycling. Current solutions to this allocation problem prioritise stoichiometric tradeoffs implemented in plant ecology. These solutions may not maximise microbial growth and fitness under all conditions, because organic nutrients are also a significant carbon resource for microbes. I created multiple allocation frameworks and simulated microbial growth using a microbial explicit biogeochemical model. I demonstrate that prioritising stoichiometric trade-offs does not optimise microbial allocation, while exploiting organic nutrients as carbon resources does. Analysis of continental-scale enzyme data supports the allocation patterns predicted by this framework, and modelling suggests large deviations in soil C loss based on which strategy is implemented. Therefore, understanding microbial allocation strategies will likely improve our understanding of carbon cycling and climate. © 2014 John Wiley & Sons Ltd/CNRS.

Study of Methanogenesis while Bioutilisation of Plant Residuals

NASA Astrophysics Data System (ADS)

Ilyin, V. K.; Korniushenkova, I. N.; Starkova, L. V.; Lauriniavichius, K. S.

respect principals of planet ecology, and compatibility with other habitability systems. For these purpose the waste management technologies, relevant to application of the biodegradation properties of bacteria are of great value. Biological treatment method is based upon the biodegradation of organic substances by various microorganisms. vegetable non-edible residual, using artificial inoculum; to study peculiarities of biogas, possibilities to optimize or to reduce the share of methane. fermentation. The biogas production achieved 46 l per 1 kg of substrate. The microbial studies of biodegradation process revealed following peculiarities: (i)gradual quantitative increasing of Lactobacillus sp. (from 103 to 105 colony forming units (CFU) per ml); (ii)activation of Clostridia sp. (from 102 to 104 CFU/ml); (iii) elimination of aerobic conventional pathogens (Enterobacteriaceae sp., Protea sp., staphylococci). methane content measures revealed traces 0.1-0.4%. granules, the amount of methane in biogas reached 80-90%. biodegradation of vegetable wastes. This inoculum consists of active sludge adapted to wastes mixed with excretes of insects which consume plant wastes. Using this inoculum the biodegradation process takes less time, then that using active sludge. Regulation of methane concentration from traces to 90% may be achieved by adding of methane reactor to the plant digester.

Disinfection by-products and microbial contamination in the treatment of pool water with granular activated carbon.

PubMed

Uhl, W; Hartmann, C

2005-01-01

For swimming pools, it is generally agreed that free chlorine levels have to be maintained to guarantee adequate disinfection. Recommended free chlorine levels can vary between 0.3 and 0.6 mg/L in Germany and up to 3 mg/L in other countries. Bathers introduce considerable amounts of organic matter, mainly in the form of such as urine and sweat, into the pool water. As a consequence, disinfection byproducts (DBPs) are formed. Regulations in Germany recommend levels of combined chlorine of less than 0.2 mg/L and levels of trihalomethanes (THMs) of less than 20 microg/L. Haloacetic acids (HAAs), haloacetonitriles (HANs), chloropicrin and chloral hydrate are also detected in considerable amounts. However, these compounds are not regulated yet. Swimming pool staff and swimmers, especially athletes, are primarily exposed to these byproducts by inhalation and/or dermal uptake. In Germany, new regulations for swimming pool water treatment generally require the use of activated carbon. In this project, three different types of granular activated carbon (GAC) (one standard GAC, two catalytic GACs) are compared for their long time behaviour in pool water treatment. In a pilot plant operated with real swimming pool water, production and removal of disinfection byproducts (THMs, HAAs, AOXs), of biodegradable substances (AOC), of bacteria (Pseudomonas aeruginosa, Legionella, coliforms, HPC) as well as the removal of chlorine and chloramines are monitored as function of GAC bed depth. Combined chlorine penetrates deeper in the filter bed than free chlorine does. However, both, free and combined chlorine removal efficiencies decrease over the time of filter operation. The decreases of removal efficiencies are also observed for parameters such as dissolved organic carbon, spectral absorption coefficient, adsorbable organic carbon and most of the disinfection byproducts. However, THMs, especially chloroform are produced in the filter bed. The GAC beds were contaminated microbially, especially with P. aeruginosa. The contamination was not removable by backwashing with chlorine concentrations up to 2 mg/l free chlorine.

Escherichia coli Removal in Biochar-Modified Biofilters: Effects of Biofilm

PubMed Central

Afrooz, A. R. M. Nabiul; Boehm, Alexandria B.

2016-01-01

The presence of microbial contaminants in urban stormwater is a significant concern for public health; however, their removal by traditional stormwater biofilters has been reported as inconsistent and inadequate. Recent work has explored the use of biochar to improve performance of stormwater biofilters under simplified conditions that do not consider potential effects of biofilm development on filter media. The present study investigates the role of biofilm on microbial contaminant removal performance of stormwater biofilters. Pseudomonas aeruginosa biofilms were formed in laboratory-scale sand and biochar-modified sand packed columns, which were then challenged with Escherichia coli laden synthetic stormwater containing natural organic matter. Results suggests that the presence of biofilm influences the removal of E. coli. However, the nature of the influence depends on the specific surface area and the relative hydrophobicity of filter media. The distribution of attached bacteria within the columns indicates that removal by filter media varies along the length of the column: the inlet was the primary removal zone regardless of experimental conditions. Findings from this research inform the design of field-scale biofilters for better and consistent performance in removing microbial contaminants from urban stormwater. PMID:27907127

Are Local Filters Blind to Provenance? Ant Seed Predation Suppresses Exotic Plants More than Natives

PubMed Central

Pearson, Dean E.; Icasatti, Nadia S.; Hierro, Jose L.; Bird, Benjamin J.

2014-01-01

The question of whether species’ origins influence invasion outcomes has been a point of substantial debate in invasion ecology. Theoretically, colonization outcomes can be predicted based on how species’ traits interact with community filters, a process presumably blind to species’ origins. Yet, exotic plant introductions commonly result in monospecific plant densities not commonly seen in native assemblages, suggesting that exotic species may respond to community filters differently than natives. Here, we tested whether exotic and native species differed in their responses to a local community filter by examining how ant seed predation affected recruitment of eighteen native and exotic plant species in central Argentina. Ant seed predation proved to be an important local filter that strongly suppressed plant recruitment, but ants suppressed exotic recruitment far more than natives (89% of exotic species vs. 22% of natives). Seed size predicted ant impacts on recruitment independent of origins, with ant preference for smaller seeds resulting in smaller seeded plant species being heavily suppressed. The disproportionate effects of provenance arose because exotics had generally smaller seeds than natives. Exotics also exhibited greater emergence and earlier peak emergence than natives in the absence of ants. However, when ants had access to seeds, these potential advantages of exotics were negated due to the filtering bias against exotics. The differences in traits we observed between exotics and natives suggest that higher-order introduction filters or regional processes preselected for certain exotic traits that then interacted with the local seed predation filter. Our results suggest that the interactions between local filters and species traits can predict invasion outcomes, but understanding the role of provenance will require quantifying filtering processes at multiple hierarchical scales and evaluating interactions between filters. PMID:25099535

Plant diversity predicts beta but not alpha diversity of soil microbes across grasslands worldwide

USGS Publications Warehouse

Prober, Suzanne M.; Leff, Jonathan W.; Bates, Scott T.; Borer, Elizabeth T.; Firn, Jennifer; Harpole, W. Stanley; Lind, Eric M.; Seabloom, Eric W.; Adler, Peter B.; Bakker, Jonathan D.; Cleland, Elsa E.; DeCrappeo, Nicole; DeLorenze, Elizabeth; Hagenah, Nicole; Hautier, Yann; Hofmockel, Kirsten S.; Kirkman, Kevin P.; Knops, Johannes M. H.; La Pierre, Kimberly J.; MacDougall, Andrew S.; McCulley, Rebecca L.; Mitchell, Charles E.; Risch, Anita C.; Schuetz, Martin; Stevens, Carly J.; Williams, Ryan J.; Fierer, Noah

2015-01-01

Aboveground–belowground interactions exert critical controls on the composition and function of terrestrial ecosystems, yet the fundamental relationships between plant diversity and soil microbial diversity remain elusive. Theory predicts predominantly positive associations but tests within single sites have shown variable relationships, and associations between plant and microbial diversity across broad spatial scales remain largely unexplored. We compared the diversity of plant, bacterial, archaeal and fungal communities in one hundred and forty-five 1 m2 plots across 25 temperate grassland sites from four continents. Across sites, the plant alpha diversity patterns were poorly related to those observed for any soil microbial group. However, plant beta diversity (compositional dissimilarity between sites) was significantly correlated with the beta diversity of bacterial and fungal communities, even after controlling for environmental factors. Thus, across a global range of temperate grasslands, plant diversity can predict patterns in the composition of soil microbial communities, but not patterns in alpha diversity.

Leaf and root C-to-N ratios are poor predictors of soil microbial biomass C and respiration across 32 tree species.

PubMed

Ferlian, Olga; Wirth, Christian; Eisenhauer, Nico

2017-11-01

Soil microorganisms are the main primary decomposers of plant material and drive biogeochemical processes like carbon and nitrogen cycles. Hence, knowledge of their nutritional demands and limitations for activity and growth is of particular importance. However, potential effects of the stoichiometry of soil and plant species on soil microbial activity and carbon use efficiency are poorly understood. Soil properties and plant traits are assumed to drive microbial carbon and community structure. We investigated the associations between C and N concentrations of leaf, root, and soil as well as their ratios and soil microbial biomass C and activity (microbial basal respiration and specific respiratory quotient) across 32 young native angiosperm tree species at two locations in Central Germany. Correlations between C:N ratios of leaves, roots, and soil were positive but overall weak. Only regressions between root and leaf C:N ratios as well as between root and soil C:N ratios were significant at one site. Soil microbial properties differed significantly between the two sites and were significantly correlated with soil C:N ratio across sites. Soil C concentrations rather than N concentrations drove significant effects of soil C:N ratio on soil microbial properties. No significant correlations between soil microbial properties and leaf as well as root C:N ratios were found. We found weak correlations of C:N ratios between plant aboveground and belowground tissues. Furthermore, microorganisms were not affected by the stoichiometry of plant tissues in the investigated young trees. The results suggest that soil stoichiometry represents a consistent determinant of soil microbial biomass and respiration. Our study indicates that stoichiometric relationships among tree organs can be weak and poor predictors of soil microbial properties in young tree stands. Further research in controlled experimental settings with a wide range of tree species is needed to study the role of plant chemical traits like the composition and stoichiometry of root exudates in determining interactions between above- and belowground compartments.

Quick counting method for estimating the number of viable microbes on food and food processing equipment.

PubMed

Winter, F H; York, G K; el-Nakhal, H

1971-07-01

A rapid method for estimating the extent of microbial contamination on food and on food processing equipment is described. Microbial cells are rinsed from food or swab samples with sterile diluent and concentrated on the surface of membrane filters. The filters are incubated on a suitable bacteriological medium for 4 hr at 30 C, heated at 105 C for 5 min, and stained. The membranes are then dried at 60 C for 15 min, rendered transparent with immersion oil, and examined microscopically. Data obtained by the rapid method were compared with counts of the same samples determined by the standard plate count method. Over 60 comparisons resulted in a correlation coefficient of 0.906. Because the rapid technique can provide reliable microbiological count information in extremely short times, it can be a most useful tool in the routine evaluation of microbial contamination of food processing facilities and for some foods.

Lake microbial communities are resilient after a whole-ecosystem disturbance

PubMed Central

Shade, Ashley; Read, Jordan S; Youngblut, Nicholas D; Fierer, Noah; Knight, Rob; Kratz, Timothy K; Lottig, Noah R; Roden, Eric E; Stanley, Emily H; Stombaugh, Jesse; Whitaker, Rachel J; Wu, Chin H; McMahon, Katherine D

2012-01-01

Disturbances act as powerful structuring forces on ecosystems. To ask whether environmental microbial communities have capacity to recover after a large disturbance event, we conducted a whole-ecosystem manipulation, during which we imposed an intense disturbance on freshwater microbial communities by artificially mixing a temperate lake during peak summer thermal stratification. We employed environmental sensors and water chemistry analyses to evaluate the physical and chemical responses of the lake, and bar-coded 16S ribosomal RNA gene pyrosequencing and automated ribosomal intergenic spacer analysis (ARISA) to assess the bacterial community responses. The artificial mixing increased mean lake temperature from 14 to 20 °C for seven weeks after mixing ended, and exposed the microorganisms to very different environmental conditions, including increased hypolimnion oxygen and increased epilimnion carbon dioxide concentrations. Though overall ecosystem conditions remained altered (with hypolimnion temperatures elevated from 6 to 20 °C), bacterial communities returned to their pre-manipulation state as some environmental conditions, such as oxygen concentration, recovered. Recovery to pre-disturbance community composition and diversity was observed within 7 (epilimnion) and 11 (hypolimnion) days after mixing. Our results suggest that some microbial communities have capacity to recover after a major disturbance. PMID:22739495

Plants Rather than Mineral Fertilization Shape Microbial Community Structure and Functional Potential in Legacy Contaminated Soil.

PubMed

Ridl, Jakub; Kolar, Michal; Strejcek, Michal; Strnad, Hynek; Stursa, Petr; Paces, Jan; Macek, Tomas; Uhlik, Ondrej

2016-01-01

Plant-microbe interactions are of particular importance in polluted soils. This study sought to determine how selected plants (horseradish, black nightshade and tobacco) and NPK mineral fertilization shape the structure of soil microbial communities in legacy contaminated soil and the resultant impact of treatment on the soil microbial community functional potential. To explore these objectives, we combined shotgun metagenomics and 16S rRNA gene amplicon high throughput sequencing with data analysis approaches developed for RNA-seq. We observed that the presence of any of the selected plants rather than fertilization shaped the microbial community structure, and the microbial populations of the root zone of each plant significantly differed from one another and/or from the bulk soil, whereas the effect of the fertilizer proved to be insignificant. When we compared microbial diversity in root zones versus bulk soil, we observed an increase in the relative abundance of Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria or Bacteroidetes, taxa which are commonly considered copiotrophic. Our results thus align with the theory that fast-growing, copiotrophic, microorganisms which are adapted to ephemeral carbon inputs are enriched in the vegetated soil. Microbial functional potential indicated that some genetic determinants associated with signal transduction mechanisms, defense mechanisms or amino acid transport and metabolism differed significantly among treatments. Genetic determinants of these categories tend to be overrepresented in copiotrophic organisms. The results of our study further elucidate plant-microbe relationships in a contaminated environment with possible implications for the phyto/rhizoremediation of contaminated areas.

Impact of artificial rearing systems on the developmental and reproductive fitness of the predatory bug, Orius laevigatus.

PubMed

Bonte, Maarten; De Clercq, Patrick

2010-01-01

This study investigated the effect of several substrate types and moisture sources on the developmental and reproductive fitness of the zoophytophagous predator Orius laevigatus (Fieber) (Hemiptera: Anthocoridae) when fed a factitious prey (i.e. unnatural prey) Ephestia kuehniella (Zeller) eggs, or a meridic artificial diet based on hen's egg yolk. O. laevigatus is known to feed on plants as an alternative food source and to oviposit in plants. E. kuehniella eggs were superior to the artificial diet. Supplementary feeding on plant materials did not compensate for the nutritional shortcomings of the artificial diet. Survival rates showed that oviposition substrates such as bean pods or lipophilic surfaces such as wax paper and plastic were more suitable for rearing O. laevigatus than household paper. The use of green bean pods as a plant substrate did not have a beneficial effect on O. laevigatus. The results indicated that O. laevigatus can successfully complete its nymphal development and realize its full reproductive potential in the absence of plant material. However, plant materials would still be required for oviposition, unless a reliable and cost-effective artificial oviposition substrate were made available. The omission of plant materials from the rearing procedures may reduce production cost of this species and other heteropteran predators.

Rooting Theories of Plant Community Ecology in Microbial Interactions

PubMed Central

Bever, James D.; Dickie, Ian A.; Facelli, Evelina; Facelli, Jose M.; Klironomos, John; Moora, Mari; Rillig, Matthias C.; Stock, William D.; Tibbett, Mark; Zobel, Martin

2010-01-01

Predominant frameworks for understanding plant ecology have an aboveground bias that neglects soil micro-organisms. This is inconsistent with recent work illustrating the importance of soil microbes in terrestrial ecology. Microbial effects have been incorporated into plant community dynamics using ideas of niche modification and plant-soil community feedbacks. Here, we expand and integrate qualitative conceptual models of plant niche and feedback to explore implications of microbial interactions for understanding plant community ecology. At the same time we review the empirical evidence for these processes. We also consider common mycorrhizal networks, and suggest these are best interpreted within the feedback framework. Finally, we apply our integrated model of niche and feedback to understanding plant coexistence, monodominance, and invasion ecology. PMID:20557974

Plant Invasions Associated with Change in Root-Zone Microbial Community Structure and Diversity.

PubMed

Rodrigues, Richard R; Pineda, Rosana P; Barney, Jacob N; Nilsen, Erik T; Barrett, John E; Williams, Mark A

2015-01-01

The importance of plant-microbe associations for the invasion of plant species have not been often tested under field conditions. The research sought to determine patterns of change in microbial communities associated with the establishment of invasive plants with different taxonomic and phenetic traits. Three independent locations in Virginia, USA were selected. One site was invaded by a grass (Microstegium vimineum), another by a shrub (Rhamnus davurica), and the third by a tree (Ailanthus altissima). The native vegetation from these sites was used as reference. 16S rRNA and ITS regions were sequenced to study root-zone bacterial and fungal communities, respectively, in invaded and non-invaded samples and analyzed using Quantitative Insights Into Microbial Ecology (QIIME). Though root-zone microbial community structure initially differed across locations, plant invasion shifted communities in similar ways. Indicator species analysis revealed that Operational Taxonomic Units (OTUs) closely related to Proteobacteria, Acidobacteria, Actinobacteria, and Ascomycota increased in abundance due to plant invasions. The Hyphomonadaceae family in the Rhodobacterales order and ammonia-oxidizing Nitrospirae phylum showed greater relative abundance in the invaded root-zone soils. Hyphomicrobiaceae, another bacterial family within the phyla Proteobacteria increased as a result of plant invasion, but the effect associated most strongly with root-zones of M. vimineum and R. davurica. Functional analysis using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) showed bacteria responsible for nitrogen cycling in soil increased in relative abundance in association with plant invasion. In agreement with phylogenetic and functional analyses, greater turnover of ammonium and nitrate was associated with plant invasion. Overall, bacterial and fungal communities changed congruently across plant invaders, and support the hypothesis that nitrogen cycling bacteria and functions are important factors in plant invasions. Whether the changes in microbial communities are driven by direct plant microbial interactions or a result of plant-driven changes in soil properties remains to be determined.

Plant Invasions Associated with Change in Root-Zone Microbial Community Structure and Diversity

PubMed Central

Rodrigues, Richard R.; Pineda, Rosana P.; Barney, Jacob N.; Nilsen, Erik T.; Barrett, John E.; Williams, Mark A.

2015-01-01

The importance of plant-microbe associations for the invasion of plant species have not been often tested under field conditions. The research sought to determine patterns of change in microbial communities associated with the establishment of invasive plants with different taxonomic and phenetic traits. Three independent locations in Virginia, USA were selected. One site was invaded by a grass (Microstegium vimineum), another by a shrub (Rhamnus davurica), and the third by a tree (Ailanthus altissima). The native vegetation from these sites was used as reference. 16S rRNA and ITS regions were sequenced to study root-zone bacterial and fungal communities, respectively, in invaded and non-invaded samples and analyzed using Quantitative Insights Into Microbial Ecology (QIIME). Though root-zone microbial community structure initially differed across locations, plant invasion shifted communities in similar ways. Indicator species analysis revealed that Operational Taxonomic Units (OTUs) closely related to Proteobacteria, Acidobacteria, Actinobacteria, and Ascomycota increased in abundance due to plant invasions. The Hyphomonadaceae family in the Rhodobacterales order and ammonia-oxidizing Nitrospirae phylum showed greater relative abundance in the invaded root-zone soils. Hyphomicrobiaceae, another bacterial family within the phyla Proteobacteria increased as a result of plant invasion, but the effect associated most strongly with root-zones of M. vimineum and R. davurica. Functional analysis using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) showed bacteria responsible for nitrogen cycling in soil increased in relative abundance in association with plant invasion. In agreement with phylogenetic and functional analyses, greater turnover of ammonium and nitrate was associated with plant invasion. Overall, bacterial and fungal communities changed congruently across plant invaders, and support the hypothesis that nitrogen cycling bacteria and functions are important factors in plant invasions. Whether the changes in microbial communities are driven by direct plant microbial interactions or a result of plant-driven changes in soil properties remains to be determined. PMID:26505627

Seeding and planting birch

Treesearch

John C. Bjorkbom

1969-01-01

Artificial regeneration of hardwoods does not have a very good reputation. Many of the early attempts to establish these species by seeding or planting resulted in failure. Then too, natural regeneration is usually adequate on cut over areas, so that there is little need for artificial regeneration on such areas. Nevertheless there are situations where artificial...

Seasonal switchgrass ecotype contributions to soil organic carbon, deep soil microbial community composition and rhizodeposit uptake during an extreme drought

USDA-ARS?s Scientific Manuscript database

The importance of rhizodeposit C and associated microbial communities in deep soil C stabilization is relatively unknown. Phenotypic variability in plant root biomass could impact C cycling through belowground plant allocation, rooting architecture, and microbial community abundance and composition...

Learned filters for object detection in multi-object visual tracking

NASA Astrophysics Data System (ADS)

Stamatescu, Victor; Wong, Sebastien; McDonnell, Mark D.; Kearney, David

2016-05-01

We investigate the application of learned convolutional filters in multi-object visual tracking. The filters were learned in both a supervised and unsupervised manner from image data using artificial neural networks. This work follows recent results in the field of machine learning that demonstrate the use learned filters for enhanced object detection and classification. Here we employ a track-before-detect approach to multi-object tracking, where tracking guides the detection process. The object detection provides a probabilistic input image calculated by selecting from features obtained using banks of generative or discriminative learned filters. We present a systematic evaluation of these convolutional filters using a real-world data set that examines their performance as generic object detectors.

Development of a Centrifugal Technique for the Microbial Bioburden Analysis of Freon (CFC-11)

NASA Technical Reports Server (NTRS)

Benardini, James N.; Koukol, Robert C.; Kazarians, Gayane A.; Morales, Fabian

2013-01-01

NASA Procedural Requirement 8020.12C entitled "Planetary Protection Provisions for Robotic Extraterrestrial Missions" states that the source-specific encapsulated microbial density for encapsulated organisms (div(0)) in nonmetallic materials ranges from 1-30 spores/cubic cm. The standard laboratory procedure, NASA Standard Procedures for the Microbial Examination of Space Hardware, NHB 5340.1B, does not provide any direction into the methodologies to understand the bioburden within such a fluid as CFC-11 (Freon). This general specification value for the Freon would be applicable to the Freon charged within the Mars Science Laboratory fs (MSL fs) Heat Rejection System. Due to the large volume required to fill this system, MSL could not afford to conservatively allocate 55.8% of the total spore budget of the entire laboratory system (rover, descent stage, cruise stage, and aeroshell) of 5.00 X 10(exp 5) spores at launch. A novel filtration approach was developed to analyze the Freon employing a 50 kDa molecular weight cutoff (MCO) filter, followed by 0.22-micron pore-size filter to establish a calculated microbial bioburden.

Investigation of the effects of slow-release fertilizer and struvite in biodegradation in filter drains and potential application of treated water in irrigation of road verges.

PubMed

Theophilus, Stephen C; Mbanaso, Fredrick U; Nnadi, Ernest O; Onyedeke, Kingsley T

2017-11-14

Filter drains are usually laid along the margins of highways. Highway runoffs are polluted with hydrocarbons and high levels of total dissolved solids. Therefore, effective pollution removal mechanism is necessary in order to avoid contamination of surrounding soils and groundwater. Biodegradation is amongst pollution removal mechanisms in filter drains, but it is a relatively slow process which is dependent on wide range of factors including the type of pollutant and availability of nutrients. This paper reports on a study conducted to investigate the impact of slow-release fertilizer and struvite in enhancement of biodegradation of hydrocarbon in filter drains. Filter drain models incorporated with geotextile were challenged with cumulative oil loading of 178 mg/m 2 /week with a view to comparing the efficiency of these two nutrient sources under high oil pollution loading and realistic rainfall conditions of 13 mm/week. Nutrients and street dust were applied at one-off rate of 17 g/m 2 and 1.55 g/rig to provide nutrient enhancement and simulate field conditions respectively. The impact of the nutrients was studied by monitoring bacterial and fungal growth using nutrient agar, Rose Bengal Agar media and CO2 evolution. EC, pH, heavy metals, TPH, elemental analysis and SAR were used to investigate water quality of effluent of filter drains for potential application as irrigation fluid for trees and flowers planted on road verges. The results show that nutrient application encouraged microbial activities and enhanced biodegradation rates with differences in type of nutrient applied. Also, it was observed that incorporation of geotextiles in filter drains improved pollution retention efficiency and there is a potential opportunity for utilization of struvite in SuDS systems as sustainable nutrient source.

Genome-wide exploration of silicon (Si) transporter genes, Lsi1 and Lsi2 in plants; insights into Si-accumulation status/capacity of plants.

PubMed

Vatansever, Recep; Ozyigit, Ibrahim Ilker; Filiz, Ertugrul; Gozukirmizi, Nermin

2017-04-01

Silicon (Si) is a nonessential, beneficial micronutrient for plants. It increases the plant stress tolerance in relation to its accumulation capacity. In this work, root Si transporter genes were characterized in 17 different plants and inferred for their Si-accumulation status. A total of 62 Si transporter genes (31 Lsi1 and 31 Lsi2) were identified in studied plants. Lsi1s were 261-324 residues protein with a MIP family domain whereas Lsi2s were 472-547 residues with a citrate transporter family domain. Lsi1s possessed characteristic sequence features that can be employed as benchmark in prediction of Si-accumulation status/capacity of the plants. Silicic acid selectivity in Lsi1s was associated with two highly conserved NPA (Asn-Pro-Ala) motifs and a Gly-Ser-Gly-Arg (GSGR) ar/R filter. Two NPA regions were present in all Lsi1 members but some Ala substituted with Ser or Val. GSGR filter was only available in the proposed high and moderate Si accumulators. In phylogeny, Lsi1s formed three clusters as low, moderate and high Si accumulators based on tree topology and availability of GSGR filter. Low-accumulators contained filters WIGR, AIGR, FAAR, WVAR and AVAR, high-accumulators only with GSGR filter, and moderate-accumulators mostly with GSGR but some with A/CSGR filters. A positive correlation was also available between sequence homology and Si-accumulation status of the tested plants. Thus, availability of GSGR selectivity filter and sequence homology degree could be used as signatures in prediction of Si-accumulation status in experimentally uncharacterized plants. Moreover, interaction partner and expression profile analyses implicated the involvement of Si transporters in plant stress tolerance.

Impact of Substratum Surface on Microbial Community Structure and Treatment Performance in Biological Aerated Filters

PubMed Central

Kim, Lavane; Pagaling, Eulyn; Zuo, Yi Y.

