Molecular Networking and Pattern-Based Genome Mining Improves discovery of biosynthetic gene clusters and their products from Salinispora species

PubMed Central

Duncan, Katherine R.; Crüsemann, Max; Lechner, Anna; Sarkar, Anindita; Li, Jie; Ziemert, Nadine; Wang, Mingxun; Bandeira, Nuno; Moore, Bradley S.; Dorrestein, Pieter C.; Jensen, Paul R.

2015-01-01

Summary Genome sequencing has revealed that bacteria contain many more biosynthetic gene clusters than predicted based on the number of secondary metabolites discovered to date. While this biosynthetic reservoir has fostered interest in new tools for natural product discovery, there remains a gap between gene cluster detection and compound discovery. Here we apply molecular networking and the new concept of pattern-based genome mining to 35 Salinispora strains including 30 for which draft genome sequences were either available or obtained for this study. The results provide a method to simultaneously compare large numbers of complex microbial extracts, which facilitated the identification of media components, known compounds and their derivatives, and new compounds that could be prioritized for structure elucidation. These efforts revealed considerable metabolite diversity and led to several molecular family-gene cluster pairings, of which the quinomycin-type depsipeptide retimycin A was characterized and linked to gene cluster NRPS40 using pattern-based bioinformatic approaches. PMID:25865308

Hydrogen Fluxes from Photosynthetic Communities: Implications for Early Earth Biogeochemistry

NASA Technical Reports Server (NTRS)

Hoehler, Tori M.; Bebout, Brad M.; DesMarais, David J.; DeVincenzi, Donald L. (Technical Monitor)

2000-01-01

More than half the history of life on Earth was dominated by photosynthetic microbial mats, which must have represented the preeminent biological influence on global geochemical cycling during that time. In modem analogs of then ancient communities, hypersaline microbial mats from Guerrero Negro, Mexico, we have observed a large flux of molecular hydrogen originating in the cyanobacteria-dominated surface layers. Hydrogen production follows a distinct diel pattern and is sensitive to both oxygen tension and microbial species composition within the mat. On an early Earth dominated by microbial mats, the observed H2 fluxes would scale to global levels far in excess of geothermal emissions. A hydrogen flux of this magnitude represents a profound transmission of reducing power from oxygenic photosynthesis, both to the anaerobic biosphere, where H2 is an almost universally-utilized substrate and regulator of microbial redox chemistry, and to the atmosphere, where subsequent escape to space could provide an important mechanism for the net oxidation of Earth's surface.

Geochemically distinct carbon isotope distributions in Allochromatium vinosum DSM 180T grown photoautotrophically and photoheterotrophically.

PubMed

Tang, T; Mohr, W; Sattin, S R; Rogers, D R; Girguis, P R; Pearson, A

2017-03-01

Anoxygenic, photosynthetic bacteria are common at redox boundaries. They are of interest in microbial ecology and geosciences through their role in linking the carbon, sulfur, and iron cycles, yet much remains unknown about how their flexible carbon metabolism-permitting either autotrophic or heterotrophic growth-is recorded in the bulk sedimentary and lipid biomarker records. Here, we investigated patterns of carbon isotope fractionation in a model photosynthetic sulfur-oxidizing bacterium, Allochromatium vinosum DSM180 T . In one treatment, A. vinosum was grown with CO 2 as the sole carbon source, while in a second treatment, it was grown on acetate. Different intracellular isotope patterns were observed for fatty acids, phytol, individual amino acids, intact proteins, and total RNA between the two experiments. Photoautotrophic CO 2 fixation yielded typical isotopic ordering for the lipid biomarkers: δ 13 C values of phytol > n-alkyl lipids. In contrast, growth on acetate greatly suppressed intracellular isotopic heterogeneity across all molecular classes, except for a marked 13 C-depletion in phytol. This caused isotopic "inversion" in the lipids (δ 13 C values of phytol < n-alkyl lipids). The finding suggests that inverse δ 13 C patterns of n-alkanes and pristane/phytane in the geologic record may be at least in part a signal for photoheterotrophy. In both experimental scenarios, the relative isotope distributions could be predicted from an isotope flux-balance model, demonstrating that microbial carbon metabolisms can be interrogated by combining compound-specific stable isotope analysis with metabolic modeling. Isotopic differences among molecular classes may be a means of fingerprinting microbial carbon metabolism, both in the modern environment and the geologic record. © 2017 John Wiley & Sons Ltd.

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

Microbial diversity and activity of an aged soil contaminated by polycyclic aromatic hydrocarbons.

PubMed

Zhao, Xiaohui; Fan, Fuqiang; Zhou, Huaidong; Zhang, Panwei; Zhao, Gaofeng

2018-06-01

In-depth understanding of indigenous microbial assemblages resulted from aged contamination by polycyclic aromatic hydrocarbons (PAHs) is of vital importance in successful in situ bioremediation treatments. Soil samples of three boreholes were collected at 12 different vertical depths. Overall, the dominating three-ring PAHs (76.2%) were closely related to distribution patterns of soil dehydrogenase activity, microbial cell numbers, and Shannon biodiversity index (H') of indigenous microorganisms. High-molecular-weight PAHs tend to yield more diverse communities. Results from 16S rRNA analysis indicated that possible functional groups of PAH degradation include three species in Bacillus cereus group, Bacillus sp. SA Ant14, Nocardioides sp., and Ralstonia pickettii. Principal component analysis indicates significant positive correlations between the content of high-molecular-weight PAHs and the distribution of Bacillus weihenstephanensis KBAB4 and Nocardioides sp. The species B. cereus 03BB102, Bacillus thuringiensis, B. weihenstephanensis KBAB4, and Nocardioides sp. were recognized as main PAH degraders and thus recommended to be utilized in further bioremediation applications. The vertical distribution characteristics of PAHs in soil profiles (1-12 m) and the internal relationship between the transport mechanisms of PAHs and the response of soil biological properties help further understand the microbial diversity and activity in an aged site.

Mapping and determinism of soil microbial community distribution across an agricultural landscape.

PubMed

Constancias, Florentin; Terrat, Sébastien; Saby, Nicolas P A; Horrigue, Walid; Villerd, Jean; Guillemin, Jean-Philippe; Biju-Duval, Luc; Nowak, Virginie; Dequiedt, Samuel; Ranjard, Lionel; Chemidlin Prévost-Bouré, Nicolas

2015-06-01

Despite the relevance of landscape, regarding the spatial patterning of microbial communities and the relative influence of environmental parameters versus human activities, few investigations have been conducted at this scale. Here, we used a systematic grid to characterize the distribution of soil microbial communities at 278 sites across a monitored agricultural landscape of 13 km². Molecular microbial biomass was estimated by soil DNA recovery and bacterial diversity by 16S rRNA gene pyrosequencing. Geostatistics provided the first maps of microbial community at this scale and revealed a heterogeneous but spatially structured distribution of microbial biomass and diversity with patches of several hundreds of meters. Variance partitioning revealed that both microbial abundance and bacterial diversity distribution were highly dependent of soil properties and land use (total variance explained ranged between 55% and 78%). Microbial biomass and bacterial richness distributions were mainly explained by soil pH and texture whereas bacterial evenness distribution was mainly related to land management. Bacterial diversity (richness, evenness, and Shannon index) was positively influenced by cropping intensity and especially by soil tillage, resulting in spots of low microbial diversity in soils under forest management. Spatial descriptors also explained a small but significant portion of the microbial distribution suggesting that landscape configuration also shapes microbial biomass and bacterial diversity. © 2015 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Molecular diagnostics for the detection and characterization of microbial pathogens.

PubMed

Procop, Gary W

2007-09-01

New and advanced methods of molecular diagnostics are changing the way we practice clinical microbiology, which affects the practice of medicine. Signal amplification and real-time nucleic acid amplification technologies offer a sensitive and specific result with a more rapid turnaround time than has ever before been possible. Numerous methods of postamplification analysis afford the simultaneous detection and differentiation of numerous microbial pathogens, their mechanisms of resistance, and the construction of disease-specific assays. The technical feasibility of these assays has already been demonstrated. How these new, often more expensive tests will be incorporated into routine practice and the impact they will have on patient care remain to be determined. One of the most attractive uses for such techniques is to achieve a more rapid characterization of the infectious agent so that a narrower-spectrum antimicrobial agent may be used, which should have an impact on resistance patterns.

Changes in Soil Organic Matter Abundance, Molecular Composition, and Diversity in an Arid Ecosystem in Response to Long-term Elevated CO2 Manipulation.

NASA Astrophysics Data System (ADS)

Hess, N. J.; Tfaily, M.; Evans, R. D.; Koyama, A.

2017-12-01

Little is known about how soils in arid ecosystems will respond to rising atmospheric CO2 concentration yet arid and semi-arid ecosystems cover more than 40% of Earth's land surface. Previous work in the Mojave Desert (Evans et al., 2014 Nature Climate Change) reported higher soil organic carbon (SOC) and total nitrogen (N) concentrations following 10 years exposure to elevated atmospheric CO2 at the Nevada Desert Free-Air-Carbon dioxide-Enrichment (FACE) Facility (NDFF). In this study, we investigated potential mechanisms that resulted in increased SOC and total N accumulation and stabilization using high resolution mass spectrometry at the NDFF site. Samples were collected from soil profiles to 1 m in depth with a 0.2 m a increment under the dominant evergreen shrub Larrea tridentata. The differences in the molecular composition and diversity of soil organic matter (SOM) were more evident in surface soils and declined with depth, and were consistent with higher SOC and total N concentrations under elevated than ambient CO2. Our molecular analysis also suggested increased root exudation and/or microbial necromass from stabilization of labile C and N contributed to SOM and N stocks. Increased microbial activity and metabolism under elevated CO2 compared to ambient plots suggested that elevated CO2 altered microbial carbon (C) use patterns, reflecting changes in the quality and quantity of SOC inputs. We found that plant-derived compounds were primary substrates for microbial activity under elevated CO2 and microbial products were the main constituents of stabilized SOM. Our results suggest that arid ecosystems are a potential large C sink under elevated CO2, give the extensive coverage of the land surface, and that labile compounds are transformed to stable SOM via microbial processes. Arid systems are limited by water, and thus may have a different C storage potential under changing climates than other ecosystems that are limited by nitrogen or phosphorus.

Two antibacterial C-type lectins from crustacean, Eriocheir sinensis, stimulated cellular encapsulation in vitro.

PubMed

Jin, Xing-Kun; Li, Shuang; Guo, Xiao-Nv; Cheng, Lin; Wu, Min-Hao; Tan, Shang-Jian; Zhu, You-Ting; Yu, Ai-Qing; Li, Wei-Wei; Wang, Qun

2013-12-01

The first step of host fighting against pathogens is that pattern recognition receptors recognized pathogen-associated molecular patterns. However, the specificity of recognition within the innate immune molecular of invertebrates remains largely unknown. In the present study, we investigated how invertebrate pattern recognition receptor (PRR) C-type lectins might be involved in the antimicrobial response in crustacean. Based on our previously obtained completed coding regions of EsLecA and EsLecG in Eriocheir sinensis, the recombinant EsLectin proteins were produced via prokaryotic expression system and affinity chromatography. Subsequently, both rEsLecA and rEsLecG were discovered to have wide spectrum binding activities towards microorganisms, and their microbial-binding was calcium-independent. Moreover, the binding activities of both rEsLecA and rEsLecG induced the aggregation against microbial pathogens. Both microorganism growth inhibitory activities assays and antibacterial activities assays revealed their capabilities of suppressing microorganisms growth and directly killing microorganisms respectively. Furthermore, the encapsulation assays signified that both rEsLecA and rEsLecG could stimulate the cellular encapsulation in vitro. Collectively, data presented here demonstrated the successful expression and purification of two C-type lectins proteins in the Chinese mitten crab, and their critical role in the innate immune system of an invertebrate. Copyright © 2013 Elsevier Ltd. All rights reserved.

Changing bacterial profile of Sundarbans, the world heritage mangrove: impact of anthropogenic interventions.

PubMed

Chakraborty, Arpita; Bera, Amit; Mukherjee, Arghya; Basak, Pijush; Khan, Imroze; Mondal, Arindam; Roy, Arunava; Bhattacharyya, Anish; SenGupta, Sohan; Roy, Debojyoti; Nag, Sudip; Ghosh, Abhrajyoti; Chattopadhyay, Dhrubajyoti; Bhattacharyya, Maitree

2015-04-01

Mangrove microbial communities and their associated activities have profound impact on biogeochemical cycles. Although microbial composition and structure are known to be influenced by biotic and abiotic factors in the mangrove sediments, finding direct correlations between them remains a challenge. In this study we have explored sediment bacterial diversity of the Sundarbans, a world heritage site using a culture-independent molecular approach. Bacterial diversity was analyzed from three different locations with a history of exposure to differential anthropogenic activities. 16S rRNA gene libraries were constructed and partial sequencing of the clones was performed to identify the microbial strains. We identified bacterial strains known to be involved in a variety of biodegradation/biotransformation processes including hydrocarbon degradation, and heavy metal resistance. Canonical Correspondence Analysis of the environmental and exploratory datasets revealed correlations between the ecological indices associated with pollutant levels and bacterial diversity across the sites. Our results indicate that sites with similar exposure of anthropogenic intervention reflect similar patterns of microbial diversity besides spatial commonalities.

Mapping spatial patterns of denitrifiers at large scales (Invited)

NASA Astrophysics Data System (ADS)

Philippot, L.; Ramette, A.; Saby, N.; Bru, D.; Dequiedt, S.; Ranjard, L.; Jolivet, C.; Arrouays, D.

2010-12-01

Little information is available regarding the landscape-scale distribution of microbial communities and its environmental determinants. Here we combined molecular approaches and geostatistical modeling to explore spatial patterns of the denitrifying community at large scales. The distribution of denitrifrying community was investigated over 107 sites in Burgundy, a 31 500 km2 region of France, using a 16 X 16 km sampling grid. At each sampling site, the abundances of denitrifiers and 42 soil physico-chemical properties were measured. The relative contributions of land use, spatial distance, climatic conditions, time and soil physico-chemical properties to the denitrifier spatial distribution were analyzed by canonical variation partitioning. Our results indicate that 43% to 85% of the spatial variation in community abundances could be explained by the measured environmental parameters, with soil chemical properties (mostly pH) being the main driver. We found spatial autocorrelation up to 739 km and used geostatistical modelling to generate predictive maps of the distribution of denitrifiers at the landscape scale. Studying the distribution of the denitrifiers at large scale can help closing the artificial gap between the investigation of microbial processes and microbial community ecology, therefore facilitating our understanding of the relationships between the ecology of denitrifiers and N-fluxes by denitrification.

Microbial carbon turnover in the plant-rhizosphere-soil continuum

NASA Astrophysics Data System (ADS)

Malik, Ashish; Dannert, Helena; Griffiths, Robert; Thomson, Bruce; Gleixner, Gerd

2014-05-01

Soil microbial biomass contributes significantly to maintenance of soil organic matter (SOM). It is well known that biochemical fractions of soil microorganisms have varying turnover and therefore contribute differentially to soil C storage. Here we compare the turnover rates of different microbial biochemical fractions using a pulse chase 13CO2 plant labelling experiment. The isotope signal was temporally traced into rhizosphere soil microorganisms using the following biomarkers: DNA, RNA, fatty acids and chloroform fumigation extraction derived microbial biomass size classes. C flow into soil microbial functional groups was assessed through phospholipid and neutral lipid fatty acid (PLFA/NLFA) analyses. Highest 13C enrichment was seen in the low molecular weight (LMW) size class of microbial biomass (Δδ13C =151) and in nucleic acids (DNA: 38o RNA: 66) immediately after the pulse followed by a sharp drop. The amount of 13C in the high molecular weight (HMW) microbial biomass (17-81) and total fatty acids (32-54) was lower initially and stayed relatively steady over the 4 weeks experimental period. We found significant differences in turnover rates of different microbial biochemical and size fractions. We infer that LMW cytosolic soluble compounds are rapidly metabolized and linked to respiratory C fluxes, whereas mid-sized products of microbial degradation and HMW polymeric compounds have lower renewal rate in that order. The turnover of cell wall fatty acids was also very slow. DNA and RNA showed faster turnover rate; and as expected RNA renewal was the fastest due to its rapid production by active microorganisms independent of cell replication. 13C incorporation into different functional groups confirmed that mutualistic arbuscular mycorrhizal fungi rely on root C and are important in the initial plant C flux. We substantiated through measurements of isotope incorporation into bacterial RNA that rhizosphere bacteria are also important in the initial C conduit from plants. Other saprophytic fungi and bacteria show a delayed 13C incorporation pattern which could suggest secondary 13C assimilation often indicative of trophic interactions. Thus, different soil microbial biochemical fractions as well as functional groups show differential C turnover which could have implications on soil C storage.

Transcriptomic responses of a simplified soil microcosm to a plant pathogen and its biocontrol agent reveal a complex reaction to harsh habitat.

PubMed

Perazzolli, Michele; Herrero, Noemí; Sterck, Lieven; Lenzi, Luisa; Pellegrini, Alberto; Puopolo, Gerardo; Van de Peer, Yves; Pertot, Ilaria

2016-10-27

Soil microorganisms are key determinants of soil fertility and plant health. Soil phytopathogenic fungi are one of the most important causes of crop losses worldwide. Microbial biocontrol agents have been extensively studied as alternatives for controlling phytopathogenic soil microorganisms, but molecular interactions between them have mainly been characterised in dual cultures, without taking into account the soil microbial community. We used an RNA sequencing approach to elucidate the molecular interplay of a soil microbial community in response to a plant pathogen and its biocontrol agent, in order to examine the molecular patterns activated by the microorganisms. A simplified soil microcosm containing 11 soil microorganisms was incubated with a plant root pathogen (Armillaria mellea) and its biocontrol agent (Trichoderma atroviride) for 24 h under controlled conditions. More than 46 million paired-end reads were obtained for each replicate and 28,309 differentially expressed genes were identified in total. Pathway analysis revealed complex adaptations of soil microorganisms to the harsh conditions of the soil matrix and to reciprocal microbial competition/cooperation relationships. Both the phytopathogen and its biocontrol agent were specifically recognised by the simplified soil microcosm: defence reaction mechanisms and neutral adaptation processes were activated in response to competitive (T. atroviride) or non-competitive (A. mellea) microorganisms, respectively. Moreover, activation of resistance mechanisms dominated in the simplified soil microcosm in the presence of both A. mellea and T. atroviride. Biocontrol processes of T. atroviride were already activated during incubation in the simplified soil microcosm, possibly to occupy niches in a competitive ecosystem, and they were not further enhanced by the introduction of A. mellea. This work represents an additional step towards understanding molecular interactions between plant pathogens and biocontrol agents within a soil ecosystem. Global transcriptional analysis of the simplified soil microcosm revealed complex metabolic adaptation in the soil environment and specific responses to antagonistic or neutral intruders.

Patterns of extracellular enzyme activities and microbial metabolism in an Arctic fjord of Svalbard and in the northern Gulf of Mexico: contrasts in carbon processing by pelagic microbial communities

PubMed Central

Arnosti, Carol; Steen, Andrew D.

2013-01-01

The microbial community composition of polar and temperate ocean waters differs substantially, but the potential functional consequences of these differences are largely unexplored. We measured bacterial production, glucose metabolism, and the abilities of microbial communities to hydrolyze a range of polysaccharides in an Arctic fjord of Svalbard (Smeerenburg Fjord), and thus to initiate remineralization of high-molecular weight organic matter. We compared these data with similar measurements previously carried out in the northern Gulf of Mexico in order to investigate whether differences in the spectrum of enzyme activities measurable in Arctic and temperate environments are reflected in “downstream” aspects of microbial metabolism (metabolism of monomers and biomass production). Only four of six polysaccharide substrates were hydrolyzed in Smeerenburg Fjord; all were hydrolyzed in the upper water column of the Gulf. These patterns are consistent on an interannual basis. Bacterial protein production was comparable at both locations, but the pathways of glucose utilization differed. Glucose incorporation rate constants were comparatively higher in Svalbard, but glucose respiration rate constants were higher in surface waters of the Gulf. As a result, at the time of sampling ca. 75% of the glucose was incorporated into biomass in Svalbard, but in the northern Gulf of Mexico most of the glucose was respired to CO2. A limited range of enzyme activities is therefore not a sign of a dormant community or one unable to further process substrates resulting from extracellular enzymatic hydrolysis. The ultimate fate of carbohydrates in marine waters, however, is strongly dependent upon the specific capabilities of heterotrophic microbial communities in these disparate environments. PMID:24198812

Detection of the plant parasite Cuscuta reflexa by a tomato cell surface receptor.

PubMed

Hegenauer, Volker; Fürst, Ursula; Kaiser, Bettina; Smoker, Matthew; Zipfel, Cyril; Felix, Georg; Stahl, Mark; Albert, Markus

2016-07-29

Parasitic plants are a constraint on agriculture worldwide. Cuscuta reflexa is a stem holoparasite that infests most dicotyledonous plants. One exception is tomato, which is resistant to C. reflexa We discovered that tomato responds to a small peptide factor occurring in Cuscuta spp. with immune responses typically activated after perception of microbe-associated molecular patterns. We identified the cell surface receptor-like protein CUSCUTA RECEPTOR 1 (CuRe1) as essential for the perception of this parasite-associated molecular pattern. CuRe1 is sufficient to confer responsiveness to the Cuscuta factor and increased resistance to parasitic C. reflexa when heterologously expressed in otherwise susceptible host plants. Our findings reveal that plants recognize parasitic plants in a manner similar to perception of microbial pathogens. Copyright © 2016, American Association for the Advancement of Science.

Plant immunity triggered by microbial molecular signatures.

PubMed

Zhang, Jie; Zhou, Jian-Min

2010-09-01

Pathogen/microbe-associated molecular patterns (PAMPs/MAMPs) are recognized by host cell surface-localized pattern-recognition receptors (PRRs) to activate plant immunity. PAMP-triggered immunity (PTI) constitutes the first layer of plant immunity that restricts pathogen proliferation. PTI signaling components often are targeted by various Pseudomonas syringae virulence effector proteins, resulting in diminished plant defenses and increased bacterial virulence. Some of the proteins targeted by pathogen effectors have evolved to sense the effector activity by associating with cytoplasmic immune receptors classically known as resistance proteins. This allows plants to activate a second layer of immunity termed effector-triggered immunity (ETI). Recent studies on PTI regulation and P. syringae effector targets have uncovered new components in PTI signaling. Although MAP kinase (MAPK) cascades have been considered crucial for PTI, emerging evidence indicates that a MAPK-independent pathway also plays an important role in PTI signaling.

Intestinal barrier dysfunction in cirrhosis: Current concepts in pathophysiology and clinical implications

PubMed Central

Tsiaoussis, Georgios I; Assimakopoulos, Stelios F; Tsamandas, Athanassios C; Triantos, Christos K; Thomopoulos, Konstantinos C

2015-01-01

The intestinal lumen is a host place for a wide range of microbiota and sets a unique interplay between local immune system, inflammatory cells and intestinal epithelium, forming a physical barrier against microbial invaders and toxins. Bacterial translocation is the migration of viable or nonviable microorganisms or their pathogen-associated molecular patterns, such as lipopolysaccharide, from the gut lumen to the mesenteric lymph nodes, systemic circulation and other normally sterile extraintestinal sites. A series of studies have shown that translocation of bacteria and their products across the intestinal barrier is a commonplace in patients with liver disease. The deterioration of intestinal barrier integrity and the consulting increased intestinal permeability in cirrhotic patients play a pivotal pathophysiological role in the development of severe complications as high rate of infections, spontaneous bacterial peritonitis, hepatic encephalopathy, hepatorenal syndrome, variceal bleeding, progression of liver injury and hepatocellular carcinoma. Nevertheless, the exact cellular and molecular mechanisms implicated in the phenomenon of microbial translocation in liver cirrhosis have not been fully elucidated yet. PMID:26301048

Commensal-Associated Molecular Patterns Induce Selective Toll-Like Receptor-Trafficking from Apical Membrane to Cytoplasmic Compartments in Polarized Intestinal Epithelium

PubMed Central

Cario, Elke; Brown, Dennis; McKee, Mary; Lynch-Devaney, Kathryn; Gerken, Guido; Podolsky, Daniel K.

2002-01-01

Commensal-associated molecular patterns, the major products of nonpathogenic bacteria, are present at high concentrations at the apical surface of the intestinal epithelium. However, the nature of the interaction of commensal-associated molecular patterns with the lumenal surface of the epithelium has not been defined. We have recently demonstrated that intestinal epithelial cells constitutively express several Toll-like receptors (TLRs) in vitro and in vivo that seem to be the key receptors responsible for immune cell activation in response to various bacterial products. In this study we characterize the subcellular distribution of two major TLRs, TLR2 and TLR4, and their ligand-specific dynamic regulation in the model human intestinal epithelial cell line T84. Immunocytochemical studies indicate that TLR2 and TLR4 are constitutively expressed at the apical pole of differentiated T84 cells. After stimulation with lipopolysaccharide or peptidoglycan, TLRs selectively traffic to cytoplasmic compartments near the basolateral membrane. Thus, we demonstrate that TLRs are positioned at the apical pole where they are poised to monitor the sensitive balance of the lumenal microbial array. The results of this dynamic epithelial surveillance can then be conveyed to the underlying cell populations of the lamina propria via these innate immune pattern recognition receptors. PMID:11786410

Study of Transport Characteristics of Motile Microorganisms Using Micro-Scale Devices

NASA Astrophysics Data System (ADS)

Parashar, R.; Scheibe, T. D.; Plymale, A.; Hu, D.; Kelly, R.; Frederick, J. M.; Yang, X.; Sund, N. L.

2016-12-01

Accurate numerical models of microbial transport are needed to support design and evaluation of bioremediation implementations. A sequence of micro-scale experiments using advanced microfluidics and imaging techniques was conducted to quantify the movement patterns of individual microbes and their interactions with solid surfaces in unobstructed medium and simple pore geometries. The set of bacteria studied encompasses strictly anaerobic, facultatively anaerobic, fermentative, and facultatively autotrophic species, with capacities to reduce a range of metals and radionuclides, as well as nitrate, using a variety of electron donors, including acetate, lactate, carbohydrates, and molecular hydrogen. Motion of motile microorganisms recorded over time provides results that can be analyzed to determine the character and several statistical attributes of microbial motion. Individual tracks on the order of several seconds to a few minutes in duration are characterized to provide information on 1) the length (distance in microns) of microbial runs, 2) velocity distributions along individual trajectories, and 3) the angle between the directions of sequential runs. Analysis of the microbial trajectories elucidates parameters related to dynamics of their motion. Comparison of these parameters with those of a classical Brownian motion yields crucial information on selection of appropriate model to account for microbial motility in relevant applications.

Factoring the intestinal microbiome into the pathogenesis of autoimmune hepatitis.

PubMed

Czaja, Albert J

2016-11-14

The intestinal microbiome is a reservoir of microbial antigens and activated immune cells. The aims of this review were to describe the role of the intestinal microbiome in generating innate and adaptive immune responses, indicate how these responses contribute to the development of systemic immune-mediated diseases, and encourage investigations that improve the understanding and management of autoimmune hepatitis. Alterations in the composition of the intestinal microflora (dysbiosis) can disrupt intestinal and systemic immune tolerances for commensal bacteria. Toll-like receptors within the intestine can recognize microbe-associated molecular patterns and shape subsets of T helper lymphocytes that may cross-react with host antigens (molecular mimicry). Activated gut-derived lymphocytes can migrate to lymph nodes, and gut-derived microbial antigens can translocate to extra-intestinal sites. Inflammasomes can form within hepatocytes and hepatic stellate cells, and they can drive the pro-inflammatory, immune-mediated, and fibrotic responses. Diet, designer probiotics, vitamin supplements, re-colonization methods, antibiotics, drugs that decrease intestinal permeability, and molecular interventions that block signaling pathways may emerge as adjunctive regimens that complement conventional immunosuppressive management. In conclusion, investigations of the intestinal microbiome are warranted in autoimmune hepatitis and promise to clarify pathogenic mechanisms and suggest alternative management strategies.

Factoring the intestinal microbiome into the pathogenesis of autoimmune hepatitis

PubMed Central

Czaja, Albert J

2016-01-01

The intestinal microbiome is a reservoir of microbial antigens and activated immune cells. The aims of this review were to describe the role of the intestinal microbiome in generating innate and adaptive immune responses, indicate how these responses contribute to the development of systemic immune-mediated diseases, and encourage investigations that improve the understanding and management of autoimmune hepatitis. Alterations in the composition of the intestinal microflora (dysbiosis) can disrupt intestinal and systemic immune tolerances for commensal bacteria. Toll-like receptors within the intestine can recognize microbe-associated molecular patterns and shape subsets of T helper lymphocytes that may cross-react with host antigens (molecular mimicry). Activated gut-derived lymphocytes can migrate to lymph nodes, and gut-derived microbial antigens can translocate to extra-intestinal sites. Inflammasomes can form within hepatocytes and hepatic stellate cells, and they can drive the pro-inflammatory, immune-mediated, and fibrotic responses. Diet, designer probiotics, vitamin supplements, re-colonization methods, antibiotics, drugs that decrease intestinal permeability, and molecular interventions that block signaling pathways may emerge as adjunctive regimens that complement conventional immunosuppressive management. In conclusion, investigations of the intestinal microbiome are warranted in autoimmune hepatitis and promise to clarify pathogenic mechanisms and suggest alternative management strategies. PMID:27895415

Energy, ecology and the distribution of microbial life.

PubMed

Macalady, Jennifer L; Hamilton, Trinity L; Grettenberger, Christen L; Jones, Daniel S; Tsao, Leah E; Burgos, William D

2013-07-19

Mechanisms that govern the coexistence of multiple biological species have been studied intensively by ecologists since the turn of the nineteenth century. Microbial ecologists in the meantime have faced many fundamental challenges, such as the lack of an ecologically coherent species definition, lack of adequate methods for evaluating population sizes and community composition in nature, and enormous taxonomic and functional diversity. The accessibility of powerful, culture-independent molecular microbiology methods offers an opportunity to close the gap between microbial science and the main stream of ecological theory, with the promise of new insights and tools needed to meet the grand challenges humans face as planetary engineers and galactic explorers. We focus specifically on resources related to energy metabolism because of their direct links to elemental cycling in the Earth's history, engineering applications and astrobiology. To what extent does the availability of energy resources structure microbial communities in nature? Our recent work on sulfur- and iron-oxidizing autotrophs suggests that apparently subtle variations in the concentration ratios of external electron donors and acceptors select for different microbial populations. We show that quantitative knowledge of microbial energy niches (population-specific patterns of energy resource use) can be used to predict variations in the abundance of specific taxa in microbial communities. Furthermore, we propose that resource ratio theory applied to micro-organisms will provide a useful framework for identifying how environmental communities are organized in space and time.

Energy, ecology and the distribution of microbial life

PubMed Central

Macalady, Jennifer L.; Hamilton, Trinity L.; Grettenberger, Christen L.; Jones, Daniel S.; Tsao, Leah E.; Burgos, William D.

2013-01-01

Mechanisms that govern the coexistence of multiple biological species have been studied intensively by ecologists since the turn of the nineteenth century. Microbial ecologists in the meantime have faced many fundamental challenges, such as the lack of an ecologically coherent species definition, lack of adequate methods for evaluating population sizes and community composition in nature, and enormous taxonomic and functional diversity. The accessibility of powerful, culture-independent molecular microbiology methods offers an opportunity to close the gap between microbial science and the main stream of ecological theory, with the promise of new insights and tools needed to meet the grand challenges humans face as planetary engineers and galactic explorers. We focus specifically on resources related to energy metabolism because of their direct links to elemental cycling in the Earth's history, engineering applications and astrobiology. To what extent does the availability of energy resources structure microbial communities in nature? Our recent work on sulfur- and iron-oxidizing autotrophs suggests that apparently subtle variations in the concentration ratios of external electron donors and acceptors select for different microbial populations. We show that quantitative knowledge of microbial energy niches (population-specific patterns of energy resource use) can be used to predict variations in the abundance of specific taxa in microbial communities. Furthermore, we propose that resource ratio theory applied to micro-organisms will provide a useful framework for identifying how environmental communities are organized in space and time. PMID:23754819

An assessment of the hypervariable domains of the 16S rRNA genes for their value in determining microbial community diversity: the paradox of traditional ecological indices.

PubMed

Mills, DeEtta K; Entry, James A; Voss, Joshua D; Gillevet, Patrick M; Mathee, Kalai

2006-09-01

Amplicon length heterogeneity PCR (LH-PCR) was investigated for its ability to distinguish between microbial community patterns from the same soil type under different land management practices. Natural sagebrush and irrigated mouldboard-ploughed soils from Idaho were queried as to which hypervariable domains, or combinations of 16S rRNA gene domains, were the best molecular markers. Using standard ecological indices to measure richness, diversity and evenness, the combination of three domains, V1, V3 and V1+V2, or the combined V1 and V3 domains were the markers that could best distinguish the undisturbed natural sagebrush communities from the mouldboard-ploughed microbial communities. Bray-Curtis similarity and multidimensional scaling were found to be better metrics to ordinate and cluster the LH-PCR community profiling data. The use/misuse of traditional ecological indices such as diversity and evenness to study microbial community profiles will remain a major point to consider when performing metagenomic studies.

Metabolic Flexibility as a Major Predictor of Spatial Distribution in Microbial Communities

PubMed Central

Carbonero, Franck; Oakley, Brian B.; Purdy, Kevin J.

2014-01-01

A better understand the ecology of microbes and their role in the global ecosystem could be achieved if traditional ecological theories can be applied to microbes. In ecology organisms are defined as specialists or generalists according to the breadth of their niche. Spatial distribution is often used as a proxy measure of niche breadth; generalists have broad niches and a wide spatial distribution and specialists a narrow niche and spatial distribution. Previous studies suggest that microbial distribution patterns are contrary to this idea; a microbial generalist genus (Desulfobulbus) has a limited spatial distribution while a specialist genus (Methanosaeta) has a cosmopolitan distribution. Therefore, we hypothesise that this counter-intuitive distribution within generalist and specialist microbial genera is a common microbial characteristic. Using molecular fingerprinting the distribution of four microbial genera, two generalists, Desulfobulbus and the methanogenic archaea Methanosarcina, and two specialists, Methanosaeta and the sulfate-reducing bacteria Desulfobacter were analysed in sediment samples from along a UK estuary. Detected genotypes of both generalist genera showed a distinct spatial distribution, significantly correlated with geographic distance between sites. Genotypes of both specialist genera showed no significant differential spatial distribution. These data support the hypothesis that the spatial distribution of specialist and generalist microbes does not match that seen with specialist and generalist large organisms. It may be that generalist microbes, while having a wider potential niche, are constrained, possibly by intrageneric competition, to exploit only a small part of that potential niche while specialists, with far fewer constraints to their niche, are more capable of filling their potential niche more effectively, perhaps by avoiding intrageneric competition. We suggest that these counter-intuitive distribution patterns may be a common feature of microbes in general and represent a distinct microbial principle in ecology, which is a real challenge if we are to develop a truly inclusive ecology. PMID:24465487

Are Longitudinal Patterns of Bacterial Community Composition and Dissolved Organic Matter Composition Linked Across a River Continuum? (Invited)

NASA Astrophysics Data System (ADS)

Mosher, J.; Kaplan, L. A.; Kan, J.; Findlay, R. H.; Podgorski, D. C.; McKenna, A. M.; Branan, T. L.; Griffith, C.

2013-12-01

The River Continuum Concept (RCC), an early meta-ecosystem idea, was developed without the benefit of new frontiers in molecular microbial ecology and ultra-high resolution mass spectrometry. We have applied technical advances in these areas to address a hypothesis implicit in the RCC that the upstream legacy of DOM processing contributes to the structure and function of downstream bacterial communities. DOM molecular structure and microbial community structure were measured across river networks within three distinct forested catchments. High-throughput pyrosequencing of bacterial 16S rRNA amplicons and phospholipid fatty acid analysis were used to characterize bacterial communities, and ultra-high resolution Fourier transform ion cyclotron resonance mass spectrometry characterized the molecular composition of stream water DOM. Total microbial biomass varied among river networks but showed a trend of decreasing biomass in sediment with increasing stream order. There were distinct shifts in bacterial community structure and a trend of decreasing richness was observed traveling downstream in both sediment and epilithic habitats. The bacterial richness in the first order stream sediment habitats was 7728 genera which decreased to 6597 genera in the second order sites and 4867 genera in the third order streams. The richness in the epilithic biofilm habitats was 2830 genera in the first order, 2322 genera in the second order and 1629 genera in the third order sites. Over 45% of the sediment biofilm genera and 37% of the epilithic genera were found in all three orders. In addition to shifts in bacterial richness, we observed a longitudinal shift in bacterial functional-types. In the sediment biofilms, Rhodoplanes spp. (containing rhodopsin pigment) and Bradyrhizobium spp. (nitrogen fixing bacteria) were predominately found in the heavily forested first order streams, while the cyanobacteria Limnothrix spp. was dominant in the second order streams. The third order streams had higher abundances of Sphingomonadaceae spp. and Nordella spp. (both Alphaproteobacteria). The cyanobacteria Chamaesiphon spp. was observed in highest abundance in the first and second order streams of the rock biofilm samples and the cyanobacteria Oscillatoria spp. was in highest abundance in the third order streams. Stream water samples from all orders had high lignin/tannin content and were enriched with carboxylic-rich alicyclic molecules (CRAM). There was an observable shift in in the molecular weight and relative abundance of the CRAM molecules with the CRAM molecules becoming less abundant and having lower molecular weight following the downstream gradient. Multivariate statistical analyses correlated the longitudinal patterns of changes in bacterial community structure to the DOM molecular structure and geochemical parameters across the river continuum.

Alkylcyclohexanes in environmental geochemistry

USGS Publications Warehouse

Hostettler, F.D.; Kvenvolden, K.A.

2002-01-01

The n-alkylated cyclohexanes (CHs) are a homologous series of hydrocarbon compounds that are commonly present in crude oil and refinery products such as diesel fuel. These compounds exhibit specific distribution patterns for different fuel types, providing useful fingerprints for characterizing petroleum products, especially after degradation of n-alkanes has occurred. However, there are no published data to show how these compounds are altered in the environment after long-term spillage of petroleum products. This paper presents two case studies of oil spills that demonstrate the changing distribution patterns resulting from long-term anaerobic microbial degradation. These spills are the 1979 crude-oil spill in Bemidji, Minnesota, and a chronic diesel-fuel spillage from 1953-1991 at Mandan, North Dakota. The alkyl CHs in both spilled oil products are affected by similar biodegradative processes in which the compounds undergo a consistent pattern of loss from the high molecular weight end of the homolog distribution. Degradation results in a measurable increase in the concentrations of the homologs in the lower molecular weight range, a gradual lowering in carbon number of the homolog maximum, and a gradual decrease of the total homolog range from the high molecular weight end. This pattern is the opposite of low-end loss expected with weathering and aerobic biodegradation. The enhancement of the low molecular mass alkyl CH homologs, if not recognized as a degradative pathway of diesel fuel in an anaerobic environment, can potentially be misinterpreted in fuel-oil fingerprinting as deriving from lower distillation-range fuels or admixture of diesel with other fuels.

General theory for integrated analysis of growth, gene, and protein expression in biofilms.

PubMed

Zhang, Tianyu; Pabst, Breana; Klapper, Isaac; Stewart, Philip S

2013-01-01

A theory for analysis and prediction of spatial and temporal patterns of gene and protein expression within microbial biofilms is derived. The theory integrates phenomena of solute reaction and diffusion, microbial growth, mRNA or protein synthesis, biomass advection, and gene transcript or protein turnover. Case studies illustrate the capacity of the theory to simulate heterogeneous spatial patterns and predict microbial activities in biofilms that are qualitatively different from those of planktonic cells. Specific scenarios analyzed include an inducible GFP or fluorescent protein reporter, a denitrification gene repressed by oxygen, an acid stress response gene, and a quorum sensing circuit. It is shown that the patterns of activity revealed by inducible stable fluorescent proteins or reporter unstable proteins overestimate the region of activity. This is due to advective spreading and finite protein turnover rates. In the cases of a gene induced by either limitation for a metabolic substrate or accumulation of a metabolic product, maximal expression is predicted in an internal stratum of the biofilm. A quorum sensing system that includes an oxygen-responsive negative regulator exhibits behavior that is distinct from any stage of a batch planktonic culture. Though here the analyses have been limited to simultaneous interactions of up to two substrates and two genes, the framework applies to arbitrarily large networks of genes and metabolites. Extension of reaction-diffusion modeling in biofilms to the analysis of individual genes and gene networks is an important advance that dovetails with the growing toolkit of molecular and genetic experimental techniques.

Social behaviour and gut microbiota in red-bellied lemurs (Eulemur rubriventer): In search of the role of immunity in the evolution of sociality.

PubMed

Raulo, Aura; Ruokolainen, Lasse; Lane, Avery; Amato, Katherine; Knight, Rob; Leigh, Steven; Stumpf, Rebecca; White, Bryan; Nelson, Karen E; Baden, Andrea L; Tecot, Stacey R

2018-03-01

Vertebrate gut microbiota form a key component of immunity and a dynamic link between an individual and the ecosystem. Microbiota might play a role in social systems as well, because microbes are transmitted during social contact and can affect host behaviour. Combining methods from behavioural and molecular research, we describe the relationship between social dynamics and gut microbiota of a group-living cooperative species of primate, the red-bellied lemur (Eulemur rubriventer). Specifically, we ask whether patterns of social contact (group membership, group size, position in social network, individual sociality) are associated with patterns of gut microbial composition (diversity and similarity) between individuals and across time. Red-bellied lemurs were found to have gut microbiota with slight temporal fluctuations and strong social group-specific composition. Contrary to expectations, individual sociality was negatively associated with gut microbial diversity. However, position within the social network predicted gut microbial composition. These results emphasize the role of the social environment in determining the microbiota of adult animals. Since social transmission of gut microbiota has the potential to enhance immunity, microbiota might have played an escalating role in the evolution of sociality. © 2017 The Authors. Journal of Animal Ecology © 2017 British Ecological Society.

Uncoupling of microbial community structure and function in decomposing litter across beech forest ecosystems in Central Europe.

PubMed

Purahong, Witoon; Schloter, Michael; Pecyna, Marek J; Kapturska, Danuta; Däumlich, Veronika; Mital, Sanchit; Buscot, François; Hofrichter, Martin; Gutknecht, Jessica L M; Krüger, Dirk

2014-11-12

The widespread paradigm in ecology that community structure determines function has recently been challenged by the high complexity of microbial communities. Here, we investigate the patterns of and connections between microbial community structure and microbially-mediated ecological function across different forest management practices and temporal changes in leaf litter across beech forest ecosystems in Central Europe. Our results clearly indicate distinct pattern of microbial community structure in response to forest management and time. However, those patterns were not reflected when potential enzymatic activities of microbes were measured. We postulate that in our forest ecosystems, a disconnect between microbial community structure and function may be present due to differences between the drivers of microbial growth and those of microbial function.

Microbial eukaryote plankton communities of high-mountain lakes from three continents exhibit strong biogeographic patterns.

PubMed

Filker, Sabine; Sommaruga, Ruben; Vila, Irma; Stoeck, Thorsten

2016-05-01

Microbial eukaryotes hold a key role in aquatic ecosystem functioning. Yet, their diversity in freshwater lakes, particularly in high-mountain lakes, is relatively unknown compared with the marine environment. Low nutrient availability, low water temperature and high ultraviolet radiation make most high-mountain lakes extremely challenging habitats for life and require specific molecular and physiological adaptations. We therefore expected that these ecosystems support a plankton diversity that differs notably from other freshwater lakes. In addition, we hypothesized that the communities under study exhibit geographic structuring. Our rationale was that geographic dispersal of small-sized eukaryotes in high-mountain lakes over continental distances seems difficult. We analysed hypervariable V4 fragments of the SSU rRNA gene to compare the genetic microbial eukaryote diversity in high-mountain lakes located in the European Alps, the Chilean Altiplano and the Ethiopian Bale Mountains. Microbial eukaryotes were not globally distributed corroborating patterns found for bacteria, multicellular animals and plants. Instead, the plankton community composition emerged as a highly specific fingerprint of a geographic region even on higher taxonomic levels. The intraregional heterogeneity of the investigated lakes was mirrored in shifts in microbial eukaryote community structure, which, however, was much less pronounced compared with interregional beta-diversity. Statistical analyses revealed that on a regional scale, environmental factors are strong predictors for plankton community structures in high-mountain lakes. While on long-distance scales (>10 000 km), isolation by distance is the most plausible scenario, on intermediate scales (up to 6000 km), both contemporary environmental factors and historical contingencies interact to shift plankton community structures. © 2016 John Wiley & Sons Ltd.

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

Cheese rind communities provide tractable systems for in situ and in vitro studies of microbial diversity

PubMed Central

Wolfe, Benjamin E.; Button, Julie E.; Santarelli, Marcela; Dutton, Rachel J.

2014-01-01

SUMMARY Tractable microbial communities are needed to bridge the gap between observations of patterns of microbial diversity and mechanisms that can explain these patterns. We developed cheese rinds as model microbial communities by characterizing in situ patterns of diversity and by developing an in vitro system for community reconstruction. Sequencing of 137 different rind communities across 10 countries revealed 24 widely distributed and culturable genera of bacteria and fungi as dominant community members. Reproducible community types formed independent of geographic location of production. Intensive temporal sampling demonstrated that assembly of these communities is highly reproducible. Patterns of community composition and succession observed in situ can be recapitulated in a simple in vitro system. Widespread positive and negative interactions were identified between bacterial and fungal community members. Cheese rind microbial communities represent an experimentally tractable system for defining mechanisms that influence microbial community assembly and function. PMID:25036636

Inferring Intra-Community Microbial Interaction Patterns from Metagenomic Datasets Using Associative Rule Mining Techniques

PubMed Central

Mande, Sharmila S.

2016-01-01

The nature of inter-microbial metabolic interactions defines the stability of microbial communities residing in any ecological niche. Deciphering these interaction patterns is crucial for understanding the mode/mechanism(s) through which an individual microbial community transitions from one state to another (e.g. from a healthy to a diseased state). Statistical correlation techniques have been traditionally employed for mining microbial interaction patterns from taxonomic abundance data corresponding to a given microbial community. In spite of their efficiency, these correlation techniques can capture only 'pair-wise interactions'. Moreover, their emphasis on statistical significance can potentially result in missing out on several interactions that are relevant from a biological standpoint. This study explores the applicability of one of the earliest association rule mining algorithm i.e. the 'Apriori algorithm' for deriving 'microbial association rules' from the taxonomic profile of given microbial community. The classical Apriori approach derives association rules by analysing patterns of co-occurrence/co-exclusion between various '(subsets of) features/items' across various samples. Using real-world microbiome data, the efficiency/utility of this rule mining approach in deciphering multiple (biologically meaningful) association patterns between 'subsets/subgroups' of microbes (constituting microbiome samples) is demonstrated. As an example, association rules derived from publicly available gut microbiome datasets indicate an association between a group of microbes (Faecalibacterium, Dorea, and Blautia) that are known to have mutualistic metabolic associations among themselves. Application of the rule mining approach on gut microbiomes (sourced from the Human Microbiome Project) further indicated similar microbial association patterns in gut microbiomes irrespective of the gender of the subjects. A Linux implementation of the Association Rule Mining (ARM) software (customised for deriving 'microbial association rules' from microbiome data) is freely available for download from the following link: http://metagenomics.atc.tcs.com/arm. PMID:27124399

Inferring Intra-Community Microbial Interaction Patterns from Metagenomic Datasets Using Associative Rule Mining Techniques.

PubMed

Tandon, Disha; Haque, Mohammed Monzoorul; Mande, Sharmila S

2016-01-01

The nature of inter-microbial metabolic interactions defines the stability of microbial communities residing in any ecological niche. Deciphering these interaction patterns is crucial for understanding the mode/mechanism(s) through which an individual microbial community transitions from one state to another (e.g. from a healthy to a diseased state). Statistical correlation techniques have been traditionally employed for mining microbial interaction patterns from taxonomic abundance data corresponding to a given microbial community. In spite of their efficiency, these correlation techniques can capture only 'pair-wise interactions'. Moreover, their emphasis on statistical significance can potentially result in missing out on several interactions that are relevant from a biological standpoint. This study explores the applicability of one of the earliest association rule mining algorithm i.e. the 'Apriori algorithm' for deriving 'microbial association rules' from the taxonomic profile of given microbial community. The classical Apriori approach derives association rules by analysing patterns of co-occurrence/co-exclusion between various '(subsets of) features/items' across various samples. Using real-world microbiome data, the efficiency/utility of this rule mining approach in deciphering multiple (biologically meaningful) association patterns between 'subsets/subgroups' of microbes (constituting microbiome samples) is demonstrated. As an example, association rules derived from publicly available gut microbiome datasets indicate an association between a group of microbes (Faecalibacterium, Dorea, and Blautia) that are known to have mutualistic metabolic associations among themselves. Application of the rule mining approach on gut microbiomes (sourced from the Human Microbiome Project) further indicated similar microbial association patterns in gut microbiomes irrespective of the gender of the subjects. A Linux implementation of the Association Rule Mining (ARM) software (customised for deriving 'microbial association rules' from microbiome data) is freely available for download from the following link: http://metagenomics.atc.tcs.com/arm.

Design and Construction of a Single-Tube, LATE-PCR, Multiplex Endpoint Assay with Lights-On/Lights-Off Probes for the Detection of Pathogens Associated with Sepsis

PubMed Central

Carver-Brown, Rachel K.; Reis, Arthur H.; Rice, Lisa M.; Czajka, John W.; Wangh, Lawrence J.

2012-01-01

Aims. The goal of this study was to construct a single tube molecular diagnostic multiplex assay for the detection of microbial pathogens commonly associated with septicemia, using LATE-PCR and Lights-On/Lights-Off probe technology. Methods and Results. The assay described here identified pathogens associated with sepsis by amplification and analysis of the 16S ribosomal DNA gene sequence for bacteria and specific gene sequences for fungi. A sequence from an unidentified gene in Lactococcus lactis subsp. cremoris served as a positive control for assay function. LATE-PCR was used to generate single-stranded amplicons that were then analyzed at endpoint over a wide temperature range in a specific fluorescent color. Each bacterial target was identified by its pattern of hybridization to Lights-On/Lights-Off probes derived from molecular beacons. Complex mixtures of targets were also detected. Conclusions. All microbial targets were identified in samples containing low starting copy numbers of pathogen genomic DNA, both as individual targets and in complex mixtures. Significance and Impact of the Study. This assay uses new technology to achieve an advance in the field of molecular diagnostics: a single-tube multiplex assay for identification of pathogens commonly associated with sepsis. PMID:23326668

Bacterial communities associated with subsurface geochemical processes in continental serpentinite springs.

PubMed

Brazelton, William J; Morrill, Penny L; Szponar, Natalie; Schrenk, Matthew O

2013-07-01

Reactions associated with the geochemical process of serpentinization can generate copious quantities of hydrogen and low-molecular-weight organic carbon compounds, which may provide energy and nutrients to sustain subsurface microbial communities independently of the photosynthetically supported surface biosphere. Previous microbial ecology studies have tested this hypothesis in deep sea hydrothermal vents, such as the Lost City hydrothermal field. This study applied similar methods, including molecular fingerprinting and tag sequencing of the 16S rRNA gene, to ultrabasic continental springs emanating from serpentinizing ultramafic rocks. These molecular surveys were linked with geochemical measurements of the fluids in an interdisciplinary approach designed to distinguish potential subsurface organisms from those derived from surface habitats. The betaproteobacterial genus Hydrogenophaga was identified as a likely inhabitant of transition zones where hydrogen-enriched subsurface fluids mix with oxygenated surface water. The Firmicutes genus Erysipelothrix was most strongly correlated with geochemical factors indicative of subsurface fluids and was identified as the most likely inhabitant of a serpentinization-powered subsurface biosphere. Both of these taxa have been identified in multiple hydrogen-enriched subsurface habitats worldwide, and the results of this study contribute to an emerging biogeographic pattern in which Betaproteobacteria occur in near-surface mixing zones and Firmicutes are present in deeper, anoxic subsurface habitats.

Bacterial Communities Associated with Subsurface Geochemical Processes in Continental Serpentinite Springs

PubMed Central

Morrill, Penny L.; Szponar, Natalie; Schrenk, Matthew O.

2013-01-01

Reactions associated with the geochemical process of serpentinization can generate copious quantities of hydrogen and low-molecular-weight organic carbon compounds, which may provide energy and nutrients to sustain subsurface microbial communities independently of the photosynthetically supported surface biosphere. Previous microbial ecology studies have tested this hypothesis in deep sea hydrothermal vents, such as the Lost City hydrothermal field. This study applied similar methods, including molecular fingerprinting and tag sequencing of the 16S rRNA gene, to ultrabasic continental springs emanating from serpentinizing ultramafic rocks. These molecular surveys were linked with geochemical measurements of the fluids in an interdisciplinary approach designed to distinguish potential subsurface organisms from those derived from surface habitats. The betaproteobacterial genus Hydrogenophaga was identified as a likely inhabitant of transition zones where hydrogen-enriched subsurface fluids mix with oxygenated surface water. The Firmicutes genus Erysipelothrix was most strongly correlated with geochemical factors indicative of subsurface fluids and was identified as the most likely inhabitant of a serpentinization-powered subsurface biosphere. Both of these taxa have been identified in multiple hydrogen-enriched subsurface habitats worldwide, and the results of this study contribute to an emerging biogeographic pattern in which Betaproteobacteria occur in near-surface mixing zones and Firmicutes are present in deeper, anoxic subsurface habitats. PMID:23584766

Molecular C dynamics downstream: the biochemical decomposition sequence and its impact on soil organic matter structure and function.

PubMed

Grandy, A Stuart; Neff, Jason C

2008-10-15

Advances in spectroscopic and other chemical methods have greatly enhanced our ability to characterize soil organic matter chemistry. As a result, the molecular characteristics of soil C are now known for a range of ecosystems, soil types, and management intensities. Placing this knowledge into a broader ecological and management context is difficult, however, and remains one of the fundamental challenges of soil organic matter research. Here we present a conceptual model of molecular soil C dynamics to stimulate inter-disciplinary research into the ecological implications of molecular C turnover and its management- and process-level controls. Our model describes three properties of soil C dynamics: 1) soil size fractions have unique molecular patterns that reflect varying degrees of biological and physical control over decomposition; 2) there is a common decomposition sequence independent of plant inputs or other ecosystem properties; and 3) molecular decomposition sequences, although consistent, are not uniform and can be altered by processes that accelerate or slow the microbial transformation of specific molecules. The consequences of this model include several key points. First, lignin presents a constraint to decomposition of plant litter and particulate C (>53 microm) but exerts little influence on more stable mineral-associated soil fractions <53 microm. Second, carbon stabilized onto mineral fractions has a distinct composition related more to microbially processed organic matter than to plant-related compounds. Third, disturbances, such as N fertilization and tillage, which alter decomposition rates, can have "downstream effects"; that is, a disturbance that directly alters the molecular dynamics of particulate C may have a series of indirect effects on C stabilization in silt and clay fractions.

Impact of Substratum Surface on Microbial Community Structure and Treatment Performance in Biological Aerated Filters

PubMed Central

Kim, Lavane; Pagaling, Eulyn; Zuo, Yi Y.

2014-01-01

The impact of substratum surface property change on biofilm community structure was investigated using laboratory biological aerated filter (BAF) reactors and molecular microbial community analysis. Two substratum surfaces that differed in surface properties were created via surface coating and used to develop biofilms in test (modified surface) and control (original surface) BAF reactors. Microbial community analysis by 16S rRNA gene-based PCR-denaturing gradient gel electrophoresis (DGGE) showed that the surface property change consistently resulted in distinct profiles of microbial populations during replicate reactor start-ups. Pyrosequencing of the bar-coded 16S rRNA gene amplicons surveyed more than 90% of the microbial diversity in the microbial communities and identified 72 unique bacterial species within 19 bacterial orders. Among the 19 orders of bacteria detected, Burkholderiales and Rhodocyclales of the Betaproteobacteria class were numerically dominant and accounted for 90.5 to 97.4% of the sequence reads, and their relative abundances in the test and control BAF reactors were different in consistent patterns during the two reactor start-ups. Three of the five dominant bacterial species also showed consistent relative abundance changes between the test and control BAF reactors. The different biofilm microbial communities led to different treatment efficiencies, with consistently higher total organic carbon (TOC) removal in the test reactor than in the control reactor. Further understanding of how surface properties affect biofilm microbial communities and functional performance would enable the rational design of new generations of substrata for the improvement of biofilm-based biological treatment processes. PMID:24141134

NOD-like receptor cooperativity in effector-triggered immunity.

PubMed

Griebel, Thomas; Maekawa, Takaki; Parker, Jane E

2014-11-01

Intracellular nucleotide-binding oligomerization domain (NOD)-like receptors (NLRs) are basic elements of innate immunity in plants and animals. Whereas animal NLRs react to conserved microbe- or damage-associated molecular patterns, plant NLRs intercept the actions of diverse pathogen virulence factors (effectors). In this review, we discuss recent genetic and molecular evidence for functional NLR pairs, and discuss the significance of NLR self-association and heteromeric NLR assemblies in the triggering of downstream signaling pathways. We highlight the versatility and impact of cooperating NLR pairs that combine pathogen sensing with the initiation of defense signaling in both plant and animal immunity. We propose that different NLR receptor molecular configurations provide opportunities for fine-tuning resistance pathways and enhancing the host's pathogen recognition spectrum to keep pace with rapidly evolving microbial populations. Copyright © 2014. Published by Elsevier Ltd.

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

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

PubMed

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

2016-07-01

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

Demonstrating microbial co-occurrence pattern analyses within and between ecosystems

PubMed Central

Williams, Ryan J.; Howe, Adina; Hofmockel, Kirsten S.

2014-01-01

Co-occurrence patterns are used in ecology to explore interactions between organisms and environmental effects on coexistence within biological communities. Analysis of co-occurrence patterns among microbial communities has ranged from simple pairwise comparisons between all community members to direct hypothesis testing between focal species. However, co-occurrence patterns are rarely studied across multiple ecosystems or multiple scales of biological organization within the same study. Here we outline an approach to produce co-occurrence analyses that are focused at three different scales: co-occurrence patterns between ecosystems at the community scale, modules of co-occurring microorganisms within communities, and co-occurring pairs within modules that are nested within microbial communities. To demonstrate our co-occurrence analysis approach, we gathered publicly available 16S rRNA amplicon datasets to compare and contrast microbial co-occurrence at different taxonomic levels across different ecosystems. We found differences in community composition and co-occurrence that reflect environmental filtering at the community scale and consistent pairwise occurrences that may be used to infer ecological traits about poorly understood microbial taxa. However, we also found that conclusions derived from applying network statistics to microbial relationships can vary depending on the taxonomic level chosen and criteria used to build co-occurrence networks. We present our statistical analysis and code for public use in analysis of co-occurrence patterns across microbial communities. PMID:25101065

Microbial Ecology of a Regional Flow System: Deep, Aerobic, Fractured Rock Aquifers of the US Basin and Range (Invited)

NASA Astrophysics Data System (ADS)

Moser, D. P.; Hamilton-Brehm, S.; Zhang, G.; Fisher, J.; Hughes, K.; Wheatley, A.; Thomas, J.; Zavarin, M.; Roberts, S. K.; Kryder, L.; McRae, R.; Howard, W.; Walker, J.; Federwisch, R.; King, M.; Friese, R.; Grim, S.; Amend, J.; Momper, L.; Sherwood Lollar, B.; Onstott, T. C.

2013-12-01

Recent decades have revealed anaerobic microbial ecosystems across a range of deep, continental settings; however, aerobic, regional aquifers represent a little-studied habitat for deep life. The US' Basin and Range Province is an extensional zone defined by deep, interconnected fracture systems that span multiple hydrologic basins and host regional aquifers. Here we describe a multi-basin microbiological assessment, applied to the Death Valley Regional Flow System (DVRFS). Our group has surveyed more than thirty deep boreholes (~ 1,000 m depth average) and deeply-sourced springs across a ~170 km inferred flow path from recharge areas in volcanic and carbonate rock highlands of the Nevada National Security Site (NNSS) and the Spring Mountains to discharge zones in Oasis, Amargosa, and Death Valleys. DVRFS waters were characterized by temperatures of 30 - 50 oC and the presence of dissolved O2 (4 - 8 mg/L in the recharge areas and ~0.2 - 2 mg/L in the discharge zones). Planktonic microbial populations, as tracked by molecular DNA approaches (e.g. 454 pyrotag), were of low abundance (e.g. ~ 10e3 ~10e6 per mL) and dominated by Proteobacteria and Nitrospirae. Archaea were also present and dominated by novel Thaumarchaeotes. Patterns of microbial diversity and the hypothesis that these patterns may have utility for recognition of hydrologic connectivity were assessed by statistical tools. At the species level, cosmopolitan, system-wide, and flow-path-specific groupings of both bacteria and archaea were detected. Even when in close proximity to aerobic springs and wells, sites sampling deep, hot, anaerobic groundwaters possessed completely distinct microbial populations (e.g. dominance by Firmicutes, ANME, and predicted methanogens). Among methodological refinements developed from this work, the repeated sampling of one deep borehole over a month-long pump test revealed that well-bore-associated contaminants required several days of pumping for complete removal and enabled the identification of the specific depth that produced most of the water. Our results reveal details of microbial community structure for a common, but little-studied microbial ecosystem and support the concept that regional flow systems possess distinct microbial populations, consistent with their geochemical and hydrologic characteristics. These results generally support the concept that microbial populations may have utility as amplifiable tracers for tracking the connectivity of fluids in the subsurface.

