Summers_FinalReport_ER64408

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

Summers, Anne; Miller, Susan M.; Lipton, Mary

2016-08-22

Elemental mercury, Hg(0) is a contaminant at many DOE sites, especially at Oak Ridge National Laboratory (ORNL) where the spread of spilled Hg and its effects on microbial populations have been monitored for decades. To explore the microbial interactions with Hg, we devised a global proteomic approach capable of directly detecting Hg-adducts of proteins. This technique developed in the facultative anaerobe, Escherichia coli, allows us to identify the proteins most vulnerable to acute exposure to organomercurials phenyl- and ethyl-mercury (as surrogates for the highly neurotoxic methyl-Hg) (Polacco, et al, 2011). We have found >300 such proteins in all metabolic functionalmore » groups and cellular compartments; most are highly conserved and can serve as markers for acute Hg exposure (Zink, et al. 2016, in preparation).« less

Detection of Bacillus spores using PCR and FTA filters.

PubMed

Lampel, Keith A; Dyer, Deanne; Kornegay, Leroy; Orlandi, Palmer A

2004-05-01

Emphasis has been placed on developing and implementing rapid detection systems for microbial pathogens. We have explored the utility of expanding FTA filter technology for the preparation of template DNA for PCR from bacterial spores. Isolated spores from several Bacillus spp., B. subtilis, B. cereus, and B. megaterium, were applied to FTA filters, and specific DNA products were amplified by PCR. Spore preparations were examined microscopically to ensure that the presence of vegetative cells, if any, did not yield misleading results. PCR primers SRM86 and SRM87 targeted a conserved region of bacterial rRNA genes, whereas primers Bsub5F and Bsub3R amplified a product from a conserved sequence of the B. subtilis rRNA gene. With the use of the latter set of primers for nested PCR, the sensitivity of the PCR-based assay was increased. Overall, 53 spores could be detected after the first round of PCR, and the sensitivity was increased to five spores by nested PCR. FTA filters are an excellent platform to remove PCR inhibitors and have universal applications for environmental, clinical, and food samples.

Sulfate-reducing bacteria are common members of bacterial communities in Altamira Cave (Spain).

PubMed

Portillo, M Carmen; Gonzalez, Juan M

2009-01-15

The conservation of paleolithic paintings such as those in Altamira Cave (Spain) is a primary objective. Recent molecular studies have shown the existence of unknown microbial communities in this cave including anaerobic microorganisms on cave walls. Herein, we analyzed an anaerobic microbial group, the sulfate-reducing bacteria (SRB), from Altamira Cave with potential negative effects on painting conservation. In the present work, the communities of bacteria and SRB were studied through PCR-DGGE analysis. Data suggest that SRB communities represent a significant, highly diverse bacterial group in Altamira Cave. These findings represent a first report on this physiological group on caves with paleolithic paintings and their potential biodegradation consequences. Expanding our knowledge on microbial communities in Altamira Cave is a priority to design appropriate conservation strategies.

Sulfide Generation by Dominant Halanaerobium Microorganisms in Hydraulically Fractured Shales

PubMed Central

Booker, Anne E.; Borton, Mikayla A.; Daly, Rebecca A.; Welch, Susan A.; Nicora, Carrie D.; Hoyt, David W.; Wilson, Travis; Purvine, Samuel O.; Wolfe, Richard A.; Sharma, Shikha; Mouser, Paula J.; Cole, David R.; Lipton, Mary S.; Wrighton, Kelly C.

2017-01-01

ABSTRACT Hydraulic fracturing of black shale formations has greatly increased United States oil and natural gas recovery. However, the accumulation of biomass in subsurface reservoirs and pipelines is detrimental because of possible well souring, microbially induced corrosion, and pore clogging. Temporal sampling of produced fluids from a well in the Utica Shale revealed the dominance of Halanaerobium strains within the in situ microbial community and the potential for these microorganisms to catalyze thiosulfate-dependent sulfidogenesis. From these field data, we investigated biogenic sulfide production catalyzed by a Halanaerobium strain isolated from the produced fluids using proteogenomics and laboratory growth experiments. Analysis of Halanaerobium isolate genomes and reconstructed genomes from metagenomic data sets revealed the conserved presence of rhodanese-like proteins and anaerobic sulfite reductase complexes capable of converting thiosulfate to sulfide. Shotgun proteomics measurements using a Halanaerobium isolate verified that these proteins were more abundant when thiosulfate was present in the growth medium, and culture-based assays identified thiosulfate-dependent sulfide production by the same isolate. Increased production of sulfide and organic acids during the stationary growth phase suggests that fermentative Halanaerobium uses thiosulfate to remove excess reductant. These findings emphasize the potential detrimental effects that could arise from thiosulfate-reducing microorganisms in hydraulically fractured shales, which are undetected by current industry-wide corrosion diagnostics. IMPORTANCE Although thousands of wells in deep shale formations across the United States have been hydraulically fractured for oil and gas recovery, the impact of microbial metabolism within these environments is poorly understood. Our research demonstrates that dominant microbial populations in these subsurface ecosystems contain the conserved capacity for the reduction of thiosulfate to sulfide and that this process is likely occurring in the environment. Sulfide generation (also known as “souring”) is considered deleterious in the oil and gas industry because of both toxicity issues and impacts on corrosion of the subsurface infrastructure. Critically, the capacity for sulfide generation via reduction of sulfate was not detected in our data sets. Given that current industry wellhead tests for sulfidogenesis target canonical sulfate-reducing microorganisms, these data suggest that new approaches to the detection of sulfide-producing microorganisms may be necessary. PMID:28685163

Application of molecular techniques for the assessment of microorganism diversity on cultural heritage objects.

PubMed

Otlewska, Anna; Adamiak, Justyna; Gutarowska, Beata

2014-01-01

As a result of their unpredictable ability to adapt to varying environmental conditions, microorganisms inhabit different types of biological niches on Earth. Owing to the key role of microorganisms in many biogeochemical processes, trends in modern microbiology emphasize the need to know and understand the structure and function of complex microbial communities. This is particularly important if the strategy relates to microbial communities that cause biodeterioration of materials that constitute our cultural heritage. Until recently, the detection and identification of microorganisms inhabiting objects of cultural value was based only on cultivation-dependent methods. In spite of many advantages, these methods provide limited information because they identify only viable organisms capable of growth under standard laboratory conditions. However, in order to carry out proper conservation and renovation, it is necessary to know the complete composition of microbial communities and their activity. This paper presents and characterizes modern techniques such as genetic fingerprinting and clone library construction for the assessment of microbial diversity based on molecular biology. Molecular methods represent a favourable alternative to culture-dependent methods and make it possible to assess the biodiversity of microorganisms inhabiting technical materials and cultural heritage objects.

[Effects of different straw recycling and tillage methods on soil respiration and microbial activity].

PubMed

Li, Xiao-sha; Wu, Ning; Liu, Ling; Feng, Yu-peng; Xu, Xu; Han, Hui-fang; Ning, Tang-yuan; Li, Zeng-jia

2015-06-01

To explore the effects of different tillage methods and straw recycling on soil respiration and microbial activity in summer maize field during the winter wheat and summer maize double cropping system, substrate induced respiration method and CO2 release method were used to determine soil microbial biomass carbon, microbial activity, soil respiration, and microbial respiratory quotient. The experiment included 3 tillage methods during the winter wheat growing season, i.e., no-tillage, subsoiling and conventional tillage. Each tillage method was companied with 2 straw management patterns, i.e., straw recycling and no straw. The results indicated that the conservation tillage methods and straw recycling mainly affected 0-10 cm soil layer. Straw recycling could significantly improve the microbial biomass carbon and microbial activity, while decrease microbial respiratory quotient. Straw recycling could improve the soil respiration at both seedling stage and anthesis, however, it could reduce the soil respiration at filling stage, wax ripeness, and harvest stage. Under the same straw application, compared with conventional tillage, the soil respiration and microbial respiratory quotient in both subsoiling and no-tillage were reduced, while the microbial biomass carbon and microbial activity were increased. During the summer maize growing season, soil microbial biomass carbon and microbial activity were increased in straw returning with conservation tillage, while the respiratory quotient was reduced. In 0-10 cm soil layer, compared with conventional tillage, straw recycling with subsoiling and no-tillage significantly increased soil microbial biomass carbon by 95.8% and 74.3%, and increased soil microbial activity by 97.1% and 74.2%, respectively.

Avoiding Pandemic Fears in the Subway and Conquering the Platypus

PubMed Central

Vázquez-Baeza, Y.; Pettengill, J. B.; Ottesen, A.; McDonald, D.; Knight, R.

2016-01-01

ABSTRACT Metagenomics is increasingly used not just to show patterns of microbial diversity but also as a culture-independent method to detect individual organisms of intense clinical, epidemiological, conservation, forensic, or regulatory interest. A widely reported metagenomic study of the New York subway suggested that the pathogens Yersinia pestis and Bacillus anthracis were part of the “normal subway microbiome.” In their article in mSystems, Hsu and collaborators (mSystems 1(3):e00018-16, 2016, http://dx.doi.org/10.1128/mSystems.00018-16) showed that microbial communities on transit surfaces in the Boston subway system are maintained from a metapopulation of human skin commensals and environmental generalists and that reanalysis of the New York subway data with appropriate methods did not detect the pathogens. We note that commonly used software pipelines can produce results that lack prima facie validity (e.g., reporting widespread distribution of notorious endemic species such as the platypus or the presence of pathogens) but that appropriate use of inclusion and exclusion sets can avoid this issue. PMID:27832215

Seasonal induced changes in spinach rhizosphere microbial community structure with varying salinity and drought.

PubMed

Mark Ibekwe, A; Ors, Selda; Ferreira, Jorge F S; Liu, Xuan; Suarez, Donald L

2017-02-01

Salinity is a common problem under irrigated agriculture, especially in low rainfall and high evaporative demand areas of southwestern United States and other semi-arid regions around the world. However, studies on salinity effects on soil microbial communities are relatively few while the effects of irrigation-induced salinity on soil chemical and physical properties and plant growth are well documented. In this study, we examined the effects of salinity, temperature, and temporal variability on soil and rhizosphere microbial communities in sand tanks irrigated with prepared solutions designed to simulate saline wastewater. Three sets of experiments with spinach (Spinacia oleracea L., cv. Racoon) were conducted under saline water during different time periods (early winter, late spring, and early summer). Bacterial 16S V4 rDNA region was amplified utilizing fusion primers designed against the surrounding conserved regions using MiSeq® Illumina sequencing platform. Across the two sample types, bacteria were relatively dominant among three phyla-the Proteobacteria, Cyanobacteria, and Bacteroidetes-accounted for 77.1% of taxa detected in the rhizosphere, while Proteobacteria, Bacteroidetes, and Actinobacteria accounted for 55.1% of taxa detected in soil. The results were analyzed using UniFrac coupled with principal coordinate analysis (PCoA) to compare diversity, abundance, community structure, and specific bacterial groups in soil and rhizosphere samples. Permutational analysis of variance (PERMANOVA) analysis showed that soil temperature (P=0.001), rhizosphere temperature (P=0.001), rhizosphere salinity (P=0.032), and evapotranspiration (P=0.002) significantly affected beta diversity of soil and rhizosphere microbial communities. Furthermore, salinity had marginal effects (P=0.078) on soil beta diversity. However, temporal variability differentially affected rhizosphere microbial communities irrigated with saline wastewater. Therefore, microbial communities in soils impacted by saline irrigation water respond differently to irrigation water quality and season of application due to temporal effects associated with temperature. Published by Elsevier B.V.

Distributions of pharmaceuticals in an urban estuary during both dry- and wet-weather conditions

USGS Publications Warehouse

Benotti, M.J.; Brownawell, Bruce J.

2007-01-01

Pharmaceuticals and selected major human metabolites are ubiquitous in Jamaica Bay, a wastewater-impacted estuary at concentrations in the low ng/L to low ??g/L range. Concentrations throughout the bay are often consistent with conservative behavior during dry-weather conditions, as evidenced by nearly linear concentration-salinity relationships. Deviation from conservative behavior is noted for some pharmaceuticals and attributed to microbial degradation. Caffeine, cotinine, nicotine, and paraxanthine were detected with the greatest analytical signal, although evidence is presented for in situ removal, especially for nicotine and caffeine. There is little evidence for significant removal of carbamazepine and sulfamethoxazole, suggesting they are more conservative and useful wastewater tracers. Immediately following heavy precipitation, which induced a combined sewer overflow (CSO) event, the concentrations of all compounds but acetaminophen and nicotine decreased or disappeared. This observation is consistent with a simple model illustrating the effect of precipitation has on pharmaceutical concentration in the wastewater stream, given the balance between dilution from rain and the bypass of treatment. ?? 2007 American Chemical Society.

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

PubMed Central

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

2011-01-01

The field experiments were conducted on sandy loam soil at New Delhi, during 2007 and 2008 to investigate the effect of conservation tillage, irrigation regimes (sub-optimal, optimal and supra-optimal water regimes), and integrated nutrient management (INM) practices on soil biological parameters in wheat cultivation. The conservation tillage soils has shown significant (p<0.05) increase in soil respiration (81.1%), soil microbial biomass carbon (SMBC) (104%) and soil dehydrogenase (DH) (59.2%) compared to the conventional tillage soil. Optimum water supply (3-irrigations) enhanced soil respiration over sub-optimum and supra-optimum irrigations by 13.32% and 79% respectively. Soil dehydrogenase (DH) activity in optimum water regime has also increased by 23.33% and 8.18% respectively over the other two irrigation regimes. Similarly, SMBC has also increased by 12.14% and 27.17% respectively in soil with optimum water supply compared to that of sub-optimum and supra-optimum water regime fields. The maximum increase in soil microbial activities is found when sole organic source (50% Farm Yard Manure+25% biofertilizer+25% Green Manure) has been used in combination with the conservation tillage and the optimum water supply. Study demonstrated that microbial activity could be regulated by tillage, water and nitrogen management in the soil in a sustainable manner. PMID:24031665

A first insight on the biodegradation of limestone: the case of the World Heritage Convent of Christ

NASA Astrophysics Data System (ADS)

Rosado, Tânia; Silva, Mara; Galvão, Andreia; Mirão, José; Candeias, António; Caldeira, Ana Teresa

2016-12-01

The present study is a multidisciplinary approach applied to architectural stone materials of the Convent of Christ in Tomar (Portugal) in order to understand and mitigate the active decay processes. The structure and appearance of the stonework from the Convent of Christ are strongly affected by stains, biofilms and structural degradation. To investigate these phenomena, a multianalytical approach comprising X-ray microdiffraction, scanning electron microscopy, microRaman and microinfrared spectroscopy was applied to the examination of altered outdoor stone areas being detected calcium oxalates, carotenoids and microbial proliferation. The presence of these alteration products seems to be correlated with the microbial activity of bacteria, microalgae, cyanobacteria and filamentous fungi. This work showed that the application of complementary methodologies is an efficient strategy to characterise the stone decay, and constitute a starting point for successful conservation intervention plans that are urgent to ensure the preservation and safeguard of this emblematic monument.

The microbiome of New World vultures.

PubMed

Roggenbuck, Michael; Bærholm Schnell, Ida; Blom, Nikolaj; Bælum, Jacob; Bertelsen, Mads Frost; Sicheritz-Pontén, Thomas; Pontén, Thomas Sicheritz; Sørensen, Søren Johannes; Gilbert, M Thomas P; Graves, Gary R; Hansen, Lars H

2014-11-25

Vultures are scavengers that fill a key ecosystem niche, in which they have evolved a remarkable tolerance to bacterial toxins in decaying meat. Here we report the first deep metagenomic analysis of the vulture microbiome. Through face and gut comparisons of 50 vultures representing two species, we demonstrate a remarkably conserved low diversity of gut microbial flora. The gut samples contained an average of 76 operational taxonomic units (OTUs) per specimen, compared with 528 OTUs on the facial skin. Clostridia and Fusobacteria, widely pathogenic to other vertebrates, dominate the vulture's gut microbiota. We reveal a likely faecal-oral-gut route for their origin. DNA of prey species detectable on facial swabs was completely degraded in the gut samples from most vultures, suggesting that the gastrointestinal tracts of vultures are extremely selective. Our findings show a strong adaption of vultures and their bacteria to their food source, exemplifying a specialized host-microbial alliance.

Multifunctional sample preparation kit and on-chip quantitative nucleic acid sequence-based amplification tests for microbial detection.

PubMed

Zhao, Xinyan; Dong, Tao

2012-10-16

This study reports a quantitative nucleic acid sequence-based amplification (Q-NASBA) microfluidic platform composed of a membrane-based sampling module, a sample preparation cassette, and a 24-channel Q-NASBA chip for environmental investigations on aquatic microorganisms. This low-cost and highly efficient sampling module, having seamless connection with the subsequent steps of sample preparation and quantitative detection, is designed for the collection of microbial communities from aquatic environments. Eight kinds of commercial membrane filters are relevantly analyzed using Saccharomyces cerevisiae, Escherichia coli, and Staphylococcus aureus as model microorganisms. After the microorganisms are concentrated on the membrane filters, the retentate can be easily conserved in a transport medium (TM) buffer and sent to a remote laboratory. A Q-NASBA-oriented sample preparation cassette is originally designed to extract DNA/RNA molecules directly from the captured cells on the membranes. Sequentially, the extract is analyzed within Q-NASBA chips that are compatible with common microplate readers in laboratories. Particularly, a novel analytical algorithmic method is developed for simple but robust on-chip Q-NASBA assays. The reported multifunctional microfluidic system could detect a few microorganisms quantitatively and simultaneously. Further research should be conducted to simplify and standardize ecological investigations on aquatic environments.

Distribution in microbial genomes of genes similar to lodA and goxA which encode a novel family of quinoproteins with amino acid oxidase activity.

PubMed

Campillo-Brocal, Jonatan C; Chacón-Verdú, María Dolores; Lucas-Elío, Patricia; Sánchez-Amat, Antonio

2015-03-24

L-Amino acid oxidases (LAOs) have been generally described as flavoproteins that oxidize amino acids releasing the corresponding ketoacid, ammonium and hydrogen peroxide. The generation of hydrogen peroxide gives to these enzymes antimicrobial characteristics. They are involved in processes such as biofilm development and microbial competition. LAOs are of great biotechnological interest in different applications such as the design of biosensors, biotransformations and biomedicine. The marine bacterium Marinomonas mediterranea synthesizes LodA, the first known LAO that contains a quinone cofactor. LodA is encoded in an operon that contains a second gene coding for LodB, a protein required for the post-translational modification generating the cofactor. Recently, GoxA, a quinoprotein with sequence similarity to LodA but with a different enzymatic activity (glycine oxidase instead of lysine-ε-oxidase) has been described. The aim of this work has been to study the distribution of genes similar to lodA and/or goxA in sequenced microbial genomes and to get insight into the evolution of this novel family of proteins through phylogenetic analysis. Genes encoding LodA-like proteins have been detected in several bacterial classes. However, they are absent in Archaea and detected only in a small group of fungi of the class Agaromycetes. The vast majority of the genes detected are in a genome region with a nearby lodB-like gene suggesting a specific interaction between both partner proteins. Sequence alignment of the LodA-like proteins allowed the detection of several conserved residues. All of them showed a Cys and a Trp that aligned with the residues that are forming part of the cysteine tryptophilquinone (CTQ) cofactor in LodA. Phylogenetic analysis revealed that LodA-like proteins can be clustered in different groups. Interestingly, LodA and GoxA are in different groups, indicating that those groups are related to the enzymatic activity of the proteins detected. Genome mining has revealed for the first time the broad distribution of LodA-like proteins containing a CTQ cofactor in many different microbial groups. This study provides a platform to explore the potentially novel enzymatic activities of the proteins detected, the mechanisms of post-translational modifications involved in their synthesis, as well as their biological relevance.

Allee effect: the story behind the stabilization or extinction of microbial ecosystem.

PubMed

Goswami, Madhurankhi; Bhattacharyya, Purnita; Tribedi, Prosun

2017-03-01

A population exhibiting Allee effect shows a positive correlation between population fitness and population size or density. Allee effect decides the extinction or conservation of a microbial population and thus appears to be an important criterion in population ecology. The underlying factor of Allee effect that decides the stabilization and extinction of a particular population density is the threshold or the critical density of their abundance. According to Allee, microbial populations exhibit a definite, critical or threshold density, beyond which the population fitness of a particular population increases with the rise in population density and below it, the population fitness goes down with the decrease in population density. In particular, microbial population displays advantageous traits such as biofilm formation, expression of virulence genes, spore formation and many more only at a high population density. It has also been observed that microorganisms exhibiting a lower population density undergo complete extinction from the residual microbial ecosystem. In reference to Allee effect, decrease in population density or size introduces deleterious mutations among the population density through genetic drift. Mutations are carried forward to successive generations resulting in its accumulation among the population density thus reducing its microbial fitness and thereby increasing the risk of extinction of a particular microbial population. However, when the microbial load is high, the chance of genetic drift is less, and through the process of biofilm formation, the cooperation existing among the microbial population increases that increases the microbial fitness. Thus, the high microbial population through the formation of microbial biofilm stabilizes the ecosystem by increasing fitness. Taken together, microbial fitness shows positive correlation with the ecosystem conservation and negative correlation with ecosystem extinction.

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

TIGER: the universal biosensor

NASA Astrophysics Data System (ADS)

Hofstadler, Steven A.; Sampath, Rangarajan; Blyn, Lawrence B.; Eshoo, Mark W.; Hall, Thomas A.; Jiang, Yun; Drader, Jared J.; Hannis, James C.; Sannes-Lowery, Kristin A.; Cummins, Lendell L.; Libby, Brian; Walcott, Demetrius J.; Schink, Amy; Massire, Christian; Ranken, Raymond; Gutierrez, Jose; Manalili, Sheri; Ivy, Cristina; Melton, Rachael; Levene, Harold; Barrett-Wilt, Greg; Li, Feng; Zapp, Vanessa; White, Neill; Samant, Vivek; McNeil, John A.; Knize, Duane; Robbins, David; Rudnick, Karl; Desai, Anjali; Moradi, Emily; Ecker, David J.

2005-03-01

In this work, we describe a strategy for the detection and characterization of microorganisms associated with a potential biological warfare attack or a natural outbreak of an emerging infectious disease. This approach, termed TIGER (Triangulation Identification for the Genetic Evaluation of Risks), relies on mass spectrometry-derived base composition signatures obtained from PCR amplification of broadly conserved regions of the microbial genome(s) in a sample. The sample can be derived from air filtration devices, clinical samples, or other sources. Core to this approach are "intelligent PCR primers" that target broadly conserved regions of microbial genomes that flank variable regions. This approach requires that high-performance mass measurements be made on PCR products in the 80-140 bp size range in a high-throughput, robust modality. As will be demonstrated, the concept is equally applicable to bacteria and viruses and could be further applied to fungi and protozoa. In addition to describing the fundamental strategy of this approach, several specific examples of TIGER are presented that illustrate the impact this approach could have on the way biological weapons attacks are detected and the way that the etiologies of infectious diseases are determined. The first example illustrates how any bacterial species might be identified, using Bacillus anthracis as the test agent. The second example demonstrates how DNA-genome viruses are identified using five members of Poxviridae family, whose members includes Variola virus, the agent responsible for smallpox. The third example demonstrates how RNA-genome viruses are identified using the Alphaviruses (VEE, WEE, and EEE) as representative examples. These examples illustrate how the TIGER technology can be applied to create a universal identification strategy for all pathogens, including those that infect humans, livestock, and plants.

Antibiotic effects on microbial community characteristics in soils under conservation management practices

USDA-ARS?s Scientific Manuscript database

Veterinary antibiotics (VAs) administered to livestock are introduced to agroecosystems via land application of manure, posing a potential human and environmental health risk. These Antibiotics may adversely affect soil microbial communities. The objectives of this research were to investigate poten...

Presence and Expression of Microbial Genes Regulating Soil Nitrogen Dynamics Along the Tanana River Successional Sequence

NASA Astrophysics Data System (ADS)

Boone, R. D.; Rogers, S. L.

2004-12-01

We report on work to assess the functional gene sequences for soil microbiota that control nitrogen cycle pathways along the successional sequence (willow, alder, poplar, white spruce, black spruce) on the Tanana River floodplain, Interior Alaska. Microbial DNA and mRNA were extracted from soils (0-10 cm depth) for amoA (ammonium monooxygenase), nifH (nitrogenase reductase), napA (nitrate reductase), and nirS and nirK (nitrite reductase) genes. Gene presence was determined by amplification of a conserved sequence of each gene employing sequence specific oligonucleotide primers and Polymerase Chain Reaction (PCR). Expression of the genes was measured via nested reverse transcriptase PCR amplification of the extracted mRNA. Amplified PCR products were visualized on agarose electrophoresis gels. All five successional stages show evidence for the presence and expression of microbial genes that regulate N fixation (free-living), nitrification, and nitrate reduction. We detected (1) nifH, napA, and nirK presence and amoA expression (mRNA production) for all five successional stages and (2) nirS and amoA presence and nifH, nirK, and napA expression for early successional stages (willow, alder, poplar). The results highlight that the existing body of previous process-level work has not sufficiently considered the microbial potential for a nitrate economy and free-living N fixation along the complete floodplain successional sequence.

Estimating phosphorus availability for microbial growth in an emerging landscape

USGS Publications Warehouse

Schmidt, S.K.; Cleveland, C.C.; Nemergut, D.R.; Reed, S.C.; King, A.J.; Sowell, P.

2011-01-01

Estimating phosphorus (P) availability is difficult—particularly in infertile soils such as those exposed after glacial recession—because standard P extraction methods may not mimic biological acquisition pathways. We developed an approach, based on microbial CO2 production kinetics and conserved carbon:phosphorus (C:P) ratios, to estimate the amount of P available for microbial growth in soils and compared this method to traditional, operationally-defined indicators of P availability. Along a primary succession gradient in the High Andes of Perú, P additions stimulated the growth-related (logistic) kinetics of glutamate mineralization in soils that had been deglaciated from 0 to 5 years suggesting that microbial growth was limited by soil P availability. We then used a logistic model to estimate the amount of C incorporated into biomass in P-limited soils, allowing us to estimate total microbial P uptake based on a conservative C:P ratio of 28:1 (mass:mass). Using this approach, we estimated that there was < 1 μg/g of microbial-available P in recently de-glaciated soils in both years of this study. These estimates fell well below estimates of available soil P obtained using traditional extraction procedures. Our results give both theoretical and practical insights into the kinetics of C and P utilization in young soils, as well as show changes in microbial P availability during early stages of soil development.

Sulfide Generation by Dominant Halanaerobium Microorganisms in Hydraulically Fractured Shales

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

Booker, Anne E.; Borton, Mikayla A.; Daly, Rebecca A.

ABSTRACT Hydraulic fracturing of black shale formations has greatly increased United States oil and natural gas recovery. However, the accumulation of biomass in subsurface reservoirs and pipelines is detrimental because of possible well souring, microbially induced corrosion, and pore clogging. Temporal sampling of produced fluids from a well in the Utica Shale revealed the dominance ofHalanaerobiumstrains within thein situmicrobial community and the potential for these microorganisms to catalyze thiosulfate-dependent sulfidogenesis. From these field data, we investigated biogenic sulfide production catalyzed by aHalanaerobiumstrain isolated from the produced fluids using proteogenomics and laboratory growth experiments. Analysis ofHalanaerobiumisolate genomes and reconstructed genomes frommore » metagenomic data sets revealed the conserved presence of rhodanese-like proteins and anaerobic sulfite reductase complexes capable of converting thiosulfate to sulfide. Shotgun proteomics measurements using aHalanaerobiumisolate verified that these proteins were more abundant when thiosulfate was present in the growth medium, and culture-based assays identified thiosulfate-dependent sulfide production by the same isolate. Increased production of sulfide and organic acids during the stationary growth phase suggests that fermentativeHalanaerobiumuses thiosulfate to remove excess reductant. These findings emphasize the potential detrimental effects that could arise from thiosulfate-reducing microorganisms in hydraulically fractured shales, which are undetected by current industry-wide corrosion diagnostics. IMPORTANCEAlthough thousands of wells in deep shale formations across the United States have been hydraulically fractured for oil and gas recovery, the impact of microbial metabolism within these environments is poorly understood. Our research demonstrates that dominant microbial populations in these subsurface ecosystems contain the conserved capacity for the reduction of thiosulfate to sulfide and that this process is likely occurring in the environment. Sulfide generation (also known as “souring”) is considered deleterious in the oil and gas industry because of both toxicity issues and impacts on corrosion of the subsurface infrastructure. Critically, the capacity for sulfide generation via reduction of sulfate was not detected in our data sets. Given that current industry wellhead tests for sulfidogenesis target canonical sulfate-reducing microorganisms, these data suggest that new approaches to the detection of sulfide-producing microorganisms may be necessary.« less

A microbial sensor for organophosphate hydrolysis exploiting an engineered specificity switch in a transcription factor

DOE PAGES

Jha, Ramesh K.; Kern, Theresa L.; Kim, Youngchang; ...

2016-08-30

A whole-cell biosensor utilizing a transcription factor (TF) is an effective tool for sensitive and selective detection of specialty chemicals or anthropogenic molecules, but requires an access to an expanded repertoire of TFs. Using ligand docked homology models for binding pocket identification, assisted by conservative mutations in the pocket, we engineered a novel specificity in an Acinetobacter TF, PobR, to ‘sense’ a chemical p-nitrophenol (pNP) and measured the response via a fluorescent protein reporter expressed from a PobR promoter. Out of 10 7 variants of PobR, four were active when pNP was added as an inducer, with two mutants showingmore » a specificity switch from the native effector 4-hydroxybenzoate (4HB). One of the mutants, pNPmut1 was then used to create a smart microbial cell responding to pNP production and detect hydrolysis of an insecticide, paraoxon, in a coupled assay involving phosphotriesterase (PTE) enzyme expressed from a separate promoter. We show that the fluorescence of the cells correlated with the catalytic efficiency of PTE variants, each cell expressed. High selectivity for similar molecules (4HB vs pNP), high sensitivity for pNP detection (~2 μM) and agreement of apo- and holo- structures of PobR scaffold with computational models are notable successes presented in this work.« less

Inflight Microbial Monitoring - An Alternative Method to Culture Based Detection Currently Used on the International Space Station

NASA Technical Reports Server (NTRS)

Khodadad, Christina L.; Birmele, Michele N.; Hummerick, Mary E.; Roman, Monsi; Smith, David J.

2015-01-01

Microorganisms including potential human pathogens have been detected on the International Space Station (ISS). The potential to introduce new microorganisms occurs with every exchange of crew or addition of equipment or supplies. Current microbial monitoring methods require enrichment of microorganisms and a 48-hour incubation time resulting in an increase in microbial load, detecting a limited number of unidentified microorganisms. An expedient, low-cost, in-flight method of microbial detection, identification, and enumeration is warranted.

Assessing the evolutionary rate of positional orthologous genes in prokaryotes using synteny data

PubMed Central

Lemoine, Frédéric; Lespinet, Olivier; Labedan, Bernard

2007-01-01

Background Comparison of completely sequenced microbial genomes has revealed how fluid these genomes are. Detecting synteny blocks requires reliable methods to determining the orthologs among the whole set of homologs detected by exhaustive comparisons between each pair of completely sequenced genomes. This is a complex and difficult problem in the field of comparative genomics but will help to better understand the way prokaryotic genomes are evolving. Results We have developed a suite of programs that automate three essential steps to study conservation of gene order, and validated them with a set of 107 bacteria and archaea that cover the majority of the prokaryotic taxonomic space. We identified the whole set of shared homologs between two or more species and computed the evolutionary distance separating each pair of homologs. We applied two strategies to extract from the set of homologs a collection of valid orthologs shared by at least two genomes. The first computes the Reciprocal Smallest Distance (RSD) using the PAM distances separating pairs of homologs. The second method groups homologs in families and reconstructs each family's evolutionary tree, distinguishing bona fide orthologs as well as paralogs created after the last speciation event. Although the phylogenetic tree method often succeeds where RSD fails, the reverse could occasionally be true. Accordingly, we used the data obtained with either methods or their intersection to number the orthologs that are adjacent in for each pair of genomes, the Positional Orthologous Genes (POGs), and to further study their properties. Once all these synteny blocks have been detected, we showed that POGs are subject to more evolutionary constraints than orthologs outside synteny groups, whichever the taxonomic distance separating the compared organisms. Conclusion The suite of programs described in this paper allows a reliable detection of orthologs and is useful for evaluating gene order conservation in prokaryotes whichever their taxonomic distance. Thus, our approach will make easy the rapid identification of POGS in the next few years as we are expecting to be inundated with thousands of completely sequenced microbial genomes. PMID:18047665

Directed evolution of FLS2 towards novel flagellin peptide recognition

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

Helft, Laura; Thompson, Mikayla; Bent, Andrew F.

Microbe-associated molecular patterns (MAMPs) are molecules, or domains within molecules, that are conserved across microbial taxa and can be recognized by a plant or animal immune system. Although MAMP receptors have evolved to recognize conserved epitopes, the MAMPs in some microbial species or strains have diverged sufficiently to render them unrecognizable by some host immune systems. In this study, we carried out in vitro evolution of the Arabidopsis thaliana flagellin receptor FLAGELLIN-SENSING 2 (FLS2) to isolate derivatives that recognize one or more flagellin peptides from bacteria for which the wildtype Arabidopsis FLS2 confers little or no response. A targeted approachmore » generated amino acid variation at FLS2 residues in a region previously implicated in flagellin recognition. The primary screen tested for elevated response to the canonical flagellin peptide from Pseudomonas aeruginosa, flg22. From this pool, we then identified five alleles of FLS2 that confer modest (quantitatively partial) recognition of an Erwinia amylovora flagellin peptide. Use of this Erwinia-based flagellin peptide to stimulate Arabidopsis plants expressing the resulting FLS2 alleles did not lead to a detectable reduction of virulent P. syringae pv. tomato growth. However, combination of two identified mutations into a single allele further increased FLS2-mediated responses to the E. amylovora flagellin peptide. Furthermore, these studies demonstrate the potential to raise the sensitivity of MAMP receptors toward particular targets.« less

Directed evolution of FLS2 towards novel flagellin peptide recognition

DOE PAGES

Helft, Laura; Thompson, Mikayla; Bent, Andrew F.

2016-06-06

Microbe-associated molecular patterns (MAMPs) are molecules, or domains within molecules, that are conserved across microbial taxa and can be recognized by a plant or animal immune system. Although MAMP receptors have evolved to recognize conserved epitopes, the MAMPs in some microbial species or strains have diverged sufficiently to render them unrecognizable by some host immune systems. In this study, we carried out in vitro evolution of the Arabidopsis thaliana flagellin receptor FLAGELLIN-SENSING 2 (FLS2) to isolate derivatives that recognize one or more flagellin peptides from bacteria for which the wildtype Arabidopsis FLS2 confers little or no response. A targeted approachmore » generated amino acid variation at FLS2 residues in a region previously implicated in flagellin recognition. The primary screen tested for elevated response to the canonical flagellin peptide from Pseudomonas aeruginosa, flg22. From this pool, we then identified five alleles of FLS2 that confer modest (quantitatively partial) recognition of an Erwinia amylovora flagellin peptide. Use of this Erwinia-based flagellin peptide to stimulate Arabidopsis plants expressing the resulting FLS2 alleles did not lead to a detectable reduction of virulent P. syringae pv. tomato growth. However, combination of two identified mutations into a single allele further increased FLS2-mediated responses to the E. amylovora flagellin peptide. Furthermore, these studies demonstrate the potential to raise the sensitivity of MAMP receptors toward particular targets.« less

Gut microbial communities of American pikas (Ochotona princeps): Evidence for phylosymbiosis and adaptations to novel diets.

PubMed

Kohl, Kevin D; Varner, Johanna; Wilkening, Jennifer L; Dearing, M Denise

2018-03-01

Gut microbial communities provide many physiological functions to their hosts, especially in herbivorous animals. We still lack an understanding of how these microbial communities are structured across hosts in nature, especially within a given host species. Studies on laboratory mice have demonstrated that host genetics can influence microbial community structure, but that diet can overwhelm these genetic effects. We aimed to test these ideas in a natural system, the American pika (Ochotona princeps). First, pikas are high-elevation specialists with significant population structure across various mountain ranges in the USA, allowing us to investigate whether similarities in microbial communities match host genetic differences. Additionally, pikas are herbivorous, with some populations exhibiting remarkable dietary plasticity and consuming high levels of moss, which is exceptionally high in fibre and low in protein. This allows us to investigate adaptations to an herbivorous diet, as well as to the especially challenging diet of moss. Here, we inventoried the microbial communities of pika caecal pellets from various populations using 16S rRNA sequencing to investigate structuring of microbial communities across various populations with different natural diets. Microbial communities varied significantly across populations, and differences in microbial community structure were congruent with genetic differences in host population structure, a pattern known as "phylosymbiosis." Several microbial members (Ruminococcus, Prevotella, Oxalobacter and Coprococcus) were detected across all samples, and thus likely represent a "core microbiome." These genera are known to perform a number of services for herbivorous hosts such as fibre fermentation and the degradation of plant defensive compounds, and thus are likely important for herbivory in pikas. Moreover, pikas that feed on moss harboured microbial communities highly enriched in Melainabacteria. This uncultivable candidate phylum has been proposed to ferment fibre for herbivores, and thus may contribute to the ability of some pika populations to consume high amounts of moss. These findings demonstrate that both host genetics and diet can influence the microbial communities of the American pika. These animals may be novel sources of fibre-degrading microbes. Last, we discuss the implications of population-specific microbial communities for conservation efforts in this species. © 2017 The Authors. Journal of Animal Ecology © 2017 British Ecological Society.

The Yeast Saccharomyces cerevisiae: a versatile model system for the identification and characterization of bacterial virulence proteins.

PubMed

Siggers, Keri A; Lesser, Cammie F

2008-07-17

Microbial pathogens utilize complex secretion systems to deliver proteins into host cells. These effector proteins target and usurp host cell processes to promote infection and cause disease. While secretion systems are conserved, each pathogen delivers its own unique set of effectors. The identification and characterization of these effector proteins has been difficult, often limited by the lack of detectable signal sequences and functional redundancy. Model systems including yeast, worms, flies, and fish are being used to circumvent these issues. This technical review details the versatility and utility of yeast Saccharomyces cerevisiae as a system to identify and characterize bacterial effectors.

Microbial Profiles and Detection Techniques in Peri-Implant Diseases: a Systematic Review

PubMed Central

Padial-Molina, Miguel; López-Martínez, Jesús; O’Valle, Francisco

2016-01-01

ABSTRACT Objectives To describe the microbial profiles of peri-implant diseases and the main detection methods. Material and Methods A literature search was performed in MEDLINE via PubMed database to identify studies on microbial composition of peri-implant surfaces in humans published in the last 5 years. Studies had to have clear implant status definition for health, peri-implant mucositis and/or peri-implantitis and specifically study microbial composition of the peri-implant sulcus. Results A total of 194 studies were screened and 47 included. Peri-implant sites are reported to be different microbial ecosystems compared to periodontal sites. However, differences between periodontal and peri-implant health and disease are not consistent across all studies, possibly due to the bias introduced by the microbial detection technique. New methods non species-oriented are being used to find ‘unexpected’ microbiota not previously described in these scenarios. Conclusions Microbial profile of peri-implant diseases usually includes classic periodontopathogens. However, correlation between studies is difficult, particularly because of the use of different detection methods. New metagenomic techniques should be promoted for future studies to avoid detection bias. PMID:27833735

Evaluation of ATP measurements to detect microbial ingress by wastewater and surface water in drinking water.

PubMed

Vang, Óluva K; Corfitzen, Charlotte B; Smith, Christian; Albrechtsen, Hans-Jørgen

2014-11-01

Fast and reliable methods are required for monitoring of microbial drinking water quality in order to protect public health. Adenosine triphosphate (ATP) was investigated as a potential real-time parameter for detecting microbial ingress in drinking water contaminated with wastewater or surface water. To investigate the ability of the ATP assay in detecting different contamination types, the contaminant was diluted with non-chlorinated drinking water. Wastewater, diluted at 10(4) in drinking water, was detected with the ATP assay, as well as 10(2) to 10(3) times diluted surface water. To improve the performance of the ATP assay in detecting microbial ingress in drinking water, different approaches were investigated, i.e. quantifying microbial ATP or applying reagents of different sensitivities to reduce measurement variations; however, none of these approaches contributed significantly in this respect. Compared to traditional microbiological methods, the ATP assay could detect wastewater and surface water in drinking water to a higher degree than total direct counts (TDCs), while both heterotrophic plate counts (HPC 22 °C and HPC 37 °C) and Colilert-18 (Escherichia coli and coliforms) were more sensitive than the ATP measurements, though with much longer response times. Continuous sampling combined with ATP measurements displays definite monitoring potential for microbial drinking water quality, since microbial ingress in drinking water can be detected in real-time with ATP measurements. The ability of the ATP assay to detect microbial ingress is influenced by both the ATP load from the contaminant itself and the ATP concentration in the specific drinking water. Consequently, a low ATP concentration of the specific drinking water facilitates a better detection of a potential contamination of the water supply with the ATP assay. Copyright © 2014 Elsevier Ltd. All rights reserved.

Sampling from living organisms: section 3 in Sampling and experiments with biofilms in the environment: chapter 6

USGS Publications Warehouse

Kellogg, Christina A.

2014-01-01

Living organisms, unlike inanimate surfaces, seem to exert some control over their surface microbiota, in many cases maintaining conserved, species-specific microbial communities. Microbial ecologists seek to characterize and identify these microbes to understand the roles they are playing in the larger organism's biology.

Predicting effects of climate change on the composition and function of soil microbial communities

NASA Astrophysics Data System (ADS)

Dubinsky, E.; Brodie, E.; Myint, C.; Ackerly, D.; van Nostrand, J.; Bird, J.; Zhou, J.; Andersen, G.; Firestone, M.

2008-12-01

Complex soil microbial communities regulate critical ecosystem processes that will be altered by climate change. A critical step towards predicting the impacts of climate change on terrestrial ecosystems is to determine the primary controllers of soil microbial community composition and function, and subsequently evaluate climate change scenarios that alter these controllers. We surveyed complex soil bacterial and archaeal communities across a range of climatic and edaphic conditions to identify critical controllers of soil microbial community composition in the field and then tested the resulting predictions using a 2-year manipulation of precipitation and temperature using mesocosms of California annual grasslands. Community DNA extracted from field soils sampled from six different ecosystems was assayed for bacterial and archaeal communities using high-density phylogenetic microarrays as well as functional gene arrays. Correlations among the relative abundances of thousands of microbial taxa and edaphic factors such as soil moisture and nutrient content provided a basis for predicting community responses to changing soil conditions. Communities of soil bacteria and archaea were strongly structured by single environmental predictors, particularly variables related to soil water. Bacteria in the Actinomycetales and Bacilli consistently demonstrated a strong negative response to increasing soil moisture, while taxa in a greater variety of lineages responded positively to increasing soil moisture. In the climate change experiment, overall bacterial community structure was impacted significantly by total precipitation but not by plant species. Changes in soil moisture due to decreased rainfall resulted in significant and predictable alterations in community structure. Over 70% of the bacterial taxa in common with the cross-ecosystem study responded as predicted to altered precipitation, with the most conserved response from Actinobacteria. The functional consequences of these predictable changes in community composition were measured with functional arrays that detect genes involved in the metabolism of carbon, nitrogen and other elements. The response of soil microbial communities to altered precipitation can be predicted from the distribution of microbial taxa across moisture gradients.

Media Ion Composition Controls Regulatory and Virulence Response of Salmonella in Spaceflight

PubMed Central

Wilson, James W.; Ott, C. Mark; Quick, Laura; Davis, Richard; zu Bentrup, Kerstin Höner; Crabbé, Aurélie; Richter, Emily; Sarker, Shameema; Barrila, Jennifer; Porwollik, Steffen; Cheng, Pui; McClelland, Michael; Tsaprailis, George; Radabaugh, Timothy; Hunt, Andrea; Shah, Miti; Nelman-Gonzalez, Mayra; Hing, Steve; Parra, Macarena; Dumars, Paula; Norwood, Kelly; Bober, Ramona; Devich, Jennifer; Ruggles, Ashleigh; CdeBaca, Autumn; Narayan, Satro; Benjamin, Joseph; Goulart, Carla; Rupert, Mark; Catella, Luke; Schurr, Michael J.; Buchanan, Kent; Morici, Lisa; McCracken, James; Porter, Marc D.; Pierson, Duane L.; Smith, Scott M.; Mergeay, Max; Leys, Natalie; Stefanyshyn-Piper, Heidemarie M.; Gorie, Dominic; Nickerson, Cheryl A.

2008-01-01

The spaceflight environment is relevant to conditions encountered by pathogens during the course of infection and induces novel changes in microbial pathogenesis not observed using conventional methods. It is unclear how microbial cells sense spaceflight-associated changes to their growth environment and orchestrate corresponding changes in molecular and physiological phenotypes relevant to the infection process. Here we report that spaceflight-induced increases in Salmonella virulence are regulated by media ion composition, and that phosphate ion is sufficient to alter related pathogenesis responses in a spaceflight analogue model. Using whole genome microarray and proteomic analyses from two independent Space Shuttle missions, we identified evolutionarily conserved molecular pathways in Salmonella that respond to spaceflight under all media compositions tested. Identification of conserved regulatory paradigms opens new avenues to control microbial responses during the infection process and holds promise to provide an improved understanding of human health and disease on Earth. PMID:19079590

Comparative analysis of sugarcane bagasse metagenome reveals unique and conserved biomass-degrading enzymes among lignocellulolytic microbial communities.

PubMed

Mhuantong, Wuttichai; Charoensawan, Varodom; Kanokratana, Pattanop; Tangphatsornruang, Sithichoke; Champreda, Verawat

2015-01-01

As one of the most abundant agricultural wastes, sugarcane bagasse is largely under-exploited, but it possesses a great potential for the biofuel, fermentation, and cellulosic biorefinery industries. It also provides a unique ecological niche, as the microbes in this lignocellulose-rich environment thrive in relatively high temperatures (50°C) with varying microenvironments of aerobic surface to anoxic interior. The microbial community in bagasse thus presents a good resource for the discovery and characterization of new biomass-degrading enzymes; however, it remains largely unexplored. We have constructed a fosmid library of sugarcane bagasse and obtained the largest bagasse metagenome to date. A taxonomic classification of the bagasse metagenome reviews the predominance of Proteobacteria, which are also found in high abundance in other aerobic environments. Based on the functional characterization of biomass-degrading enzymes, we have demonstrated that the bagasse microbial community benefits from a large repertoire of lignocellulolytic enzymes, which allows them to digest different components of lignocelluoses into single molecule sugars. Comparative genomic analyses with other lignocellulolytic and non-lignocellulolytic metagenomes show that microbial communities are taxonomically separable by their aerobic "open" or anoxic "closed" environments. Importantly, a functional analysis of lignocellulose-active genes (based on the CAZy classifications) reveals core enzymes highly conserved within the lignocellulolytic group, regardless of their taxonomic compositions. Cellulases, in particular, are markedly more pronounced compared to the non-lignocellulolytic group. In addition to the core enzymes, the bagasse fosmid library also contains some uniquely enriched glycoside hydrolases, as well as a large repertoire of the newly defined auxiliary activity proteins. Our study demonstrates a conservation and diversification of carbohydrate-active genes among diverse microbial species in different biomass-degrading niches, and signifies the importance of taking a global approach to functionally investigate a microbial community as a whole, as compared to focusing on individual organisms.

Microbial Profiling of Combat Wound Infection through Detection Microarray and Next-Generation Sequencing

PubMed Central

Allen, Jonathan E.; Brown, Trevor S.; Gardner, Shea N.; McLoughlin, Kevin S.; Forsberg, Jonathan A.; Kirkup, Benjamin C.; Chromy, Brett A.; Luciw, Paul A.; Elster, Eric A.

2014-01-01

Combat wound healing and resolution are highly affected by the resident microbial flora. We therefore sought to achieve comprehensive detection of microbial populations in wounds using novel genomic technologies and bioinformatics analyses. We employed a microarray capable of detecting all sequenced pathogens for interrogation of 124 wound samples from extremity injuries in combat-injured U.S. service members. A subset of samples was also processed via next-generation sequencing and metagenomic analysis. Array analysis detected microbial targets in 51% of all wound samples, with Acinetobacter baumannii being the most frequently detected species. Multiple Pseudomonas species were also detected in tissue biopsy specimens. Detection of the Acinetobacter plasmid pRAY correlated significantly with wound failure, while detection of enteric-associated bacteria was associated significantly with successful healing. Whole-genome sequencing revealed broad microbial biodiversity between samples. The total wound bioburden did not associate significantly with wound outcome, although temporal shifts were observed over the course of treatment. Given that standard microbiological methods do not detect the full range of microbes in each wound, these data emphasize the importance of supplementation with molecular techniques for thorough characterization of wound-associated microbes. Future application of genomic protocols for assessing microbial content could allow application of specialized care through early and rapid identification and management of critical patterns in wound bioburden. PMID:24829242

Phylogenetically conserved resource partitioning in the coastal microbial loop

DOE PAGES

Bryson, Samuel; Li, Zhou; Chavez, Francisco; ...

2017-08-11

Resource availability influences marine microbial community structure, suggesting that population-specific resource partitioning defines discrete niches. Identifying how resources are partitioned among populations, thereby characterizing functional guilds within the communities, remains a challenge for microbial ecologists. We used proteomic stable isotope probing (SIP) and NanoSIMS analysis of phylogenetic microarrays (Chip-SIP) along with 16S rRNA gene amplicon and metagenomic sequencing to characterize the assimilation of six 13C-labeled common metabolic substrates and changes in the microbial community structure within surface water collected from Monterey Bay, CA. Both sequencing approaches indicated distinct substrate-specific community shifts. However, observed changes in relative abundance for individual populationsmore » did not correlate well with directly measured substrate assimilation. The complementary SIP techniques identified assimilation of all six substrates by diverse taxa, but also revealed differential assimilation of substrates into protein and ribonucleotide biomass between taxa. Substrate assimilation trends indicated significantly conserved resource partitioning among populations within the Flavobacteriia, Alphaproteobacteria and Gammaproteobacteria classes, suggesting that functional guilds within marine microbial communities are phylogenetically cohesive. However, populations within these classes exhibited heterogeneity in biosynthetic activity, which distinguished high-activity copiotrophs from low-activity oligotrophs. These results indicate distinct growth responses between populations that is not apparent by genome sequencing alone.« less

Phylogenetically conserved resource partitioning in the coastal microbial loop

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

Bryson, Samuel; Li, Zhou; Chavez, Francisco

Resource availability influences marine microbial community structure, suggesting that population-specific resource partitioning defines discrete niches. Identifying how resources are partitioned among populations, thereby characterizing functional guilds within the communities, remains a challenge for microbial ecologists. We used proteomic stable isotope probing (SIP) and NanoSIMS analysis of phylogenetic microarrays (Chip-SIP) along with 16S rRNA gene amplicon and metagenomic sequencing to characterize the assimilation of six 13C-labeled common metabolic substrates and changes in the microbial community structure within surface water collected from Monterey Bay, CA. Both sequencing approaches indicated distinct substrate-specific community shifts. However, observed changes in relative abundance for individual populationsmore » did not correlate well with directly measured substrate assimilation. The complementary SIP techniques identified assimilation of all six substrates by diverse taxa, but also revealed differential assimilation of substrates into protein and ribonucleotide biomass between taxa. Substrate assimilation trends indicated significantly conserved resource partitioning among populations within the Flavobacteriia, Alphaproteobacteria and Gammaproteobacteria classes, suggesting that functional guilds within marine microbial communities are phylogenetically cohesive. However, populations within these classes exhibited heterogeneity in biosynthetic activity, which distinguished high-activity copiotrophs from low-activity oligotrophs. These results indicate distinct growth responses between populations that is not apparent by genome sequencing alone.« less

Phylogenetically conserved resource partitioning in the coastal microbial loop

PubMed Central

Bryson, Samuel; Li, Zhou; Chavez, Francisco; Weber, Peter K; Pett-Ridge, Jennifer; Hettich, Robert L; Pan, Chongle; Mayali, Xavier; Mueller, Ryan S

2017-01-01

Resource availability influences marine microbial community structure, suggesting that population-specific resource partitioning defines discrete niches. Identifying how resources are partitioned among populations, thereby characterizing functional guilds within the communities, remains a challenge for microbial ecologists. We used proteomic stable isotope probing (SIP) and NanoSIMS analysis of phylogenetic microarrays (Chip-SIP) along with 16S rRNA gene amplicon and metagenomic sequencing to characterize the assimilation of six 13C-labeled common metabolic substrates and changes in the microbial community structure within surface water collected from Monterey Bay, CA. Both sequencing approaches indicated distinct substrate-specific community shifts. However, observed changes in relative abundance for individual populations did not correlate well with directly measured substrate assimilation. The complementary SIP techniques identified assimilation of all six substrates by diverse taxa, but also revealed differential assimilation of substrates into protein and ribonucleotide biomass between taxa. Substrate assimilation trends indicated significantly conserved resource partitioning among populations within the Flavobacteriia, Alphaproteobacteria and Gammaproteobacteria classes, suggesting that functional guilds within marine microbial communities are phylogenetically cohesive. However, populations within these classes exhibited heterogeneity in biosynthetic activity, which distinguished high-activity copiotrophs from low-activity oligotrophs. These results indicate distinct growth responses between populations that is not apparent by genome sequencing alone. PMID:28800138

On the conservation of easel paintings: evaluation of microbial contamination and artists materials

NASA Astrophysics Data System (ADS)

Salvador, Cátia; Bordalo, Rui; Silva, Mara; Rosado, Tânia; Candeias, António; Caldeira, Ana Teresa

2017-01-01

Easel paintings have been considered one of the most important art expressions, constituting today outstanding works of art with important historic and cultural value. Unfortunately, due to the presence of several organic materials, these artworks have been affected by microbial contamination that among other factors can be responsible for different aesthetic and structural alterations. For this study, four easel paintings from the late nineteenth century by Giorgio Marini with evident chromatic and structural alterations due to biocontamination were analysed in order to better understand the materials used and the source of high microbial contamination within a focused conservation intervention process. For this end, both the biofilms and the painting materials were characterised by several analytical techniques. Fungal communities were found to prevail in areas with evident structural and aesthetic damages, which were confirmed by scanning electron microscopy analyses that allowed the observation of the fungal hyphae proliferation capacity. Energy-dispersive X-ray spectroscopy, μ-X-ray diffraction, μ-Raman, μ-FTIR and optical microscopy were used to further identify the painting materials. Immunological assays revealed the presence of a mixture of proteins of ovalbumin, collagen and casein, suggesting that the presence of these proteinaceous materials in these paintings is one of the main reasons of microbial biofilms appearance on the painting's surface. These approaches contribute for a better knowledge of these artworks providing at the same time relevant information for the ongoing conservation-restoration intervention.

Soil microbial community restoration in conservation reserve program semi-arid grasslands

USDA-ARS?s Scientific Manuscript database

The Conservation Reserve Program (CRP) in the Southern High Plains (SHP) is known to play a crucial role in maintaining ecosystem health by reducing soil erosion. However, the restoration of its soil biological health (biological community and its function) over time have not been clearly elucidated...

Microbial Biosensors for Selective Detection of Disaccharides

USDA-ARS?s Scientific Manuscript database

Seven microbial strains were screened for their ability to detect disaccharides as components of Clark-type oxygen biosensors. Sensors responded to varying degrees to maltose, cellobiose, sucrose, and melibiose, but none responded strongly to lactose. Although microbial sensors are relatively nons...

Soil acidity amelioration in a no-till system in west Tennessee USA differs by cover crop type and nitrogen application rate

USDA-ARS?s Scientific Manuscript database

Conservation soil management practices may influence the soil acidity. Surface application of lime may be required in no-till systems to ameliorate soil acidity and to improve crop yields. The application of lime may also increase microbial activity on soil. Specifically, the microbial activity of s...

Development of lower Triassic wrinkle structures: implications for the search for life on other planets.

PubMed

Mata, Scott A; Bottjer, David J

2009-11-01

Wrinkle structures are microbially mediated sedimentary structures that are a common feature of Proterozoic and earliest Phanerozoic siliciclastic seafloors on Earth and occur only rarely in post-Cambrian strata. These macroscopic microbially induced sedimentary structures are readily identifiable at the outcrop scale, and their recognition on other planetary bodies by landed missions may suggest the presence of past microbial life. Wrinkle structures of the Lower Triassic (Spathian) Virgin Limestone Member of the Moenkopi Formation in the western United States record an occurrence of widespread microbialite formation in the wake of the end-Permian mass extinction, the largest biotic crisis of the Phanerozoic. Wrinkle structures occur on proximal sandy tempestites deposited within the offshore transition. Storm layers appear to have been rapidly colonized by microbial mats and were subsequently buried by mud during fair-weather conditions. Wrinkle structures exhibit flat-topped crests and sinuous troughs, with associated mica grains oriented parallel to bedding, suggestive of trapping and binding activity. Although Lower Triassic wrinkle structures postdate the widespread occurrence of these features during the Proterozoic and Cambrian, they exhibit many of the same characteristics and environmental trends, which suggests a conservation of microbial formational and preservational processes in subtidal siliciclastic settings on Earth from the Precambrian into the Phanerozoic. In the search for extraterrestrial life, it may be these conservative characteristics that prove to be the most useful and robust for recognizing microbial features on other planetary bodies, and may add to an ever-growing foundation of knowledge for directing future explorations aimed at seeking out macroscopic microbial signatures.

Theory of microbial genome evolution

NASA Astrophysics Data System (ADS)

Koonin, Eugene

Bacteria and archaea have small genomes tightly packed with protein-coding genes. This compactness is commonly perceived as evidence of adaptive genome streamlining caused by strong purifying selection in large microbial populations. In such populations, even the small cost incurred by nonfunctional DNA because of extra energy and time expenditure is thought to be sufficient for this extra genetic material to be eliminated by selection. However, contrary to the predictions of this model, there exists a consistent, positive correlation between the strength of selection at the protein sequence level, measured as the ratio of nonsynonymous to synonymous substitution rates, and microbial genome size. By fitting the genome size distributions in multiple groups of prokaryotes to predictions of mathematical models of population evolution, we show that only models in which acquisition of additional genes is, on average, slightly beneficial yield a good fit to genomic data. Thus, the number of genes in prokaryotic genomes seems to reflect the equilibrium between the benefit of additional genes that diminishes as the genome grows and deletion bias. New genes acquired by microbial genomes, on average, appear to be adaptive. Evolution of bacterial and archaeal genomes involves extensive horizontal gene transfer and gene loss. Many microbes have open pangenomes, where each newly sequenced genome contains more than 10% `ORFans', genes without detectable homologues in other species. A simple, steady-state evolutionary model reveals two sharply distinct classes of microbial genes, one of which (ORFans) is characterized by effectively instantaneous gene replacement, whereas the other consists of genes with finite, distributed replacement rates. These findings imply a conservative estimate of at least a billion distinct genes in the prokaryotic genomic universe.

Planetary protection - assaying new methods

NASA Astrophysics Data System (ADS)

Nellen, J.; Rettberg, P.; Horneck, G.

Space age began in 1957 when the USSR launched the first satellite into earth orbit. In response to this new challenge the International Council for Science, formerly know as International Council of Scientific Unions (ICSU), established the Committee on Space Research (COSPAR) in 1958. The role of COSPAR was to channel the international scientific research in space and establish an international forum. Through COSPAR the scientific community agreed on the need for screening interplanetary probes for forward (contamination of foreign planets) and backward (contamination of earth by returned samples/probes) contamination. To prevent both forms of contamination a set of rules, as a guideline was established. Nowadays the standard implementation of the planetary protection rules is based on the experience gained during NASA's Viking project in 1975/76. Since then the evaluation-methods for microbial contamination of spacecrafts have been changed or updated just slowly. In this study the standard method of sample taking will be evaluated. New methods for examination of those samples, based on the identification of life on the molecular level, will be reviewed and checked for their feasibility as microbial detection systems. The methods will be examined for their qualitative (detection and verification of different organisms) and quantitative (detection limit and concentration verification) qualities. Amongst the methods analyzed will be i.e. real-time / PCR (poly-chain-reaction), using specific primer-sets for the amplification of highly conserved rRNA or DNA regions. Measurement of intrinsic fluorescence, i.e ATP using luciferin-luciferase reagents. The use of FAME (fatty acid methyl esters) and microchips for microbial identification purposes. The methods will be chosen to give a good overall coverage of different possible molecular markers and approaches. The most promising methods shall then be lab-tested and evaluated for their use under spacecraft assembly conditions. Since mars became one of the most sought-after planets in our solar system and will be visited by man-made probes quiet often in the near future, planetary protection is as important as never before.

Rapid detection of microbial cell abundance in aquatic systems

DOE PAGES

Rocha, Andrea M.; Yuan, Quan; Close, Dan M.; ...

2016-06-01

The detection and quantification of naturally occurring microbial cellular densities is an essential component of environmental systems monitoring. While there are a number of commonly utilized approaches for monitoring microbial abundance, capacitance-based biosensors represent a promising approach because of their low-cost and label-free detection of microbial cells, but are not as well characterized as more traditional methods. Here, we investigate the applicability of enhanced alternating current electrokinetics (ACEK) capacitive sensing as a new application for rapidly detecting and quantifying microbial cellular densities in cultured and environmentally sourced aquatic samples. ACEK capacitive sensor performance was evaluated using two distinct and dynamicmore » systems the Great Australian Bight and groundwater from the Oak Ridge Reservation in Oak Ridge, TN. Results demonstrate that ACEK capacitance-based sensing can accurately determine microbial cell counts throughout cellular concentrations typically encountered in naturally occurring microbial communities (10 3 – 10 6 cells/mL). A linear relationship was observed between cellular density and capacitance change correlations, allowing a simple linear curve fitting equation to be used for determining microbial abundances in unknown samples. As a result, this work provides a foundation for understanding the limits of capacitance-based sensing in natural environmental samples and supports future efforts focusing on evaluating the robustness ACEK capacitance-based within aquatic environments.« less

Rapid detection of microbial cell abundance in aquatic systems

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

Rocha, Andrea M.; Yuan, Quan; Close, Dan M.

The detection and quantification of naturally occurring microbial cellular densities is an essential component of environmental systems monitoring. While there are a number of commonly utilized approaches for monitoring microbial abundance, capacitance-based biosensors represent a promising approach because of their low-cost and label-free detection of microbial cells, but are not as well characterized as more traditional methods. Here, we investigate the applicability of enhanced alternating current electrokinetics (ACEK) capacitive sensing as a new application for rapidly detecting and quantifying microbial cellular densities in cultured and environmentally sourced aquatic samples. ACEK capacitive sensor performance was evaluated using two distinct and dynamicmore » systems the Great Australian Bight and groundwater from the Oak Ridge Reservation in Oak Ridge, TN. Results demonstrate that ACEK capacitance-based sensing can accurately determine microbial cell counts throughout cellular concentrations typically encountered in naturally occurring microbial communities (10 3 – 10 6 cells/mL). A linear relationship was observed between cellular density and capacitance change correlations, allowing a simple linear curve fitting equation to be used for determining microbial abundances in unknown samples. As a result, this work provides a foundation for understanding the limits of capacitance-based sensing in natural environmental samples and supports future efforts focusing on evaluating the robustness ACEK capacitance-based within aquatic environments.« less

Microbial contributions to coupled arsenic and sulfur cycling in the acid-sulfide hot spring Champagne Pool, New Zealand.

PubMed

Hug, Katrin; Maher, William A; Stott, Matthew B; Krikowa, Frank; Foster, Simon; Moreau, John W

2014-01-01

Acid-sulfide hot springs are analogs of early Earth geothermal systems where microbial metal(loid) resistance likely first evolved. Arsenic is a metalloid enriched in the acid-sulfide hot spring Champagne Pool (Waiotapu, New Zealand). Arsenic speciation in Champagne Pool follows reaction paths not yet fully understood with respect to biotic contributions and coupling to biogeochemical sulfur cycling. Here we present quantitative arsenic speciation from Champagne Pool, finding arsenite dominant in the pool, rim and outflow channel (55-75% total arsenic), and dithio- and trithioarsenates ubiquitously present as 18-25% total arsenic. In the outflow channel, dimethylmonothioarsenate comprised ≤9% total arsenic, while on the outflow terrace thioarsenates were present at 55% total arsenic. We also quantified sulfide, thiosulfate, sulfate and elemental sulfur, finding sulfide and sulfate as major species in the pool and outflow terrace, respectively. Elemental sulfur concentration reached a maximum at the terrace. Phylogenetic analysis of 16S rRNA genes from metagenomic sequencing revealed the dominance of Sulfurihydrogenibium at all sites and an increased archaeal population at the rim and outflow channel. Several phylotypes were found closely related to known sulfur- and sulfide-oxidizers, as well as sulfur- and sulfate-reducers. Bioinformatic analysis revealed genes underpinning sulfur redox transformations, consistent with sulfur speciation data, and illustrating a microbial role in sulfur-dependent transformation of arsenite to thioarsenate. Metagenomic analysis also revealed genes encoding for arsenate reductase at all sites, reflecting the ubiquity of thioarsenate and a need for microbial arsenate resistance despite anoxic conditions. Absence of the arsenite oxidase gene, aio, at all sites suggests prioritization of arsenite detoxification over coupling to energy conservation. Finally, detection of methyl arsenic in the outflow channel, in conjunction with increased sequences from Aquificaceae, supports a role for methyltransferase in thermophilic arsenic resistance. Our study highlights microbial contributions to coupled arsenic and sulfur cycling at Champagne Pool, with implications for understanding the evolution of microbial arsenic resistance in sulfidic geothermal systems.

The Impact of Population Bottlenecks on Microbial Adaptation

NASA Astrophysics Data System (ADS)

LeClair, Joshua S.; Wahl, Lindi M.

2018-07-01

Population bottlenecks—sudden, severe reductions in population size—are ubiquitous in nature. Because of their critical implications for conservation genetics, the effects of population bottlenecks on the loss of genetic diversity have been well studied. Bottlenecks also have important implications for adaptation, however, and these effects have been addressed more recently, typically in microbial populations. In this short review, we survey both experimental and theoretical work describing the impact of population bottlenecks on microbial adaptation. Focusing on theoretical contributions, we highlight emerging insights and conclude with several open questions of interest in the field.

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

Vitamin and Amino Acid Auxotrophy in Anaerobic Consortia Operating under Methanogenic Conditions

PubMed Central

Hubalek, Valerie; Buck, Moritz; Tan, BoonFei; Foght, Julia; Wendeberg, Annelie; Berry, David; Bertilsson, Stefan

2017-01-01

ABSTRACT Syntrophy among Archaea and Bacteria facilitates the anaerobic degradation of organic compounds to CH4 and CO2. Particularly during aliphatic and aromatic hydrocarbon mineralization, as in the case of crude oil reservoirs and petroleum-contaminated sediments, metabolic interactions between obligate mutualistic microbial partners are of central importance. Using micromanipulation combined with shotgun metagenomic approaches, we describe the genomes of complex consortia within short-chain alkane-degrading cultures operating under methanogenic conditions. Metabolic reconstruction revealed that only a small fraction of genes in the metagenome-assembled genomes encode the capacity for fermentation of alkanes facilitated by energy conservation linked to H2 metabolism. Instead, the presence of inferred lifestyles based on scavenging anabolic products and intermediate fermentation products derived from detrital biomass was a common feature. Additionally, inferred auxotrophy for vitamins and amino acids suggests that the hydrocarbon-degrading microbial assemblages are structured and maintained by multiple interactions beyond the canonical H2-producing and syntrophic alkane degrader-methanogen partnership. Compared to previous work, our report points to a higher order of complexity in microbial consortia engaged in anaerobic hydrocarbon transformation. IMPORTANCE Microbial interactions between Archaea and Bacteria mediate many important chemical transformations in the biosphere from degrading abundant polymers to synthesis of toxic compounds. Two of the most pressing issues in microbial interactions are how consortia are established and how we can modulate these microbial communities to express desirable functions. Here, we propose that public goods (i.e., metabolites of high energy demand in biosynthesis) facilitate energy conservation for life under energy-limited conditions and determine the assembly and function of the consortia. Our report suggests that an understanding of public good dynamics could result in new ways to improve microbial pollutant degradation in anaerobic systems. PMID:29104938

Antimicrobial Materials for Advanced Microbial Control in Spacecraft Water Systems

NASA Technical Reports Server (NTRS)

Birmele, Michele; Caro, Janicce; Newsham, Gerard; Roberts, Michael; Morford, Megan; Wheeler, Ray

2012-01-01

Microbial detection, identification, and control are essential for the maintenance and preservation of spacecraft water systems. Requirements set by NASA put limitations on the energy, mass, materials, noise, cost, and crew time that can be devoted to microbial control. Efforts are being made to attain real-time detection and identification of microbial contamination in microgravity environments. Research for evaluating technologies for capability enhancement on-orbit is currently focused on the use of adenosine triphosphate (ATP) analysis for detection purposes and polymerase chain reaction (peR) for microbial identification. Additional research is being conducted on how to control for microbial contamination on a continual basis. Existing microbial control methods in spacecraft utilize iodine or ionic silver biocides, physical disinfection, and point-of-use sterilization filters. Although these methods are effective, they require re-dosing due to loss of efficacy, have low human toxicity thresholds, produce poor taste, and consume valuable mass and crew time. Thus, alternative methods for microbial control are needed. This project also explores ultraviolet light-emitting diodes (UV-LEDs), surface passivation methods for maintaining residual biocide levels, and several antimicrobial materials aimed at improving current microbial control techniques, as well as addressing other materials presently under analysis and future directions to be pursued.

Indirect microbial detection

NASA Technical Reports Server (NTRS)

Wilkins, J. R. (Inventor)

1981-01-01

The growth of microorganisms in a sample is detected and monitored by culturing microorganisms in a growth medium and detecting a change in potential between two electrodes, separated from the microbial growth by a barrier which is permeable to charged paticles but microorganism impermeable.

Rapid culture-independent microbial analysis aboard the international space station (ISS) stage two: quantifying three microbial biomarkers.

PubMed

Morris, Heather C; Damon, Michael; Maule, Jake; Monaco, Lisa A; Wainwright, Norm

2012-09-01

Abstract A portable, rapid, microbial detection unit, the Lab-On-a-Chip Application Development Portable Test System (LOCAD-PTS), was launched to the International Space Station (ISS) as a technology demonstration unit in December 2006. Results from the first series of experiments designed to detect Gram-negative bacteria on ISS surfaces by quantifying a single microbial biomarker lipopolysaccharide (LPS) were reported in a previous article. Herein, we report additional technology demonstration experiments expanding the on-orbit capabilities of the LOCAD-PTS to detecting three different microbial biomarkers on ISS surfaces. Six different astronauts on more than 20 occasions participated in these experiments, which were designed to test the new beta-glucan (fungal cell wall molecule) and lipoteichoic acid (LTA; Gram-positive bacterial cell wall component) cartridges individually and in tandem with the existing Limulus Amebocyte Lysate (LAL; Gram-negative bacterial LPS detection) cartridges. Additionally, we conducted the sampling side by side with the standard culture-based detection method currently used on the ISS. Therefore, we present data on the distribution of three microbial biomarkers collected from various surfaces in every module present on the ISS at the time of sampling. In accordance with our previous experiments, we determined that spacecraft surfaces known to be frequently in contact with crew members demonstrated higher values of all three microbial molecules. Key Words: Planetary protection-Spaceflight-Microbiology-Biosensor. Astrobiology 12, 830-840.

MBGD update 2013: the microbial genome database for exploring the diversity of microbial world.

PubMed

Uchiyama, Ikuo; Mihara, Motohiro; Nishide, Hiroyo; Chiba, Hirokazu

2013-01-01

The microbial genome database for comparative analysis (MBGD, available at http://mbgd.genome.ad.jp/) is a platform for microbial genome comparison based on orthology analysis. As its unique feature, MBGD allows users to conduct orthology analysis among any specified set of organisms; this flexibility allows MBGD to adapt to a variety of microbial genomic study. Reflecting the huge diversity of microbial world, the number of microbial genome projects now becomes several thousands. To efficiently explore the diversity of the entire microbial genomic data, MBGD now provides summary pages for pre-calculated ortholog tables among various taxonomic groups. For some closely related taxa, MBGD also provides the conserved synteny information (core genome alignment) pre-calculated using the CoreAligner program. In addition, efficient incremental updating procedure can create extended ortholog table by adding additional genomes to the default ortholog table generated from the representative set of genomes. Combining with the functionalities of the dynamic orthology calculation of any specified set of organisms, MBGD is an efficient and flexible tool for exploring the microbial genome diversity.

Review: Microbial Analysis in Dielectrophoretic Microfluidic Systems

PubMed Central

Fernandez, Renny E.; Rohani, Ali; Farmehini, Vahid; Swami, Nathan S.

2017-01-01

Infections caused by various known and emerging pathogenic microorganisms, including antibiotic-resistant strains, are a major threat to global health and well-being. This highlights the urgent need for detection systems for microbial identification, quantification and characterization towards assessing infections, prescribing therapies and understanding the dynamic cellular modifications. Current state-of-the-art microbial detection systems exhibit a trade-off between sensitivity and assay time, which could be alleviated by selective and label-free microbial capture onto the sensor surface from dilute samples. AC electrokinetic methods, such as dielectrophoresis, enable frequency-selective capture of viable microbial cells and spores due to polarization based on their distinguishing size, shape and sub-cellular compositional characteristics, for downstream coupling to various detection modalities. Following elucidation of the polarization mechanisms that distinguish bacterial cells from each other, as well as from mammalian cells, this review compares the microfluidic platforms for dielectrophoretic manipulation of microbials and their coupling to various detection modalities, including immuno-capture, impedance measurement, Raman spectroscopy and nucleic acid amplification methods, as well as for phenotypic assessment of microbial viability and antibiotic susceptibility. Based on the urgent need within point-of-care diagnostics towards reducing assay times and enhancing capture of the target organism, as well as the emerging interest in isolating intact microbials based on their phenotype and subcellular features, we envision widespread adoption of these label-free and selective electrokinetic techniques. PMID:28372723

Characterization of Microbial Community in Lascaux Cave by High Throughput Sequencing

NASA Astrophysics Data System (ADS)

Alonso, Lise; Dubost, Audrey; Luis, Patricia; Pommier, Thomas; Moënne-Loccoz, Yvan

2017-04-01

The Lascaux Cave in South-Est France is an archeological landmark renowned for its Paleolithic paintings dating back c.18.000 years. Extensive touristic frequenting and repeated chemical treatments have resulted in the development of microbial stains on cave walls, which is a major issue in terms of art conservation. Therefore, it is of prime importance to better understand the microbial ecology of Lascaux Cave. Like many other caves, Lascaux is quite heterogeneous in terms of the nature and surface properties of rock walls within cave rooms, as well as the succession of rooms/galleries from the entrance to deeper areas of the cave. Lascaux Cave displays an additional levels of heterogeneity related to the presence of discontinuous stains on certain types of cave walls. We compared the microbial community (i.e. both prokaryotic and eukaryotic microbial populations) colonizing cave walls of different rooms/galleries, in and outside stains and in different cave layers, in successive years. Quantitative PCR analysis of cave wall samples gave in the order of 102 copies of 18S rRNA genes and 105 copies of 16S rRNA genes per ng of DNA, indicating significant colonization of all cave walls by micro-eukaryotes and especially bacteria. Illumina metagenomic analyses of cave wall samples was carried out based on four ribosomal DNA markers targeting bacteria, archaea, fungi, and other micro-eukaryotes. The results showed that the four microbial communities were highly diverse in and outside stains, as several hundred genera of microorganisms were identified in each. Proteobacteria were more prominent within stains whereas Bacteroidetes and Sordariomycetes were more prominent outside stains. High-throughput sequencing also showed that the nature/surface properties of cave walls were the main factor determining the structure and composition of microbial communities, ahead of the other heterogeneity factors studied i.e. location within the cave, presence of stain and sampling season. This work provides a global view of the microbial community of Lascaux Cave, which could be useful to guide conservation efforts.

Biogeochemistry of Stinking Springs, Utah. Part II: Microbial Diversity and Photo- and Chemo-Autotrophic Growth Rates in a Layered Microbial Mat

NASA Astrophysics Data System (ADS)

Monteverde, D.; Metzger, J. G.; Bournod, C.; Kelly, H.; Johnson, H.; Sessions, A. L.; Osburn, M.; Shapiro, R. S.; Rideout, J.; Johnston, D. T.; Stevenson, B.; Stamps, B. W.; Vuono, D.; Hanselmann, K.; Spear, J. R.

2013-12-01

Layered microbial mats have garnered attention for their high phylogenetic diversity and exploitation of geochemical gradients often on the mm scale. However, despite their novelty and implications for early life diversification, little is known about layered microbial mat growth rates or the interdependence of the microbial communities within the system. Stinking Springs, a warm, sulfidic, saline spring northeast of the Great Salt Lake, serves as our test-site to investigate some of these questions. Stinking Springs undergoes downstream changes in pH (6.59-8.14), sulfide (527μM - below detection), sulfate (13-600μM), TCO2 (7.77-3.71mM), and temperature (40-21°C) along its ~150m flow path. The first 10m of discharge is channelized, beyond that, the spring supports a 10 to 40mm-thick layered microbial mat covering ~40% of the total spring runoff area. The mat was divided into four texturally-distinct layers which were each analyzed for 16S rRNA, lipid abundance, and bicarbonate and acetate uptake rates in addition to standard microscopy analyses. 16S rRNA analyses confirmed high taxa diversity within each layer, which varied significantly in taxa makeup such that no single phylum dominated the abundance (>33%) in more than one mat layer. The taxonomic diversity tended to increase with mat depth, a similar finding to other studies on layered microbial mats. A mat sampling transect across 16 meters showed that layer taxonomic diversity was conserved horizontally for all four mat layers, which implies mat depth has a larger control on diversity than physical or chemical parameters. Microscopy indicated the presence of diatoms in all layers which was confirmed by lipid abundance of sterols and long-branch fatty acid methyl esters. Incubation experiments were conducted in light and dark conditions over 24 hours with separate 13C-tagged bicarbonate and acetate additions. Heterotrophic growth rates (acetate uptake; 0.03-0.65%/day) were higher than autotrophic growth rates (bicarbonate uptake; 0-0.16%/day) under both dark and light conditions. Light conditions yielded higher growth rates for both heterotrophs and autotrophs and the highest rates were consistently found in the top mat layer and decreased with depth. The addition of 13C-acetate and concomitant high uptake is a measure of potential heterotrophy since in situ acetate concentrations are unlikely to be as high. 13C-bicarbonate uptake, on the other hand, should quantitatively represent the autotrophic growth rate. The Stinking Spring layered microbial mats display high taxonomic diversity, which is conserved horizontally across distances of meters and varies significantly with depth. Mats experience highest growth in the surface layer likely driven by phototrophs; high rates of bicarbonate uptake in the dark indicate considerable chemoautotrophy. Covariation in the heterotroph growth rates and 16S rRNA heterotroph abundance with mat depth indicates that heterotrophy may play an important role in the growth of these layered mats.

Current Technical Approaches for the Early Detection of Foodborne Pathogens: Challenges and Opportunities.

PubMed

Cho, Il-Hoon; Ku, Seockmo

2017-09-30

The development of novel and high-tech solutions for rapid, accurate, and non-laborious microbial detection methods is imperative to improve the global food supply. Such solutions have begun to address the need for microbial detection that is faster and more sensitive than existing methodologies (e.g., classic culture enrichment methods). Multiple reviews report the technical functions and structures of conventional microbial detection tools. These tools, used to detect pathogens in food and food homogenates, were designed via qualitative analysis methods. The inherent disadvantage of these analytical methods is the necessity for specimen preparation, which is a time-consuming process. While some literature describes the challenges and opportunities to overcome the technical issues related to food industry legal guidelines, there is a lack of reviews of the current trials to overcome technological limitations related to sample preparation and microbial detection via nano and micro technologies. In this review, we primarily explore current analytical technologies, including metallic and magnetic nanomaterials, optics, electrochemistry, and spectroscopy. These techniques rely on the early detection of pathogens via enhanced analytical sensitivity and specificity. In order to introduce the potential combination and comparative analysis of various advanced methods, we also reference a novel sample preparation protocol that uses microbial concentration and recovery technologies. This technology has the potential to expedite the pre-enrichment step that precedes the detection process.

Removal of microbial pathogens in a sandy gravel aquifer under forced-gradient subsurface flow conditions

NASA Astrophysics Data System (ADS)

Oudega, Thomas James; Derx, Julia; van Driezum, Inge; Cisneros, Anibal; Sommer, Regina; Kirschner, Alexander; Farnleitner, Andreas; Blaschke, Alfred Paul

2017-04-01

Subsurface media are being used around the world as a means to mitigate microbial contamination, but vary widely in their ability to remove pathogens. To help to provide accurate risk assessments of microbial contamination of groundwaters, and establish safe setback distances between receiving waters and disposal fields, this study aims to use aquifer tracer tests to evaluate the ability of subsurface media to attenuate these pathogens. The novelty of this work is the use of a variety of different tracer substances (e.g. phages, spores, microspheres, conservative tracers) together in field experiments. This will be done by means of injecting these substances under a forced gradient in a sandy gravel aquifer in Lobau, Austria. The extraction of the tracers will be monitored in a pumping well at a distrance of 50m downgradient. This will be able to provide us with insight to the characteristics of microbial transport and how the microorganisms react to the subsurface in the study site. Subsequent numerical modelling of the experiments can tell us more about quantification of subsurface processes such as attachment/detachment, inactivation and die-off of these substances. The first field experiment with conservative tracers (NaCl) has been carried out in December 2016, and subsequent tests are being planned for the next months.