2014-01-01

The impact of substratum surface property change on biofilm community structure was investigated using laboratory biological aerated filter (BAF) reactors and molecular microbial community analysis. Two substratum surfaces that differed in surface properties were created via surface coating and used to develop biofilms in test (modified surface) and control (original surface) BAF reactors. Microbial community analysis by 16S rRNA gene-based PCR-denaturing gradient gel electrophoresis (DGGE) showed that the surface property change consistently resulted in distinct profiles of microbial populations during replicate reactor start-ups. Pyrosequencing of the bar-coded 16S rRNA gene amplicons surveyed more than 90% of the microbial diversity in the microbial communities and identified 72 unique bacterial species within 19 bacterial orders. Among the 19 orders of bacteria detected, Burkholderiales and Rhodocyclales of the Betaproteobacteria class were numerically dominant and accounted for 90.5 to 97.4% of the sequence reads, and their relative abundances in the test and control BAF reactors were different in consistent patterns during the two reactor start-ups. Three of the five dominant bacterial species also showed consistent relative abundance changes between the test and control BAF reactors. The different biofilm microbial communities led to different treatment efficiencies, with consistently higher total organic carbon (TOC) removal in the test reactor than in the control reactor. Further understanding of how surface properties affect biofilm microbial communities and functional performance would enable the rational design of new generations of substrata for the improvement of biofilm-based biological treatment processes. PMID:24141134

Amino acid production exceeds plant nitrogen demand in Siberian tundra

NASA Astrophysics Data System (ADS)

Wild, Birgit; Eloy Alves, Ricardo J.; Bárta, Jiři; Čapek, Petr; Gentsch, Norman; Guggenberger, Georg; Hugelius, Gustaf; Knoltsch, Anna; Kuhry, Peter; Lashchinskiy, Nikolay; Mikutta, Robert; Palmtag, Juri; Prommer, Judith; Schnecker, Jörg; Shibistova, Olga; Takriti, Mounir; Urich, Tim; Richter, Andreas

2018-03-01

Arctic plant productivity is often limited by low soil N availability. This has been attributed to slow breakdown of N-containing polymers in litter and soil organic matter (SOM) into smaller, available units, and to shallow plant rooting constrained by permafrost and high soil moisture. Using 15N pool dilution assays, we here quantified gross amino acid and ammonium production rates in 97 active layer samples from four sites across the Siberian Arctic. We found that amino acid production in organic layers alone exceeded literature-based estimates of maximum plant N uptake 17-fold and therefore reject the hypothesis that arctic plant N limitation results from slow SOM breakdown. High microbial N use efficiency in organic layers rather suggests strong competition of microorganisms and plants in the dominant rooting zone. Deeper horizons showed lower amino acid production rates per volume, but also lower microbial N use efficiency. Permafrost thaw together with soil drainage might facilitate deeper plant rooting and uptake of previously inaccessible subsoil N, and thereby promote plant productivity in arctic ecosystems. We conclude that changes in microbial decomposer activity, microbial N utilization and plant root density with soil depth interactively control N availability for plants in the Arctic.

Comparing methods of artificially regenerating loblolly and slash pines: container planting, bareroot planting, and spot seeding

Treesearch

James D. Haywood; James P Barnett

1994-01-01

In central Louisiana, loblolly (Pinus taeda L.) and slash (P. elliottii Engelm. var. elliottii,) pines were artificially regenerated by three methods: (1)planting 14-week-old container stock, (2)planting 1+0 bareroot stock, and (3)spot seeding. A common seed source was use for each species for all regeneration...

Genome-Based Models to Optimize In Situ Bioremediation of Uranium and Harvesting Electrical Energy from Waste Organic Matter

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lovley, Derek R

2012-12-28

The goal of this research was to provide computational tools to predictively model the behavior of two microbial communities of direct relevance to Department of Energy interests: 1) the microbial community responsible for in situ bioremediation of uranium in contaminated subsurface environments; and 2) the microbial community capable of harvesting electricity from waste organic matter and renewable biomass. During this project the concept of microbial electrosynthesis, a novel form of artificial photosynthesis for the direct production of fuels and other organic commodities from carbon dioxide and water was also developed and research was expanded into this area as well.

Flatness-based model inverse for feed-forward braking control

NASA Astrophysics Data System (ADS)

de Vries, Edwin; Fehn, Achim; Rixen, Daniel

2010-12-01

For modern cars an increasing number of driver assistance systems have been developed. Some of these systems interfere/assist with the braking of a car. Here, a brake actuation algorithm for each individual wheel that can respond to both driver inputs and artificial vehicle deceleration set points is developed. The algorithm consists of a feed-forward control that ensures, within the modelled system plant, the optimal behaviour of the vehicle. For the quarter-car model with LuGre-tyre behavioural model, an inverse model can be derived using v x as the 'flat output', that is, the input for the inverse model. A number of time derivatives of the flat output are required to calculate the model input, brake torque. Polynomial trajectory planning provides the needed time derivatives of the deceleration request. The transition time of the planning can be adjusted to meet actuator constraints. It is shown that the output of the trajectory planning would ripple and introduce a time delay when a gradual continuous increase of deceleration is requested by the driver. Derivative filters are then considered: the Bessel filter provides the best symmetry in its step response. A filter of same order and with negative real-poles is also used, exhibiting no overshoot nor ringing. For these reasons, the 'real-poles' filter would be preferred over the Bessel filter. The half-car model can be used to predict the change in normal load on the front and rear axle due to the pitching of the vehicle. The anticipated dynamic variation of the wheel load can be included in the inverse model, even though it is based on a quarter-car. Brake force distribution proportional to normal load is established. It provides more natural and simpler equations than a fixed force ratio strategy.

Design of order statistics filters using feedforward neural networks

NASA Astrophysics Data System (ADS)

Maslennikova, Yu. S.; Bochkarev, V. V.

2016-08-01

In recent years significant progress have been made in the development of nonlinear data processing techniques. Such techniques are widely used in digital data filtering and image enhancement. Many of the most effective nonlinear filters based on order statistics. The widely used median filter is the best known order statistic filter. Generalized form of these filters could be presented based on Lloyd's statistics. Filters based on order statistics have excellent robustness properties in the presence of impulsive noise. In this paper, we present special approach for synthesis of order statistics filters using artificial neural networks. Optimal Lloyd's statistics are used for selecting of initial weights for the neural network. Adaptive properties of neural networks provide opportunities to optimize order statistics filters for data with asymmetric distribution function. Different examples demonstrate the properties and performance of presented approach.

Advancing the science of microbial symbiosis to support invasive species management: a case study on Phragmites in the Great Lakes

PubMed Central

Kowalski, Kurt P.; Bacon, Charles; Bickford, Wesley; Braun, Heather; Clay, Keith; Leduc-Lapierre, Michèle; Lillard, Elizabeth; McCormick, Melissa K.; Nelson, Eric; Torres, Monica; White, James; Wilcox, Douglas A.

2015-01-01

A growing body of literature supports microbial symbiosis as a foundational principle for the competitive success of invasive plant species. Further exploration of the relationships between invasive species and their associated microbiomes, as well as the interactions with the microbiomes of native species, can lead to key new insights into invasive success and potentially new and effective control approaches. In this manuscript, we review microbial relationships with plants, outline steps necessary to develop invasive species control strategies that are based on those relationships, and use the invasive plant species Phragmites australis (common reed) as an example of how development of microbial-based control strategies can be enhanced using a collective impact approach. The proposed science agenda, developed by the Collaborative for Microbial Symbiosis and Phragmites Management, contains a foundation of sequential steps and mutually-reinforcing tasks to guide the development of microbial-based control strategies for Phragmites and other invasive species. Just as the science of plant-microbial symbiosis can be transferred for use in other invasive species, so too can the model of collective impact be applied to other avenues of research and management. PMID:25745417

Advancing the science of microbial symbiosis to support invasive species management: a case study on Phragmites in the Great Lakes.

PubMed

Kowalski, Kurt P; Bacon, Charles; Bickford, Wesley; Braun, Heather; Clay, Keith; Leduc-Lapierre, Michèle; Lillard, Elizabeth; McCormick, Melissa K; Nelson, Eric; Torres, Monica; White, James; Wilcox, Douglas A

2015-01-01

A growing body of literature supports microbial symbiosis as a foundational principle for the competitive success of invasive plant species. Further exploration of the relationships between invasive species and their associated microbiomes, as well as the interactions with the microbiomes of native species, can lead to key new insights into invasive success and potentially new and effective control approaches. In this manuscript, we review microbial relationships with plants, outline steps necessary to develop invasive species control strategies that are based on those relationships, and use the invasive plant species Phragmites australis (common reed) as an example of how development of microbial-based control strategies can be enhanced using a collective impact approach. The proposed science agenda, developed by the Collaborative for Microbial Symbiosis and Phragmites Management, contains a foundation of sequential steps and mutually-reinforcing tasks to guide the development of microbial-based control strategies for Phragmites and other invasive species. Just as the science of plant-microbial symbiosis can be transferred for use in other invasive species, so too can the model of collective impact be applied to other avenues of research and management.

Advancing the science of microbial symbiosis to support invasive species management: a case study on Phragmites in the Great Lakes

USGS Publications Warehouse

Kowalski, Kurt P.; Bacon, Charles R.; Bickford, Wesley A.; Braun, Heather A.; Clay, Keith; Leduc-Lapierre, Michele; Lillard, Elizabeth; McCormick, Melissa K.; Nelson, Eric; Torres, Monica; White, James W. C.; Wilcox, Douglas A.

2015-01-01

A growing body of literature supports microbial symbiosis as a foundational principle for the competitive success of invasive plant species. Further exploration of the relationships between invasive species and their associated microbiomes, as well as the interactions with the microbiomes of native species, can lead to key new insights into invasive success and potentially new and effective control approaches. In this manuscript, we review microbial relationships with plants, outline steps necessary to develop invasive species control strategies that are based on those relationships, and use the invasive plant species Phragmites australis (common reed) as an example of how development of microbial-based control strategies can be enhanced using a collective impact approach. The proposed science agenda, developed by the Collaborative for Microbial Symbiosis andPhragmites Management, contains a foundation of sequential steps and mutually-reinforcing tasks to guide the development of microbial-based control strategies for Phragmites and other invasive species. Just as the science of plant-microbial symbiosis can be transferred for use in other invasive species, so too can the model of collective impact be applied to other avenues of research and management.

DNA Isolation of Microbial Contaminants in Aviation Turbine Fuel via Traditional Polymerase Chain Reaction (PCR) and Direct PCR. Preliminary Results

DTIC Science & Technology

2005-11-01

fuel gauge malfunctions, fuel line and filter plugging, and corrosion. As a result, there is considerable interest in identifying microbial growth ...corrosion. As a result, there is considerable interest in identifying microbial growth and finding strategies to mitigate it. Previous research to... Rhodotorula sp. Yes Yes Trichosporium sp. Yes Trichoderma sp. (viride + others) Yes Yes 4 Table 2. Culturability Determined as a Percentage of

Implications of altered rainfall and exotic plants on soil microbial communities and carbon biomass

NASA Astrophysics Data System (ADS)

Castro, S.; Lipson, D.; Cleland, E. E.

2016-12-01

Climate and exotic plant disturbances are among the most significant threats to Mediterranean-type ecosystems, compromising their renowned biodiversity and role in the global carbon cycle. Predicted shifts in rainfall patterns have become a particular concern, especially when interactions with other stressors and effects on biogeochemical processes remain poorly understood. To understand the impacts of altered rainfall on belowground dynamics as well as the role of inter- and intra-annual variation and plant community composition, we monitored soil microbial communities under native and exotic plant dominated plots with rainfall manipulation treatments in a semi-arid Mediterranean-type ecosystem. We measured microbial biomass, respiration rates, and community structure across treatments and vegetation types. Soil moisture and dissolved organic carbon were also measured to characterize abiotic soil properties. The soil moisture gradient established by the rainfall treatments had a positive correlation with microbial biomass carbon under native- and exotic-dominated plots but had no effect on respiration rates. A significant reduction in microbial biomass under exotic plants was found in 2013 but not in 2014 and 2015. Substrate-induced respiration values were higher in the exotic-dominated plots during the spring seasons, resulting in a significant interaction between plant community type and season. Bacterial communities showed little variation except in the Proteobacteria phyla, which was lower in exotic plants-dominated plots. Dissolved organic carbon was significantly reduced in exotic-dominated plots by approximately 26% based on average values of all plots throughout. Our results illustrate that rainfall quantity and exotic plants can cause changes in microbial biomass, community composition and respiration rates jeopardizing soil carbon storage. They also reinforce the importance of temporal variability and the need for repeated sampling to correctly interpret environmental changes in semi-arid ecosystems. We conclude that to improve predictions of the implications of global stressors on biogeochemical cycles in semi-arid ecosystems, there is a need to incorporate microbial data with the understanding that it is highly dependent on temporal dynamics and plant community.

Apparatus and process for microbial detection and enumeration

NASA Technical Reports Server (NTRS)

Wilkins, J. R.; Grana, D. (Inventor)

1982-01-01

An apparatus and process for detecting and enumerating specific microorganisms from large volume samples containing small numbers of the microorganisms is presented. The large volume samples are filtered through a membrane filter to concentrate the microorganisms. The filter is positioned between two absorbent pads and previously moistened with a growth medium for the microorganisms. A pair of electrodes are disposed against the filter and the pad electrode filter assembly is retained within a petri dish by retainer ring. The cover is positioned on base of petri dish and sealed at the edges by a parafilm seal prior to being electrically connected via connectors to a strip chart recorder for detecting and enumerating the microorganisms collected on filter.

Ion Permeability of Artificial Membranes Evaluated by Diffusion Potential and Electrical Resistance Measurements

ERIC Educational Resources Information Center

Shlyonsky, Vadim

2013-01-01

In the present article, a novel model of artificial membranes that provides efficient assistance in teaching the origins of diffusion potentials is proposed. These membranes are made of polycarbonate filters fixed to 12-mm plastic rings and then saturated with a mixture of creosol and "n"-decane. The electrical resistance and potential…

Removal of Cr, Mn, and Co from textile wastewater by horizontal rotating tubular bioreactor.

PubMed

Zeiner, Michaela; Rezić, Tonci; Santek, Bozidar; Rezić, Iva; Hann, Stephan; Stingeder, Gerhard

2012-10-02

Environmental pollution by industrial wastewaters polluted with toxic heavy metals is of great concern. Various guidelines regulate the quality of water released from industrial plants and of surface waters. In wastewater treatment, bioreactors with microbial biofilms are widely used. A horizontal rotating tubular bioreactor (HRTB) is a combination of a thin layer and a biodisc reactor with an interior divided by O-ring shaped partition walls as carriers for microbial biomass. Using a biofilm of heavy metal resistant bacteria in combination with this special design provides various advantages for wastewater treatment proven in a pilot study. In the presented study, the applicability of HRTB for removing metals commonly present in textile wastewaters (chromium, manganese, cobalt) was investigated. Artificial wastewaters with a load of 125 mg/L of each metal underwent the bioreactor treatment. Different process parameters (inflow rate, rotation speed) were applied for optimizing the removal efficiency. Samples were drawn along the bioreactor length for monitoring the metal contents on site by UV-vis spectrometry. The metal uptake of the biomass was determined by ICP-MS after acidic microwave assisted digestion. The maximum removal rates obtained for chromium, manganese, and cobalt were: 100%, 94%, and 69%, respectively.

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

NASA Astrophysics Data System (ADS)

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.

Management of Bottom Sediments Containing Toxic Substances: Proceedings of the U.S./Japan Experts Meeting (9th) Held at Jacksonville, Florida on 17-19 October 1983

DTIC Science & Technology

1985-03-01

maturation process in the laboratory. Females can then be artificially inseminated . One advantage of this technology is a much reduced cost of obtaining...installed at canal zones. Artificial cascades and dams are also considered effective when installed at canal zones. Therefore, these two types have...centrifuge or a filter press "procedure. These methods release nutrients dynami- cally by artificial forces duri 4 water separation. However, the

Levels and limits in artificial selection of communities.

PubMed

Blouin, Manuel; Karimi, Battle; Mathieu, Jérôme; Lerch, Thomas Z

2015-10-01

Artificial selection of individuals has been determinant in the elaboration of the Darwinian theory of natural selection. Nowadays, artificial selection of ecosystems has proven its efficiency and could contribute to a theory of natural selection at several organisation levels. Here, we were not interested in identifying mechanisms of adaptation to selection, but in establishing the proof of principle that a specific structure of interaction network emerges under ecosystem artificial selection. We also investigated the limits in ecosystem artificial selection to evaluate its potential in terms of managing ecosystem function. By artificially selecting microbial communities for low CO2 emissions over 21 generations (n = 7560), we found a very high heritability of community phenotype (52%). Artificial selection was responsible for simpler interaction networks with lower interaction richness. Phenotype variance and heritability both decreased across generations, suggesting that selection was more likely limited by sampling effects than by stochastic ecosystem dynamics. © 2015 John Wiley & Sons Ltd/CNRS.

Toward Understanding, Managing, and Protecting Microbial Ecosystems

PubMed Central

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

Weathering of pyrogenic organic matter induces fungal oxidative enzyme response in single culture inoculation experiments.

PubMed

Gibson, Christy; Berry, Timothy D; Wang, Ruzhen; Spencer, Julie A; Johnston, Cliff T; Jiang, Yong; Bird, Jeffrey A; Filley, Timothy R

2016-02-01

The addition of pyrogenic organic matter (PyOM), the aromatic carbon-rich product of the incomplete combustion of plant biomass or fossil fuels, to soil can influence the rate of microbial metabolism of native soil carbon. The interaction of soil heterotrophs with PyOM may be governed by the surficial chemical and physical properties of PyOM that evolve with environmental exposure. We present results of a 36-day laboratory incubation investigating the interaction of a common white-rot fungus, Trametes versicolor, with three forms of 13 C-enriched (2.08 atom% 13 C) PyOM derived from Pinus ponderosa (450 °C): one freshly produced, and two artificially weathered (254 nm, UV light-water treatment and water-leaching alone). Analysis (FTIR, XPS) of the UV-weathered PyOM showed increased aliphatic C-H content and oxidation of aromatic carbon relative to both the original and water-leached PyOM. The addition of both weathered forms of PyOM stimulated (positively primed) fungal respiration of the growth media, while the unaltered PyOM mildly inhibited (negatively primed) respiration. Artificial weathering resulted in higher oxidative (laccase and peroxidase) enzyme activity than unaltered PyOM, possibly the result of a diminished capacity to bind reactive substrates and extracellular enzymes after weathering. However, and contrary to expectations, simple water-leached weathering resulted in a relatively higher enzyme activity and respiration than that of UV-weathering. The 13 C content of respired CO 2 indicated negligible fungal oxidation of PyOM for all treatments, demonstrating the overall low microbial reactivity of this high temperature PyOM. The increased enzymatic and positive priming response of T. versicolor to weathered PyOM highlights the importance of weathering-induced chemistry in controlling PyOM-microbe-soil carbon interactions.

The coupling of the plant and microbial catabolisms of phenanthrene in the rhizosphere of Medicago sativa.

PubMed

Muratova, Anna; Dubrovskaya, Ekaterina; Golubev, Sergey; Grinev, Vyacheslav; Chernyshova, Marina; Turkovskaya, Olga

2015-09-01

We studied the catabolism of the polycyclic aromatic hydrocarbon phenanthrene by four rhizobacterial strains and the possibility of enzymatic oxidation of this compound and its microbial metabolites by the root exudates of alfalfa (Medicago sativa L.) in order to detect the possible coupling of the plant and microbial metabolisms under the rhizospheric degradation of the organic pollutant. A comparative study of phenanthrene degradation pathways in the PAH-degrading rhizobacteria Ensifer meliloti, Pseudomonas kunmingensis, Rhizobium petrolearium, and Stenotrophomonas sp. allowed us to identify the key metabolites from the microbial transformation of phenanthrene, including 9,10-phenanthrenequinone, 2-carboxybenzaldehyde, and 1-hydroxy-2-naphthoic, salicylic, and o-phthalic acids. Sterile alfalfa plants were grown in the presence and absence of phenanthrene (0.03 g kg(-1)) in quartz sand under controlled environmental conditions to obtain plant root exudates. The root exudates were collected, concentrated by ultrafiltration, and the activity of oxidoreductases was detected spectrophotometrically by the oxidation rate for various substrates. The most marked activity was that of peroxidase, whereas the presence of oxidase and tyrosinase was detected on the verge of the assay sensitivity. Using alfalfa root exudates as a crude enzyme preparation, we found that in the presence of the synthetic mediator, the plant peroxidase could oxidize phenanthrene and its microbial metabolites. The results indicate the possibility of active participation of plants in the rhizospheric degradation of polycyclic aromatic hydrocarbons and their microbial metabolites, which makes it possible to speak about the coupling of the plant and microbial catabolisms of these contaminants in the rhizosphere. Copyright © 2015 Elsevier GmbH. All rights reserved.

Soil fertility and plant diversity enhance microbial performance in metal-polluted soils.

PubMed

Stefanowicz, Anna M; Kapusta, Paweł; Szarek-Łukaszewska, Grażyna; Grodzińska, Krystyna; Niklińska, Maria; Vogt, Rolf D

2012-11-15

This study examined the effects of soil physicochemical properties (including heavy metal pollution) and vegetation parameters on soil basal respiration, microbial biomass, and the activity and functional richness of culturable soil bacteria and fungi. In a zinc and lead mining area (S Poland), 49 sites were selected to represent all common plant communities and comprise the area's diverse soil types. Numerous variables describing habitat properties were reduced by PCA to 7 independent factors, mainly representing subsoil type (metal-rich mining waste vs. sand), soil fertility (exchangeable Ca, Mg and K, total C and N, organic C), plant species richness, phosphorus content, water-soluble heavy metals (Zn, Cd and Pb), clay content and plant functional diversity (based on graminoids, legumes and non-leguminous forbs). Multiple regression analysis including these factors explained much of the variation in most microbial parameters; in the case of microbial respiration and biomass, it was 86% and 71%, respectively. The activity of soil microbes was positively affected mainly by soil fertility and, apparently, by the presence of mining waste in the subsoil. The mining waste contained vast amounts of trace metals (total Zn, Cd and Pb), but it promoted microbial performance due to its inherently high content of macronutrients (total Ca, Mg, K and C). Plant species richness had a relatively strong positive effect on all microbial parameters, except for the fungal component. In contrast, plant functional diversity was practically negligible in its effect on microbes. Other explanatory variables had only a minor positive effect (clay content) or no significant influence (phosphorus content) on microbial communities. The main conclusion from this study is that high nutrient availability and plant species richness positively affected the soil microbes and that this apparently counteracted the toxic effects of metal contamination. Copyright © 2012 Elsevier B.V. All rights reserved.

The core microbiome bonds the Alpine bog vegetation to a transkingdom metacommunity.

PubMed

Bragina, Anastasia; Berg, Christian; Berg, Gabriele

2015-09-01

Bog ecosystems fulfil important functions in Earth's carbon and water turnover. While plant communities and their keystone species Sphagnum have been well studied, less is known about the microbial communities associated with them. To study our hypothesis that bog plants share an essential core of their microbiome despite their different phylogenetic origins, we analysed four plant community plots with 24 bryophytes, vascular plants and lichen species in two Alpine bogs in Austria by 16S rDNA amplicon sequencing followed by bioinformatic analyses. The overall bog microbiome was classified into 32 microbial phyla, while Proteobacteria (30.8%), Verrucomicrobia (20.3%) and Planctomycetes (15.1%) belonged to the most abundant groups. Interestingly, the archaeal phylum Euryarcheota represented 7.2% of total microbial abundance. However, a high portion of micro-organisms remained unassigned at phylum and class level, respectively. The core microbiome of the bog vegetation contained 177 operational taxonomic units (OTUs) (150 526 seq.) and contributed to 49.5% of the total microbial abundance. Only a minor portion of associated core micro-organisms was host specific for examined plant groups (5.9-11.6%). Using our new approach to analyse plant-microbial communities in an integral framework of ecosystem, vegetation and microbiome, we demonstrated that bog vegetation harboured a core microbiome that is shared between plants and lichens over the whole ecosystem and formed a transkingdom metacommunity. All micro- and macro-organisms are connected to keystone Sphagnum mosses via set of microbial species, for example Burkholderia bryophila which was found associated with a wide spectrum of host plants and is known for a beneficial plant-microbe interaction. © 2015 John Wiley & Sons Ltd.

Microbial biomass as a significant source of soil organic matter

NASA Astrophysics Data System (ADS)

Miltner, Anja; Kindler, Reimo; Schweigert, Michael; Achtenhagen, Jan; Bombach, Petra; Fester, Thomas; Kästner, Matthias

2014-05-01

Soil organic matter (SOM) plays an important role for soil fertility and in the global carbon cycle. SOM management should be based on knowledge about the chemical composition as well as the spatial distribution of SOM and its individual components in soils. Both parameters strongly depend on the direct precursors of SOM. In the past, microbial biomass has been neglected as a potential source of SOM, mainly because of its small pool size. Recent studies, however, show that a substantial portion of SOM is derived from microbial biomass residues. We therefore investigated the fate of microbial biomass residues in soils by means of incubation experiments with 13C-labelled microbial biomass. For our studies, we selected model organisms representing the three types of soil microorganisms and their characteristic cell wall structures: Escherichia coli (a Gram-negative bacterium), Bacillus subtilis (a Gram-positive bacterium) and Laccaria bicolor (an ectomycorrhizal fungus). We labelled the organisms by growing them on 13C glucose and incubated them in soil. During incubation, we followed the mineralisation of the labelled C, its incorporation into microbial biomass, and its transformation to non-living SOM. We found that 50-65% of the microbial biomass C remained in the soil during incubation. However, only a small part remained in the microbial biomass, the majority was transformed to SOM. In particular, proteins seemed to be rather stable in our experiments. In addition, we used scanning electron microscopy to identify microbial residues in soils and, for comparison, in artificial groundwater microcosms. Scanning electron micrographs showed a low number of intact cells, but mainly fragments of about 200-500 nm size. Similar fragments were found in artificial groundwater microcosms where the only possible origin was microbial biomass residues. Based on the results obtained, we provide a mechanistic model which explains how microbial biomass residues are formed and stabilized in soils. This model also explains a number of chemical and physical properties of SOM such as the abundance and stability of microbial biomolecules, the low C/N ratio and the water repellency of SOM.

Depth dependent microbial carbon use efficiency in the capillary fringe as affected by water table fluctuations in a column incubation experiment

NASA Astrophysics Data System (ADS)

Pronk, G. J.; Mellage, A.; Milojevic, T.; Smeaton, C. M.; Rezanezhad, F.; Van Cappellen, P.