Emerging spatial patterns in Antarctic prokaryotes

PubMed Central

Chong, Chun-Wie; Pearce, David A.; Convey, Peter

2015-01-01

Recent advances in knowledge of patterns of biogeography in terrestrial eukaryotic organisms have led to a fundamental paradigm shift in understanding of the controls and history of life on land in Antarctica, and its interactions over the long term with the glaciological and geological processes that have shaped the continent. However, while it has long been recognized that the terrestrial ecosystems of Antarctica are dominated by microbes and their processes, knowledge of microbial diversity and distributions has lagged far behind that of the macroscopic eukaryote organisms. Increasing human contact with and activity in the continent is leading to risks of biological contamination and change in a region whose isolation has protected it for millions of years at least; these risks may be particularly acute for microbial communities which have, as yet, received scant recognition and attention. Even a matter apparently as straightforward as Protected Area designation in Antarctica requires robust biodiversity data which, in most parts of the continent, remain almost completely unavailable. A range of important contributing factors mean that it is now timely to reconsider the state of knowledge of Antarctic terrestrial prokaryotes. Rapid advances in molecular biological approaches are increasingly demonstrating that bacterial diversity in Antarctica may be far greater than previously thought, and that there is overlap in the environmental controls affecting both Antarctic prokaryotic and eukaryotic communities. Bacterial dispersal mechanisms and colonization patterns remain largely unaddressed, although evidence for regional evolutionary differentiation is rapidly accruing and, with this, there is increasing appreciation of patterns in regional bacterial biogeography in this large part of the globe. In this review, we set out to describe the state of knowledge of Antarctic prokaryote diversity patterns, drawing analogy with those of eukaryote groups where appropriate. Based on our synthesis, it is clear that spatial patterns of Antarctic prokaryotes can be unique at local scales, while the limited evidence available to date supports the group exhibiting overall regional biogeographical patterns similar to the eukaryotes. We further consider the applicability of the concept of “functional redundancy” for the Antarctic microbial community and highlight the requirements for proper consideration of their important and distinctive roles in Antarctic terrestrial ecosystems. PMID:26483777

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...

Microbial Source Tracking: Current and Future Molecular Tools in Microbial Water Quality Forensics

EPA Science Inventory

Current regulations in the United States stipulate that the microbial quality of waters used for consumption and recreational activities should be determined regularly by measuring microbial indicators of fecal pollution. Hence, the microbial risk associated with these waters is...

Long-term monitoring of molecular markers can distinguish different seasonal patterns of fecal indicating bacteria sources.

PubMed

Riedel, Timothy E; Thulsiraj, Vanessa; Zimmer-Faust, Amity G; Dagit, Rosi; Krug, Jenna; Hanley, Kaitlyn T; Adamek, Krista; Ebentier, Darcy L; Torres, Robert; Cobian, Uriel; Peterson, Sophie; Jay, Jennifer A

2015-03-15

Elevated levels of fecal indicator bacteria (FIB) have been observed at Topanga Beach, CA, USA. To identify the FIB sources, a microbial source tracking study using a dog-, a gull- and two human-associated molecular markers was conducted at 10 sites over 21 months. Historical data suggest that episodic discharge from the lagoon at the mouth of Topanga Creek is the main source of bacteria to the beach. A decline in creek FIB/markers downstream from upper watershed development and a sharp increase in FIB/markers at the lagoon sites suggest sources are local to the lagoon. At the lagoon and beach, human markers are detected sporadically, dog marker peaks in abundance mid-winter, and gull marker is chronically elevated. Varied seasonal patterns of FIB and source markers were identified showing the importance of applying a suite of markers over long-term spatial and temporal sampling to identify a complex combination of sources of contamination. Copyright © 2014 Elsevier Ltd. All rights reserved.

Microbial colonization and lung function in adolescents with cystic fibrosis.

PubMed

Hector, Andreas; Kirn, Tobias; Ralhan, Anjali; Graepler-Mainka, Ute; Berenbrinker, Sina; Riethmueller, Joachim; Hogardt, Michael; Wagner, Marlies; Pfleger, Andreas; Autenrieth, Ingo; Kappler, Matthias; Griese, Matthias; Eber, Ernst; Martus, Peter; Hartl, Dominik

2016-05-01

With intensified antibiotic therapy and longer survival, patients with cystic fibrosis (CF) are colonized with a more complex pattern of bacteria and fungi. However, the clinical relevance of these emerging pathogens for lung function remains poorly defined. The aim of this study was to assess the association of bacterial and fungal colonization patterns with lung function in adolescent patients with CF. Microbial colonization patterns and lung function parameters were assessed in 770 adolescent European (German/Austrian) CF patients in a retrospective study (median follow-up time: 10years). Colonization with Pseudomonas aeruginosa and MRSA were most strongly associated with loss of lung function, while mainly colonization with Haemophilus influenzae was associated with preserved lung function. Aspergillus fumigatus was the only species that was associated with an increased risk for infection with P. aeruginosa. Microbial interaction analysis revealed three distinct microbial clusters within the longitudinal course of CF lung disease. Collectively, this study identified potentially protective and harmful microbial colonization patterns in adolescent CF patients. Further studies in different patient cohorts are required to evaluate these microbial patterns and to assess their clinical relevance. Copyright © 2016 European Cystic Fibrosis Society. Published by Elsevier B.V. All rights reserved.

Microbial Abundances in Salt Marsh Soils: A Molecular Approach for Small Spatial Scales

NASA Astrophysics Data System (ADS)

Granse, Dirk; Mueller, Peter; Weingartner, Magdalena; Hoth, Stefan; Jensen, Kai

2016-04-01

The rate of biological decomposition greatly determines the carbon sequestration capacity of salt marshes. Microorganisms are involved in the decomposition of biomass and the rate of decomposition is supposed to be related to microbial abundance. Recent studies quantified microbial abundance by means of quantitative polymerase chain reaction (QPCR), a method that also allows determining the microbial community structure by applying specific primers. The main microbial community structure can be determined by using primers specific for 16S rRNA (Bacteria) and 18S rRNA (Fungi) of the microbial DNA. However, the investigation of microbial abundance pattern at small spatial scales, such as locally varying abiotic conditions within a salt-marsh system, requires high accuracy in DNA extraction and QPCR methods. Furthermore, there is evidence that a single extraction may not be sufficient to reliably quantify rRNA gene copies. The aim of this study was to establish a suitable DNA extraction method and stable QPCR conditions for the measurement of microbial abundances in semi-terrestrial environments. DNA was extracted from two soil samples (top WE{5}{cm}) by using the PowerSoil DNA Extraction Kit (Mo Bio Laboratories, Inc., Carlsbad, CA) and applying a modified extraction protocol. The DNA extraction was conducted in four consecutive DNA extraction loops from three biological replicates per soil sample by reusing the PowerSoil bead tube. The number of Fungi and Bacteria rRNA gene copies of each DNA extraction loop and a pooled DNA solution (extraction loop 1 - 4) was measured by using the QPCR method with taxa specific primer pairs (Bacteria: B341F, B805R; Fungi: FR1, FF390). The DNA yield of the replicates varied at DNA extraction loop 1 between WE{25 and 85}{ng

Electron acceptors for anaerobic oxidation of methane drive microbial community structure and diversity in mud volcanoes.

PubMed

Ren, Ge; Ma, Anzhou; Zhang, Yanfen; Deng, Ye; Zheng, Guodong; Zhuang, Xuliang; Zhuang, Guoqiang; Fortin, Danielle

2018-04-06

Mud volcanoes (MVs) emit globally significant quantities of methane into the atmosphere, however, methane cycling in such environments is not yet fully understood, as the roles of microbes and their associated biogeochemical processes have been largely overlooked. Here, we used data from high-throughput sequencing of microbial 16S rRNA gene amplicons from six MVs in the Junggar Basin in northwest China to quantify patterns of diversity and characterize the community structure of archaea and bacteria. We found anaerobic methanotrophs and diverse sulfate- and iron-reducing microbes in all of the samples, and the diversity of both archaeal and bacterial communities was strongly linked to the concentrations of sulfate, iron and nitrate, which could act as electron acceptors in anaerobic oxidation of methane (AOM). The impacts of sulfate/iron/nitrate on AOM in the MVs were verified by microcosm experiments. Further, two representative MVs were selected to explore the microbial interactions based on phylogenetic molecular ecological networks. The sites showed distinct network structures, key species and microbial interactions, with more complex and numerous linkages between methane-cycling microbes and their partners being observed in the iron/sulfate-rich MV. These findings suggest that electron acceptors are important factors driving the structure of microbial communities in these methane-rich environments. © 2018 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Rational Design of Pathogen-Mimicking Amphiphilic Materials as Nanoadjuvants

NASA Astrophysics Data System (ADS)

Ulery, Bret D.; Petersen, Latrisha K.; Phanse, Yashdeep; Kong, Chang Sun; Broderick, Scott R.; Kumar, Devender; Ramer-Tait, Amanda E.; Carrillo-Conde, Brenda; Rajan, Krishna; Wannemuehler, Michael J.; Bellaire, Bryan H.; Metzger, Dennis W.; Narasimhan, Balaji

2011-12-01

An opportunity exists today for cross-cutting research utilizing advances in materials science, immunology, microbial pathogenesis, and computational analysis to effectively design the next generation of adjuvants and vaccines. This study integrates these advances into a bottom-up approach for the molecular design of nanoadjuvants capable of mimicking the immune response induced by a natural infection but without the toxic side effects. Biodegradable amphiphilic polyanhydrides possess the unique ability to mimic pathogens and pathogen associated molecular patterns with respect to persisting within and activating immune cells, respectively. The molecular properties responsible for the pathogen-mimicking abilities of these materials have been identified. The value of using polyanhydride nanovaccines was demonstrated by the induction of long-lived protection against a lethal challenge of Yersinia pestis following a single administration ten months earlier. This approach has the tantalizing potential to catalyze the development of next generation vaccines against diseases caused by emerging and re-emerging pathogens.

Molecular Insights into Plant-Microbial Processes and Carbon Storage in Mangrove Ecosystems

NASA Astrophysics Data System (ADS)

Romero, I. C.; Ziegler, S. E.; Fogel, M.; Jacobson, M.; Fuhrman, J. A.; Capone, D. G.

2009-12-01

Mangrove forests, in tropical and subtropical coastal zones, are among the most productive ecosystems, representing a significant global carbon sink. We report new molecular insights into the functional relationship among microorganisms, mangrove trees and sediment geochemistry. The interactions among these elements were studied in peat-based mangrove sediments (Twin Cays, Belize) subjected to a long-term fertilization experiment with N and P, providing an analog for eutrophication. The composition and δ13C of bacterial PLFA showed that bacteria and mangrove trees had similar nutrient limitation patterns (N in the fringe mangrove zone, P in the interior zone), and that fertilization with N or P can affect bacterial metabolic processes and bacterial carbon uptake (from diverse mangrove sources including leaf litter, live and dead roots). PCR amplified nifH genes showed a high diversity (26% nifH novel clones) and a remarkable spatial and temporal variability in N-fixing microbial populations in the rhizosphere, varying primarily with the abundance of dead roots, PO4-3 and H2S concentrations in natural and fertilized environments. Our results indicate that eutrophication of mangrove ecosystems has the potential to alter microbial organic matter remineralization and carbon release with important implications for the coastal carbon budget. In addition, we will present preliminary data from a new study exploring the modern calibration of carbon and hydrogen isotopes of plant leaf waxes as a proxy recorder of past environmental change in mangrove ecosystems.

Analysis of Soil Vapor Extraction Expenses to Estimate Bioventing Expenses

DTIC Science & Technology

1995-11-01

Performance and Cost Summary. Brooks Air Force Base, Texas, July 1994. 2. Atlas , Ronald M, and Richard Bartha . Microbial Ecology : Fundamentals and...and straight-chain alkanes is highly dependent on molecular weight (carbon chain length) and the degree of branching. The book " Microbial Ecology ...must first be the presence of lower- molecular-weight aromatics (Heitkamp and Cerniglia 1988). The " Microbial Ecology " book also points out, on page

Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates.

PubMed

Xia, Li C; Steele, Joshua A; Cram, Jacob A; Cardon, Zoe G; Simmons, Sheri L; Vallino, Joseph J; Fuhrman, Jed A; Sun, Fengzhu

2011-01-01

The increasing availability of time series microbial community data from metagenomics and other molecular biological studies has enabled the analysis of large-scale microbial co-occurrence and association networks. Among the many analytical techniques available, the Local Similarity Analysis (LSA) method is unique in that it captures local and potentially time-delayed co-occurrence and association patterns in time series data that cannot otherwise be identified by ordinary correlation analysis. However LSA, as originally developed, does not consider time series data with replicates, which hinders the full exploitation of available information. With replicates, it is possible to understand the variability of local similarity (LS) score and to obtain its confidence interval. We extended our LSA technique to time series data with replicates and termed it extended LSA, or eLSA. Simulations showed the capability of eLSA to capture subinterval and time-delayed associations. We implemented the eLSA technique into an easy-to-use analytic software package. The software pipeline integrates data normalization, statistical correlation calculation, statistical significance evaluation, and association network construction steps. We applied the eLSA technique to microbial community and gene expression datasets, where unique time-dependent associations were identified. The extended LSA analysis technique was demonstrated to reveal statistically significant local and potentially time-delayed association patterns in replicated time series data beyond that of ordinary correlation analysis. These statistically significant associations can provide insights to the real dynamics of biological systems. The newly designed eLSA software efficiently streamlines the analysis and is freely available from the eLSA homepage, which can be accessed at http://meta.usc.edu/softs/lsa.

Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates

PubMed Central

2011-01-01

Background The increasing availability of time series microbial community data from metagenomics and other molecular biological studies has enabled the analysis of large-scale microbial co-occurrence and association networks. Among the many analytical techniques available, the Local Similarity Analysis (LSA) method is unique in that it captures local and potentially time-delayed co-occurrence and association patterns in time series data that cannot otherwise be identified by ordinary correlation analysis. However LSA, as originally developed, does not consider time series data with replicates, which hinders the full exploitation of available information. With replicates, it is possible to understand the variability of local similarity (LS) score and to obtain its confidence interval. Results We extended our LSA technique to time series data with replicates and termed it extended LSA, or eLSA. Simulations showed the capability of eLSA to capture subinterval and time-delayed associations. We implemented the eLSA technique into an easy-to-use analytic software package. The software pipeline integrates data normalization, statistical correlation calculation, statistical significance evaluation, and association network construction steps. We applied the eLSA technique to microbial community and gene expression datasets, where unique time-dependent associations were identified. Conclusions The extended LSA analysis technique was demonstrated to reveal statistically significant local and potentially time-delayed association patterns in replicated time series data beyond that of ordinary correlation analysis. These statistically significant associations can provide insights to the real dynamics of biological systems. The newly designed eLSA software efficiently streamlines the analysis and is freely available from the eLSA homepage, which can be accessed at http://meta.usc.edu/softs/lsa. PMID:22784572

Weathering Patterns of Forensic Biomarker Compounds and PAHs in Coastal Marsh Sediment Samples since the 2010 Deepwater Horizon Oil Spill

NASA Astrophysics Data System (ADS)

Overton, E. B.; Meyer, B.; Miles, S.; Olson, G.; Adhikari, P. L.

2016-02-01

It has been well established that the composition of oil, when spilled into the marine environment, undergoes substantial changes caused by weathering. The general sequence of this compositional change begins with straight chain alkanes (the fastest to degrade), followed by low molecular weight branched and cyclic alkanes and, finally the aromatics. Most resistant to weathering are the higher molecular weight cyclic and branched alkanes (i.e., the "forensic biomarker compounds" such as the hopanes and steranes) and tri-aromatic ringed steroids. The composition of these biomarker compounds is particularly resistant to change because they are not affected by evaporative weathering, are not water soluble, and are not readily degraded by microbial and/or photo-oxidation. However, after extensive time in the environment, being subjected to numerous weathering factors, biomarker compositional patterns are beginning to exhibit significant changes. This presentation will describe the general weathering patterns of petroleum residues in sediment samples collected from marsh areas of coastal Louisiana over a five year period. Particular attention will focus on compositional changes that have been observed in the steranes and diasteranes compounds that traditionally have been considered the most resistant to compositional changes due to weathering.

Molecular recognition of microbial lipid-based antigens by T cells.

PubMed

Gras, Stephanie; Van Rhijn, Ildiko; Shahine, Adam; Le Nours, Jérôme

2018-05-01

The immune system has evolved to protect hosts from pathogens. T cells represent a critical component of the immune system by their engagement in host defence mechanisms against microbial infections. Our knowledge of the molecular recognition by T cells of pathogen-derived peptidic antigens that are presented by the major histocompatibility complex glycoproteins is now well established. However, lipids represent an additional, distinct chemical class of molecules that when presented by the family of CD1 antigen-presenting molecules can serve as antigens, and be recognized by specialized subsets of T cells leading to antigen-specific activation. Over the past decades, numerous CD1-presented self- and bacterial lipid-based antigens have been isolated and characterized. However, our understanding at the molecular level of T cell immunity to CD1 molecules presenting microbial lipid-based antigens is still largely unexplored. Here, we review the insights and the molecular basis underpinning the recognition of microbial lipid-based antigens by T cells.

New technologies, human-microbe interactions, and the search for previously unrecognized pathogens.

PubMed

Relman, David A

2002-12-01

Evidence suggests that a significant number of clinically important microbial pathogens remain unrecognized. Observations from the natural world, from patterns of disease in human populations, from the bedside, and from the clinical laboratory all contribute to this body of evidence. A variety of acute and chronic neurologic syndromes illustrate this point; despite features of infection, most cases of aseptic meningitis, encephalitis, and cerebral vasculitis cannot be assigned a microbiologic diagnosis. The development and clinical application of molecular methods have led to the discovery of novel members of the endogenous normal flora as well as putative disease agents. Current challenges include the establishment of criteria for disease causation and further characterization of the human microbiome during states of health. These challenges and the goal of understanding microbial contributions to inflammatory disease may be addressed effectively through the thoughtful integration of modern technologies and clinical insight.

Fine-scale phylogenetic architecture of a complex bacterial community.

PubMed

Acinas, Silvia G; Klepac-Ceraj, Vanja; Hunt, Dana E; Pharino, Chanathip; Ceraj, Ivica; Distel, Daniel L; Polz, Martin F

2004-07-29

Although molecular data have revealed the vast scope of microbial diversity, two fundamental questions remain unanswered even for well-defined natural microbial communities: how many bacterial types co-exist, and are such types naturally organized into phylogenetically discrete units of potential ecological significance? It has been argued that without such information, the environmental function, population biology and biogeography of microorganisms cannot be rigorously explored. Here we address these questions by comprehensive sampling of two large 16S ribosomal RNA clone libraries from a coastal bacterioplankton community. We show that compensation for artefacts generated by common library construction techniques reveals fine-scale patterns of community composition. At least 516 ribotypes (unique rRNA sequences) were detected in the sample and, by statistical extrapolation, at least 1,633 co-existing ribotypes in the sampled population. More than 50% of the ribotypes fall into discrete clusters containing less than 1% sequence divergence. This pattern cannot be accounted for by interoperon variation, indicating a large predominance of closely related taxa in this community. We propose that such microdiverse clusters arise by selective sweeps and persist because competitive mechanisms are too weak to purge diversity from within them.

Leaf-FISH: Microscale Imaging of Bacterial Taxa on Phyllosphere

PubMed Central

Peredo, Elena L.; Simmons, Sheri L.

2018-01-01

Molecular methods for microbial community characterization have uncovered environmental and plant-associated factors shaping phyllosphere communities. Variables undetectable using bulk methods can play an important role in shaping plant-microbe interactions. Microscale analysis of bacterial dynamics in the phyllosphere requires imaging techniques specially adapted to the high autoflouresence and 3-D structure of the leaf surface. We present an easily-transferable method (Leaf-FISH) to generate high-resolution tridimensional images of leaf surfaces that allows simultaneous visualization of multiple bacterial taxa in a structurally informed context, using taxon-specific fluorescently labeled oligonucleotide probes. Using a combination of leaf pretreatments coupled with spectral imaging confocal microscopy, we demonstrate the successful imaging bacterial taxa at the genus level on cuticular and subcuticular leaf areas. Our results confirm that different bacterial species, including closely related isolates, colonize distinct microhabitats in the leaf. We demonstrate that highly related Methylobacterium species have distinct colonization patterns that could not be predicted by shared physiological traits, such as carbon source requirements or phytohormone production. High-resolution characterization of microbial colonization patterns is critical for an accurate understanding of microbe-microbe and microbe-plant interactions, and for the development of foliar bacteria as plant-protective agents. PMID:29375531

Influence of aeolian activities on the distribution of microbial abundance in glacier ice

NASA Astrophysics Data System (ADS)

Chen, Y.; Li, X.-K.; Si, J.; Wu, G.-J.; Tian, L.-D.; Xiang, S.-R.

2014-10-01

Microorganisms are continuously blown onto the glacier snow, and thus the glacial depth profiles provide excellent archives of microbial communities and climatic and environmental changes. However, it is uncertain about how aeolian processes that cause climatic changes control the distribution of microorganisms in the glacier ice. In the present study, microbial density, stable isotopic ratios, 18O / 16O in the precipitation, and mineral particle concentrations along the glacial depth profiles were collected from ice cores from the Muztag Ata glacier and the Dunde ice cap. The ice core data showed that microbial abundance was often, but not always associated with high concentrations of particles. Results also revealed clear seasonal patterning with high microbial abundance occurring in both the cooling autumn and warming spring-summer seasons. Microbial comparisons among the neighbouring glaciers display a heterogeneous spatial pattern, with the highest microbial cell density in the glaciers lying adjacent to the central Asian deserts and lowest microbial density in the southwestern margin of the Tibetan Plateau. In conclusion, microbial data of the glaciers indicates the aeolian deposits of microorganisms in the glacier ice and that the spatial patterns of microorgansisms are related to differences in sources of microbial flux and intensity of aeolian activities in the current regions. The results strongly support our hypothesis of aeolian activities being the main agents controlling microbial load in the glacier ice.

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

PubMed

Wang, Gang; Or, Dani

2014-10-24

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

Expression of toll-like receptors in hepatic cirrhosis and hepatocellular carcinoma.

PubMed

Sun, L; Dai, J J; Hu, W F; Wang, J

2016-07-14

Toll-like receptors (TLRs) can specifically identify pathogen-associated molecular patterns (PAMPs) by recognizing structural patterns in diverse microbial molecules, and can provide an effective defense against multiple microbial infectious. A variety of TLRs can be expressed on the surface of liver parenchymal as well as nonparenchymal cells. Kupffer cells are a type of hepatic nonparenchymal macrophage, and are positively associated with the severity of liver fibrosis. They play an important role in the synthesis and deposition of the extracellular matrix by upregulating the expression of tissue inhibitor of metalloproteinases and downregulating the activity of matrix metalloproteinases. Cirrhosis, a chronic diffuse lesion usually accompanying extensive liver fibrosis and nodular regeneration, is caused by liver parenchymal cells repeating injury-repair following reconstruction of organizational structure in the hepatic lobules. Hepatocellular carcinoma is caused by repeated and persistent chronic severe liver injury, and partial hepatocytes can eventually transform into hepatoma cells. Multiple TLRs such as TLR2, TLR3, TLR4, and TLR9, as well as other receptors, can be expressed in cirrhosis and hepatocellular carcinoma. About 53 and 85% of hepatocellular carcinoma patients frequently express TLR3 and TLR9, respectively. The chronic and repeated liver injury caused by alcohol, and HBV, HCV, or other pathogens can be recognized by TLRs through the PAMP pathway, which directly increases the risk for hepatic cirrhosis and hepatocellular carcinoma. In this review, we briefly present evidence that the novel cellular molecular mechanisms of TLRs may provide more information about new therapeutics targets of the anti-inflammatory immune response.

Delineating Molecular Interaction Mechanisms in an In Vitro Microbial-Plant Community (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

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

Larsen, Peter

2013-03-01

Peter Larsen of Argonne National Lab on "Delineating molecular interaction mechanisms in an in vitro microbial-plant community" at the 8th Annual Genomics of Energy & Environment Meeting in Walnut Creek, CA.

Microbial biogeography: putting microorganisms on the map.

PubMed

Martiny, Jennifer B Hughes; Bohannan, Brendan J M; Brown, James H; Colwell, Robert K; Fuhrman, Jed A; Green, Jessica L; Horner-Devine, M Claire; Kane, Matthew; Krumins, Jennifer Adams; Kuske, Cheryl R; Morin, Peter J; Naeem, Shahid; Ovreås, Lise; Reysenbach, Anna-Louise; Smith, Val H; Staley, James T

2006-02-01

We review the biogeography of microorganisms in light of the biogeography of macroorganisms. A large body of research supports the idea that free-living microbial taxa exhibit biogeographic patterns. Current evidence confirms that, as proposed by the Baas-Becking hypothesis, 'the environment selects' and is, in part, responsible for spatial variation in microbial diversity. However, recent studies also dispute the idea that 'everything is everywhere'. We also consider how the processes that generate and maintain biogeographic patterns in macroorganisms could operate in the microbial world.

Silage review: Using molecular approaches to define the microbial ecology of silage.

PubMed

McAllister, T A; Dunière, L; Drouin, P; Xu, S; Wang, Y; Munns, K; Zaheer, R

2018-05-01

Ensiling of forages was recognized as a microbial-driven process as early as the late 1800s, when it was associated with the production of "sweet" or "sour" silage. Classical microbiological plating techniques defined the epiphytic microbial populations associated with fresh forage, the pivotal role of lactic acid-producing bacteria in the ensiling process, and the contribution of clostridia, bacilli, yeast, and molds to the spoilage of silage. Many of these classical studies focused on the enumeration and characterization of a limited number of microbial species that could be readily isolated on selective media. Evidence suggested that many of the members of these microbial populations were viable but unculturable, resulting in classical studies underestimating the true microbial diversity associated with ensiling. Polymerase chain reaction-based techniques, including length heterogeneity PCR, terminal RFLP, denaturing gradient gel electrophoresis, and automated ribosomal intergenic spacer analysis, were the first molecular methods used to study silage microbial communities. Further advancements in whole comparative genomic, metagenomic, and metatranscriptomic sequencing have or are in the process of superseding these methods, enabling microbial communities during ensiling to be defined with a degree of detail that is impossible using classical microbiology. These methods have identified new microbial species in silage, as well as characterized shifts in microbial communities with forage type and composition, ensiling method, and in response to aerobic exposure. Strain- and species-specific primers have been used to track the persistence and contribution of silage inoculants to the ensiling process and the role of specific species of yeast and fungi in silage spoilage. Sampling and the methods used to isolate genetic materials for further molecular analysis can have a profound effect on results. Primer selection for PCR amplification and the presence of inhibitors can also lead to biases in the interpretation of sequence data. Bioinformatic analyses are reliant on the integrity and presence of sequence data within established databases and can be subject to low taxonomic resolution. Despite these limitations, advancements in molecular biology are poised to revolutionize our current understanding of the microbial ecology of silage. Published by FASS Inc. and Elsevier Inc. on behalf of the American Dairy Science Association®. All rights reserved.

The niche of an invasive marine microbe in a subtropical freshwater impoundment

PubMed Central

David Hambright, K; Beyer, Jessica E; Easton, James D; Zamor, Richard M; Easton, Anne C; Hallidayschult, Thayer C

2015-01-01

Growing attention in aquatic ecology is focusing on biogeographic patterns in microorganisms and whether these potential patterns can be explained within the framework of general ecology. The long-standing microbiologist's credo ‘Everything is everywhere, but, the environment selects' suggests that dispersal is not limiting for microbes, but that the environment is the primary determining factor in microbial community composition. Advances in molecular techniques have provided new evidence that biogeographic patterns exist in microbes and that dispersal limitation may actually have an important role, yet more recent study using extremely deep sequencing predicts that indeed everything is everywhere. Using a long-term field study of the ‘invasive' marine haptophyte Prymnesium parvum, we characterize the environmental niche of P. parvum in a subtropical impoundment in the southern United States. Our analysis contributes to a growing body of evidence that indicates a primary role for environmental conditions, but not dispersal, in the lake-wide abundances and seasonal bloom patterns in this globally important microbe. PMID:24950108

Ecological Patterns Among Bacteria and Microbial Eukaryotes Derived from Network Analyses in a Low-Salinity Lake.

PubMed

Jones, Adriane Clark; Hambright, K David; Caron, David A

2018-05-01

Microbial communities are comprised of complex assemblages of highly interactive taxa. We employed network analyses to identify and describe microbial interactions and co-occurrence patterns between microbial eukaryotes and bacteria at two locations within a low salinity (0.5-3.5 ppt) lake over an annual cycle. We previously documented that the microbial diversity and community composition within Lake Texoma, southwest USA, were significantly affected by both seasonal forces and a site-specific bloom of the harmful alga, Prymnesium parvum. We used network analyses to answer ecological questions involving both the bacterial and microbial eukaryotic datasets and to infer ecological relationships within the microbial communities. Patterns of connectivity at both locations reflected the seasonality of the lake including a large rain disturbance in May, while a comparison of the communities between locations revealed a localized response to the algal bloom. A network built from shared nodes (microbial operational taxonomic units and environmental variables) and correlations identified conserved associations at both locations within the lake. Using network analyses, we were able to detect disturbance events, characterize the ecological extent of a harmful algal bloom, and infer ecological relationships not apparent from diversity statistics alone.

Research advances on microbial genetics in China in 2015.

PubMed

Xie, Jian-ping; Han, Yu-bo; Liu, Gang; Bai, Lin-quan

2016-09-01

In 2015, there are significant progresses in many aspects of the microbial genetics in China. To showcase the contribution of Chinese scientists in microbial genetics, this review surveys several notable progresses in microbial genetics made largely by Chinese scientists, and some key findings are highlighted. For the basic microbial genetics, the components, structures and functions of many macromolecule complexes involved in gene expression regulation have been elucidated. Moreover, the molecular basis underlying the recognition of foreign nucleic acids by microbial immune systems was unveiled. We also illustrated the biosynthetic pathways and regulators of multiple microbial compounds, novel enzyme reactions, and new mechanisms regulating microbial gene expression. And new findings were obtained in the microbial development, evolution and population genetics. For the industrial microbiology, more understanding on the molecular basis of the microbial factory has been gained. For the pathogenic microbiology, the genetic circuits of several pathogens were depicted, and significant progresses were achieved for understanding the pathogen-host interaction and revealing the genetic mechanisms underlying antimicrobial resistance, emerging pathogens and environmental microorganisms at the genomic level. In future, the genetic diversity of microbes can be used to obtain specific products, while gut microbiome is gathering momentum.

Molecular and Microbial Mechanisms Increasing Soil C Storage Under Future Rates of Anthropogenic N Deposition

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

Zak, Donald R.

A growing body of evidence reveals that anthropogenic N deposition can reduce the microbial decay of plant detritus and increase soil C storage across a wide range of terrestrial ecosystems. This aspect of global change has the potential to constrain the accumulation of anthropogenic CO 2 in the Earth’s atmosphere, and hence slow the pace of climate warming. The molecular and microbial mechanisms underlying this biogeochemical response are not understood, and they are not a component of any coupled climate-biogeochemical model estimating ecosystem C storage, and hence, the future climate of an N-enriched Earth. Here, we report the use ofmore » genomic-enabled approaches to identify the molecular underpinnings of the microbial mechanisms leading to greater soil C storage in response to anthropogenic N deposition, thereby enabling us to better anticipate changes in soil C storage.« less

Advanced Mass Spectrometry Technologies for the Study of Microbial Pathogenesis

PubMed Central

Moore, Jessica L.; Caprioli, Richard M.; Skaar, Eric P.

2014-01-01

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) has been successfully applied to the field of microbial pathogenesis with promising results, principally in diagnostic microbiology to rapidly identify bacteria based on the molecular profiles of small cell populations. Direct profiling of molecules from serum and tissue samples by MALDI MS providesa means to study the pathogen-host interaction and to discover potential markers of infection. Systematic molecular profiling across tissue sections represents a new imaging modality, enabling regiospecific molecular measurements to be made in situ, in both two- and three-dimensional analyses. Herein, we briefly summarize work that employs MALDI MS to study the pathogenesis of microbial infection. PMID:24997399

Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology.

PubMed

Binga, Erik K; Lasken, Roger S; Neufeld, Josh D

2008-03-01

Microbial ecology is a field that applies molecular techniques to analyze genes and communities associated with a plethora of unique environments on this planet. In the past, low biomass and the predominance of a few abundant community members have impeded the application of techniques such as PCR, microarray analysis and metagenomics to complex microbial populations. In the absence of suitable cultivation methods, it was not possible to obtain DNA samples from individual microorganisms. Recently, a method called multiple displacement amplification (MDA) has been used to circumvent these limitations by amplifying DNA from microbial communities in low-biomass environments, individual cells from uncultivated microbial species and active organisms obtained through stable isotope probing incubations. This review describes the development and applications of MDA, discusses its strengths and limitations and highlights the impact of MDA on the field of microbial ecology. Whole genome amplification via MDA has increased access to the genomic DNA of uncultivated microorganisms and low-biomass environments and represents a 'power tool' in the molecular toolbox of microbial ecologists.

CRENAME, A Molecular Microbiology Method Enabling Multiparametric Assessment of Potable/Drinking Water.

PubMed

Bissonnette, Luc; Maheux, Andrée F; Bergeron, Michel G

2017-01-01

The microbial assessment of potable/drinking water is done to ensure that the resource is free of fecal contamination indicators or waterborne pathogens. Culture-based methods for verifying the microbial safety are limited in the sense that a standard volume of water is generally tested for only one indicator (family) or pathogen.In this work, we describe a membrane filtration-based molecular microbiology method, CRENAME (Concentration Recovery Extraction of Nucleic Acids and Molecular Enrichment), exploiting molecular enrichment by whole genome amplification (WGA) to yield, in less than 4 h, a nucleic acid preparation which can be repetitively tested by real-time PCR for example, to provide multiparametric presence/absence tests (1 colony forming unit or microbial particle per standard volume of 100-1000 mL) for bacterial or protozoan parasite cells or particles susceptible to contaminate potable/drinking water.

IDENTIFYING THE SIGNATURE OF THE NATURAL ATTENUATION IN THE MICROBIAL ECOLOGY OF HYDROCARBON CONTAMINATED GROUNDWATER USING MOLECULAR METHODS AND &LDQUO;BUG TRAPS&RDQUO;

EPA Science Inventory

These related projects have combined biological molecular methods and a novel passive sampling system (bio-trap) to produce a technology that will allow the active component of any contaminated groundwater microbial community to be investigated. Conventional sampling methods c...

Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets.

PubMed

Washburne, Alex D; Silverman, Justin D; Leff, Jonathan W; Bennett, Dominic J; Darcy, John L; Mukherjee, Sayan; Fierer, Noah; David, Lawrence A

2017-01-01

Marker gene sequencing of microbial communities has generated big datasets of microbial relative abundances varying across environmental conditions, sample sites and treatments. These data often come with putative phylogenies, providing unique opportunities to investigate how shared evolutionary history affects microbial abundance patterns. Here, we present a method to identify the phylogenetic factors driving patterns in microbial community composition. We use the method, "phylofactorization," to re-analyze datasets from the human body and soil microbial communities, demonstrating how phylofactorization is a dimensionality-reducing tool, an ordination-visualization tool, and an inferential tool for identifying edges in the phylogeny along which putative functional ecological traits may have arisen.

The Inter-Valley Soil Comparative Survey: the ecology of Dry Valley edaphic microbial communities

PubMed Central

Lee, Charles K; Barbier, Béatrice A; Bottos, Eric M; McDonald, Ian R; Cary, Stephen Craig

2012-01-01

Recent applications of molecular genetics to edaphic microbial communities of the McMurdo Dry Valleys and elsewhere have rejected a long-held belief that Antarctic soils contain extremely limited microbial diversity. The Inter-Valley Soil Comparative Survey aims to elucidate the factors shaping these unique microbial communities and their biogeography by integrating molecular genetic approaches with biogeochemical analyses. Although the microbial communities of Dry Valley soils may be complex, there is little doubt that the ecosystem's food web is relatively simple, and evidence suggests that physicochemical conditions may have the dominant role in shaping microbial communities. To examine this hypothesis, bacterial communities from representative soil samples collected in four geographically disparate Dry Valleys were analyzed using molecular genetic tools, including pyrosequencing of 16S rRNA gene PCR amplicons. Results show that the four communities are structurally and phylogenetically distinct, and possess significantly different levels of diversity. Strikingly, only 2 of 214 phylotypes were found in all four valleys, challenging a widespread assumption that the microbiota of the Dry Valleys is composed of a few cosmopolitan species. Analysis of soil geochemical properties indicated that salt content, alongside altitude and Cu2+, was significantly correlated with differences in microbial communities. Our results indicate that the microbial ecology of Dry Valley soils is highly localized and that physicochemical factors potentially have major roles in shaping the microbiology of ice-free areas of Antarctica. These findings hint at links between Dry Valley glacial geomorphology and microbial ecology, and raise previously unrecognized issues related to environmental management of this unique ecosystem. PMID:22170424

Microbial interactions: ecology in a molecular perspective.

PubMed

Braga, Raíssa Mesquita; Dourado, Manuella Nóbrega; Araújo, Welington Luiz

2016-12-01

The microorganism-microorganism or microorganism-host interactions are the key strategy to colonize and establish in a variety of different environments. These interactions involve all ecological aspects, including physiochemical changes, metabolite exchange, metabolite conversion, signaling, chemotaxis and genetic exchange resulting in genotype selection. In addition, the establishment in the environment depends on the species diversity, since high functional redundancy in the microbial community increases the competitive ability of the community, decreasing the possibility of an invader to establish in this environment. Therefore, these associations are the result of a co-evolution process that leads to the adaptation and specialization, allowing the occupation of different niches, by reducing biotic and abiotic stress or exchanging growth factors and signaling. Microbial interactions occur by the transference of molecular and genetic information, and many mechanisms can be involved in this exchange, such as secondary metabolites, siderophores, quorum sensing system, biofilm formation, and cellular transduction signaling, among others. The ultimate unit of interaction is the gene expression of each organism in response to an environmental (biotic or abiotic) stimulus, which is responsible for the production of molecules involved in these interactions. Therefore, in the present review, we focused on some molecular mechanisms involved in the microbial interaction, not only in microbial-host interaction, which has been exploited by other reviews, but also in the molecular strategy used by different microorganisms in the environment that can modulate the establishment and structuration of the microbial community. Copyright © 2016 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Molecular ecological network analyses.

PubMed

Deng, Ye; Jiang, Yi-Huei; Yang, Yunfeng; He, Zhili; Luo, Feng; Zhou, Jizhong

2012-05-30

Understanding the interaction among different species within a community and their responses to environmental changes is a central goal in ecology. However, defining the network structure in a microbial community is very challenging due to their extremely high diversity and as-yet uncultivated status. Although recent advance of metagenomic technologies, such as high throughout sequencing and functional gene arrays, provide revolutionary tools for analyzing microbial community structure, it is still difficult to examine network interactions in a microbial community based on high-throughput metagenomics data. Here, we describe a novel mathematical and bioinformatics framework to construct ecological association networks named molecular ecological networks (MENs) through Random Matrix Theory (RMT)-based methods. Compared to other network construction methods, this approach is remarkable in that the network is automatically defined and robust to noise, thus providing excellent solutions to several common issues associated with high-throughput metagenomics data. We applied it to determine the network structure of microbial communities subjected to long-term experimental warming based on pyrosequencing data of 16 S rRNA genes. We showed that the constructed MENs under both warming and unwarming conditions exhibited topological features of scale free, small world and modularity, which were consistent with previously described molecular ecological networks. Eigengene analysis indicated that the eigengenes represented the module profiles relatively well. In consistency with many other studies, several major environmental traits including temperature and soil pH were found to be important in determining network interactions in the microbial communities examined. To facilitate its application by the scientific community, all these methods and statistical tools have been integrated into a comprehensive Molecular Ecological Network Analysis Pipeline (MENAP), which is open-accessible now (http://ieg2.ou.edu/MENA). The RMT-based molecular ecological network analysis provides powerful tools to elucidate network interactions in microbial communities and their responses to environmental changes, which are fundamentally important for research in microbial ecology and environmental microbiology.

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

PubMed

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

2009-10-01

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

Some New Windows into Terrestrial Deep Subsurface Microbial Ecosystems

NASA Astrophysics Data System (ADS)

Moser, D. P.

2011-12-01

Over the past several years, our group has surveyed the microbial ecology and biogeochemistry of a range of fracture rock subsurface ecosystems via deep mine boreholes in South Africa, the United States, and Canada; and boreholes from surface or deeply-sourced natural springs of the U.S. Great Basin. Collectively, these mostly unexplored habitats represent a wide range of geologic provinces, host rock types, aquatic chemistries, and the vast potential for biogeographic isolation. Thus, patterns of microbial diversity are of interest from the perspective of filling a fundamental knowledge gap; and while not necessarily expected, the detection of closely related microorganisms from geographically isolated settings would be noteworthy. Across these sample sets, microbial communities were invariably very low in biomass (e.g. 10e3 - 10e4 cells per mL) and dominated by deeply-branching bacterial lineages, particularly from the phyla Firmicutes and Nitrospira. In several cases, the Firmicutes have shown very close phylogenetic affiliations to lineages detected at divergent locations. For example, one abundant lineage from a new artesian well drilled into the Furnace Creek Fault of Death Valley, CA bears a very close phylogenetic relatedness to environmental DNA sequences (SSU rRNA gene) detected in one of the world's deepest mines (Tau Tona of South Africa) and what was North America's deepest gold mine (Homestake of South Dakota). Several radioactive wells from the Nevada National Security Site have produced rRNA gene sequences very close (e.g. greater than 99% identity) to that of Desulforudis audaxviator, a rarely detected microorganism thought to subsist as a single species ecosystem on the products of radiochemical reactions in deep crustal rocks from the South African Witwatersrand Basin. These sequences, along with more distantly related sequences from the marine subsurface (ridge flank basalt and mud volcanoes) and groundwater in Europe, hint at a role in certain hydrogen-rich subsurface settings for this group. Likewise, patterns of archaeal diversity across many of our Great Basin sites suggest shared deep lineages, particularly with the phylum, Thaumarchaeota. Here we will explore the possible significance of these patterns of diversity and discuss future research plans involving high throughput molecular techniques.

A Recombinant Horseshoe Crab Plasma Lectin Recognizes Specific Pathogen-Associated Molecular Patterns of Bacteria through Rhamnose

PubMed Central

Ng, Sim-Kun; Huang, Yu-Tsyr; Lee, Yuan-Chuan; Low, Ee-Ling; Chiu, Cheng-Hsun; Chen, Shiu-Ling; Mao, Liang-Chi; Chang, Margaret Dah-Tsyr

2014-01-01

Horseshoe crab is an ancient marine arthropod that, in the absence of a vertebrate-like immune system, relies solely on innate immune responses by defense molecules found in hemolymph plasma and granular hemocytes for host defense. A plasma lectin isolated from the hemolymph of Taiwanese Tachypleus tridentatus recognizes bacteria and lipopolysaccharides (LPSs), yet its structure and mechanism of action remain unclear, largely because of limited availability of horseshoe crabs and the lack of a heterogeneous expression system. In this study, we have successfully expressed and purified a soluble and functional recombinant horseshoe crab plasma lectin (rHPL) in an Escherichia coli system. Interestingly, rHPL bound not only to bacteria and LPSs like the native HPL but also to selective medically important pathogens isolated from clinical specimens, such as Gram-negative Pseudomonas aeruginosa and Klebsiella pneumoniae and Gram-positive Streptococcus pneumoniae serotypes. The binding was demonstrated to occur through a specific molecular interaction with rhamnose in pathogen-associated molecular patterns (PAMPs) on the bacterial surface. Additionally, rHPL inhibited the growth of P. aeruginosa PAO1 in a concentration-dependent manner. The results suggest that a specific protein-glycan interaction between rHPL and rhamnosyl residue may further facilitate development of novel diagnostic and therapeutic strategies for microbial pathogens. PMID:25541995

Molecular Survey of Concrete Biofilm Microbial Communities

EPA Science Inventory

Although several studies have shown that bacteria can deteriorate concrete structures, there is very little information on the composition of concrete microbial communities. To this end, we studied different microbial communities associated with concrete biofilms using 16S rRNA g...

Effects of microbial transglutaminase on physicochemical properties, electrophoretic patterns and sensory attributes of veggie burger.

PubMed

Forghani, Zahra; Eskandari, Mohammad Hadi; Aminlari, Mahmoud; Shekarforoush, Seyed Shahram

2017-07-01

The main objective of this study was to investigate the effects of microbial-transglutaminase (MTGase 0-0.75%)/sodium-caseinate (SC 0-2%) as crosslinker agents on proximate analysis, binding properties (expressible moisture and shrinkage), texture analysis, electrophoretic patterns, instrumental color, and sensory properties of veggie burgers. Addition of SC and MTGase positively affected shrinkage and expressible moisture. It also increased hardness, springiness, chewiness, and cutting-force of burgers. Presence of SC had no effects on cohesiveness of burgers. Total protein and ash of samples were increased by treatment with SC. The lightness (L*) of samples was significantly decreased by 0.75% MTGase. No significant influence of SC on samples color parameters was observed. The results indicated that distinct protein bands were not formed on the SDS-PAGE of burger samples and resulted in a smearing pattern on the gel. When soy-protein was incubated with MTGase, a progressive decrease in the intensity of the bands corresponding to the subunits 7S and 11S globulins was observed concomitant with disappearance of A3 and B3 bands. Electrophoresis pattern of gluten was slightly changed after MTGase treatment. There were significant differences in color, taste, appearance, mouth feel, and overall acceptability between treated and control samples. Results suggest that production of veggie burgers using MTGase alone or in combination with SC brings about covalent cross-linking between homologous and heterologous proteins to form high-molecular weight polymers, thereby improving the mechanical properties of veggie burgers and profoundly increases the acceptability of the end product.

Microbial eukaryotic distributions and diversity patterns in a deep-sea methane seep ecosystem.

PubMed

Pasulka, Alexis L; Levin, Lisa A; Steele, Josh A; Case, David H; Landry, Michael R; Orphan, Victoria J

2016-09-01

Although chemosynthetic ecosystems are known to support diverse assemblages of microorganisms, the ecological and environmental factors that structure microbial eukaryotes (heterotrophic protists and fungi) are poorly characterized. In this study, we examined the geographic, geochemical and ecological factors that influence microbial eukaryotic composition and distribution patterns within Hydrate Ridge, a methane seep ecosystem off the coast of Oregon using a combination of high-throughput 18S rRNA tag sequencing, terminal restriction fragment length polymorphism fingerprinting, and cloning and sequencing of full-length 18S rRNA genes. Microbial eukaryotic composition and diversity varied as a function of substrate (carbonate versus sediment), activity (low activity versus active seep sites), sulfide concentration, and region (North versus South Hydrate Ridge). Sulfide concentration was correlated with changes in microbial eukaryotic composition and richness. This work also revealed the influence of oxygen content in the overlying water column and water depth on microbial eukaryotic composition and diversity, and identified distinct patterns from those previously observed for bacteria, archaea and macrofauna in methane seep ecosystems. Characterizing the structure of microbial eukaryotic communities in response to environmental variability is a key step towards understanding if and how microbial eukaryotes influence seep ecosystem structure and function. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

[Progress in expression and molecular modification of microbial transglutaminase].

PubMed

Liu, Song; Zhang, Dongxu; Du, Guocheng; Chen, Jian

2011-12-01

Microbial transglutaminase, which could catalyze the cross-linking of many proteins or non-protein materials, has been widely used in food, pharmaceutical and textile industry. To enhance the yield of the enzyme and establish corresponding platform for molecular modification, the researchers of Japanese Ajinomoto began to construct the recombinant strain producing transglutaminase in the 1990s. So far, the enzyme has been successfully expressed in different expression systems. Some of the recombinant strains are more productive than wild strains. Recently, progress has been made in the molecular modification of microbial transglutaminase, and the activity, thermo-stability and specificity of the enzyme are improved. This review briefly summarized and analyzed the strategies involved in these studies, and noted its trends.

Statistical differences between relative quantitative molecular fingerprints from microbial communities.

PubMed

Portillo, M C; Gonzalez, J M

2008-08-01

Molecular fingerprints of microbial communities are a common method for the analysis and comparison of environmental samples. The significance of differences between microbial community fingerprints was analyzed considering the presence of different phylotypes and their relative abundance. A method is proposed by simulating coverage of the analyzed communities as a function of sampling size applying a Cramér-von Mises statistic. Comparisons were performed by a Monte Carlo testing procedure. As an example, this procedure was used to compare several sediment samples from freshwater ponds using a relative quantitative PCR-DGGE profiling technique. The method was able to discriminate among different samples based on their molecular fingerprints, and confirmed the lack of differences between aliquots from a single sample.

Graft-versus-host disease: regulation by microbe-associated molecules and innate immune receptors.

PubMed

Penack, Olaf; Holler, Ernst; van den Brink, Marcel R M

2010-03-11

Acute graft-versus-host disease (GVHD) remains the major obstacle to a more favorable therapeutic outcome of allogeneic hematopoietic stem cell transplantation (HSCT). GVHD is characterized by tissue damage in gut, liver, and skin, caused by donor T cells that are critical for antitumor and antimicrobial immunity after HSCT. One obstacle in combating GVHD used to be the lack of understanding the molecular mechanisms that are involved in the initiation phase of this syndrome. Recent research has demonstrated that interactions between microbial-associated molecules (pathogen-associated molecular patterns [PAMPs]) and innate immune receptors (pathogen recognition receptors [PRRs]), such as NOD-like receptors (NLRs) and Toll-like receptors (TLRs), control adaptive immune responses in inflammatory disorders. Polymorphisms of the genes encoding NOD2 and TLR4 are associated with a higher incidence of GVHD in HSC transplant recipients. Interestingly, NOD2 regulates GVHD through its inhibitory effect on antigen-presenting cell (APC) function. These insights identify important mechanisms regarding the induction of GVHD through the interplay of microbial molecules and innate immunity, thus opening a new area for future therapeutic approaches. This review covers current knowledge of the role of PAMPs and PRRs in the control of adaptive immune responses during inflammatory diseases, particularly GVHD.

Microbial quality and molecular identification of cultivable microorganisms isolated from an urban drinking water distribution system (Limassol, Cyprus).

PubMed

Botsaris, George; Kanetis, Loukas; Slaný, Michal; Parpouna, Christiana; Makris, Konstantinos C

2015-12-01

Microorganisms can survive and multiply in aged urban drinking water distribution systems, leading to potential health risks. The objective of this work was to investigate the microbial quality of tap water and molecularly identify its predominant cultivable microorganisms. Tap water samples collected from 24 different households scattered in the urban area of Limassol, Cyprus, were microbiologically tested following standard protocols for coliforms, E. coli, Pseudomonas spp., Enterococcus spp., and total viable count at 22 and 37 °C. Molecular identification was performed on isolated predominant single colonies using 16SrRNA sequencing. Approximately 85% of the household water samples were contaminated with one or more microorganisms belonging to the genera of Pseudomonas, Corynebacterium, Agrobacterium, Staphylococcus, Bacillus, Delftia, Acinetobacter, Enterococcus, Enterobacter, and Aeromonas. However, all samples tested were free from E. coli. This is the first report in Cyprus molecularly confirming specific genera of relevant microbial communities in tap water.

Oxidation-Specific Epitopes are Danger Associated Molecular Patterns Recognized by Pattern Recognition Receptors of Innate Immunity

PubMed Central

Miller, Yury I.; Choi, Soo-Ho; Wiesner, Philipp; Fang, Longhou; Harkewicz, Richard; Hartvigsen, Karsten; Boullier, Agnès; Gonen, Ayelet; Diehl, Cody J.; Que, Xuchu; Montano, Erica; Shaw, Peter X.; Tsimikas, Sotirios; Binder, Christoph J.; Witztum, Joseph L.

2010-01-01

Oxidation reactions are vital parts of metabolism and signal transduction. However, they also produce reactive oxygen species, which damage lipids, proteins and DNA, generating “oxidation-specific” epitopes. In this review, we will discuss the hypothesis that such common oxidation-specific epitopes are a major target of innate immunity, recognized by a variety of “pattern recognition receptors” (PRRs). By analogy with microbial “pathogen associated molecular patterns” (PAMPs), we postulate that host-derived, oxidation-specific epitopes can be considered to represent “danger (or damage) associated molecular patterns” (DAMPs). We also argue that oxidation-specific epitopes present on apoptotic cells and their cellular debris provided the primary evolutionary pressure for the selection of such PRRs. Further, because many PAMPs on microbes share molecular identity and/or mimicry with oxidation-specific epitopes, such PAMPs provided a strong secondary selecting pressure for the same set of oxidation-specific PRRs as well. Because lipid peroxidation is ubiquitous and a major component of the inflammatory state associated with atherosclerosis, the understanding that oxidation-specific epitopes are DAMPs, and thus the target of multiple arcs of innate immunity, provides novel insights into the pathogenesis of atherosclerosis. As examples, we show that both cellular and soluble PRRs, such as CD36, toll-like receptor-4, natural antibodies, and CRP recognize common oxidation-specific DAMPs, such as oxidized phospholipids and oxidized cholesteryl esters, and mediate a variety of immune responses, from expression of proinflammatory genes to excessive intracellular lipoprotein accumulation to atheroprotective humoral immunity. These insights may lead to improved understanding of inflammation and atherogenesis and suggest new approaches to diagnosis and therapy. PMID:21252151

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

Organic layer serves as a hotspot of microbial activity and abundance in Arctic tundra soils.

PubMed

Lee, Seung-Hoon; Jang, Inyoung; Chae, Namyi; Choi, Taejin; Kang, Hojeong

2013-02-01

Tundra ecosystem is of importance for its high accumulation of organic carbon and vulnerability to future climate change. Microorganisms play a key role in carbon dynamics of the tundra ecosystem by mineralizing organic carbon. We assessed both ecosystem process rates and community structure of Bacteria, Archaea, and Fungi in different soil layers (surface organic layer and subsurface mineral soil) in an Arctic soil ecosystem located at Spitsbergen, Svalbard during the summer of 2008 by using biochemical and molecular analyses, such as enzymatic assay, terminal restriction fragment length polymorphism (T-RFLP), quantitative polymerase chain reaction (qPCR), and pyrosequencing. Activity of hydrolytic enzymes showed difference according to soil type. For all three microbial communities, the average gene copy number did not significantly differ between soil types. However, archaeal diversities appeared to differ according to soil type, whereas bacterial and fungal diversity indices did not show any variation. Correlation analysis between biogeochemical and microbial parameters exhibited a discriminating pattern according to microbial or soil types. Analysis of the microbial community structure showed that bacterial and archaeal communities have different profiles with unique phylotypes in terms of soil types. Water content and hydrolytic enzymes were found to be related with the structure of bacterial and archaeal communities, whereas soil organic matter (SOM) and total organic carbon (TOC) were related with bacterial communities. The overall results of this study indicate that microbial enzyme activity were generally higher in the organic layer than in mineral soils and that bacterial and archaeal communities differed between the organic layer and mineral soils in the Arctic region. Compared to mineral soil, peat-covered organic layer may represent a hotspot for secondary productivity and nutrient cycling in this ecosystem.

Microbial functional diversity plays an important role in the degradation of polyhydroxybutyrate (PHB) in soil.

PubMed

Dey, Samrat; Tribedi, Prosun

2018-03-01

Towards bioremediation of recalcitrant materials like synthetic polymer, soil has been recognized as a traditional site for disposal and subsequent degradation as some microorganisms in soil can degrade the polymer in a non-toxic, cost-effective, and environment friendly way. Microbial functional diversity is a constituent of biodiversity that includes wide range of metabolic activities that can influence numerous aspects of ecosystem functioning like ecosystem stability, nutrient availability, ecosystem dynamics, etc. Thus, in the current study, we assumed that microbial functional diversity could play an important role in polymer degradation in soil. To verify this hypothesis, we isolated soil from five different sites of landfill and examined several microbiological parameters wherein we observed a significant variation in heterotrophic microbial count as well as microbial activities among the soil microcosms tested. Multivariate analysis (principle component analysis) based on the carbon sources utilization pattern revealed that soil microcosms showed different metabolic patterns suggesting the variable distribution of microorganisms among the soil microcosms tested. Since microbial functional diversity depends on both microbial richness and evenness, Shannon diversity index was determined to measure microbial richness and Gini coefficient was determined to measure microbial evenness. The tested soil microcosms exhibited variation in both microbial richness and evenness suggesting the considerable difference in microbial functional diversity among the tested microcosms. We then measured polyhydroxybutyrate (PHB) degradation in soil microcosms after desired period of incubation of PHB in soil wherein we found that soil microcosms having higher functional diversity showed enhanced PHB degradation and soil microcosms having lower functional diversity showed reduced PHB degradation. We also noticed that all the tested soil microcosms showed similar pattern in both microbial functional diversity and PHB degradation suggesting a strong positive correlation ( r  = 0.95) between microbial functional diversity and PHB degradation. Thus, the results demonstrate that microbial functional diversity plays an important role in PHB degradation in soil by exhibiting versatile microbial metabolic potentials that lead to the enhanced degradation of PHB.

Patterns of Nitrogen Fixation and Related Genetic Diversity (nifH) in Microbial Mats and Stromatolites from Different Environments

NASA Astrophysics Data System (ADS)

Beltrán, Y. Y.; Centeno, C.; Falcón, L. I.

2010-04-01

We want to estimate the patterns of nitrogen fixation and the related genetic diversity (nifH) of microbial mats and microbialites on dial and temporal scales along a physicochemical and geographical gradient.

Dynamics of Molecular Hydrogen in Hypersaline Microbial Mars

NASA Technical Reports Server (NTRS)

Hoehler, Tori M.; Bebout, Brad M.; Visscher, Pieter T.; DesMarais, David J.; DeVincenzi, Donald L. (Technical Monitor)

2000-01-01

Early Earth microbial communities that centered around the anaerobic decomposition of organic molecular hydrogen as a carrier of electrons, regulator of energy metabolism, and facilitator of syntroph'c microbial interactions. The advent of oxygenic photosynthetic organisms added a highly dynamic and potentially dominant term to the hydrogen economy of these communities. We have examined the daily variations of hydrogen concentrations in cyanobacteria-dominated microbial mats from hypersaline ponds in Baja California Sur, Mexico. These mats bring together phototrophic and anaerobic bacteria (along with virtually all other trophic groups) in a spatially ordered and chemically dynamic matrix that provides a good analog for early Earth microbial ecosystems. Hydrogen concentrations in the photic zone of the mat can be three orders of magnitude or more higher than in the photic zone, which are, in turn, an order of magnitude higher than in the unconsolidated sediments underlying the mat community. Within the photic zone, hydrogen concentrations can fluctuate dramatically during the diel (24 hour day-night) cycle, ranging from less than 0.001% during the day to nearly 10% at night. The resultant nighttime flux of hydrogen from the mat to the environment was up to 17% of the daytime oxygen flux. The daily pattern observed is highly dependent on cyanobacterial species composition within the mat, with Lyngbya-dominated systems having a much greater dynamic range than those dominated by Microcoleus; this may relate largely to differing degrees of nitrogen-fixing and fermentative activity in the two mats. The greatest H2 concentrations and fluxes were observed in the absence of oxygen, suggesting an important potential feedback control in the context of the evolution of atmospheric composition. The impact of adding this highly dynamic photosynthetic term to the hydrogen economy of early microbial ecosystems must have been substantial. From an evolutionary standpoint, the H2 generated in mats could have represented a very important new source of electrons and energy - but one that could not be harnessed without substantial adaptation to the highly variable chemistry of the mat surface. In addition, the emergent chemistry of anaerobic communities is often highly dependent on ambient hydrogen concentrations, so that incorporation of these communities into photosynthetic mats could have significantly affected the composition and flux of reduced "biosignature' gases to the environment.

The Microbial Fecal Indicator Paradigm: Tools in the Toolbox Applications in Recreational Waters

EPA Science Inventory

Summary of ORD’s recent research to develop tools for assessing microbial water quality in recreational waters. Methods discussed include the development of health associations between microbial fecal indicators and the development of culture, and molecular methods for fec...

Genetic Comparison of B. Anthracis and its Close Relatives Using AFLP and PCR Analysis

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

Jackson, P.J.; Hill, K.K.; Laker, M.T.