Comparison of the microbial communities of hot springs waters and the microbial biofilms in the acidic geothermal area of Copahue (Neuquén, Argentina).

PubMed

Urbieta, María Sofía; González-Toril, Elena; Bazán, Ángeles Aguilera; Giaveno, María Alejandra; Donati, Edgardo

2015-03-01

Copahue is a natural geothermal field (Neuquén province, Argentina) dominated by the Copahue volcano. As a consequence of the sustained volcanic activity, Copahue presents many acidic pools, hot springs and solfataras with different temperature and pH conditions that influence their microbial diversity. The occurrence of microbial biofilms was observed on the surrounding rocks and the borders of the ponds, where water movements and thermal activity are less intense. Microbial biofilms are particular ecological niches within geothermal environments; they present different geochemical conditions from that found in the water of the ponds and hot springs which is reflected in different microbial community structure. The aim of this study is to compare microbial community diversity in the water of ponds and hot springs and in microbial biofilms in the Copahue geothermal field, with particular emphasis on Cyanobacteria and other photosynthetic species that have not been detected before in Copahue. In this study, we report the presence of Cyanobacteria, Chloroflexi and chloroplasts of eukaryotes in the microbial biofilms not detected in the water of the ponds. On the other hand, acidophilic bacteria, the predominant species in the water of moderate temperature ponds, are almost absent in the microbial biofilms in spite of having in some cases similar temperature conditions. Species affiliated with Sulfolobales in the Archaea domain are the predominant microorganism in high temperature ponds and were also detected in the microbial biofilms.

Microbial Risk Assessment

NASA Technical Reports Server (NTRS)

Ott, C. M.; Mena, K. D.; Nickerson, C.A.; Pierson, D. L.

2009-01-01

Historically, microbiological spaceflight requirements have been established in a subjective manner based upon expert opinion of both environmental and clinical monitoring results and the incidence of disease. The limited amount of data, especially from long-duration missions, has created very conservative requirements based primarily on the concentration of microorganisms. Periodic reevaluations of new data from later missions have allowed some relaxation of these stringent requirements. However, the requirements remain very conservative and subjective in nature, and the risk of crew illness due to infectious microorganisms is not well defined. The use of modeling techniques for microbial risk has been applied in the food and potable water industries and has exceptional potential for spaceflight applications. From a productivity standpoint, this type of modeling can (1) decrease unnecessary costs and resource usage and (2) prevent inadequate or inappropriate data for health assessment. In addition, a quantitative model has several advantages for risk management and communication. By identifying the variable components of the model and the knowledge associated with each component, this type of modeling can: (1) Systematically identify and close knowledge gaps, (2) Systematically identify acceptable and unacceptable risks, (3) Improve communication with stakeholders as to the reasons for resource use, and (4) Facilitate external scientific approval of the NASA requirements. The modeling of microbial risk involves the evaluation of several key factors including hazard identification, crew exposure assessment, dose-response assessment, and risk characterization. Many of these factors are similar to conditions found on Earth; however, the spaceflight environment is very specialized as the inhabitants live in a small, semi-closed environment that is often dependent on regenerative life support systems. To further complicate modeling efforts, microbial dose-response characteristics may be affected by a potentially dysfunctional crew immune system during a mission. In addition, microbial virulence has been shown to change under certain conditions during spaceflight, further complicating dose-response characterization. An initial study of the applicability of microbial risk assessment techniques was performed using Crew Health Care System (CHeCS) operational data from the International Space Station potable water systems. The risk of infection from potable water was selected as the flight systems and microbial ecology are well defined. This initial study confirmed the feasibility of using microbial risk assessment modeling for spaceflight systems. While no immediate threat was detected, the study identified several medically significant microorganisms that could pose a health risk if uncontrolled. The study also identified several specific knowledge gaps in making a risk assessment and noted that filling these knowledge gaps is essential as the risk estimates may change by orders of magnitude depending on the answers. The current phase of the microbial risk assessment studies focuses on the dose-response relationship of specific infectious agents, focusing on Salmonella enterica Typhimurium, Pseudomonas spp., and Escherichia coli, as their evaluation will provide a better baseline for determining the overall hazard characterization. The organisms were chosen as they either have been isolated on spacecraft or have an identified route of infection during a mission. The characterization will utilize dose-response models selected either from the peer-reviewed literature and/or by using statistical approaches. Development of these modeling and risk assessment techniques will help to optimize flight requirements and to protect the safety, health, and performance of the crew.

In situ detection of microbial c-type cytochrome based on intrinsic peroxidase-like activity using screen-printed carbon electrode.

PubMed

Wen, Junlin; He, Daigui; Yu, Zhen; Zhou, Shungui

2018-08-15

C-type cytochromes (c-cyts) facilitate microbial extracellular electron transfer and play critical roles in biogeochemical cycling, bioelectricity generation and bioremediation. In this study, a simple and effective method has been developed to detect microbial c-cyts by means of peroxidase mimetic reaction on screen-printed carbon electrode (SPCE). To this end, bacteria cells were immobilized onto the working electrode surface of SPCE by a simple drop casting. After introducing 3,3',5,5'-tetramethylbenzidine (TMB) solution, microbial c-cyts with peroxidase-like activity catalyze the oxidation of TMB in the presence of hydrogen peroxide. The oxidized TMB was electrochemically determined and the current signal was employed to calculate the c-cyts content. This electrochemical method is highly sensitive for microbial c-cyts with a low detection limit of 40.78 fmol and a wide detection range between 51.70 fmol and 6.64 pmol. Moreover, the proposed technique can be universally expanded to detect c-cyts in other bacteria species such as Fontibacter ferrireducens, Pseudomonas aeruginosa, Comamonas guangdongensis and Escherichia coli. Furthermore, the proposed method confers an in situ facile and quantitative c-cyts detection without any destructive sample preparations, complex electrode modifications and expensive enzyme- or metal particle- based signal amplification. The suggested method advances an intelligent strategy for in situ quantification of microbial c-cyts and consequently holds promising application potential in microbiology and environmental science. Copyright © 2018 Elsevier B.V. All rights reserved.

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

PubMed

Salter, Ian

2018-01-01

Environmental DNA (eDNA) can be defined as the DNA pool recovered from an environmental sample that includes both extracellular and intracellular DNA. There has been a significant increase in the number of recent studies that have demonstrated the possibility to detect macroorganisms using eDNA. Despite the enormous potential of eDNA to serve as a biomonitoring and conservation tool in aquatic systems, there remain some important limitations concerning its application. One significant factor is the variable persistence of eDNA over natural environmental gradients, which imposes a critical constraint on the temporal and spatial scales of species detection. In the present study, a radiotracer bioassay approach was used to quantify the kinetic parameters of dissolved eDNA (d-eDNA), a component of extracellular DNA, over an annual cycle in the coastal Northwest Mediterranean. Significant seasonal variability in the biological uptake and turnover of d-eDNA was observed, the latter ranging from several hours to over one month. Maximum uptake rates of d-eDNA occurred in summer during a period of intense phosphate limitation (turnover <5 hrs). Corresponding increases in bacterial production and uptake of adenosine triphosphate (ATP) demonstrated the microbial utilization of d-eDNA as an organic phosphorus substrate. Higher temperatures during summer may amplify this effect through a general enhancement of microbial metabolism. A partial least squares regression (PLSR) model was able to reproduce the seasonal cycle in d-eDNA persistence and explained 60% of the variance in the observations. Rapid phosphate turnover and low concentrations of bioavailable phosphate, both indicative of phosphate limitation, were the most important parameters in the model. Abiotic factors such as pH, salinity and oxygen exerted minimal influence. The present study demonstrates significant seasonal variability in the persistence of d-eDNA in a natural marine environment that can be linked to the metabolic response of microbial communities to nutrient limitation. Future studies should consider the effect of natural environmental gradients on the seasonal persistence of eDNA, which will be of particular relevance for time-series biomonitoring programs.

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

PubMed Central

2018-01-01

Environmental DNA (eDNA) can be defined as the DNA pool recovered from an environmental sample that includes both extracellular and intracellular DNA. There has been a significant increase in the number of recent studies that have demonstrated the possibility to detect macroorganisms using eDNA. Despite the enormous potential of eDNA to serve as a biomonitoring and conservation tool in aquatic systems, there remain some important limitations concerning its application. One significant factor is the variable persistence of eDNA over natural environmental gradients, which imposes a critical constraint on the temporal and spatial scales of species detection. In the present study, a radiotracer bioassay approach was used to quantify the kinetic parameters of dissolved eDNA (d-eDNA), a component of extracellular DNA, over an annual cycle in the coastal Northwest Mediterranean. Significant seasonal variability in the biological uptake and turnover of d-eDNA was observed, the latter ranging from several hours to over one month. Maximum uptake rates of d-eDNA occurred in summer during a period of intense phosphate limitation (turnover <5 hrs). Corresponding increases in bacterial production and uptake of adenosine triphosphate (ATP) demonstrated the microbial utilization of d-eDNA as an organic phosphorus substrate. Higher temperatures during summer may amplify this effect through a general enhancement of microbial metabolism. A partial least squares regression (PLSR) model was able to reproduce the seasonal cycle in d-eDNA persistence and explained 60% of the variance in the observations. Rapid phosphate turnover and low concentrations of bioavailable phosphate, both indicative of phosphate limitation, were the most important parameters in the model. Abiotic factors such as pH, salinity and oxygen exerted minimal influence. The present study demonstrates significant seasonal variability in the persistence of d-eDNA in a natural marine environment that can be linked to the metabolic response of microbial communities to nutrient limitation. Future studies should consider the effect of natural environmental gradients on the seasonal persistence of eDNA, which will be of particular relevance for time-series biomonitoring programs. PMID:29474423

Miniprimer PCR, a New Lens for Viewing the Microbial World▿ †

PubMed Central

Isenbarger, Thomas A.; Finney, Michael; Ríos-Velázquez, Carlos; Handelsman, Jo; Ruvkun, Gary

2008-01-01

Molecular methods based on the 16S rRNA gene sequence are used widely in microbial ecology to reveal the diversity of microbial populations in environmental samples. Here we show that a new PCR method using an engineered polymerase and 10-nucleotide “miniprimers” expands the scope of detectable sequences beyond those detected by standard methods using longer primers and Taq polymerase. After testing the method in silico to identify divergent ribosomal genes in previously cloned environmental sequences, we applied the method to soil and microbial mat samples, which revealed novel 16S rRNA gene sequences that would not have been detected with standard primers. Deeply divergent sequences were discovered with high frequency and included representatives that define two new division-level taxa, designated CR1 and CR2, suggesting that miniprimer PCR may reveal new dimensions of microbial diversity. PMID:18083877

mRNA-Based Parallel Detection of Active Methanotroph Populations by Use of a Diagnostic Microarray

PubMed Central

Bodrossy, Levente; Stralis-Pavese, Nancy; Konrad-Köszler, Marianne; Weilharter, Alexandra; Reichenauer, Thomas G.; Schöfer, David; Sessitsch, Angela

2006-01-01

A method was developed for the mRNA-based application of microbial diagnostic microarrays to detect active microbial populations. DNA- and mRNA-based analyses of environmental samples were compared and confirmed via quantitative PCR. Results indicated that mRNA-based microarray analyses may provide additional information on the composition and functioning of microbial communities. PMID:16461725

Microbial survey of the mummies from the Capuchin Catacombs of Palermo, Italy: biodeterioration risk and contamination of the indoor air

PubMed Central

Piñar, Guadalupe; Piombino-Mascali, Dario; Maixner, Frank; Zink, Albert; Sterflinger, Katja

2013-01-01

The Capuchin Catacombs of Palermo contain over 1800 preserved bodies dating from the 16th to 20th centuries AD and showing evidence of biodeterioration. An extensive microbiological and molecular investigation was recently performed. Samples were taken from skin, muscle, hair, bone, stuffing materials, clothes, and surrounding walls as well as from the indoor air. In this study, we witnessed that the different degradation phenomena observed on the variety of materials located at the Capuchin Catacombs of Palermo are biological in origin. Molecular techniques showed the dominance of halophilic species of the domains Bacteria and Archaea on the walls and – as a result of salt emanating from the walls – on the mummies themselves. Nevertheless, specialized microorganisms belonging to taxa well-known for their cellulolytic and proteolytic activities were detected on clothes and stuffing material, and on skin, muscle, hair, and bone, respectively. This specialized microbiota is threatening the conservation of the mummies themselves. Additionally, sequences related to the human skin microbiome and to some pathogenic Bacteria (order Clostridiales) and fungi (genus Phialosimplex) were identified on samples derived from the mummies. Furthermore, a phosphate-reducing fungus, Penicillium radicum, was detected on bone. Finally, the high concentration of airborne fungal spores is not conducive to the conservation of the human remains and is posing a potential health risk for visitors. PMID:23772650

Formation of 2,4-D bound residues in soils: New insights into microbial metabolism.

PubMed

Botero, Liliana Rocío; Mougin, Chistian; Peñuela, Gustavo; Barriuso, Enrique

2017-04-15

The microbial contribution to the formation of bound residues in soils is studied by characterizing the metabolic activity of three microorganisms (Trametes versicolor, Fusarium solani and Ralstonia eutropha) on 14 C-2,4-dichlorophenoxyacetic acid (2,4-D) during incubation in synthetic liquid media and soil. A fractionation protocol was applied to quantify the 14 C-2,4-D that was incorporated into the biomass among biomolecular-like fractions. Successive fractionation of microbial biomass was implemented to break up and quantify the methanol/dichloromethane fraction (corresponding to the 14 C-lipid-like fraction), the trichloroacetic acid fraction (or hydrolysed 14 C-polysaccharide-like fraction) and the acid hydrolysable fraction (or the hydrolysed 14 C-protein-like fraction). Relevant differences in the 2,4-D degradation and biomass radioactivity distribution among the three microorganisms were found. The 14 C-protein-like fraction was the most consistent biomass fraction for reflecting the pesticide use capacity of the microorganisms under liquid and soil conditions. 2,4-D and its metabolite 4-chlorophenol were detected in methanol/dichloromethane and trichloroacetic acid fractions of the biomass of microorganisms exhibiting a low capacity to mineralize 2,4-D, thus proving that the microbial participation in the formation of bound residues while conserving the initial pesticide structure under natural soil conditions may be intimately associated with the lipid- and polysaccharide-like constituents. The fractionation protocol differentiates between 14 C that is incorporated into biomass as a biomolecular constituent and the pesticide or its metabolites that accumulate in the biomass and thus correspond to the stricto sensu definition of bound residues. Copyright © 2017 Elsevier B.V. All rights reserved.

History, applications, methodological issues and perspectives for the use of environmental DNA (eDNA) in marine and freshwater environments.

PubMed

Díaz-Ferguson, Edgardo E; Moyer, Gregory R

2014-12-01

Genetic material (short DNA fragments) left behind by species in nonliving components of the environment (e.g. soil, sediment, or water) is defined as environmental DNA (eDNA). This DNA has been previously described as particulate DNA and has been used to detect and describe microbial communities in marine sediments since the mid-1980's and phytoplankton communities in the water column since the early-1990's. More recently, eDNA has been used to monitor invasive or endangered vertebrate and invertebrate species. While there is a steady increase in the applicability of eDNA as a monitoring tool, a variety of eDNA applications are emerging in fields such as forensics, population and community ecology, and taxonomy. This review provides scientist with an understanding of the methods underlying eDNA detection as well as applications, key methodological considerations, and emerging areas of interest for its use in ecology and conservation of freshwater and marine environments.

Electing a candidate: a speculative history of the bacterial phylum OP10.

PubMed

Dunfield, Peter F; Tamas, Ivica; Lee, Kevin C; Morgan, Xochitl C; McDonald, Ian R; Stott, Matthew B

2012-12-01

In 1998, a cultivation-independent survey of the microbial community in Obsidian Pool, Yellowstone National Park, detected 12 new phyla within the Domain Bacteria. These were dubbed 'candidate divisions' OP1 to OP12. Since that time the OP10 candidate division has been commonly detected in various environments, usually as part of the rare biosphere, but occasionally as a predominant community component. Based on 16S rRNA gene phylogeny, OP10 comprises at least 12 class-level subdivisions. However, despite this broad ecological and evolutionary diversity, all OP10 bacteria have eluded cultivation until recently. In 2011, two reference species of OP10 were taxonomically validated, removing the phylum from its 'candidate' status. Construction of a highly resolved phylogeny based on 29 universally conserved genes verifies its standing as a unique bacterial phylum. In the following paper we summarize what is known and what is suspected about the newest described bacterial phylum, the Armatimonadetes. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

Biogeochemistry of a submerged groundwater seep ecosystem in Lake Huron near karst region of Alpena, MI

NASA Astrophysics Data System (ADS)

Kinsman-Costello, L. E.; Dick, G.; Sheik, C.; Burton, G. A.; Sheldon, N. D.

2015-12-01

Submerged groundwater seeps in Lake Huron establish ecosystems with distinctive geochemical conditions. In the Middle Island Sinkhole (MIS), a 23-m deep seep, groundwater seepage establishes low O2 (< 4 mg L-1), high sulfate (6 mM) conditions, in which a purple cyanobacteria-dominated mat thrives. The mat is capable of anoxygenic photosynthesis, oxygenic photosynthesis, and chemosynthesis. Within the top 3 cm of the mat-water interface, hydrogen sulfide concentrations increase to 1-7 mM. Little is known about the structure and function of microbes within organic-rich, high-sulfide sediments beneath the mat. Using pore water and sediment geochemical characterization along with microbial community analysis, we elucidated relationships between microbial community structure and ecosystem function along vertical gradients. In sediment pore waters, biologically reactive solutes (SO42-, NH4+, PO43-, and CH4) displayed steep vertical gradients, reflecting biological and geochemical functioning. In contrast, more conservative ions (Ca+2, Mg+2, Na+, and Cl-), did not change significantly with depth in MIS sediments, indicating groundwater influence in the sediment profile. MIS sediments contained more organic matter than typical Lake Huron sediments, and were generally higher in nutrients, metals, and sulfur (acid volatile sulfide). Using the Illumina MiSeq platform we detected 14,127 unique operational taxonomic units across sediment and surface mat samples. Microbial community composition in the MIS was distinctly different from non-groundwater affected areas at similar depth nearby in Lake Huron (ANOSIM, R= 0.74, p=0.002). MIS sediment communities were more diverse that MIS surface mat communities and changed with depth into sediments. MIS sediment community composition was related to several geochemical variables, including organic matter and multiple indicators of phosphorus availability. Elucidating the structure and function of microbial consortia in MIS, a highly unique and environmentally vulnerable ecosystem, provides a rare opportunity to understand relationships between microbial species and their environment and may provide insights into the evolution of life under ancient low-oxygen, high-sulfur conditions.

Shifts in taxonomic and functional microbial diversity with agriculture: How fragile is the Brazilian Cerrado?

PubMed

Souza, Renata Carolini; Mendes, Iêda Carvalho; Reis-Junior, Fábio Bueno; Carvalho, Fabíola Marques; Nogueira, Marco Antonio; Vasconcelos, Ana Tereza Ribeiro; Vicente, Vânia Aparecida; Hungria, Mariangela

2016-03-16

The Cerrado--an edaphic type of savannah--comprises the second largest biome of the Brazilian territory and is the main area for grain production in the country, but information about the impact of land conversion to agriculture on microbial diversity is still scarce. We used a shotgun metagenomic approach to compare undisturbed (native) soil and soils cropped for 23 years with soybean/maize under conservation tillage--"no-till" (NT)--and conventional tillage (CT) systems in the Cerrado biome. Soil management and fertilizer inputs with the introduction of agriculture improved chemical properties, but decreased soil macroporosity and microbial biomass of carbon and nitrogen. Principal coordinates analyses confirmed different taxonomic and functional profiles for each treatment. There was predominance of the Bacteria domain, especially the phylum Proteobacteria, with higher numbers of sequences in the NT and CT treatments; Archaea and Viruses also had lower numbers of sequences in the undisturbed soil. Within the Alphaproteobacteria, there was dominance of Rhizobiales and of the genus Bradyrhizobium in the NT and CT systems, attributed to massive inoculation of soybean, and also of Burkholderiales. In contrast, Rhizobium, Azospirillum, Xanthomonas, Pseudomonas and Acidobacterium predominated in the native Cerrado. More Eukaryota, especially of the phylum Ascomycota were detected in the NT. The functional analysis revealed lower numbers of sequences in the five dominant categories for the CT system, whereas the undisturbed Cerrado presented higher abundance. High impact of agriculture in taxonomic and functional microbial diversity in the biome Cerrado was confirmed. Functional diversity was not necessarily associated with taxonomic diversity, as the less conservationist treatment (CT) presented increased taxonomic sequences and reduced functional profiles, indicating a strategy to try to maintain soil functioning by favoring taxa that are probably not the most efficient for some functions. Our results highlight that underneath the rustic appearance of the Cerrado vegetation there is a fragile soil microbial community.

Molecular Ecology of Drinking Water

EPA Science Inventory

The presentation consists of examples of molecular research: –Detection and control (removal and/or inactivation) of microbes in drinking source waters –Changing microbial quality of water during distribution and storage –Detection and identification of microbial agents, incl...

Rapid Clinical Bacteriology and Its Future Impact

PubMed Central

Durand, Géraldine; Peyret, Michel; Chatellier, Sonia; Zambardi, Gilles; Schrenzel, Jacques; Shortridge, Dee; Engelhardt, Anette; Dunne, William Michael

2013-01-01

Clinical microbiology has always been a slowly evolving and conservative science. The sub-field of bacteriology has been and still is dominated for over a century by culture-based technologies. The integration of serological and molecular methodologies during the seventies and eighties of the previous century took place relatively slowly and in a cumbersome fashion. When nucleic acid amplification technologies became available in the early nineties, the predicted "revolution" was again slow but in the end a real paradigm shift did take place. Several of the culture-based technologies were successfully replaced by tests aimed at nucleic acid detection. More recently a second revolution occurred. Mass spectrometry was introduced and broadly accepted as a new diagnostic gold standard for microbial species identification. Apparently, the diagnostic landscape is changing, albeit slowly, and the combination of newly identified infectious etiologies and the availability of innovative technologies has now opened new avenues for modernizing clinical microbiology. However, the improvement of microbial antibiotic susceptibility testing is still lagging behind. In this review we aim to sketch the most recent developments in laboratory-based clinical bacteriology and to provide an overview of emerging novel diagnostic approaches. PMID:23301218

Identifying Key Proteins in Hg Methylation Pathways of Desulfovibrio by Global Proteomics, Final Technical Report

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

Summers, Anne O.; Miller, Susan M.; Wall, Judy

2016-06-18

Elemental mercury, Hg(0) is a contaminant at many DOE sites, especially at Oak Ridge National Laboratory (ORNL) where the spread of spilled Hg and its effects on microbial populations have been monitored for decades. To explore the microbial interactions with Hg, we have devised a global proteomic approach capable of directly detecting Hg-adducts of proteins. This technique developed in the facultative anaerobe, Escherichia coli, allows us to identify the proteins most vulnerable to acute exposure to organomercurials phenyl- and ethyl-mercury (as surrogates for the highly neurotoxic methyl-Hg) (Polacco, et al, 2011). We have found >300 such proteins in all metabolicmore » functional groups and cellular compartments; most are highly conserved and can serve as markers for acute Hg exposure (Zink, et al. 2016, in preparation). We have also discovered that acute Hg exposure severely disrupts thiol, iron and redox homeostases, and electrolyte balance (LaVoie, et al., 2015) Thus, we proposed to bring these techniques to bear on the central problem of identifying the cellular proteins involved in bacterial uptake and methylation of mercury and its release from the cell.« less

Microbial communities and bioactive compounds in marine sponges of the family irciniidae-a review.

PubMed

Hardoim, Cristiane C P; Costa, Rodrigo

2014-09-30

Marine sponges harbour complex microbial communities of ecological and biotechnological importance. Here, we propose the application of the widespread sponge family Irciniidae as an appropriate model in microbiology and biochemistry research. Half a gram of one Irciniidae specimen hosts hundreds of bacterial species-the vast majority of which are difficult to cultivate-and dozens of fungal and archaeal species. The structure of these symbiont assemblages is shaped by the sponge host and is highly stable over space and time. Two types of quorum-sensing molecules have been detected in these animals, hinting at microbe-microbe and host-microbe signalling being important processes governing the dynamics of the Irciniidae holobiont. Irciniids are vulnerable to disease outbreaks, and concerns have emerged about their conservation in a changing climate. They are nevertheless amenable to mariculture and laboratory maintenance, being attractive targets for metabolite harvesting and experimental biology endeavours. Several bioactive terpenoids and polyketides have been retrieved from Irciniidae sponges, but the actual producer (host or symbiont) of these compounds has rarely been clarified. To tackle this, and further pertinent questions concerning the functioning, resilience and physiology of these organisms, truly multi-layered approaches integrating cutting-edge microbiology, biochemistry, genetics and zoology research are needed.

Microbial immigration across the Mediterranean via airborne dust

PubMed Central

Rosselli, Riccardo; Fiamma, Maura; Deligios, Massimo; Pintus, Gabriella; Pellizzaro, Grazia; Canu, Annalisa; Duce, Pierpaolo; Squartini, Andrea; Muresu, Rosella; Cappuccinelli, Pietro

2015-01-01

Dust particles lifting and discharge from Africa to Europe is a recurring phenomenon linked to air circulation conditions. The possibility that microorganisms are conveyed across distances entails important consequences in terms of biosafety and pathogens spread. Using culture independent DNA-based analyses via next generation sequencing of the 16 S genes from the airborne metagenome, the atmospheric microbial community was characterized and the hypothesis was tested that shifts in species diversity could be recorded in relation to dust discharge. As sampling ground the island of Sardinia was chosen, being an ideal cornerstone within the Mediterranean and a crossroad of wind circulation amidst Europe and Africa. Samples were collected in two opposite coastal sites and in two different weather conditions comparing dust-conveying winds from Africa with a control situation with winds from Europe. A major conserved core microbiome was evidenced but increases in species richness and presence of specific taxa were nevertheless observed in relation to each wind regime. Taxa which can feature strains with clinical implications were also detected. The approach is reported as a recommended model monitoring procedure for early warning alerts in frameworks of biosafety against natural spread of clinical microbiota across countries as well as to prevent bacteriological warfare. PMID:26542754

DAMPs, MAMPs, and NAMPs in plant innate immunity.

PubMed

Choi, Hyong Woo; Klessig, Daniel F

2016-10-26

Multicellular organisms have evolved systems/mechanisms to detect various forms of danger, including attack by microbial pathogens and a variety of pests, as well as tissue and cellular damage. Detection via cell-surface receptors activates an ancient and evolutionarily conserved innate immune system. Potentially harmful microorganisms are recognized by the presence of molecules or parts of molecules that have structures or chemical patterns unique to microbes and thus are perceived as non-self/foreign. They are referred to as Microbe-Associated Molecular Patterns (MAMPs). Recently, a class of small molecules that is made only by nematodes, and that functions as pheromones in these organisms, was shown to be recognized by a wide range of plants. In the presence of these molecules, termed Nematode-Associated Molecular Patterns (NAMPs), plants activate innate immune responses and display enhanced resistance to a broad spectrum of microbial and nematode pathogens. In addition to pathogen attack, the relocation of various endogenous molecules or parts of molecules, generally to the extracellular milieu, as a result of tissue or cellular damage is perceived as a danger signal, and it leads to the induction of innate immune responses. These relocated endogenous inducers are called Damage-Associated Molecular Patterns (DAMPs). This mini-review is focused on plant DAMPs, including the recently discovered Arabidopsis HMGB3, which is the counterpart of the prototypic animal DAMP HMGB1. The plant DAMPs will be presented in the context of plant MAMPs and NAMPs, as well as animal DAMPs.

Similarity-based gene detection: using COGs to find evolutionarily-conserved ORFs.

PubMed

Powell, Bradford C; Hutchison, Clyde A

2006-01-19

Experimental verification of gene products has not kept pace with the rapid growth of microbial sequence information. However, existing annotations of gene locations contain sufficient information to screen for probable errors. Furthermore, comparisons among genomes become more informative as more genomes are examined. We studied all open reading frames (ORFs) of at least 30 codons from the genomes of 27 sequenced bacterial strains. We grouped the potential peptide sequences encoded from the ORFs by forming Clusters of Orthologous Groups (COGs). We used this grouping in order to find homologous relationships that would not be distinguishable from noise when using simple BLAST searches. Although COG analysis was initially developed to group annotated genes, we applied it to the task of grouping anonymous DNA sequences that may encode proteins. "Mixed COGs" of ORFs (clusters in which some sequences correspond to annotated genes and some do not) are attractive targets when seeking errors of gene prediction. Examination of mixed COGs reveals some situations in which genes appear to have been missed in current annotations and a smaller number of regions that appear to have been annotated as gene loci erroneously. This technique can also be used to detect potential pseudogenes or sequencing errors. Our method uses an adjustable parameter for degree of conservation among the studied genomes (stringency). We detail results for one level of stringency at which we found 83 potential genes which had not previously been identified, 60 potential pseudogenes, and 7 sequences with existing gene annotations that are probably incorrect. Systematic study of sequence conservation offers a way to improve existing annotations by identifying potentially homologous regions where the annotation of the presence or absence of a gene is inconsistent among genomes.

Similarity-based gene detection: using COGs to find evolutionarily-conserved ORFs

PubMed Central

Powell, Bradford C; Hutchison, Clyde A

2006-01-01

Background Experimental verification of gene products has not kept pace with the rapid growth of microbial sequence information. However, existing annotations of gene locations contain sufficient information to screen for probable errors. Furthermore, comparisons among genomes become more informative as more genomes are examined. We studied all open reading frames (ORFs) of at least 30 codons from the genomes of 27 sequenced bacterial strains. We grouped the potential peptide sequences encoded from the ORFs by forming Clusters of Orthologous Groups (COGs). We used this grouping in order to find homologous relationships that would not be distinguishable from noise when using simple BLAST searches. Although COG analysis was initially developed to group annotated genes, we applied it to the task of grouping anonymous DNA sequences that may encode proteins. Results "Mixed COGs" of ORFs (clusters in which some sequences correspond to annotated genes and some do not) are attractive targets when seeking errors of gene predicion. Examination of mixed COGs reveals some situations in which genes appear to have been missed in current annotations and a smaller number of regions that appear to have been annotated as gene loci erroneously. This technique can also be used to detect potential pseudogenes or sequencing errors. Our method uses an adjustable parameter for degree of conservation among the studied genomes (stringency). We detail results for one level of stringency at which we found 83 potential genes which had not previously been identified, 60 potential pseudogenes, and 7 sequences with existing gene annotations that are probably incorrect. Conclusion Systematic study of sequence conservation offers a way to improve existing annotations by identifying potentially homologous regions where the annotation of the presence or absence of a gene is inconsistent among genomes. PMID:16423288

The Microbiology of Subsurface, Salt-Based Nuclear Waste Repositories: Using Microbial Ecology, Bioenergetics, and Projected Conditions to Help Predict Microbial Effects on Repository Performance

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

Swanson, Juliet S.; Cherkouk, Andrea; Arnold, Thuro

This report summarizes the potential role of microorganisms in salt-based nuclear waste repositories using available information on the microbial ecology of hypersaline environments, the bioenergetics of survival under high ionic strength conditions, and “repository microbiology” related studies. In areas where microbial activity is in question, there may be a need to shift the research focus toward feasibility studies rather than studies that generate actual input for performance assessments. In areas where activity is not necessary to affect performance (e.g., biocolloid transport), repository-relevant data should be generated. Both approaches will lend a realistic perspective to a safety case/performance scenario that willmore » most likely underscore the conservative value of that case.« less

The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome

PubMed Central

Sela, D. A.; Chapman, J.; Adeuya, A.; Kim, J. H.; Chen, F.; Whitehead, T. R.; Lapidus, A.; Rokhsar, D. S.; Lebrilla, C. B.; German, J. B.; Price, N. P.; Richardson, P. M.; Mills, D. A.

2008-01-01

Following birth, the breast-fed infant gastrointestinal tract is rapidly colonized by a microbial consortium often dominated by bifidobacteria. Accordingly, the complete genome sequence of Bifidobacterium longum subsp. infantis ATCC15697 reflects a competitive nutrient-utilization strategy targeting milk-borne molecules which lack a nutritive value to the neonate. Several chromosomal loci reflect potential adaptation to the infant host including a 43 kbp cluster encoding catabolic genes, extracellular solute binding proteins and permeases predicted to be active on milk oligosaccharides. An examination of in vivo metabolism has detected the hallmarks of milk oligosaccharide utilization via the central fermentative pathway using metabolomic and proteomic approaches. Finally, conservation of gene clusters in multiple isolates corroborates the genomic mechanism underlying milk utilization for this infant-associated phylotype. PMID:19033196

SPECIES-SPECIFIC DETECTION OF HYDROCARBON UTILIZING BACTERIA. (R825810)

EPA Science Inventory

Rapid detection and quantitative assessment of specific microbial species in environmental samples is desirable for monitoring changes in ecosystems and for tracking natural or introduced microbial species during bioremediation of contaminated sites. In the interests of develo...

Seasonal dynamics alter taxonomical and functional microbial profiles in Pampa biome soils under natural grasslands

PubMed Central

Barboza, Anthony Diego Muller; Pylro, Victor Satler; Jacques, Rodrigo Josemar Seminot; Gubiani, Paulo Ivonir; de Quadros, Fernando Luiz Ferreira; da Trindade, Júlio Kuhn; Triplett, Eric W.

2018-01-01

Soil microbial communities’ assembly is strongly tied to changes in temperature and moisture. Although microbial functional redundancy seems to overcome taxonomical composition changes, the sensitivity and resilience of soil microbial communities from subtropical regions in response to seasonal variations are still poorly understood. Thus, the development of new strategies for biodiversity conservation and sustainable management require a complete understanding of the soil abiotic process involved in the selection of microbial taxa and functions. In this work, we used state of the art molecular methodologies (Next Generation Sequencing) to compare the taxonomic (metataxonomics) and functional (metatranscriptomics) profiles among soil samples from two subtropical natural grasslands located in the Pampa biome, Brazil, in response to short-term seasonal variations. Our data suggest that grasslands maintained a stable microbial community membership along the year with oscillation in abundance. Apparently soil microbial taxa are more susceptible to natural climatic disturbances while functions are more stable and change with less intensity along the year. Finally, our data allow us to conclude that the most abundant microbial groups and functions were shared between seasons and locations reflecting the existence of a stable taxonomical and functional core microbiota.

Available nitrogen is the key factor influencing soil microbial functional gene diversity in tropical rainforest.

PubMed

Cong, Jing; Liu, Xueduan; Lu, Hui; Xu, Han; Li, Yide; Deng, Ye; Li, Diqiang; Zhang, Yuguang

2015-08-20

Tropical rainforests cover over 50% of all known plant and animal species and provide a variety of key resources and ecosystem services to humans, largely mediated by metabolic activities of soil microbial communities. A deep analysis of soil microbial communities and their roles in ecological processes would improve our understanding on biogeochemical elemental cycles. However, soil microbial functional gene diversity in tropical rainforests and causative factors remain unclear. GeoChip, contained almost all of the key functional genes related to biogeochemical cycles, could be used as a specific and sensitive tool for studying microbial gene diversity and metabolic potential. In this study, soil microbial functional gene diversity in tropical rainforest was analyzed by using GeoChip technology. Gene categories detected in the tropical rainforest soils were related to different biogeochemical processes, such as carbon (C), nitrogen (N) and phosphorus (P) cycling. The relative abundance of genes related to C and P cycling detected mostly derived from the cultured bacteria. C degradation gene categories for substrates ranging from labile C to recalcitrant C were all detected, and gene abundances involved in many recalcitrant C degradation gene categories were significantly (P < 0.05) different among three sampling sites. The relative abundance of genes related to N cycling detected was significantly (P < 0.05) different, mostly derived from the uncultured bacteria. The gene categories related to ammonification had a high relative abundance. Both canonical correspondence analysis and multivariate regression tree analysis showed that soil available N was the most correlated with soil microbial functional gene structure. Overall high microbial functional gene diversity and different soil microbial metabolic potential for different biogeochemical processes were considered to exist in tropical rainforest. Soil available N could be the key factor in shaping the soil microbial functional gene structure and metabolic potential.

Microbial fuel cells applied to the metabolically based detection of extraterrestrial life.

PubMed

Abrevaya, Ximena C; Mauas, Pablo J D; Cortón, Eduardo

2010-12-01

Since the 1970s, when the Viking spacecrafts carried out experiments to detect microbial metabolism on the surface of Mars, the search for nonspecific methods to detect life in situ has been one of the goals of astrobiology. It is usually required that a methodology detect life independently from its composition or form and that the chosen biological signature point to a feature common to all living systems, such as the presence of metabolism. In this paper, we evaluate the use of microbial fuel cells (MFCs) for the detection of microbial life in situ. MFCs are electrochemical devices originally developed as power electrical sources and can be described as fuel cells in which the anode is submerged in a medium that contains microorganisms. These microorganisms, as part of their metabolic process, oxidize organic material, releasing electrons that contribute to the electric current, which is therefore proportional to metabolic and other redox processes. We show that power and current density values measured in MFCs that use microorganism cultures or soil samples in the anode are much larger than those obtained with a medium free of microorganisms or sterilized soil samples, respectively. In particular, we found that this is true for extremophiles, which have been proposed as potential inhabitants of extraterrestrial environments. Therefore, our results show that MFCs have the potential to be used for in situ detection of microbial life.

Microbial Fuel Cells Applied to the Metabolically Based Detection of Extraterrestrial Life

NASA Astrophysics Data System (ADS)

Abrevaya, Ximena C.; Mauas, Pablo J. D.; Cortón, Eduardo

2010-12-01

Since the 1970s, when the Viking spacecrafts carried out experiments to detect microbial metabolism on the surface of Mars, the search for nonspecific methods to detect life in situ has been one of the goals of astrobiology. It is usually required that a methodology detect life independently from its composition or form and that the chosen biological signature point to a feature common to all living systems, such as the presence of metabolism. In this paper, we evaluate the use of microbial fuel cells (MFCs) for the detection of microbial life in situ. MFCs are electrochemical devices originally developed as power electrical sources and can be described as fuel cells in which the anode is submerged in a medium that contains microorganisms. These microorganisms, as part of their metabolic process, oxidize organic material, releasing electrons that contribute to the electric current, which is therefore proportional to metabolic and other redox processes. We show that power and current density values measured in MFCs that use microorganism cultures or soil samples in the anode are much larger than those obtained with a medium free of microorganisms or sterilized soil samples, respectively. In particular, we found that this is true for extremophiles, which have been proposed as potential inhabitants of extraterrestrial environments. Therefore, our results show that MFCs have the potential to be used for in situ detection of microbial life.

Microbial Monitoring of Common Opportunistic Pathogens by Comparing Multiple Real-time PCR Platforms for Potential Space Applications

NASA Technical Reports Server (NTRS)

Roman, Monserrate C.; Jones, Kathy U.; Oubre, Cherie M.; Castro, Victoria; Ott, Mark C.; Birmele, Michele; Venkateswaran, Kasthuri J.; Vaishampayan, Parag A.

2013-01-01

Current methods for microbial detection: a) Labor & time intensive cultivation-based approaches that can fail to detect or characterize all cells present. b) Requires collection of samples on orbit and transportation back to ground for analysis. Disadvantages to current detection methods: a) Unable to perform quick and reliable detection on orbit. b) Lengthy sampling intervals. c) No microbe identification.

In-Flight Microbial Monitor

NASA Technical Reports Server (NTRS)

Zeitlin, Nancy; Mullenix, Pamela; Wheeler, Raymond M.; Ruby, Anna Maria

2015-01-01

Previous research has shown that potential human pathogens have been detected on the International Space Station (ISS). New microorganisms are introduced with every exchange of crew and cargo. Microorganisms introduced to the ISS are readily transferred between crew and subsystems (i.e., ECLSS, environmental control and life support systems). Current microbial characterization methods require a culture-based enrichment of microorganisms and at least a 48-hour incubation time. This increases the microbial load while detecting only a limited number of microorganisms. The culture-based method detects approximately 1-10% of the total organisms present and provides no identification. To identify and enumerate ISS samples requires that the microbes be returned to Earth for complete analysis. Therefore, a more expedient, low-cost, inflight method of microbial detection, identification, and enumeration is needed. The RAZOR EX, a ruggedized, commercial off the shelf, real-time PCR field instrument was tested for its ability to detect microorganisms at low concentrations within one hour. Escherichia coli, Salmonella enterica Typhimurium, and Pseudomonas aeruginosa were detected at low levels using real-time DNA amplification. Total heterotrophic counts could also be detected using a 16S gene marker that can identify up to 98% of all bacteria. To reflect viable cells found in the samples, RNA was also detectable using a modified, single-step reverse transcription reaction.

Multiple genome alignment for identifying the core structure among moderately related microbial genomes.

PubMed

Uchiyama, Ikuo

2008-10-31

Identifying the set of intrinsically conserved genes, or the genomic core, among related genomes is crucial for understanding prokaryotic genomes where horizontal gene transfers are common. Although core genome identification appears to be obvious among very closely related genomes, it becomes more difficult when more distantly related genomes are compared. Here, we consider the core structure as a set of sufficiently long segments in which gene orders are conserved so that they are likely to have been inherited mainly through vertical transfer, and developed a method for identifying the core structure by finding the order of pre-identified orthologous groups (OGs) that maximally retains the conserved gene orders. The method was applied to genome comparisons of two well-characterized families, Bacillaceae and Enterobacteriaceae, and identified their core structures comprising 1438 and 2125 OGs, respectively. The core sets contained most of the essential genes and their related genes, which were primarily included in the intersection of the two core sets comprising around 700 OGs. The definition of the genomic core based on gene order conservation was demonstrated to be more robust than the simpler approach based only on gene conservation. We also investigated the core structures in terms of G+C content homogeneity and phylogenetic congruence, and found that the core genes primarily exhibited the expected characteristic, i.e., being indigenous and sharing the same history, more than the non-core genes. The results demonstrate that our strategy of genome alignment based on gene order conservation can provide an effective approach to identify the genomic core among moderately related microbial genomes.

Molecular monitoring of the microbial dynamics occurring on historical limestone buildings during and after the in situ application of different bio-consolidation treatments

PubMed Central

Ettenauer, Jörg; Piñar, Guadalupe; Sterflinger, Katja; Gonzalez-Muñoz, Maria Teresa; Jroundi, Fadwa

2011-01-01

Microbially Induced Carbonate Precipitation is proposed as an environmentally friendly method to protect decayed ornamental stone and introduced in the field of preservation of Cultural Heritage. Recent conservation studies performed under laboratory conditions on non-sterile calcarenite stones have successfully reported on the application of a suitable nutritional solution, inoculated and non-inoculated with Myxococcus xanthus, as a bioconsolidation treatment. Furthermore, this procedure has been applied in situ, very recently, to selected historical buildings in Granada, Spain. For the first time, we evaluate the efficiency and risks of the in situ application of the above mentioned treatments onto two historical buildings in Granada. The evaluation consists of a detailed investigation of the micro-biota actively growing during the seven days of the treatments – short-term monitoring and of that remaining on the stones after six and twelve months of the application – long-term monitoring. A molecular strategy, including DNA extraction, PCR amplification of 16S rRNA sequences, construction of clone libraries and fingerprinting by DGGE (Denaturing Gradient Gel Electrophoresis) analysis followed by sequencing was used to gain insight into the microbial diversity present on the differentially treated stones. The monitoring of M. xanthus was performed by PCR using species-specific primers. Similar dynamics were triggered on both buildings by the application of the nutritional solution (inoculated or non-inoculated). 16S rDNA sequencing revealed the dominant occurrence of members belonging to the Firmicutes and Proteobacteria during the seven days of the treatment, whereas after one year the order Bacillales of the phylum Firmicutes was the predominantly detected microorganisms. M. xanthus could be detected only during the seven days of the treatment. The treatments seem to activate no dangerous microorganisms and furthermore, to select the remainder of a homogeneous group of carbonatogenic bacteria on the stones after a long period of time. PMID:21944202

Screening For Alcohol-Producing Microbes

NASA Technical Reports Server (NTRS)

Schubert, Wayne W.

1988-01-01

Dye reaction rapidly identifies alcohol-producing microbial colonies. Method visually detects alcohol-producing micro-organisms, and distinguishes them from other microbial colonies that do not produce alcohol. Method useful for screening mixed microbial populations in environmental samples.

Temporal variation in airborne microbial populations and microbially-derived allergens in a tropical urban landscape

NASA Astrophysics Data System (ADS)

Woo, Anthony C.; Brar, Manreetpal S.; Chan, Yuki; Lau, Maggie C. Y.; Leung, Frederick C. C.; Scott, James A.; Vrijmoed, Lilian L. P.; Zawar-Reza, Peyman; Pointing, Stephen B.

2013-08-01

The microbial component of outdoor aerosols was assessed along a gradient of urban development from inner-city to rural in the seasonal-tropical metropolis of Hong Kong. Sampling over a continuous one-year period was conducted, with molecular analyses to characterize bacterial and eukaryal microbial populations, immuno-assays to detect microbially-derived allergens and extensive environmental and meteorological observations. The data revealed bio-aerosol populations were not significantly impacted by the level of urban development as measured by anthropogenic pollutants and human population levels, but instead exhibited a strong seasonal trend related to general climatic variables. We applied back-trajectory analysis to establish sources of air masses and this allowed further explanation of urban bio-aerosols largely in terms of summer-marine and winter-continental origins. We also evaluated bio-aerosols for the potential to detect human health threats. Many samples supported bacterial and fungal phylotypes indicative of known pathogenic taxa, together with common indicators of human presence. The occurrence of allergenic endotoxins and beta-glucans generally tracked trends in microbial populations, with levels known to induce symptoms detected during summer months when microbial loading was higher. This strengthens calls for bio-aerosols to be considered in future risk assessments and surveillance of air quality, along with existing chemical and particulate indices.

Inflight Microbial Monitoring- An Alternative Method to Culture Based Detection Currently Used on the International Space Station

NASA Technical Reports Server (NTRS)

Khodadad, Christina L.; Birmele, Michele N.; Roman, Monsi; Hummerick, Mary E.; Smith, David J.; Wheeler, Raymond M.

2015-01-01

Previous research has shown that potentially destructive microorganisms and human pathogens have been detected on the International Space Station (ISS). The likelihood of introducing new microorganisms occurs with every exchange of crew or addition of equipment or supplies. Microorganisms introduced to the ISS are readily transferred between crew and subsystems (i.e. ECLSS, environmental control and life support systems). Current microbial characterization methods require enrichment of microorganisms and at least a 48-hour incubation time. This increases the microbial load while detecting only a limited number of the total microorganisms. The culture based method detects approximately 1-10% of the total organisms present and provides no identification. To identify and enumerate ISS microbes requires that samples be returned to Earth for complete analysis. Therefore, a more expedient, low-cost, in-flight method of microbial detection, identification, and enumeration is warranted. The RAZOR EX, a ruggedized, commercial off the shelf, real-time PCR field instrument was tested for its ability to detect microorganisms at low concentrations within one hour. Escherichia coli, Salmonella enterica Typhimurium, and Pseudomonas aeruginosa were detected at low levels using real-time DNA amplification. Total heterotrophic counts could also be detected using a 16S gene marker that can identify up to 98% of all bacteria. To reflect viable cells found in the samples, RNA was also detectable using a modified, single-step reverse transcription reaction.

Inflight Microbial Monitoring-An Alternative Method to Culture Based Detection Currently Used on International Space Station

NASA Technical Reports Server (NTRS)

Khodadad, Christina L.; Birmele, Michele N.; Roman, Monsi; Hummerick, Mary E.; Smith, David J.; Wheeler, Raymond M.

2015-01-01

Previous research has shown that microorganisms and potential human pathogens have been detected on the International Space Station (ISS). The potential to introduce new microorganisms occurs with every exchange of crew or addition of equipment or supplies. Previous research has shown that microorganisms introduced to the ISS are readily transferred between crew and subsystems and back (i.e. ECLSS, environmental control and life support systems). Current microbial characterization methods require enrichment of microorganisms and a 48-hour incubation time. This increases the microbial load while detecting a limited number of microorganisms. The culture based method detects approximately 1-10% of the total organisms present and provides no identification, To identify and enumerate ISS samples requires that samples to be returned to Earth for complete analysis. Therefore, a more expedient, low-cost, in-flight method of microbial detection, identification, and enumeration is warranted. The RAZOR EX, a ruggedized, commercial off the shelf, real-time PCR field instrument was tested for its ability to detect microorganism at low concentrations within one hour. Escherichia coli, Salmonella enterica Typhimurium, and Pseudomonas aeruginosa were detected at low levels using real-time DNA amplification. Total heterotrophic counts could also be detected using a 16S gene marker that can identify up to 98% of all bacteria. To reflect viable cells found in the samples, RNA was also detectable using a modified, single-step reverse transcription reaction.

Effects of cryopreservation on microbial-contaminated cord blood.

PubMed

Clark, Pamela; Trickett, Annette; Saffo, Sandra; Stark, Damien

2014-03-01

Cord blood units (CBUs) are associated with significant risk of exposure to microbial contamination during collection and processing; however, the survival of bacteria within a CBU is poorly understood. This study aimed to determine whether contaminating organisms in CBU survive the cryopreservation, frozen storage, and subsequent thawing conditions before infusion. A total of 134 CBUs rejected from banking due to known contamination were thawed and rescreened using blood culture bottles (BacT/ALERT, bioMérieux). An additional 61 fresh CBUs were deliberately spiked with a range of microbial organisms and evaluated both before freeze and after thaw. Microbial contaminants were detected after thaw in 63% of stored contaminated CBUs and 85% of spiked CBUs. Postthaw organism detection in spiked cord blood (CB) was higher in adult culture bottles (80%) than pediatric culture bottles (61%). Twenty percent of spiked organisms, particularly Bacillus subtilis, Escherichia coli, Clostridium sporogenes, and Propionibacterium acnes, were not detected in prefreeze samples but were detectable after thaw. This study demonstrates that the majority of contaminating organisms isolated in a prefreeze sample of CB have the ability to survive cryopreservation, frozen storage, and thawing. Further, CBUs reported as microbial free may contain microbial contamination, which could result in transplantation of contaminated CB and be potentially deleterious to a patient. © 2013 The Sydney Children's Hospital Network. Transfusion © 2013 American Association of Blood Banks.

[Detection of toxic substances in microbial fuel cells].

PubMed

Wang, Jiefu; Niu, Hao; Wu, Wenguo

2017-05-25

Microbial fuel cells (MFCs) is a highly promising bioelectrochemical technology and uses microorganisms as catalyst to convert chemical energy directly to electrical energy. Microorganisms in the anodic chamber of MFC oxidize the substrate and generate electrons. The electrons are absorbed by the anode and transported through an external circuit to the cathode for corresponding reduction. The flow of electrons is measured as current. This current is a linear measure of the activity of microorganisms. If a toxic event occurs, microbial activity will change, most likely decrease. Hence, fewer electrons are transported and current decreases as well. In this way, a microbial fuel cell-based biosensor provides a direct measure to detect toxicity for samples. This paper introduces the detection of antibiotics, heavy metals, organic pollutants and acid in MFCs. The existing problems and future application of MFCs are also analyzed.

Innovative biological approaches for monitoring and improving water quality

PubMed Central

Aracic, Sanja; Manna, Sam; Petrovski, Steve; Wiltshire, Jennifer L.; Mann, Gülay; Franks, Ashley E.

2015-01-01

Water quality is largely influenced by the abundance and diversity of indigenous microbes present within an aquatic environment. Physical, chemical and biological contaminants from anthropogenic activities can accumulate in aquatic systems causing detrimental ecological consequences. Approaches exploiting microbial processes are now being utilized for the detection, and removal or reduction of contaminants. Contaminants can be identified and quantified in situ using microbial whole-cell biosensors, negating the need for water samples to be tested off-site. Similarly, the innate biodegradative processes can be enhanced through manipulation of the composition and/or function of the indigenous microbial communities present within the contaminated environments. Biological contaminants, such as detrimental/pathogenic bacteria, can be specifically targeted and reduced in number using bacteriophages. This mini-review discusses the potential application of whole-cell microbial biosensors for the detection of contaminants, the exploitation of microbial biodegradative processes for environmental restoration and the manipulation of microbial communities using phages. PMID:26322034

A new rate law describing microbial respiration.

PubMed

Jin, Qusheng; Bethke, Craig M

2003-04-01

The rate of microbial respiration can be described by a rate law that gives the respiration rate as the product of a rate constant, biomass concentration, and three terms: one describing the kinetics of the electron-donating reaction, one for the kinetics of the electron-accepting reaction, and a thermodynamic term accounting for the energy available in the microbe's environment. The rate law, derived on the basis of chemiosmotic theory and nonlinear thermodynamics, is unique in that it accounts for both forward and reverse fluxes through the electron transport chain. Our analysis demonstrates how a microbe's respiration rate depends on the thermodynamic driving force, i.e., the net difference between the energy available from the environment and energy conserved as ATP. The rate laws commonly applied in microbiology, such as the Monod equation, are specific simplifications of the general law presented. The new rate law is significant because it affords the possibility of extrapolating in a rigorous manner from laboratory experiment to a broad range of natural conditions, including microbial growth where only limited energy is available. The rate law also provides a new explanation of threshold phenomena, which may reflect a thermodynamic equilibrium where the energy released by electron transfer balances that conserved by ADP phosphorylation.

NF-κB/Rel Proteins and the Humoral Immune Responses of Drosophila melanogaster

PubMed Central

Ganesan, Sandhya; Aggarwal, Kamna; Paquette, Nicholas; Silverman, Neal

2011-01-01

Nuclear Factor-κB (NF-κB)/Rel transcription factors form an integral part of innate immune defenses and are conserved throughout the animal kingdom. Studying the function, mechanism of activation and regulation of these factors is crucial for understanding host responses to microbial infections. The fruit fly Drosophila melanogaster has proved to be a valuable model system to study these evolutionarily conserved NF-κB mediated immune responses. Drosophila combats pathogens through humoral and cellular immune responses. These humoral responses are well characterized and are marked by the robust production of a battery of anti-microbial peptides. Two NF-κB signaling pathways, the Toll and the IMD pathways, are responsible for the induction of these antimicrobial peptides. Signal transduction in these pathways is strikingly similar to that in mammalian TLR pathways. In this chapter, we discuss in detail the molecular mechanisms of microbial recognition, signal transduction and NF-κB regulation, in both the Toll and the IMD pathways. Similarities and differences relative to their mammalian counterparts are discussed, and recent advances in our understanding of the intricate regulatory networks in these NF-κB signaling pathways are also highlighted. PMID:20852987

Microarray-Based Analysis of Subnanogram Quantities of Microbial Community DNAs by Using Whole-Community Genome Amplification†

PubMed Central

Wu, Liyou; Liu, Xueduan; Schadt, Christopher W.; Zhou, Jizhong

2006-01-01

Microarray technology provides the opportunity to identify thousands of microbial genes or populations simultaneously, but low microbial biomass often prevents application of this technology to many natural microbial communities. We developed a whole-community genome amplification-assisted microarray detection approach based on multiple displacement amplification. The representativeness of amplification was evaluated using several types of microarrays and quantitative indexes. Representative detection of individual genes or genomes was obtained with 1 to 100 ng DNA from individual or mixed genomes, in equal or unequal abundance, and with 1 to 500 ng community DNAs from groundwater. Lower concentrations of DNA (as low as 10 fg) could be detected, but the lower template concentrations affected the representativeness of amplification. Robust quantitative detection was also observed by significant linear relationships between signal intensities and initial DNA concentrations ranging from (i) 0.04 to 125 ng (r2 = 0.65 to 0.99) for DNA from pure cultures as detected by whole-genome open reading frame arrays, (ii) 0.1 to 1,000 ng (r2 = 0.91) for genomic DNA using community genome arrays, and (iii) 0.01 to 250 ng (r2 = 0.96 to 0.98) for community DNAs from ethanol-amended groundwater using 50-mer functional gene arrays. This method allowed us to investigate the oligotrophic microbial communities in groundwater contaminated with uranium and other metals. The results indicated that microorganisms containing genes involved in contaminant degradation and immobilization are present in these communities, that their spatial distribution is heterogeneous, and that microbial diversity is greatly reduced in the highly contaminated environment. PMID:16820490

Possibilities for the detection of microbial life on extrasolar planets.

PubMed

Knacke, Roger F

2003-01-01

We consider possibilities for the remote detection of microbial life on extrasolar planets. The Darwin/Terrestrial Planet Finder (TPF) telescope concepts for observations of terrestrial planets focus on indirect searches for life through the detection of atmospheric gases related to life processes. Direct detection of extraterrestrial life may also be possible through well-designed searches for microbial life forms. Satellites in Earth orbit routinely monitor colonies of terrestrial algae in oceans and lakes by analysis of reflected ocean light in the visible region of the spectrum. These remote sensing techniques suggest strategies for extrasolar searches for signatures of chlorophylls and related photosynthetic compounds associated with life. However, identification of such life-related compounds on extrasolar planets would require observations through strong, interfering absorptions and scattering radiances from the remote atmospheres and landmasses. Techniques for removal of interfering radiances have been extensively developed for remote sensing from Earth orbit. Comparable techniques would have to be developed for extrasolar planet observations also, but doing so would be challenging for a remote planet. Darwin/TPF coronagraph concepts operating in the visible seem to be best suited for searches for extrasolar microbial life forms with instruments that can be projected for the 2010-2020 decades, although resolution and signal-to-noise ratio constraints severely limit detection possibilities on terrestrial-type planets. The generation of telescopes with large apertures and extremely high spatial resolutions that will follow Darwin/TPF could offer striking possibilities for the direct detection of extrasolar microbial life.

A microbiology-based multi-parametric approach towards assessing biological stability in drinking water distribution networks.

PubMed

Lautenschlager, Karin; Hwang, Chiachi; Liu, Wen-Tso; Boon, Nico; Köster, Oliver; Vrouwenvelder, Hans; Egli, Thomas; Hammes, Frederik

2013-06-01

Biological stability of drinking water implies that the concentration of bacterial cells and composition of the microbial community should not change during distribution. In this study, we used a multi-parametric approach that encompasses different aspects of microbial water quality including microbial growth potential, microbial abundance, and microbial community composition, to monitor biological stability in drinking water of the non-chlorinated distribution system of Zürich. Drinking water was collected directly after treatment from the reservoir and in the network at several locations with varied average hydraulic retention times (6-52 h) over a period of four months, with a single repetition two years later. Total cell concentrations (TCC) measured with flow cytometry remained remarkably stable at 9.5 (± 0.6) × 10(4) cells/ml from water in the reservoir throughout most of the distribution network, and during the whole time period. Conventional microbial methods like heterotrophic plate counts, the concentration of adenosine tri-phosphate, total organic carbon and assimilable organic carbon remained also constant. Samples taken two years apart showed more than 80% similarity for the microbial communities analysed with denaturing gradient gel electrophoresis and 454 pyrosequencing. Only the two sampling locations with the longest water retention times were the exceptions and, so far for unknown reasons, recorded a slight but significantly higher TCC (1.3 (± 0.1) × 10(5) cells/ml) compared to the other locations. This small change in microbial abundance detected by flow cytometry was also clearly observed in a shift in the microbial community profiles to a higher abundance of members from the Comamonadaceae (60% vs. 2% at other locations). Conventional microbial detection methods were not able to detect changes as observed with flow cytometric cell counts and microbial community analysis. Our findings demonstrate that the multi-parametric approach used provides a powerful and sensitive tool to assess and evaluate biological stability and microbial processes in drinking water distribution systems. Copyright © 2013 Elsevier Ltd. All rights reserved.

Biodiversity of the microbial mat of the Garga hot spring.

PubMed

Rozanov, Alexey Sergeevich; Bryanskaya, Alla Victorovna; Ivanisenko, Timofey Vladimirovich; Malup, Tatyana Konstantinovna; Peltek, Sergey Evgenievich

2017-12-28

Microbial mats are a good model system for ecological and evolutionary analysis of microbial communities. There are more than 20 alkaline hot springs on the banks of the Barguzin river inflows. Water temperature reaches 75 °C and pH is usually 8.0-9.0. The formation of microbial mats is observed in all hot springs. Microbial communities of hot springs of the Baikal rift zone are poorly studied. Garga is the biggest hot spring in this area. In this study, we investigated bacterial and archaeal diversity of the Garga hot spring (Baikal rift zone, Russia) using 16S rRNA metagenomic sequencing. We studied two types of microbial communities: (i) small white biofilms on rocks in the points with the highest temperature (75 °C) and (ii) continuous thick phototrophic microbial mats observed at temperatures below 70 °C. Archaea (mainly Crenarchaeota; 19.8% of the total sequences) were detected only in the small biofilms. The high abundance of Archaea in the sample from hot springs of the Baikal rift zone supplemented our knowledge of the distribution of Archaea. Most archaeal sequences had low similarity to known Archaea. In the microbial mats, primary products were formed by cyanobacteria of the genus Leptolyngbya. Heterotrophic microorganisms were mostly represented by Actinobacteria and Proteobacteria in all studied samples of the microbial mats. Planctomycetes, Chloroflexi, and Chlorobi were abundant in the middle layer of the microbial mats, while heterotrophic microorganisms represented mostly by Firmicutes (Clostridia, strict anaerobes) dominated in the bottom part. Besides prokaryotes, we detect some species of Algae with help of detection their chloroplasts 16 s rRNA. High abundance of Archaea in samples from hot springs of the Baikal rift zone supplemented our knowledge of the distribution of Archaea. Most archaeal sequences had low similarity to known Archaea. Metagenomic analysis of microbial communities of the microbial mat of Garga hot spring showed that the three studied points sampled at 70 °C, 55 °C, and 45 °C had similar species composition. Cyanobacteria of the genus Leptolyngbya dominated in the upper layer of the microbial mat. Chloroflexi and Chlorobi were less abundant and were mostly observed in the middle part of the microbial mat. We detected domains of heterotrophic organisms in high abundance (Proteobacteria, Firmicutes, Verrucomicrobia, Planctomicetes, Bacteroidetes, Actinobacteria, Thermi), according to metabolic properties of known relatives, which can form complete cycles of carbon, sulphur, and nitrogen in the microbial mat. The studied microbial mats evolved in early stages of biosphere formation. They can live autonomously, providing full cycles of substances and preventing live activity products poisoning.

Cloning, expression and phylogenetic analysis of Hemolin, from the Chinese oak silkmoth, Antheraea pernyi.

PubMed

Li, Wenli; Terenius, Olle; Hirai, Makoto; Nilsson, Anders S; Faye, Ingrid

2005-01-01

The Chinese oak silk moth Antheraea pernyi is an important silk producer. To understand microbial resistance of this moth, we cloned Hemolin, encoding a multifunctional immune protein belonging to the immunoglobulin superfamily, and examined the expression in gonads and fat body. The ApHemolin amino acid sequence was compared to other Hemolin sequences in order to predict functional sites. Several sites were conserved; among them a phosphate binding site, which according to 3D structure modelling does not appear in neuroglian, the phylogenetically closest related protein. In addition, two conserved KDG sequences in the C-C' loop of immunoglobulin domains 1 and 3, give rise to gamma-turns, which is a common motif in the C'-C'' loop of the hypervariable region L2 in vertebrate immunoglobulins. The comparisons also show variable regions of specific interest for future studies of hemolin and its interaction with microbial entities.

Long-term no-tillage and organic input management enhanced the diversity and stability of soil microbial community.

PubMed

Wang, Yi; Li, Chunyue; Tu, Cong; Hoyt, Greg D; DeForest, Jared L; Hu, Shuijin

2017-12-31

Intensive tillage and high inputs of chemicals are frequently used in conventional agriculture management, which critically depresses soil properties and causes soil erosion and nonpoint source pollution. Conservation practices, such as no-tillage and organic farming, have potential to enhance soil health. However, the long-term impact of no-tillage and organic practices on soil microbial diversity and community structure has not been fully understood, particularly in humid, warm climate regions such as the southeast USA. We hypothesized that organic inputs will lead to greater microbial diversity and a more stable microbial community, and that the combination of no-tillage and organic inputs will maximize soil microbial diversity. We conducted a long-term experiment in the southern Appalachian mountains of North Carolina, USA to test these hypotheses. The results showed that soil microbial diversity and community structure diverged under different management regimes after long term continuous treatments. Organic input dominated the effect of management practices on soil microbial properties, although no-tillage practice also exerted significant impacts. Both no-tillage and organic inputs significantly promoted soil microbial diversity and community stability. The combination of no-tillage and organic management increased soil microbial diversity over the conventional tillage and led to a microbial community structure more similar to the one in an adjacent grassland. These results indicate that effective management through reducing tillage and increasing organic C inputs can enhance soil microbial diversity and community stability. Copyright © 2017 Elsevier B.V. All rights reserved.

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

PubMed

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

2016-09-01

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

Bacterial profiling of White Plague Disease across corals and oceans indicates a conserved and distinct disease microbiome

PubMed Central

Roder, Cornelia; Arif, Chatchanit; Daniels, Camille; Weil, Ernesto; Voolstra, Christian R

2014-01-01

Coral diseases are characterized by microbial community shifts in coral mucus and tissue, but causes and consequences of these changes are vaguely understood due to the complexity and dynamics of coral-associated bacteria. We used 16S rRNA gene microarrays to assay differences in bacterial assemblages of healthy and diseased colonies displaying White Plague Disease (WPD) signs from two closely related Caribbean coral species, Orbicella faveolata and Orbicella franksi. Analysis of differentially abundant operational taxonomic units (OTUs) revealed strong differences between healthy and diseased specimens, but not between coral species. A subsequent comparison to data from two Indo-Pacific coral species (Pavona duerdeni and Porites lutea) revealed distinct microbial community patterns associated with ocean basin, coral species and health state. Coral species were clearly separated by site, but also, the relatedness of the underlying bacterial community structures resembled the phylogenetic relationship of the coral hosts. In diseased samples, bacterial richness increased and putatively opportunistic bacteria were consistently more abundant highlighting the role of opportunistic conditions in structuring microbial community patterns during disease. Our comparative analysis shows that it is possible to derive conserved bacterial footprints of diseased coral holobionts that might help in identifying key bacterial species related to the underlying etiopathology. Furthermore, our data demonstrate that similar-appearing disease phenotypes produce microbial community patterns that are consistent over coral species and oceans, irrespective of the putative underlying pathogen. Consequently, profiling coral diseases by microbial community structure over multiple coral species might allow the development of a comparative disease framework that can inform on cause and relatedness of coral diseases. PMID:24350609

Microbial survey of the mummies from the Capuchin Catacombs of Palermo, Italy: biodeterioration risk and contamination of the indoor air.

PubMed

Piñar, Guadalupe; Piombino-Mascali, Dario; Maixner, Frank; Zink, Albert; Sterflinger, Katja

2013-11-01

The Capuchin Catacombs of Palermo contain over 1800 preserved bodies dating from the 16th to 20th centuries AD and showing evidence of biodeterioration. An extensive microbiological and molecular investigation was recently performed. Samples were taken from skin, muscle, hair, bone, stuffing materials, clothes, and surrounding walls as well as from the indoor air. In this study, we witnessed that the different degradation phenomena observed on the variety of materials located at the Capuchin Catacombs of Palermo are biological in origin. Molecular techniques showed the dominance of halophilic species of the domains Bacteria and Archaea on the walls and - as a result of salt emanating from the walls - on the mummies themselves. Nevertheless, specialized microorganisms belonging to taxa well-known for their cellulolytic and proteolytic activities were detected on clothes and stuffing material, and on skin, muscle, hair, and bone, respectively. This specialized microbiota is threatening the conservation of the mummies themselves. Additionally, sequences related to the human skin microbiome and to some pathogenic Bacteria (order Clostridiales) and fungi (genus Phialosimplex) were identified on samples derived from the mummies. Furthermore, a phosphate-reducing fungus, Penicillium radicum, was detected on bone. Finally, the high concentration of airborne fungal spores is not conducive to the conservation of the human remains and is posing a potential health risk for visitors. © 2013 The Authors. FEMS Microbiology Ecology published by John Wiley & Sons Ltd on behalf of the Federation of European Microbiological Societies.

Detecting contaminating microorganism in human food and water from Raman mapping through biofilms

USDA-ARS?s Scientific Manuscript database

Detecting microbial growth can help experts determine how to prevent the outbreaks especially if human food or water has been contaminated. Biofilms are a group of microbial cells that can either grow on living surfaces or surrounding themselves as they progress. Biofilms are not necessarily uniform...

Why does carbon increase in highly weathered soil under no-till upon lime and gypsum use?

PubMed

Inagaki, Thiago Massao; de Moraes Sá, João Carlos; Caires, Eduardo Fávero; Gonçalves, Daniel Ruiz Potma

2017-12-01

Field experiments have been used to explain how soil organic carbon (SOC) dynamics is affected by lime and gypsum applications, however, how SOC storage occurs is still debatable. We hypothesized that although many studies conclude that Ca-based soil amendments such as lime and gypsum may lead to SOC depletion due to the enhancement of microbial activity, the same does not occur under conservation agriculture conditions. Thus, the objective of this study was to elucidate the effects of lime and gypsum applications on soil microbial activity and SOC stocks in a no-till field and in a laboratory incubation study simulating no-till conditions. The field experiment was established in 1998 in a clayey Oxisol in southern Brazil following a completely randomized blocks design with a split-plot arrangement and three replications. Lime and gypsum were surface applied in 1998 and reapplied in 2013. Undisturbed soil samples were collected before the treatments reapplications, and one year after. The incubation experiment was carried out during 16months using these samples adding crop residues on the soil surface to simulate no-till field conditions. Lime and gypsum applications significantly increased the labile SOC stocks, microbial activity and soil fertility attributes in both field and laboratory experiments. Although the microbial activity was increased, no depletion of SOC stocks was observed in both experiments. Positive correlations were observed between microbial activity increase and SOC gains. Labile SOC and Ca 2+ content increase leads to forming complex with mineral soil fractions. Gypsum applications performed a higher influence on labile SOC pools in the field than in the laboratory experiment, which may be related to the presence of active root system in the soil profile. We conclude that incubation experiments using lime and gypsum in undisturbed samples confirm that soil microbial activity increase does not deplete SOC stocks under conservation agriculture. Copyright © 2017 Elsevier B.V. All rights reserved.

Monitoring of oil hydrocarbons pollution in the Sea of Japan, based on detection of marker genes in microbial communities

NASA Astrophysics Data System (ADS)

Kim, A. V.; Buzoleva, L. S.; Bogatyrenko, E. A.; Zemskaya, T. I.; Mamaeva, E. V.

2018-01-01

By means of molecular biology techniques, metabolic potential of microbial communities within the regions of inshore water areas in the Sea of Japan with various anthropogenic load was explored. Presence of functional genes, responsible for oil hydrocarbons destruction, for microbial communities within the regions of inshore water areas in the Sea of Japan was first researched. In total microbial DNA from water mass in the regions with chronic anthropogenic pollution, the genes, responsible for oxidation of broad range of n-alkanes and polycyclic aromatic hydrocarbons, were found. Detection of marker genes in the background water area (in the Vostok Bay) was ever indicating ecological deterioration within this territory. Thereby, it was demonstrated, that molecular genetic methods, aimed at marker gene detection in total bacterial DNA from environment objects, proved themselves to be more effective technique for identification of oil hydrocarbons water pollution, in comparison with trivial culturable methods.

Challenging a bioinformatic tool's ability to detect microbial contaminants using in silico whole genome sequencing data.

PubMed

Olson, Nathan D; Zook, Justin M; Morrow, Jayne B; Lin, Nancy J

2017-01-01

High sensitivity methods such as next generation sequencing and polymerase chain reaction (PCR) are adversely impacted by organismal and DNA contaminants. Current methods for detecting contaminants in microbial materials (genomic DNA and cultures) are not sensitive enough and require either a known or culturable contaminant. Whole genome sequencing (WGS) is a promising approach for detecting contaminants due to its sensitivity and lack of need for a priori assumptions about the contaminant. Prior to applying WGS, we must first understand its limitations for detecting contaminants and potential for false positives. Herein we demonstrate and characterize a WGS-based approach to detect organismal contaminants using an existing metagenomic taxonomic classification algorithm. Simulated WGS datasets from ten genera as individuals and binary mixtures of eight organisms at varying ratios were analyzed to evaluate the role of contaminant concentration and taxonomy on detection. For the individual genomes the false positive contaminants reported depended on the genus, with Staphylococcus , Escherichia , and Shigella having the highest proportion of false positives. For nearly all binary mixtures the contaminant was detected in the in-silico datasets at the equivalent of 1 in 1,000 cells, though F. tularensis was not detected in any of the simulated contaminant mixtures and Y. pestis was only detected at the equivalent of one in 10 cells. Once a WGS method for detecting contaminants is characterized, it can be applied to evaluate microbial material purity, in efforts to ensure that contaminants are characterized in microbial materials used to validate pathogen detection assays, generate genome assemblies for database submission, and benchmark sequencing methods.

PanCoreGen - Profiling, detecting, annotating protein-coding genes in microbial genomes.

PubMed

Paul, Sandip; Bhardwaj, Archana; Bag, Sumit K; Sokurenko, Evgeni V; Chattopadhyay, Sujay

2015-12-01

A large amount of genomic data, especially from multiple isolates of a single species, has opened new vistas for microbial genomics analysis. Analyzing the pan-genome (i.e. the sum of genetic repertoire) of microbial species is crucial in understanding the dynamics of molecular evolution, where virulence evolution is of major interest. Here we present PanCoreGen - a standalone application for pan- and core-genomic profiling of microbial protein-coding genes. PanCoreGen overcomes key limitations of the existing pan-genomic analysis tools, and develops an integrated annotation-structure for a species-specific pan-genomic profile. It provides important new features for annotating draft genomes/contigs and detecting unidentified genes in annotated genomes. It also generates user-defined group-specific datasets within the pan-genome. Interestingly, analyzing an example-set of Salmonella genomes, we detect potential footprints of adaptive convergence of horizontally transferred genes in two human-restricted pathogenic serovars - Typhi and Paratyphi A. Overall, PanCoreGen represents a state-of-the-art tool for microbial phylogenomics and pathogenomics study. Copyright © 2015 Elsevier Inc. All rights reserved.

Impact of the reusing of food manufacturing wastewater for irrigation in a closed system on the microbiological quality of the food crops.

PubMed

Beneduce, Luciano; Gatta, Giuseppe; Bevilacqua, Antonio; Libutti, Angela; Tarantino, Emanuele; Bellucci, Micol; Troiano, Eleonora; Spano, Giuseppe

2017-11-02

In order to evaluate if the reuse of food industry treated wastewater is compatible for irrigation of food crops, without increased health risk, in the present study a cropping system, in which ground water and treated wastewater were used for irrigation of tomato and broccoli, during consecutive crop seasons was monitored. Water, crop environment and final products were monitored for microbial indicators and pathogenic bacteria, by conventional and molecular methods. The microbial quality of the irrigation waters influenced sporadically the presence of microbial indicators in soil. No water sample was found positive for pathogenic bacteria, independently from the source. Salmonella spp. and Listeria monocytogenes were detected in soil samples, independently from the irrigation water source. No pathogen was found to contaminate tomato plants, while Listeria monocytogenes and E. coli O157:H7 were detected on broccoli plant, but when final produce were harvested, no pathogen was detected on edible part. The level of microbial indicators and detection of pathogenic bacteria in field and plant was not dependent upon wastewater used. Our results, suggest that reuse of food industry wastewater for irrigation of agricultural crop can be applied without significant increase of potential health risk related to microbial quality. Copyright © 2017 Elsevier B.V. All rights reserved.

In situ microbial detection in Mojave Desert soil using native fluorescence.

PubMed

Smith, H D; Duncan, A G; Neary, P L; Lloyd, C R; Anderson, A J; Sims, R C; McKay, C P

2012-03-01

We report on the use of a portable instrument for microbial detection in the Mojave Desert soil and the potential for its use on Mars. The instrument is based on native fluorescence and employs four excitation wavelengths combined with four emission wavelengths. A soil dilution series in which known numbers of Bacillus subtilis spores were added to soil was used to determine the sensitivity of the instrument. We found that the fluorescence of the biological and organic components of the desert soil samples studied can be as strong as the fluorescence of the mineral component of these soils. Using the calibration derived from B. subtilis spores, we estimated that microbial content at our primary sampling site was 10(7) bacteria per gram of soil, a level confirmed by phospholipid fatty acid analysis. At a nearby site, but in a slightly different geological setting, we tested the instrument's ability to map out microbial concentrations in situ. Over a ∼50 m diameter circle, soil microbial concentrations determined with the B. subtilis calibration indicate that the concentrations of microorganisms detected varies from 10(4) to 10(7) cells per gram of soil. We conclude that fluorescence is a promising method for detecting soil microbes in noncontact applications in extreme environments on Earth and may have applications on future missions to Mars.

Using 13C labeled glucose to determine soil microbial and physical controls of new C incorporation under drying-rewetting cycles and conservation agricultural management

NASA Astrophysics Data System (ADS)

Li, L.; Schaeffer, S. M.

2017-12-01

Drying-rewetting cycles can induce carbon (C) depletion in soil, while conservation agricultural management aims at soil C sequestration. Understanding the combined effect of drying-rewetting cycles and conservation management is critical for sustaining agricultural soil under climate change. Soil organic C can be stored in a relatively rapidly cycling active pool, or a more slowly cycling passive pool. We conducted a 24-days mesocosm incubation using an agricultural soil from western Tennessee under 35-years of conservation management. Different lengths of drought period before rewetting of 0, 3, 6, and 24 days were applied on the mesocosms. To trace the fate of newly added C, 13C labeled glucose was added to the mesocosms at the beginning of the incubation. After 24 days, dissolvable organic C, microbial biomass C, accumulative microbial respiration, and extracellular enzyme activity were analyzed to evaluate the active C pool; hydrogen peroxide oxidation and aggregate size fractionation were used to examine the passive C pool. The highest cumulative microbial respiration was found in the 6-days treatment combining a N-fixing cover crop with no-tillage, and the lowest in the 24-day treatment with a wheat cover crop combined with conventional-tillage (1000.0±20.5 and 106.8±17.5 µg C-CO2 g-1 dry soil, respectively). The 6-days treatment induced 0.5-4.3 times higher cumulative C-CO2 emission than the 3-days treatment. The proportion of macroaggregates in bulk soil varied between 97.2% and 76.7%, and it was negatively correlated with drying-rewetting frequency. The proportion of microaggregates in bulk soil varied between 21.9% and 2.1%, and it was positively correlated with drying-rewetting frequency. 13C recovery rate in bulk soil varied between 11-53%. The vetch-cover-crop-with-no-tillage treatment facilitated 13C accumulation the most. Our results show that the N fixing cover crops combined with no-tillage treatment induced the highest C accumulation in bulk soil, while the no cover crop combined with conventional tillage induced the lowest C concentration. Our results show that frequent drying-rewetting cycles disrupt macroaggregates and release the microaggregates within macroaggregates, and favor greater C loss combined with greater C storage in less stable aggregate fractions.

Biodiversity of air-borne microorganisms at Halley Station, Antarctica.

PubMed

Pearce, David A; Hughes, K A; Lachlan-Cope, T; Harangozo, S A; Jones, A E

2010-03-01

A study of air-borne microbial biodiversity over an isolated scientific research station on an ice-shelf in continental Antarctica was undertaken to establish the potential source of microbial colonists. The study aimed to assess: (1) whether microorganisms were likely to have a local (research station) or distant (marine or terrestrial) origin, (2) the effect of changes in sea ice extent on microbial biodiversity and (3) the potential human impact on the environment. Air samples were taken above Halley Research Station during the austral summer and austral winter over a 2-week period. Overall, a low microbial biodiversity was detected, which included many sequence replicates. No significant patterns were detected in the aerial biodiversity between the austral summer and the austral winter. In common with other environmental studies, particularly in the polar regions, many of the sequences obtained were from as yet uncultivated organisms. Very few marine sequences were detected irrespective of the distance to open water, and around one-third of sequences detected were similar to those identified in human studies, though both of these might reflect prevailing wind conditions. The detected aerial microorganisms were markedly different from those obtained in earlier studies over the Antarctic Peninsula in the maritime Antarctic.

Microbial Composition of Near-Boiling Silica-Depositing Thermal Springs throughout Yellowstone National Park

PubMed Central

Blank, Carrine E.; Cady, Sherry L.; Pace, Norman R.