2017-12-01

Microbial growth and turnover of soil organic carbon (SOC) depend on the availability of electron donors and acceptors. The steep geochemical gradients in the capillary fringe between the saturated and unsaturated zones provide hotspots of soil microbial activity. Water table fluctuations and the associated drying and wetting cycles within these zones have been observed to lead to enhanced turnover of SOC and adaptation of the local microbial communities. To improve our understanding of SOC degradation under changing moisture conditions, we carried out an automated soil column experiment with integrated of hydro-bio-geophysical monitoring under both constant and oscillating water table conditions. An artificial soil mixture composed of quartz sand, montmorillonite, goethite and humus was used to provide a well-defined system. This material was inoculated with a microbial community extracted from a forested riparian zone. The soils were packed into 6 columns (60 cm length and 7.5 cm inner diameter) to a height of 45 cm; and three replicate columns were incubated under constant water table while another three were saturated and drained monthly. The initial soil development, carbon cycling and microbial community development were then characterized during 10 months of incubation. This system provides an ideal artificial gradient from the saturated to the unsaturated zone to study soil development from initially homogeneous materials and the same microbial community composition under controlled conditions. Depth profiles of SOC and microbial biomass after 329 days of incubation showed a depletion of carbon in the transition drying and wetting zone that was not associated with higher accumulation of microbial biomass, indicating a lower carbon use efficiency of the microbial community established within the water table fluctuation zone. This was supported by a higher ATP to microbial biomass carbon ratio within the same zone. The findings from this study highlight the importance of considering the effects of transient soil moisture and oxygen availability on microbial mediated SOC transformations. The effects of these changes in carbon use efficiency need to be included in soil models in order to accurately predict SOC turnover.

Incorporating the soil environment and microbial community into plant competition theory

PubMed Central

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

Effects of Different Regeneration Scenarios and Fertilizer Treatments on Soil Microbial Ecology in Reclaimed Opencast Mining Areas on the Loess Plateau, China

PubMed Central

Li, Junjian; Zheng, Yuanming; Yan, Junxia; Li, Hongjian; Wang, Xiang; He, Jizheng; Ding, Guangwei

2013-01-01

The soil microbial community in reclaimed mining areas is fundamental to vegetative establishment. However, how this community responds to different regeneration scenarios and fertilizer treatments is poorly understood. This research evaluated plant and soil microbial communities from different regeneration scenarios and different fertilizer treatments. Regeneration scenarios significantly influenced soil bacterial, archaeal, and fungal rDNA abundance. The ratios of fungi to bacteria or archaea were increased with fertilizer application. The diversity of both plants and microbes was lowest in Lotus corniculatus grasslands. Regeneration scenario, fertilizer treatment, and their interaction influenced soil microbial richness, diversity and evenness indices. Labile carbon pool 2 was a significant factor affected plant and microbe communities in July, suggesting that plants and microbes may be competing for nutrients. The higher ratios of positive to negative association were found in soil bacteria and total microbe than in archaea and fungi. Stronger clustering of microbial communities from the same regeneration scenario indicated that the vegetative composition of regeneration site may have a greater influence on soil microbial communities than fertilizer treatment. PMID:23658819

Aquatic Plants Aid Sewage Filter

NASA Technical Reports Server (NTRS)

Wolverton, B. C.

1985-01-01

Method of wastewater treatment combines micro-organisms and aquatic plant roots in filter bed. Treatment occurs as liquid flows up through system. Micro-organisms, attached themselves to rocky base material of filter, act in several steps to decompose organic matter in wastewater. Vascular aquatic plants (typically, reeds, rushes, cattails, or water hyacinths) absorb nitrogen, phosphorus, other nutrients, and heavy metals from water through finely divided roots.

The Microbial Efficiency-Matrix Stabilization (MEMS) framework integrates plant litter decomposition with soil organic matter stabilization: do labile plant inputs form stable soil organic matter?

PubMed

Cotrufo, M Francesca; Wallenstein, Matthew D; Boot, Claudia M; Denef, Karolien; Paul, Eldor

2013-04-01

The decomposition and transformation of above- and below-ground plant detritus (litter) is the main process by which soil organic matter (SOM) is formed. Yet, research on litter decay and SOM formation has been largely uncoupled, failing to provide an effective nexus between these two fundamental processes for carbon (C) and nitrogen (N) cycling and storage. We present the current understanding of the importance of microbial substrate use efficiency and C and N allocation in controlling the proportion of plant-derived C and N that is incorporated into SOM, and of soil matrix interactions in controlling SOM stabilization. We synthesize this understanding into the Microbial Efficiency-Matrix Stabilization (MEMS) framework. This framework leads to the hypothesis that labile plant constituents are the dominant source of microbial products, relative to input rates, because they are utilized more efficiently by microbes. These microbial products of decomposition would thus become the main precursors of stable SOM by promoting aggregation and through strong chemical bonding to the mineral soil matrix. © 2012 Blackwell Publishing Ltd.

New Methods for Analysis of Spatial Distribution and Coaggregation of Microbial Populations in Complex Biofilms

PubMed Central

Almstrand, Robert; Daims, Holger; Persson, Frank; Sörensson, Fred

2013-01-01

In biofilms, microbial activities form gradients of substrates and electron acceptors, creating a complex landscape of microhabitats, often resulting in structured localization of the microbial populations present. To understand the dynamic interplay between and within these populations, quantitative measurements and statistical analysis of their localization patterns within the biofilms are necessary, and adequate automated tools for such analyses are needed. We have designed and applied new methods for fluorescence in situ hybridization (FISH) and digital image analysis of directionally dependent (anisotropic) multispecies biofilms. A sequential-FISH approach allowed multiple populations to be detected in a biofilm sample. This was combined with an automated tool for vertical-distribution analysis by generating in silico biofilm slices and the recently developed Inflate algorithm for coaggregation analysis of microbial populations in anisotropic biofilms. As a proof of principle, we show distinct stratification patterns of the ammonia oxidizers Nitrosomonas oligotropha subclusters I and II and the nitrite oxidizer Nitrospira sublineage I in three different types of wastewater biofilms, suggesting niche differentiation between the N. oligotropha subclusters, which could explain their coexistence in the same biofilms. Coaggregation analysis showed that N. oligotropha subcluster II aggregated closer to Nitrospira than did N. oligotropha subcluster I in a pilot plant nitrifying trickling filter (NTF) and a moving-bed biofilm reactor (MBBR), but not in a full-scale NTF, indicating important ecophysiological differences between these phylogenetically closely related subclusters. By using high-resolution quantitative methods applicable to any multispecies biofilm in general, the ecological interactions of these complex ecosystems can be understood in more detail. PMID:23892743

Division of Energy Biosciences annual report and summaries of FY 1996 activities

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1997-04-01

The mission of the Division of Energy Biosciences is to support research that advances the fundamental knowledge necessary for the future development of biotechnologies related to the Department of Energy`s mission. The departmental civilian objectives include effective and efficient energy production, energy conservation, environmental restoration, and waste management. The Energy Biosciences program emphasizes research in the microbiological and plant sciences, as these understudied areas offer numerous scientific opportunities to dramatically influence environmentally sensible energy production and conservation. The research supported is focused on the basic mechanism affecting plant productivity, conversion of biomass and other organic materials into fuels and chemicalsmore » by microbial systems, and the ability of biological systems to replace energy-intensive or pollutant-producing processes. The Division also addresses the increasing number of new opportunities arising at the interface of biology with other basic energy-related sciences such as biosynthesis of novel materials and the influence of soil organisms on geological processes. This report gives summaries on 225 projects on photosynthesis, membrane or ion transport, plant metabolism and biosynthesis, carbohydrate metabolism lipid metabolism, plant growth and development, plant genetic regulation and genetic mechanisms, plant cell wall development, lignin-polysaccharide breakdown, nitrogen fixation and plant-microbial symbiosis, mechanism for plant adaptation, fermentative microbial metabolism, one and two carbon microbial metabolism, extremophilic microbes, microbial respiration, nutrition and metal metabolism, and materials biosynthesis.« less

Microbial Community Structure in the Rhizosphere of Rice Plants

PubMed Central

Breidenbach, Björn; Pump, Judith; Dumont, Marc G.

2016-01-01

The microbial community in the rhizosphere environment is critical for the health of land plants and the processing of soil organic matter. The objective of this study was to determine the extent to which rice plants shape the microbial community in rice field soil over the course of a growing season. Rice (Oryza sativa) was cultivated under greenhouse conditions in rice field soil from Vercelli, Italy and the microbial community in the rhizosphere of planted soil microcosms was characterized at four plant growth stages using quantitative PCR and 16S rRNA gene pyrotag analysis and compared to that of unplanted bulk soil. The abundances of 16S rRNA genes in the rice rhizosphere were on average twice that of unplanted bulk soil, indicating a stimulation of microbial growth in the rhizosphere. Soil environment type (i.e., rhizosphere versus bulk soil) had a greater effect on the community structure than did time (e.g., plant growth stage). Numerous phyla were affected by the presence of rice plants, but the strongest effects were observed for Gemmatimonadetes, Proteobacteria, and Verrucomicrobia. With respect to functional groups of microorganisms, potential iron reducers (e.g., Geobacter, Anaeromyxobacter) and fermenters (e.g., Clostridiaceae, Opitutaceae) were notably enriched in the rhizosphere environment. A Herbaspirillum species was always more abundant in the rhizosphere than bulk soil and was enriched in the rhizosphere during the early stage of plant growth. PMID:26793175

An Ankle-Foot Orthosis Powered by Artificial Pneumatic Muscles

PubMed Central

Ferris, Daniel P.; Czerniecki, Joseph M.; Hannaford, Blake

2005-01-01

We developed a pneumatically powered orthosis for the human ankle joint. The orthosis consisted of a carbon fiber shell, hinge joint, and two artificial pneumatic muscles. One artificial pneumatic muscle provided plantar flexion torque and the second one provided dorsiflexion torque. Computer software adjusted air pressure in each artificial muscle independently so that artificial muscle force was proportional to rectified low-pass-filtered electromyography (EMG) amplitude (i.e., proportional myoelectric control). Tibialis anterior EMG activated the artificial dorsiflexor and soleus EMG activated the artificial plantar flexor. We collected joint kinematic and artificial muscle force data as one healthy participant walked on a treadmill with the orthosis. Peak plantar flexor torque provided by the orthosis was 70 Nm, and peak dorsiflexor torque provided by the orthosis was 38 Nm. The orthosis could be useful for basic science studies on human locomotion or possibly for gait rehabilitation after neurological injury. PMID:16082019

Application of Aspergillus niger-treated agrowaste residue and Glomus mosseae for improving growth and nutrition of Trifolium repens in a Cd-contaminated soil.

PubMed

Medina, A; Vassilev, N; Barea, J M; Azcón, R

2005-04-06

The microbial transformation of sugar beet (SB) agrowaste with or without rock-phosphate (RP) has utility for the improvement of plant growth in a Cd (5 microg g-1) artificially contaminated soil, particularly when the soil is co-inoculated with arbuscular mycorrhizal (AM) fungus Glomus mosseae isolated from a Cd-polluted area. Under such Cd-polluted conditions, the limited growth, mineral nutrition, symbiotic developments (nodulation and AM-colonization) and soil enzymatic activities were stimulated using SB or SB+RP as soil amendments and G. mosseae as inoculant. G. mosseae enhanced plant establishment in a higher extent in amended soil; it is probably due to the interactive effect increasing the potential fertility of such compounds and its ability for decreasing Cd transfer from soil to plant. The amount of Cd transferred from soil solution to biomass of AM-colonized plants ranged from 0.09 microg Cd g-1 (in SB+RP-amended soil) to 0.6 microg Cd g-1 (in non-amended soil). Nodule formation was more sensitive to Cd than AM-colonization, and both symbioses were stimulated in amended soils. Not only AM-colonization but also amendments were critical for plant growth and nutrition in Cd-polluted soil. The high effectiveness of AM inoculum increasing nutrients and decreasing Cd in amended soil indicated the positive interaction of these treatments in increasing plant tolerance to Cd contamination.

Artificial light at night as a new threat to pollination.

PubMed

Knop, Eva; Zoller, Leana; Ryser, Remo; Gerpe, Christopher; Hörler, Maurin; Fontaine, Colin

2017-08-10

Pollinators are declining worldwide and this has raised concerns for a parallel decline in the essential pollination service they provide to both crops and wild plants. Anthropogenic drivers linked to this decline include habitat changes, intensive agriculture, pesticides, invasive alien species, spread of pathogens and climate change. Recently, the rapid global increase in artificial light at night has been proposed to be a new threat to terrestrial ecosystems; the consequences of this increase for ecosystem function are mostly unknown. Here we show that artificial light at night disrupts nocturnal pollination networks and has negative consequences for plant reproductive success. In artificially illuminated plant-pollinator communities, nocturnal visits to plants were reduced by 62% compared to dark areas. Notably, this resulted in an overall 13% reduction in fruit set of a focal plant even though the plant also received numerous visits by diurnal pollinators. Furthermore, by merging diurnal and nocturnal pollination sub-networks, we show that the structure of these combined networks tends to facilitate the spread of the negative consequences of disrupted nocturnal pollination to daytime pollinator communities. Our findings demonstrate that artificial light at night is a threat to pollination and that the negative effects of artificial light at night on nocturnal pollination are predicted to propagate to the diurnal community, thereby aggravating the decline of the diurnal community. We provide perspectives on the functioning of plant-pollinator communities, showing that nocturnal pollinators are not redundant to diurnal communities and increasing our understanding of the human-induced decline in pollinators and their ecosystem service.

50 CFR 23.23 - What information is required on U.S. and foreign CITES documents?

Code of Federal Regulations, 2012 CFR

2012-10-01

... artificially propagated plants, certificate for wildlife bred in captivity, certificate of origin, certificate..., EXPORTATION, AND IMPORTATION OF WILDLIFE AND PLANTS (CONTINUED) CONVENTION ON INTERNATIONAL TRADE IN... CITES certificate for artificially propagated plants in paragraph (f) of this section, or a customs...

50 CFR 23.23 - What information is required on U.S. and foreign CITES documents?

Code of Federal Regulations, 2013 CFR

2013-10-01

... artificially propagated plants, certificate for wildlife bred in captivity, certificate of origin, certificate..., EXPORTATION, AND IMPORTATION OF WILDLIFE AND PLANTS (CONTINUED) CONVENTION ON INTERNATIONAL TRADE IN... CITES certificate for artificially propagated plants in paragraph (f) of this section, or a customs...

50 CFR 23.23 - What information is required on U.S. and foreign CITES documents?

Code of Federal Regulations, 2010 CFR

2010-10-01

... artificially propagated plants, certificate for wildlife bred in captivity, certificate of origin, certificate..., EXPORTATION, AND IMPORTATION OF WILDLIFE AND PLANTS (CONTINUED) CONVENTION ON INTERNATIONAL TRADE IN... CITES certificate for artificially propagated plants in paragraph (f) of this section, or a customs...

50 CFR 23.23 - What information is required on U.S. and foreign CITES documents?

Code of Federal Regulations, 2011 CFR

2011-10-01

... artificially propagated plants, certificate for wildlife bred in captivity, certificate of origin, certificate..., EXPORTATION, AND IMPORTATION OF WILDLIFE AND PLANTS (CONTINUED) CONVENTION ON INTERNATIONAL TRADE IN... CITES certificate for artificially propagated plants in paragraph (f) of this section, or a customs...

Field-scale investigations on the biodegradation of chlorinated aromatic compounds and HCH in the subsurface environment

NASA Astrophysics Data System (ADS)

Feidieker, Doris; Kämpfer, Peter; Dott, Wolfgang

1995-08-01

The biological in situ remediation of a former pesticide production site, highly contaminated with chlorobenzenes, chlorophenols and hexachlorocyclohexanes, was studied for a period of one year. Field experiments testing the remediation technology were carried out in the subsurface to a depth of 5.5 m. Detailed monitoring of several chemical and microbiological parameters was made in order to evaluate the remediation success. The initial pollution of this site ranged from 0.03-0.30 g EOX (extractable halogenated organic compounds)/kg soil in the saturated layer to 1-20 g kg -1 EOX in the unsaturated layer, whereas the impounded water was polluted with 8-13 mg L -1 AOX (adsorbable halogenated organic compounds). No significant decrease of the pollutants in the subsoil was observed, although oxygen and nutrients were supplied in sufficient concentrations. In contrast, several of the chlorinated organic compounds were eliminated from the water treatment plant, either by physical or biological processes. Based on measurements of AOX in different parts of the plant, 26% of the pollutants was found adsorbed on the activated carbon and 3% was found in the sludge of the filter back-wash. Dependent on these measurements, elimination of ˜ 70% of the pollutants was attributed to microbial degradation. The latter fact is supported by oxygen consumption data, by increase in the microbial counts and by changes in the distribution of the pollutants in the plant effluent. Among the chlorobenzenes, 1,2,4-trichlorobenzene, and among the hexachlorocyclohexanes, a-hexachlorocyclohexane were eliminated preferentially. The results suggest that an in situ remediation of a site polluted with chlorinated organic compounds cannot be recommended; however, an on site circulation water treatment is possible by a combination of physical and biological processes.

Bacterial diversity and active biomass in full-scale granular activated carbon filters operated at low water temperatures.

PubMed

Kaarela, Outi E; Härkki, Heli A; Palmroth, Marja R T; Tuhkanen, Tuula A

2015-01-01

Granular activated carbon (GAC) filtration enhances the removal of natural organic matter and micropollutants in drinking water treatment. Microbial communities in GAC filters contribute to the removal of the biodegradable part of organic matter, and thus help to control microbial regrowth in the distribution system. Our objectives were to investigate bacterial community dynamics, identify the major bacterial groups, and determine the concentration of active bacterial biomass in full-scale GAC filters treating cold (3.7-9.5°C), physicochemically pretreated, and ozonated lake water. Three sampling rounds were conducted to study six GAC filters of different operation times and flow modes in winter, spring, and summer. Total organic carbon results indicated that both the first-step and second-step filters contributed to the removal of organic matter. Length heterogeneity analysis of amplified 16S rRNA genes illustrated that bacterial communities were diverse and considerably stable over time. α-Proteobacteria, β-Proteobacteria, and Nitrospira dominated in all of the GAC filters, although the relative proportion of dominant phylogenetic groups in individual filters differed. The active bacterial biomass accumulation, measured as adenosine triphosphate, was limited due to low temperature, low flux of nutrients, and frequent backwashing. The concentration of active bacterial biomass was not affected by the moderate seasonal temperature variation. In summary, the results provided an insight into the biological component of GAC filtration in cold water temperatures and the operational parameters affecting it.

Final Report for Project "A high-throughput pipeline for mapping inter-species interactions and metabolic synergy relevant to next-generation biofuel production"

DOE Office of Scientific and Technical Information (OSTI.GOV)

Segre, Daniel; Marx, Christopher J.; Northen, Trent

The goal of our project was to implement a pipeline for the systematic, computationally-driven study and optimization of microbial interactions and their effect on lignocellulose degradation and biofuel production. We specifically sought to design and construct artificial microbial consortia that could collectively degrade lignocellulose from plant biomass, and produce precursors of energy-rich biofuels. This project fits into the bigger picture goal of helping identify a sustainable strategy for the production of energy-rich biofuels that would satisfy the existing energy constraints and demand of our society. Based on the observation that complex natural microbial communities tend to be metabolically efficient andmore » ecologically robust, we pursued the study of a microbial system in which the desired engineering function is achieved through division of labor across multiple microbial species. Our approach was aimed at bypassing the complexity of natural communities by establishing a rational approach to design small synthetic microbial consortia. Towards this goal, we combined multiple approaches, including computer modeling of ecosystem-level microbial metabolism, mass spectrometry of metabolites, genetic engineering, and experimental evolution. The microbial production of biofuels from lignocellulose is a complex, multi-step process. Microbial consortia are an ideal approach to consolidated bioprocessing: a community of microorganisms performs a wide variety of functions more efficiently and is more resilient to environmental perturbations than a microbial monoculture. Each organism we chose for this project addresses a specific challenge: lignin degradation (Pseudomonas putida); (hemi)cellulose degradation (Cellulomonas fimi); lignin degradation product demethoxylation (Methylobacterium spp); generation of biofuel lipid precursors (Yarrowia lipolytica). These organisms are genetically tractable, aerobic, and have been used in biotechnological applications. Throughout the project, we have used mass spectrometry to characterize and measure the metabolic inputs and outputs of each of these consortium members, providing valuable information for model refinement, and enabling the establishment of metabolism-mediated interactions. In addition to lignocellulose degradation, we have started addressing the challenge of removing metabolites (e.g. formaldehyde) produced by the demethoxylation of lignin monomers, which can otherwise inhibit microbial growth due to their toxicity. On the computational side, we have implemented genome-scale models for all consortium members, based on KBase reconstructions and literature curation, and we studied small consortia and their properties. Overall, our project has identified a complex landscape of interactions types and metabolic processes relevant to community-level functions, illustrating the challenges and opportunities of microbial community engineering for the transformation of biomass into bioproducts.« less

Among-Population Variation in Microbial Community Structure in the Floral Nectar of the Bee-Pollinated Forest Herb Pulmonaria officinalis L

PubMed Central

Jacquemyn, Hans; Lenaerts, Marijke; Brys, Rein; Willems, Kris; Honnay, Olivier; Lievens, Bart

2013-01-01

Background Microbial communities in floral nectar have been shown to be characterized by low levels of species diversity, yet little is known about among-plant population variation in microbial community composition. Methodology/Principal Findings We investigated the microbial community structure (yeasts and bacteria) in floral nectar of ten fragmented populations of the bee-pollinated forest herb Pulmonaria officinalis. We also explored possible relationships between plant population size and microbial diversity in nectar, and related microbial community composition to the distance separating plant populations. Culturable bacteria and yeasts occurring in the floral nectar of a total of 100 plant individuals were isolated and identified by partially sequencing the 16S rRNA gene and D1/D2 domains of the 26S rRNA gene, respectively. A total of 9 and 11 yeast and 28 and 39 bacterial OTUs was found, taking into account a 3% (OTU0.03) and 1% sequence dissimilarity cut-off (OTU0.01). OTU richness at the plant population level (i.e. the number of OTUs per population) was low for yeasts (mean: 1.7, range: 0–4 OTUs0.01/0.03 per population), whereas on average 6.9 (range: 2–13) OTUs0.03 and 7.9 (range 2–16) OTUs0.01 per population were found for bacteria. Both for yeasts and bacteria, OTU richness was not significantly related to plant population size. Similarity in community composition among populations was low (average Jaccard index: 0.14), and did not decline with increasing distance between populations. Conclusions/Significance We found low similarity in microbial community structure among populations, suggesting that the assembly of nectar microbiota is to a large extent context-dependent. Although the precise factors that affect variation in microbial community structure in floral nectar require further study, our results indicate that both local and regional processes may contribute to among-population variation in microbial community structure in nectar. PMID:23536759

Among-population variation in microbial community structure in the floral nectar of the bee-pollinated forest herb Pulmonaria officinalis L.

PubMed

Jacquemyn, Hans; Lenaerts, Marijke; Brys, Rein; Willems, Kris; Honnay, Olivier; Lievens, Bart

2013-01-01

Microbial communities in floral nectar have been shown to be characterized by low levels of species diversity, yet little is known about among-plant population variation in microbial community composition. We investigated the microbial community structure (yeasts and bacteria) in floral nectar of ten fragmented populations of the bee-pollinated forest herb Pulmonaria officinalis. We also explored possible relationships between plant population size and microbial diversity in nectar, and related microbial community composition to the distance separating plant populations. Culturable bacteria and yeasts occurring in the floral nectar of a total of 100 plant individuals were isolated and identified by partially sequencing the 16S rRNA gene and D1/D2 domains of the 26S rRNA gene, respectively. A total of 9 and 11 yeast and 28 and 39 bacterial OTUs was found, taking into account a 3% (OTU0.03) and 1% sequence dissimilarity cut-off (OTU0.01). OTU richness at the plant population level (i.e. the number of OTUs per population) was low for yeasts (mean: 1.7, range: 0-4 OTUs0.01/0.03 per population), whereas on average 6.9 (range: 2-13) OTUs0.03 and 7.9 (range 2-16) OTUs0.01 per population were found for bacteria. Both for yeasts and bacteria, OTU richness was not significantly related to plant population size. Similarity in community composition among populations was low (average Jaccard index: 0.14), and did not decline with increasing distance between populations. We found low similarity in microbial community structure among populations, suggesting that the assembly of nectar microbiota is to a large extent context-dependent. Although the precise factors that affect variation in microbial community structure in floral nectar require further study, our results indicate that both local and regional processes may contribute to among-population variation in microbial community structure in nectar.

Dynamics of microorganism populations in recirculating nutrient solutions

NASA Technical Reports Server (NTRS)

Strayer, R. F.

1994-01-01

This overview covers the basic microbial ecology of recirculating hydroponic solutions. Examples from NASA and Soviet CELSS tests and the commercial hydroponic industry will be used. The sources of microorganisms in nutrient solutions include air, water, seeds, plant containers and plumbing, biological vectors, and personnel. Microbial fates include growth, death, and emigration. Important microbial habitats within nutrient delivery systems are root surfaces, hardware surfaces (biofilms), and solution suspension. Numbers of bacteria on root surfaces usually exceed those from the other habitats by several orders of magnitude. Gram negative bacteria dominate the microflora with fungal counts usually much lower. Trends typically show a decrease in counts with increasing time unless stressed plants increase root exudates. Important microbial activities include carbon mineralization and nitrogen transformations. Important detrimental interactions include competition with plants, and human and plant pathogenesis.

Impact of relative humidity, inoculum carrier and size, and native microbiota on Salmonella ser. Typhimurium survival in baby lettuce.

PubMed

López-Gálvez, Francisco; Gil, Maria Isabel; Allende, Ana

2018-04-01

The effects of relative humidity (RH), fluctuating climate conditions, inoculum size and carrier on the survival of Salmonella enterica serovar Typhimurium on baby lettuce in environmental test chambers were studied. Buffered peptone water (BPW), distilled water (DW), and irrigation water (IW) were compared as inoculum carriers. Additionally, survival of Salmonella in suspensions prepared using filtered and unfiltered IW was assessed. Salmonella Typhimurium survived better on baby lettuce plants at high RH independently of the inoculum size. When lettuce plants were grown under fluctuating environmental conditions, Salmonella survival was similar under both RH conditions. Regarding the inoculum carrier, the inoculated microorganism survived better on lettuce plants when BPW was used as carrier both at high and low RH. Survival rate of Salmonella in IW was affected by the presence of native microbiota. Native microbiota present in IW did not affect survival of Salmonella or the levels of mesophilic bacteria on the baby lettuce leaves. The information obtained in the present study contributes to the knowledge on the effect of environmental conditions on pathogenic bacteria survival on growing edible plants. These results are useful when selecting the methodology to carry out experimental studies on the survival of microbial pathogens under different pre-harvest conditions. Copyright © 2017 Elsevier Ltd. All rights reserved.

Metagenomic analysis of the airborne environment in urban spaces.