1999-02-01

Amplified Fragment length Polymorphism (AFLP) analysis allows a rapid, relatively simple analysis of a large portion of a microbial genome, providing information about the species and its phylogenetic relationship to other microbes (Vos, et al., 1995). The method simply surveys the genome for length and sequence polymorphisms. The pattern identified can be used for comparison to the genomes of other species. Unlike other methods, it does not rely on analysis of a single genetic locus that may bias the interpretation of results and it does not require any prior knowledge of the targeted organism. Moreover, a standard set of reagentsmore » can be applied to any species without using species-specific information or molecular probes. The authors are using AFLP's to rapidly identify different bacterial species. A comparison of AFLP profiles generated from a large battery of B. anthracis strains shows very little variability among different isolates (Keim, et al., 1997). By contrast, there is a significant difference between AFLP profiles generated for any B. anthracis strain and even the most closely related Bacillus species. Sufficient variability is apparent among all known microbial species to allow phylogenetic analysis based on large numbers of genetically unlinked loci. These striking differences among AFLP profiles allow unambiguous identification of previously identified species and phylogenetic placement of newly characterized isolates relative to known species based on a large number of independent genetic loci. Data generated thus far show that the method provides phylogenetic analyses that are consistent with other widely accepted phylogenetic methods. However, AFLP analysis provides a more detailed analysis of the targets and samples a much larger portion of the genome. Consequently, it provides an inexpensive, rapid means of characterizing microbial isolates to further differentiate among strains and closely related microbial species. Such information cannot be rapidly generated by other means. AFLP sample analysis quickly generates a very large amount of molecular information about microbial genomes. However, this information cannot be analyzed rapidly using manual methods. The authors are developing a large archive of electronic AFLP signatures that is being used to identify isolates collected from medical, veterinary, forensic and environmental samples. They are also developing the computational packages necessary to rapidly and unambiguously analyze the AFLP profiles and conduct a phylogenetic comparison of these data relative to information already in the database. They will use this archive and the associated algorithms to determine the species identity of previously uncharacterized isolates and place them phylogenetically relative to other microbes based on their AFLP signatures. This study provides significant new information about microbes with environmental, veterinary and medical significance. This information can be used in further studies to understand the relationships among these species and the factors that distinguish them from one another. It should also allow identification of unique factors that contribute to important microbial traits including pathogenicity and virulence. They are also using AFLP data to identify, isolate and sequence DNA fragments that are unique to particular microbial species and strains. The fragment patterns and sequence information provide insights into the complexity and organization of bacterial genomes relative to one another. They also provide the information necessary for development of species-specific PCR primers that can be used to interrogate complex samples for the presence of B. anthracis, other microbial pathogens or their remnants.« less

Patterns and Processes of Microbial Community Assembly

PubMed Central

Schmidt, Steven K.; Fukami, Tadashi; O'Neill, Sean P.; Bilinski, Teresa M.; Stanish, Lee F.; Knelman, Joseph E.; Darcy, John L.; Lynch, Ryan C.; Wickey, Phillip; Ferrenberg, Scott

2013-01-01

SUMMARY Recent research has expanded our understanding of microbial community assembly. However, the field of community ecology is inaccessible to many microbial ecologists because of inconsistent and often confusing terminology as well as unnecessarily polarizing debates. Thus, we review recent literature on microbial community assembly, using the framework of Vellend (Q. Rev. Biol. 85:183–206, 2010) in an effort to synthesize and unify these contributions. We begin by discussing patterns in microbial biogeography and then describe four basic processes (diversification, dispersal, selection, and drift) that contribute to community assembly. We also discuss different combinations of these processes and where and when they may be most important for shaping microbial communities. The spatial and temporal scales of microbial community assembly are also discussed in relation to assembly processes. Throughout this review paper, we highlight differences between microbes and macroorganisms and generate hypotheses describing how these differences may be important for community assembly. We end by discussing the implications of microbial assembly processes for ecosystem function and biodiversity. PMID:24006468

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

PubMed

Averill, Colin

2014-10-01

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

Spatial patterns of cyanobacterial mat growth on sand ripples

NASA Astrophysics Data System (ADS)

Mariotti, G.; Klepac-Ceraj, V.; Perron, J. T.; Bosak, T.

2016-02-01

Photosynthetic microbial mats produce organic matter, cycle nutrients, bind pollutants and stabilize sediment in sandy marine environments. Here, we investigate the influence of bedforms and wave motion on the growth rate, composition and spatial variability of microbial mats by growing cyanobacterial mats on a rippled bed of carbonate sand in a wave tank. The tank was forced with an oscillatory flow with velocities below the threshold for sediment motion yet able to induce a porewater flow within the sediment. Different spatial patterns developed in mats depending on the initial biochemistry of the water medium. When growing in a medium rich in nitrogen, phosphorous and micronutrients, mats grew faster on ripple troughs than on ripple crests. After two months, mats covered the bed surface uniformly, and the microbial communities on the crests and in the troughs had similar compositions. Differences in bed shear stress and nutrient availability between crests and troughs were not able to explain the faster growth in the troughs. We hypothesize that this growth pattern is due to a "strainer" effect, i.e. the suspended bacteria from the inoculum were preferentially delivered to troughs by the wave-induced porewater flow. In the experiments initiated in a medium previously used up by a microbial mat and thus depleted in nutrients, mats grew preferentially on the ripple crests. This spatial pattern persisted for nearly two years, and the microbial composition on troughs and crests was different. We attribute this pattern to the upwelling of porewater in the crests, which increased the delivery of nutrients from sediment to the cyanobacteria on the bed surface. Thus, the macroscopic patterns formed by photosynthetic microbial mats on sand ripples may be used to infer whether mats are nutrient-limited and whether they are recently colonized or older than a month.

Simultaneous construction of PCR-DGGE-based predictive models of Listeria monocytogenes and Vibrio parahaemolyticus on cooked shrimps.

PubMed

Liao, C; Peng, Z Y; Li, J B; Cui, X W; Zhang, Z H; Malakar, P K; Zhang, W J; Pan, Y J; Zhao, Y

2015-03-01

The aim of this study was to simultaneously construct PCR-DGGE-based predictive models of Listeria monocytogenes and Vibrio parahaemolyticus on cooked shrimps at 4 and 10°C. Calibration curves were established to correlate peak density of DGGE bands with microbial counts. Microbial counts derived from PCR-DGGE and plate methods were fitted by Baranyi model to obtain molecular and traditional predictive models. For L. monocytogenes, growing at 4 and 10°C, molecular predictive models were constructed. It showed good evaluations of correlation coefficients (R(2) > 0.92), bias factors (Bf ) and accuracy factors (Af ) (1.0 ≤ Bf ≤ Af ≤ 1.1). Moreover, no significant difference was found between molecular and traditional predictive models when analysed on lag phase (λ), maximum growth rate (μmax ) and growth data (P > 0.05). But for V. parahaemolyticus, inactivated at 4 and 10°C, molecular models show significant difference when compared with traditional models. Taken together, these results suggest that PCR-DGGE based on DNA can be used to construct growth models, but it is inappropriate for inactivation models yet. This is the first report of developing PCR-DGGE to simultaneously construct multiple molecular models. It has been known for a long time that microbial predictive models based on traditional plate methods are time-consuming and labour-intensive. Denaturing gradient gel electrophoresis (DGGE) has been widely used as a semiquantitative method to describe complex microbial community. In our study, we developed DGGE to quantify bacterial counts and simultaneously established two molecular predictive models to describe the growth and survival of two bacteria (Listeria monocytogenes and Vibrio parahaemolyticus) at 4 and 10°C. We demonstrated that PCR-DGGE could be used to construct growth models. This work provides a new approach to construct molecular predictive models and thereby facilitates predictive microbiology and QMRA (Quantitative Microbial Risk Assessment). © 2014 The Society for Applied Microbiology.

Bacterial Community Dynamics during Production of Registered Designation of Origin Salers Cheese as Evaluated by 16S rRNA Gene Single-Strand Conformation Polymorphism Analysis

PubMed Central

Duthoit, Frédérique; Godon, Jean-Jacques; Montel, Marie-Christine

2003-01-01

Microbial dynamics during processing and ripening of traditional cheeses such as registered designation of origin Salers cheese, an artisanal cheese produced in France, play an important role in the elaboration of sensory qualities. The aim of the present study was to obtain a picture of the dynamics of the microbial ecosystem of RDO Salers cheese by using culture-independent methods. This included DNA extraction, PCR, and single-strand conformation polymorphism (SSCP) analysis. Bacterial and high-GC% gram-positive bacterial primers were used to amplify V2 or V3 regions of the 16S rRNA gene. SSCP patterns revealed changes during the manufacturing of the cheese. Patterns of the ecosystems of cheeses that were provided by three farmers were also quite different. Cloning and sequencing of the 16S rRNA gene revealed sequences related to lactic acid bacteria (Lactococcus lactis, Streptococcus thermophilus, Enterococcus faecium, Leuconostoc mesenteroides, Leuconostoc pseudomesenteroides, Lactobacillus plantarum, and Lactobacillus pentosus), which were predominant during manufacturing and ripening. Bacteria belonging to the high-GC% gram-positive group (essentially corynebacteria) were found by using specific primers. The present molecular approach can effectively describe the ecosystem of artisanal dairy products. PMID:12839752

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.

Microbial pattern of pressure ulcer in pediatric patients

NASA Astrophysics Data System (ADS)

Paramita, D. A.; Khairina; Lubis, N. Z.

2018-03-01

Pressure ulcer (PU) is a localized trauma to the skin and or tissue beneath which lies in bony prominence due to pressure or pressure that combines with a sharp surface. Several studies have found that PU is a common problem in pediatrics population. Infection at the site of a PU is the most common complication in which the PU may host a resistant microorganism and may turn into a local infection that will be the source of bacteremia in hospitalized patients. To reveal which is the most common microbial species that underlie in pressure ulcer of pediatrics patients.A cross-sectional study was conducted in July-September 2017, involving 18 PU pediatric patients in Haji Adam Malik Hospital. To each subject, swab culture from the ulcer was madein microbial laboratory in Haji Adam Malik Hospital to determine the microbial pattern. This study found that the most common microbial pattern in pressure ulcers of pediatrics patient in Haji Adam Malik Hospital is Acinetobacter baumannii (22.2%).

The Biogeography of Putative Microbial Antibiotic Production

PubMed Central

Bryant, Jessica A.; Charkoudian, Louise K.; Docherty, Kathryn M.; Jones, Evan; Kembel, Steven W.; Green, Jessica L.; Bohannan, Brendan J. M.

2015-01-01

Understanding patterns in the distribution and abundance of functional traits across a landscape is of fundamental importance to ecology. Mapping these distributions is particularly challenging for species-rich groups with sparse trait measurement coverage, such as flowering plants, insects, and microorganisms. Here, we use likelihood-based character reconstruction to infer and analyze the spatial distribution of unmeasured traits. We apply this framework to a microbial dataset comprised of 11,732 ketosynthase alpha gene sequences extracted from 144 soil samples from three continents to document the spatial distribution of putative microbial polyketide antibiotic production. Antibiotic production is a key competitive strategy for soil microbial survival and performance. Additionally, novel antibiotic discovery is highly relevant to human health, making natural antibiotic production by soil microorganisms a major target for bioprospecting. Our comparison of trait-based biogeographical patterns to patterns based on taxonomy and phylogeny is relevant to our basic understanding of microbial biogeography as well as the pressing need for new antibiotics. PMID:26102275

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).

Assessing the potential for rhizoremediation of PCB contaminated soils in northern regions using native species

PubMed Central

Slater, Heather; Gouin, Todd; Leigh, Mary Beth

2011-01-01

Rhizosphere bioremediation of polychlorinated biphenyls (PCBs) offers a potentially inexpensive approach to remediating contaminated soils that is particularly attractive in remote regions including the Arctic. We assessed the abilities of two tree species native to Alaska, Salix alaxensis (felt-leaf willow) and Picea glauca (white spruce), to promote microbial biodegradation of PCBs via the release of phytochemicals upon fine root death. Crushed fine roots, biphenyl (PCB analogue) or salicylate (willow secondary compound) were added to microcosms containing soil spiked with PCBs and resultant PCB disappearance, soil toxicity and microbial community changes were examined. After 180 d, soil treated with willow root crushates showed a significantly greater PCB loss than untreated soils for some PCB congeners, including the toxic congeners, PCB 77, 105 and 169, and showed a similar PCB loss pattern (in both extent of degradation and congeners degraded) to biphenyl-treated microcosms. Neither P. glauca (white spruce) roots nor salicylate enhanced PCB loss, indicating that biostimulation is plant species specific and was not mediated by salicylate. Soil toxicity assessed using the Microtox bioassay indicated that the willow treatment resulted in a less toxic soil environment. Molecular microbial community analyses indicated that biphenyl and salicylate promoted shifts in microbial community structure and composition that differed distinctly from each other and from the crushed root treatments. The biphenyl utilizing bacterium, Cupriavidus spp. was isolated from the soil. The findings suggest that S. alaxensis may be an effective plant for rhizoremediation by altering microbial community structure, enhancing the loss of some PCB congeners and reducing the toxicity of the soil environment. PMID:21596420

The biochemistry and molecular biology of xenobiotic polymer degradation by microorganisms.

PubMed

Kawai, Fusako

2010-01-01

Research on microbial degradation of xenobiotic polymers has been underway for more than 40 years. It has exploited a new field not only in applied microbiology but also in environmental microbiology, and has greatly contributed to polymer science by initiating the design of biodegradable polymers. Owing to the development of analytical tools and technology, molecular biological and biochemical advances have made it possible to prospect for degrading microorganisms in the environment and to determine the mechanisms involved in biodegradation when xenobiotic polymers are introduced into the environment and are exposed to microbial attack. In this review, the molecular biological and biochemical aspects of the microbial degradation of xenobiotic polymers are summarized, and possible applications of potent microorganisms, enzymes, and genes in environmental biotechnology are suggested.

Molecular analysis of microbial diversity in corrosion samples from energy transmission towers.

PubMed

Oliveira, Valéria M; Lopes-Oliveira, Patrícia F; Passarini, Michel R Z; Menezes, Claudia B A; Oliveira, Walter R C; Rocha, Adriano J; Sette, Lara D

2011-04-01

Microbial diversity in corrosion samples from energy transmission towers was investigated using molecular methods. Ribosomal DNA fragments were used to assemble gene libraries. Sequence analysis indicated 10 bacterial genera within the phyla Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. In the two libraries generated from corroded screw-derived samples, the genus Acinetobacter was the most abundant. Acinetobacter and Clostridium spp. dominated, with similar percentages, in the libraries derived from corrosion scrapings. Fungal clones were affiliated with 14 genera belonging to the phyla Ascomycota and Basidiomycota; of these, Capnobotryella and Fellomyces were the most abundant fungi observed. Several of the microorganisms had not previously been associated with biofilms and corrosion, reinforcing the need to use molecular techniques to achieve a more comprehensive assessment of microbial diversity in environmental samples.

Comparison of microbial taxonomic and functional shift pattern along contamination gradient.

PubMed

Ren, Youhua; Niu, Jiaojiao; Huang, Wenkun; Peng, Deliang; Xiao, Yunhua; Zhang, Xian; Liang, Yili; Liu, Xueduan; Yin, Huaqun

2016-06-14

The interaction mechanism between microbial communities and environment is a key issue in microbial ecology. Microbial communities usually change significantly under environmental stress, which has been studied both phylogenetically and functionally, however which method is more effective in assessing the relationship between microbial communities shift and environmental changes still remains controversial. By comparing the microbial taxonomic and functional shift pattern along heavy metal contamination gradient, we found that both sedimentary composition and function shifted significantly along contamination gradient. For example, the relative abundance of Geobacter and Fusibacter decreased along contamination gradient (from high to low), while Janthinobacterium and Arthrobacter increased their abundances. Most genes involved in heavy metal resistance (e.g., metc, aoxb and mer) showed higher intensity in sites with higher concentration of heavy metals. Comparing the two shift patterns, there were correlations between them, because functional and phylogenetic β-diversities were significantly correlated, and many heavy metal resistance genes were derived from Geobacter, explaining their high abundance in heavily contaminated sites. However, there was a stronger link between functional composition and environmental drivers, while stochasticity played an important role in formation and succession of phylogenetic composition demonstrated by null model test. Overall our research suggested that the responses of functional traits depended more on environmental changes, while stochasticity played an important role in formation and succession of phylogenetic composition for microbial communities. So profiling microbial functional composition seems more appropriate to study the relationship between microbial communities and environment, as well as explore the adaptation and remediation mechanism of microbial communities to heavy metal contamination.

Aerobic Toluene Degraders in the Rhizosphere of a Constructed Wetland Model Show Diurnal Polyhydroxyalkanoate Metabolism.

PubMed

Lünsmann, Vanessa; Kappelmeyer, Uwe; Taubert, Anja; Nijenhuis, Ivonne; von Bergen, Martin; Heipieper, Hermann J; Müller, Jochen A; Jehmlich, Nico

2016-07-15

Constructed wetlands (CWs) are successfully applied for the treatment of waters contaminated with aromatic compounds. In these systems, plants provide oxygen and root exudates to the rhizosphere and thereby stimulate microbial degradation processes. Root exudation of oxygen and organic compounds depends on photosynthetic activity and thus may show day-night fluctuations. While diurnal changes in CW effluent composition have been observed, information on respective fluctuations of bacterial activity are scarce. We investigated microbial processes in a CW model system treating toluene-contaminated water which showed diurnal oscillations of oxygen concentrations using metaproteomics. Quantitative real-time PCR was applied to assess diurnal expression patterns of genes involved in aerobic and anaerobic toluene degradation. We observed stable aerobic toluene turnover by Burkholderiales during the day and night. Polyhydroxyalkanoate synthesis was upregulated in these bacteria during the day, suggesting that they additionally feed on organic root exudates while reutilizing the stored carbon compounds during the night via the glyoxylate cycle. Although mRNA copies encoding the anaerobic enzyme benzylsuccinate synthase (bssA) were relatively abundant and increased slightly at night, the corresponding protein could not be detected in the CW model system. Our study provides insights into diurnal patterns of microbial processes occurring in the rhizosphere of an aquatic ecosystem. Constructed wetlands are a well-established and cost-efficient option for the bioremediation of contaminated waters. While it is commonly accepted knowledge that the function of CWs is determined by the interplay of plants and microorganisms, the detailed molecular processes are considered a black box. Here, we used a well-characterized CW model system treating toluene-contaminated water to investigate the microbial processes influenced by diurnal plant root exudation. Our results indicated stable aerobic toluene degradation by members of the Burkholderiales during the day and night. Polyhydroxyalkanoate synthesis in these bacteria was higher during the day, suggesting that they additionally fed on organic root exudates and reutilized the stored carbon compounds during the night. Our study illuminates microbial processes occurring in the rhizosphere of an aquatic ecosystem. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Aerobic Toluene Degraders in the Rhizosphere of a Constructed Wetland Model Show Diurnal Polyhydroxyalkanoate Metabolism

PubMed Central

Lünsmann, Vanessa; Kappelmeyer, Uwe; Taubert, Anja; Nijenhuis, Ivonne; von Bergen, Martin; Müller, Jochen A.; Jehmlich, Nico

2016-01-01

ABSTRACT Constructed wetlands (CWs) are successfully applied for the treatment of waters contaminated with aromatic compounds. In these systems, plants provide oxygen and root exudates to the rhizosphere and thereby stimulate microbial degradation processes. Root exudation of oxygen and organic compounds depends on photosynthetic activity and thus may show day-night fluctuations. While diurnal changes in CW effluent composition have been observed, information on respective fluctuations of bacterial activity are scarce. We investigated microbial processes in a CW model system treating toluene-contaminated water which showed diurnal oscillations of oxygen concentrations using metaproteomics. Quantitative real-time PCR was applied to assess diurnal expression patterns of genes involved in aerobic and anaerobic toluene degradation. We observed stable aerobic toluene turnover by Burkholderiales during the day and night. Polyhydroxyalkanoate synthesis was upregulated in these bacteria during the day, suggesting that they additionally feed on organic root exudates while reutilizing the stored carbon compounds during the night via the glyoxylate cycle. Although mRNA copies encoding the anaerobic enzyme benzylsuccinate synthase (bssA) were relatively abundant and increased slightly at night, the corresponding protein could not be detected in the CW model system. Our study provides insights into diurnal patterns of microbial processes occurring in the rhizosphere of an aquatic ecosystem. IMPORTANCE Constructed wetlands are a well-established and cost-efficient option for the bioremediation of contaminated waters. While it is commonly accepted knowledge that the function of CWs is determined by the interplay of plants and microorganisms, the detailed molecular processes are considered a black box. Here, we used a well-characterized CW model system treating toluene-contaminated water to investigate the microbial processes influenced by diurnal plant root exudation. Our results indicated stable aerobic toluene degradation by members of the Burkholderiales during the day and night. Polyhydroxyalkanoate synthesis in these bacteria was higher during the day, suggesting that they additionally fed on organic root exudates and reutilized the stored carbon compounds during the night. Our study illuminates microbial processes occurring in the rhizosphere of an aquatic ecosystem. PMID:27129963

Pan-Arctic patterns of planktonic heterotrophic microbial abundance and processes: Controlling factors and potential impacts of warming

NASA Astrophysics Data System (ADS)

Maranger, Roxane; Vaqué, Dolors; Nguyen, Dan; Hébert, Marie-Pier; Lara, Elena

2015-12-01

The Arctic Ocean is rapidly changing where increasing water temperatures and rapid loss of summer sea-ice will likely influence the structure and functioning of the entire ecosystem. The aim of this study was to synthesize the current state of knowledge on microbial abundances and processes from a regional Pan-Arctic perspective, characterize regulating factors and attempt to predict how patterns may change under a warming scenario. Here we identify some generalized patterns of different microbial variables between the Pacific-fed and the Atlantic-fed sectors of the Arctic Ocean. Bacterial production (BP), abundance and grazing rates by protists (GT) were all higher in the Atlantic-fed region. Bacterial loss by viral lyses (VL) was proportionally more important in the Pacific-fed sector, suggesting a reduced C transfer efficiency within the microbial loop of that region. Using a cross-comparative approach and all available data to build Arrhenius plots, we found a differential response to warming temperatures among various microbial processes. BP and GT responded similarly and more strongly to increases in temperature than VL did, suggesting a shift in the overall influence of viral mortality under a warming scenario. However, together with temperature, resource-related factors also exerted an influence in regulating these rates. We identified large information gaps for more classically studied microbial variable from several Arctic seas. Furthermore, there is limited information on less conventional pathways such as grazing by mixotrophic species, which may be playing a significant role in Arctic microbial trophodynamics. Although generalized patterns could be elucidated, more information is needed to predict and understand how a changing Arctic will alter microbial C pathways and major biogeochemical cycles on regional and seasonal scales.

Gut microbiota and allergy: the importance of the pregnancy period.

PubMed

Abrahamsson, Thomas R; Wu, Richard You; Jenmalm, Maria C

2015-01-01

Limited microbial exposure is suggested to underlie the increase of allergic diseases in affluent countries, and bacterial diversity seems to be more important than specific bacteria taxa. Prospective studies indicate that the gut microbiota composition during the first months of life influences allergy development, and support the theory that factors influencing the early maturation of the immune system might be important for subsequent allergic disease. However, recent research indicates that microbial exposure during pregnancy may be even more important for the preventative effects against allergic disease. This review gives a background of the epidemiology, immunology, and microbiology literature in this field. It focuses on possible underlying mechanisms such as immune-regulated epigenetic imprinting and bacterial translocation during pregnancy, potentially providing the offspring with a pioneer microbiome. We suggest that a possible reason for the initial exposure of bacterial molecular patterns to the fetus in utero is to prime the immune system and/or the epithelium to respond appropriately to pathogens and commensals after birth.

Gene transfers can date the tree of life.

PubMed

Davín, Adrián A; Tannier, Eric; Williams, Tom A; Boussau, Bastien; Daubin, Vincent; Szöllősi, Gergely J

2018-05-01

Biodiversity has always been predominantly microbial, and the scarcity of fossils from bacteria, archaea and microbial eukaryotes has prevented a comprehensive dating of the tree of life. Here, we show that patterns of lateral gene transfer deduced from an analysis of modern genomes encode a novel and abundant source of information about the temporal coexistence of lineages throughout the history of life. We use state-of-the-art species tree-aware phylogenetic methods to reconstruct the history of thousands of gene families and demonstrate that dates implied by gene transfers are consistent with estimates from relaxed molecular clocks in Bacteria, Archaea and Eukarya. We present the order of speciations according to lateral gene transfer data calibrated to geological time for three datasets comprising 40 genomes for Cyanobacteria, 60 genomes for Archaea and 60 genomes for Fungi. An inspection of discrepancies between transfers and clocks and a comparison with mammalian fossils show that gene transfer in microbes is potentially as informative for dating the tree of life as the geological record in macroorganisms.

Expanded functions for a family of plant intracellular immune receptors beyond specific recognition of pathogen effectors

PubMed Central

Bonardi, Vera; Tang, Saijun; Stallmann, Anna; Roberts, Melinda; Cherkis, Karen; Dangl, Jeffery L.

2011-01-01

Plants and animals deploy intracellular immune receptors that perceive specific pathogen effector proteins and microbial products delivered into the host cell. We demonstrate that the ADR1 family of Arabidopsis nucleotide-binding leucine-rich repeat (NB-LRR) receptors regulates accumulation of the defense hormone salicylic acid during three different types of immune response: (i) ADRs are required as “helper NB-LRRs” to transduce signals downstream of specific NB-LRR receptor activation during effector-triggered immunity; (ii) ADRs are required for basal defense against virulent pathogens; and (iii) ADRs regulate microbial-associated molecular pattern-dependent salicylic acid accumulation induced by infection with a disarmed pathogen. Remarkably, these functions do not require an intact P-loop motif for at least one ADR1 family member. Our results suggest that some NB-LRR proteins can serve additional functions beyond canonical, P-loop–dependent activation by specific virulence effectors, extending analogies between intracellular innate immune receptor function from plants and animals. PMID:21911370

Ecological effects of soil properties and metal concentrations on the composition and diversity of microbial communities associated with land use patterns in an electronic waste recycling region.

PubMed

Wu, Wencheng; Dong, Changxun; Wu, Jiahui; Liu, Xiaowen; Wu, Yingxin; Chen, Xianbin; Yu, Shixiao

2017-12-01

Soil microbes play vital roles in ecosystem functions, and soil microbial communities may be strongly structured by land use patterns associated with electronic waste (e-waste) recycling activities, which can increase the heavy metal concentration in soils. In this study, a suite of soils from five land use types (paddy field, vegetable field, dry field, forest field, and e-waste recycling site) were collected in Longtang Town, Guangdong Province, South China. Soil physicochemical properties and heavy metal concentrations were measured, and the indigenous microbial assemblages were profiled using 16S rRNA high-throughput sequencing and clone library analyses. The results showed that mercury concentration was positively correlated with both Faith's PD and Chao1 estimates, suggesting that the soil microbial alpha diversity was predominantly regulated by mercury. In addition, redundancy analysis indicated that available phosphorus, soil moisture, and mercury were the three major drivers affecting the microbial assemblages. Overall, the microbial composition was determined primarily by land use patterns, and this study provides a novel insight on the composition and diversity of microbial communities in soils associated with e-waste recycling activities. Copyright © 2017 Elsevier B.V. All rights reserved.

Recognition of microbial molecular patterns and stimulation of prophenoloxidase activation by a β-1,3-glucanase-related protein in Manduca sexta larval plasma

PubMed Central

Wang, Yang; Sumathipala, Niranji; Rayaprolu, Subrahmanyam; Jiang, Haobo

2011-01-01

Detection of pathogenic invaders is the essential first step of a successful defense response in multicellular organisms. In this study, we have identified a new member of the β-1,3-glucanase-related protein superfamily from the tobacco hornworm Manduca sexta. This protein, designated microbe binding protein (MBP), is 61% identical in sequence to Bombyx mori Gram-negative bacteria binding protein, but only 34-36% identical to M. sexta β-1,3-glucan recognition protein-1 and 2. Its mRNA levels were strongly up-regulated in hemocytes and fat body of immune challenged larvae, along with an increase in concentration of the plasma protein. We expressed M. sexta MBP in a baculovirus-insect cell system. The purified protein associated with intact bacteria and fungi. It specifically bound to lipoteichoic acid, lipopolysaccharide, diaminopimelic acid-type peptidoglycans (DAP-PGs) from Escherichia coli and Bacillus subtilis, but less so to laminarin or Lys-type PG from Staphylococcus aureus. The complex binding pattern was influenced by other plasma factors and additional microbial surface molecules. After different amounts of MBP had been incubated with larval plasma on ice, a concentration-dependent increase in phenoloxidase (PO) activity occurred in the absence of any microbial elicitor. The activity increase was also observed in the mixture of plasma and a bacterial or fungal cell wall component. The prophenoloxidase (proPO) activation became more prominent when DAP-PGs, Micrococcus luteus Lys-PG, or lipoteichoic acid was included in the mixture of MBP and plasma. Statistic analysis suggested that a synergistic enhancement of proPO activation was caused by an interaction between MBP and these elicitors, but not S. aureus Lys-PG, lipopolysaccharide, curdlan, or laminarin. These data indicate that M. sexta MBP is a component of the surveillance mechanism and, by working together with other pattern recognition molecules and serine proteinases, triggers the proPO activation system. PMID:21296155

Recognition of bacterial plant pathogens: local, systemic and transgenerational immunity.

PubMed

Henry, Elizabeth; Yadeta, Koste A; Coaker, Gitta

2013-09-01

Bacterial pathogens can cause multiple plant diseases and plants rely on their innate immune system to recognize and actively respond to these microbes. The plant innate immune system comprises extracellular pattern recognition receptors that recognize conserved microbial patterns and intracellular nucleotide binding leucine-rich repeat (NLR) proteins that recognize specific bacterial effectors delivered into host cells. Plants lack the adaptive immune branch present in animals, but still afford flexibility to pathogen attack through systemic and transgenerational resistance. Here, we focus on current research in plant immune responses against bacterial pathogens. Recent studies shed light onto the activation and inactivation of pattern recognition receptors and systemic acquired resistance. New research has also uncovered additional layers of complexity surrounding NLR immune receptor activation, cooperation and sub-cellular localizations. Taken together, these recent advances bring us closer to understanding the web of molecular interactions responsible for coordinating defense responses and ultimately resistance. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

PHYLOGENETIC AND FUNCTIONAL DIVERSITY OF SEAGULL AND CANADIAN GEESE FECAL MICROBIAL COMMUNITIES

EPA Science Inventory

In spite of increasing public health concerns on the risks associated with swimming in waters contaminated with waterfowl feces, there is little information on the gut microbial communities of aquatic birds. To address the molecular microbial diversity of waterfowl, 16S rDNA and ...

Characterization of chlorinated and chloraminated drinking water microbial communities in a distribution system simulator using pyrosequencing data analysis

EPA Science Inventory

The molecular analysis of drinking water microbial communities has focused primarily on 16S rRNA gene sequence analysis. Since this approach provides limited information on function potential of microbial communities, analysis of whole-metagenome pyrosequencing data was used to...

Low-molecular-weight poly(alpha-methyl beta,L-malate) of microbial origin: synthesis and crystallization.

PubMed

Fernández, Carlos E; Mancera, Manuel; Holler, Eggehard; Bou, Jordi J; Galbis, Juan A; Muñoz-Guerra, Sebastián

2005-02-23

Low-molecular-weight poly(alpha-methyl beta,L-malate) made of approximately 25-30 units was prepared from microbial poly(beta,L-malic acid) by treatment with diazomethane. The thermal characterization of the polymalate methyl ester was carried out and its crystalline structure was preliminary examined. Its ability to crystallize both from solution and from the melt was comparatively evaluated.

Molecular tools for bathing water assessment in Europe: Balancing social science research with a rapidly developing environmental science evidence-base.

PubMed

Oliver, David M; Hanley, Nick D; van Niekerk, Melanie; Kay, David; Heathwaite, A Louise; Rabinovici, Sharyl J M; Kinzelman, Julie L; Fleming, Lora E; Porter, Jonathan; Shaikh, Sabina; Fish, Rob; Chilton, Sue; Hewitt, Julie; Connolly, Elaine; Cummins, Andy; Glenk, Klaus; McPhail, Calum; McRory, Eric; McVittie, Alistair; Giles, Amanna; Roberts, Suzanne; Simpson, Katherine; Tinch, Dugald; Thairs, Ted; Avery, Lisa M; Vinten, Andy J A; Watts, Bill D; Quilliam, Richard S

2016-02-01

The use of molecular tools, principally qPCR, versus traditional culture-based methods for quantifying microbial parameters (e.g., Fecal Indicator Organisms) in bathing waters generates considerable ongoing debate at the science-policy interface. Advances in science have allowed the development and application of molecular biological methods for rapid (~2 h) quantification of microbial pollution in bathing and recreational waters. In contrast, culture-based methods can take between 18 and 96 h for sample processing. Thus, molecular tools offer an opportunity to provide a more meaningful statement of microbial risk to water-users by providing near-real-time information enabling potentially more informed decision-making with regard to water-based activities. However, complementary studies concerning the potential costs and benefits of adopting rapid methods as a regulatory tool are in short supply. We report on findings from an international Working Group that examined the breadth of social impacts, challenges, and research opportunities associated with the application of molecular tools to bathing water regulations.

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.

Spatial pattern formation of microbes at the soil microscale affect soil C and N turnover in an individual-based microbial community model

NASA Astrophysics Data System (ADS)

Kaiser, Christina; Evans, Sarah; Dieckmann, Ulf; Widder, Stefanie

2016-04-01

At the μm-scale, soil is a highly structured and complex environment, both in physical as well as in biological terms, characterized by non-linear interactions between microbes, substrates and minerals. As known from mathematics and theoretical ecology, spatial structure significantly affects the system's behaviour by enabling synergistic dynamics, facilitating diversity, and leading to emergent phenomena such as self-organisation and self-regulation. Such phenomena, however, are rarely considered when investigating mechanisms of microbial soil organic matter turnover. Soil organic matter is the largest terrestrial reservoir for organic carbon (C) and nitrogen (N) and plays a pivotal role in global biogeochemical cycles. Still, the underlying mechanisms of microbial soil organic matter buildup and turnover remain elusive. We explored mechanisms of microbial soil organic matter turnover using an individual-based, stoichiometrically and spatially explicit computer model, which simulates the microbial de-composer system at the soil microscale (i.e. on a grid of 100 x 100 soil microsites). Soil organic matter dynamics in our model emerge as the result of interactions among individual microbes with certain functional traits (f.e. enzyme production rates, growth rates, cell stoichiometry) at the microscale. By degrading complex substrates, and releasing labile substances microbes in our model continusly shape their environment, which in turn feeds back to spatiotemporal dynamics of the microbial community. In order to test the effect of microbial functional traits and organic matter input rate on soil organic matter turnover and C and N storage, we ran the model into steady state using continuous inputs of fresh organic material. Surprisingly, certain parameter settings that induce resource limitation of microbes lead to regular spatial pattern formation (f.e. moving spiral waves) of microbes and substrate at the μm-scale at steady-state. The occurrence of these pattern can be explained by the Turing mechanism. These pattern formation had strong consequences for process rates, as well as for C and N storage in the soil at the steady state: Scenarios that exhibited pattern formation were generally associated with higher C storage at steady state compared to those without pattern formation (i.e. at non-limiting conditions for microbes). Moreover, pattern formation lead to a spatial decoupling of C and N turnover processes, and to a spatial decoupling of microbial N mineralization and N immobilization. Taken together, our theoretical analysis shows that self-organisation may be a feature of the soil decomposer system, with consequences for process rates of microbial C and N turnover. Pattern formation through spatial self-organization, which has been observed on larger spatial scales in other resource-limited communities (e.g., vegetation patterns in arid or wetland eco-systems), may also occur at the soil microscale, leaving its mark on the soil's storage capacity for C and N.

Functions and Unique Diversity of Genes and Microorganisms Involved in Arsenite Oxidation from the Tailings of a Realgar Mine

PubMed Central

E, Guoji; Wang, Jianing; Wang, Nian; Chen, Xiaoming; Mu, Yao; Li, Hao; Yang, Ye; Liu, Yichen; Wang, Yanxin

2016-01-01

ABSTRACT The tailings of the Shimen realgar mine have unique geochemical features. Arsenite oxidation is one of the major biogeochemical processes that occurs in the tailings. However, little is known about the functional and molecular aspects of the microbial community involved in arsenite oxidation. Here, we fully explored the functional and molecular features of the microbial communities from the tailings of the Shimen realgar mine. We collected six samples of tailings from sites A, B, C, D, E, and F. Microcosm assays indicated that all of the six sites contain both chemoautotrophic and heterotrophic arsenite-oxidizing microorganisms; their activities differed considerably from each other. The microbial arsenite-oxidizing activities show a positive correlation with soluble arsenic concentrations. The microbial communities of the six sites contain 40 phyla of bacteria and 2 phyla of archaea that show extremely high diversity. Soluble arsenic, sulfate, pH, and total organic carbon (TOC) are the key environmental factors that shape the microbial communities. We further identified 114 unique arsenite oxidase genes from the samples; all of them code for new or new-type arsenite oxidases. We also isolated 10 novel arsenite oxidizers from the samples, of which 4 are chemoautotrophic and 6 are heterotrophic. These data highlight the unique diversities of the arsenite-oxidizing microorganisms and their oxidase genes from the tailings of the Shimen realgar mine. To the best of our knowledge, this is the first report describing the functional and molecular features of microbial communities from the tailings of a realgar mine. IMPORTANCE This study focused on the functional and molecular characterizations of microbial communities from the tailings of the Shimen realgar mine. We fully explored, for the first time, the arsenite-oxidizing activities and the functional gene diversities of microorganisms from the tailings, as well as the correlation of the microbial activities/diversities with environmental factors. The findings of this study help us to better understand the diversities of the arsenite-oxidizing bacteria and the geochemical cycle of arsenic in the tailings of the Shimen realgar mine and gain insights into the microbial mechanisms by which the secondary minerals of the tailings were formed. This work also offers a set of unique arsenite-oxidizing bacteria for basic research of the molecular regulation of arsenite oxidation in bacterial cells and for the environmentally friendly bioremediation of arsenic-contaminated groundwater. PMID:27663031

Functions and Unique Diversity of Genes and Microorganisms Involved in Arsenite Oxidation from the Tailings of a Realgar Mine.

PubMed

Zeng, Xian-Chun; E, Guoji; Wang, Jianing; Wang, Nian; Chen, Xiaoming; Mu, Yao; Li, Hao; Yang, Ye; Liu, Yichen; Wang, Yanxin

2016-12-15

The tailings of the Shimen realgar mine have unique geochemical features. Arsenite oxidation is one of the major biogeochemical processes that occurs in the tailings. However, little is known about the functional and molecular aspects of the microbial community involved in arsenite oxidation. Here, we fully explored the functional and molecular features of the microbial communities from the tailings of the Shimen realgar mine. We collected six samples of tailings from sites A, B, C, D, E, and F. Microcosm assays indicated that all of the six sites contain both chemoautotrophic and heterotrophic arsenite-oxidizing microorganisms; their activities differed considerably from each other. The microbial arsenite-oxidizing activities show a positive correlation with soluble arsenic concentrations. The microbial communities of the six sites contain 40 phyla of bacteria and 2 phyla of archaea that show extremely high diversity. Soluble arsenic, sulfate, pH, and total organic carbon (TOC) are the key environmental factors that shape the microbial communities. We further identified 114 unique arsenite oxidase genes from the samples; all of them code for new or new-type arsenite oxidases. We also isolated 10 novel arsenite oxidizers from the samples, of which 4 are chemoautotrophic and 6 are heterotrophic. These data highlight the unique diversities of the arsenite-oxidizing microorganisms and their oxidase genes from the tailings of the Shimen realgar mine. To the best of our knowledge, this is the first report describing the functional and molecular features of microbial communities from the tailings of a realgar mine. This study focused on the functional and molecular characterizations of microbial communities from the tailings of the Shimen realgar mine. We fully explored, for the first time, the arsenite-oxidizing activities and the functional gene diversities of microorganisms from the tailings, as well as the correlation of the microbial activities/diversities with environmental factors. The findings of this study help us to better understand the diversities of the arsenite-oxidizing bacteria and the geochemical cycle of arsenic in the tailings of the Shimen realgar mine and gain insights into the microbial mechanisms by which the secondary minerals of the tailings were formed. This work also offers a set of unique arsenite-oxidizing bacteria for basic research of the molecular regulation of arsenite oxidation in bacterial cells and for the environmentally friendly bioremediation of arsenic-contaminated groundwater. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Dramatic Increases of Soil Microbial Functional Gene Diversity at the Treeline Ecotone of Changbai Mountain.

PubMed

Shen, Congcong; Shi, Yu; Ni, Yingying; Deng, Ye; Van Nostrand, Joy D; He, Zhili; Zhou, Jizhong; Chu, Haiyan

2016-01-01

The elevational and latitudinal diversity patterns of microbial taxa have attracted great attention in the past decade. Recently, the distribution of functional attributes has been in the spotlight. Here, we report a study profiling soil microbial communities along an elevation gradient (500-2200 m) on Changbai Mountain. Using a comprehensive functional gene microarray (GeoChip 5.0), we found that microbial functional gene richness exhibited a dramatic increase at the treeline ecotone, but the bacterial taxonomic and phylogenetic diversity based on 16S rRNA gene sequencing did not exhibit such a similar trend. However, the β-diversity (compositional dissimilarity among sites) pattern for both bacterial taxa and functional genes was similar, showing significant elevational distance-decay patterns which presented increased dissimilarity with elevation. The bacterial taxonomic diversity/structure was strongly influenced by soil pH, while the functional gene diversity/structure was significantly correlated with soil dissolved organic carbon (DOC). This finding highlights that soil DOC may be a good predictor in determining the elevational distribution of microbial functional genes. The finding of significant shifts in functional gene diversity at the treeline ecotone could also provide valuable information for predicting the responses of microbial functions to climate change.

Molecular phylogenetic and chemical analyses of the microbial mats in deep-sea cold seep sediments at the northeastern Japan Sea.

PubMed

Arakawa, Shizuka; Sato, Takako; Sato, Rumi; Zhang, Jing; Gamo, Toshitaka; Tsunogai, Urumu; Hirota, Akinari; Yoshida, Yasuhiko; Usami, Ron; Inagaki, Fumio; Kato, Chiaki

2006-08-01

Microbial communities inhabiting deep-sea cold seep sediments at the northeastern Japan Sea were characterized by molecular phylogenetic and chemical analyses. White patchy microbial mats were observed along the fault offshore the Hokkaido Island and sediment samples were collected from two stations at the southern foot of the Shiribeshi seamount (M1 site at a depth of 2,961 m on the active fault) and off the Motta Cape site (M2 site at a depth of 3,064 m off the active fault). The phylogenetic and terminal-restriction fragment polymorphism analyses of PCR-amplified 16S rRNA genes revealed that microbial community structures were different between two sampling stations. The members of ANME-2 archaea and diverse bacterial components including sulfate reducers within Deltaproteobacteria were detected from M1 site, indicating the occurrence of biologically mediated anaerobic oxidation of methane, while microbial community at M2 site was predominantly composed of members of Marine Crenarchaeota group I, sulfate reducers of Deltaproteobacteria, and sulfur oxidizers of Epsilonproteobacteria. Chemical analyses of seawater above microbial mats suggested that concentrations of sulfate and methane at M1 site were largely decreased relative to those at M2 site and carbon isotopic composition of methane at M1 site shifted heavier ((13)C-enriched), the results of which are consistent with molecular analyses. These results suggest that the mat microbial communities in deep-sea cold seep sediments at the northeastern Japan Sea are significantly responsible for sulfur and carbon circulations and the geological activity associated with plate movements serves unique microbial habitats in deep-sea environments.

New challenges and opportunities for industrial biotechnology.

PubMed

Chen, Guo-Qiang

2012-08-20

Industrial biotechnology has not developed as fast as expected due to some challenges including the emergences of alternative energy sources, especially shale gas, natural gas hydrate (or gas hydrate) and sand oil et al. The weaknesses of microbial or enzymatic processes compared with the chemical processing also make industrial biotech products less competitive with the chemical ones. However, many opportunities are still there if industrial biotech processes can be as similar as the chemical ones. Taking advantages of the molecular biology and synthetic biology methods as well as changing process patterns, we can develop bioprocesses as competitive as chemical ones, these including the minimized cells, open and continuous fermentation processes et al.

Printing-assisted surface modifications of patterned ultrafiltration membranes

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

Wardrip, Nathaniel C.; Dsouza, Melissa; Urgun-Demirtas, Meltem

Understanding and restricting microbial surface attachment will enhance wastewater treatment with membranes. We report a maskless lithographic patterning technique for the generation of patterned polymer coatings on ultrafiltration membranes. Polyethylene glycol, zwitterionic, or negatively charged hydrophilic polymer compositions in parallel- or perpendicular-striped patterns with respect to feed flow were evaluated using wastewater. Membrane fouling was dependent on the orientation and chemical composition of the coatings. Modifications reduced alpha diversity in the attached microbial community (Shannon indices decreased from 2.63 to 1.89) which nevertheless increased with filtration time. Sphingomonas species, which condition membrane surfaces and facilitate cellular adhesion, were depleted inmore » all modified membranes. Microbial community structure was significantly different between control, different patterns, and different chemistries. Lastly, this study broadens the tools for surface modification of membranes with polymer coatings and for understanding and optimization of antifouling surfaces.« less

Printing-assisted surface modifications of patterned ultrafiltration membranes

DOE PAGES

Wardrip, Nathaniel C.; Dsouza, Melissa; Urgun-Demirtas, Meltem; ...

2016-10-17

Understanding and restricting microbial surface attachment will enhance wastewater treatment with membranes. We report a maskless lithographic patterning technique for the generation of patterned polymer coatings on ultrafiltration membranes. Polyethylene glycol, zwitterionic, or negatively charged hydrophilic polymer compositions in parallel- or perpendicular-striped patterns with respect to feed flow were evaluated using wastewater. Membrane fouling was dependent on the orientation and chemical composition of the coatings. Modifications reduced alpha diversity in the attached microbial community (Shannon indices decreased from 2.63 to 1.89) which nevertheless increased with filtration time. Sphingomonas species, which condition membrane surfaces and facilitate cellular adhesion, were depleted inmore » all modified membranes. Microbial community structure was significantly different between control, different patterns, and different chemistries. Lastly, this study broadens the tools for surface modification of membranes with polymer coatings and for understanding and optimization of antifouling surfaces.« less

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.

Cellulose-Derived Oligomers Act as Damage-Associated Molecular Patterns and Trigger Defense-Like Responses1

PubMed Central

Li, Shundai; Zipfel, Cyril

2017-01-01

The plant cell wall, often the site of initial encounters between plants and their microbial pathogens, is composed of a complex mixture of cellulose, hemicellulose, and pectin polysaccharides as well as proteins. The concept of damage-associated molecular patterns (DAMPs) was proposed to describe plant elicitors like oligogalacturonides (OGs), which can be derived by the breakdown of the pectin homogalacturon by pectinases. OGs act via many of the same signaling steps as pathogen- or microbe-associated molecular patterns (PAMPs) to elicit defenses and provide protection against pathogens. Given both the complexity of the plant cell wall and the fact that many pathogens secrete a wide range of cell wall-degrading enzymes, we reasoned that the breakdown products of other cell wall polymers may be similarly biologically active as elicitors and may help to reinforce the perception of danger by plant cells. Our results indicate that oligomers derived from cellulose are perceived as signal molecules in Arabidopsis (Arabidopsis thaliana), triggering a signaling cascade that shares some similarities to responses to well-known elicitors such as chitooligomers and OGs. However, in contrast to other known PAMPs/DAMPs, cellobiose stimulates neither detectable reactive oxygen species production nor callose deposition. Confirming our idea that both PAMPs and DAMPs are likely to cooccur at infection sites, cotreatments of cellobiose with flg22 or chitooligomers led to synergistic increases in gene expression. Thus, the perception of cellulose-derived oligomers may participate in cell wall integrity surveillance and represents an additional layer of signaling following plant cell wall breakdown during cell wall remodeling or pathogen attack. PMID:28242654

Mapping microbial ecosystems and spoilage-gene flow in breweries highlights patterns of contamination and resistance

PubMed Central

Bokulich, Nicholas A; Bergsveinson, Jordyn; Ziola, Barry; Mills, David A

2015-01-01

Distinct microbial ecosystems have evolved to meet the challenges of indoor environments, shaping the microbial communities that interact most with modern human activities. Microbial transmission in food-processing facilities has an enormous impact on the qualities and healthfulness of foods, beneficially or detrimentally interacting with food products. To explore modes of microbial transmission and spoilage-gene frequency in a commercial food-production scenario, we profiled hop-resistance gene frequencies and bacterial and fungal communities in a brewery. We employed a Bayesian approach for predicting routes of contamination, revealing critical control points for microbial management. Physically mapping microbial populations over time illustrates patterns of dispersal and identifies potential contaminant reservoirs within this environment. Habitual exposure to beer is associated with increased abundance of spoilage genes, predicting greater contamination risk. Elucidating the genetic landscapes of indoor environments poses important practical implications for food-production systems and these concepts are translatable to other built environments. DOI: http://dx.doi.org/10.7554/eLife.04634.001 PMID:25756611

Molecular ecology of Listeria spp., Salmonella, Escherichia coli O157:H7 and non-O157 Shiga toxin-producing E. coli in pristine natural environments in Northern Colorado.

PubMed

Ahlstrom, C A; Manuel, C S; Den Bakker, H C; Wiedmann, M; Nightingale, K K

2018-02-01

Molecular subtyping is commonly used in foodborne disease surveillance and microbial source tracking. There is a knowledge gap regarding the molecular ecology of foodborne pathogens in non-food-associated environments. The objective of this study was to isolate and subtype foodborne pathogens from pristine natural environments with minimal anthropogenic inputs. Five locations (wilderness areas) in Northern Colorado were sampled during the spring, summer and fall over a 2-year period. Soil, water, sediment, surface soil and wildlife faecal samples were microbiologically analysed to detect Listeria, Salmonella and Shiga toxin-producing Escherichia coli (STEC), and resultant isolates were subtyped. Three samples tested positive for Listeria monocytogenes and 19 samples contained other Listeria spp. Salmonella was isolated from two samples, five samples contained non-O157 STEC, and E. coli O157:H7 was not detected. Two L. monocytogenes isolates from faecal samples collected from the same wilderness area over a year apart shared the same PFGE pattern, while all other isolates had a unique type. Our data indicate that (i) there was a rare presence of human foodborne pathogens in pristine natural environments in Northern Colorado, (ii) there was genetic diversity between organisms isolated within a given wilderness area, and (iii) the Northern Colorado climate and topography may contribute to the low occurrence of these organisms. Relatively little is known about the molecular ecology of foodborne pathogens in pristine natural environments. While foodborne pathogens were rarely detected in wildlife faecal and environmental samples from the wilderness areas in this study, some isolates shared DNA fingerprint types with human clinical isolates from same region during the same time frame, highlighting the need for environmental isolate subtype data. The availability of molecular subtyping data for non-food-associated foodborne pathogen isolates can facilitate epidemiological and microbial source tracking investigations. © 2017 The Society for Applied Microbiology.

EVIDENCE FOR MICROBIAL ENHANCED ELECTRICAL CONDUCTIVITY IN HYDROCARBON-CONTAMINATED SEDIMENTS

EPA Science Inventory

Electrical conductivity of sediments during microbial mineralization of diesel was investigated in a mesoscale column experiment consisting of biotic contaminated and uncontaminated columns. Microbial population numbers increased with a clear pattern of depth zonation within the ...

Uses of antimicrobial genes from microbial genome

DOEpatents

Sorek, Rotem; Rubin, Edward M.

2013-08-20

We describe a method for mining microbial genomes to discover antimicrobial genes and proteins having broad spectrum of activity. Also described are antimicrobial genes and their expression products from various microbial genomes that were found using this method. The products of such genes can be used as antimicrobial agents or as tools for molecular biology.

Microbial mat of the thermal springs Kuchiger Republic of Buryatia: species composition, biochemical properties and electrogenic activity in biofuel cell

NASA Astrophysics Data System (ADS)

Aleksandrovich Yuriev, Denis; Viktorovna Zaitseva, Svetlana; Olegovna Zhdanova, Galina; Yurievich Tolstoy, Mikhail; Dondokovna Barkhutova, Darima; Feodorovna Vyatchina, Olga; Yuryevna Konovalova, Elena; Iosifovich Stom, Devard

2018-02-01

Electrogenic, molecular and some other properties of a microbial mat isolated from the Kuchiger hot spring (Kurumkansky District, Republic of Buryatia) were studied. Molecular analysis showed that representatives of Proteobacteria (85.5 % of the number of classified bacterial sequences) prevailed in the microbial mat of the Kuchiger springs, among which sulfur bacteria of the genus Thiothrix were the most numerous. In the microbial mat there were bacteria from the families Rhodocyclaceae, Comamonadaceae and Flavobacteriaceae. Phylum Bacteroidetes, Cyanobacteria/Chloroplast, Fusobacteria, Fibrobacteres, Acidobacteria, Chlorobi, Spirochaetes, Verrucomicrobia, Firmicutes, Deinococcus-Thermus, Chloroflexi and Actinobacteria are also noted in the composition of the microbial mat. Under the experimental conditions using Kuchiger-mat 16 as bioagents, glucose and peptone as substrates, the power of BFC was 240 and 221 mW / m2, respectively. When replacing the substrate with sodium acetate, the efficiency of the BFC was reduced by a factor of 10 (20 mW / m2). The prospects of using a microbial mat “Kuchiger-16” as an electrogen in BFC when utilizing alkaline waste water components to generate electricity are discussed.

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

USGS Publications Warehouse

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

2006-01-01

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

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.

Gene-centric approach to integrating environmental genomics and biogeochemical models.

PubMed

Reed, Daniel C; Algar, Christopher K; Huber, Julie A; Dick, Gregory J

2014-02-04

Rapid advances in molecular microbial ecology have yielded an unprecedented amount of data about the evolutionary relationships and functional traits of microbial communities that regulate global geochemical cycles. Biogeochemical models, however, are trailing in the wake of the environmental genomics revolution, and such models rarely incorporate explicit representations of bacteria and archaea, nor are they compatible with nucleic acid or protein sequence data. Here, we present a functional gene-based framework for describing microbial communities in biogeochemical models by incorporating genomics data to provide predictions that are readily testable. To demonstrate the approach in practice, nitrogen cycling in the Arabian Sea oxygen minimum zone (OMZ) was modeled to examine key questions about cryptic sulfur cycling and dinitrogen production pathways in OMZs. Simulations support previous assertions that denitrification dominates over anammox in the central Arabian Sea, which has important implications for the loss of fixed nitrogen from the oceans. Furthermore, cryptic sulfur cycling was shown to attenuate the secondary nitrite maximum often observed in OMZs owing to changes in the composition of the chemolithoautotrophic community and dominant metabolic pathways. Results underscore the need to explicitly integrate microbes into biogeochemical models rather than just the metabolisms they mediate. By directly linking geochemical dynamics to the genetic composition of microbial communities, the method provides a framework for achieving mechanistic insights into patterns and biogeochemical consequences of marine microbes. Such an approach is critical for informing our understanding of the key role microbes play in modulating Earth's biogeochemistry.

A Study of the Microbial Spatial Heterogeneity of Bahamian Thrombolites Using Molecular, Biochemical, and Stable Isotope Analyses

NASA Astrophysics Data System (ADS)

Louyakis, Artemis S.; Mobberley, Jennifer M.; Vitek, Brooke E.; Visscher, Pieter T.; Hagan, Paul D.; Reid, R. Pamela; Kozdon, Reinhard; Orland, Ian J.; Valley, John W.; Planavsky, Noah J.; Casaburi, Giorgio; Foster, Jamie S.

2017-05-01

Thrombolites are buildups of carbonate that exhibit a clotted internal structure formed through the interactions of microbial mats and their environment. Despite recent advances, we are only beginning to understand the microbial and molecular processes associated with their formation. In this study, a spatial profile of the microbial and metabolic diversity of thrombolite-forming mats of Highborne Cay, The Bahamas, was generated by using 16S rRNA gene sequencing and predictive metagenomic analyses. These molecular-based approaches were complemented with microelectrode profiling and in situ stable isotope analysis to examine the dominant taxa and metabolic activities within the thrombolite-forming communities. Analyses revealed three distinctive zones within the thrombolite-forming mats that exhibited stratified populations of bacteria and archaea. Predictive metagenomics also revealed vertical profiles of metabolic capabilities, such as photosynthesis and carboxylic and fatty acid synthesis within the mats that had not been previously observed. The carbonate precipitates within the thrombolite-forming mats exhibited isotopic geochemical signatures suggesting that the precipitation within the Bahamian thrombolites is photosynthetically induced. Together, this study provides the first look at the spatial organization of the microbial populations within Bahamian thrombolites and enables the distribution of microbes to be correlated with their activities within modern thrombolite systems.

Mapping the distribution of the denitrifier community at large scales (Invited)

NASA Astrophysics Data System (ADS)

Philippot, L.; Bru, D.; Ramette, A.; Dequiedt, S.; Ranjard, L.; Jolivet, C.; Arrouays, D.

2010-12-01

Little information is available regarding the landscape-scale distribution of microbial communities and its environmental determinants. Here we combined molecular approaches and geostatistical modeling to explore spatial patterns of the denitrifying community at large scales. The distribution of denitrifrying community was investigated over 107 sites in Burgundy, a 31 500 km2 region of France, using a 16 X 16 km sampling grid. At each sampling site, the abundances of denitrifiers and 42 soil physico-chemical properties were measured. The relative contributions of land use, spatial distance, climatic conditions, time and soil physico-chemical properties to the denitrifier spatial distribution were analyzed by canonical variation partitioning. Our results indicate that 43% to 85% of the spatial variation in community abundances could be explained by the measured environmental parameters, with soil chemical properties (mostly pH) being the main driver. We found spatial autocorrelation up to 740 km and used geostatistical modelling to generate predictive maps of the distribution of denitrifiers at the landscape scale. Studying the distribution of the denitrifiers at large scale can help closing the artificial gap between the investigation of microbial processes and microbial community ecology, therefore facilitating our understanding of the relationships between the ecology of denitrifiers and N-fluxes by denitrification.

Spatial autocorrelation of microbial communities atop a debris-covered glacier is evidence of a supraglacial chronosequence.

PubMed

Darcy, John L; King, Andrew J; Gendron, Eli M S; Schmidt, Steven K

2017-08-01

Although microbial communities from many glacial environments have been analyzed, microbes living in the debris atop debris-covered glaciers represent an understudied frontier in the cryosphere. The few previous molecular studies of microbes in supraglacial debris have either had limited phylogenetic resolution, limited spatial resolution (e.g. only one sample site on the glacier) or both. Here, we present the microbiome of a debris-covered glacier across all three domains of life, using a spatially-explicit sampling scheme to characterize the Middle Fork Toklat Glacier's microbiome from its terminus to sites high on the glacier. Our results show that microbial communities differ across the supraglacial transect, but surprisingly these communities are strongly spatially autocorrelated, suggesting the presence of a supraglacial chronosequence. This pattern is dominated by phototrophic microbes (both bacteria and eukaryotes) which are less abundant near the terminus and more abundant higher on the glacier. We use these data to refute the hypothesis that the inhabitants of the glacier are randomly deposited atmospheric microbes, and to provide evidence that succession from a predominantly photosynthetic to a more heterotrophic community is occurring on the glacier. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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.

Contrasting microbial functional genes in two distinct saline-alkali and slightly acidic oil-contaminated sites.

PubMed

Liang, Yuting; Zhao, Huihui; Zhang, Xu; Zhou, Jizhong; Li, Guanghe

2014-07-15

To compare the functional gene structure and diversity of microbial communities in saline-alkali and slightly acidic oil-contaminated sites, 40 soil samples were collected from two typical oil exploration sites in North and South China and analyzed with a comprehensive functional gene array (GeoChip 3.0). The overall microbial pattern was significantly different between the two sites, and a more divergent pattern was observed in slightly acidic soils. Response ratio was calculated to compare the microbial functional genes involved in organic contaminant degradation and carbon, nitrogen, phosphorus, and sulfur cycling. The results indicated a significantly low abundance of most genes involved in organic contaminant degradation and in the cycling of nitrogen and phosphorus in saline-alkali soils. By contrast, most carbon degradation genes and all carbon fixation genes had similar abundance at both sites. Based on the relationship between the environmental variables and microbial functional structure, pH was the major factor influencing the microbial distribution pattern in the two sites. This study demonstrated that microbial functional diversity and heterogeneity in oil-contaminated environments can vary significantly in relation to local environmental conditions. The limitation of nitrogen and phosphorus and the low degradation capacity of organic contaminant should be carefully considered, particularly in most oil-exploration sites with saline-alkali soils. Copyright © 2014 Elsevier B.V. All rights reserved.

Diversity, dynamics, and activity of bacterial communities during production of an artisanal Sicilian cheese as evaluated by 16S rRNA analysis.

PubMed

Randazzo, Cinzia L; Torriani, Sandra; Akkermans, Antoon D L; de Vos, Willem M; Vaughan, Elaine E

2002-04-01

The diversity and dynamics of the microbial communities during the manufacturing of Ragusano cheese, an artisanal cheese produced in Sicily (Italy), were investigated by a combination of classical and culture-independent approaches. The latter included PCR, reverse transcriptase-PCR (RT-PCR), and denaturing gradient gel electrophoresis (DGGE) of 16S rRNA genes (rDNA). Bacterial and Lactobacillus group-specific primers were used to amplify the V6 to V8 and V1 to V3 regions of the 16S rRNA gene, respectively. DGGE profiles from samples taken during cheese production indicated dramatic shifts in the microbial community structure. Cloning and sequencing of rDNA amplicons revealed that mesophilic lactic acid bacteria (LAB), including species of Leuconostoc, Lactococcus lactis, and Macrococcus caseolyticus were dominant in the raw milk, while Streptococcus thermophilus prevailed during lactic fermentation. Other thermophilic LAB, especially Lactobacillus delbrueckii and Lactobacillus fermentum, also flourished during ripening. Comparison of the rRNA-derived patterns obtained by RT-PCR to the rDNA DGGE patterns indicated a substantially different degree of metabolic activity for the microbial groups detected. Identification of cultivated LAB isolates by phenotypic characterization and 16S rDNA analysis indicated a variety of species, reflecting to a large extent the results obtained from the 16S rDNA clone libraries, with the significant exception of the Lactobacillus delbrueckii species, which dominated in the ripening cheese but was not detected by cultivation. The present molecular approaches combined with culture can effectively describe the complex ecosystem of natural fermented dairy products, giving useful information for starter culture design and preservation of artisanal fermented food technology.

TLR9-based immunotherapy for the treatment of allergic diseases.

PubMed

Farrokhi, Shokrollah; Abbasirad, Narjes; Movahed, Ali; Khazaei, Hossein Ali; Pishjoo, Masoud; Rezaei, Nima

2017-03-01

Toll-like receptors (TLRs), a family of pattern recognition receptors expressed on many cell types of innate immunity, recognize the pathogen-associated molecular patterns of microbes. The hygiene hypothesis suggests that a reduced microbial exposure in early childhood increases the susceptibility to allergic diseases due to deviation in development of the immune system. TLRs are key roles in the right and healthy direction of adaptive immunity with the induction of T-helper 2 toward Th1 immune responses and regulatory T cells. TLR ligand CpG-ODN-based immunomodulation is independent of allergen and it mainly affects innate immune system. While, CpG-oligodeoxynucleotide-based vaccination is allergen specific and induces adaptive immune system. The use of agonists of TLR9 in two distinct strategies of immunotherapy, immunomodulation and vaccination, could be presented as the curative method for the treatment of allergic diseases.