2002-01-01

The extent of hyperthermophilic microbial diversity associated with siliceous sinter (geyserite) was characterized in seven near-boiling silica-depositing springs throughout Yellowstone National Park using environmental PCR amplification of small-subunit rRNA genes (SSU rDNA), large-subunit rDNA, and the internal transcribed spacer (ITS). We found that Thermocrinis ruber, a member of the order Aquificales, is ubiquitous, an indication that primary production in these springs is driven by hydrogen oxidation. Several other lineages with no known close relatives were identified that branch among the hyperthermophilic bacteria. Although they all branch deep in the bacterial tree, the precise phylogenetic placement of many of these lineages is unresolved at this time. While some springs contained a fair amount of phylogenetic diversity, others did not. Within the same spring, communities in the subaqueous environment were not appreciably different than those in the splash zone at the edge of the pool, although a greater number of phylotypes was found along the pool's edge. Also, microbial community composition appeared to have little correlation with the type of sinter morphology. The number of cell morphotypes identified by fluorescence in situ hybridization and scanning electron microscopy was greater than the number of phylotypes in SSU clone libraries. Despite little variation in Thermocrinis ruber SSU sequences, abundant variation was found in the hypervariable ITS region. The distribution of ITS sequence types appeared to be correlated with distinct morphotypes of Thermocrinis ruber in different pools. Therefore, species- or subspecies-level divergences are present but not detectable in highly conserved SSU sequences. PMID:12324363

Microbial Communities and Bioactive Compounds in Marine Sponges of the Family Irciniidae—A Review

PubMed Central

Hardoim, Cristiane C. P.; Costa, Rodrigo

2014-01-01

Marine sponges harbour complex microbial communities of ecological and biotechnological importance. Here, we propose the application of the widespread sponge family Irciniidae as an appropriate model in microbiology and biochemistry research. Half a gram of one Irciniidae specimen hosts hundreds of bacterial species—the vast majority of which are difficult to cultivate—and dozens of fungal and archaeal species. The structure of these symbiont assemblages is shaped by the sponge host and is highly stable over space and time. Two types of quorum-sensing molecules have been detected in these animals, hinting at microbe-microbe and host-microbe signalling being important processes governing the dynamics of the Irciniidae holobiont. Irciniids are vulnerable to disease outbreaks, and concerns have emerged about their conservation in a changing climate. They are nevertheless amenable to mariculture and laboratory maintenance, being attractive targets for metabolite harvesting and experimental biology endeavours. Several bioactive terpenoids and polyketides have been retrieved from Irciniidae sponges, but the actual producer (host or symbiont) of these compounds has rarely been clarified. To tackle this, and further pertinent questions concerning the functioning, resilience and physiology of these organisms, truly multi-layered approaches integrating cutting-edge microbiology, biochemistry, genetics and zoology research are needed. PMID:25272328

Exploitation of microbial forensics and nanotechnology for the monitoring of emerging pathogens.

PubMed

Bokhari, Habib

2018-03-07

Emerging infectious diseases remain among the leading causes of global mortality. Traditional laboratory diagnostic approaches designed to detect and track infectious disease agents provide a framework for surveillance of bio threats. However, surveillance and outbreak investigations using such time-consuming approaches for early detection of pathogens remain the major pitfall. Hence, reasonable real-time surveillance systems to anticipate threats to public health and environment are critical for identifying specific aetiologies and preventing the global spread of infectious disease. The current review discusses the growing need for monitoring and surveillance of pathogens with the same zeal and approach as adopted by microbial forensics laboratories, and further strengthening it by integrating with the innovative nanotechnology for rapid detection of microbial pathogens. Such innovative diagnostics platforms will help to track pathogens from high risk areas and environment by pre-emptive approach that will minimize damages. The various scenarios with the examples are discussed where the high risk associated human pathogens in particular were successfully detected using various nanotechnology approaches with potential future prospects in the field of microbial forensics.

Detection of antibiotics in goat's milk: effect of detergents on the response of microbial inhibitor tests.

PubMed

Romero, Tamara; Beltrán, María Carmen; Althaus, Rafael Lisandro; Molina, María Pilar

2014-08-01

The aim of the study was to evaluate the interference of acid and alkaline detergents employed in the cleaning of milking equipment of caprine dairy farms on the performance of microbial tests used in antibiotic control (BRT MRL, Delvotest MCS, and Eclipse 100). Eight concentrations of commercial detergents, five acid (0-0.25%) and five alkaline (0-1%) were add to antimicrobial-free goat's milk to evaluate the detergent effect on the response of microbial inhibitor tests. To evaluate the effect of detergents on the detection capability of microbial tests two detergents at 0.5 ml/l (one acid and one basic) and eight concentrations of four β-lactam antibiotics (ampicillin, amoxicillin, cloxacillin and benzylpenicillin) were used. Milk without detergents was used as control. The spiked samples were analysed twelve times by three microbial tests. The results showed that the presence of acid detergents did not affect the response of microbial tests for any of the concentrations tested. However, at concentrations equal to or greater than 2 ml/l alkaline detergents positive results were found in microbial tests (16.7-100%). The detection limits of the screening tests for penicillins were not modified substantially by the presence of detergents. In general, the presence of acid and alkaline detergents in goat's milk did not produce a great interference in the microbial tests, only high concentrations of detergents could cause non-compliant results, but these concentrations are difficult to find in practice if proper cleaning procedures are applied in goat dairy farms.

A multiplex real-time polymerase chain reaction assay with two internal controls for the detection of Brucella species in tissues, blood, and feces from marine mammals.

PubMed

Sidor, Inga F; Dunn, J Lawrence; Tsongalis, Gregory J; Carlson, Jolene; Frasca, Salvatore

2013-01-01

Brucellosis has emerged as a disease of concern in marine mammals in the last 2 decades. Molecular detection techniques have the potential to address limitations of other methods for detecting infection with Brucella in these species. Presented herein is a real-time polymerase chain reaction (PCR) method targeting the Brucella genus-specific bcsp31 gene. The method also includes a target to a conserved region of the eukaryotic mitochondrial 16S ribosomal RNA gene to assess suitability of extracted DNA and a plasmid-based internal control to detect failure of PCR due to inhibition. This method was optimized and validated to detect Brucella spp. in multiple sample matrices, including fresh or frozen tissue, blood, and feces. The analytical limit of detection was low, with 95% amplification at 24 fg, or an estimated 7 bacterial genomic copies. When Brucella spp. were experimentally added to tissue or fecal homogenates, the assay detected an estimated 1-5 bacteria/µl. An experiment simulating tissue autolysis showed relative persistence of bacterial DNA compared to host mitochondrial DNA. When used to screen 1,658 field-collected marine mammal tissues in comparison to microbial culture, diagnostic sensitivity and specificity were 70.4% and 98.3%, respectively. In addition to amplification in fresh and frozen tissues, Brucella spp. were detected in feces and formalin-fixed, paraffin-embedded tissues from culture-positive animals. Results indicate the utility of this real-time PCR for the detection of Brucella spp. in marine species, which may have applications in surveillance or epidemiologic investigations.

Ecology and exploration of the rare biosphere.

PubMed

Lynch, Michael D J; Neufeld, Josh D

2015-04-01

The profound influence of microorganisms on human life and global biogeochemical cycles underlines the value of studying the biogeography of microorganisms, exploring microbial genomes and expanding our understanding of most microbial species on Earth: that is, those present at low relative abundance. The detection and subsequent analysis of low-abundance microbial populations—the 'rare biosphere'—have demonstrated the persistence, population dynamics, dispersion and predation of these microbial species. We discuss the ecology of rare microbial populations, and highlight molecular and computational methods for targeting taxonomic 'blind spots' within the rare biosphere of complex microbial communities.

Characterizing The Microbial Lability And Isotopic (14C, 13C) Signatures Of Marine Organic Matter With A Novel Culture Vessel System

NASA Astrophysics Data System (ADS)

Beaupre, S. R.; Mahmoudi, N.; Pearson, A.

2016-02-01

The rate at which non-living organic matter is respired in the ocean is an unconstrained and important property of the marine carbon cycle. Studies of inherent mineralization rates are complicated by the fact that marine organic matter is a mixture of compounds that vary in reactivity and concentration. While natural radiocarbon ages (14C, half-life = 5730 yr) have served as proxies for lability, they have not been used extensively to characterize that fraction of marine organic matter that is biologically accessible. To address this problem, we developed a novel batch culture system to monitor the time-dependent production rates and isotopic signatures of CO2 released during microbial degradation of natural organic matter. The system simulated a nepheloid layer by maintaining a slurry of decarbonated sediment and minimal media (M9) in a custom 2-liter culture vessel. The natural microbial community was allowed to develop within the sediment, and respired CO2 was continuously sparged from the medium with helium and oxygen, quantified in real time with an infrared gas analyzer, and isolated as a series of contiguous fractions for subsequent isotopic (∆14C, d13C) characterization. Control experiments indicated the accumulation of just 4.5 mg of background carbon per hour of continuous gas flow, which constituted ≤ 10 % of the respired carbon mass in each fraction. Since ∆14C values are conserved during molecular transformations, this low-blank system enables the detection of subtle shifts in the "age" of organic matter respired during the course of a culture experiment. Analyses of sediments from Falmouth, MA revealed both a variable CO2 production rate and an increase in post-bomb ∆14C values during a 10-day incubation. This suggests that the microbial lability of organic matter at this site decreased non-linearly with apparent 14C age, and that the least labile fraction observed was not more than 50 years old. These results underscore the complex relationship between microbial communities, organic matter composition, and its 14C age distribution.

Field Analysis of Microbial Contamination Using Three Molecular Methods in Parallel

NASA Technical Reports Server (NTRS)

Morris, H.; Stimpson, E.; Schenk, A.; Kish, A.; Damon, M.; Monaco, L.; Wainwright, N.; Steele, A.

2010-01-01

Advanced technologies with the capability of detecting microbial contamination remain an integral tool for the next stage of space agency proposed exploration missions. To maintain a clean, operational spacecraft environment with minimal potential for forward contamination, such technology is a necessity, particularly, the ability to analyze samples near the point of collection and in real-time both for conducting biological scientific experiments and for performing routine monitoring operations. Multiple molecular methods for detecting microbial contamination are available, but many are either too large or not validated for use on spacecraft. Two methods, the adenosine- triphosphate (ATP) and Limulus Amebocyte Lysate (LAL) assays have been approved by the NASA Planetary Protection Office for the assessment of microbial contamination on spacecraft surfaces. We present the first parallel field analysis of microbial contamination pre- and post-cleaning using these two methods as well as universal primer-based polymerase chain reaction (PCR).

Terroir is a key driver of seed-associated microbial assemblages.

PubMed

Klaedtke, Stephanie; Jacques, Marie-Agnès; Raggi, Lorenzo; Préveaux, Anne; Bonneau, Sophie; Negri, Valeria; Chable, Véronique; Barret, Matthieu

2016-06-01

Seeds have evolved in association with diverse microbial assemblages that may influence plant growth and health. However, little is known about the composition of seed-associated microbial assemblages and the ecological processes shaping their structures. In this work, we monitored the relative influence of the host genotypes and terroir on the structure of the seed microbiota through metabarcoding analysis of different microbial assemblages associated to five different bean cultivars harvested in two distinct farms. Overall, few bacterial and fungal operational taxonomic units (OTUs) were conserved across all seed samples. The lack of shared OTUs between samples is explained by a significant effect of the farm site on the structure of microbial assemblage, which explained 12.2% and 39.7% of variance in bacterial and fungal diversity across samples. This site-specific effect is reflected by the significant enrichment of 70 OTUs in Brittany and 88 OTUs in Luxembourg that lead to differences in co-occurrence patterns. In contrast, variance in microbial assemblage structure was not explained by host genotype. Altogether, these results suggest that seed-associated microbial assemblage is determined by niche-based processes and that the terroir is a key driver of these selective forces. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

New directions in coral reef microbial ecology.

PubMed

Garren, Melissa; Azam, Farooq

2012-04-01

Microbial processes largely control the health and resilience of coral reef ecosystems, and new technologies have led to an exciting wave of discovery regarding the mechanisms by which microbial communities support the functioning of these incredibly diverse and valuable systems. There are three questions at the forefront of discovery: What mechanisms underlie coral reef health and resilience? How do environmental and anthropogenic pressures affect ecosystem function? What is the ecology of microbial diseases of corals? The goal is to understand the functioning of coral reefs as integrated systems from microbes and molecules to regional and ocean-basin scale ecosystems to enable accurate predictions of resilience and responses to perturbations such as climate change and eutrophication. This review outlines recent discoveries regarding the microbial ecology of different microenvironments within coral ecosystems, and highlights research directions that take advantage of new technologies to build a quantitative and mechanistic understanding of how coral health is connected through microbial processes to its surrounding environment. The time is ripe for natural resource managers and microbial ecologists to work together to create an integrated understanding of coral reef functioning. In the context of long-term survival and conservation of reefs, the need for this work is immediate. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

Challenging a bioinformatic tool’s ability to detect microbial contaminants using in silico whole genome sequencing data

PubMed Central

Zook, Justin M.; Morrow, Jayne B.; Lin, Nancy J.

2017-01-01

High sensitivity methods such as next generation sequencing and polymerase chain reaction (PCR) are adversely impacted by organismal and DNA contaminants. Current methods for detecting contaminants in microbial materials (genomic DNA and cultures) are not sensitive enough and require either a known or culturable contaminant. Whole genome sequencing (WGS) is a promising approach for detecting contaminants due to its sensitivity and lack of need for a priori assumptions about the contaminant. Prior to applying WGS, we must first understand its limitations for detecting contaminants and potential for false positives. Herein we demonstrate and characterize a WGS-based approach to detect organismal contaminants using an existing metagenomic taxonomic classification algorithm. Simulated WGS datasets from ten genera as individuals and binary mixtures of eight organisms at varying ratios were analyzed to evaluate the role of contaminant concentration and taxonomy on detection. For the individual genomes the false positive contaminants reported depended on the genus, with Staphylococcus, Escherichia, and Shigella having the highest proportion of false positives. For nearly all binary mixtures the contaminant was detected in the in-silico datasets at the equivalent of 1 in 1,000 cells, though F. tularensis was not detected in any of the simulated contaminant mixtures and Y. pestis was only detected at the equivalent of one in 10 cells. Once a WGS method for detecting contaminants is characterized, it can be applied to evaluate microbial material purity, in efforts to ensure that contaminants are characterized in microbial materials used to validate pathogen detection assays, generate genome assemblies for database submission, and benchmark sequencing methods. PMID:28924496

Microbial fuel cells for biosensor applications.

PubMed

Yang, Huijia; Zhou, Minghua; Liu, Mengmeng; Yang, Weilu; Gu, Tingyue

2015-12-01

Microbial fuel cells (MFCs) face major hurdles for real-world applications as power generators with the exception of powering small sensor devices. Despite tremendous improvements made in the last two decades, MFCs are still too expensive to build and operate and their power output is still too small. In view of this, in recently years, intensive researches have been carried out to expand the applications into other areas such as acid and alkali production, bioremediation of aquatic sediments, desalination and biosensors. Unlike power applications, MFC sensors have the immediate prospect to be practical. This review covers the latest developments in various proposed biosensor applications using MFCs including monitoring microbial activity, testing biochemical oxygen demand, detection of toxicants and detection of microbial biofilms that cause biocorrosion.

A New Rate Law Describing Microbial Respiration

PubMed Central

Jin, Qusheng; Bethke, Craig M.

2003-01-01

The rate of microbial respiration can be described by a rate law that gives the respiration rate as the product of a rate constant, biomass concentration, and three terms: one describing the kinetics of the electron-donating reaction, one for the kinetics of the electron-accepting reaction, and a thermodynamic term accounting for the energy available in the microbe's environment. The rate law, derived on the basis of chemiosmotic theory and nonlinear thermodynamics, is unique in that it accounts for both forward and reverse fluxes through the electron transport chain. Our analysis demonstrates how a microbe's respiration rate depends on the thermodynamic driving force, i.e., the net difference between the energy available from the environment and energy conserved as ATP. The rate laws commonly applied in microbiology, such as the Monod equation, are specific simplifications of the general law presented. The new rate law is significant because it affords the possibility of extrapolating in a rigorous manner from laboratory experiment to a broad range of natural conditions, including microbial growth where only limited energy is available. The rate law also provides a new explanation of threshold phenomena, which may reflect a thermodynamic equilibrium where the energy released by electron transfer balances that conserved by ADP phosphorylation. PMID:12676718

Community structure of rare methanogenic archaea: insight from a single functional group

PubMed Central

Winkel, Matthias; Wagner, Dirk

2017-01-01

Abstract The rare biosphere, the low abundant microbial populations, is suggested to be a conserved way of microbial life. Here we conducted a molecular survey of rare methanogenic archaea in the environment targeting the mcrA gene in order to test if general concepts associated with the structure of the rare bacterial biosphere also apply to single functional groups. Similar to what is known about rare bacterial communities, the contribution of rare methanogens to the alpha diversity is much larger than to Bray-Curtis measures. Moreover, a similar core group of methanogens harbored by the abundant and rare communities suggests similar sources and environmental controls of both groups. Among the communities of different levels of rarity, the conditionally rare methanogenic taxa largely account for the overall community dynamics of the rare biosphere and likely enter the dominant community under favorable environmental conditions. In addition, we observed a positive correlation between the alpha diversity and the production of methane when the rare taxa were taken into account. This supports the concept that increasing microbial biodiversity enhances ecological function. The composition and environmental associations of the rare methanogenic biosphere allow us to conclude that rarity is a conserved way also for single functional groups. PMID:29029047

Engineering microbial cell factories for the production of plant natural products: from design principles to industrial-scale production.

PubMed

Liu, Xiaonan; Ding, Wentao; Jiang, Huifeng

2017-07-19

Plant natural products (PNPs) are widely used as pharmaceuticals, nutraceuticals, seasonings, pigments, etc., with a huge commercial value on the global market. However, most of these PNPs are still being extracted from plants. A resource-conserving and environment-friendly synthesis route for PNPs that utilizes microbial cell factories has attracted increasing attention since the 1940s. However, at the present only a handful of PNPs are being produced by microbial cell factories at an industrial scale, and there are still many challenges in their large-scale application. One of the challenges is that most biosynthetic pathways of PNPs are still unknown, which largely limits the number of candidate PNPs for heterologous microbial production. Another challenge is that the metabolic fluxes toward the target products in microbial hosts are often hindered by poor precursor supply, low catalytic activity of enzymes and obstructed product transport. Consequently, despite intensive studies on the metabolic engineering of microbial hosts, the fermentation costs of most heterologously produced PNPs are still too high for industrial-scale production. In this paper, we review several aspects of PNP production in microbial cell factories, including important design principles and recent progress in pathway mining and metabolic engineering. In addition, implemented cases of industrial-scale production of PNPs in microbial cell factories are also highlighted.

In-Situ 13C-Labeling of Microbial Phospholipid Fatty Acids: Tracing Substrate Assimilation in a Petroleum-Contaminated Aquifer

NASA Astrophysics Data System (ADS)

Pombo, S. A.; Schroth, M. H.; Pelz, O.; Zeyer, J.

2001-12-01

Stable isotope analysis of phospholipid-derived fatty acids (PLFA) is a novel tool to trace assimilation of organic carbon in microbial communities. The 13C-labeling of biomarker fatty acids allows the identification of specific microbial populations involved in the metabolism of particular substrates, supplemented in 13C-labeled form. The goal of this study was to investigate the feasibility of 13C-labeling of PLFA and produced dissolved inorganic carbon (DIC) in a petroleum hydrocarbon (PHC)-contaminated aquifer during an in-situ experiment. To this end, we performed a single-well "push-pull" test in a monitoring well located in the denitrifying zone of a PHC-contaminated aquifer in Studen, Switzerland. During the experiment, we injected 500 L of site groundwater that was amended with 13C-labeled acetate (50% [2-13C]) and nitrate as reactants, and bromide as conservative tracer. Following the injection, we extracted a total of 1000 L of test solution/groundwater mixture after 4, 23 and 46 h from the same location. Concentrations of anions were measured in samples collected during the extraction. From these data, we computed first order rate coefficients for consumption of acetate (0.70 +/- 0.05 1/d) and nitrate (0.63 +/- 0.08 1/d). In addition, we extracted and identified PLFA, and measured \\delta13C values of PLFA and DIC. After only 4 h of incubation, we detected 13C-enrichment of certain PLFA in suspended biomass of extracted groundwater. After 46 h, we measured enrichments of up to 5000 per mil in certain PLFA (e.g. 16:1ω 7c), and up to 1500 per mil in the produced DIC. Our results demonstrate the feasibility of in-situ 13C-labeling of PLFA and DIC using push-pull tests to determine microbial activities in-situ in a natural ecosystem.

Evaluation of microbial diversity in the pilot-scale beer brewing process by culture-dependent and culture-independent method.

PubMed

Takahashi, M; Kita, Y; Kusaka, K; Mizuno, A; Goto-Yamamoto, N

2015-02-01

In the brewing industry, microbial management is very important for stabilizing the quality of the product. We investigated the detailed microbial community of beer during fermentation and maturation, to manage beer microbiology in more detail. We brewed a beer (all-malt) and two beerlike beverages (half- and low-malt) in pilot-scale fermentation and investigated the microbial community of them using a next-generation sequencer (454 GS FLX titanium), quantitative PCR, flow cytometry and a culture-dependent method. From 28 to 88 genera of bacteria and from 9 to 38 genera of eukaryotic micro-organisms were detected in each sample. Almost all micro-organisms died out during the boiling process. However, bacteria belonging to the genera Acidovorax, Bacillus, Brevundimonas, Caulobacter, Chryseobacterium, Methylobacterium, Paenibacillus, Polaromonas, Pseudomonas, Ralstonia, Sphingomonas, Stenotrophomonas, Tepidimonas and Tissierella were detected at the early and middle stage of fermentation, even though their cell densities were low (below approx. 10(3) cells ml(-1) ) and they were not almost detected at the end of fermentation. We revealed that the microbial community of beer during fermentation and maturation is very diverse and several bacteria possibly survive during fermentation. In this study, we revealed the detailed microbial communities of beer using next-generation sequencing. Some of the micro-organisms detected in this study were found in beer brewing process for the first time. Additionally, the possibility of growth of several bacteria at the early and middle stage of fermentation was suggested. © 2014 The Society for Applied Microbiology.

State-of-the-art molecular approaches to elucidate the genetic inventory of spacecraft surfaces and associated environments

NASA Astrophysics Data System (ADS)

Venkateswaran, Kasthuri; La Duc, Myron; James; Osman, Shariff; Andersen, Gary; Huber, Julie; Sogin, Mitchell

The scientific literature teems with reports of microbial diversity from seemingly every niche imaginable, from deep within Antarctic ice to ocean-floor hydrothermal systems. The fields of applied microbiology and molecular biology have made enormous technological advancements over the past two decades, from the development of PCR-amplification of DNA to the forensic detection of what many consider to be "miniscule" amounts of blood and other such biomatter. Despite advances in the specificity and sensitivity of molecular biological technologies, the abilities to efficiently sample and extract nucleic acids from low-biomass matrices, and accurately describe the true microbial diversity housed in such samples, remain significant challenges. To minimize the likelihood of forward contamination of Mars, Europa, or any other extraterrestrial environment, significant effort is invested to ensure that environments in which spacecraft are assembled are maintained appropriately and kept as free of microbial contamination as possible. To this end, routine analyses, largely based on spore-counts and cultivation-based approaches, are carried out to validate the cleanliness of such surfaces. However, only by applying the most efficient and accurate molecular means of analysis can conclusions be drawn on the actual bioburden and microbial diversity associated with these environments. For any measure of sample-derived bioburden, a large portion is inevitably lost in sampling. Furthermore, a 90 Since the surface area of a spacecraft is fixed, it is not possible to simply increase sample size to improve yield. It is therefore critical to assure that current methods of purification of biomolecules sampled from this limited resource are 1) optimal for achieving total yield of biota present and 2) conserving of the true microbial diversity of the sampled environment. This project focuses on the development of capabilities to effectively and efficiently generate a genetic inventory of microbes present about the surfaces of spacecraft and associated clean-room facilities. This entails the evaluation and optimization of molecular-based strategies designed to assess microbial burden and diversity arising from samples of low biomass. Such strategies include conventional clone library analysis, DNA microarray screening, and V6-Tag Sequencing. The capabilities resulting from this work will enable NASA to establish genetic inventories of spacecraft, as recommended by the National Research Council, to better understand the risk of forward contamination.

A PILOT STUDY TO COMPARE MICROBIAL AND CHEMICAL INDICATORS OF HUMAN FECAL CONTAMINATION IN WATER

EPA Science Inventory

Limitations exist in applying traditional microbial methods for the detection of human fecal contamination of water. A pilot study was undertaken to compare the microbial and chemical indicators of human fecal contamination of water. Sixty-four water samples were collected in O...

Biosignature Preservation Vulnerability Associated with Stress Response Metabolic Redox Mode Switching in a Mars Analogue Coupled Microbial Mat Transiting Near-Space

NASA Astrophysics Data System (ADS)

Archer, R.; Ralat, A.

2016-05-01

Examination of a coupled microbial mat recovered from Death Valley failed to detect rosickyte, both before and after exposure to near-space conditions; associated redox proxies suggest diagenesis caused by rapid adaptive microbial stress response.

Living microorganisms change the information (Shannon) content of a geophysical system.

PubMed

Tang, Fiona H M; Maggi, Federico

2017-06-12

The detection of microbial colonization in geophysical systems is becoming of interest in various disciplines of Earth and planetary sciences, including microbial ecology, biogeochemistry, geomicrobiology, and astrobiology. Microorganisms are often observed to colonize mineral surfaces, modify the reactivity of minerals either through the attachment of their own biomass or the glueing of mineral particles with their mucilaginous metabolites, and alter both the physical and chemical components of a geophysical system. Here, we hypothesise that microorganisms engineer their habitat, causing a substantial change to the information content embedded in geophysical measures (e.g., particle size and space-filling capacity). After proving this hypothesis, we introduce and test a systematic method that exploits this change in information content to detect microbial colonization in geophysical systems. Effectiveness and robustness of this method are tested using a mineral sediment suspension as a model geophysical system; tests are carried out against 105 experiments conducted with different suspension types (i.e., pure mineral and microbially-colonized) subject to different abiotic conditions, including various nutrient and mineral concentrations, and different background entropy production rates. Results reveal that this method can systematically detect microbial colonization with less than 10% error in geophysical systems with low-entropy background production rate.

Microbial Relatives of the Seed Storage Proteins of Higher Plants: Conservation of Structure and Diversification of Function during Evolution of the Cupin Superfamily

PubMed Central

Dunwell, Jim M.; Khuri, Sawsan; Gane, Paul J.

2000-01-01

This review summarizes the recent discovery of the cupin superfamily (from the Latin term “cupa,” a small barrel) of functionally diverse proteins that initially were limited to several higher plant proteins such as seed storage proteins, germin (an oxalate oxidase), germin-like proteins, and auxin-binding protein. Knowledge of the three-dimensional structure of two vicilins, seed proteins with a characteristic β-barrel core, led to the identification of a small number of conserved residues and thence to the discovery of several microbial proteins which share these key amino acids. In particular, there is a highly conserved pattern of two histidine-containing motifs with a varied intermotif spacing. This cupin signature is found as a central component of many microbial proteins including certain types of phosphomannose isomerase, polyketide synthase, epimerase, and dioxygenase. In addition, the signature has been identified within the N-terminal effector domain in a subgroup of bacterial AraC transcription factors. As well as these single-domain cupins, this survey has identified other classes of two-domain bicupins including bacterial gentisate 1,2-dioxygenases and 1-hydroxy-2-naphthoate dioxygenases, fungal oxalate decarboxylases, and legume sucrose-binding proteins. Cupin evolution is discussed from the perspective of the structure-function relationships, using data from the genomes of several prokaryotes, especially Bacillus subtilis. Many of these functions involve aspects of sugar metabolism and cell wall synthesis and are concerned with responses to abiotic stress such as heat, desiccation, or starvation. Particular emphasis is also given to the oxalate-degrading enzymes from microbes, their biological significance, and their value in a range of medical and other applications. PMID:10704478

Microbial Functional Gene Diversity with a Shift of Subsurface Redox Conditions during In Situ Uranium Reduction

PubMed Central

Liang, Yuting; Van Nostrand, Joy D.; N′Guessan, Lucie A.; Peacock, Aaron D.; Deng, Ye; Long, Philip E.; Resch, C. Tom; Wu, Liyou; He, Zhili; Li, Guanghe; Hazen, Terry C.; Lovley, Derek R.

2012-01-01

To better understand the microbial functional diversity changes with subsurface redox conditions during in situ uranium bioremediation, key functional genes were studied with GeoChip, a comprehensive functional gene microarray, in field experiments at a uranium mill tailings remedial action (UMTRA) site (Rifle, CO). The results indicated that functional microbial communities altered with a shift in the dominant metabolic process, as documented by hierarchical cluster and ordination analyses of all detected functional genes. The abundance of dsrAB genes (dissimilatory sulfite reductase genes) and methane generation-related mcr genes (methyl coenzyme M reductase coding genes) increased when redox conditions shifted from Fe-reducing to sulfate-reducing conditions. The cytochrome genes detected were primarily from Geobacter sp. and decreased with lower subsurface redox conditions. Statistical analysis of environmental parameters and functional genes indicated that acetate, U(VI), and redox potential (Eh) were the most significant geochemical variables linked to microbial functional gene structures, and changes in microbial functional diversity were strongly related to the dominant terminal electron-accepting process following acetate addition. The study indicates that the microbial functional genes clearly reflect the in situ redox conditions and the dominant microbial processes, which in turn influence uranium bioreduction. Microbial functional genes thus could be very useful for tracking microbial community structure and dynamics during bioremediation. PMID:22327592

A comparative analysis of microbial profile of Guinea fowl and chicken using metagenomic approach

PubMed Central

Bhogoju, Sarayu; Wang, Xiaofei; Darris, Carl; Kilonzo-Nthenge, Agnes

2018-01-01

Probiotics are live microbial feed supplements that promote growth and health to the host by minimizing non-essential and pathogenic microorganisms in the host’s gastrointestinal tract (GIT). The campaign to minimize excessive use of antibiotics in poultry production has necessitated development of probiotics with broad application in multiple poultry species. Design of such probiotics requires understanding of the diversity or similarity in microbial profiles among avian species of economic importance. Therefore, the objective of this research was to establish and compare the microbial profiles of the GIT of Guinea fowl and chicken and to establish the microbial diversity or similarity between the two avian species. A metagenomic approach consisting of the amplification and sequence analysis of the hypervariable regions V1-V9 of the 16S rRNA gene was used to identify the GIT microbes. Collectively, we detected more than 150 microbial families. The total number of microbial species detected in the chicken GIT was higher than that found in the Guinea Fowl GIT. Our studies also revealed phylogenetic diversity among the microbial species found in chicken and guinea fowl. The phylum Firmicutes was most abundant in both avian species whereas Phylum Actinobacteria was most abundant in chickens than Guinea fowls. The diversity of the microbial profiles found in broiler chickens and Guinea fowls suggest that the design of effective avian probiotics would require species specificity. PMID:29494648

Soil microbial communities influence seedling growth of a rare conifer independent of plant-soil feedback.

PubMed

Rigg, Jessica L; Offord, Cathy A; Singh, Brajesh K; Anderson, Ian; Clarke, Steve; Powell, Jeff R

2016-12-01

Plant-soil feedback, the reciprocal relationship between a plant and its associated microbial communities, has been proposed to be an important driver of plant populations and community dynamics. While rarely considered, understanding how plant-soil feedback contributes to plant rarity may have implications for conservation and management of rare species. Wollemi pine (Wollemia nobilis) is a critically endangered species, of which fewer than 100 trees are known to exist in the wild. Seedling survival within the first year after germination and subsequent recruitment of Wollemi pine is limited in the wild. We used a plant-soil feedback approach to investigate the functional effect of species-specific differences previously observed in the microbial communities underneath adult Wollemi pine and a neighboring species, coachwood (Ceratopetalum apetalum), and also whether additional variation in microbial communities in the wild could impact seedling growth. There was no evidence for seedling growth being affected by tree species associated with soil inocula, suggesting that plant-soil feedbacks are not limiting recruitment in the natural population. However, there was evidence of fungal, but not bacterial, community variation impacting seedling growth independently of plant-soil feedbacks. Chemical (pH) and physical (porosity) soil characteristics were identified as potential drivers of the functional outcomes of these fungal communities. The empirical approach described here may provide opportunities to identify the importance of soil microbes to conservation efforts targeting other rare plant species and is also relevant to understanding the importance of soil microbes and plant-soil feedbacks for plant community dynamics more broadly. © 2016 by the Ecological Society of America.

Metabolic Activity and Biosignatures of Microbes in the Lower Ocean Crust of Atlantis Bank, IODP Expedition 360

NASA Astrophysics Data System (ADS)

Wee, S. Y.; Edgcomb, V. P.; Burgaud, G.; Klein, F.; Schubotz, F.; Yvon-Lewis, S. A.; Sylvan, J. B.

2017-12-01

International Ocean Discovery Program (IODP) Expedition 360 represents the first leg of a multi-phase drilling program, SloMo, aimed at investigating the nature of the lower crust and Moho at slow spreading ridges. The goal of Expedition 360 was to recover a representative transect of the lower oceanic crust formed at Atlantis Bank, an oceanic core complex on the SW Indian Ridge. Recovered cores were primarily gabbro and olivine gabbro, which may potentially host serpentinization reactions and associated microbial life. Our goal was to sample this subseafloor environment and determine quantity, diversity and metabolic capabilities of any resident microbial life. Hole U1473A was drilled during Expedition 360 down to 790 m below seafloor and samples for detection of microbial communities and microbial biosignatures were collected throughout. We present here quantification of microbial biomass via fluorescence microscopy, preliminary analysis of nutrient addition experiments, data from sequencing of microbial 16S rRNA genes, analysis of microbial lipids, and data from Raman spectra of subsurface isolates. We initiated and sampled 12 nutrient addition experiments from 71-745 mbsf by adding sampled rocks to artificial seawater with no additions, added ammonium, added ammonium plus phosphate, and added organic acids. In nearly all of the experiment bottles, methane was detected when samples were collected at six months and again after one year of incubation. Phosphate in the incubations was drawn down, indicating active microbial metabolism, and archaeal lipids from in situ samples indicate the presence of methanogens, corroborating the likelihood of methanogens as the source of detected methane in the nutrient addition incubations. Altogether, the interdisciplinary approach used here provides a peek into life in the subseafloor upper ocean crust.

Microbial responses to southward and northward Cambisol soil transplant

DOE PAGES

Wang, Mengmeng; Liu, Shanshan; Wang, Feng; ...

2015-10-26

We report that soil transplant serves as a proxy to simulate climate changes. Recently, we have shown that southward transplant of black soil and northward transplant of red soil altered soil microbial communities and biogeochemical variables. However, fundamental differences in soil types have prevented direct comparison between southward and northward transplants. To tackle it, herein we report an analysis of microbial communities of Cambisol soil in an agriculture field after 4 years of adaptation to southward and northward soil transplants over large transects. Analysis of bare fallow soils revealed concurrent increase in microbial functional diversity and coarse-scale taxonomic diversity atmore » both transplanted sites, as detected by GeoChip 3.0 and DGGE, respectively. Furthermore, a correlation between microbial functional diversity and taxonomic diversity was detected, which was masked in maize cropped soils. Mean annual temperature, soil moisture, and nitrate (NO 3¯-N) showed strong correlations with microbial communities. In addition, abundances of ammonium-oxidizing genes (amoA) and denitrification genes were correlated with nitrification capacity and NO 3¯-N contents, suggesting that microbial responses to soil transplant could alter microbe-mediated biogeochemical cycle at the ecosystem level.« less

MALDI-TOF mass spectrometry: an emerging technology for microbial identification and diagnosis

PubMed Central

Singhal, Neelja; Kumar, Manish; Kanaujia, Pawan K.; Virdi, Jugsharan S.

2015-01-01

Currently microorganisms are best identified using 16S rRNA and 18S rRNA gene sequencing. However, in recent years matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has emerged as a potential tool for microbial identification and diagnosis. During the MALDI-TOF MS process, microbes are identified using either intact cells or cell extracts. The process is rapid, sensitive, and economical in terms of both labor and costs involved. The technology has been readily imbibed by microbiologists who have reported usage of MALDI-TOF MS for a number of purposes like, microbial identification and strain typing, epidemiological studies, detection of biological warfare agents, detection of water- and food-borne pathogens, detection of antibiotic resistance and detection of blood and urinary tract pathogens etc. The limitation of the technology is that identification of new isolates is possible only if the spectral database contains peptide mass fingerprints of the type strains of specific genera/species/subspecies/strains. This review provides an overview of the status and recent applications of mass spectrometry for microbial identification. It also explores the usefulness of this exciting new technology for diagnosis of diseases caused by bacteria, viruses, and fungi. PMID:26300860

MALDI-TOF mass spectrometry: an emerging technology for microbial identification and diagnosis.

PubMed

Singhal, Neelja; Kumar, Manish; Kanaujia, Pawan K; Virdi, Jugsharan S

2015-01-01

Currently microorganisms are best identified using 16S rRNA and 18S rRNA gene sequencing. However, in recent years matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has emerged as a potential tool for microbial identification and diagnosis. During the MALDI-TOF MS process, microbes are identified using either intact cells or cell extracts. The process is rapid, sensitive, and economical in terms of both labor and costs involved. The technology has been readily imbibed by microbiologists who have reported usage of MALDI-TOF MS for a number of purposes like, microbial identification and strain typing, epidemiological studies, detection of biological warfare agents, detection of water- and food-borne pathogens, detection of antibiotic resistance and detection of blood and urinary tract pathogens etc. The limitation of the technology is that identification of new isolates is possible only if the spectral database contains peptide mass fingerprints of the type strains of specific genera/species/subspecies/strains. This review provides an overview of the status and recent applications of mass spectrometry for microbial identification. It also explores the usefulness of this exciting new technology for diagnosis of diseases caused by bacteria, viruses, and fungi.

Normalization of environmental metagenomic DNA enhances the discovery of under-represented microbial community members.

PubMed

Ramond, J-B; Makhalanyane, T P; Tuffin, M I; Cowan, D A

2015-04-01

Normalization is a procedure classically employed to detect rare sequences in cellular expression profiles (i.e. cDNA libraries). Here, we present a normalization protocol involving the direct treatment of extracted environmental metagenomic DNA with S1 nuclease, referred to as normalization of metagenomic DNA: NmDNA. We demonstrate that NmDNA, prior to post hoc PCR-based experiments (16S rRNA gene T-RFLP fingerprinting and clone library), increased the diversity of sequences retrieved from environmental microbial communities by detection of rarer sequences. This approach could be used to enhance the resolution of detection of ecologically relevant rare members in environmental microbial assemblages and therefore is promising in enabling a better understanding of ecosystem functioning. This study is the first testing 'normalization' on environmental metagenomic DNA (mDNA). The aim of this procedure was to improve the identification of rare phylotypes in environmental communities. Using hypoliths as model systems, we present evidence that this post-mDNA extraction molecular procedure substantially enhances the detection of less common phylotypes and could even lead to the discovery of novel microbial genotypes within a given environment. © 2014 The Society for Applied Microbiology.

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...

Soil Ecosystem Recovery Should Be Quantifiable

USDA-ARS?s Scientific Manuscript database

Conservation Reserve Program (CRP) costs close to two billion dollars in federal funds every year; and yet, it is challenging to evaluate its effectiveness to assist the decision making process. Using a combination of physical properties and microbial indicators, we found that it is possible to make...

The Potential of Berries to Serve as Selective Inhibitors of Pathogens and Promoters of Beneficial Microorganisms

USDA-ARS?s Scientific Manuscript database

Berries are distinct from other foods because of their unique compounds with bioprotective effects and antimicrobial/prebiotic properties. With new knowledge of how these unique phytochemicals differentially affect microbial communities, inhibit foodborne pathogens, and conserve beneficial species, ...

Epilithic and endolithic bacterial communities in limestone from a Maya archaeological site.

PubMed

McNamara, Christopher J; Perry, Thomas D; Bearce, Kristen A; Hernandez-Duque, Guillermo; Mitchell, Ralph

2006-01-01

Biodeterioration of archaeological sites and historic buildings is a major concern for conservators, archaeologists, and scientists involved in preservation of the world's cultural heritage. The Maya archaeological sites in southern Mexico, some of the most important cultural artifacts in the Western Hemisphere, are constructed of limestone. High temperature and humidity have resulted in substantial microbial growth on stone surfaces at many of the sites. Despite the porous nature of limestone and the common occurrence of endolithic microorganisms in many habitats, little is known about the microbial flora living inside the stone. We found a large endolithic bacterial community in limestone from the interior of the Maya archaeological site Ek' Balam. Analysis of 16S rDNA clones demonstrated disparate communities (endolithic: >80% Actinobacteria, Acidobacteria, and Low GC Firmicutes; epilithic: >50% Proteobacteria). The presence of differing epilithic and endolithic bacterial communities may be a significant factor for conservation of stone cultural heritage materials and quantitative prediction of carbonate weathering.

Analysis of Low-Biomass Microbial Communities in the Deep Biosphere.

PubMed

Morono, Y; Inagaki, F

2016-01-01

Over the past few decades, the subseafloor biosphere has been explored by scientific ocean drilling to depths of about 2.5km below the seafloor. Although organic-rich anaerobic sedimentary habitats in the ocean margins harbor large numbers of microbial cells, microbial populations in ultraoligotrophic aerobic sedimentary habitats in the open ocean gyres are several orders of magnitude less abundant. Despite advances in cultivation-independent molecular ecological techniques, exploring the low-biomass environment remains technologically challenging, especially in the deep subseafloor biosphere. Reviewing the historical background of deep-biosphere analytical methods, the importance of obtaining clean samples and tracing contamination, as well as methods for detecting microbial life, technological aspects of molecular microbiology, and detecting subseafloor metabolic activity will be discussed. Copyright © 2016 Elsevier Inc. All rights reserved.

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

Wang, Mengmeng; Liu, Shanshan; Wang, Feng

We report that soil transplant serves as a proxy to simulate climate changes. Recently, we have shown that southward transplant of black soil and northward transplant of red soil altered soil microbial communities and biogeochemical variables. However, fundamental differences in soil types have prevented direct comparison between southward and northward transplants. To tackle it, herein we report an analysis of microbial communities of Cambisol soil in an agriculture field after 4 years of adaptation to southward and northward soil transplants over large transects. Analysis of bare fallow soils revealed concurrent increase in microbial functional diversity and coarse-scale taxonomic diversity atmore » both transplanted sites, as detected by GeoChip 3.0 and DGGE, respectively. Furthermore, a correlation between microbial functional diversity and taxonomic diversity was detected, which was masked in maize cropped soils. Mean annual temperature, soil moisture, and nitrate (NO 3¯-N) showed strong correlations with microbial communities. In addition, abundances of ammonium-oxidizing genes (amoA) and denitrification genes were correlated with nitrification capacity and NO 3¯-N contents, suggesting that microbial responses to soil transplant could alter microbe-mediated biogeochemical cycle at the ecosystem level.« less

Alternations of Structure and Functional Activity of Below Ground Microbial Communities at Elevated Atmospheric Carbon Dioxide

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

He, Zhili; Xu, Meiying; Deng, Ye

2010-05-17

The global atmospheric concentration of CO2 has increased by more than 30percent since the industrial revolution. Although the stimulating effects of elevated CO2 (eCO2) on plant growth and primary productivity have been well studied, its influences on belowground microbial communities are poorly understood and controversial. In this study, we showed a significant change in the structure and functional potential of soil microbial communities at eCO2 in a grassland ecosystem, the BioCON (Biodiversity, CO2 and Nitrogen) experimental site (http://www.biocon.umn.edu/) using a comprehensive functional gene array, GeoChip 3.0, which contains about 28,0000 probes and covers approximately 57,000 gene variants from 292 functionalmore » gene families involved in carbon, nitrogen, phosphorus and sulfur cycles as well as other functional processes. GeoChip data indicated that the functional structure of microbial communities was markedly different between ambient CO2 (aCO2) and eCO2 by detrended correspondence analysis (DCA) of all 5001 detected functional gene probes although no significant differences were detected in the overall microbial diversity. A further analysis of 1503 detected functional genes involved in C, N, P, and S cycles showed that a considerable portion (39percent) of them were only detected under either aCO2 (14percent) or eCO2 (25percent), indicating that the functional characteristics of the microbial community were significantly altered by eCO2. Also, for those shared genes (61percent) detected, some significantly (p<0.05) changed their abundance at eCO2. Especially, genes involved in labile C degradation, such as amyA, egl, and ara for starch, cellulose, and hemicelluloses, respectively, C fixation (e.g., rbcL, pcc/acc), N fixation (nifH), and phosphorus utilization (ppx) were significantly increased under eCO2, while those involved in decomposing recalcitrant C, such as glx, lip, and mnp for lignin degradation remained unchanged. This study provides insights into our understanding of belowground microbial communities and their feedbacks to terrestrial ecosystems at eCO2.« less

Discriminative detection and enumeration of microbial life in marine subsurface sediments.

PubMed

Morono, Yuki; Terada, Takeshi; Masui, Noriaki; Inagaki, Fumio

2009-05-01

Detection and enumeration of microbial life in natural environments provide fundamental information about the extent of the biosphere on Earth. However, it has long been difficult to evaluate the abundance of microbial cells in sedimentary habitats because non-specific binding of fluorescent dye and/or auto-fluorescence from sediment particles strongly hampers the recognition of cell-derived signals. Here, we show a highly efficient and discriminative detection and enumeration technique for microbial cells in sediments using hydrofluoric acid (HF) treatment and automated fluorescent image analysis. Washing of sediment slurries with HF significantly reduced non-biological fluorescent signals such as amorphous silica and enhanced the efficiency of cell detachment from the particles. We found that cell-derived SYBR Green I signals can be distinguished from non-biological backgrounds by dividing green fluorescence (band-pass filter: 528/38 nm (center-wavelength/bandwidth)) by red (617/73 nm) per image. A newly developed automated microscope system could take a wide range of high-resolution image in a short time, and subsequently enumerate the accurate number of cell-derived signals by the calculation of green to red fluorescence signals per image. Using our technique, we evaluated the microbial population in deep marine sediments offshore Peru and Japan down to 365 m below the seafloor, which provided objective digital images as evidence for the quantification of the prevailing microbial life. Our method is hence useful to explore the extent of sub-seafloor life in the future scientific drilling, and moreover widely applicable in the study of microbial ecology.

SOPROCARE - 450 nm wavelength detection tool for microbial plaque and gingival inflammation: a clinical study

NASA Astrophysics Data System (ADS)

Rechmann, P.; Liou, Shasan W.; Rechmann, Beate M.; Featherstone, John D.

2014-02-01

Gingivitis due to microbial plaque and calculus can lead over time if left untreated to advanced periodontal disease with non-physiological pocket formation. Removal of microbial plaque in the gingivitis stage typically achieves gingival health. The SOPROCARE camera system emits blue light at 450 nm wavelength using three blue diodes. The 450 nm wavelength is located in the non-ionizing, visible spectral wavelength region and thus is not dangerous. It is assumed that using the SOPROCARE camera in perio-mode inflamed gingiva can easily be observed and inflammation can be scored due to fluorescence from porphyrins in blood. The assumption is also that illumination of microbial plaque with blue light induces fluorescence due to the bacteria and porphyrin content of the plaque and thus can help to make microbial plaque and calculus visible. Aim of the study with 55 subjects was to evaluate the ability of the SOPROCARE fluorescence camera system to detect, visualize and allow scoring of microbial plaque in comparison to the Turesky modification of the Quigley and Hein plaque index. A second goal was to detect and score gingival inflammation and correlated the findings to the Silness and Löe gingival inflammation index. The study showed that scoring of microbial plaque as well as gingival inflammation levels similar to the established Turesky modified Quigley Hein index and the Silness and Löe gingival inflammation index can easily be done using the SOPROCARE fluorescence system in periomode. Linear regression fits between the different clinical indices and SOPROCARE scores in fluorescence perio-mode revealed the system's capacity for effective discrimination between scores.

Medical Devices; Immunology and Microbiology Devices; Classification of the Device To Detect and Identify Microbial Pathogen Nucleic Acids in Cerebrospinal Fluid. Final order.

PubMed

2017-10-20

The Food and Drug Administration (FDA or we) is classifying the device to detect and identify microbial pathogen nucleic acids in cerebrospinal fluid into class II (special controls). The special controls that will apply to the device type are identified in this order and will be part of the codified language for the device to detect and identify microbial pathogen nucleic acids in cerebrospinal fluid’s classification. We are taking this action because we have determined that classifying the device into class II (special controls) will provide a reasonable assurance of safety and effectiveness of the device. We believe this action will also enhance patients' access to beneficial innovative devices, in part by reducing regulatory burdens.

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

Jha, Ramesh K.; Kern, Theresa L.; Kim, Youngchang

A whole-cell biosensor utilizing a transcription factor (TF) is an effective tool for sensitive and selective detection of specialty chemicals or anthropogenic molecules, but requires an access to an expanded repertoire of TFs. Using ligand docked homology models for binding pocket identification, assisted by conservative mutations in the pocket, we engineered a novel specificity in an Acinetobacter TF, PobR, to ‘sense’ a chemical p-nitrophenol (pNP) and measured the response via a fluorescent protein reporter expressed from a PobR promoter. Out of 10 7 variants of PobR, four were active when pNP was added as an inducer, with two mutants showingmore » a specificity switch from the native effector 4-hydroxybenzoate (4HB). One of the mutants, pNPmut1 was then used to create a smart microbial cell responding to pNP production and detect hydrolysis of an insecticide, paraoxon, in a coupled assay involving phosphotriesterase (PTE) enzyme expressed from a separate promoter. We show that the fluorescence of the cells correlated with the catalytic efficiency of PTE variants, each cell expressed. High selectivity for similar molecules (4HB vs pNP), high sensitivity for pNP detection (~2 μM) and agreement of apo- and holo- structures of PobR scaffold with computational models are notable successes presented in this work.« less

PMA-PhyloChip DNA Microarray to Elucidate Viable Microbial Community Structure

NASA Technical Reports Server (NTRS)

Venkateswaran, Kasthuri J.; Stam, Christina N.; Andersen, Gary L.; DeSantis, Todd

2011-01-01

Since the Viking missions in the mid-1970s, traditional culture-based methods have been used for microbial enumeration by various NASA programs. Viable microbes are of particular concern for spacecraft cleanliness, for forward contamination of extraterrestrial bodies (proliferation of microbes), and for crew health/safety (viable pathogenic microbes). However, a "true" estimation of viable microbial population and differentiation from their dead cells using the most sensitive molecular methods is a challenge, because of the stability of DNA from dead cells. The goal of this research is to evaluate a rapid and sensitive microbial detection concept that will selectively estimate viable microbes. Nucleic acid amplification approaches such as the polymerase chain reaction (PCR) have shown promise for reducing time to detection for a wide range of applications. The proposed method is based on the use of a fluorescent DNA intercalating agent, propidium monoazide (PMA), which can only penetrate the membrane of dead cells. The PMA-quenched reaction mixtures can be screened, where only the DNA from live cells will be available for subsequent PCR reaction and microarray detection, and be identified as part of the viable microbial community. An additional advantage of the proposed rapid method is that it will detect viable microbes and differentiate from dead cells in only a few hours, as opposed to less comprehensive culture-based assays, which take days to complete. This novel combination approach is called the PMA-Microarray method. DNA intercalating agents such as PMA have previously been used to selectively distinguish between viable and dead bacterial cells. Once in the cell, the dye intercalates with the DNA and, upon photolysis under visible light, produces stable DNA adducts. DNA cross-linked in this way is unavailable for PCR. Environmental samples suspected of containing a mixture of live and dead microbial cells/spores will be treated with PMA, and then incubated in the dark. Thereafter, the sample is exposed to visible light for five minutes, so that the DNA from dead cells will be cross-linked. Following this PMA treatment step, the sample is concentrated by centrifugation and washed (to remove excessive PMA) before DNA is extracted. The 16S rRNA gene fragments will be amplified by PCR to screen the total microbial community using PhyloChip DNA microarray analysis. This approach will detect only the viable microbial community since the PMA intercalated DNA from dead cells would be unavailable for PCR amplification. The total detection time including PCR reaction for low biomass samples will be a few hours. Numerous markets may use this technology. The food industry uses spore detection to validate new alternative food processing technologies, sterility, and quality. Pharmaceutical and medical equipment companies also detect spores as a marker for sterility. This system can be used for validating sterilization processes, water treatment systems, and in various public health and homeland security applications.

Comparative analysis on microbial community associated with different gastrointestinal regions of wild northern snakehead Channa argus Cantor, 1842

NASA Astrophysics Data System (ADS)

Miao, Shuyan; Zhao, Chenze; Zhu, Jinyu; Pan, Mingzhu

2018-03-01

Microbial communities in different gastrointestinal regions (stomach, foregut, midgut, and hindgut) of the northern snakehead Channa argus (Cantor, 1842) were compared by polymerase chain reaction and partial 16S rDNA sequencing. A total of 194, 140, 212, and 122 OTUs were detected in the stomach, foregut, midgut, and hindgut, respectively. Significant differences were found in the Sobs, ACE, Shannon, and Simpson indices among samples ( P<0.05). The gastrointestinal microbial community of C. argus consisted predominantly of Proteobacteria with either Halomonas, Shewanella, Plesiomonas, or Sphingomonas. Fusobacteria, Firmicutes, and Bacteroidetes also existed in the gastrointestinal tracts. However, significant differences were found in the compositions of microbial community among the four regions ( P<0.05). Cyanobacteria and Spirochetes were significantly higher in the midgut and hindgut ( P<0.05). Fusobacteria and Firmicutes were dominant in the hindgut and foregut, respectively ( P<0.05). Proteobacteria was the lowest in the hindgut ( P<0.05). At genus level, Cetobacterium and Plesiomonas were significantly higher in the hindgut than in the other three samples ( P<0.05). Clostridium and Prevotella were the highest in the midgut ( P<0.05). Halomonas, Shewanella, and Sphingomonas were the highest in the foregut ( P<0.05). Paracoccus and Vibrio were the highest in the stomach. Several genera were only detected in certain regions, as follows: stomach, Paracoccus and Vibrio; foregut, Halomonas, Shewanella, and Sphingomonas; midgut, Clostridium and Prevotella; and hindgut, Cetobacterium and Plesiomonas ( P<0.05). At the species level, Acinetobacter rhizosphaerae was only detected in the stomach. Prevotella copri and Clostridium perfring were not detected in the foregut and midgut, respectively, whereas Prevotella copri and Faecalibacterium pra were not detected in the hindgut. These findings provide valuable information on the microbial community in each gastrointestinal region of C. argus. Moreover, this study indicated that microbial community was not only related to rearing environment but also to the physico-chemical characteristics of each gastrointestinal region.

Rapid detection of rRNA group I pseudomonads in contaminated metalworking fluids and biofilm formation by fluorescent in situ hybridization.

PubMed

Saha, Ratul; Donofrio, Robert S; Goeres, Darla M; Bagley, Susan T

2012-05-01

Metalworking fluids (MWFs), used in different machining operations, are highly prone to microbial degradation. Microbial communities present in MWFs lead to biofilm formation in the MWF systems, which act as a continuous source of contamination. Species of rRNA group I Pseudomonas dominate in contaminated MWFs. However, their actual distribution is typically underestimated when using standard culturing techniques as most fail to grow on the commonly used Pseudomonas Isolation Agar. To overcome this, fluorescent in situ hybridization (FISH) was used to study their abundance along with biofilm formation by two species recovered from MWFs, Pseudomonas fluorescens MWF-1 and the newly described Pseudomonas oleovorans subsp. lubricantis. Based on 16S rRNA sequences, a unique fluorescent molecular probe (Pseudo120) was designed targeting a conserved signature sequence common to all rRNA group I Pseudomonas. The specificity of the probe was evaluated using hybridization experiments with whole cells of different Pseudomonas species. The probe's sensitivity was determined to be 10(3) cells/ml. It successfully detected and enumerated the abundance and distribution of Pseudomonas indicating levels between 3.2 (± 1.1) × 10(6) and 5.0 (± 2.3) × 10(6) cells/ml in four different industrial MWF samples collected from three different locations. Biofilm formation was visualized under stagnant conditions using high and low concentrations of cells for both P. fluorescens MWF-1 and P. oleovorans subsp. lubricantis stained with methylene blue and Pseudo120. On the basis of these observations, this molecular probe can be successfully be used in the management of MWF systems to monitor the levels and biofilm formation of rRNA group I pseudomonads.

Petroleum hydrocarbon biodegradation under seasonal freeze-thaw soil temperature regimes in contaminated soils from a sub-Arctic site.

PubMed

Chang, Wonjae; Klemm, Sara; Beaulieu, Chantale; Hawari, Jalal; Whyte, Lyle; Ghoshal, Subhasis

2011-02-01

Several studies have shown that biostimulation in ex situ systems such as landfarms and biopiles can facilitate remediation of petroleum hydrocarbon contaminated soils at sub-Arctic sites during summers when temperatures are above freezing. In this study, we examine the biodegradation of semivolatile (F2: C10-C16) and nonvolatile (F3: C16-C34) petroleum hydrocarbons and microbial respiration and population dynamics at post- and presummer temperatures ranging from -5 to 14 °C. The studies were conducted in pilot-scale tanks with soils obtained from a historically contaminated sub-Arctic site in Resolution Island (RI), Canada. In aerobic, nutrient-amended, unsaturated soils, the F2 hydrocarbons decreased by 32% during the seasonal freeze-thaw phase where soils were cooled from 2 to -5 °C at a freezing rate of -0.12 °C d(-1) and then thawed from -5 to 4 °C at a thawing rate of +0.16 °C d(-1). In the unamended (control) tank, the F2 fraction only decreased by 14% during the same period. Biodegradation of individual hydrocarbon compounds in the nutrient-amended soils was also confirmed by comparing their abundance over time to that of the conserved diesel biomarker, bicyclic sesquiterpanes (BS). During this period, microbial respiration was observed, even at subzero temperatures when unfrozen liquid water was detected during the freeze-thaw period. An increase in culturable heterotrophs and 16S rDNA copy numbers was noted during the freezing phase, and the (14)C-hexadecane mineralization in soil samples obtained from the nutrient-amended tank steadily increased. Hydrocarbon degrading bacterial populations identified as Corynebacterineae- and Alkanindiges-related strains emerged during the freezing and thawing phases, respectively, indicating there were temperature-based microbial community shifts.

Loss of a Tyrosine-Dependent Trafficking Motif in the Simian Immunodeficiency Virus Envelope Cytoplasmic Tail Spares Mucosal CD4 Cells but Does Not Prevent Disease Progression

PubMed Central

Breed, Matthew W.; Jordan, Andrea P. O.; Aye, Pyone P.; Lichtveld, Cornelis F.; Midkiff, Cecily C.; Schiro, Faith R.; Haggarty, Beth S.; Sugimoto, Chie; Alvarez, Xavier; Sandler, Netanya G.; Douek, Daniel C.; Kuroda, Marcelo J.; Pahar, Bapi; Piatak, Michael; Lifson, Jeffrey D.; Keele, Brandon F.; Hoxie, James A.

2013-01-01

A hallmark of pathogenic simian immunodeficiency virus (SIV) and human immunodeficiency virus (HIV) infections is the rapid and near-complete depletion of mucosal CD4+ T lymphocytes from the gastrointestinal tract. Loss of these cells and disruption of epithelial barrier function are associated with microbial translocation, which has been proposed to drive chronic systemic immune activation and disease progression. Here, we evaluate in rhesus macaques a novel attenuated variant of pathogenic SIVmac239, termed ΔGY, which contains a deletion of a Tyr and a proximal Gly from a highly conserved YxxØ trafficking motif in the envelope cytoplasmic tail. Compared to SIVmac239, ΔGY established a comparable acute peak of viremia but only transiently infected lamina propria and caused little or no acute depletion of mucosal CD4+ T cells and no detectable microbial translocation. Nonetheless, these animals developed T-cell activation and declining peripheral blood CD4+ T cells and ultimately progressed with clinical or pathological features of AIDS. ΔGY-infected animals also showed no infection of macrophages or central nervous system tissues even in late-stage disease. Although the ΔGY mutation persisted, novel mutations evolved, including the formation of new YxxØ motifs in two of four animals. These findings indicate that disruption of this trafficking motif by the ΔGY mutation leads to a striking alteration in anatomic distribution of virus with sparing of lamina propria and a lack of microbial translocation. Because these animals exhibited wild-type levels of acute viremia and immune activation, our findings indicate that these pathological events are dissociable and that immune activation unrelated to gut damage can be sufficient for the development of AIDS. PMID:23152518

A bioenergetics-kinetics coupled modeling study on subsurface microbial metabolism in a field biostimulation experiment

NASA Astrophysics Data System (ADS)

Jin, Q.; Zheng, Z.; Zhu, C.

2006-12-01

Microorganisms in nature conserve energy by catalyzing various geochemical reactions. To build a quantitative relationship between geochemical conditions and metabolic rates, we propose a bioenergetics-kinetics coupled modeling approach. This approach describes microbial community as a metabolic network, i.e., fermenting microbes degrade organic substrates while aerobic respirer, nitrate reducer, metal reducer, sulfate reducer, and methanogen consume the fermentation products. It quantifies the control of substrate availability and biological energy conservation on the metabolic rates using thermodynamically consistent rate laws. We applied this simulation approach to study the progress of microbial metabolism during a field biostimulation experiment conducted in Oak Ridge, Tennessee. In the experiment, ethanol was injected into a monitoring well and groundwater was sampled to monitor changes in the chemistry. With time, concentrations of ethanol and SO42- decreased while those of NH4+, Fe2+, and Mn2+ increased. The simulation results fitted well to the observation, indicating simultaneous ethanol degradation and terminal electron accepting processes. The rates of aerobic respiration and denitrification were mainly controlled by substrate concentrations while those of ethanol degradation, sulfate reduction, and methanogenesis were controlled dominantly by the energy availability. The simulation results suggested two different microbial growth statuses in the subsurface. For the functional groups with significant growth, variations with time in substrate concentrations demonstrated a typical S curve. For the groups without significant growth, initial decreases in substrate concentrations were linear with time. Injecting substrates followed by monitoring environmental chemistry therefore provides a convenient approach to characterize microbial growth in the subsurface where methods for direct observation are currently unavailable. This research was funded by the NABIR program, DOE, under grant No. DE-FG02-04ER63740 to CZ. We thank J. Istok, David Watson, and Philip Jardine for their help. The views and opinions of authors expressed herein do not necessarily state or reflect those of the DOE.

Designer cells programming quorum-sensing interference with microbes.

PubMed

Sedlmayer, Ferdinand; Hell, Dennis; Müller, Marius; Ausländer, David; Fussenegger, Martin

2018-05-08

Quorum sensing is a promising target for next-generation anti-infectives designed to address evolving bacterial drug resistance. The autoinducer-2 (AI-2) is a key quorum-sensing signal molecule which regulates bacterial group behaviors and is recognized by many Gram-negative and Gram-positive bacteria. Here we report a synthetic mammalian cell-based microbial-control device that detects microbial chemotactic formyl peptides through a formyl peptide sensor (FPS) and responds by releasing AI-2. The microbial-control device was designed by rewiring an artificial receptor-based signaling cascade to a modular biosynthetic AI-2 production platform. Mammalian cells equipped with the microbial-control gene circuit detect formyl peptides secreted from various microbes with high sensitivity and respond with robust AI-2 production, resulting in control of quorum sensing-related behavior of pathogenic Vibrio harveyi and attenuation of biofilm formation by the human pathogen Candida albicans. The ability to manipulate mixed microbial populations through fine-tuning of AI-2 levels may provide opportunities for future anti-infective strategies.

Anterior cingulate cortex and intuitive bias detection during number conservation.

PubMed

Simon, Grégory; Lubin, Amélie; Houdé, Olivier; De Neys, Wim

2015-01-01

Children's number conservation is often biased by misleading intuitions but the precise nature of these conservation errors is not clear. A key question is whether children detect that their erroneous conservation judgment is unwarranted. The present study reanalyzed available fMRI data to test the implication of the anterior cingulate cortex (ACC) in this detection process. We extracted mean BOLD (Blood Oxygen Level Dependent) signal values in an independently defined ACC region of interest (ROI) during presentation of classic and control number conservation problems. In classic trials, an intuitively cued visuospatial response conflicted with the correct conservation response, whereas this conflict was not present in the control trials. Results showed that ACC activation increased when solving the classic conservation problems. Critically, this increase did not differ between participants who solved the classic problems correctly (i.e., so-called conservers) and incorrectly (i.e., so-called non-conservers). Additional control analyses of inferior and lateral prefrontal ROIs showed that the group of conservers did show stronger activation in the right inferior frontal gyrus and right lateral middle frontal gyrus. In line with recent behavioral findings, these data lend credence to the hypothesis that even non-conserving children detect the biased nature of their judgment. The key difference between conservers and non-conservers seems to lie in a differential recruitment of inferior and lateral prefrontal regions associated with inhibitory control.

Enzyme Amplified Detection of Microbial Cell Wall Components

NASA Technical Reports Server (NTRS)

Wainwright, Norman R.

2004-01-01

This proposal is MBL's portion of NASA's Johnson Space Center's Astrobiology Center led by Principal Investigator, Dr. David McKay, entitled: 'Institute for the Study of Biomarkers in Astromaterials.' Dr. Norman Wainwright is the principal investigator at MBL and is responsible for developing methods to detect trace quantities of microbial cell wall chemicals using the enzyme amplification system of Limulus polyphemus and other related methods.

Performance of two quantitative PCR methods for microbial source tracking of human sewage and implications for microbial risk assessment in recreational waters

EPA Science Inventory

Before new, rapid quantitative PCR (qPCR) methods for recreational water quality assessment and microbial source tracking (MST) can be useful in a regulatory context, an understanding of the ability of the method to detect a DNA target (marker) when the contaminant soure has been...

Natural attenuation of contaminated marine sediments from an old floating dock Part II: changes of sediment microbial community structure and its relationship with environmental variables.

PubMed

Wang, Ya-Fen; Tam, Nora Fung-Yee

2012-04-15

Changes of microbial community structure and its relationship with various environmental variables in surface marine sediments were examined for a one-year period after the removal of an old floating dock in Hong Kong SAR, South China. Temporal variations in the microbial community structure were clearly revealed by principal component analysis (PCA) of the microbial ester-linked fatty acid methyl ester (EL-FAME) profiles. The most obvious shift in microbial community structure was detected 6 months after the removal of the dock, although no significant decline in the levels of pollutants could be detected. As determined by EL-FAME profiles, the microbial diversity recovered and the predominance of gram-negative bacteria was gradually replaced by gram-positive bacteria and fungi in the impacted stations. With redundancy analysis (RDA), the concentration of total polycyclic aromatic hydrocarbons (PAHs) was found to be the second important determinant of microbial community structure, next to Time. The relative abundance of 18:1ω9c and hydroxyl fatty acids enriched in the PAH hot spots, whereas 16:1ω9 and 18:1ω9t were negatively correlated to total PAH concentration. The significant relationships observed between microbial EL-FAME profiles and pollutants, exampled by PAHs in the present study, suggested the potential of microbial community analysis in the assessment of the natural attenuation process in contaminated environments. Copyright © 2012 Elsevier B.V. All rights reserved.

Microbial responses to microgravity and other low-shear environments.

PubMed

Nickerson, Cheryl A; Ott, C Mark; Wilson, James W; Ramamurthy, Rajee; Pierson, Duane L

2004-06-01

Microbial adaptation to environmental stimuli is essential for survival. While several of these stimuli have been studied in detail, recent studies have demonstrated an important role for a novel environmental parameter in which microgravity and the low fluid shear dynamics associated with microgravity globally regulate microbial gene expression, physiology, and pathogenesis. In addition to analyzing fundamental questions about microbial responses to spaceflight, these studies have demonstrated important applications for microbial responses to a ground-based, low-shear stress environment similar to that encountered during spaceflight. Moreover, the low-shear growth environment sensed by microbes during microgravity of spaceflight and during ground-based microgravity analogue culture is relevant to those encountered during their natural life cycles on Earth. While no mechanism has been clearly defined to explain how the mechanical force of fluid shear transmits intracellular signals to microbial cells at the molecular level, the fact that cross talk exists between microbial signal transduction systems holds intriguing possibilities that future studies might reveal common mechanotransduction themes between these systems and those used to sense and respond to low-shear stress and changes in gravitation forces. The study of microbial mechanotransduction may identify common conserved mechanisms used by cells to perceive changes in mechanical and/or physical forces, and it has the potential to provide valuable insight for understanding mechanosensing mechanisms in higher organisms. This review summarizes recent and future research trends aimed at understanding the dynamic effects of changes in the mechanical forces that occur in microgravity and other low-shear environments on a wide variety of important microbial parameters.

Microbial Responses to Microgravity and Other Low-Shear Environments

NASA Technical Reports Server (NTRS)

Nickerson, Cheryl A.; Ott, C. Mark; Wilson, James W.; Ramamurthy, Rajee; Pierson, Duane L.

2004-01-01

Microbial adaptation to environmental stimuli is essential for survival. While several of these stimuli have been studied in detail, recent studies have demonstrated an important role for a novel environmental parameter in which microgravity and the low fluid shear dynamics associated with microgravity globally regulate microbial gene expression, physiology, and pathogenesis. In addition to analyzing fundamental questions about microbial responses to spaceflight, these studies have demonstrated important applications for microbial responses to a ground-based, low-shear stress environment similar to that encountered during spaceflight. Moreover, the low-shear growth environment sensed by microbes during microgravity of spaceflight and during ground-based microgravity analogue culture is relevant to those encountered during their natural life cycles on Earth. While no mechanism has been clearly defined to explain how the mechanical force of fluid shear transmits intracellular signals to microbial cells at the molecular level, the fact that cross talk exists between microbial signal transduction systems holds intriguing possibilities that future studies might reveal common mechanotransduction themes between these systems and those used to sense and respond to low-shear stress and changes in gravitation forces. The study of microbial mechanotransduction may identify common conserved mechanisms used by cells to perceive changes in mechanical and/or physical forces, and it has the potential to provide valuable insight for understanding mechanosensing mechanisms in higher organisms. This review summarizes recent and future research trends aimed at understanding the dynamic effects of changes in the mechanical forces that occur in microgravity and other low-shear environments on a wide variety of important microbial parameters.

Exploration of Microbial Diversity and Community Structure of Lonar Lake: The Only Hypersaline Meteorite Crater Lake within Basalt Rock

PubMed Central

Paul, Dhiraj; Kumbhare, Shreyas V.; Mhatre, Snehit S.; Chowdhury, Somak P.; Shetty, Sudarshan A.; Marathe, Nachiket P.; Bhute, Shrikant; Shouche, Yogesh S.

2016-01-01

Lonar Lake is a hypersaline and hyperalkaline soda lake and the only meteorite impact crater in the world situated in basalt rocks. Although culture-dependent studies have been reported, a comprehensive understanding of microbial community composition and structure in Lonar Lake remains elusive. In the present study, microbial community structure associated with Lonar Lake sediment and water samples was investigated using high-throughput sequencing. Microbial diversity analysis revealed the existence of diverse, yet largely consistent communities. Proteobacteria (30%), Actinobacteria (24%), Firmicutes (11%), and Cyanobacteria (5%) predominated in the sequencing survey, whereas Bacteroidetes (1.12%), BD1-5 (0.5%), Nitrospirae (0.41%), and Verrucomicrobia (0.28%) were detected in relatively minor abundances in the Lonar Lake ecosystem. Within the Proteobacteria phylum, the Gammaproteobacteria represented the most abundantly detected class (21–47%) within sediment samples, but only a minor population in the water samples. Proteobacteria and Firmicutes were found at significantly higher abundance (p ≥ 0.05) in sediment samples, whereas members of Actinobacteria, Candidate division TM7 and Cyanobacteria (p ≥ 0.05) were significantly abundant in water samples. Compared to the microbial communities of other hypersaline soda lakes, those of Lonar Lake formed a distinct cluster, suggesting a different microbial community composition and structure. Here we report for the first time, the difference in composition of indigenous microbial communities between the sediment and water samples of Lonar Lake. An improved census of microbial community structure in this Lake ecosystem provides a foundation for exploring microbial biogeochemical cycling and microbial function in hypersaline lake environments. PMID:26834712

Potential Research and Development Synergies between Life support and Planetary protection

NASA Astrophysics Data System (ADS)

Lasseur, Ch.; Kminek, G.; Mergeay, M.

Long term manned missions of our Russian colleagues have demonstrated the risks associated with microbial contamination These risks concern both crew health via the metabolic consumables contamination water air but and also the hardware degradation Over the last six years ESA and IBMP have developed a collaboration to elaborate and document these microbial contamination issues The collaboration involved the mutual exchanges of knowledge as well as microbial samples and leads up to the microbial survey of the Russian module of the ISS Based on these results and in addition to an external expert report commissioned by ESA the agency initiated the development of a rapid and automated microbial detection and identification tool for use in future space missions In parallel to these developments and via several international meetings planetary protection experts have agreed to place clear specification of the microbial quality of future hardware landing on virgin planets as well as elaborate the preliminary requirements of contamination for manned missions on surface For these activities its is necessary to have a better understanding of microbial activity to create culture collection and to develop on-line detection tools Within this paper we present more deeply the life support activities related to microbial issues we identify some potential synergies with Planetary protection developments and we propose some pathway for collaboration between these two communities

Exploring ancient microbial community assemblages by creating complex lipid biomarker profiles for stromatolites and microbial mats in Hamelin Pool, Shark Bay, Australia

NASA Astrophysics Data System (ADS)

Myers, E.; Summons, R. E.; Schubotz, F.; Matys, E. D.

2015-12-01

Stromatolites that are biogenic in origin, a characteristic that can be determined by the coexistence of microbial mats (active microbial communities) and stromatolites (lithified structures) like in Hamelin Pool, comprise one of the best modern analogs to ancient microbial community assemblages. Comprehensive lipid biomarker profiles that include lipids of varying persistence in the rock record can help determine how previously living microbial communities are represented in lithified stromatolites. To create these profiles, the samples analyzed included non-lithified smooth, pustular, and colloform microbial mats, as well as smooth and colloform stromatolites. Select samples were separated into upper and lower layers of 5cm depth each. Intact polar lipids, glycerol dialkyl glycerol tetraethers, and bacteriohopanepolyols were analyzed via liquid chromatography-mass spectrometry (LC-MS) coupled to a Quadropole Time-of-Flight (QTOF) mass spectrometer; additionally, fatty acids from each sample were analyzed using gas chromatography-mass spectrometry (GC-MS) to prove consistent signatures with those determined by Allen et al. in 2010 for similar microbial mat samples. In accordance with those findings, 2-methylhopanoids were detected, as well as limited signals from higher (vascular) plants, the latter of which suggests terrestrial inputs, potentially from runoff. The rarely detected presence of 3-methylhopanoids appears in a significant portion of the samples, though further isolations of the molecule are needed to confirm. While all lipid profiles were relatively similar, certain differences in relative composition are likely attributable to morphological differences of the mats, some of which allow deeper oxygen and/or sunlight penetration, which influence the microbial community. However, overall similarities of transient and persistent lipids suggest that the microbial communities of both the non-lithified microbial mats and stromatolites are similar.

Microbial Load Monitor

NASA Technical Reports Server (NTRS)

Gibson, S. F.; Royer, E. R.

1979-01-01

The Microbial Load Monitor (MLM) is an automated and computerized system for detection and identification of microorganisms. Additionally, the system is designed to enumerate and provide antimicrobic susceptibility profiles for medically significant bacteria. The system is designed to accomplish these tasks in a time of 13 hours or less versus the traditional time of 24 hours for negatives and 72 hours or more for positives usually required for standard microbiological analysis. The MLM concept differs from other methods of microbial detection in that the system is designed to accept raw untreated clinical samples and to selectively identify each group or species that may be present in a polymicrobic sample.

Rapid System to Quantitatively Characterize the Airborne Microbial Community

NASA Technical Reports Server (NTRS)

Macnaughton, Sarah J.

1998-01-01

Bioaerosols have been linked to a wide range of different allergies and respiratory illnesses. Currently, microorganism culture is the most commonly used method for exposure assessment. Such culture techniques, however, generally fail to detect between 90-99% of the actual viable biomass. Consequently, an unbiased technique for detecting airborne microorganisms is essential. In this Phase II proposal, a portable air sampling device his been developed for the collection of airborne microbial biomass from indoor (and outdoor) environments. Methods were evaluated for extracting and identifying lipids that provide information on indoor air microbial biomass, and automation of these procedures was investigated. Also, techniques to automate the extraction of DNA were explored.

Current molecular and emerging nanobiotechnology approaches for the detection of microbial pathogens.

PubMed

Theron, Jacques; Eugene Cloete, Thomas; de Kwaadsteniet, Michele

2010-11-01

Waterborne microbial diseases are escalating worldwide increasing the need for powerful and sensitive diagnostics tools. Molecular methodologies, including immunological and nucleic acid-based methods, have only recently been applied in the water sector. Advances in nanotechnology and nanomaterials have opened the door for the development of new diagnostic tools with increased sensitivity and speed, and reduced cost and labor. Quantum dots, flo dots, gold nanoparticles, magnetic nanoparticles, carbon nanotubes, nanowires, and nanocantilevers, with their unique optical and physical properties, have already been applied in nanodiagnostics. Nanobiotechnology, once remaining technical and practical problems has been addressed, will play an important role in the detection of microbial pathogens.

In situ Detection of Microbial Life in the Deep Biosphere in Igneous Ocean Crust.

PubMed

Salas, Everett C; Bhartia, Rohit; Anderson, Louise; Hug, William F; Reid, Ray D; Iturrino, Gerardo; Edwards, Katrina J

2015-01-01

The deep biosphere is a major frontier to science. Recent studies have shown the presence and activity of cells in deep marine sediments and in the continental deep biosphere. Volcanic lavas in the deep ocean subsurface, through which substantial fluid flow occurs, present another potentially massive deep biosphere. We present results from the deployment of a novel in situ logging tool designed to detect microbial life harbored in a deep, native, borehole environment within igneous oceanic crust, using deep ultraviolet native fluorescence spectroscopy. Results demonstrate the predominance of microbial-like signatures within the borehole environment, with densities in the range of 10(5) cells/mL. Based on transport and flux models, we estimate that such a concentration of microbial cells could not be supported by transport through the crust, suggesting in situ growth of these communities.

Tracking heavy water (D2O) incorporation for identifying and sorting active microbial cells

PubMed Central

Berry, David; Mader, Esther; Lee, Tae Kwon; Woebken, Dagmar; Wang, Yun; Zhu, Di; Palatinszky, Marton; Schintlmeister, Arno; Schmid, Markus C.; Hanson, Buck T.; Shterzer, Naama; Mizrahi, Itzhak; Rauch, Isabella; Decker, Thomas; Bocklitz, Thomas; Popp, Jürgen; Gibson, Christopher M.; Fowler, Patrick W.; Huang, Wei E.; Wagner, Michael

2015-01-01

Microbial communities are essential to the function of virtually all ecosystems and eukaryotes, including humans. However, it is still a major challenge to identify microbial cells active under natural conditions in complex systems. In this study, we developed a new method to identify and sort active microbes on the single-cell level in complex samples using stable isotope probing with heavy water (D2O) combined with Raman microspectroscopy. Incorporation of D2O-derived D into the biomass of autotrophic and heterotrophic bacteria and archaea could be unambiguously detected via C-D signature peaks in single-cell Raman spectra, and the obtained labeling pattern was confirmed by nanoscale-resolution secondary ion MS. In fast-growing Escherichia coli cells, label detection was already possible after 20 min. For functional analyses of microbial communities, the detection of D incorporation from D2O in individual microbial cells via Raman microspectroscopy can be directly combined with FISH for the identification of active microbes. Applying this approach to mouse cecal microbiota revealed that the host-compound foragers Akkermansia muciniphila and Bacteroides acidifaciens exhibited distinctive response patterns to amendments of mucin and sugars. By Raman-based cell sorting of active (deuterated) cells with optical tweezers and subsequent multiple displacement amplification and DNA sequencing, novel cecal microbes stimulated by mucin and/or glucosamine were identified, demonstrating the potential of the nondestructive D2O-Raman approach for targeted sorting of microbial cells with defined functional properties for single-cell genomics. PMID:25550518

Molecular Viability Testing of UV-Inactivated Bacteria.

PubMed

Weigel, Kris M; Nguyen, Felicia K; Kearney, Moira R; Meschke, John S; Cangelosi, Gerard A

2017-05-15

PCR is effective in detecting bacterial DNA in samples, but it is unable to differentiate viable bacteria from inactivated cells or free DNA fragments. New PCR-based analytical strategies have been developed to address this limitation. Molecular viability testing (MVT) correlates bacterial viability with the ability to rapidly synthesize species-specific rRNA precursors (pre-rRNA) in response to brief nutritional stimulation. Previous studies demonstrated that MVT can assess bacterial inactivation by chlorine, serum, and low-temperature pasteurization. Here, we demonstrate that MVT can detect inactivation of Escherichia coli , Aeromonas hydrophila , and Enterococcus faecalis cells by UV irradiation. Some UV-inactivated E. coli cells transiently retained the ability to synthesize pre-rRNA postirradiation (generating false-positive MVT results), but this activity ceased within 1 h following UV exposure. Viable but transiently undetectable (by culture) E. coli cells were consistently detected by MVT. An alternative viability testing method, viability PCR (vPCR), correlates viability with cell envelope integrity. This method did not distinguish viable bacteria from UV-inactivated bacteria under some conditions, indicating that the inactivated cells retained intact cell envelopes. MVT holds promise as a means to rapidly assess microbial inactivation by UV treatment. IMPORTANCE UV irradiation is increasingly being used to disinfect water, food, and other materials for human use. Confirming the effectiveness of UV disinfection remains a challenging task. In particular, microbiological methods that rely on rapid detection of microbial DNA can yield misleading results, due to the detection of remnant DNA associated with dead microbial cells. This report describes a novel method that rapidly distinguishes living microbial cells from dead microbial cells after UV disinfection. Copyright © 2017 American Society for Microbiology.

Pyrosequencing for Microbial Identification and Characterization

PubMed Central

Cummings, Patrick J.; Ahmed, Ray; Durocher, Jeffrey A.; Jessen, Adam; Vardi, Tamar; Obom, Kristina M.

2013-01-01

Pyrosequencing is a versatile technique that facilitates microbial genome sequencing that can be used to identify bacterial species, discriminate bacterial strains and detect genetic mutations that confer resistance to anti-microbial agents. The advantages of pyrosequencing for microbiology applications include rapid and reliable high-throughput screening and accurate identification of microbes and microbial genome mutations. Pyrosequencing involves sequencing of DNA by synthesizing the complementary strand a single base at a time, while determining the specific nucleotide being incorporated during the synthesis reaction. The reaction occurs on immobilized single stranded template DNA where the four deoxyribonucleotides (dNTP) are added sequentially and the unincorporated dNTPs are enzymatically degraded before addition of the next dNTP to the synthesis reaction. Detection of the specific base incorporated into the template is monitored by generation of chemiluminescent signals. The order of dNTPs that produce the chemiluminescent signals determines the DNA sequence of the template. The real-time sequencing capability of pyrosequencing technology enables rapid microbial identification in a single assay. In addition, the pyrosequencing instrument, can analyze the full genetic diversity of anti-microbial drug resistance, including typing of SNPs, point mutations, insertions, and deletions, as well as quantification of multiple gene copies that may occur in some anti-microbial resistance patterns. PMID:23995536

Pyrosequencing for microbial identification and characterization.