PubMed

Be, Nicholas A; Thissen, James B; Fofanov, Viacheslav Y; Allen, Jonathan E; Rojas, Mark; Golovko, George; Fofanov, Yuriy; Koshinsky, Heather; Jaing, Crystal J

2015-02-01

The organisms in aerosol microenvironments, especially densely populated urban areas, are relevant to maintenance of public health and detection of potential epidemic or biothreat agents. To examine aerosolized microorganisms in this environment, we performed sequencing on the material from an urban aerosol surveillance program. Whole metagenome sequencing was applied to DNA extracted from air filters obtained during periods from each of the four seasons. The composition of bacteria, plants, fungi, invertebrates, and viruses demonstrated distinct temporal shifts. Bacillus thuringiensis serovar kurstaki was detected in samples known to be exposed to aerosolized spores, illustrating the potential utility of this approach for identification of intentionally introduced microbial agents. Together, these data demonstrate the temporally dependent metagenomic complexity of urban aerosols and the potential of genomic analytical techniques for biosurveillance and monitoring of threats to public health.

Deep-Sea Hydrothermal-Vent Sampler

NASA Technical Reports Server (NTRS)

Behar, Alberto E.; Venkateswaran, Kasthur; Matthews, Jaret B.

2008-01-01

An apparatus is being developed for sampling water for signs of microbial life in an ocean hydrothermal vent at a depth of as much as 6.5 km. Heretofore, evidence of microbial life in deep-sea hydrothermal vents has been elusive and difficult to validate. Because of the extreme conditions in these environments (high pressures and temperatures often in excess of 300 C), deep-sea hydrothermal- vent samplers must be robust. Because of the presumed low density of biomass of these environments, samplers must be capable of collecting water samples of significant volume. It is also essential to prevent contamination of samples by microbes entrained from surrounding waters. Prior to the development of the present apparatus, no sampling device was capable of satisfying these requirements. The apparatus (see figure) includes an intake equipped with a temperature probe, plus several other temperature probes located away from the intake. The readings from the temperature probes are utilized in conjunction with readings from flowmeters to determine the position of the intake relative to the hydrothermal plume and, thereby, to position the intake to sample directly from the plume. Because it is necessary to collect large samples of water in order to obtain sufficient microbial biomass but it is not practical to retain all the water from the samples, four filter arrays are used to concentrate the microbial biomass (which is assumed to consist of particles larger than 0.2 m) into smaller volumes. The apparatus can collect multiple samples per dive and is designed to process a total volume of 10 L of vent fluid, of which most passes through the filters, leaving a total possibly-microbe-containing sample volume of 200 mL remaining in filters. A rigid titanium nose at the intake is used for cooling the sample water before it enters a flexible inlet hose connected to a pump. As the water passes through the titanium nose, it must be cooled to a temperature that is above a mineral-precipitation temperature of 100 C but below the upper working temperature (230 C) of switching valves and tubes in the apparatus. The sample water then passes into a manifold tube, from whence the switching valves can direct the water through either a bypass tube or any one of the filter arrays, without contamination from a previous sample. Each filter array consists of series of filters having pore sizes decreasing in the direction of flow: 90-, 60-, 15-, and 7-micron prefilters and a large-surface-area 0.2-micron collection filter. All the filter taps are located between the intake and the bypass tube so that each time the bypass tube is used, the entire manifold tube is flushed as well.

De novo prediction of the genomic components and capabilities for microbial plant biomass degradation from (meta-)genomes

PubMed Central

2013-01-01

Background Understanding the biological mechanisms used by microorganisms for plant biomass degradation is of considerable biotechnological interest. Despite of the growing number of sequenced (meta)genomes of plant biomass-degrading microbes, there is currently no technique for the systematic determination of the genomic components of this process from these data. Results We describe a computational method for the discovery of the protein domains and CAZy families involved in microbial plant biomass degradation. Our method furthermore accurately predicts the capability to degrade plant biomass for microbial species from their genome sequences. Application to a large, manually curated data set of microbial degraders and non-degraders identified gene families of enzymes known by physiological and biochemical tests to be implicated in cellulose degradation, such as GH5 and GH6. Additionally, genes of enzymes that degrade other plant polysaccharides, such as hemicellulose, pectins and oligosaccharides, were found, as well as gene families which have not previously been related to the process. For draft genomes reconstructed from a cow rumen metagenome our method predicted Bacteroidetes-affiliated species and a relative to a known plant biomass degrader to be plant biomass degraders. This was supported by the presence of genes encoding enzymatically active glycoside hydrolases in these genomes. Conclusions Our results show the potential of the method for generating novel insights into microbial plant biomass degradation from (meta-)genome data, where there is an increasing production of genome assemblages for uncultured microbes. PMID:23414703

Coupled effect of chemotaxis and growth on microbial distributions in organic-amended aquifer sediments: Observations from laboratory and field studies

USGS Publications Warehouse

Wang, M.; Ford, R.M.; Harvey, R.W.

2008-01-01

The inter-relationship of growth and chemotactic response exhibited by two common soil-inhabiting bacteria was investigated to determine its impact on bacterial migration. Filter-chambers were used to simulate aquifer sediments characterized by vertical gradients of organic contaminants in both artificial groundwater flow systems in the laboratory and within the screened intervals of observation wells in a sandy aquifer. A labile model contaminant (acetate) was added to the top compartments of the three-part chambers, whereas bacteria with a demonstrated propensity to grow on and chemotactically respond to acetate were introduced to the lower compartments, The motility and chemotactic response of Pseudomonas putida F1 resulted in 40 to 110% greater abundances in the upper compartments and concomitant 22 to 70% depletions in the lower compartments relative to the nonchemotactic controls over 2 days. Bacteria were in greatest abundance within the sand plug that separated the upper and lower compartments where sharp acetate gradients induced a strong chemotactic response. This observation was consistent with predictions from a mathematical model. In agreement with the laboratory results, the down-well filter-chamber incubations with Pseudomonas stutzeri in the aquifer indicated that 91% fewer bacteria resided in the lower compartment than the control experiment without acetate at 15 h. The combination of chemotaxis and growth greatly accelerated the migration of bacteria toward and subsequent abundance at the higher acetate concentration. ?? 2008 American Chemical Society.

Plant Growth Models Using Artificial Neural Networks

NASA Technical Reports Server (NTRS)

Bubenheim, David

1997-01-01

In this paper, we descrive our motivation and approach to devloping models and the neural network architecture. Initial use of the artificial neural network for modeling the single plant process of transpiration is presented.

Therapeutic Potential of Plants as Anti-microbials for Drug Discovery

PubMed Central

Perumal Samy, Ramar

2010-01-01

The uses of traditional medicinal plants for primary health care have steadily increased worldwide in recent years. Scientists are in search of new phytochemicals that could be developed as useful anti-microbials for treatment of infectious diseases. Currently, out of 80% of pharmaceuticals derived from plants, very few are now being used as anti-microbials. Plants are rich in a wide variety of secondary metabolites that have found anti-microbial properties. This review highlights the current status of traditional medicine, its contribution to modern medicine, recent trends in the evaluation of anti-microbials with a special emphasis upon some tribal medicine, in vitro and in vivo experimental design for screening, and therapeutic efficacy in safety and human clinical trails for commercial outlet. Many of these commercially available compounds are crude preparations administered without performing human clinical trials. Recent methods are useful to standardize the extraction for scientific investigation of new phytochemicals and anti-microbials of traditionally used plants. It is concluded that once the local ethnomedical preparations of traditional sources are scientifically evaluated before dispensing they should replace existing drugs commonly used for the therapeutic treatment of infection. This method should be put into practice for future investigations in the field of ethnopharmacology, phytochemistry, ethnobotany and other biological fields for drug discovery. PMID:18955349

Phytotechnological purification of water and bio energy utilization of plant biomass

NASA Astrophysics Data System (ADS)

Stom, D. I.; Gruznych, O. V.; Zhdanova, G. O.; Timofeeva, S. S.; Kashevsky, A. V.; Saksonov, M. N.; Balayan, A. E.

2017-01-01

The aim of the study was to explore the possibility of using the phytomass of aquatic plants as the substrate in the microbial fuel cells and selection of microorganisms suitable for the generation of electricity on this substrate. The conversion of chemical energy of phytomass of aquatic plants to the electrical energy was carried out in a microbial fuel cells by biochemical transformation. As biological agents in the generation of electricity in the microbial fuel cells was used commercial microbial drugs “Doctor Robic 109K” and “Vostok-EM-1”. The results of evaluation of the characteristics of electrogenic (amperage, voltage) and the dynamics of the growth of microorganisms in the microbial fuel cells presents in the experimental part. As a source of electrogenic microorganisms is possible to use drugs “Dr. Robic 109K” and “Vostok-EM-1” was established. The possibility of utilization of excess phytomass of aquatic plants, formed during the implementation of phytotechnological purification of water, in microbial fuel cells, was demonstrated. The principal possibility of creating hybrid phytotechnology (plant-microbe cells), allowing to obtain electricity as a product, which can be used to ensure the operation of the pump equipment and the creation of a full cycle of resource-saving technologies for water treatment, was reviewed.

Harnessing Insect-Microbe Chemical Communications To Control Insect Pests of Agricultural Systems.

PubMed

Beck, John J; Vannette, Rachel L

2017-01-11

Insect pests cause serious economic, yield, and food safety problems to managed crops worldwide. Compounding these problems, insect pests often vector pathogenic or toxigenic microbes to plants. Previous work has considered plant-insect and plant-microbe interactions separately. Although insects are well-understood to use plant volatiles to locate hosts, microorganisms can produce distinct and abundant volatile compounds that in some cases strongly attract insects. In this paper, we focus on the microbial contribution to plant volatile blends, highlighting the compounds emitted and the potential for variation in microbial emission. We suggest that these aspects of microbial volatile emission may make these compounds ideal for use in agricultural applications, as they may be more specific or enhance methods currently used in insect control or monitoring. Our survey of microbial volatiles in insect-plant interactions suggests that these emissions not only signal host suitability but may indicate a distinctive time frame for optimal conditions for both insect and microbe. Exploitation of these host-specific microbe semiochemicals may provide important microbe- and host-based attractants and a basis for future plant-insect-microbe chemical ecology investigations.

The influence of microbial-based inoculants on N2O emissions from soil planted with corn (Zea mays L.) under greenhouse conditions with different nitrogen fertilizer regimens.

PubMed

Calvo, Pamela; Watts, Dexter B; Kloepper, Joseph W; Torbert, H Allen

2016-12-01

Nitrous oxide (N 2 O) emissions are increasing at an unprecedented rate owing to the increased use of nitrogen (N) fertilizers. Thus, new innovative management tools are needed to reduce emissions. One potential approach is the use of microbial inoculants in agricultural production. In a previous incubation study, we observed reductions in N 2 O emissions when microbial-based inoculants were added to soil (no plants present) with N fertilizers under laboratory incubations. This present study evaluated the effects of microbial-based inoculants on N 2 O and carbon dioxide (CO 2 ) emissions when applied to soil planted with corn (Zea mays L.) under controlled greenhouse conditions. Inoculant treatments consisted of (i) SoilBuilder (SB), (ii) a metabolite extract of SoilBuilder (SBF), and (iii) a mixture of 4 strains of plant-growth-promoting Bacillus spp. (BM). Experiments included an unfertilized control and 3 N fertilizers: urea, urea - ammonium nitrate with 32% N (UAN-32), and calcium - ammonium nitrate with 17% N (CAN-17). Cumulative N 2 O fluxes from pots 41 days after planting showed significant reductions in N 2 O of 15% (SB), 41% (BM), and 28% (SBF) with CAN-17 fertilizer. When UAN-32 was used, reductions of 34% (SB), 35% (SBF), and 49% (BM) were obtained. However, no reductions in N 2 O emissions occurred with urea. Microbial-based inoculants did not affect total CO 2 emissions from any of the fertilized treatments or the unfertilized control. N uptake was increased by an average of 56% with microbial inoculants compared with the control (nonmicrobial-based treatments). Significant increases in plant height, SPAD chlorophyll readings, and fresh and dry shoot mass were also observed when the microbial-based treatments were applied (with and without N). Overall, results demonstrate that microbial inoculants can reduce N 2 O emissions following fertilizer application depending on the N fertilizer type used and can enhance N uptake and plant growth. Future studies are planned to evaluate the effectiveness of these microbial inoculants in field-based trials and determine the mechanisms involved in N 2 O reduction.

Bio-control and plant growth promotion potential of Salicaceae endophytes

USDA-ARS?s Scientific Manuscript database

Microbial endophytes are important for growth benefits in a variety of plant species. Microbial communities of the poplar (Populus sp.) and willow (Salix sp.) endosphere have been demonstrated to be important for plant growth promotion, protection from abiotic stresses, and degradation of toxic subs...

An investigation into the microbial clogging potential of selected filter media as a result of biodegradation of a high-strength sulphate-rich alkaline leachate.

PubMed

Wang, Zhengjian; Banks, Charles

2006-10-01

The research examines the potential for bio-clogging in filter packs containing fine sand of the type typically used in extraction wells for pumping leachates containing fine particulate matter, such as cement kiln dust (CKD). Three filter media with different particle sizes were used: 1.7-4.75, 0.35-1.0, and 0.235-0.45 mm. Each sand filter was tested using a leachate recirculating column reactor with a free drainage layer, on top of which was placed the filtration medium which was kept saturated and at a positive hydrostatic head by a 2-l reservoir of leachate. The leachate was collected from a landfill site that had been used for the co-disposal of municipal solid waste (MSW) and CKD. The leachate used was filtered by passing through a Whatman GFA filter paper before being added to the reactors in order to eliminate as far as possible the non-biological clogging which might have resulted from the introduction of particulate matter in the form of CKD. The filters and a control experiment were run under anaerobic conditions at 35 degrees C. The bio-clogging potential was observed by taking differential manometer readings from manometers located in the drainage and reservoir sections of the reactor. No clogging was detected using the coarser of the filter media, but there was some clogging when a finer filter medium was used. Head space gas analysis indicated that methanogenic activity was inhibited and analysis of the liquid phase indicated that the microbial process responsible for removal of chemical oxygen demand (COD) was principally one of sulphate reduction.

Preservation and Faithful Expression of Transgene via Artificial Seeds in Alfalfa

PubMed Central

Liu, Wenting; Liang, Zongsuo; Wang, Xinhua; Sibbald, Susan; Hunter, David; Tian, Lining

2013-01-01

Proper preservation of transgenes and transgenic materials is important for wider use of transgenic technology in plants. Here, we report stable preservation and faithful expression of a transgene via artificial seed technology in alfalfa. DNA constructs containing the uid reporter gene coding for β-glucuronidase (GUS) driven by a 35S promoter or a tCUP promoter were introduced into alfalfa via Agrobacterium-mediated genetic transformation. Somatic embryos were subsequently induced from transgenic alfalfa plants via in vitro technology. These embryos were treated with abscisic acid to induce desiccation tolerance and were subjected to a water loss process. After the desiccation procedure, the water content in dried embryos, or called artificial seeds, was about 12–15% which was equivalent to that in true seeds. Upon water rehydration, the dried somatic embryos showed high degrees of viability and exhibited normal germination. Full plants were subsequently developed and recovered in a greenhouse. The progeny plants developed from artificial seeds showed GUS enzyme activity and the GUS expression level was comparable to that of plants developed from somatic embryos without the desiccation process. Polymerase chain reaction analysis indicated that the transgene was well retained in the plants and Southern blot analysis showed that the transgene was stably integrated in plant genome. The research showed that the transgene and the new trait can be well preserved in artificial seeds and the progeny developed. The research provides a new method for transgenic germplasm preservation in different plant species. PMID:23690914

Developing a comprehensive framework for eutrophication management in off-stream artificial lakes

NASA Astrophysics Data System (ADS)

Khorasani, Hamed; Kerachian, Reza; Malakpour-Estalaki, Siamak

2018-07-01

In this paper, a comprehensive and interdisciplinary framework for management of eutrophication in off-stream artificial lakes in semi-arid and arid regions is proposed. Identification of the lake's water resources system components and stakeholders, simulation of Phosphorus (P) export from upstream watershed, simulation of the lake water quality as well as simulation of water demands and supply, development of management scenarios for the lake and selecting the best scenario using social choice methods (i.e. discrete and fuzzy Borda counts) are the four main parts of the framework. The proposed framework is applied on Chitgar Artificial Lake (ChAL), the largest intra-urban artificial lake in Tehran which has been constructed in 2010-2013 for recreational purposes. The Load Apportionment Model (LAM) is used for the simulation of P loads from the point and non-point (diffusive) sources and the LakeMab model is used for the simulation of P dynamics in the lake. The management scenarios contain optimized rule curves for water intake/outtake blended with P management plans (i.e. removal of point sources of P load in the upstream watershed, construction of a hydroponic bio-filter or an advanced water treatment plant beside the lake for reduction of external loading of P and recycling lake water, alum treatment of lake sediments for controlling the internal loading of P as well as construction of a dry detention basin). The most preferred scenarios selected by the discrete Borda count are the low-cost alum treatment and dry detention basin, while the most preferred scenario according to fuzzy Borda count, which considers the uncertainty of model inputs, is the costly water treatment plant. In all preferred scenarios, water intake is conducted from flood flows in order to avoid conflict with downstream agricultural demands. In addition to decentralized decision making and stakeholders' participation, the proposed framework promotes the integration of the technical aspects such as the role of internal loading in lake eutrophication and separation of flood and non-flood flows in the off-stream lakes' systems.

Influences of space, soil, nematodes and plants on microbial community composition of chalk grassland soils.

PubMed

Yergeau, Etienne; Bezemer, T Martijn; Hedlund, Katarina; Mortimer, Simon R; Kowalchuk, George A; Van Der Putten, Wim H

2010-08-01

Microbial communities respond to a variety of environmental factors related to resources (e.g. plant and soil organic matter), habitat (e.g. soil characteristics) and predation (e.g. nematodes, protozoa and viruses). However, the relative contribution of these factors on microbial community composition is poorly understood. Here, we sampled soils from 30 chalk grassland fields located in three different chalk hill ridges of Southern England, using a spatially explicit sampling scheme. We assessed microbial communities via phospholipid fatty acid (PLFA) analyses and PCR-denaturing gradient gel electrophoresis (DGGE) and measured soil characteristics, as well as nematode and plant community composition. The relative influences of space, soil, vegetation and nematodes on soil microorganisms were contrasted using variation partitioning and path analysis. Results indicate that soil characteristics and plant community composition, representing habitat and resources, shape soil microbial community composition, whereas the influence of nematodes, a potential predation factor, appears to be relatively small. Spatial variation in microbial community structure was detected at broad (between fields) and fine (within fields) scales, suggesting that microbial communities exhibit biogeographic patterns at different scales. Although our analysis included several relevant explanatory data sets, a large part of the variation in microbial communities remained unexplained (up to 92% in some analyses). However, in several analyses, significant parts of the variation in microbial community structure could be explained. The results of this study contribute to our understanding of the relative importance of different environmental and spatial factors in driving the composition of soil-borne microbial communities. © 2009 Society for Applied Microbiology and Blackwell Publishing Ltd.

Remediation of incomplete nitrification and capacity increase of biofilters at different drinking water treatment plants through copper dosing.

PubMed

Wagner, Florian B; Nielsen, Peter Borch; Boe-Hansen, Rasmus; Albrechtsen, Hans-Jørgen

2018-04-01

Drinking water treatment plants based on groundwater may suffer from incomplete ammonium removal, which deteriorates drinking water quality and constrains water utilities in the operation of their plants. Ammonium is normally removed through nitrification in biological granular media filters, and recent studies have demonstrated that dosing of copper can stimulate the removal of ammonium. Here, we investigated if copper dosing could generically improve ammonium removal of biofilters, at treatment plants with different characteristics. Copper was dosed at ≤1.5 μg Cu/L to biofilters at 10 groundwater treatment plants, all of which had displayed several years of incomplete nitrification. Plants exceeded the Danish national water quality standard of 0.05 mg NH 4 + /L by a factor of 2-12. Within only 2-3 weeks of dosing, ammonium removal rates increased significantly (up to 150%). Nitrification was fully established, with ammonium effluent concentrations of <0.01 mg NH 4 + -N/L at most plants, regardless of the differences in raw water chemistry, ammonium loading rates, filter design and operation, or treatment plant configuration. However, for filters without primary filtration, it took longer time to reach complete ammonium removal than for filters receiving prefiltered water, likely due to sorption of copper to iron oxides, at plants without prefiltration. With complete ammonium removal, we subjected two plants to short-term loading rate upshifts, to examine the filters' ability to cope with loading rate variations. After 2 months of dosing and an average loading rate of 1.0 g NH 4 + -N/m 3 filter material/h, the loading rate was upshifted by 50%. Yet, a filter managed to completely remove all the influent ammonium, showing that with copper dosing the filter had extra capacity to remove ammonium even beyond its normal loading rates. Depth sampling revealed that the ammonium removal rate of the filter's upper 10 cm increased more than 7-fold from 0.67 to 4.90 g NH 4 + -N/m 3 /h, and that nitrite produced from increased ammonium oxidation was completely oxidized further to nitrate. Hence, no problems with nitrite accumulation or breakthrough occurred. Overall, copper dosing generically enhanced nitrification efficiency and allowed a range of quite different plants to meet water quality standards, even at increased loading rates. The capacity increase is highly relevant in practice, as it makes filters more robust towards sudden ammonium loading rate variations. Copyright © 2017 Elsevier Ltd. All rights reserved.

Plant, fungal, bacterial, and nitrogen interactions in the litter layer of a native Patagonian forest.

PubMed

Vivanco, Lucía; Rascovan, Nicolás; Austin, Amy T

2018-01-01

Plant-microbial interactions in the litter layer represent one of the most relevant interactions for biogeochemical cycling as litter decomposition is a key first step in carbon and nitrogen turnover. However, our understanding of these interactions in the litter layer remains elusive. In an old-growth mixed Nothofagus forest in Patagonia, we studied the effects of single tree species identity and the mixture of three tree species on the fungal and bacterial composition in the litter layer. We also evaluated the effects of nitrogen (N) addition on these plant-microbial interactions. In addition, we compared the magnitude of stimulation of litter decomposition due to home field advantage (HFA, decomposition occurs more rapidly when litter is placed beneath the plant species from which it had been derived than beneath a different plant species) and N addition that we previously demonstrated in this same forest, and used microbial information to interpret these results. Tree species identity had a strong and significant effect on the composition of fungal communities but not on the bacterial community of the litter layer. The microbial composition of the litter layer under the tree species mixture show an averaged contribution of each single tree species. N addition did not erase the plant species footprint on the fungal community, and neither altered the bacterial community. N addition stimulated litter decomposition as much as HFA for certain tree species, but the mechanisms behind N and HFA stimulation may have differed. Our results suggest that stimulation of decomposition from N addition might have occurred due to increased microbial activity without large changes in microbial community composition, while HFA may have resulted principally from plant species' effects on the litter fungal community. Together, our results suggest that plant-microbial interactions can be an unconsidered driver of litter decomposition in temperate forests.

Microbial stowaways: Addressing oil spill impacts and the artificial reef effect on deep-sea microbiomes

NASA Astrophysics Data System (ADS)

Hamdan, L. J.; Salerno, J. L.; Blackwell, C. A.; Little, B.; McGown, C.; Fitzgerald, L. A.; Damour, M.

2016-02-01

Shipwrecks enhance macro-biological diversity in the deep ocean, but, to date, studies have not explored the reef effect on deep-sea microbiological diversity. This is an important concept to address in a restoration framework, as microbial biogeochemical function impacts recruitment and adhesion of higher trophic levels on artificial reefs. In addition, microbial biofilms influence the preservation of shipwrecks through biologically mediated corrosion. Oil and gas-related activities have potential to disrupt the base of the reef trophic web; therefore, bacterial diversity and gene function at six shipwrecks (3 steel-hulled; 3 wood-hulled) in the northern Gulf of Mexico was investigated as part of the GOM-SCHEMA (Shipwreck Corrosion, Hydrocarbon Exposure, Microbiology, and Archaeology) project. Sites were selected based on proximity to the Deepwater Horizon spill's subsurface plume, depth, hull type, and existing archaeological data. Classification of taxa in sediments adjacent to and at distance from wrecks, in water, and on experimental steel coupons was used to evaluate how the presence of shipwrecks and spill contaminants in the deep biosphere influenced diversity. At all sites, and in all sample types, Proteobacteria were most abundant. Biodiversity was highest in surface sediments and in coupon biofilms adjacent to two steel-hulled wrecks in the study (Halo and Anona) and decreased with sediment depth and distance from the wrecks. Sequences associated with the iron oxidizing Mariprofundus genus were elevated at steel-hulled sites, indicating wreck-specific environmental selection. Despite evidence of the reef effect on microbiomes, bacterial composition was structured primarily by proximity to the spill and secondarily by hull material at all sites. This study provides the first evidence of an artificial reef effect on deep-sea microbial communities and suggests that biodiversity and function of primary colonizers of shipwrecks may be impacted by the spill.

Development, registration and commercialization of microbial pesticides for plant protection.

PubMed

Montesinos, Emilio

2003-12-01

Plant protection against pathogens, pests and weeds has been progressively reoriented from a therapeutic approach to a rational use of pesticide chemicals in which consumer health and environmental preservation prevail over any other productive or economic considerations. Microbial pesticides are being introduced in this new scenario of crop protection and currently several beneficial microorganisms are the active ingredients of a new generation of microbial pesticides or the basis for many natural products of microbial origin. The development of a microbial pesticide requires several steps addressed to its isolation in pure culture and screening by means of efficacy bioassays performed in vitro, ex vivo, in vivo, or in pilot trials under real conditions of application (field, greenhouse, post-harvest). For the commercial delivery of a microbial pesticide, the biocontrol agent must be produced at an industrial scale (fermentation), preserved for storage and formulated by means of biocompatible additives to increase survival and to improve the application and stability of the final product. Despite the relative high number of patents for biopesticides, only a few of them have materialized in a register for agricultural use. The excessive specificity in most cases and biosafety or environmental concerns in others are major limiting factors. Non-target effects may be possible in particular cases, such as displacement of beneficial microorganisms, allergenicity, toxinogencity (production of secondary metabolites toxic to plants, animals, or humans), pathogenicity (to plants or animals) by the agent itself or due to contaminants, or horizontal gene transfer of these characteristics to non-target microorganisms. However, these non-target effects should not be evaluated in an absolute manner, but relative to chemical control or the absence of any control of the target disease (for example, toxins derived from the pathogen). Consumer concerns about live microbes due to emerging food-borne diseases and bioterrorism do not help to create a socially receptive environment to microbial pesticides. The future of microbial pesticides is not only in developing new active ingredients based on microorganisms beneficial to plants, but in producing self-protected plants (so-called plant-incorporated pesticides) by transforming agronomically high-value crop plants with genes from biological control agents.

Indoor-biofilter growth and exposure to airborne chemicals drive similar changes in plant root bacterial communities.