Tracking microbial colonization patterns associated with micro-environments of rice

NASA Astrophysics Data System (ADS)

Schmidt, Hannes; Eickhorst, Thilo

2015-04-01

The interface between soil and roots (i.e. the rhizosphere) represents a highly dynamic micro-environment for microbial populations. Root-derived compounds are released into the rhizosphere and may attract, stimulate, or inhibit native soil microorganisms. Microbes associated with the rhizosphere, in turn, may have deleterious, neutral, or promoting effects on the plant. Such influences of microbial populations on the plant and vice versa are likely to be greatest in close vicinity to the root surface. It is therefore essential to detect and visualize preferential micro-sites of microbial root colonization to identify potential areas of microbe-plant interaction. We present a single-cell based approach allowing for the localization, quantification, and visualization of native microbial populations in the rhizosphere and on the rhizoplane of soil-grown roots in situ. Catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) in combination with confocal laser scanning microscopy was applied to observe colonization densities and patterns of microbial populations associated with wetland rice. Hybridizations with domain- and phylum-specific oligonucleotide probes showed that the growth stage of the rice plant as well as the distance to the root surface had a strong influence on microbial colonization patterns. Three-dimensional visualizations of root-associated microbes revealed micro-sites of preferential colonization. Highest cell numbers of archaea and bacteria were found at flowering stage of rice plant development. Irregular distribution patterns of microbiota observed at early growth stages shifted towards more uniform colonization with plant age. Accordingly, the highest colonization densities shifted from the tip to more mature regions of rice roots. Methanogenic archaea and methanotrophic bacteria were found to be co-localized at basal regions of lateral roots. Beneficial effects of a close association with root surfaces were indicated by proportionally higher numbers of methane-oxidizing bacteria on the rhizoplane compared to the rhizosphere. Such spatial effects could not be observed for methanogenic archaea. As a consequence, the detection and visualization of microbial colonization patterns on a micro-scale via CARD-FISH represents an instrumental approach in revealing potential sites of interaction between microbes and plants in soil micro-environments.

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

Unveiling Microbial Carbon Cycling Processes in Key U.S. Soils using ''Omics''

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

Myrold, David D.; Bottomely, Peter J.; Jumpponen, Ari

2014-09-17

Soils process and store large amounts of C; however, considerable uncertainty still exists about the details of that influence microbial partitioning of C into soil C pools, and what are the main influential forces that control the fraction of the C input that is stabilized. The soil microbial community is genotypically and phenotypically diverse. Despite our ability to predict the kinds of regional environmental changes that will accompany global climate change, it is not clear how the microbial community will respond to climate-induced modification of precipitation and inter-precipitation intervals, and if this response will affect the fate of C depositedmore » into soil by the local plant community. Part of this uncertainty lies with our ignorance of how the microbial community adapts genotypically and physiologically to changes in soil moisture brought about by shifts in precipitation. Our overarching goal is to harness the power of multiple meta-omics tools to gain greater understanding of the functioning of whole-soil microbial communities and their role in C cycling. We will do this by meeting the following three objectives: 1. Further develop and optimize a combination of meta-omics approaches to study how environmental factors affect microbially-mediated C cycling processes. 2. Determine the impacts of long-term changes in precipitation timing on microbial C cycling using an existing long-term field manipulation of a tallgrass prairie soil. 3. Conduct laboratory experiments that vary moisture and C inputs to confirm field observations of the linkages between microbial communities and C cycling processes. We took advantage of our state-of-the-art expertise in community “omics” to better understand the functioning soil C cycling within the Great Prairie ecosystem, including our ongoing Konza Prairie soil metagenome flagship project at JGI and the unique rainfall manipulation plots (RaMPs) established at this site more than a decade ago. We employed a systems biology approach, considering the complex soil microbial community as a functioning system and using state-of-the-art metatranscriptomic, metaproteomic, and metabolomic approaches. These omics tools were refined, applied to field experiments, and confirmed with controlled laboratory studies. Our experiments were designed to specifically identify microbial community members and processes that are instrumental players in processing of C in the prairie soils and how these processes are impacted by wetting and drying events. This project addresses a key ecosystem in the United States that current climate models predict will be subjected to dramatic changes in rainfall patterns as a result of global warming. Currently Mollisols, such as those of the tallgrass prairie, are thought to sequester more C than is released into the atmosphere, but it is not known what changes in rainfall patterns will have on future C fluxes. Through an analysis of the molecular response of the soil microbial community to shifts in precipitation cycles that are accompanied by phenologically driven changes in quality of plant C rhizodeposits, we gained deeper insight into how the metabolism of microbes has adapted to different precipitation regimes and the impact of this adaption on the fate of C deposited into soil. In doing so, we addressed key questions about the microbial cycling of C in soils that have been identified by the DOE.« less

Assessing the potential for rhizoremediation of PCB contaminated soils in northern regions using native tree species.

PubMed

Slater, Heather; Gouin, Todd; Leigh, Mary Beth

2011-06-01

Rhizosphere bioremediation of polychlorinated biphenyls (PCBs) offers a potentially inexpensive approach to remediating contaminated soils that is particularly attractive in remote regions including the Arctic. We assessed the abilities of two tree species native to Alaska, Salix alaxensis (felt-leaf willow) and Picea glauca (white spruce), to promote microbial biodegradation of PCBs via the release of phytochemicals upon fine root death. Crushed fine roots, biphenyl (PCB analogue) or salicylate (willow secondary compound) were added to microcosms containing soil spiked with PCBs and resultant PCB disappearance, soil toxicity and microbial community changes were examined. After 180d, soil treated with willow root crushates showed a significantly greater PCB loss than untreated soils for some PCB congeners, including the toxic congeners, PCB 77, 105 and 169, and showed a similar PCB loss pattern (in both extent of degradation and congeners degraded) to biphenyl-treated microcosms. Neither P. glauca (white spruce) roots nor salicylate enhanced PCB loss, indicating that biostimulation is plant species specific and was not mediated by salicylate. Soil toxicity assessed using the Microtox bioassay indicated that the willow treatment resulted in a less toxic soil environment. Molecular microbial community analyses indicated that biphenyl and salicylate promoted shifts in microbial community structure and composition that differed distinctly from each other and from the crushed root treatments. The biphenyl utilizing bacterium, Cupriavidus spp. was isolated from the soil. The findings suggest that S. alaxensis may be an effective plant for rhizoremediation by altering microbial community structure, enhancing the loss of some PCB congeners and reducing the toxicity of the soil environment. Copyright © 2011 Elsevier Ltd. All rights reserved.

Correlating Microbial Diversity Patterns with Geochemistry in an Extreme and Heterogeneous Environment of Mine Tailings

PubMed Central

Liu, Jun; Hua, Zheng-Shuang; Chen, Lin-Xing; Kuang, Jia-Liang; Li, Sheng-Jin; Shu, Wen-Sheng

2014-01-01

Recent molecular surveys have advanced our understanding of the forces shaping the large-scale ecological distribution of microbes in Earth's extreme habitats, such as hot springs and acid mine drainage. However, few investigations have attempted dense spatial analyses of specific sites to resolve the local diversity of these extraordinary organisms and how communities are shaped by the harsh environmental conditions found there. We have applied a 16S rRNA gene-targeted 454 pyrosequencing approach to explore the phylogenetic differentiation among 90 microbial communities from a massive copper tailing impoundment generating acidic drainage and coupled these variations in community composition with geochemical parameters to reveal ecological interactions in this extreme environment. Our data showed that the overall microbial diversity estimates and relative abundances of most of the dominant lineages were significantly correlated with pH, with the simplest assemblages occurring under extremely acidic conditions and more diverse assemblages associated with neutral pHs. The consistent shifts in community composition along the pH gradient indicated that different taxa were involved in the different acidification stages of the mine tailings. Moreover, the effect of pH in shaping phylogenetic structure within specific lineages was also clearly evident, although the phylogenetic differentiations within the Alphaproteobacteria, Deltaproteobacteria, and Firmicutes were attributed to variations in ferric and ferrous iron concentrations. Application of the microbial assemblage prediction model further supported pH as the major factor driving community structure and demonstrated that several of the major lineages are readily predictable. Together, these results suggest that pH is primarily responsible for structuring whole communities in the extreme and heterogeneous mine tailings, although the diverse microbial taxa may respond differently to various environmental conditions. PMID:24727268

Microbial Burden Approach : New Monitoring Approach for Measuring Microbial Burden

NASA Technical Reports Server (NTRS)

Venkateswaran, Kasthuri; Vaishampayan, Parag; Barmatz, Martin

2013-01-01

Advantages of new approach for differentiating live cells/ spores from dead cells/spores. Four examples of Salmonella outbreaks leading to costly destruction of dairy products. List of possible collaboration activities between JPL and other industries (for future discussion). Limitations of traditional microbial monitoring approaches. Introduction to new approach for rapid measurement of viable (live) bacterial cells/spores and its areas of application. Detailed example for determining live spores using new approach (similar procedure for determining live cells). JPL has developed a patented approach for measuring amount of live and dead cells/spores. This novel "molecular" method takes less than 5 to 7 hrs. compared to the seven days required using conventional techniques. Conventional "molecular" techniques can not discriminate live cells/spores among dead cells/spores. The JPL-developed novel method eliminates false positive results obtained from conventional "molecular" techniques that lead to unnecessary delay in the processing and to unnecessary destruction of food products.

Dramatic Increases of Soil Microbial Functional Gene Diversity at the Treeline Ecotone of Changbai Mountain

PubMed Central

Shen, Congcong; Shi, Yu; Ni, Yingying; Deng, Ye; Van Nostrand, Joy D.; He, Zhili; Zhou, Jizhong; Chu, Haiyan

2016-01-01

The elevational and latitudinal diversity patterns of microbial taxa have attracted great attention in the past decade. Recently, the distribution of functional attributes has been in the spotlight. Here, we report a study profiling soil microbial communities along an elevation gradient (500–2200 m) on Changbai Mountain. Using a comprehensive functional gene microarray (GeoChip 5.0), we found that microbial functional gene richness exhibited a dramatic increase at the treeline ecotone, but the bacterial taxonomic and phylogenetic diversity based on 16S rRNA gene sequencing did not exhibit such a similar trend. However, the β-diversity (compositional dissimilarity among sites) pattern for both bacterial taxa and functional genes was similar, showing significant elevational distance-decay patterns which presented increased dissimilarity with elevation. The bacterial taxonomic diversity/structure was strongly influenced by soil pH, while the functional gene diversity/structure was significantly correlated with soil dissolved organic carbon (DOC). This finding highlights that soil DOC may be a good predictor in determining the elevational distribution of microbial functional genes. The finding of significant shifts in functional gene diversity at the treeline ecotone could also provide valuable information for predicting the responses of microbial functions to climate change. PMID:27524983

Estuarine microbial food web patterns in a Lake Erie coastal wetland.

PubMed

Lavrentyev, P J; McCarthy, M J; Klarer, D M; Jochem, F; Gardner, W S

2004-11-01

Composition and distribution of planktonic protists were examined relative to microbial food web dynamics (growth, grazing, and nitrogen cycling rates) at the Old Woman Creek (OWC) National Estuarine Research Reserve during an episodic storm event in July 2003. More than 150 protistan taxa were identified based on morphology. Species richness and microbial biomass measured via microscopy and flow cytometry increased along a stream-lake (Lake Erie) transect and peaked at the confluence. Water column ammonium (NH4+) uptake (0.06 to 1.82 microM N h(-1)) and regeneration (0.04 to 0.55 microM N h(-1)) rates, measured using 15NH4+ isotope dilution, followed the same pattern. Large light/dark NH4+ uptake differences were observed in the hypereutrophic OWC interior, but not at the phosphorus-limited Lake Erie site, reflecting the microbial community structural shift from net autotrophic to net heterotrophic. Despite this shift, microbial grazers (mostly choreotrich ciliates, taxon-specific growth rates up to 2.9 d(-1)) controlled nanophytoplankton and bacteria at all sites by consuming 76 to 110% and 56 to 97% of their daily production, respectively, in dilution experiments. Overall, distribution patterns and dynamics of microbial communities in OWC resemble those in marine estuaries, where plankton productivity increases along the river-sea gradient and reaches its maximum at the confluence.

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

PubMed

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

2012-09-01

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

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

NASA Astrophysics Data System (ADS)

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

2018-01-01

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

Microbial diversity in European and South American spacecraft assembly clean rooms

NASA Astrophysics Data System (ADS)

Moissl-Eichinger, Christine; Stieglmeier, Michaela; Schwendner, Petra

Spacecraft assembly clean rooms are unique environments for microbes: Due to low nutri-ent levels, desiccated, clean conditions, constant control of humidity and temperature, these environments are quite inhospitable to microbial life and even considered "extreme". Many procedures keep the contamination as low as possible, but these conditions are also highly se-lective for indigenous microbial communities. For space missions under planetary protection requirements, it is crucial to control the contaminating bioburden as much as possible; but for the development of novel cleaning/sterilization methods it is also important to identify and characterize (understand) the present microbial community of spacecraft clean rooms. In prepa-ration for the recently approved ESA ExoMars mission, two European and one South American spacecraft assembly clean rooms were analyzed with respect to their microbial diversity, using standard procedures, new cultivation approaches and molecular methods, that should shed light onto the presence of planetary protection relevant microorganisms. For this study, the Her-schel Space Observatory (launched in May 2009) and its housing clean rooms in Friedrichshafen (Germany), at ESTEC (The Netherlands) and CSG, Kourou (French Guyana) were sampled during assembly, test and launch operations. Although Herschel does not demand planetary protection requirements, all clean rooms were in a fully operating state during sampling. This gave us the opportunity to sample the microbial diversity under strict particulate and molecular contamination-control. Samples were collected from spacecraft and selected clean room surface areas and were subjected to cultivation assays (32 different media), molecular studies (based on 16S rRNA gene sequence analysis) and quantitative PCR. The results from different strategies will be compared and critically discussed, showing the advantages and limits of the selected methodologies. This talk will sum up the lessons learned from this microbial diversity project.

Plant innate immunity: an updated insight into defense mechanism.

PubMed

Muthamilarasan, Mehanathan; Prasad, Manoj

2013-06-01

Plants are invaded by an array of pathogens of which only a few succeed in causing disease. The attack by others is countered by a sophisticated immune system possessed by the plants. The plant immune system is broadly divided into two, viz. microbial-associated molecular-patterns-triggered immunity (MTI) and effector-triggered immunity (ETI). MTI confers basal resistance, while ETI confers durable resistance, often resulting in hypersensitive response. Plants also possess systemic acquired resistance (SAR), which provides long-term defense against a broad-spectrum of pathogens. Salicylic-acid-mediated systemic acquired immunity provokes the defense response throughout the plant system during pathogen infection at a particular site. Trans-generational immune priming allows the plant to heritably shield their progeny towards pathogens previously encountered. Plants circumvent the viral infection through RNA interference phenomena by utilizing small RNAs. This review summarizes the molecular mechanisms of plant immune system, and the latest breakthroughs reported in plant defense. We discuss the plant–pathogen interactions and integrated defense responses in the context of presenting an integral understanding in plant molecular immunity.

Challenges for Complex Microbial Ecosystems: Combination of Experimental Approaches with Mathematical Modeling

PubMed Central

Haruta, Shin; Yoshida, Takehito; Aoi, Yoshiteru; Kaneko, Kunihiko; Futamata, Hiroyuki

2013-01-01

In the past couple of decades, molecular ecological techniques have been developed to elucidate microbial diversity and distribution in microbial ecosystems. Currently, modern techniques, represented by meta-omics and single cell observations, are revealing the incredible complexity of microbial ecosystems and the large degree of phenotypic variation. These studies propound that microbiological techniques are insufficient to untangle the complex microbial network. This minireview introduces the application of advanced mathematical approaches in combination with microbiological experiments to microbial ecological studies. These combinational approaches have successfully elucidated novel microbial behaviors that had not been recognized previously. Furthermore, the theoretical perspective also provides an understanding of the plasticity, robustness and stability of complex microbial ecosystems in nature. PMID:23995424

Enhanced methane production via repeated batch bioaugmentation pattern of enriched microbial consortia.

PubMed

Yang, Zhiman; Guo, Rongbo; Xu, Xiaohui; Wang, Lin; Dai, Meng

2016-09-01

Using batch and repeated batch cultivations, this study investigated the effects of bioaugmentation with enriched microbial consortia (named as EMC) on methane production from effluents of hydrogen-producing stage of potato slurry, as well as on the indigenous bacterial community. The results demonstrated that the improved methane production and shift of the indigenous bacterial community structure were dependent on the EMC/sludge ratio and bioaugmentation patterns. The methane yield and production rate in repeated batch bioaugmentation pattern of EMC were, respectively, average 15% and 10% higher than in one-time bioaugmentation pattern of EMC. DNA-sequencing approach showed that the enhanced methane production in the repeated batch bioaugmentation pattern of EMC mainly resulted from the enriched iron-reducing bacteria and the persistence of the introduced Syntrophomonas, which led to a rapid degradation of individual VFAs to methane. The findings contributed to understanding the correlation between the bioaugmentation of microbial consortia, community shift, and methane production. Copyright © 2016 Elsevier Ltd. All rights reserved.

Mercury in water and biomass of microbial communities in hot springs of Yellowstone National Park, USA

USGS Publications Warehouse

King, S.A.; Behnke, S.; Slack, K.; Krabbenhoft, D.P.; Nordstrom, D. Kirk; Burr, M.D.; Striegl, Robert G.

2006-01-01

Ultra-clean sampling methods and approaches typically used in pristine environments were applied to quantify concentrations of Hg species in water and microbial biomass from hot springs of Yellowstone National Park, features that are geologically enriched with Hg. Microbial populations of chemically-diverse hot springs were also characterized using modern methods in molecular biology as the initial step toward ongoing work linking Hg speciation with microbial processes. Molecular methods (amplification of environmental DNA using 16S rDNA primers, cloning, denatured gradient gel electrophoresis (DGGE) screening of clone libraries, and sequencing of representative clones) were used to examine the dominant members of microbial communities in hot springs. Total Hg (THg), monomethylated Hg (MeHg), pH, temperature, and other parameters influential to Hg speciation and microbial ecology are reported for hot springs water and associated microbial mats. Several hot springs indicate the presence of MeHg in microbial mats with concentrations ranging from 1 to 10 ng g-1 (dry weight). Concentrations of THg in mats ranged from 4.9 to 120,000 ng g-1 (dry weight). Combined data from surveys of geothermal water, lakes, and streams show that aqueous THg concentrations range from l to 600 ng L-1. Species and concentrations of THg in mats and water vary significantly between hot springs, as do the microorganisms found at each site. ?? 2006.

Gayle Bentley | NREL

Science.gov Websites

Areas of Expertise Metabolic engineering Synthetic biology Molecular microbiology Gas chromatography biosynthesis Education Ph.D., Molecular Microbiology and Microbial Pathogenesis, Washington University in St

Post-Fire Spatial Patterns of Soil Nitrogen Mineralization and Microbial Abundance

PubMed Central

Smithwick, Erica A. H.; Naithani, Kusum J.; Balser, Teri C.; Romme, William H.; Turner, Monica G.

2012-01-01

Stand-replacing fires influence soil nitrogen availability and microbial community composition, which may in turn mediate post-fire successional dynamics and nutrient cycling. However, fires create patchiness at both local and landscape scales and do not result in consistent patterns of ecological dynamics. The objectives of this study were to (1) quantify the spatial structure of microbial communities in forest stands recently affected by stand-replacing fire and (2) determine whether microbial variables aid predictions of in situ net nitrogen mineralization rates in recently burned stands. The study was conducted in lodgepole pine (Pinus contorta var. latifolia) and Engelmann spruce/subalpine fir (Picea engelmannii/Abies lasiocarpa) forest stands that burned during summer 2000 in Greater Yellowstone (Wyoming, USA). Using a fully probabilistic spatial process model and Bayesian kriging, the spatial structure of microbial lipid abundance and fungi-to-bacteria ratios were found to be spatially structured within plots two years following fire (for most plots, autocorrelation range varied from 1.5 to 10.5 m). Congruence of spatial patterns among microbial variables, in situ net N mineralization, and cover variables was evident. Stepwise regression resulted in significant models of in situ net N mineralization and included variables describing fungal and bacterial abundance, although explained variance was low (R2<0.29). Unraveling complex spatial patterns of nutrient cycling and the biotic factors that regulate it remains challenging but is critical for explaining post-fire ecosystem function, especially in Greater Yellowstone, which is projected to experience increased fire frequencies by mid 21st Century. PMID:23226324

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

NASA Astrophysics Data System (ADS)

Daly, Amanda; Grandy, A. Stuart

2016-04-01

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

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

PubMed

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

2013-08-01

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

Molecular ecology of hydrothermal vent microbial communities.

PubMed

Jeanthon, C

2000-02-01

The study of the structure and diversity of hydrothermal vent microbial communities has long been restricted to the morphological description of microorganisms and the use of enrichment culture-based techniques. Until recently the identification of the culturable fraction required the isolation of pure cultures followed by testing for multiple physiological and biochemical traits. However, peculiar inhabitants of the hydrothermal ecosystem such as the invertebrate endosymbionts and the dense microbial mat filaments have eluded laboratory cultivation. Substantial progress has been achieved in recent years in techniques for the identification of microorganisms in natural environments. Application of molecular approaches has revealed the existence of unique and previously unrecognized microorganisms. These have provided fresh insight into the ecology, diversity and evolution of mesophilic and thermophilic microbial communities from the deep-sea hydrothermal ecosystem. This review reports the main discoveries made through the introduction of these powerful techniques in the study of deep-sea hydrothermal vent microbiology.

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.

Small-scale spatial variability of soil microbial community composition and functional diversity in a mixed forest

NASA Astrophysics Data System (ADS)

Wang, Qiufeng; Tian, Jing; Yu, Guirui

2014-05-01

Patterns in the spatial distribution of organisms provide important information about mechanisms that regulate the diversity and complexity of soil ecosystems. Therefore, information on spatial distribution of microbial community composition and functional diversity is urgently necessary. The spatial variability on a 26×36 m plot and vertical distribution (0-10 cm and 10-20 cm) of soil microbial community composition and functional diversity were studied in a natural broad-leaved Korean pine (Pinus koraiensis) mixed forest soil in Changbai Mountain. The phospholipid fatty acid (PLFA) pattern was used to characterize the soil microbial community composition and was compared with the community substrate utilization pattern using Biolog. Bacterial biomass dominated and showed higher variability than fungal biomass at all scales examined. The microbial biomass decreased with soil depths increased and showed less variability in lower 10-20 cm soil layer. The Shannon-Weaver index value for microbial functional diversity showed higher variability in upper 0-10 cm than lower 10-20 cm soil layer. Carbohydrates, carboxylic acids, polymers and amino acids are the main carbon sources possessing higher utilization efficiency or utilization intensity. At the same time, the four carbon source types contributed to the differentiation of soil microbial communities. This study suggests the higher diversity and complexity for this mix forest ecosystem. To determine the driving factors that affect this spatial variability of microorganism is the next step for our study.

The role of ecological theory in microbial ecology.

PubMed

Prosser, James I; Bohannan, Brendan J M; Curtis, Tom P; Ellis, Richard J; Firestone, Mary K; Freckleton, Rob P; Green, Jessica L; Green, Laura E; Killham, Ken; Lennon, Jack J; Osborn, A Mark; Solan, Martin; van der Gast, Christopher J; Young, J Peter W

2007-05-01

Microbial ecology is currently undergoing a revolution, with repercussions spreading throughout microbiology, ecology and ecosystem science. The rapid accumulation of molecular data is uncovering vast diversity, abundant uncultivated microbial groups and novel microbial functions. This accumulation of data requires the application of theory to provide organization, structure, mechanistic insight and, ultimately, predictive power that is of practical value, but the application of theory in microbial ecology is currently very limited. Here we argue that the full potential of the ongoing revolution will not be realized if research is not directed and driven by theory, and that the generality of established ecological theory must be tested using microbial systems.

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

USGS Publications Warehouse

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

2015-01-01

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

Biofilm community succession: a neutral perspective.

PubMed

Woodcock, Stephen; Sloan, William T

2017-05-22

Although biofilms represent one of the dominant forms of life in aqueous environments, our understanding of the assembly and development of their microbial communities remains relatively poor. In recent years, several studies have addressed this and have extended the concepts of succession theory in classical ecology into microbial systems. From these datasets, niche-based conceptual models have been developed explaining observed biodiversity patterns and their dynamics. These models have not, however, been formulated mathematically and so remain untested. Here, we further develop spatially resolved neutral community models and demonstrate that these can also explain these patterns and offer alternative explanations of microbial succession. The success of neutral models suggests that stochastic effects alone may have a much greater influence on microbial community succession than previously acknowledged. Furthermore, such models are much more readily parameterised and can be used as the foundation of more complex and realistic models of microbial community succession.

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

PubMed Central

DeBry, Ronald W.; Lytle, Darren A.

2012-01-01

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

Bench-to-bedside review: Toll-like receptors and their role in septic shock

PubMed Central

Opal, Steven M; Huber, Christian E

2002-01-01

The Toll-like receptors (TLRs) are essential transmembrane signaling receptors of the innate immune system that alert the host to the presence of a microbial invader. The recent discovery of the TLRs has rapidly expanded our knowledge of molecular events that initiate host–pathogen interactions. These functional attributes of the cellular receptors provide insights into the nature of pattern recognition receptors that activate the human antimicrobial defense systems. The fundamental significance of the TLRs in the generation of systemic inflammation and the pathogenesis of septic shock is reviewed. The potential clinical implications of therapeutic modulation of these recently characterized receptors of innate immunity are also discussed. PMID:11983038

New challenges and opportunities for industrial biotechnology

PubMed Central

2012-01-01

Industrial biotechnology has not developed as fast as expected due to some challenges including the emergences of alternative energy sources, especially shale gas, natural gas hydrate (or gas hydrate) and sand oil et al. The weaknesses of microbial or enzymatic processes compared with the chemical processing also make industrial biotech products less competitive with the chemical ones. However, many opportunities are still there if industrial biotech processes can be as similar as the chemical ones. Taking advantages of the molecular biology and synthetic biology methods as well as changing process patterns, we can develop bioprocesses as competitive as chemical ones, these including the minimized cells, open and continuous fermentation processes et al. PMID:22905695

Molecular Insights on Dissolved Organic Matter Transformation by Supraglacial Microbial Communities.

PubMed

Antony, Runa; Willoughby, Amanda S; Grannas, Amanda M; Catanzano, Victoria; Sleighter, Rachel L; Thamban, Meloth; Hatcher, Patrick G; Nair, Shanta

2017-04-18

Snow overlays the majority of Antarctica and is an important repository of dissolved organic matter (DOM). DOM transformations by supraglacial microbes are not well understood. We use ultrahigh resolution mass spectrometry to elucidate molecular changes in snowpack DOM by in situ microbial processes (up to 55 days) in a coastal Antarctic site. Both autochthonous and allochthonous DOM is highly bioavailable and is transformed by resident microbial communities through parallel processes of degradation and synthesis. DOM thought to be of a more refractory nature, such as dissolved black carbon and carboxylic-rich alicyclic molecules, was also rapidly and extensively reworked. Microbially reworked DOM exhibits an increase in the number and magnitude of N-, S-, and P-containing formulas, is less oxygenated, and more aromatic when compared to the initial DOM. Shifts in the heteroatom composition suggest that microbial processes may be important in the cycling of not only C, but other elements such as N, S, and P. Microbial reworking also produces photoreactive compounds, with potential implications for DOM photochemistry. Refined measurements of supraglacial DOM and their cycling by microbes is critical for improving our understanding of supraglacial DOM cycling and the biogeochemical and ecological impacts of DOM export to downstream environments.

Molecular analysis of microbial community structures in pristine and contaminated aquifers--Field and laboratory microcosm experiments

USGS Publications Warehouse

Shi, Y.; Zwolinski, M.D.; Schreiber, M.E.; Bahr, J.M.; Sewell, G.W.; Hickey, W.J.

1999-01-01

Molecular Analysis of Microbial Community Structures in Pristine and Contaminated Aquifers: Field and Laboratory Microcosm Experimentsvar callbackToken='531E8ACDB6C8511'; var subCode='asmjournal_sub'; var OAS_sitepage = 'aem.asm.org'; This study used phylogenetic probes in hybridization analysis to (i) determine in situ microbial community structures in regions of a shallow sand aquifer that were oxygen depleted and fuel contaminated (FC) or aerobic and noncontaminated (NC) and (ii) examine alterations in microbial community structures resulting from exposure to toluene and/or electron acceptor supplementation (nitrate). The latter objective was addressed by using the NC and FC aquifer materials for anaerobic microcosm studies in which phylogenetic probe analysis was complemented by microbial activity assays. Domain probe analysis of the aquifer samples showed that the communities were predominantlyBacteria; Eucarya and Archaea were not detectable. At the phylum and subclass levels, the FC and NC aquifer material had similar relative abundance distributions of 43 to 65% β- and γ-Proteobacteria (B+G), 31 to 35% α-Proteobacteria (ALF), 15 to 18% sulfate-reducing bacteria, and 5 to 10% high G+C gram positive bacteria. Compared to that of the NC region, the community structure of the FC material differed mainly in an increased abundance of B+G relative to that of ALF. The microcosm communities were like those of the field samples in that they were predominantly Bacteria (83 to 101%) and lacked detectable Archaea but differed in that a small fraction (2 to 8%) of Eucarya was detected regardless of the treatment applied. The latter result was hypothesized to reflect enrichment of anaerobic protozoa. Addition of nitrate and/or toluene stimulated microbial activity in the microcosms, but only supplementation of toluene alone significantly altered community structures. For the NC material, the dominant subclass shifted from B+G to ALF, while in the FC microcosms 55 to 65% of theBacteria community was no longer identifiable by the phylum or subclass probes used. The latter result suggested that toluene exposure fostered the proliferation of phylotype(s) that were otherwise minor constituents of the FC aquifer community. These studies demonstrated that alterations in aquifer microbial communities resulting from specific anthropogenic perturbances can be inferred from microcosm studies integrating chemical and phylogenetic probe analysis and in the case of hydrocarbon contamination may facilitate the identification of organisms important for in situ biodegradation processes. Further work integrating and coordinating microcosm and field experiments is needed to explore how differences in scale, substrate complexity, and other hydrogeological conditions may affect patterns observed in these systems.

Bioavailability of riverine dissolved organic matter in three Baltic Sea estuaries and the effect of catchment land use

NASA Astrophysics Data System (ADS)

Asmala, E.; Autio, R.; Kaartokallio, H.; Pitkänen, L.; Stedmon, C. A.; Thomas, D. N.

2013-11-01

The microbial degradation of dissolved organic carbon and nitrogen (DOC, DON) was studied in three Finnish boreal estuaries with contrasting land use patterns (Kiiminkijoki - natural forest and peatland; Kyrönjoki - agricultural; Karjaanjoki - mixed/urban). Bioassays of 12-18 d long durations were used in 3 seasons at in situ temperatures. Besides the bulk parameters, a suite of dissolved organic matter (DOM) quality parameters were also investigated, including colored DOM (CDOM), fluorescent DOM and the molecular weight of DOM. Bioavailable DOC and DON pools varied significantly between the estuaries, from 7.9 to 10.6% and from 5.5 to 21.9%, respectively. DOM originating from the catchment dominated by natural forests and peatlands (Kiiminkijoki) had the lowest DOC and DON degradation rates, as well as the lowest proportions of biodegradable DOC and DON. A greater proportion of agricultural land in the catchment increased the bioavailability of DON, but not the bioavailability of DOC (Kyrönjoki). Additionally, DOM quality varied significantly between the estuaries, and DOM originating from the agricultural Kyrönjoki catchment sustained higher DOC and DON degradation rates and higher bacterial growth efficiency (BGE) compared to those of the natural forest and peat dominated Kiiminkijoki catchment. The quality of DOM, indicated by differences in CDOM, fluorescent DOM and molecular weight, varied between estuaries with differing land use and was concluded to be major driver of BGE of these systems and thereafter to the microbial CO2 fluxes from the estuaries. The differences in BGE resulted in a 5-fold difference in the calculated daily bacterial CO2 emissions between the study's estuaries due to bacterial activity, ranging from 40 kg C d-1 in the Karjaanjoki estuary to 200 kg C d-1 in the Kyrönjoki estuary. Lower DOC:DON ratios, smaller molecular weight and higher CDOM absorption spectral slope values of DOM resulted in higher proportion of the initial DOC and DON being transferred to microbial growth and therefore to the pelagic food web. The pristine, peatland and forest-dominated Kiiminkijoki catchment had the lowest BGE, and therefore proportionally highest CO2 fluxes.

Chemotactic preferences govern competition and pattern formation in simulated two-strain microbial communities.

PubMed

Centler, Florian; Thullner, Martin

2015-01-01

Substrate competition is a common mode of microbial interaction in natural environments. While growth properties play an important and well-studied role in competition, we here focus on the influence of motility. In a simulated two-strain community populating a homogeneous two-dimensional environment, strains competed for a common substrate and only differed in their chemotactic preference, either responding more sensitively to a chemoattractant excreted by themselves or responding more sensitively to substrate. Starting from homogeneous distributions, three possible behaviors were observed depending on the competitors' chemotactic preferences: (i) distributions remained homogeneous, (ii) patterns formed but dissolved at a later time point, resulting in a shifted community composition, and (iii) patterns emerged and led to the extinction of one strain. When patterns formed, the more aggregating strain populated the core of microbial aggregates where starving conditions prevailed, while the less aggregating strain populated the more productive zones at the fringe or outside aggregates, leading to a competitive advantage of the less aggregating strain. The presence of a competitor was found to modulate a strain's behavior, either suppressing or promoting aggregate formation. This observation provides a potential mechanism by which an aggregated lifestyle might evolve even if it is initially disadvantageous. Adverse effects can be avoided as a competitor hinders aggregate formation by a strain which has just acquired this ability. The presented results highlight both, the importance of microbial motility for competition and pattern formation, and the importance of the temporal evolution, or history, of microbial communities when trying to explain an observed distribution.

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

Surface, Water and Air Biocharacterization - A Comprehensive Characterization of Microorganisms and Allergens in Spacecraft Environment

NASA Technical Reports Server (NTRS)

Pierson, Duane L.; Ott, C. Mark; Cruz, Patricia; Buttner, Mark P.

2009-01-01

A Comprehensive Characterization of Microorganisms and Allergens in Spacecraft (SWAB) will use advanced molecular techniques to comprehensively evaluate microbes on board the space station, including pathogens (organisms that may cause disease). It also will track changes in the microbial community as spacecraft visit the station and new station modules are added. This study will allow an assessment of the risk of microbes to the crew and the spacecraft. Research Summary: Previous microbial analysis of spacecraft only identify microorganisms that will grow in culture, omitting greater than 90% of all microorganisms including pathogens such as Legionella (the bacterium which causes Legionnaires' disease) and Cryptosporidium (a parasite common in contaminated water) The incidence of potent allergens, such as dust mites, has never been systematically studied in spacecraft environments and microbial toxins have not been previously monitored. This study will use modern molecular techniques to identify microorganisms and allergens. Direct sampling of the ISS allows identification of the microbial communities present, and determination of whether these change or mutate over time. SWAB complements the nominal ISS environmental monitoring by providing a comparison of analyses from current media-based and advanced molecular-based technologies.

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.

Anti-fibrinolytic and anti-microbial activities of a serine protease inhibitor from honeybee (Apis cerana) venom.

PubMed

Yang, Jie; Lee, Kwang Sik; Kim, Bo Yeon; Choi, Yong Soo; Yoon, Hyung Joo; Jia, Jingming; Jin, Byung Rae

2017-10-01

Bee venom contains a variety of peptide constituents, including low-molecular-weight protease inhibitors. While the putative low-molecular-weight serine protease inhibitor Api m 6 containing a trypsin inhibitor-like cysteine-rich domain was identified from honeybee (Apis mellifera) venom, no anti-fibrinolytic or anti-microbial roles for this inhibitor have been elucidated. In this study, we identified an Asiatic honeybee (A. cerana) venom serine protease inhibitor (AcVSPI) that was shown to act as a microbial serine protease inhibitor and plasmin inhibitor. AcVSPI was found to consist of a trypsin inhibitor-like domain that displays ten cysteine residues. Interestingly, the AcVSPI peptide sequence exhibited high similarity to the putative low-molecular-weight serine protease inhibitor Api m 6, which suggests that AcVSPI is an allergen Api m 6-like peptide. Recombinant AcVSPI was expressed in baculovirus-infected insect cells, and it demonstrated inhibitory activity against trypsin, but not chymotrypsin. Additionally, AcVSPI has inhibitory effects against plasmin and microbial serine proteases; however, it does not have any detectable inhibitory effects on thrombin or elastase. Consistent with these inhibitory effects, AcVSPI inhibited the plasmin-mediated degradation of fibrin to fibrin degradation products. AcVSPI also bound to bacterial and fungal surfaces and exhibited anti-microbial activity against fungi as well as gram-positive and gram-negative bacteria. These findings demonstrate the anti-fibrinolytic and anti-microbial roles of AcVSPI as a serine protease inhibitor. Copyright © 2017 Elsevier Inc. All rights reserved.

Experimental design and quantitative analysis of microbial community multiomics.

PubMed

Mallick, Himel; Ma, Siyuan; Franzosa, Eric A; Vatanen, Tommi; Morgan, Xochitl C; Huttenhower, Curtis

2017-11-30

Studies of the microbiome have become increasingly sophisticated, and multiple sequence-based, molecular methods as well as culture-based methods exist for population-scale microbiome profiles. To link the resulting host and microbial data types to human health, several experimental design considerations, data analysis challenges, and statistical epidemiological approaches must be addressed. Here, we survey current best practices for experimental design in microbiome molecular epidemiology, including technologies for generating, analyzing, and integrating microbiome multiomics data. We highlight studies that have identified molecular bioactives that influence human health, and we suggest steps for scaling translational microbiome research to high-throughput target discovery across large populations.

Molecular analyses of two bacterial sampling methods in ligature-induced periodontitis in rats.

PubMed

Fontana, Carla Raquel; Grecco, Clovis; Bagnato, Vanderlei Salvador; de Freitas, Laura Marise; Boussios, Constantinos I; Soukos, Nikolaos S

2018-02-01

The prevalence profile of periodontal pathogens in dental plaque can vary as a function of the detection method; however, the sampling technique may also play a role in determining dental plaque microbial profiles. We sought to determine the bacterial composition comparing two sampling methods, one well stablished and a new one proposed here. In this study, a ligature-induced periodontitis model was used in 30 rats. Twenty-seven days later, ligatures were removed and microbiological samples were obtained directly from the ligatures as well as from the periodontal pockets using absorbent paper points. Microbial analysis was performed using DNA probes to a panel of 40 periodontal species in the checkerboard assay. The bacterial composition patterns were similar for both sampling methods. However, detection levels for all species were markedly higher for ligatures compared with paper points. Ligature samples provided more bacterial counts than paper points, suggesting that the technique for induction of periodontitis could also be applied for sampling in rats. Our findings may be helpful in designing studies of induced periodontal disease-associated microbiota.

A resurgence in field research is essential to better understand the diversity, ecology, and evolution of microbial eukaryotes.

PubMed

Heger, Thierry J; Edgcomb, Virginia P; Kim, Eunsoo; Lukeš, Julius; Leander, Brian S; Yubuki, Naoji

2014-01-01

The discovery and characterization of protist communities from diverse environments are crucial for understanding the overall evolutionary history of life on earth. However, major questions about the diversity, ecology, and evolutionary history of protists remain unanswered, notably because data obtained from natural protist communities, especially of heterotrophic species, remain limited. In this review, we discuss the challenges associated with "field protistology", defined here as the exploration, characterization, and interpretation of microbial eukaryotic diversity within the context of natural environments or field experiments, and provide suggestions to help fill this important gap in knowledge. We also argue that increased efforts in field studies that combine molecular and microscopical methods offer the most promising path toward (1) the discovery of new lineages that expand the tree of eukaryotes; (2) the recognition of novel evolutionary patterns and processes; (3) the untangling of ecological interactions and functions, and their roles in larger ecosystem processes; and (4) the evaluation of protist adaptations to a changing climate. © 2013 The Author(s) Journal of Eukaryotic Microbiology © 2013 International Society of Protistologists.

Eric P. Knoshaug | NREL

Science.gov Websites

P. Knoshaug Photo of Eric P. Knoshaug Eric Knoshaug Researcher IV-Molecular Biology Eric.Knoshaug , molecular biology, and microbial physiology Fermentation and growth systems development Metabolic

Genetic diversity patterns of microeukaryotic plankton communities in Shenhu Bay, southeast China

NASA Astrophysics Data System (ADS)

Zhang, Wenjing; Pan, Yongbo; Yu, Lingyu; Liu, Lemian

2017-06-01

Microeukaryotic plankton is an abundant and diverse component of marine environments and plays an important role in microbial food webs. However, few studies have been conducted on the genetic diversity of microeukaryotes in the subtropical bays of China. In the present study, we investigated the microeukaryotic plankton in the Shenhu Bay by using denaturing gradient gel electrophoresis (DGGE) and sequencing of prominent bands. Our results indicated that Copepoda and Dinophyceae were the most diverse groups, and that the microeukaryotic communities varied significantly between summer and autumn, with the autumn communities exhibited a higher diversity than summer communities. Furthermore, the community composition and diversity from both surface and bottom waters showed more significant differences in summer than in autumn. Environmental parameters also displayed obvious seasonal patterns. Redundancy analysis (RDA) showed that temperature was the most significant environmental factor shaping the seasonal patterns of the microplanktonic members in the Shenhu Bay. Community-level molecular techniques such as DGGE appear as useful tools to detect the presence of red tide causing species and to guide the management of coastal water mariculture.

A trait-based approach for examining microbial community assembly

NASA Astrophysics Data System (ADS)

Prest, T. L.; Nemergut, D.

2015-12-01

Microorganisms regulate all of Earth's major biogeochemical cycles and an understanding of how microbial communities assemble is a key part in evaluating controls over many types of ecosystem processes. Rapid advances in technology and bioinformatics have led to a better appreciation for the variation in microbial community structure in time and space. Yet, advances in theory are necessary to make sense of these data and allow us to generate unifying hypotheses about the causes and consequences of patterns in microbial biodiversity and what they mean for ecosystem function. Here, I will present a metaanalysis of microbial community assembly from a variety of successional and post-disturbance systems. Our analysis shows various distinct patterns in community assembly, and the potential importance of nutrients and dispersal in shaping microbial community beta diversity in these systems. We also used a trait-based approach to generate hypotheses about the mechanisms driving patterns of microbial community assembly and the implications for function. Our work reveals the importance of rRNA operon copy number as a community aggregated trait in helping to reconcile differences in community dynamics between distinct types of successional and disturbed systems. Specifically, our results demonstrate that decreases in average copy number can be a common feature of communities across various drivers of ecological succession, supporting a transition from an r-selected to a K-selected community. Importantly, our work supports the scaling of the copy number trait over multiple levels of biological organization, from cells to populations and communities, and has implications for both ecology and evolution. Trait-based approaches are an important next step to generate and test hypotheses about the forces structuring microbial communities and the subsequent consequences for ecosystem function.

Investigative modalities in infectious keratitis.

PubMed

Gupta, Noopur; Tandon, Radhika

2008-01-01

Standard recommended guidelines for diagnosis of infectious keratitis do exist. Based on an extensive Medline literature search, the various investigative modalities available for aiding the diagnosis of microbial keratitis have been reviewed and described briefly. Preferred practice patterns have been outlined and the importance of routine pre-treatment cultures in the primary management of infectious keratitis has been highlighted. Corneal scraping, tear samples and corneal biopsy are few of the specimens needed to carry out the investigative procedures for diagnosis and for initiating therapy in cases of microbial keratitis. In bacterial, fungal and amoebic keratitis, microscopic examination of smears is essential for rapid diagnosis. Potassium hydroxide (KOH) wet mount, Gram's stain and Giemsa stain are widely used and are important for clinicians to start empirical therapy before microbial culture results are available. The usefulness of performing corneal cultures in all cases of suspected infectious keratitis has been well established. In cases of suspected viral keratitis, therapy can be initiated on clinical judgment alone. If a viral culture is needed, scrapings should directly be inoculated into the viral transport media. In vivo confocal microscopy is a useful adjunct to slit lamp bio-microscopy for supplementing diagnosis in most cases and establishing early diagnosis in many cases of non-responding fungal and amoebic keratitis. This is a non-invasive, high resolution technique which allows rapid detection of Acanthamoeba cysts and trophozoites and fungal hyphae in the cornea long before laboratory cultures give conclusive results. Other new modalities for detection of microbial keratitis include molecular diagnostic techniques like polymerase chain reaction, and genetic finger printing by pulsed field gel electrophoresis.

Microbe observation and cultivation array (MOCA) for cultivating and analyzing environmental microbiota.

PubMed

Gao, Weimin; Navarroli, Dena; Naimark, Jared; Zhang, Weiwen; Chao, Shih-Hui; Meldrum, Deirdre R

2013-01-09

The use of culture-independent nucleic acid techniques, such as ribosomal RNA gene cloning library analysis, has unveiled the tremendous microbial diversity that exists in natural environments. In sharp contrast to this great achievement is the current difficulty in cultivating the majority of bacterial species or phylotypes revealed by molecular approaches. Although recent new technologies such as metagenomics and metatranscriptomics can provide more functionality information about the microbial communities, it is still important to develop the capacity to isolate and cultivate individual microbial species or strains in order to gain a better understanding of microbial physiology and to apply isolates for various biotechnological applications. We have developed a new system to cultivate bacteria in an array of droplets. The key component of the system is the microbe observation and cultivation array (MOCA), which consists of a Petri dish that contains an array of droplets as cultivation chambers. MOCA exploits the dominance of surface tension in small amounts of liquid to spontaneously trap cells in well-defined droplets on hydrophilic patterns. During cultivation, the growth of the bacterial cells across the droplet array can be monitored using an automated microscope, which can produce a real-time record of the growth. When bacterial cells grow to a visible microcolony level in the system, they can be transferred using a micropipette for further cultivation or analysis. MOCA is a flexible system that is easy to set up, and provides the sensitivity to monitor growth of single bacterial cells. It is a cost-efficient technical platform for bioassay screening and for cultivation and isolation of bacteria from natural environments.

Macroecology of unicellular organisms - patterns and processes.

PubMed

Soininen, Janne

2012-02-01

Macroecology examines the relationship between organisms and their environment at large spatial (and temporal) scales. Typically, macroecologists explain the large-scale patterns of abundance, distribution and diversity. Despite the difficulties in sampling and characterizing microbial diversity, macroecologists have recently also been interested in unicellular organisms. Here, I review the current advances made in microbial macroecology, as well as discuss related ecosystem functions. Overall, it seems that microorganisms suit surprisingly well to known species abundance distributions and show positive relationship between distribution and adundance. Microbial species-area and distance-decay relationships tend to be weaker than for macroorganisms, but nonetheless significant. Few findings on altitudinal gradients in unicellular taxa seem to differ greatly from corresponding findings for larger taxa, whereas latitudinal gradients among microorganisms have either been clearly evident or absent depending on the context. Literature also strongly emphasizes the role of spatial scale for the patterns of diversity and suggests that patterns are affected by species traits as well as ecosystem characteristics. Finally, I discuss the large role of local biotic and abiotic variables driving the community assembly in unicellular taxa and eventually dictating how multiple ecosystem processes are performed. Present review highlights the fact that most microorganisms may not differ fundamentally from larger taxa in their large-scale distribution patterns. Yet, review also shows that many aspects of microbial macroecology are still relatively poorly understood and specific patterns depend on focal taxa and ecosystem concerned. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

Engineering microbial electrocatalysis for chemical and fuel production.

PubMed

Rosenbaum, Miriam A; Henrich, Alexander W

2014-10-01

In many biotechnological areas, metabolic engineering and synthetic biology have become core technologies for biocatalyst development. Microbial electrocatalysis for biochemical and fuel production is still in its infancy and reactions rates and the product spectrum are currently very low. Therefore, molecular engineering strategies will be crucial for the advancement and realization of many new bioproduction routes using electroactive microorganisms. The complex and unresolved biochemistry and physiology of extracellular electron transfer and the lack of molecular tools for these new non-model hosts for genetic engineering constitute the major challenges for this effort. This review is providing an insight into the current status, challenges and promising approaches of pathway engineering for microbial electrocatalysis. Copyright © 2014 Elsevier Ltd. All rights reserved.

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.

Molecular Survey of Concrete Sewer Biofilm Microbial Communities

EPA Science Inventory

Although bacteria are implicated in deteriorating concrete structures, there is very little information on the composition of concrete microbial communities. To this end, we studied different concrete biofilms by performing sequence analysis of 16S rDNA concrete clone libraries. ...

Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate

PubMed Central

Bokulich, Nicholas A.; Thorngate, John H.; Richardson, Paul M.; Mills, David A.

2014-01-01

Wine grapes present a unique biogeography model, wherein microbial biodiversity patterns across viticultural zones not only answer questions of dispersal and community maintenance, they are also an inherent component of the quality, consumer acceptance, and economic appreciation of a culturally important food product. On their journey from the vineyard to the wine bottle, grapes are transformed to wine through microbial activity, with indisputable consequences for wine quality parameters. Wine grapes harbor a wide range of microbes originating from the surrounding environment, many of which are recognized for their role in grapevine health and wine quality. However, determinants of regional wine characteristics have not been identified, but are frequently assumed to stem from viticultural or geological factors alone. This study used a high-throughput, short-amplicon sequencing approach to demonstrate that regional, site-specific, and grape-variety factors shape the fungal and bacterial consortia inhabiting wine-grape surfaces. Furthermore, these microbial assemblages are correlated to specific climatic features, suggesting a link between vineyard environmental conditions and microbial inhabitation patterns. Taken together, these factors shape the unique microbial inputs to regional wine fermentations, posing the existence of nonrandom “microbial terroir” as a determining factor in regional variation among wine grapes. PMID:24277822

Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate.

PubMed

Bokulich, Nicholas A; Thorngate, John H; Richardson, Paul M; Mills, David A

2014-01-07

Wine grapes present a unique biogeography model, wherein microbial biodiversity patterns across viticultural zones not only answer questions of dispersal and community maintenance, they are also an inherent component of the quality, consumer acceptance, and economic appreciation of a culturally important food product. On their journey from the vineyard to the wine bottle, grapes are transformed to wine through microbial activity, with indisputable consequences for wine quality parameters. Wine grapes harbor a wide range of microbes originating from the surrounding environment, many of which are recognized for their role in grapevine health and wine quality. However, determinants of regional wine characteristics have not been identified, but are frequently assumed to stem from viticultural or geological factors alone. This study used a high-throughput, short-amplicon sequencing approach to demonstrate that regional, site-specific, and grape-variety factors shape the fungal and bacterial consortia inhabiting wine-grape surfaces. Furthermore, these microbial assemblages are correlated to specific climatic features, suggesting a link between vineyard environmental conditions and microbial inhabitation patterns. Taken together, these factors shape the unique microbial inputs to regional wine fermentations, posing the existence of nonrandom "microbial terroir" as a determining factor in regional variation among wine grapes.

Effects of lead and cadmium nitrate on biomass and substrate utilization pattern of soil microbial communities.

PubMed

Muhammad, Akmal; Xu, Jianming; Li, Zhaojun; Wang, Haizhen; Yao, Huaiying

2005-07-01

A study was conducted to evaluate the effects of different concentrations of lead (Pb) and cadmium (Cd) applied as their nitrates on soil microbial biomass carbon (C(mic)) and nitrogen (N(mic)), and substrate utilization pattern of soil microbial communities. The C(mic) and N(mic) contents were determined at 0, 14, 28, 42 and 56 days after heavy metal application (DAA). The results showed a significant decline in the C(mic) for all Pb and Cd amended soils from the start to 28 DAA. From 28 to 56 DAA, C(mic) contents changed non-significantly for all other treatments except for 600 mgkg(-1) Pb and 100 mgkg(-1) Cd in which it declined significantly from 42 to 56 DAA. The N(mic) contents also decreased significantly from start to 28 DAA for all other Pb and Cd treatments except for 200 mgkg(-1) Pb which did not show significant difference from the control. Control and 200 mgkg(-1) Pb had significantly lower soil microbial biomass C:N ratio as compared with other Pb treatments from 14 to 42 DAA, however at 56 DAA, only 1000 mgkg(-1) Pb showed significantly higher C:N ratio compared with other treatments. No significant difference in C:N ratio for all Cd treated soils was seen from start to 28 DAA, however from 42 to 56 DAA, 100 mgkg(-1) Pb showed significantly higher C:N ratio compared with other treatments. On 56 DAA, substrate utilization pattern of soil microbial communities was determined by inoculating Biolog ECO plates. The results indicated that Pb and Cd addition inhibited the functional activity of soil microbial communities as indicated by the intensity of average well color development (AWCD) during 168 h of incubation. Multivariate analysis of sole carbon source utilization pattern demonstrated that higher levels of heavy metal application had significantly affected soil microbial community structure.

Variance and potential niche separation of microbial communities in subseafloor sediments off Shimokita Peninsula, Japan.

PubMed

Nunoura, Takuro; Takaki, Yoshihiro; Shimamura, Shigeru; Kakuta, Jungo; Kazama, Hiromi; Hirai, Miho; Masui, Noriaki; Tomaru, Hitoshi; Morono, Yuki; Imachi, Hiroyuki; Inagaki, Fumio; Takai, Ken

2016-06-01

Subseafloor pelagic sediments with high concentrations of organic matter form habitats for diverse microorganisms. Here, we determined depth profiles of genes for SSU rRNA, mcrA, dsrA and amoA from just beneath the seafloor to 363.3 m below the seafloor (mbsf) using core samples obtained from the forearc basin off the Shimokita Peninsula. The molecular profiles were combined with data on lithostratigraphy, depositional age, sedimentation rate and pore-water chemistry. The SSU rRNA gene tag structure and diversity changed at around the sulfate-methane transition zone (SMTZ), whereas the profiles varied further with depth below the SMTZ, probably in connection with the variation in pore-water chemistry. The depth profiles of diversity and abundance of dsrA, a key gene for sulfate reduction, suggested the possible niche separations of sulfate-reducing populations, even below the SMTZ. The diversity and abundance patterns of mcrA, a key gene for methanogenesis/anaerobic methanotrophy, suggested a stratified distribution and separation of anaerobic methanotrophy and hydrogenotrophic or methylotrophic methanogensis below the SMTZ. This study provides novel insights into the relationships between the composition and function of microbial communities and the chemical environment in the nutrient-rich continental margin subseafloor sediments, which may result in niche separation and variability in subseafloor microbial populations. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Changes in coral-associated microbial communities during a bleaching event.

PubMed

Bourne, David; Iida, Yuki; Uthicke, Sven; Smith-Keune, Carolyn

2008-04-01

Environmental stressors such as increased sea surface temperatures are well-known for contributing to coral bleaching; however, the effect of increased temperatures and subsequent bleaching on coral-associated microbial communities is poorly understood. Colonies of the hard coral Acropora millepora were tagged on a reef flat off Magnetic Island (Great Barrier Reef) and surveyed over 2.5 years, which included a severe bleaching event in January/February 2002. Daily average water temperatures exceeded the previous 10-year average by more than 1 degrees C for extended periods with field-based visual surveys recording all tagged colonies displaying signs of bleaching. During the bleaching period, direct counts of coral zooxanthellae densities decreased by approximately 64%, before recovery to pre-bleaching levels after the thermal stress event. A subset of three tagged coral colonies were sampled through the bleaching event and changes in the microbial community elucidated. Denaturing gradient gel electrophoresis (DGGE) analysis demonstrated conserved bacterial banding profiles between the three coral colonies, confirming previous studies highlighting specific microbial associations. As coral colonies bleached, the microbial community shifted and redundancy analysis (RDA) of DGGE banding patterns revealed a correlation of increasing temperature with the appearance of Vibrio-affiliated sequences. Interestingly, this shift to a Vibrio-dominated community commenced prior to visual signs of bleaching. Clone libraries hybridized with Vibrio-specific oligonucleotide probes confirmed an increase in the fraction of Vibrio-affiliated clones during the bleaching period. Post bleaching, the coral microbial associations again shifted, returning to a profile similar to the fingerprints prior to bleaching. This provided further evidence for corals selecting and shaping their microbial partners. For non-bleached samples, a close association with Spongiobacter-related sequences were revealed by both clone libraries and DGGE profiling. Despite Vibrio species being previously implicated in bleaching of specific coral species, it is unsure if the relative increase in retrieved Vibrio sequences is due to bacterial infection or an opportunistic response to compromised health and changing environmental parameters of the coral host. This study provides the first molecular-based study demonstrating changes in coral-associated bacterial assemblages during a bleaching event on a natural reef system.

Microbial communities may modify how litter quality affects potential decomposition rates as tree species migrate

Treesearch

Ashley D. Keiser; Jennifer D. Knoepp; Mark A. Bradford

2013-01-01

Background and aims Climate change alters regional plant species distributions, creating new combinations of litter species and soil communities. Biogeographic patterns in microbial communities relate to dissimilarity in microbial community function, meaning novel litters to communities may decompose differently than predicted from their chemical composition. Therefore...

A communal catalogue reveals Earth’s multiscale microbial diversity

DOE PAGES

Thompson, Luke R.; Sanders, Jon G.; McDonald, Daniel; ...

2017-11-01

Our growing awareness of the importance and diversity of the microbial world contrasts starkly with our limited understanding of its fundamental structure. Despite remarkable advances in DNA sequence generation, a lack of standardized protocols and common analytical framework impede useful comparison between studies, hindering development of global inferences about microbial life on Earth. Here, we show that with coordinated protocols, exact microbial 16S rRNA gene sequences can be followed across scores of individual studies, revealing patterns of diversity, community structure, and life history strategy at a planetary scale. Using 27,751 crowdsourced environmental samples comprising more than 2.2 billion reads, wemore » find sharp divides between host-associated and free-living communities. We show that the distribution of taxonomic and sequence diversity follows consistent trends across samples types and along gradients of environmental parameters, highlighting some of the global evolutionary patterns and ecological principles that underpin Earth’s microbiome. Here, this dataset provides the most complete environmental survey of our microbial world to date, and serves as a growing reference to provide immediate global context to future microbial surveys.« less

A communal catalogue reveals Earth’s multiscale microbial diversity

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

Thompson, Luke R.; Sanders, Jon G.; McDonald, Daniel

Our growing awareness of the importance and diversity of the microbial world contrasts starkly with our limited understanding of its fundamental structure. Despite remarkable advances in DNA sequence generation, a lack of standardized protocols and common analytical framework impede useful comparison between studies, hindering development of global inferences about microbial life on Earth. Here, we show that with coordinated protocols, exact microbial 16S rRNA gene sequences can be followed across scores of individual studies, revealing patterns of diversity, community structure, and life history strategy at a planetary scale. Using 27,751 crowdsourced environmental samples comprising more than 2.2 billion reads, wemore » find sharp divides between host-associated and free-living communities. We show that the distribution of taxonomic and sequence diversity follows consistent trends across samples types and along gradients of environmental parameters, highlighting some of the global evolutionary patterns and ecological principles that underpin Earth’s microbiome. Here, this dataset provides the most complete environmental survey of our microbial world to date, and serves as a growing reference to provide immediate global context to future microbial surveys.« less

Stress-evoked sterile inflammation, danger associated molecular patterns (DAMPs), microbial associated molecular patterns (MAMPs) and the inflammasome.

PubMed

Fleshner, Monika

2013-01-01

Since the inception of the field of psychoneuroimmunolology research, there has been an appreciation that the physiological response to stressors includes modulation of immune function. Investigators initially focused on the effect of stress on cellular migration and immunosuppression and the resultant decreases in tumor surveillance, anti-viral T cell immunity and antigen-specific antibody responses. More recently, it has become clear that exposure to stressors also potentiate innate immune processes. Stressor exposure, for example, can change the activation status of myeloid lineage cells such as monocytes, macrophages, neutrophils, and microglia, leading to a primed state. In addition, stressor exposure increases the synthesis and release of a vast cadre' of inflammatory proteins both in the blood and within tissues (i.e., spleen, liver, adipose, vasculature and brain). The mechanisms for stress-evoked innate immune 'arousal' remain unknown. The goals of this presidential address are the following: (1) offer a personalized, brief overview of stress and immunity with a focus on 'aroused' innate immunity; (2) describe sterile inflammatory processes and the role of the inflammasome; and (3) suggest that these same processes likely contribute to primed myeloid cells and inflammatory protein responses (systemic and tissue) produced by stress in the absence of pathogens. Copyright © 2012 Elsevier Inc. All rights reserved.

Ionotropic glutamate receptor (iGluR)-like channels mediate MAMP-induced calcium influx in Arabidopsis thaliana.

PubMed

Kwaaitaal, Mark; Huisman, Rik; Maintz, Jens; Reinstädler, Anja; Panstruga, Ralph

2011-12-15

Binding of specific microbial epitopes [MAMPs (microbe-associated molecular patterns)] to PRRs (pattern recognition receptors) and subsequent receptor kinase activation are key steps in plant innate immunity. One of the earliest detectable events after MAMP perception is a rapid and transient rise in cytosolic Ca2+ levels. In plants, knowledge about the signalling events leading to Ca2+ influx and on the molecular identity of the channels involved is scarce. We used a transgenic Arabidopsis thaliana line stably expressing the luminescent aequorin Ca2+ biosensor to monitor pharmacological interference with Ca2+ signatures following treatment with the bacterial peptide MAMPs flg22 and elf18, and the fungal carbohydrate MAMP chitin. Using a comprehensive set of compounds known to impede Ca2+-transport processes in plants and animals we found strong evidence for a prominent role of amino acid-controlled Ca2+ fluxes, probably through iGluR (ionotropic glutamate receptor)-like channels. Interference with amino acid-mediated Ca2+ fluxes modulates MAMP-triggered MAPK (mitogen-activated protein kinase) activity and affects MAMP-induced accumulation of defence gene transcripts. We conclude that the initiation of innate immune responses upon flg22, elf18 and chitin recognition involves apoplastic Ca2+ influx via iGluR-like channels.