PubMed

Cummings, Patrick J; Ahmed, Ray; Durocher, Jeffrey A; Jessen, Adam; Vardi, Tamar; Obom, Kristina M

2013-08-22

Pyrosequencing is a versatile technique that facilitates microbial genome sequencing that can be used to identify bacterial species, discriminate bacterial strains and detect genetic mutations that confer resistance to anti-microbial agents. The advantages of pyrosequencing for microbiology applications include rapid and reliable high-throughput screening and accurate identification of microbes and microbial genome mutations. Pyrosequencing involves sequencing of DNA by synthesizing the complementary strand a single base at a time, while determining the specific nucleotide being incorporated during the synthesis reaction. The reaction occurs on immobilized single stranded template DNA where the four deoxyribonucleotides (dNTP) are added sequentially and the unincorporated dNTPs are enzymatically degraded before addition of the next dNTP to the synthesis reaction. Detection of the specific base incorporated into the template is monitored by generation of chemiluminescent signals. The order of dNTPs that produce the chemiluminescent signals determines the DNA sequence of the template. The real-time sequencing capability of pyrosequencing technology enables rapid microbial identification in a single assay. In addition, the pyrosequencing instrument, can analyze the full genetic diversity of anti-microbial drug resistance, including typing of SNPs, point mutations, insertions, and deletions, as well as quantification of multiple gene copies that may occur in some anti-microbial resistance patterns.

Application of clone library analysis and real-time PCR for comparison of microbial communities in a low-grade copper sulfide ore bioheap leachate.

PubMed

Bowei, Chen; Xingyu, Liu; Wenyan, Liu; Jiankang, Wen

2009-11-01

The microbial communities of leachate from a bioleaching heap located in China were analyzed using the 16S rRNA gene clone library and real-time quantitative PCR. Both methods showed that Leptospirillum spp. were the dominant bacteria, and Ferroplasma acidiphilum were the only archaea detected in the leachate. Clone library results indicated that nine operational taxonomic units (OTUs) were obtained, which fell into four divisions, the Nitrospirae (74%), the gamma-Proteobacteria (14%), the Actinobacteria (6%) and the Euryarchaeota (6%). The results obtained by real-time PCR in some ways were the same as clone library analysis. Furthermore, Sulfobacillus spp., detected only by real-time PCR, suggests that real-time PCR was a reliable technology to study the microbial communities in bioleaching environments. It is a useful tool to assist clone library analysis, to further understand microbial consortia and to have comprehensive and exact microbiological information about bioleaching environments. Finally, the interactions among the microorganisms detected in the leachate were summarized according to the characteristics of these species.

Assessing the genetic diversity of Cu resistance in mine tailings through high-throughput recovery of full-length copA genes

PubMed Central

Li, Xiaofang; Zhu, Yong-Guan; Shaban, Babak; Bruxner, Timothy J. C.; Bond, Philip L.; Huang, Longbin

2015-01-01

Characterizing the genetic diversity of microbial copper (Cu) resistance at the community level remains challenging, mainly due to the polymorphism of the core functional gene copA. In this study, a local BLASTN method using a copA database built in this study was developed to recover full-length putative copA sequences from an assembled tailings metagenome; these sequences were then screened for potentially functioning CopA using conserved metal-binding motifs, inferred by evolutionary trace analysis of CopA sequences from known Cu resistant microorganisms. In total, 99 putative copA sequences were recovered from the tailings metagenome, out of which 70 were found with high potential to be functioning in Cu resistance. Phylogenetic analysis of selected copA sequences detected in the tailings metagenome showed that topology of the copA phylogeny is largely congruent with that of the 16S-based phylogeny of the tailings microbial community obtained in our previous study, indicating that the development of copA diversity in the tailings might be mainly through vertical descent with few lateral gene transfer events. The method established here can be used to explore copA (and potentially other metal resistance genes) diversity in any metagenome and has the potential to exhaust the full-length gene sequences for downstream analyses. PMID:26286020

Transport of a conservative and "smart" tracers' in a first-order creek: role of transient storage type

USDA-ARS?s Scientific Manuscript database

Quantification of microbial fate and transport in streams has become one of most important topics in studying biogeochemical properties and behavior of stream ecosystems. Using "smart" tracer such as resazurin (Raz) allows assessment of sediment-water interactions and associated biological activity ...

Multiple microbial activity-based measures reflect effects of cover cropping and tillage on soils

USDA-ARS?s Scientific Manuscript database

Agricultural producers, conservation professionals, and policy makers are eager to learn of soil analytical techniques and data that document improvement in soil health by agricultural practices such as no-till and incorporation of cover crops. However, there is considerable uncertainty within the r...

Glyphosate applications,glyphosate resistant corn, and tillage on nitrification rates and distribution of nitrifying microbial communities

USDA-ARS?s Scientific Manuscript database

Conservation tillage practices have combined genetically modified glyphosate resistant corn crops along with applications of the herbicide glyphosate. We tested the null hypothesis that the soil process of nitrification and the distribution of archaeal and bacterial nitrifying communities would not ...

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.

Single gene-based distinction of individual microbial genomes from a mixed population of microbial cells.

PubMed

Tamminen, Manu V; Virta, Marko P J

2015-01-01

Recent progress in environmental microbiology has revealed vast populations of microbes in any given habitat that cannot be detected by conventional culturing strategies. The use of sensitive genetic detection methods such as CARD-FISH and in situ PCR have been limited by the cell wall permeabilization requirement that cannot be performed similarly on all cell types without lysing some and leaving some nonpermeabilized. Furthermore, the detection of low copy targets such as genes present in single copies in the microbial genomes, has remained problematic. We describe an emulsion-based procedure to trap individual microbial cells into picoliter-volume polyacrylamide droplets that provide a rigid support for genetic material and therefore allow complete degradation of cellular material to expose the individual genomes. The polyacrylamide droplets are subsequently converted into picoliter-scale reactors for genome amplification. The amplified genomes are labeled based on the presence of a target gene and differentiated from those that do not contain the gene by flow cytometry. Using the Escherichia coli strains XL1 and MC1061, which differ with respect to the presence (XL1), or absence (MC1061) of a single copy of a tetracycline resistance gene per genome, we demonstrate that XL1 genomes present at 0.1% of MC1061 genomes can be differentiated using this method. Using a spiked sediment microbial sample, we demonstrate that the method is applicable to highly complex environmental microbial communities as a target gene-based screen for individual microbes. The method provides a novel tool for enumerating functional cell populations in complex microbial communities. We envision that the method could be optimized for fluorescence-activated cell sorting to enrich genetic material of interest from complex environmental samples.

Microbial community functional structure in response to antibiotics in pharmaceutical wastewater treatment systems.

PubMed

Zhang, Yu; Xie, Jianping; Liu, Miaomiao; Tian, Zhe; He, Zhili; van Nostrand, Joy D; Ren, Liren; Zhou, Jizhong; Yang, Min

2013-10-15

It is widely demonstrated that antibiotics in the environment affect microbial community structure. However, direct evidence regarding the impacts of antibiotics on microbial functional structures in wastewater treatment systems is limited. Herein, a high-throughput functional gene array (GeoChip 3.0) in combination with quantitative PCR and clone libraries were used to evaluate the microbial functional structures in two biological wastewater treatment systems, which treat antibiotic production wastewater mainly containing oxytetracycline. Despite the bacteriostatic effects of antibiotics, the GeoChip detected almost all key functional gene categories, including carbon cycling, nitrogen cycling, etc., suggesting that these microbial communities were functionally diverse. Totally 749 carbon-degrading genes belonging to 40 groups (24 from bacteria and 16 from fungi) were detected. The abundance of several fungal carbon-degrading genes (e.g., glyoxal oxidase (glx), lignin peroxidase or ligninase (lip), manganese peroxidase (mnp), endochitinase, exoglucanase_genes) was significantly correlated with antibiotic concentrations (Mantel test; P < 0.05), showing that the fungal functional genes have been enhanced by the presence of antibiotics. However, from the fact that the majority of carbon-degrading genes were derived from bacteria and diverse antibiotic resistance genes were detected in bacteria, it was assumed that many bacteria could survive in the environment by acquiring antibiotic resistance and may have maintained the position as a main player in nutrient removal. Variance partitioning analysis showed that antibiotics could explain 24.4% of variations in microbial functional structure of the treatment systems. This study provides insights into the impacts of antibiotics on microbial functional structure of a unique system receiving antibiotic production wastewater, and reveals the potential importance of the cooperation between fungi and bacteria with antibiotic resistance in maintaining the stability and performance of the systems. Copyright © 2013 Elsevier Ltd. All rights reserved.

Effects of Environmental Toxicants on Metabolic Activity of Natural Microbial Communities

PubMed Central

Barnhart, Carole L. H.; Vestal, J. Robie

1983-01-01

Two methods of measuring microbial activity were used to study the effects of toxicants on natural microbial communities. The methods were compared for suitability for toxicity testing, sensitivity, and adaptability to field applications. This study included measurements of the incorporation of 14C-labeled acetate into microbial lipids and microbial glucosidase activity. Activities were measured per unit biomass, determined as lipid phosphate. The effects of various organic and inorganic toxicants on various natural microbial communities were studied. Both methods were useful in detecting toxicity, and their comparative sensitivities varied with the system studied. In one system, the methods showed approximately the same sensitivities in testing the effects of metals, but the acetate incorporation method was more sensitive in detecting the toxicity of organic compounds. The incorporation method was used to study the effects of a point source of pollution on the microbiota of a receiving stream. Toxic doses were found to be two orders of magnitude higher in sediments than in water taken from the same site, indicating chelation or adsorption of the toxicant by the sediment. The microbiota taken from below a point source outfall was 2 to 100 times more resistant to the toxicants tested than was that taken from above the outfall. Downstream filtrates in most cases had an inhibitory effect on the natural microbiota taken from above the pollution source. The microbial methods were compared with commonly used bioassay methods, using higher organisms, and were found to be similar in ability to detect comparative toxicities of compounds, but were less sensitive than methods which use standard media because of the influences of environmental factors. PMID:16346432

Medium-Throughput Screen of Microbially Produced Serotonin via a G-Protein-Coupled Receptor-Based Sensor.

PubMed

Ehrenworth, Amy M; Claiborne, Tauris; Peralta-Yahya, Pamela

2017-10-17

Chemical biosensors, for which chemical detection triggers a fluorescent signal, have the potential to accelerate the screening of noncolorimetric chemicals produced by microbes, enabling the high-throughput engineering of enzymes and metabolic pathways. Here, we engineer a G-protein-coupled receptor (GPCR)-based sensor to detect serotonin produced by a producer microbe in the producer microbe's supernatant. Detecting a chemical in the producer microbe's supernatant is nontrivial because of the number of other metabolites and proteins present that could interfere with sensor performance. We validate the two-cell screening system for medium-throughput applications, opening the door to the rapid engineering of microbes for the increased production of serotonin. We focus on serotonin detection as serotonin levels limit the microbial production of hydroxystrictosidine, a modified alkaloid that could accelerate the semisynthesis of camptothecin-derived anticancer pharmaceuticals. This work shows the ease of generating GPCR-based chemical sensors and their ability to detect specific chemicals in complex aqueous solutions, such as microbial spent medium. In addition, this work sets the stage for the rapid engineering of serotonin-producing microbes.

Specific capture and detection of Staphylococcus aureus with high-affinity modified aptamers to cell surface components

PubMed Central

Baumstummler, A; Lehmann, D; Janjic, N; Ochsner, UA

2014-01-01

Slow off-rate modified aptamer (SOMAmer) reagents were generated to several Staphylococcus aureus cell surface-associated proteins via SELEX with multiple modified DNA libraries using purified recombinant or native proteins. High-affinity binding agents with sub-nanomolar Kd's were obtained for staphylococcal protein A (SpA), clumping factors (ClfA, ClfB), fibronectin-binding proteins (FnbA, FnbB) and iron-regulated surface determinants (Isd). Further screening revealed several SOMAmers that specifically bound to Staph. aureus cells from all strains that were tested, but not to other staphylococci or other bacteria. SpA and ClfA SOMAmers proved useful for the selective capture and enrichment of Staph. aureus cells, as shown by culture and PCR, leading to improved limits of detection and efficient removal of PCR inhibitors. Detection of Staph. aureus cells was enhanced by several orders of magnitude when the bacterial cell surface was coated with SOMAmers followed by qPCR of the SOMAmers. Furthermore, fluorescence-labelled SpA SOMAmers demonstrated their utility as direct detection agents in flow cytometry. Significance and Impact of the Study Monitoring for microbial contamination of food, water, nonsterile products or the environment is typically based on culture, PCR or antibodies. Aptamers that bind with high specificity and affinity to well-conserved cell surface epitopes represent a promising novel type of reagents to detect bacterial cells without the need for culture or cell lysis, including for the capture and enrichment of bacteria present at low cell densities and for the direct detection via qPCR or fluorescent staining. PMID:24935714

Polythiophene biosensor for rapid detection of microbial particles in water.

PubMed

Plante, Marie-Pier; Bérubé, Eve; Bissonnette, Luc; Bergeron, Michel G; Leclerc, Mario

2013-06-12

Most microbial particles have a negatively charged surface and in this work, we describe a water quality monitoring application of a cationic polythiophene derivative (AH-35) for the rapid assessment of microbial contamination of water. Using E. coli as a prototype microbial particle, we demonstrate that the AH-35 polymer can provide a qualitative assessment of water if exposed to more than 500 CFU/mL, thereby paving the way to a new family of biosensors potentially useful for monitoring drinking water distribution systems.

Microbial response to environmental gradients in a ceramic-based diffusion system.

PubMed

Wolfaardt, G M; Hendry, M J; Birkham, T; Bressel, A; Gardner, M N; Sousa, A J; Korber, D R; Pilaski, M

2008-05-01

A solid, porous matrix was used to establish steady-state concentration profiles upon which microbial responses to concentration gradients of nutrients or antimicrobial agents could be quantified. This technique relies on the development of spatially defined concentration gradients across a ceramic plate resulting from the diffusion of solutes through the porous ceramic matrix. A two-dimensional, finite-element numerical transport model was used to predict the establishment of concentration profiles, after which concentration profiles of conservative tracers were quantified fluorometrically and chemically at the solid-liquid interface to verify the simulated profiles. Microbial growth responses to nutrient, hypochloride, and antimicrobial concentration gradients were then quantified using epifluorescent or scanning confocal laser microscopy. The observed microbial response verified the establishment and maintenance of stable concentration gradients along the solid-liquid interface. These results indicate the ceramic diffusion system has potential for the isolation of heterogeneous microbial communities as well as for testing the efficacy of antimicrobial agents. In addition, the durability of the solid matrix allowed long-term investigations, making this approach preferable to conventional gel-stabilized systems that are impeded by erosion as well as expansion or shrinkage of the gel. Copyright 2008 Wiley Periodicals, Inc.

The life sulfuric: microbial ecology of sulfur cycling in marine sediments

PubMed Central

Wasmund, Kenneth; Mußmann, Marc

2017-01-01

Summary Almost the entire seafloor is covered with sediments that can be more than 10 000 m thick and represent a vast microbial ecosystem that is a major component of Earth's element and energy cycles. Notably, a significant proportion of microbial life in marine sediments can exploit energy conserved during transformations of sulfur compounds among different redox states. Sulfur cycling, which is primarily driven by sulfate reduction, is tightly interwoven with other important element cycles (carbon, nitrogen, iron, manganese) and therefore has profound implications for both cellular‐ and ecosystem‐level processes. Sulfur‐transforming microorganisms have evolved diverse genetic, metabolic, and in some cases, peculiar phenotypic features to fill an array of ecological niches in marine sediments. Here, we review recent and selected findings on the microbial guilds that are involved in the transformation of different sulfur compounds in marine sediments and emphasise how these are interlinked and have a major influence on ecology and biogeochemistry in the seafloor. Extraordinary discoveries have increased our knowledge on microbial sulfur cycling, mainly in sulfate‐rich surface sediments, yet many questions remain regarding how sulfur redox processes may sustain the deep‐subsurface biosphere and the impact of organic sulfur compounds on the marine sulfur cycle. PMID:28419734

The nanostructure of microbially-reduced graphene oxide fosters thick and highly-performing electrochemically-active biofilms

NASA Astrophysics Data System (ADS)

Virdis, Bernardino; Dennis, Paul G.

2017-07-01

Biofilms of electrochemically-active organisms are used in microbial electrochemical technologies (METs) to catalyze bioreactions otherwise not possible at bare electrodes. At present, however, achievable current outputs are still below levels considered sufficient for economic viability of large-scale METs implementations. Here, we report three-dimensional, self-aggregating biofilm composites comprising of microbial cells embedded with microbially-reduced graphene oxide (rGO) nanoparticles to form a thick macro-porous network with superior electrochemical properties. In the presence of metabolic substrate, these hybrid biofilms are capable of producing up to five times more catalytic current than the control biofilms. Cyclic voltammetry, linear sweep voltammetry, and electrochemical impedance spectroscopy, show that in spite of the increased thickness, the biofilms amended with GO display lower polarization/charge transfer resistance compared to the controls, which we ascribe to the incorporation of rGO into the biofilms, which (1) promotes fast electron transfer, yet conserving a macroporous structure that allows free diffusion of reactants and products, and (2) enhances the interfacial dynamics by allowing a higher load of microbial cells per electrode surface area. These results suggest an easy-to-apply and cost-effective method to produce high-performing electrochemically-active biofilms in situ.

Distribution and abundance of microbial biomass in Rocky Mountain spring snowpacks

Treesearch

P. D. Brooks; S. K. Schmidt; R. Sommerfeld; R. Musselman

1993-01-01

Snowpacks in both Colorado and Wyoming were sampled on 15 dates for total microbial biomass, ratio of bacteria to fungi, and major inorganic ions. Levels of viable microbial biomass remained low throughout the period, peaking at 0.05 micrograms carbon/mi. Microscopic analyses indicated this biomass was composed primarily of bacteria. Fungi were not detected in samples...

Linking microbial community structure and microbial processes: An empirical and conceptual overview

USGS Publications Warehouse

Bier, R.L.; Bernhardt, Emily S.; Boot, Claudia M.; Graham, Emily B.; Hall, Edward K.; Lennon, Jay T.; Nemergut, Diana R.; Osborne, Brooke B.; Ruiz-Gonzalez, Clara; Schimel, Joshua P.; Waldrop, Mark P.; Wallenstein, Matthew D.

2015-01-01

A major goal of microbial ecology is to identify links between microbial community structure and microbial processes. Although this objective seems straightforward, there are conceptual and methodological challenges to designing studies that explicitly evaluate this link. Here, we analyzed literature documenting structure and process responses to manipulations to determine the frequency of structure-process links and whether experimental approaches and techniques influence link detection. We examined nine journals (published 2009–13) and retained 148 experimental studies measuring microbial community structure and processes. Many qualifying papers (112 of 148) documented structure and process responses, but few (38 of 112 papers) reported statistically testing for a link. Of these tested links, 75% were significant and typically used Spearman or Pearson's correlation analysis (68%). No particular approach for characterizing structure or processes was more likely to produce significant links. Process responses were detected earlier on average than responses in structure or both structure and process. Together, our findings suggest that few publications report statistically testing structure-process links. However, when links are tested for they often occur but share few commonalities in the processes or structures that were linked and the techniques used for measuring them.

Plasmonic cell nanocoating: a new concept for rapid microbial screening.

PubMed

Xu, Ke; Bui, Minh-Phuong N; Fang, Aiqin; Abbas, Abdennour

2017-11-01

Nanocoating of single microbial cells with gold nanostructures can confer optical, electrical, thermal, and mechanical properties to microorganisms, thus enabling new avenues for their control, study, application, and detection. Cell nanocoating is often performed using layer-by-layer (LbL) deposition. LbL is time-consuming and relies on nonspecific electrostatic interactions, which limit potential applications for microbial diagnostics. Here, we show that, by taking advantage of surface molecules densely present in the microbial outer layers, cell nanocoating with gold nanoparticles can be achieved within seconds using surface molecules, including disulfide- bond-containing (Dsbc) proteins and chitin. A simple activation of these markers and their subsequent interaction with gold nanoparticles allow specific microbial screening and quantification of bacteria and fungi within 5 and 30 min, respectively. The use of plasmonics and fluorescence as transduction methods offers a limit of detection below 35 cfu mL -1 for E. coli bacteria and 1500 cfu mL -1 for M. circinelloides fungi using a hand-held fluorescent reader. Graphical abstract A new concept for rapid microbial screening by targeting disulfide - bond-containing (Dsbc) proteins and chitin with reducing agents and gold nanoparticles.

Rapid Electrochemical Detection and Identification of Microbiological and Chemical Contaminants for Manned Spaceflight Project

NASA Technical Reports Server (NTRS)

Pierson, Duane; Botkin, Douglas; Gazda, Daniel

2014-01-01

Microbial control in the spacecraft environment is a daunting task, especially in the presence of human crew members. Currently, assessing the potential crew health risk associated with a microbial contamination event requires return of representative environmental samples that are analyzed in a ground-based laboratory. It is therefore not currently possible to quickly identify microbes during spaceflight. This project addresses the unmet need for spaceflight-compatible microbial identification technology. The electrochemical detection and identification platform is expected to provide a sensitive, specific, and rapid sample-to-answer capability for in-flight microbial monitoring that can distinguish between related microorganisms (pathogens and non-pathogens) as well as chemical contaminants. This will dramatically enhance our ability to monitor the spacecraft environment and the health risk to the crew. Further, the project is expected to eliminate the need for sample return while significantly reducing crew time required for detection of multiple targets. Initial work will focus on the optimization of bacterial detection and identification. The platform is designed to release nucleic acids (DNA and RNA) from microorganisms without the use of harmful chemicals. Bacterial DNA or RNA is captured by bacteria-specific probe molecules that are bound to a microelectrode, and that capture event can generate a small change in the electrical current (Lam, et al. 2012. Anal. Chem. 84(1): 21-5.). This current is measured, and a determination is made whether a given microbe is present in the sample analyzed. Chemical detection can be accomplished by directly applying a sample to the microelectrode and measuring the resulting current change. This rapid microbial and chemical detection device is designed to be a low-cost, low-power platform anticipated to be operated independently of an external power source, characteristics optimal for manned spaceflight and areas where power and computing resources are scarce.

Reproducibility and quantitation of amplicon sequencing-based detection

PubMed Central

Zhou, Jizhong; Wu, Liyou; Deng, Ye; Zhi, Xiaoyang; Jiang, Yi-Huei; Tu, Qichao; Xie, Jianping; Van Nostrand, Joy D; He, Zhili; Yang, Yunfeng

2011-01-01

To determine the reproducibility and quantitation of the amplicon sequencing-based detection approach for analyzing microbial community structure, a total of 24 microbial communities from a long-term global change experimental site were examined. Genomic DNA obtained from each community was used to amplify 16S rRNA genes with two or three barcode tags as technical replicates in the presence of a small quantity (0.1% wt/wt) of genomic DNA from Shewanella oneidensis MR-1 as the control. The technical reproducibility of the amplicon sequencing-based detection approach is quite low, with an average operational taxonomic unit (OTU) overlap of 17.2%±2.3% between two technical replicates, and 8.2%±2.3% among three technical replicates, which is most likely due to problems associated with random sampling processes. Such variations in technical replicates could have substantial effects on estimating β-diversity but less on α-diversity. A high variation was also observed in the control across different samples (for example, 66.7-fold for the forward primer), suggesting that the amplicon sequencing-based detection approach could not be quantitative. In addition, various strategies were examined to improve the comparability of amplicon sequencing data, such as increasing biological replicates, and removing singleton sequences and less-representative OTUs across biological replicates. Finally, as expected, various statistical analyses with preprocessed experimental data revealed clear differences in the composition and structure of microbial communities between warming and non-warming, or between clipping and non-clipping. Taken together, these results suggest that amplicon sequencing-based detection is useful in analyzing microbial community structure even though it is not reproducible and quantitative. However, great caution should be taken in experimental design and data interpretation when the amplicon sequencing-based detection approach is used for quantitative analysis of the β-diversity of microbial communities. PMID:21346791

Microbial succession and stimulation following a test well injection simulating CO2 leakage into shallow Newark Basin aquifers

NASA Astrophysics Data System (ADS)

Dueker, M.; Clauson, K.; Yang, Q.; Umemoto, K.; Seltzer, A. M.; Zakharova, N. V.; Matter, J. M.; Stute, M.; Takahashi, T.; Goldberg, D.; O'Mullan, G. D.

2012-12-01

Despite growing appreciation for the importance of microbes in altering geochemical reactions in the subsurface, the microbial response to geological carbon sequestration injections and the role of microbes in altering metal mobilization following leakage scenarios in shallow aquifers remain poorly constrained. A Newark Basin test well was utilized in field experiments to investigate patterns of microbial succession following injection of CO2 saturated water into isolated aquifer intervals. Additionally, laboratory mesocosm experiments, including microbially-active and inactive (autoclave sterilized) treatments, were used to constrain the microbial role in mineral dissolution, trace metal release, and gas production (e.g. hydrogen and methane). Hydrogen production was detected in both sterilized and unsterilized laboratory mesocosm treatments, indicating abiotic hydrogen production may occur following CO2 leakage, and methane production was detected in unsterilized, microbially active mesocosms. In field experiments, a decrease in pH following injection of CO2 saturated aquifer water was accompanied by mobilization of trace elements (e.g. Fe and Mn), the production of hydrogen gas, and increased bacterial cell concentrations. 16S ribosomal RNA clone libraries, from samples collected before and after the test well injection, were compared in an attempt to link variability in geochemistry to changes in aquifer microbiology. Significant changes in microbial composition, compared to background conditions, were found following the test well injection, including a decrease in Proteobacteria, and an increased presence of Firmicutes, Verrucomicrobia, Acidobacteria and other microbes associated with iron reducing and syntrophic metabolism. The concurrence of increased microbial cell concentration, and rapid microbial community succession, with increased concentrations of hydrogen gas suggests that abiotically produced hydrogen may serve as an ecologically-relevant energy source stimulating changes in aquifer microbial communities immediately following CO2 leakage.

Similar soil microbial community structure across different environments after long-term succession: evidence from volcanoes of different ages.

PubMed

Xu, Shangqi; Zhang, Jianfeng; Luo, Shasha; Zhou, Xue; Shi, Shaohua; Tian, Chunjie

2018-06-08

Soil microbes play critical roles in global biogeochemical cycles, but their succession patterns across long temporal scales have rarely been studied. In this study, soil samples were collected from three volcanoes in Wudalianchi, northeastern China: Laoheishan (LH, approximately 240 years old), Dongjiaodebushan (DJ, 0.45-0.6 million years old), and Nangelaqiushan (NG, 0.8-1.3 million years old). For each volcano, both southern (S) and northern (N) slope aspects were sampled. Soil microbial communities were analyzed using phospholipid fatty acid analysis (PLFA). The results showed that soil properties and microbial biomass changed perceptibly among different volcanoes and different slope aspects. Almost all of the detected soil nutrient contents of LH were lowest, and total microbial biomass of LH was 40 and 36% lower than those of NG and DJ, respectively. LH was significantly different from NG and DJ in soil microbial community structure with a higher relative abundance of fungi and a lower relative abundance of actinomycetes and bacteria. However, for the two ancient volcanoes (NG and DJ), soil microbial community structures were highly similar among different ages and different slope aspects. No difference was detected in any of the measured microbial indices, including richness, evenness, Shannon's diversity, Simpson's diversity and the relative abundance of different microbial groups. The results indicated that while soil microbial biomass may change across different soil environments after long-term succession, soil microbial community structure can remain relatively stable. The results further indicated that soil microbes may show different successional patterns in different stages of succession. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

In situ Detection of Microbial Life in the Deep Biosphere in Igneous Ocean Crust

PubMed Central

Salas, Everett C.; Bhartia, Rohit; Anderson, Louise; Hug, William F.; Reid, Ray D.; Iturrino, Gerardo; Edwards, Katrina J.

2015-01-01

The deep biosphere is a major frontier to science. Recent studies have shown the presence and activity of cells in deep marine sediments and in the continental deep biosphere. Volcanic lavas in the deep ocean subsurface, through which substantial fluid flow occurs, present another potentially massive deep biosphere. We present results from the deployment of a novel in situ logging tool designed to detect microbial life harbored in a deep, native, borehole environment within igneous oceanic crust, using deep ultraviolet native fluorescence spectroscopy. Results demonstrate the predominance of microbial-like signatures within the borehole environment, with densities in the range of 105 cells/mL. Based on transport and flux models, we estimate that such a concentration of microbial cells could not be supported by transport through the crust, suggesting in situ growth of these communities. PMID:26617595

A controlled comparison of the BacT/ALERT® 3D and VIRTUO™ microbial detection systems.

PubMed

Totty, H; Ullery, M; Spontak, J; Viray, J; Adamik, M; Katzin, B; Dunne, W M; Deol, P

2017-10-01

The performance of the next-generation BacT/ALERT® VIRTUO™ Microbial Detection System (VIRTUO™, bioMérieux Inc., Hazelwood, MO) was compared to the BacT/ALERT® 3D Microbial Detection System (3D, bioMérieux Inc., Durham, NC) using BacT/ALERT® FA Plus (FA Plus), BacT/ALERT® PF Plus (PF Plus), BacT/ALERT® FN Plus (FN Plus), BacT/ALERT® Standard Aerobic (SA), and BacT/ALERT® Standard Anaerobic (SN) blood culture bottles (bioMérieux Inc., Durham, NC). A seeded limit of detection (LoD) study was performed for each bottle type in both systems. The LoD studies demonstrated that both systems were capable of detecting organisms at nearly identical levels [<10 colony-forming units (CFU) per bottle], with no significant difference. Following LoD determination, a seeded study was performed to compare the time to detection (TTD) between the systems using a panel of clinically relevant microorganisms inoculated at or near the LoD with 0, 4, or 10 mL of healthy human blood. VIRTUO™ exhibited a faster TTD by an average of 3.5 h, as well as demonstrated a significantly improved detection rate of 99.9% compared to 98.8% with 3D (p-value <0.05).

Monitoring microbial metabolites using an inductively coupled resonance circuit

NASA Astrophysics Data System (ADS)

Karnaushenko, Daniil; Baraban, Larysa; Ye, Dan; Uguz, Ilke; Mendes, Rafael G.; Rümmeli, Mark H.; de Visser, J. Arjan G. M.; Schmidt, Oliver G.; Cuniberti, Gianaurelio; Makarov, Denys

2015-08-01

We present a new approach to monitor microbial population dynamics in emulsion droplets via changes in metabolite composition, using an inductively coupled LC resonance circuit. The signal measured by such resonance detector provides information on the magnetic field interaction with the bacterial culture, which is complementary to the information accessible by other detection means, based on electric field interaction, i.e. capacitive or resistive, as well as optical techniques. Several charge-related factors, including pH and ammonia concentrations, were identified as possible contributors to the characteristic of resonance detector profile. The setup enables probing the ionic byproducts of microbial metabolic activity at later stages of cell growth, where conventional optical detection methods have no discriminating power.

Complementary Microorganisms in Highly Corrosive Biofilms from an Offshore Oil Production Facility.

PubMed

Vigneron, Adrien; Alsop, Eric B; Chambers, Brian; Lomans, Bartholomeus P; Head, Ian M; Tsesmetzis, Nicolas

2016-04-01

Offshore oil production facilities are frequently victims of internal piping corrosion, potentially leading to human and environmental risks and significant economic losses. Microbially influenced corrosion (MIC) is believed to be an important factor in this major problem for the petroleum industry. However, knowledge of the microbial communities and metabolic processes leading to corrosion is still limited. Therefore, the microbial communities from three anaerobic biofilms recovered from the inside of a steel pipe exhibiting high corrosion rates, iron oxide deposits, and substantial amounts of sulfur, which are characteristic of MIC, were analyzed in detail. Bacterial and archaeal community structures were investigated by automated ribosomal intergenic spacer analysis, multigenic (16S rRNA and functional genes) high-throughput Illumina MiSeq sequencing, and quantitative PCR analysis. The microbial community analysis indicated that bacteria, particularly Desulfovibrio species, dominated the biofilm microbial communities. However, other bacteria, such as Pelobacter, Pseudomonas, and Geotoga, as well as various methanogenic archaea, previously detected in oil facilities were also detected. The microbial taxa and functional genes identified suggested that the biofilm communities harbored the potential for a number of different but complementary metabolic processes and that MIC in oil facilities likely involves a range of microbial metabolisms such as sulfate, iron, and elemental sulfur reduction. Furthermore, extreme corrosion leading to leakage and exposure of the biofilms to the external environment modify the microbial community structure by promoting the growth of aerobic hydrocarbon-degrading organisms. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Potential microbial risk factors related to soil amendments and irrigation water of potato crops.

PubMed

Selma, M V; Allende, A; López-Gálvez, F; Elizaquível, P; Aznar, R; Gil, M I

2007-12-01

This study assesses the potential microbial risk factors related to the use of soil amendments and irrigation water on potato crops, cultivated in one traditional and two intensive farms during two harvest seasons. The natural microbiota and potentially pathogenic micro-organisms were evaluated in the soil amendment, irrigation water, soil and produce. Uncomposted amendments and residual and creek water samples showed the highest microbial counts. The microbial load of potatoes harvested in spring was similar among the tested farms despite the diverse microbial levels of Listeria spp. and faecal coliforms in the potential risk sources. However, differences in total coliform load of potato were found between farms cultivated in the autumn. Immunochromatographic rapid tests and the BAM's reference method (Bacteriological Analytical Manual; AOAC International) were used to detect Escherichia coli O157:H7 from the potential risk sources and produce. Confirmation of the positive results by polymerase chain reaction procedures showed that the immunochromatographic assay was not reliable as it led to false-positive results. The potentially pathogenic micro-organisms of soil amendment, irrigation water and soil samples changed with the harvest seasons and the use of different agricultural practices. However, the microbial load of the produce was not always influenced by these risk sources. Improvements in environmental sample preparation are needed to avoid interferences in the use of immunochromatographic rapid tests. The potential microbial risk sources of fresh produce should be regularly controlled using reliable detection methods to guarantee their microbial safety.

Complementary Microorganisms in Highly Corrosive Biofilms from an Offshore Oil Production Facility

PubMed Central

Alsop, Eric B.; Chambers, Brian; Lomans, Bartholomeus P.; Head, Ian M.; Tsesmetzis, Nicolas

2016-01-01

Offshore oil production facilities are frequently victims of internal piping corrosion, potentially leading to human and environmental risks and significant economic losses. Microbially influenced corrosion (MIC) is believed to be an important factor in this major problem for the petroleum industry. However, knowledge of the microbial communities and metabolic processes leading to corrosion is still limited. Therefore, the microbial communities from three anaerobic biofilms recovered from the inside of a steel pipe exhibiting high corrosion rates, iron oxide deposits, and substantial amounts of sulfur, which are characteristic of MIC, were analyzed in detail. Bacterial and archaeal community structures were investigated by automated ribosomal intergenic spacer analysis, multigenic (16S rRNA and functional genes) high-throughput Illumina MiSeq sequencing, and quantitative PCR analysis. The microbial community analysis indicated that bacteria, particularly Desulfovibrio species, dominated the biofilm microbial communities. However, other bacteria, such as Pelobacter, Pseudomonas, and Geotoga, as well as various methanogenic archaea, previously detected in oil facilities were also detected. The microbial taxa and functional genes identified suggested that the biofilm communities harbored the potential for a number of different but complementary metabolic processes and that MIC in oil facilities likely involves a range of microbial metabolisms such as sulfate, iron, and elemental sulfur reduction. Furthermore, extreme corrosion leading to leakage and exposure of the biofilms to the external environment modify the microbial community structure by promoting the growth of aerobic hydrocarbon-degrading organisms. PMID:26896143

Innate immunity in rice

PubMed Central

Chen, Xuewei; Ronald, Pamela C.

2011-01-01

Advances in studies of rice innate immunity have led to the identification and characterization of host sensors encoding receptor kinases that perceive conserved microbial signatures. The non-RD domain, a newly recognized hallmark of these receptor kinases is highly expanded in rice (Oryza sativa) compared with Arabidopsis (Arabidopsis thaliana). Researchers have also identified a diverse array of microbial effectors from bacterial and fungal pathogens that triggers immune responses upon perception. These include both, effectors that indirectly target host Nucleotide binding site/Leucine rice repeat (NBS-LRR) proteins and transcription activator-like (TAL) effectors that directly bind promoters of host genes. Here we review the recognition and signaling events that govern rice innate immunity. PMID:21602092

Medical Devices; Immunology and Microbiology Devices; Classification of the Device To Detect and Measure Non-Microbial Analyte(s) in Human Clinical Specimens To Aid in Assessment of Patients With Suspected Sepsis. Final order.

PubMed

2017-10-24

The Food and Drug Administration (FDA or we) is classifying the device to detect and measure non-microbial analyte(s) in human clinical specimens to aid in assessment of patients with suspected sepsis into class II (special controls). The special controls that apply to the device type are identified in this order and will be part of the codified language for the device to detect and measure non-microbial analyte(s) in human clinical specimens to aid in assessment of patients with suspected sepsis's classification. We are taking this action because we have determined that classifying the device into class II (special controls) will provide a reasonable assurance of safety and effectiveness of the device. We believe this action will also enhance patients' access to beneficial innovative devices, in part by reducing regulatory burdens.

Probing Metabolic Activity of Deep Subseafloor Life with NanoSIMS

NASA Astrophysics Data System (ADS)

Morono, Y.; Terada, T.; Itoh, M.; Inagaki, F.

2014-12-01

There are very few natural environments where life is absent in the Earth's surface biosphere. However, uninhabitable region is expected to be exist in the deep subsurface biosphere, of which extent and constraining factor(s) have still remained largly unknown. Scientific ocean drilling have revealed that microbial communities in sediments are generally phylogenetically distinct from known spieces isolated from the Earth's surface biosphere, and hence metabolic functions of the deep subseafloor life remain unknown. In addition, activity of subseafloor microbial cells are thought to be extraordinally slow, as indicated by limited supply of neutrient and energy substrates. To understand the limits of the Earth's subseafloor biosphere and metabolic functions of microbial populations, detection and quantification of the deeply buried microbial cells in geological habitats are fundamentary important. Using newly developed cell separation techniques as well as an discriminative cell detection system, the current quantification limit of sedimentary microbial cells approaches to 102 cells/cm3. These techniques allow not only to assess very small microbial population close to the subsurface biotic fringe, but also to separate and sort the target cells using flow cytometric cell sorter. Once the deep subseafloor microbial cells are detached from mineral grains and sorted, it opens new windows to subsequent molecular ecological and element/isotopic analyses. With a combined use of nano-scale secondary ion masspectrometry (NanoSIMS) and stable isotope-probing techniques, it is possible to detect and measure activity of substrate incorporation into biomass, even for extremely slow metabolic processes such as uncharacteriszed deep subseafloor life. For example, it was evidenced by NanoSIMS that at least over 80% of microbial cells at ~200 meters-deep, 460,000-year-old sedimentary habitat are indeed live, which substrate incooporation was found to be low (10-15 gC/cell/day) even under the lab incubation condition. Also microbial activity in ultraoligotrophic biosphere samples such as the South Pacific Gyre (i.e., IODP Expeditions 329) will be shown. Our results demonstrates metabolic potential of microbes that have been survived for geological timescale in extremely starved condition.

GeoChip-based Analysis of Groundwater Microbial Diversity in Norman Landfill

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

Lu, Zhenmei; He, Zhili; Parisi, Victoria

The Norman Landfill is a closed municipal solid waste landfill located on an alluvium associated with the Canadian River in Norman, Oklahoma. It has operated as a research site since 1994 because it is typical of many closed landfill sites across the U.S. Leachate from the unlined landfill forms a groundwater plume that extends downgradient approximately 250 m from the landfill toward the Canadian River. To investigate the impact of the landfill leachate on the diversity and functional structure of microbial communities, groundwater samples were taken from eight monitoring wells at a depth of 5m, and analyzed using a comprehensivemore » functional gene array covering about 50,000 genes involved in key microbial processes, such as biogeochemical cycling of C, N, P, and S, and bioremediation of organic contaminants and metals. Wells are located within a transect along a presumed flow path with different distances to the center of the leachate plume. Our analyses showed that microbial communities were obviously impacted by the leachate-component from the landfill. The number of genes detected and microbial diversity indices in the center (LF2B) and its closest (MLS35) wells were significantly less than those detected in other more downgradient wells, while no significant changes were observed in the relative abundance (i.e., percentage of each gene category) for most gene categories. However, the microbial community composition or structure of the landfill groundwater did not clearly show a significant correlation with the distance from well LF2B. Burkholderia sp. and Pseudomonas sp. were found to be the dominant microbial populations detected in all wells, while Bradyrhizobium sp. and Ralstonia sp. were dominant populations for seven wells except LF2B. In addition, Mantel test and canonical correspondence analysis (CCA) indicate that pH, sulfate, ammonia nitrogen and dissolved organic carbon (DOC) have significant effects on the microbial community structure. The results suggest that the leachate from unlined landfills significantly impact the structures of groundwater microbial communities, and that more distal wells recover by natural attenuation.« less

Tracking heavy water (D 2O) incorporation for identifying and sorting active microbial cells

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

Berry, David; Mader, Esther; Lee, Tae Kwon

Here, microbial communities are essential to the function of virtually all ecosystems and eukaryotes, including humans. However, it is still a major challenge to identify microbial cells active under natural conditions in complex systems. Here in this study, we developed a new method to identify and sort active microbes on the single-cell level in complex samples using stable isotope probing with heavy water (D 2O) combined with Raman microspectroscopy. Incorporation of D 2O-derived D into the biomass of autotrophic and heterotrophic bacteria and archaea could be unambiguously detected via C-D signature peaks in single-cell Raman spectra, and the obtained labelingmore » pattern was confirmed by nanoscale-resolution secondary ion MS. In fast-growing Escherichia coli cells, label detection was already possible after 20 min. For functional analyses of microbial communities, the detection of D incorporation from D 2O in individual microbial cells via Raman microspectroscopy can be directly combined with FISH for the identification of active microbes. Applying this approach to mouse cecal microbiota revealed that the host-compound foragers Akkermansia muciniphila and Bacteroides acidifaciens exhibited distinctive response patterns to amendments of mucin and sugars. By Raman-based cell sorting of active (deuterated) cells with optical tweezers and subsequent multiple displacement amplification and DNA sequencing, novel cecal microbes stimulated by mucin and/or glucosamine were identified, demonstrating the potential of the nondestructive D 2O-Raman approach for targeted sorting of microbial cells with defined functional properties for single-cell genomics.« less

Tracking heavy water (D 2O) incorporation for identifying and sorting active microbial cells

DOE PAGES

Berry, David; Mader, Esther; Lee, Tae Kwon; ...

2014-12-30

Here, microbial communities are essential to the function of virtually all ecosystems and eukaryotes, including humans. However, it is still a major challenge to identify microbial cells active under natural conditions in complex systems. Here in this study, we developed a new method to identify and sort active microbes on the single-cell level in complex samples using stable isotope probing with heavy water (D 2O) combined with Raman microspectroscopy. Incorporation of D 2O-derived D into the biomass of autotrophic and heterotrophic bacteria and archaea could be unambiguously detected via C-D signature peaks in single-cell Raman spectra, and the obtained labelingmore » pattern was confirmed by nanoscale-resolution secondary ion MS. In fast-growing Escherichia coli cells, label detection was already possible after 20 min. For functional analyses of microbial communities, the detection of D incorporation from D 2O in individual microbial cells via Raman microspectroscopy can be directly combined with FISH for the identification of active microbes. Applying this approach to mouse cecal microbiota revealed that the host-compound foragers Akkermansia muciniphila and Bacteroides acidifaciens exhibited distinctive response patterns to amendments of mucin and sugars. By Raman-based cell sorting of active (deuterated) cells with optical tweezers and subsequent multiple displacement amplification and DNA sequencing, novel cecal microbes stimulated by mucin and/or glucosamine were identified, demonstrating the potential of the nondestructive D 2O-Raman approach for targeted sorting of microbial cells with defined functional properties for single-cell genomics.« less

Microbial Signatures of Cadaver Gravesoil During Decomposition.

PubMed

Finley, Sheree J; Pechal, Jennifer L; Benbow, M Eric; Robertson, B K; Javan, Gulnaz T

2016-04-01

Genomic studies have estimated there are approximately 10(3)-10(6) bacterial species per gram of soil. The microbial species found in soil associated with decomposing human remains (gravesoil) have been investigated and recognized as potential molecular determinants for estimates of time since death. The nascent era of high-throughput amplicon sequencing of the conserved 16S ribosomal RNA (rRNA) gene region of gravesoil microbes is allowing research to expand beyond more subjective empirical methods used in forensic microbiology. The goal of the present study was to evaluate microbial communities and identify taxonomic signatures associated with the gravesoil human cadavers. Using 16S rRNA gene amplicon-based sequencing, soil microbial communities were surveyed from 18 cadavers placed on the surface or buried that were allowed to decompose over a range of decomposition time periods (3-303 days). Surface soil microbial communities showed a decreasing trend in taxon richness, diversity, and evenness over decomposition, while buried cadaver-soil microbial communities demonstrated increasing taxon richness, consistent diversity, and decreasing evenness. The results show that ubiquitous Proteobacteria was confirmed as the most abundant phylum in all gravesoil samples. Surface cadaver-soil communities demonstrated a decrease in Acidobacteria and an increase in Firmicutes relative abundance over decomposition, while buried soil communities were consistent in their community composition throughout decomposition. Better understanding of microbial community structure and its shifts over time may be important for advancing general knowledge of decomposition soil ecology and its potential use during forensic investigations.

Towards a rapid and comprehensive microbial detection and identification system for life support and planetary protection applications

NASA Astrophysics Data System (ADS)

Lasseur, Christophe

Long term manned missions of our Russian colleagues have demonstrated the risks associated with microbial contamination. These risks concern both crew health via the metabolic consumables contamination (water, air,.) but and also the hardware degradation. In parallel to these life support issues, planetary protection experts have agreed to place clear specifications of the microbial quality of future hardware landing on extraterrestrial planets as well as elaborate the requirements of contamination for manned missions on surface. For these activities, it is necessary to have a better understanding of microbial activity, to create culture collections and to develop on-line detection tools. . In this respect, over the last 6 years , ESA has supported active scientific research on the choice of critical genes and functions, including those linked to horizontal gene pool of bacteria and its dissemination. In parallel, ESA and European industries have been developing an automated instrument for rapid microbial detection on air and surface samples. Within this paper, we first present the life support and planetary protection requirements, and the state of the art of the instrument development. Preliminary results at breadboard level, including a mock-up view of the final instrument are also presented. Finally, the remaining steps required to reach a functional instrument for planetary hardware integration and life support flight hardware are also presented.

Effect of Increasing Nitrogen Deposition on Soil Microbial Communities

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

Xiao, Shengmu; Xue, Kai; He, Zhili

2010-05-17

Increasing nitrogen deposition, increasing atmospheric CO2, and decreasing biodiversity are three main environmental changes occurring on a global scale. The BioCON (Biodiversity, CO2, and Nitrogen) ecological experiment site at the University of Minnesota's Cedar Creek Ecosystem Science Reserve started in 1997, to better understand how these changes would affect soil systems. To understand how increasing nitrogen deposition affects the microbial community diversity, heterogeneity, and functional structure impact soil microbial communities, 12 samples were collected from the BioCON plots in which nitrogenous fertilizer was added to simulate the effect of increasing nitrogen deposition and 12 samples from without added fertilizer. DNAmore » from the 24 samples was extracted using a freeze-grind protocol, amplified, labeled with a fluorescent dye, and then hybridized to GeoChip, a functional gene array containing probes for genes involved in N, S and C cycling, metal resistance and organic contaminant degradation. Detrended correspondence analysis (DCA) of all genes detected was performed to analyze microbial community patterns. The first two axes accounted for 23.5percent of the total variation. The samples fell into two major groups: fertilized and non-fertilized, suggesting that nitrogenous fertilizer had a significant impact on soil microbial community structure and diversity. The functional gene numbers detected in fertilized samples was less that detected in non-fertilizer samples. Functional genes involving in the N cycling were mainly discussed.« less

Microbial degradation of chloroethenes: a review.

PubMed

Dolinová, Iva; Štrojsová, Martina; Černík, Miroslav; Němeček, Jan; Macháčková, Jiřina; Ševců, Alena

2017-05-01

Contamination by chloroethenes has a severe negative effect on both the environment and human health. This has prompted intensive remediation activity in recent years, along with research into the efficacy of natural microbial communities for degrading toxic chloroethenes into less harmful compounds. Microbial degradation of chloroethenes can take place either through anaerobic organohalide respiration, where chloroethenes serve as electron acceptors; anaerobic and aerobic metabolic degradation, where chloroethenes are used as electron donors; or anaerobic and aerobic co-metabolic degradation, with chloroethene degradation occurring as a by-product during microbial metabolism of other growth substrates, without energy or carbon benefit. Recent research has focused on optimising these natural processes to serve as effective bioremediation technologies, with particular emphasis on (a) the diversity and role of bacterial groups involved in dechlorination microbial processes, and (b) detection of bacterial enzymes and genes connected with dehalogenation activity. In this review, we summarise the different mechanisms of chloroethene bacterial degradation suitable for bioremediation and provide a list of dechlorinating bacteria. We also provide an up-to-date summary of primers available for detecting functional genes in anaerobic and aerobic bacteria degrading chloroethenes metabolically or co-metabolically.

Bacterial dominance in subseafloor sediments characterized by methane hydrates

USGS Publications Warehouse

Briggs, Brandon R.; Inagaki, Fumio; Morono, Yuki; Futagami, Taiki; Huguet, Carme; Rosell-Mele, Antoni; Lorenson, T.D.; Colwell, Frederick S.

2015-01-01

The degradation of organic carbon in subseafloor sediments on continental margins contributes to the largest reservoir of methane on Earth. Sediments in the Andaman Sea are composed of ~ 1% marine-derived organic carbon and biogenic methane is present. Our objective was to determine microbial abundance and diversity in sediments that transition the gas hydrate occurrence zone (GHOZ) in the Andaman Sea. Microscopic cell enumeration revealed that most sediment layers harbored relatively low microbial abundance (103–105 cells cm−3). Archaea were never detected despite the use of both DNA- and lipid-based methods. Statistical analysis of terminal restriction fragment length polymorphisms revealed distinct microbial communities from above, within, and below the GHOZ, and GHOZ samples were correlated with a decrease in organic carbon. Primer-tagged pyrosequences of bacterial 16S rRNA genes showed that members of the phylum Firmicutes are predominant in all zones. Compared with other seafloor settings that contain biogenic methane, this deep subseafloor habitat has a unique microbial community and the low cell abundance detected can help to refine global subseafloor microbial abundance.

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.

Microbial Contamination Detection in Water Resources: Interest of Current Optical Methods, Trends and Needs in the Context of Climate Change

PubMed Central

Jung, Aude-Valérie; Le Cann, Pierre; Roig, Benoit; Thomas, Olivier; Baurès, Estelle; Thomas, Marie-Florence

2014-01-01

Microbial pollution in aquatic environments is one of the crucial issues with regard to the sanitary state of water bodies used for drinking water supply, recreational activities and harvesting seafood due to a potential contamination by pathogenic bacteria, protozoa or viruses. To address this risk, microbial contamination monitoring is usually assessed by turbidity measurements performed at drinking water plants. Some recent studies have shown significant correlations of microbial contamination with the risk of endemic gastroenteresis. However the relevance of turbidimetry may be limited since the presence of colloids in water creates interferences with the nephelometric response. Thus there is a need for a more relevant, simple and fast indicator for microbial contamination detection in water, especially in the perspective of climate change with the increase of heavy rainfall events. This review focuses on the one hand on sources, fate and behavior of microorganisms in water and factors influencing pathogens’ presence, transportation and mobilization, and on the second hand, on the existing optical methods used for monitoring microbiological risks. Finally, this paper proposes new ways of research. PMID:24747537

Comparative genomic analysis of isoproturon-mineralizing sphingomonads reveals the isoproturon catabolic mechanism.

PubMed

Yan, Xin; Gu, Tao; Yi, Zhongquan; Huang, Junwei; Liu, Xiaowei; Zhang, Ji; Xu, Xihui; Xin, Zhihong; Hong, Qing; He, Jian; Spain, Jim C; Li, Shunpeng; Jiang, Jiandong

2016-12-01

The worldwide use of the phenylurea herbicide, isoproturon (IPU), has resulted in considerable concern about its environmental fate. Although many microbial metabolites of IPU are known and IPU-mineralizing bacteria have been isolated, the molecular mechanism of IPU catabolism has not been elucidated yet. In this study, complete genes that encode the conserved IPU catabolic pathway were revealed, based on comparative analysis of the genomes of three IPU-mineralizing sphingomonads and subsequent experimental validation. The complete genes included a novel hydrolase gene ddhA, which is responsible for the cleavage of the urea side chain of the IPU demethylated products; a distinct aniline dioxygenase gene cluster adoQTA1A2BR, which has a broad substrate range; and an inducible catechol meta-cleavage pathway gene cluster adoXEGKLIJC. Furthermore, the initial mono-N-demethylation genes pdmAB were further confirmed to be involved in the successive N-demethylation of the IPU mono-N-demethylated product. These IPU-catabolic genes were organized into four transcription units and distributed on three plasmids. They were flanked by multiple mobile genetic elements and highly conserved among IPU-mineralizing sphingomonads. The elucidation of the molecular mechanism of IPU catabolism will enhance our understanding of the microbial mineralization of IPU and provide insights into the evolutionary scenario of the conserved IPU-catabolic pathway. © 2016 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Employment of Near Full-Length Ribosome Gene TA-Cloning and Primer-Blast to Detect Multiple Species in a Natural Complex Microbial Community Using Species-Specific Primers Designed with Their Genome Sequences.

PubMed

Zhang, Huimin; He, Hongkui; Yu, Xiujuan; Xu, Zhaohui; Zhang, Zhizhou

2016-11-01

It remains an unsolved problem to quantify a natural microbial community by rapidly and conveniently measuring multiple species with functional significance. Most widely used high throughput next-generation sequencing methods can only generate information mainly for genus-level taxonomic identification and quantification, and detection of multiple species in a complex microbial community is still heavily dependent on approaches based on near full-length ribosome RNA gene or genome sequence information. In this study, we used near full-length rRNA gene library sequencing plus Primer-Blast to design species-specific primers based on whole microbial genome sequences. The primers were intended to be specific at the species level within relevant microbial communities, i.e., a defined genomics background. The primers were tested with samples collected from the Daqu (also called fermentation starters) and pit mud of a traditional Chinese liquor production plant. Sixteen pairs of primers were found to be suitable for identification of individual species. Among them, seven pairs were chosen to measure the abundance of microbial species through quantitative PCR. The combination of near full-length ribosome RNA gene library sequencing and Primer-Blast may represent a broadly useful protocol to quantify multiple species in complex microbial population samples with species-specific primers.

Quantitative microbial faecal source tracking with sampling guided by hydrological catchment dynamics.

PubMed

Reischer, G H; Haider, J M; Sommer, R; Stadler, H; Keiblinger, K M; Hornek, R; Zerobin, W; Mach, R L; Farnleitner, A H

2008-10-01

The impairment of water quality by faecal pollution is a global public health concern. Microbial source tracking methods help to identify faecal sources but the few recent quantitative microbial source tracking applications disregarded catchment hydrology and pollution dynamics. This quantitative microbial source tracking study, conducted in a large karstic spring catchment potentially influenced by humans and ruminant animals, was based on a tiered sampling approach: a 31-month water quality monitoring (Monitoring) covering seasonal hydrological dynamics and an investigation of flood events (Events) as periods of the strongest pollution. The detection of a ruminant-specific and a human-specific faecal Bacteroidetes marker by quantitative real-time PCR was complemented by standard microbiological and on-line hydrological parameters. Both quantitative microbial source tracking markers were detected in spring water during Monitoring and Events, with preponderance of the ruminant-specific marker. Applying multiparametric analysis of all data allowed linking the ruminant-specific marker to general faecal pollution indicators, especially during Events. Up to 80% of the variation of faecal indicator levels during Events could be explained by ruminant-specific marker levels proving the dominance of ruminant faecal sources in the catchment. Furthermore, soil was ruled out as a source of quantitative microbial source tracking markers. This study demonstrates the applicability of quantitative microbial source tracking methods and highlights the prerequisite of considering hydrological catchment dynamics in source tracking study design.

The preservation of microbial DNA in archived soils of various genetic types.

PubMed

Ivanova, Ekaterina A; Korvigo, Ilia O; Aparin, Boris F; Chirak, Evgenii L; Pershina, Elizaveta V; Romaschenko, Nikolay S; Provorov, Nikolai A; Andronov, Evgeny E

2017-01-01

This study is a comparative analysis of samples of archived (stored for over 70-90 years) and modern soils of two different genetic types-chernozem and sod-podzolic soils. We revealed a reduction in biodiversity of archived soils relative to their modern state. Particularly, long-term storage in the museum exerted a greater impact on the microbiomes of sod-podzolic soils, while chernozem samples better preserved the native community. Thus, the persistence of microbial DNA in soil is largely determined by the physico-chemical characteristics that differ across soil types. Chernozems create better conditions for the long-term DNA preservation than sod-podzolic soils. This results in supposedly higher levels of biodiversity conservation in the microbiomes of chernozem with preservation of major microbial taxa dominant in the modern (control) soil samples, which makes archived chernozems a promising object for paleosoil studies.

Alternative cytoskeletal landscapes: cytoskeletal novelty and evolution in basal excavate protists

PubMed Central

Dawson, Scott C.; Paredez, Alexander R.

2016-01-01

Microbial eukaryotes encompass the majority of eukaryotic evolutionary and cytoskeletal diversity. The cytoskeletal complexity observed in multicellular organisms appears to be an expansion of components present in genomes of diverse microbial eukaryotes such as the basal lineage of flagellates, the Excavata. Excavate protists have complex and diverse cytoskeletal architectures and life cycles – essentially alternative cytoskeletal “landscapes” – yet still possess conserved microtubule- and actin-associated proteins. Comparative genomic analyses have revealed that a subset of excavates, however, lack many canonical actin-binding proteins central to actin cytoskeleton function in other eukaryotes. Overall, excavates possess numerous uncharacterized and “hypothetical” genes, and may represent an undiscovered reservoir of novel cytoskeletal genes and cytoskeletal mechanisms. The continued development of molecular genetic tools in these complex microbial eukaryotes will undoubtedly contribute to our overall understanding of cytoskeletal diversity and evolution. PMID:23312067

The preservation of microbial DNA in archived soils of various genetic types

PubMed Central

Korvigo, Ilia O.; Aparin, Boris F.; Chirak, Evgenii L.; Pershina, Elizaveta V.; Romaschenko, Nikolay S.; Provorov, Nikolai A.; Andronov, Evgeny E.

2017-01-01

This study is a comparative analysis of samples of archived (stored for over 70–90 years) and modern soils of two different genetic types–chernozem and sod-podzolic soils. We revealed a reduction in biodiversity of archived soils relative to their modern state. Particularly, long-term storage in the museum exerted a greater impact on the microbiomes of sod-podzolic soils, while chernozem samples better preserved the native community. Thus, the persistence of microbial DNA in soil is largely determined by the physico-chemical characteristics that differ across soil types. Chernozems create better conditions for the long-term DNA preservation than sod-podzolic soils. This results in supposedly higher levels of biodiversity conservation in the microbiomes of chernozem with preservation of major microbial taxa dominant in the modern (control) soil samples, which makes archived chernozems a promising object for paleosoil studies. PMID:28339464

Can cover crops pull double duty: Conservation and profitable forage production in the Midwestern U.S.?

USDA-ARS?s Scientific Manuscript database

Data from a recent survey suggests that the major reasons Nebraska farmer’s plant cover crops are to: improve soil organic matter, reduce erosion, improve soil water holding capacity, produce forage, and increase soil microbial biomass. Many of these benefits appear to be positively correlated with...

Microbial responses to disturbance following the conversion of CRP land to cropland under water limiting conditions

USDA-ARS?s Scientific Manuscript database

The conversion of Conservation Reserve Program (CRP) lands to croplands potentially reduces ecological benefits such as high soil health condition that resist to disturbance (i.e. extreme weather). Soil CO2 flux primarily comes from root and microbes’ respirations and is sensitive to changes in soil...

Effects of long-term soil management on the mutual interaction among soil organic matter, microbial activity and aggregates in vineyard

USDA-ARS?s Scientific Manuscript database

Vineyard management practices to enhance soil conservation principally focus on increasing carbon (C) input, whereas mitigating impacts of disturbance through reduced tillage has been rarely considered. Furthermore, information is lacking on the effects of soil management practices adopted in the un...

The microbial diversity, distribution, and ecology of permafrost in China: a review.

PubMed

Hu, Weigang; Zhang, Qi; Tian, Tian; Cheng, Guodong; An, Lizhe; Feng, Huyuan

2015-07-01

Permafrost in China mainly located in high-altitude areas. It represents a unique and suitable ecological niche that can be colonized by abundant microbes. Permafrost microbial community varies across geographically separated locations in China, and some lineages are novel and possible endemic. Besides, Chinese permafrost is a reservoir of functional microbial groups involved in key biogeochemical cycling processes. In future, more work is necessary to determine if these phylogenetic groups detected by DNA-based methods are part of the viable microbial community, and their functional roles and how they potentially respond to climate change. This review summaries recent studies describing microbial biodiversity found in permafrost and associated environments in China, and provides a framework for better understanding the microbial ecology of permafrost.

Electron Bifurcation Makes the Puzzle Pieces Fall Energetically into Place in Methanogenic Energy Conservation

DOE PAGES

Lubner, Carolyn E.; Peters, John W.

2017-10-06

Microbial life has evolved a wide range of metabolisms exploiting in many cases unanticipated suites of oxidation-reduction reactions to generate energy. Although many of these suites of reactions don't allow these microbes to enjoy the same quality of energetic life that we enjoy via respiration/oxidative phosphorylation, it has conferred the ability for life to exploit almost any oxidation-reduction reaction. We find in many of these cases when energy is sparing, the difference between life and death may be conserving the maximal amount of energy and minimizing loss of free energy through heat.

Electron Bifurcation Makes the Puzzle Pieces Fall Energetically into Place in Methanogenic Energy Conservation

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

Lubner, Carolyn E.; Peters, John W.

Microbial life has evolved a wide range of metabolisms exploiting in many cases unanticipated suites of oxidation-reduction reactions to generate energy. Although many of these suites of reactions don't allow these microbes to enjoy the same quality of energetic life that we enjoy via respiration/oxidative phosphorylation, it has conferred the ability for life to exploit almost any oxidation-reduction reaction. We find in many of these cases when energy is sparing, the difference between life and death may be conserving the maximal amount of energy and minimizing loss of free energy through heat.

Nationwide reconnaissance of contaminants of emerging ...

EPA Pesticide Factsheets

When chemical or microbial contaminants are assessed for potential effect or possible regulation in ambient and drinking waters, a critical first step is determining if the contaminants occur and if they are at concentrations that may cause human or ecological health concerns. To this end, source and treated drinking water samples from 29 drinking water treatment plants (DWTPs) were analyzed as part of a two-phase study to determine whether chemical and microbial constituents, many of which are considered contaminants of emerging concern, were detectable in the waters. Of the 84 chemicals monitored in the 9 Phase I DWTPs, 27 were detected at least once in the source water, and 21 were detected at least once in treated drinking water. In Phase II, which was a broader and more comprehensive assessment, 247 chemical and microbial analytes were measured in 25 DWTPs, with 148 detected at least once in the source water, and 121 detected at least once in the treated drinking water. The frequency of detection was often related to the analyte's contaminant class, as pharmaceuticals and anthropogenic waste indicators tended to be infrequently detected and more easily removed during treatment, while per and polyfluoroalkyl substances and inorganic constituents were both more frequently detected and, overall, more resistant to treatment. The data collected as part of this project will be used to help inform evaluation of unregulated contaminants in surface water, groundwate

A thiotrophic microbial community in an acidic brine lake in Northern Chile.

PubMed

Escudero, Lorena; Oetiker, Nia; Gallardo, Karem; Tebes-Cayo, Cinthya; Guajardo, Mariela; Nuñez, Claudia; Davis-Belmar, Carol; Pueyo, J J; Chong Díaz, Guillermo; Demergasso, Cecilia

2018-05-10

The endorheic basins of the Northern Chilean Altiplano contain saline lakes and salt flats. Two of the salt flats, Gorbea and Ignorado, have high acidic brines. The causes of the local acidity have been attributed to the occurrence of volcanic native sulfur, the release of sulfuric acid by oxidation, and the low buffering capacity of the rocks in the area. Understanding the microbial community composition and available energy in this pristine ecosystem is relevant in determining the origin of the acidity and in supporting the rationale of conservation policies. Besides, a comparison between similar systems in Australia highlights key microbial components and specific ones associated with geological settings and environmental conditions. Sediment and water samples from the Salar de Gorbea were collected, physicochemical parameters measured and geochemical and molecular biological analyses performed. A low diversity microbial community was observed in brines and sediments dominated by Actinobacteria, Algae, Firmicutes and Proteobacteria. Most of the constituent genera have been reported to be either sulfur oxidizing microorganisms or ones having the potential for sulfur oxidation given available genomic data and information drawn from the literature on cultured relatives. In addition, a link between sulfur oxidation and carbon fixation was observed. In contrast, to acid mine drainage communities, Gorbea microbial diversity is mainly supported by chemolithoheterotrophic, facultative chemolithoautotrophic and oligotrophic sulfur oxidizing populations indicating that microbial activity should also be considered as a causative agent of local acidity.

Gold-FISH: A correlative approach to microscopic imaging of single microbial cells in environmental samples

NASA Astrophysics Data System (ADS)

Schmidt, Hannes; Seki, David; Woebken, Dagmar; Eickhorst, Thilo

2017-04-01

Fluorescence in situ hybridization (FISH) is routinely used for the phylogenetic identification, detection, and quantification of single microbial cells environmental microbiology. Oligonucleotide probes that match the 16S rRNA sequence of target organisms are generally applied and the resulting signals are visualized via fluorescence microscopy. Consequently, the detection of the microbial cells of interest is limited by the resolution and the sensitivity of light microscopy where objects smaller than 0.2 µm can hardly be represented. Visualizing microbial cells at magnifications beyond light microscopy, however, can provide information on the composition and potential complexity of microbial habitats - the actual sites of nutrient cycling in soil and sediments. We present a recently developed technique that combines (1) the phylogenetic identification and detection of individual microorganisms by epifluorescence microscopy, with (2) the in situ localization of gold-labelled target cells on an ultrastructural level by SEM. Based on 16S rRNA targeted in situ hybridization combined with catalyzed reporter deposition, a streptavidin conjugate labeled with a fluorescent dye and nanogold particles is introduced into whole microbial cells. A two-step visualization process including an autometallographic enhancement of nanogold particles then allows for either fluorescence or electron microscopy, or a correlative application thereof. We will present applications of the Gold-FISH protocol to samples of marine sediments, agricultural soils, and plant roots. The detection and enumeration of bacterial cells in soil and sediment samples was comparable to CARD-FISH applications via fluorescence microscopy. Examples of microbe-surface interaction analysis will be presented on the basis of bacteria colonizing the rhizoplane of rice roots. In principle, Gold-FISH can be performed on any material to give a snapshot of microbe-surface interactions and provides a promising tool for the acquisition of correlative information on microorganisms within their respective habitats.

Microbial Habitability in Gale Crater: Sample Analysis at Mars (SAM) Instrument Detection of Microbial Essential Carbon and Nitrogen

NASA Technical Reports Server (NTRS)

Sutter, B.; Ming, D. W.; Eigenbrode, J. E.; Steele, A.; Stern, J. C.; Gonzalez, R. N.; McAdam, A. C.; Mahaffy, P. R.

2016-01-01

Chemical analyses of Mars soils and sediments from previous landed missions have demonstrated that Mars surface materials possessed major (e.g., P, K, Ca, Mg, S) and minor (e.g., Fe, Mn, Zn, Ni, Cl) elements essential to support microbial life. However, the detection of microbial essential organic-carbon (C) and nitrate have been more elusive until the Mars Science Laboratory (MSL) rover mission. Nitrate and organic-C in Gale Crater, Mars have been detected by the Sample Analysis at Mars (SAM) instrument onboard the MSL Curiosity rover. Eolian fines and drilled sedimentary rock samples were heated in the SAM oven from approximately 30 to 860 degrees Centigrade where evolved gases (e.g., nitrous oxide (NO) and CO2) were released and analyzed by SAM’s quadrupole mass spectrometer (MS). The temperatures of evolved NO was assigned to nitrate while evolved CO2 was assigned to organic-C and carbonate. The CO2 releases in several samples occurred below 450 degrees Centigrade suggesting organic-C dominated in those samples. As much as 7 micromoles NO3-N per gram and 200 micromoles CO2-C per gram have been detected in the Gale Crater materials. These N and C levels coupled with assumed microbial biomass (9 x 10 (sup -7) micrograms per cell) C (0.5 micrograms C per micrograms cell) and N (0.14 micrograms N per micrograms cell) requirements, suggests that less than 1 percent and less than 10 percent of Gale Crater C and N, respectively, would be required if available, to accommodate biomass requirements of 1 by 10 (sup 5) cells per gram sediment. While nitrogen is the limiting nutrient, the potential exists that sufficient N and organic-C were present to support limited heterotrophic microbial populations that may have existed on ancient Mars.

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.

Microfluidics and microbial engineering.

PubMed

Kou, Songzi; Cheng, Danhui; Sun, Fei; Hsing, I-Ming

2016-02-07

The combination of microbial engineering and microfluidics is synergistic in nature. For example, microfluidics is benefiting from the outcome of microbial engineering and many reported point-of-care microfluidic devices employ engineered microbes as functional parts for the microsystems. In addition, microbial engineering is facilitated by various microfluidic techniques, due to their inherent strength in high-throughput screening and miniaturization. In this review article, we firstly examine the applications of engineered microbes for toxicity detection, biosensing, and motion generation in microfluidic platforms. Secondly, we look into how microfluidic technologies facilitate the upstream and downstream processes of microbial engineering, including DNA recombination, transformation, target microbe selection, mutant characterization, and microbial function analysis. Thirdly, we highlight an emerging concept in microbial engineering, namely, microbial consortium engineering, where the behavior of a multicultural microbial community rather than that of a single cell/species is delineated. Integrating the disciplines of microfluidics and microbial engineering opens up many new opportunities, for example in diagnostics, engineering of microbial motors, development of portable devices for genetics, high throughput characterization of genetic mutants, isolation and identification of rare/unculturable microbial species, single-cell analysis with high spatio-temporal resolution, and exploration of natural microbial communities.

Advantages and limitations of quantitative PCR (Q-PCR)-based approaches in microbial ecology.

PubMed

Smith, Cindy J; Osborn, A Mark

2009-01-01

Quantitative PCR (Q-PCR or real-time PCR) approaches are now widely applied in microbial ecology to quantify the abundance and expression of taxonomic and functional gene markers within the environment. Q-PCR-based analyses combine 'traditional' end-point detection PCR with fluorescent detection technologies to record the accumulation of amplicons in 'real time' during each cycle of the PCR amplification. By detection of amplicons during the early exponential phase of the PCR, this enables the quantification of gene (or transcript) numbers when these are proportional to the starting template concentration. When Q-PCR is coupled with a preceding reverse transcription reaction, it can be used to quantify gene expression (RT-Q-PCR). This review firstly addresses the theoretical and practical implementation of Q-PCR and RT-Q-PCR protocols in microbial ecology, highlighting key experimental considerations. Secondly, we review the applications of (RT)-Q-PCR analyses in environmental microbiology and evaluate the contribution and advances gained from such approaches. Finally, we conclude by offering future perspectives on the application of (RT)-Q-PCR in furthering understanding in microbial ecology, in particular, when coupled with other molecular approaches and more traditional investigations of environmental systems.

Assessment of test methods for evaluating effectiveness of cleaning flexible endoscopes.

PubMed

Washburn, Rebecca E; Pietsch, Jennifer J

2018-06-01

Strict adherence to each step of reprocessing is imperative to removing potentially infectious agents. Multiple methods for verifying proper reprocessing exist; however, each presents challenges and limitations, and best practice within the industry has not been established. Our goal was to evaluate endoscope cleaning verification tests with particular interest in the evaluation of the manual cleaning step. The results of the cleaning verification tests were compared with microbial culturing to see if a positive cleaning verification test would be predictive of microbial growth. This study was conducted at 2 high-volume endoscopy units within a multisite health care system. Each of the 90 endoscopes were tested for adenosine triphosphate, protein, microbial growth via agar plate, and rapid gram-negative culture via assay. The endoscopes were tested in 3 locations: the instrument channel, control knob, and elevator mechanism. This analysis showed substantial level of agreement between protein detection postmanual cleaning and protein detection post-high-level disinfection at the control head for scopes sampled sequentially. This study suggests that if protein is detected postmanual cleaning, there is a significant likelihood that protein will also be detected post-high-level disinfection. It also infers that a cleaning verification test is not predictive of microbial growth. Copyright © 2018 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

Microbial community pattern detection in human body habitats via ensemble clustering framework.

PubMed

Yang, Peng; Su, Xiaoquan; Ou-Yang, Le; Chua, Hon-Nian; Li, Xiao-Li; Ning, Kang

2014-01-01

The human habitat is a host where microbial species evolve, function, and continue to evolve. Elucidating how microbial communities respond to human habitats is a fundamental and critical task, as establishing baselines of human microbiome is essential in understanding its role in human disease and health. Recent studies on healthy human microbiome focus on particular body habitats, assuming that microbiome develop similar structural patterns to perform similar ecosystem function under same environmental conditions. However, current studies usually overlook a complex and interconnected landscape of human microbiome and limit the ability in particular body habitats with learning models of specific criterion. Therefore, these methods could not capture the real-world underlying microbial patterns effectively. To obtain a comprehensive view, we propose a novel ensemble clustering framework to mine the structure of microbial community pattern on large-scale metagenomic data. Particularly, we first build a microbial similarity network via integrating 1920 metagenomic samples from three body habitats of healthy adults. Then a novel symmetric Nonnegative Matrix Factorization (NMF) based ensemble model is proposed and applied onto the network to detect clustering pattern. Extensive experiments are conducted to evaluate the effectiveness of our model on deriving microbial community with respect to body habitat and host gender. From clustering results, we observed that body habitat exhibits a strong bound but non-unique microbial structural pattern. Meanwhile, human microbiome reveals different degree of structural variations over body habitat and host gender. In summary, our ensemble clustering framework could efficiently explore integrated clustering results to accurately identify microbial communities, and provide a comprehensive view for a set of microbial communities. The clustering results indicate that structure of human microbiome is varied systematically across body habitats and host genders. Such trends depict an integrated biography of microbial communities, which offer a new insight towards uncovering pathogenic model of human microbiome.

Microbial community pattern detection in human body habitats via ensemble clustering framework

PubMed Central

2014-01-01

Background The human habitat is a host where microbial species evolve, function, and continue to evolve. Elucidating how microbial communities respond to human habitats is a fundamental and critical task, as establishing baselines of human microbiome is essential in understanding its role in human disease and health. Recent studies on healthy human microbiome focus on particular body habitats, assuming that microbiome develop similar structural patterns to perform similar ecosystem function under same environmental conditions. However, current studies usually overlook a complex and interconnected landscape of human microbiome and limit the ability in particular body habitats with learning models of specific criterion. Therefore, these methods could not capture the real-world underlying microbial patterns effectively. Results To obtain a comprehensive view, we propose a novel ensemble clustering framework to mine the structure of microbial community pattern on large-scale metagenomic data. Particularly, we first build a microbial similarity network via integrating 1920 metagenomic samples from three body habitats of healthy adults. Then a novel symmetric Nonnegative Matrix Factorization (NMF) based ensemble model is proposed and applied onto the network to detect clustering pattern. Extensive experiments are conducted to evaluate the effectiveness of our model on deriving microbial community with respect to body habitat and host gender. From clustering results, we observed that body habitat exhibits a strong bound but non-unique microbial structural pattern. Meanwhile, human microbiome reveals different degree of structural variations over body habitat and host gender. Conclusions In summary, our ensemble clustering framework could efficiently explore integrated clustering results to accurately identify microbial communities, and provide a comprehensive view for a set of microbial communities. The clustering results indicate that structure of human microbiome is varied systematically across body habitats and host genders. Such trends depict an integrated biography of microbial communities, which offer a new insight towards uncovering pathogenic model of human microbiome. PMID:25521415

Microbial limitation in a changing world: A stoichiometric approach for predicting microbial resource limitation and fluxes

NASA Astrophysics Data System (ADS)

Midgley, M.; Phillips, R.

2014-12-01

Microbes mediate fluxes of carbon (C), nitrogen (N), and phosphorus (P) in soils depending on ratios of available C, N, and P relative to microbial demand. Hence, characterizing microbial C and nutrient limitation in soils is critical for predicting how ecosystems will respond to human alterations of climate and nutrient availability. Here, we take a stoichiometric approach to assessing microbial C, N, and P limitation by using threshold element ratios (TERs). TERs enable shifting resource limitation to be assessed by matching C, N and P ratios from microbial biomass, extracellular enzyme activities, and soil nutrient concentrations. We assessed microbial nutrient limitation in temperate forests dominated by trees that associate with one of two mycorrhizal symbionts: arbsucular mycorrhizal (AM) or ectomycorrhizal (ECM) fungi. We found that both ECM and AM microbial communities were co-limited by C and N, supporting conventional wisdom that microbes are C-limited and temperate forests are N-limited. However, AM microbial communities were relatively more C-limited than ECM communities (P=0.001). In response to chronic field N fertilization, both AM and ECM communities became relatively more P-limited (P=0.011), but they remained N- and C-limited overall. Thus, realistic levels of N deposition may not dampen microbial N limitation. Reflecting differences in relative limitation, N mineralization rates were higher in AM soils than in ECM soils (P=0.004) while C mineralization rates were higher in ECM soils than in AM soils (P=0.023). There were no significant differences in P flux between AM and ECM soils or detectable mineralization responses to N addition, indicating that mineralization rates are closely tied to C and nutrient limitation. Overall, we found that 1) microbial resource limitation can be detected without resource addition; and 2) TERs and ratios of labile resources are viable tools for predicting mineralization responses to resource additions.

Functional gene array-based analysis of microbial community structure in groundwaters with a gradient of contaminant levels

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

Waldron, P.J.; Wu, L.; Van Nostrand, J.D.

2009-06-15

To understand how contaminants affect microbial community diversity, heterogeneity, and functional structure, six groundwater monitoring wells from the Field Research Center of the U.S. Department of Energy Environmental Remediation Science Program (ERSP; Oak Ridge, TN), with a wide range of pH, nitrate, and heavy metal contamination were investigated. DNA from the groundwater community was analyzed with a functional gene array containing 2006 probes to detect genes involved in metal resistance, sulfate reduction, organic contaminant degradation, and carbon and nitrogen cycling. Microbial diversity decreased in relation to the contamination levels of the wells. Highly contaminated wells had lower gene diversity butmore » greater signal intensity than the pristine well. The microbial composition was heterogeneous, with 17-70% overlap between different wells. Metal-resistant and metal-reducing microorganisms were detected in both contaminated and pristine wells, suggesting the potential for successful bioremediation of metal-contaminated groundwaters. In addition, results of Mantel tests and canonical correspondence analysis indicate that nitrate, sulfate, pH, uranium, and technetium have a significant (p < 0.05) effect on microbial community structure. This study provides an overall picture of microbial community structure in contaminated environments with functional gene arrays by showing that diversity and heterogeneity can vary greatly in relation to contamination.« less

Humans differ in their personal microbial cloud

PubMed Central

Altrichter, Adam E.; Bateman, Ashley C.; Stenson, Jason; Brown, GZ; Green, Jessica L.; Bohannan, Brendan J.M.

2015-01-01

Dispersal of microbes between humans and the built environment can occur through direct contact with surfaces or through airborne release; the latter mechanism remains poorly understood. Humans emit upwards of 106 biological particles per hour, and have long been known to transmit pathogens to other individuals and to indoor surfaces. However it has not previously been demonstrated that humans emit a detectible microbial cloud into surrounding indoor air, nor whether such clouds are sufficiently differentiated to allow the identification of individual occupants. We used high-throughput sequencing of 16S rRNA genes to characterize the airborne bacterial contribution of a single person sitting in a sanitized custom experimental climate chamber. We compared that to air sampled in an adjacent, identical, unoccupied chamber, as well as to supply and exhaust air sources. Additionally, we assessed microbial communities in settled particles surrounding each occupant, to investigate the potential long-term fate of airborne microbial emissions. Most occupants could be clearly detected by their airborne bacterial emissions, as well as their contribution to settled particles, within 1.5–4 h. Bacterial clouds from the occupants were statistically distinct, allowing the identification of some individual occupants. Our results confirm that an occupied space is microbially distinct from an unoccupied one, and demonstrate for the first time that individuals release their own personalized microbial cloud. PMID:26417541

The Risk of Microbial Contamination in Multiple-Dose Preservative-Free Ophthalmic Preparations.