PubMed

Russell, Jacob A; Hu, Yi; Chau, Linh; Pauliushchyk, Margarita; Anastopoulos, Ioannis; Anandan, Shivanthi; Waring, Michael S

2014-08-01

Due to the long durations spent inside by many humans, indoor air quality has become a growing concern. Biofiltration has emerged as a potential mechanism to clean indoor air of harmful volatile organic compounds (VOCs), which are typically found at concentrations higher indoors than outdoors. Root-associated microbes are thought to drive the functioning of plant-based biofilters, or biowalls, converting VOCs into biomass, energy, and carbon dioxide, but little is known about the root microbial communities of such artificially grown plants, how or whether they differ from those of plants grown in soil, and whether any changes in composition are driven by VOCs. In this study, we investigated how bacterial communities on biofilter plant roots change over time and in response to VOC exposure. Through 16S rRNA amplicon sequencing, we compared root bacterial communities from soil-grown plants with those from two biowalls, while also comparing communities from roots exposed to clean versus VOC-laden air in a laboratory biofiltration system. The results showed differences in bacterial communities between soil-grown and biowall-grown plants and between bacterial communities from plant roots exposed to clean air and those from VOC-exposed plant roots. Both biowall-grown and VOC-exposed roots harbored enriched levels of bacteria from the genus Hyphomicrobium. Given their known capacities to break down aromatic and halogenated compounds, we hypothesize that these bacteria are important VOC degraders. While different strains of Hyphomicrobium proliferated in the two studied biowalls and our lab experiment, strains were shared across plant species, suggesting that a wide range of ornamental houseplants harbor similar microbes of potential use in living biofilters. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Indoor-Biofilter Growth and Exposure to Airborne Chemicals Drive Similar Changes in Plant Root Bacterial Communities

PubMed Central

Hu, Yi; Chau, Linh; Pauliushchyk, Margarita; Anastopoulos, Ioannis; Anandan, Shivanthi; Waring, Michael S.

2014-01-01

Due to the long durations spent inside by many humans, indoor air quality has become a growing concern. Biofiltration has emerged as a potential mechanism to clean indoor air of harmful volatile organic compounds (VOCs), which are typically found at concentrations higher indoors than outdoors. Root-associated microbes are thought to drive the functioning of plant-based biofilters, or biowalls, converting VOCs into biomass, energy, and carbon dioxide, but little is known about the root microbial communities of such artificially grown plants, how or whether they differ from those of plants grown in soil, and whether any changes in composition are driven by VOCs. In this study, we investigated how bacterial communities on biofilter plant roots change over time and in response to VOC exposure. Through 16S rRNA amplicon sequencing, we compared root bacterial communities from soil-grown plants with those from two biowalls, while also comparing communities from roots exposed to clean versus VOC-laden air in a laboratory biofiltration system. The results showed differences in bacterial communities between soil-grown and biowall-grown plants and between bacterial communities from plant roots exposed to clean air and those from VOC-exposed plant roots. Both biowall-grown and VOC-exposed roots harbored enriched levels of bacteria from the genus Hyphomicrobium. Given their known capacities to break down aromatic and halogenated compounds, we hypothesize that these bacteria are important VOC degraders. While different strains of Hyphomicrobium proliferated in the two studied biowalls and our lab experiment, strains were shared across plant species, suggesting that a wide range of ornamental houseplants harbor similar microbes of potential use in living biofilters. PMID:24878602

Using a trait-based approach to link microbial community composition and functioning to soil salinity

NASA Astrophysics Data System (ADS)

Rath, Kristin; Fierer, Noah; Rousk, Johannes

2017-04-01

Our knowledge of the dynamics structuring microbial communities and the consequences this has for soil functions is rudimentary. In particular, predictions of the response of microbial communities to environmental change and the implications for associated ecosystem processes remain elusive. Understanding how environmental factors structure microbial communities and regulate the functions they perform is key to a mechanistic understanding of how biogeochemical cycles respond to environmental change. Soil salinization is an agricultural problem in many parts of the world. The activity of soil microorganisms is reduced in saline soils compared to non-saline soil. However, soil salinity often co-varies with other factors, making it difficult to assign responses of microbial communities to direct effects of salinity. A trait-based approach allows us to connect the environmental factor salinity with the responses of microbial community composition and functioning. Salinity along a salinity gradient serves as a filter for the community trait distribution of salt tolerance, selecting for higher salt tolerance at more saline sites. This trait-environment relationship can be used to predict responses of microbial communities to environmental change. Our aims were to (i) use salinity along natural salinity gradients as an environmental filter, and (ii) link the resulting filtered trait-distributions of the communities (the trait being salt tolerance) to the community composition. Soil samples were obtained from two replicated salinity gradients along an Australian salt lake, spanning a wide range of soil salinities (0.1 dS m-1 to >50 dS m-1). In one of the two gradients salinity was correlated with pH. Community trait distributions for salt tolerance were assessed by establishing dose-dependences for extracted bacterial communities using growth rate assays. In addition, functional parameters were measured along the salt gradients. Community composition of sites was compared through 16S rRNA gene amplicon sequencing. Microbial community composition changed greatly along the salinity gradients. Using the salt-tolerance assessments to estimate bacterial trait-distributions we could determine substantial differences in tolerance to salt revealing a strong causal connection between environment and trait distributions. By constraining the community composition with salinity tolerance in ordinations, we could assign which community differences were directly due to a shift in community trait distributions. These analyses revealed that a substantial part (up to 30%) of the community composition differences were directly driven by environmental salt concentrations.. Even though communities in saline soils had trait-distributions aligned to their environment, their performance (respiration, growth rates) was lower than those in non-saline soils and remained low even after input of organic material. Using a trait-based approach we could connect filtered trait distributions along environmental gradients, to the composition of the microbial community. We show that soil salinity played an important role in shaping microbial community composition by selecting for communities with higher salt tolerance. The shift toward bacterial communities with trait distributions matched to salt environments probably compensated for much of the potential loss of function induced by salinity, resulting in a degree of apparent functional redundancy for decomposition. However, more tolerant communities still showed reduced functioning, suggesting a trade-off between salt tolerance and performance.

A supervised 'lesion-enhancement' filter by use of a massive-training artificial neural network (MTANN) in computer-aided diagnosis (CAD).

PubMed

Suzuki, Kenji

2009-09-21

Computer-aided diagnosis (CAD) has been an active area of study in medical image analysis. A filter for the enhancement of lesions plays an important role for improving the sensitivity and specificity in CAD schemes. The filter enhances objects similar to a model employed in the filter; e.g. a blob-enhancement filter based on the Hessian matrix enhances sphere-like objects. Actual lesions, however, often differ from a simple model; e.g. a lung nodule is generally modeled as a solid sphere, but there are nodules of various shapes and with internal inhomogeneities such as a nodule with spiculations and ground-glass opacity. Thus, conventional filters often fail to enhance actual lesions. Our purpose in this study was to develop a supervised filter for the enhancement of actual lesions (as opposed to a lesion model) by use of a massive-training artificial neural network (MTANN) in a CAD scheme for detection of lung nodules in CT. The MTANN filter was trained with actual nodules in CT images to enhance actual patterns of nodules. By use of the MTANN filter, the sensitivity and specificity of our CAD scheme were improved substantially. With a database of 69 lung cancers, nodule candidate detection by the MTANN filter achieved a 97% sensitivity with 6.7 false positives (FPs) per section, whereas nodule candidate detection by a difference-image technique achieved a 96% sensitivity with 19.3 FPs per section. Classification-MTANNs were applied for further reduction of the FPs. The classification-MTANNs removed 60% of the FPs with a loss of one true positive; thus, it achieved a 96% sensitivity with 2.7 FPs per section. Overall, with our CAD scheme based on the MTANN filter and classification-MTANNs, an 84% sensitivity with 0.5 FPs per section was achieved.

New plant-growth medium for increased power output of the Plant-Microbial Fuel Cell.

PubMed

Helder, M; Strik, D P B T B; Hamelers, H V M; Kuijken, R C P; Buisman, C J N

2012-01-01

In a Plant-Microbial Fuel Cell anode-conditions must be created that are favorable for plant growth and electricity production. One of the major aspects in this is the composition of the plant-growth medium. Hoagland medium has been used until now, with added phosphate buffer to reduce potential losses over the membrane because of differences in pH between anode and cathode. We developed a new, improved plant-growth medium that improves current production, while the plant keeps growing. This medium is a nitrate-less, ammonium-rich medium that contains all macro- and micro-nutrients necessary for plant growth, with a balanced amount of bicarbonate buffer. Sulphate presence in the plant-growth medium helps to keep a low anode-potential. With the new plant-growth medium the maximum current production of the Plant-Microbial Fuel Cell increased from 186 mA/m(2) to 469 mA/m(2). Copyright © 2011 Elsevier Ltd. All rights reserved.

Standard filtration practices may significantly distort planktonic microbial diversity estimates.

PubMed

Padilla, Cory C; Ganesh, Sangita; Gantt, Shelby; Huhman, Alex; Parris, Darren J; Sarode, Neha; Stewart, Frank J

2015-01-01

Fractionation of biomass by filtration is a standard method for sampling planktonic microbes. It is unclear how the taxonomic composition of filtered biomass changes depending on sample volume. Using seawater from a marine oxygen minimum zone, we quantified the 16S rRNA gene composition of biomass on a prefilter (1.6 μm pore-size) and a downstream 0.2 μm filter over sample volumes from 0.05 to 5 L. Significant community shifts occurred in both filter fractions, and were most dramatic in the prefilter community. Sequences matching Vibrionales decreased from ~40 to 60% of prefilter datasets at low volumes (0.05-0.5 L) to less than 5% at higher volumes, while groups such at the Chromatiales and Thiohalorhabdales followed opposite trends, increasing from minor representation to become the dominant taxa at higher volumes. Groups often associated with marine particles, including members of the Deltaproteobacteria, Planctomycetes, and Bacteroidetes, were among those showing the greatest increase with volume (4 to 27-fold). Taxon richness (97% similarity clusters) also varied significantly with volume, and in opposing directions depending on filter fraction, highlighting potential biases in community complexity estimates. These data raise concerns for studies using filter fractionation for quantitative comparisons of aquatic microbial diversity, for example between free-living and particle-associated communities.

Plant attributes explain the distribution of soil microbial communities in two contrasting regions of the globe.

PubMed

Delgado-Baquerizo, Manuel; Fry, Ellen L; Eldridge, David J; de Vries, Franciska T; Manning, Peter; Hamonts, Kelly; Kattge, Jens; Boenisch, Gerhard; Singh, Brajesh K; Bardgett, Richard D

2018-04-19

We lack strong empirical evidence for links between plant attributes (plant community attributes and functional traits) and the distribution of soil microbial communities at large spatial scales. Using datasets from two contrasting regions and ecosystem types in Australia and England, we report that aboveground plant community attributes, such as diversity (species richness) and cover, and functional traits can predict a unique portion of the variation in the diversity (number of phylotypes) and community composition of soil bacteria and fungi that cannot be explained by soil abiotic properties and climate. We further identify the relative importance and evaluate the potential direct and indirect effects of climate, soil properties and plant attributes in regulating the diversity and community composition of soil microbial communities. Finally, we deliver a list of examples of common taxa from Australia and England that are strongly related to specific plant traits, such as specific leaf area index, leaf nitrogen and nitrogen fixation. Together, our work provides new evidence that plant attributes, especially plant functional traits, can predict the distribution of soil microbial communities at the regional scale and across two hemispheres. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

Coastal urbanisation affects microbial communities on a dominant marine holobiont.

PubMed

Marzinelli, Ezequiel M; Qiu, Zhiguang; Dafforn, Katherine A; Johnston, Emma L; Steinberg, Peter D; Mayer-Pinto, Mariana

2018-01-01

Host-associated microbial communities play a fundamental role in the life of eukaryotic hosts. It is increasingly argued that hosts and their microbiota must be studied together as 'holobionts' to better understand the effects of environmental stressors on host functioning. Disruptions of host-microbiota interactions by environmental stressors can negatively affect host performance and survival. Substantial ecological impacts are likely when the affected hosts are habitat-forming species (e.g., trees, kelps) that underpin local biodiversity. In marine systems, coastal urbanisation via the addition of artificial structures is a major source of stress to habitat formers, but its effect on their associated microbial communities is unknown. We characterised kelp-associated microbial communities in two of the most common and abundant artificial structures in Sydney Harbour-pier-pilings and seawalls-and in neighbouring natural rocky reefs. The kelp Ecklonia radiata is the dominant habitat-forming species along 8000 km of the temperate Australian coast. Kelp-associated microbial communities on pilings differed significantly from those on seawalls and natural rocky reefs, possibly due to differences in abiotic (e.g., shade) and biotic (e.g., grazing) factors between habitats. Many bacteria that were more abundant on kelp on pilings belonged to taxa often associated with macroalgal diseases, including tissue bleaching in Ecklonia . There were, however, no differences in kelp photosynthetic capacity between habitats. The observed differences in microbial communities may have negative effects on the host by promoting fouling by macroorganisms or by causing and spreading disease over time. This study demonstrates that urbanisation can alter the microbiota of key habitat-forming species with potential ecological consequences.

Evolution under domestication: ongoing artificial selection and divergence of wild and managed Stenocereus pruinosus (Cactaceae) populations in the Tehuacán Valley, Mexico

PubMed Central

Parra, Fabiola; Casas, Alejandro; Peñaloza-Ramírez, Juan Manuel; Cortés-Palomec, Aurea C.; Rocha-Ramírez, Víctor; González-Rodríguez, Antonio

2010-01-01

Background and Aims The Tehuacán Valley in Mexico is a principal area of plant domestication in Mesoamerica. There, artificial selection is currently practised on nearly 120 native plant species with coexisting wild, silvicultural and cultivated populations, providing an excellent setting for studying ongoing mechanisms of evolution under domestication. One of these species is the columnar cactus Stenocereus pruinosus, in which we studied how artificial selection is operating through traditional management and whether it has determined morphological and genetic divergence between wild and managed populations. Methods Semi-structured interviews were conducted with 83 households of three villages to investigate motives and mechanisms of artificial selection. Management effects were studied by comparing variation patterns of 14 morphological characters and population genetics (four microsatellite loci) of 264 plants from nine wild, silvicultural and cultivated populations. Key Results Variation in fruit characters was recognized by most people, and was the principal target of artificial selection directed to favour larger and sweeter fruits with thinner or thicker peel, fewer spines and pulp colours others than red. Artificial selection operates in agroforestry systems favouring abundance (through not felling plants and planting branches) of the preferred phenotypes, and acts more intensely in household gardens. Significant morphological divergence between wild and managed populations was observed in fruit characters and plant vigour. On average, genetic diversity in silvicultural populations (HE = 0·743) was higher than in wild (HE = 0·726) and cultivated (HE = 0·700) populations. Most of the genetic variation (90·58 %) occurred within populations. High gene flow (NmFST > 2) was identified among almost all populations studied, but was slightly limited by mountains among wild populations, and by artificial selection among wild and managed populations. Conclusions Traditional management of S. pruinosus involves artificial selection, which, despite the high levels of gene flow, has promoted morphological divergence and moderate genetic structure between wild and managed populations, while conserving genetic diversity. PMID:20729372

Evolution under domestication: ongoing artificial selection and divergence of wild and managed Stenocereus pruinosus (Cactaceae) populations in the Tehuacan Valley, Mexico.

PubMed

Parra, Fabiola; Casas, Alejandro; Peñaloza-Ramírez, Juan Manuel; Cortés-Palomec, Aurea C; Rocha-Ramírez, Víctor; González-Rodríguez, Antonio

2010-09-01

The Tehuacán Valley in Mexico is a principal area of plant domestication in Mesoamerica. There, artificial selection is currently practised on nearly 120 native plant species with coexisting wild, silvicultural and cultivated populations, providing an excellent setting for studying ongoing mechanisms of evolution under domestication. One of these species is the columnar cactus Stenocereus pruinosus, in which we studied how artificial selection is operating through traditional management and whether it has determined morphological and genetic divergence between wild and managed populations. Semi-structured interviews were conducted with 83 households of three villages to investigate motives and mechanisms of artificial selection. Management effects were studied by comparing variation patterns of 14 morphological characters and population genetics (four microsatellite loci) of 264 plants from nine wild, silvicultural and cultivated populations. Variation in fruit characters was recognized by most people, and was the principal target of artificial selection directed to favour larger and sweeter fruits with thinner or thicker peel, fewer spines and pulp colours other than red. Artificial selection operates in agroforestry systems favouring abundance (through not felling plants and planting branches) of the preferred phenotypes, and acts more intensely in household gardens. Significant morphological divergence between wild and managed populations was observed in fruit characters and plant vigour. On average, genetic diversity in silvicultural populations (H(E) = 0.743) was higher than in wild (H(E) = 0.726) and cultivated (H(E) = 0.700) populations. Most of the genetic variation (90.58 %) occurred within populations. High gene flow (Nm(FST) > 2) was identified among almost all populations studied, but was slightly limited by mountains among wild populations, and by artificial selection among wild and managed populations. Traditional management of S. pruinosus involves artificial selection, which, despite the high levels of gene flow, has promoted morphological divergence and moderate genetic structure between wild and managed populations, while conserving genetic diversity.

Microbial Community in the Hydrothermal System at Southern Mariana Trough

NASA Astrophysics Data System (ADS)

Kato, S.; Itahashi, S.; Kakegawa, T.; Utsumi, M.; Maruyama, A.; Ishibashi, J.; Marumo, K.; Urabe, T.; Yamagishi, A.

2004-12-01

There is unique ecosystem around deep-sea hydrothermal area. Living organisms are supported by chemical free energy provided by the hydrothermal water. The ecosystem is expected to be similar to those in early stage of life history on the earth, when photosynthetic organisms have not emerged. In this study, we have analyzed the microbial diversity in the hydrothermal area at southern Mariana trough. In the "Archaean Park Project" supported by special Coordination Fund, four holes were bored and cased by titanium pipes near hydrothermal vents in the southern Mariana trough in 2004. Hydrothermal fluids were collected from these cased holes and natural vents in this area. Microbial cells were collected by filtering the hydrothermal fluid in situ or in the mother sip. Filters were stored at -80C and used for DNA extraction. Chimneys at this area was also collected and stored at -80C. The filters and chimney samples were crushed and DNA was extracted. DNA samples were used for amplification of 16S rDNA fragments by PCR using archaea specific primers and universal primers. The PCR fragments were cloned and sequenced. These PCR clones of different samples will be compared. We will extend our knowledge about microbiological diversity at Southern Mariana trough to compare the results obtained at other area.

The interacting roles of climate, soils, and plant production on soil microbial communities at a continental scale

USGS Publications Warehouse

Waldrop, Mark P.; Holloway, JoAnn M.; Smith, David; Goldhaber, Martin B.; Drenovsky, R.E.; Scow, K.M.; Dick, R.; Howard, Daniel M.; Wylie, Bruce K.; Grace, James B.

2017-01-01

Soil microbial communities control critical ecosystem processes such as decomposition, nutrient cycling, and soil organic matter formation. Continental scale patterns in the composition and functioning of microbial communities are related to climatic, biotic, and edaphic factors such as temperature and precipitation, plant community composition, and soil carbon, nitrogen, and pH. Although these relationships have been well explored individually, the examination of the factors that may act directly on microbial communities vs. those that may act indirectly through other ecosystem properties has not been well developed. To further such understanding, we utilized structural equation modeling (SEM) to evaluate a set of hypotheses about the direct and indirect effects of climatic, biotic, and edaphic variables on microbial communities across the continental United States. The primary goals of this work were to test our current understanding of the interactions among climate, soils, and plants in affecting microbial community composition, and to examine whether variation in the composition of the microbial community affects potential rates of soil enzymatic activities. A model of interacting factors created through SEM shows several expected patterns. Distal factors such as climate had indirect effects on microbial communities by influencing plant productivity, soil mineralogy, and soil pH, but factors related to soil organic matter chemistry had the most direct influence on community composition. We observed that both plant productivity and soil mineral composition were important indirect influences on community composition at the continental scale, both interacting to affect organic matter content and microbial biomass and ultimately community composition. Although soil hydrolytic enzymes were related to the moisture regime and soil carbon, oxidative enzymes were also affected by community composition, reflected in the abundance of soil fungi. These results highlight that soil microbial communities can be modeled within the context of multiple interacting ecosystem properties acting both directly and indirectly on their composition and function, and this provides a rich and informative context with which to examine communities. This work also highlights that variation in climate, microbial biomass, and microbial community composition can affect maximum rates of soil enzyme activities, potentially influencing rates of decomposition and nutrient mineralization in soils.

Nitrogen Cycling in the Mycorrhizosphere: Multipartite Interactions and Plant Nitrogen Uptake Vary with Fertilization Legacy

NASA Astrophysics Data System (ADS)

Hestrin, R.; Lehmann, J.

2017-12-01

Soil microbes play an important role in rhizosphere nutrient cycling and plant productivity. In this study, the contributions of soil microbes to organic matter mineralization and plant nitrogen uptake were investigated using incubation and microcosm experiments. Microbial inocula included arbuscular mycorrhizal fungi and microbial communities sampled across a long-term gradient of nitrogen fertilization. Stable isotopes, nanoSIMS imaging, and phospholipid fatty acid analysis were used to track carbon and nitrogen movement from organic matter into microbes, mycorrhizal fungi, and plants. Results show that multipartite relationships between plants and microbes increased plant growth and access to nitrogen from organic matter, and that nitrogen fertilization history had a lasting effect on microbial contributions to fungal and plant nitrogen uptake. This research links rhizosphere ecology and land management with terrestrial biogeochemistry.

Control of Boreal Forest Soil Microbial Communities and Processes by Plant Secondary Compounds

NASA Astrophysics Data System (ADS)

Leewis, M. C.; Leigh, M. B.

2016-12-01

Plants release an array of secondary plant metabolites (SPMEs), which vary widely between plant species/progenies and may drive shifts in soil microbial community structure and function. We hypothesize that SPMEs released through litterfall and root turnover in the boreal forest control ecosystem carbon cycling by inhibiting microbial decomposition processes, which are overcome partially by increased aromatic biodegradation of microbial communities that also fortuitously prime soils for accelerated biodegradation of contaminants. Soils and litter (stems, roots, senescing leaves) were collected from 3 different birch progenies from Iceland, Finland, and Siberia that have been reported to contain different SPME content (low, medium, high, respectively) due to differences in herbivory pressure over their natural history, as well as black spruce, all growing in a long-term common tree garden at the Kevo Subarctic Field Research Institute, Finland. We characterized the SPME content of these plant progenies and used a variety of traditional microbiological techniques (e.g., enzyme assays, litter decomposition and contaminant biodegradation rates) and molecular techniques (e.g., high-throughput amplicon sequencing for bacteria and fungi) to assess how different levels of SPMEs may correlate to shifts in microbial community structure and function. Microbial communities (bacterial and fungal) significantly varied in composition as well as leaf litter and diesel biodegradation rates, in accordance with the phytochemistry of the trees present. This study offers novel, fundamental information about phytochemical controls on ecosystem processes, resilience to contaminants, and microbial decomposition processes.

Census of the bacterial community of the gypsy moth larval midgut by using culturing and culture-independent methods.

PubMed

Broderick, Nichole A; Raffa, Kenneth F; Goodman, Robert M; Handelsman, Jo

2004-01-01

Little is known about bacteria associated with Lepidoptera, the large group of mostly phytophagous insects comprising the moths and butterflies. We inventoried the larval midgut bacteria of a polyphagous foliivore, the gypsy moth (Lymantria dispar L.), whose gut is highly alkaline, by using traditional culturing and culture-independent methods. We also examined the effects of diet on microbial composition. Analysis of individual third-instar larvae revealed a high degree of similarity of microbial composition among insects fed on the same diet. DNA sequence analysis indicated that most of the PCR-amplified 16S rRNA genes belong to the gamma-Proteobacteria and low G+C gram-positive divisions and that the cultured members represented more than half of the phylotypes identified. Less frequently detected taxa included members of the alpha-Proteobacterium, Actinobacterium, and Cytophaga/Flexibacter/Bacteroides divisions. The 16S rRNA gene sequences from 7 of the 15 cultured organisms and 8 of the 9 sequences identified by PCR amplification diverged from previously reported bacterial sequences. The microbial composition of midguts differed substantially among larvae feeding on a sterilized artificial diet, aspen, larch, white oak, or willow. 16S rRNA analysis of cultured isolates indicated that an Enterococcus species and culture-independent analysis indicated that an Entbacter sp. were both present in all larvae, regardless of the feeding substrate; the sequences of these two phylotypes varied less than 1% among individual insects. These results provide the first comprehensive description of the microbial diversity of a lepidopteran midgut and demonstrate that the plant species in the diet influences the composition of the gut bacterial community.

Overcoming antibiotic resistance: Is siderophore Trojan horse conjugation an answer to evolving resistance in microbial pathogens?

PubMed

Dhusia, Kalyani; Bajpai, Archana; Ramteke, P W

2018-01-10

Comparative study of siderophore biosynthesis pathway in pathogens provides potential targets for antibiotics and host drug delivery as a part of computationally feasible microbial therapy. Iron acquisition using siderophore models is an essential and well established model in all microorganisms and microbial infections a known to cause great havoc to both plant and animal. Rapid development of antibiotic resistance in bacterial as well as fungal pathogens has drawn us at a verge where one has to get rid of the traditional way of obstructing pathogen using single or multiple antibiotic/chemical inhibitors or drugs. 'Trojan horse' strategy is an answer to this imperative call where antibiotic are by far sneaked into the pathogenic cell via the siderophore receptors at cell and outer membrane. This antibiotic once gets inside, generates a 'black hole' scenario within the opportunistic pathogens via iron scarcity. For pathogens whose siderophore are not compatible to smuggle drug due to their complex conformation and stiff valence bonds, there is another approach. By means of the siderophore biosynthesis pathways, potential targets for inhibition of these siderophores in pathogenic bacteria could be achieved and thus control pathogenic virulence. Method to design artificial exogenous siderophores for pathogens that would compete and succeed the battle of intake is also covered with this review. These manipulated siderophore would enter pathogenic cell like any other siderophore but will not disperse iron due to which iron inadequacy and hence pathogens control be accomplished. The aim of this review is to offer strategies to overcome the microbial infections/pathogens using siderophore. Copyright © 2017 Elsevier B.V. All rights reserved.

Simplification of the Kalman filter for meteorological data assimilation

NASA Technical Reports Server (NTRS)

Dee, Dick P.

1991-01-01

The paper proposes a new statistical method of data assimilation that is based on a simplification of the Kalman filter equations. The forecast error covariance evolution is approximated simply by advecting the mass-error covariance field, deriving the remaining covariances geostrophically, and accounting for external model-error forcing only at the end of each forecast cycle. This greatly reduces the cost of computation of the forecast error covariance. In simulations with a linear, one-dimensional shallow-water model and data generated artificially, the performance of the simplified filter is compared with that of the Kalman filter and the optimal interpolation (OI) method. The simplified filter produces analyses that are nearly optimal, and represents a significant improvement over OI.

Electron shuttles in biotechnology.