Oestrogen promotes healing in a bacterial LPS model of delayed cutaneous wound repair.

PubMed

Crompton, Rachel; Williams, Helen; Ansell, David; Campbell, Laura; Holden, Kirsty; Cruickshank, Sheena; Hardman, Matthew J

2016-04-01

Wound infection is a major clinical problem, yet understanding of bacterial host interactions in the skin remains limited. Microbe-derived molecules, known as pathogen-associated molecular patterns, are recognised in barrier tissues by pattern-recognition receptors. In particular, the pathogen-associated molecular pattern, lipopolysaccharide (LPS), a component of microbial cell walls and a specific ligand for Toll-like receptor 4, has been widely used to mimic systemic and local infection across a range of tissues. Here we administered LPS derived from Klebsiella pneumoniae, a species of bacteria that is emerging as a wound-associated pathogen, to full-thickness cutaneous wounds in C57/BL6 mice. Early in healing, LPS-treated wounds displayed increased local apoptosis and reduced proliferation. Subsequent healing progression was delayed with reduced re-epithelialisation, increased proliferation, a heightened inflammatory response and perturbed wound matrix deposition. Our group and others have previously demonstrated the beneficial effects of 17β-estradiol treatment across a range of preclinical wound models. Here we asked whether oestrogen would effectively promote healing in our LPS bacterial infection model. Intriguingly, co-treatment with 17β-estradiol was able to promote re-epithelialisation, dampen inflammation and induce collagen deposition in our LPS-delayed healing model. Collectively, these studies validate K. pneumoniae-derived LPS treatment as a simple yet effective model of bacterial wound infection, while providing the first indication that oestrogen could promote cutaneous healing in the presence of infection, further strengthening the case for its therapeutic use.

The diagnosis of chronic endometritis in infertile asymptomatic women: a comparative study of histology, microbial cultures, hysteroscopy, and molecular microbiology.

PubMed

Moreno, Inmaculada; Cicinelli, Ettore; Garcia-Grau, Iolanda; Gonzalez-Monfort, Marta; Bau, Davide; Vilella, Felipe; De Ziegler, Dominique; Resta, Leonardo; Valbuena, Diana; Simon, Carlos

2018-06-01

Chronic endometritis is a persistent inflammation of the endometrial mucosa caused by bacterial pathogens such as Enterobacteriaceae, Enterococcus, Streptococcus, Staphylococcus, Mycoplasma, and Ureaplasma. Although chronic endometritis can be asymptomatic, it is found in up to 40% of infertile patients and is responsible for repeated implantation failure and recurrent miscarriage. Diagnosis of chronic endometritis is based on hysteroscopy of the uterine cavity, endometrial biopsy with plasma cells being identified histologically, while specific treatment is determined based on microbial culture. However, not all microorganisms implicated are easily or readily culturable needing a turnaround time of up to 1 week. We sought to develop a molecular diagnostic tool for chronic endometritis based on real-time polymerase chain reaction equivalent to using the 3 classic methods together, overcoming the bias of using any of them alone. Endometrial samples from patients assessed for chronic endometritis (n = 113) using at least 1 or several conventional diagnostic methods namely histology, hysteroscopy, and/or microbial culture, were blindly evaluated by real-time polymerase chain reaction for the presence of 9 chronic endometritis pathogens: Chlamydia trachomatis, Enterococcus, Escherichia coli, Gardnerella vaginalis, Klebsiella pneumoniae, Mycoplasma hominis, Neisseria gonorrhoeae, Staphylococcus, and Streptococcus. The sensitivity and specificity of the molecular analysis vs the classic diagnostic techniques were compared in the 65 patients assessed by all 3 recognized classic methods. The molecular method showed concordant results with histological diagnosis in 30 samples (14 double positive and 16 double negative) with a matching accuracy of 46.15%. Concordance of molecular and hysteroscopic diagnosis was observed in 38 samples (37 double positive and 1 double negative), with an accuracy of 58.46%. When the molecular method was compared to microbial culture, concordance was present in 37 samples (22 double positive and 15 double negative), a matching rate of 56.92%. When cases of potential contamination and/or noncultivable bacteria were considered, the accuracy increased to 66.15%. Of these 65 patients, only 27 patients had consistent histological + hysteroscopic diagnosis, revealing 58.64% of nonconcordant results. Only 13 of 65 patients (20%) had consistent histology + hysteroscopy + microbial culture results. In these cases, the molecular microbiology matched in 10 cases showing a diagnostic accuracy of 76.92%. Interestingly, the molecular microbiology confirmed over half of the isolated pathogens and provided additional detection of nonculturable microorganisms. These results were confirmed by the microbiome assessed by next-generation sequencing. In the endometrial samples with concordant histology + hysteroscopy + microbial culture results, the molecular microbiology diagnosis demonstrates 75% sensitivity, 100% specificity, 100% positive and 25% negative predictive values, and 0% false-positive and 25% false-negative rates. The molecular microbiology method describe herein is a fast and inexpensive diagnostic tool that allows for the identification of culturable and nonculturable endometrial pathogens associated with chronic endometritis. The results obtained were similar to all 3 classic diagnostic methods together with a degree of concordance of 76.92% providing an opportunity to improve the clinical management of infertile patients with a risk of experiencing this ghost endometrial pathology. Copyright © 2018 Elsevier Inc. All rights reserved.

Molecular fossils of prokaryotes in ancient authigenic minerals: archives of microbial activity in reefs and mounds?

NASA Astrophysics Data System (ADS)

Heindel, Katrin; Birgel, Daniel; Richoz, Sylvain; Westphal, Hildegard; Peckmann, Jörn

2016-04-01

Molecular fossils (lipid biomarkers) are commonly used as proxies in organic-rich sediments of various sources, including eukaryotes and prokaryotes. Usually, molecular fossils of organisms transferred from the water column to the sediment are studied to monitor environmental changes (e.g., temperature, pH). Apart from these 'allochthonous' molecular fossils, prokaryotes are active in sediments and mats on the seafloor and leave behind 'autochthonous' molecular fossils in situ. In contrast to many phototrophic organisms, most benthic sedimentary prokaryotes are obtaining their energy from oxidation or reduction of organic or inorganic substrates. A peculiarity of some of the sediment-thriving prokaryotes is their ability to trigger in situ mineral precipitation, often but not only due to metabolic activity, resulting in authigenic rocks (microbialites). During that process, prokaryotes are rapidly entombed in the mineral matrix, where the molecular fossils are protected from early (bio)degradation. In contrast to other organic compounds (DNA, proteins etc.), molecular fossils can be preserved over very long time periods (millions of years). Thus, molecular fossils in authigenic mineral phases are perfectly suitable to trace microbial activity back in time. Among the best examples of molecular fossils, which are preserved in authigenic rocks are various microbialites, forming e.g. in phototrophic microbial mats and at cold seeps. Microbialite formation is reported throughout earth history. We here will focus on reefal microbialites form the Early Triassic and the Holocene. After the End-Permian mass extinction, microbialites covered wide areas on the ocean margins. In microbialites from the Griesbachian in Iran and Turkey (both Neotethys), molecular fossils of cyanobacteria, archaea, anoxygenic phototrophs, and sulphate-reducing bacteria indicate the presence of layered microbial mats on the seafloor, in which carbonate precipitation was induced. In association with metazoans other than corals (sponges, bivalves, gastropods, ostracods) and foraminifera, first metazoan-microbialite reefs developed on the Early Triassic seafloor. After the last glacial maximum, microbialites formed in coral reefs. Our evidence shows that sulphate-reducing bacteria played an intrinsic role in the precipitation of these microbialites during the Holocene sea-level rise. With more nutrients and organic matter distributed in the reef ecosystem, anoxic microenvironments preferentially developed. Such conditions favored heterotrophic bacteria, particularly, sulphate-reducing bacteria. It is suggested that matrix-solute interaction related to the activity of sulphate reducers induced carbonate precipitation in extracellular polymeric substances. Overall, authigenic mineral phases from various environments can be used as excellent archives to describe former microbial activity in sediments. The early entombment of the lipids in the mineral matrix avoids the loss of specific and important information, which may have been lost in soft sediments rather quick.

MOLECULAR DIVERSITY OF DRINKING WATER MICROBIAL COMMUNITIES: A PHYLOGENETIC APPROACH

EPA Science Inventory

The microbiological quality of drinking water is assessed using culture-based methods that are highly selective and that tend to underestimate the densities and diversity of microbial populations inhabiting distribution systems. In order to better understand the effect of differe...

Molecular Characterization of Swine Manure Lagoon Microbial and Antibiotic Resistant Populations

USDA-ARS?s Scientific Manuscript database

Background: The differences in swine manure lagoon effluent based on differing management styles or approaches such as different stages of swine rearing determines the presence of variable antibiotic resistance determinants and functional microbial populations. These concerns determine the suitabil...

Neutrophil-mediated oxidative burst and host defense are controlled by a Vav-PLCγ2 signaling axis in mice

PubMed Central

Graham, Daniel B.; Robertson, Charles M.; Bautista, Jhoanne; Mascarenhas, Francesca; Diacovo, M. Julia; Montgrain, Vivianne; Lam, Siu Kit; Cremasco, Viviana; Dunne, W. Michael; Faccio, Roberta; Coopersmith, Craig M.; Swat, Wojciech

2007-01-01

Oxidative burst, a critical antimicrobial mechanism of neutrophils, involves the rapid generation and release of reactive oxygen intermediates (ROIs) by the NADPH oxidase complex. Genetic mutations in an NADPH oxidase subunit, gp91 (also referred to as NOX2), are associated with chronic granulomatous disease (CGD), which is characterized by recurrent and life-threatening microbial infections. To combat such infections, ROIs are produced by neutrophils after stimulation by integrin-dependent adhesion to the ECM in conjunction with stimulation from inflammatory mediators, or microbial components containing pathogen-associated molecular patterns. In this report, we provide genetic evidence that both the Vav family of Rho GTPase guanine nucleotide exchange factors (GEFs) and phospholipase C–γ2 (PLC-γ2) are critical mediators of adhesion-dependent ROI production by neutrophils in mice. We also demonstrated that Vav was critically required for neutrophil-dependent host defense against systemic infection by Staphylococcus aureus and Pseudomonas aeruginosa, 2 common pathogens associated with fatal cases of hospital-acquired pneumonia. We identified a molecular pathway in which Vav GEFs linked integrin-mediated signaling with PLC-γ2 activation, release of intracellular Ca2+ cations, and generation of diacylglycerol to control assembly of the NADPH oxidase complex and ROI production by neutrophils. Taken together, our data indicate that integrin-dependent signals generated during neutrophil adhesion contribute to the activation of NADPH oxidase by a variety of distinct effector pathways, all of which require Vav. PMID:17932569

Fabrication of three dimensional patterns of wide dimensional range using microbes and their applications

NASA Astrophysics Data System (ADS)

Mehta, Sunita; Murugeson, Saravanan; Prakash, Balaji; Deepak

2015-10-01

Inspired by the wound healing property of certain trees, we report a novel microbes based additive process for producing three dimensional patterns, which has a potential of engineering applications in a variety of fields. Imposing a two dimensional pattern of microbes on a gel media and allowing them to grow in the third dimension is known from its use in biological studies. Instead, we have introduced an intermediate porous substrate between the gel media and the microbial growth, which enables three dimensional patterns in specific forms that can be lifted off and used in engineering applications. In order to demonstrate the applicability of this idea in a diverse set of areas, two applications are selected. In one, using this method of microbial growth, we have fabricated microlenses for enhanced light extraction in organic light emitting diodes, where densely packed microlenses of the diameters of hundreds of microns lead to luminance increase by a factor of 1.24X. In another entirely different type of application, braille text patterns are prepared on a normal office paper where the grown microbial colonies serve as braille tactile dots. Braille dot patterns thus prepared meet the standard specifications (size and spacing) for braille books.

Molecular and Imaging Insights into the Formation of Soil Organic Matter in a Red Pine Rhizosphere

NASA Astrophysics Data System (ADS)

Dohnalkova, A.; Tfaily, M.; Smith, A. P.; Chu, R. K.; Crump, A.; Brislawn, C.; Varga, T.; Shi, Z.; Thomashow, L. S.; Harsh, J. B.; Balogh-Brunstad, Z.; Keller, C. K.

2017-12-01

Microbially-derived carbon inputs to soils play an important role in forming soil organic matter (SOM), but detailed knowledge of basic mechanisms of carbon (C) cycling, such as stabilization of organic C compounds originating from rhizodeposition, is limited. The objective of this study aimed to investigate the stability of rhizosphere-produced carbon components in a model laboratory mesocosm of Pinus resinosa grown in a designed mineral soil mix. We hypothesized that nutrient limitation would cause formation of microbially-produced C constituents that would contribute to SOM stabilization. We focused on the processes of rhizodeposition in the rhizosphere, and we utilized a suite of advanced imaging and molecular techniques to obtain a molecular-level identification of the microbial community and the newly-formed SOM compounds in the rhizosphere and the bulk soil. We considered implications regarding their degree of long-term stability. The microbes in this controlled, nutrient-limited system, without pre-existing organic matter, produced extracellular polymeric substances that formed associations with nutrient-bearing minerals and contributed to the microbial mineral weathering process. Electron microscopy revealed unique ultrastructural residual signatures of biogenic C compounds, and the increased presence of an amorphous organic phase associated with the mineral phase was evidenced by X-ray diffraction. These findings provide insight into the various degrees of stability of microbial SOM products in ecosystems and evidence that the residual biogenic material associated with mineral matrices may be important components in current carbon cycle models.

Anoxia stimulates microbially catalyzed metal release from Animas River sediments.

PubMed

Saup, Casey M; Williams, Kenneth H; Rodríguez-Freire, Lucía; Cerrato, José M; Johnston, Michael D; Wilkins, Michael J

2017-04-19

The Gold King Mine spill in August 2015 released 11 million liters of metal-rich mine waste to the Animas River watershed, an area that has been previously exposed to historical mining activity spanning more than a century. Although adsorption onto fluvial sediments was responsible for rapid immobilization of a significant fraction of the spill-associated metals, patterns of longer-term mobility are poorly constrained. Metals associated with river sediments collected downstream of the Gold King Mine in August 2015 exhibited distinct presence and abundance patterns linked to location and mineralogy. Simulating riverbed burial and development of anoxic conditions, sediment microcosm experiments amended with Animas River dissolved organic carbon revealed the release of specific metal pools coupled to microbial Fe- and SO 4 2- -reduction. Results suggest that future sedimentation and burial of riverbed materials may drive longer-term changes in patterns of metal remobilization linked to anaerobic microbial metabolism, potentially driving decreases in downstream water quality. Such patterns emphasize the need for long-term water monitoring efforts in metal-impacted watersheds.

Spatial and temporal microbial pollution patterns in a tropical estuary during high and low river flow conditions.

PubMed

Wiegner, T N; Edens, C J; Abaya, L M; Carlson, K M; Lyon-Colbert, A; Molloy, S L

2017-01-30

Spatial and temporal patterns of coastal microbial pollution are not well documented. Our study examined these patterns through measurements of fecal indicator bacteria (FIB), nutrients, and physiochemical parameters in Hilo Bay, Hawai'i, during high and low river flow. >40% of samples tested positive for the human-associated Bacteroides marker, with highest percentages near rivers. Other FIB were also higher near rivers, but only Clostridium perfringens concentrations were related to discharge. During storms, FIB concentrations were three times to an order of magnitude higher, and increased with decreasing salinity and water temperature, and increasing turbidity. These relationships and high spatial resolution data for these parameters were used to create Enterococcus spp. and C. perfringens maps that predicted exceedances with 64% and 95% accuracy, respectively. Mapping microbial pollution patterns and predicting exceedances is a valuable tool that can improve water quality monitoring and aid in visualizing FIB hotspots for management actions. Copyright © 2016 Elsevier Ltd. All rights reserved.

Deconvolving molecular signatures of interactions between microbial colonies

PubMed Central

Harn, Y.-C.; Powers, M. J.; Shank, E. A.; Jojic, V.

2015-01-01

Motivation: The interactions between microbial colonies through chemical signaling are not well understood. A microbial colony can use different molecules to inhibit or accelerate the growth of other colonies. A better understanding of the molecules involved in these interactions could lead to advancements in health and medicine. Imaging mass spectrometry (IMS) applied to co-cultured microbial communities aims to capture the spatial characteristics of the colonies’ molecular fingerprints. These data are high-dimensional and require computational analysis methods to interpret. Results: Here, we present a dictionary learning method that deconvolves spectra of different molecules from IMS data. We call this method MOLecular Dictionary Learning (MOLDL). Unlike standard dictionary learning methods which assume Gaussian-distributed data, our method uses the Poisson distribution to capture the count nature of the mass spectrometry data. Also, our method incorporates universally applicable information on common ion types of molecules in MALDI mass spectrometry. This greatly reduces model parameterization and increases deconvolution accuracy by eliminating spurious solutions. Moreover, our method leverages the spatial nature of IMS data by assuming that nearby locations share similar abundances, thus avoiding overfitting to noise. Tests on simulated datasets show that this method has good performance in recovering molecule dictionaries. We also tested our method on real data measured on a microbial community composed of two species. We confirmed through follow-up validation experiments that our method recovered true and complete signatures of molecules. These results indicate that our method can discover molecules in IMS data reliably, and hence can help advance the study of interaction of microbial colonies. Availability and implementation: The code used in this paper is available at: https://github.com/frizfealer/IMS_project. Contact: vjojic@cs.unc.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26072476

Impacts of Sampling and Handling Procedures on DNA- and RNA-based Microbial Characterization and Quantification of Groundwater and Saturated Soil

DTIC Science & Technology

2012-07-01

use of molecular biological techniques (MBTs) has allowed microbial ecologists and environmental engineers to determine microbial community...metabolic genes). The most common approaches used in bioremediation research are those based on the polymerase chain reaction (PCR) amplification of... bioremediation . Because of its sensitivity compared to direct hybridization/probing, PCR is increasingly used to analyze groundwater samples and soil samples

Aerobic microbial taxa dominate deep subsurface cores from the Alberta oil sands.

PubMed

Ridley, Christina M; Voordouw, Gerrit

2018-06-01

Little is known about the microbial ecology of the subsurface oil sands in Northern Alberta, Canada. Biodegradation of low molecular weight hydrocarbons by indigenous microbes has enriched high molecular weight hydrocarbons, resulting in highly viscous bitumen. This extreme subsurface environment is further characterized by low nutrient availability and limited access to water, thus resulting in low microbial biomass. Improved DNA isolation protocols and increasingly sensitive sequencing methods have allowed an in-depth investigation of the microbial ecology of this unique subsurface environmental niche. Community analysis was performed on core samples (n = 62) that were retrieved from two adjacent sites located in the Athabasca Oil Sands at depths from 220 to 320 m below the surface. Microbial communities were dominated by aerobic taxa, including Pseudomonas and Acinetobacter. Only one core sample microbial community was dominated by anaerobic taxa, including the methanogen Methanoculleus, as well as Desulfomicrobium and Thauera. Although the temperature of the bitumen-containing subsurface is low (8°C), two core samples had high fractions of the potentially thermophilic taxon, Thermus. Predominance of aerobic taxa in the subsurface suggests the potential for in situ aerobic hydrocarbon degradation; however, more studies are required to determine the functional role of these taxa within this unique environment.

Marine Protists Are Not Just Big Bacteria.

PubMed

Keeling, Patrick J; Campo, Javier Del

2017-06-05

The study of marine microbial ecology has been completely transformed by molecular and genomic data: after centuries of relative neglect, genomics has revealed the surprising extent of microbial diversity and how microbial processes transform ocean and global ecosystems. But the revolution is not complete: major gaps in our understanding remain, and one obvious example is that microbial eukaryotes, or protists, are still largely neglected. Here we examine various ways in which protists might be better integrated into models of marine microbial ecology, what challenges this will present, and why understanding the limitations of our tools is a significant concern. In part this is a technical challenge - eukaryotic genomes are more difficult to characterize - but eukaryotic adaptations are also more dependent on morphology and behaviour than they are on the metabolic diversity that typifies bacteria, and these cannot be inferred from genomic data as readily as metabolism can be. We therefore cannot simply follow in the methodological footsteps of bacterial ecology and hope for similar success. Understanding microbial eukaryotes will require different approaches, including greater emphasis on taxonomically and trophically diverse model systems. Molecular sequencing will continue to play a role, and advances in environmental sequence tag studies and single-cell methods for genomic and transcriptomics offer particular promise. Copyright © 2017 Elsevier Ltd. All rights reserved.

Microbial ecology to manage processes in environmental biotechnology.

PubMed

Rittmann, Bruce E

2006-06-01

Microbial ecology and environmental biotechnology are inherently tied to each other. The concepts and tools of microbial ecology are the basis for managing processes in environmental biotechnology; and these processes provide interesting ecosystems to advance the concepts and tools of microbial ecology. Revolutionary advancements in molecular tools to understand the structure and function of microbial communities are bolstering the power of microbial ecology. A push from advances in modern materials along with a pull from a societal need to become more sustainable is enabling environmental biotechnology to create novel processes. How do these two fields work together? Five principles illuminate the way: (i) aim for big benefits; (ii) develop and apply more powerful tools to understand microbial communities; (iii) follow the electrons; (iv) retain slow-growing biomass; and (v) integrate, integrate, integrate.

Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience.

PubMed

Mandakovic, Dinka; Rojas, Claudia; Maldonado, Jonathan; Latorre, Mauricio; Travisany, Dante; Delage, Erwan; Bihouée, Audrey; Jean, Géraldine; Díaz, Francisca P; Fernández-Gómez, Beatriz; Cabrera, Pablo; Gaete, Alexis; Latorre, Claudio; Gutiérrez, Rodrigo A; Maass, Alejandro; Cambiazo, Verónica; Navarrete, Sergio A; Eveillard, Damien; González, Mauricio

2018-04-12

Understanding the factors that modulate bacterial community assembly in natural soils is a longstanding challenge in microbial community ecology. In this work, we compared two microbial co-occurrence networks representing bacterial soil communities from two different sections of a pH, temperature and humidity gradient occurring along a western slope of the Andes in the Atacama Desert. In doing so, a topological graph alignment of co-occurrence networks was used to determine the impact of a shift in environmental variables on OTUs taxonomic composition and their relationships. We observed that a fraction of association patterns identified in the co-occurrence networks are persistent despite large environmental variation. This apparent resilience seems to be due to: (1) a proportion of OTUs that persist across the gradient and maintain similar association patterns within the community and (2) bacterial community ecological rearrangements, where an important fraction of the OTUs come to fill the ecological roles of other OTUs in the other network. Actually, potential functional features suggest a fundamental role of persistent OTUs along the soil gradient involving nitrogen fixation. Our results allow identifying factors that induce changes in microbial assemblage configuration, altering specific bacterial soil functions and interactions within the microbial communities in natural environments.

Decoding molecular interactions in microbial communities

PubMed Central

Abreu, Nicole A.; Taga, Michiko E.

2016-01-01

Microbial communities govern numerous fundamental processes on earth. Discovering and tracking molecular interactions among microbes is critical for understanding how single species and complex communities impact their associated host or natural environment. While recent technological developments in DNA sequencing and functional imaging have led to new and deeper levels of understanding, we are limited now by our inability to predict and interpret the intricate relationships and interspecies dependencies within these communities. In this review, we highlight the multifaceted approaches investigators have taken within their areas of research to decode interspecies molecular interactions that occur between microbes. Understanding these principles can give us greater insight into ecological interactions in natural environments and within synthetic consortia. PMID:27417261

Contrasting effects of photochemical and microbial degradation on Cu(II) binding with fluorescent DOM from different origins.

PubMed

Xu, Huacheng; Guan, Dong-Xing; Zou, Li; Lin, Hui; Guo, Laodong

2018-08-01

Effects of photochemical and microbial degradation on variations in composition and molecular-size of dissolved organic matter (DOM) from different sources (algal and soil) and the subsequent influence on Cu(II) binding were investigated using UV-Vis, fluorescence excitation-emission matrices coupled with parallel factor analysis, flow field-flow fractionation (FlFFF), and metal titration. The degradation processes resulted in an initial rapid decline in the bulk dissolved organic carbon and chromophoric and fluorescent DOM components, followed by a small or little decrease. Specifically, photochemical reaction decreased the aromaticity, humification and apparent molecular weights of all DOM samples, whereas a reverse trend was observed during microbial degradation. The FlFFF fractograms revealed that coagulation of both protein- and humic-like DOM induced an increase in molecular weights for algal-DOM, while the molecular weight enhancement for allochthonous soil samples was mainly attributed to the self-assembly of humic-like components. The Cu(II) binding capacity of algal-derived humic-like and fulvic-like DOM consistently increased during photo- and bio-degradation, while the soil-derived DOM exhibited a slight decline in Cu(II) binding capacity during photo-degradation but a substantial increase during microbial degradation, indicating source- and degradation-dependent metal binding heterogeneities. Pearson correlation analysis demonstrated that the Cu(II) binding potential was mostly related with aromaticity and molecular size for allochthonous soil-derived DOM, but was regulated by both DOM properties and specific degradation processes for autochthonous algal-derived DOM. This study highlighted the coupling role of inherent DOM properties and external environmental processes in regulating metal binding, and provided new insights into metal-DOM interactions and the behavior and fate of DOM-bound metals in aquatic environments. Copyright © 2018 Elsevier Ltd. All rights reserved.

Microbial competition between Bacillus subtilis and Staphylococcus aureus monitored by imaging mass spectrometry

PubMed Central

Gonzalez, David J.; Haste, Nina M.; Hollands, Andrew; Fleming, Tinya C.; Hamby, Matthew; Pogliano, Kit; Nizet, Victor

2011-01-01

Microbial competition exists in the general environment, such as soil or aquatic habitats, upon or within unicellular or multicellular eukaryotic life forms. The molecular actions that govern microbial competition, leading to niche establishment and microbial monopolization, remain undetermined. The emerging technology of imaging mass spectrometry (IMS) enabled the observation that there is directionality in the metabolic output of the organism Bacillus subtilis when co-cultured with Staphylococcus aureus. The directionally released antibiotic alters S. aureus virulence factor production and colonization. Therefore, IMS provides insight into the largely hidden nature of competitive microbial encounters and niche establishment, and provides a paradigm for future antibiotic discovery. PMID:21719540

Bioenergy Research | Bioenergy | NREL

Science.gov Websites

range of research from exploring biomass at the molecular level through biorefinery process optimization Bioenergetics We work at the molecular and cellular level to understand and optimize microbial production of biofuels and bioproducts. fanciful illustration of fuel nozzle with molecular structures drawn in

Co-occurrence Networks Among Bacteria and Microbial Eukaryotes of Lake Baikal During a Spring Phytoplankton Bloom.

PubMed

Mikhailov, Ivan S; Zakharova, Yulia R; Bukin, Yuri S; Galachyants, Yuri P; Petrova, Darya P; Sakirko, Maria V; Likhoshway, Yelena V

2018-06-07

The pelagic zone of Lake Baikal is an ecological niche where phytoplankton bloom causes increasing microbial abundance in spring which plays a key role in carbon turnover in the freshwater lake. Co-occurrence patterns revealed among different microbes can be applied to predict interactions between the microbes and environmental conditions in the ecosystem. We used 454 pyrosequencing of 16S rRNA and 18S rRNA genes to study bacterial and microbial eukaryotic communities and their co-occurrence patterns at the pelagic zone of Lake Baikal during a spring phytoplankton bloom. We found that microbes within one domain mostly correlated positively with each other and are highly interconnected. The highly connected taxa in co-occurrence networks were operational taxonomic units (OTUs) of Actinobacteria, Bacteroidetes, Alphaproteobacteria, and autotrophic and unclassified Eukaryota which might be analogous to microbial keystone taxa. Constrained correspondence analysis revealed the relationships of bacterial and microbial eukaryotic communities with geographical location.

Characterizing Low Molecular Weight Organic Matter in Arctic Polygonal Tundra Soils to Identify Biogeochemical Hotspots Using a Dual-Separation, High-Resolution Mass Spectrometry Approach

NASA Astrophysics Data System (ADS)

Ladd, M.; Wullschleger, S. D.; Iversen, C. M.; Hettich, R.

2016-12-01

Reliably modeling biogeochemical processes (e.g. decomposition, plant-microbial competition for nutrients) across spatial or temporal scales requires elucidating the chemical composition of low molecular weight (LMW) dissolved soil organic matter (DOM). Our understanding is limited, however, by the wide-ranging physicochemical properties and high fluxes of these compounds, posing major challenges in detection, isolation, and quantification. Here, we developed and evaluated a sensitive, non-targeted approach to characterize LMW DOM in the Arctic, a unique system that is warming at a rate twice that of the global average and may have significant feedbacks to global C and N cycles. Soil cores were collected from a continuous permafrost, polygonal tundra landscape near Barrow, Alaska (71° 16' N) and sectioned into 5 cm increments. Water and salt extracts from each section were filtered and injected onto C18 reversed-phase or zwitterionic-type hydrophilic interaction chromatography (ZIC-pHILIC) columns for separation. LMW DOM profiles were obtained using high-resolution mass spectrometry (HRMS), and unique features, known and unknown, were characterized by LC retention time, accurate mass (m/z), and molecular fragmentation pattern. Coupling two orthogonal chromatographic separations with HRMS enabled the characterization of hundreds of analytes in a single measurement providing enhanced, high-throughput coverage of LMW DOM from soil extracts. The complexity and relative/absolute intensities of LMW DOM features (e.g. organic acids, amino sugars, peptides) varied across polygon type (high- or low-centered), extract condition, and with depth, providing an information-rich, molecular signal of LMW DOM availability across scales. Comprehensively profiling this complex mixture of small molecules of both biotic and abiotic origin provides a chemical signature of biological function, allowing for more reliable predictions of how discrete, molecular-scale processes may control landscape dynamics. In the Arctic, this platform can be leveraged to identify biogeochemical hotspots to gain insight into to how warming temperatures will impact microbial dynamics and CO2 and CH4 fluxes from these systems.

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, ...

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.

The polycyclic aromatic hydrocarbon degradation potential of Gulf of Mexico native coastal microbial communities after the Deepwater Horizon oil spill

PubMed Central

Kappell, Anthony D.; Wei, Yin; Newton, Ryan J.; Van Nostrand, Joy D.; Zhou, Jizhong; McLellan, Sandra L.; Hristova, Krassimira R.

2014-01-01

The Deepwater Horizon (DWH) blowout resulted in oil transport, including polycyclic aromatic hydrocarbons (PAHs) to the Gulf of Mexico shoreline. The microbial communities of these shorelines are thought to be responsible for the intrinsic degradation of PAHs. To investigate the Gulf Coast beach microbial community response to hydrocarbon exposure, we examined the functional gene diversity, bacterial community composition, and PAH degradation capacity of a heavily oiled and non-oiled beach following the oil exposure. With a non-expression functional gene microarray targeting 539 gene families, we detected 28,748 coding sequences. Of these sequences, 10% were uniquely associated with the severely oil-contaminated beach and 6.0% with the non-oiled beach. There was little variation in the functional genes detected between the two beaches; however the relative abundance of functional genes involved in oil degradation pathways, including polycyclic aromatic hydrocarbons (PAHs), were greater in the oiled beach. The microbial PAH degradation potentials of both beaches, were tested in mesocosms. Mesocosms were constructed in glass columns using sands with native microbial communities, circulated with artificial sea water and challenged with a mixture of PAHs. The low-molecular weight PAHs, fluorene and naphthalene, showed rapid depletion in all mesocosms while the high-molecular weight benzo[α]pyrene was not degraded by either microbial community. Both the heavily oiled and the non-impacted coastal communities showed little variation in their biodegradation ability for low molecular weight PAHs. Massively-parallel sequencing of 16S rRNA genes from mesocosm DNA showed that known PAH degraders and genera frequently associated with oil hydrocarbon degradation represented a major portion of the bacterial community. The observed similar response by microbial communities from beaches with a different recent history of oil exposure suggests that Gulf Coast beach communities are primed for PAH degradation. PMID:24847320

Origin of microbial life: Nano- and molecular events, thermodynamics/entropy, quantum mechanisms and genetic instructions.

PubMed

Trevors, J T

2011-03-01

Currently, there are no agreed upon mechanisms and supporting evidence for the origin of the first microbial cells on the Earth. However, some hypotheses have been proposed with minimal supporting evidence and experimentation/observations. The approach taken in this article is that life originated at the nano- and molecular levels of biological organization, using quantum mechanic principles that became manifested as classical microbial cell(s), allowing the origin of microbial life on the Earth with a core or minimal, organic, genetic code containing the correct instructions for cell(s) for growth and division, in a micron dimension environment, with a local entropy range conducive to life (present about 4 billion years ago), and obeying the laws of thermodynamics. An integrated approach that explores all encompassing factors necessary for the origin of life, may bring forth plausible hypotheses (and mechanisms) with much needed supporting experimentation and observations for an origin of life theory. Copyright © 2010 Elsevier B.V. All rights reserved.

The theory and application of space microbiology: China's experiences in space experiments and beyond.

PubMed

Liu, Changting

2017-02-01

Microorganisms exhibit high adaptability to extreme environments of outer space via phenotypic and genetic changes. These changes may affect astronauts in the space environment as well as on Earth because mutant microbes will inevitably return with the spacecraft. However, the role and significance of these phenotypic changes and the underlying mechanisms are important unresolved questions in the field of space biology. By reviewing, especially the Chinese studies, we propose a space microbial molecular effect theory, that is, the space environment affects the nature of genes and the molecular structure of microorganisms to produce phenotypic changes. In this review, we discussed three basic theories for the research of space microbiology, including (1) space microbial pathogenicity and virulence mutations and the human mutualism theory; (2) space microbial drug-resistance mutations and metabolism associated with space pharmaceuticals theory; (3) space corrosion, microbial decontamination, and new materials technology theory. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Degradation of oxytetracycline and its impacts on biogas-producing microbial community structure.

PubMed

Coban, Halil; Ertekin, Emine; Ince, Orhan; Turker, Gokhan; Akyol, Çağrı; Ince, Bahar

2016-07-01

The effect of veterinary antibiotics in anaerobic digesters is a concern where methane production efficiency is highly dependent on microbial community structure. In this study, both anaerobic degradation of a common veterinary antibiotic, oxytetracycline (OTC), and its effects on an anaerobic digester microbial community were investigated. Qualitative and quantitative molecular tools were used to monitor changes in microbial community structure during a 60-day batch incubation period of cow manure with the addition of different concentrations of the antibiotic. Molecular data were interpreted by a further redundancy analysis as a multivariate statistics approach. At the end of the experiment, approximately 48, 33, and 17 % of the initially added 50, 100, and 200 mg l(-1) of OTC was still present in the serum bottles which reduced the biogas production via accumulation of some of the volatile fatty acids (VFAs). Biogas production was highly correlated with Methanobacteriales and Methanosarcinales gene copy numbers, and those parameters were negatively affected with oxytetracycline and VFA concentrations.

Soil microbial community successional patterns during forest ecosystem restoration.

PubMed

Banning, Natasha C; Gleeson, Deirdre B; Grigg, Andrew H; Grant, Carl D; Andersen, Gary L; Brodie, Eoin L; Murphy, D V

2011-09-01

Soil microbial community characterization is increasingly being used to determine the responses of soils to stress and disturbances and to assess ecosystem sustainability. However, there is little experimental evidence to indicate that predictable patterns in microbial community structure or composition occur during secondary succession or ecosystem restoration. This study utilized a chronosequence of developing jarrah (Eucalyptus marginata) forest ecosystems, rehabilitated after bauxite mining (up to 18 years old), to examine changes in soil bacterial and fungal community structures (by automated ribosomal intergenic spacer analysis [ARISA]) and changes in specific soil bacterial phyla by 16S rRNA gene microarray analysis. This study demonstrated that mining in these ecosystems significantly altered soil bacterial and fungal community structures. The hypothesis that the soil microbial community structures would become more similar to those of the surrounding nonmined forest with rehabilitation age was broadly supported by shifts in the bacterial but not the fungal community. Microarray analysis enabled the identification of clear successional trends in the bacterial community at the phylum level and supported the finding of an increase in similarity to nonmined forest soil with rehabilitation age. Changes in soil microbial community structure were significantly related to the size of the microbial biomass as well as numerous edaphic variables (including pH and C, N, and P nutrient concentrations). These findings suggest that soil bacterial community dynamics follow a pattern in developing ecosystems that may be predictable and can be conceptualized as providing an integrated assessment of numerous edaphic variables.

Soil Microbial Community Successional Patterns during Forest Ecosystem Restoration ▿†

PubMed Central

Banning, Natasha C.; Gleeson, Deirdre B.; Grigg, Andrew H.; Grant, Carl D.; Andersen, Gary L.; Brodie, Eoin L.; Murphy, D. V.

2011-01-01

Soil microbial community characterization is increasingly being used to determine the responses of soils to stress and disturbances and to assess ecosystem sustainability. However, there is little experimental evidence to indicate that predictable patterns in microbial community structure or composition occur during secondary succession or ecosystem restoration. This study utilized a chronosequence of developing jarrah (Eucalyptus marginata) forest ecosystems, rehabilitated after bauxite mining (up to 18 years old), to examine changes in soil bacterial and fungal community structures (by automated ribosomal intergenic spacer analysis [ARISA]) and changes in specific soil bacterial phyla by 16S rRNA gene microarray analysis. This study demonstrated that mining in these ecosystems significantly altered soil bacterial and fungal community structures. The hypothesis that the soil microbial community structures would become more similar to those of the surrounding nonmined forest with rehabilitation age was broadly supported by shifts in the bacterial but not the fungal community. Microarray analysis enabled the identification of clear successional trends in the bacterial community at the phylum level and supported the finding of an increase in similarity to nonmined forest soil with rehabilitation age. Changes in soil microbial community structure were significantly related to the size of the microbial biomass as well as numerous edaphic variables (including pH and C, N, and P nutrient concentrations). These findings suggest that soil bacterial community dynamics follow a pattern in developing ecosystems that may be predictable and can be conceptualized as providing an integrated assessment of numerous edaphic variables. PMID:21724890

The evolution of ecological tolerance in prokaryotes

NASA Technical Reports Server (NTRS)

Knoll, A. H.; Bauld, J.

1989-01-01

The ecological ranges of Archaeobacteria and Eubacteria are constrained by a requirement for liquid water and the physico-chemical stability limits of biomolecules, but within this broad envelope, prokaryotes have evolved adaptations that permit them to tolerate a remarkable spectrum of habitats. Laboratory experiments indicate that prokaryotes can adapt rapidly to novel environmental conditions, yet geological studies suggest early diversification and long-term stasis within the prokaryotic kingdoms. These apparently contradictory perspectives can be reconciled by understanding that, in general, rates and patterns of prokaryotic evolution reflect the developmental history of the Earth's surface environments. Our understanding of modern microbial ecology provides a lens through which our accumulating knowledge of physiology, molecular phylogeny and the Earth's history can be integrated and focussed on the phenomenon of prokaryotic evolution.

Analysis of PAMP-Triggered ROS Burst in Plant Immunity.

PubMed

Sang, Yuying; Macho, Alberto P

2017-01-01

The plant perception of pathogen-associated molecular patterns triggers a plethora of cellular immune responses. One of these responses is a rapid and transient burst of reactive oxygen species (ROS) mediated by plasma membrane-localized NADPH oxidases. The ROS burst requires a functional receptor complex and the contribution of several additional regulatory components. In laboratory conditions, the ROS burst can be detected a few minutes after the treatment with an immunogenic microbial elicitor. For these reasons, the elicitor-triggered ROS burst has been often exploited as readout to probe the contribution of plant components to early immune responses. Here, we describe a detailed protocol for the measurement of elicitor-triggered ROS burst in a simple, fast, and easy manner.

The Oral Microbiota in Health and Disease: An Overview of Molecular Findings.

PubMed

Siqueira, José F; Rôças, Isabela N

2017-01-01

Culture-independent nucleic acid technologies have been extensively applied to the analysis of oral bacterial communities associated with healthy and diseased conditions. These methods have confirmed and substantially expanded the findings from culture studies to reveal the oral microbial inhabitants and candidate pathogens associated with the major oral diseases. Over 1000 bacterial distinct species-level taxa have been identified in the oral cavity and studies using next-generation DNA sequencing approaches indicate that the breadth of bacterial diversity may be even much larger. Nucleic acid technologies have also been helpful in profiling bacterial communities and identifying disease-related patterns. This chapter provides an overview of the diversity and taxonomy of oral bacteria associated with health and disease.

Stratification Modelling of Key Bacterial Taxa Driven by Metabolic Dynamics in Meromictic Lakes.

PubMed

Zhu, Kaicheng; Lauro, Federico M; Su, Haibin

2018-06-22

In meromictic lakes, the water column is stratified into distinguishable steady layers with different physico-chemical properties. The bottom portion, known as monimolimnion, has been studied for the functional stratification of microbial populations. Recent experiments have reported the profiles of bacterial and nutrient spatial distributions, but quantitative understanding is invoked to unravel the underlying mechanism of maintaining the discrete spatial organization. Here a reaction-diffusion model is developed to highlight the spatial pattern coupled with the light-driven metabolism of bacteria, which is resilient to a wide range of dynamical correlation between bacterial and nutrient species at the molecular level. Particularly, exact analytical solutions of the system are presented together with numerical results, in a good agreement with measurements in Ace lake and Rogoznica lake. Furthermore, one quantitative prediction is reported here on the dynamics of the seasonal stratification patterns in Ace lake. The active role played by the bacterial metabolism at microscale clearly shapes the biogeochemistry landscape of lake-wide ecology at macroscale.

Functional gene diversity of soil microbial communities from five oil-contaminated fields in China.

PubMed

Liang, Yuting; Van Nostrand, Joy D; Deng, Ye; He, Zhili; Wu, Liyou; Zhang, Xu; Li, Guanghe; Zhou, Jizhong

2011-03-01

To compare microbial functional diversity in different oil-contaminated fields and to know the effects of oil contaminant and environmental factors, soil samples were taken from typical oil-contaminated fields located in five geographic regions of China. GeoChip, a high-throughput functional gene array, was used to evaluate the microbial functional genes involved in contaminant degradation and in other major biogeochemical/metabolic processes. Our results indicated that the overall microbial community structures were distinct in each oil-contaminated field, and samples were clustered by geographic locations. The organic contaminant degradation genes were most abundant in all samples and presented a similar pattern under oil contaminant stress among the five fields. In addition, alkane and aromatic hydrocarbon degradation genes such as monooxygenase and dioxygenase were detected in high abundance in the oil-contaminated fields. Canonical correspondence analysis indicated that the microbial functional patterns were highly correlated to the local environmental variables, such as oil contaminant concentration, nitrogen and phosphorus contents, salt and pH. Finally, a total of 59% of microbial community variation from GeoChip data can be explained by oil contamination, geographic location and soil geochemical parameters. This study provided insights into the in situ microbial functional structures in oil-contaminated fields and discerned the linkages between microbial communities and environmental variables, which is important to the application of bioremediation in oil-contaminated sites.

Functional gene diversity of soil microbial communities from five oil-contaminated fields in China

PubMed Central

Liang, Yuting; Van Nostrand, Joy D; Deng, Ye; He, Zhili; Wu, Liyou; Zhang, Xu; Li, Guanghe; Zhou, Jizhong

2011-01-01

To compare microbial functional diversity in different oil-contaminated fields and to know the effects of oil contaminant and environmental factors, soil samples were taken from typical oil-contaminated fields located in five geographic regions of China. GeoChip, a high-throughput functional gene array, was used to evaluate the microbial functional genes involved in contaminant degradation and in other major biogeochemical/metabolic processes. Our results indicated that the overall microbial community structures were distinct in each oil-contaminated field, and samples were clustered by geographic locations. The organic contaminant degradation genes were most abundant in all samples and presented a similar pattern under oil contaminant stress among the five fields. In addition, alkane and aromatic hydrocarbon degradation genes such as monooxygenase and dioxygenase were detected in high abundance in the oil-contaminated fields. Canonical correspondence analysis indicated that the microbial functional patterns were highly correlated to the local environmental variables, such as oil contaminant concentration, nitrogen and phosphorus contents, salt and pH. Finally, a total of 59% of microbial community variation from GeoChip data can be explained by oil contamination, geographic location and soil geochemical parameters. This study provided insights into the in situ microbial functional structures in oil-contaminated fields and discerned the linkages between microbial communities and environmental variables, which is important to the application of bioremediation in oil-contaminated sites. PMID:20861922

Unravelling ancient microbial history with community proteogenomics and lipid geochemistry.

PubMed

Brocks, Jochen J; Banfield, Jillian

2009-08-01

Our window into the Earth's ancient microbial past is narrow and obscured by missing data. However, we can glean information about ancient microbial ecosystems using fossil lipids (biomarkers) that are extracted from billion-year-old sedimentary rocks. In this Opinion article, we describe how environmental genomics and related methodologies will give molecular fossil research a boost, by increasing our knowledge about how evolutionary innovations in microorganisms have changed the surface of planet Earth.

Biosynthesis and derivatization of microbial glycolipids and their potential application in tribology

USDA-ARS?s Scientific Manuscript database

Microbial-produced glycolipids are biobased products with immense potential for commercial applications. Advances in the production process have led to the lowering of production cost and the appearance of commercial products in niche markets. The ability to manipulate the molecular structure by f...

The plastid genome as a platform for the expression of microbial resistance genes

USDA-ARS?s Scientific Manuscript database

In recent years, our fundamental understanding of host-microbe interaction has developed considerably. We have begun to tease out the genetic components that influence host resistance to microbial colonization. The use of advancing molecular technologies such as microarray expression profiling and...

Taxonomic concepts and practice with complex microbial communities

USDA-ARS?s Scientific Manuscript database

This brief review discusses the main points of the Keynote Lecture to be given at the 3rd International Conference on Microbial Diversity, October 27-29, 2015, Perugia, Italy. Key points include the necessity of molecular identification of microorganisms in order to understand their ecology. DNA-bas...

Microbial Degradation of Octamethylcyclotetrasiloxane

PubMed Central

Grümping, R.; Michalke, K.; Hirner, A. V.; Hensel, R.

1999-01-01

The microbial degradation of low-molecular-weight polydimethylsiloxanes was investigated through laboratory experiments. Octamethylcyclotetrasiloxane was found to be biodegraded under anaerobic conditions in composted sewage sludge, as monitored by the occurrence of the main polydimethylsiloxane degradation product, dimethylsilanediol, compared to that found in experiments with sterilized control samples. PMID:10224038

Patterns and drivers of soil microbial communities in temperate grasslands on the Mongolian plateau

NASA Astrophysics Data System (ADS)

Yang, Y.; Hu, H.; Hao, B.; Liu, Y.; Chen, Y.; Ma, W.

2016-12-01

Soil microorganisms play key roles in regulating many important ecosystem processes. However, our understanding of the patterns and drivers of soil microbial communities at the regional scale remains limited. In this study, on the basis of phospholipid fatty acid (PLFA) analysis, we investigated large-scale patterns and drivers of soil microbial communities using data from 78 sites between two depths (0-10 cm and 10-20 cm) within three major grassland types (desert steppe, typical steppe, and meadow steppe) on the Mongolian Plateau. Our findings demonstrated that, at the regional scale, the total soil microbial biomass, fungal biomass, bacterial biomass, and actinomycete biomass in Inner Mongolian temperate grasslands were all positively associated with mean annual precipitation (MAP), soil organic carbon (SOC), soil total nitrogen (TN), C:N ratio, plant aboveground biomass (AGB), and plant species richness (SR), but negatively correlated with mean annual temperature (MAT), soil bulk density (BD), and soil pH in both depths, except actinomycete biomass with MAP and BD in 10-20 cm. A stepwise regression analysis revealed that soil microbial community variations in Inner Mongolian temperate grasslands were mainly explained by C : N ratio in 0-10 cm, but by SR (total soil microbial biomass, fungal biomass, and actinomycete biomass) and MAT (bacterial biomass) in 10-20 cm. Our findings strongly indicate that the dominant drivers of spatial variations in soil microbial communities between 0-10 cm and 10-20 cm in the Inner Mongolia grasslands are significantly different, with edaphic factors (e.g., C: N ratio) in 0-10 cm but climatic (e.g, MAT) and/or biotic (e.g, SR) in 10-20 cm.

An analysis of species boundaries and biogeographic patterns in a cryptic species complex: the rotifer--Brachionus plicatilis.

PubMed

Suatoni, Elizabeth; Vicario, Saverio; Rice, Sean; Snell, Terry; Caccone, Adalgisa

2006-10-01

Since the advent of molecular phylogenetics, there is increasing evidence that many small aquatic and marine invertebrates--once believed to be single, cosmopolitan species--are in fact cryptic species complexes. Although the application of the biological species concept is central to the identification of species boundaries in these cryptic complexes, tests of reproductive isolation do not frequently accompany phylogenetic studies. Because different species concepts generally identify different boundaries in cryptic complexes, studies that apply multiple species concepts are needed to gain a more detailed understanding of patterns of diversification in these taxa. Here we explore different methods of empirically delimiting species boundaries in the salt water rotifer Brachionus plicatilis by comparing reproductive data (i.e., the traditional biological species concept) to phylogenetic data (the genealogical species concept). Based on a high degree of molecular sequence divergence and largely concordant genetic patterns in COI and ITS1, the genealogical species hypothesis indicates the existence of at least 14 species--the highest estimate for the group thus far. A test of the genealogical species concept with biological crosses shows a fairly high level of concordance, depending on the degree of reproductive success used to draw boundaries. The convergence of species concepts in this group suggests that many of the species within the group may be old. Although the diversity of the group is higher than previously understood, geographic distributions remain broad. Efficient passive dispersal has resulted in global distributions for many species with some evidence of isolation by distance over large geographic scales. These patterns concur with expectations that micro-meiofauna (0.1-1mm) have biogeographies intermediate to microbial organisms and large vertebrates. Sympatry of genetically distant strains is common.

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

PubMed

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

2011-07-01

To promote rational and sustainable use of soil resources and to maintain the urban soil quality, it is essential to assess urban ecosystem health. In this study, the microbiological properties of urban soils in Beijing and their spatial distribution patterns across the city were evaluated based on measurements of microbial biomass carbon and urease and invertase activities of the soils for the purpose of assessing the urban ecosystem health of Beijing. Grid sampling design, normal Kriging technique, and the multiple comparisons among different land use types were used in soil sampling and data treatment. The inherent chemical characteristics of urban soils in Beijing, e.g., soil pH, electronic conductivity, heavy metal contents, total N, P and K contents, and soil organic matter contents were detected. The size and diversity of microbial community and the extent of microbial activity in Beijing urban soils were measured as the microbial biomass carbon content and the ratio of microbial biomass carbon content to total soil organic carbon. The microbial community health measured in terms of microbial biomass carbon, urease, and invertase activities varied with the organic substrate and nutrient contents of the soils and were not adversely affected by the presence of heavy metals at p < 0.01. It was shown that the older and the biologically more stable part of city exhibited higher microbial activity levels than the more recently developed part of the city and the road areas of heavy traffic. It was concluded that the land use patterns in Beijing urban soils influenced the nature and activities of the microbial communities.

Successional and seasonal variations in soil and litter microbial community structure and function during tropical postagricultural forest regeneration: a multiyear study.

PubMed

Smith, A Peyton; Marín-Spiotta, Erika; Balser, Teri

2015-09-01

Soil microorganisms regulate fundamental biochemical processes in plant litter decomposition and soil organic matter (SOM) transformations. Understanding how microbial communities respond to changes in vegetation is critical for improving predictions of how land-cover change affects belowground carbon storage and nutrient availability. We measured intra- and interannual variability in soil and forest litter microbial community composition and activity via phospholipid fatty acid analysis (PLFA) and extracellular enzyme activity across a well-replicated, long-term chronosequence of secondary forests growing on abandoned pastures in the wet subtropical forest life zone of Puerto Rico. Microbial community PLFA structure differed between young secondary forests and older secondary and primary forests, following successional shifts in tree species composition. These successional patterns held across seasons, but the microbial groups driving these patterns differed over time. Microbial community composition from the forest litter differed greatly from those in the soil, but did not show the same successional trends. Extracellular enzyme activity did not differ with forest succession, but varied by season with greater rates of potential activity in the dry seasons. We found few robust significant relationships among microbial community parameters and soil pH, moisture, carbon, and nitrogen concentrations. Observed inter- and intrannual variability in microbial community structure and activity reveal the importance of a multiple, temporal sampling strategy when investigating microbial community dynamics with land-use change. Successional control over microbial composition with forest recovery suggests strong links between above and belowground communities. © 2015 John Wiley & Sons Ltd.

Microbial production of polyhydroxybutyrate with tailor-made properties: an integrated modelling approach and experimental validation.

PubMed

Penloglou, Giannis; Chatzidoukas, Christos; Kiparissides, Costas

2012-01-01

The microbial production of polyhydroxybutyrate (PHB) is a complex process in which the final quantity and quality of the PHB depend on a large number of process operating variables. Consequently, the design and optimal dynamic operation of a microbial process for the efficient production of PHB with tailor-made molecular properties is an extremely interesting problem. The present study investigates how key process operating variables (i.e., nutritional and aeration conditions) affect the biomass production rate and the PHB accumulation in the cells and its associated molecular weight distribution. A combined metabolic/polymerization/macroscopic modelling approach, relating the process performance and product quality with the process variables, was developed and validated using an extensive series of experiments and measurements. The model predicts the dynamic evolution of the biomass growth, the polymer accumulation, the consumption of carbon and nitrogen sources and the average molecular weights of the PHB in a bioreactor, under batch and fed-batch operating conditions. The proposed integrated model was used for the model-based optimization of the production of PHB with tailor-made molecular properties in Azohydromonas lata bacteria. The process optimization led to a high intracellular PHB accumulation (up to 95% g of PHB per g of DCW) and the production of different grades (i.e., different molecular weight distributions) of PHB. Copyright © 2011 Elsevier Inc. All rights reserved.

Microbial response to modified precipitation patterns in tallgrass prairie soil: molecular mechanisms, activity rates and organic matter dynamics

NASA Astrophysics Data System (ADS)

Zeglin, L. H.; David, M.; Bottomley, P.; Hettich, R. L.; Jansson, J.; Jumpponen, A.; Rice, C. W.; Tringe, S.; VerBerkmoes, N. C.; Myrold, D.

2011-12-01

A significant amount of carbon (C) is processed and stored in prairie soils: grasslands cover 6.1-7.4% of the earth's land surface and hold 7.3-11.4% of global soil C. Global change models predict that the future precipitation regime across the North American Great Plains will entail less frequent but larger rainfall events. The response of prairie soil microbial C processing and allocation to this scenario of higher hydrologic variability is not known, but will be a key determiner of the future capacity for prairie soil C sequestration. We are approaching this problem by assessing soil microbial function (respiration, C utilization efficiency, extracellular enzyme activity) and molecular indicators of dominant C allocation pathways (soil transcriptome, proteome and metabolome) under ambient and experimentally modified precipitation regimes. The rainfall manipulation plots (RaMPs) at the Konza Prairie Long-Term Ecological Research (LTER) site in eastern Kansas, USA is a replicated field manipulation of the magnitude and frequency of natural precipitation that was established in 1998. We collected soil before, during and after a rainfall event in both ambient and modified precipitation treatments and measured the microbial response. Microbial respiration doubled in both treatments during the water addition, and cellobiohydrolase enzyme potential activity (a catalyst of cellulose hydrolysis) increased slightly, but no significant effect of altered precipitation treatment has emerged. The fungal and bacterial ribosomal gene composition was also similar between precipitation treatments. Although pools of genes and extracellular enzymes may be relatively static during short-term dynamic conditions, transcript and intracellular protein abundances may be more indicative of the active microbial metabolic response to rapid shifts in soil moisture. Thus, analysis of transcript and protein composition is underway. In addition, we have implemented a series of lab experiments to optimize and link transcript and protein recovery and analysis procedures using the model soil bacterium Arthrobacter chlorophenicolus strain A6 (ArtchA6). Konza prairie soil was inoculated with ArchA6 and incubated for 72 h with no supplemental C, with acetate or with 4-chlorophenol (a xenobiotic compound that ArtchA6 can utilize as its sole C source), then RNA and protein were extracted from the soil. Quantitatively representative recovery of ArtchA6 genes, rRNA, mRNA and protein was successful. The ratio of ArtchA6 isocitrate lyase (icl, indicative of 2-C metabolism) to succinyl CoA synthetase (suCAB, indicative of total respiratory activity) transcript was highest in soils amended with acetate. Proteomic signatures were distinct in soils with different supplemental C sources. This experiment confirms our capability of recovering transcript and protein from the study soil and of identifying the functional molecules representative of distinct C metabolism pathways.

Studying plant-pathogen interactions in the genomics era: beyond molecular Koch’s postulates to systems biology

USDA-ARS?s Scientific Manuscript database

Molecular factors enabling microbial pathogens to cause plant diseases have been sought with increasing efficacy over three research eras, which successively introduced the tools of disease physiology, single-gene molecular genetics, and genomics. From this work emerged a unified model of the intera...

Habitat generalists and specialists in microbial communities across a terrestrial-freshwater gradient

NASA Astrophysics Data System (ADS)

Monard, C.; Gantner, S.; Bertilsson, S.; Hallin, S.; Stenlid, J.

2016-11-01

Observations of distributions of microorganisms and their differences in community composition across habitats provide evidence of biogeographical patterns. However, little is known about the processes controlling transfers across habitat gradients. By analysing the overall microbial community composition (bacteria, fungi, archaea) across a terrestrial-freshwater gradient, the aim of this study was to understand the spatial distribution patterns of populations and identify taxa capable of crossing biome borders. Barcoded 454 pyrosequencing of taxonomic gene markers was used to describe the microbial communities in adjacent soil, freshwater and sediment samples and study the role of biotic and spatial factors in shaping their composition. Few habitat generalists but a high number of specialists were detected indicating that microbial community composition was mainly regulated by species sorting and niche partitioning. Biotic interactions within microbial groups based on an association network underlined the importance of Actinobacteria, Sordariomycetes, Agaricomycetes and Nitrososphaerales in connecting among biomes. Even if dispersion seemed limited, the shore of the lake represented a transition area, allowing populations to cross the biome boundaries. In finding few broadly distributed populations, our study points to biome specialization within microbial communities with limited potential for dispersal and colonization of new habitats along the terrestrial-freshwater continuum.

Effect of invader litter chemistries on soil organic matter compositions: consequences of Polygonum cuspidatum and Pueraria lobata invasions

NASA Astrophysics Data System (ADS)

Tharayil, N.; Tamura, M.

2012-12-01

Carbon fixation during photosynthesis forms the precursor of all organic carbon in soil and the predominant source of energy that drives soil microbial processes; hence the molecular identity of the fixed carbon could influence the formation of soil organic matter (SOM). Due to their high resource acquisition and resource use efficiencies, some invasive plants can input disproportionately high quantities of litter that are qualitatively distinctive, and this could influence the accrual of organic carbon and overall carbon cycling in invaded habitats. Hence, we hypothesized that invasive plants with unique litter chemistries would significantly influence the overall carbon cycling in the invaded soils. We tested this hypothesis by comparing plants exhibiting recalcitrant vs. labile litter chemistries using japanese knotweed (Polygonum cuspidatum) and kudzu (Pueraria lobata), respectively. Japanese knotweed produces low litter abundant in polyphenols which selectively hinders microbially mediated decomposition and re-synthesis; whereas kudzu produces low C:N, high quality litter that can stimulate microbial decomposition. Soil samples were collected at 5-cm intervals and from inside and outside 15 to 20 year old stands of the invasive species. The novelty of our study was that both of our study species were invading into soils of contrasting substrate qualities relative to the invading litter quality. The molecular composition of carbon in the soils and the degradation stage of the SOM were assessed with a biomarker approach using gas chromatography-mass spectrometry to determine the source of biomolecules (plant or microbes). Stability of SOM fractions was assessed through oxidation with hydrogen peroxide, serving as a proxy of biological degradation, followed by stable isotope analysis. Fungal communities dominated the uppermost soils under knotweed whereas kudzu litter suppressed fungal biomass in the top 10-cm. In constrast, increase in active microbial biomass C was observed under kudzu for all depths while it was suppressed at the top soil of knotweed invasion. Principal component analyses on biomarkers revealed a convergence of soils under knotweed and kudzu, based on profiles of lignin derived phenolics, cutin derived long chain n-alkanoic acid, and plant or microbe derived steroids. Knotweed soil was consisted of higher concentration of higher plant wax derived long chain alkanoic acid, phenolics (ferulic and p-coumaric acid), and both microbe (ergosterol) and plant (campesterol) derived steroids. Kudzu soil was characterized by lower lignin monomers and long-chain plant derived alkanoic acid, suggesting rapid litter decomposition. Increase in δ13C (%) after hydrogen peroxide treatment indicated difference in degradation pattern among biochemical components varying in natural abundance. In conclusion, molecular level characterization of the soil has a potential to link the organic matter composition to the estimated stability. These results indicate that both invaders can significantly influence the molecular-level characteristics of carbon accrued in soils by producing a high biomass of litter.

MOLECULAR ANALYSIS OF MICROBIAL COMMUNITY STRUCTURES IN PRISTINE AND CONTAMINATED AQUIFERS: FIELD AND LABORATORY MICROCOSM EXPERIMENTS

EPA Science Inventory

This study used phylogenetic probes in hybridization analysis to (i) determine in situ microbial community structures in regions of a shallow sand aquifer that were oxygen depleted and fuel contaminated (FC) or aerobic and noncontaminted (NC) and (ii) examine alterations in micro...