PubMed

Saisyo, Atsuyuki; Shimono, Rima; Oie, Shigeharu; Kimura, Kazuhiro; Furukawa, Hiroyuki

2017-01-01

Multiple-dose ophthalmic preparations that do not contain preservatives carry high risks of microbial contamination. However, there are various types of hospital preparations, with different physicochemical properties. In the present study, we evaluated the association between physicochemical properties and microbial contamination in ophthalmic preparations. The investigated hospital preparations included ophthalmic preparations of physiological saline, 0.2% fluconazole, 0.5% vancomycin hydrochloride, and 2% cyclosporine. We investigated the microbial dynamics of each ophthalmic preparation and microbial contamination in ophthalmic preparations used by patients. Remarkable growth of Pseudomonas aeruginosa, Burkholderia cepacia, and Serratia marcescens was observed in ophthalmic preparations of physiological saline and 0.2% fluconazole. All tested microorganisms displayed decreased counts after inoculation in 0.5% vancomycin hydrochloride. In 2% cyclosporine, all investigated microorganisms were below the limit of detection after inoculation for 6 h. The microbial contamination rates of ophthalmic preparations used by patients were 16.7% (3/18 samples) for 0.5% vancomycin hydrochloride and 0% (0/30 samples) for 2% cyclosporine. All detected contaminants in 0.5% vancomycin hydrochloride were Candida spp., one of which was present at a level of 1×10 4 colony-forming units/mL. The storage method for in-use ophthalmic preparations should be considered on the basis of their physicochemical properties.

Cellulolytic potential under environmental changes in microbial communities from grassland litter

DOE PAGES

Berlemont, Renaud; Allison, Steven D.; Weihe, Claudia; ...

2014-11-25

We report that in many ecosystems, global changes are likely to profoundly affect microorganisms. In Southern California, changes in precipitation and nitrogen deposition may influence the composition and functional potential of microbial communities and their resulting ability to degrade plant material. To test whether such environmental changes impact the distribution of functional groups involved in leaf litter degradation, we determined how the genomic diversity of microbial communities in a semi-arid grassland ecosystem changed under reduced precipitation or increased N deposition. We monitored communities seasonally over a period of 2 years to place environmental change responses into the context of naturalmore » variation. Fungal and bacterial communities displayed strong seasonal patterns, Fungi being mostly detected during the dry season whereas Bacteria were common during wet periods. Most putative cellulose degraders were associated with 33 bacterial genera and predicted to constitute 18% of the microbial community. Precipitation reduction reduced bacterial abundance and cellulolytic potential whereas nitrogen addition did not affect the cellulolytic potential of the microbial community. Finally, we detected a strong correlation between the frequencies of genera of putative cellulose degraders and cellulase genes. Thus, microbial taxonomic composition was predictive of cellulolytic potential. This work provides a framework for how environmental changes affect microorganisms responsible for plant litter deconstruction.« less

GreenLight Model 960.

PubMed

Fernandes, Richard; Carey, Conn; Hynes, James; Papkovsky, Dmitri

2013-01-01

The importance of food safety has resulted in a demand for a more rapid, high-throughput method for total viable count (TVC). The industry standard for TVC determination (ISO 4833:2003) is widely used but presents users with some drawbacks. The method is materials- and labor-intensive, requiring multiple agar plates per sample. More importantly, the method is slow, with 72 h typically required for a definitive result. Luxcel Biosciences has developed the GreenLight Model 960, a microtiter plate-based assay providing a rapid high-throughput method of aerobic bacterial load assessment through analysis of microbial oxygen consumption. Results are generated in 1-12 h, depending on microbial load. The mix and measure procedure allows rapid detection of microbial oxygen consumption and equates oxygen consumption to microbial load (CFU/g), providing a simple, sensitive means of assessing the microbial contamination levels in foods (1). As bacteria in the test sample grow and respire, they deplete O2, which is detected as an increase in the GreenLight probe signal above the baseline level (2). The time required to reach this increase in signal can be used to calculate the CFU/g of the original sample, based on a predetermined calibration. The higher the initial microbial load, the earlier this threshold is reached (1).

In vitro study on the effect of doxycycline on the microbial activity of soil determined by redox-potential measuring system.

PubMed

Szakmár, Katalin; Reichart, Olivér; Szatmári, István; Erdősi, Orsolya; Szili, Zsuzsanna; László, Noémi; Székely Körmöczy, Péter; Laczay, Péter

2014-09-01

The potential effect of doxycycline on the microbial activity was investigated in three types of soil. Soil samples were spiked with doxycycline, incubated at 25°C and tested at 0, 2, 4 and 6 days after treatment. The microbiological activity of the soil was characterized by the viable count determined by plate pouring and by the time necessary to reach a defined rate of the redox-potential decrease termed as time to detection (TTD).The viable count of the samples was not changed during the storage. The TTD values, however exhibited a significant increase in the 0.2-1.6 mg/kg doxycycline concentration range compared to the untreated samples indicating concentration-dependent inhibitory effect on microbial activity. The potency of the effect was different in the 3 soil types. To describe the combined effect of the doxycycline concentration and time on the biological activity of one type of soil a mathematical model was constructed and applied.The change of microbial metabolic rate could be measured also without (detectable) change of microbial count when the traditional microbiological methods are not applicable. The applied new redox potential measurement-based method is a simple and useful procedure for the examination of microbial activity of soil and its potential inhibition by antibiotics.

Microbial dynamics during production of lesser mealworms (Alphitobius diaperinus) for human consumption at industrial scale.

PubMed

Wynants, E; Crauwels, S; Verreth, C; Gianotten, N; Lievens, B; Claes, J; Van Campenhout, L

2018-04-01

In this study, the microbial dynamics during an industrial production cyle of lesser mealworms (Alphitobius diaperinus), sold for human consumption, were characterised. The microbial numbers as well as the microbial diversity were generally higher for the substrate, existing of remaining feed, faeces and exuviae, than for the larvae. Most of the species-level operational taxonomic units, identified using Illumina MiSeq sequencing, that were present in the feed were also detected in the larvae and vice versa. However, bacterial diversity decreased in the larvae during rearing. These results suggested that the feed is an important determinant of the insect bacterial community, but that some bacterial species show a competitive advantage inside the insect gut and become dominant. A blanching treatment of the larvae after harvest reduced most microbial counts, but the number of aerobic endospores remained at 4.0 log cfu/g. Whereas food pathogens Salmonella spp., Listeria monocytogenes, Bacillus cereus or coagulase-positive staphylococci were not detected in our study, fungal isolates corresponding to the genera Aspergillus and Fusarium were recovered. Therefore, it cannot be excluded that mycotoxins were present. The results of this study contribute to a better understanding of the microbial dynamics and food safety aspects during the production of edible insects. Copyright © 2017 Elsevier Ltd. All rights reserved.

Forensic analysis of tertiary-butyl alcohol (TBA) detections in a hydrocarbon-rich groundwater basin.

PubMed

Quast, Konrad W; Levine, Audrey D; Kester, Janet E; Fordham, Carolyn L

2016-04-01

Tertiary-butyl alcohol (TBA), a high-production volume (HPV) chemical, was sporadically detected in groundwater and coalbed methane (CBM) wells in southeastern Colorado's hydrocarbon-rich Raton Basin. TBA concentrations in shallow water wells averaged 75.1 μg/L, while detections in deeper CBM wells averaged 14.4 μg/L. The detection of TBA prompted a forensic investigation to try to identify potential sources. Historic and recent data were reviewed to determine if there was a discernable pattern of TBA occurrence. Supplemental samples from domestic water wells, monitor wells, CBM wells, surface waters, and hydraulic fracturing (HF) fluids were analyzed for TBA in conjunction with methyl tertiary-butyl ether (MTBE) and ethyl tertiary-butyl ether (ETBE), proxies for evidence of contamination from reformulated gasoline or associated oxygenates. Exploratory microbiological sampling was conducted to determine if methanotrophic organisms co-occurred with TBA in individual wells. Meaningful comparisons of historic TBA data were limited due to widely varying reporting limits. Mapping of TBA occurrence did not reveal any spatial patterns or physical associations with CBM operations or contamination plumes. Additionally, TBA was not detected in HF fluids or surface water samples. Given the widespread use of TBA in industrial and consumer products, including water well completion materials, it is likely that multiple diffuse sources exist. Exploratory data on stable isotopes, dissolved gases, and microbial profiling provide preliminary evidence that methanotrophic activity may be producing TBA from naturally occurring isobutane. Reported TBA concentrations were significantly below a conservative risk-based drinking water screening level of 8000 μg/L derived from animal toxicity data.

Metagenomics Reveals the Influence of Land Use and Rain on the Benthic Microbial Communities in a Tropical Urban Waterway

PubMed Central

2018-01-01

ABSTRACT Growing demands for potable water have led to extensive reliance on waterways in tropical megacities. Attempts to manage these waterways in an environmentally sustainable way generally lack an understanding of microbial processes and how they are influenced by urban factors, such as land use and rain. Here, we describe the composition and functional potential of benthic microbial communities from an urban waterway network and analyze the effects of land use and rain perturbations on these communities. With a sequence depth of 3 billion reads from 48 samples, these metagenomes represent nearly full coverage of microbial communities. The predominant taxa in these waterways were Nitrospira and Coleofasciculus, indicating the presence of nitrogen and carbon fixation in this system. Gene functions from carbohydrate, protein, and nucleic acid metabolism suggest the presence of primary and secondary productivity in such nutrient-deficient systems. Comparison of microbial communities by land use type and rain showed that while there are significant differences in microbial communities in land use, differences due to rain perturbations were rain event specific. The more diverse microbial communities in the residential areas featured a higher abundance of reads assigned to genes related to community competition. However, the less diverse communities from industrial areas showed a higher abundance of reads assigned to specialized functions such as organic remediation. Finally, our study demonstrates that microbially diverse populations in well-managed waterways, where contaminant levels are within defined limits, are comparable to those in other relatively undisturbed freshwater systems. IMPORTANCE Unravelling the microbial metagenomes of urban waterway sediments suggest that well-managed urban waterways have the potential to support diverse sedimentary microbial communities, similar to those of undisturbed natural freshwaters. Despite the fact that these urban waterways are well managed, our study shows that environmental pressures from land use and rain perturbations play a role in shaping the structure and functions of microbial communities in these waterways. We propose that although pulsed disturbances, such as rain perturbations, influence microbial communities, press disturbances, including land usage history, have a long-term and stronger influence on microbial communities. Our study found that the functions of microbial communities were less affected by environmental factors than the structure of microbial communities was, indicating that core microbial functions largely remain conserved in challenging environments. PMID:29896568

Metagenomics Reveals the Influence of Land Use and Rain on the Benthic Microbial Communities in a Tropical Urban Waterway.

PubMed

Saxena, Gourvendu; Mitra, Suparna; Marzinelli, Ezequiel M; Xie, Chao; Wei, Toh Jun; Steinberg, Peter D; Williams, Rohan B H; Kjelleberg, Staffan; Lauro, Federico M; Swarup, Sanjay

2018-01-01

Growing demands for potable water have led to extensive reliance on waterways in tropical megacities. Attempts to manage these waterways in an environmentally sustainable way generally lack an understanding of microbial processes and how they are influenced by urban factors, such as land use and rain. Here, we describe the composition and functional potential of benthic microbial communities from an urban waterway network and analyze the effects of land use and rain perturbations on these communities. With a sequence depth of 3 billion reads from 48 samples, these metagenomes represent nearly full coverage of microbial communities. The predominant taxa in these waterways were Nitrospira and Coleofasciculus , indicating the presence of nitrogen and carbon fixation in this system. Gene functions from carbohydrate, protein, and nucleic acid metabolism suggest the presence of primary and secondary productivity in such nutrient-deficient systems. Comparison of microbial communities by land use type and rain showed that while there are significant differences in microbial communities in land use, differences due to rain perturbations were rain event specific. The more diverse microbial communities in the residential areas featured a higher abundance of reads assigned to genes related to community competition. However, the less diverse communities from industrial areas showed a higher abundance of reads assigned to specialized functions such as organic remediation. Finally, our study demonstrates that microbially diverse populations in well-managed waterways, where contaminant levels are within defined limits, are comparable to those in other relatively undisturbed freshwater systems. IMPORTANCE Unravelling the microbial metagenomes of urban waterway sediments suggest that well-managed urban waterways have the potential to support diverse sedimentary microbial communities, similar to those of undisturbed natural freshwaters. Despite the fact that these urban waterways are well managed, our study shows that environmental pressures from land use and rain perturbations play a role in shaping the structure and functions of microbial communities in these waterways. We propose that although pulsed disturbances, such as rain perturbations, influence microbial communities, press disturbances, including land usage history, have a long-term and stronger influence on microbial communities. Our study found that the functions of microbial communities were less affected by environmental factors than the structure of microbial communities was, indicating that core microbial functions largely remain conserved in challenging environments.

Assessment of the microbial removal capabilities of riverbank filtration

NASA Astrophysics Data System (ADS)

Partinoudi, V.; Collins, M.; Margolin, A.; Brannaka, L.

2003-04-01

Riverbank filtrate includes both groundwater and river water that has percolated through the banks or bed of a river to an extraction well. One of the primary objectives of this study was to assess the microbial removal capabilities of riverbank filtration (RBF) independent of any groundwater dilution, i.e. a worse case scenario. A total of five sites were chosen: the Pembroke Waterworks (NH), the Milford State Fish Hatchery (NH), Jackson (NH) (where an infiltration gallery exists), Louisville Water Company (KY), and Cedar Rapids (IA). This study has been monitoring total coliforms, E.coli and aerobic spore forming bacteria amongst other water quality parameters over the past twelve months. Male specific (MS2) and somatic coliphage viruses were also monitored intensively for two weeks, using a single agar overlay and a two-step enrichment method, in December 2002 in Louisville, KY and in Cedar Rapids, IA. This intensive coliphage monitoring was followed by the collection of samples for special analysis of enteric viruses (Adenovirus type 40 and 41, Astrovirus, Poliovirus, Coxsackie virus, Rotavirus and Echovirus). The virus samples were analyzed using the ICC-nPCR method, due to its high specificity and sensitivity. Typical river water total coliforms, E.coli and aerobic spore forming bacteria concentrations ranged between 43-145000 CFU/100mL, 0-24192 CFU/100mL and 83-1997 CFU/100mL, respectively. All three of these microbial concentrations were below detection limits (<1CFU/100mL) in the riverbank filtration extraction well water, even after eliminating the “dilution” effects with groundwater. The male specific and the somatic coliphages ranged between 328-491 PFU/25mL and 3-21 PFU/25mL, respectively, in the river water. The concentration of the male specific coliphages was reduced by as much as 77% by the riverbank passage whereas the concentrations of the somatic coliphages were reduced by 100%. In summary the sites evaluated in this study indicated the conservative effectiveness of RBF in removing bacteria and virus indicators. Any groundwater dilution with the RBF extract should contribute to even lower microbial concentrations.

Mind the gut: genomic insights to population divergence and gut microbial composition of two marine keystone species.

PubMed

Fietz, Katharina; Rye Hintze, Christian Olaf; Skovrind, Mikkel; Kjærgaard Nielsen, Tue; Limborg, Morten T; Krag, Marcus A; Palsbøll, Per J; Hestbjerg Hansen, Lars; Rask Møller, Peter; Gilbert, M Thomas P

2018-05-02

Deciphering the mechanisms governing population genetic divergence and local adaptation across heterogeneous environments is a central theme in marine ecology and conservation. While population divergence and ecological adaptive potential are classically viewed at the genetic level, it has recently been argued that their microbiomes may also contribute to population genetic divergence. We explored whether this might be plausible along the well-described environmental gradient of the Baltic Sea in two species of sand lance (Ammodytes tobianus and Hyperoplus lanceolatus). Specifically, we assessed both their population genetic and gut microbial composition variation and investigated not only which environmental parameters correlate with the observed variation, but whether host genome also correlates with microbiome variation. We found a clear genetic structure separating the high-salinity North Sea from the low-salinity Baltic Sea sand lances. The observed genetic divergence was not simply a function of isolation by distance, but correlated with environmental parameters, such as salinity, sea surface temperature, and, in the case of A. tobianus, possibly water microbiota. Furthermore, we detected two distinct genetic groups in Baltic A. tobianus that might represent sympatric spawning types. Investigation of possible drivers of gut microbiome composition variation revealed that host species identity was significantly correlated with the microbial community composition of the gut. A potential influence of host genetic factors on gut microbiome composition was further confirmed by the results of a constrained analysis of principal coordinates. The host genetic component was among the parameters that best explain observed variation in gut microbiome composition. Our findings have relevance for the population structure of two commercial species but also provide insights into potentially relevant genomic and microbial factors with regards to sand lance adaptation across the North Sea-Baltic Sea environmental gradient. Furthermore, our findings support the hypothesis that host genetics may play a role in regulating the gut microbiome at both the interspecific and intraspecific levels. As sequencing costs continue to drop, we anticipate that future studies that include full genome and microbiome sequencing will be able to explore the full relationship and its potential adaptive implications for these species.

The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide.

PubMed

He, Zhili; Piceno, Yvette; Deng, Ye; Xu, Meiying; Lu, Zhenmei; Desantis, Todd; Andersen, Gary; Hobbie, Sarah E; Reich, Peter B; Zhou, Jizhong

2012-02-01

One of the major factors associated with global change is the ever-increasing concentration of atmospheric CO(2). Although the stimulating effects of elevated CO(2) (eCO(2)) on plant growth and primary productivity have been established, its impacts on the diversity and function of soil microbial communities are poorly understood. In this study, phylogenetic microarrays (PhyloChip) were used to comprehensively survey the richness, composition and structure of soil microbial communities in a grassland experiment subjected to two CO(2) conditions (ambient, 368 p.p.m., versus elevated, 560 p.p.m.) for 10 years. The richness based on the detected number of operational taxonomic units (OTUs) significantly decreased under eCO(2). PhyloChip detected 2269 OTUs derived from 45 phyla (including two from Archaea), 55 classes, 99 orders, 164 families and 190 subfamilies. Also, the signal intensity of five phyla (Crenarchaeota, Chloroflexi, OP10, OP9/JS1, Verrucomicrobia) significantly decreased at eCO(2), and such significant effects of eCO(2) on microbial composition were also observed at the class or lower taxonomic levels for most abundant phyla, such as Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Acidobacteria, suggesting a shift in microbial community composition at eCO(2). Additionally, statistical analyses showed that the overall taxonomic structure of soil microbial communities was altered at eCO(2). Mantel tests indicated that such changes in species richness, composition and structure of soil microbial communities were closely correlated with soil and plant properties. This study provides insights into our understanding of shifts in the richness, composition and structure of soil microbial communities under eCO(2) and environmental factors shaping the microbial community structure.

Impact of long-term conservation management on soil microbial N cycling and greenhouse gas emissions in a humid agroecosystem in West Tennessee

NASA Astrophysics Data System (ADS)

Schaeffer, S. M.; Konkel, J. M.; Jin, V.

2017-12-01

Conservation practices such as no-tillage, cover crops, and reduced mineral fertilizer application are thought to help mitigate atmospheric greenhouse gas (GHG) concentrations through building soil organic matter. However, some studies have shown that both no-till and cover crops can increase GHG emissions, perhaps due to increased microbial activity. It is possible that these results are confounded by perturbations caused when management practices are newly implemented. There is a clear lack of data from long-term sites where experimental plots are well equilibrated to the management systems. Starting in 2016, we measured fluxes of nitrous oxide (N2O), methane (CH4) and carbon dioxide (CO2) in twelve combinations of tillage (disk, no-till), N fertilizer rate (0, 67 kg N ha-1), and winter cover crops (none, hairy vetch, winter wheat) under continuous cotton production for 35 years. During the cotton growing season, the largest daily fluxes of N2O (36.9±11.9 g N ha-1 d-1) occurred in tilled plots regardless of cover crop or fertilization rate. However, over the entire year, the largest fluxes were observed during winter cover crop growth (63.0±21.4 g N ha-1 d-1). Overall, N2O fluxes were lower in no-till compared to tilled soils, save those under hairy vetch, a nitrogen fixing cover crop. These results, combined with our observation of higher rates of microbial N mineralization and nitrification in no-till and vetch plots, suggest vetch cover crops may stimulate both GHG and inorganic N production. We observed seasonal patterns in CH4 flux with net CH4 production during Spring and early Summer (from 0.2±0.8 to 4.8±3.2 g C ha-1 d-1), switching to net CH4 consumption by late summer (from -6.3±3.4 to 0.8±0.5 g C ha-1 d-1). Cumulative CH4 fluxes suggest that reduced tillage and fertilization may change these agroecosystems from weak sources to weak sinks for CH4. Our results highlight the impact of nitrogen availability on GHG emissions, and the need for improved understanding of the soil microbial and physical processes driving coupled N and C transformations, as well as the interactive effect of conservation management practices.

Monitoring microbial metabolites using an inductively coupled resonance circuit

PubMed Central

Karnaushenko, Daniil; Baraban, Larysa; Ye, Dan; Uguz, Ilke; Mendes, Rafael G.; Rümmeli, Mark H.; de Visser, J. Arjan G. M.; Schmidt, Oliver G.; Cuniberti, Gianaurelio; Makarov, Denys

2015-01-01

We present a new approach to monitor microbial population dynamics in emulsion droplets via changes in metabolite composition, using an inductively coupled LC resonance circuit. The signal measured by such resonance detector provides information on the magnetic field interaction with the bacterial culture, which is complementary to the information accessible by other detection means, based on electric field interaction, i.e. capacitive or resistive, as well as optical techniques. Several charge-related factors, including pH and ammonia concentrations, were identified as possible contributors to the characteristic of resonance detector profile. The setup enables probing the ionic byproducts of microbial metabolic activity at later stages of cell growth, where conventional optical detection methods have no discriminating power. PMID:26264183

A review of current and future molecular diagnostic tests for use in the microbiology laboratory.

PubMed

Jannes, Geert; De Vos, Daniel

2006-01-01

Nucleic acid-based diagnostics gradually are replacing or complementing culture-based, biochemical, and immunological assays in routine microbiology laboratories. Similar to conventional tests, the first-generation deoxyribonucleic acid assays determined only a single analyte. Recent improvements in detection technologies have paved the way for the development of multiparameter assays using macroarrays or micro-arrays, while the introduction of closed-tube real-time polymerase chain reaction systems has resulted in the development of rapid microbial diagnostics with a reduced contamination risk. The use of these new molecular technologies is not restricted to detection and identification of microbial pathogens but also can be used for genotyping, allowing one to determine antibiotic resistance or to perform microbial fingerprinting.

An assessment of water quality and microbial risk in Rio Grande Basin in the United States-Mexican border region.

PubMed

Ryu, Hodon; Alum, Absar; Alvarez, Maria; Mendoza, Jose; Abbaszadegan, Morteza

2005-06-01

Increased reliance of urban populations on Rio Grande water has necessitated an expanded microbial surveillance of the river to help identify and evaluate sources of human pathogens, which could pose a public health risk. The objectives of this study were to investigate microbial and chemical water quality in Rio Grande water and to perform risk assessment analyses for Cryptosporidium. No oocysts in any of the ten-litre samples were detected. However, the limit of detection in the water samples ranged between 20 and 200 oocysts/100 L. The limits of detection obtained in this study would result in one to two orders of magnitude higher risk of infection for Cryptosporidium than the U.S.EPA annual acceptable risk level of 10(-4). The bacterial data showed the significance of animal farming and raw sewage as sources of fecal pollution. Male specific and somatic coliphages were detected in 52% (11/21) and 62% (24/39) of the samples, respectively. Somatic coliphages were greater by one order of magnitude, and were better correlated with total (r2 = 0.6801; p < or = 0.05) and fecal coliform bacteria (r2 = 0.7366; p < or = 0.05) than male specific coliphages. The dissolved organic carbon (DOC) and specific ultraviolet absorbance (SUVA) values ranged 2.58-5.59mg/L and 1.23-2.29 m(-1) (mg/I)(-1), respectively. Low SUVA values of raw water condition make it difficult to remove DOC during physical and chemical treatment processes. The microbial and chemical data provided from this study can help drinking water utilities to maintain balance between greater microbial inactivation and reduced disinfection by-products (DBPs) formation.

Nanomaterials-based biosensors for detection of microorganisms and microbial toxins.

PubMed

Sutarlie, Laura; Ow, Sian Yang; Su, Xiaodi

2017-04-01

Detection of microorganisms and microbial toxins is important for health and safety. Due to their unique physical and chemical properties, nanomaterials have been extensively used to develop biosensors for rapid detection of microorganisms with microbial cells and toxins as target analytes. In this paper, the design principles of nanomaterials-based biosensors for four selected analyte categories (bacteria cells, toxins, mycotoxins, and protozoa cells), closely associated with the target analytes' properties is reviewed. Five signal transducing methods that are less equipment intensive (colorimetric, fluorimetric, surface enhanced Raman scattering, electrochemical, and magnetic relaxometry methods) is described and compared for their sensory performance (in term oflimit of detection, dynamic range, and response time) for all analyte categories. In the end, the suitability of these five sensing principles for on-site or field applications is discussed. With a comprehensive coverage of nanomaterials, design principles, sensing principles, and assessment on the sensory performance and suitability for on-site application, this review offers valuable insight and perspective for designing suitable nanomaterials-based microorganism biosensors for a given application. Copyright © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

THE NEAR-EQUILIBRIUM OF MICROBIALLY MEDIATED REDOX COUPLES IN REDUCING GROUNDWATER ENVIRONMENTS

EPA Science Inventory

Redox couples are commonly held to be in disequilibrium among each other in most natural waters. To evaluate this view for microbially mediated, reducing, groundwater environments, monitoring data were examined for several couples under conditions ranging from nitrate-detectable...

Identification of Bacterial DNA Markers for the Detection of Human and Cattle Fecal Pollution - SLIDES

EPA Science Inventory

Technological advances in DNA sequencing and computational biology allow scientists to compare entire microbial genomes. However, the use of these approaches to discern key genomic differences between natural microbial communities remains prohibitively expensive for most laborato...

IDENTIFICATION OF BACTERIAL DNA MARKERS FOR THE DETECTION OF HUMAN AND CATTLE FECAL POLLUTION

EPA Science Inventory

Technological advances in DNA sequencing and computational biology allow scientists to compare entire microbial genomes. However, the use of these approaches to discern key genomic differences between natural microbial communities remains prohibitively expensive for most laborato...

The life sulfuric: microbial ecology of sulfur cycling in marine sediments.

PubMed

Wasmund, Kenneth; Mußmann, Marc; Loy, Alexander

2017-08-01

Almost the entire seafloor is covered with sediments that can be more than 10 000 m thick and represent a vast microbial ecosystem that is a major component of Earth's element and energy cycles. Notably, a significant proportion of microbial life in marine sediments can exploit energy conserved during transformations of sulfur compounds among different redox states. Sulfur cycling, which is primarily driven by sulfate reduction, is tightly interwoven with other important element cycles (carbon, nitrogen, iron, manganese) and therefore has profound implications for both cellular- and ecosystem-level processes. Sulfur-transforming microorganisms have evolved diverse genetic, metabolic, and in some cases, peculiar phenotypic features to fill an array of ecological niches in marine sediments. Here, we review recent and selected findings on the microbial guilds that are involved in the transformation of different sulfur compounds in marine sediments and emphasise how these are interlinked and have a major influence on ecology and biogeochemistry in the seafloor. Extraordinary discoveries have increased our knowledge on microbial sulfur cycling, mainly in sulfate-rich surface sediments, yet many questions remain regarding how sulfur redox processes may sustain the deep-subsurface biosphere and the impact of organic sulfur compounds on the marine sulfur cycle. © 2017 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Microbial diversity in Brazilian mangrove sediments – a mini review

PubMed Central

Ghizelini, Angela Michelato; Mendonça-Hagler, Leda Cristina Santana; Macrae, Andrew

2012-01-01

The importance and protection of mangrove ecosystems has been recognized in Brazilian Federal law since 1965. Being protected in law, however, has not always guaranteed their protection in practice. Mangroves are found in coastal and estuarine locations, which are prime real estate for the growth of cities, ports and other economic activities important for Brazilian development. In this mini-review we introduce what mangroves are and why they are so important. We give a brief overview of the microbial diversity found in mangrove sediments and then focus on diversity studies from Brazilian mangroves. We highlight the breadth and depth of knowledge about mangrove microbial communities gained from studying Brazilian mangroves. We report on the exciting findings of molecular microbial ecology methods that have been very successfully applied to study bacterial communities. We note that there have been fewer studies that focus on fungal communities and that fungal diversity studies deserve more attention. The review ends with a look at how a combination of new molecular biology methods and isolation studies are being developed to monitor and conserve mangrove ecosystems and their associated microbial communities. These recent studies are having a global impact and we hope they will help to protect and re-establish mangrove ecosystems. PMID:24031949

In-Field Implementation of a Recombinant Factor C Assay for the Detection of Lipopolysaccharide as a Biomarker of Extant Life within Glacial Environments

PubMed Central

Barnett, Megan J.; Wadham, Jemma L.; Jackson, Miriam; Cullen, David C.

2012-01-01

The discovery over the past two decades of viable microbial communities within glaciers has promoted interest in the role of glaciers and ice sheets (the cryosphere) as contributors to subglacial erosion, global biodiversity, and in regulating global biogeochemical cycles. In situ or in-field detection and characterisation of microbial communities is becoming recognised as an important approach to improve our understanding of such communities. Within this context we demonstrate, for the first time, the ability to detect Gram-negative bacteria in glacial field-environments (including subglacial environments) via the detection of lipopolysaccharide (LPS); an important component of Gram-negative bacterial cell walls. In-field measurements were performed using the recently commercialised PyroGene® recombinant Factor C (rFC) endotoxin detection system and used in conjunction with a handheld fluorometer to measure the fluorescent endpoint of the assay. Twenty-seven glacial samples were collected from the surface, bed and terminus of a low-biomass Arctic valley glacier (Engabreen, Northern Norway), and were analysed in a field laboratory using the rFC assay. Sixteen of these samples returned positive LPS detection. This work demonstrates that LPS detection via rFC assay is a viable in-field method and is expected to be a useful proxy for microbial cell concentrations in low biomass environments. PMID:25585634

Microbially derived biosensors for diagnosis, monitoring and epidemiology.

PubMed

Chang, Hung-Ju; Voyvodic, Peter L; Zúñiga, Ana; Bonnet, Jérôme

2017-09-01

Living cells have evolved to detect and process various signals and can self-replicate, presenting an attractive platform for engineering scalable and affordable biosensing devices. Microbes are perfect candidates: they are inexpensive and easy to manipulate and store. Recent advances in synthetic biology promise to streamline the engineering of microbial biosensors with unprecedented capabilities. Here we review the applications of microbially-derived biosensors with a focus on environmental monitoring and healthcare applications. We also identify critical challenges that need to be addressed in order to translate the potential of synthetic microbial biosensors into large-scale, real-world applications. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Microbial distributions detected by an oligonucleotide microarray across geochemical zones associated with methane in marine sediments from the Ulleung Basin

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

Briggs, Brandon R; Graw, Michael; Brodie, Eoin L

2013-11-01

The biogeochemical processes that occur in marine sediments on continental margins are complex; however, from one perspective they can be considered with respect to three geochemical zones based on the presence and form of methane: sulfate–methane transition (SMTZ), gas hydrate stability zone (GHSZ), and free gas zone (FGZ). These geochemical zones may harbor distinct microbial communities that are important in biogeochemical carbon cycles. The objective of this study was to describe the microbial communities in sediments from the SMTZ, GHSZ, and FGZ using molecular ecology methods (i.e. PhyloChip microarray analysis and terminal restriction fragment length polymorphism (T-RFLP)) and examining themore » results in the context of non-biological parameters in the sediments. Non-metric multidimensional scaling and multi-response permutation procedures were used to determine whether microbial community compositions were significantly different in the three geochemical zones and to correlate samples with abiotic characteristics of the sediments. This analysis indicated that microbial communities from all three zones were distinct from one another and that variables such as sulfate concentration, hydrate saturation of the nearest gas hydrate layer, and depth (or unmeasured variables associated with depth e.g. temperature, pressure) were correlated to differences between the three zones. The archaeal anaerobic methanotrophs typically attributed to performing anaerobic oxidation of methane were not detected in the SMTZ; however, the marine benthic group-B, which is often found in SMTZ, was detected. Within the GHSZ, samples that were typically closer to layers that contained higher hydrate saturation had indicator sequences related to Vibrio-type taxa. These results suggest that the biogeographic patterns of microbial communities in marine sediments are distinct based on geochemical zones defined by methane.« less

GeoChip-based analysis of metabolic diversity of microbial communities at the Juan de Fuca Ridge hydrothermal vent

PubMed Central

Wang, Fengping; Zhou, Huaiyang; Meng, Jun; Peng, Xiaotong; Jiang, Lijing; Sun, Ping; Zhang, Chuanlun; Van Nostrand, Joy D.; Deng, Ye; He, Zhili; Wu, Liyou; Zhou, Jizhong; Xiao, Xiang

2009-01-01

Deep-sea hydrothermal vents are one of the most unique and fascinating ecosystems on Earth. Although phylogenetic diversity of vent communities has been extensively examined, their physiological diversity is poorly understood. In this study, a GeoChip-based, high-throughput metagenomics technology revealed dramatic differences in microbial metabolic functions in a newly grown protochimney (inner section, Proto-I; outer section, Proto-O) and the outer section of a mature chimney (4143-1) at the Juan de Fuca Ridge. Very limited numbers of functional genes were detected in Proto-I (113 genes), whereas much higher numbers of genes were detected in Proto-O (504 genes) and 4143-1 (5,414 genes). Microbial functional genes/populations in Proto-O and Proto-I were substantially different (around 1% common genes), suggesting a rapid change in the microbial community composition during the growth of the chimney. Previously retrieved cbbL and cbbM genes involved in the Calvin Benson Bassham (CBB) cycle from deep-sea hydrothermal vents were predominant in Proto-O and 4143-1, whereas photosynthetic green-like cbbL genes were the major components in Proto-I. In addition, genes involved in methanogenesis, aerobic and anaerobic methane oxidation (e.g., ANME1 and ANME2), nitrification, denitrification, sulfate reduction, degradation of complex carbon substrates, and metal resistance were also detected. Clone libraries supported the GeoChip results but were less effective than the microarray in delineating microbial populations of low biomass. Overall, these results suggest that the hydrothermal microbial communities are metabolically and physiologically highly diverse, and the communities appear to be undergoing rapid dynamic succession and adaptation in response to the steep temperature and chemical gradients across the chimney. PMID:19273854

Recovery of microbial communities and carbon cycling processes following drought manipulation in southern California

NASA Astrophysics Data System (ADS)

Allison, S. D.; Martiny, J. B. H.; Martiny, A.; Berlemont, R.; Treseder, K. K.; Goulden, M.; Brodie, E.

2016-12-01

Predicting the functioning of microbial communities under changing environmental conditions remains a key challenge in Earth system science. Metagenomics and other high-throughput molecular approaches can help address this challenge by revealing the functional potential of microbial communities. We coupled metagenomics with models and experimental manipulations to address microbial responses to drought in a California grassland ecosystem along with the consequences for carbon cycling. We developed an approach for extracting trait information from metagenomic data and asked: 1) What is the phylogenetic structure of drought response traits? 2) What is the relationship between these traits and those involved in carbohydrate degradation? 3) How do both classes of traits vary seasonally and with precipitation manipulation? 4) How resilient are these traits in the face of perturbation? We found that drought response traits are phylogenetically conserved at an equivalent of 5-8% ribosomal RNA gene sequence dissimilarity. Experimental drought treatment selected for the genetic potential to degrade starch, xylan, and mixed polysaccharides, suggesting a link between drought response and carbon cycling traits. In addition, microbial communities exposed to experimental drought showed a reduced potential to degrade plant biomass. Particularly among bacteria, seasonal drought had a larger impact on microbial composition, abundance, and carbohydrate-degrading genes compared to experimental drought. Bacterial communities were also more resilient to drought perturbation than fungal communities, which showed legacies of drought perturbation for up to three years. Altogether, these findings imply that microbial communities exhibit trait diversity that facilitates resilience but with substantial time lags and consequences for carbon turnover. This information is being used to inform new trait-based models that address the challenge of predicting microbial functioning under precipitation change.

From Metchnikoff to Monsanto and beyond: the path of microbial control.

PubMed

Lord, Jeffrey C

2005-05-01

In 125 years since Metchnikoff proposed the use of Metarhizium anisopliae to control the wheat cockchafer and brought about the first field trials, microbial control has progressed from the application of naturalists' observations to biotechnology and precision delivery. This review highlights major milestones in its evolution and presents a perspective on its current direction. Fungal pathogens, the most eye-catching agents, dominated the early period, but major mycological control efforts for chinch bugs and citrus pests in the US had questionable success, and interest waned. The discoveries of Bacillus popilliae and Bacillus thuringiensis began the era of practical and commercially viable microbial control. A program to control the Japanese beetle in the US led to the discovery of both B. popilliae and Steinernema glaseri, the first nematode used as a microbial control agent. Viral insect control became practical in the latter half of the 20th century, and the first registration was obtained with the Heliothis nuclear polyhedrosis virus in 1975. Now strategies are shifting for microbial control. While Bt transgenic crops are now planted on millions of hectares, the successes of more narrowly defined microbial control are mainly in small niches. Commercial enthusiasm for traditional microbial control agents has been unsteady in recent years. The prospects of microbial insecticide use on vast areas of major crops are now viewed more realistically. Regulatory constraints, activist resistance, benign and efficacious chemicals, and limited research funding all drive changes in focus. Emphasis is shifting to monitoring, conservation, integration with chemical pesticides, and selection of favorable venues such as organic agriculture and countries that have low costs, mild regulatory climates, modest chemical inputs, and small scale farming.

Microbial consortia in Oman oil fields: a possible use in enhanced oil recovery.

PubMed

Al-Bahry, Saif N; Elshafie, Abdulkader E; Al-Wahaibi, Yahya M; Al-Bemani, Ali S; Joshi, Sanket J; Al-Maaini, Ratiba A; Al-Alawi, Wafa J; Sugai, Yuichi; Al-Mandhari, Mussalam

2013-01-01

Microbial enhanced oil recovery (MEOR) is one of the most economical and efficient methods for extending the life of production wells in a declining reservoir. Microbial consortia from Wafra oil wells and Suwaihat production water, Al-Wusta region, Oman were screened. Microbial consortia in brine samples were identified using denaturing gradient gel electrophoresis and 16S rRNA gene sequences. The detected microbial consortia of Wafra oil wells were completely different from microbial consortia of Suwaihat formation water. A total of 33 genera and 58 species were identified in Wafra oil wells and Suwaihat production water. All of the identified microbial genera were first reported in Oman, with Caminicella sporogenes for the first time reported from oil fields. Most of the identified microorganisms were found to be anaerobic, thermophilic, and halophilic, and produced biogases, biosolvants, and biosurfactants as by-products, which may be good candidates for MEOR.

A Natural View of Microbial Biodiversity within Hot Spring Cyanobacterial Mat Communities

PubMed Central

Ward, David M.; Ferris, Michael J.; Nold, Stephen C.; Bateson, Mary M.

1998-01-01

This review summarizes a decade of research in which we have used molecular methods, in conjunction with more traditional approaches, to study hot spring cyanobacterial mats as models for understanding principles of microbial community ecology. Molecular methods reveal that the composition of these communities is grossly oversimplified by microscopic and cultivation methods. For example, none of 31 unique 16S rRNA sequences detected in the Octopus Spring mat, Yellowstone National Park, matches that of any prokaryote previously cultivated from geothermal systems; 11 are contributed by genetically diverse cyanobacteria, even though a single cyanobacterial species was suspected based on morphologic and culture analysis. By studying the basis for the incongruity between culture and molecular samplings of community composition, we are beginning to cultivate isolates whose 16S rRNA sequences are readily detected. By placing the genetic diversity detected in context with the well-defined natural environmental gradients typical of hot spring mat systems, the relationship between gene and species diversity is clarified and ecological patterns of species occurrence emerge. By combining these ecological patterns with the evolutionary patterns inherently revealed by phylogenetic analysis of gene sequence data, we find that it may be possible to understand microbial biodiversity within these systems by using principles similar to those developed by evolutionary ecologists to understand biodiversity of larger species. We hope that such an approach guides microbial ecologists to a more realistic and predictive understanding of microbial species occurrence and responsiveness in both natural and disturbed habitats. PMID:9841675

A natural view of microbial biodiversity within hot spring cyanobacterial mat communities

NASA Technical Reports Server (NTRS)

Ward, D. M.; Ferris, M. J.; Nold, S. C.; Bateson, M. M.

1998-01-01

This review summarizes a decade of research in which we have used molecular methods, in conjunction with more traditional approaches, to study hot spring cyanobacterial mats as models for understanding principles of microbial community ecology. Molecular methods reveal that the composition of these communities is grossly oversimplified by microscopic and cultivation methods. For example, none of 31 unique 16S rRNA sequences detected in the Octopus Spring mat, Yellowstone National Park, matches that of any prokaryote previously cultivated from geothermal systems; 11 are contributed by genetically diverse cyanobacteria, even though a single cyanobacterial species was suspected based on morphologic and culture analysis. By studying the basis for the incongruity between culture and molecular samplings of community composition, we are beginning to cultivate isolates whose 16S rRNA sequences are readily detected. By placing the genetic diversity detected in context with the well-defined natural environmental gradients typical of hot spring mat systems, the relationship between gene and species diversity is clarified and ecological patterns of species occurrence emerge. By combining these ecological patterns with the evolutionary patterns inherently revealed by phylogenetic analysis of gene sequence data, we find that it may be possible to understand microbial biodiversity within these systems by using principles similar to those developed by evolutionary ecologists to understand biodiversity of larger species. We hope that such an approach guides microbial ecologists to a more realistic and predictive understanding of microbial species occurrence and responsiveness in both natural and disturbed habitats.

Microbial models of mammalian metabolism: microbial transformation of naproxen.

PubMed

el Sayed, K A

2000-12-01

Preparative-scale fermentation of S-naproxen, the known antiinflammatory, analgesic and antipyretic drug, with Cunninghamella elegans ATCC 9245 afforded S-demethylnaproxen, the known human active metabolite of naproxen, in a 90% yield. Demethylnaproxen was also detected as the major metabolite of naproxen using Cunninghamella blakesleeana ATCC 8688a. A review of the previous microbial metabolism studies using the fungi Cunninghamella species suggested that it could be a plausible in vitro predictor for mammalian metabolism.

Targeting physiological activities to modify the ecology and functionality of rumen and gastrointestinal ecosystems, prototypical anaerobic digester

USDA-ARS?s Scientific Manuscript database

The rumen microbial ecosystem is highly regarded for its ability to digest and transform low quality plant material into chemical forms of use by the host. However, less than 35% of the dietary energy consumed by the ruminant is conserved by the host. Methane production within the rumen contribute...

Relationship between proteolysis in the silo and efficiency of utilization of dietary protein by lactating dairy cows

USDA-ARS?s Scientific Manuscript database

Ensiling is used widely to conserve forages for feeding to dairy cows. However, the protein in hay-crop silages is particularly susceptible to microbial breakdown in the rumen, and utilization of protein in alfalfa and grass silages by dairy cows is particularly poor. Dependent on maturity, hay-crop...

Genes encoding a callose synthase and phytochrome A are adjacent to a MAP3Ka-like gene in Beta vulgaris USH20

USDA-ARS?s Scientific Manuscript database

MAP3Ka encodes a key conserved protein kinase responsible for orchestrating a rapid cascade of cellular events ultimately leading to localized cell death. Hypersensitive response, as it is termed, enables genetically-resistant plants to limit microbial invasion under the right environmental conditio...

Microbial communities in soil profile are more responsive to legacy effects of wheat-cover crop rotations than tillage systems

USDA-ARS?s Scientific Manuscript database

Declining trends in soil health under continuous monoculture systems of winter wheat are a concern for sustainable production in the Southern Great Plains of the US. This study was conducted to evaluate the long-term implementation of conservation tillage in combination with nitrogen treatments and ...

Non-biological synthetic spike-in controls and the AMPtk software pipeline improve mycobiome data

Treesearch

Jonathan M. Palmer; Michelle A. Jusino; Mark T. Banik; Daniel L. Lindner

2018-01-01

High-throughput amplicon sequencing (HTAS) of conserved DNA regions is a powerful technique to characterize microbial communities. Recently, spike-in mock communities have been used to measure accuracy of sequencing platforms and data analysis pipelines. To assess the ability of sequencing platforms and data processing pipelines using fungal internal transcribed spacer...

Specific capture and detection of Staphylococcus aureus with high-affinity modified aptamers to cell surface components.

PubMed

Baumstummler, A; Lehmann, D; Janjic, N; Ochsner, U A

2014-10-01

Slow off-rate modified aptamer (SOMAmer) reagents were generated to several Staphylococcus aureus cell surface-associated proteins via SELEX with multiple modified DNA libraries using purified recombinant or native proteins. High-affinity binding agents with sub-nanomolar Kd 's were obtained for staphylococcal protein A (SpA), clumping factors (ClfA, ClfB), fibronectin-binding proteins (FnbA, FnbB) and iron-regulated surface determinants (Isd). Further screening revealed several SOMAmers that specifically bound to Staph. aureus cells from all strains that were tested, but not to other staphylococci or other bacteria. SpA and ClfA SOMAmers proved useful for the selective capture and enrichment of Staph. aureus cells, as shown by culture and PCR, leading to improved limits of detection and efficient removal of PCR inhibitors. Detection of Staph. aureus cells was enhanced by several orders of magnitude when the bacterial cell surface was coated with SOMAmers followed by qPCR of the SOMAmers. Furthermore, fluorescence-labelled SpA SOMAmers demonstrated their utility as direct detection agents in flow cytometry. Significance and impact of the study: Monitoring for microbial contamination of food, water, nonsterile products or the environment is typically based on culture, PCR or antibodies. Aptamers that bind with high specificity and affinity to well-conserved cell surface epitopes represent a promising novel type of reagents to detect bacterial cells without the need for culture or cell lysis, including for the capture and enrichment of bacteria present at low cell densities and for the direct detection via qPCR or fluorescent staining. © 2014 Soma Logic, Inc. published by John Wiley & Sons Ltd On behalf of the society for Applied Microbiology.

GeoChip-Based Analysis of the Functional Gene Diversity and Metabolic Potential of Microbial Communities in Acid Mine Drainage▿ †

PubMed Central

Xie, Jianping; He, Zhili; Liu, Xinxing; Liu, Xueduan; Van Nostrand, Joy D.; Deng, Ye; Wu, Liyou; Zhou, Jizhong; Qiu, Guanzhou

2011-01-01

Acid mine drainage (AMD) is an extreme environment, usually with low pH and high concentrations of metals. Although the phylogenetic diversity of AMD microbial communities has been examined extensively, little is known about their functional gene diversity and metabolic potential. In this study, a comprehensive functional gene array (GeoChip 2.0) was used to analyze the functional diversity, composition, structure, and metabolic potential of AMD microbial communities from three copper mines in China. GeoChip data indicated that these microbial communities were functionally diverse as measured by the number of genes detected, gene overlapping, unique genes, and various diversity indices. Almost all key functional gene categories targeted by GeoChip 2.0 were detected in the AMD microbial communities, including carbon fixation, carbon degradation, methane generation, nitrogen fixation, nitrification, denitrification, ammonification, nitrogen reduction, sulfur metabolism, metal resistance, and organic contaminant degradation, which suggested that the functional gene diversity was higher than was previously thought. Mantel test results indicated that AMD microbial communities are shaped largely by surrounding environmental factors (e.g., S, Mg, and Cu). Functional genes (e.g., narG and norB) and several key functional processes (e.g., methane generation, ammonification, denitrification, sulfite reduction, and organic contaminant degradation) were significantly (P < 0.10) correlated with environmental variables. This study presents an overview of functional gene diversity and the structure of AMD microbial communities and also provides insights into our understanding of metabolic potential in AMD ecosystems. PMID:21097602

Soil microbial communities and enzyme activities in sea-buckthorn (Hippophae rhamnoides) plantation at different ages.

PubMed

Yang, Miao; Yang, Dan; Yu, Xuan

2018-01-01

The aim of this study was to assess the impact of forest age and season on the soil microbial community and enzyme activities in sea-buckthorn plantation system and to determine the relative contributions to soil microbial properties. Soil sampling was carried out in the dry season (April) and wet season (September) in four areas, including: abandoned farmland (NH), an 8-year- old plantation (young plantation, 8Y), a 13-year-old plantation (middle-aged plantation, 13Y), and an 18-year-old plantation (mature plantation, 18Y). The results showed that forest age and season have a significant effect on soil microbial community structure and enzyme activities. The total, bacterial, fungal, Gram-negative (G+), and Gram-positive (G-) PLFAs increased gradually with forest age, with the highest values detected in 18Y. All the detected enzyme activities showed the trend as a consequence of forest age. The microbial PLFAs and soil enzyme activities were higher in the wet season than the dry season. However, there were no significant interactions between forest age and season. A Correlation analysis suggested that soil microbial communities and enzyme activities were significantly and positively correlated with pH, total nitrogen (TN) and available phosphorus (AP). Season had a stronger influence on soil microbial communities than forest age. In general, sea-buckthorn plantations establishment might be a potential tool for maintaining and increasing soil fertility in arid and semi-arid regions.

Soil microbial communities and enzyme activities in sea-buckthorn (Hippophae rhamnoides) plantation at different ages

PubMed Central

Yang, Miao; Yang, Dan

2018-01-01

The aim of this study was to assess the impact of forest age and season on the soil microbial community and enzyme activities in sea-buckthorn plantation system and to determine the relative contributions to soil microbial properties. Soil sampling was carried out in the dry season (April) and wet season (September) in four areas, including: abandoned farmland (NH), an 8-year- old plantation (young plantation, 8Y), a 13-year-old plantation (middle-aged plantation, 13Y), and an 18-year-old plantation (mature plantation, 18Y). The results showed that forest age and season have a significant effect on soil microbial community structure and enzyme activities. The total, bacterial, fungal, Gram-negative (G+), and Gram-positive (G-) PLFAs increased gradually with forest age, with the highest values detected in 18Y. All the detected enzyme activities showed the trend as a consequence of forest age. The microbial PLFAs and soil enzyme activities were higher in the wet season than the dry season. However, there were no significant interactions between forest age and season. A Correlation analysis suggested that soil microbial communities and enzyme activities were significantly and positively correlated with pH, total nitrogen (TN) and available phosphorus (AP). Season had a stronger influence on soil microbial communities than forest age. In general, sea-buckthorn plantations establishment might be a potential tool for maintaining and increasing soil fertility in arid and semi-arid regions. PMID:29324845

Flow cytometric analysis of microbial contamination in food industry technological lines--initial study.

PubMed

Józwa, Wojciech; Czaczyk, Katarzyna

2012-04-02

Flow cytometry constitutes an alternative for traditional methods of microorganisms identification and analysis, including methods requiring cultivation step. It enables the detection of pathogens and other microorganisms contaminants without the need to culture microbial cells meaning that the sample (water, waste or food e.g. milk, wine, beer) may be analysed directly. This leads to a significant reduction of time required for analysis allowing monitoring of production processes and immediate reaction in case of contamination or any disruption occurs. Apart from the analysis of raw materials or products on different stages of manufacturing process, the flow cytometry seems to constitute an ideal tool for the assessment of microbial contamination on the surface of technological lines. In the present work samples comprising smears from 3 different surfaces of technological lines from fruit and vegetable processing company from Greater Poland were analysed directly with flow cytometer. The measured parameters were forward and side scatter of laser light signals allowing the estimation of microbial cell contents in each sample. Flow cytometric analysis of the surface of food industry production lines enable the preliminary evaluation of microbial contamination within few minutes from the moment of sample arrival without the need of sample pretreatment. The presented method of fl ow cytometric initial evaluation of microbial state of food industry technological lines demonstrated its potential for developing a robust, routine method for the rapid and labor-saving detection of microbial contamination in food industry.

Prey Range and Genome Evolution of Halobacteriovorax marinus Predatory Bacteria from an Estuary

PubMed Central

Enos, Brett G.; Anthony, Molly K.; DeGiorgis, Joseph A.

2018-01-01

ABSTRACT Halobacteriovorax strains are saltwater-adapted predatory bacteria that attack Gram-negative bacteria and may play an important role in shaping microbial communities. To understand how Halobacteriovorax strains impact ecosystems and develop them as biocontrol agents, it is important to characterize variation in predation phenotypes and investigate Halobacteriovorax genome evolution. We isolated Halobacteriovorax marinus BE01 from an estuary in Rhode Island using Vibrio from the same site as prey. Small, fast-moving, attack-phase BE01 cells attach to and invade prey cells, consistent with the intraperiplasmic predation strategy of the H. marinus type strain, SJ. BE01 is a prey generalist, forming plaques on Vibrio strains from the estuary, Pseudomonas from soil, and Escherichia coli. Genome analysis revealed extremely high conservation of gene order and amino acid sequences between BE01 and SJ, suggesting strong selective pressure to maintain the genome in this H. marinus lineage. Despite this, we identified two regions of gene content difference that likely resulted from horizontal gene transfer. Analysis of modal codon usage frequencies supports the hypothesis that these regions were acquired from bacteria with different codon usage biases than H. marinus. In one of these regions, BE01 and SJ carry different genes associated with mobile genetic elements. Acquired functions in BE01 include the dnd operon, which encodes a pathway for DNA modification, and a suite of genes involved in membrane synthesis and regulation of gene expression that was likely acquired from another Halobacteriovorax lineage. This analysis provides further evidence that horizontal gene transfer plays an important role in genome evolution in predatory bacteria. IMPORTANCE Predatory bacteria attack and digest other bacteria and therefore may play a role in shaping microbial communities. To investigate phenotypic and genotypic variation in saltwater-adapted predatory bacteria, we isolated Halobacteriovorax marinus BE01 from an estuary in Rhode Island, assayed whether it could attack different prey bacteria, and sequenced and analyzed its genome. We found that BE01 is a prey generalist, attacking bacteria from different phylogenetic groups and environments. Gene order and amino acid sequences are highly conserved between BE01 and the H. marinus type strain, SJ. By comparative genomics, we detected two regions of gene content difference that likely occurred via horizontal gene transfer events. Acquired genes encode functions such as modification of DNA, membrane synthesis and regulation of gene expression. Understanding genome evolution and variation in predation phenotypes among predatory bacteria will inform their development as biocontrol agents and clarify how they impact microbial communities. PMID:29359184

Challenges of microarray applications for microbial detection and gene expression profiling in food

USDA-ARS?s Scientific Manuscript database

Microarray technology represents one of the latest advances in molecular biology. The diverse types of microarrays have been applied to clinical and environmental microbiology, microbial ecology, and in human, veterinary, and plant diagnostics. Since multiple genes can be analyzed simultaneously, ...

Depth-resolved microbial community analyses in the anaerobic co-digester of dewatered sewage sludge with food waste.

PubMed

Xu, Rui; Yang, Zhao-Hui; Zheng, Yue; Zhang, Hai-Bo; Liu, Jian-Bo; Xiong, Wei-Ping; Zhang, Yan-Ru; Ahmad, Kito

2017-11-01

This study evaluated the impacts of FW addition on co-digestion in terms of microbial community. Anaerobic co-digestion (AcoD) reactors were conducted at gradually increased addition of food waste (FW) from 0 to 4kg-VSm -3 d -1 for 220days. Although no markable acidification was found at an OLR of 4kg-VSm -3 d -1 , the unhealthy operation was observed in aspect of an inhibited methane yield (185mLg -1 VS added ), which was restricted by 40% when compared with its peak value. Deterioration of digestion process was timely indicated by the dramatic decrease of archaeal population and microbial biodiversity. Furthermore, the cooperation network showed a considerable number of rare species (<1%) were strongly correlated with methane production, which were frequently overlooked due to the limits of detecting resolution or analysis methods before. Advances in the analysis of sensitive microbial community enable us to detect the early disturbances in AcoD reactors. Copyright © 2017 Elsevier Ltd. All rights reserved.

Microbial community analysis in rice paddy soils irrigated by acid mine drainage contaminated water.

PubMed

Sun, Min; Xiao, Tangfu; Ning, Zengping; Xiao, Enzong; Sun, Weimin

2015-03-01

Five rice paddy soils located in southwest China were selected for geochemical and microbial community analysis. These rice fields were irrigated with river water which was contaminated by Fe-S-rich acid mine drainage. Microbial communities were characterized by high-throughput sequencing, which showed 39 different phyla/groups in these samples. Among these phyla/groups, Proteobacteria was the most abundant phylum in all samples. Chloroflexi, Acidobacteria, Nitrospirae, and Bacteroidetes exhibited higher relative abundances than other phyla. A number of rare and candidate phyla were also detected. Moreover, canonical correspondence analysis suggested that pH, sulfate, and nitrate were significant factors that shaped the microbial community structure. In addition, a wide diversity of Fe- and S-related bacteria, such as GOUTA19, Shewanella, Geobacter, Desulfobacca, Thiobacillus, Desulfobacterium, and Anaeromyxobacter, might be responsible for biogeochemical Fe and S cycles in the tested rice paddy soils. Among the dominant genera, GOUTA19 and Shewanella were seldom detected in rice paddy soils.

Effects of bamboo charcoal on fouling and microbial diversity in a flat-sheet ceramic membrane bioreactor.

PubMed

Zhang, Wenjie; Liu, Xiaoning; Wang, Dunqiu; Jin, Yue

2017-11-01

Membrane fouling is a problem in full-scale membrane bioreactors. In this study, bamboo charcoal (BC) was evaluated for its efficacy in alleviating membrane fouling in flat-sheet membrane bioreactors treating municipal wastewater. The results showed that BC addition markedly improved treatment performance based on COD, NH 4 + -N, total nitrogen, and total phosphorus levels. Adding BC slowed the increase in the trans-membrane pressure rate and resulted in lower levels of soluble microbial products and extracellular polymeric substances detected in the flat-sheet membrane bioreactor. BC has a porous structure, and a large quantity of biomass was detected using scanning electron microscopy. The microbial community analysis results indicated that BC increased the microbial diversity and Aminomonas, Anaerofustis, uncultured Anaerolineaceae, Anaerolinea, and Anaerotruncus were found in higher abundances in the reactor with BC. BC addition is an effective method for reducing membrane fouling, and can be applied to full-scale flat-sheet membrane bioreactors to improve their function. Copyright © 2017 Elsevier Ltd. All rights reserved.

Aerobic stability of maize silage stored under plastic films with different oxygen permeability.

PubMed

Borreani, Giorgio; Piano, Serenella; Tabacco, Ernesto

2014-10-01

The most important factor that can influence silage quality is the degree of anaerobiosis maintained during conservation. The quality of the plastic film is a key factor, since the permeability of polyethylene to oxygen is too high for silage conservation. The aim of this work was to assess the effects of the interaction between three plastic films with different degrees of oxygen permeability and two different maize silage conservation times on fermentation, microbial quality and aerobic stability. The conservation time affected the pH, lactic and acetic acids, 1,2-propanediol and lactic/acetic acid ratio, with higher pH, lower lactic acid concentration and lactic/acetic acid ratio but higher acetic acid and 1,2-propanediol concentrations being found in silages conserved for 110 days versus silages conserved for 55 days. The plastic film affected the pH, lactic and acetic acids and lactic/acetic acid ratio. The yeast count was lower and aerobic stability higher for silage conserved under the oxygen barrier film for both conservation periods. The positive interaction between length of storage and the increased anaerobiosis of silage during conservation provided by the oxygen barrier compared with polyethylene film helped reduce the yeast count and increase the aerobic stability of maize silage, even when less acetic acid was produced during ensiling. © 2014 Society of Chemical Industry.

Validation Study of Rapid Assays of Bioburden, Endotoxins and Other Contamination.

PubMed

Shintani, Hideharu

2016-01-01

Microbial testing performed in support of pharmaceutical and biopharmaceutical production falls into three main categories: detection (qualitative), enumeration (quantitative), and characterization/identification. Traditional microbiological methods are listed in the compendia and discussed by using the conventional growth-based techniques, which are labor intensive and time consuming. In general, such tests require several days of incubation for microbial contamination (bioburden) to be detected, and therefore management seldom is able to take proactive corrective measures. In addition, microbial growth is limited by the growth medium used and incubation conditions, thus impacting testing sensitivity, accuracy, and reproducibility. 　For more than 20 years various technology platforms for rapid microbiological methods (RMM) have been developed, and many have been readily adopted by the food industry and clinical microbiology laboratories. Their use would certainly offer drug companies faster test turnaround times to accommodate the aggressive deadlines for manufacturing processes and product release. Some rapid methods also offer the possibility for real-time microbial analyses, enabling management to respond to microbial contamination events in a more timely fashion, and can provide cost savings and higher efficiencies in quality control testing laboratories. Despite the many proven business and quality benefits and the fact that the FDA's initiative to promote the use of process analytical technology (PAT) includes rapid microbial methods, pharmaceutical and biopharmaceutical industries have been somewhat slow to embrace alternative microbial methodologies for several reasons. The major reason is that the bioburden counts detected by the incubation method and rapid assay are greatly divergent. 　The use of rapid methods is a dynamic field in applied microbiology and one that has gained increased attention nationally and internationally over time. This topic has been extensively addressed at conferences and in published documents around the world. More recently, the use of alternative methods for control of the microbiological quality of pharmaceutical products and materials used in pharmaceutical production has been addressed by the compendia in an attempt to facilitate implementation of these technologies by pharmaceutical companies. The author presents some of the rapid method technologies under evaluation or in use by pharmaceutical microbiologists and the current status of the implementation of alternative microbial methods.

Potential microbial contamination during sampling of permafrost soil assessed by tracers

NASA Astrophysics Data System (ADS)

Bang-Andreasen, Toke; Schostag, Morten; Priemé, Anders; Elberling, Bo; Jacobsen, Carsten S.

2017-02-01

Drilling and handling of permanently frozen soil cores without microbial contamination is of concern because contamination e.g. from the active layer above may lead to incorrect interpretation of results in experiments investigating potential and actual microbial activity in these low microbial biomass environments. Here, we present an example of how microbial contamination from active layer soil affected analysis of the potentially active microbial community in permafrost soil. We also present the development and use of two tracers: (1) fluorescent plastic microspheres and (2) Pseudomonas putida genetically tagged with Green Fluorescent Protein production to mimic potential microbial contamination of two permafrost cores. A protocol with special emphasis on avoiding microbial contamination was developed and employed to examine how far microbial contamination can penetrate into permafrost cores. The quantity of tracer elements decreased with depth into the permafrost cores, but the tracers were detected as far as 17 mm from the surface of the cores. The results emphasize that caution should be taken to avoid microbial contamination of permafrost cores and that the application of tracers represents a useful tool to assess penetration of potential microbial contamination into permafrost cores.

Potential microbial contamination during sampling of permafrost soil assessed by tracers.

PubMed

Bang-Andreasen, Toke; Schostag, Morten; Priemé, Anders; Elberling, Bo; Jacobsen, Carsten S

2017-02-23

Drilling and handling of permanently frozen soil cores without microbial contamination is of concern because contamination e.g. from the active layer above may lead to incorrect interpretation of results in experiments investigating potential and actual microbial activity in these low microbial biomass environments. Here, we present an example of how microbial contamination from active layer soil affected analysis of the potentially active microbial community in permafrost soil. We also present the development and use of two tracers: (1) fluorescent plastic microspheres and (2) Pseudomonas putida genetically tagged with Green Fluorescent Protein production to mimic potential microbial contamination of two permafrost cores. A protocol with special emphasis on avoiding microbial contamination was developed and employed to examine how far microbial contamination can penetrate into permafrost cores. The quantity of tracer elements decreased with depth into the permafrost cores, but the tracers were detected as far as 17 mm from the surface of the cores. The results emphasize that caution should be taken to avoid microbial contamination of permafrost cores and that the application of tracers represents a useful tool to assess penetration of potential microbial contamination into permafrost cores.

Potential microbial contamination during sampling of permafrost soil assessed by tracers

PubMed Central

Bang-Andreasen, Toke; Schostag, Morten; Priemé, Anders; Elberling, Bo; Jacobsen, Carsten S.

2017-01-01

Drilling and handling of permanently frozen soil cores without microbial contamination is of concern because contamination e.g. from the active layer above may lead to incorrect interpretation of results in experiments investigating potential and actual microbial activity in these low microbial biomass environments. Here, we present an example of how microbial contamination from active layer soil affected analysis of the potentially active microbial community in permafrost soil. We also present the development and use of two tracers: (1) fluorescent plastic microspheres and (2) Pseudomonas putida genetically tagged with Green Fluorescent Protein production to mimic potential microbial contamination of two permafrost cores. A protocol with special emphasis on avoiding microbial contamination was developed and employed to examine how far microbial contamination can penetrate into permafrost cores. The quantity of tracer elements decreased with depth into the permafrost cores, but the tracers were detected as far as 17 mm from the surface of the cores. The results emphasize that caution should be taken to avoid microbial contamination of permafrost cores and that the application of tracers represents a useful tool to assess penetration of potential microbial contamination into permafrost cores. PMID:28230151

Nationwide reconnaissance of contaminants of emerging concern in source and treated drinking waters of the United States

USGS Publications Warehouse

Glassmeyer, Susan T.; Furlong, Edward T.; Kolpin, Dana W.; Batt, Angela L.; Benson, Robert; Boone, J. Scott; Conerly, Octavia D.; Donohue, Maura J.; King, Dawn N.; Kostich, Mitchell S.; Mash, Heath E.; Pfaller, Stacy; Schenck, Kathleen M.; Simmons, Jane Ellen; Varughese, Eunice A.; Vesper, Stephen J.; Villegas, Eric N.; Wilson, Vickie S.

2017-01-01

When chemical or microbial contaminants are assessed for potential effect or possible regulation in ambient and drinking waters, a critical first step is determining if the contaminants occur and if they are at concentrations that may cause human or ecological health concerns. To this end, source and treated drinking water samples from 29 drinking water treatment plants (DWTPs) were analyzed as part of a two-phase study to determine whether chemical and microbial constituents, many of which are considered contaminants of emerging concern, were detectable in the waters. Of the 84 chemicals monitored in the 9 Phase I DWTPs, 27 were detected at least once in the source water, and 21 were detected at least once in treated drinking water. In Phase II, which was a broader and more comprehensive assessment, 247 chemical and microbial analytes were measured in 25 DWTPs, with 148 detected at least once in the source water, and 121 detected at least once in the treated drinking water. The frequency of detection was often related to the analyte's contaminant class, as pharmaceuticals and anthropogenic waste indicators tended to be infrequently detected and more easily removed during treatment, while per and polyfluoroalkyl substances and inorganic constituents were both more frequently detected and, overall, more resistant to treatment. The data collected as part of this project will be used to help inform evaluation of unregulated contaminants in surface water, groundwater, and drinking water.

Nationwide reconnaissance of contaminants of emerging concern in source and treated drinking waters of the United States.

PubMed

Glassmeyer, Susan T; Furlong, Edward T; Kolpin, Dana W; Batt, Angela L; Benson, Robert; Boone, J Scott; Conerly, Octavia; Donohue, Maura J; King, Dawn N; Kostich, Mitchell S; Mash, Heath E; Pfaller, Stacy L; Schenck, Kathleen M; Simmons, Jane Ellen; Varughese, Eunice A; Vesper, Stephen J; Villegas, Eric N; Wilson, Vickie S

2017-03-01

When chemical or microbial contaminants are assessed for potential effect or possible regulation in ambient and drinking waters, a critical first step is determining if the contaminants occur and if they are at concentrations that may cause human or ecological health concerns. To this end, source and treated drinking water samples from 29 drinking water treatment plants (DWTPs) were analyzed as part of a two-phase study to determine whether chemical and microbial constituents, many of which are considered contaminants of emerging concern, were detectable in the waters. Of the 84 chemicals monitored in the 9 Phase I DWTPs, 27 were detected at least once in the source water, and 21 were detected at least once in treated drinking water. In Phase II, which was a broader and more comprehensive assessment, 247 chemical and microbial analytes were measured in 25 DWTPs, with 148 detected at least once in the source water, and 121 detected at least once in the treated drinking water. The frequency of detection was often related to the analyte's contaminant class, as pharmaceuticals and anthropogenic waste indicators tended to be infrequently detected and more easily removed during treatment, while per and polyfluoroalkyl substances and inorganic constituents were both more frequently detected and, overall, more resistant to treatment. The data collected as part of this project will be used to help inform evaluation of unregulated contaminants in surface water, groundwater, and drinking water. Published by Elsevier B.V.

A virus or more in (nearly) every cell: ubiquitous networks of virus-host interactions in extreme environments.

PubMed

Munson-McGee, Jacob H; Peng, Shengyun; Dewerff, Samantha; Stepanauskas, Ramunas; Whitaker, Rachel J; Weitz, Joshua S; Young, Mark J

2018-06-01

The application of viral and cellular metagenomics to natural environments has expanded our understanding of the structure, functioning, and diversity of microbial and viral communities. The high diversity of many communities, e.g., soils, surface ocean waters, and animal-associated microbiomes, make it difficult to establish virus-host associations at the single cell (rather than population) level, assign cellular hosts, or determine the extent of viral host range from metagenomics studies alone. Here, we combine single-cell sequencing with environmental metagenomics to characterize the structure of virus-host associations in a Yellowstone National Park (YNP) hot spring microbial community. Leveraging the relatively low diversity of the YNP environment, we are able to overlay evidence at the single-cell level with contextualized viral and cellular community structure. Combining evidence from hexanucelotide analysis, single cell read mapping, network-based analytics, and CRISPR-based inference, we conservatively estimate that >60% of cells contain at least one virus type and a majority of these cells contain two or more virus types. Of the detected virus types, nearly 50% were found in more than 2 cellular clades, indicative of a broad host range. The new lens provided by the combination of metaviromics and single-cell genomics reveals a network of virus-host interactions in extreme environments, provides evidence that extensive virus-host associations are common, and further expands the unseen impact of viruses on cellular life.

How conserved are the bacterial communities associated with aphids? A detailed assessment of the Brevicoryne brassicae (Hemiptera: Aphididae) using 16S rDNA.

PubMed

Clark, E L; Daniell, T J; Wishart, J; Hubbard, S F; Karley, A J

2012-12-01

Aphids harbor a community of bacteria that include obligate and facultative endosymbionts belonging to the Enterobacteriaceae along with opportunistic, commensal, or pathogenic bacteria. This study represents the first detailed analysis of the identity and diversity of the bacterial community associated with the cabbage aphid, Brevicoryne brassicae (L.). 16S rDNA sequence analysis revealed that the community of bacteria associated with B. brassicae was diverse, with at least four different bacterial community types detected among aphid lines, collected from widely dispersed sites in Northern Britain. The bacterial sequence types isolated from B. brassicae showed little similarity to any bacterial endosymbionts characterized in insects; instead, they were closely related to free-living extracellular bacterial species that have been isolated from the aphid gut or that are known to be present in the environment, suggesting that they are opportunistic bacteria transmitted between the aphid gut and the environment. To quantify variation in bacterial community between aphid lines, which was driven largely by differences in the proportions of two dominant bacterial orders, the Pseudomonales and the Enterobacteriales, we developed a novel real-time (Taqman) qPCR assay. By improving our knowledge of aphid microbial ecology, and providing novel molecular tools to examine the presence and function of the microbial community, this study forms the basis of further research to explore the influence of the extracellular bacterial community on aphid fitness, pest status, and susceptibility to control by natural enemies.

Epitopes of Microbial and Human Heat Shock Protein 60 and Their Recognition in Myalgic Encephalomyelitis

PubMed Central

Elfaitouri, Amal; Herrmann, Björn; Bölin-Wiener, Agnes; Wang, Yilin; Gottfries, Carl-Gerhard; Zachrisson, Olof; Pipkorn, Rϋdiger; Rönnblom, Lars; Blomberg, Jonas

2013-01-01

Myalgic encephalomyelitis (ME, also called Chronic Fatigue Syndrome), a common disease with chronic fatigability, cognitive dysfunction and myalgia of unknown etiology, often starts with an infection. The chaperonin human heat shock protein 60 (HSP60) occurs in mitochondria and in bacteria, is highly conserved, antigenic and a major autoantigen. The anti-HSP60 humoral (IgG and IgM) immune response was studied in 69 ME patients and 76 blood donors (BD) (the Training set) with recombinant human and E coli HSP60, and 136 30-mer overlapping and targeted peptides from HSP60 of humans, Chlamydia, Mycoplasma and 26 other species in a multiplex suspension array. Peptides from HSP60 helix I had a chaperonin-like activity, but these and other HSP60 peptides also bound IgG and IgM with an ME preference, theoretically indicating a competition between HSP60 function and antibody binding. A HSP60-based panel of 25 antigens was selected. When evaluated with 61 other ME and 399 non-ME samples (331 BD, 20 Multiple Sclerosis and 48 Systemic Lupus Erythematosus patients), a peptide from Chlamydia pneumoniae HSP60 detected IgM in 15 of 61 (24%) of ME, and in 1 of 399 non-ME at a high cutoff (p<0.0001). IgM to specific cross-reactive epitopes of human and microbial HSP60 occurs in a subset of ME, compatible with infection-induced autoimmunity. PMID:24312270

Functional Potential of Soil Microbial Communities in the Maize Rhizosphere

PubMed Central

Xiong, Jingbo; Li, Jiabao; He, Zhili; Zhou, Jizhong; Yannarell, Anthony C.; Mackie, Roderick I.

2014-01-01

Microbial communities in the rhizosphere make significant contributions to crop health and nutrient cycling. However, their ability to perform important biogeochemical processes remains uncharacterized. Here, we identified important functional genes that characterize the rhizosphere microbial community to understand metabolic capabilities in the maize rhizosphere using the GeoChip-based functional gene array method. Significant differences in functional gene structure were apparent between rhizosphere and bulk soil microbial communities. Approximately half of the detected gene families were significantly (p<0.05) increased in the rhizosphere. Based on the detected gyrB genes, Gammaproteobacteria, Betaproteobacteria, Firmicutes, Bacteroidetes and Cyanobacteria were most enriched in the rhizosphere compared to those in the bulk soil. The rhizosphere niche also supported greater functional diversity in catabolic pathways. The maize rhizosphere had significantly enriched genes involved in carbon fixation and degradation (especially for hemicelluloses, aromatics and lignin), nitrogen fixation, ammonification, denitrification, polyphosphate biosynthesis and degradation, sulfur reduction and oxidation. This research demonstrates that the maize rhizosphere is a hotspot of genes, mostly originating from dominant soil microbial groups such as Proteobacteria, providing functional capacity for the transformation of labile and recalcitrant organic C, N, P and S compounds. PMID:25383887

Critical moisture content for microbial growth in dried food-processing residues.

PubMed

Rezaei, Farzaneh; Vandergheynst, Jean S

2010-09-01

Food-processing residues are good feedstocks for biofuel and biochemical production because they have high energy content and are abundant. Year-round biofuel and biochemical production requires proper storage to prevent microbial decomposition and thermal runaway. In this study, microbial activity of tomato pomace (TP), grape pomace (GP), fermented grape pomace (FGP) and sugar beet pulp (SBP) was monitored at nine different moisture contents. Maximum and cumulative respirations for each feedstock with respect to moisture content followed a sigmoidal relationship. The critical moisture content below which no microbial activity was detected for SBP, TP, FGP and GP was 24-31, 16-21, 23-33 and 43-46% (dry basis) respectively. A logarithmic relationship was observed (R(2) = 0.94) between critical moisture content and initial water-soluble carbohydrate (WSC) content of the processing residues. The critical moisture content below which no microbial activity was detected and the relationship between critical moisture content and initial WSC content were determined in this study for four food-processing residues. Both parameters permit evaluation of the potential for deterioration of food-processing residues during storage based on moisture content and WSC content. Copyright 2010 Society of Chemical Industry.

[Microbial Community Structure on the Root Surface of Patients with Periodontitis.

PubMed

Zhang, Ju-Mei; Zhou, Jian-Ye; Bo, Lei; Hu, Xiao-Pan; Jiao, Kang-Li; Li, Zhi-Jie; Li, Yue-Hong; Li, Zhi-Qiang

2016-11-01

To study the microbial community structure on the root surface of patients with periodontitis. Bacterial plaque and tissues from the root neck (RN group),root middle (RM group) and root tine (RT group) of six teeth with mobility 3 in one patient with periodontitis were sampled.The V3V4 region of 16S rRNA was sequenced on the Illumina MiSeq platform.The microbial community structure was analyzed by Mothur,Qiime and SPSS software. The principal component analysis (PCoA) results indicated that the RM samples had a similar microbial community structure as that of the RT samples,which was significant different from that of the RN samples.Thirteen phyla were detected in the three groups of samples,which included 7 dominant phyla.29 dominant genera were detected in 184 genera.The abundance of Bacteroidetes _[G-6] and Peptostre ptococcaceae _[XI][G-4] had a positive correlation with the depth of the collection site of samples ( P <0.05),while the abundance of Prevotella,Selenomonas,Corynebacterium and Olsenella had a negative correlation with the depth of the collection site of samples ( P <0.05). There is region-specificity of microbial community structure on the root surface of patients with periodontitis.

Abundance and diversity of microbial inhabitants in European spacecraft-associated clean rooms.

PubMed

Stieglmeier, Michaela; Rettberg, Petra; Barczyk, Simon; Bohmeier, Maria; Pukall, Rüdiger; Wirth, Reinhard; Moissl-Eichinger, Christine

2012-06-01

The determination of the microbial load of a spacecraft en route to interesting extraterrestrial environments is mandatory and currently based on the culturable, heat-shock-surviving portion of microbial contaminants. Our study compared these classical bioburden measurements as required by NASA's and ESA's guidelines for the microbial examination of flight hardware, with molecular analysis methods (16S rRNA gene cloning and quantitative PCR) to further develop our understanding of the diversity and abundance of the microbial communities of spacecraft-associated clean rooms. Three samplings of the Herschel Space Observatory and its surrounding clean rooms were performed in two different European facilities. Molecular analyses detected a broad diversity of microbes typically found in the human microbiome with three bacterial genera (Staphylococcus, Propionibacterium, and Brevundimonas) common to all three locations. Bioburden measurements revealed a low, but heterogeneous, abundance of spore-forming and other heat-resistant microorganisms. Total cell numbers estimated by quantitative real-time PCR were typically 3 orders of magnitude greater than those determined by viable counts, which indicates a tendency for traditional methods to underestimate the extent of clean room bioburden. Furthermore, the molecular methods allowed the detection of a much broader diversity than traditional culture-based methods.

Noise-free accurate count of microbial colonies by time-lapse shadow image analysis.

PubMed

Ogawa, Hiroyuki; Nasu, Senshi; Takeshige, Motomu; Funabashi, Hisakage; Saito, Mikako; Matsuoka, Hideaki

2012-12-01

Microbial colonies in food matrices could be counted accurately by a novel noise-free method based on time-lapse shadow image analysis. An agar plate containing many clusters of microbial colonies and/or meat fragments was trans-illuminated to project their 2-dimensional (2D) shadow images on a color CCD camera. The 2D shadow images of every cluster distributed within a 3-mm thick agar layer were captured in focus simultaneously by means of a multiple focusing system, and were then converted to 3-dimensional (3D) shadow images. By time-lapse analysis of the 3D shadow images, it was determined whether each cluster comprised single or multiple colonies or a meat fragment. The analytical precision was high enough to be able to distinguish a microbial colony from a meat fragment, to recognize an oval image as two colonies contacting each other, and to detect microbial colonies hidden under a food fragment. The detection of hidden colonies is its outstanding performance in comparison with other systems. The present system attained accuracy for counting fewer than 5 colonies and is therefore of practical importance. Copyright © 2012 Elsevier B.V. All rights reserved.

The role of coastal fog in increased viability of marine microbial aerosols

NASA Astrophysics Data System (ADS)

Dueker, M.; O'Mullan, G. D.; Weathers, K. C.; Juhl, A. R.; Uriarte, M.

2011-12-01

Microbes in the atmosphere (microbial aerosols) play an important role in climate and provide an ecological and biogeochemical connection between oceanic, atmospheric, and terrestrial environments. Despite the ubiquity of these bacteria (concentration estimates range from 1 x 10^4 to 6 x 10^5 cells m-3), much is still being learned about their source, viability, and interactions with climatic controls. They can be attached to ambient aerosol particles or exist singly in the air. They affect climate by serving as ice, cloud, and fog nucleators, and have the metabolic potential to alter atmospheric chemistry. Fog presence in particular has been shown to greatly increase the deposition of viable microbial aerosols in both urban and coastal environments, but the mechanisms behind this are not fully understood. To address this gap, we examined the diversity of culturable microbial aerosols from a relatively pristine coastal environment in Maine (USA) and determined the effect of fog presence on viability and community composition of microbial aerosols. 16S rRNA sequencing of culturable ocean surface bacteria and depositing microbial aerosols (under clear and foggy conditions) resulted in the detection of 31 bacterial genera, with 5 dominant genera (Vibrio, Bacillus, Pseudoalteromonas, Psychrobacter, Salinibacterium) making up 66% of all sequences. Seventy-five percent of the viable microbial aerosols falling out under foggy conditions were most similar to GenBank-published sequences detected in marine environments. The fog and ocean surface sequence libraries were significantly more similar in microbial community composition than clear (non-foggy) and ocean surface libraries. These findings support a dual role for fog in enhancing the fallout of viable marine microbial aerosols via increased gravitational settling rates and decreased aerosolization stress on the organisms. The dominant presence of marine bacteria in coastal microbial aerosols provides a strong case for an ecologically-relevant ocean to terrestrial transport of microbes, creating a potential connection between water and air quality in the coastal environment.

Seasonal succession leads to habitat-dependent differentiation in ribosomal RNA:DNA ratios among freshwater lake bacteria

DOE PAGES

Denef, Vincent J.; Fujimoto, Masanori; Berry, Michelle A.; ...