PubMed

Watanabe, Kazuya; Manefield, Mike; Lee, Matthew; Kouzuma, Atsushi

2009-12-01

Electron-shuttling compounds (electron shuttles [ESs], or redox mediators) are essential components in intracellular electron transfer, while microbes also utilize self-produced and naturally present ESs for extracellular electron transfer. These compounds assist in microbial energy metabolism by facilitating electron transfer between microbes, from electron-donating substances to microbes, and/or from microbes to electron-accepting substances. Artificially supplemented ESs can create new routes of electron flow in the microbial energy metabolism, thereby opening up new possibilities for the application of microbes to biotechnology processes. Typical examples of such processes include halogenated-organics bioremediation, azo-dye decolorization, and microbial fuel cells. Herein we suggest that ESs can be applied widely to create new microbial biotechnology processes.

Inhospitable sweetness: nectar filtering of pollinator-borne inocula leads to impoverished, phylogenetically clustered yeast communities

PubMed Central

Herrera, Carlos M.; Canto, Azucena; Pozo, María I.; Bazaga, Pilar

2010-01-01

Identifying the rules and mechanisms that determine the composition and diversity of naturally co-occurring species assemblages is a central topic in community ecology. Although micro-organisms represent the ‘unseen majority’ of species, individuals and biomass in many ecosystems and play pivotal roles in community development and function, the study of the factors influencing the assembly of microbial communities has lagged behind that of plant and animal communities. In this paper, we investigate experimentally the mechanisms accounting for the low species richness of yeast communities inhabiting the nectar of the bumble-bee-pollinated Helleborus foetidus (Ranunculaceae), and explore the relationships between community assembly rules and phylogenetic relatedness. By comparing yeast communities on the glossae of foraging bumble-bees (the potential species pool) with those eventually establishing in virgin nectar probed with bee glossae (the realized community), we address the questions: (i) does nectar filter yeast inocula, so that the communities eventually established there are not random subsamples of species on bumble-bee glossae? and (ii) do yeast communities establishing in H. foetidus nectar exhibit some phylogenetic bias relative to the species pool on bumble-bee glossae? Results show that nectar filtering leads to species-poor, phylogenetically clustered yeast communities that are a predictable subset of pollinator-borne inocula. Such strong habitat filtering is probably due to H. foetidus nectar representing a harsh environment for most yeasts, where only a few phylogenetically related nectar specialists physiologically endowed to tolerate a combination of high osmotic pressure and fungicidal compounds are able to develop. PMID:19889702

8. MAIN INLET FROM FILTER GALLERY AND CANAL INTO HINDS ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

8. MAIN INLET FROM FILTER GALLERY AND CANAL INTO HINDS PLANT. VIEW LOOKING DUE WEST OF HINDS COMPLEX IN BACKGROUND OF SAND FILTERS. - Hinds Pump Plant, East of Joshua Tree National Monument, 5 miles north of Route 10, Hayfield, Riverside County, CA

Dynamics of microorganism populations in recirculating nutrient solutions

NASA Technical Reports Server (NTRS)

Strayer, R. F.

1994-01-01

This overview covers the basic microbial ecology of recirculating hydroponic solutions. Examples from NASA and Soviet Controlled Ecological Life Support Systems (CELSS) tests and the commercial hydroponic industry will be used. The sources of microorganisms in nutrient solutions include air, water, seeds, plant containers and plumbing, biological vectors, and personnel. Microbial fates include growth, death, and emigration. Important microbial habitats within nutrient delivery systems are root surfaces, hardware surfaces (biofilms), and solution suspension. Numbers of bacteria on root surfaces usually exceed those from the other habitats by several orders of magnitude. Gram negative bacteria dominate the microflora with fungal counts usually much lower. Trends typically show a decrease in counts with increasing time unless stressed plants increase root exudates. Important microbial activities include carbon mineralization and nitrogen transformations. Important detrimental interactions include competition with plants, and human and plant pathogenesis.

Rhizosphere Microbial Community Composition Affects Cadmium and Zinc Uptake by the Metal-Hyperaccumulating Plant Arabidopsis halleri

PubMed Central

Muehe, E. Marie; Weigold, Pascal; Adaktylou, Irini J.; Planer-Friedrich, Britta; Kraemer, Ute; Kappler, Andreas

2015-01-01

The remediation of metal-contaminated soils by phytoextraction depends on plant growth and plant metal accessibility. Soil microorganisms can affect the accumulation of metals by plants either by directly or indirectly stimulating plant growth and activity or by (im)mobilizing and/or complexing metals. Understanding the intricate interplay of metal-accumulating plants with their rhizosphere microbiome is an important step toward the application and optimization of phytoremediation. We compared the effects of a “native” and a strongly disturbed (gamma-irradiated) soil microbial communities on cadmium and zinc accumulation by the plant Arabidopsis halleri in soil microcosm experiments. A. halleri accumulated 100% more cadmium and 15% more zinc when grown on the untreated than on the gamma-irradiated soil. Gamma irradiation affected neither plant growth nor the 1 M HCl-extractable metal content of the soil. However, it strongly altered the soil microbial community composition and overall cell numbers. Pyrosequencing of 16S rRNA gene amplicons of DNA extracted from rhizosphere samples of A. halleri identified microbial taxa (Lysobacter, Streptomyces, Agromyces, Nitrospira, “Candidatus Chloracidobacterium”) of higher relative sequence abundance in the rhizospheres of A. halleri plants grown on untreated than on gamma-irradiated soil, leading to hypotheses on their potential effect on plant metal uptake. However, further experimental evidence is required, and wherefore we discuss different mechanisms of interaction of A. halleri with its rhizosphere microbiome that might have directly or indirectly affected plant metal accumulation. Deciphering the complex interactions between A. halleri and individual microbial taxa will help to further develop soil metal phytoextraction as an efficient and sustainable remediation strategy. PMID:25595759

Predicting Microbial Fuel Cell Biofilm Communities and Bioreactor Performance using Artificial Neural Networks.

PubMed

Lesnik, Keaton Larson; Liu, Hong

2017-09-19

The complex interactions that occur in mixed-species bioelectrochemical reactors, like microbial fuel cells (MFCs), make accurate predictions of performance outcomes under untested conditions difficult. While direct correlations between any individual waste stream characteristic or microbial community structure and reactor performance have not been able to be directly established, the increase in sequencing data and readily available computational power enables the development of alternate approaches. In the current study, 33 MFCs were evaluated under a range of conditions including eight separate substrates and three different wastewaters. Artificial Neural Networks (ANNs) were used to establish mathematical relationships between wastewater/solution characteristics, biofilm communities, and reactor performance. ANN models that incorporated biotic interactions predicted reactor performance outcomes more accurately than those that did not. The average percent error of power density predictions was 16.01 ± 4.35%, while the average percent error of Coulombic efficiency and COD removal rate predictions were 1.77 ± 0.57% and 4.07 ± 1.06%, respectively. Predictions of power density improved to within 5.76 ± 3.16% percent error through classifying taxonomic data at the family versus class level. Results suggest that the microbial communities and performance of bioelectrochemical systems can be accurately predicted using data-mining, machine-learning techniques.

Evaluation and control of microbial and chemical contamination in dialysis water plants of Italian nephrology wards.

PubMed

Totaro, M; Casini, B; Valentini, P; Miccoli, M; Giorgi, S; Porretta, A; Privitera, G; Lopalco, P L; Baggiani, A

2017-10-01

Patients receiving haemodialysis are exposed to a large volume of dialysis fluid. The Italian Society of Nephrology (ISN) has published guidelines and microbial quality standards on dialysis water (DW) and solutions to ensure patient safety. To identify microbial and chemical hazards, and evaluate the quality of disinfection treatment in DW plants. In 2015 and 2016, water networks and DW plants (closed loop and online monitors) of nine dialysis wards of Italian hospitals, hosting 162 dialysis beds overall, were sampled on a monthly basis to determine the parameters provided by ISN guidelines. Chlorinated drinking water was desalinated by reverse osmosis and distributed to the closed loop which feeds all online monitors. Disinfection with peracetic acid was performed in all DW plants on a monthly basis. Over the 24-month study period, seven out of nine DW plants (78%) recorded negative results for all investigated parameters. Closed loop contamination with Burkholderia cepacia was detected in a DW plant from January 2015 to March 2015. Pseudomonas aeruginosa was isolated from March 2016 to May 2016 in the closed loop of another DW plant. These microbial contaminations were eradicated by shock disinfection with sodium hypochlorite and peracetic acid, followed by water flushing. These results highlight the importance of chemical and physical methods of DW disinfection. The maintenance of control measures in water plants hosted in dialysis wards ensures a microbial risk reduction for all dialysis patients. Copyright © 2017 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.

41 CFR 101-26.103-2 - Restriction on personal convenience items.

Code of Federal Regulations, 2012 CFR

2012-07-01

... funds may be expended for pictures, objects of art, plants, or flowers (both artificial and real), or... expended for pictures, objects of art, plants, flowers (both artificial and real), or any other similar...

41 CFR 101-26.103-2 - Restriction on personal convenience items.

Code of Federal Regulations, 2011 CFR

2011-07-01

... funds may be expended for pictures, objects of art, plants, or flowers (both artificial and real), or... expended for pictures, objects of art, plants, flowers (both artificial and real), or any other similar...

41 CFR 101-26.103-2 - Restriction on personal convenience items.

Code of Federal Regulations, 2013 CFR

2013-07-01

... funds may be expended for pictures, objects of art, plants, or flowers (both artificial and real), or... expended for pictures, objects of art, plants, flowers (both artificial and real), or any other similar...

41 CFR 101-26.103-2 - Restriction on personal convenience items.

Code of Federal Regulations, 2014 CFR

2014-07-01

... funds may be expended for pictures, objects of art, plants, or flowers (both artificial and real), or... expended for pictures, objects of art, plants, flowers (both artificial and real), or any other similar...

41 CFR 101-26.103-2 - Restriction on personal convenience items.

Code of Federal Regulations, 2010 CFR

2010-07-01

... funds may be expended for pictures, objects of art, plants, or flowers (both artificial and real), or... expended for pictures, objects of art, plants, flowers (both artificial and real), or any other similar...

The analysis and application of a new hybrid pollutants forecasting model using modified Kolmogorov-Zurbenko filter.

PubMed

Li, Peizhi; Wang, Yong; Dong, Qingli

2017-04-01

Cities in China suffer from severe smog and haze, and a forecasting system with high accuracy is of great importance to foresee the concentrations of the airborne particles. Compared with chemical transport models, the growing artificial intelligence models can simulate nonlinearities and interactive relationships and getting more accurate results. In this paper, the Kolmogorov-Zurbenko (KZ) filter is modified and firstly applied to construct the model using an artificial intelligence method. The concentration of inhalable particles and fine particulate matter in Dalian are used to analyze the filtered components and test the forecasting accuracy. Besides, an extended experiment is made by implementing a comprehensive comparison and a stability test using data in three other cities in China. Results testify the excellent performance of the developed hybrid models, which can be utilized to better understand the temporal features of pollutants and to perform a better air pollution control and management. Copyright © 2017 Elsevier B.V. All rights reserved.

Light transmission and ultraviolet protection of contact lenses under artificial illumination.

PubMed

Artigas, José M; Navea, Amparo; García-Domene, M Carmen; Gené, Andrés; Artigas, Cristina

2016-04-01

To determine the spectral transmission of contact lenses (CLs), with and without an ultraviolet (UV) filter to evaluate their capacity for protection under UV radiation from artificial illumination (incandescent, fluorescent, xenon (Xe) lamps, or white LEDs (light-emitting diode)). The transmission curves of nine soft CLs were obtained by using a PerkinElmer Lambda 35 UV-vis spectrophotometer. A CIE standard was used for the emission spectra of incandescent and fluorescent lamps, and Xe lamps and white LEDs were measured by using an International Light Technologies ILT-950 spectroradiometer. Five of the nine soft CLs analysed state that they incorporate UV filters, but the other four do not specify anything in this regard. The spectral transmission of all the CLs studied is excellent in the visible region. The CLs with UV filters filter out this radiation more or less effectively. Xe lamps emit a part in the UV region. Incandescent, fluorescent and white LEDs do not emit at all in the UV. Incorporating UV filters is important when the illumination is from a Xe lamp since this light source emits in the UV region. This, however, does not occur with incandescent and fluorescent lamps or white LEDs. The CLs that do incorporate UV filters meet all the standard requirements that the U.S. FDA (Food and Drug Administration) has for UV-blocking CLs Class II (OcularScience, CooperVision and Neolens), and AcuvueMoist and HydronActifresh400 even comply with the stricter Class I. The CLs without UV filters let UVA, UVB and even some UVC through. Copyright © 2015. Published by Elsevier Ltd.

Microbial Brokers of Insect-Plant Interactions Revisited

PubMed Central

Douglas, Angela E

2013-01-01

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. PMID:23793897

Colloidal Nanomolybdenum Influence upon the Antioxidative Reaction of Chickpea Plants ( Cicer arietinum L.)

NASA Astrophysics Data System (ADS)

Taran, Nataliya; Batsmanova, Ludmila; Kosyk, Oksana; Smirnov, Oleksandr; Kovalenko, Mariia; Honchar, Liubov; Okanenko, Alexander

2016-10-01

The use of colloidal solutions of metals as micronutrients enhances plant resistance to unfavorable environmental conditions and ensures high yields of food crops. The purpose of the study was a comparative evaluation of presowing treatment with nanomolybdenum and microbiological preparation impact upon the development of adaptive responses in chickpea plants. Oxidative processes did not develop in all variants of the experiment but in variants treated with microbial preparation, and joint action of microbial and nanopreparations even declined, as evidenced by the reduction of thiobarbituric acid reactive substances in photosynthetic tissues by 15 %. The activity of superoxide dismutase increased (by 15 %) in variant "nanomolybdenum" and joint action "microbial + nanomolybdenum," but it decreased by 20 % in variants with microbial preparation treatment. The same dependence was observed in changes of catalase activity. Antioxidant status factor, which takes into account the ratio of antioxidant to pro-oxidant, was the highest in variants with joint action of microbial preparation and nanomolybdenum (0.7), the lowest in variants with microbial treatment only (0.1). Thus, the results show that the action of nanoparticles of molybdenum activated antioxidant enzymes and decreased oxidative processes, thus promoting adaptation of plants.

Bacterial Endophyte Colonization and Distribution within Plants

PubMed Central

Kandel, Shyam L.; Joubert, Pierre M.

2017-01-01

The plant endosphere contains a diverse group of microbial communities. There is general consensus that these microbial communities make significant contributions to plant health. Both recently adopted genomic approaches and classical microbiology techniques continue to develop the science of plant-microbe interactions. Endophytes are microbial symbionts residing within the plant for the majority of their life cycle without any detrimental impact to the host plant. The use of these natural symbionts offers an opportunity to maximize crop productivity while reducing the environmental impacts of agriculture. Endophytes promote plant growth through nitrogen fixation, phytohormone production, nutrient acquisition, and by conferring tolerance to abiotic and biotic stresses. Colonization by endophytes is crucial for providing these benefits to the host plant. Endophytic colonization refers to the entry, growth and multiplication of endophyte populations within the host plant. Lately, plant microbiome research has gained considerable attention but the mechanism allowing plants to recruit endophytes is largely unknown. This review summarizes currently available knowledge about endophytic colonization by bacteria in various plant species, and specifically discusses the colonization of maize plants by Populus endophytes. PMID:29186821

Microbial quality of soft drinks served by the dispensing machines in fast food restaurants and convenience stores in Griffin, Georgia, and surrounding areas.

PubMed

Park, Yoen Ju; Chen, Jinru

2009-12-01

This study was undertaken to evaluate the microbial quality of the soft drinks served by fast food restaurants and gas station convenience stores in Griffin, GA, and surrounding areas. The soft drinks were collected from the dispensing machines in 8 fast food restaurants or gas station convenience stores in 2005 (n = 25) and in 10 fast food restaurants or gas station convenience stores in 2006 (n = 43) and 2007 (n = 43). One hundred milliliters of each soft drink was filtered through a hydrophobic grid membrane filter. The remaining portion of the soft drink was kept at room temperature for 4 h before sampling in order to mimic the possible holding time between purchase and consumption. The membrane filters were sampled for total aerobic bacteria, Enterobacteriaceae, lactic acid bacteria, and yeasts and molds. The microbial counts in the 2006 samples were numerically higher than the counts in the 2007 samples except for the average lactic acid bacteria counts, and were either significantly or numerically higher than the counts in the 2005 samples. Soft drinks sampled after the 4-h holding period had relatively higher counts than those sampled initially, with a few exceptions. Some soft drinks had over 4 log CFU/100 ml of total aerobic bacteria, Enterobacteriaceae, lactic acid bacteria, and yeast and mold cells. The study revealed the microbial quality of soft drinks served by dispensing machines in Griffin, GA, and surrounding areas, emphasizing the importance of effective sanitizing practice in retail settings.

Analysis of Bacterial and Archaeal Communities along a High-Molecular-Weight Polyacrylamide Transportation Pipeline System in an Oil Field

PubMed Central

Li, Cai-Yun; Li, Jing-Yan; Mbadinga, Serge Maurice; Liu, Jin-Feng; Gu, Ji-Dong; Mu, Bo-Zhong

2015-01-01

Viscosity loss of high-molecular-weight partially hydrolyzed polyacrylamide (HPAM) solution was observed in a water injection pipeline before being injected into subterranean oil wells. In order to investigate the possible involvement of microorganisms in HPAM viscosity loss, both bacterial and archaeal community compositions of four samples collected from different points of the transportation pipeline were analyzed using PCR-amplification of the 16S rRNA gene and clone library construction method together with the analysis of physicochemical properties of HPAM solution and environmental factors. Further, the relationship between environmental factors and HPAM properties with microorganisms were delineated by canonical correspondence analysis (CCA). Diverse bacterial and archaeal groups were detected in the four samples. The microbial community of initial solution S1 gathered from the make-up tank is similar to solution S2 gathered from the first filter, and that of solution S3 obtained between the first and the second filter is similar to that of solution S4 obtained between the second filter and the injection well. Members of the genus Acinetobacter sp. were detected with high abundance in S3 and S4 in which HPAM viscosity was considerably reduced, suggesting that they likely played a considerable role in HPAM viscosity loss. This study presents information on microbial community diversity in the HPAM transportation pipeline and the possible involvement of microorganisms in HPAM viscosity loss and biodegradation. The results will help to understand the microbial community contribution made to viscosity change and are beneficial for providing information for microbial control in oil fields. PMID:25849654

Analysis of bacterial and archaeal communities along a high-molecular-weight polyacrylamide transportation pipeline system in an oil field.

PubMed

Li, Cai-Yun; Li, Jing-Yan; Mbadinga, Serge Maurice; Liu, Jin-Feng; Gu, Ji-Dong; Mu, Bo-Zhong

2015-04-02

Viscosity loss of high-molecular-weight partially hydrolyzed polyacrylamide (HPAM) solution was observed in a water injection pipeline before being injected into subterranean oil wells. In order to investigate the possible involvement of microorganisms in HPAM viscosity loss, both bacterial and archaeal community compositions of four samples collected from different points of the transportation pipeline were analyzed using PCR-amplification of the 16S rRNA gene and clone library construction method together with the analysis of physicochemical properties of HPAM solution and environmental factors. Further, the relationship between environmental factors and HPAM properties with microorganisms were delineated by canonical correspondence analysis (CCA). Diverse bacterial and archaeal groups were detected in the four samples. The microbial community of initial solution S1 gathered from the make-up tank is similar to solution S2 gathered from the first filter, and that of solution S3 obtained between the first and the second filter is similar to that of solution S4 obtained between the second filter and the injection well. Members of the genus Acinetobacter sp. were detected with high abundance in S3 and S4 in which HPAM viscosity was considerably reduced, suggesting that they likely played a considerable role in HPAM viscosity loss. This study presents information on microbial community diversity in the HPAM transportation pipeline and the possible involvement of microorganisms in HPAM viscosity loss and biodegradation. The results will help to understand the microbial community contribution made to viscosity change and are beneficial for providing information for microbial control in oil fields.

Model system for studies of microbial dynamics at exuding surfaces such as the rhizosphere.

PubMed Central

Odham, G; Tunlid, A; Valeur, A; Sundin, P; White, D C

1986-01-01

An autoclavable all-glass system for studying microbial dynamics at permeable surfaces is described. Standard hydrophobic or hydrophilic membranes (46-mm diameter) of various pore sizes were supported on a glass frit through which nutrient solutions were pumped by a peristaltic pump. The pump provided a precisely controlled flow at speeds of 0.5 to 500 ml of defined or natural cell exudates per h, which passed through the membrane into a receiving vessel. The construction allowed a choice of membranes, which could be modified. The system was tested with a bacterium, isolated from rape plant roots (Brassica napus L.), that was inoculated on a hydrophilic membrane filter and allowed to develop into a biofilm. A defined medium with a composition resembling that of natural rape root exudate was pumped through the membrane at 0.5 ml/h. Scanning electron microscopic examinations indicated that the inoculum formed microcolonies embedded in exopolymers evenly distributed over the membrane surface. The lipid composition and content of poly-beta-hydroxybutyrate in free-living and adhered cells were determined by gas chromatography. The bacterial consumption of amino acids in the exudate was also studied. Images PMID:11536565

Model system for studies of microbial dynamics at exuding surfaces such as the rhizosphere

NASA Technical Reports Server (NTRS)

Odham, G.; Tunlid, A.; Valeur, A.; Sundin, P.; White, D. C.

1986-01-01

An autoclavable all-glass system for studying microbial dynamics at permeable surfaces is described. Standard hydrophobic or hydrophilic membranes (46-mm diameter) of various pore sizes were supported on a glass frit through which nutrient solutions were pumped by a peristaltic pump. The pump provided a precisely controlled flow at speeds of 0.5 to 500 ml of defined or natural cell exudates per h, which passed through the membrane into a receiving vessel. The construction allowed a choice of membranes, which could be modified. The system was tested with a bacterium, isolated from rape plant roots (Brassica napus L.), that was inoculated on a hydrophilic membrane filter and allowed to develop into a biofilm. A defined medium with a composition resembling that of natural rape root exudate was pumped through the membrane at 0.5 ml/h. Scanning electron microscopic examinations indicated that the inoculum formed microcolonies embedded in exopolymers evenly distributed over the membrane surface. The lipid composition and content of poly-beta-hydroxybutyrate in free-living and adhered cells were determined by gas chromatography. The bacterial consumption of amino acids in the exudate was also studied.

Microbial production of isoquinoline alkaloids as plant secondary metabolites based on metabolic engineering research.

PubMed

Sato, Fumihiko; Kumagai, Hidehiko

2013-01-01

Plants produce a variety of secondary metabolites that possess strong physiological activities. Unfortunately, however, their production can suffer from a variety of serious problems, including low levels of productivity and heterogeneous quality, as well as difficulty in raw material supply. In contrast, microorganisms can be used to produce their primary and some of their secondary metabolites in a controlled environment, thus assuring high levels of efficiency and uniform quality. In an attempt to overcome the problems associated with secondary metabolite production in plants, we developed a microbial platform for the production of plant isoquinoline alkaloids involving the unification of the microbial and plant metabolic pathways into a single system. The potential applications of this system have also been discussed.

Microbial production of isoquinoline alkaloids as plant secondary metabolites based on metabolic engineering research

PubMed Central

SATO, Fumihiko; KUMAGAI, Hidehiko

2013-01-01

Plants produce a variety of secondary metabolites that possess strong physiological activities. Unfortunately, however, their production can suffer from a variety of serious problems, including low levels of productivity and heterogeneous quality, as well as difficulty in raw material supply. In contrast, microorganisms can be used to produce their primary and some of their secondary metabolites in a controlled environment, thus assuring high levels of efficiency and uniform quality. In an attempt to overcome the problems associated with secondary metabolite production in plants, we developed a microbial platform for the production of plant isoquinoline alkaloids involving the unification of the microbial and plant metabolic pathways into a single system. The potential applications of this system have also been discussed. PMID:23666088

Cascading effects of artificial light at night: resource-mediated control of herbivores in a grassland ecosystem

PubMed Central

Bennie, Jonathan; Davies, Thomas W.; Cruse, David; Inger, Richard; Gaston, Kevin J.

2015-01-01

Artificial light at night has a wide range of biological effects on both plants and animals. Here, we review mechanisms by which artificial light at night may restructure ecological communities by modifying the interactions between species. Such mechanisms may be top-down (predator, parasite or grazer controlled), bottom-up (resource-controlled) or involve non-trophic processes, such as pollination, seed dispersal or competition. We present results from an experiment investigating both top-down and bottom-up effects of artificial light at night on the population density of pea aphids Acyrthosiphon pisum in a diverse artificial grassland community in the presence and absence of predators and under low-level light of different spectral composition. We found no evidence for top-down control of A. pisum in this system, but did find evidence for bottom-up effects mediated through the impact of light on flower head density in a leguminous food plant. These results suggest that physiological effects of light on a plant species within a diverse plant community can have detectable demographic effects on a specialist herbivore. PMID:25780243

[Distribution characteristics of soil organic carbon of burned area under different restorations.

PubMed

Li, Hong Yun; Xin, Ying; Zhao, Yu Sen

2016-09-01

The distribution characteristics of soil organic carbon (SOC), soil dissolved organic carbon (DOC) and soil microbial biomass carbon (MBC) under different restorations were studied in Larix gmelinii plantation, Pinus sylvestris var. mongolica plantation, artificial promotion poplar-birch forest and the natural secondary poplar-birch forest restored from burned area after the severe fire of Greater Xing' an Mountains in 1987. The results showed that the variations in SOC, DOC and MBC ranged from 9.63 to 79.72 g·kg -1 , from 33.21 to 186.30 mg·kg -1 and from 200.85 to 1755.63 mg·kg -1 , respectively, which decreased with soil depth increasing. There was significant diffe-rence in SOC, DOC and MBC among different restorations, with the maximum carbon contents for artificial promotion poplar-birch forest, followed by L. gmelinii plantation, natural secondary poplar-birch forest and P. sylvestris var. mongolica plantation successively. The soil microbial quotient va-ried from 1.1% under P. sylvestris var. mongolica plantation to 2.3% under artificial promotion poplar-birch forest, and its vertical distributions were different in the four restoration forests. Correlation analysis indicated that MBC had a significant positive correlation with SOC and DOC, respectively. The activity of soil organic carbon in artificial promotion poplar-birch forest was higher than in other forest stands, suggesting a stronger capacity of the soil carbon cycle through natural regeneration with artificial promotion on burned area in Greater Xing'an Mountains.

Environmental factors influencing the structural dynamics of soil microbial communities during assisted phytostabilization of acid-generating mine tailings: a mesocosm experiment.