Effects of 18 pharmaceuticals on the physiological diversity of edaphic microorganisms.

PubMed

Pino-Otín, Mª Rosa; Muñiz, Selene; Val, Jonatan; Navarro, Enrique

2017-10-01

Pharmaceutical residues can enter the terrestrial environment through the application of recycled water and contaminated biosolids to agricultural soils, were edaphic microfauna can would be threatened. This study thus assessed the effect of 18 widely consumed pharmaceuticals, belonging to four groups: antibiotics, non-steroidal anti-inflammatory drugs (NSAIDs), blood lipid-lowering agents (BLLA) and β-blockers, on the physiology of soil microbial communities from a ecological crop field. Biolog EcoPlates, containing 31 of the most common carbon sources found in forest and crop soils, were used to calculate both the averaged well colour development (AWCD), as an indicator of the entire capacity of degrading carbon sources, and the diversity of carbon source utilization, as an indicator of the physiological diversity. The results show that pharmaceuticals impact microbial communities by changing the ability of microbes to metabolize different carbon sources, thus affecting the metabolic diversity of the soil community. The toxicity of the pharmaceuticals was inversely related to the log K ow ; indeed, NSAIDs were the least toxic and antibiotics were the most toxic, while BLLA and β-blockers presented intermediate toxicity. The antibiotic sulfamethoxazole imposed the greatest impact on microbial communities at concentrations from 100 mg/L, followed by the other two antibiotics (trimethoprim and tetracycline) and the β-blocker nadolol. Other chemical parameters (i.e. melting point, molecular weight, pK a or solubility) had little influence on toxicity. Microbial communities exposed to pharmaceuticals having similar physicochemical characteristics presented similar physiological diversity patterns of carbon substrate utilization. These results suggest that the repeated amendment of agricultural soils with biosolids or sludges containing pharmaceutical residuals may result in soil concentrations of concern regarding key ecological functions (i.e. the carbon cycle). Copyright © 2017 Elsevier B.V. All rights reserved.

Phylogeography of microbial phototrophs in the dry valleys of the high Himalayas and Antarctica.

PubMed

Schmidt, S K; Lynch, R C; King, A J; Karki, D; Robeson, M S; Nagy, L; Williams, M W; Mitter, M S; Freeman, K R

2011-03-07

High-elevation valleys in dry areas of the Himalayas are among the most extreme, yet least explored environments on Earth. These barren, rocky valleys are subjected to year-round temperature fluctuations across the freezing point and very low availability of water and nutrients, causing previous workers to hypothesize that no photoautotrophic life (primary producers) exists in these locations. However, there has been no work using modern biogeochemical or culture-independent molecular methods to test the hypothesis that photoautotrophs are absent from high Himalayan soil systems. Here, we show that although microbial biomass levels are as low as those of the Dry Valleys of Antarctica, there are abundant microbial photoautotrophs, displaying unexpected phylogenetic diversity, in barren soils from just below the permanent ice line of the central Himalayas. Furthermore, we discovered that one of the dominant algal clades from the high Himalayas also contains the dominant algae in culture-independent surveys of both soil and ice samples from the Dry Valleys of Antarctica, revealing an unexpected link between these environmentally similar but geographically very distant systems. Phylogenetic and biogeographic analyses demonstrated that although this algal clade is globally distributed to other high-altitude and high-latitude soils, it shows significant genetic isolation by geographical distance patterns, indicating local adaptation and perhaps speciation in each region. Our results are the first to demonstrate the remarkable similarities of microbial life of arid soils of Antarctica and the high Himalayas. Our findings are a starting point for future comparative studies of the dry valleys of the Himalayas and Antarctica that will yield new insights into the cold and dry limits to life on Earth.

Bioavailability of riverine dissolved organic matter in three Baltic Sea estuaries and the effect of catchment land-use

NASA Astrophysics Data System (ADS)

Asmala, E.; Autio, R.; Kaartokallio, H.; Pitkänen, L.; Stedmon, C. A.; Thomas, D. N.

2013-06-01

The microbial degradation of dissolved organic carbon and nitrogen (DOC, DON) was studied in three boreal estuaries with contrasting land use patterns (Kiiminkijoki - natural forest and peatland; Kyrönjoki - agricultural; Karjaanjoki - mixed/urban). Bioassays conducted for 12-18 days were used in 3 seasons at in situ temperatures. Besides the bulk parameters, a suite of dissolved organic matter (DOM) quality parameters were investigated, including colored DOM (CDOM), fluorescent DOM and the molecular weight of DOM. Bioavailable DOC and DON pools varied significantly between the estuaries, from 7.9% in Kiiminkijoki to 10.6% in Karjaanjoki and from 5.5% in Kiiminkijoki to 21.9% in Kyrönjoki, respectively. DOM originating from catchment dominated by natural forests and peatlands had the lowest DOC and DON degradation rates, as well as the lowest proportions of biodegradable DOC and DON. A greater proportion of agricultural land in the catchment increased the bioavailability of DON, but not the bioavailability of DOC. Also DOM quality varied significantly between the estuaries, and DOM originating from the agricultural Kyrönjoki catchment sustained higher DOC and DON degradation rates and higher bacterial growth efficiency (BGE) compared to those of the natural forest and peat dominated Kiiminkijoki catchment. The quality of DOM, indicated by differences in CDOM, fluorescent DOM and molecular weight, varied between estuaries with differing land use and was concluded to be major driver of BGE of these systems and thereafter to the microbial CO2 fluxes from the estuaries. The differences in BGE resulted in a 5-fold differences in the calculated daily bacterial CO2-emissions between the study estuaries due to bacterial activity, ranging from 40 kg C d-1 in Karjaanjoki estuary to 200 kg C d-1 in Kyrönjoki estuary. Two of the study systems (Karjaanjoki, mixed land use; Kyrönjoki, intensive agriculture) in which the DOM pool had lower DOC : DON ratio, smaller molecular weight and higher CDOM absorption spectral slope values resulted in higher proportion of the initial DOC and DON being transferred to microbial growth and therefore to the pelagic food web. The pristine, peatland and forest-dominated Kiiminkijoki catchment had the lowest BGE, and therefore proportionally highest CO2 fluxes. The slope coefficient S275-295 was a good proxy of molecular weight across estuaries and seasons, and also for different diagenetic stages of DOM during biological degradation.

Microbial and long-range terrestrial contributions of organic matter to Antarctica

NASA Astrophysics Data System (ADS)

Antony, R.; Grannas, A. M.; Priest, A. S.; Sleighter, R. L.; Meloth, T.; Hatcher, P.

2012-12-01

Composition and cycling of dissolved organic matter in glacial systems is important because of its great significance to global carbon dynamics, snow photochemistry, and air-snow exchange processes. But, due to the trace nature of specific organic components in Polar ice sheets, detecting and studying these species in molecular level detail has been an analytical challenge. Electrospray ionization coupled with Fourier transform ion cyclotron resonance mass spectrometry (ESI FT-ICR MS) enabled the elucidation of molecular level details of natural organic matter in snow samples collected along a coast to inland transect from the Princesses Elizabeth Land, East Antarctica. Thousands of distinct molecular species comprising of different compound classes were identified providing clues to the nature and sources of organic carbon in Antarctic snow. The major biochemical classes of compounds detected were lignins, tannins, carbohydrates, proteins, amino sugars, lipids, unsaturated hydrocarbons and condensed aromatics. Specifically, lignin molecules comprising up to 50% and compounds derived from algal and microbial biomass comprising up to 45% of the total assigned formulas dominated the organic carbon pool. The identification of a variety of lignin compounds demonstrates substantial input of vascular plant-derived materials to the identified molecular species, presumably from long range atmospheric transport and deposition. The detection of proteins, lipids and amino sugars suggests that a large proportion of the identified supraglacial organic matter likely originates from in situ microbial activity. This corroborates well with the presence of significant numbers of bacteria, picoplankton and microalgae in these samples. These results suggest that organic matter in the supraglacial environments have both a microbial and terrestrial provenance.

Fabrication of three dimensional patterns of wide dimensional range using microbes and their applications

PubMed Central

Mehta, Sunita; Murugeson, Saravanan; Prakash, Balaji; Deepak

2015-01-01

Inspired by the wound healing property of certain trees, we report a novel microbes based additive process for producing three dimensional patterns, which has a potential of engineering applications in a variety of fields. Imposing a two dimensional pattern of microbes on a gel media and allowing them to grow in the third dimension is known from its use in biological studies. Instead, we have introduced an intermediate porous substrate between the gel media and the microbial growth, which enables three dimensional patterns in specific forms that can be lifted off and used in engineering applications. In order to demonstrate the applicability of this idea in a diverse set of areas, two applications are selected. In one, using this method of microbial growth, we have fabricated microlenses for enhanced light extraction in organic light emitting diodes, where densely packed microlenses of the diameters of hundreds of microns lead to luminance increase by a factor of 1.24X. In another entirely different type of application, braille text patterns are prepared on a normal office paper where the grown microbial colonies serve as braille tactile dots. Braille dot patterns thus prepared meet the standard specifications (size and spacing) for braille books. PMID:26486847

Microbial Communities and Organic Matter Composition in Surface and Subsurface Sediments of the Helgoland Mud Area, North Sea

PubMed Central

Oni, Oluwatobi E.; Schmidt, Frauke; Miyatake, Tetsuro; Kasten, Sabine; Witt, Matthias; Hinrichs, Kai-Uwe; Friedrich, Michael W.

2015-01-01

The role of microorganisms in the cycling of sedimentary organic carbon is a crucial one. To better understand relationships between molecular composition of a potentially bioavailable fraction of organic matter and microbial populations, bacterial and archaeal communities were characterized using pyrosequencing-based 16S rRNA gene analysis in surface (top 30 cm) and subsurface/deeper sediments (30–530 cm) of the Helgoland mud area, North Sea. Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS) was used to characterize a potentially bioavailable organic matter fraction (hot-water extractable organic matter, WE-OM). Algal polymer-associated microbial populations such as members of the Gammaproteobacteria, Bacteroidetes, and Verrucomicrobia were dominant in surface sediments while members of the Chloroflexi (Dehalococcoidales and candidate order GIF9) and Miscellaneous Crenarchaeota Groups (MCG), both of which are linked to degradation of more recalcitrant, aromatic compounds and detrital proteins, were dominant in subsurface sediments. Microbial populations dominant in subsurface sediments (Chloroflexi, members of MCG, and Thermoplasmata) showed strong correlations to total organic carbon (TOC) content. Changes of WE-OM with sediment depth reveal molecular transformations from oxygen-rich [high oxygen to carbon (O/C), low hydrogen to carbon (H/C) ratios] aromatic compounds and highly unsaturated compounds toward compounds with lower O/C and higher H/C ratios. The observed molecular changes were most pronounced in organic compounds containing only CHO atoms. Our data thus, highlights classes of sedimentary organic compounds that may serve as microbial energy sources in methanic marine subsurface environments. PMID:26635758

Global investigation of composition and interaction networks in gut microbiomes of individuals belonging to diverse geographies and age-groups.

PubMed

Yadav, Deepak; Ghosh, Tarini Shankar; Mande, Sharmila S

2016-01-01

Factors like ethnicity, diet and age of an individual have been hypothesized to play a role in determining the makeup of gut microbiome. In order to investigate the gut microbiome structure as well as the inter-microbial associations present therein, we have performed a comprehensive global comparative profiling of the structure (composition, relative heterogeneity and diversity) and the inter-microbial networks in the gut microbiomes of 399 individuals of eight different nationalities. The study identified certain geography-specific trends with respect to composition, intra-group heterogeneity and diversity of the gut microbiomes. Interestingly, the gut microbial association/mutual-exlusion networks were observed to exhibit several cross-geography trends. It was seen that though the composition of gut microbiomes of the American and European individuals were similar, there were distinct patterns in their microbial interaction networks. Amongst European gut-microbiomes, the co-occurrence network obtained for the Danish population was observed to be most dense. Distinct patterns were also observed within Chinese, Japanese and Indian datasets. While performing an age-wise comparison, it was observed that the microbial interactions increased with the age of individuals. Furthermore, certain bacterial groups were identified to be present only in the older age groups. The trends observed in gut microbial networks could be due to the inherent differences in the diet of individuals belonging to different nationalities. For example, the higher number of microbial associations in the Danish population as compared to the Spanish population, may be attributed to the evenly distributed diet of the later. This is in line with previously reported findings which indicate an increase in functional interdependency of microbes in individuals with higher nutritional status. To summarise, the present study identifies geography and age specific patterns in the composition as well as microbial interactions in gut microbiomes.

Freezing and hungry? Hydrocarbon degrading microbial communities in Barents Sea sediments around Svalbard

NASA Astrophysics Data System (ADS)

Krueger, Martin; Straaten, Nontje

2017-04-01

The Polar Regions are characterised by varying temperatures and changing ice coverage, so most of the primary production take place in the warmer season. Consequently, sedimentation rates and nutrient input are low. The diversity and metabolic potentials of the microbial communities inhabiting these sediments in the Northern Barents Sea are largely unknown. Recent reports on natural methane seeps as well as the increase in hydrocarbon exploration activities in the Arctic initiated our studies on the potential of indigenous microbial communities to degrade methane and higher hydrocarbons under in situ pressure and temperature conditions. Furthermore, the subseafloor geochemistry in these areas was studied, together with important microbial groups, like methanotrophs, methanogens, metal and sulfate reducers, which may drive seafloor ecosystems in the Northern Barents Sea. Sediment samples were collected in several areas around Svalbard in the years 2013-2016 ranging from shallow (200m) areas on the Svalbard shelf to deep sea areas on the eastern Yermak Plateau (3200m water depths). Shelf sediments showed the highest organic carbon content which decreased with increasing depths. Iron and manganese as potential electron acceptors were found in the porewater especially in the top 50 cm of the cores, while sulfate was always present in substantial amounts in porewater samples down to the end of the up to two metre long cores. Concentrations of dissolved methane and carbon dioxide were low. The potential of the indigenous microorganisms to degrade methane and higher hydrocarbons as well as different oils under in situ temperatures and pressures was widespread in surface sediments. Degradation rates were higher under aerobic than under anaerobic conditions, and decreased with increasing sediment as well as water depths. Similar pattern were found for other metabolic processes, including sulfate, Fe and Mn reduction as well as carbon dioxide and methane production rates. Ongoing molecular biological analyses of original sediments and enrichment cultures indicate the presence of diverse and varying microbial communities.

How Redox Fluctuation Shapes Microbial Community Structure and Mineral-Organic Matter Relationships in a Humid Tropical Forest Soil

NASA Astrophysics Data System (ADS)

Campbell, A.; Bhattacharyya, A.; Lin, Y.; Tfaily, M. M.; Paša-Tolić, L.; Chu, R. K.; Silver, W. L.; Nico, P. S.; Pett-Ridge, J.

2016-12-01

Wet tropical soils can alternate frequently between fully oxygenated and anaerobic conditions, constraining both the metabolism of tropical soil microorganisms, and the mineral-organic matter relationships that regulate many aspects of soil C cycling. Tropical forests are predicted to experience a 2-5°C temperature increase and substantial differences in the amount and timing of rainfall in the coming half century. Yet we have a poor understanding of how soil microbial activity and C cycling in these systems will respond to changes in environmental variability caused by climate change. Using a 44 day redox manipulation and isotope tracing experiment with soils from the Luquillo Experimental Forest, Puerto Rico, we examined patterns of tropical soil microorganisms, metabolites and soil chemistry when soils were exposed to different redox regimes - static oxic, static anoxic, high frequency redox fluctuation (4 days oxic, 4 days anoxic), or low frequency redox fluctuation (8 days oxic, 4 days anoxic). Replicate microcosms were harvested throughout the incubation to understand how changes in redox oscillation frequency altered microbial community structure and activity, organic matter turnover and fate, and soil chemistry. While gross soil respiration was highest in static oxic soils, respiration derived from added litter was highest in static anoxic soils, suggesting that decomposition of preexisting SOM was limited by O2 availability in the anoxic treatment. Microbial communities responded to shifting O2 availability in the different treatments, resulting in significant differences in DOC concentration and molecular composition (measured by FTICR-MS). DOC and Fe2+ concentrations were positively correlated for all four redox treatments, and rapidly increased following oscillation from oxic to anoxic conditions. These results, along with parallel studies of biogeochemical responses (Fe speciation, pH, P availability), suggest a highly responsive microbial and geochemical system, where the frequency of low-redox events controls exchanges of C between mineral-sorbed and aqueous pools.

A microbial perspective of human developmental biology.

PubMed

Charbonneau, Mark R; Blanton, Laura V; DiGiulio, Daniel B; Relman, David A; Lebrilla, Carlito B; Mills, David A; Gordon, Jeffrey I

2016-07-07

When most people think of human development, they tend to consider only human cells and organs. Yet there is another facet that involves human-associated microbial communities. A microbial perspective of human development provides opportunities to refine our definitions of healthy prenatal and postnatal growth and to develop innovative strategies for disease prevention and treatment. Given the dramatic changes in lifestyles and disease patterns that are occurring with globalization, we issue a call for the establishment of 'human microbial observatories' designed to examine microbial community development in birth cohorts representing populations with diverse anthropological characteristics, including those undergoing rapid change.

Human developmental biology viewed from a microbial perspective

PubMed Central

Charbonneau, Mark R.; Blanton, Laura V.; DiGiulio, Daniel B.; Relman, David A.; Lebrilla, Carlito B.; Mills, David A.; Gordon, Jeffrey I.

2017-01-01

Preface Most people think of human development only in terms of ‘human’ cells and organs. Here, we discuss another facet involving human-associated microbial communities. A microbial perspective of human development provides opportunities to refine our definitions of healthy pre- and postnatal growth and to develop new strategies for disease prevention and treatment. Considering the dramatic changes in lifestyles and disease patterns that are occurring with globalization, we issue a call for human microbial observatory programs designed to examine microbial community development in birth cohorts representing populations with diverse anthropologic characteristics, including those undergoing rapid change. PMID:27383979

Microbial Biogeography on the Legacies of Historical Events in the Arctic Subsurface Sediments

NASA Astrophysics Data System (ADS)

Han, Dukki; Nam, Seung-Il; Hur, Hor-Gil

2017-04-01

The Arctic marine environment consists of various microbial habitats. The niche preference of microbial assemblages in the Arctic Ocean has been surveyed with the modern environmental change by oceanographic traits such as sea-ice dynamics, current circulation, and sedimentation. The North Pacific inflow from the shallow and narrow Bering Strait is highly susceptible to sea-level fluctuations, and thus the water mass exchange mediated by the history of sea-ice between the North Pacific and the Chukchi Sea in the Arctic Ocean. Over geological timescale, the climate change may provide putative evidences for ecological niche for the Arctic microbial assemblages as well as geological records in response to the paleoclimate change. In the present study, the multidisciplinary approach, based on microbiology, geology, and geochemistry, was applied to survey the microbial assemblages in the Arctic subsurface sediments and help further integrate the microbial biogeography and biogeochemical patterns in the Arctic subsurface biosphere. Our results describe microbial assemblages with high-resolution paleoceanographic records in the Chukchi Sea sediment core (ARA02B/01A-GC; 5.4 mbsf) to show the processes that drive microbial biogeographic patterns in the Arctic subsurface sediments. We found microbial habitat preferences closely linked to Holocene paleoclimate records as well as geological, geochemical, and microbiological evidence for the inference of the sulphate-methane transition zone (SMTZ) in the Chukchi Sea. Especially, the vertically distributed predominant populations of Gammaproteobacteria and Marine Group II Euryarchaeota in the ARA02B/01A-GC consistent with the patterns of the known global SMTZs and Holocene sedimentary records, suggesting that in-depth microbiological profiles integrated with geological records may be indirectly useful for reconstructing Arctic paleoclimate changes. In the earliest phase of Mid Holocene in the ARA02B/01A-GC with concentrated crenarchaeol (a unique biomarker for Marine Group I Thaumarchaea), the most abundant archaeal population was Marine Group II Euryarchaeota rather than Marine Group I Thaumarchaea, suggesting that the interpretation of archaeal tetraether lipids in subsurface sediments needs careful consideration for paleoceanography. In conclusion, our findings have important implications for the availability of microbial biogeography in the sedimentary record. The present study offers a deeper understanding of the legacies of historical events during the Holocene and implies that the survey of microbial biogeography may be an appropriate tool to monitor potential effects from the climate change in the Arctic Ocean.

Molecular insights into the microbial formation of marine dissolved organic matter: recalcitrant or labile?

NASA Astrophysics Data System (ADS)

Koch, B. P.; Kattner, G.; Witt, M.; Passow, U.

2014-08-01

The degradation of marine dissolved organic matter (DOM) is an important control variable in the global carbon cycle. For our understanding of the kinetics of organic matter cycling in the ocean, it is crucial to achieve a mechanistic and molecular understanding of its transformation processes. A long-term microbial experiment was performed to follow the production of non-labile DOM by marine bacteria. Two different glucose concentrations and dissolved algal exudates were used as substrates. We monitored the bacterial abundance, concentrations of dissolved and particulate organic carbon (DOC, POC), nutrients, amino acids and transparent exopolymer particles (TEP) for 2 years. The molecular characterization of extracted DOM was performed by ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) after 70 days and after ∼2 years of incubation. Although glucose quickly degraded, a non-labile DOC background (5-9% of the initial DOC) was generated in the glucose incubations. Only 20% of the organic carbon from the algal exudate degraded within the 2 years of incubation. The degradation rates for the non-labile DOC background in the different treatments varied between 1 and 11 μmol DOC L-1 year-1. Transparent exopolymer particles, which are released by microorganisms, were produced during glucose degradation but decreased back to half of the maximum concentration within less than 3 weeks (degradation rate: 25 μg xanthan gum equivalents L-1 d-1) and were below detection in all treatments after 2 years. Additional glucose was added after 2 years to test whether labile substrate can promote the degradation of background DOC (co-metabolism; priming effect). A priming effect was not observed but the glucose addition led to a slight increase of background DOC. The molecular analysis demonstrated that DOM generated during glucose degradation differed appreciably from DOM transformed during the degradation of the algal exudates. Our results led to several conclusions: (i) based on our experimental setup, higher substrate concentration resulted in a higher concentration of non-labile DOC; (ii) TEP, generated by bacteria, degrade rapidly, thus limiting their potential contribution to carbon sequestration; (iii) the molecular signatures of DOM derived from algal exudates and glucose after 70 days of incubation differed strongly from refractory DOM. After 2 years, however, the molecular patterns of DOM in glucose incubations were more similar to deep ocean DOM whereas the degraded exudate was still different.

Bacterial and fungal DNA extraction from blood samples: automated protocols.

PubMed

Lorenz, Michael G; Disqué, Claudia; Mühl, Helge

2015-01-01

Automation in DNA isolation is a necessity for routine practice employing molecular diagnosis of infectious agents. To this end, the development of automated systems for the molecular diagnosis of microorganisms directly in blood samples is at its beginning. Important characteristics of systems demanded for routine use include high recovery of microbial DNA, DNA-free containment for the reduction of DNA contamination from exogenous sources, DNA-free reagents and consumables, ideally a walkaway system, and economical pricing of the equipment and consumables. Such full automation of DNA extraction evaluated and in use for sepsis diagnostics is yet not available. Here, we present protocols for the semiautomated isolation of microbial DNA from blood culture and low- and high-volume blood samples. The protocols include a manual pretreatment step followed by automated extraction and purification of microbial DNA.

Microbial Diversity Analysis of the Bacterial and Archaeal Population in Present Day Stromatolites

NASA Technical Reports Server (NTRS)

Ortega, Maya C.

2011-01-01

Stromatolites are layered sedimentary structures resulting from microbial mat communities that remove carbon dioxide from their environment and biomineralize it as calcium carbonate. Although prevalent in the fossil record, stromatolites are rare in the modem world and are only found in a few locations including Highbome Cay in the Bahamas. The stromatolites found at this shallow marine site are analogs to ancient microbial mat ecosystems abundant in the Precambrian period on ancient Earth. To understand how stromatolites form and develop, it is important to identify what microorganisms are present in these mats, and how these microbes contribute to geological structure. These results will provide insight into the molecular and geochemical processes of microbial communities that prevailed on ancient Earth. Since stromatolites are formed by lithifying microbial mats that are able to mineralize calcium carbonate, understanding the biological mechanisms involved may lead to the development of carbon sequestration technologies that will be applicable in human spaceflight, as well as improve our understanding of global climate and its sustainability. The objective of my project was to analyze the archaeal and bacterial dIversity in stromatolites from Highborn Cay in the Bahamas. The first step in studying the molecular processes that the microorganisms carry out is to ascertain the microbial complexity within the mats, which includes identifying and estimating the numbers of different microbes that comprise these mats.

The role of microbial low-molecular-weight autoregulatory factors (alkylhydroxybenzenes) in resistance of microorganisms to radiation and heat shock

NASA Astrophysics Data System (ADS)

El-Registan, Galina I.; Mulyukin, Andrey L.; Nikolaev, Yuri A.; Stepanenko, Irina Yu.; Kozlova, Alla N.; Martirosova, Elena I.; Shanenko, Elena F.; Strakhovskaya, Marina G.; Revina, Aleksandra A.

Low-molecular-weight cell-to-cell communication factors are produced by various pro- and eukaryotes and involved in autoregulation of the growth and development of microbial cultures. As for some bacterial and yeast species, these factors were identified as isomers and homologues of alkylhydroxybenzenes (AHB). Depending on the concentration, they participate in controlling the transition to stationary phase, entering the resting state, and stress resistance of vegetative cells to gamma-irradiation, photooxidation (singlet oxygen), and heat shock. Chemical analogues of microbial AHB protected microbial cultures from stressful situations and exerted (1) the stabilizing activity toward macromolecules and (2) the ability to scavenge active oxygen species. The stabilizing effect of AHBs resulted from their complex formation with protected macromolecules due to intermolecular hydrogen bonds, hydrophobic and electrostatic interactions and was demonstrated on models of individual enzymes (trypsin). Particularly, AHBs protected the yeast from the action of (a) active oxygen species formed during gamma-irradiation (500 Gy, 1.96 Gy/s) or (b) singlet oxygen generated in cells photosensitized by chlorin e 6 (10 μg/L). It is important that microbial AHBs were not species-specific and defended cultured microbial and animal cells from the action of organic toxicants. The use of AHBs as protectants and adaptogens is discussed as well as perspectives of further investigations.

Microorganisms with a Taste for Vanilla: Microbial Ecology of Traditional Indonesian Vanilla Curing

PubMed Central

Röling, Wilfred F. M.; Kerler, Josef; Braster, Martin; Apriyantono, Anton; Stam, Hein; van Verseveld, Henk W.

2001-01-01

The microbial ecology of traditional postharvesting processing of vanilla beans (curing) was examined using a polyphasic approach consisting of conventional cultivation, substrate utilization-based and molecular identification of isolates, and cultivation-independent community profiling by 16S ribosomal DNA based PCR-denaturing gradient gel electrophoresis. At two different locations, a batch of curing beans was monitored. In both batches a major shift in microbial communities occurred after short-term scalding of the beans in hot water. Fungi and yeast disappeared, although regrowth of fungi occurred in one batch during a period in which process conditions were temporarily not optimal. Conventional plating showed that microbial communities consisting of thermophilic and thermotolerant bacilli (mainly closely related to Bacillus subtilis, B. licheniformis,, and B. smithii) developed under the high temperatures (up to 65°C) that were maintained for over a week after scalding. Only small changes in the communities of culturable bacteria occurred after this period. Molecular analysis revealed that a proportion of the microbial communities could not be cultured on conventional agar medium, especially during the high-temperature period. Large differences between both batches were observed in the numbers of microorganisms, in species composition, and in the enzymatic abilities of isolated bacteria. These large differences indicate that the effects of microbial activities on the development of vanilla flavor could be different for each batch of cured vanilla beans. PMID:11319073

Isolation of a thermophilic bacterium capable of low-molecular-weight polyethylene degradation.

PubMed

Jeon, Hyun Jeong; Kim, Mal Nam

2013-02-01

A thermophilic bacterium capable of low-molecular-weight polyethylene (LMWPE) degradation was isolated from a compost sample, and was identified as Chelatococcus sp. E1, through sequencing of the 16S rRNA gene. LMWPE was prepared by thermal degradation of commercial PE in a strict nitrogen atmosphere. LMWPE with a weight-average-molecular-weight (Mw) in the range of 1,700-23,700 was noticeably mineralized into CO(2) by the bacterium. The biodegradability of LMWPE decreased as the Mw increased. The low molecular weight fraction of LMWPE decreased significantly as a result of the degradation process, and thereby both the number-average-molecular-weight and Mw increased after biodegradation. The polydispersity of LMWPE was either narrowed or widened, depending on the initial Mw of LMWPE, due to the preferential elimination of the low molecular weight fraction, in comparison to the high molecular weight portion. LMWPE free from an extremely low molecular weight fraction was also mineralized by the strain at a remarkable rate, and FTIR peaks assignable to C-O stretching appeared as a result of microbial action. The FTIR peaks corresponding to alkenes also became more intense, indicating that dehydrogenations occurred concomitantly with microbial induced oxidation.

High Carbon Use Efficiency is Not Explained by Production of Storage Compounds

NASA Astrophysics Data System (ADS)

Dijkstra, Paul; van Groenigen, Kees-Jan

2015-04-01

The efficiency with which microbes use substrate to make new microbial biomass (Carbon Use Efficiency or CUE; mol C / mol C) is an important variable in soil and ecosystem C cycling models. Estimates of CUE in soil microbial communities vary widely. It has been hypothesized that high values of CUE are associated with production of storage compounds following a sudden increases in substrate availability during CUE measurements. In that case, these high CUE values would not be representative for balanced microbial growth (i.e. the production of all compounds needed to make new microbial cells). To test this hypothesis, we added position-specific 13C-labeled glucose isotopomers in parallel incubations of a ponderosa pine and piñon-juniper soil. We compared the measured pattern of CO2 release for the six glucose C atoms with patterns of CO2 production expected for balanced growth with a low, medium, or high CUE, and with CO2 production patterns associated with production of storage compounds (glycogen, lipids, or polyhydroxybutyrate). The measured position-specific CO2 production did not match that for production of glycogen, lipids, or polyhydroxybutyrate, but agreed closely with that expected for balanced growth at high CUE and high pentose phosphate pathway activity. We conclude that soil microbial communities utilize glucose substrate for biomass growth with high CUE, and that addition of small amounts of 13C-labeled glucose tracers do not affect CUE or induce storage compounds production. We submit that the measurement of position-specific CO2 production offers a quick and easy way to test biochemically explicit hypotheses concerning microbial growth metabolism.

Gut microbiota and cardiometabolic outcomes: influence of dietary patterns and their associated components.

PubMed

Wong, Julia M W

2014-07-01

Many dietary patterns have been associated with cardiometabolic risk reduction. A commonality between these dietary patterns is the emphasis on plant-based foods. Studies in individuals who consume vegetarian and vegan diets have shown a reduced risk of cardiovascular events and incidence of diabetes. Plant-based dietary patterns may promote a more favorable gut microbial profile. Such diets are high in dietary fiber and fermentable substrate (ie, nondigestible or undigested carbohydrates), which are sources of metabolic fuel for gut microbial fermentation and, in turn, result in end products that may be used by the host (eg, short-chain fatty acids). These end products may have direct or indirect effects on modulating the health of their host. Modulation of the gut microbiota is an area of growing interest, and it has been suggested to have the potential to reduce risk factors associated with chronic diseases. Examples of dietary components that alter the gut microbial composition include prebiotics and resistant starches. Emerging evidence also suggests a potential link between interindividual differences in the gut microbiota and variations in physiology or predisposition to certain chronic disease risk factors. Alterations in the gut microbiota may also stimulate certain populations and may assist in biotransformation of bioactive components found in plant foods. Strategies to modify microbial communities may therefore provide a novel approach in the treatment and management of chronic diseases. © 2014 American Society for Nutrition.

Development of a microbial high-throughput screening instrument based on elastic light scatter patterns

NASA Astrophysics Data System (ADS)

Bae, Euiwon; Patsekin, Valery; Rajwa, Bartek; Bhunia, Arun K.; Holdman, Cheryl; Davisson, V. Jo; Hirleman, E. Daniel; Robinson, J. Paul

2012-04-01

A microbial high-throughput screening (HTS) system was developed that enabled high-speed combinatorial studies directly on bacterial colonies. The system consists of a forward scatterometer for elastic light scatter (ELS) detection, a plate transporter for sample handling, and a robotic incubator for automatic incubation. To minimize the ELS pattern-capturing time, a new calibration plate and correction algorithms were both designed, which dramatically reduced correction steps during acquisition of the circularly symmetric ELS patterns. Integration of three different control software programs was implemented, and the performance of the system was demonstrated with single-species detection for library generation and with time-resolved measurement for understanding ELS colony growth correlation, using Escherichia coli and Listeria. An in-house colony-tracking module enabled researchers to easily understand the time-dependent variation of the ELS from identical colony, which enabled further analysis in other biochemical experiments. The microbial HTS system provided an average scan time of 4.9 s per colony and the capability of automatically collecting more than 4000 ELS patterns within a 7-h time span.

Anoxia stimulates microbially catalyzed metal release from Animas River sediments

DOE PAGES

Saup, Casey M.; Williams, Kenneth H.; Rodríguez-Freire, Lucía; ...

2017-03-06

The Gold King Mine spill in August 2015 released 11 million liters of metal-rich mine waste to the Animas River watershed, an area that has been previously exposed to historical mining activity spanning more than a century. Although adsorption onto fluvial sediments was responsible for rapid immobilization of a significant fraction of the spill-associated metals, patterns of longer-term mobility are poorly constrained. Metals associated with river sediments collected downstream of the Gold King Mine in August 2015 exhibited distinct presence and abundance patterns linked to location and mineralogy. Simulating riverbed burial and development of anoxic conditions, sediment microcosm experiments amendedmore » with Animas River dissolved organic carbon revealed the release of specific metal pools coupled to microbial Fe- and SO 4 2-reduction. Results suggest that future sedimentation and burial of riverbed materials may drive longer-term changes in patterns of metal remobilization linked to anaerobic microbial metabolism, potentially driving decreases in downstream water quality. Such patterns emphasize the need for long-term water monitoring efforts in metal-impacted watersheds.« less

Anoxia stimulates microbially catalyzed metal release from Animas River sediments

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

Saup, Casey M.; Williams, Kenneth H.; Rodríguez-Freire, Lucía

The Gold King Mine spill in August 2015 released 11 million liters of metal-rich mine waste to the Animas River watershed, an area that has been previously exposed to historical mining activity spanning more than a century. Although adsorption onto fluvial sediments was responsible for rapid immobilization of a significant fraction of the spill-associated metals, patterns of longer-term mobility are poorly constrained. Metals associated with river sediments collected downstream of the Gold King Mine in August 2015 exhibited distinct presence and abundance patterns linked to location and mineralogy. Simulating riverbed burial and development of anoxic conditions, sediment microcosm experiments amendedmore » with Animas River dissolved organic carbon revealed the release of specific metal pools coupled to microbial Fe- and SO 4 2-reduction. Results suggest that future sedimentation and burial of riverbed materials may drive longer-term changes in patterns of metal remobilization linked to anaerobic microbial metabolism, potentially driving decreases in downstream water quality. Such patterns emphasize the need for long-term water monitoring efforts in metal-impacted watersheds.« less

A critical evaluation of ecological indices for the comparative analysis of microbial communities based on molecular datasets.

PubMed

Lucas, Rico; Groeneveld, Jürgen; Harms, Hauke; Johst, Karin; Frank, Karin; Kleinsteuber, Sabine

2017-01-01

In times of global change and intensified resource exploitation, advanced knowledge of ecophysiological processes in natural and engineered systems driven by complex microbial communities is crucial for both safeguarding environmental processes and optimising rational control of biotechnological processes. To gain such knowledge, high-throughput molecular techniques are routinely employed to investigate microbial community composition and dynamics within a wide range of natural or engineered environments. However, for molecular dataset analyses no consensus about a generally applicable alpha diversity concept and no appropriate benchmarking of corresponding statistical indices exist yet. To overcome this, we listed criteria for the appropriateness of an index for such analyses and systematically scrutinised commonly employed ecological indices describing diversity, evenness and richness based on artificial and real molecular datasets. We identified appropriate indices warranting interstudy comparability and intuitive interpretability. The unified diversity concept based on 'effective numbers of types' provides the mathematical framework for describing community composition. Additionally, the Bray-Curtis dissimilarity as a beta-diversity index was found to reflect compositional changes. The employed statistical procedure is presented comprising commented R-scripts and example datasets for user-friendly trial application. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Molecular methods for pathogen and microbial community detection and characterization: current and potential application in diagnostic microbiology.

PubMed

Sibley, Christopher D; Peirano, Gisele; Church, Deirdre L

2012-04-01

Clinical microbiology laboratories worldwide have historically relied on phenotypic methods (i.e., culture and biochemical tests) for detection, identification and characterization of virulence traits (e.g., antibiotic resistance genes, toxins) of human pathogens. However, limitations to implementation of molecular methods for human infectious diseases testing are being rapidly overcome allowing for the clinical evaluation and implementation of diverse technologies with expanding diagnostic capabilities. The advantages and limitation of molecular techniques including real-time polymerase chain reaction, partial or whole genome sequencing, molecular typing, microarrays, broad-range PCR and multiplexing will be discussed. Finally, terminal restriction fragment length polymorphism (T-RFLP) and deep sequencing are introduced as technologies at the clinical interface with the potential to dramatically enhance our ability to diagnose infectious diseases and better define the epidemiology and microbial ecology of a wide range of complex infections. Copyright © 2012 Elsevier B.V. All rights reserved.

Ab initio genotype–phenotype association reveals intrinsic modularity in genetic networks

PubMed Central

Slonim, Noam; Elemento, Olivier; Tavazoie, Saeed

2006-01-01

Microbial species express an astonishing diversity of phenotypic traits, behaviors, and metabolic capacities. However, our molecular understanding of these phenotypes is based almost entirely on studies in a handful of model organisms that together represent only a small fraction of this phenotypic diversity. Furthermore, many microbial species are not amenable to traditional laboratory analysis because of their exotic lifestyles and/or lack of suitable molecular genetic techniques. As an adjunct to experimental analysis, we have developed a computational information-theoretic framework that produces high-confidence gene–phenotype predictions using cross-species distributions of genes and phenotypes across 202 fully sequenced archaea and eubacteria. In addition to identifying the genetic basis of complex traits, our approach reveals the organization of these genes into generic preferentially co-inherited modules, many of which correspond directly to known enzymatic pathways, molecular complexes, signaling pathways, and molecular machines. PMID:16732191

Seasonal Changes in Bacterial and Archaeal Gene Expression Patterns across Salinity Gradients in the Columbia River Coastal Margin

PubMed Central

Smith, Maria W.; Herfort, Lydie; Tyrol, Kaitlin; Suciu, Dominic; Campbell, Victoria; Crump, Byron C.; Peterson, Tawnya D.; Zuber, Peter; Baptista, Antonio M.; Simon, Holly M.

2010-01-01

Through their metabolic activities, microbial populations mediate the impact of high gradient regions on ecological function and productivity of the highly dynamic Columbia River coastal margin (CRCM). A 2226-probe oligonucleotide DNA microarray was developed to investigate expression patterns for microbial genes involved in nitrogen and carbon metabolism in the CRCM. Initial experiments with the environmental microarrays were directed toward validation of the platform and yielded high reproducibility in multiple tests. Bioinformatic and experimental validation also indicated that >85% of the microarray probes were specific for their corresponding target genes and for a few homologs within the same microbial family. The validated probe set was used to query gene expression responses by microbial assemblages to environmental variability. Sixty-four samples from the river, estuary, plume, and adjacent ocean were collected in different seasons and analyzed to correlate the measured variability in chemical, physical and biological water parameters to differences in global gene expression profiles. The method produced robust seasonal profiles corresponding to pre-freshet spring (April) and late summer (August). Overall relative gene expression was high in both seasons and was consistent with high microbial abundance measured by total RNA, heterotrophic bacterial production, and chlorophyll a. Both seasonal patterns involved large numbers of genes that were highly expressed relative to background, yet each produced very different gene expression profiles. April patterns revealed high differential gene expression in the coastal margin samples (estuary, plume and adjacent ocean) relative to freshwater, while little differential gene expression was observed along the river-to-ocean transition in August. Microbial gene expression profiles appeared to relate, in part, to seasonal differences in nutrient availability and potential resource competition. Furthermore, our results suggest that highly-active particle-attached microbiota in the Columbia River water column may perform dissimilatory nitrate reduction (both dentrification and DNRA) within anoxic particle microniches. PMID:20967204

Lineage-specific responses of microbial communities to environmental change.

PubMed

Youngblut, Nicholas D; Shade, Ashley; Read, Jordan S; McMahon, Katherine D; Whitaker, Rachel J

2013-01-01

A great challenge facing microbial ecology is how to define ecologically relevant taxonomic units. To address this challenge, we investigated how changing the definition of operational taxonomic units (OTUs) influences the perception of ecological patterns in microbial communities as they respond to a dramatic environmental change. We used pyrosequenced tags of the bacterial V2 16S rRNA region, as well as clone libraries constructed from the cytochrome oxidase C gene ccoN, to provide additional taxonomic resolution for the common freshwater genus Polynucleobacter. At the most highly resolved taxonomic scale, we show that distinct genotypes associated with the abundant Polynucleobacter lineages exhibit divergent spatial patterns and dramatic changes over time, while the also abundant Actinobacteria OTUs are highly coherent. This clearly demonstrates that different bacterial lineages demand different taxonomic definitions to capture ecological patterns. Based on the temporal distribution of highly resolved taxa in the hypolimnion, we demonstrate that change in the population structure of a single genotype can provide additional insight into the mechanisms of community-level responses. These results highlight the importance and feasibility of examining ecological change in microbial communities across taxonomic scales while also providing valuable insight into the ecological characteristics of ecologically coherent groups in this system.

Two-dimensional distribution of microbial activity and flow patterns within naturally fractured chalk.

PubMed

Arnon, Shai; Ronen, Zeev; Adar, Eilon; Yakirevich, Alexander; Nativ, Ronit

2005-10-01

The two-dimensional distribution of flow patterns and their dynamic change due to microbial activity were investigated in naturally fractured chalk cores. Long-term biodegradation experiments were conducted in two cores ( approximately 20 cm diameter, 31 and 44 cm long), intersected by a natural fracture. 2,4,6-tribromophenol (TBP) was used as a model contaminant and as the sole carbon source for aerobic microbial activity. The transmissivity of the fractures was continuously reduced due to biomass accumulation in the fracture concurrent with TBP biodegradation. From multi-tracer experiments conducted prior to and following the microbial activity, it was found that biomass accumulation causes redistribution of the preferential flow channels. Zones of slow flow near the fracture inlet were clogged, thus further diverting the flow through zones of fast flow, which were also partially clogged. Quantitative evaluation of biodegradation and bacterial counts supported the results of the multi-tracer tests, indicating that most of the bacterial activity occurs close to the inlet. The changing flow patterns, which control the nutrient supply, resulted in variations in the concentrations of the chemical constituents (TBP, bromide and oxygen), used as indicators of biodegradation.

Nitrogen controls spatial and temporal variability of substrate-induced respiration within seven years of bare fallow

NASA Astrophysics Data System (ADS)

Meyer, Nele; Bornemann, Ludger; Welp, Gerhard; Amelung, Wulf

2015-04-01

Bare fallow management goes along with lacking supply of new C sources; yet, little is known on the spatio-temporal controls of microbial adaptation processes. Here we hypothesized that microbial activity parameters decline upon bare fallow but that their spatial patterns are increasingly controlled by nutrient status as fallow management proceeds. To test these hypotheses, we investigated spatial and temporal patterns of substrate-induced respiration (SIR) and basal respiration curves in an arable field after 1, 3, and 7 years of bare fallow but with large within-field heterogeneity of physicochemical soil parameters. The analyses comprised the contents of SOC, mineral nitrogen (Nmin), particulate organic matter (POM), texture of the fine earth, and the proportion of rock fragments as well as basal respiration and several SIR fitting parameters (microbial biomass, microbial growth rates, peak respiration rates, cumulative CO2 release) each with and without additions of mineral N and P. We also repeated substrate (i.e. glucose) additions following the first SIR measurement. The results revealed that most respiration parameters like basal respiration, microbial biomass, and growth rates showed no or inconsistent responses to spatial and temporal patterns of basic soil properties like SOC, Nmin or texture. However, bare fallow changed the shape of the SIR curves; it developed two distinct microbial growth peaks at advanced stages of fallow, i.e. a delayed CO2 release. Likewise, the maximum respiration rate during the first growth phase declined during 7 years of fallow by 47% but its spatial distribution was always correlated with Nmin contents (r = 0.43 - 0.79). The nutrient additions suggested that these changes in SIR curves were caused by N deficiency; the first peak increased after N additions while the second growth phase diminished. Intriguingly, a repeated glucose addition had a similar effect on the SIR curves as the glucose+N addition. Thus, N deficiency apparently subsided during SIR. The results suggested that soil microbes acquire nitrogen from refractory SOM pools (i.e. microbial nitrogen mining). Hence, there was no significant decrease in cumulative CO2 evolution with proceeding time of fallow. As soil microorganisms maintained their functionality there was no overall loss in potential microbial activity, irrespective of the spatial patterns of other soil properties.

Effect of Substrate Conversion on Performance of Microbial Fuel Cells and Anodic Microbial Communities.

PubMed

Zhao, Yang-Guo; Zhang, Yi; She, Zonglian; Shi, Yue; Wang, Min; Gao, Mengchun; Guo, Liang

2017-09-01

Performance of microbial fuel cells (MFCs) was monitored during the influent nutrient change from lactate to glucose/acetate/propionate and then to lactate. Meanwhile, anodic microbial communities were characterized by culture-independent molecular biotechnologies. Results showed MFC performance recovered rapidly when the lactate was replaced by one of its metabolic intermediates acetate, while it needed a longer time to recover if lactate substrate was converted to glucose/propionate or acetate to lactate. Secondary lactate feed enhanced the enrichment of bacterial populations dominating in first lactate feed. Electricity-producing bacteria, Geobacter spp., and beneficial helpers, Anaeromusa spp. and Pseudomonas spp., revived from a low abundance as lactate secondary supply, but microbial communities were hard to achieve former profiles in structure and composition. Hence, microbial community profiles tended to recover when outside environmental condition were restored. Different substrates selected unique functional microbial populations.

Drilling Fluid Contamination during Riser Drilling Quantified by Chemical and Molecular Tracers

NASA Astrophysics Data System (ADS)

Inagaki, F.; Lever, M. A.; Morono, Y.; Hoshino, T.

2012-12-01

Stringent contamination controls are essential to any type of microbiological investigation, and are particularly challenging in ocean drilling, where samples are retrieved from hundreds of meters below the seafloor. In summer 2012, Integrated Ocean Drilling Expedition 337 aboard the Japanese vessel Chikyu pioneered the use of chemical tracers in riser drilling while exploring the microbial ecosystem of coalbeds 2 km below the seafloor off Shimokita, Japan. Contamination tests involving a perfluorocarbon tracer that had been successfully used during past riserless drilling expeditions were complemented by DNA-based contamination tests. In the latter, likely microbial contaminants were targeted via quantitative polymerase chain reaction assays using newly designed, group-specific primers. Target groups included potential indicators of (a) drilling mud viscosifiers (Xanthomonas, Halomonas), (b) anthropogenic wastewater (Bifidobacterium, Blautia, Methanobrevibacter), and (c) surface seawater (SAR 11, Marine Group I Archaea). These target groups were selected based on past evidence suggesting viscosifiers, wastewater, and seawater as the main sources of microbial contamination in cores retrieved by ocean drilling. Analyses of chemical and molecular tracers are in good agreement, and indicate microorganisms associated with mud viscosifiers as the main contaminants during riser drilling. These same molecular analyses are then extended to subseafloor samples obtained during riserless drilling operations. General strategies to further reduce the risk of microbial contamination during riser and riserless drilling operations are discussed.

Predicting Biological Information Flow in a Model Oxygen Minimum Zone

NASA Astrophysics Data System (ADS)

Louca, S.; Hawley, A. K.; Katsev, S.; Beltran, M. T.; Bhatia, M. P.; Michiels, C.; Capelle, D.; Lavik, G.; Doebeli, M.; Crowe, S.; Hallam, S. J.

2016-02-01

Microbial activity drives marine biochemical fluxes and nutrient cycling at global scales. Geochemical measurements as well as molecular techniques such as metagenomics, metatranscriptomics and metaproteomics provide great insight into microbial activity. However, an integration of molecular and geochemical data into mechanistic biogeochemical models is still lacking. Recent work suggests that microbial metabolic pathways are, at the ecosystem level, strongly shaped by stoichiometric and energetic constraints. Hence, models rooted in fluxes of matter and energy may yield a holistic understanding of biogeochemistry. Furthermore, such pathway-centric models would allow a direct consolidation with meta'omic data. Here we present a pathway-centric biogeochemical model for the seasonal oxygen minimum zone in Saanich Inlet, a fjord off the coast of Vancouver Island. The model considers key dissimilatory nitrogen and sulfur fluxes, as well as the population dynamics of the genes that mediate them. By assuming a direct translation of biocatalyzed energy fluxes to biosynthesis rates, we make predictions about the distribution and activity of the corresponding genes. A comparison of the model to molecular measurements indicates that the model explains observed DNA, RNA, protein and cell depth profiles. This suggests that microbial activity in marine ecosystems such as oxygen minimum zones is well described by DNA abundance, which, in conjunction with geochemical constraints, determines pathway expression and process rates. Our work further demonstrates how meta'omic data can be mechanistically linked to environmental redox conditions and biogeochemical processes.

Contrasting Microbial Community Assembly Hypotheses: A Reconciling Tale from the Río Tinto

PubMed Central

Palacios, Carmen; Zettler, Erik; Amils, Ricardo; Amaral-Zettler, Linda

2008-01-01

Background The Río Tinto (RT) is distinguished from other acid mine drainage systems by its natural and ancient origins. Microbial life from all three domains flourishes in this ecosystem, but bacteria dominate metabolic processes that perpetuate environmental extremes. While the patchy geochemistry of the RT likely influences the dynamics of bacterial populations, demonstrating which environmental variables shape microbial diversity and unveiling the mechanisms underlying observed patterns, remain major challenges in microbial ecology whose answers rely upon detailed assessments of community structures coupled with fine-scale measurements of physico-chemical parameters. Methodology/Principal Findings By using high-throughput environmental tag sequencing we achieved saturation of richness estimators for the first time in the RT. We found that environmental factors dictate the distribution of the most abundant taxa in this system, but stochastic niche differentiation processes, such as mutation and dispersal, also contribute to observed diversity patterns. Conclusions/Significance We predict that studies providing clues to the evolutionary and ecological processes underlying microbial distributions will reconcile the ongoing debate between the Baas Becking vs. Hubbell community assembly hypotheses. PMID:19052647

Contrasting microbial community assembly hypotheses: a reconciling tale from the Río Tinto.

PubMed

Palacios, Carmen; Zettler, Erik; Amils, Ricardo; Amaral-Zettler, Linda

2008-01-01

The Río Tinto (RT) is distinguished from other acid mine drainage systems by its natural and ancient origins. Microbial life from all three domains flourishes in this ecosystem, but bacteria dominate metabolic processes that perpetuate environmental extremes. While the patchy geochemistry of the RT likely influences the dynamics of bacterial populations, demonstrating which environmental variables shape microbial diversity and unveiling the mechanisms underlying observed patterns, remain major challenges in microbial ecology whose answers rely upon detailed assessments of community structures coupled with fine-scale measurements of physico-chemical parameters. By using high-throughput environmental tag sequencing we achieved saturation of richness estimators for the first time in the RT. We found that environmental factors dictate the distribution of the most abundant taxa in this system, but stochastic niche differentiation processes, such as mutation and dispersal, also contribute to observed diversity patterns. We predict that studies providing clues to the evolutionary and ecological processes underlying microbial distributions will reconcile the ongoing debate between the Baas Becking vs. Hubbell community assembly hypotheses.

Seasonal Patterns in Microbial Community Composition in Denitrifying Bioreactors Treating Subsurface Agricultural Drainage.

PubMed

Porter, Matthew D; Andrus, J Malia; Bartolerio, Nicholas A; Rodriguez, Luis F; Zhang, Yuanhui; Zilles, Julie L; Kent, Angela D

2015-10-01

Denitrifying bioreactors, consisting of water flow control structures and a woodchip-filled trench, are a promising approach for removing nitrate from agricultural subsurface or tile drainage systems. To better understand the seasonal dynamics and the ecological drivers of the microbial communities responsible for denitrification in these bioreactors, we employed microbial community "fingerprinting" techniques in a time-series examination of three denitrifying bioreactors over 2 years, looking at bacteria, fungi, and the denitrifier functional group responsible for the final step of complete denitrification. Our analysis revealed that microbial community composition responds to depth and seasonal variation in moisture content and inundation of the bioreactor media, as well as temperature. Using a geostatistical analysis approach, we observed recurring temporal patterns in bacterial and denitrifying bacterial community composition in these bioreactors, consistent with annual cycling. The fungal communities were more stable, having longer temporal autocorrelations, and did not show significant annual cycling. These results suggest a recurring seasonal cycle in the denitrifying bioreactor microbial community, likely due to seasonal variation in moisture content.

Reproducing stone monument photosynthetic-based colonization under laboratory conditions.

PubMed

Miller, Ana Zélia; Laiz, Leonila; Gonzalez, Juan Miguel; Dionísio, Amélia; Macedo, Maria Filomena; Saiz-Jimenez, Cesareo

2008-11-01

In order to understand the biodeterioration process occurring on stone monuments, we analyzed the microbial communities involved in these processes and studied their ability to colonize stones under controlled laboratory experiments. In this study, a natural green biofilm from a limestone monument was cultivated, inoculated on stone probes of the same lithotype and incubated in a laboratory chamber. This incubation system, which exposes stone samples to intermittently sprinkling water, allowed the development of photosynthetic biofilms similar to those occurring on stone monuments. Denaturing gradient gel electrophoresis (DGGE) analysis was used to evaluate the major microbial components of the laboratory biofilms. Cyanobacteria, green microalgae, bacteria and fungi were identified by DNA-based molecular analysis targeting the 16S and 18S ribosomal RNA genes. The natural green biofilm was mainly composed by the Chlorophyta Chlorella, Stichococcus, and Trebouxia, and by Cyanobacteria belonging to the genera Leptolyngbya and Pleurocapsa. A number of bacteria belonging to Alphaproteobacteria, Bacteroidetes and Verrucomicrobia were identified, as well as fungi from the Ascomycota. The laboratory colonization experiment on stone probes showed a colonization pattern similar to that occurring on stone monuments. The methodology described in this paper allowed to reproduce a colonization equivalent to the natural biodeteriorating process.

Glyburide inhibits the Cryopyrin/Nalp3 inflammasome

PubMed Central

Lamkanfi, Mohamed; Mueller, James L.; Vitari, Alberto C.; Misaghi, Shahram; Fedorova, Anna; Deshayes, Kurt; Lee, Wyne P.; Hoffman, Hal M.

2009-01-01

Inflammasomes activate caspase-1 for processing and secretion of the cytokines interleukin-1β (IL-1β) and IL-18. Cryopyrin/NALP3/NLRP3 is an essential component of inflammasomes triggered by microbial ligands, danger-associated molecular patterns (DAMPs), and crystals. Inappropriate Cryopyrin activity has been incriminated in the pathogenesis of gouty arthritis, Alzheimer's, and silicosis. Therefore, inhibitors of the Nalp3 inflammasome offer considerable therapeutic promise. In this study, we show that the type 2 diabetes drug glyburide prevented activation of the Cryopyrin inflammasome. Glyburide's cyclohexylurea group, which binds to adenosine triphosphatase (ATP)–sensitive K+ (KATP) channels for insulin secretion, is dispensable for inflammasome inhibition. Macrophages lacking KATP subunits or ATP-binding cassette transporters also activate the Cryopyrin inflammasome normally. Glyburide analogues inhibit ATP- but not hypothermia-induced IL-1β secretion from human monocytes expressing familial cold-associated autoinflammatory syndrome–associated Cryopyrin mutations, thus suggesting that inhibition occurs upstream of Cryopyrin. Concurrent with the role of Cryopyrin in endotoxemia, glyburide significantly delays lipopolysaccharide-induced lethality in mice. Therefore, glyburide is the first identified compound to prevent Cryopyrin activation and microbial ligand-, DAMP-, and crystal-induced IL-1β secretion. PMID:19805629

Glyburide inhibits the Cryopyrin/Nalp3 inflammasome.

PubMed

Lamkanfi, Mohamed; Mueller, James L; Vitari, Alberto C; Misaghi, Shahram; Fedorova, Anna; Deshayes, Kurt; Lee, Wyne P; Hoffman, Hal M; Dixit, Vishva M

2009-10-05

Inflammasomes activate caspase-1 for processing and secretion of the cytokines interleukin-1beta (IL-1beta) and IL-18. Cryopyrin/NALP3/NLRP3 is an essential component of inflammasomes triggered by microbial ligands, danger-associated molecular patterns (DAMPs), and crystals. Inappropriate Cryopyrin activity has been incriminated in the pathogenesis of gouty arthritis, Alzheimer's, and silicosis. Therefore, inhibitors of the Nalp3 inflammasome offer considerable therapeutic promise. In this study, we show that the type 2 diabetes drug glyburide prevented activation of the Cryopyrin inflammasome. Glyburide's cyclohexylurea group, which binds to adenosine triphosphatase (ATP)-sensitive K(+) (K(ATP)) channels for insulin secretion, is dispensable for inflammasome inhibition. Macrophages lacking K(ATP) subunits or ATP-binding cassette transporters also activate the Cryopyrin inflammasome normally. Glyburide analogues inhibit ATP- but not hypothermia-induced IL-1beta secretion from human monocytes expressing familial cold-associated autoinflammatory syndrome-associated Cryopyrin mutations, thus suggesting that inhibition occurs upstream of Cryopyrin. Concurrent with the role of Cryopyrin in endotoxemia, glyburide significantly delays lipopolysaccharide-induced lethality in mice. Therefore, glyburide is the first identified compound to prevent Cryopyrin activation and microbial ligand-, DAMP-, and crystal-induced IL-1beta secretion.

Direct effects of temperature on forest nitrogen cycling revealed through analysis of long-term watershed records

Treesearch

E.N. Jack Brookshire; Stefan Gerber; Jackson R. Webster; James M. Vose; Wayne T. Swank

2010-01-01

The microbial conversion of organic nitrogen (N) to plant available forms is a critical determinant of plant growth and carbon sequestration in forests worldwide. In temperate zones, microbial activity is coupled to variations in temperature, yet at the ecosystem level, microbial N mineralization seems to play a minor role in determining patterns of N loss. Rather, N...

Microbial Communities as Environmental Indicators of Ecological Disturbance in Restored Carbonate Fen-Results of 10 Years of Studies.

PubMed

Mieczan, Tomasz; Tarkowska-Kukuryk, Monika

2017-08-01

Interactions between bacteria and protists are essential to the ecosystem ecology of fens. Until now, however, there has been almost no information on how restoration procedures in carbonate fens affect the functioning of microbial food webs. Changes in vegetation patterns resulting from restoration may take years to be observed, whereas microbial processes display effects even after short-term exposure to changes in environmental conditions caused by restoration. Therefore, microbial processes and patterns can be used as sensitive indicators of changes in environmental conditions. The present study attempts to verify the hypothesis that the species richness and abundance of microbial loop components would differ substantially before and after restoration. The effect of restoration processes on the functioning of the food web was investigated for a 10 years in a carbonate-rich fen, before and after restoration. The restoration procedure (particularly the improvement in hydrological conditions) distinctly modified the taxonomic composition and functioning of microbial food webs. This is reflected in the increased abundance and diversity of testate amoeba, i.e. top predators, within the microbial food web and in the pronounced increase in the abundance of bacteria. This study suggests potential use of microbial loop components as bio-indicators and bio-monitoring tools for hydrological status of fens and concentrations of nutrients. Better understanding of what regulates microbial populations and activity in fens and unravelling of these fundamental mechanisms are particularly critical in order to more accurately predict how fens will respond to global change or anthropogenic disturbances.

Molecular Phylogenetic Analysis of Archaeal Intron-Containing Genes Coding for rRNA Obtained from a Deep-Subsurface Geothermal Water Pool

PubMed Central

Takai, Ken; Horikoshi, Koki

1999-01-01

Molecular phylogenetic analysis of a naturally occurring microbial community in a deep-subsurface geothermal environment indicated that the phylogenetic diversity of the microbial population in the environment was extremely limited and that only hyperthermophilic archaeal members closely related to Pyrobaculum were present. All archaeal ribosomal DNA sequences contained intron-like sequences, some of which had open reading frames with repeated homing-endonuclease motifs. The sequence similarity analysis and the phylogenetic analysis of these homing endonucleases suggested the possible phylogenetic relationship among archaeal rRNA-encoded homing endonucleases. PMID:10584021

Dissolved organic matter (DOM) in pore water of Arctic Ocean sediments: linking DOM molecular composition with microbial community structure

NASA Astrophysics Data System (ADS)

Rossel, P. E.; Bienhold, C.; Boetius, A.; Dittmar, T.