2016-04-29

Relative abundance profiles of bacterial populations measured by sequencing DNA or RNA of marker genes can widely differ. These differences, made apparent when calculating ribosomal RNA:DNA ratios, have been interpreted as variable activities of bacterial populations. However, inconsistent correlations between ribosomal RNA:DNA ratios and metabolic activity or growth rates have led to a more conservative interpretation of this metric as the cellular protein synthesis potential (PSP). Little is known, particularly in freshwater systems, about how PSP varies for specific taxa across temporal and spatial environmental gradients and how conserved PSP is across bacterial phylogeny. Here, we generated 16S rRNA genemore » sequencing data using simultaneously extracted DNA and RNA from fractionated (free-living and particulate) water samples taken seasonally along a eutrophic freshwater estuary to oligotrophic pelagic transect in Lake Michigan. In contrast to previous reports, we observed frequent clustering of DNA and RNA data from the same sample. Analysis of the overlap in taxa detected at the RNA and DNA level indicated that microbial dormancy may be more common in the estuary, the particulate fraction, and during the stratified period. Across spatiotemporal gradients, PSP was often conserved at the phylum and class levels. PSPs for specific taxa were more similar across habitats in spring than in summer and fall. This was most notable for PSPs of the same taxa when located in the free-living or particulate fractions, but also when contrasting surface to deep, and estuary to Lake Michigan communities. Our results show that community composition assessed by RNA and DNA measurements are more similar than previously assumed in freshwater systems. Furthermore, the similarity between RNA and DNA measurements and taxa-specific PSPs that drive community-level similarities are conditional on spatiotemporal factors.« less

Seasonal succession leads to habitat-dependent differentiation in ribosomal RNA:DNA ratios among freshwater lake bacteria

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

Denef, Vincent J.; Fujimoto, Masanori; Berry, Michelle A.

Relative abundance profiles of bacterial populations measured by sequencing DNA or RNA of marker genes can widely differ. These differences, made apparent when calculating ribosomal RNA:DNA ratios, have been interpreted as variable activities of bacterial populations. However, inconsistent correlations between ribosomal RNA:DNA ratios and metabolic activity or growth rates have led to a more conservative interpretation of this metric as the cellular protein synthesis potential (PSP). Little is known, particularly in freshwater systems, about how PSP varies for specific taxa across temporal and spatial environmental gradients and how conserved PSP is across bacterial phylogeny. Here, we generated 16S rRNA genemore » sequencing data using simultaneously extracted DNA and RNA from fractionated (free-living and particulate) water samples taken seasonally along a eutrophic freshwater estuary to oligotrophic pelagic transect in Lake Michigan. In contrast to previous reports, we observed frequent clustering of DNA and RNA data from the same sample. Analysis of the overlap in taxa detected at the RNA and DNA level indicated that microbial dormancy may be more common in the estuary, the particulate fraction, and during the stratified period. Across spatiotemporal gradients, PSP was often conserved at the phylum and class levels. PSPs for specific taxa were more similar across habitats in spring than in summer and fall. This was most notable for PSPs of the same taxa when located in the free-living or particulate fractions, but also when contrasting surface to deep, and estuary to Lake Michigan communities. Our results show that community composition assessed by RNA and DNA measurements are more similar than previously assumed in freshwater systems. Furthermore, the similarity between RNA and DNA measurements and taxa-specific PSPs that drive community-level similarities are conditional on spatiotemporal factors.« less

Microbial detection in microfluidic devices through dual staining of quantum dots-labeled immunoassay and RNA hybridization.

PubMed

Zhang, Qing; Zhu, Liang; Feng, Hanhua; Ang, Simon; Chau, Fook Siong; Liu, Wen-Tso

2006-01-18

This paper reported the development of a microfludic device for the rapid detection of viable and nonviable microbial cells through dual labeling by fluorescent in situ hybridization (FISH) and quantum dots (QDs)-labeled immunofluorescent assay (IFA). The coin sized device consists of a microchannel and filtering pillars (gap=1-2 microm) and was demonstrated to effectively trap and concentrate microbial cells (i.e. Giardia lamblia). After sample injection, FISH probe solution and QDs-labeled antibody solution were sequentially pumped into the device to accelerate the fluorescent labeling reactions at optimized flow rates (i.e. 1 and 20 microL/min, respectively). After 2 min washing for each assay, the whole process could be finished within 30 min, with minimum consumption of labeling reagents and superior fluorescent signal intensity. The choice of QDs 525 for IFA resulted in bright and stable fluorescent signal, with minimum interference with the Cy3 signal from FISH detection.

New Performance Metrics for Quantitative Polymerase Chain Reaction-Based Microbial Source Tracking Methods

EPA Science Inventory

Binary sensitivity and specificity metrics are not adequate to describe the performance of quantitative microbial source tracking methods because the estimates depend on the amount of material tested and limit of detection. We introduce a new framework to compare the performance ...

Mineralization Of PAHs In Coal-Tar Impacted Aquifer Sediments And Associated Microbial Community Structure Investigated With FISH

EPA Science Inventory

The microbial community structure and mineralization of polycyclic aromatic hydrocarbons (PAHs) in a coal-tar contaminated aquifer were investigated spatially using fluorescence in situ hybridization (FISH) and in laboratory-scale incubations of the aquifer sediments. DAPI-detect...

Optimized MOL-PCR for Characterization of Microbial Pathogens.

PubMed

Wuyts, Véronique; Roosens, Nancy H C; Bertrand, Sophie; Marchal, Kathleen; De Keersmaecker, Sigrid C J

2016-01-06

Characterization of microbial pathogens is necessary for surveillance, outbreak detection, and tracing of outbreak sources. This unit describes a multiplex oligonucleotide ligation-PCR (MOL-PCR) optimized for characterization of microbial pathogens. With MOL-PCR, different types of markers, like unique sequences, single-nucleotide polymorphisms (SNPs) and indels, can be simultaneously analyzed in one assay. This assay consists of a multiplex ligation for detection of the markers, a singleplex PCR for signal amplification, and hybridization to MagPlex-TAG beads for readout on a Luminex platform after fluorescent staining. The current protocol describes the MOL-PCR, as well as methods for DNA isolation, probe design, and data interpretation and it is based on an optimized MOL-PCR assay for subtyping of Salmonella Typhimurium. Copyright © 2016 John Wiley & Sons, Inc.

Temporal and Spatial Variations in Transcriptional Patterns among Closely Related Marine Microbial Taxa

NASA Astrophysics Data System (ADS)

Shilova, I. N.; Robidart, J.; DeLong, E.; Zehr, J. P.

2016-02-01

Marine microbial communities are complex, and even closely related marine microbial populations are genetically and physiologically diverse. Despite such great diversity, conserved and highly synchronized rhythmic transcriptional patterns have been observed in microbial communities worldwide. The current widely used approaches analyzing high-throughput sequence data from microbiomes are not designed to differentiate transcription at strain or ecotype level. We used a novel MicroArray-inspired Gene-Centric (MAGC) bioinformatics approach to discern daily transcription by individual strains in previously analyzed metatranscriptomes from two oceanic regions, California Current System and central North Pacific. The results demonstrated that marine microbial taxa (within cyanobacteria Prochlorococcus and Synechococcus, Alphaproteobacterium Pelagibacter and picoeukaryote Ostreococcus) have unique transcription patterns and respond differentially to variability in space and time in the ocean. For example, the timing of maximum transcription for the photosynthesis and pigments genes varied among Synechococcus strains in the California Current study, likely for optimizing light utilization based on their differences in genetics and physiology. While several Prochlorococcus genotypes were present in the North Pacific study, transcription of the phosphate transporter gene, pstS, in specific genotypes was negatively correlated with phosphate concentrations. These individual transcriptional patterns underlie whole microbial community responses and may be sensitive indicators of environmental conditions, including those associated with long-term environmental change. The MAGC applied here to ocean ecosystems is a promising complementary approach that can enhance the ability to analyze metatranscriptomic data from a variety of environmental microbiomes.

Assessment of Anaerobic Metabolic Activity and Microbial Diversity in a Petroleum-Contaminated Aquifer Using Push-Pull Tests in Combination With Molecular Tools and Stable Isotopes

NASA Astrophysics Data System (ADS)

Schroth, M. H.; Kleikemper, J.; Pombo, S. A.; Zeyer, J.

2002-12-01

In the past, studies on microbial communities in natural environments have typically focused on either their structure or on their metabolic function. However, linking structure and function is important for understanding microbial community dynamics, in particular in contaminated environments. We will present results of a novel combination of a hydrogeological field method (push-pull tests) with molecular tools and stable isotope analysis, which was employed to quantify anaerobic activities and associated microbial diversity in a petroleum-contaminated aquifer in Studen, Switzerland. Push-pull tests consisted of the injection of test solution containing a conservative tracer and reactants (electron acceptors, 13C-labeled carbon sources) into the aquifer anoxic zone. Following an incubation period, the test solution/groundwater mixture was extracted from the same location. Metabolic activities were computed from solute concentrations measured during extraction. Simultaneously, microbial diversity in sediment and groundwater was characterized by using fluorescence in situ hybridization (FISH), denaturing gradient gel electrophoresis (DGGE), as well as phospholipids fatty acid (PLFA) analysis in combination with 13C isotopic measurements. Results from DGGE analyses provided information on the general community structure before, during and after the tests, while FISH yielded information on active populations. Moreover, using 13C-labeling of microbial PLFA we were able to directly link carbon source assimilation in an aquifer to indigenous microorganisms while providing quantitative information on respective carbon source consumption.

A Seafloor Microbial Biome Hosted within Incipient Ferromanganese Crusts

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

Templeton, Alexis S.; Knowles, A. S.; Eldridge, D. L.

2009-11-15

Unsedimented volcanic rocks exposed on the seafloor at ridge systems and Seamounts host complex, abundant and diverse microbial communities that are relatively cosmopolitan in distribution (Lysnes, Thorseth et al. 2004; Mason, Stingl et al. 2007; Santelli, Orcutt et al. 2008). The most commonly held hypothesis is that the energy released by the hydration, dissolution and oxidative alteration of volcanic glasses in seawater drives the formation of an ocean crust biosphere (Thorseth, Furnes et al. 1992; Fisk, Giovannoni et al. 1998; Furnes and Staudigel 1999). The combined thermodynamically favorable weathering reactions could theoretically support anywhere from 105 to 109 cells/gram ofmore » rock depending upon the metabolisms utilized and cellular growth rates and turnover (Bach and Edwards 2003; Santelli, Orcutt et al. 2008). Yet microbially-mediated basalt alteration and energy conservation has not been directly demonstrated on the seafloor. By using synchrotron-based x-ray microprobe mapping, x-ray absorption spectroscopy and high-resolution scanning and transmission electron microscopy observations of young volcanic glasses recovered from the outer flanks of Loihi Seamount, we intended to identify the initial rates and mechanisms of microbial basalt colonization and bioalteration. Instead, here we show that microbial biofilms are intimately associated with ferromanganese crusts precipitating onto basalt surfaces from cold seawater. Thus we hypothesize that microbial communities colonizing seafloor rocks are established and sustained by external inputs of potential energy sources, such as dissolved and particulate Fe(II), Mn(II) and organic matter, rather than rock dissolution.« less

[Characterization of microbial activities in marine mudflat sediment using FDA hydrolase analysis].

PubMed

Liu, Ye; Zou, Li; Liu, Lu; Gao, Dong-Mei

2013-10-01

A method based on fluorescence spectrometry was developed to detect the microbial activities in marine mudflat sediment, where is characterized by high salinity, complex organic compounds and low microbial biomass. This paper optimized the sample extracts, the detection equipment for reaction products, the pretreatment methods, and the experimental conditions. The optimal procedure is described as following. Fresh sediment was first extracted with sterilized and aged seawater, followed by the addition of Tween-80 solution, then uniformly dispersed by thorough oscillating, and kept steady for precipitation. After filtration through a sterilized membrane (1. 2 microm, sterilized in boiling water repeatedly) , the supernatant was supplemented with an appropriate amount of FDA solution and allowed to react in dark for 180 min at temperature ranged 25-30 degrees C . The reaction was terminated by the addition of acetone, and the fluorescence intensity of the reaction mixture was measured within 25 min using a molecular fluorescence photometer at an excitation wavelength of 488 nm and an emission wavelength of 530 nm, and the detection range of this method (dry weight) was 3.0 x10(3)-1. 1 x 10(5) ind.g-1. The microbial activity was reported as fluorescence content in per unit sediment mass (microg.g-1, dry weight).

Assessment of Anaerobic Toluene Biodegradation Activity by bssA Transcript/Gene Ratios

PubMed Central

Brow, Christina N.; O'Brien Johnson, Reid; Johnson, Richard L.

2013-01-01

Benzylsuccinate synthase (bssA) genes associated with toluene degradation were profiled across a groundwater contaminant plume under nitrate-reducing conditions and were detected in significant numbers throughout the plume. However, differences between groundwater and core sediment samples suggested that microbial transport, rather than local activity, was the underlying cause of the high copy numbers within the downgradient plume. Both gene transcript and reactant concentrations were consistent with this hypothesis. Expression of bssA genes from denitrifying toluene degraders was induced by toluene but only in the presence of nitrate, and transcript abundance dropped rapidly following the removal of either toluene or nitrate. The drop in bssA transcripts following the removal of toluene could be described by an exponential decay function with a half-life on the order of 1 h. Interestingly, bssA transcripts never disappeared completely but were always detected at some level if either inducer was present. Therefore, the detection of transcripts alone may not be sufficient evidence for contaminant degradation. To avoid mistakenly associating basal-level gene expression with actively degrading microbial populations, an integrated approach using the ratio of functional gene transcripts to gene copies is recommended. This approach minimizes the impact of microbial transport on activity assessment and allows reliable assessments of microbial activity to be obtained from water samples. PMID:23811506

Monitoring of the microbial communities involved in the soy sauce manufacturing process by PCR-denaturing gradient gel electrophoresis.

PubMed

Tanaka, Yasushi; Watanabe, Jun; Mogi, Yoshinobu

2012-08-01

Soy sauce is a traditional seasoning produced through the fermentation of soybeans and wheat using microbes. In this study, the microbial communities involved in the soy sauce manufacturing process were analyzed by PCR-Denaturing Gradient Gel Electrophoresis (PCR-DGGE). The bacterial DGGE profile indicated that the bacterial microbes in the koji were Weissella cibaria (Weissella confusa, Weissella kimchii, Weissella salipiscis, Lactobacillus fermentum, Lactobacillus plantarum, Lactobacillus iners, or Streptococcus thermophilus), Staphylococcus gallinarum (or Staphylococcus xylosus), and Staphylococcus kloosii. In addition to these bacteria, Tetragenococcus halophilus was also detected in the mash during lactic acid fermentation. The fungal DGGE profile indicated that the fungal microbes in the koji were not only Aspergillus oryzae but also several yeasts. In the mash, Zygosaccharomyces rouxii appeared in the early fermentation stage, Candida etchellsii (or Candida nodaensis) and Candida versatilis were detected at the middle fermentation stage, and Candida etchellsii was detected at the mature fermentation stage. These results suggest that the microbial communities present during the soy sauce manufacturing process change drastically throughout its production. This is the first report to reveal the microbial communities involved in the soy sauce manufacturing process using a culture-independent method. Crown Copyright © 2012. Published by Elsevier Ltd. All rights reserved.

Reactivity and mobilization of permafrost-derived organic matter along the Lena River Delta - Laptev Sea transition

NASA Astrophysics Data System (ADS)

Koch, Boris P.; Dubinenkov, Ivan; Flerus, Ruth; Schmitt-Kopplin, Philippe; Kattner, Gerhard

2015-04-01

The impact of global warming on organic carbon budgets in permafrost systems are not well constrained. Changes in organic carbon fluxes caused by permafrost thaw depend on microbial activity, coastal erosion, mobilization of organic matter by increased porewater fluxes, and the inherent chemical stability of organic matter in permafrost soils. Here we aim at the identification and molecular characterization of active and inactive dissolved organic matter (DOM) components within the river-ocean transition. We studied four transects in the coastal Laptev Sea characterized by steep physico-chemical gradients. Molecular information on solid-phase extracted DOM was derived from ultrahigh resolution mass spectrometry. Changes of the chemical composition with salinity were used as a measure for DOM reactivity. Although changes of dissolved organic carbon (DOC) in the estuary suggested conservative mixing, only 27% of the identified molecular formulas behaved conservatively, 32% were moderately affected, and 41% were actively involved in estuarine processes. The molecular complexity in the DOM samples increased with growing marine influence and the average elemental composition (i.e. relative contribution of organic nitrogen and oxygen compounds) changed significantly with increasing salinity. These chemical changes were consistent with the results of a 20-day microbial incubation experiment, during which more than half of the permafrost-derived DOC was mineralized. We conclude that, although the DOC gradient in the estuary suggests conservative behavior, terrestrial DOM is substantially affected by estuarine processes which in turn also impact organic carbon budgets in the Lena Delta.

Evaluating Microbial Purification during Soil Treatment of Wastewater with Multicomponent Tracer and Surrogate Tests

USGS Publications Warehouse

Van Cuyk, S.; Siegrist, R.L.; Lowe, K.; Harvey, R.W.

2004-01-01

Soil treatment of wastewater has the potential to achieve high purification efficiency, yet the understanding and predictability of purification with respect to removal of viruses and other pathogens is limited. Research has been completed to quantify the removal of virus and bacteria through the use of microbial surrogates and conservative tracers during controlled experiments with three-dimensional pilot-scale soil treatment systems in the laboratory and during the testing of full-scale systems under field conditions. The surrogates and tracers employed included two viruses (MS-2 and PRID-1 bacteriophages), one bacterium (ice-nucleating active Pseudomonas), and one conservative tracer (bromide ion). Efforts have also been made to determine the relationship between viruses and fecal coliform bacteria in soil samples below the wastewater infiltrative surface, and the correlation between Escherichia coil concentrations measured in percolating soil solution as compared with those estimated from analyses of soil solids. The results suggest episodic breakthrough of virus and bacteria during soil treatment of wastewater and a 2 to 3 log (99-99.9%) removal of virus and near complete removal of fecal coliform bacteria during unsaturated flow through 60 to 90 cm of sandy medium. Results also suggest that the fate of fecal coliform bacteria may be indicative of that of viruses in soil media near the infiltrative surface receiving wastewater effluent. Concentrations of fecal coliform in percolating soil solution may be conservatively estimated from analysis of extracted soil solids.

Conserved Responses in a War of Small Molecules between a Plant-Pathogenic Bacterium and Fungi.

PubMed

Spraker, Joseph E; Wiemann, Philipp; Baccile, Joshua A; Venkatesh, Nandhitha; Schumacher, Julia; Schroeder, Frank C; Sanchez, Laura M; Keller, Nancy P

2018-05-22

Small-molecule signaling is one major mode of communication within the polymicrobial consortium of soil and rhizosphere. While microbial secondary metabolite (SM) production and responses of individual species have been studied extensively, little is known about potentially conserved roles of SM signals in multilayered symbiotic or antagonistic relationships. Here, we characterize the SM-mediated interaction between the plant-pathogenic bacterium Ralstonia solanacearum and the two plant-pathogenic fungi Fusarium fujikuroi and Botrytis cinerea We show that cellular differentiation and SM biosynthesis in F. fujikuroi are induced by the bacterially produced lipopeptide ralsolamycin (synonym ralstonin A). In particular, fungal bikaverin production is induced and preferentially accumulates in fungal survival spores (chlamydospores) only when exposed to supernatants of ralsolamycin-producing strains of R. solanacearum Although inactivation of bikaverin biosynthesis moderately increases chlamydospore invasion by R. solanacearum , we show that other metabolites such as beauvericin are also induced by ralsolamycin and contribute to suppression of R. solanacearum growth in vitro Based on our findings that bikaverin antagonizes R. solanacearum and that ralsolamycin induces bikaverin biosynthesis in F. fujikuroi , we asked whether other bikaverin-producing fungi show similar responses to ralsolamycin. Examining a strain of B. cinerea that horizontally acquired the bikaverin gene cluster from Fusarium , we found that ralsolamycin induced bikaverin biosynthesis in this fungus. Our results suggest that conservation of microbial SM responses across distantly related fungi may arise from horizontal transfer of protective gene clusters that are activated by conserved regulatory cues, e.g., a bacterial lipopeptide, providing consistent fitness advantages in dynamic polymicrobial networks. IMPORTANCE Bacteria and fungi are ubiquitous neighbors in many environments, including the rhizosphere. Many of these organisms are notorious as economically devastating plant pathogens, but little is known about how they communicate chemically with each other. Here, we uncover a conserved antagonistic communication between the widespread bacterial wilt pathogen Ralstonia solanacearum and plant-pathogenic fungi from disparate genera, Fusarium and Botrytis Exposure of Fusarium fujikuroi to the bacterial lipopeptide ralsolamycin resulted in production of the antibacterial metabolite bikaverin specifically in fungal tissues invaded by Ralstonia Remarkably, ralsolamycin induction of bikaverin was conserved in a Botrytis cinerea isolate carrying a horizontally transferred bikaverin gene cluster. These results indicate that horizontally transferred gene clusters may carry regulatory prompts that contribute to conserved fitness functions in polymicrobial environments. Copyright © 2018 Spraker et al.

Microbial Community Analysis of a Coastal Salt Marsh Affected by the Deepwater Horizon Oil Spill

PubMed Central

Beazley, Melanie J.; Martinez, Robert J.; Rajan, Suja; Powell, Jessica; Piceno, Yvette M.; Tom, Lauren M.; Andersen, Gary L.; Hazen, Terry C.; Van Nostrand, Joy D.; Zhou, Jizhong; Mortazavi, Behzad; Sobecky, Patricia A.

2012-01-01

Coastal salt marshes are highly sensitive wetland ecosystems that can sustain long-term impacts from anthropogenic events such as oil spills. In this study, we examined the microbial communities of a Gulf of Mexico coastal salt marsh during and after the influx of petroleum hydrocarbons following the Deepwater Horizon oil spill. Total hydrocarbon concentrations in salt marsh sediments were highest in June and July 2010 and decreased in September 2010. Coupled PhyloChip and GeoChip microarray analyses demonstrated that the microbial community structure and function of the extant salt marsh hydrocarbon-degrading microbial populations changed significantly during the study. The relative richness and abundance of phyla containing previously described hydrocarbon-degrading bacteria (Proteobacteria, Bacteroidetes, and Actinobacteria) increased in hydrocarbon-contaminated sediments and then decreased once hydrocarbons were below detection. Firmicutes, however, continued to increase in relative richness and abundance after hydrocarbon concentrations were below detection. Functional genes involved in hydrocarbon degradation were enriched in hydrocarbon-contaminated sediments then declined significantly (p<0.05) once hydrocarbon concentrations decreased. A greater decrease in hydrocarbon concentrations among marsh grass sediments compared to inlet sediments (lacking marsh grass) suggests that the marsh rhizosphere microbial communities could also be contributing to hydrocarbon degradation. The results of this study provide a comprehensive view of microbial community structural and functional dynamics within perturbed salt marsh ecosystems. PMID:22815990

Detection of microbial contamination during human islet isolation.

PubMed

Kin, Tatsuya; Rosichuk, Shawn; Shapiro, A M James; Lakey, Jonathan R T

2007-01-01

Current good manufacturing practice (cGMP) islet processing facilities provide an ultraclean environment for the safe production of clinical grade islets for transplantation into immunosuppressed diabetic recipients. The objective of this study was to monitor the rate of microbial contamination in islet products after implementation of good manufacturing practice conditions. Fluid samples for microbial contamination were collected at the following steps: from the pancreas transport solution upon arrival of the organ (n=157), after surface decontamination of the pancreas with antiseptic agents (n=89), from islet supernatant at the end of the isolation (n=104), and from islet supernatant as a final transplantable product after culture (n=53). Bacterial, fungal, and mycoplasma cultures were conducted for 2, 2, and 3 weeks, respectively. Microbial contamination was detected in 31% of transport solution. The contamination was not associated with the presence of the duodenum during the preservation, cold ischemia time, or procurement team (local vs. distant). Surface decontamination of the pancreas resulted in clearance of 92% of the microbial contamination. Six preparations at the end of the isolation revealed microbial growth. All were de novo contamination during the processing. Fifty-three preparations that met our release criteria in terms of product sterility were transplanted into type 1 diabetic patients. In two instances, positive culture of the islet preparation was reported after transplantation had occurred. No patient showed any clinical findings suggestive of infection or any radiological abnormalities suggestive of abscess; a single dose of antibiotic coverage was given routinely to recipients prior to islet infusion. Although transport solution carries a high risk of microbial contamination, most contaminants become undetectable during islet processing. Microbial contamination in final products is rare, but de novo contamination still occurs during processing even under cGMP conditions.

Detection of Microbial Contamination during Human Islet Isolation.

PubMed

Kin, Tatsuya; Rosichuk, Shawn; Shapiro, A M James; Lakey, Jonathan R T

2007-01-01

Current good manufacturing practice (cGMP) islet processing facilities provide an ultraclean environment for the safe production of clinical grade islets for transplantation into immunosuppressed diabetic recipients. The objective of this study was to monitor the rate of microbial contamination in islet products after implementation of good manufacturing practice conditions. Fluid samples for microbial contamination were collected at the following steps: from the pancreas transport solution upon arrival of the organ (n = 157), after surface decontamination of the pancreas with antiseptic agents (n = 89), from islet supernatant at the end of the isolation (n = 104), and from islet supernatant as a final transplantable product after culture (n = 53). Bacterial, fungal, and mycoplasma cultures were conducted for 2, 2, and 3 weeks, respectively. Microbial contamination was detected in 31% of transport solution. The contamination was not associated with the presence of the duodenum during the preservation, cold ischemia time, or procurement team (local vs. distant). Surface decontamination of the pancreas resulted in clearance of 92% of the microbial contamination. Six preparations at the end of the isolation revealed microbial growth. All were de novo contamination during the processing. Fifty-three preparations that met our release criteria in terms of product sterility were transplanted into type 1 diabetic patients. In two instances, positive culture of the islet preparation was reported after transplantation had occurred. No patient showed any clinical findings suggestive of infection or any radiological abnormalities suggestive of abscess; a single dose of antibiotic coverage was given routinely to recipients prior to islet infusion. Although transport solution carries a high risk of microbial contamination, most contaminants become undetectable during islet processing. Microbial contamination in final products is rare, but de novo contamination still occurs during processing even under cGMP conditions.

A Comparison of Microbial Community Structures by Depth and Season Under Switchgrass

NASA Astrophysics Data System (ADS)

Fansler, S. J.; Smith, J. L.; Bolton, H.; Bailey, V. L.

2008-12-01

As part of a multidisciplinary study of C sequestration in switchgrass production systems, the soil microbial community structure was monitored at 6 different depths (reaching 90 cm) in both spring and autumn. Microbial community structure was assessed using ribosomal intergenic spacer analysis (RISA), and primers were used specific to either bacteria or fungi, generating microbial community fingerprints for each taxonomic group. Diverse microbial communities for both groups were detected throughout the soil profile. It is notable that while community structure clearly changed with depth, there was the deepest soil samples still retained relatively diverse communities. Seasonally, differences are clearly evident within plots at the surface. As the plots were replicated, significant differences in the community fingerprints with depth and season are reported.

Molecular detection and quantification of viable probiotic strains in animal feedstuffs using the commercial direct fed microbial Lactobacillus animalis NP51 as a model.

PubMed

Ayala, D I; Chen, J C; Bugarel, M; Loneragan, G H; den Bakker, H C; Kottapalli, K R; Brashears, M M; Nightingale, K K

2018-04-17

Lactobacillus animalis NP51 is a direct-fed microbial strain (DFM) extensively used as a pre-harvest food safety mitigation in feedlot cattle due to its antagonistic effects against human foodborne pathogens such as Salmonella and Escherichia coli O157:H7. NP51 not only promotes overall gut health but interferes with the ability of these pathogens to colonize the gastrointestinal tract of cattle. As a result, NP51 reduces fecal shedding of Salmonella and E. coli O157:H7 in cattle presented for harvest and the load of these pathogens that enter the human food chain. Cattle are administered a high dose (1 × 10 9  CFU/head/day) of NP51 to reduce fecal shedding of foodborne pathogens. Ensiled animal feedstuffs naturally contain a high load of lactic acid bacteria (LAB) and it is not possible to detect and quantify the level of a specific LAB strain (e.g., NP51) in this matrix using traditional microbiological culture. The purpose of this study was to develop a molecular method to detect and quantify viable populations of a specific LAB strain (e.g., NP51) in cattle feedstuffs. The NP51 whole genome sequence was aligned with closely related LAB clustering within the same well-supported clade in a LAB phylogeny derived from 30 conserved amino acid encoding sequence to identify orthologs. A sequence encoding recombinational DNA repair protein RecT was found to be unique to NP51 and used to design primers and a probe for molecular detection and quantification of NP51. The primers and probe were confirmed to be specific to NP51 in vitro. Total RNA was extracted from silage samples, including samples naturally inoculated in the field and control samples that were artificially spiked with a range of NP51 concentrations in the laboratory. Reverse-transcriptase quantitative real-time (RT-qRTi) PCR was used to quantify cDNA copies in samples and cycle threshold (Ct) values were compared to a standard curve to estimate NP51 concentrations. Our results indicate this novel molecular method is suitable to confirm the presence and estimate the concentration of a specific LAB strain in animal feedstuffs containing high background levels of LAB. Copyright © 2018. Published by Elsevier B.V.

Microbial management of arthropod pests of tea: current state and prospects.

PubMed

Roy, Somnath; Muraleedharan, Narayanannair

2014-06-01

Sustainable tea cultivation will rely increasingly on alternatives to conventional chemical insecticides for pest management that are environment-friendly and reduce the amount of pesticide residues in made tea. Entomopathogens can provide effective control, conserve biodiversity, and serve as alternatives to chemical insecticides under several conditions. Due to their specificity for insects, these pathogens including viruses, bacteria, and fungi are ideal candidates for incorporation in the integrated pest management strategies for tea where their effects on other natural enemies will be minimal. Biological and ecological characteristics of several dominant natural entomopathogenic microorganisms have been well documented throughout the tea-growing countries particularly China, Japan, and India. But research to convert them to microbial insecticide formulations for tea pest control by evolving suitable techniques for production, standardization, formulation, and application has not progressed well except in Japan and China to some extent. Increased use of microbial control will depend on a variety of factors including improvements in the pathogens' virulence, formulation, delivery, etc. and an increased awareness of their attributes by growers and the general public. In this review, we provide an overview of microbial control of the key insect pests of tea and also the scope for future studies for their better utilization.

Type II NKT Cells in Inflammation, Autoimmunity, Microbial Immunity, and Cancer

PubMed Central

Marrero, Idania; Ware, Randle; Kumar, Vipin

2015-01-01

Natural killer T cells (NKT) recognize self and microbial lipid antigens presented by non-polymorphic CD1d molecules. Two major NKT cell subsets, type I and II, express different types of antigen receptors (TCR) with distinct mode of CD1d/lipid recognition. Though type II NKT cells are less frequent in mice and difficult to study, they are predominant in human. One of the major subsets of type II NKT cells reactive to the self-glycolipid sulfatide is the best characterized and has been shown to induce a dominant immune regulatory mechanism that controls inflammation in autoimmunity and in anti-cancer immunity. Recently, type II NKT cells reactive to other self-glycolipids and phospholipids have been identified suggesting both promiscuous and specific TCR recognition in microbial immunity as well. Since the CD1d pathway is highly conserved, a detailed understanding of the biology and function of type II NKT cells as well as their interplay with type I NKT cells or other innate and adaptive T cells will have major implications for potential novel interventions in inflammatory and autoimmune diseases, microbial immunity, and cancer. PMID:26136748

The dual role of microbes in corrosion

PubMed Central

Kip, Nardy; van Veen, Johannes A

2015-01-01

Corrosion is the result of a series of chemical, physical and (micro) biological processes leading to the deterioration of materials such as steel and stone. It is a world-wide problem with great societal and economic consequences. Current corrosion control strategies based on chemically produced products are under increasing pressure of stringent environmental regulations. Furthermore, they are rather inefficient. Therefore, there is an urgent need for environmentally friendly and sustainable corrosion control strategies. The mechanisms of microbially influenced corrosion and microbially influenced corrosion inhibition are not completely understood, because they cannot be linked to a single biochemical reaction or specific microbial species or groups. Corrosion is influenced by the complex processes of different microorganisms performing different electrochemical reactions and secreting proteins and metabolites that can have secondary effects. Information on the identity and role of microbial communities that are related to corrosion and corrosion inhibition in different materials and in different environments is scarce. As some microorganisms are able to both cause and inhibit corrosion, we pay particular interest to their potential role as corrosion-controlling agents. We show interesting interfaces in which scientists from different disciplines such as microbiology, engineering and art conservation can collaborate to find solutions to the problems caused by corrosion. PMID:25259571

The dual role of microbes in corrosion.

PubMed

Kip, Nardy; van Veen, Johannes A

2015-03-01

Corrosion is the result of a series of chemical, physical and (micro) biological processes leading to the deterioration of materials such as steel and stone. It is a world-wide problem with great societal and economic consequences. Current corrosion control strategies based on chemically produced products are under increasing pressure of stringent environmental regulations. Furthermore, they are rather inefficient. Therefore, there is an urgent need for environmentally friendly and sustainable corrosion control strategies. The mechanisms of microbially influenced corrosion and microbially influenced corrosion inhibition are not completely understood, because they cannot be linked to a single biochemical reaction or specific microbial species or groups. Corrosion is influenced by the complex processes of different microorganisms performing different electrochemical reactions and secreting proteins and metabolites that can have secondary effects. Information on the identity and role of microbial communities that are related to corrosion and corrosion inhibition in different materials and in different environments is scarce. As some microorganisms are able to both cause and inhibit corrosion, we pay particular interest to their potential role as corrosion-controlling agents. We show interesting interfaces in which scientists from different disciplines such as microbiology, engineering and art conservation can collaborate to find solutions to the problems caused by corrosion.

VirSorter: mining viral signal from microbial genomic data.

PubMed

Roux, Simon; Enault, Francois; Hurwitz, Bonnie L; Sullivan, Matthew B

2015-01-01

Viruses of microbes impact all ecosystems where microbes drive key energy and substrate transformations including the oceans, humans and industrial fermenters. However, despite this recognized importance, our understanding of viral diversity and impacts remains limited by too few model systems and reference genomes. One way to fill these gaps in our knowledge of viral diversity is through the detection of viral signal in microbial genomic data. While multiple approaches have been developed and applied for the detection of prophages (viral genomes integrated in a microbial genome), new types of microbial genomic data are emerging that are more fragmented and larger scale, such as Single-cell Amplified Genomes (SAGs) of uncultivated organisms or genomic fragments assembled from metagenomic sequencing. Here, we present VirSorter, a tool designed to detect viral signal in these different types of microbial sequence data in both a reference-dependent and reference-independent manner, leveraging probabilistic models and extensive virome data to maximize detection of novel viruses. Performance testing shows that VirSorter's prophage prediction capability compares to that of available prophage predictors for complete genomes, but is superior in predicting viral sequences outside of a host genome (i.e., from extrachromosomal prophages, lytic infections, or partially assembled prophages). Furthermore, VirSorter outperforms existing tools for fragmented genomic and metagenomic datasets, and can identify viral signal in assembled sequence (contigs) as short as 3kb, while providing near-perfect identification (>95% Recall and 100% Precision) on contigs of at least 10kb. Because VirSorter scales to large datasets, it can also be used in "reverse" to more confidently identify viral sequence in viral metagenomes by sorting away cellular DNA whether derived from gene transfer agents, generalized transduction or contamination. Finally, VirSorter is made available through the iPlant Cyberinfrastructure that provides a web-based user interface interconnected with the required computing resources. VirSorter thus complements existing prophage prediction softwares to better leverage fragmented, SAG and metagenomic datasets in a way that will scale to modern sequencing. Given these features, VirSorter should enable the discovery of new viruses in microbial datasets, and further our understanding of uncultivated viral communities across diverse ecosystems.

VirSorter: mining viral signal from microbial genomic data

PubMed Central

Roux, Simon; Enault, Francois; Hurwitz, Bonnie L.

2015-01-01

Viruses of microbes impact all ecosystems where microbes drive key energy and substrate transformations including the oceans, humans and industrial fermenters. However, despite this recognized importance, our understanding of viral diversity and impacts remains limited by too few model systems and reference genomes. One way to fill these gaps in our knowledge of viral diversity is through the detection of viral signal in microbial genomic data. While multiple approaches have been developed and applied for the detection of prophages (viral genomes integrated in a microbial genome), new types of microbial genomic data are emerging that are more fragmented and larger scale, such as Single-cell Amplified Genomes (SAGs) of uncultivated organisms or genomic fragments assembled from metagenomic sequencing. Here, we present VirSorter, a tool designed to detect viral signal in these different types of microbial sequence data in both a reference-dependent and reference-independent manner, leveraging probabilistic models and extensive virome data to maximize detection of novel viruses. Performance testing shows that VirSorter’s prophage prediction capability compares to that of available prophage predictors for complete genomes, but is superior in predicting viral sequences outside of a host genome (i.e., from extrachromosomal prophages, lytic infections, or partially assembled prophages). Furthermore, VirSorter outperforms existing tools for fragmented genomic and metagenomic datasets, and can identify viral signal in assembled sequence (contigs) as short as 3kb, while providing near-perfect identification (>95% Recall and 100% Precision) on contigs of at least 10kb. Because VirSorter scales to large datasets, it can also be used in “reverse” to more confidently identify viral sequence in viral metagenomes by sorting away cellular DNA whether derived from gene transfer agents, generalized transduction or contamination. Finally, VirSorter is made available through the iPlant Cyberinfrastructure that provides a web-based user interface interconnected with the required computing resources. VirSorter thus complements existing prophage prediction softwares to better leverage fragmented, SAG and metagenomic datasets in a way that will scale to modern sequencing. Given these features, VirSorter should enable the discovery of new viruses in microbial datasets, and further our understanding of uncultivated viral communities across diverse ecosystems. PMID:26038737

Gut microbiomes of free-ranging and captive Namibian cheetahs: Diversity, putative functions and occurrence of potential pathogens.

PubMed

Wasimuddin; Menke, Sebastian; Melzheimer, Jörg; Thalwitzer, Susanne; Heinrich, Sonja; Wachter, Bettina; Sommer, Simone

2017-10-01

Although the significance of the gut microbiome for host health is well acknowledged, the impact of host traits and environmental factors on the interindividual variation of gut microbiomes of wildlife species is not well understood. Such information is essential; however, as changes in the composition of these microbial communities beyond the natural range might cause dysbiosis leading to increased susceptibility to infections. We examined the potential influence of sex, age, genetic relatedness, spatial tactics and the environment on the natural range of the gut microbiome diversity in free-ranging Namibian cheetahs (Acinonyx jubatus). We further explored the impact of an altered diet and frequent contact with roaming dogs and cats on the occurrence of potential bacterial pathogens by comparing free-ranging and captive individuals living under the same climatic conditions. Abundance patterns of particular bacterial genera differed between the sexes, and bacterial diversity and richness were higher in older (>3.5 years) than in younger individuals. In contrast, male spatial tactics, which probably influence host exposure to environmental bacteria, had no discernible effect on the gut microbiome. The profound resemblance of the gut microbiome of kin in contrast to nonkin suggests a predominant role of genetics in shaping bacterial community characteristics and functional similarities. We also detected various Operational Taxonomic Units (OTUs) assigned to potential pathogenic bacteria known to cause diseases in humans and wildlife species, such as Helicobacter spp., and Clostridium perfringens. Captive individuals did not differ in their microbial alpha diversity but exhibited higher abundances of OTUs related to potential pathogenic bacteria and shifts in disease-associated functional pathways. Our study emphasizes the need to integrate ecological, genetic and pathogenic aspects to improve our comprehension of the main drivers of natural variation and shifts in gut microbial communities possibly affecting host health. This knowledge is essential for in situ and ex situ conservation management. © 2017 John Wiley & Sons Ltd.

Heat Stress Dictates Microbial Lipid Composition along a Thermal Gradient in Marine Sediments

PubMed Central

Sollich, Miriam; Yoshinaga, Marcos Y.; Häusler, Stefan; Price, Roy E.; Hinrichs, Kai-Uwe; Bühring, Solveig I.

2017-01-01

Temperature exerts a first-order control on microbial populations, which constantly adjust the fluidity and permeability of their cell membrane lipids to minimize loss of energy by ion diffusion across the membrane. Analytical advances in liquid chromatography coupled to mass spectrometry have allowed the detection of a stunning diversity of bacterial and archaeal lipids in extreme environments such as hot springs, hydrothermal vents and deep subsurface marine sediments. Here, we investigated a thermal gradient from 18 to 101°C across a marine sediment field and tested the hypothesis that cell membrane lipids provide a major biochemical basis for the bioenergetics of archaea and bacteria under heat stress. This paper features a detailed lipidomics approach with the focus on membrane lipid structure-function. Membrane lipids analyzed here include polar lipids of bacteria and polar and core lipids of archaea. Reflecting the low permeability of their ether-linked isoprenoids, we found that archaeal polar lipids generally dominate over bacterial lipids in deep layers of the sediments influenced by hydrothermal fluids. A close examination of archaeal and bacterial lipids revealed a membrane quandary: not only low permeability, but also increased fluidity of membranes are required as a unified property of microbial membranes for energy conservation under heat stress. For instance, bacterial fatty acids were composed of longer chain lengths in concert with higher degree of unsaturation while archaea modified their tetraethers by incorporation of additional methyl groups at elevated sediment temperatures. It is possible that these configurations toward a more fluidized membrane at elevated temperatures are counterbalanced by the high abundance of archaeal glycolipids and bacterial sphingolipids, which could reduce membrane permeability through strong intermolecular hydrogen bonding. Our results provide a new angle for interpreting membrane lipid structure-function enabling archaea and bacteria to survive and grow in hydrothermal systems. PMID:28878741

Performance of Two Quantitative PCR Methods for Microbial Source Tracking of Human Sewage and Implications for Microbial Risk Assessment in Recreational Waters

PubMed Central

Staley, Christopher; Gordon, Katrina V.; Schoen, Mary E.

2012-01-01

Before new, rapid quantitative PCR (qPCR) methods for assessment of recreational water quality and microbial source tracking (MST) can be useful in a regulatory context, an understanding of the ability of the method to detect a DNA target (marker) when the contaminant source has been diluted in environmental waters is needed. This study determined the limits of detection and quantification of the human-associated Bacteroides sp. (HF183) and human polyomavirus (HPyV) qPCR methods for sewage diluted in buffer and in five ambient, Florida water types (estuarine, marine, tannic, lake, and river). HF183 was quantifiable in sewage diluted up to 10−6 in 500-ml ambient-water samples, but HPyVs were not quantifiable in dilutions of >10−4. Specificity, which was assessed using fecal composites from dogs, birds, and cattle, was 100% for HPyVs and 81% for HF183. Quantitative microbial risk assessment (QMRA) estimated the possible norovirus levels in sewage and the human health risk at various sewage dilutions. When juxtaposed with the MST marker detection limits, the QMRA analysis revealed that HF183 was detectable when the modeled risk of gastrointestinal (GI) illness was at or below the benchmark of 10 illnesses per 1,000 exposures, but the HPyV method was generally not sensitive enough to detect potential health risks at the 0.01 threshold for frequency of illness. The tradeoff between sensitivity and specificity in the MST methods indicates that HF183 data should be interpreted judiciously, preferably in conjunction with a more host-specific marker, and that better methods of concentrating HPyVs from environmental waters are needed if this method is to be useful in a watershed management or monitoring context. PMID:22885746

Comprehensive Analysis of Secondary Dental Root Canal Infections: A Combination of Culture and Culture-Independent Approaches Reveals New Insights

PubMed Central

Anderson, Annette Carola; Hellwig, Elmar; Vespermann, Robin; Wittmer, Annette; Schmid, Michael; Karygianni, Lamprini; Al-Ahmad, Ali

2012-01-01

Persistence of microorganisms or reinfections are the main reasons for failure of root canal therapy. Very few studies to date have included culture-independent methods to assess the microbiota, including non-cultivable microorganisms. The aim of this study was to combine culture methods with culture-independent cloning methods to analyze the microbial flora of root-filled teeth with periradicular lesions. Twenty-one samples from previously root-filled teeth were collected from patients with periradicular lesions. Microorganisms were cultivated, isolated and biochemically identified. In addition, ribosomal DNA of bacteria, fungi and archaea derived from the same samples was amplified and the PCR products were used to construct clone libraries. DNA of selected clones was sequenced and microbial species were identified, comparing the sequences with public databases. Microorganisms were found in 12 samples with culture-dependent and -independent methods combined. The number of bacterial species ranged from 1 to 12 in one sample. The majority of the 26 taxa belonged to the phylum Firmicutes (14 taxa), followed by Actinobacteria, Proteobacteria and Bacteroidetes. One sample was positive for fungi, and archaea could not be detected. The results obtained with both methods differed. The cloning technique detected several as-yet-uncultivated taxa. Using a combination of both methods 13 taxa were detected that had not been found in root-filled teeth so far. Enterococcus faecalis was only detected in two samples using culture methods. Combining the culture-dependent and –independent approaches revealed new candidate endodontic pathogens and a high diversity of the microbial flora in root-filled teeth with periradicular lesions. Both methods yielded differing results, emphasizing the benefit of combined methods for the detection of the actual microbial diversity in apical periodontitis. PMID:23152922

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

Jha, Ramesh K.; Kern, Teresa L.; Kim, Youngchang

A whole-cell biosensor utilizing a transcription factor (TF) is an effective tool for sensitive and selective detection of specialty chemicals or anthropogenic molecules, but requires access to an expanded repertoire of TFs. Using homology modeling and ligand docking for binding pocket identification, assisted by conservative mutations in the pocket, we engineered a novel specificity in an Acinetobacter TF, PobR, to ‘sense’ a chemical p-nitrophenol (pNP) and measured the response via a fluorescent protein reporter expressed from a PobR promoter. Out of 107 variants of PobR, four were active when dosed with pNP, with two mutants showing a specificity switch frommore » the native effector 4-hydroxybenzoate (4HB). One of the mutants, pNPmut1 was then used to create a smart microbial cell responding to pNP production from hydrolysis of an insecticide, paraoxon, in a coupled assay involving phosphotriesterase (PTE) enzyme expressed from a separate promoter. We show the fluorescence of the cells correlated with the catalytic efficiency of the PTE variant expressed in each cell. High selectivity between similar molecules (4HB versus pNP), high sensitivity for pNP detection (~2 μM) and agreement of apo- and holo-structures of PobR scaffold with predetermined computational models are other significant results presented in this work.« less

Microbial-sized, carboxylate-modified microspheres as surrogate tracers in a variety of subsurface environments: An overview

USGS Publications Warehouse

Harvey, Ronald W.; Metge, David W.; LeBlanc, Denis R.

2017-01-01

Since 1986, fluorescent carboxylate-modified polystyrene/latex microspheres (FCM) have been co-injected into aquifers along with conservative tracers and viruses, bacteria, and (or) protozoa. Use of FCM has resulted in new information about subsurface transport behaviors of microorganisms in fractured crystalline rock, karst limestone, soils, and granular aquifers. FCM have been used as surrogates for oocysts of the pathogenic protist Cryptosporidium parvum in karst limestone and granular drinking-water aquifers. The advantages of FCM in subsurface transport studies are that they are safe in tracer applications, negatively charged, easy to detect, chemically inert, and available in wide range of sizes. The limitations of FCM are that the quantities needed for some field transport studies can be prohibitively expensive and that their surface characteristics may not match the microorganisms of interest. These limitations may be ameliorated, in part by using chemically modified FCM so that their surface characteristics are a better match to that of the organisms. Also, more sensitive methods of detection may allow using smaller quantities of FCM. To assess how the transport behaviors of FCM and pathogens might compare at the field scale, it is helpful to conduct side-by-side comparisons of their transport behaviors using the geologic media and site-specific conditions that characterize the field site.

Pharmaceutical container/closure integrity. II: The relationship between microbial ingress and helium leak rates in rubber-stoppered glass vials.

PubMed

Kirsch, L E; Nguyen, L; Moeckly, C S; Gerth, R

1997-01-01

Helium leak rate measurements were quantitatively correlated to the probability of microbial ingress for rubber-stoppered glass vials subjected to immersion challenge. Standard 10-mL tubing glass vials were modified by inserting micropipettes of various sizes (0.1 to 10 microns nominal diameter) into a side wall hole and securing them with epoxy. Butyl rubber closures and aluminum crimps were used to seal the vials. The test units were sealed in a helium-filled glove bag, then the absolute helium leak rates were determined. The test units were disassembled, filled with media, resealed, and autoclaved. The test units were thermally treated to eliminate airlocks within the micropipette lumen and establish a liquid path between microbial challenge media and the test units' contents. Microbial challenge was performed by immersing the test units in a 35 degrees C bath containing magnesium ion and 8 to 10 logs of viable P. diminuta and E. coli for 24 hours. The test units were then incubated at 35 degrees C for an additional 13 days. Microbial ingress was detected by turbidity and plating on blood agar. The elimination of airlocks was confirmed by the presence of magnesium ions in the vial contents by atomic absorption spectrometry. A total of 288 vials were subjected to microbial challenge testing. Those test units whose contents failed to show detectable magnesium ions were eliminated from further analysis. At large leak rates, the probability of microbial ingress approached 100% and at very low leak rates microbial ingress rates were 0%. A dramatic increase in microbial failure occurred in the leak rate region 10(-4.5) to 10(-3) std cc/sec, which roughly corresponded to leak diameters ranging from 0.4 to 2 microns. Below a leak rate of 10(-4.5) std cc/sec the microbial failure rate was < 10%. The critical leak rate in our studies, i.e. the value below which microbial ingress cannot occur because the leak is too small, was observed to be between 10(-5) and 10(-5.8) std cc/sec, which corresponds to an approximate leak diameter of 0.2-0.3 micron.

Single cell genomic study of dehalogenating Chloroflexi from deep sea sediments of Peruvian Margin

NASA Astrophysics Data System (ADS)

Spormann, A.; Kaster, A.; Meyer-Blackwell, K.; Biddle, J.

2012-12-01

Dehalogenating Chloroflexi, such as Dehalococcoidites (Dhc), are members of the rare biosphere of deep sea sediments but were originally discovered as the key microbes mediating reductive dehalogenation of the prevalent groundwater contaminants tetrachloroethene and trichloroethene to ethene. Dhc are slow growing, highly niche adapted microbes that are specialized to organohalide respiration as the sole mode of energy conservation. These strictly anaerobic microbes depend on a supporting microbial community to mitigate electron donor and cofactor requirements among other factors. Molecular and genomic studies on the key enzymes for energy conservation, reductive dehalogenases, have provided evidence for rapid adaptive evolution in terrestrial environments. However, the metabolic life style of Dhc in the absence of anthropogenic contaminants, such as in pristine deep sea sediments, is still unknown. In order to provide fundamental insights into life style, genomic population structure and evolution of Dhc, we analyzed a non-contaminated deep sea sediment sample of the Peru Margin 1230 site collected 6 mbf by a metagenomic and single cell genomic. We present for the first time single cell genomic data on dehalogenating Chloroflexi, a significant microbial population in the poorly understood oligotrophic marine sub-surface environments.

Single cell genomic study of dehalogenating Chloroflexi in deep sea sediments of Peru Margin 1230

NASA Astrophysics Data System (ADS)

Kaster, A.; Meyer-Blackwell, K.; Biddle, J.; Spormann, A.

2012-12-01

Dehalogenating Chloroflexi, such as Dehalococcoidites (Dhc), are members of the rare biosphere of deep sea sediments but were originally discovered as the key microbes mediating reductive dehalogenation of the prevalent groundwater contaminants tetrachloroethene and trichloroethene to ethene. Dhc are slow growing, highly niche adapted microbes that are specialized to organohalide respiration as the sole mode of energy conservation. They are strictly anaerobic microbes that depend on a supporting microbial community for electron donor and cofactor requirements among other factors. Molecular and genomic studies on the key enzymes for energy conservation, reductive dehalogenases, have provided evidence for rapid adaptive evolution in terrestrial environments. However, the metabolic life style of Dhc in the absence of anthropogenic contaminants, such as in pristine deep sea sediments, is still unknown. In order to provide fundamental insights into life style, genomic population structure and evolution of Dhc, we analyzed a non-contaminated deep sea sediment sample of the Peru Margin 1230 site collected 6 mbsf by a metagenomic and single cell genomic approach. We present for the first time single cell genomic data on dehalogenating Chloroflexi, a significant microbial population in the poorly understood oligotrophic marine sub-surface environment.

Microbial culture collections as pillars for promoting fungal diversity, conservation and exploitation.

PubMed

Sette, Lara Durães; Pagnocca, Fernando Carlos; Rodrigues, André

2013-11-01

Fungi are a diverse group of organisms with an overall global number of 1.5M up to 3.3M species on Earth. Besides their ecological roles as decomposers, fungi are important in several aspects of applied research. Here, we review how culture collections may promote the knowledge on diversity, conservation and biotechnological exploitation of fungi. The impact of fungi diversity on biotechnological studies is discussed. We point out the major roles of microbial repositories, including fungal preservation, prospecting, identification, authentication and supply. A survey on the World Data Center for Microorganisms (WDCM) powered by the World Federation for Culture Collections and on the Genetic Heritage Management Council (CGEN) database revealed that 46 Brazilian culture collections registered in these databases are dedicate to preserving fungi. Most of these culture collections are located in the Southeast of Brazil. This scenario also demonstrates that Brazil has many collections focused on fungal strains, but the lack of up-to-date information in WDCM as well as of a solid national platform for culture collections registration do not allow accurate assessment of fungal preservation. Copyright © 2013 Elsevier Inc. All rights reserved.

Effects of combining microbial and chemical insecticides on mortality of the Pecan Weevil (Coleoptera: Curculionidae).

PubMed

Shapiro-Ilan, David I; Cottrell, Ted E; Wood, Bruce W

2011-02-01

The pecan weevil, Curculio caryae (Horn), is a key pest of pecan [Carya illinoinensis (Wangenh.) K. Koch]. Current control recommendations are based on chemical insecticide applications. Microbial control agents such as the entomopathogenic nematode, Steinernema carpocapsae (Weiser) and the fungus Beauveria bassiana (Balsamo) Vuillemin occur naturally in southeastern U.S. pecan orchards and have shown promise as alternative control agents for C. caryjae. Conceivably, the chemical and microbial agents occur simultaneously within pecan orchards or might be applied concurrently. The objective of this study was to determine the interactions between two chemical insecticides that are used in commercial C. caryae control (i.e., carbaryl and cypermethrin applied below field rates) and the microbial agents B. bassiana and S. carpocapsae. In laboratory experiments, pecan weevil larval or adult mortality was assessed after application of microbial or chemical treatments applied singly or in combination (microbial + chemical agent). The nature of interactions (antagonism, additivity, or synergy) in terms of weevil mortality was evaluated over 9 d (larvae) or 5 d (adults). Results for B. bassiana indicated synergistic activity with carbaryl and antagonism with cypermethrin in C. caryae larvae and adults. For S. carpocapsae, synergy was detected with both chemicals in C. caryae larvae, but only additive effects were detected in adult weevils. Our results indicate that the chemical-microbial combinations tested are compatible with the exception of B. bassiana and cypermethrin. In addition, combinations that exhibited synergistic interactions may provide enhanced C. caryae control in commercial field applications; thus, their potential merits further exploration.

Detection of Metabolism Function of Microbial Community of Corpses by Biolog-Eco Method.

PubMed

Jiang, X Y; Wang, J F; Zhu, G H; Ma, M Y; Lai, Y; Zhou, H

2016-06-01

To detect the changes of microbial community functional diversity of corpses with different postmortem interval （PMI） and to evaluate forensic application value for estimating PMI. The cultivation of microbial community from the anal swabs of a Sus scrofa and a human corpse placed in field environment from 0 to 240 h after death was performed using the Biolog-Eco Microplate and the variations of the absorbance values were also monitored. Combined with the technology of forensic pathology and flies succession, the metabolic characteristics and changes of microbial community on the decomposed corpse under natural environment were also observed. The diversity of microbial metabolism function was found to be negatively correlated with the number of maggots in the corpses. The freezing processing had the greatest impact on average well color development value at 0 h and the impact almost disappeared after 48 h. The diversity of microbial metabolism of the samples became relatively unstable after 192 h. The principal component analysis showed that 31 carbon sources could be consolidated for 5 principal components （accumulative contribution ratio >90%）.The carbon source tsquare-analysis showed that N -acetyl- D -glucosamine and L -serine were the dominant carbon sources for estimating the PMI （0=240 h） of the Sus scrofa and human corpse. The Biolog-Eco method can be used to reveal the metabolic differences of the carbon resources utilization of the microbial community on the corpses during 0-240 h after death, which could provide a new basis for estimating the PMI. Copyright© by the Editorial Department of Journal of Forensic Medicine

Energy conservation using face detection

NASA Astrophysics Data System (ADS)

Deotale, Nilesh T.; Kalbande, Dhananjay R.; Mishra, Akassh A.

2011-10-01

Computerized Face Detection, is concerned with the difficult task of converting a video signal of a person to written text. It has several applications like face recognition, simultaneous multiple face processing, biometrics, security, video surveillance, human computer interface, image database management, digital cameras use face detection for autofocus, selecting regions of interest in photo slideshows that use a pan-and-scale and The Present Paper deals with energy conservation using face detection. Automating the process to a computer requires the use of various image processing techniques. There are various methods that can be used for Face Detection such as Contour tracking methods, Template matching, Controlled background, Model based, Motion based and color based. Basically, the video of the subject are converted into images are further selected manually for processing. However, several factors like poor illumination, movement of face, viewpoint-dependent Physical appearance, Acquisition geometry, Imaging conditions, Compression artifacts makes Face detection difficult. This paper reports an algorithm for conservation of energy using face detection for various devices. The present paper suggests Energy Conservation can be done by Detecting the Face and reducing the brightness of complete image and then adjusting the brightness of the particular area of an image where the face is located using histogram equalization.

Antibody to a conserved antigenic target is protective against diverse prokaryotic and eukaryotic pathogens

PubMed Central

Cywes-Bentley, Colette; Skurnik, David; Zaidi, Tanweer; Roux, Damien; DeOliveira, Rosane B.; Garrett, Wendy S.; Lu, Xi; O’Malley, Jennifer; Kinzel, Kathryn; Zaidi, Tauqeer; Rey, Astrid; Perrin, Christophe; Fichorova, Raina N.; Kayatani, Alexander K. K.; Maira-Litràn, Tomas; Gening, Marina L.; Tsvetkov, Yury E.; Nifantiev, Nikolay E.; Bakaletz, Lauren O.; Pelton, Stephen I.; Golenbock, Douglas T.; Pier, Gerald B.

2013-01-01

Microbial capsular antigens are effective vaccines but are chemically and immunologically diverse, resulting in a major barrier to their use against multiple pathogens. A β-(1→6)–linked poly-N-acetyl-d-glucosamine (PNAG) surface capsule is synthesized by four proteins encoded in genetic loci designated intercellular adhesion in Staphylococcus aureus or polyglucosamine in selected Gram-negative bacterial pathogens. We report that many microbial pathogens lacking an identifiable intercellular adhesion or polyglucosamine locus produce PNAG, including Gram-positive, Gram-negative, and fungal pathogens, as well as protozoa, e.g., Trichomonas vaginalis, Plasmodium berghei, and sporozoites and blood-stage forms of Plasmodium falciparum. Natural antibody to PNAG is common in humans and animals and binds primarily to the highly acetylated glycoform of PNAG but is not protective against infection due to lack of deposition of complement opsonins. Polyclonal animal antibody raised to deacetylated glycoforms of PNAG and a fully human IgG1 monoclonal antibody that both bind to native and deacetylated glycoforms of PNAG mediated complement-dependent opsonic or bactericidal killing and protected mice against local and/or systemic infections by Streptococcus pyogenes, Streptococcus pneumoniae, Listeria monocytogenes, Neisseria meningitidis serogroup B, Candida albicans, and P. berghei ANKA, and against colonic pathology in a model of infectious colitis. PNAG is also a capsular polysaccharide for Neisseria gonorrhoeae and nontypable Hemophilus influenzae, and protects cells from environmental stress. Vaccination targeting PNAG could contribute to immunity against serious and diverse prokaryotic and eukaryotic pathogens, and the conserved production of PNAG suggests that it is a critical factor in microbial biology. PMID:23716675

Application of laser scanning speckle-microscopy for high-resolution express diagnostics of chlamydial infection

NASA Astrophysics Data System (ADS)

Ulyanov, Sergey; Larionova, Olga; Ulianova, Onega; Zaitsev, Sergey; Saltykov, Yury; Polyanina, Tatiana; Lyapina, Anna; Filonova, Nadezhda; Subbotina, Irina; Kalduzova, Irina; Utz, Sergey; Moiseeva, Yulia; Feodorova, Valentina

2018-04-01

Method of speckle-microscopy has been adapted to the problem of detection of Chlamydia trachomatis microbial cells in clinical samples. Prototype of laser scanning speckle-microscope has been designed. Spatial resolution and output characteristics of this microscope have been analyzed for the case of scanning of C. trachomatis bacteria inclusions - Elementary Bodies (EBs) inside the human cells, fixed on the glass. It has been demonstrated, that presence of C. trachomatis microbial cells in the sample can be easily detected using speckle microscopy.

Microbial water quality before and after the repair of a failing onsite wastewater treatment system adjacent to coastal waters

USGS Publications Warehouse

Conn, K.E.; Habteselassie, M.Y.; Denene, Blackwood A.; Noble, R.T.

2012-01-01

Aims: The objective was to assess the impacts of repairing a failing onsite wastewater treatment system (OWTS, i.e., septic system) as related to coastal microbial water quality. Methods and Results: Wastewater, groundwater and surface water were monitored for environmental parameters, faecal indicator bacteria (total coliforms, Escherichia coli, enterococci) and the viral tracer MS2 before and after repairing a failing OWTS. MS2 results using plaque enumeration and quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) often agreed, but inhibition limited the qRT-PCR assay sensitivity. Prerepair, MS2 persisted in groundwater and was detected in the nearby creek; postrepair, it was not detected. In groundwater, total coliform concentrations were lower and E.??coli was not detected, while enterococci concentrations were similar to prerepair levels. E.??coli and enterococci surface water concentrations were elevated both before and after the repair. Conclusions: Repairing the failing OWTS improved groundwater microbial water quality, although persistence of bacteria in surface water suggests that the OWTS was not the singular faecal contributor to adjacent coastal waters. A suite of tracers is needed to fully assess OWTS performance in treating microbial contaminants and related impacts on receiving waters. Molecular methods like qRT-PCR have potential but require optimization. Significance and Impact of Study: This is the first before and after study of a failing OWTS and provides guidance on selection of microbial tracers and methods. ?? 2011 The Authors. Journal of Applied Microbiology ?? 2011 The Society for Applied Microbiology.

Investigating bacterial populations in styrene-degrading biofilters by 16S rDNA tag pyrosequencing.

PubMed

Portune, Kevin J; Pérez, M Carmen; Álvarez-Hornos, F Javier; Gabaldón, Carmen

2015-01-01

Microbial biofilms are essential components in the elimination of pollutants within biofilters, yet still little is known regarding the complex relationships between microbial community structure and biodegradation function within these engineered ecosystems. To further explore this relationship, 16S rDNA tag pyrosequencing was applied to samples taken at four time points from a styrene-degrading biofilter undergoing variable operating conditions. Changes in microbial structure were observed between different stages of biofilter operation, and the level of styrene concentration was revealed to be a critical factor affecting these changes. Bacterial genera Azoarcus and Pseudomonas were among the dominant classified genera in the biofilter. Canonical correspondence analysis (CCA) and correlation analysis revealed that the genera Brevundimonas, Hydrogenophaga, and Achromobacter may play important roles in styrene degradation under increasing styrene concentrations. No significant correlations (P > 0.05) could be detected between biofilter operational/functional parameters and biodiversity measurements, although biological heterogeneity within biofilms and/or technical variability within pyrosequencing may have considerably affected these results. Percentages of selected bacterial taxonomic groups detected by fluorescence in situ hybridization (FISH) were compared to results from pyrosequencing in order to assess the effectiveness and limitations of each method for identifying each microbial taxon. Comparison of results revealed discrepancies between the two methods in the detected percentages of numerous taxonomic groups. Biases and technical limitations of both FISH and pyrosequencing, such as the binding of FISH probes to non-target microbial groups and lack of classification of sequences for defined taxonomic groups from pyrosequencing, may partially explain some differences between the two methods.

Performance of Kiestra Total Laboratory Automation Combined with MS in Clinical Microbiology Practice

PubMed Central

Hodiamont, Caspar J.; de Jong, Menno D.; Overmeijer, Hendri P. J.; van den Boogaard, Mandy; Visser, Caroline E.

2014-01-01

Background Microbiological laboratories seek technologically innovative solutions to cope with large numbers of samples and limited personnel and financial resources. One platform that has recently become available is the Kiestra Total Laboratory Automation (TLA) system (BD Kiestra B.V., the Netherlands). This fully automated sample processing system, equipped with digital imaging technology, allows superior detection of microbial growth. Combining this approach with matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MS) (Bruker Daltonik, Germany) is expected to enable more rapid identification of pathogens. Methods Early growth detection by digital imaging using Kiestra TLA combined with MS was compared to conventional methods (CM) of detection. Accuracy and time taken for microbial identification were evaluated for the two methods in 219 clinical blood culture isolates. The possible clinical impact of earlier microbial identification was assessed according to antibiotic treatment prescription. Results Pathogen identification using Kiestra TLA combined with MS resulted in a 30.6 hr time gain per isolate compared to CM. Pathogens were successfully identified in 98.4% (249/253) of all tested isolates. Early microbial identification without susceptibility testing led to an adjustment of antibiotic regimen in 12% (24/200) of patients. Conclusions The requisite 24 hr incubation time for microbial pathogens to reach sufficient growth for susceptibility testing and identification would be shortened by the implementation of Kiestra TLA in combination with MS, compared to the use of CM. Not only can this method optimize workflow and reduce costs, but it can allow potentially life-saving switches in antibiotic regimen to be initiated sooner. PMID:24624346

Microbial responses to chitin and chitosan in oxic and anoxic agricultural soil slurries

NASA Astrophysics Data System (ADS)

Wieczorek, A. S.; Hetz, S. A.; Kolb, S.

2014-06-01

Microbial degradation of chitin in soil substantially contributes to carbon cycling in terrestrial ecosystems. Chitin is globally the second most abundant biopolymer after cellulose and can be deacetylated to chitosan or can be hydrolyzed to N,N'-diacetylchitobiose and oligomers of N-acetylglucosamine by aerobic and anaerobic microorganisms. Which pathway of chitin hydrolysis is preferred by soil microbial communities is unknown. Supplementation of chitin stimulated microbial activity under oxic and anoxic conditions in agricultural soil slurries, whereas chitosan had no effect. Thus, the soil microbial community likely was more adapted to chitin as a substrate. In addition, this finding suggested that direct hydrolysis of chitin was preferred to the pathway that starts with deacetylation. Chitin was apparently degraded by aerobic respiration, ammonification, and nitrification to carbon dioxide and nitrate under oxic conditions. When oxygen was absent, fermentation products (acetate, butyrate, propionate, hydrogen, and carbon dioxide) and ammonia were detected, suggesting that butyric and propionic acid fermentation, along with ammonification, were likely responsible for anaerobic chitin degradation. In total, 42 different chiA genotypes were detected of which twenty were novel at an amino acid sequence dissimilarity of less than 50%. Various chiA genotypes responded to chitin supplementation and affiliated with a novel deep-branching bacterial chiA genotype (anoxic conditions), genotypes of Beta- and Gammaproteobacteria (oxic and anoxic conditions), and Planctomycetes (oxic conditions). Thus, this study provides evidence that detected chitinolytic bacteria were catabolically diverse and occupied different ecological niches with regard to oxygen availability enabling chitin degradation under various redox conditions on community level.

Microbial responses to chitin and chitosan in oxic and anoxic agricultural soil slurries

NASA Astrophysics Data System (ADS)

Wieczorek, A. S.; Hetz, S. A.; Kolb, S.

2014-02-01

Chitin is the second most abundant biopolymer in terrestrial ecosystems and is subject to microbial degradation. Chitin can be deacetylated to chitosan or can be hydrolyzed to N,N'-diacetylchitobiose and oligomers of N-acetylglucosamine by aerobic and anaerobic microorganisms. Which pathway of chitin hydrolysis is preferred by soil microbial communities has previously been unknown. Supplementation of chitin stimulated microbial activity under oxic and anoxic conditions in agricultural soil slurries, whereas chitosan had no effect. Thus, the soil microbial community likely was more adapted to chitin as a substrate. In addition, this finding suggested that direct hydrolysis of chitin was preferred to the pathway that starts with deacetylation. Chitin was apparently degraded by aerobic respiration, ammonification, and nitrification to carbon dioxide and nitrate under oxic conditions. When oxygen was absent, fermentation products (acetate, butyrate, propionate, hydrogen, carbon dioxide) and ammonia were detected, suggesting that butyric and propionic acid fermentation were along with ammonification likely responsible for apparent anaerobic chitin degradation. In total, 42 different chiA genotypes were detected of which twenty were novel at an amino acid sequence dissimilarity of >50%. Various chiA genotypes responded to chitin supplementation and affiliated with a novel deep-branching bacterial chiA genotype (anoxic conditions), genotypes of Beta- and Gammaproteobacteria (oxic and anoxic conditions), and Planctomycetes (oxic conditions). Thus, this study provides evidence that detected chitinolytic bacteria were catabolically diverse and occupied different ecological niches with regard to oxygen availability enabling chitin degradation under various redox conditions at the level of the community.

Subsurface metabolic potential on the Costa Rican Margin

NASA Astrophysics Data System (ADS)

Biddle, J.; Leon, Z. R.; Martino, A. J.; Bousses, K.; House, C. H.

2017-12-01

The distribution of archaea and bacteria and their associated metabolic abilities in the deep subseafloor are poorly understood. In order to explore this, we focused on samples from the Costa Rica margin IODP Expedition 334. The microbial community was analyzed via metagenomics in two different sites at multiple depths. At Site 1378, samples are from 2 meters below the sea floor (mbsf), 33 mbsf and 93 mbsf, and at Site 1379 from 22 mbsf to 45 mbsf. Whole community analysis of conserved gene markers in the metagenome show that the microbial community varies with depth, and drastically differs between the two geographically close sites. Thirty-two genomes were recovered from the metagenomic data with more than 30% completion. Archaea make 49% of all genomes recovered and over 90% of these recovered genomes belong to recently discovered and poorly characterized groups of Archaea. This study explored the relative dynamics of microbial communities in the deep biosphere and presents the metabolic potential of distinct subsurface biosphere archaeal groups.

Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range

PubMed Central

Henderson, Gemma; Cox, Faith; Ganesh, Siva; Jonker, Arjan; Young, Wayne; Abecia, Leticia; Angarita, Erika; Aravena, Paula; Nora Arenas, Graciela; Ariza, Claudia; Attwood, Graeme T.; Mauricio Avila, Jose; Avila-Stagno, Jorge; Bannink, André; Barahona, Rolando; Batistotti, Mariano; Bertelsen, Mads F.; Brown-Kav, Aya; Carvajal, Andres M.; Cersosimo, Laura; Vieira Chaves, Alexandre; Church, John; Clipson, Nicholas; Cobos-Peralta, Mario A.; Cookson, Adrian L.; Cravero, Silvio; Cristobal Carballo, Omar; Crosley, Katie; Cruz, Gustavo; Cerón Cucchi, María; de la Barra, Rodrigo; De Menezes, Alexandre B.; Detmann, Edenio; Dieho, Kasper; Dijkstra, Jan; dos Reis, William L. S.; Dugan, Mike E. R.; Hadi Ebrahimi, Seyed; Eythórsdóttir, Emma; Nde Fon, Fabian; Fraga, Martín; Franco, Francisco; Friedeman, Chris; Fukuma, Naoki; Gagić, Dragana; Gangnat, Isabelle; Javier Grilli, Diego; Guan, Le Luo; Heidarian Miri, Vahideh; Hernandez-Sanabria, Emma; Gomez, Alma Ximena Ibarra; Isah, Olubukola A.; Ishaq, Suzanne; Jami, Elie; Jelincic, Juan; Kantanen, Juha; Kelly, William J.; Kim, Seon-Ho; Klieve, Athol; Kobayashi, Yasuo; Koike, Satoshi; Kopecny, Jan; Nygaard Kristensen, Torsten; Julie Krizsan, Sophie; LaChance, Hannah; Lachman, Medora; Lamberson, William R.; Lambie, Suzanne; Lassen, Jan; Leahy, Sinead C.; Lee, Sang-Suk; Leiber, Florian; Lewis, Eva; Lin, Bo; Lira, Raúl; Lund, Peter; Macipe, Edgar; Mamuad, Lovelia L.; Cuquetto Mantovani, Hilário; Marcoppido, Gisela Ariana; Márquez, Cristian; Martin, Cécile; Martinez, Gonzalo; Eugenia Martinez, Maria; Lucía Mayorga, Olga; McAllister, Tim A.; McSweeney, Chris; Mestre, Lorena; Minnee, Elena; Mitsumori, Makoto; Mizrahi, Itzhak; Molina, Isabel; Muenger, Andreas; Munoz, Camila; Murovec, Bostjan; Newbold, John; Nsereko, Victor; O’Donovan, Michael; Okunade, Sunday; O’Neill, Brendan; Ospina, Sonia; Ouwerkerk, Diane; Parra, Diana; Pereira, Luiz Gustavo Ribeiro; Pinares-Patino, Cesar; Pope, Phil B.; Poulsen, Morten; Rodehutscord, Markus; Rodriguez, Tatiana; Saito, Kunihiko; Sales, Francisco; Sauer, Catherine; Shingfield, Kevin; Shoji, Noriaki; Simunek, Jiri; Stojanović-Radić, Zorica; Stres, Blaz; Sun, Xuezhao; Swartz, Jeffery; Liang Tan, Zhi; Tapio, Ilma; Taxis, Tasia M.; Tomkins, Nigel; Ungerfeld, Emilio; Valizadeh, Reza; van Adrichem, Peter; Van Hamme, Jonathan; Van Hoven, Woulter; Waghorn, Garry; John Wallace, R.; Wang, Min; Waters, Sinéad M.; Keogh, Kate; Witzig, Maren; Wright, Andre-Denis G.; Yamano, Hidehisa; Yan, Tianhai; Yanez-Ruiz, David R.; Yeoman, Carl J.; Zambrano, Ricardo; Zeitz, Johanna; Zhou, Mi; Wei Zhou, Hua; Xia Zou, Cai; Zunino, Pablo; Janssen, Peter H.

2015-01-01

Ruminant livestock are important sources of human food and global greenhouse gas emissions. Feed degradation and methane formation by ruminants rely on metabolic interactions between rumen microbes and affect ruminant productivity. Rumen and camelid foregut microbial community composition was determined in 742 samples from 32 animal species and 35 countries, to estimate if this was influenced by diet, host species, or geography. Similar bacteria and archaea dominated in nearly all samples, while protozoal communities were more variable. The dominant bacteria are poorly characterised, but the methanogenic archaea are better known and highly conserved across the world. This universality and limited diversity could make it possible to mitigate methane emissions by developing strategies that target the few dominant methanogens. Differences in microbial community compositions were predominantly attributable to diet, with the host being less influential. There were few strong co-occurrence patterns between microbes, suggesting that major metabolic interactions are non-selective rather than specific. PMID:26449758

Monitoring of microbial communities in anaerobic digestion sludge for biogas optimisation.

PubMed

Lim, Jun Wei; Ge, Tianshu; Tong, Yen Wah

2018-01-01

This study characterised and compared the microbial communities of anaerobic digestion (AD) sludge using three different methods - (1) Clone library; (2) Pyrosequencing; and (3) Terminal restriction fragment length polymorphism (T-RFLP). Although high-throughput sequencing techniques are becoming increasingly popular and affordable, the reliance of such techniques for frequent monitoring of microbial communities may be a financial burden for some. Furthermore, the depth of microbial analysis revealed by high-throughput sequencing may not be required for monitoring purposes. This study aims to develop a rapid, reliable and economical approach for the monitoring of microbial communities in AD sludge. A combined approach where genetic information of sequences from clone library was used to assign phylogeny to T-RFs determined experimentally was developed in this study. In order to assess the effectiveness of the combined approach, microbial communities determined by the combined approach was compared to that characterised by pyrosequencing. Results showed that both pyrosequencing and clone library methods determined the dominant bacteria phyla to be Proteobacteria, Firmicutes, Bacteroidetes, and Thermotogae. Both methods also found that sludge A and B were predominantly dominated by acetogenic methanogens followed by hydrogenotrophic methanogens. The number of OTUs detected by T-RFLP was significantly lesser than that detected by the clone library. In this study, T-RFLP analysis identified majority of the dominant species of the archaeal consortia. However, many of the more highly diverse bacteria consortia were missed. Nevertheless, the combined approach developed in this study where clone sequences from the clone library were used to assign phylogeny to T-RFs determined experimentally managed to accurately predict the same dominant microbial groups for both sludge A and sludge B, as compared to the pyrosequencing results. Results showed that the combined approach of clone library and T-RFLP accurately predicted the dominant microbial groups and thus is a reliable and more economical way to monitor the evolution of microbial systems in AD sludge. Copyright © 2017 Elsevier Ltd. All rights reserved.

Dining local: the microbial diet of a snail that grazes microbial communities is geographically structured.

PubMed

O'Rorke, Richard; Cobian, Gerald M; Holland, Brenden S; Price, Melissa R; Costello, Vincent; Amend, Anthony S

2015-05-01

Achatinella mustelina is a critically endangered tree snail that subsists entirely by grazing microbes from leaf surfaces of native trees. Little is known about the fundamental aspects of these microbe assemblages: not taxonomic composition, how this varies with host plant or location, nor whether snails selectively consume microbes. To address these questions, we collected 102 snail faecal samples as a proxy for diet, and 102 matched-leaf samples from four locations. We used Illumina amplicon sequencing to determine bacterial and fungal community composition. Microbial community structure was significantly distinct between snail faeces and leaf samples, but the same microbes occurred in both. We conclude that snails are not 'picky' eaters at the microbial level, but graze the surface of whatever plant they are on. In a second experiment, the gut was dissected from non-endangered native tree snails in the same family as Achatinella to confirm that faecal samples reflect gut contents. Over 60% of fungal reads were shared between faeces, gut and leaf samples. Overall, location, sample type (faeces or leaf) and host plant identity all significantly explained the community composition and variation among samples. Understanding the microbial ecology of microbes grazed by tree snails enables effective management when conservation requires captive breeding or field relocation. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Effects of vegetation type on microbial biomass carbon and nitrogen in subalpine mountain forest soils.

PubMed

Ravindran, Anita; Yang, Shang-Shyng

2015-08-01

Microbial biomass plays an important role in nutrient transformation and conservation of forest and grassland ecosystems. The objective of this study was to determine the microbial biomass among three vegetation types in subalpine mountain forest soils of Taiwan. Tatachia is a typical high-altitude subalpine temperate forest ecosystem in Taiwan with an elevation of 1800-3952 m and consists of three vegetation types: spruce, hemlock, and grassland. Three plots were selected in each vegetation type. Soil samples were collected from the organic layer, topsoil, and subsoil. Microbial biomass carbon (Cmic) was determined by the chloroform fumigation-extraction method, and microbial biomass nitrogen (Nmic) was determined from the total nitrogen (Ntot) released during fumigation-extraction. Bacteria, actinomycetes, fungi, cellulolytic microbes, phosphate-solubilizing microbes, and nitrogen-fixing microbes were also counted. The Cmic and Nmic were highest in the surface soil and declined with the soil depth. These were also highest in spruce soils, followed by in hemlock soils, and were lowest in grassland soils. Cmic and Nmic had the highest values in the spring season and the lowest values in the winter season. Cmic and Nmic had significantly positive correlations with total organic carbon (Corg) and Ntot. Contributions of Cmic and Nmic, respectively, to Corg and Ntot indicated that the microbial biomass was immobilized more in spruce and hemlock soils than in grassland soils. Microbial populations of the tested vegetation types decreased with increasing soil depth. Cmic and Nmic were high in the organic layer and decreased with the depth of layers. These values were higher for spruce and hemlock soils than for grassland soils. Positive correlations were observed between Cmic and Nmic and between Corg and Ntot. Copyright © 2014. Published by Elsevier B.V.

Microbial P450 Enzymes in Bioremediation and Drug Discovery: Emerging Potentials and Challenges.

PubMed

Bhattacharya, Sukanta S; Yadav, Jagjit S

2018-01-01

Cytochrome P450 enzymes are a structurally conserved but functionally diverse group of heme-containing mixed function oxidases found across both prokaryotic and eukaryotic forms of the microbial world. Microbial P450s are known to perform diverse functions ranging from the synthesis of cell wall components to xenobiotic/drug metabolism to biodegradation of environmental chemicals. Conventionally, many microbial systems have been reported to mimic mammalian P450-like activation of drugs and were proposed as the in-vitro models of mammalian drug metabolism. Recent reports suggest that native or engineered forms of specific microbial P450s from these and other microbial systems could be employed for desired specific biotransformation reactions toward natural and synthetic (drug) compounds underscoring their emerging potential in drug improvement and discovery. On the other hand, microorganisms particularly fungi and actinomycetes have been shown to possess catabolic P450s with unusual potential to degrade toxic environmental chemicals including persistent organic pollutants (POPs). Wood-rotting basidiomycete fungi in particular have revealed the presence of exceptionally large P450 repertoire (P450ome) in their genomes, majority of which are however orphan (with no known function). Our pre- and post-genomic studies have led to functional characterization of several fungal P450s inducible in response to exposure to several environmental toxicants and demonstration of their potential in bioremediation of these chemicals. This review is an attempt to summarize the postgenomic unveiling of this versatile enzyme superfamily in microbial systems and investigation of their potential to synthesize new drugs and degrade persistent pollutants, among other biotechnological applications. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Electrochemical selective detection of dopamine on microbial carbohydrate-doped multiwall carbon nanotube-modified electrodes.