PubMed

Valentín-Vargas, Alexis; Root, Robert A; Neilson, Julia W; Chorover, Jon; Maier, Raina M

2014-12-01

Compost-assisted phytostabilization has recently emerged as a robust alternative for reclamation of metalliferous mine tailings. Previous studies suggest that root-associated microbes may be important for facilitating plant establishment on the tailings, yet little is known about the long-term dynamics of microbial communities during reclamation. A mechanistic understanding of microbial community dynamics in tailings ecosystems undergoing remediation is critical because these dynamics profoundly influence both the biogeochemical weathering of tailings and the sustainability of a plant cover. Here we monitor the dynamics of soil microbial communities (i.e. bacteria, fungi, archaea) during a 12-month mesocosm study that included 4 treatments: 2 unplanted controls (unamended and compost-amended tailings) and 2 compost-amended seeded tailings treatments. Bacterial, fungal and archaeal communities responded distinctively to the revegetation process and concurrent changes in environmental conditions and pore water chemistry. Compost addition significantly increased microbial diversity and had an immediate and relatively long-lasting buffering-effect on pH, allowing plants to germinate and thrive during the early stages of the experiment. However, the compost buffering capacity diminished after six months and acidification took over as the major factor affecting plant survival and microbial community structure. Immediate changes in bacterial communities were observed following plant establishment, whereas fungal communities showed a delayed response that apparently correlated with the pH decline. Fluctuations in cobalt pore water concentrations, in particular, had a significant effect on the structure of all three microbial groups, which may be linked to the role of cobalt in metal detoxification pathways. The present study represents, to our knowledge, the first documentation of the dynamics of the three major microbial groups during revegetation of compost-amended, metalliferous mine tailings. Copyright © 2014 Elsevier B.V. All rights reserved.

Environmental Factors Influencing the Structural Dynamics of Soil Microbial Communities During Assisted Phytostabilization of Acid-Generating Mine Tailings: a Mesocosm Experiment

PubMed Central

Valentín-Vargas, Alexis; Root, Robert A.; Neilson, Julia W; Chorover, Jon; Maier, Raina M.

2014-01-01

Compost-assisted phytostabilization has recently emerged as a robust alternative for reclamation of metalliferous mine tailings. Previous studies suggest that root-associated microbes may be important for facilitating plant establishment on the tailings, yet little is known about the long-term dynamics of microbial communities during reclamation. A mechanistic understanding of microbial community dynamics in tailings ecosystems undergoing remediation is critical because these dynamics profoundly influence both the biogeochemical weathering of tailings and the sustainability of a plant cover. Here we monitor the dynamics of soil microbial communities (i.e. bacteria, fungi, archaea) during a 12-month mesocosm study that included 4 treatments: 2 unplanted controls (unamended and compost-amended tailings) and 2 compost-amended seeded tailings treatments. Bacterial, fungal and archaeal communities responded distinctively to the revegetation process and concurrent changes in environmental conditions and pore water chemistry. Compost addition significantly increased microbial diversity and had an immediate and relatively long-lasting buffering-effect on pH, allowing plants to germinate and thrive during the early stages of the experiment. However, the compost buffering capacity diminished after six months and acidification took over as the major factor affecting plant survival and microbial community structure. Immediate changes in bacterial communities were observed following plant establishment, whereas fungal communities showed a delayed response that apparently correlated with the pH decline. Fluctuations in cobalt pore water concentrations, in particular, had a significant effect on the structure of all three microbial groups, which may be linked to the role of cobalt in metal detoxification pathways. The present study represents, to our knowledge, the first documentation of the dynamics of the three major microbial groups during revegetation of compost-amended, metalliferous mine tailings. PMID:25237788

Soluble microbial products in pilot-scale drinking water biofilters with acetate as sole carbon source.

PubMed

Zhang, Ying; Ye, Chengsong; Gong, Song; Wei, Gu; Yu, Xin; Feng, Lin

2013-04-01

A comprehensive study on formation and characteristics of soluble microbial products (SMP) during drinking water biofiltration was made in four parallel pilot-scale ceramic biofilters with acetate as the substrate. Excellent treatment performance was achieved while microbial biomass and acetate carbon both declined with the depth of filter. The SMP concentration was determined by calculating the difference between the concentration of dissolved organic carbon (DOC), biodegradable dissolved organic carbon (BDOC) and acetate carbon. The results revealed that SMP showed an obvious increase from 0 to 100 cm depth of the filter. A rising specific ultraviolet absorbance (SUVA) was also found, indicating that benzene or carbonyl might exist in these compounds. SMP produced during this drinking water biological process were proved to have weak mutagenicity and were not precursors of by-products of chlorination disinfection. The volatile parts of SMP were half-quantity analyzed and most of them were dicarboxyl acids, others were hydrocarbons or benzene with 16-17 carbon atoms.

Strategies for microbial synthesis of high-value phytochemicals

NASA Astrophysics Data System (ADS)

Li, Sijin; Li, Yanran; Smolke, Christina D.

2018-03-01

Phytochemicals are of great pharmaceutical and agricultural importance, but often exhibit low abundance in nature. Recent demonstrations of industrial-scale production of phytochemicals in yeast have shown that microbial production of these high-value chemicals is a promising alternative to sourcing these molecules from native plant hosts. However, a number of challenges remain in the broader application of this approach, including the limited knowledge of plant secondary metabolism and the inefficient reconstitution of plant metabolic pathways in microbial hosts. In this Review, we discuss recent strategies to achieve microbial biosynthesis of complex phytochemicals, including strategies to: (1) reconstruct plant biosynthetic pathways that have not been fully elucidated by mining enzymes from native and non-native hosts or by enzyme engineering; (2) enhance plant enzyme activity, specifically cytochrome P450 activity, by improving efficiency, selectivity, expression or electron transfer; and (3) enhance overall reaction efficiency of multi-enzyme pathways by dynamic control, compartmentalization or optimization with the host's metabolism. We also highlight remaining challenges to — and future opportunities of — this approach.

Artificial Leaks in Container Closure Integrity Testing: Nonlinear Finite Element Simulation of Aperture Size Originated by a Copper Wire Sandwiched between the Stopper and the Glass Vial.

PubMed

Nieto, Alejandra; Roehl, Holger; Brown, Helen; Adler, Michael; Chalus, Pascal; Mahler, Hanns-Christian

2016-01-01

Container closure integrity (CCI) testing is required by different regulatory authorities in order to provide assurance of tightness of the container closure system against possible contamination, for example, by microorganisms. Microbial ingress CCI testing is performed by incubation of the container closure system with microorganisms under specified testing conditions. Physical CCI uses surrogate endpoints, such as coloration by dye solution ingress or gas flow (helium leakage testing). In order to correlate microbial CCI and physical CCI test methods and to evaluate the methods' capability to detect a given leak, artificial leaks are being introduced into the container closure system in a variety of different ways. In our study, artificial leaks were generated using inserted copper wires between the glass vial opening and rubber stopper. However, the insertion of copper wires introduces leaks of unknown size and shape. With nonlinear finite element simulations, the aperture size between the rubber stopper and the glass vial was calculated, depending on wire diameter and capping force. The dependency of the aperture size on the copper wire diameter was quadratic. With the data obtained, we were able to calculate the leak size and model leak shape. Our results suggest that the size as well as the shape of the artificial leaks should be taken into account when evaluating critical leak sizes, as flow rate does not, independently, correlate to hole size. Capping force also affected leak size. An increase in the capping force from 30 to 70 N resulted in a reduction of the aperture (leak size) by approximately 50% for all wire diameters. From 30 to 50 N, the reduction was approximately 33%. Container closure integrity (CCI) testing is required by different regulatory authorities in order to provide assurance of tightness of the container closure system against contamination, for example, by microorganisms. Microbial ingress CCI testing is performed by incubation of the container closure system with microorganisms under specified testing conditions. Physical CCI uses surrogate endpoints, such as coloration by dye solution ingress or gas flow. In order to correlate microbial ingress CCI and physical CCI test methods and to evaluate the methods' capability to detect a given leak, artificially created defects (artificial leaks) are being introduced into the container closure system in a variety of different ways. In our study, artificial leaks were generated using inserted copper wires between the glass vial opening and rubber stopper. Up to date, the insertion of copper wires introduced leaks of unknown size and shape. With nonlinear finite element simulations, the effective aperture size between the rubber stopper and the glass vial was calculated, depending on wire diameter and capping force, and the leak shape was modelled. Our results suggest that the size as well as the shape of the artificial leaks should be taken into account when evaluating critical leak sizes, as flow rate does not, independently, correlate to the hole size. © PDA, Inc. 2016.

Differential responses of soil microbial biomass, diversity, and compositions to altitudinal gradients depend on plant and soil characteristics.

PubMed

Ren, Chengjie; Zhang, Wei; Zhong, ZeKun; Han, Xinhui; Yang, Gaihe; Feng, Yongzhong; Ren, Guangxin

2018-01-01

Alt'itudinal gradients strongly affect plant biodiversity, but the effects on microbial patterns remain unclear, especially in the large scale. We therefore designed an altitudinal gradient experiment that covered three climate zones to monitor soil microbial community dynamics and to compare those with plant and soil characteristics. Illumina sequencing of the 16S rRNA gene and ITS gene was used to analyze soil microbial (bacterial and fungal) diversity and composition, and fumigation-extraction was used to determine microbial biomass; the plant community metrics (i.e., percent cover, Shannon-Wiener, grass biomass, and carbon/nitrogen in leaf and biomass) and soil properties (i.e., soil moisture, soil temperature, bulk density, organic carbon, total nitrogen, and available nitrogen) were determined. The results showed that carbon/nitrogen in microbial biomass was higher at medium altitude and was positively related to carbon and nitrogen in both soil and grass biomass along the altitudinal gradients. Soil bacterial alpha diversity was significantly higher at medium altitude but fungal alpha diversity did not affected by altitudinal gradients; the effect of altitudinal gradients on bacterial beta diversity was larger than that on fungal beta diversity, although both groups were significantly affected by altitudinal gradients. Moreover, Alpha-proteobacteria, Beta-proteobacteria, and Gemmatimonadetes were significantly more abundant in higher altitude than in lower altitude, both Acidobacteria and Actinobacteria significantly declined with increasing altitude; other bacterial taxa such as Chloroflexi, Nitrospirae, Gamma-proteobacteria, and Delta-proteobacteria were significantly higher at medium altitudes. For fungal taxa, Basidiomycota and Ascomycota were the dominant phyla and responded insignificantly to the altitudinal gradients. The responses of microbial alpha diversity were mostly associated with plant Shannon index, organic carbon, and total nitrogen, whereas microbial beta diversity and composition mainly depended on soil moisture and temperature. Overall, these results suggest that soil bacteria rather than fungi can reflect changes in plant and soil characteristics along altitudinal gradients. Copyright © 2017 Elsevier B.V. All rights reserved.

Relationships among plants, soils and microbial communities along a hydrological gradient in the New Jersey Pinelands, USA

PubMed Central

Yu, Shen; Ehrenfeld, Joan G.

2010-01-01

Background and Aims Understanding the role of different components of hydrology in structuring wetland communities is not well developed. A sequence of adjacent wetlands located on a catenary sequence of soils and receiving the same sources and qualities of water is used to examine specifically the role of water-table median position and variability in affecting plant and microbial community composition and soil properties. Methods Two replicates of three types of wetland found adjacent to each other along a hydrological gradient in the New Jersey Pinelands (USA) were studied. Plant-community and water-table data were obtained within a 100-m2 plot in each community (pine swamp, maple swamp and Atlantic-white-cedar swamp). Monthly soil samples from each plot were analysed for soil moisture, organic matter, extractable nitrogen fractions, N mineralization rate and microbial community composition. Multivariate ordination methods were used to compare patterns among sites within and between data sets. Key Results The maple and pine wetlands were more similar to each other in plant community composition, soil properties and microbial community composition than either was to the cedar swamps. However, maple and pine wetlands differed from each other in water-table descriptors as much as they differed from the cedar swamps. All microbial communities were dominated by Gram-positive bacteria despite hydrologic differences among the sites. Water-table variability was as important as water-table level in affecting microbial communities. Conclusions Water tables affect wetland communities through both median level and variability. Differentiation of both plant and microbial communities are not simple transforms of differences in water-table position, even when other hydrologic factors are kept constant. Rather, soil genesis, a result of both water-table position and geologic history, appears to be the main factor affecting plant and microbial community similarities. PMID:19643908

Linking the development and functioning of a carnivorous pitcher plant's microbial digestive community.

PubMed

Armitage, David W

2017-11-01

Ecosystem development theory predicts that successional turnover in community composition can influence ecosystem functioning. However, tests of this theory in natural systems are made difficult by a lack of replicable and tractable model systems. Using the microbial digestive associates of a carnivorous pitcher plant, I tested hypotheses linking host age-driven microbial community development to host functioning. Monitoring the yearlong development of independent microbial digestive communities in two pitcher plant populations revealed a number of trends in community succession matching theoretical predictions. These included mid-successional peaks in bacterial diversity and metabolic substrate use, predictable and parallel successional trajectories among microbial communities, and convergence giving way to divergence in community composition and carbon substrate use. Bacterial composition, biomass, and diversity positively influenced the rate of prey decomposition, which was in turn positively associated with a host leaf's nitrogen uptake efficiency. Overall digestive performance was greatest during late summer. These results highlight links between community succession and ecosystem functioning and extend succession theory to host-associated microbial communities.

Microbial community structure elucidates performance of Glyceria maxima plant microbial fuel cell.

PubMed

Timmers, Ruud A; Rothballer, Michael; Strik, David P B T B; Engel, Marion; Schulz, Stephan; Schloter, Michael; Hartmann, Anton; Hamelers, Bert; Buisman, Cees

2012-04-01

The plant microbial fuel cell (PMFC) is a technology in which living plant roots provide electron donor, via rhizodeposition, to a mixed microbial community to generate electricity in a microbial fuel cell. Analysis and localisation of the microbial community is necessary for gaining insight into the competition for electron donor in a PMFC. This paper characterises the anode-rhizosphere bacterial community of a Glyceria maxima (reed mannagrass) PMFC. Electrochemically active bacteria (EAB) were located on the root surfaces, but they were more abundant colonising the graphite granular electrode. Anaerobic cellulolytic bacteria dominated the area where most of the EAB were found, indicating that the current was probably generated via the hydrolysis of cellulose. Due to the presence of oxygen and nitrate, short-chain fatty acid-utilising denitrifiers were the major competitors for the electron donor. Acetate-utilising methanogens played a minor role in the competition for electron donor, probably due to the availability of graphite granules as electron acceptors.

Effects of soil depth and plant-soil interaction on microbial community in temperate grasslands of northern China.

PubMed

Yao, Xiaodong; Zhang, Naili; Zeng, Hui; Wang, Wei

2018-07-15

Although the patterns and drivers of soil microbial community composition are well studied, little is known about the effects of plant-soil interactions and soil depth on soil microbial distribution at a regional scale. We examined 195 soil samples from 13 sites along a climatic transect in the temperate grasslands of northern China to measure the composition of and factors influencing soil microbial communities within a 1-m soil profile. Soil microbial community composition was measured using phospholipid fatty acids (PLFA) analysis. Fungi predominated in topsoil (0-10 cm) and bacteria and actinomycetes in deep soils (40-100 cm), independent of steppe types. This variation was explained by contemporary environmental factors (including above- and below-ground plant biomass, soil physicochemical and climatic factors) >58% in the 0-40 cm of soil depth, but <45% in deep soils. Interestingly, when we considered the interactive effects between plant traits (above ground biomass and root biomass) and soil factors (pH, clay content, and soil total carbon, nitrogen, phosphorous), we observed a significant interaction effect occurring at depths of 10-20 cm soil layer, due to different internal and external factors of the plant-soil system along the soil profile. These results improve understanding of the drivers of soil microbial community composition at regional scales. Copyright © 2018 Elsevier B.V. All rights reserved.

Manipulation of the rhizosphere microbial community through application of a new bio-organic fertilizer improves watermelon quality and health

PubMed Central

Huang, Jing; Chen, Zhe; Nie, Yuanjun; Wang, Changbiao

2018-01-01

Bio-organic fertilizers (BOFs) combine functional microbes with a suitable substrate and have been shown to effectively suppress soil-borne diseases and promote plant growth. Here, we developed a novel bio-organic fertilizer (BOF) by fermentation of a cow plus chicken manure (M) compost using Fen-liquor Daqu (FLD) as a fermentation starter and compared the compositions of bacterial and fungal communities in the rhizosphere soil of watermelon plants after treatment with different fertilizers. Further, we aimed to explore the mechanisms underlying plant-promoting and disease (Fusarium wilt)-suppressing activities of each rhizosphere microbial community. The microbial communities of soil amended with cow plus chicken manure compost (S+M), soil amended with the BOF (S+BOF), and untreated control soil (S) without plants were analyzed through sequence analysis using the Illumina MiSeq platform. The results showed that a new microbial community was formed in the manure compost after fermentation by the Daqu. Application of the BOF to the soil induced remarkable changes in the rhizosphere microbial communities, with increased bacterial diversity and decreased fungal diversity. Most importantly, S+BOF showed the lowest abundance of Fusarium. Moreover, watermelon quality was higher (P < 0.05) in the S+BOF than in the S+M treatment. Thus, application of the BOF favorably altered the composition of the rhizosphere microbial community, suppressing Fusarium wilt disease and promoting plant quality. PMID:29451918

Manipulation of the rhizosphere microbial community through application of a new bio-organic fertilizer improves watermelon quality and health.

PubMed

Zhao, Jia; Liu, Jiang; Liang, Hong; Huang, Jing; Chen, Zhe; Nie, Yuanjun; Wang, Changbiao; Wang, Yuguo

2018-01-01

Bio-organic fertilizers (BOFs) combine functional microbes with a suitable substrate and have been shown to effectively suppress soil-borne diseases and promote plant growth. Here, we developed a novel bio-organic fertilizer (BOF) by fermentation of a cow plus chicken manure (M) compost using Fen-liquor Daqu (FLD) as a fermentation starter and compared the compositions of bacterial and fungal communities in the rhizosphere soil of watermelon plants after treatment with different fertilizers. Further, we aimed to explore the mechanisms underlying plant-promoting and disease (Fusarium wilt)-suppressing activities of each rhizosphere microbial community. The microbial communities of soil amended with cow plus chicken manure compost (S+M), soil amended with the BOF (S+BOF), and untreated control soil (S) without plants were analyzed through sequence analysis using the Illumina MiSeq platform. The results showed that a new microbial community was formed in the manure compost after fermentation by the Daqu. Application of the BOF to the soil induced remarkable changes in the rhizosphere microbial communities, with increased bacterial diversity and decreased fungal diversity. Most importantly, S+BOF showed the lowest abundance of Fusarium. Moreover, watermelon quality was higher (P < 0.05) in the S+BOF than in the S+M treatment. Thus, application of the BOF favorably altered the composition of the rhizosphere microbial community, suppressing Fusarium wilt disease and promoting plant quality.

METHODS FOR IMPROVEMENT OF TRICKLING FILTER PLANT PERFORMANCE. PART II. CHEMICAL ADDITION

EPA Science Inventory

An experimental program to explore potential methods for removing phosphorus and generally enhancing trickling filter plant performance was conducted at the Mason Farm Wastewater Treatment Plant, Chapel Hill, North Carolina. Preliminary investigations included jar testing with se...

Difference of microbial community stressed in artificial pit muds for Luzhou-flavour liquor brewing revealed by multiphase culture-independent technology.

PubMed

Zhang, L; Zhou, R; Niu, M; Zheng, J; Wu, C

2015-11-01

Artificial pit muds (APMs) is produced by peats, aged pit muds, yellow and black clays etc. and is one of essential factors for Luzhou-flavour liquor production. The microbial community of APMs significantly influence the quality of Luzhou-flavour liquor. The aim of this study was to investigate the differences in bacterial, archaeal and fungal community of APMs, starters and materials. Multiphase culture-independent technology were employed in this study, including nested PCR-denaturing gradient gel electrophoresis (nested PCR-DGGE), phospholipid fatty acid (PLFA), phospholipid ether lipids (PLEL) and fluorescence in situ hybridization (FISH) analysis. Results suggested that the microbial diversity significantly changed under environmental stress and different culture patterns during APMs cultivation. The dominant bacteria in APMs mainly fell into Clostridiales, Lactobacillales, Bacteroidales and Rhizobiales, Archaea affiliated with Methanomicrobiales and Methanosarcinales, and fungi belonged to Saccharomycetales and Eurotiales. Furthermore, the microbial community structures of APMs cultured by ground pile pattern were more similar with that of aged pit muds, meanwhile, the relative bands intensities of microbes, which are the main contributors for liquor brewing, increased with the culture times. Not only the niche selection and biogeochemical properties of APMs, but also the mutual collaboration and constraint between different microbes may result in enriching different liquor-brewing microbes into APMs. APM cultivation technology was necessary to promote enriching functional liquor-brewing microbes into APMs. These results may facilitate understanding the microbial succession during APMs manufacture. © 2015 The Society for Applied Microbiology.

Headwater fish population responses to planting grass filter strips adjacent to channelized agricultural headwater streams

USDA-ARS?s Scientific Manuscript database

Grass filter strips are a widely used conservation practice in the Midwestern United States for reducing nutrient, pesticide, and sediment inputs into agricultural streams. Only a limited amount of information is available on the ecological effects of planting grass filter strips adjacent to channe...

Risk Assessment of Arsenic Mitigation Options in Bangladesh

PubMed Central

Ahmed, M. Feroze; Shamsuddin, Abu Jafar; Mahmud, Shamsul Gafur; Deere, Daniel

2006-01-01

The provision of alternative water sources is the principal arsenic mitigation strategy in Bangladesh, but can lead to risk substitution. A study of arsenic mitigation options was undertaken to assess water quality and sanitary condition and to estimate the burden of disease associated with each technology in disability-adjusted life years (DALYs). Dugwells and pond-sand filters showed heavy microbial contamination in both dry and monsoon seasons, and the estimated burden of disease was high. Rainwater was of good quality in the monsoon but deteriorated in the dry season. Deep tubewells showed microbial contamination in the monsoon but not in the dry season and was the only technology to approach the World Health Organization's reference level of risk of 10-6 DALYs. A few dugwells and one pond-sand filter showed arsenic in excess of 50 μg/L. The findings suggest that deep tubewells and rainwater harvesting provide safer water than dugwells and pond-sand filters and should be the preferred options. PMID:17366776

Method and apparatus for optimizing operation of a power generating plant using artificial intelligence techniques

DOEpatents

Wroblewski, David [Mentor, OH; Katrompas, Alexander M [Concord, OH; Parikh, Neel J [Richmond Heights, OH

2009-09-01

A method and apparatus for optimizing the operation of a power generating plant using artificial intelligence techniques. One or more decisions D are determined for at least one consecutive time increment, where at least one of the decisions D is associated with a discrete variable for the operation of a power plant device in the power generating plant. In an illustrated embodiment, the power plant device is a soot cleaning device associated with a boiler.

Symbiotic in vitro seed propagation of Dendrobium: fungal and bacterial partners and their influence on plant growth and development.

PubMed

Teixeira da Silva, Jaime A; Tsavkelova, Elena A; Zeng, Songjun; Ng, Tzi Bun; Parthibhan, S; Dobránszki, Judit; Cardoso, Jean Carlos; Rao, M V

2015-07-01

The genus Dendrobium is one of the largest genera of the Orchidaceae Juss. family, although some of its members are the most threatened today. The reason why many species face a vulnerable or endangered status is primarily because of anthropogenic interference in natural habitats and commercial overexploitation. The development and application of modern techniques and strategies directed towards in vitro propagation of orchids not only increases their number but also provides a viable means to conserve plants in an artificial environment, both in vitro and ex vitro, thus providing material for reintroduction. Dendrobium seed germination and propagation are challenging processes in vivo and in vitro, especially when the extreme specialization of these plants is considered: (1) their biotic relationships with pollinators and mycorrhizae; (2) adaptation to epiphytic or lithophytic life-styles; (3) fine-scale requirements for an optimal combination of nutrients, light, temperature, and pH. This review also aims to summarize the available data on symbiotic in vitro Dendrobium seed germination. The influence of abiotic factors as well as composition and amounts of different exogenous nutrient substances is examined. With a view to better understanding how to optimize and control in vitro symbiotic associations, a part of the review describes the strong biotic relations of Dendrobium with different associative microorganisms that form microbial communities with adult plants, and also influence symbiotic seed germination. The beneficial role of plant growth-promoting bacteria is also discussed.

Microbial decomposers not constrained by climate history along a Mediterranean climate gradient in southern California.

PubMed

Baker, Nameer R; Khalili, Banafshe; Martiny, Jennifer B H; Allison, Steven D

2018-06-01

Microbial decomposers mediate the return of CO 2 to the atmosphere by producing extracellular enzymes to degrade complex plant polymers, making plant carbon available for metabolism. Determining if and how these decomposer communities are constrained in their ability to degrade plant litter is necessary for predicting how carbon cycling will be affected by future climate change. We analyzed mass loss, litter chemistry, microbial biomass, extracellular enzyme activities, and enzyme temperature sensitivities in grassland litter transplanted along a Mediterranean climate gradient in southern California. Microbial community composition was manipulated by caging litter within bags made of nylon membrane that prevent microbial immigration. To test whether grassland microbes were constrained by climate history, half of the bags were inoculated with local microbial communities native to each gradient site. We determined that temperature and precipitation likely interact to limit microbial decomposition in the extreme sites along our gradient. Despite their unique climate history, grassland microbial communities were not restricted in their ability to decompose litter under different climate conditions across the gradient, although microbial communities across our gradient may be restricted in their ability to degrade different types of litter. We did find some evidence that local microbial communities were optimized based on climate, but local microbial taxa that proliferated after inoculation into litterbags did not enhance litter decomposition. Our results suggest that microbial community composition does not constrain C-cycling rates under climate change in our system, but optimization to particular resource environments may act as more general constraints on microbial communities. © 2018 by the Ecological Society of America.

Depth Filters Containing Diatomite Achieve More Efficient Particle Retention than Filters Solely Containing Cellulose Fibers

PubMed Central

Buyel, Johannes F.; Gruchow, Hannah M.; Fischer, Rainer

2015-01-01

The clarification of biological feed stocks during the production of biopharmaceutical proteins is challenging when large quantities of particles must be removed, e.g., when processing crude plant extracts. Single-use depth filters are often preferred for clarification because they are simple to integrate and have a good safety profile. However, the combination of filter layers must be optimized in terms of nominal retention ratings to account for the unique particle size distribution in each feed stock. We have recently shown that predictive models can facilitate filter screening and the selection of appropriate filter layers. Here we expand our previous study by testing several filters with different retention ratings. The filters typically contain diatomite to facilitate the removal of fine particles. However, diatomite can interfere with the recovery of large biopharmaceutical molecules such as virus-like particles and aggregated proteins. Therefore, we also tested filtration devices composed solely of cellulose fibers and cohesive resin. The capacities of both filter types varied from 10 to 50 L m−2 when challenged with tobacco leaf extracts, but the filtrate turbidity was ~500-fold lower (~3.5 NTU) when diatomite filters were used. We also tested pre–coat filtration with dispersed diatomite, which achieved capacities of up to 120 L m−2 with turbidities of ~100 NTU using bulk plant extracts, and in contrast to the other depth filters did not require an upstream bag filter. Single pre-coat filtration devices can thus replace combinations of bag and depth filters to simplify the processing of plant extracts, potentially saving on time, labor and consumables. The protein concentrations of TSP, DsRed and antibody 2G12 were not affected by pre-coat filtration, indicating its general applicability during the manufacture of plant-derived biopharmaceutical proteins. PMID:26734037

Depth Filters Containing Diatomite Achieve More Efficient Particle Retention than Filters Solely Containing Cellulose Fibers.