2016-02-01

Marine organic matter (OM) that sinks from surface waters to the seafloor is the energy and carbon source for benthic communities. These communities produce dissolved organic matter (DOM) in the process of remineralization, enriching the sediment porewater with fresh DOM compounds. In the Arctic Ocean, primary production is limited by nutrients and light and is thus strongly influenced by sea ice cover. Ice cover is expected to further decrease due to global warming, which may have important consequences for primary production and the quantity and quality of OM exported to the seafloor. This study focused on: 1) the molecular composition of the DOM in sediment pore waters of the deep Eurasian Arctic basins, 2) whether there is any relation between Arctic Ocean ice cover and DOM composition and 3) whether the DOM composition correlates with microbial community structure. Molecular data, obtained via 15 Tesla Fourier transform ion cyclotron resonance mass spectrometry, were statistically correlated with environmental parameters. The productive ice margin stations showed higher abundances of molecular formulae of peptides, unsaturated aliphatics and saturated fatty acids. This molecular trend is indicative of fresh OM and phytodetritus deposition, compared to the northernmost, ice-covered stations which had stronger aromatic signals. Benthic bacterial community structure, as assessed with the fingerprinting method ARISA, was significantly correlated with DOM molecular composition. Further analyses using Illumina next-generation sequencing will enable the taxonomic identification of specific bacterial groups and their interdependence with DOM compounds. This study contributes to the understanding of the coupling between Arctic Ocean productivity and its depositional regime, and provides first insights into potential links between microbial community structure and DOM molecular composition in Arctic sediments

Final Technical Report to DOE for the Award DE-SC0004601

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

Zhou, Jizhong

Understanding the responses, adaptations and feedback mechanisms of biological communities to climate change is critical to project future state of earth and climate systems. Although significant amount of knowledge is available on the feedback responses of aboveground communities to climate change, little is known about the responses of belowground microbial communities due to the challenges in analyzing soil microbial community structure. Thus the goal overall goal of this study is to provide system-level, predictive mechanistic understanding of the temperature sensitivity of soil carbon (C) decomposition to climate warming by using cutting-edge integrated metagenomic technologies. Towards this goal, the following fourmore » objectives will be pursued: (i) To determine phylogenetic composition and metabolic diversity of microbial communities in the temperate grassland and tundra ecosystems; (ii) To delineate the responses of microbial community structure, functions and activities to climate change in the temperate grassland and tundra ecosystems; (iii) To determine the temperature sensitivity of microbial respiration in soils with different mixtures of labile versus recalcitrant C, and the underlying microbiological basis for temperature sensitivity of these pools; and (iv) To synthesize all experimental data for revealing microbial control of ecosystem carbon processes in responses to climate change. We have achieved our goals for all four proposed objectives. First, we determined the phylogenetic composition and metabolic diversity of microbial communities in the temperate grassland and tundra ecosystems. For this objective, we have developed a novel phasing amplicon sequencing (PAS) approach for MiSeq sequencing of amplicons. This approach has been used for sequencing various phylogenetic and functional genes related to ecosystem functioning. A comprehensive functional gene array (e.g., GeoChip 5.0) has also been developed and used for soil microbial community analysis in this study. In addition, shot-gun metagenome sequencing along with the above approaches have been used to understand the phylogenetic and functional diversity, composition, and structure of soil microbial communities in both temperature grassland and tundra ecosystems. Second, we determined the response of soil microbial communities to climate warming in both temperate grassland and tundra ecosystems using various methods. Our major findings are: (i) Microorganisms are very rapid to respond to climate warming in the tundra ecosystem, AK, which is vulnerable, too. (ii) Climate warming also significantly shifted the metabolic diversity, composition and structure of microbial communities, and key metabolic pathways related to carbon turnover, such as cellulose degradation (~13%) and CO2 production (~10%), and to nitrogen cycling, including denitrification (~12%) were enriched by warming. (iii) Warming also altered the expression patterns of microbial functional genes important to ecosystem functioning and stability through GeoChip and metatranscriptomic analysis of soil microbial communities at the OK site. Third, we analyzed temperature sensitivity of C decomposition to climate warming for both AK and OK soils through laboratory incubations. Key results include: (i) Alaska tundra soils showed that after one year of incubation, CT in the top 15 cm could be as high as 25% and 15% of the initial soil C content at 25°C and 15°C incubations, respectively. (ii) analysis of 456 incubated soil samples with 16S rRNA gene, ITS and GeoChip hybridization showed that warming shifted the phylogenretic and functional diversity, composition, structure and metabolic potential of soil microbial communities, and at different stages of incubation, key populations and functional genes significantly changed along with soil substrate changes. Functional gene diversity and functional genes for degrading labile C components decrease along incubation when labile C components are exhausting, but the genes related to degrading recalcitrant C increase. These molecular data will be directly used for modeling. Fourth, we have developed novel approaches to integrate and model experimental data to understand microbial control of ecosystem C processes in response to climate change. We compared different methods to calculate Q10 for estimating temperature sensitivity, and new approaches for Q10 calculation and molecular ecological network analysis were also developed. Using those newly developed approaches, our result indicated that Q10s increased with the recalcitrance of C pools, suggesting that longer incubation studies are needed in order to assess the temperature sensitivity of slower C pools, especially at low temperature regimes. This project has been very productive, resulting in 42 papers published or in press, 4 submitted, and 13 in preparation.« less

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.

Microbial Diversity in Sediment Ecosystems (Evaporites Domes, Microbial Mats, and Crusts) of Hypersaline Laguna Tebenquiche, Salar de Atacama, Chile.

PubMed

Fernandez, Ana B; Rasuk, Maria C; Visscher, Pieter T; Contreras, Manuel; Novoa, Fernando; Poire, Daniel G; Patterson, Molly M; Ventosa, Antonio; Farias, Maria E

2016-01-01

We combined nucleic acid-based molecular methods, biogeochemical measurements, and physicochemical characteristics to investigate microbial sedimentary ecosystems of Laguna Tebenquiche, Atacama Desert, Chile. Molecular diversity, and biogeochemistry of hypersaline microbial mats, rhizome-associated concretions, and an endoevaporite were compared with: The V4 hypervariable region of the 16S rRNA gene was amplified by pyrosequencing to analyze the total microbial diversity (i.e., bacteria and archaea) in bulk samples, and in addition, in detail on a millimeter scale in one microbial mat and in one evaporite. Archaea were more abundant than bacteria. Euryarchaeota was one of the most abundant phyla in all samples, and particularly dominant (97% of total diversity) in the most lithified ecosystem, the evaporite. Most of the euryarchaeal OTUs could be assigned to the class Halobacteria or anaerobic and methanogenic archaea. Planctomycetes potentially also play a key role in mats and rhizome-associated concretions, notably the aerobic organoheterotroph members of the class Phycisphaerae. In addition to cyanobacteria, members of Chromatiales and possibly the candidate family Chlorotrichaceae contributed to photosynthetic carbon fixation. Other abundant uncultured taxa such as the candidate division MSBL1, the uncultured MBGB, and the phylum Acetothermia potentially play an important metabolic role in these ecosystems. Lithifying microbial mats contained calcium carbonate precipitates, whereas endoevoporites consisted of gypsum, and halite. Biogeochemical measurements revealed that based on depth profiles of O2 and sulfide, metabolic activities were much higher in the non-lithifying mat (peaking in the least lithified systems) than in lithifying mats with the lowest activity in endoevaporites. This trend in decreasing microbial activity reflects the increase in salinity, which may play an important role in the biodiversity.

Microbial Diversity in Sediment Ecosystems (Evaporites Domes, Microbial Mats, and Crusts) of Hypersaline Laguna Tebenquiche, Salar de Atacama, Chile

PubMed Central

Fernandez, Ana B.; Rasuk, Maria C.; Visscher, Pieter T.; Contreras, Manuel; Novoa, Fernando; Poire, Daniel G.; Patterson, Molly M.; Ventosa, Antonio; Farias, Maria E.

2016-01-01

We combined nucleic acid-based molecular methods, biogeochemical measurements, and physicochemical characteristics to investigate microbial sedimentary ecosystems of Laguna Tebenquiche, Atacama Desert, Chile. Molecular diversity, and biogeochemistry of hypersaline microbial mats, rhizome-associated concretions, and an endoevaporite were compared with: The V4 hypervariable region of the 16S rRNA gene was amplified by pyrosequencing to analyze the total microbial diversity (i.e., bacteria and archaea) in bulk samples, and in addition, in detail on a millimeter scale in one microbial mat and in one evaporite. Archaea were more abundant than bacteria. Euryarchaeota was one of the most abundant phyla in all samples, and particularly dominant (97% of total diversity) in the most lithified ecosystem, the evaporite. Most of the euryarchaeal OTUs could be assigned to the class Halobacteria or anaerobic and methanogenic archaea. Planctomycetes potentially also play a key role in mats and rhizome-associated concretions, notably the aerobic organoheterotroph members of the class Phycisphaerae. In addition to cyanobacteria, members of Chromatiales and possibly the candidate family Chlorotrichaceae contributed to photosynthetic carbon fixation. Other abundant uncultured taxa such as the candidate division MSBL1, the uncultured MBGB, and the phylum Acetothermia potentially play an important metabolic role in these ecosystems. Lithifying microbial mats contained calcium carbonate precipitates, whereas endoevoporites consisted of gypsum, and halite. Biogeochemical measurements revealed that based on depth profiles of O2 and sulfide, metabolic activities were much higher in the non-lithifying mat (peaking in the least lithified systems) than in lithifying mats with the lowest activity in endoevaporites. This trend in decreasing microbial activity reflects the increase in salinity, which may play an important role in the biodiversity. PMID:27597845

Distinct microbial communities in the active and permafrost layers on the Tibetan Plateau.

PubMed

Chen, Yong-Liang; Deng, Ye; Ding, Jin-Zhi; Hu, Hang-Wei; Xu, Tian-Le; Li, Fei; Yang, Gui-Biao; Yang, Yuan-He

2017-12-01

Permafrost represents an important understudied genetic resource. Soil microorganisms play important roles in regulating biogeochemical cycles and maintaining ecosystem function. However, our knowledge of patterns and drivers of permafrost microbial communities is limited over broad geographic scales. Using high-throughput Illumina sequencing, this study compared soil bacterial, archaeal and fungal communities between the active and permafrost layers on the Tibetan Plateau. Our results indicated that microbial alpha diversity was significantly higher in the active layer than in the permafrost layer with the exception of fungal Shannon-Wiener index and Simpson's diversity index, and microbial community structures were significantly different between the two layers. Our results also revealed that environmental factors such as soil fertility (soil organic carbon, dissolved organic carbon and total nitrogen contents) were the primary drivers of the beta diversity of bacterial, archaeal and fungal communities in the active layer. In contrast, environmental variables such as the mean annual precipitation and total phosphorus played dominant roles in driving the microbial beta diversity in the permafrost layer. Spatial distance was important for predicting the bacterial and archaeal beta diversity in both the active and permafrost layers, but not for fungal communities. Collectively, these results demonstrated different driving factors of microbial beta diversity between the active layer and permafrost layer, implying that the drivers of the microbial beta diversity observed in the active layer cannot be used to predict the biogeographic patterns of the microbial beta diversity in the permafrost layer. © 2017 John Wiley & Sons Ltd.

Old Lineages in a New Ecosystem: Diversification of Arcellinid Amoebae (Amoebozoa) and Peatland Mosses

PubMed Central

Leander, Brian S.

2014-01-01

Arcellinid testate amoebae (Amoebozoa) form a group of free-living microbial eukaryotes with one of the oldest fossil records known, yet several aspects of their evolutionary history remain poorly understood. Arcellinids occur in a range of terrestrial, freshwater and even brackish habitats; however, many arcellinid morphospecies such as Hyalosphenia papilio are particularly abundant in Sphagnum-dominated peatlands, a relatively new ecosystem that appeared during the diversification of Sphagnum species in the Miocene (5–20 Myr ago). Here, we reconstruct divergence times in arcellinid testate amoebae after selecting several fossils for clock calibrations and then infer whether or not arcellinids followed a pattern of diversification that parallels the pattern described for Sphagnum. We found that the diversification of core arcellinids occurred during the Phanerozoic, which is congruent with most arcellinid fossils but not with the oldest known amoebozoan fossil (i.e. at ca. 662 or ca. 750 Myr). Overall, Sphagnum and the Hyalospheniidae exhibit different patterns of diversification. However, an extensive molecular phylogenetic analysis of distinct clades within H. papilio species complex demonstrated a correlation between the recent diversification of H. papilio, the recent diversification of Sphagnum mosses, and the establishment of peatlands. PMID:24762929

Developing planetary protection technology- microbial diversity of the Mars Orbiter Odyssey and the spacecraft assembly and encapsulation facility II

NASA Technical Reports Server (NTRS)

Duc, M. La; Chen, F.; Kern, R.; Koukol, R.; Baker, A.; Venkateswaran, K.

2001-01-01

A study in which several surface samples, retrieved from both the Mars Odyssey Spacecraft and the Kennedy Space Center (KSC) Spacecraft Assembly and Encapsulation Facility II (SAEF-II), were prcesed and evaluated by both molecular and traditional culture-based methods for the microbial diversity.

[Microbial secondary metabolites as potential reserve of pharmaceuticals].

PubMed

Orlova, T I; Bulgakova, V G; Polin, A N

2014-01-01

The major characteristics of new bioactive microbial secondary metabolites are summarized in the review. A wide range of new molecular targets are implicated in discovery of new nonantibiotic compounds with some other pharmacological activities (noninfectious diseases). Microorganisms represent fascinating resources due to their production of novel products with broad spectra of bioactivities.

Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes

NASA Astrophysics Data System (ADS)

Hultman, Jenni; Waldrop, Mark P.; Mackelprang, Rachel; David, Maude M.; McFarland, Jack; Blazewicz, Steven J.; Harden, Jennifer; Turetsky, Merritt R.; McGuire, A. David; Shah, Manesh B.; Verberkmoes, Nathan C.; Lee, Lang Ho; Mavrommatis, Kostas; Jansson, Janet K.

2015-05-01

Over 20% of Earth's terrestrial surface is underlain by permafrost with vast stores of carbon that, once thawed, may represent the largest future transfer of carbon from the biosphere to the atmosphere. This process is largely dependent on microbial responses, but we know little about microbial activity in intact, let alone in thawing, permafrost. Molecular approaches have recently revealed the identities and functional gene composition of microorganisms in some permafrost soils and a rapid shift in functional gene composition during short-term thaw experiments. However, the fate of permafrost carbon depends on climatic, hydrological and microbial responses to thaw at decadal scales. Here we use the combination of several molecular `omics' approaches to determine the phylogenetic composition of the microbial communities, including several draft genomes of novel species, their functional potential and activity in soils representing different states of thaw: intact permafrost, seasonally thawed active layer and thermokarst bog. The multi-omics strategy reveals a good correlation of process rates to omics data for dominant processes, such as methanogenesis in the bog, as well as novel survival strategies for potentially active microbes in permafrost.

Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes.

PubMed

Hultman, Jenni; Waldrop, Mark P; Mackelprang, Rachel; David, Maude M; McFarland, Jack; Blazewicz, Steven J; Harden, Jennifer; Turetsky, Merritt R; McGuire, A David; Shah, Manesh B; VerBerkmoes, Nathan C; Lee, Lang Ho; Mavrommatis, Kostas; Jansson, Janet K

2015-05-14

Over 20% of Earth's terrestrial surface is underlain by permafrost with vast stores of carbon that, once thawed, may represent the largest future transfer of carbon from the biosphere to the atmosphere. This process is largely dependent on microbial responses, but we know little about microbial activity in intact, let alone in thawing, permafrost. Molecular approaches have recently revealed the identities and functional gene composition of microorganisms in some permafrost soils and a rapid shift in functional gene composition during short-term thaw experiments. However, the fate of permafrost carbon depends on climatic, hydrological and microbial responses to thaw at decadal scales. Here we use the combination of several molecular 'omics' approaches to determine the phylogenetic composition of the microbial communities, including several draft genomes of novel species, their functional potential and activity in soils representing different states of thaw: intact permafrost, seasonally thawed active layer and thermokarst bog. The multi-omics strategy reveals a good correlation of process rates to omics data for dominant processes, such as methanogenesis in the bog, as well as novel survival strategies for potentially active microbes in permafrost.

Characterization of Outer Space Radiation Induced Changes in Extremophiles Utilizing Deep Space Gateway Opportunities

NASA Astrophysics Data System (ADS)

Venkateswaran, K.; Wang, C.; Smith, D.; Mason, C.; Landry, K.; Rettberg, P.

2018-02-01

Extremophilic microbial survival, adaptation, biological functions, and molecular mechanisms associated with outer space radiation can be tested by exposing them onto Deep Space Gateway hardware (inside/outside) using microbiology and molecular biology techniques.

Preparation of BAC libraries from marine microbial populations.

PubMed

Sabehi, Gazalah; Béjà, Oded

2013-01-01

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

Modes of action of microbially-produced phytotoxins.

PubMed

Duke, Stephen O; Dayan, Franck E

2011-08-01

Some of the most potent phytotoxins are synthesized by microbes. A few of these share molecular target sites with some synthetic herbicides, but many microbial toxins have unique target sites with potential for exploitation by the herbicide industry. Compounds from both non-pathogenic and pathogenic microbes are discussed. Microbial phytotoxins with modes of action the same as those of commercial herbicides and those with novel modes of action of action are covered. Examples of the compounds discussed are tentoxin, AAL-toxin, auscaulitoxin aglycone, hydantocidin, thaxtomin, and tabtoxin.

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

PubMed

Saleem, Muhammad; Moe, Luke A

2014-10-01

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

Development and application of the microbial fate and transport module for the Agricultural Policy/Environmental eXtender (APEX) model

NASA Astrophysics Data System (ADS)

Hong, E.; Park, Y.; Muirhead, R.; Jeong, J.; Pachepsky, Y. A.

2017-12-01

Pathogenic microorganisms in recreational and irrigation waters remain the subject of concern. Water quality models are used to estimate microbial quality of water sources, to evaluate microbial contamination-related risks, to guide the microbial water quality monitoring, and to evaluate the effect of agricultural management on the microbial water quality. The Agricultural Policy/Environmental eXtender (APEX) is the watershed-scale water quality model that includes highly detailed representation of agricultural management. The APEX currently does not have microbial fate and transport simulation capabilities. The objective of this work was to develop the first APEX microbial fate and transport module that could use the APEX conceptual model of manure removal together with recently introduced conceptualizations of the in-stream microbial fate and transport. The module utilizes manure erosion rates found in the APEX. Bacteria survival in soil-manure mixing layer was simulated with the two-stage survival model. Individual survival patterns were simulated for each manure application date. Simulated in-stream microbial fate and transport processes included the reach-scale passive release of bacteria with resuspended bottom sediment during high flow events, the transport of bacteria from bottom sediment due to the hyporheic exchange during low flow periods, the deposition with settling sediment, and the two-stage survival. Default parameter values were available from recently published databases. The APEX model with the newly developed microbial fate and transport module was applied to simulate seven years of monitoring data for the Toenepi watershed in New Zealand. Based on calibration and testing results, the APEX with the microbe module reproduced well the monitored pattern of E. coli concentrations at the watershed outlet. The APEX with the microbial fate and transport module will be utilized for predicting microbial quality of water under various agricultural practices, evaluating monitoring protocols, and supporting the selection of management practices based on regulations that rely on fecal indicator bacteria concentrations.

Induced Genome-Wide Binding of Three Arabidopsis WRKY Transcription Factors during Early MAMP-Triggered Immunity

PubMed Central

Birkenbihl, Rainer P.; Kracher, Barbara; Roccaro, Mario

2017-01-01

During microbial-associated molecular pattern-triggered immunity (MTI), molecules derived from microbes are perceived by cell surface receptors and upon signaling to the nucleus initiate a massive transcriptional reprogramming critical to mount an appropriate host defense response. WRKY transcription factors play an important role in regulating these transcriptional processes. Here, we determined on a genome-wide scale the flg22-induced in vivo DNA binding dynamics of three of the most prominent WRKY factors, WRKY18, WRKY40, and WRKY33. The three WRKY factors each bound to more than 1000 gene loci predominantly at W-box elements, the known WRKY binding motif. Binding occurred mainly in the 500-bp promoter regions of these genes. Many of the targeted genes are involved in signal perception and transduction not only during MTI but also upon damage-associated molecular pattern-triggered immunity, providing a mechanistic link between these functionally interconnected basal defense pathways. Among the additional targets were genes involved in the production of indolic secondary metabolites and in modulating distinct plant hormone pathways. Importantly, among the targeted genes were numerous transcription factors, encoding predominantly ethylene response factors, active during early MTI, and WRKY factors, supporting the previously hypothesized existence of a WRKY subregulatory network. Transcriptional analysis revealed that WRKY18 and WRKY40 function redundantly as negative regulators of flg22-induced genes often to prevent exaggerated defense responses. PMID:28011690

Adenovirus-mediated gene transfer of pathogen-associated molecular patterns for cancer immunotherapy.

PubMed

Tosch, C; Geist, M; Ledoux, C; Ziller-Remi, C; Paul, S; Erbs, P; Corvaia, N; Von Hoegen, P; Balloul, J-M; Haegel, H

2009-04-01

The delivery of stimulatory signals to dendritic cells (DCs) in the tumor microenvironment could be an effective means to break tumor-induced tolerance. The work presented here evaluates the immunostimulatory properties of pathogen-associated molecular patterns (PAMPs), microbial molecules which bind Toll-like receptors and deliver activating signals to immune cells, when expressed in tumor cells using adenoviral (Ad) vectors. In vitro, transduction of A549 tumor cells with Ad vectors expressing either flagellin from Listeria monocytogenes or P40 protein from Klebsiella pneumoniae induced the maturation of human monocyte-derived DCs in co-cultures. In mixed lymphocyte reactions (MLRs), Ad-flagellin and Ad-P40 transduction of tumor cells stimulated lymphocyte proliferation and the secretion of IFN-gamma. In vivo, these vectors were used either as stand-alone immunoadjuvants injected intratumorally or as vaccine adjuvants combined with a tumor antigen-expressing vector. When Ad-PAMPs were administered intratumorally to mice bearing subcutaneous syngeneic B16F0-CAR (cocksackie-adenovirus receptor) melanomas, tumor progression was transiently inhibited by Ad-P40. In a therapeutic vaccine setting, the combination of Ad-MUC1 and Ad-PAMP vectors injected subcutaneously delayed the growth of implanted RenCa-MUC1 tumors and improved tumor rejection when compared with vaccination with Ad-MUC1 alone. These results suggest that Ad-PAMPs could be effective immunoadjuvants for cancer immunotherapy.

Deep-Subterranean Microbial Habitats in the Hishikari Epithermal Gold Mine: Active Thermophilic Microbial Communities and Endolithic Ancient Microbial Relicts.

NASA Astrophysics Data System (ADS)

Hirayama, H.; Takai, K.; Inagaki, F.; Horikoshi, K.

2001-12-01

Deep subterranean microbial community structures in an epithermal gold-silver deposit, Hishikari gold mine, southern part of Kyusyu Japan, were evaluated through the combined use of enrichment culture methods and culture-independent molecular surveys. The geologic setting of the Hishikari deposit is composed of three lithologies; basement oceanic sediments of the Cretaceous Shimanto Supergroup, Quaternary andesites, and auriferous quartz vein. We studied the drilled core rock of these, and the geothermal hot waters from the basement aquifers collected by means of the dewatering system located at the deepest level in the mining sites. Culture-independent molecular phylogenetic analyses of PCR-amplified ribosomal DNA (rDNA) recovered from drilled cores suggested that the deep-sea oceanic microbial communities were present as ancient indigenous relicts confined in the Shimanto basement. On the other hand, genetic signals of active thermophilic microbial communities, mainly consisting of thermophilic hydrogen-oxidizer within Aquificales, thermophilic methanotroph within g-Proteobacteria and yet-uncultivated bacterium OPB37 within b-Proteobacteria, were detected with these of oceanic relicts from the subterranean geothermal hot aquifers (temp. 70-100ºC). Successful cultivation and FISH analyses strongly supported that these thermophilic lithotrophic microorganisms could be exactly active and they grew using geochemically produced hydrogen and methane gasses as nutrients. Based on these results, the deep-subsurface biosphere occurring in the Hishikari epithermal gold mine was delineated as endolithic ancient microbial relicts and modern habitats raising active lithotrophic thermophiles associated with the geological and geochemical features of the epithermal gold deposit.

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

Diversity of anaerobic microbes in spacecraft assembly clean rooms.

PubMed

Probst, Alexander; Vaishampayan, Parag; Osman, Shariff; Moissl-Eichinger, Christine; Andersen, Gary L; Venkateswaran, Kasthuri

2010-05-01

Although the cultivable and noncultivable microbial diversity of spacecraft assembly clean rooms has been previously documented using conventional and state-of-the-art molecular techniques, the occurrence of obligate anaerobes within these clean rooms is still uncertain. Therefore, anaerobic bacterial communities of three clean-room facilities were analyzed during assembly of the Mars Science Laboratory rover. Anaerobic bacteria were cultured on several media, and DNA was extracted from suitable anaerobic enrichments and examined with conventional 16S rRNA gene clone library, as well as high-density phylogenetic 16S rRNA gene microarray (PhyloChip) technologies. The culture-dependent analyses predominantly showed the presence of clostridial and propionibacterial strains. The 16S rRNA gene sequences retrieved from clone libraries revealed distinct microbial populations associated with each clean-room facility, clustered exclusively within gram-positive organisms. PhyloChip analysis detected a greater microbial diversity, spanning many phyla of bacteria, and provided a deeper insight into the microbial community structure of the clean-room facilities. This study presents an integrated approach for assessing the anaerobic microbial population within clean-room facilities, using both molecular and cultivation-based analyses. The results reveal that highly diverse anaerobic bacterial populations persist in the clean rooms even after the imposition of rigorous maintenance programs and will pose a challenge to planetary protection implementation activities.

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

Microbial sequencing methods for monitoring of anaerobic treatment of antibiotics to optimize performance and prevent system failure.

PubMed

Aydin, Sevcan

2016-06-01

As a result of developments in molecular technologies and the use of sequencing technologies, the analyses of the anaerobic microbial community in biological treatment process has become increasingly prevalent. This review examines the ways in which microbial sequencing methods can be applied to achieve an extensive understanding of the phylogenetic and functional characteristics of microbial assemblages in anaerobic reactor if the substrate is contaminated by antibiotics which is one of the most important toxic compounds. It will discuss some of the advantages and disadvantages associated with microbial sequencing techniques that are more commonly employed and will assess how a combination of the existing methods may be applied to develop a more comprehensive understanding of microbial communities and improve the validity and depth of the results for the enhancement of the stability of anaerobic reactors.

Microbial Diversity Aboard Spacecraft: Evaluation of the International Space Station

NASA Technical Reports Server (NTRS)

Castro, Victoria A.; Thrasher, Adrianna N.; Healy, Mimi; Ott, C. Mark; Pierson, Duane L.

2003-01-01

An evaluation of the microbial flora from air, water, and surface samples provided a baseline of microbial diversity onboard the International Space Station (ISS) to gain insight into bacterial and fungal contamination during the initial stages of construction and habitation. Using 16S genetic sequencing and rep-PeR, 63 bacterial strains were isolated for identification and fingerprinted for microbial tracking. The use of these molecular tools allowed for the identification of bacteria not previously identified using automated biochemical analysis and provided a clear indication of the source of several ISS contaminants. Fungal and bacterial data acquired during monitoring do not suggest there is a current microbial hazard to the spacecraft, nor does any trend indicate a potential health risk. Previous spacecraft environmental analysis indicated that microbial contamination will increase with time and require continued surveillance.

Influence of Precipitation Regime on Microbial Decomposition Patterns in Semi-Arid Ecosystems

NASA Astrophysics Data System (ADS)

Feris, K. P.; Jilek, C.; Huber, D. P.; Reinhardt, K.; deGraaff, M.; Lohse, K.; Germino, M.

2011-12-01

In water-limited semi-arid sagebrush steppe ecosystems predicted changes in climate may manifest as a shift from historically winter/snow-dominated precipitation regimes to one dominated by spring rains. In these ecosystems soil microorganisms play a vital role in linking the effects of water availability and plant productivity to biogeochemical cycling. Patterns of soil microbial catalyzed organic matter decomposition patters (i.e. patterns of extracellular enzyme activity (EEA)) are thought to depend upon the quantity and quality of soil organic matter (SOM), pH, and mean annual precipitation (Sinsabaugh, 2008), and less on the timing and magnitude of precipitation. However, sagebrush-steppe plant communities respond strongly to changes in the timing and magnitude of precipitation, and preliminary findings by our group suggest that corresponding changes in SOM quantity, quality, N-cycle dynamics, and soil structure are occurring. Therefore, we hypothesized: 1) Shifts in the timing and magnitude of precipitation would indirectly affect soil microbial decomposition patterns via responses in the plant community structure; and 2) Changes in precipitation patterns can directly affect soil microbial community structure and function, in effect uncoupling the interaction between plant community structure and soil community structure. We tested our hypotheses by determining the influence of experimentally manipulated timing and magnitude of precipitation on soil microbial EEA using standard flourometric assays in soils sampled under plant canopies and plant interspaces. We assessed this response in a mature (18 + years) ecohydrologic field experiment in eastern Idaho that annually imitates three possible post climatic-shift precipitation regimes (Ambient (AMB): no additional precipitation, ~200mm annually; Summer (SUMM): 200mm provisioned at 50mm bi-weekly starting in June; and Fall/Spring (F/S): 200mm provisioned over 1-2 weeks in October or April) (n=3). Within plant interspaces Beta glucosaminide activity increased by 18% in treatments receiving additional F/S precipitation, whereas alpha glucopyranoside activity was lower in the F/S and SUMM plots. Conversely, underplant canopies alpha glucopyranoside activity increased by 15% in the SUMM and F/S precipitation treatments. Across treatments and sampling types (i.e. plant canopy vs. interspace), cellobioside activity levels are consistently elevated in response to additional precipitation compared to those of the control plots. When coupled with recent preliminary findings by our group regarding changes in plant and microbial community structure and SOM, C-storage, and soil structural responses, these preliminary findings suggest that 1) microbial community structure and function respond both directly and indirectly to changes in climate, and 2) thus provide a mechanism for changes in plant community structure to feed-forward to affect soil carbon decomposition patterns and ultimately soil carbon storage potential.

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

Molecular approaches for the detection and monitoring of microbial communities in bioaerosols: A review.

PubMed

Yoo, Keunje; Lee, Tae Kwon; Choi, Eun Joo; Yang, Jihoon; Shukla, Sudheer Kumar; Hwang, Sang-Il; Park, Joonhong

2017-01-01

Bioaerosols significantly affect atmospheric processes while they undergo long-range vertical and horizontal transport and influence atmospheric chemistry and physics and climate change. Accumulating evidence suggests that exposure to bioaerosols may cause adverse health effects, including severe disease. Studies of bioaerosols have primarily focused on their chemical composition and largely neglected their biological composition and the negative effects of biological composition on ecosystems and human health. Here, current molecular methods for the identification, quantification, and distribution of bioaerosol agents are reviewed. Modern developments in environmental microbiology technology would be favorable in elucidation of microbial temporal and spatial distribution in the atmosphere at high resolution. In addition, these provide additional supports for growing evidence that microbial diversity or composition in the bioaerosol is an indispensable environmental aspect linking with public health. Copyright © 2016. Published by Elsevier B.V.

The Sponge Hologenome

PubMed Central

Thomas, Torsten

2016-01-01

ABSTRACT A paradigm shift has recently transformed the field of biological science; molecular advances have revealed how fundamentally important microorganisms are to many aspects of a host’s phenotype and evolution. In the process, an era of “holobiont” research has emerged to investigate the intricate network of interactions between a host and its symbiotic microbial consortia. Marine sponges are early-diverging metazoa known for hosting dense, specific, and often highly diverse microbial communities. Here we synthesize current thoughts about the environmental and evolutionary forces that influence the diversity, specificity, and distribution of microbial symbionts within the sponge holobiont, explore the physiological pathways that contribute to holobiont function, and describe the molecular mechanisms that underpin the establishment and maintenance of these symbiotic partnerships. The collective genomes of the sponge holobiont form the sponge hologenome, and we highlight how the forces that define a sponge’s phenotype in fact act on the genomic interplay between the different components of the holobiont. PMID:27103626

Molecular Ecology of Hypersaline Microbial Mats: Current Insights and New Directions.

PubMed

Wong, Hon Lun; Ahmed-Cox, Aria; Burns, Brendan Paul

2016-01-05

Microbial mats are unique geobiological ecosystems that form as a result of complex communities of microorganisms interacting with each other and their physical environment. Both the microorganisms present and the network of metabolic interactions govern ecosystem function therein. These systems are often found in a range of extreme environments, and those found in elevated salinity have been particularly well studied. The purpose of this review is to briefly describe the molecular ecology of select model hypersaline mat systems (Guerrero Negro, Shark Bay, S'Avall, and Kiritimati Atoll), and any potentially modulating effects caused by salinity to community structure. In addition, we discuss several emerging issues in the field (linking function to newly discovered phyla and microbial dark matter), which illustrate the changing paradigm that is seen as technology has rapidly advanced in the study of these extreme and evolutionally significant ecosystems.

2012 Gordon Research Conference on Microbial Stress Response, Schedule and Speaker/Poster Program

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

Donohue, Timothy J.

2012-07-20

The Gordon Research Conference on Microbial Stress Response was held at Mount Holyoke College, South Hadley, Massachusetts, July 15-20, 2012. The Conference was well-attended with 180 participants. The 2012 Microbial Stress Responses Gordon Research Conference will provide a forum for the open reporting of recent discoveries on the diverse mechanisms employed by microbes to respond to stress. Approaches range from analysis at the molecular level (how are signals perceived and transmitted to change gene expression or function) to cellular and microbial community responses. Attached is a copy of the formal schedule and speaker program and the poster program.

Mineralogical Control on Microbial Diversity in a Weathered Granite?

NASA Astrophysics Data System (ADS)

Gleeson, D.; Clipson, N.; McDermott, F.

2003-12-01

Mineral transformation reactions and the behaviour of metals in rock and soils are affected not only by physicochemical parameters but also by biological factors, particularly by microbial activity. Microbes inhabit a wide range of niches in surface and subsurface environments, with mineral-microbe interactions being generally poorly understood. The focus of this study is to elucidate the role of microbial activity in the weathering of common silicate minerals in granitic rocks. A site in the Wicklow Mountains (Ireland) has been identified that consists of an outcrop surface of Caledonian (ca. 400 million years old) pegmatitic granite from which large intact crystals of variably weathered muscovite, plagioclase, K-feldspar and quartz were sampled, together with whole-rock granite. Culture-based microbial approaches have been widely used to profile microbial communities, particularly from copiotrophic environments, but it is now well established that for oligotrophic environments such as those that would be expected on weathering faces, perhaps less than 1% of microbial diversity can be profiled by cultural means. A number of culture-independent molecular based approaches have been developed to profile microbial diversity and community structure. These rely on successfully isolating environmental DNA from a given environment, followed by the use of the polymerase chain reaction (PCR) to amplify the typically small quantities of extracted DNA. Amplified DNA can then be analysed using cloning based approaches as well as community fingerprinting systems such as denaturing gradient gel electrophoresis (DGGE), terminal restriction fragment length polymorphism (TRFLP) and ribosomal intergenic spacer analysis (RISA). Community DNA was extracted and the intergenic spacer region (ITS) between small (16S) and large (23S) bacterial subunit rRNA genes was amplified. RISA fragments were then electrophoresed on a non-denaturing polyacrylamide gel. Banding patterns suggest that the bacterial population in whole rock, which contained approximately 30 separated bands (indicative of the number of bacterial ribotypes), is greater than muscovite (20), K-feldspar (15), and plagioclase feldspar (12) with quartz exhibiting the lowest number (6). These bands were excised from the gel for sequencing, allowing identification of the major populations. An automated approach was also used to assess similarity of bacterial communities present on each sample type, and this allowed for a statistical evaluation of bacterial diversity. Petrographic studies were carried out to assess mineral alteration effects. Scanning electron microscopy (SEM) was used to visualise in-situ bacterial cells.

Biogeography and ecology of the rare and abundant microbial lineages in deep-sea hydrothermal vents.

PubMed

Anderson, Rika E; Sogin, Mitchell L; Baross, John A

2015-01-01

Environmental gradients generate countless ecological niches in deep-sea hydrothermal vent systems, which foster diverse microbial communities. The majority of distinct microbial lineages in these communities occur in very low abundance. However, the ecological role and distribution of rare and abundant lineages, particularly in deep, hot subsurface environments, remain unclear. Here, we use 16S rRNA tag sequencing to describe biogeographic patterning and microbial community structure of both rare and abundant archaea and bacteria in hydrothermal vent systems. We show that while rare archaeal lineages and almost all bacterial lineages displayed geographically restricted community structuring patterns, the abundant lineages of archaeal communities displayed a much more cosmopolitan distribution. Finally, analysis of one high-volume, high-temperature fluid sample representative of the deep hot biosphere described a unique microbial community that differed from microbial populations in diffuse flow fluid or sulfide samples, yet the rare thermophilic archaeal groups showed similarities to those that occur in sulfides. These results suggest that while most archaeal and bacterial lineages in vents are rare and display a highly regional distribution, a small percentage of lineages, particularly within the archaeal domain, are successful at widespread dispersal and colonization. © FEMS 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Microbial Community Profiles in Wastewaters from Onsite Wastewater Treatment Systems Technology

PubMed Central

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

2016-01-01

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

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.

Molecular epidemiology of mastitis pathogens of dairy cattle and comparative relevance to humans.

PubMed

Zadoks, Ruth N; Middleton, John R; McDougall, Scott; Katholm, Jorgen; Schukken, Ynte H

2011-12-01

Mastitis, inflammation of the mammary gland, can be caused by a wide range of organisms, including gram-negative and gram-positive bacteria, mycoplasmas and algae. Many microbial species that are common causes of bovine mastitis, such as Escherichia coli, Klebsiella pneumoniae, Streptococcus agalactiae and Staphylococcus aureus also occur as commensals or pathogens of humans whereas other causative species, such as Streptococcus uberis, Streptococcus dysgalactiae subsp. dysgalactiae or Staphylococcus chromogenes, are almost exclusively found in animals. A wide range of molecular typing methods have been used in the past two decades to investigate the epidemiology of bovine mastitis at the subspecies level. These include comparative typing methods that are based on electrophoretic banding patterns, library typing methods that are based on the sequence of selected genes, virulence gene arrays and whole genome sequencing projects. The strain distribution of mastitis pathogens has been investigated within individual animals and across animals, herds, countries and host species, with consideration of the mammary gland, other animal or human body sites, and environmental sources. Molecular epidemiological studies have contributed considerably to our understanding of sources, transmission routes, and prognosis for many bovine mastitis pathogens and to our understanding of mechanisms of host-adaptation and disease causation. In this review, we summarize knowledge gleaned from two decades of molecular epidemiological studies of mastitis pathogens in dairy cattle and discuss aspects of comparative relevance to human medicine.

Associations among Wine Grape Microbiome, Metabolome, and Fermentation Behavior Suggest Microbial Contribution to Regional Wine Characteristics.

PubMed

Bokulich, Nicholas A; Collins, Thomas S; Masarweh, Chad; Allen, Greg; Heymann, Hildegarde; Ebeler, Susan E; Mills, David A

2016-06-14

Regionally distinct wine characteristics (terroir) are an important aspect of wine production and consumer appreciation. Microbial activity is an integral part of wine production, and grape and wine microbiota present regionally defined patterns associated with vineyard and climatic conditions, but the degree to which these microbial patterns associate with the chemical composition of wine is unclear. Through a longitudinal survey of over 200 commercial wine fermentations, we demonstrate that both grape microbiota and wine metabolite profiles distinguish viticultural area designations and individual vineyards within Napa and Sonoma Counties, California. Associations among wine microbiota and fermentation characteristics suggest new links between microbiota, fermentation performance, and wine properties. The bacterial and fungal consortia of wine fermentations, composed from vineyard and winery sources, correlate with the chemical composition of the finished wines and predict metabolite abundances in finished wines using machine learning models. The use of postharvest microbiota as an early predictor of wine chemical composition is unprecedented and potentially poses a new paradigm for quality control of agricultural products. These findings add further evidence that microbial activity is associated with wine terroir Wine production is a multi-billion-dollar global industry for which microbial control and wine chemical composition are crucial aspects of quality. Terroir is an important feature of consumer appreciation and wine culture, but the many factors that contribute to terroir are nebulous. We show that grape and wine microbiota exhibit regional patterns that correlate with wine chemical composition, suggesting that the grape microbiome may influence terroir In addition to enriching our understanding of how growing region and wine properties interact, this may provide further economic incentive for agricultural and enological practices that maintain regional microbial biodiversity. Copyright © 2016 Bokulich et al.

Metabolic Network Modeling of Microbial Interactions in Natural and Engineered Environmental Systems

PubMed Central

Perez-Garcia, Octavio; Lear, Gavin; Singhal, Naresh

2016-01-01

We review approaches to characterize metabolic interactions within microbial communities using Stoichiometric Metabolic Network (SMN) models for applications in environmental and industrial biotechnology. SMN models are computational tools used to evaluate the metabolic engineering potential of various organisms. They have successfully been applied to design and optimize the microbial production of antibiotics, alcohols and amino acids by single strains. To date however, such models have been rarely applied to analyze and control the metabolism of more complex microbial communities. This is largely attributed to the diversity of microbial community functions, metabolisms, and interactions. Here, we firstly review different types of microbial interaction and describe their relevance for natural and engineered environmental processes. Next, we provide a general description of the essential methods of the SMN modeling workflow including the steps of network reconstruction, simulation through Flux Balance Analysis (FBA), experimental data gathering, and model calibration. Then we broadly describe and compare four approaches to model microbial interactions using metabolic networks, i.e., (i) lumped networks, (ii) compartment per guild networks, (iii) bi-level optimization simulations, and (iv) dynamic-SMN methods. These approaches can be used to integrate and analyze diverse microbial physiology, ecology and molecular community data. All of them (except the lumped approach) are suitable for incorporating species abundance data but so far they have been used only to model simple communities of two to eight different species. Interactions based on substrate exchange and competition can be directly modeled using the above approaches. However, interactions based on metabolic feedbacks, such as product inhibition and synthropy require extensions to current models, incorporating gene regulation and compounding accumulation mechanisms. SMN models of microbial interactions can be used to analyze complex “omics” data and to infer and optimize metabolic processes. Thereby, SMN models are suitable to capitalize on advances in high-throughput molecular and metabolic data generation. SMN models are starting to be applied to describe microbial interactions during wastewater treatment, in-situ bioremediation, microalgae blooms methanogenic fermentation, and bioplastic production. Despite their current challenges, we envisage that SMN models have future potential for the design and development of novel growth media, biochemical pathways and synthetic microbial associations. PMID:27242701

Greatest soil microbial diversity found in micro-habitats

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

Bach, Elizabeth M.; Williams, Ryan J.; Hargreaves, Sarah K.

Microbial interactions occur in habitats much smaller than typically considered in classic ecological studies. This study uses soil aggregates to examine soil microbial community composition and structure of both bacteria and fungi at a microbially relevant scale. Aggregates were isolated from three land management systems in central Iowa, USA to test if aggregate-level microbial responses were sensitive to large-scale shifts in plant community and management practices. Bacteria and fungi exhibited similar patterns of community structure and diversity among soil aggregates, regardless of land management. Microaggregates supported more diverse microbial communities, both taxonomically and functionally. Calculation of a weighted proportional wholemore » soil diversity, which accounted for microbes found in aggregate fractions, resulted in 65% greater bacterial richness and 100% greater fungal richness over independently sampled whole soil. Our results show microaggregates support a previously unrecognized diverse microbial community that likely effects microbial access and metabolism of soil substrates.« less

Trait-based approaches for understanding microbial biodiversity and ecosystem functioning

PubMed Central

Krause, Sascha; Le Roux, Xavier; Niklaus, Pascal A.; Van Bodegom, Peter M.; Lennon, Jay T.; Bertilsson, Stefan; Grossart, Hans-Peter; Philippot, Laurent; Bodelier, Paul L. E.

2014-01-01

In ecology, biodiversity-ecosystem functioning (BEF) research has seen a shift in perspective from taxonomy to function in the last two decades, with successful application of trait-based approaches. This shift offers opportunities for a deeper mechanistic understanding of the role of biodiversity in maintaining multiple ecosystem processes and services. In this paper, we highlight studies that have focused on BEF of microbial communities with an emphasis on integrating trait-based approaches to microbial ecology. In doing so, we explore some of the inherent challenges and opportunities of understanding BEF using microbial systems. For example, microbial biologists characterize communities using gene phylogenies that are often unable to resolve functional traits. Additionally, experimental designs of existing microbial BEF studies are often inadequate to unravel BEF relationships. We argue that combining eco-physiological studies with contemporary molecular tools in a trait-based framework can reinforce our ability to link microbial diversity to ecosystem processes. We conclude that such trait-based approaches are a promising framework to increase the understanding of microbial BEF relationships and thus generating systematic principles in microbial ecology and more generally ecology. PMID:24904563

Analysis of microbial communities in the oil reservoir subjected to CO2-flooding by using functional genes as molecular biomarkers for microbial CO2 sequestration

PubMed Central

Liu, Jin-Feng; Sun, Xiao-Bo; Yang, Guang-Chao; Mbadinga, Serge M.; Gu, Ji-Dong; Mu, Bo-Zhong

2015-01-01

Sequestration of CO2 in oil reservoirs is considered to be one of the feasible options for mitigating atmospheric CO2 building up and also for the in situ potential bioconversion of stored CO2 to methane. However, the information on these functional microbial communities and the impact of CO2 storage on them is hardly available. In this paper a comprehensive molecular survey was performed on microbial communities in production water samples from oil reservoirs experienced CO2-flooding by analysis of functional genes involved in the process, including cbbM, cbbL, fthfs, [FeFe]-hydrogenase, and mcrA. As a comparison, these functional genes in the production water samples from oil reservoir only experienced water-flooding in areas of the same oil bearing bed were also analyzed. It showed that these functional genes were all of rich diversity in these samples, and the functional microbial communities and their diversity were strongly affected by a long-term exposure to injected CO2. More interestingly, microorganisms affiliated with members of the genera Methanothemobacter, Acetobacterium, and Halothiobacillus as well as hydrogen producers in CO2 injected area either increased or remained unchanged in relative abundance compared to that in water-flooded area, which implied that these microorganisms could adapt to CO2 injection and, if so, demonstrated the potential for microbial fixation and conversion of CO2 into methane in subsurface oil reservoirs. PMID:25873911

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.

The microbial perspective of organic matter turnover and nutrient cycling in tropical soils

NASA Astrophysics Data System (ADS)

Rasche, Frank

2017-04-01

A primary goal of low-input small-holder farming systems in the tropics is the appropriate management of organic matter (OM) turnover and nutrient cycling via adapted agricultural practices. These emphasize the promotion of soil organic matter (SOM) turnover and carbon (C) sequestration, nutrient use efficiency and soil microbial activity. Since soil microbial communities are acknowledged as key players in the terrestrial C and nutrient (e.g., nitrogen (N), phosphorus (P)) cycles, they may respond sensitively to agricultural management with shifts in their community structure as well as functional traits (i.e., decomposition, mineralization). This may be in particular evident for tropical, agricultural soils which show an accelerated microbial decomposition activity induced by favourable climatic and unique physico-chemical soil conditions. While modern molecular techniques advanced primarily the understanding about the microbiome and their functional traits interacting closely with SOM dynamics in temperate soils, tropical soils under agricultural use have been still neglected to a great extent. The majority of available studies revealed mainly descriptive data on the structural composition of microbial communities rather than questioning if detected structural alterations of the soil microbiome influenced key processes in N and P cycling which actually maintain ecosystem functioning and soil productivity. This talk highlights latest efforts in deploying molecular techniques to study the compositional status of soil microbial decomposer communities and their functional attributes in response to land use change and OM management in tropical agro-ecosystems.

Molecular imprinted hydrogel polymer (MIHP) as microbial immobilization media in artificial produced water treatment

NASA Astrophysics Data System (ADS)

Kardena, E.; Ridhati, S. L.; Helmy, Q.

2018-01-01

Produced water generated during oil and gas exploration and drilling, consists of many chemicals which used in drilling process. The production of produced water is over three fold of the oil production. The water-cut has increased over time and continues to do so because the fraction of oil in the reservoir decreases and it is more difficult to get the oil out from an old oil-field. It therefore requires more sea water to be injected in order to force the oil out; hence more produced water is generated. Produced water can pollute the environment if it is not treated properly. In this research, produced water will be treated biologically using bacterial consortium which is isolated from petroleum processing facility with Molecular Imprinted Hydrogel Polymer (MIHP) for microbial immobilization media. Microbial growth rate is determined by measuring the MLVSS and hydrogel mass, also by SEM-EDS analysis. SEM-EDS analysis is an analysis to evidence the presence of microbe trapped in hydrogel, and also to determine the types and weight of the molecules of hydrogel. From this research, suspended microbial growth rate was found at 0.1532/days and attached microbial growth rate was 0.3322/days. Furthermore, based on SEM analysis, microbe is entrapped inside the hydrogel. Effectiveness of microbial degradation activity was determined by measuring organic materials as COD. Based on COD measurement, degradation rate of organic materials in wastewater is 0.3089/days, with maximum COD removal efficiency of 76.67%.

Sewage Reflects the Microbiomes of Human Populations

PubMed Central

Newton, Ryan J.; McLellan, Sandra L.; Dila, Deborah K.; Vineis, Joseph H.; Morrison, Hilary G.; Eren, A. Murat

2015-01-01

ABSTRACT Molecular characterizations of the gut microbiome from individual human stool samples have identified community patterns that correlate with age, disease, diet, and other human characteristics, but resources for marker gene studies that consider microbiome trends among human populations scale with the number of individuals sampled from each population. As an alternative strategy for sampling populations, we examined whether sewage accurately reflects the microbial community of a mixture of stool samples. We used oligotyping of high-throughput 16S rRNA gene sequence data to compare the bacterial distribution in a stool data set to a sewage influent data set from 71 U.S. cities. On average, only 15% of sewage sample sequence reads were attributed to human fecal origin, but sewage recaptured most (97%) human fecal oligotypes. The most common oligotypes in stool matched the most common and abundant in sewage. After informatically separating sequences of human fecal origin, sewage samples exhibited ~3× greater diversity than stool samples. Comparisons among municipal sewage communities revealed the ubiquitous and abundant occurrence of 27 human fecal oligotypes, representing an apparent core set of organisms in U.S. populations. The fecal community variability among U.S. populations was significantly lower than among individuals. It clustered into three primary community structures distinguished by oligotypes from either: Bacteroidaceae, Prevotellaceae, or Lachnospiraceae/Ruminococcaceae. These distribution patterns reflected human population variation and predicted whether samples represented lean or obese populations with 81 to 89% accuracy. Our findings demonstrate that sewage represents the fecal microbial community of human populations and captures population-level traits of the human microbiome. PMID:25714718

Principal Component Analysis of Microbial Community Data from an Accelerated Decay Cellar Test

Treesearch

Grant T. Kirker; Patricia K. Lebow

2014-01-01

Analysis of microbial communities is a valuable tool for characterization and identification of microbes in a myriad of environments. We are currently using the molecular method terminal restriction fragment length polymorphism (T-RFLP) analysis to characterize changes in bacterial and fungal communities on treated and untreated wood in soil. T-RFLP uses fluorescently...

Correlation between vegetation and underground microbial communities on a micro-landscape of the Tibetan Plateau

NASA Astrophysics Data System (ADS)

Zhang, G.; Hu, A.; Wang, J.

2016-12-01

Aboveground vegetation and underground microbes are tightly associated and form a systematic entity to maintain terrestrial ecosystem functions; however, the roles and relative importance of vegetation to corresponding underlying microbial community remain clearly unresolved. Here we studied the vegetation and corresponding underground microbial communities along an elevation range of 704-3,760 m a.s.l on the Tibetan Plateau, which covering from a tropical forest to frigid shrub meadow ecosystem. By substituting space for time, we explored how the alteration of vegetation and abiotic environments jointly affect the underlying microbial communities. We found that vegetation showed a hump-shaped elevational pattern in diversity, while microbial community exhibited a two-section elevational pattern at a tipping point of 2400m elevation where vegetation diversity approximately peaks. The statistical analyses and regression modelling of the measures of underground microbial community including biomass, diversity, phylogenetic structure and community composition provided evidences of this threshold. Our findings highlighted that vegetation is a good predictor of underground microbial communities. Further statistical analyses suggested that alteration of vegetation and environmental filtering processes might be the vital driving forces jointly structuring underground microbial communities along an elevational gradient. Specifically, vegetation is a major contributor to underground microbes primarily through soil pH below the threshold (that is, in tropical and subtropical zones), while vegetation could directly influence underground microbes and also partly through its effects on several abiotic factors such as soil pH and WSOC above the threshold (that is, in temperate and frigid zones). These insights into the alteration of vegetation types and corresponding underground microbial communities provide new perspective on the aboveground and belowground interactions in forest ecosystems.

Soil microbial biomass, activity and community composition along altitudinal gradients in the High Arctic (Billefjorden, Svalbard)

NASA Astrophysics Data System (ADS)

Kotas, Petr; Šantrůčková, Hana; Elster, Josef; Kaštovská, Eva

2018-03-01

The unique and fragile High Arctic ecosystems are vulnerable to global climate warming. The elucidation of factors driving microbial distribution and activity in arctic soils is essential for a comprehensive understanding of ecosystem functioning and its response to environmental change. The goals of this study were to investigate microbial biomass and activity, microbial community structure (MCS), and their environmental controls in soils along three elevational transects in the coastal mountains of Billefjorden, central Svalbard. Soils from four different altitudes (25, 275, 525 and 765 m above sea level) were analyzed for a suite of characteristics including temperature regimes, organic matter content, base cation availability, moisture, pH, potential respiration, and microbial biomass and community structure using phospholipid fatty acids (PLFAs). We observed significant spatial heterogeneity of edaphic properties among transects, resulting in transect-specific effects of altitude on most soil parameters. We did not observe any clear elevation pattern in microbial biomass, and microbial activity revealed contrasting elevational patterns between transects. We found relatively large horizontal variability in MCS (i.e., between sites of corresponding elevation in different transects), mainly due to differences in the composition of bacterial PLFAs, but also a systematic altitudinal shift in MCS related to different habitat preferences of fungi and bacteria, which resulted in high fungi-to-bacteria ratios at the most elevated sites. The biological soil crusts on these most elevated, unvegetated sites can host microbial assemblages of a size and activity comparable to those of the arctic tundra ecosystem. The key environmental factors determining horizontal and vertical changes in soil microbial properties were soil pH, organic carbon content, soil moisture and Mg2+ availability.

Long-term pattern and magnitude of soil carbon feedback to the climate system in a warming world.

PubMed

Melillo, J M; Frey, S D; DeAngelis, K M; Werner, W J; Bernard, M J; Bowles, F P; Pold, G; Knorr, M A; Grandy, A S

2017-10-06

In a 26-year soil warming experiment in a mid-latitude hardwood forest, we documented changes in soil carbon cycling to investigate the potential consequences for the climate system. We found that soil warming results in a four-phase pattern of soil organic matter decay and carbon dioxide fluxes to the atmosphere, with phases of substantial soil carbon loss alternating with phases of no detectable loss. Several factors combine to affect the timing, magnitude, and thermal acclimation of soil carbon loss. These include depletion of microbially accessible carbon pools, reductions in microbial biomass, a shift in microbial carbon use efficiency, and changes in microbial community composition. Our results support projections of a long-term, self-reinforcing carbon feedback from mid-latitude forests to the climate system as the world warms. Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Predator identity more than predator richness structures aquatic microbial assemblages in Sarracenia purpurea leaves.

PubMed

Canter, Erin J; Cuellar-Gempeler, Catalina; Pastore, Abigail I; Miller, Thomas E; Mason, Olivia U

2018-03-01

The importance of predators in influencing community structure is a well-studied area of ecology. However, few studies test ecological hypotheses of predation in multi-predator microbial communities. The phytotelmic community found within the water-filled leaves of the pitcher plant, Sarracenia purpurea, exhibits a simple trophic structure that includes multiple protozoan predators and microbial prey. Using this system, we sought to determine whether different predators target distinct microorganisms, how interactions among protozoans affect resource (microorganism) use, and how predator diversity affects prey community diversity. In particular, we endeavored to determine if protozoa followed known ecological patterns such as keystone predation or generalist predation. For these experiments, replicate inquiline microbial communities were maintained for seven days with five protozoan species. Microbial community structure was determined by 16S rRNA gene amplicon sequencing (iTag) and analysis. Compared to the control (no protozoa), two ciliates followed patterns of keystone predation by increasing microbial evenness. In pairwise competition treatments with a generalist flagellate, prey communities resembled the microbial communities of the respective keystone predator in monoculture. The relative abundance of the most common bacterial Operational Taxonomic Unit (OTU) in our system decreased compared to the control in the presence of these ciliates. This OTU was 98% similar to a known chitin degrader and nitrate reducer, important functions for the microbial community and the plant host. Collectively, the data demonstrated that predator identity had a greater effect on prey diversity and composition than overall predator diversity. © 2018 by the Ecological Society of America.

Formation of Kinneyia via shear-induced instabilities in microbial mats.

PubMed

Thomas, Katherine; Herminghaus, Stephan; Porada, Hubertus; Goehring, Lucas

2013-01-01

Kinneyia are a class of microbially mediated sedimentary fossils. Characterized by clearly defined ripple structures, Kinneyia are generally found in areas that were formally littoral habitats and covered by microbial mats. To date, there has been no conclusive explanation of the processes involved in the formation of these fossils. Microbial mats behave like viscoelastic fluids. We propose that the key mechanism involved in the formation of Kinneyia is a Kelvin-Helmholtz-type instability induced in a viscoelastic film under flowing water. A ripple corrugation is spontaneously induced in the film and grows in amplitude over time. Theoretical predictions show that the ripple instability has a wavelength proportional to the thickness of the film. Experiments carried out using viscoelastic films confirm this prediction. The ripple pattern that forms has a wavelength roughly three times the thickness of the film. This behaviour is independent of the viscosity of the film and the flow conditions. Laboratory-analogue Kinneyia were formed via the sedimentation of glass beads, which preferentially deposit in the troughs of the ripples. Well-ordered patterns form, with both honeycomb-like and parallel ridges being observed, depending on the flow speed. These patterns correspond well with those found in Kinneyia, with similar morphologies, wavelengths and amplitudes being observed.

Formation of Kinneyia via shear-induced instabilities in microbial mats.

PubMed

Thomas, Katherine; Herminghaus, Stephan; Porada, Hubertus; Goehring, Lucas

2013-12-13

Kinneyia are a class of microbially mediated sedimentary fossils. Characterized by clearly defined ripple structures, Kinneyia are generally found in areas that were formally littoral habitats and covered by microbial mats. To date, there has been no conclusive explanation of the processes involved in the formation of these fossils. Microbial mats behave like viscoelastic fluids. We propose that the key mechanism involved in the formation of Kinneyia is a Kelvin-Helmholtz-type instability induced in a viscoelastic film under flowing water. A ripple corrugation is spontaneously induced in the film and grows in amplitude over time. Theoretical predictions show that the ripple instability has a wavelength proportional to the thickness of the film. Experiments carried out using viscoelastic films confirm this prediction. The ripple pattern that forms has a wavelength roughly three times the thickness of the film. This behaviour is independent of the viscosity of the film and the flow conditions. Laboratory-analogue Kinneyia were formed via the sedimentation of glass beads, which preferentially deposit in the troughs of the ripples. Well-ordered patterns form, with both honeycomb-like and parallel ridges being observed, depending on the flow speed. These patterns correspond well with those found in Kinneyia, with similar morphologies, wavelengths and amplitudes being observed.

A genomic perspective on stoichiometric regulation of soil carbon cycling.

PubMed

Hartman, Wyatt H; Ye, Rongzhong; Horwath, William R; Tringe, Susannah G

2017-12-01

Similar to plant growth, soil carbon (C) cycling is constrained by the availability of nitrogen (N) and phosphorus (P). We hypothesized that stoichiometric control over soil microbial C cycling may be shaped by functional guilds with distinct nutrient substrate preferences. Across a series of rice fields spanning 5-25% soil C (N:P from 1:12 to 1:70), C turnover was best correlated with P availability and increased with experimental N addition only in lower C (mineral) soils with N:P⩽16. Microbial community membership also varied with soil stoichiometry but not with N addition. Shotgun metagenome data revealed changes in community functions with increasing C turnover, including a shift from aromatic C to carbohydrate utilization accompanied by lower N uptake and P scavenging. Similar patterns of C, N and P acquisition, along with higher ribosomal RNA operon copy numbers, distinguished that microbial taxa positively correlated with C turnover. Considering such tradeoffs in genomic resource allocation patterns among taxa strengthened correlations between microbial community composition and C cycling, suggesting simplified guilds amenable to ecosystem modeling. Our results suggest that patterns of soil C turnover may reflect community-dependent metabolic shifts driven by resource allocation strategies, analogous to growth rate-stoichiometry coupling in animal and plant communities.

Characteristics and fates of soluble microbial products in ceramic membrane bioreactor at various sludge retention times.

PubMed

Shin, Hang-Sik; Kang, Seok-Tae

2003-01-01

The formation and fate of soluble microbial products (SMP) in membrane bioreactor (MBR) was investigated at various sludge retention times (SRT) for 170 days. The SMP concentration was estimated by feeding glucose, which could be completely degraded, and by measuring the dissolved organic carbon (DOC) of the effluent from MBR. Under the conditions of SRT of 20 days, influent DOC of 112 mg/l and HRT of 6 h, the produced SMP was 4.7 mg DOC/l of which 57% was removed or retained by the membrane. DOC of MBR supernatant increased during 100 days and then gradually decreased. Specific UV absorbance showed that the accumulated compounds had a portion of larger, more aromatic, more hydrophobic and double-bond-rich organics, which originated from the decayed biomass. Molecular weight distributions of SMP in MBR supernatant showed that the acclimated microorganisms in a long SRT could decompose high molecular weight organics, it caused the shift of molecular weight distributions of SMP to a lower range. During the operation period, enumeration of active cells in the MBR showed that microbial inhibitions by accumulated SMP was not observed.