PubMed

Jin, Joon-Hyung; Cho, Eunae; Jung, Seunho

2010-03-01

Microbial carbohydrate-doped multiwall carbon nanotube (MWNT)-modified electrodes were prepared for the purpose of determining if 4-(2-aminoethyl)benzene-1,2-diol (3,4-dihydroxyphenylalanine; dopamine) exists in the presence of 0.5 mM ascorbic acid, a representative interfering agent in neurotransmitter detection. The microbial carbohydrate dopants were alpha-cyclosophorohexadecaose (alpha-C16) from Xanthomonas oryzae and cyclic-(1 --> 2)-beta-d-glucan (Cys) from Rhizobium meliloti. The cyclic voltammetric responses showed that the highest sensitivity (5.8 x 10(-3) mA cm(-2) microM(-1)) is attained with the Cys-doped MWNT-modified ultra-trace carbon electrode, and that the alpha-C16-doped MWNT-modified glassy carbon electrode displays the best selectivity to dopamine (the approximate peak potential separation is 310 mV).

Transmutation of Personal Glucose Meters into Portable and Highly Sensitive Microbial Pathogen Detection Platform.

PubMed

Wang, Zhenzhen; Chen, Zhaowei; Gao, Nan; Ren, Jinsong; Qu, Xiaogang

2015-10-07

Herein, for the first time, we presented a simple and general approach by using personal glucose meters (PGM) for portable and ultrasensitive detection of microbial pathogens. Upon addition of pathogenic bacteria, glucoamylase-quaternized magnetic nanoparticles (GA-QMNPS) conjugates were disrupted by the competitive multivalent interactions between bacteria and QMNPS, resulting in the release of GA. After magnetic separation, the free GA could catalyze the hydrolysis of amylose into glucose for quantitative readout by PGM. In such way, PGM was transmuted into a bacterial detection device and extremely low detection limits down to 20 cells mL(-1) was achieved. More importantly, QMNPS could inhibit the growth of the bacteria and destroy its cellular structure, which enabled bacteria detection and inhibition simultaneously. The simplicity, portability, sensitivity and low cost of presented work make it attractive for clinical applications. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Association of TLR1, TLR2, TLR4, TLR6, and TIRAP polymorphisms with disease susceptibility.

PubMed

Noreen, Mamoona; Arshad, Muhammad

2015-06-01

Toll like receptors (TLRs) play a crucial role in regulation of innate as well as adaptive immunity. TLRs recognize a distinct but limited repertoire of conserved microbial products. Ligand binding to TLRs activates the signaling cascade and results in activation of multiple inflammatory genes. Variation in this immune response is under genetic control. Polymorphisms in genes associated with inflammatory pathway especially influence the outcome of diseases. TLR2 makes heterodimer with TLR1 or TLR6 and recognizes a wide variety of microbial ligands. In this review, we summarize studies of polymorphisms in genes encoding TLR1, TLR2, TLR4, TLR6, and most polymorphic adaptor protein, Mal/TIRAP, revealing their effect on susceptibility to diseases.

Metaproteomics Reveals Functional Shifts in Microbial and Human Proteins During Infant Gut Colonization Case

DOE PAGES

Young, Jacque C.; Pan, Chongle; Adams, Rachel M.; ...

2015-01-01

The microbial colonization of the human gastrointestinal tract plays an important role in establishing health and homeostasis. However, the time-dependent functional signatures of microbial and human proteins during early colonization of the gut have yet to be determined. Thus, we employed shotgun proteomics to simultaneously monitor microbial and human proteins in fecal samples from a preterm infant during the first month of life. Microbial community complexity and functions increased over time, with compositional changes that were consistent with previous metagenomic and rRNA gene data indicating three distinct colonization phases. Overall microbial community functions were established relatively early in development andmore » remained stable. Human proteins detected included those responsible for epithelial barrier function and antimicrobial activity. Some neutrophil-derived proteins increased in abundance early in the study period, suggesting activation of the innate immune system. Moreover, abundances of cytoskeletal and mucin proteins increased later in the time course, suggestive of subsequent adjustment to the increased microbial load. Our study provides the first snapshot of coordinated human and microbial protein expression in the infant gut during early development.« less

Lava Cave Microbial Communities Within Mats and Secondary Mineral Deposits: Implications for Life Detection on Other Planets

PubMed Central

Melim, L.A.; Spilde, M.N.; Hathaway, J.J.M.; Garcia, M.G.; Moya, M.; Stone, F.D.; Boston, P.J.; Dapkevicius, M.L.N.E.; Riquelme, C.

2011-01-01

Abstract Lava caves contain a wealth of yellow, white, pink, tan, and gold-colored microbial mats; but in addition to these clearly biological mats, there are many secondary mineral deposits that are nonbiological in appearance. Secondary mineral deposits examined include an amorphous copper-silicate deposit (Hawai‘i) that is blue-green in color and contains reticulated and fuzzy filament morphologies. In the Azores, lava tubes contain iron-oxide formations, a soft ooze-like coating, and pink hexagons on basaltic glass, while gold-colored deposits are found in lava caves in New Mexico and Hawai‘i. A combination of scanning electron microscopy (SEM) and molecular techniques was used to analyze these communities. Molecular analyses of the microbial mats and secondary mineral deposits revealed a community that contains 14 phyla of bacteria across three locations: the Azores, New Mexico, and Hawai‘i. Similarities exist between bacterial phyla found in microbial mats and secondary minerals, but marked differences also occur, such as the lack of Actinobacteria in two-thirds of the secondary mineral deposits. The discovery that such deposits contain abundant life can help guide our detection of life on extraterrestrial bodies. Key Words: Biosignatures—Astrobiology—Bacteria—Caves—Life detection—Microbial mats. Astrobiology 11, 601–618. PMID:21879833

Insights into microbial involvement in desert varnish formation retrieved from metagenomic analysis.

PubMed

Lang-Yona, Naama; Maier, Stefanie; Macholdt, Dorothea S; Müller-Germann, Isabell; Yordanova, Petya; Rodriguez-Caballero, Emilio; Jochum, Klaus P; Al-Amri, Abdullah; Andreae, Meinrat O; Fröhlich-Nowoisky, Janine; Weber, Bettina

2018-02-28

Desert varnishes are dark rock coatings observed in arid environments and might resemble Mn-rich coatings found on Martian rocks. Their formation mechanism is not fully understood and the possible microbial involvement is under debate. In this study, we applied DNA metagenomic Shotgun sequencing of varnish and surrounding soil to evaluate the composition of the microbial community and its potential metabolic function. We found that the α diversity was lower in varnish compared to soil samples (p value < 0.05), suggesting distinct populations with significantly higher abundance of Actinobacteria, Proteobacteria and Cyanobacteria within the varnish. Additionally, we observed increased levels of transition metal metabolic processes in varnish compared to soil samples. Nevertheless, potentially relevant enzymes for varnish formation were detected at low to insignificant levels in both niches, indicating no current direct microbial involvement in Mn oxidation. This finding is supported by quantitative genomic analysis, elemental analysis, fluorescence imaging and scanning transmission X-ray microscopy. We thus conclude that the distinct microbial communities detected in desert varnish originate from settled Aeolian microbes, which colonized this nutrient-enriched niche, and discuss possible indirect contributions of microorganisms to the formation of desert varnish. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

Diversity of the Sediment Microbial Community in the Aha Watershed (Southwest China) in Response to Acid Mine Drainage Pollution Gradients

PubMed Central

Sun, Weimin; Sun, Min; Dong, Yiran; Ning, Zengping; Xiao, Enzong; Tang, Song; Li, Jiwei

2015-01-01

Located in southwest China, the Aha watershed is continually contaminated by acid mine drainage (AMD) produced from upstream abandoned coal mines. The watershed is fed by creeks with elevated concentrations of aqueous Fe (total Fe > 1 g/liter) and SO42− (>6 g/liter). AMD contamination gradually decreases throughout downstream rivers and reservoirs, creating an AMD pollution gradient which has led to a suite of biogeochemical processes along the watershed. In this study, sediment samples were collected along the AMD pollution sites for geochemical and microbial community analyses. High-throughput sequencing found various bacteria associated with microbial Fe and S cycling within the watershed and AMD-impacted creek. A large proportion of Fe- and S-metabolizing bacteria were detected in this watershed. The dominant Fe- and S-metabolizing bacteria were identified as microorganisms belonging to the genera Metallibacterium, Aciditerrimonas, Halomonas, Shewanella, Ferrovum, Alicyclobacillus, and Syntrophobacter. Among them, Halomonas, Aciditerrimonas, Metallibacterium, and Shewanella have previously only rarely been detected in AMD-contaminated environments. In addition, the microbial community structures changed along the watershed with different magnitudes of AMD pollution. Moreover, the canonical correspondence analysis suggested that temperature, pH, total Fe, sulfate, and redox potentials (Eh) were significant factors that structured the microbial community compositions along the Aha watershed. PMID:25979900

Spatial and Temporal Variation in Enterococcal Abundance and Its Relationship to the Microbial Community in Hawaii Beach Sand and Water

PubMed Central

Cui, Henglin; Yang, Kun; Pagaling, Eulyn

2013-01-01

Recent studies have reported high levels of fecal indicator enterococci in marine beach sand. This study aimed to determine the spatial and temporal variation of enterococcal abundance and to evaluate its relationships with microbial community parameters in Hawaii beach sand and water. Sampling at 23 beaches on the Island of Oahu detected higher levels of enterococci in beach foreshore sand than in beach water on a mass unit basis. Subsequent 8-week consecutive samplings at two selected beaches (Waialae and Kualoa) consistently detected significantly higher levels of enterococci in backshore sand than in foreshore/nearshore sand and beach water. Comparison between the abundance of enterococci and the microbial communities showed that enterococci correlated significantly with total Vibrio in all beach zones but less significantly with total bacterial density and Escherichia coli. Samples from the different zones of Waialae beach were sequenced by 16S rRNA gene pyrosequencing to determine the microbial community structure and diversity. The backshore sand had a significantly more diverse community and contained different major bacterial populations than the other beach zones, which corresponded to the spatial distribution pattern of enterococcal abundance. Taken together, multiple lines of evidence support the possibility of enterococci as autochthonous members of the microbial community in Hawaii beach sand. PMID:23563940

HMMerThread: detecting remote, functional conserved domains in entire genomes by combining relaxed sequence-database searches with fold recognition.

PubMed

Bradshaw, Charles Richard; Surendranath, Vineeth; Henschel, Robert; Mueller, Matthias Stefan; Habermann, Bianca Hermine

2011-03-10

Conserved domains in proteins are one of the major sources of functional information for experimental design and genome-level annotation. Though search tools for conserved domain databases such as Hidden Markov Models (HMMs) are sensitive in detecting conserved domains in proteins when they share sufficient sequence similarity, they tend to miss more divergent family members, as they lack a reliable statistical framework for the detection of low sequence similarity. We have developed a greatly improved HMMerThread algorithm that can detect remotely conserved domains in highly divergent sequences. HMMerThread combines relaxed conserved domain searches with fold recognition to eliminate false positive, sequence-based identifications. With an accuracy of 90%, our software is able to automatically predict highly divergent members of conserved domain families with an associated 3-dimensional structure. We give additional confidence to our predictions by validation across species. We have run HMMerThread searches on eight proteomes including human and present a rich resource of remotely conserved domains, which adds significantly to the functional annotation of entire proteomes. We find ∼4500 cross-species validated, remotely conserved domain predictions in the human proteome alone. As an example, we find a DNA-binding domain in the C-terminal part of the A-kinase anchor protein 10 (AKAP10), a PKA adaptor that has been implicated in cardiac arrhythmias and premature cardiac death, which upon stress likely translocates from mitochondria to the nucleus/nucleolus. Based on our prediction, we propose that with this HLH-domain, AKAP10 is involved in the transcriptional control of stress response. Further remotely conserved domains we discuss are examples from areas such as sporulation, chromosome segregation and signalling during immune response. The HMMerThread algorithm is able to automatically detect the presence of remotely conserved domains in proteins based on weak sequence similarity. Our predictions open up new avenues for biological and medical studies. Genome-wide HMMerThread domains are available at http://vm1-hmmerthread.age.mpg.de.

HMMerThread: Detecting Remote, Functional Conserved Domains in Entire Genomes by Combining Relaxed Sequence-Database Searches with Fold Recognition

PubMed Central

Bradshaw, Charles Richard; Surendranath, Vineeth; Henschel, Robert; Mueller, Matthias Stefan; Habermann, Bianca Hermine

2011-01-01

Conserved domains in proteins are one of the major sources of functional information for experimental design and genome-level annotation. Though search tools for conserved domain databases such as Hidden Markov Models (HMMs) are sensitive in detecting conserved domains in proteins when they share sufficient sequence similarity, they tend to miss more divergent family members, as they lack a reliable statistical framework for the detection of low sequence similarity. We have developed a greatly improved HMMerThread algorithm that can detect remotely conserved domains in highly divergent sequences. HMMerThread combines relaxed conserved domain searches with fold recognition to eliminate false positive, sequence-based identifications. With an accuracy of 90%, our software is able to automatically predict highly divergent members of conserved domain families with an associated 3-dimensional structure. We give additional confidence to our predictions by validation across species. We have run HMMerThread searches on eight proteomes including human and present a rich resource of remotely conserved domains, which adds significantly to the functional annotation of entire proteomes. We find ∼4500 cross-species validated, remotely conserved domain predictions in the human proteome alone. As an example, we find a DNA-binding domain in the C-terminal part of the A-kinase anchor protein 10 (AKAP10), a PKA adaptor that has been implicated in cardiac arrhythmias and premature cardiac death, which upon stress likely translocates from mitochondria to the nucleus/nucleolus. Based on our prediction, we propose that with this HLH-domain, AKAP10 is involved in the transcriptional control of stress response. Further remotely conserved domains we discuss are examples from areas such as sporulation, chromosome segregation and signalling during immune response. The HMMerThread algorithm is able to automatically detect the presence of remotely conserved domains in proteins based on weak sequence similarity. Our predictions open up new avenues for biological and medical studies. Genome-wide HMMerThread domains are available at http://vm1-hmmerthread.age.mpg.de. PMID:21423752

Microbial Source Tracking Markers for Detection of Fecal Contamination in Environmental Waters: Relationships Between Pathogens and Human Health Outcomes

EPA Science Inventory

Microbial source tracking (MST) describes a suite of methods and an investigative strategy designed to identify the dominant sources of fecal pollution in environmental waters. The methods rely on the close association of certain fecal microorganisms with a particular host speci...

Isolation of cultivation-resistant oomycetes, first detected as amplicon sequences, from roots of herbicide-terminated winter rye

USDA-ARS?s Scientific Manuscript database

The dynamics of microbial communities associated with dying cover crops are of interest because of potential impacts on disease in a subsequent crop, and because of the importance of microbial activity on plant residue to soil organic matter dynamics and nutrient cycling. High throughput amplicon se...

Impedance Spectroscopy as a Tool for Non-Intrusive Detection of Extracellular Mediators in Microbial Fuel Cells

DTIC Science & Technology

2009-12-01

bioseparation. Hoboken, NJ: John Wiley & Sons, p. 267. HernandezME, Kappler A, Newman DK. 2004. Phenazines and other redox active antibiotics promote...Verstraete W. 2005. Microbial phenazine production enhances electron transfer in biofuel cells. Environ Sci Technol 39:3401. Ramasamy RP, Ren Z, Mench MM

Development of a new pentaplex real-time PCR assay for the identification of poly-microbial specimens containing Staphylococcus aureus and other staphylococci, with simultaneous detection of staphylococcal virulence and methicillin resistance markers.

PubMed

Okolie, Charles E; Wooldridge, Karl G; Turner, David P; Cockayne, Alan; James, Richard

2015-06-01

Staphylococcus aureus strains harbouring genes encoding virulence and antibiotic resistance are of public health importance. In clinical samples, pathogenic S. aureus is often mixed with putatively less pathogenic coagulase-negative staphylococci (CoNS), both of which can harbour mecA, the gene encoding staphylococcal methicillin-resistance. There have been previous attempts at distinguishing MRSA from MRCoNS, most of which were based on the detection of one of the pathognomonic markers of S. aureus, such as coa, nuc or spa. That approach might suffice for discrete colonies and mono-microbial samples; it is inadequate for identification of clinical specimens containing mixtures of S. aureus and CoNS. In the present study, a real-time pentaplex PCR assay has been developed which simultaneously detects markers for bacteria (16S rRNA), coagulase-negative staphylococcus (cns), S. aureus (spa), Panton-Valentine leukocidin (pvl) and methicillin resistance (mecA). Staphylococcal and non-staphylococcal bacterial strains (n = 283) were used to validate the new assay. The applicability of this test to clinical samples was evaluated using spiked blood cultures (n = 43) containing S. aureus and CoNS in mono-microbial and poly-microbial models, which showed that the 5 markers were all detected as expected. Cycling completes within 1 h, delivering 100% specificity, NPV and PPV with a detection limit of 1.0 × 10(1) to 3.0 × 10(1) colony forming units (CFU)/ml, suggesting direct applicability in routine diagnostic microbiology. This is the most multiplexed real-time PCR-based PVL-MRSA assay and the first detection of a unique marker for CoNS without recourse to the conventional elimination approach. There was no evidence that this new assay produced invalid/indeterminate test results. Copyright © 2015 Elsevier Ltd. All rights reserved.

Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity

DOE PAGES

Shade, Ashley; Jones, Stuart E.; Caporaso, J. Gregory; ...

2014-07-15

Microbial communities typically contain many rare taxa that make up the majority of the observed membership, yet the contribution of this microbial “rare biosphere” to community dynamics is unclear. Using 16S rRNA amplicon sequencing of 3,237 samples from 42 time series of microbial communities from nine different ecosystems (air; marine; lake; stream; adult human skin, tongue, and gut; infant gut; and brewery wastewater treatment), we introduce a new method to detect typically rare microbial taxa that occasionally become very abundant (conditionally rare taxa [CRT]) and then quantify their contributions to temporal shifts in community structure. We discovered that CRT mademore » up 1.5 to 28% of the community membership, represented a broad diversity of bacterial and archaeal lineages, and explained large amounts of temporal community dissimilarity (i.e., up to 97% of Bray-Curtis dissimilarity). Most of the CRT were detected at multiple time points, though we also identified “one-hit wonder” CRT that were observed at only one time point. Using a case study from a temperate lake, we gained additional insights into the ecology of CRT by comparing routine community time series to large disturbance events. Our results reveal that many rare taxa contribute a greater amount to microbial community dynamics than is apparent from their low proportional abundances. In conclusion, this observation was true across a wide range of ecosystems, indicating that these rare taxa are essential for understanding community changes over time.« less

Microflora of root filled teeth with apical periodontitis in Latvian patients.

PubMed

Mindere, Anda; Kundzina, Rita; Nikolajeva, Vizma; Eze, Daina; Petrina, Zaiga

2010-01-01

The aim of the present study was to investigate the microbial flora of root filled teeth with apical periodontitis and to determine the prevalence of β-lactamase producing strains in isolated bacteria in Latvian patients. 33 root filled teeth with asymptomatic persisting periapical lesions were selected for the present study. During nonsurgical endodontic retreatment, the root filling material was removed and canals were sampled. Determination of microbial species was based on series of biochemical tests using identification kits. All strains of bacteria were tested for β-lactamase production by using chromogenic nitrocefin-impregnated slides. Bacteria were found in 32 (97%) of initial specimens from the teeth. The number of isolated microbial strains in the specimens ranged from one to six (mean 2.7). 79% of the isolated microbial species were Gram-positive bacteria. The most common isolates were Streptococcus (27%), Actinomyces (27%), Staphylococcus (18%), Enterococcus (18%) and Lactobacillus (18%) spp. Yeasts were found as four isolates in 3 cases (9%). β-lactamase-producing bacterial strains were detected in 12 specimens, 36% of the patients. The most common enzyme-producing bacteria belonged to Actinomyces and Staphylococcus spp. The microbial flora in previously treated root canals with apical periodontitis is limited to a small number of predominantly Gram-positive microbial species. The most common isolates are Streptococcus, Actinomyces, Staphylococcus, Enterococcus and Lactobacillus spp. A moderately high prevalence of β-lactamase producing bacterial strains was detected in patients with root filled teeth with apical periodontitis.

[Effects of Perfluoroalkyl Substances on the Microbial Community Structure in Surface Sediments of Typical River, China].

PubMed

Sun, Ya-jun; Wang, Tie-yu; Peng, Xia-wei; Wang, Pei

2015-07-01

In order to reveal the relationship between Perfluoroalkyl substances (PFASs) contamination and the bacterial community composition, surface sediment samples were collected along the Xiaoqing River in Shandong Province in April and July 2014 (XQ1-XQ10), where many PFASs manufacturers were located. PFASs were quantified by HPLC/MS-MS, related environmental factors affecting the microbial community structure were measured, and the microbial community structure in surface sediments was measured by the second-generation sequencing technology Illumina MiSeq. The results not only revealed the degree of PFASs pollution in the sediments of Xiaoqing River, but also illustrated the relationship between PFASs pollution and the microbial community structure. Among the twelve kinds of PFASs detected in this study, PFOA was the predominant compound, and the highest PFOA concentrations were detected in the sample of XQ5 (April: 456. 2 ng. g-1; July: 748.7 ng . g-1) located at the downstream of Xiaoqing River with many fluoropolymer producing facilities. PFOA contamination was the main factor affecting the microbial community structure in April, accordingly community richness and evenness were significantly negatively correlated with PFOA levels. The abundance of Thiobacillus increased with the increasing PFOA concentration in the sediment PFOA. This suggested that Thiobacillus was sensitive to PFOA pollution and might be the potential indicator to reveal the degree of PFOA pollution in sediment. When the concentrations of PFOA were below 100 ng . g-1, no significant effects on the microbial community structure were observed.

The Chthonomonas calidirosea Genome Is Highly Conserved across Geographic Locations and Distinct Chemical and Microbial Environments in New Zealand's Taupō Volcanic Zone.

PubMed

Lee, Kevin C; Stott, Matthew B; Dunfield, Peter F; Huttenhower, Curtis; McDonald, Ian R; Morgan, Xochitl C

2016-06-15

Chthonomonas calidirosea T49(T) is a low-abundance, carbohydrate-scavenging, and thermophilic soil bacterium with a seemingly disorganized genome. We hypothesized that the C. calidirosea genome would be highly responsive to local selection pressure, resulting in the divergence of its genomic content, genome organization, and carbohydrate utilization phenotype across environments. We tested this hypothesis by sequencing the genomes of four C. calidirosea isolates obtained from four separate geothermal fields in the Taupō Volcanic Zone, New Zealand. For each isolation site, we measured physicochemical attributes and defined the associated microbial community by 16S rRNA gene sequencing. Despite their ecological and geographical isolation, the genome sequences showed low divergence (maximum, 1.17%). Isolate-specific variations included single-nucleotide polymorphisms (SNPs), restriction-modification systems, and mobile elements but few major deletions and no major rearrangements. The 50-fold variation in C. calidirosea relative abundance among the four sites correlated with site environmental characteristics but not with differences in genomic content. Conversely, the carbohydrate utilization profiles of the C. calidirosea isolates corresponded to the inferred isolate phylogenies, which only partially paralleled the geographical relationships among the sample sites. Genomic sequence conservation does not entirely parallel geographic distance, suggesting that stochastic dispersal and localized extinction, which allow for rapid population homogenization with little restriction by geographical barriers, are possible mechanisms of C. calidirosea distribution. This dispersal and extinction mechanism is likely not limited to C. calidirosea but may shape the populations and genomes of many other low-abundance free-living taxa. This study compares the genomic sequence variations and metabolisms of four strains of Chthonomonas calidirosea, a rare thermophilic bacterium from the phylum Armatimonadetes It additionally compares the microbial communities and chemistry of each of the geographically distinct sites from which the four C. calidirosea strains were isolated. C. calidirosea was previously reported to possess a highly disorganized genome, but it was unclear whether this reflected rapid evolution. Here, we show that each isolation site has a distinct chemistry and microbial community, but despite this, the C. calidirosea genome is highly conserved across all isolation sites. Furthermore, genomic sequence differences only partially paralleled geographic distance, suggesting that C. calidirosea genotypes are not primarily determined by adaptive evolution. Instead, the presence of C. calidirosea may be driven by stochastic dispersal and localized extinction. This ecological mechanism may apply to many other low-abundance taxa. Copyright © 2016 Lee et al.

The Chthonomonas calidirosea Genome Is Highly Conserved across Geographic Locations and Distinct Chemical and Microbial Environments in New Zealand's Taupō Volcanic Zone

PubMed Central

Lee, Kevin C.; Stott, Matthew B.; Dunfield, Peter F.; Huttenhower, Curtis; McDonald, Ian R.

2016-01-01

ABSTRACT Chthonomonas calidirosea T49T is a low-abundance, carbohydrate-scavenging, and thermophilic soil bacterium with a seemingly disorganized genome. We hypothesized that the C. calidirosea genome would be highly responsive to local selection pressure, resulting in the divergence of its genomic content, genome organization, and carbohydrate utilization phenotype across environments. We tested this hypothesis by sequencing the genomes of four C. calidirosea isolates obtained from four separate geothermal fields in the Taupō Volcanic Zone, New Zealand. For each isolation site, we measured physicochemical attributes and defined the associated microbial community by 16S rRNA gene sequencing. Despite their ecological and geographical isolation, the genome sequences showed low divergence (maximum, 1.17%). Isolate-specific variations included single-nucleotide polymorphisms (SNPs), restriction-modification systems, and mobile elements but few major deletions and no major rearrangements. The 50-fold variation in C. calidirosea relative abundance among the four sites correlated with site environmental characteristics but not with differences in genomic content. Conversely, the carbohydrate utilization profiles of the C. calidirosea isolates corresponded to the inferred isolate phylogenies, which only partially paralleled the geographical relationships among the sample sites. Genomic sequence conservation does not entirely parallel geographic distance, suggesting that stochastic dispersal and localized extinction, which allow for rapid population homogenization with little restriction by geographical barriers, are possible mechanisms of C. calidirosea distribution. This dispersal and extinction mechanism is likely not limited to C. calidirosea but may shape the populations and genomes of many other low-abundance free-living taxa. IMPORTANCE This study compares the genomic sequence variations and metabolisms of four strains of Chthonomonas calidirosea, a rare thermophilic bacterium from the phylum Armatimonadetes. It additionally compares the microbial communities and chemistry of each of the geographically distinct sites from which the four C. calidirosea strains were isolated. C. calidirosea was previously reported to possess a highly disorganized genome, but it was unclear whether this reflected rapid evolution. Here, we show that each isolation site has a distinct chemistry and microbial community, but despite this, the C. calidirosea genome is highly conserved across all isolation sites. Furthermore, genomic sequence differences only partially paralleled geographic distance, suggesting that C. calidirosea genotypes are not primarily determined by adaptive evolution. Instead, the presence of C. calidirosea may be driven by stochastic dispersal and localized extinction. This ecological mechanism may apply to many other low-abundance taxa. PMID:27060125

Cost-effective scat-detection dogs: unleashing a powerful new tool for international mammalian conservation biology.

PubMed

Orkin, Joseph D; Yang, Yuming; Yang, Chunyan; Yu, Douglas W; Jiang, Xuelong

2016-10-10

Recently, detection dogs have been utilized to collect fecal samples from cryptic and rare mammals. Despite the great promise of this technique for conservation biology, its broader application has been limited by the high cost (tens to hundreds of thousands of dollars) and logistical challenges of employing a scat-detection dog team while conducting international, collaborative research. Through an international collaboration of primatologists and the Chinese Ministry of Public Security, we trained and used a detection dog to find scat from three species of unhabituated, free-ranging primates, for less than $3,000. We collected 137 non-human primate fecal samples that we confirmed by sequencing taxonomically informative genetic markers. Our detection dog team had a 92% accuracy rate, significantly outperforming our human-only team. Our results demonstrate that detection dogs can locate fecal samples from unhabituated primates with variable diets, locomotion, and grouping patterns, despite challenging field conditions. We provide a model for in-country training, while also building local capacity for conservation and genetic monitoring. Unlike previous efforts, our approach will allow for the wide adoption of scat-detection dogs in international conservation biology.

Cost-effective scat-detection dogs: unleashing a powerful new tool for international mammalian conservation biology

PubMed Central

Orkin, Joseph D.; Yang, Yuming; Yang, Chunyan; Yu, Douglas W.; Jiang, Xuelong

2016-01-01

Recently, detection dogs have been utilized to collect fecal samples from cryptic and rare mammals. Despite the great promise of this technique for conservation biology, its broader application has been limited by the high cost (tens to hundreds of thousands of dollars) and logistical challenges of employing a scat-detection dog team while conducting international, collaborative research. Through an international collaboration of primatologists and the Chinese Ministry of Public Security, we trained and used a detection dog to find scat from three species of unhabituated, free-ranging primates, for less than $3,000. We collected 137 non-human primate fecal samples that we confirmed by sequencing taxonomically informative genetic markers. Our detection dog team had a 92% accuracy rate, significantly outperforming our human-only team. Our results demonstrate that detection dogs can locate fecal samples from unhabituated primates with variable diets, locomotion, and grouping patterns, despite challenging field conditions. We provide a model for in-country training, while also building local capacity for conservation and genetic monitoring. Unlike previous efforts, our approach will allow for the wide adoption of scat-detection dogs in international conservation biology. PMID:27721442

Simultaneous UPLC-MS/MS analysis of native catechins and procyanidins and their microbial metabolites in intestinal contents and tissues of male Wistar Furth inbred rats.

PubMed

Goodrich, Katheryn M; Neilson, Andrew P

2014-05-01

Procyanidins have been extensively investigated for their potential health protective activities. However, the potential bioactivities of procyanidins are limited by their poor bioavailability. The majority of the ingested dose remains unabsorbed and reaches the colon where extensive microbial metabolism occurs. Most existing analytical methods measure either native compounds (catechins and procyanidins), or their microbial metabolites. The objectives of this study were to develop a high-throughput extraction and UPLC-MS/MS method for simultaneous measurement of both native procyanidins and their metabolites, facilitating high-throughput analysis of native and metabolite profiles in various regions of the colon. The present UPLC-MS/MS method facilitates simultaneous resolution and detection of authentic standards of 14 native catechin monomers and procyanidins, as well as 24 microbial metabolites. Detection and resolution of an additional 3 procyanidin dimers and 10 metabolites for which standards were not available was achieved. Elution and adequate resolution of both native compounds and metabolites were achieved within 10min. The intraday repeatability for native compounds was between 1.1 and 16.5%, and the interday repeatability for native compounds was between 2.2 and 25%. Intraday and interday repeatability for metabolites was between 0.6 and 24.1% and 1 and 23.9%, respectively. Observed lower limits of quantification for native compounds were ∼9-350fmol on-column, and for the microbial metabolites were ∼0.8-12,000fmol on-column. Observed lower limits of detection for native compounds were ∼4.5-190fmol on-column, and for metabolites were 0.304-6020fmol on-column. For native monomers and procyanidins, extraction recoveries ranged from 38 to 102%. Extraction recoveries for the 9 microbial metabolites tested ranged from 41 to 95%. Data from tissue analysis of rats gavaged with grape seed extract indicate fairly high accumulation of native compounds, primarily monomers and dimers, in the cecum and colon. Metabolite data indicate the progressive nature of microbial metabolism as the digesta moves through the lower GI tract. This method facilitates the high-throughput, sensitive, and simultaneous analysis of both native compounds and their microbial metabolites in biological samples and provides a more efficient means of extraction and analysis than previous methods. Copyright © 2014 Elsevier B.V. All rights reserved.

Modern Microbial Ecosystems are a Key to Understanding Our Biosphere's Early Evolution and its Contributions To The Atmosphere and Rock Record

NASA Technical Reports Server (NTRS)

DesMarais, David J.; DeVincenzi, Donald L. (Technical Monitor)

2000-01-01

The survival of our early biosphere depended upon efficient coordination anion- diverse microbial populations. Microbial mats exhibit a 3.46-billion-year fossil record, thus they are the oldest known ecosystems. Photosynthetic microbial mats were key because, today, sunlight powers more than 99 percent of global primary productivity. Thus photosynthetic ecosystems have affected the atmosphere profoundly and have created the most pervasive, easily-detected fossils. Photosynthetic biospheres elsewhere will be most detectible via telescopes or spacecraft. As a part of the Astrobiology Institute, our Ames Microbial Ecosystems group examines the roles played by ecological processes in the early evolution of our biosphere, as recorded in geologic fossils and in the macromolecules of living cells: (1) We are defining the microbial mat microenvironment, which was an important milieu for early evolution. (2) We are comparing mats in contrasting environments to discern strategies of adaptation and diversification, traits that were key for long-term survival. (3) We have selected sites that mimic key environmental attributes of early Earth and thereby focus upon evolutionary adaptations to long-term changes in the global environment. (4) Our studies of gas exchange contribute to better estimates of biogenic gases in Earth's early atmosphere. This group therefore directly addresses the question: How have the Earth and its biosphere influenced each other over time Our studies strengthen the systematics for interpreting the microbial fossil record and thereby enhance astrobiological studies of martian samples. Our models of biogenic gas emissions will enhance models of atmospheres that might be detected on inhabited extrasolar planets. This work therefore also addresses the question: How can other biospheres be recogniZed" Our choice of field sites helps us explore Earth's evolving early environment. For example, modern mats that occupy thermal springs and certain freshwater environments experience conditions such as low O2 and sulfate and high inorganic carbon and sulfide levels that resemble those of ancient marine environments. Later in history, both biologically-induced carbonate precipitation and the trapping and binding of suspended grains of carbonate became a dominant mechanism for carbonate deposition. Modern marine carbonate platforms and alkaline offer good examples of microbiologically-induced calcification. Both marine platforms and solar salterns illustrate microbially-driven trapping and binding. We are also exploring the effects of water composition upon the exchange of biogenic gases with the atmosphere.

The CRISPR Spacer Space Is Dominated by Sequences from Species-Specific Mobilomes

PubMed Central

Shmakov, Sergey A.; Sitnik, Vassilii; Makarova, Kira S.; Wolf, Yuri I.; Severinov, Konstantin V.

2017-01-01

ABSTRACT Clustered regularly interspaced short palindromic repeats and CRISPR-associated protein (CRISPR-Cas) systems store the memory of past encounters with foreign DNA in unique spacers that are inserted between direct repeats in CRISPR arrays. For only a small fraction of the spacers, homologous sequences, called protospacers, are detectable in viral, plasmid, and microbial genomes. The rest of the spacers remain the CRISPR “dark matter.” We performed a comprehensive analysis of the spacers from all CRISPR-cas loci identified in bacterial and archaeal genomes, and we found that, depending on the CRISPR-Cas subtype and the prokaryotic phylum, protospacers were detectable for 1% to about 19% of the spacers (~7% global average). Among the detected protospacers, the majority, typically 80 to 90%, originated from viral genomes, including proviruses, and among the rest, the most common source was genes that are integrated into microbial chromosomes but are involved in plasmid conjugation or replication. Thus, almost all spacers with identifiable protospacers target mobile genetic elements (MGE). The GC content, as well as dinucleotide and tetranucleotide compositions, of microbial genomes, their spacer complements, and the cognate viral genomes showed a nearly perfect correlation and were almost identical. Given the near absence of self-targeting spacers, these findings are most compatible with the possibility that the spacers, including the dark matter, are derived almost completely from the species-specific microbial mobilomes. PMID:28928211

Microbial community structure associated with the high loading anaerobic codigestion of olive mill and abattoir wastewaters.

PubMed

Gannoun, Hana; Omri, Ilhem; Chouari, Rakia; Khelifi, Eltaief; Keskes, Sajiaa; Godon, Jean-Jacques; Hamdi, Moktar; Sghir, Abdelghani; Bouallagui, Hassib

2016-02-01

The effect of increasing the organic loading rates (OLRs) on the performance of the anaerobic codigestion of olive mill (OMW) and abattoir wastewaters (AW) was investigated under mesophilic and thermophilic conditions. The structure of the microbial community was also monitored. Increasing OLR to 9g of chemical oxygen demand (COD) L(-1)d(-1) affected significantly the biogas yield and microbial diversity at 35°C. However, at 55°C digester remained stable until OLR of 12g of CODL(-1)d(-1) with higher COD removal (80%) and biogas yield (0.52Lg(-1) COD removed). Significant differences in the bacterial communities were detected between mesophilic and thermophilic conditions. The dominant phyla detected in the digester at both phases were the Firmicutes, Actinobacteria, Bacteroidetes, Synergistetes and Spirochaete. However, Verrucomicrobia, Proteobacteria and the candidate division BRC1 were only detected at thermophilic conditions. The Methanobacteriales and the Thermoplasmales were found as a high predominant archaeal member in the anaerobic sludge. Copyright © 2015 Elsevier Ltd. All rights reserved.

Ancient pathogen DNA in archaeological samples detected with a Microbial Detection Array.

PubMed

Devault, Alison M; McLoughlin, Kevin; Jaing, Crystal; Gardner, Shea; Porter, Teresita M; Enk, Jacob M; Thissen, James; Allen, Jonathan; Borucki, Monica; DeWitte, Sharon N; Dhody, Anna N; Poinar, Hendrik N

2014-03-06

Ancient human remains of paleopathological interest typically contain highly degraded DNA in which pathogenic taxa are often minority components, making sequence-based metagenomic characterization costly. Microarrays may hold a potential solution to these challenges, offering a rapid, affordable, and highly informative snapshot of microbial diversity in complex samples without the lengthy analysis and/or high cost associated with high-throughput sequencing. Their versatility is well established for modern clinical specimens, but they have yet to be applied to ancient remains. Here we report bacterial profiles of archaeological and historical human remains using the Lawrence Livermore Microbial Detection Array (LLMDA). The array successfully identified previously-verified bacterial human pathogens, including Vibrio cholerae (cholera) in a 19th century intestinal specimen and Yersinia pestis ("Black Death" plague) in a medieval tooth, which represented only minute fractions (0.03% and 0.08% alignable high-throughput shotgun sequencing reads) of their respective DNA content. This demonstrates that the LLMDA can identify primary and/or co-infecting bacterial pathogens in ancient samples, thereby serving as a rapid and inexpensive paleopathological screening tool to study health across both space and time.

Detection of microbial concentration in ice-cream using the impedance technique.

PubMed

Grossi, M; Lanzoni, M; Pompei, A; Lazzarini, R; Matteuzzi, D; Riccò, B

2008-06-15

The detection of microbial concentration, essential for safe and high quality food products, is traditionally made with the plate count technique, that is reliable, but also slow and not easily realized in the automatic form, as required for direct use in industrial machines. To this purpose, the method based on impedance measurements represents an attractive alternative since it can produce results in about 10h, instead of the 24-48h needed by standard plate counts and can be easily realized in automatic form. In this paper such a method has been experimentally studied in the case of ice-cream products. In particular, all main ice-cream compositions of real interest have been considered and no nutrient media has been used to dilute the samples. A measurement set-up has been realized using benchtop instruments for impedance measurements on samples whose bacteria concentration was independently measured by means of standard plate counts. The obtained results clearly indicate that impedance measurement represents a feasible and reliable technique to detect total microbial concentration in ice-cream, suitable to be implemented as an embedded system for industrial machines.

In situ detection of microbial respiration in soils and salt flats. [Nevada desert

NASA Technical Reports Server (NTRS)

Tew, R. W.

1973-01-01

Increase in CO2 partial pressures over a desert soil treated with casamino-acids glucose solution correlated with bacterial growth. Few or no increases in numbers of bacteria or CO2 concentrations were noted in similar plots treated with water only or receiving no treatment. Growth in the soil appeared to be severely nutrient limited during the 10 day experiment. Especially rapid growth took place between the third and fifth day, when temperatures ranged from 0 deg. (night) to a maximum of 17.4 deg. (day). Under the conditions of the experiment, intermittent CO2 assay was an insensitive indicator of growth, possibly because of restiction of gas escape by the desert pavement or solution, exchange, or precipitation of carbonate, but more likely because of inefficient sealing of hoods to and below the soil surface. CO2 assay was unable to detect microbial successions. The unpredictable course of these successions, plus unpredictable relative retentions mitigates against assay of organic gases as reliable in situ detection of microbial activity, except perhaps in very alkaline environments such as Owens Lake salts.

Burning fire-prone Mediterranean shrublands: immediate changes in soil microbial community structure and ecosystem functions.

PubMed

Goberna, M; García, C; Insam, H; Hernández, M T; Verdú, M

2012-07-01

Wildfires subject soil microbes to extreme temperatures and modify their physical and chemical habitat. This might immediately alter their community structure and ecosystem functions. We burned a fire-prone shrubland under controlled conditions to investigate (1) the fire-induced changes in the community structure of soil archaea, bacteria and fungi by analysing 16S or 18S rRNA gene amplicons separated through denaturing gradient gel electrophoresis; (2) the physical and chemical variables determining the immediate shifts in the microbial community structure; and (3) the microbial drivers of the change in ecosystem functions related to biogeochemical cycling. Prokaryotes and eukaryotes were structured by the local environment in pre-fire soils. Fire caused a significant shift in the microbial community structure, biomass C, respiration and soil hydrolases. One-day changes in bacterial and fungal community structure correlated to the rise in total organic C and NO(3)(-)-N caused by the combustion of plant residues. In the following week, bacterial communities shifted further forced by desiccation and increasing concentrations of macronutrients. Shifts in archaeal community structure were unrelated to any of the 18 environmental variables measured. Fire-induced changes in the community structure of bacteria, rather than archaea or fungi, were correlated to the enhanced microbial biomass, CO(2) production and hydrolysis of C and P organics. This is the first report on the combined effects of fire on the three biological domains in soils. We concluded that immediately after fire the biogeochemical cycling in Mediterranean shrublands becomes less conservative through the increased microbial biomass, activity and changes in the bacterial community structure.

The Biogeographic Pattern of Microbial Functional Genes along an Altitudinal Gradient of the Tibetan Pasture

PubMed Central

Qi, Qi; Zhao, Mengxin; Wang, Shiping; Ma, Xingyu; Wang, Yuxuan; Gao, Ying; Lin, Qiaoyan; Li, Xiangzhen; Gu, Baohua; Li, Guoxue; Zhou, Jizhong; Yang, Yunfeng

2017-01-01

As the highest place of the world, the Tibetan plateau is a fragile ecosystem. Given the importance of microbial communities in driving soil nutrient cycling, it is of interest to document the microbial biogeographic pattern here. We adopted a microarray-based tool named GeoChip 4.0 to investigate grassland microbial functional genes along an elevation gradient from 3200 to 3800 m above sea level open to free grazing by local herdsmen and wild animals. Interestingly, microbial functional diversities increase with elevation, so does the relative abundances of genes associated with carbon degradation, nitrogen cycling, methane production, cold shock and oxygen limitation. The range of Shannon diversities (10.27–10.58) showed considerably smaller variation than what was previously observed at ungrazed sites nearby (9.95–10.65), suggesting the important role of livestock grazing on microbial diversities. Closer examination showed that the dissimilarity of microbial community at our study sites increased with elevations, revealing an elevation-decay relationship of microbial functional genes. Both microbial functional diversity and the number of unique genes increased with elevations. Furthermore, we detected a tight linkage of greenhouse gas (CO2) and relative abundances of carbon cycling genes. Our biogeographic study provides insights on microbial functional diversity and soil biogeochemical cycling in Tibetan pastures. PMID:28659870

Environmental proteomics of microbial plankton in a highly productive coastal upwelling system

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

Sowell, Sarah; Abraham, Paul E; Shah, Manesh B

2011-01-01

Metaproteomics is one of a suite of new approaches providing insights into the activities of microorganisms in natural environments. Proteins, the final products of gene expression, indicate cellular priorities, taking into account both transcriptional and posttranscriptional control mechanisms that control adaptive responses. Here, we report the proteomic composition of the o 1.2 lm fraction of a microbial community from Oregon coast summer surface waters, detected with two-dimensional liquid chromatography coupled with electrospray tandem mass spectrometry. Spectra corresponding to proteins involved in protein folding and biosynthesis, transport, and viral capsid structure were the most frequently detected. A total of 36% ofmore » all the detected proteins were best matches to the SAR11 clade, and other abundant coastal microbial clades were also well represented, including the Roseobacter clade (17%), oligotrophic marine gammaproteobacteria group (6%), OM43 clade (1%). Viral origins were attributed to 2.5% of proteins. In contrast to oligotrophic waters, phosphate transporters were not highly detected in this nutrient-rich system. However, transporters for amino acids, taurine, polyamines and glutamine synthetase were among the most highly detected proteins, supporting predictions that carbon and nitrogen are more limiting than phosphate in this environment. Intriguingly, one of the highly detected proteins was methanol dehydrogenase originating from the OM43 clade, providing further support for recent reports that the metabolism of one-carbon compounds by these streamlined methylotrophs might be an important feature of coastal ocean biogeochemistry.« less

Remote detection of buried explosives by fluorescent and bioluminescent microbial sensors (Conference Presentation)

NASA Astrophysics Data System (ADS)

Belkin, Shimshon; Yagur-Kroll, Sharon; Zohar, Cheinat; Rabinovitz, Zahi; Nussinovitch, Amos; Kabessa, Yossi; Agranat, Aharon J.

2017-06-01

Current landmine detection methodologies are not much different in principle from those employed 75 years ago, in that they require actual presence in the minefield, with obvious risks to personnel and equipment. Other limitations include an extremely large ratio of false positives, as well as a very limited ability to detect non-metallic landmines. In this lecture a microbial-based solution for the remote detection of buried landmines described. The small size requirements, rapid responses and sensing versatility of bacterial bioreporters allow their integration into diverse types of devices, for laboratory as well as field applications. The relative ease by which molecular sensing and reporting elements can be fused together to generate dose-dependent quantifiable physical (luminescent, fluorescent, colorimetric, electrochemical) responses to pre-determined conditions allows the construction of diverse classes of sensors. Over the last two decades we and others have employed this principle to design and construct microbial bioreporter strains for the sensitive detection of (a) specific chemicals of environmental concern (heavy metals, halogenated organics etc.) or (b) their deleterious biological effects on living systems (such as toxicity or genotoxicity). In many of these cases, additional molecular manipulations beyond the initial sensor-reporter fusion may be highly beneficial for enhancing the performance of the engineered sensor systems. This presentation highlights several of the approaches we have adopted over the years to achieve this aim, while focusing on the application of live cell microbeads for the remote detection of buried landmines and other explosive devices.

Perchlorate Salts in the Martian Surface Environment - A Reexamination of the 1976 Viking Biology Results

NASA Astrophysics Data System (ADS)

Dillon, James; Quinn, R. C.

2010-01-01

The Viking Mars landers of 1976 conducted three biology experiments designed to detect the presence of microbial life in the Martian surface. The gas exchange experiment carried out by the Viking landers periodically sampled the gaseous headspace of Mars soil samples saturated with an organic/inorganic aqueous mixture, M4 nutrient. A gas chromatograph measured the change in concentrations of N2, O2, CO2, Kr, H2, and CH4 over various time intervals. The presence of metabolically active microbial life would be confirmed by the consumption or release of one of these gases. A significant release of O2 was detected after the addition of nutrient, however since the Gas Chromatograph - Mass Spectrometer experiment did not detect organics in the soil, this rapid release of O2 could not be attributed to microbial life, but rather a chemical reaction. The recent discovery of the oxidizer perchlorate in the Martian soil by the Phoenix Mars lander was investigated as the principal cause of this O2 release detected by the Viking gas exchange experiment. A variety of oxychloride salts ranging from hypochlorite to perchlorate were examined under conditions similar to the Viking experiment in order to determine if a rapid release of O2 would be detected upon addition of M4 nutrient. No oxychloride species examined decomposed with the kinetics required to support an oxychloride as the cause of the O2 response detected by the Viking experiment.

Rapid filtration separation-based sample preparation method for Bacillus spores in powdery and environmental matrices.

PubMed

Isabel, Sandra; Boissinot, Maurice; Charlebois, Isabelle; Fauvel, Chantal M; Shi, Lu-E; Lévesque, Julie-Christine; Paquin, Amélie T; Bastien, Martine; Stewart, Gale; Leblanc, Eric; Sato, Sachiko; Bergeron, Michel G

2012-03-01

Authorities frequently need to analyze suspicious powders and other samples for biothreat agents in order to assess environmental safety. Numerous nucleic acid detection technologies have been developed to detect and identify biowarfare agents in a timely fashion. The extraction of microbial nucleic acids from a wide variety of powdery and environmental samples to obtain a quality level adequate for these technologies still remains a technical challenge. We aimed to develop a rapid and versatile method of separating bacteria from these samples and then extracting their microbial DNA. Bacillus atrophaeus subsp. globigii was used as a simulant of Bacillus anthracis. We studied the effects of a broad variety of powdery and environmental samples on PCR detection and the steps required to alleviate their interference. With a benchmark DNA extraction procedure, 17 of the 23 samples investigated interfered with bacterial lysis and/or PCR-based detection. Therefore, we developed the dual-filter method for applied recovery of microbial particles from environmental and powdery samples (DARE). The DARE procedure allows the separation of bacteria from contaminating matrices that interfere with PCR detection. This procedure required only 2 min, while the DNA extraction process lasted 7 min, for a total of <10 min. This sample preparation procedure allowed the recovery of cleaned bacterial spores and relieved detection interference caused by a wide variety of samples. Our procedure was easily completed in a laboratory facility and is amenable to field application and automation.

Rapid Filtration Separation-Based Sample Preparation Method for Bacillus Spores in Powdery and Environmental Matrices

PubMed Central

Isabel, Sandra; Boissinot, Maurice; Charlebois, Isabelle; Fauvel, Chantal M.; Shi, Lu-E; Lévesque, Julie-Christine; Paquin, Amélie T.; Bastien, Martine; Stewart, Gale; Leblanc, Éric; Sato, Sachiko

2012-01-01

Authorities frequently need to analyze suspicious powders and other samples for biothreat agents in order to assess environmental safety. Numerous nucleic acid detection technologies have been developed to detect and identify biowarfare agents in a timely fashion. The extraction of microbial nucleic acids from a wide variety of powdery and environmental samples to obtain a quality level adequate for these technologies still remains a technical challenge. We aimed to develop a rapid and versatile method of separating bacteria from these samples and then extracting their microbial DNA. Bacillus atrophaeus subsp. globigii was used as a simulant of Bacillus anthracis. We studied the effects of a broad variety of powdery and environmental samples on PCR detection and the steps required to alleviate their interference. With a benchmark DNA extraction procedure, 17 of the 23 samples investigated interfered with bacterial lysis and/or PCR-based detection. Therefore, we developed the dual-filter method for applied recovery of microbial particles from environmental and powdery samples (DARE). The DARE procedure allows the separation of bacteria from contaminating matrices that interfere with PCR detection. This procedure required only 2 min, while the DNA extraction process lasted 7 min, for a total of <10 min. This sample preparation procedure allowed the recovery of cleaned bacterial spores and relieved detection interference caused by a wide variety of samples. Our procedure was easily completed in a laboratory facility and is amenable to field application and automation. PMID:22210204

The Microbial Detection Array Combined with Random Phi29-Amplification Used as a Diagnostic Tool for Virus Detection in Clinical Samples

PubMed Central

Erlandsson, Lena; Rosenstierne, Maiken W.; McLoughlin, Kevin; Jaing, Crystal; Fomsgaard, Anders

2011-01-01

A common technique used for sensitive and specific diagnostic virus detection in clinical samples is PCR that can identify one or several viruses in one assay. However, a diagnostic microarray containing probes for all human pathogens could replace hundreds of individual PCR-reactions and remove the need for a clear clinical hypothesis regarding a suspected pathogen. We have established such a diagnostic platform for random amplification and subsequent microarray identification of viral pathogens in clinical samples. We show that Phi29 polymerase-amplification of a diverse set of clinical samples generates enough viral material for successful identification by the Microbial Detection Array, demonstrating the potential of the microarray technique for broad-spectrum pathogen detection. We conclude that this method detects both DNA and RNA virus, present in the same sample, as well as differentiates between different virus subtypes. We propose this assay for diagnostic analysis of viruses in clinical samples. PMID:21853040

The applicability of TaqMan-based quantitative real-time PCR assays for detecting and enumeratIng Cryptosporidium spp. oocysts in the environment

EPA Science Inventory

Molecular detection methods such as PCR have been extensively used to type Cryptosporidium oocysts detected in the environment. More recently, studies have developed quantitative real-time PCR assays for detection and quantification of microbial contaminants in water as well as ...

Robotic Astrobiology: Searching for Life with Rovers

NASA Astrophysics Data System (ADS)

Cabrol, N. A.; Wettergreen, D. S.; Team, L.

2006-05-01

The Life In The Atacama (LITA) project has developed and field tested a long-range, solar-powered, automated rover platform (Zoe) and a science payload assembled to search for microbial life in the Atacama desert. Life is hardly detectable over most of the extent of the driest desert on Earth. Its geological, climatic, and biological evolution provides a unique training ground for designing and testing exploration strategies and life detection methods for the robotic search for life on Mars. LITA opens the path to a new generation of rover missions that will transition from the current study of habitability (MER) to the upcoming search for, and study of, habitats and life on Mars. Zoe's science payload reflects this transition by combining complementary elements, some directed towards the remote sensing of the environment (geology, morphology, mineralogy, weather/climate) for the detection of conditions favorable to microbial habitats and oases along survey traverses, others directed toward the in situ detection of life' signatures (biological and physical, such as biological constructs and patterns). New exploration strategies specifically adapted to the search for microbial life were designed and successfully tested in the Atacama between 2003-2005. They required the development and implementation in the field of new technological capabilities, including navigation beyond the horizon, obstacle avoidance, and "science-on-the-fly" (automated detection of targets of science value), and that of new rover planning tools in the remote science operation center.

Metagenomics of Microbial Communities in Gallbladder Bile from Patients with Gallbladder Cancer or Cholelithiasis

PubMed

Tsuchiya, Yasuo; Loza, Ernest; Villa-Gomez, Guido; Trujillo, Carlos C; Baez, Sergio; Asai, Takao; Ikoma, Toshikazu; Endoh, Kazuo; Nakamura, Kazutoshi

2018-04-25

Salmonella typhi and Helicobacter infections have been shown to increase risk of gallbladder cancer (GBC), but findings have been inconsistent. Other bacterial infections may also be associated with GBC. However, information on microbial pathogens in gallbladder bile of GBC patients is scarce. We aimed to investigate the microbial communities in gallbladder bile of patients with GBC and cholelithiasis (CL). Seven GBC patients and 30 CL patients were enrolled in this study. Genomic DNA was extracted from bile and the V3-V4 region of 16S rRNA was amplified. The sequencing results were compared with the 16S database, and the bacteria were identified by homology searches and phylogenetic analysis. DNA was detected in the bile of three GBC (42.9%; Bolivia, 1; Chile, 2) and four CL patients (13.3%; Bolivia, 1; Chile, 3). Of the 37 patients, 30 (81.1%) were negative and unable to analyze. Salmonella typhi and Helicobacter sp. were not detected in bile from any GBC patients. As the predominant species, Fusobacterium nucleatum, Escherichia coli, and Enetrobacter sp. were detected in bile from GBC patients. Those in bile from CL patients were Escherichia coli, Salmonella sp., and Enerococcus gallinarum. Escherichia coli was detected in bile samples from both GBC and CL patients. Whether the bacteria detected in bile from GBC patients would associated with the development of GBC warrant further investigation. Creative Commons Attribution License

Microbial Diagnostic Array Workstation (MDAW): a web server for diagnostic array data storage, sharing and analysis

PubMed Central

Scaria, Joy; Sreedharan, Aswathy; Chang, Yung-Fu

2008-01-01

Background Microarrays are becoming a very popular tool for microbial detection and diagnostics. Although these diagnostic arrays are much simpler when compared to the traditional transcriptome arrays, due to the high throughput nature of the arrays, the data analysis requirements still form a bottle neck for the widespread use of these diagnostic arrays. Hence we developed a new online data sharing and analysis environment customised for diagnostic arrays. Methods Microbial Diagnostic Array Workstation (MDAW) is a database driven application designed in MS Access and front end designed in ASP.NET. Conclusion MDAW is a new resource that is customised for the data analysis requirements for microbial diagnostic arrays. PMID:18811969

Microbial Diagnostic Array Workstation (MDAW): a web server for diagnostic array data storage, sharing and analysis.

PubMed

Scaria, Joy; Sreedharan, Aswathy; Chang, Yung-Fu

2008-09-23

Microarrays are becoming a very popular tool for microbial detection and diagnostics. Although these diagnostic arrays are much simpler when compared to the traditional transcriptome arrays, due to the high throughput nature of the arrays, the data analysis requirements still form a bottle neck for the widespread use of these diagnostic arrays. Hence we developed a new online data sharing and analysis environment customised for diagnostic arrays. Microbial Diagnostic Array Workstation (MDAW) is a database driven application designed in MS Access and front end designed in ASP.NET. MDAW is a new resource that is customised for the data analysis requirements for microbial diagnostic arrays.

Influence of indoor microbial aerosol on the welfare of meat ducks.

PubMed

Yu, G L; Wei, L M; Liu, Y Y; Liu, J Y; Wang, Y; Gao, J; Chai, T J; Cai, Y M

2016-01-01

The aim of the study was to evaluate the effects of microbial aerosols on ducks' welfare and provide information on which to establish microbial aerosol concentration standards for poultry. A total of 1800 1-d-old Cherry Valley ducks were randomly divided into 5 groups (A, B, C, D and E) with 360 ducks in each. To obtain objective data, each group had three replications. Different microbial aerosol concentrations in different groups were created by controlling ventilation and bedding cleaning frequency. Group A was the control group and hygienic conditions deteriorated progressively from group B to E. A 6-stage Andersen impactor was used to detect the aerosol concentration of aerobes, fungi, gram-negative bacteria and an AGI-30 microbial air sampler detected endotoxins. Physiological stress was evaluated in the ducks by adrenocorticotropic hormone (ACTH) values in serum. To assess the effects of bioaerosol factors, welfare indicators including fluctuating asymmetry (FA), appearance and gait as well as the Lactobacillus caecal concentration were evaluated. The data showed group D had already reached the highest limit of concentration of airborne aerobic bacteria, airborne fungi, airborne gram-negative bacteria and airborne endotoxin. The ducks in this group had significantly increased serum ACTH values and significantly decreased caecal lactobacilli concentration. Furthermore, appearance and gait scores, wing length and overall FA and caecal Lactobacillus concentration in this group were significantly increased at 6 and 8 weeks of age. In conclusion, high concentrations of microbial aerosol adversely affected the welfare of meat ducks. The microbial aerosol values in group D suggest a preliminary upper limit concentration of bioaerosols in ambient air for healthy meat ducks.

Microbial diversity in hummock and hollow soils of three wetlands on the Qinghai-Tibetan Plateau revealed by 16S rRNA pyrosequencing.

PubMed

Deng, Yongcui; Cui, Xiaoyong; Hernández, Marcela; Dumont, Marc G

2014-01-01

The wetlands of the Qinghai-Tibetan Plateau are believed to play an important role in global nutrient cycling, but the composition and diversity of microorganisms in this ecosystem are poorly characterized. An understanding of the effects of geography and microtopography on microbial populations will provide clues to the underlying mechanisms that structure microbial communities. In this study, we used pyrosequencing-based analysis of 16S rRNA gene sequences to assess and compare the composition of soil microbial communities present in hummock and hollow soils from three wetlands (Dangxiong, Hongyuan and Maduo) on the Qinghai-Tibetan Plateau, the world's highest plateau. A total of 36 bacterial phyla were detected. Proteobacteria (34.5% average relative abundance), Actinobacteria (17.3%) and Bacteroidetes (11%) had the highest relative abundances across all sites. Chloroflexi, Acidobacteria, Verrucomicrobia, Firmicutes, and Planctomycetes were also relatively abundant (1-10%). In addition, archaeal sequences belonging to Euryarchaea, Crenarchaea and Thaumarchaea were detected. Alphaproteobacteria sequences, especially of the order Rhodospirillales, were significantly more abundant in Maduo than Hongyuan and Dangxiong wetlands. Compared with Hongyuan soils, Dangxiong and Maduo had significantly higher relative abundances of Gammaproteobacteria sequences (mainly order Xanthomonadales). Hongyuan wetland had a relatively high abundance of methanogens (mainly genera Methanobacterium, Methanosarcina and Methanosaeta) and methanotrophs (mainly Methylocystis) compared with the other two wetlands. Principal coordinate analysis (PCoA) indicated that the microbial community structure differed between locations and microtopographies and canonical correspondence analysis indicated an association between microbial community structure and soil properties or geography. These insights into the microbial community structure and the main controlling factors in wetlands of the Qinghai-Tibetan Plateau provide a valuable background for further studies on biogeochemical processes in this distinct ecosystem.

Depletion of Unwanted Nucleic Acid Templates by Selective Cleavage: LNAzymes, Catalytically Active Oligonucleotides Containing Locked Nucleic Acids, Open a New Window for Detecting Rare Microbial Community Members

PubMed Central

Dolinšek, Jan; Dorninger, Christiane; Lagkouvardos, Ilias; Wagner, Michael

2013-01-01

Many studies of molecular microbial ecology rely on the characterization of microbial communities by PCR amplification, cloning, sequencing, and phylogenetic analysis of genes encoding rRNAs or functional marker enzymes. However, if the established clone libraries are dominated by one or a few sequence types, the cloned diversity is difficult to analyze by random clone sequencing. Here we present a novel approach to deplete unwanted sequence types from complex nucleic acid mixtures prior to cloning and downstream analyses. It employs catalytically active oligonucleotides containing locked nucleic acids (LNAzymes) for the specific cleavage of selected RNA targets. When combined with in vitro transcription and reverse transcriptase PCR, this LNAzyme-based technique can be used with DNA or RNA extracts from microbial communities. The simultaneous application of more than one specific LNAzyme allows the concurrent depletion of different sequence types from the same nucleic acid preparation. This new method was evaluated with defined mixtures of cloned 16S rRNA genes and then used to identify accompanying bacteria in an enrichment culture dominated by the nitrite oxidizer “Candidatus Nitrospira defluvii.” In silico analysis revealed that the majority of publicly deposited rRNA-targeted oligonucleotide probes may be used as specific LNAzymes with no or only minor sequence modifications. This efficient and cost-effective approach will greatly facilitate tasks such as the identification of microbial symbionts in nucleic acid preparations dominated by plastid or mitochondrial rRNA genes from eukaryotic hosts, the detection of contaminants in microbial cultures, and the analysis of rare organisms in microbial communities of highly uneven composition. PMID:23263968

Microbial Diversity in Hummock and Hollow Soils of Three Wetlands on the Qinghai-Tibetan Plateau Revealed by 16S rRNA Pyrosequencing

PubMed Central

Deng, Yongcui; Cui, Xiaoyong; Hernández, Marcela; Dumont, Marc G.

2014-01-01

The wetlands of the Qinghai-Tibetan Plateau are believed to play an important role in global nutrient cycling, but the composition and diversity of microorganisms in this ecosystem are poorly characterized. An understanding of the effects of geography and microtopography on microbial populations will provide clues to the underlying mechanisms that structure microbial communities. In this study, we used pyrosequencing-based analysis of 16S rRNA gene sequences to assess and compare the composition of soil microbial communities present in hummock and hollow soils from three wetlands (Dangxiong, Hongyuan and Maduo) on the Qinghai-Tibetan Plateau, the world’s highest plateau. A total of 36 bacterial phyla were detected. Proteobacteria (34.5% average relative abundance), Actinobacteria (17.3%) and Bacteroidetes (11%) had the highest relative abundances across all sites. Chloroflexi, Acidobacteria, Verrucomicrobia, Firmicutes, and Planctomycetes were also relatively abundant (1–10%). In addition, archaeal sequences belonging to Euryarchaea, Crenarchaea and Thaumarchaea were detected. Alphaproteobacteria sequences, especially of the order Rhodospirillales, were significantly more abundant in Maduo than Hongyuan and Dangxiong wetlands. Compared with Hongyuan soils, Dangxiong and Maduo had significantly higher relative abundances of Gammaproteobacteria sequences (mainly order Xanthomonadales). Hongyuan wetland had a relatively high abundance of methanogens (mainly genera Methanobacterium, Methanosarcina and Methanosaeta) and methanotrophs (mainly Methylocystis) compared with the other two wetlands. Principal coordinate analysis (PCoA) indicated that the microbial community structure differed between locations and microtopographies and canonical correspondence analysis indicated an association between microbial community structure and soil properties or geography. These insights into the microbial community structure and the main controlling factors in wetlands of the Qinghai-Tibetan Plateau provide a valuable background for further studies on biogeochemical processes in this distinct ecosystem. PMID:25078273

Changes in the Structure and Function of Microbial Communities in Drinking Water Treatment Bioreactors upon Addition of Phosphorus▿ †

PubMed Central

Li, Xu; Upadhyaya, Giridhar; Yuen, Wangki; Brown, Jess; Morgenroth, Eberhard; Raskin, Lutgarde

2010-01-01

Phosphorus was added as a nutrient to bench-scale and pilot-scale biologically active carbon (BAC) reactors operated for perchlorate and nitrate removal from contaminated groundwater. The two bioreactors responded similarly to phosphorus addition in terms of microbial community function (i.e., reactor performance), while drastically different responses in microbial community structure were detected. Improvement in reactor performance with respect to perchlorate and nitrate removal started within a few days after phosphorus addition for both reactors. Microbial community structures were evaluated using molecular techniques targeting 16S rRNA genes. Clone library results showed that the relative abundance of perchlorate-reducing bacteria (PRB) Dechloromonas and Azospira in the bench-scale reactor increased from 15.2% and 0.6% to 54.2% and 11.7% after phosphorus addition, respectively. Real-time quantitative PCR (qPCR) experiments revealed that these increases started within a few days after phosphorus addition. In contrast, after phosphorus addition, the relative abundance of Dechloromonas in the pilot-scale reactor decreased from 7.1 to 0.6%, while Zoogloea increased from 17.9 to 52.0%. The results of this study demonstrated that similar operating conditions for bench-scale and pilot-scale reactors resulted in similar contaminant removal performances, despite dramatically different responses from microbial communities. These findings suggest that it is important to evaluate the microbial community compositions inside bioreactors used for drinking water treatment, as they determine the microbial composition in the effluent and impact downstream treatment requirements for drinking water production. This information could be particularly relevant to drinking water safety, if pathogens or disinfectant-resistant bacteria are detected in the bioreactors. PMID:20889793

18 CFR 401.36 - Water supply projects-Conservation requirements.

Code of Federal Regulations, 2010 CFR

2010-04-01

... leak detection and control program; (2) Use of the best practicable water-conserving devices and... 18 Conservation of Power and Water Resources 2 2010-04-01 2010-04-01 false Water supply projects-Conservation requirements. 401.36 Section 401.36 Conservation of Power and Water Resources DELAWARE RIVER BASIN...

On-line detection of Escherichia coli intrusion in a pilot-scale drinking water distribution system.

PubMed

Ikonen, Jenni; Pitkänen, Tarja; Kosse, Pascal; Ciszek, Robert; Kolehmainen, Mikko; Miettinen, Ilkka T

2017-08-01

Improvements in microbial drinking water quality monitoring are needed for the better control of drinking water distribution systems and for public health protection. Conventional water quality monitoring programmes are not always able to detect a microbial contamination of drinking water. In the drinking water production chain, in addition to the vulnerability of source waters, the distribution networks are prone to contamination. In this study, a pilot-scale drinking-water distribution network with an on-line monitoring system was utilized for detecting bacterial intrusion. During the experimental Escherichia coli intrusions, the contaminant was measured by applying a set of on-line sensors for electric conductivity (EC), pH, temperature (T), turbidity, UV-absorbance at 254 nm (UVAS SC) and with a device for particle counting. Monitored parameters were compared with the measured E. coli counts using the integral calculations of the detected peaks. EC measurement gave the strongest signal compared with the measured baseline during the E. coli intrusion. Integral calculations showed that the peaks in the EC, pH, T, turbidity and UVAS SC data were detected corresponding to the time predicted. However, the pH and temperature peaks detected were barely above the measured baseline and could easily be mixed with the background noise. The results indicate that on-line monitoring can be utilized for the rapid detection of microbial contaminants in the drinking water distribution system although the peak interpretation has to be performed carefully to avoid being mixed up with normal variations in the measurement data. Copyright © 2017 Elsevier Ltd. All rights reserved.

Management of microbial contamination in storm runoff from California coastal dairy pastures.

PubMed

Lewis, David J; Atwill, Edward R; Lennox, Michael S; Pereira, Maria D G; Miller, Woutrina A; Conrad, Patricia A; Tate, Kenneth W

2010-01-01

A survey of storm runoff fecal coliform bacteria (FCB) from working farm and ranch pastures is presented in conjunction with a survey of FCB in manure management systems (MMS). The cross-sectional survey of pasture runoff was conducted on 34 pastures on five different dairies over 2 yr under varying conditions of precipitation, slope, manure management, and use of conservation practices such as vegetative filter strips. The MMS cross-sectional survey consisted of samples collected during 1 yr on nine different dairies from six loafing barns, nine primary lagoons, 12 secondary lagoons, and six irrigation sample points. Pasture runoff samples were additionally analyzed for Cryptosporidium sp. and Giardia duodenalis, whereby detectable concentrations occurred sporadically at higher FCB concentrations resulting in poor correlations with FCB. Prevalence of both parasites was lower relative to high-use areas studied simultaneously on these same farms. Application of manure to pastures more than 2 wk in advance of storm-associated runoff was related to a > or =80% reduction in FCB concentration and load compared to applications within 2 wk before a runoff event. For every 10 m of buffer length, a 24% reduction in FCB concentration was documented. A one-half (75%), one (90%), and two (99%) log10 reduction in manure FCB concentration was observed for manure holding times in MMS of approximately 20, 66, and 133 d, respectively. These results suggest that there are several management and conservation practices for working farms that may result in reduced FCB fluxes from agricultural operations.

Extensive Management Promotes Plant and Microbial Nitrogen Retention in Temperate Grassland

PubMed Central

de Vries, Franciska T.; Bloem, Jaap; Quirk, Helen; Stevens, Carly J.; Bol, Roland; Bardgett, Richard D.

2012-01-01

Leaching losses of nitrogen (N) from soil and atmospheric N deposition have led to widespread changes in plant community and microbial community composition, but our knowledge of the factors that determine ecosystem N retention is limited. A common feature of extensively managed, species-rich grasslands is that they have fungal-dominated microbial communities, which might reduce soil N losses and increase ecosystem N retention, which is pivotal for pollution mitigation and sustainable food production. However, the mechanisms that underpin improved N retention in extensively managed, species-rich grasslands are unclear. We combined a landscape-scale field study and glasshouse experiment to test how grassland management affects plant and soil N retention. Specifically, we hypothesised that extensively managed, species-rich grasslands of high conservation value would have lower N loss and greater N retention than intensively managed, species-poor grasslands, and that this would be due to a greater immobilisation of N by a more fungal-dominated microbial community. In the field study, we found that extensively managed, species-rich grasslands had lower N leaching losses. Soil inorganic N availability decreased with increasing abundance of fungi relative to bacteria, although the best predictor of soil N leaching was the C/N ratio of aboveground plant biomass. In the associated glasshouse experiment we found that retention of added 15N was greater in extensively than in intensively managed grasslands, which was attributed to a combination of greater root uptake and microbial immobilisation of 15N in the former, and that microbial immobilisation increased with increasing biomass and abundance of fungi. These findings show that grassland management affects mechanisms of N retention in soil through changes in root and microbial uptake of N. Moreover, they support the notion that microbial communities might be the key to improved N retention through tightening linkages between plants and microbes and reducing N availability. PMID:23227252

Coral-Associated Bacterial Diversity Is Conserved across Two Deep-Sea Anthothela Species

PubMed Central

Lawler, Stephanie N.; Kellogg, Christina A.; France, Scott C.; Clostio, Rachel W.; Brooke, Sandra D.; Ross, Steve W.

2016-01-01

Cold-water corals, similar to tropical corals, contain diverse and complex microbial assemblages. These bacteria provide essential biological functions within coral holobionts, facilitating increased nutrient utilization and production of antimicrobial compounds. To date, few cold-water octocoral species have been analyzed to explore the diversity and abundance of their microbial associates. For this study, 23 samples of the family Anthothelidae were collected from Norfolk (n = 12) and Baltimore Canyons (n = 11) from the western Atlantic in August 2012 and May 2013. Genetic testing found that these samples comprised two Anthothela species (Anthothela grandiflora and Anthothela sp.) and Alcyonium grandiflorum. DNA was extracted and sequenced with primers targeting the V4–V5 variable region of the 16S rRNA gene using 454 pyrosequencing with GS FLX Titanium chemistry. Results demonstrated that the coral host was the primary driver of bacterial community composition. Al. grandiflorum, dominated by Alteromonadales and Pirellulales had much higher species richness, and a distinct bacterial community compared to Anthothela samples. Anthothela species (A. grandiflora and Anthothela sp.) had very similar bacterial communities, dominated by Oceanospirillales and Spirochaetes. Additional analysis of core-conserved bacteria at 90% sample coverage revealed genus level conservation across Anthothela samples. This core included unclassified Oceanospirillales, Kiloniellales, Campylobacterales, and genus Spirochaeta. Members of this core were previously recognized for their functional capabilities in nitrogen cycling and suggest the possibility of a nearly complete nitrogen cycle within Anthothela species. Overall, many of the bacterial associates identified in this study have the potential to contribute to the acquisition and cycling of nutrients within the coral holobiont. PMID:27092120

Coral-associated bacterial diversity is conserved across two deep-sea Anthothela species

USGS Publications Warehouse

Lawler, Stephanie N.; Kellogg, Christina A.; France, Scott C; Clostio, Rachel W; Brooke, Sandra D.; Ross, Steve W.

2016-01-01

Cold-water corals, similar to tropical corals, contain diverse and complex microbial assemblages. These bacteria provide essential biological functions within coral holobionts, facilitating increased nutrient utilization and production of antimicrobial compounds. To date, few cold-water octocoral species have been analyzed to explore the diversity and abundance of their microbial associates. For this study, 23 samples of the family Anthothelidae were collected from Norfolk (n = 12) and Baltimore Canyons (n = 11) from the western Atlantic in August 2012 and May 2013. Genetic testing found that these samples comprised two Anthothela species (Anthothela grandiflora and Anthothela sp.) and Alcyonium grandiflorum. DNA was extracted and sequenced with primers targeting the V4-V5 variable region of the 16S rRNA gene using 454 pyrosequencing with GS FLX Titanium chemistry. Results demonstrated that the coral host was the primary driver of bacterial community composition. Al. grandiflorum, dominated by Alteromonadales and Pirellulales had much higher species richness, and a distinct bacterial community compared to Anthothela samples. Anthothela species (A. grandiflora and Anthothela sp.) had very similar bacterial communities, dominated by Oceanospirillales and Spirochaetes. Additional analysis of core-conserved bacteria at 90% sample coverage revealed genus level conservation across Anthothela samples. This core included unclassified Oceanospirillales, Kiloniellales, Campylobacterales, and genus Spirochaeta. Members of this core were previously recognized for their functional capabilities in nitrogen cycling and suggest the possibility of a nearly complete nitrogen cycle within Anthothela species. Overall, many of the bacterial associates identified in this study have the potential to contribute to the acquisition and cycling of nutrients within the coral holobiont.

International Space Station environmental microbiome - microbial inventories of ISS filter debris.

PubMed

Venkateswaran, Kasthuri; Vaishampayan, Parag; Cisneros, Jessica; Pierson, Duane L; Rogers, Scott O; Perry, Jay

2014-01-01

Despite an expanding array of molecular approaches for detecting microorganisms in a given sample, rapid and robust means of assessing the differential viability of the microbial cells, as a function of phylogenetic lineage, remain elusive. A propidium monoazide (PMA) treatment coupled with downstream quantitative polymerase chain reaction (qPCR) and pyrosequencing analyses was carried out to better understand the frequency, diversity, and distribution of viable microorganisms associated with debris collected from the crew quarters of the International Space Station (ISS). The cultured bacterial counts were more in the ISS samples than cultured fungal population. The rapid molecular analyses targeted to estimate viable population exhibited 5-fold increase in bacterial (qPCR-PMA assay) and 25-fold increase in microbial (adenosine triphosphate assay) burden than the cultured bacterial population. The ribosomal nucleic acid-based identification of cultivated strains revealed the presence of only four to eight bacterial species in the ISS samples, however, the viable bacterial diversity detected by the PMA-pyrosequencing method was far more diverse (12 to 23 bacterial taxa) with the majority consisting of members of actinobacterial genera (Propionibacterium, Corynebacterium) and Staphylococcus. Sample fractions not treated with PMA (inclusive of both live and dead cells) yielded a great abundance of highly diverse bacterial (94 to 118 taxa) and fungal lineages (41 taxa). Even though deep sequencing capability of the molecular analysis widened the understanding about the microbial diversity, the cultivation assay also proved to be essential since some of the spore-forming microorganisms were detected only by the culture-based method. Presented here are the findings of the first comprehensive effort to assess the viability of microbial cells associated with ISS surfaces, and correlate differential viability with phylogenetic affiliation.

Microbial Performance of Food Safety Control and Assurance Activities in a Fresh Produce Processing Sector Measured Using a Microbial Assessment Scheme and Statistical Modeling.

PubMed

Njage, Patrick Murigu Kamau; Sawe, Chemutai Tonui; Onyango, Cecilia Moraa; Habib, I; Njagi, Edmund Njeru; Aerts, Marc; Molenberghs, Geert

2017-01-01

Current approaches such as inspections, audits, and end product testing cannot detect the distribution and dynamics of microbial contamination. Despite the implementation of current food safety management systems, foodborne outbreaks linked to fresh produce continue to be reported. A microbial assessment scheme and statistical modeling were used to systematically assess the microbial performance of core control and assurance activities in five Kenyan fresh produce processing and export companies. Generalized linear mixed models and correlated random-effects joint models for multivariate clustered data followed by empirical Bayes estimates enabled the analysis of the probability of contamination across critical sampling locations (CSLs) and factories as a random effect. Salmonella spp. and Listeria monocytogenes were not detected in the final products. However, none of the processors attained the maximum safety level for environmental samples. Escherichia coli was detected in five of the six CSLs, including the final product. Among the processing-environment samples, the hand or glove swabs of personnel revealed a higher level of predicted contamination with E. coli , and 80% of the factories were E. coli positive at this CSL. End products showed higher predicted probabilities of having the lowest level of food safety compared with raw materials. The final products were E. coli positive despite the raw materials being E. coli negative for 60% of the processors. There was a higher probability of contamination with coliforms in water at the inlet than in the final rinse water. Four (80%) of the five assessed processors had poor to unacceptable counts of Enterobacteriaceae on processing surfaces. Personnel-, equipment-, and product-related hygiene measures to improve the performance of preventive and intervention measures are recommended.

Raman Spectroscopy of Microbial Pigments

PubMed Central

Edwards, Howell G. M.; Oren, Aharon

2014-01-01

Raman spectroscopy is a rapid nondestructive technique providing spectroscopic and structural information on both organic and inorganic molecular compounds. Extensive applications for the method in the characterization of pigments have been found. Due to the high sensitivity of Raman spectroscopy for the detection of chlorophylls, carotenoids, scytonemin, and a range of other pigments found in the microbial world, it is an excellent technique to monitor the presence of such pigments, both in pure cultures and in environmental samples. Miniaturized portable handheld instruments are available; these instruments can be used to detect pigments in microbiological samples of different types and origins under field conditions. PMID:24682303

Increased performance of hydrogen production in microbial electrolysis cells under alkaline conditions.

PubMed

Rago, Laura; Baeza, Juan A; Guisasola, Albert

2016-06-01

This work reports the first successful enrichment and operation of alkaline bioelectrochemical systems (microbial fuel cells, MFC, and microbial electrolysis cells, MEC). Alkaline (pH=9.3) bioelectrochemical hydrogen production presented better performance (+117%) compared to conventional neutral conditions (2.6 vs 1.2 litres of hydrogen gas per litre of reactor per day, LH2·L(-1)REACTOR·d(-1)). Pyrosequencing results of the anodic biofilm showed that while Geobacter was mainly detected under conventional neutral conditions, Geoalkalibacter sp. was highly detected in the alkaline MFC (21%) and MEC (48%). This is the first report of a high enrichment of Geoalkalibacter from an anaerobic mixed culture using alkaline conditions in an MEC. Moreover, Alkalibacter sp. was highly present in the anodic biofilm of the alkaline MFC (37%), which would indicate its potentiality as a new exoelectrogen. Copyright © 2016 Elsevier B.V. All rights reserved.

Application of genetically engineered microbial whole-cell biosensors for combined chemosensing.

PubMed

He, Wei; Yuan, Sheng; Zhong, Wen-Hui; Siddikee, Md Ashaduzzaman; Dai, Chuan-Chao

2016-02-01

The progress of genetically engineered microbial whole-cell biosensors for chemosensing and monitoring has been developed in the last 20 years. Those biosensors respond to target chemicals and produce output signals, which offer a simple and alternative way of assessment approaches. As actual pollution caused by human activities usually contains a combination of different chemical substances, how to employ those biosensors to accurately detect real contaminant samples and evaluate biological effects of the combined chemicals has become a realistic object of environmental researches. In this review, we outlined different types of the recent method of genetically engineered microbial whole-cell biosensors for combined chemical evaluation, epitomized their detection performance, threshold, specificity, and application progress that have been achieved up to now. We also discussed the applicability and limitations of this biosensor technology and analyzed the optimum conditions for their environmental assessment in a combined way.