PubMed

Buyel, Johannes F; Gruchow, Hannah M; Fischer, Rainer

2015-01-01

The clarification of biological feed stocks during the production of biopharmaceutical proteins is challenging when large quantities of particles must be removed, e.g., when processing crude plant extracts. Single-use depth filters are often preferred for clarification because they are simple to integrate and have a good safety profile. However, the combination of filter layers must be optimized in terms of nominal retention ratings to account for the unique particle size distribution in each feed stock. We have recently shown that predictive models can facilitate filter screening and the selection of appropriate filter layers. Here we expand our previous study by testing several filters with different retention ratings. The filters typically contain diatomite to facilitate the removal of fine particles. However, diatomite can interfere with the recovery of large biopharmaceutical molecules such as virus-like particles and aggregated proteins. Therefore, we also tested filtration devices composed solely of cellulose fibers and cohesive resin. The capacities of both filter types varied from 10 to 50 L m(-2) when challenged with tobacco leaf extracts, but the filtrate turbidity was ~500-fold lower (~3.5 NTU) when diatomite filters were used. We also tested pre-coat filtration with dispersed diatomite, which achieved capacities of up to 120 L m(-2) with turbidities of ~100 NTU using bulk plant extracts, and in contrast to the other depth filters did not require an upstream bag filter. Single pre-coat filtration devices can thus replace combinations of bag and depth filters to simplify the processing of plant extracts, potentially saving on time, labor and consumables. The protein concentrations of TSP, DsRed and antibody 2G12 were not affected by pre-coat filtration, indicating its general applicability during the manufacture of plant-derived biopharmaceutical proteins.

Saving seed microbiomes.

PubMed

Berg, Gabriele; Raaijmakers, Jos M

2018-05-01

Plant seeds are home to diverse microbial communities whose composition is determined by plant genotype, environment, and management practices. Plant domestication is now recognized as an important driver of plant-associated microbial diversity. To what extent and how domestication affects seed microbiomes is less well studied. Here we propose a 'back-to-the-future' approach to harness seed microbiomes of wild relatives of crop cultivars to save and re-instate missing beneficial seed microbes for improved plant tolerance to biotic and abiotic stress.

A Community-Based Culture Collection for Targeting Novel Plant Growth-Promoting Bacteria from the Sugarcane Microbiome

PubMed Central

Armanhi, Jaderson Silveira Leite; de Souza, Rafael Soares Correa; Damasceno, Natália de Brito; de Araújo, Laura M.; Imperial, Juan; Arruda, Paulo

2018-01-01

The soil-plant ecosystem harbors an immense microbial diversity that challenges investigative approaches to study traits underlying plant-microbe association. Studies solely based on culture-dependent techniques have overlooked most microbial diversity. Here we describe the concomitant use of culture-dependent and -independent techniques to target plant-beneficial microbial groups from the sugarcane microbiome. The community-based culture collection (CBC) approach was used to access microbes from roots and stalks. The CBC recovered 399 unique bacteria representing 15.9% of the rhizosphere core microbiome and 61.6–65.3% of the endophytic core microbiomes of stalks. By cross-referencing the CBC (culture-dependent) with the sugarcane microbiome profile (culture-independent), we designed a synthetic community comprised of naturally occurring highly abundant bacterial groups from roots and stalks, most of which has been poorly explored so far. We then used maize as a model to probe the abundance-based synthetic inoculant. We show that when inoculated in maize plants, members of the synthetic community efficiently colonize plant organs, displace the natural microbiota and dominate at 53.9% of the rhizosphere microbial abundance. As a result, inoculated plants increased biomass by 3.4-fold as compared to uninoculated plants. The results demonstrate that abundance-based synthetic inoculants can be successfully applied to recover beneficial plant microbes from plant microbiota. PMID:29354144

Interspecific Plant Interactions Reflected in Soil Bacterial Community Structure and Nitrogen Cycling in Primary Succession.

PubMed

Knelman, Joseph E; Graham, Emily B; Prevéy, Janet S; Robeson, Michael S; Kelly, Patrick; Hood, Eran; Schmidt, Steve K

2018-01-01

Past research demonstrating the importance plant-microbe interactions as drivers of ecosystem succession has focused on how plants condition soil microbial communities, impacting subsequent plant performance and plant community assembly. These studies, however, largely treat microbial communities as a black box. In this study, we sought to examine how emblematic shifts from early successional Alnus viridus ssp. sinuata (Sitka alder) to late successional Picea sitchensis (Sitka spruce) in primary succession may be reflected in specific belowground changes in bacterial community structure and nitrogen cycling related to the interaction of these two plants. We examined early successional alder-conditioned soils in a glacial forefield to delineate how alders alter the soil microbial community with increasing dominance. Further, we assessed the impact of late-successional spruce plants on these early successional alder-conditioned microbiomes and related nitrogen cycling through a leachate addition microcosm experiment. We show how increasingly abundant alder select for particular bacterial taxa. Additionally, we found that spruce leachate significantly alters the composition of these microbial communities in large part by driving declines in taxa that are enriched by alder, including bacterial symbionts. We found these effects to be spruce specific, beyond a general leachate effect. Our work also demonstrates a unique influence of spruce on ammonium availability. Such insights bolster theory relating the importance of plant-microbe interactions with late-successional plants and interspecific plant interactions more generally.

Tracking microbial colonization patterns associated with micro-environments of rice

NASA Astrophysics Data System (ADS)

Schmidt, Hannes; Eickhorst, Thilo

2015-04-01

The interface between soil and roots (i.e. the rhizosphere) represents a highly dynamic micro-environment for microbial populations. Root-derived compounds are released into the rhizosphere and may attract, stimulate, or inhibit native soil microorganisms. Microbes associated with the rhizosphere, in turn, may have deleterious, neutral, or promoting effects on the plant. Such influences of microbial populations on the plant and vice versa are likely to be greatest in close vicinity to the root surface. It is therefore essential to detect and visualize preferential micro-sites of microbial root colonization to identify potential areas of microbe-plant interaction. We present a single-cell based approach allowing for the localization, quantification, and visualization of native microbial populations in the rhizosphere and on the rhizoplane of soil-grown roots in situ. Catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) in combination with confocal laser scanning microscopy was applied to observe colonization densities and patterns of microbial populations associated with wetland rice. Hybridizations with domain- and phylum-specific oligonucleotide probes showed that the growth stage of the rice plant as well as the distance to the root surface had a strong influence on microbial colonization patterns. Three-dimensional visualizations of root-associated microbes revealed micro-sites of preferential colonization. Highest cell numbers of archaea and bacteria were found at flowering stage of rice plant development. Irregular distribution patterns of microbiota observed at early growth stages shifted towards more uniform colonization with plant age. Accordingly, the highest colonization densities shifted from the tip to more mature regions of rice roots. Methanogenic archaea and methanotrophic bacteria were found to be co-localized at basal regions of lateral roots. Beneficial effects of a close association with root surfaces were indicated by proportionally higher numbers of methane-oxidizing bacteria on the rhizoplane compared to the rhizosphere. Such spatial effects could not be observed for methanogenic archaea. As a consequence, the detection and visualization of microbial colonization patterns on a micro-scale via CARD-FISH represents an instrumental approach in revealing potential sites of interaction between microbes and plants in soil micro-environments.

Direct effects of temperature on forest nitrogen cycling revealed through analysis of long-term watershed records

Treesearch

E.N. Jack Brookshire; Stefan Gerber; Jackson R. Webster; James M. Vose; Wayne T. Swank

2010-01-01

The microbial conversion of organic nitrogen (N) to plant available forms is a critical determinant of plant growth and carbon sequestration in forests worldwide. In temperate zones, microbial activity is coupled to variations in temperature, yet at the ecosystem level, microbial N mineralization seems to play a minor role in determining patterns of N loss. Rather, N...

FILTER PLANT DESIGN FOR ASBESTOS FIBER REMOVAL

EPA Science Inventory

Water filtration plants used to remove asbestos fibers should be designed to produce filtered water with very low turbidity (0.10 ntu or lower). Flexibility in plant operation, especially with respect to conditioning raw water for filtration, is a key design factor. Preconditioni...

Comparing the plant diversity between artificial forest and nature growth forest in a giant panda habitat.

PubMed

Kang, Dongwei; Wang, Xiaorong; Li, Shuang; Li, Junqing

2017-06-15

Artificial restoration is an important way to restore forests, but little is known about its effect on the habitat restoration of the giant panda. In the present study, we investigated the characteristics of artificial forest in the Wanglang Nature Reserve to determine whether through succession it has formed a suitable habitat for the giant panda. We compared artificial forest characteristics with those of natural habitat used by the giant panda. We found that the dominant tree species in artificial forest differed from those in the natural habitat. The artificial forest had lower plant species richness and diversity in the tree and shrub layers than did the latter, and its community structure was characterized by smaller tree and bamboo sizes, and fewer and lower bamboo clumps, but more trees and larger shrub sizes. The typical community collocation of artificial forest was a "Picea asperata + no-bamboo" model, which differs starkly from the giant panda's natural habitat. After several years of restoration, the artificial forest has failed to become a suitable habitat for the giant panda. Therefore, a simple way of planting individual trees cannot restore giant panda habitat; instead, habitat restoration should be based on the habitat requirements of the giant panda.

Spatio temporal analysis of microbial habitats in soil-root interfaces

NASA Astrophysics Data System (ADS)

Eickhorst, Thilo; Schmidt, Hannes

2017-04-01

Microbial habitats in soils are formed by the arrangement and availability of inorganic and organic compounds. They can be characterized by physico-chemical parameters and the resulting colonization by microorganisms. Areas being preferably colonized are known as microbial hot spots which can be found in (bio)pores within the aggregatusphere or in the rhizosphere. The latter is directly influenced by plants i.e. the growth and activity of plant roots which has an influence on physico-chemical dynamics in the rhizosphere and can even shape plants' root microbiome. As microbial communities play an important role in nutrient cycling their response in soil-root interfaces is of great importance. Especially in complex systems such as paddy soils used for the cultivation of wetland rice the analysis of spatio-temporal aspects is important to get knowledge about their influence on the microbial dynamics in the respective habitats. But also other spatial variations on larger scales up to landscape scale may have an impact on the soil microorganisms in their habitats. This PICO presentation will introduce a set of techniques which are useful to analyze both the physico-chemical characteristics of microbial habitats and the microbial colonization and dynamics in soil-root interfaces. Examples will be given on various studies from rice cultivation in different paddy soils up to an European transect representing rhizosphere soils of selected plant species.

Effect of rhizosphere on soil microbial community and in-situ pyrene biodegradation

USGS Publications Warehouse

Su, Y.; Yang, X.; Chiou, C.T.

2008-01-01

To access the influence of a vegetation on soil microorganisms toward organic pollutant biogegration, this study examined the rhizospheric effects of four plant species (sudan grass, white clover, alfalfa, and fescue) on the soil microbial community and in-situ pyrene (PYR) biodegradation. The results indicated that the spiked PYR levels in soils decreased substantially compared to the control soil without planting. With equal planted densities, the efficiencies of PYR degradation in rhizosphere with sudan grass, white clover, alfalfa and fescue were 34.0%, 28.4%, 27.7%, and 9.9%, respectively. However, on the basis of equal root biomass the efficiencies were in order of white clover >> alfalfa > sudan > fescue. The increased PYR biodegradation was attributed to the enhanced bacterial population and activity induced by plant roots in the rhizosphere. Soil microbial species and biomasses were elucidated in terms of microbial phospholipid ester-linked fatty acid (PLFA) biomarkers. The principal component analysis (PCA) revealed significant changes in PLFA pattern in planted and non-planted soils spiked with PYR. Total PLFAs in planted soils were all higher than those in non-planted soils. PLFA assemblages indicated that bacteria were the primary PYR degrading microorganisms, and that Gram-positive bacteria exhibited higher tolerance to PYR than Gram-negative bacteria did. ?? 2008 Higher Education Press and Springer-Verlag GmbH.

Effect of immobilized rhizobacteria and organic amendment in bulk and rhizospheric soil of Cistus albidus L.

NASA Astrophysics Data System (ADS)

Mengual, Carmen Maria; del Mar Alguacil, Maria; Roldan, Antonio; Schoebitz, Mauricio

2013-04-01

A field experiment was carried out to assess the effectiveness of the immobilized microbial inoculant and the addition of organic olive residue. The microbial inoculant contained two rhizobacterial species identified as Azospirillum brasilense and Pantoea dispersa immobilized in a natural inert support. Bacterial population densities were 3.5×109 and 4.1×109 CFU g-1 of A. brasilense M3 and P. dispersa C3, respectively. The amendment used was the organic fraction extracted with KOH from composted "alperujo". The raw material was collected from an olive-mill and mixed with fresh cow bedding as bulking agent for composting. The inoculation of rhizobacteria and the addition of organic residue were employed for plant growth promotion of Cistus albidus L. and enhancement of soil physicochemical, biochemical and biological properties in a degraded semiarid Mediterranean area. One year after planting, the available phosphorus and potassium content in the amended soils was about 100 and 70% respectively higher than in the non-amended soil. Microbial inoculant and their interaction with organic residue increased the aggregate stability of the rhizosphere soil of C. albidus (by 12% with respect to control soil) while the organic residue alone not increased the aggregate stability of the rhizosphere of C. albidus. Microbial biomass C content and enzyme activities (dehydrogenase, urease, protease-BAA and alkaline phosphatase) of the rhizosphere of C. albidus were increased by microbial inoculant and organic residue interaction but not by microbial inoculation alone. The microbial inoculant and organic residue interaction were the most effective treatment for stimulating the roots dry weight of C. albidus (by 133% with respect to control plants) and microbial inoculant was the most effective treatment for increase the shoot dry weigh of plants (by 106% with respect to control plants). The combined treatment, involving microbial inoculant and addition of the organic residue directly into the soil, had additive effect on the root growth of C. albidus and chemical and biological quality of soil.

Microbial biofilm formation and its consequences for the CELSS program

NASA Technical Reports Server (NTRS)

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.

Formation of higher plant component microbial community in closed ecological system

NASA Astrophysics Data System (ADS)

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.

Microbial diversity in the floral nectar of Linaria vulgaris along an urbanization gradient.

PubMed

Bartlewicz, Jacek; Lievens, Bart; Honnay, Olivier; Jacquemyn, Hans

2016-03-30

Microbes are common inhabitants of floral nectar and are capable of influencing plant-pollinator interactions. All studies so far investigated microbial communities in floral nectar in plant populations that were located in natural environments, but nothing is known about these communities in nectar of plants inhabiting urban environments. However, at least some microbes are vectored into floral nectar by pollinators, and because urbanization can have a profound impact on pollinator communities and plant-pollinator interactions, it can be expected that it affects nectar microbes as well. To test this hypothesis, we related microbial diversity in floral nectar to the degree of urbanization in the late-flowering plant Linaria vulgaris. Floral nectar was collected from twenty populations along an urbanization gradient and culturable bacteria and yeasts were isolated and identified by partially sequencing the genes coding for small and large ribosome subunits, respectively. A total of seven yeast and 13 bacterial operational taxonomic units (OTUs) were found at 3 and 1% sequence dissimilarity cut-offs, respectively. In agreement with previous studies, Metschnikowia reukaufii and M. gruessi were the main yeast constituents of nectar yeast communities, whereas Acinetobacter nectaris and Rosenbergiella epipactidis were the most frequently found bacterial species. Microbial incidence was high and did not change along the investigated urbanization gradient. However, microbial communities showed a nested subset structure, indicating that species-poor communities were a subset of species-rich communities. The level of urbanization was putatively identified as an important driver of nestedness, suggesting that environmental changes related to urbanization may impact microbial communities in floral nectar of plants growing in urban environments.

Microbial Transformations of Nitrogen, Sulfur, and Iron Dictate Vegetation Composition in Wetlands: A Review

PubMed Central

Lamers, Leon P. M.; van Diggelen, Josepha M. H.; Op den Camp, Huub J. M.; Visser, Eric J. W.; Lucassen, Esther C. H. E. T.; Vile, Melanie A.; Jetten, Mike S. M.; Smolders, Alfons J. P.; Roelofs, Jan G. M.

2012-01-01

The majority of studies on rhizospheric interactions focus on pathogens, mycorrhizal symbiosis, or carbon transformations. Although the biogeochemical transformations of N, S, and Fe have profound effects on vegetation, these effects have received far less attention. This review, meant for microbiologists, biogeochemists, and plant scientists includes a call for interdisciplinary research by providing a number of challenging topics for future ecosystem research. Firstly, all three elements are plant nutrients, and microbial activity significantly changes their availability. Secondly, microbial oxidation with oxygen supplied by radial oxygen loss from roots in wetlands causes acidification, while reduction using alternative electron acceptors leads to generation of alkalinity, affecting pH in the rhizosphere, and hence plant composition. Thirdly, reduced species of all three elements may become phytotoxic. In addition, Fe cycling is tightly linked to that of S and P. As water level fluctuations are very common in wetlands, rapid changes in the availability of oxygen and alternative terminal electron acceptors will result in strong changes in the prevalent microbial redox reactions, with significant effects on plant growth. Depending on geological and hydrological settings, these interacting microbial transformations change the conditions and resource availability for plants, which are both strong drivers of vegetation development and composition by changing relative competitive strengths. Conversely, microbial composition is strongly driven by vegetation composition. Therefore, the combination of microbiological and plant ecological knowledge is essential to understand the biogeochemical and biological key factors driving heterogeneity and total (i.e., microorganisms and vegetation) community composition at different spatial and temporal scales. PMID:22539932

A highly diverse, desert-like microbial biocenosis on solar panels in a Mediterranean city.

PubMed

Dorado-Morales, Pedro; Vilanova, Cristina; Peretó, Juli; Codoñer, Francisco M; Ramón, Daniel; Porcar, Manuel

2016-07-05

Microorganisms colonize a wide range of natural and artificial environments although there are hardly any data on the microbial ecology of one the most widespread man-made extreme structures: solar panels. Here we show that solar panels in a Mediterranean city (Valencia, Spain) harbor a highly diverse microbial community with more than 500 different species per panel, most of which belong to drought-, heat- and radiation-adapted bacterial genera, and sun-irradiation adapted epiphytic fungi. The taxonomic and functional profiles of this microbial community and the characterization of selected culturable bacteria reveal the existence of a diverse mesophilic microbial community on the panels' surface. This biocenosis proved to be more similar to the ones inhabiting deserts than to any human or urban microbial ecosystem. This unique microbial community shows different day/night proteomic profiles; it is dominated by reddish pigment- and sphingolipid-producers, and is adapted to withstand circadian cycles of high temperatures, desiccation and solar radiation.

A highly diverse, desert-like microbial biocenosis on solar panels in a Mediterranean city

PubMed Central

Dorado-Morales, Pedro; Vilanova, Cristina; Peretó, Juli; Codoñer, Francisco M.; Ramón, Daniel; Porcar, Manuel

2016-01-01

Microorganisms colonize a wide range of natural and artificial environments although there are hardly any data on the microbial ecology of one the most widespread man-made extreme structures: solar panels. Here we show that solar panels in a Mediterranean city (Valencia, Spain) harbor a highly diverse microbial community with more than 500 different species per panel, most of which belong to drought-, heat- and radiation-adapted bacterial genera, and sun-irradiation adapted epiphytic fungi. The taxonomic and functional profiles of this microbial community and the characterization of selected culturable bacteria reveal the existence of a diverse mesophilic microbial community on the panels’ surface. This biocenosis proved to be more similar to the ones inhabiting deserts than to any human or urban microbial ecosystem. This unique microbial community shows different day/night proteomic profiles; it is dominated by reddish pigment- and sphingolipid-producers, and is adapted to withstand circadian cycles of high temperatures, desiccation and solar radiation. PMID:27378552

Prediction of the thickness of the compensator filter in radiation therapy using computational intelligence

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dehlaghi, Vahab; Taghipour, Mostafa; Haghparast, Abbas

In this study, artificial neural networks (ANNs) and adaptive neuro-fuzzy inference system (ANFIS) are investigated to predict the thickness of the compensator filter in radiation therapy. In the proposed models, the input parameters are field size (S), off-axis distance, and relative dose (D/D{sub 0}), and the output is the thickness of the compensator. The obtained results show that the proposed ANN and ANFIS models are useful, reliable, and cheap tools to predict the thickness of the compensator filter in intensity-modulated radiation therapy.

The application of dummy noise adaptive Kalman filter in underwater navigation

NASA Astrophysics Data System (ADS)

Li, Song; Zhang, Chun-Hua; Luan, Jingde

2011-10-01

The track of underwater target is easy to be affected by the various by the various factors, which will cause poor performance in Kalman filter with the error in the state and measure model. In order to solve the situation, a method is provided with dummy noise compensative technology. Dummy noise is added to state and measure model artificially, and then the question can be solved by the adaptive Kalman filter with unknown time-changed statistical character. The simulation result of underwater navigation proves the algorithm is effective.

Optimized Extraction Method To Remove Humic Acid Interferences from Soil Samples Prior to Microbial Proteome Measurements.

PubMed

Qian, Chen; Hettich, Robert L

2017-07-07

The microbial composition and their activities in soil environments play a critical role in organic matter transformation and nutrient cycling. Liquid chromatography coupled to high-performance mass spectrometry provides a powerful approach to characterize soil microbiomes; however, the limited microbial biomass and the presence of abundant interferences in soil samples present major challenges to proteome extraction and subsequent MS measurement. To this end, we have designed an experimental method to improve microbial proteome measurement by removing the soil-borne humic substances coextraction from soils. Our approach employs an in situ detergent-based microbial lysis/TCA precipitation coupled to an additional cleanup step involving acidified precipitation and filtering at the peptide level to remove most of the humic acid interferences prior to proteolytic peptide measurement. The novelty of this approach is an integration to exploit two different characteristics of humic acids: (1) Humic acids are insoluble in acidic solution but should not be removed at the protein level, as undesirable protein removal may also occur. Rather it is better to leave the humics acids in the samples until the peptide level, at which point the significant differential solubility of humic acids versus peptides at low pH can be exploited very efficiently. (2) Most of the humic acids have larger molecule weights than the peptides. Therefore, filtering a pH 2 to 3 peptide solution with a 10 kDa filter will remove most of the humic acids. This method is easily interfaced with normal proteolytic processing approaches and provides a reliable and straightforward protein extraction method that efficiently removes soil-borne humic substances without inducing proteome sample loss or biasing protein identification in mass spectrometry. In general, this humic acid removal step is universal and can be adopted by any workflow to effectively remove humic acids to avoid them negatively competing with peptides for binding with reversed-phase resin or ionization in the electrospray.

A robust, simple, high-throughput technique for time-resolved plant volatile analysis in field experiments

PubMed Central

Kallenbach, Mario; Oh, Youngjoo; Eilers, Elisabeth J.; Veit, Daniel; Baldwin, Ian T.; Schuman, Meredith C.

2014-01-01

Summary Plant volatiles (PVs) mediate interactions between plants and arthropods, microbes, and other plants, and are involved in responses to abiotic stress. PV emissions are therefore influenced by many environmental factors, including herbivore damage, microbial invasion, and cues from neighboring plants, but also light regime, temperature, humidity, and nutrient availability. Thus an understanding of the physiological and ecological functions of PVs must be grounded in measurements reflecting PV emissions under natural conditions. However, PVs are usually sampled in the artificial environments of laboratories or climate chambers. Sampling of PVs in natural environments is difficult, limited by the need to transport, maintain, and power instruments, or use expensive sorbent devices in replicate. Ideally, PVs should be measured in natural settings with high replication, spatiotemporal resolution, and sensitivity, and at modest costs. Polydimethysiloxane (PDMS), a sorbent commonly used for PV sampling, is available as silicone tubing (ST) for as little as 0.60 €/m (versus 100-550 € apiece for standard PDMS sorbent devices). Small (mm-cm) ST pieces (STs) can be placed in any environment and used for headspace sampling with little manipulation of the organism or headspace. STs have sufficiently fast absorption kinetics and large capacity to sample plant headspaces on a timescale of minutes to hours, and thus can produce biologically meaningful “snapshots” of PV blends. When combined with thermal desorption (TD)-GC-MS analysis – a 40-year-old and widely available technology – STs yield reproducible, sensitive, spatiotemporally resolved, quantitative data from headspace samples taken in natural environments. PMID:24684685

The role of adaptive immunity as an ecological filter on the gut microbiota in zebrafish.

PubMed

Stagaman, Keaton; Burns, Adam R; Guillemin, Karen; Bohannan, Brendan Jm

2017-07-01

All animals live in intimate association with communities of microbes, collectively referred to as their microbiota. Certain host traits can influence which microbial taxa comprise the microbiota. One potentially important trait in vertebrate animals is the adaptive immune system, which has been hypothesized to act as an ecological filter, promoting the presence of some microbial taxa over others. Here we surveyed the intestinal microbiota of 68 wild-type zebrafish, with functional adaptive immunity, and 61 rag1 - zebrafish, lacking functional B- and T-cell receptors, to test the role of adaptive immunity as an ecological filter on the intestinal microbiota. In addition, we tested the robustness of adaptive immunity's filtering effects to host-host interaction by comparing the microbiota of fish populations segregated by genotype to those containing both genotypes. The presence of adaptive immunity individualized the gut microbiota and decreased the contributions of neutral processes to gut microbiota assembly. Although mixing genotypes led to increased phylogenetic diversity in each, there was no significant effect of adaptive immunity on gut microbiota composition in either housing condition. Interestingly, the most robust effect on microbiota composition was co-housing within a tank. In all, these results suggest that adaptive immunity has a role as an ecological filter of the zebrafish gut microbiota, but it can be overwhelmed by other factors, including transmission of microbes among hosts.

The effect of dosages of microbial consortia formulation and synthetic fertilizer on the growth and yield of field-grown chili

NASA Astrophysics Data System (ADS)

Istifadah, N.; Sapta, D.; Krestini, H.; Natalie, B.; Suryatmana, P.; Nurbaity, A.; Hidersah, R.

2018-03-01

Chili (Capsicum annuum, L) is one of important horticultural crop in Indonesia. Formulation of microbial consortia containing Bacillus subtilis, Pseudomonas sp., Azotobacter chroococcum and Trichoderma harzianum has been developed. This study evaluated the effects of dosage of the microbial formulation combined with NPK fertilizer on growth and yield of chili plants in the field experiment. The experiment was arranged in completely randomized design of factorial, in which the first factor was dosage of formulation (0, 2.5, 5.0, 7.5, 10 g per plant) and the second factor was NPK fertilizer dosage (0, 25, 50 and 75% of the standard dosage). The treatments were replicated three times. For application, the formulation was mixed with chicken manure 1:10 (w/v). The results showed that application of microbial formulation solely improved the chili growth. There was interaction between dosages of the microbial formulation and NPK fertilizer in improving plant height, nitrogen availability and the chili yield, while there was no interaction between those dosages in improving the root length. Combination between microbial formulation at the dosage of 5.0-7.5 g per plant combined with NPK fertilizer with the dosage 50 or 75% of the standard dosage support relatively better growth and the chili yield.