Biomarker Analysis of Samples Visually Identified as Microbial in the Eocene Green River Formation: An Analogue for Mars.

PubMed

Olcott Marshall, Alison; Cestari, Nicholas A

2015-09-01

One of the major exploration targets for current and future Mars missions are lithofacies suggestive of biotic activity. Although such lithofacies are not confirmation of biotic activity, they provide a way to identify samples for further analyses. To test the efficacy of this approach, we identified carbonate samples from the Eocene Green River Formation as "microbial" or "non-microbial" based on the macroscale morphology of their laminations. These samples were then crushed and analyzed by gas chromatography/mass spectroscopy (GC/MS) to determine their lipid biomarker composition. GC/MS analysis revealed that carbonates visually identified as "microbial" contained a higher concentration of more diverse biomarkers than those identified as "non-microbial," suggesting that this could be a viable detection strategy for selecting samples for further analysis or caching on Mars.

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

Zhen Li; Rishika Haynes; Eugene Sato

Microbial fuel cells (MFCs) convert chemical energy to electrical energy via bioelectrochemical reactions mediated by microorganisms. We investigated the diversity of the microbial community in an air cathode single chamber MFC that utilized potato-process wastewater as substrate. Terminal Restriction Fragment Length Polymorphism (T-RFLP) results indicated that the bacterial communities on the anode, cathode, control electrode, and MFC bulk fluid were similar, but differed dramatically from that of the anaerobic domestic sludge and potato wastewater inoculum. The 16S rDNA sequencing results showed that microbial species detected on the anode were predominantly within the phyla of Proteobacteria, Firmicutes, and Bacteroidetes. Fluorescent microscopymore » results indicated that there was a clear enhancement of biofilm formation on the anode. Results of this study could help improve understanding of the complexity of microbial communities and optimize the microbial composition for generating electricity by MFCs that utilize potato wastewater.« less

Criteria For Evaluation of Proposed Protozoan Detection Methods

EPA Science Inventory

Currently, the only EPA approved method for detection and quantitation of protozoan cysts and oöcysts in source and drinking water, is the “ICR Protozoan Method for Detecting Giardia Cysts and Cryptosporidium Oöcysts in Water by a Fluorescent Antibody Procedure (ICR Microbial La...

Activation of the innate immune receptor Dectin-1 upon formation of a “phagocytic synapse”

PubMed Central

Goodridge, Helen S.; Reyes, Christopher N.; Becker, Courtney A.; Katsumoto, Tamiko R.; Ma, Jun; Wolf, Andrea J.; Bose, Nandita; Chan, Anissa S. H.; Magee, Andrew S.; Danielson, Michael E.; Weiss, Arthur; Vasilakos, John P.; Underhill, David M.

2011-01-01

Innate immune cells must be able to distinguish between direct binding to microbes and detection of components shed from the surface of microbes located at a distance. Dectin-1 is a pattern recognition receptor expressed by myeloid phagocytes (macrophages, dendritic cells and neutrophils) that detects β-glucans in fungal cell walls and triggers direct cellular anti-microbial activity, including phagocytosis and production of reactive oxygen species1, 2. In contrast to inflammatory responses stimulated upon detection of soluble ligands by other pattern recognition receptors, such as Toll-like receptors (TLRs), these responses are only useful when a cell comes into direct contact with a microbe and must not be spuriously activated by soluble stimuli. In this study we show that despite its ability to bind both soluble and particulate β-glucan polymers, Dectin-1 signalling is only activated by particulate β-glucans, which cluster the receptor in synapse-like structures from which regulatory tyrosine phosphatases CD45 and CD148 are excluded (Supplementary Figure 1). The “phagocytic synapse” now provides a model mechanism by which innate immune receptors can distinguish direct microbial contact from detection of microbes at a distance, thereby initiating direct cellular anti-microbial responses only when they are required. PMID:21525931

Identification of dominant pathogens in periapical lesions associated with persistent apical periodontitis.

PubMed

Zhang, Shuang; Wang, Qian Qian; Zhang, Cheng Fei; Soo, Irwan

2010-01-01

to identify dominant pathogens in the periapical lesions associated with persistent apical periodontitis. thirty-three root-filled teeth with persistent apical periodontitis referred for surgical treatment were selected. Microbial samples were collected from the periapical lesions during apical surgery. Microbial identification was performed with species-specific primers prepared according to the sequence analysis data using a 16S rRNA technique. among the 33 cases, in 5 cases none of the target species were detected, 6 cases showed the presence of only one species, and 22 cases showed more than two species. Porphyromonas endodontalis (45% of sample) was the most commonly detected dominant microbial species in the study sample, followed by Actinomyces viscosus (42%), Candida albicans (36%) and Porphyromonas gingivalis (27%). Fusobacterium, Actinomyces israelii and Enterococcus faecalis were also detected in 27%, 21% and 15% of the sample, respectively. The most frequently isolated species, P. endodontalis, was in most cases detected together with Actinomyces (14 cases) and P. gingivalis (6 cases). None of the lesions analysed in the present study contained Prevotella intermedia. There was no correlation in relation to the presence of sinus tracts and the bacterial species. a mixed population of pathogens was found in the endodontic lesions associated with persistent apical periodontitis. P. endodontalis, A. viscosus, C. albicans and P. gingivalis were the dominant species identified.

Distinct enzymatic and cellular characteristics of two secretory phospholipases A2 in the filamentous fungus Aspergillus oryzae.

PubMed

Nakahama, Tomoyuki; Nakanishi, Yoshito; Viscomi, Arturo R; Takaya, Kohei; Kitamoto, Katsuhiko; Ottonello, Simone; Arioka, Manabu

2010-04-01

Microbial secretory phospholipases A(2) (sPLA(2)s) are among the last discovered and least known members of this functionally diverse family of enzymes. We analyzed here two sPLA(2)s, named sPlaA and sPlaB, of the filamentous ascomycete Aspergillus oryzae. sPlaA and sPlaB consist of 222 and 160 amino acids, respectively, and share the conserved Cys and catalytic His-Asp residues typical of microbial sPLA(2)s. Two sPLA(2)s differ in pH optimum, Ca(2+) requirement and expression profile. The splaA mRNA was strongly upregulated in response to carbon starvation, oxidative stress and during conidiation, while splaB was constitutively expressed at low levels and was weakly upregulated by heat shock. Experiments with sPLA(2) overexpressing strains demonstrated that two enzymes produce subtly different phospholipid composition variations and also differ in their subcellular localization: sPlaA is most abundant in hyphal tips and secreted to the medium, whereas sPlaB predominantly localizes to the ER-like intracellular compartment. Both sPLA(2) overexpressing strains were defective in conidiation, which was more pronounced for sPlaB overexpressors. Although no major morphological abnormality was detected in either DeltasplaA or DeltasplaB mutants, hyphal growth of DeltasplaB, but not that of DeltasplaA, displayed increased sensitivity to H(2)O(2) treatment. These data indicate that two A. oryzae sPLA(2) enzymes display distinct, presumably non-redundant, physiological functions.

hypD as a Marker for [NiFe]-Hydrogenases in Microbial Communities of Surface Waters

PubMed Central

Beimgraben, Christian; Gutekunst, Kirstin; Opitz, Friederike

2014-01-01

Hydrogen is an important trace gas in the atmosphere. Soil microorganisms are known to be an important part of the biogeochemical H2 cycle, contributing 80 to 90% of the annual hydrogen uptake. Different aquatic ecosystems act as either sources or sinks of hydrogen, but the contribution of their microbial communities is unknown. [NiFe]-hydrogenases are the best candidates for hydrogen turnover in these environments since they are able to cope with oxygen. As they lack sufficiently conserved sequence motifs, reliable markers for these enzymes are missing, and consequently, little is known about their environmental distribution. We analyzed the essential maturation genes of [NiFe]-hydrogenases, including their frequency of horizontal gene transfer, and found hypD to be an applicable marker for the detection of the different known hydrogenase groups. Investigation of two freshwater lakes showed that [NiFe]-hydrogenases occur in many prokaryotic orders. We found that the respective hypD genes cooccur with oxygen-tolerant [NiFe]-hydrogenases (groups 1 and 5) mainly of Actinobacteria, Acidobacteria, and Burkholderiales; cyanobacterial uptake hydrogenases (group 2a) of cyanobacteria; H2-sensing hydrogenases (group 2b) of Burkholderiales, Rhizobiales, and Rhodobacterales; and two groups of multimeric soluble hydrogenases (groups 3b and 3d) of Legionellales and cyanobacteria. These findings support and expand a previous analysis of metagenomic data (M. Barz et al., PLoS One 5:e13846, 2010, http://dx.doi.org/10.1371/journal.pone.0013846) and further identify [NiFe]-hydrogenases that could be involved in hydrogen cycling in aquatic surface waters. PMID:24727276

Methodological approaches for studying the microbial ecology of drinking water distribution systems.

PubMed

Douterelo, Isabel; Boxall, Joby B; Deines, Peter; Sekar, Raju; Fish, Katherine E; Biggs, Catherine A

2014-11-15

The study of the microbial ecology of drinking water distribution systems (DWDS) has traditionally been based on culturing organisms from bulk water samples. The development and application of molecular methods has supplied new tools for examining the microbial diversity and activity of environmental samples, yielding new insights into the microbial community and its diversity within these engineered ecosystems. In this review, the currently available methods and emerging approaches for characterising microbial communities, including both planktonic and biofilm ways of life, are critically evaluated. The study of biofilms is considered particularly important as it plays a critical role in the processes and interactions occurring at the pipe wall and bulk water interface. The advantages, limitations and usefulness of methods that can be used to detect and assess microbial abundance, community composition and function are discussed in a DWDS context. This review will assist hydraulic engineers and microbial ecologists in choosing the most appropriate tools to assess drinking water microbiology and related aspects. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

Galectins as self/non-self recognition receptors in innate and adaptive immunity: an unresolved paradox

PubMed Central

Vasta, Gerardo R.; Ahmed, Hafiz; Nita-Lazar, Mihai; Banerjee, Aditi; Pasek, Marta; Shridhar, Surekha; Guha, Prasun; Fernández-Robledo, José A.

2012-01-01

Galectins are characterized by their binding affinity for β-galactosides, a unique binding site sequence motif, and wide taxonomic distribution and structural conservation in vertebrates, invertebrates, protista, and fungi. Since their initial description, galectins were considered to bind endogenous (“self”) glycans and mediate developmental processes and cancer. In the past few years, however, numerous studies have described the diverse effects of galectins on cells involved in both innate and adaptive immune responses, and the mechanistic aspects of their regulatory roles in immune homeostasis. More recently, however, evidence has accumulated to suggest that galectins also bind exogenous (“non-self”) glycans on the surface of potentially pathogenic microbes, parasites, and fungi, suggesting that galectins can function as pattern recognition receptors (PRRs) in innate immunity. Thus, a perplexing paradox arises by the fact that galectins also recognize lactosamine-containing glycans on the host cell surface during developmental processes and regulation of immune responses. According to the currently accepted model for non-self recognition, PRRs recognize pathogens via highly conserved microbial surface molecules of wide distribution such as LPS or peptidoglycan (pathogen-associated molecular patterns; PAMPs), which are absent in the host. Hence, this would not apply to galectins, which apparently bind similar self/non-self molecular patterns on host and microbial cells. This paradox underscores first, an oversimplification in the use of the PRR/PAMP terminology. Second, and most importantly, it reveals significant gaps in our knowledge about the diversity of the host galectin repertoire, and the subcellular targeting, localization, and secretion. Furthermore, our knowledge about the structural and biophysical aspects of their interactions with the host and microbial carbohydrate moieties is fragmentary, and warrants further investigation. PMID:22811679

Common themes in microbial pathogenicity revisited.

PubMed Central

Finlay, B B; Falkow, S

1997-01-01

Bacterial pathogens employ a number of genetic strategies to cause infection and, occasionally, disease in their hosts. Many of these virulence factors and their regulatory elements can be divided into a smaller number of groups based on the conservation of similar mechanisms. These common themes are found throughout bacterial virulence factors. For example, there are only a few general types of toxins, despite a large number of host targets. Similarly, there are only a few conserved ways to build the bacterial pilus and nonpilus adhesins used by pathogens to adhere to host substrates. Bacterial entry into host cells (invasion) is a complex mechanism. However, several common invasion themes exist in diverse microorganisms. Similarly, once inside a host cell, pathogens have a limited number of ways to ensure their survival, whether remaining within a host vacuole or by escaping into the cytoplasm. Avoidance of the host immune defenses is key to the success of a pathogen. Several common themes again are employed, including antigenic variation, camouflage by binding host molecules, and enzymatic degradation of host immune components. Most virulence factors are found on the bacterial surface or secreted into their immediate environment, yet virulence factors operate through a relatively small number of microbial secretion systems. The expression of bacterial pathogenicity is dependent upon complex regulatory circuits. However, pathogens use only a small number of biochemical families to express distinct functional factors at the appropriate time that causes infection. Finally, virulence factors maintained on mobile genetic elements and pathogenicity islands ensure that new strains of pathogens evolve constantly. Comprehension of these common themes in microbial pathogenicity is critical to the understanding and study of bacterial virulence mechanisms and to the development of new "anti-virulence" agents, which are so desperately needed to replace antibiotics. PMID:9184008

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

PubMed

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

2012-08-01

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

Enrichment of arsenic transforming and resistant heterotrophic bacteria from sediments of two salt lakes in Northern Chile.

PubMed

Lara, José; Escudero González, Lorena; Ferrero, Marcela; Chong Díaz, Guillermo; Pedrós-Alió, Carlos; Demergasso, Cecilia

2012-05-01

Microbial populations are involved in the arsenic biogeochemical cycle in catalyzing arsenic transformations and playing indirect roles. To investigate which ecotypes among the diverse microbial communities could have a role in cycling arsenic in salt lakes in Northern Chile and to obtain clues to facilitate their isolation in pure culture, sediment samples from Salar de Ascotán and Salar de Atacama were cultured in diluted LB medium amended with NaCl and arsenic, at different incubation conditions. The samples and the cultures were analyzed by nucleic acid extraction, fingerprinting analysis, and sequencing. Microbial reduction of As was evidenced in all the enrichments carried out in anaerobiosis. The results revealed that the incubation factors were more important for determining the microbial community structure than arsenic species and concentrations. The predominant microorganisms in enrichments from both sediments belonged to the Firmicutes and Proteobacteria phyla, but most of the bacterial ecotypes were confined to only one system. The occurrence of an active arsenic biogeochemical cycle was suggested in the system with the highest arsenic content that included populations compatible with microorganisms able to transform arsenic for energy conservation, accumulate arsenic, produce H(2), H(2)S and acetic acid (potential sources of electrons for arsenic reduction) and tolerate high arsenic levels.

The genome sequence of Dyella jiangningensis FCAV SCS01 from a lignocellulose-decomposing microbial consortium metagenome reveals potential for biotechnological applications.

PubMed

Desiderato, Joana G; Alvarenga, Danillo O; Constancio, Milena T L; Alves, Lucia M C; Varani, Alessandro M

2018-05-14

Cellulose and its associated polymers are structural components of the plant cell wall, constituting one of the major sources of carbon and energy in nature. The carbon cycle is dependent on cellulose- and lignin-decomposing microbial communities and their enzymatic systems acting as consortia. These microbial consortia are under constant exploration for their potential biotechnological use. Herein, we describe the characterization of the genome of Dyella jiangningensis FCAV SCS01, recovered from the metagenome of a lignocellulose-degrading microbial consortium, which was isolated from a sugarcane crop soil under mechanical harvesting and covered by decomposing straw. The 4.7 Mbp genome encodes 4,194 proteins, including 36 glycoside hydrolases (GH), supporting the hypothesis that this bacterium may contribute to lignocellulose decomposition. Comparative analysis among fully sequenced Dyella species indicate that the genome synteny is not conserved, and that D. jiangningensis FCAV SCS01 carries 372 unique genes, including an alpha-glucosidase and maltodextrin glucosidase coding genes, and other potential biomass degradation related genes. Additional genomic features, such as prophage-like, genomic islands and putative new biosynthetic clusters were also uncovered. Overall, D. jiangningensis FCAV SCS01 represents the first South American Dyella genome sequenced and shows an exclusive feature among its genus, related to biomass degradation.

Hydraulic fracturing offers view of microbial life in the deep terrestrial subsurface.

PubMed

Mouser, Paula J; Borton, Mikayla; Darrah, Thomas H; Hartsock, Angela; Wrighton, Kelly C

2016-11-01

Horizontal drilling and hydraulic fracturing are increasingly used for recovering energy resources in black shales across the globe. Although newly drilled wells are providing access to rocks and fluids from kilometer depths to study the deep biosphere, we have much to learn about microbial ecology of shales before and after 'fracking'. Recent studies provide a framework for considering how engineering activities alter this rock-hosted ecosystem. We first provide data on the geochemical environment and microbial habitability in pristine shales. Next, we summarize data showing the same pattern across fractured shales: diverse assemblages of microbes are introduced into the subsurface, eventually converging to a low diversity, halotolerant, bacterial and archaeal community. Data we synthesized show that the shale microbial community predictably shifts in response to temporal changes in geochemistry, favoring conservation of key microorganisms regardless of inputs, shale location or operators. We identified factors that constrain diversity in the shale and inhibit biodegradation at the surface, including salinity, biocides, substrates and redox. Continued research in this engineered ecosystem is required to assess additive biodegradability, quantify infrastructure biocorrosion, treat wastewaters that return to the surface and potentially enhance energy production through in situ methanogenesis. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

The Effect Of microbial Mats In The Decay Of Anurans With Implications For Understanding Taphonomic Processes In The Fossil Record

PubMed Central

Iniesto, M.; Villalba, I.; Buscalioni, A. D.; Guerrero, M. C.; López-Archilla, A. I.

2017-01-01

The pattern and sequence of the decomposition of the Pipidae African dwarf frog (Hymenochirus boettgeri) is tracked in an experiment with microbial mats in order to explore soft tissue preservation over three years. Frog decay in microbial mats is preceded by rapid entombment (25–30 days) and mediated by the formation of a sarcophagus, which is built by a complex microbial community. The frog carcasses maintained a variety of soft tissues for years. Labile organic structures show greater durability within the mat, cells maintain their general shape (bone marrow cells and adipocytes), and muscles and connective tissues (adipose and fibrous tendons) exhibit their original organic structures. In addition, other soft tissues are promptly mineralized (day 540) in a Ca-rich carbonate phase (encephalic tectum) or enriched in sulphur residues (integumentary system). The result is coherent with a bias in soft-tissue preservation, as some tissues are more likely to be conserved than others. The outcomes support observations of exceptionally preserved fossil anurans (adults and tadpoles). Decomposition in mats shows singular conditions of pH and dissolved oxygen. Mineralization processes could be more diverse than in simple heterotrophic biofilms, opening new taphonomic processes that have yet to be explored. PMID:28338095

Modified Pressure Imaging for Egg Crack Detection and Resulting Egg Quality

USDA-ARS?s Scientific Manuscript database

Cracks in the shell surface impair the primary barrier for external microbial contamination of the egg. Microcracks are very small cracks in the shell surface which are difficult to detect by human graders. New technology has been developed which utilizes modified pressure and imaging to detect mi...

Soil microbial communities of three grassland ecosystems in the Bayinbuluke, China.

PubMed

Shao, Keqiang; Gao, Guang

2018-03-01

The microbial community plays an important role in soil nutrient cycles and energy transformations in alpine grassland. In this study, we investigated the composition of the soil microbial community collected from alpine cold swamp meadow (ASM), alpine cold meadow (AM), and alpine cold desert steppe (ADS) within the Bayinbuluke alpine grassland, China, using Illumina amplicon sequencing. Of the 147 271 sequences obtained, 36 microbial phyla or groups were detected. The results showed that the ADS had lower microbial diversity than the ASM and AM, as estimated by the Shannon index. The Verrucomicrobia, Chloroflexi, Planctomycetes, Proteobacteria, and Actinobacteria were the predominant phyla in all 3 ecosystems. Particularly, Thaumarchaeota was only abundant in ASM, Bacteroidetes in AM, and Acidobacteria in ADS. Additionally, the predominant genus also differed with each ecosystem. Candidatus Nitrososphaera was predominant in ADS, the Pir4 lineage in ASM, and Sphingomonas in AM. Our results indicated that the soil microbial community structure was different for each grassland ecosystem in the Bayinbuluke.

Signatures of natural selection and ecological differentiation in microbial genomes.

PubMed

Shapiro, B Jesse

2014-01-01

We live in a microbial world. Most of the genetic and metabolic diversity that exists on earth - and has existed for billions of years - is microbial. Making sense of this vast diversity is a daunting task, but one that can be approached systematically by analyzing microbial genome sequences. This chapter explores how the evolutionary forces of recombination and selection act to shape microbial genome sequences, leaving signatures that can be detected using comparative genomics and population-genetic tests for selection. I describe the major classes of tests, paying special attention to their relative strengths and weaknesses when applied to microbes. Specifically, I apply a suite of tests for selection to a set of closely-related bacterial genomes with different microhabitat preferences within the marine water column, shedding light on the genomic mechanisms of ecological differentiation in the wild. I will focus on the joint problem of simultaneously inferring the boundaries between microbial populations, and the selective forces operating within and between populations.

Effects of heavy metals on soil microbial community

NASA Astrophysics Data System (ADS)

Chu, Dian

2018-02-01

Soil is one of the most important environmental natural resources for human beings living, which is of great significance to the quality of ecological environment and human health. The study of the function of arable soil microbes exposed to heavy metal pollution for a long time has a very important significance for the usage of farmland soil. In this paper, the effects of heavy metals on soil microbial community were reviewed. The main contents were as follows: the effects of soil microbes on soil ecosystems; the effects of heavy metals on soil microbial activity, soil enzyme activities and the composition of soil microbial community. In addition, a brief description of main methods of heavy metal detection for soil pollution is given, and the means of researching soil microbial community composition are introduced as well. Finally, it is concluded that the study of soil microbial community can well reflect the degree of soil heavy metal pollution and the impact of heavy metal pollution on soil ecology.

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

PubMed

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

2010-06-01

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

Recycling of treated domestic effluent from an on-site wastewater treatment system for hydroponics.

PubMed

Oyama, N; Nair, J; Ho, G E

2005-01-01

An alternative method to conserve water and produce crops in arid regions is through hydroponics. Application of treated wastewater for hydroponics will help in stripping off nutrients from wastewater, maximising reuse through reduced evaporation losses, increasing control on quality of water and reducing risk of pathogen contamination. This study focuses on the efficiency of treated wastewater from an on-site aerobic wastewater treatment unit. The experiment aimed to investigate 1) nutrient reduction 2) microbial reduction and 3) growth rate of plants fed on wastewater compared to a commercial hydroponics medium. The study revealed that the chemical and microbial quality of wastewater after hydroponics was safe and satisfactory for irrigation and plant growth rate in wastewater hydroponics was similar to those grown in a commercial medium.

Identification of microbes from the surfaces of food-processing lines based on the flow cytometric evaluation of cellular metabolic activity combined with cell sorting.

PubMed

Juzwa, W; Duber, A; Myszka, K; Białas, W; Czaczyk, K

2016-09-01

In this study the design of a flow cytometry-based procedure to facilitate the detection of adherent bacteria from food-processing surfaces was evaluated. The measurement of the cellular redox potential (CRP) of microbial cells was combined with cell sorting for the identification of microorganisms. The procedure enhanced live/dead cell discrimination owing to the measurement of the cell physiology. The microbial contamination of the surface of a stainless steel conveyor used to process button mushrooms was evaluated in three independent experiments. The flow cytometry procedure provided a step towards monitoring of contamination and enabled the assessment of microbial food safety hazards by the discrimination of active, mid-active and non-active bacterial sub-populations based on determination of their cellular vitality and subsequently single cell sorting to isolate microbial strains from discriminated sub-populations. There was a significant correlation (r = 0.97; p < 0.05) between the bacterial cell count estimated by the pour plate method and flow cytometry, despite there being differences in the absolute number of cells detected. The combined approach of flow cytometric CRP measurement and cell sorting allowed an in situ analysis of microbial cell vitality and the identification of species from defined sub-populations, although the identified microbes were limited to culturable cells.

Use of real-time qPCR to quantify members of the unculturable heterotrophic bacterial community in a deep sea marine sponge, Vetulina sp.

PubMed

Cassler, M; Peterson, C L; Ledger, A; Pomponi, S A; Wright, A E; Winegar, R; McCarthy, P J; Lopez, J V

2008-04-01

In this report, real-time quantitative PCR (TaqMan qPCR) of the small subunit (SSU) 16S-like rRNA molecule, a universal phylogenetic marker, was used to quantify the relative abundance of individual bacterial members of a diverse, yet mostly unculturable, microbial community from a marine sponge. Molecular phylogenetic analyses of bacterial communities derived from Caribbean Lithistid sponges have shown a wide diversity of microbes that included at least six major subdivisions; however, very little overlap was observed between the culturable and unculturable microbial communities. Based on sequence data of three culture-independent Lithistid-derived representative bacteria, we designed probe/primer sets for TaqMan qPCR to quantitatively characterize selected microbial residents in a Lithistid sponge, Vetulina, metagenome. TaqMan assays included specificity testing, DNA limit of detection analysis, and quantification of specific microbial rRNA sequences such as Nitrospira-like microbes and Actinobacteria up to 172 million copies per microgram per Lithistid sponge metagenome. By contrast, qPCR amplification with probes designed for common previously cultured sponge-associated bacteria in the genera Rheinheimera and Marinomonas and a representative of the CFB group resulted in only minimal detection of the Rheiheimera in total DNA extracted from the sponge. These data verify that a large portion of the microbial community within Lithistid sponges may consist of currently unculturable microorganisms.

Diversity of the Sediment Microbial Community in the Aha Watershed (Southwest China) in Response to Acid Mine Drainage Pollution Gradients.

PubMed

Sun, Weimin; Xiao, Tangfu; Sun, Min; Dong, Yiran; Ning, Zengping; Xiao, Enzong; Tang, Song; Li, Jiwei

2015-08-01

Located in southwest China, the Aha watershed is continually contaminated by acid mine drainage (AMD) produced from upstream abandoned coal mines. The watershed is fed by creeks with elevated concentrations of aqueous Fe (total Fe > 1 g/liter) and SO4 (2-) (>6 g/liter). AMD contamination gradually decreases throughout downstream rivers and reservoirs, creating an AMD pollution gradient which has led to a suite of biogeochemical processes along the watershed. In this study, sediment samples were collected along the AMD pollution sites for geochemical and microbial community analyses. High-throughput sequencing found various bacteria associated with microbial Fe and S cycling within the watershed and AMD-impacted creek. A large proportion of Fe- and S-metabolizing bacteria were detected in this watershed. The dominant Fe- and S-metabolizing bacteria were identified as microorganisms belonging to the genera Metallibacterium, Aciditerrimonas, Halomonas, Shewanella, Ferrovum, Alicyclobacillus, and Syntrophobacter. Among them, Halomonas, Aciditerrimonas, Metallibacterium, and Shewanella have previously only rarely been detected in AMD-contaminated environments. In addition, the microbial community structures changed along the watershed with different magnitudes of AMD pollution. Moreover, the canonical correspondence analysis suggested that temperature, pH, total Fe, sulfate, and redox potentials (Eh) were significant factors that structured the microbial community compositions along the Aha watershed. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Something new from something old? Fracking stimulated microbial processes

NASA Astrophysics Data System (ADS)

Wrighton, K. C.; Daly, R. A.; Hoyt, D.; Trexler, R.; McRae, J.; Wilkins, M.; Mouser, P. J.

2015-12-01

Hydraulic fracturing, colloquially known as "fracking", is employed for effective gas and oil recovery in deep shales. This process injects organisms and liquids from the surface into the deep subsurface (~2500 m), exposing microorganisms to high pressures, elevated temperatures, chemical additives, and brine-level salinities. Here we use assembly-based metagenomics to create a metabolic blueprint from an energy-producing Marcellus shale well over a 328-day period. Using this approach we ask the question: What abiotic and biotic factors drive microbial metabolism and thus biogeochemical cycling during natural gas extraction? We found that after 49 days, increased salinity in produced waters corresponded to a shift in the microbial community, with only organisms that encode salinity adaptations detected. We posit that organic compatible solutes, produced by organisms adapting to increased salinity, fuels a methylamine-driven ecosystem in fractured shale. This metabolic network ultimately results in biogenic methane production from members of Methanohalophilus and Methanolobus. Proton NMR validated these genomic hypotheses, with mono-methylamine being highest in the input material, but detected throughout the sampling. Beyond abiotic constraints, our genomic investigations revealed that viruses can be linked to key members of the microbial community, potentially releasing methylamine osmoprotectants and impacting bacterial strain variation. Collectively our results indicate that adaptation to high salinity, metabolism in the absence of oxidized electron acceptors, and viral predation are controlling factors mediating microbial community metabolism during hydraulic fracturing of the deep subsurface.

Microbial Genetic Memory to Study Heterogeneous Soil Processes

NASA Astrophysics Data System (ADS)

Fulk, E. M.; Silberg, J. J.; Masiello, C. A.

2017-12-01

Microbes can be engineered to sense environmental conditions and produce a detectable output. These microbial biosensors have traditionally used visual outputs that are difficult to detect in soil. However, recently developed gas-producing biosensors can be used to noninvasively monitor complex soil processes such as horizontal gene transfer or cell-cell signaling. While these biosensors report on the fraction of a microbial population exposed to a process or chemical signal at the time of measurement, they do not record a "memory" of past exposure. Synthetic biologists have recently developed a suite of genetically encoded memory circuits capable of reporting on historical exposure to the signal rather than just the current state. We will provide an overview of the microbial memory systems that may prove useful to studying microbial decision-making in response to environmental conditions. Simple memory circuits can give a yes/no report of any past exposure to the signal (for example anaerobic conditions, osmotic stress, or high nitrate concentrations). More complicated systems can report on the order of exposure of a population to multiple signals or the experiences of spatially distinct populations, such as those in root vs. bulk soil. We will report on proof-of-concept experiments showing the function of a simple permanent memory system in soil-cultured microbes, and we will highlight additional applications. Finally, we will discuss challenges still to be addressed in applying these memory circuits for biogeochemical studies.

Semi-quantitative evaluation of fecal contamination potential by human and ruminant sources using multiple lines of evidence

USGS Publications Warehouse

Stoeckel, D.M.; Stelzer, E.A.; Stogner, R.W.; Mau, D.P.

2011-01-01

Protocols for microbial source tracking of fecal contamination generally are able to identify when a source of contamination is present, but thus far have been unable to evaluate what portion of fecal-indicator bacteria (FIB) came from various sources. A mathematical approach to estimate relative amounts of FIB, such as Escherichia coli, from various sources based on the concentration and distribution of microbial source tracking markers in feces was developed. The approach was tested using dilute fecal suspensions, then applied as part of an analytical suite to a contaminated headwater stream in the Rocky Mountains (Upper Fountain Creek, Colorado). In one single-source fecal suspension, a source that was not present could not be excluded because of incomplete marker specificity; however, human and ruminant sources were detected whenever they were present. In the mixed-feces suspension (pet and human), the minority contributor (human) was detected at a concentration low enough to preclude human contamination as the dominant source of E. coli to the sample. Without the semi-quantitative approach described, simple detects of human-associated marker in stream samples would have provided inaccurate evidence that human contamination was a major source of E. coli to the stream. In samples from Upper Fountain Creek the pattern of E. coli, general and host-associated microbial source tracking markers, nutrients, and wastewater-associated chemical detections-augmented with local observations and land-use patterns-indicated that, contrary to expectations, birds rather than humans or ruminants were the predominant source of fecal contamination to Upper Fountain Creek. This new approach to E. coli allocation, validated by a controlled study and tested by application in a relatively simple setting, represents a widely applicable step forward in the field of microbial source tracking of fecal contamination. ?? 2011 Elsevier Ltd.

Trial watch

PubMed Central

Vacchelli, Erika; Galluzzi, Lorenzo; Eggermont, Alexander; Fridman, Wolf Hervé; Galon, Jerome; Sautès-Fridman, Catherine; Tartour, Eric; Zitvogel, Laurence; Kroemer, Guido

2012-01-01

Toll-like receptors (TLRs) have first been characterized for their capacity to detect conserved microbial components like lipopolysaccharide (LPS) and double-stranded RNA, resulting in the elicitation of potent (innate) immune responses against invading pathogens. More recently, TLRs have also been shown to promote the activation of the cognate immune system against cancer cells. Today, only three TLR agonists are approved by FDA for use in humans: the bacillus Calmette-Guérin (BCG), monophosphoryl lipid A (MPL) and imiquimod. BCG (an attenuated strain of Mycobacterium bovis) is mainly used as a vaccine against tuberculosis, but also for the immunotherapy of in situ bladder carcinoma. MPL (derived from the LPS of Salmonella minnesota) is included in the formulation of Cervarix®, a vaccine against human papillomavirus-16 and -18. Imiquimod (a synthetic imidazoquinoline) is routinely employed for actinic keratosis, superficial basal cell carcinoma, and external genital warts (condylomata acuminata). In this Trial Watch, we will summarize the results of recently completed clinical trials and discuss the progress of ongoing studies that have evaluated/are evaluating FDA-approved TLR agonists as off-label medications for cancer therapy. PMID:23162757

Does microbial contamination influence the success of the hematopoietic cell transplantation outcomes?

PubMed

Dal, Mehmet Sinan; Tekgündüz, Emre; Çakar, Merih Kızıl; Kaya, Ali Hakan; Namdaroğu, Sinem; Batgi, Hikmetullah; Bekdemir, Filiz; Uncu Ulu, Bahar; Yiğenoğlu, Tuğçe Nur; Kılınç, Ali; İskender, Dicle; Uğur, Bilge; Koçubaba, Şerife; İskender, Gülşen; Altuntaş, Fevzi

2016-08-01

Microbial contamination can be a marker for faulty process and is assumed to play an important role in the collection of hematopoietic progenitor cell (HPC) and infusion procedure. We aimed to determine the microbial contamination rates and evaluate the success of hematopoietic cell transplantation (HCT) in patients who received contaminated products. We analyzed microbial contamination records of HPC grafts between 2012 and 2015, retrospectively. Contamination rates of autologous donors were evaluated for at three steps: at the end of mobilization, following processing with dimethyl sulfoxide, and just before stem cell infusion. Grafts of allogeneic donors were assessed only before HCT. A total of 445 mobilization procedures were carried out on 333 (167 autologous and 166 allogeneic) donors. The microbiological contamination of peripheral blood (323/333 donations) and bone marrow (10/333 donations) products were analyzed. Bacterial contamination was detected in 18 of 1552 (1.15 %) culture bottles of 333 donors. During the study period 248 patients underwent HCT and among these patients microbial contamination rate on sample basis was 1.3 % (16/1212). Microbial contamination detected in nine patients (7 autologous; 2 allogeneic). In 8 of 9 patients, a febrile neutropenic attack was observed. The median day for the neutropenic fever was 4 days (0-9). None of the patients died within the post-transplant 30 days who received contaminated products. The use of contaminated products with antibiotic prophylaxis may be safe in terms of the first day of fever, duration of fever, neutrophil, platelet engraftment and duration of hospitalization. Copyright © 2016 Elsevier Ltd. All rights reserved.

Cultivation of methanogenic community from subseafloor sediments using a continuous-flow bioreactor

PubMed Central

Imachi, Hiroyuki; Aoi, Ken; Tasumi, Eiji; Saito, Yumi; Yamanaka, Yuko; Saito, Yayoi; Yamaguchi, Takashi; Tomaru, Hitoshi; Takeuchi, Rika; Morono, Yuki; Inagaki, Fumio; Takai, Ken

2011-01-01

Microbial methanogenesis in subseafloor sediments is a key process in the carbon cycle on the Earth. However, the cultivation-dependent evidences have been poorly demonstrated. Here we report the cultivation of a methanogenic microbial consortium from subseafloor sediments using a continuous-flow-type bioreactor with polyurethane sponges as microbial habitats, called down-flow hanging sponge (DHS) reactor. We anaerobically incubated methane-rich core sediments collected from off Shimokita Peninsula, Japan, for 826 days in the reactor at 10 °C. Synthetic seawater supplemented with glucose, yeast extract, acetate and propionate as potential energy sources was provided into the reactor. After 289 days of operation, microbiological methane production became evident. Fluorescence in situ hybridization analysis revealed the presence of metabolically active microbial cells with various morphologies in the reactor. DNA- and RNA-based phylogenetic analyses targeting 16S rRNA indicated the successful growth of phylogenetically diverse microbial components during cultivation in the reactor. Most of the phylotypes in the reactor, once it made methane, were more closely related to culture sequences than to the subsurface environmental sequence. Potentially methanogenic phylotypes related to the genera Methanobacterium, Methanococcoides and Methanosarcina were predominantly detected concomitantly with methane production, while uncultured archaeal phylotypes were also detected. Using the methanogenic community enrichment as subsequent inocula, traditional batch-type cultivations led to the successful isolation of several anaerobic microbes including those methanogens. Our results substantiate that the DHS bioreactor is a useful system for the enrichment of numerous fastidious microbes from subseafloor sediments and will enable the physiological and ecological characterization of pure cultures of previously uncultivated subseafloor microbial life. PMID:21654849

Cultivation of methanogenic community from subseafloor sediments using a continuous-flow bioreactor.

PubMed

Imachi, Hiroyuki; Aoi, Ken; Tasumi, Eiji; Saito, Yumi; Yamanaka, Yuko; Saito, Yayoi; Yamaguchi, Takashi; Tomaru, Hitoshi; Takeuchi, Rika; Morono, Yuki; Inagaki, Fumio; Takai, Ken

2011-12-01

Microbial methanogenesis in subseafloor sediments is a key process in the carbon cycle on the Earth. However, the cultivation-dependent evidences have been poorly demonstrated. Here we report the cultivation of a methanogenic microbial consortium from subseafloor sediments using a continuous-flow-type bioreactor with polyurethane sponges as microbial habitats, called down-flow hanging sponge (DHS) reactor. We anaerobically incubated methane-rich core sediments collected from off Shimokita Peninsula, Japan, for 826 days in the reactor at 10 °C. Synthetic seawater supplemented with glucose, yeast extract, acetate and propionate as potential energy sources was provided into the reactor. After 289 days of operation, microbiological methane production became evident. Fluorescence in situ hybridization analysis revealed the presence of metabolically active microbial cells with various morphologies in the reactor. DNA- and RNA-based phylogenetic analyses targeting 16S rRNA indicated the successful growth of phylogenetically diverse microbial components during cultivation in the reactor. Most of the phylotypes in the reactor, once it made methane, were more closely related to culture sequences than to the subsurface environmental sequence. Potentially methanogenic phylotypes related to the genera Methanobacterium, Methanococcoides and Methanosarcina were predominantly detected concomitantly with methane production, while uncultured archaeal phylotypes were also detected. Using the methanogenic community enrichment as subsequent inocula, traditional batch-type cultivations led to the successful isolation of several anaerobic microbes including those methanogens. Our results substantiate that the DHS bioreactor is a useful system for the enrichment of numerous fastidious microbes from subseafloor sediments and will enable the physiological and ecological characterization of pure cultures of previously uncultivated subseafloor microbial life.

Restricted-Range Fishes and the Conservation of Brazilian Freshwaters

PubMed Central

Nogueira, Cristiano; Buckup, Paulo A.; Menezes, Naercio A.; Oyakawa, Osvaldo T.; Kasecker, Thais P.; Ramos Neto, Mario B.; da Silva, José Maria C.

2010-01-01

Background Freshwaters are the most threatened ecosystems on earth. Although recent assessments provide data on global priority regions for freshwater conservation, local scale priorities remain unknown. Refining the scale of global biodiversity assessments (both at terrestrial and freshwater realms) and translating these into conservation priorities on the ground remains a major challenge to biodiversity science, and depends directly on species occurrence data of high taxonomic and geographic resolution. Brazil harbors the richest freshwater ichthyofauna in the world, but knowledge on endemic areas and conservation in Brazilian rivers is still scarce. Methodology/Principal Findings Using data on environmental threats and revised species distribution data we detect and delineate 540 small watershed areas harboring 819 restricted-range fishes in Brazil. Many of these areas are already highly threatened, as 159 (29%) watersheds have lost more than 70% of their original vegetation cover, and only 141 (26%) show significant overlap with formally protected areas or indigenous lands. We detected 220 (40%) critical watersheds overlapping hydroelectric dams or showing both poor formal protection and widespread habitat loss; these sites harbor 344 endemic fish species that may face extinction if no conservation action is in place in the near future. Conclusions/Significance We provide the first analysis of site-scale conservation priorities in the richest freshwater ecosystems of the globe. Our results corroborate the hypothesis that freshwater biodiversity has been neglected in former conservation assessments. The study provides a simple and straightforward method for detecting freshwater priority areas based on endemism and threat, and represents a starting point for integrating freshwater and terrestrial conservation in representative and biogeographically consistent site-scale conservation strategies, that may be scaled-up following naturally linked drainage systems. Proper management (e. g. forestry code enforcement, landscape planning) and conservation (e. g. formal protection) of the 540 watersheds detected herein will be decisive in avoiding species extinction in the richest aquatic ecosystems on the planet. PMID:20613986

Restricted-range fishes and the conservation of Brazilian freshwaters.

PubMed

Nogueira, Cristiano; Buckup, Paulo A; Menezes, Naercio A; Oyakawa, Osvaldo T; Kasecker, Thais P; Ramos Neto, Mario B; da Silva, José Maria C

2010-06-30

Freshwaters are the most threatened ecosystems on earth. Although recent assessments provide data on global priority regions for freshwater conservation, local scale priorities remain unknown. Refining the scale of global biodiversity assessments (both at terrestrial and freshwater realms) and translating these into conservation priorities on the ground remains a major challenge to biodiversity science, and depends directly on species occurrence data of high taxonomic and geographic resolution. Brazil harbors the richest freshwater ichthyofauna in the world, but knowledge on endemic areas and conservation in Brazilian rivers is still scarce. Using data on environmental threats and revised species distribution data we detect and delineate 540 small watershed areas harboring 819 restricted-range fishes in Brazil. Many of these areas are already highly threatened, as 159 (29%) watersheds have lost more than 70% of their original vegetation cover, and only 141 (26%) show significant overlap with formally protected areas or indigenous lands. We detected 220 (40%) critical watersheds overlapping hydroelectric dams or showing both poor formal protection and widespread habitat loss; these sites harbor 344 endemic fish species that may face extinction if no conservation action is in place in the near future. We provide the first analysis of site-scale conservation priorities in the richest freshwater ecosystems of the globe. Our results corroborate the hypothesis that freshwater biodiversity has been neglected in former conservation assessments. The study provides a simple and straightforward method for detecting freshwater priority areas based on endemism and threat, and represents a starting point for integrating freshwater and terrestrial conservation in representative and biogeographically consistent site-scale conservation strategies, that may be scaled-up following naturally linked drainage systems. Proper management (e. g. forestry code enforcement, landscape planning) and conservation (e. g. formal protection) of the 540 watersheds detected herein will be decisive in avoiding species extinction in the richest aquatic ecosystems on the planet.

A Fast Alignment-Free Approach for De Novo Detection of Protein Conserved Regions

PubMed Central

Abnousi, Armen; Broschat, Shira L.; Kalyanaraman, Ananth

2016-01-01

Background Identifying conserved regions in protein sequences is a fundamental operation, occurring in numerous sequence-driven analysis pipelines. It is used as a way to decode domain-rich regions within proteins, to compute protein clusters, to annotate sequence function, and to compute evolutionary relationships among protein sequences. A number of approaches exist for identifying and characterizing protein families based on their domains, and because domains represent conserved portions of a protein sequence, the primary computation involved in protein family characterization is identification of such conserved regions. However, identifying conserved regions from large collections (millions) of protein sequences presents significant challenges. Methods In this paper we present a new, alignment-free method for detecting conserved regions in protein sequences called NADDA (No-Alignment Domain Detection Algorithm). Our method exploits the abundance of exact matching short subsequences (k-mers) to quickly detect conserved regions, and the power of machine learning is used to improve the prediction accuracy of detection. We present a parallel implementation of NADDA using the MapReduce framework and show that our method is highly scalable. Results We have compared NADDA with Pfam and InterPro databases. For known domains annotated by Pfam, accuracy is 83%, sensitivity 96%, and specificity 44%. For sequences with new domains not present in the training set an average accuracy of 63% is achieved when compared to Pfam. A boost in results in comparison with InterPro demonstrates the ability of NADDA to capture conserved regions beyond those present in Pfam. We have also compared NADDA with ADDA and MKDOM2, assuming Pfam as ground-truth. On average NADDA shows comparable accuracy, more balanced sensitivity and specificity, and being alignment-free, is significantly faster. Excluding the one-time cost of training, runtimes on a single processor were 49s, 10,566s, and 456s for NADDA, ADDA, and MKDOM2, respectively, for a data set comprised of approximately 2500 sequences. PMID:27552220

The Biogeographic Pattern of Microbial Functional Genes along an Altitudinal Gradient of the Tibetan Pasture

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

Qi, Qi; Zhao, Mengxin; Wang, Shiping

As the highest place of the world, the Tibetan plateau is a fragile ecosystem. Given the importance of microbial communities in driving soil nutrient cycling, it is of interest to document the microbial biogeographic pattern here. We adopted a microarray-based tool named GeoChip 4.0 to investigate grassland microbial functional genes along an elevation gradient from 3200 to 3800 m above sea level open to free grazing by local herdsmen and wild animals. Interestingly, microbial functional diversities increase with elevation, so does the relative abundances of genes associated with carbon degradation, nitrogen cycling, methane production, cold shock and oxygen limitation. Themore » range of Shannon diversities (10.27–10.58) showed considerably smaller variation than what was previously observed at ungrazed sites nearby (9.95–10.65), suggesting the important role of livestock grazing on microbial diversities. Closer examination showed that the dissimilarity of microbial community at our study sites increased with elevations, revealing an elevation-decay relationship of microbial functional genes. Both microbial functional diversity and the number of unique genes increased with elevations. Furthermore, we detected a tight linkage of greenhouse gas (CO2) and relative abundances of carbon cycling genes. Our biogeographic study provides insights on microbial functional diversity and soil biogeochemical cycling in Tibetan pastures.« less

Inhibition, Conflict Detection, and Number Conservation

ERIC Educational Resources Information Center

Lubin, Amélie; Simon, Grégory; Houdé, Olivier; De Neys, Wim

2015-01-01

The acquisition of number conservation is a critical step in children's numerical and mathematical development. Classic developmental studies have established that children's number conservation is often biased by misleading intuitions. However, the precise nature of these conservation errors is not clear. A key question is whether conservation…

Baseline Assessment of Mesophotic Reefs of the Vitória-Trindade Seamount Chain Based on Water Quality, Microbial Diversity, Benthic Cover and Fish Biomass Data.

PubMed

Meirelles, Pedro M; Amado-Filho, Gilberto M; Pereira-Filho, Guilherme H; Pinheiro, Hudson T; de Moura, Rodrigo L; Joyeux, Jean-Christophe; Mazzei, Eric F; Bastos, Alex C; Edwards, Robert A; Dinsdale, Elizabeth; Paranhos, Rodolfo; Santos, Eidy O; Iida, Tetsuya; Gotoh, Kazuyoshi; Nakamura, Shota; Sawabe, Tomoo; Rezende, Carlos E; Gadelha, Luiz M R; Francini-Filho, Ronaldo B; Thompson, Cristiane; Thompson, Fabiano L

2015-01-01

Seamounts are considered important sources of biodiversity and minerals. However, their biodiversity and health status are not well understood; therefore, potential conservation problems are unknown. The mesophotic reefs of the Vitória-Trindade Seamount Chain (VTC) were investigated via benthic community and fish surveys, metagenomic and water chemistry analyses, and water microbial abundance estimations. The VTC is a mosaic of reef systems and includes fleshy algae dominated rhodolith beds, crustose coralline algae (CCA) reefs, and turf algae dominated rocky reefs of varying health levels. Macro-carnivores and larger fish presented higher biomass at the CCA reefs (4.4 kg per frame) than in the rhodolith beds and rocky reefs (0.0 to 0.1 kg per frame). A larger number of metagenomic sequences identified as primary producers (e.g., Chlorophyta and Streptophyta) were found at the CCA reefs. However, the rocky reefs contained more diseased corals (>90%) than the CCA reefs (~40%) and rhodolith beds (~10%). Metagenomic analyses indicated a heterotrophic and fast-growing microbiome in rocky reef corals that may possibly lead to unhealthy conditions possibly enhanced by environmental features (e.g. light stress and high loads of labile dissolved organic carbon). VTC mounts represent important hotspots of biodiversity that deserve further conservation actions.

Biodegradation of artificial monolayers applied to water storages to reduce evaporative loss.

PubMed

Pittaway, P; Herzig, M; Stuckey, N; Larsen, K

2015-01-01

Repeat applications of an artificial monolayer to the interfacial boundary layer of large agricultural water storages during periods of high evaporative demand remains the most commercially feasible water conservation strategy. However, the interfacial boundary layer (or microlayer) is ecologically distinct from subsurface water, and repeat monolayer applications may adversely affect microlayer processes. In this study, the natural cleansing mechanisms operating within the microlayer were investigated to compare the biodegradability of two fatty alcohol (C16OH and C18OH) and one glycol ether (C18E1) monolayer compound. The C16OH and C18OH compounds were more susceptible to microbial degradation, but the C18E1 compound was most susceptible to indirect photodegradation. On clean water the surface pressure and evaporation reduction achieved with a compressed C18E1 monolayer was superior to the C18OH monolayer, but on brown water the surface pressure dropped rapidly. These results suggest artificial monolayers are readily degraded by the synergy between photo and microbial degradation. The residence time of C18OH and C18E1 monolayers on clear water is sufficient for cost-effective water conservation. However, the susceptibility of C18E1 to photodegradation indicates the application of this monolayer to brown water may not be cost-effective.

Surveying the expanding prokaryotic Rubisco multiverse.

PubMed

Liu, Di; Ramya, Ramaswamy Chettiyan Seetharaman; Mueller-Cajar, Oliver

2017-09-01

The universal, but catalytically modest, CO2-fixing enzyme Rubisco is currently experiencing intense interest by researchers aiming to enhance crop photosynthesis. These efforts are mostly focused on the highly conserved hexadecameric enzyme found in land plants. In comparison, prokaryotic organisms harbor a far greater diversity in Rubisco forms. Recent work towards improving our appreciation of microbial Rubisco properties and harnessing their potential is surveyed. New structural models are providing informative glimpses into catalytic subtleties and diverse oligomeric states. Ongoing characterization is informing us about the conservation of constraints, such as sugar phosphate inhibition and the associated dependence on Rubisco activase helper proteins. Prokaryotic Rubiscos operate under a far wider range of metabolic contexts than the photosynthetic function of higher plant enzymes. Relaxed selection pressures may have resulted in the exploration of a larger volume of sequence space than permitted in organisms performing oxygenic photosynthesis. To tap into the potential of microbial Rubiscos, in vivo selection systems are being used to discover functional metagenomic Rubiscos. Various directed evolution systems to optimize their function have been developed. It is anticipated that this approach will provide access to biotechnologically valuable enzymes that cannot be encountered in the higher plant Rubisco space. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Linear relations in microbial reaction systems: a general overview of their origin, form, and use.

PubMed

Noorman, H J; Heijnen, J J; Ch A M Luyben, K

1991-09-01

In microbial reaction systems, there are a number of linear relations among net conversion rates. These can be very useful in the analysis of experimental data. This article provides a general approach for the formation and application of the linear relations. Two type of system descriptions, one considering the biomass as a black box and the other based on metabolic pathways, are encountered. These are defined in a linear vector and matrix algebra framework. A correct a priori description can be obtained by three useful tests: the independency, consistency, and observability tests. The independency are different. The black box approach provides only conservations relations. They are derived from element, electrical charge, energy, and Gibbs energy balances. The metabolic approach provides, in addition to the conservation relations, metabolic and reaction relations. These result from component, energy, and Gibbs energy balances. Thus it is more attractive to use the metabolic description than the black box approach. A number of different types of linear relations given in the literature are reviewed. They are classified according to the different categories that result from the black box or the metabolic system description. Validation of hypotheses related to metabolic pathways can be supported by experimental validation of the linear metabolic relations. However, definite proof from biochemical evidence remains indispensable.

Microbial communities along biogeochemical gradients in a hydrocarbon-contaminated aquifer.

PubMed

Tischer, Karolin; Kleinsteuber, Sabine; Schleinitz, Kathleen M; Fetzer, Ingo; Spott, Oliver; Stange, Florian; Lohse, Ute; Franz, Janett; Neumann, Franziska; Gerling, Sarah; Schmidt, Christian; Hasselwander, Eyk; Harms, Hauke; Wendeberg, Annelie

2013-09-01

Micro-organisms are known to degrade a wide range of toxic substances. How the environment shapes microbial communities in polluted ecosystems and thus influences degradation capabilities is not yet fully understood. In this study, we investigated microbial communities in a highly complex environment: the capillary fringe and subjacent sediments in a hydrocarbon-contaminated aquifer. Sixty sediment sections were analysed using terminal restriction fragment length polymorphism (T-RFLP) fingerprinting, cloning and sequencing of bacterial and archaeal 16S rRNA genes, complemented by chemical analyses of petroleum hydrocarbons, methane, oxygen and alternative terminal electron acceptors. Multivariate statistics revealed concentrations of contaminants and the position of the water table as significant factors shaping the microbial community composition. Micro-organisms with highest T-RFLP abundances were related to sulphate reducers belonging to the genus Desulfosporosinus, fermenting bacteria of the genera Sedimentibacter and Smithella, and aerobic hydrocarbon degraders of the genus Acidovorax. Furthermore, the acetoclastic methanogens Methanosaeta, and hydrogenotrophic methanogens Methanocella and Methanoregula were detected. Whereas sulphate and sulphate reducers prevail at the contamination source, the detection of methane, fermenting bacteria and methanogenic archaea further downstream points towards syntrophic hydrocarbon degradation. © 2013 John Wiley & Sons Ltd and Society for Applied Microbiology.

Lava cave microbial communities within mats and secondary mineral deposits: implications for life detection on other planets.

PubMed

Northup, D E; Melim, L A; Spilde, M N; Hathaway, J J M; Garcia, M G; Moya, M; Stone, F D; Boston, P J; Dapkevicius, M L N E; Riquelme, C

2011-09-01

Lava caves contain a wealth of yellow, white, pink, tan, and gold-colored microbial mats; but in addition to these clearly biological mats, there are many secondary mineral deposits that are nonbiological in appearance. Secondary mineral deposits examined include an amorphous copper-silicate deposit (Hawai'i) that is blue-green in color and contains reticulated and fuzzy filament morphologies. In the Azores, lava tubes contain iron-oxide formations, a soft ooze-like coating, and pink hexagons on basaltic glass, while gold-colored deposits are found in lava caves in New Mexico and Hawai'i. A combination of scanning electron microscopy (SEM) and molecular techniques was used to analyze these communities. Molecular analyses of the microbial mats and secondary mineral deposits revealed a community that contains 14 phyla of bacteria across three locations: the Azores, New Mexico, and Hawai'i. Similarities exist between bacterial phyla found in microbial mats and secondary minerals, but marked differences also occur, such as the lack of Actinobacteria in two-thirds of the secondary mineral deposits. The discovery that such deposits contain abundant life can help guide our detection of life on extraterrestrial bodies.

Molecular Detection of Legionella spp. and their associations with Mycobacterium spp., Pseudomonas aeruginosa and amoeba hosts in a drinking water distribution system.

PubMed

Lu, J; Struewing, I; Vereen, E; Kirby, A E; Levy, K; Moe, C; Ashbolt, N

2016-02-01

This study investigated waterborne opportunistic pathogens (OPs) including potential hosts, and evaluated the use of Legionella spp. for indicating microbial water quality for OPs within a full-scale operating drinking water distribution system (DWDS). To investigate the occurrence of specific microbial pathogens within a major city DWDS we examined large volume (90 l drinking water) ultrafiltration (UF) concentrates collected from six sites between February, 2012 and June, 2013. The detection frequency and concentration estimates by qPCR were: Legionella spp. (57%/85 cell equivalent, CE l(-1) ), Mycobacterium spp. (88%/324 CE l(-1) ), Pseudomonas aeruginosa (24%/2 CE l(-1) ), Vermamoeba vermiformis (24%/2 CE l(-1) ) and Acanthamoeba spp. (42%/5 cyst equivalent, CE l(-1) ). There was no detection of the following microorganisms: human faecal indicator Bacteroides (HF183), Salmonella enterica, Campylobacter spp., Escherichia coli O157:H7, Giardia intestinalis, Cryptosporidium spp. or Naegleria fowleri. There were significant correlations between the qPCR signals of Legionella spp. and Mycobacterium spp., and their potential hosts V. vermiformis and Acanthamoeba spp. Sequencing of Legionella spp. demonstrated limited diversity, with most sequences coming from two dominant groups, of which the larger dominant group was an unidentified species. Other known species including Legionella pneumophila were detected, but at low frequency. The densities of Legionella spp. and Mycobacterium spp. were generally higher (17 and 324 folds, respectively) for distal sites relative to the entry point to the DWDS. Legionella spp. occurred, had significant growth and were strongly associated with free-living amoebae (FLA) and Mycobacterium spp., suggesting that Legionella spp. could provide a useful DWDS monitoring role to indicate potential conditions for non-faecal OPs. The results provide insight into microbial pathogen detection that may aid in the monitoring of microbial water quality within DWDS prior to customer exposures. © 2015 The Society for Applied Microbiology.

Oil Biodegradation and Oil-Degrading Microbial Populations in Marsh Sediments Impacted by Oil from the Deepwater Horizon Well Blowout.

PubMed

Atlas, Ronald M; Stoeckel, Donald M; Faith, Seth A; Minard-Smith, Angela; Thorn, Jonathan R; Benotti, Mark J

2015-07-21

To study hydrocarbon biodegradation in marsh sediments impacted by Macondo oil from the Deepwater Horizon well blowout, we collected sediment cores 18-36 months after the accident at the marshes in Bay Jimmy (Upper Barataria Bay), Louisiana, United States. The highest concentrations of oil were found in the top 2 cm of sediment nearest the waterline at the shorelines known to have been heavily oiled. Although petroleum hydrocarbons were detectable, Macondo oil could not be identified below 8 cm in 19 of the 20 surveyed sites. At the one site where oil was detected below 8 cm, concentrations were low. Residual Macondo oil was already highly weathered at the start of the study, and the concentrations of individual saturated hydrocarbons and polycyclic aromatic hydrocarbons continued to decrease over the course of the study due to biodegradation. Desulfococcus oleovorans, Marinobacter hydrocarbonoclasticus, Mycobacterium vanbaalenii, and related mycobacteria were the most abundant oil-degrading microorganisms detected in the top 2 cm at the oiled sites. Relative populations of these taxa declined as oil concentrations declined. The diversity of the microbial community was low at heavily oiled sites compared to that of the unoiled reference sites. As oil concentrations decreased over time, microbial diversity increased and approached the diversity levels of the reference sites. These trends show that the oil continues to be biodegraded, and microbial diversity continues to increase, indicating ongoing overall ecological recovery.

Phylogenetic analysis of TCE-dechlorinating consortia enriched on a variety of electron donors.

PubMed

Freeborn, Ryan A; West, Kimberlee A; Bhupathiraju, Vishvesh K; Chauhan, Sadhana; Rahm, Brian G; Richardson, Ruth E; Alvarez-Cohen, Lisa

2005-11-01

Two rapidly fermented electron donors, lactate and methanol, and two slowly fermented electron donors, propionate and butyrate, were selected for enrichment studies to evaluate the characteristics of anaerobic microbial consortia that reductively dechlorinate TCE to ethene. Each electron donor enrichment subculture demonstrated the ability to dechlorinate TCE to ethene through several serial transfers. Microbial community analyses based upon 16S rDNA, including terminal restriction fragment length polymorphism (T-RFLP) and clone library/sequencing, were performed to assess major changes in microbial community structure associated with electron donors capable of stimulating reductive dechlorination. Results demonstrated that five phylogenic subgroups or genera of bacteria were present in all consortia, including Dehalococcoides sp., low G+C Gram-positives (mostly Clostridium and Eubacterium sp.), Bacteroides sp., Citrobacter sp., and delta Proteobacteria (mostly Desulfovibrio sp.). Phylogenetic association indicates that only minor shifts in the microbial community structure occurred between the four alternate electron donor enrichments and the parent consortium. Inconsistent detection of Dehalococcoides spp. in clone libraries and T-RFLP of enrichment subcultures was resolved using quantitative polymerase chain reaction (Q-PCR). Q-PCR with primers specific to Dehalococcoides 16S rDNA resulted in positive detection of this species in all enrichments. Our results suggest that TCE-dechlorinating consortia can be stably maintained on a variety of electron donors and that quantities of Dehalococcoides cells detected with Dehalococcoides specific 16S rDNA primer/probe sets do not necessarily correlate well with solvent degradation rates.

Microbial activity in an acid resin deposit: biodegradation potential and ecotoxicology in an extremely acidic hydrocarbon contamination.

PubMed

Kloos, Karin; Schloter, Michael; Meyer, Ortwin

2006-11-01

Acid resins are residues produced in a recycling process for used oils that was in use in the forties and fifties of the last century. The resin-like material is highly contaminated with mineral oil hydrocarbons, extremely acidic and co-contaminated with substituted and aromatic hydrocarbons, and heavy metals. To determine the potential for microbial biodegradation the acid resin deposit and its surroundings were screened for microbial activity by soil respiration measurements. No microbial activity was found in the core deposit. However, biodegradation of hydrocarbons was possible in zones with a lower degree of contamination surrounding the deposit. An extreme acidophilic microbial community was detected close to the core deposit. With a simple ecotoxicological approach it could be shown that the pure acid resin that formed the major part of the core deposit, was toxic to the indigenous microflora due to its extremely low pH of 0-1.

Effect of gamma irradiation under various atmospheres of packaging on the microbial and physicochemical properties of turmeric powder

NASA Astrophysics Data System (ADS)

Esmaeili, Saeideh; Barzegar, Mohsen; Sahari, Mohammad Ali; Berengi-Ardestani, Samira

2018-07-01

This study investigated the effect of gamma irradiation (0, 5, 10, and 15 kGy) under various atmospheres of packaging (air, N₂, and vacuum) on the microbial load and physicochemical properties of turmeric powder, including antioxidant activities, total phenolic content (TPC), color parameters, and curcuminoid content. The efficiency of irradiation in reducing microbial contamination in the samples was observed even at the lowest dose. By increasing the irradiation dose, the microbial load was not detectable. Irradiation in the presence of oxygen had synergistic effects on the extraction of curcuminoids and TPC, and increased the antioxidant activity of the methanolic extracts: highest activity was observed at 15 kGy. Generally, gamma irradiation up to the dose of 10 kGy under air atmosphere not only ensured microbial safety and desirability of turmeric powder, but also improved the extraction yield of bioactive compounds and, consequently, antioxidant activities of the samples.

Microbial Diagnostic Microarrays for the Detection and Typing of Food- and Water-Borne (Bacterial) Pathogens

PubMed Central

Kostić, Tanja; Sessitsch, Angela

2011-01-01

Reliable and sensitive pathogen detection in clinical and environmental (including food and water) samples is of greatest importance for public health. Standard microbiological methods have several limitations and improved alternatives are needed. Most important requirements for reliable analysis include: (i) specificity; (ii) sensitivity; (iii) multiplexing potential; (iv) robustness; (v) speed; (vi) automation potential; and (vii) low cost. Microarray technology can, through its very nature, fulfill many of these requirements directly and the remaining challenges have been tackled. In this review, we attempt to compare performance characteristics of the microbial diagnostic microarrays developed for the detection and typing of food and water pathogens, and discuss limitations, points still to be addressed and issues specific for the analysis of food, water and environmental samples. PMID:27605332

A fosmid cloning strategy for detecting the widest possible spectrum of microbes from the international space station drinking water system.

PubMed

Choi, Sangdun; Chang, Mi Sook; Stuecker, Tara; Chung, Christine; Newcombe, David A; Venkateswaran, Kasthuri

2012-12-01

In this study, fosmid cloning strategies were used to assess the microbial populations in water from the International Space Station (ISS) drinking water system (henceforth referred to as Prebiocide and Tank A water samples). The goals of this study were: to compare the sensitivity of the fosmid cloning strategy with that of traditional culture-based and 16S rRNA-based approaches and to detect the widest possible spectrum of microbial populations during the water purification process. Initially, microbes could not be cultivated, and conventional PCR failed to amplify 16S rDNA fragments from these low biomass samples. Therefore, randomly primed rolling-circle amplification was used to amplify any DNA that might be present in the samples, followed by size selection by using pulsed-field gel electrophoresis. The amplified high-molecular-weight DNA from both samples was cloned into fosmid vectors. Several hundred clones were randomly selected for sequencing, followed by Blastn/Blastx searches. Sequences encoding specific genes from Burkholderia, a species abundant in the soil and groundwater, were found in both samples. Bradyrhizobium and Mesorhizobium, which belong to rhizobia, a large community of nitrogen fixers often found in association with plant roots, were present in the Prebiocide samples. Ralstonia, which is prevalent in soils with a high heavy metal content, was detected in the Tank A samples. The detection of many unidentified sequences suggests the presence of potentially novel microbial fingerprints. The bacterial diversity detected in this pilot study using a fosmid vector approach was higher than that detected by conventional 16S rRNA gene sequencing.

Electron microscopy study of microbial mat in the North Fiji basin hydrothermal vent

NASA Astrophysics Data System (ADS)

Park, H.; Kim, J. W.; Lee, J. W.

2017-12-01

Hydrothermal vent systems consisting of hydrothermal vent, hydrothermal sediment and microbial mat are widely spread around the ocean, particularly spreading axis, continental margin and back-arc basin. Scientists have perceived that the hydrothermal systems, which reflect the primeval earth environment, are one of the best places to reveal the origin of life and extensive biogeochemical process of microbe-mineral interaction. In the present study multiline of analytical methods (X-Ray Diffraction (XRD), Scanning Electron Microscopy (SEM) and Transmission Electron Microscopy (TEM)) were utilized to investigate the mineralogy/chemistry of microbe-mineral interaction in hydrothermal microbial mat. Microbial mat samples were recovered by Canadian scientific submersible ROPOS on South Pacific North Fiji basin KIOST hydrothermal vent expedition 1602. XRD analysis showed that red-colored microbial mat contains Fe-oxides and Fe-oxyhydroxides. Various morphologies of minerals in the red-colored microbial mat observed by SEM are mainly showed sheath shaped, resembled with Leptothrix microbial structure, stalks shaped, similar with Marioprofundus microbial structure and globule shaped microbial structures. They are also detected with DNA analysis. The cross sectional observation of microbial structures encrusted with Fe-oxide and Fe-oxyhydroxide at a nano scale by Transmission Electron Microscopy (TEM) and Focused Ion Beam (FIB) technique was developed to verify the structural/biogeochemical properties in the microbe-mineral interaction. Systematic nano-scale measurements on the biomineralization in the microbial mat leads the understandings of biogeochemical environments around the hydrothermal vent.

Metabolite exchange between microbiome members produces compounds that influence Drosophila behavior

PubMed Central

Fischer, Caleb N; Trautman, Eric P; Crawford, Jason M; Stabb, Eric V; Handelsman, Jo; Broderick, Nichole A

2017-01-01

Animals host multi-species microbial communities (microbiomes) whose properties may result from inter-species interactions; however, current understanding of host-microbiome interactions derives mostly from studies in which elucidation of microbe-microbe interactions is difficult. In exploring how Drosophila melanogaster acquires its microbiome, we found that a microbial community influences Drosophila olfactory and egg-laying behaviors differently than individual members. Drosophila prefers a Saccharomyces-Acetobacter co-culture to the same microorganisms grown individually and then mixed, a response mainly due to the conserved olfactory receptor, Or42b. Acetobacter metabolism of Saccharomyces-derived ethanol was necessary, and acetate and its metabolic derivatives were sufficient, for co-culture preference. Preference correlated with three emergent co-culture properties: ethanol catabolism, a distinct volatile profile, and yeast population decline. Egg-laying preference provided a context-dependent fitness benefit to larvae. We describe a molecular mechanism by which a microbial community affects animal behavior. Our results support a model whereby emergent metabolites signal a beneficial multispecies microbiome. DOI: http://dx.doi.org/10.7554/eLife.18855.001 PMID:28068220

Integrative computational approach for genome-based study of microbial lipid-degrading enzymes.

PubMed

Vorapreeda, Tayvich; Thammarongtham, Chinae; Laoteng, Kobkul

2016-07-01

Lipid-degrading or lipolytic enzymes have gained enormous attention in academic and industrial sectors. Several efforts are underway to discover new lipase enzymes from a variety of microorganisms with particular catalytic properties to be used for extensive applications. In addition, various tools and strategies have been implemented to unravel the functional relevance of the versatile lipid-degrading enzymes for special purposes. This review highlights the study of microbial lipid-degrading enzymes through an integrative computational approach. The identification of putative lipase genes from microbial genomes and metagenomic libraries using homology-based mining is discussed, with an emphasis on sequence analysis of conserved motifs and enzyme topology. Molecular modelling of three-dimensional structure on the basis of sequence similarity is shown to be a potential approach for exploring the structural and functional relationships of candidate lipase enzymes. The perspectives on a discriminative framework of cutting-edge tools and technologies, including bioinformatics, computational biology, functional genomics and functional proteomics, intended to facilitate rapid progress in understanding lipolysis mechanism and to discover novel lipid-degrading enzymes of microorganisms are discussed.

Captivity results in disparate loss of gut microbial diversity in closely related hosts

PubMed Central

Kohl, Kevin D.; Skopec, Michele M.; Dearing, M. Denise

2014-01-01

The gastrointestinal tracts of animals contain diverse communities of microbes that provide a number of services to their hosts. There is recent concern that these communities may be lost as animals enter captive breeding programmes, due to changes in diet and/or exposure to environmental sources. However, empirical evidence documenting the effects of captivity and captive birth on gut communities is lacking. We conducted three studies to advance our knowledge in this area. First, we compared changes in microbial diversity of the gut communities of two species of woodrats (Neotoma albigula, a dietary generalist, and Neotoma stephensi, which specializes on juniper) before and after 6–9 months in captivity. Second, we investigated whether reintroduction of the natural diet of N. stephensi could restore microbial diversity. Third, we compared the microbial communities between offspring born in captivity and their mothers. We found that the dietary specialist, N. stephensi, lost a greater proportion of its native gut microbiota and overall diversity in response to captivity compared with N. albigula. Addition of the natural diet increased the proportion of the original microbiota but did not restore overall diversity in N. stephensi. Offspring of N. albigula more closely resembled their mothers compared with offspring–mother pairs of N. stephensi. This research suggests that the microbiota of dietary specialists may be more susceptible to captivity. Furthermore, this work highlights the need for further studies investigating the mechanisms underlying how loss of microbial diversity may vary between hosts and what an acceptable level of diversity loss may be to a host. This knowledge will aid conservation biologists in designing captive breeding programmes effective at maintaining microbial diversity. Sequence Accession Numbers: NCBI's Sequence Read Archive (SRA) – SRP033616 PMID:27293630

Microbial electron transport and energy conservation – the foundation for optimizing bioelectrochemical systems

PubMed Central

Kracke, Frauke; Vassilev, Igor; Krömer, Jens O.

2015-01-01

Microbial electrochemical techniques describe a variety of emerging technologies that use electrode–bacteria interactions for biotechnology applications including the production of electricity, waste and wastewater treatment, bioremediation and the production of valuable products. Central in each application is the ability of the microbial catalyst to interact with external electron acceptors and/or donors and its metabolic properties that enable the combination of electron transport and carbon metabolism. And here also lies the key challenge. A wide range of microbes has been discovered to be able to exchange electrons with solid surfaces or mediators but only a few have been studied in depth. Especially electron transfer mechanisms from cathodes towards the microbial organism are poorly understood but are essential for many applications such as microbial electrosynthesis. We analyze the different electron transport chains that nature offers for organisms such as metal respiring bacteria and acetogens, but also standard biotechnological organisms currently used in bio-production. Special focus lies on the essential connection of redox and energy metabolism, which is often ignored when studying bioelectrochemical systems. The possibility of extracellular electron exchange at different points in each organism is discussed regarding required redox potentials and effect on cellular redox and energy levels. Key compounds such as electron carriers (e.g., cytochromes, ferredoxin, quinones, flavins) are identified and analyzed regarding their possible role in electrode–microbe interactions. This work summarizes our current knowledge on electron transport processes and uses a theoretical approach to predict the impact of different modes of transfer on the energy metabolism. As such it adds an important piece of fundamental understanding of microbial electron transport possibilities to the research community and will help to optimize and advance bioelectrochemical techniques. PMID:26124754

Impact of adding Saccharomyces strains on fermentation, aerobic stability, nutritive value, and select lactobacilli populations in corn silage.

PubMed

Duniere, L; Jin, L; Smiley, B; Qi, M; Rutherford, W; Wang, Y; McAllister, T

2015-05-01

Bacterial inoculants can improve the conservation and nutritional quality of silages. Inclusion of the yeast Saccharomyces in the diet of dairy cattle has also been reported to be beneficial. The present study assessed the ability of silage to be used as a means of delivering Saccharomyces strains to ruminants. Two strains of Saccharomyces cerevisiae (strain 1 and 3)and 1 strain of Saccharomyces paradoxus (strain 2) were inoculated (10(3) cfu/g) individually onto corn forage that was ensiled in mini silos for 90 d. Fermentation characteristics, aerobic stability, and nutritive value of silages were determined and real-time quantitative PCR (RT-qPCR) was used to quantify S. cerevisiae, S.paradoxus, total Saccharomyces, fungal, and bacterial populations. Fermentation characteristics of silage inoculated with S1 were similar to control silage. Although strain 3 inoculation increased ash and decreased OM contents of silage (P = 0.017), no differences were observed in nutrient composition or fermentation profiles after 90 d of ensiling. Inoculation with Saccharomyces had no detrimental effect on the aerobic stability of silage. In vitro DM disappearance, gas production, and microbial protein synthesis were not affected by yeast inoculation.Saccharomyces strain 1 was quantified throughout ensiling, whereas strain 2 was detected only immediately after inoculation. Saccharomyces cerevisiae strain 3 was quantified until d 7 and detectable 90 d after ensiling. All inoculants were detected and quantified during aerobic exposure. Inoculation with Saccharomyces did not alter lactobacilli populations. Saccharomycetales were detected by RT-qPCR throughout ensiling in all silages. Both S. cerevisiae and S. paradoxus populations increased during aerobic exposure, demonstrating that the density of these yeast strains would increase between the time that silage was removed from storage and the time it was fed.

Measurement of microbial activity in soil by colorimetric observation of in situ dye reduction: an approach to detection of extraterrestrial life

PubMed Central

Crawford, Ronald L; Paszczynski, Andrzej; Lang, Qingyong; Erwin, Daniel P; Allenbach, Lisa; Corti, Giancarlo; Anderson, Tony J; Cheng, I Francis; Wai, Chien; Barnes, Bruce; Wells, Richard; Assefi, Touraj; Mojarradi, Mohammad

2002-01-01

Background Detecting microbial life in extraterrestrial locations is a goal of space exploration because of ecological and health concerns about possible contamination of other planets with earthly organisms, and vice versa. Previously we suggested a method for life detection based on the fact that living entities require a continual input of energy accessed through coupled oxidations and reductions (an electron transport chain). We demonstrated using earthly soils that the identification of extracted components of electron transport chains is useful for remote detection of a chemical signature of life. The instrument package developed used supercritical carbon dioxide for soil extraction, followed by chromatography or electrophoresis to separate extracted compounds, with final detection by voltammetry and tandem mass-spectrometry. Results Here we used Earth-derived soils to develop a related life detection system based on direct observation of a biological redox signature. We measured the ability of soil microbial communities to reduce artificial electron acceptors. Living organisms in pure culture and those naturally found in soil were shown to reduce 2,3-dichlorophenol indophenol (DCIP) and the tetrazolium dye 2,3-bis(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide inner salt (XTT). Uninoculated or sterilized controls did not reduce the dyes. A soil from Antarctica that was determined by chemical signature and DNA analysis to be sterile also did not reduce the dyes. Conclusion Observation of dye reduction, supplemented with extraction and identification of only a few specific signature redox-active biochemicals such as porphyrins or quinones, provides a simplified means to detect a signature of life in the soils of other planets or their moons. PMID:12150716

Remote sensing techniques for the detection of soil erosion and the identification of soil conservation practices

NASA Technical Reports Server (NTRS)

Pelletier, R. E.; Griffin, R. H.

1985-01-01

The following paper is a summary of a number of techniques initiated under the AgRISTARS (Agriculture and Resources Inventory Surveys Through Aerospace Remote Sensing) project for the detection of soil degradation caused by water erosion and the identification of soil conservation practices for resource inventories. Discussed are methods to utilize a geographic information system to determine potential soil erosion through a USLE (Universal Soil Loss Equation) model; application of the Kauth-Thomas Transform to detect present erosional status; and the identification of conservation practices through visual interpretation and a variety of enhancement procedures applied to digital remotely sensed data.

Using Remote Sensing and GIS Techniques to Detect Changes to the Prince Alfred Hamlet Conservation Area in the Western Cape, South Africa

NASA Astrophysics Data System (ADS)

Duncan, P.; Lewarne, M.

2016-06-01

Understanding and identifying the spatial-temporal changes in the natural environment is crucial for monitoring and evaluating conservation efforts, as well as understanding the impact of human activities on natural resources, informing responsible land management, and promoting better decision-making. Conservation areas are often under pressure from expanding farming and related industry, invasive alien vegetation, and an ever-increasing human settlement footprint. This study focuses on detecting changes to the Prince Alfred Hamlet commonage, near Ceres in the Cape Floral Kingdom. It was chosen for its high conservation value and significance as a critical water source area. The study area includes a fast-growing human settlement footprint in a highly productive farming landscape. There are conflicting development needs as well as risks to agricultural production, and both of these threaten the integrity of the ecosystems which supply underlying services to both demands on the land. Using a multi-disciplinary approach and high-resolution satellite imagery, land use and land cover changes can be detected and classified, and the results used to support the conservation of biodiversity and wildlife, and protect our natural resources. The aim of this research is to study the efficacy of using remote sensing and GIS techniques to detect changes to critical conservation areas where disturbances can be understood, and therefore better managed and mitigated before these areas are degraded beyond repair.

Characterization of Microbial Communities Associated With Deep-Sea Hydrothermal Vent Animals of the East Pacific Rise and the Galápagos Rift

NASA Astrophysics Data System (ADS)

Ward, N.; Page, S.; Heidelberg, J.; Eisen, J. A.; Fraser, C. M.

2002-12-01

The composition of microbial communities associated with deep-sea hydrothermal vent animals is of interest because of the key role of bacterial symbionts in driving the chemosynthetic food chain of the vent system, and also because bacterial biofilms attached to animal exterior surfaces may play a part in settlement of larval forms. Sequence analysis of 16S ribosomal RNA (rRNA) genes from such communities provides a snapshot of community structure, as this gene is present in all Bacteria and Archaea, and a useful phylogenetic marker for both cultivated microbial species, and uncultivated species such as many of those found in the deep-sea environment. Specimens of giant tube worms (Riftia pachyptila), mussels (Bathymodiolus thermophilus), and clams (Calyptogena magnifica) were collected during the 2002 R/V Atlantis research cruises to the East Pacific Rise (9N) and Galápagos Rift. Microbial biofilms attached to the exterior surfaces of individual animals were sampled, as were tissues known to harbor chemosynthetic bacterial endosymbionts. Genomic DNA was extracted from the samples using a commercially available kit, and 16S rRNA genes amplified from the mixed bacterial communities using the polymerase chain reaction (PCR) and oligonucleotide primers targeting conserved terminal regions of the 16S rRNA gene. The PCR products obtained were cloned into a plasmid vector and the recombinant plasmids transformed into cells of Escherichia coli. Individual cloned 16S rRNA genes were sequenced at the 5' end of the gene (the most phylogenetically informative region in most taxa) and the sequence data compared to publicly available gene sequence databases, to allow a preliminary assignment of clones to taxonomic groups within the Bacteria and Archaea, and to determine the overall composition and phylogenetic diversity of the animal-associated microbial communities. Analysis of Riftia pachyptila exterior biofilm samples revealed the presence of members of the delta and epsilon proteobacteria, low GC Gram positive bacteria (firmicutes), spirochetes, CFB (Cytophaga-Flavobacterium-Bacteroides) group, green nonsulfur bacteria, acidobacteria, verrucomicrobia, and planctomycetes. The presence of the latter three taxonomic groups is of special interest, as they represent phylogenetically distinct groups within the Bacteria for which specific ecological functions have not yet been identified, but which have been found to be widely distributed and often numerically significant in diverse terrestrial and aquatic habitats. Although further sequencing is required to demonstrate the presence of a Riftia-associated microbial population distinct from that of the surrounding seawater, results available from three Riftia individuals from the East Pacific Rise suggest this to be the case. Analysis of microbial communities associated with the gill tissue of the mussel Bathymodiolus thermophilus shows a population dominated by gamma-Proteobacterial chemoautotrophic symbionts, although lower frequency novel phylotypes have been detected. Representatives of specific taxonomic groups have been selected for sequencing of the complete 16S rRNA gene, and the sequences used to reconstruct phylogenetic trees to more accurately determine the evolutionary relationships between the novel sequences, and available sequences for both cultured and non-cultured bacteria.