Diversity and Function of Microbial Community in Chinese Strong-Flavor Baijiu Ecosystem: A Review

PubMed Central

Zou, Wei; Zhao, Changqing; Luo, Huibo

2018-01-01

Strong flavor baijiu (SFB), also called Luzhou-flavor liquor, is the most popular Chinese baijiu. It is manufactured via solid fermentation, with daqu as the starter. Microbial diversity of the SFB ecosystem and the synergistic effects of the enzymes and compounds produced by them are responsible for the special flavor and mouthfeel of SFB. The present review covers research studies focused on microbial community analysis of the SFB ecosystem, including the culturable microorganisms, their metabolic functions, microbial community diversity and their interactions. The review specifically emphasizes on the most recently conducted culture-independent analysis of SFB microbial community diversity. Furthermore, the possible application of systems biology approaches for elucidating the molecular mechanisms of SFB production were also reviewed and prospected. PMID:29686656

Dysbiosis of gut microbiota and microbial metabolites in Parkinson's Disease.

PubMed

Sun, Meng-Fei; Shen, Yan-Qin

2018-04-26

Gut microbial dysbiosis and alteration of microbial metabolites in Parkinson's disease (PD) have been increasingly reported. Dysbiosis in the composition and abundance of gut microbiota can affect both the enteric nervous system and the central nervous system (CNS), indicating the existence of a microbiota-gut-brain axis and thereby causing CNS diseases. Disturbance of the microbiota-gut-brain axis has been linked to specific microbial products that are related to gut inflammation and neuroinflammation. Future directions should therefore focus on the exploration of specific gut microbes or microbial metabolites that contribute to the development of PD. Microbiota-targeted interventions, such as antibiotics, probiotics and fecal microbiota transplantation, have been shown to favorably affect host health. In this review, recent findings regarding alterations and the role of gut microbiota and microbial metabolites in PD are summarized, and potential molecular mechanisms and microbiota-targeted interventions in PD are discussed. Copyright © 2018. Published by Elsevier B.V.

Distribution Patterns of Microbial Community Structure Along a 7000-Mile Latitudinal Transect from the Mediterranean Sea Across the Atlantic Ocean to the Brazilian Coastal Sea.

PubMed

Zhou, Jin; Song, Xiao; Zhang, Chun-Yun; Chen, Guo-Fu; Lao, Yong-Min; Jin, Hui; Cai, Zhong-Hua

2018-02-14

A central goal in marine microecology is to understand the ecological factors shaping spatiotemporal microbial patterns and the underlying processes. We hypothesized that abiotic and/or biotic interactions are probably more important for explaining the distribution patterns of marine bacterioplankton than environmental filtering. In this study, surface seawater samples were collected about 7000 miles from the Mediterranean Sea, transecting the North Atlantic Ocean, to the Brazilian marginal sea. In bacterial biosphere, SAR11, SAR86, Rhodobacteraceae, and Rhodospiriaceae were predominant in the Mediterranean Sea; Prochlorococcus was more frequent in Atlantic Ocean; whereas in the Brazilian coastal sea, the main bacterial members were Synechococcus and SAR11. With respect to archaea, Euryarchaeota were predominant in the Atlantic Ocean and Thaumarchaeota in the Mediterranean Sea. With respect to the eukaryotes, Syndiniales, Spumellaria, Cryomonadida, and Chlorodendrales were predominant in the open ocean, while diatoms and microzooplankton were dominant in the coastal sea. Distinct clusters of prokaryotes and eukaryotes displayed clear spatial heterogeneity. Among the environmental parameters measured, temperature and salinity were key factors controlling bacterial and archaeal community structure, respectively, whereas N/P/Si contributed to eukaryotic variation. The relative contribution of environmental parameters to the microbial distribution pattern was 45.2%. Interaction analysis showed that Gammaproteobacteria, Alphaproteobacteria, and Flavobacteriia were the keystone taxa within the positive-correlation network, while Thermoplasmata was the main contributor in the negative-correlation network. Our study demonstrated that microbial communities are co-governed by environmental filtering and biotic interactions, which are the main deterministic driving factors modulating the spatiotemporal patterns of marine plankton synergistically at the regional or global levels.

Connectivity to the surface determines diversity patterns in subsurface aquifers of the Fennoscandian shield.

PubMed

Hubalek, Valerie; Wu, Xiaofen; Eiler, Alexander; Buck, Moritz; Heim, Christine; Dopson, Mark; Bertilsson, Stefan; Ionescu, Danny

2016-10-01

Little research has been conducted on microbial diversity deep under the Earth's surface. In this study, the microbial communities of three deep terrestrial subsurface aquifers were investigated. Temporal community data over 6 years revealed that the phylogenetic structure and community dynamics were highly dependent on the degree of isolation from the earth surface biomes. The microbial community at the shallow site was the most dynamic and was dominated by the sulfur-oxidizing genera Sulfurovum or Sulfurimonas at all-time points. The microbial community in the meteoric water filled intermediate aquifer (water turnover approximately every 5 years) was less variable and was dominated by candidate phylum OD1. Metagenomic analysis of this water demonstrated the occurrence of key genes for nitrogen and carbon fixation, sulfate reduction, sulfide oxidation and fermentation. The deepest water mass (5000 year old waters) had the lowest taxon richness and surprisingly contained Cyanobacteria. The high relative abundance of phylogenetic groups associated with nitrogen and sulfur cycling, as well as fermentation implied that these processes were important in these systems. We conclude that the microbial community patterns appear to be shaped by the availability of energy and nutrient sources via connectivity to the surface or from deep geological processes.

Microbial secondary succession in soil microcosms of a desert oasis in the Cuatro Cienegas Basin, Mexico.

PubMed

López-Lozano, Nguyen E; Heidelberg, Karla B; Nelson, William C; García-Oliva, Felipe; Eguiarte, Luis E; Souza, Valeria

2013-01-01

Ecological succession is one of the most important concepts in ecology. However for microbial community succession, there is a lack of a solid theoretical framework regarding succession in microorganisms. This is in part due to microbial community complexity and plasticity but also because little is known about temporal patterns of microbial community shifts in different kinds of ecosystems, including arid soils. The Cuatro Cienegas Basin (CCB) in Coahuila, Mexico, is an arid zone with high diversity and endemisms that has recently been threatened by aquifer overexploitation. The gypsum-based soil system of the CCB is one of the most oligotrophic places in the world. We undertook a comparative 16S rRNA 454 pyrosequencing study to evaluate microbial community succession and recovery over a year after disturbance at two sites. Results were related to concurrent measurements of humidity, organic matter and total C and N content. While each site differed in both biogeochemistry and biodiversity, both present similar pattern of change at the beginning of the succession that diverged in later stages. After one year, experimentally disturbed soil was not similar to established and undisturbed adjacent soil communities indicating recovery and succession in disturbed soils is a long process.

Changes in microbial communities along redox gradients in polygonized Arctic wet tundra soils

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

Lipson, David A.; Raab, Theodore K.; Parker, Melanie

2015-08-01

Summary This study investigated how microbial community structure and diversity varied with depth and topography in ice wedge polygons of wet tundra of the Arctic Coastal Plain in northern Alaska and what soil variables explain these patterns. We observed strong changes in community structure and diversity with depth, and more subtle changes between areas of high and low topography, with the largest differences apparent near the soil surface. These patterns are most strongly correlated with redox gradients (measured using the ratio of reduced Fe to total Fe in acid extracts as a proxy): conditions grew more reducing with depth andmore » were most oxidized in shallow regions of polygon rims. Organic matter and pH also changed with depth and topography but were less effective predictors of the microbial community structure and relative abundance of specific taxa. Of all other measured variables, lactic acid concentration was the best, in combination with redox, for describing the microbial community. We conclude that redox conditions are the dominant force in shaping microbial communities in this landscape. Oxygen and other electron acceptors allowed for the greatest diversity of microbes: at depth the community was reduced to a simpler core of anaerobes,« less

First Investigation of Microbial Community Composition in the Bridge (Gadeok Channel) between the Jinhae-Masan Bay and the South Sea of Korea

NASA Astrophysics Data System (ADS)

Lee, Jiyoung; Lim, Jae-Hyun; Park, Junhyung; Youn, Seok-Hyun; Oh, Hyun-Ju; Kim, Ju-Hyoung; Kim, Myung Kyum; Cho, Hyeyoun; Yoon, Joo-Eun; Kim, Soyeon; Markkandan, Kesavan; Park, Ki-Tae; Kim, Il-Nam

2018-02-01

Microbial community composition varies based on seasonal dynamics (summer: strongly stratified water column; autumn: weakly stratified water column; winter: vertically homogeneous water column) and vertical distributions (surface, middle, and bottom depths) in the Gadeok Channel, which is the primary passage to exchange waters and materials between the Jinhae-Masan Bay and the South Sea waters. The microbial community composition was analyzed from June to December 2016 using 16S rRNA gene sequencing. The community was dominated by the phyla Proteobacteria (45%), Bacteroidetes (18%), Cyanobacteria (15%), Verrucomicrobia (6%), and Actinobacteria (6%). Alphaproteobacteria (29%) was the most abundant microbial class, followed by Flavobacteria (15%) and Gammaproteobacteria (15%) in all samples. The composition of the microbial communities was found to vary vertically and seasonally. The orders Flavobacteriales and Stramenopiles showed opposing seasonal patterns; Flavobacteriales was more abundant in August and December while Stramenopiles showed high abundance in June and October at all depths. The genus Synechococcus reached extremely high abundance (14%) in the June surface water column, but was much less abundant in December water columns. Clustering analysis showed that there was a difference in the microbial community composition pattern between the strongly stratified season and well-mixed season. These results indicate that the seasonal dynamics of physicochemical and hydrologic conditions throughout the water column are important parameters in shaping the microbial community composition in the Gadeok Channel.

Determination of natural organic matter and iron binding capacity in fen samples

NASA Astrophysics Data System (ADS)

Kügler, Stefan; Cooper, Rebecca E.; Frieder Mohr, Jan; Wichard, Thomas; Küsel, Kirsten

2017-04-01

Natural organic matter (NOM) plays an important role in ecosystem processes such as soil carbon stabilization, nutrient availability and metal complexation. Iron-NOM-complexes, for example, are known to increase the solubility and, as a result, the bioavailability of iron in natural environments leading to several effects on the microbial community. Due to the various functions of NOM in natural environments, there is a high level of interest in the characterization of the molecular composition. The complexity of NOM presents a significant challenge in the elucidation of its composition. However, the development and utilization of high resolution mass spectrometry (HR-MS) as a tool to detect single compounds in complex samples has spearheaded the effort to elucidate the composition of NOM. Over the past years, the accuracy of ion cyclotron- or Orbitrap mass spectrometers has increased dramatically resulting in the possibility to obtain a mass differentiation of the large number of compounds in NOM. Together these tools provide significant and powerful insight into the molecular composition of NOM. In the current study, we aim to understand abiotic and biotic interactions between NOM and metals, such as iron, found in the Schlöppnerbrunnen fen (Fichtelgebirge, Germany) and how these interactions impact the microbial consortia. We characterized the dissolved organic matter (DOM) as well as basic chemical parameters in the iron-rich (up to 20 mg (g wt peat)-1), slightly acidic (pH 4.8) fen to gain more information about DOM-metal interactions. This minerotrophic peatland connected to the groundwater has received Fe(II) released from the surrounding soils in the Lehstenbach catchment. Absorption spectroscopy (AAS), differential pulse polarography (DPP) and high resolution electrospray ionization mass spectrometry (HR-ESI-Orbitrap-MS) was applied to characterize the molecular composition of DOM in the peat water extract (PWE). We identified typical patterns for DOM illustrated by van Krevelen plots, which indicate the presence of different substance classes including condensed aromatics, lignins and tannins known to complex iron. Our results indicate a variety of potential Fe-DOM-complexes present in the PWE samples when iron is incorporated into the elemental composition search. Using DPP we determine the complexation capacity of iron in the natural matrix of the fen along with the identification of ligands in order to estimate the iron bioavailability for bacteria. As the microbial redox system of the fen is impacted by other metals in the environment, we perform comprehensive analysis of the entirety of metal ions and concentrations in the water samples. Dialysis chambers are currently installed in the iron-rich fen from which pore water samples will be collected at 1 cm increments between 0-20 cm depth to determine the depth profiles of Fe(II)- and Fe(III)-concentration and evaluate the influence of the depth profiles on the interplay between microorganism comprising the natural microbial redox system of the fen. We have shown that metal-DOM-pH interactions affect the bioavailable metal concentration in fen water systems. This information will pave the way for a better understanding of the bacterial recruitment of trace elements and microbial redox reactions.

Molecular Tools for Investigating the Gut Microbiota

NASA Astrophysics Data System (ADS)

Lay, Christophe

The “microbial world within us” (Zoetendal et al., 2006) is populated by a complex society of indigenous microorganisms that feature different “ethnic” populations. Those microbial cells thriving within us are estimated to outnumber human body cells by a factor of ten to one. Insights into the relation between the intestinal microbial community and its host have been gained through gnotobiology. Indeed, the influence of the gut microbiota upon human development, physiology, immunity, and nutrition has been inferred by comparing gnotoxenic and axenic murine models (Hooper et al., 1998, 2002, 2003; Hooper and Gordon, 2001).

Modes of Action of Microbially-Produced Phytotoxins

PubMed Central

Duke, Stephen O.; Dayan, Franck E.

2011-01-01

Some of the most potent phytotoxins are synthesized by microbes. A few of these share molecular target sites with some synthetic herbicides, but many microbial toxins have unique target sites with potential for exploitation by the herbicide industry. Compounds from both non-pathogenic and pathogenic microbes are discussed. Microbial phytotoxins with modes of action the same as those of commercial herbicides and those with novel modes of action of action are covered. Examples of the compounds discussed are tentoxin, AAL-toxin, auscaulitoxin aglycone, hydantocidin, thaxtomin, and tabtoxin. PMID:22069756

Buried treasure: evolutionary perspectives on microbial iron piracy

PubMed Central

Barber, Matthew F.; Elde, Nels C.

2015-01-01

Host-pathogen interactions provide valuable systems for the study of evolutionary genetics and natural selection. The sequestration of essential iron has emerged as a critical innate defense system termed nutritional immunity, leading pathogens to evolve mechanisms of `iron piracy' to scavenge this metal from host proteins. This battle for iron carries numerous consequences not only for host-pathogen evolution, but also microbial community interactions. Here we highlight recent and potential future areas of investigation on the evolutionary implications of microbial iron piracy in relation to molecular arms races, host range, competition, and virulence. Applying evolutionary genetic approaches to the study of microbial iron acquisition could also provide new inroads for understanding and combating infectious disease. PMID:26431675

Microbial Enzymes: Tools for Biotechnological Processes

PubMed Central

Adrio, Jose L.; Demain, Arnold L.

2014-01-01

Microbial enzymes are of great importance in the development of industrial bioprocesses. Current applications are focused on many different markets including pulp and paper, leather, detergents and textiles, pharmaceuticals, chemical, food and beverages, biofuels, animal feed and personal care, among others. Today there is a need for new, improved or/and more versatile enzymes in order to develop more novel, sustainable and economically competitive production processes. Microbial diversity and modern molecular techniques, such as metagenomics and genomics, are being used to discover new microbial enzymes whose catalytic properties can be improved/modified by different strategies based on rational, semi-rational and random directed evolution. Most industrial enzymes are recombinant forms produced in bacteria and fungi. PMID:24970208

Development of a program to fit data to a new logistic model for microbial growth.

PubMed

Fujikawa, Hiroshi; Kano, Yoshihiro

2009-06-01

Recently we developed a mathematical model for microbial growth in food. The model successfully predicted microbial growth at various patterns of temperature. In this study, we developed a program to fit data to the model with a spread sheet program, Microsoft Excel. Users can instantly get curves fitted to the model by inputting growth data and choosing the slope portion of a curve. The program also could estimate growth parameters including the rate constant of growth and the lag period. This program would be a useful tool for analyzing growth data and further predicting microbial growth.

Extracellular enzymes facilitate electron uptake in biocorrosion and bioelectrosynthesis.

PubMed

Deutzmann, Jörg S; Sahin, Merve; Spormann, Alfred M

2015-04-21

Direct, mediator-free transfer of electrons between a microbial cell and a solid phase in its surrounding environment has been suggested to be a widespread and ecologically significant process. The high rates of microbial electron uptake observed during microbially influenced corrosion of iron [Fe(0)] and during microbial electrosynthesis have been considered support for a direct electron uptake in these microbial processes. However, the underlying molecular mechanisms of direct electron uptake are unknown. We investigated the electron uptake characteristics of the Fe(0)-corroding and electromethanogenic archaeon Methanococcus maripaludis and discovered that free, surface-associated redox enzymes, such as hydrogenases and presumably formate dehydrogenases, are sufficient to mediate an apparent direct electron uptake. In genetic and biochemical experiments, we showed that these enzymes, which are released from cells during routine culturing, catalyze the formation of H2 or formate when sorbed to an appropriate redox-active surface. These low-molecular-weight products are rapidly consumed by M. maripaludis cells when present, thereby preventing their accumulation to any appreciable or even detectable level. Rates of H2 and formate formation by cell-free spent culture medium were sufficient to explain the observed rates of methane formation from Fe(0) and cathode-derived electrons by wild-type M. maripaludis as well as by a mutant strain carrying deletions in all catabolic hydrogenases. Our data collectively show that cell-derived free enzymes can mimic direct extracellular electron transfer during Fe(0) corrosion and microbial electrosynthesis and may represent an ecologically important but so far overlooked mechanism in biological electron transfer. The intriguing trait of some microbial organisms to engage in direct electron transfer is thought to be widespread in nature. Consequently, direct uptake of electrons into microbial cells from solid surfaces is assumed to have a significant impact not only on fundamental microbial and biogeochemical processes but also on applied bioelectrochemical systems, such as microbial electrosynthesis and biocorrosion. This study provides a simple mechanistic explanation for frequently observed fast electron uptake kinetics in microbiological systems without a direct transfer: free, cell-derived enzymes can interact with cathodic surfaces and catalyze the formation of intermediates that are rapidly consumed by microbial cells. This electron transfer mechanism likely plays a significant role in various microbial electron transfer reactions in the environment. Copyright © 2015 Deutzmann et al.

Microbial Succession and Flavor Production in the Fermented Dairy Beverage Kefir

PubMed Central

Walsh, Aaron M.; Crispie, Fiona; Kilcawley, Kieran; O’Sullivan, Orla; O’Sullivan, Maurice G.; Claesson, Marcus J.

2016-01-01

ABSTRACT Kefir is a putatively health-promoting dairy beverage that is produced when a kefir grain, consisting of a consortium of microorganisms, is added to milk to initiate a natural fermentation. Here, a detailed analysis was carried out to determine how the microbial population, gene content, and flavor of three kefirs from distinct geographic locations change over the course of 24-h fermentations. Metagenomic sequencing revealed that Lactobacillus kefiranofaciens was the dominant bacterial species in kefir during early stages of fermentations but that Leuconostoc mesenteroides became more prevalent in later stages. This pattern is consistent with an observation that genes involved in aromatic amino acid biosynthesis were absent from L. kefiranofaciens but were present in L. mesenteroides. Additionally, these shifts in the microbial community structure, and associated pathways, corresponded to changes in the levels of volatile compounds. Specifically, Acetobacter spp. correlated with acetic acid; Lactobacillus spp. correlated with carboxylic acids, esters and ketones; Leuconostoc spp. correlated with acetic acid and 2,3-butanedione; and Saccharomyces spp. correlated with esters. The correlation data suggest a causal relationship between microbial taxa and flavor that is supported by observations that addition of L. kefiranofaciens NCFB 2797 increased the levels of esters and ketones whereas addition of L. mesenteroides 213M0 increased the levels of acetic acid and 2,3-butanedione. Finally, we detected genes associated with probiotic functionalities in the kefir microbiome. Our results illustrate the dynamic nature of kefir fermentations and microbial succession patterns therein and can be applied to optimize the fermentation processes, flavors, and health-related attributes of this and other fermented foods. IMPORTANCE Traditional fermented foods represent relatively low-complexity microbial environments that can be used as model microbial communities to understand how microbes interact in natural environments. Our results illustrate the dynamic nature of kefir fermentations and microbial succession patterns therein. In the process, the link between individual species, and associated pathways, with flavor compounds is revealed and several genes that could be responsible for the purported gut health-associated benefits of consuming kefir are identified. Ultimately, in addition to providing an important fundamental insight into microbial interactions, this information can be applied to optimize the fermentation processes, flavors, and health-related attributes of this and other fermented foods. Author Video: An author video summary of this article is available. PMID:27822552

Microbial Succession and Flavor Production in the Fermented Dairy Beverage Kefir.

PubMed

Walsh, Aaron M; Crispie, Fiona; Kilcawley, Kieran; O'Sullivan, Orla; O'Sullivan, Maurice G; Claesson, Marcus J; Cotter, Paul D

2016-01-01

Kefir is a putatively health-promoting dairy beverage that is produced when a kefir grain, consisting of a consortium of microorganisms, is added to milk to initiate a natural fermentation. Here, a detailed analysis was carried out to determine how the microbial population, gene content, and flavor of three kefirs from distinct geographic locations change over the course of 24-h fermentations. Metagenomic sequencing revealed that Lactobacillus kefiranofaciens was the dominant bacterial species in kefir during early stages of fermentations but that Leuconostoc mesenteroides became more prevalent in later stages. This pattern is consistent with an observation that genes involved in aromatic amino acid biosynthesis were absent from L. kefiranofaciens but were present in L. mesenteroides . Additionally, these shifts in the microbial community structure, and associated pathways, corresponded to changes in the levels of volatile compounds. Specifically, Acetobacter spp. correlated with acetic acid; Lactobacillus spp. correlated with carboxylic acids, esters and ketones; Leuconostoc spp. correlated with acetic acid and 2,3-butanedione; and Saccharomyces spp. correlated with esters. The correlation data suggest a causal relationship between microbial taxa and flavor that is supported by observations that addition of L. kefiranofaciens NCFB 2797 increased the levels of esters and ketones whereas addition of L. mesenteroides 213M0 increased the levels of acetic acid and 2,3-butanedione. Finally, we detected genes associated with probiotic functionalities in the kefir microbiome. Our results illustrate the dynamic nature of kefir fermentations and microbial succession patterns therein and can be applied to optimize the fermentation processes, flavors, and health-related attributes of this and other fermented foods. IMPORTANCE Traditional fermented foods represent relatively low-complexity microbial environments that can be used as model microbial communities to understand how microbes interact in natural environments. Our results illustrate the dynamic nature of kefir fermentations and microbial succession patterns therein. In the process, the link between individual species, and associated pathways, with flavor compounds is revealed and several genes that could be responsible for the purported gut health-associated benefits of consuming kefir are identified. Ultimately, in addition to providing an important fundamental insight into microbial interactions, this information can be applied to optimize the fermentation processes, flavors, and health-related attributes of this and other fermented foods.

Key factors controlling microbial community response after a fire: importance of severity and recurrence

NASA Astrophysics Data System (ADS)

Lombao, Alba; Barreiro, Ana; Martín, Ángela; Díaz-Raviña, Montserrat

2015-04-01

Microorganisms play an important role in forest ecosystems, especially after fire when vegetation is destroyed and soil is bared. Fire severity and recurrence might be one of main factors controlling the microbial response after a wildfire but information about this topic is scarce. The aim of this study is to evaluate the influence of fire regimen (recurrence and severity) on soil microbial community structure by means of the analysis of phospholipid fatty acid (PLFA). The study was performed with unburned and burned samples collected from the top layer of a soil affected by a high severity fire (Laza, NW Spain) heated under laboratory conditions at different temperatures (50°C, 75°C, 100°C, 125°C, 150°C, 175°C, 200°C, 300°C) to simulate different fire intensities; the process was repeated after further soil recovery (1 month incubation) to simulate fire recurrence. The soil temperature was measured with thermocouples and used to calculate the degree-hours as estimation of the amount of heat supplied to the samples (fire severity). The PLFA analysis was used to estimate total biomass and the biomass of specific groups (bacteria, fungi, gram-positive bacteria and gram-negative bacteria) as well as microbial community structure (PLFA pattern) and PLFA data were analyzed by means of principal component analysis (PCA) in order to identify main factors determining microbial community structure. The results of PCA, performed with the whole PLFA data set, showed that first component explained 35% of variation and clearly allow us to differentiate unburned samples from the corresponding burned samples, while the second component, explaining 16% of variation, separated samples according the heating temperature. A marked impact of fire regimen on soil microorganisms was detected; the microbial community response varied depending on previous history of soil heating and the magnitude of changes in the PLFA pattern was related to the amount of heat supplied to the samples. Thus, wildfire was the main factor determining the microbial community structure followed, in less extent, by fire severity. The total biomass and the biomass of specifics microbial groups decreased notably as consequence of wildfire and minor changes were detected due to soil heating under laboratory conditions. The results clearly showed the usefulness of PLFA pattern combined with PCA to study the relationships between fire regimen (recurrence and severity) and associated direct and indirect changes in soil microorganisms. The data also indicated that degree-hours methodology rather than temperature is adequate for evaluating the impact of soil heating on microbial communities. Keywords: wildfire, heating temperature, degree-hours, PLFA pattern, microbial biomass Acknowledgements. This study was supported by the Ministerio Español de Economía y Competitividad (AGL2012-39688-C02-01). A Lombao is recipient of FPU grant from Ministerio Español de Educación.

Surface, Water, and Air Biocharacterization (SWAB) Flight Experiment

NASA Technical Reports Server (NTRS)

Castro, V. A.; Ott, C. M.; Pierson, D. L.

2012-01-01

The determination of risk from infectious disease during spaceflight missions is composed of several factors including both the concentration and characteristics of the microorganisms to which the crew are exposed. Thus, having a good understanding of the microbial ecology aboard spacecraft provides the necessary information to mitigate health risks to the crew. While preventive measures are taken to minimize the presence of pathogens on spacecraft, medically significant organisms have been isolated from both the Mir and International Space Station (ISS). Historically, the method for isolation and identification of microorganisms from spacecraft environmental samples depended upon their growth on culture media. Unfortunately, only a fraction of the organisms may grow on a specific culture medium, potentially omitting those microorganisms whose nutritional and physical requirements for growth are not met. To address this bias in our understanding of the ISS environment, the Surface, Water, and Air Biocharacterization (SWAB) Flight Experiment was designed to investigate and develop monitoring technology to provide better microbial characterization. For the SWAB flight experiment, we hypothesized that environmental analysis using non-culture-based technologies would reveal microorganisms, allergens, and microbial toxins not previously reported in spacecraft, allowing for a more complete health assessment. Key findings during this experiment included: a) Generally, advanced molecular techniques were able to reveal a few organisms not recovered using culture-based methods; however, there is no indication that current monitoring is "missing" any medically significant bacteria or fungi. b) Molecular techniques have tremendous potential for microbial monitoring, however, sample preparation and data analysis present challenges for spaceflight hardware. c) Analytical results indicate that some molecular techniques, such as denaturing gradient gel electrophoresis (DGGE), can be much less sensitive than culture-based methods. d) More sensitive molecular techniques, such as quantitative polymerase chain reaction (QPCR), were able to identify viral DNA from ISS environments, suggesting potential transfer of the organism between crewmembers. In addition, the hardware selected for this experiment represented advances for next-generation sample collection. The advanced nature of this collection hardware was noted, when the Sartorius MD8 Air Port air sampler from the SWAB experiment remained on board ISS at the request of JAXA investigators, who intend to use it in completion of their microbial ecology experiment.

Characterization of Antimicrobial Resistance Patterns and Detection of Virulence Genes in Campylobacter Isolates in Italy

PubMed Central

Di Giannatale, Elisabetta; Di Serafino, Gabriella; Zilli, Katiuscia; Alessiani, Alessandra; Sacchini, Lorena; Garofolo, Giuliano; Aprea, Giuseppe; Marotta, Francesca

2014-01-01

Campylobacter has developed resistance to several antimicrobial agents over the years, including macrolides, quinolones and fluoroquinolones, becoming a significant public health hazard. A total of 145 strains derived from raw milk, chicken faeces, chicken carcasses, cattle faeces and human faeces collected from various Italian regions, were screened for antimicrobial susceptibility, molecular characterization (SmaI pulsed-field gel electrophoresis) and detection of virulence genes (sequencing and DNA microarray analysis). The prevalence of C. jejuni and C. coli was 62.75% and 37.24% respectively. Antimicrobial susceptibility revealed a high level of resistance for ciprofloxacin (62.76%), tetracycline (55.86%) and nalidixic acid (55.17%). Genotyping of Campylobacter isolates using PFGE revealed a total of 86 unique SmaI patterns. Virulence gene profiles were determined using a new microbial diagnostic microarray composed of 70-mer oligonucleotide probes targeting genes implicated in Campylobacter pathogenicity. Correspondence between PFGE and microarray clusters was observed. Comparisons of PFGE and virulence profiles reflected the high genetic diversity of the strains examined, leading us to speculate different degrees of pathogenicity inside Campylobacter populations. PMID:24556669

Characterization of antimicrobial resistance patterns and detection of virulence genes in Campylobacter isolates in Italy.

PubMed

Di Giannatale, Elisabetta; Di Serafino, Gabriella; Zilli, Katiuscia; Alessiani, Alessandra; Sacchini, Lorena; Garofolo, Giuliano; Aprea, Giuseppe; Marotta, Francesca

2014-02-19

Campylobacter has developed resistance to several antimicrobial agents over the years, including macrolides, quinolones and fluoroquinolones, becoming a significant public health hazard. A total of 145 strains derived from raw milk, chicken faeces, chicken carcasses, cattle faeces and human faeces collected from various Italian regions, were screened for antimicrobial susceptibility, molecular characterization (SmaI pulsed-field gel electrophoresis) and detection of virulence genes (sequencing and DNA microarray analysis). The prevalence of C. jejuni and C. coli was 62.75% and 37.24% respectively. Antimicrobial susceptibility revealed a high level of resistance for ciprofloxacin (62.76%), tetracycline (55.86%) and nalidixic acid (55.17%). Genotyping of Campylobacter isolates using PFGE revealed a total of 86 unique SmaI patterns. Virulence gene profiles were determined using a new microbial diagnostic microarray composed of 70-mer oligonucleotide probes targeting genes implicated in Campylobacter pathogenicity. Correspondence between PFGE and microarray clusters was observed. Comparisons of PFGE and virulence profiles reflected the high genetic diversity of the strains examined, leading us to speculate different degrees of pathogenicity inside Campylobacter populations.

A Modular Approach to a Library of Semi-Synthetic Fucosylated Chondroitin Sulfate Polysaccharides with Different Sulfation and Fucosylation Patterns.

PubMed

Laezza, Antonio; Iadonisi, Alfonso; Pirozzi, Anna V A; Diana, Paola; De Rosa, Mario; Schiraldi, Chiara; Parrilli, Michelangelo; Bedini, Emiliano

2016-12-12

Fucosylated chondroitin sulfate (fCS)-a glycosaminoglycan (GAG) found in sea cucumbers-has recently attracted much attention owing to its biological properties. In particular, a low molecular mass fCS polysaccharide has very recently been suggested as a strong candidate for the development of an antithrombotic drug that would be safer and more effective than heparin. To avoid the use of animal sourced drugs, here we present the chemical transformation of a microbial sourced unsulfated chondroitin polysaccharide into a small library of fucosylated (and sulfated) derivatives thereof. To this aim, a modular approach based on the different combination of only five reactions was employed, with an almost unprecedented polysaccharide branching by O-glycosylation as the key step. The library was differentiated for sulfation patterns and/or positions of the fucose branches, as confirmed by detailed 2D NMR spectroscopic analysis. These semi-synthetic polysaccharides will allow a wider and more accurate structure-activity relationship study with respect to those reported in literature to date. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Microbial populations in contaminant plumes

USGS Publications Warehouse

Haack, S.K.; Bekins, B.A.

2000-01-01

Efficient biodegradation of subsurface contaminants requires two elements: (1) microbial populations with the necessary degradative capabilities, and (2) favorable subsurface geochemical and hydrological conditions. Practical constraints on experimental design and interpretation in both the hydrogeological and microbiological sciences have resulted in limited knowledge of the interaction between hydrogeological and microbiological features of subsurface environments. These practical constraints include: (1) inconsistencies between the scales of investigation in the hydrogeological and microbiological sciences, and (2) practical limitations on the ability to accurately define microbial populations in environmental samples. However, advances in application of small-scale sampling methods and interdisciplinary approaches to site investigations are beginning to significantly improve understanding of hydrogeological and microbiological interactions. Likewise, culture-based and molecular analyses of microbial populations in subsurface contaminant plumes have revealed significant adaptation of microbial populations to plume environmental conditions. Results of recent studies suggest that variability in subsurface geochemical and hydrological conditions significantly influences subsurface microbial-community structure. Combined investigations of site conditions and microbial-community structure provide the knowledge needed to understand interactions between subsurface microbial populations, plume geochemistry, and contaminant biodegradation.

The microorganisms used for working in microbial fuel cells

NASA Astrophysics Data System (ADS)

Konovalova, E. Yu.; Stom, D. I.; Zhdanova, G. O.; Yuriev, D. A.; Li, Youming; Barbora, Lepakshi; Goswami, Pranab

2018-04-01

Investigated the use as biological object in microbial fuel cells (MFC) of various microorganisms performing the transport of electrons in the processing of various substrates. Most MFC, uses complex substrates. Such MFC filled with associations of microorganisms. The article deals with certain types of microorganisms for use in the MFC, shows the characteristics of molecular electron transfer mechanisms microorganisms into the environment.

Molecular Interactions at Marine Interfaces

DTIC Science & Technology

1994-09-20

Microbial Attachment and Biofilm Formation 9:00 Michael Sinnott Structure of Extracellular Polysaccharides of Pseudomonas atlantica 9:30 Herb Waite...sit/ i u~ . Direct Measurements of the Intermolecular F~rccs Between Polysaccharide Exopolymers from marine Bacter"a and Solid Substrates Georges...aqueous medium of high ionic strength. Effect of Polysaccharide Surface Structurt on Microbial Attachment and Biofilm Formation David C. White and A

The usual suspects : fingerprinting microbial communities involved in decay of treated southern yellow pine

Treesearch

Grant T. Kirker; Susan V. Diehl; M. Lynn Prewitt

2010-01-01

Currrent standards for soil-block testing have long been based on the effectiveness of preservative systems against only a small number of wood decay fungi and even fewer bacteria. Culture-independent molecular methods offer simple, reproducible means to obtain a more holistic view of the microbial communities that colonize wood throughout the decay process. By using a...

Environmental proteomics reveals taxonomic and functional changes in an enriched aquatic ecosystem.

PubMed

Northrop, Amanda C; Brooks, Rachel; Ellison, Aaron M; Gotelli, Nicholas J; Ballif, Bryan A

2017-10-01

Aquatic ecosystem enrichment can lead to distinct and irreversible changes to undesirable states. Understanding changes in active microbial community function and composition following organic-matter loading in enriched ecosystems can help identify biomarkers of such state changes. In a field experiment, we enriched replicate aquatic ecosystems in the pitchers of the northern pitcher plant, Sarracenia purpurea . Shotgun metaproteomics using a custom metagenomic database identified proteins, molecular pathways, and contributing microbial taxa that differentiated control ecosystems from those that were enriched. The number of microbial taxa contributing to protein expression was comparable between treatments; however, taxonomic evenness was higher in controls. Functionally active bacterial composition differed significantly among treatments and was more divergent in control pitchers than enriched pitchers. Aerobic and facultative anaerobic bacteria contributed most to identified proteins in control and enriched ecosystems, respectively. The molecular pathways and contributing taxa in enriched pitcher ecosystems were similar to those found in larger enriched aquatic ecosystems and are consistent with microbial processes occurring at the base of detrital food webs. Detectable differences between protein profiles of enriched and control ecosystems suggest that a time series of environmental proteomics data may identify protein biomarkers of impending state changes to enriched states.

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.

Ex situ bioremediation of oil-contaminated soil.

PubMed

Lin, Ta-Chen; Pan, Po-Tsen; Cheng, Sheng-Shung

2010-04-15

An innovative bioprocess method, Systematic Environmental Molecular Bioremediation Technology (SEMBT) that combines bioaugmentation and biostimulation with a molecular monitoring microarray biochip, was developed as an integrated bioremediation technology to treat S- and T-series biopiles by using the landfarming operation and reseeding process to enhance the bioremediation efficiency. After 28 days of the bioremediation process, diesel oil (TPH(C10-C28)) and fuel oil (TPH(C10-C40)) were degraded up to approximately 70% and 63% respectively in the S-series biopiles. When the bioaugmentation and biostimulation were applied in the beginning of bioremediation, the microbial concentration increased from approximately 10(5) to 10(6) CFU/g dry soil along with the TPH biodegradation. Analysis of microbial diversity in the contaminated soils by microarray biochips revealed that Acinetobacter sp. and Pseudomonas aeruginosa were the predominant groups in indigenous consortia, while the augmented consortia were Gordonia alkanivorans and Rhodococcus erythropolis in both series of biopiles during bioremediation. Microbial respiration as influenced by the microbial activity reflected directly the active microbial population and indirectly the biodegradation of TPH. Field experimental results showed that the residual TPH concentration in the complex biopile was reduced to less than 500 mg TPH/kg dry soil. The above results demonstrated that the SEMBT technology is a feasible alternative to bioremediate the oil-contaminated soil. Crown Copyright 2009. Published by Elsevier B.V. All rights reserved.

Diversity of Anaerobic Microbes in Spacecraft Assembly Clean Rooms ▿ †

PubMed Central

Probst, Alexander; Vaishampayan, Parag; Osman, Shariff; Moissl-Eichinger, Christine; Andersen, Gary L.; Venkateswaran, Kasthuri

2010-01-01

Although the cultivable and noncultivable microbial diversity of spacecraft assembly clean rooms has been previously documented using conventional and state-of-the-art molecular techniques, the occurrence of obligate anaerobes within these clean rooms is still uncertain. Therefore, anaerobic bacterial communities of three clean-room facilities were analyzed during assembly of the Mars Science Laboratory rover. Anaerobic bacteria were cultured on several media, and DNA was extracted from suitable anaerobic enrichments and examined with conventional 16S rRNA gene clone library, as well as high-density phylogenetic 16S rRNA gene microarray (PhyloChip) technologies. The culture-dependent analyses predominantly showed the presence of clostridial and propionibacterial strains. The 16S rRNA gene sequences retrieved from clone libraries revealed distinct microbial populations associated with each clean-room facility, clustered exclusively within gram-positive organisms. PhyloChip analysis detected a greater microbial diversity, spanning many phyla of bacteria, and provided a deeper insight into the microbial community structure of the clean-room facilities. This study presents an integrated approach for assessing the anaerobic microbial population within clean-room facilities, using both molecular and cultivation-based analyses. The results reveal that highly diverse anaerobic bacterial populations persist in the clean rooms even after the imposition of rigorous maintenance programs and will pose a challenge to planetary protection implementation activities. PMID:20228115

Metagenomic analysis of the rhizosphere soil microbiome with respect to phytic acid utilization.

PubMed

Unno, Yusuke; Shinano, Takuro

2013-01-01

While phytic acid is a major form of organic phosphate in many soils, plant utilization of phytic acid is normally limited; however, culture trials of Lotus japonicus using experimental field soil that had been managed without phosphate fertilizer for over 90 years showed significant usage of phytic acid applied to soil for growth and flowering and differences in the degree of growth, even in the same culture pot. To understand the key metabolic processes involved in soil phytic acid utilization, we analyzed rhizosphere soil microbial communities using molecular ecological approaches. Although molecular fingerprint analysis revealed changes in the rhizosphere soil microbial communities from bulk soil microbial community, no clear relationship between the microbiome composition and flowering status that might be related to phytic acid utilization of L. japonicus could be determined. However, metagenomic analysis revealed changes in the relative abundance of the classes Bacteroidetes, Betaproteobacteria, Chlorobi, Dehalococcoidetes and Methanobacteria, which include strains that potentially promote plant growth and phytic acid utilization, and some gene clusters relating to phytic acid utilization, such as alkaline phosphatase and citrate synthase, with the phytic acid utilization status of the plant. This study highlights phylogenetic and metabolic features of the microbial community of the L. japonicus rhizosphere and provides a basic understanding of how rhizosphere microbial communities affect the phytic acid status in soil.

Belowground Response to Drought in a Tropical Forest Soil. II. Change in Microbial Function Impacts Carbon Composition

Treesearch

Nicholas J. Bouskill; Tana E. Wood; Richard Baran; Zhao Hao; Zaw Ye; Ben P. Bowen; Hsiao Chien Lim; Peter S. Nico; Hoi-Ying Holman; Benjamin Gilbert; Whendee L. Silver; Trent R. Northen; Eoin L. Brodie

2016-01-01

Climate model projections for tropical regions show clear perturbation of precipitation patterns leading to increased frequency and severity of drought in some regions. Previous work has shown declining soil moisture to be a strong driver of changes in microbial trait distribution, however...

Effects of Bacillus subtilis-based direct-fed microbials on growth performance, immune characteristics and resistance against experimental coccidiosis in broiler chickens

USDA-ARS?s Scientific Manuscript database

The present experiment was conducted to study the effects of dietary Bacillus-based direct-fed microbials (DFMs) on cytokine expression patterns, intestinal intraepithelial lymphocyte (IEL) subpopulation, splenocyte proliferation, macrophage functions and resistance against experimental coccidiosis ...

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Geographical patterns of the standing and active human gut microbiome in health and IBD.

PubMed

Rehman, Ateequr; Rausch, Philipp; Wang, Jun; Skieceviciene, Jurgita; Kiudelis, Gediminas; Bhagalia, Ketan; Amarapurkar, Deepak; Kupcinskas, Limas; Schreiber, Stefan; Rosenstiel, Philip; Baines, John F; Ott, Stephan

2016-02-01

A global increase of IBD has been reported, especially in countries that previously had low incidence rates. Also, the knowledge of the human gut microbiome is steadily increasing, however, limited information regarding its variation on a global scale is available. In the light of the microbial involvement in IBDs, we aimed to (1) identify shared and distinct IBD-associated mucosal microbiota patterns from different geographical regions including Europe (Germany, Lithuania) and South Asia (India) and (2) determine whether profiling based on 16S rRNA transcripts provides additional resolution, both of which may hold important clinical relevance. In this study, we analyse a set of 89 mucosal biopsies sampled from individuals of German, Lithuanian and Indian origins, using bacterial community profiling of a roughly equal number of healthy controls, patients with Crohn's disease and UC from each location, and analyse 16S rDNA and rRNA as proxies for standing and active microbial community structure, respectively. We find pronounced population-specific as well as general disease patterns in the major phyla and patterns of diversity, which differ between the standing and active communities. The geographical origin of samples dominates the patterns of β diversity with locally restricted disease clusters and more pronounced effects in the active microbial communities. However, two genera belonging to the Clostridium leptum subgroup, Faecalibacteria and Papillibacter, display consistent patterns with respect to disease status and may thus serve as reliable 'microbiomarkers'. These analyses reveal important interactions of patients' geographical origin and disease in the interpretation of disease-associated changes in microbial communities and highlight the added value of analysing communities on both the 16S rRNA gene (DNA) and transcript (RNA) level. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Multiparametric monitoring of microbial faecal pollution reveals the dominance of human contamination along the whole Danube River

PubMed Central

Kirschner, A.K.T.; Reischer, G.H.; Jakwerth, S.; Savio, D.; Ixenmaier, S.; Toth, E.; Sommer, R.; Mach, R.L.; Linke, R.; Eiler, A.; Kolarevic, S.; Farnleitner, A.H.

2017-01-01

The microbial faecal pollution of rivers has wide-ranging impacts on a variety of human activities that rely on appropriate river water quality. Thus, detailed knowledge of the extent and origin of microbial faecal pollution is crucial for watershed management activities to maintain safe water use. In this study, the microbial faecal pollution levels were monitored by standard faecal indicator bacteria (SFIB) along a 2580 km stretch of the Danube, the world's most international river, as well as the Danube's most important tributaries. To track the origin of faecal pollution, host-associated Bacteroidetes genetic faecal marker qPCR assays for different host groups were applied in concert with SFIB. The spatial resolution analysis was followed by a time resolution analysis of faecal pollution patterns over 1 year at three selected sites. In this way, a comprehensive faecal pollution map of the total length of the Danube was created, combining substantiated information on both the extent and origin of microbial faecal pollution. Within the environmental data matrix for the river, microbial faecal pollution constituted an independent component and did not cluster with any other measured environmental parameters. Generally, midstream samples representatively depicted the microbial pollution levels at the respective river sites. However, at a few, somewhat unexpected sites, high pollution levels occurred in the lateral zones of the river while the midstream zone had good water quality. Human faecal pollution was demonstrated as the primary pollution source along the whole river, while animal faecal pollution was of minor importance. This study demonstrates that the application of host-associated genetic microbial source tracking markers in concert with the traditional concept of microbial faecal pollution monitoring based on SFIB significantly enhances the knowledge of the extent and origin of microbial faecal pollution patterns in large rivers. It constitutes a powerful tool to guide target-oriented water quality management in large river basins. PMID:28806705

Multiparametric monitoring of microbial faecal pollution reveals the dominance of human contamination along the whole Danube River.

PubMed

Kirschner, A K T; Reischer, G H; Jakwerth, S; Savio, D; Ixenmaier, S; Toth, E; Sommer, R; Mach, R L; Linke, R; Eiler, A; Kolarevic, S; Farnleitner, A H

2017-11-01

The microbial faecal pollution of rivers has wide-ranging impacts on a variety of human activities that rely on appropriate river water quality. Thus, detailed knowledge of the extent and origin of microbial faecal pollution is crucial for watershed management activities to maintain safe water use. In this study, the microbial faecal pollution levels were monitored by standard faecal indicator bacteria (SFIB) along a 2580 km stretch of the Danube, the world's most international river, as well as the Danube's most important tributaries. To track the origin of faecal pollution, host-associated Bacteroidetes genetic faecal marker qPCR assays for different host groups were applied in concert with SFIB. The spatial resolution analysis was followed by a time resolution analysis of faecal pollution patterns over 1 year at three selected sites. In this way, a comprehensive faecal pollution map of the total length of the Danube was created, combining substantiated information on both the extent and origin of microbial faecal pollution. Within the environmental data matrix for the river, microbial faecal pollution constituted an independent component and did not cluster with any other measured environmental parameters. Generally, midstream samples representatively depicted the microbial pollution levels at the respective river sites. However, at a few, somewhat unexpected sites, high pollution levels occurred in the lateral zones of the river while the midstream zone had good water quality. Human faecal pollution was demonstrated as the primary pollution source along the whole river, while animal faecal pollution was of minor importance. This study demonstrates that the application of host-associated genetic microbial source tracking markers in concert with the traditional concept of microbial faecal pollution monitoring based on SFIB significantly enhances the knowledge of the extent and origin of microbial faecal pollution patterns in large rivers. It constitutes a powerful tool to guide target-oriented water quality management in large river basins. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Optical Measurement of Cell Colonization Patterns on Individual Suspended Sediment Aggregates

NASA Astrophysics Data System (ADS)

Nguyen, Thu Ha; Tang, Fiona H. M.; Maggi, Federico

2017-10-01

Microbial processes can make substantial differences to the way in which particles settle in aquatic environments. A novel method (OMCEC, optical measurement of cell colonization) is introduced to systematically map the biological spatial distribution over individual suspended sediment aggregates settling through a water column. OMCEC was used to investigate (1) whether a carbon source concentration has an impact on cell colonization, (2) how cells colonize minerals, and (3) if a correlation between colonization patterns and aggregate geometry exists. Incubations of Saccharomyces cerevisiae and stained montmorillonite at four sucrose concentrations were tested in a settling column equipped with a full-color microparticle image velocimetry system. The acquired high-resolution images were processed to map the cell distribution on aggregates based on emission spectra separation. The likelihood of cells colonizing minerals increased with increasing sucrose concentration. Colonization patterns were classified into (i) scattered, (ii) well touched, and (iii) poorly touched, with the second being predominant. Cell clusters in well-touched patterns were found to have lower capacity dimension than those in other patterns, while the capacity dimension of the corresponding aggregates was relatively high. A strong correlation of colonization patterns with aggregate biomass fraction and properties suggests dynamic colonization mechanisms from cell attachment to minerals, to joining of isolated cell clusters, and finally cell growth over the entire aggregate. This paper introduces a widely applicable method for analyses of microbial-affected sediment dynamics and highlights the microbial control on aggregate geometry, which can improve the prediction of large-scale morphodynamics processes.

The interacting roles of climate, soils, and plant production on soil microbial communities at a continental scale

USGS Publications Warehouse

Waldrop, Mark P.; Holloway, JoAnn M.; Smith, David; Goldhaber, Martin B.; Drenovsky, R.E.; Scow, K.M.; Dick, R.; Howard, Daniel M.; Wylie, Bruce K.; Grace, James B.

2017-01-01

Soil microbial communities control critical ecosystem processes such as decomposition, nutrient cycling, and soil organic matter formation. Continental scale patterns in the composition and functioning of microbial communities are related to climatic, biotic, and edaphic factors such as temperature and precipitation, plant community composition, and soil carbon, nitrogen, and pH. Although these relationships have been well explored individually, the examination of the factors that may act directly on microbial communities vs. those that may act indirectly through other ecosystem properties has not been well developed. To further such understanding, we utilized structural equation modeling (SEM) to evaluate a set of hypotheses about the direct and indirect effects of climatic, biotic, and edaphic variables on microbial communities across the continental United States. The primary goals of this work were to test our current understanding of the interactions among climate, soils, and plants in affecting microbial community composition, and to examine whether variation in the composition of the microbial community affects potential rates of soil enzymatic activities. A model of interacting factors created through SEM shows several expected patterns. Distal factors such as climate had indirect effects on microbial communities by influencing plant productivity, soil mineralogy, and soil pH, but factors related to soil organic matter chemistry had the most direct influence on community composition. We observed that both plant productivity and soil mineral composition were important indirect influences on community composition at the continental scale, both interacting to affect organic matter content and microbial biomass and ultimately community composition. Although soil hydrolytic enzymes were related to the moisture regime and soil carbon, oxidative enzymes were also affected by community composition, reflected in the abundance of soil fungi. These results highlight that soil microbial communities can be modeled within the context of multiple interacting ecosystem properties acting both directly and indirectly on their composition and function, and this provides a rich and informative context with which to examine communities. This work also highlights that variation in climate, microbial biomass, and microbial community composition can affect maximum rates of soil enzyme activities, potentially influencing rates of decomposition and nutrient mineralization in soils.

Min Zhang | NREL

Science.gov Websites

Min Zhang Photo of Min Zhang Min Zhang Researcher V-Molecular Biology Min.Zhang@nrel.gov | 303-384 -7753 Research Interests Using a systems biology approach to identify, analyze, and engineer pathways Metabolic engineering Molecular biology Microbial physiology Systems biology Fermentation development Enzyme

Microbial community in persistent apical periodontitis: a 16S rRNA gene clone library analysis.

PubMed

Zakaria, M N; Takeshita, T; Shibata, Y; Maeda, H; Wada, N; Akamine, A; Yamashita, Y

2015-08-01

To characterize the microbial composition of persistent periapical lesions of root filled teeth using a molecular genetics approach. Apical lesion samples were collected from 12 patients (23-80 years old) who visited the Kyushu University Hospital for apicectomy with persistent periapical lesions associated with root filled teeth. DNA was directly extracted from each sample and the microbial composition was comprehensively analysed using clone library analysis of the 16S rRNA gene. Enterococcus faecalis, Candida albicans and specific fimA genotypes of Porphyromonas gingivalis were confirmed using polymerase chain reaction (PCR) analysis with specific primers. Bacteria were detected in all samples, and the dominant findings were P. gingivalis (19.9%), Fusobacterium nucleatum (11.2%) and Propionibacterium acnes (9%). Bacterial diversity was greater in symptomatic lesions than in asymptomatic ones. In addition, the following bacteria or bacterial combinations were characteristic to symptomatic lesions: Prevotella spp., Treponema spp., Peptostreptococcaceae sp. HOT-113, Olsenella uli, Slackia exigua, Selemonas infelix, P. gingivalis with type IV fimA, and a combination of P. gingivalis, F. nucleatum, and Peptostreptococcaceae sp. HOT-113 and predominance of Streptococcus spp. On the other hand, neither Enterococcus faecalis nor C. albicans were detected in any of the samples. Whilst a diverse bacterial species were observed in the persistent apical lesions, some characteristic patterns of bacterial community were found in the symptomatic lesions. The diverse variation of community indicates that bacterial combinations as a community may cause persistent inflammation in periapical tissues rather than specific bacterial species. © 2014 International Endodontic Journal. Published by John Wiley & Sons Ltd.

Integrating biogeochemistry with multiomic sequence information in a model oxygen minimum zone

PubMed Central

Hawley, Alyse K.; Katsev, Sergei; Torres-Beltran, Monica; Bhatia, Maya P.; Kheirandish, Sam; Michiels, Céline C.; Capelle, David; Lavik, Gaute; Doebeli, Michael; Crowe, Sean A.; Hallam, Steven J.

2016-01-01

Microorganisms are the most abundant lifeform on Earth, mediating global fluxes of matter and energy. Over the past decade, high-throughput molecular techniques generating multiomic sequence information (DNA, mRNA, and protein) have transformed our perception of this microcosmos, conceptually linking microorganisms at the individual, population, and community levels to a wide range of ecosystem functions and services. Here, we develop a biogeochemical model that describes metabolic coupling along the redox gradient in Saanich Inlet—a seasonally anoxic fjord with biogeochemistry analogous to oxygen minimum zones (OMZs). The model reproduces measured biogeochemical process rates as well as DNA, mRNA, and protein concentration profiles across the redox gradient. Simulations make predictions about the role of ubiquitous OMZ microorganisms in mediating carbon, nitrogen, and sulfur cycling. For example, nitrite “leakage” during incomplete sulfide-driven denitrification by SUP05 Gammaproteobacteria is predicted to support inorganic carbon fixation and intense nitrogen loss via anaerobic ammonium oxidation. This coupling creates a metabolic niche for nitrous oxide reduction that completes denitrification by currently unidentified community members. These results quantitatively improve previous conceptual models describing microbial metabolic networks in OMZs. Beyond OMZ-specific predictions, model results indicate that geochemical fluxes are robust indicators of microbial community structure and reciprocally, that gene abundances and geochemical conditions largely determine gene expression patterns. The integration of real observational data, including geochemical profiles and process rate measurements as well as metagenomic, metatranscriptomic and metaproteomic sequence data, into a biogeochemical model, as shown here, enables holistic insight into the microbial metabolic network driving nutrient and energy flow at ecosystem scales. PMID:27655888

Integrating biogeochemistry with multiomic sequence information in a model oxygen minimum zone.

PubMed

Louca, Stilianos; Hawley, Alyse K; Katsev, Sergei; Torres-Beltran, Monica; Bhatia, Maya P; Kheirandish, Sam; Michiels, Céline C; Capelle, David; Lavik, Gaute; Doebeli, Michael; Crowe, Sean A; Hallam, Steven J

2016-10-04

Microorganisms are the most abundant lifeform on Earth, mediating global fluxes of matter and energy. Over the past decade, high-throughput molecular techniques generating multiomic sequence information (DNA, mRNA, and protein) have transformed our perception of this microcosmos, conceptually linking microorganisms at the individual, population, and community levels to a wide range of ecosystem functions and services. Here, we develop a biogeochemical model that describes metabolic coupling along the redox gradient in Saanich Inlet-a seasonally anoxic fjord with biogeochemistry analogous to oxygen minimum zones (OMZs). The model reproduces measured biogeochemical process rates as well as DNA, mRNA, and protein concentration profiles across the redox gradient. Simulations make predictions about the role of ubiquitous OMZ microorganisms in mediating carbon, nitrogen, and sulfur cycling. For example, nitrite "leakage" during incomplete sulfide-driven denitrification by SUP05 Gammaproteobacteria is predicted to support inorganic carbon fixation and intense nitrogen loss via anaerobic ammonium oxidation. This coupling creates a metabolic niche for nitrous oxide reduction that completes denitrification by currently unidentified community members. These results quantitatively improve previous conceptual models describing microbial metabolic networks in OMZs. Beyond OMZ-specific predictions, model results indicate that geochemical fluxes are robust indicators of microbial community structure and reciprocally, that gene abundances and geochemical conditions largely determine gene expression patterns. The integration of real observational data, including geochemical profiles and process rate measurements as well as metagenomic, metatranscriptomic and metaproteomic sequence data, into a biogeochemical model, as shown here, enables holistic insight into the microbial metabolic network driving nutrient and energy flow at ecosystem scales.

Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat.

PubMed

Harris, J Kirk; Caporaso, J Gregory; Walker, Jeffrey J; Spear, John R; Gold, Nicholas J; Robertson, Charles E; Hugenholtz, Philip; Goodrich, Julia; McDonald, Daniel; Knights, Dan; Marshall, Paul; Tufo, Henry; Knight, Rob; Pace, Norman R

2013-01-01

The microbial mats of Guerrero Negro (GN), Baja California Sur, Mexico historically were considered a simple environment, dominated by cyanobacteria and sulfate-reducing bacteria. Culture-independent rRNA community profiling instead revealed these microbial mats as among the most phylogenetically diverse environments known. A preliminary molecular survey of the GN mat based on only ∼1500 small subunit rRNA gene sequences discovered several new phylum-level groups in the bacterial phylogenetic domain and many previously undetected lower-level taxa. We determined an additional ∼119,000 nearly full-length sequences and 28,000 >200 nucleotide 454 reads from a 10-layer depth profile of the GN mat. With this unprecedented coverage of long sequences from one environment, we confirm the mat is phylogenetically stratified, presumably corresponding to light and geochemical gradients throughout the depth of the mat. Previous shotgun metagenomic data from the same depth profile show the same stratified pattern and suggest that metagenome properties may be predictable from rRNA gene sequences. We verify previously identified novel lineages and identify new phylogenetic diversity at lower taxonomic levels, for example, thousands of operational taxonomic units at the family-genus levels differ considerably from known sequences. The new sequences populate parts of the bacterial phylogenetic tree that previously were poorly described, but indicate that any comprehensive survey of GN diversity has only begun. Finally, we show that taxonomic conclusions are generally congruent between Sanger and 454 sequencing technologies, with the taxonomic resolution achieved dependent on the abundance of reference sequences in the relevant region of the rRNA tree of life.

Extracellular Enzymes Facilitate Electron Uptake in Biocorrosion and Bioelectrosynthesis

PubMed Central

Deutzmann, Jörg S.; Sahin, Merve

2015-01-01

ABSTRACT Direct, mediator-free transfer of electrons between a microbial cell and a solid phase in its surrounding environment has been suggested to be a widespread and ecologically significant process. The high rates of microbial electron uptake observed during microbially influenced corrosion of iron [Fe(0)] and during microbial electrosynthesis have been considered support for a direct electron uptake in these microbial processes. However, the underlying molecular mechanisms of direct electron uptake are unknown. We investigated the electron uptake characteristics of the Fe(0)-corroding and electromethanogenic archaeon Methanococcus maripaludis and discovered that free, surface-associated redox enzymes, such as hydrogenases and presumably formate dehydrogenases, are sufficient to mediate an apparent direct electron uptake. In genetic and biochemical experiments, we showed that these enzymes, which are released from cells during routine culturing, catalyze the formation of H2 or formate when sorbed to an appropriate redox-active surface. These low-molecular-weight products are rapidly consumed by M. maripaludis cells when present, thereby preventing their accumulation to any appreciable or even detectable level. Rates of H2 and formate formation by cell-free spent culture medium were sufficient to explain the observed rates of methane formation from Fe(0) and cathode-derived electrons by wild-type M. maripaludis as well as by a mutant strain carrying deletions in all catabolic hydrogenases. Our data collectively show that cell-derived free enzymes can mimic direct extracellular electron transfer during Fe(0) corrosion and microbial electrosynthesis and may represent an ecologically important but so far overlooked mechanism in biological electron transfer. PMID:25900658

Automated DNA extraction platforms offer solutions to challenges of assessing microbial biofouling in oil production facilities.

PubMed

Oldham, Athenia L; Drilling, Heather S; Stamps, Blake W; Stevenson, Bradley S; Duncan, Kathleen E

2012-11-20

The analysis of microbial assemblages in industrial, marine, and medical systems can inform decisions regarding quality control or mitigation. Modern molecular approaches to detect, characterize, and quantify microorganisms provide rapid and thorough measures unbiased by the need for cultivation. The requirement of timely extraction of high quality nucleic acids for molecular analysis is faced with specific challenges when used to study the influence of microorganisms on oil production. Production facilities are often ill equipped for nucleic acid extraction techniques, making the preservation and transportation of samples off-site a priority. As a potential solution, the possibility of extracting nucleic acids on-site using automated platforms was tested. The performance of two such platforms, the Fujifilm QuickGene-Mini80™ and Promega Maxwell®16 was compared to a widely used manual extraction kit, MOBIO PowerBiofilm™ DNA Isolation Kit, in terms of ease of operation, DNA quality, and microbial community composition. Three pipeline biofilm samples were chosen for these comparisons; two contained crude oil and corrosion products and the third transported seawater. Overall, the two more automated extraction platforms produced higher DNA yields than the manual approach. DNA quality was evaluated for amplification by quantitative PCR (qPCR) and end-point PCR to generate 454 pyrosequencing libraries for 16S rRNA microbial community analysis. Microbial community structure, as assessed by DGGE analysis and pyrosequencing, was comparable among the three extraction methods. Therefore, the use of automated extraction platforms should enhance the feasibility of rapidly evaluating microbial biofouling at remote locations or those with limited resources.

Automated DNA extraction platforms offer solutions to challenges of assessing microbial biofouling in oil production facilities

PubMed Central

2012-01-01

The analysis of microbial assemblages in industrial, marine, and medical systems can inform decisions regarding quality control or mitigation. Modern molecular approaches to detect, characterize, and quantify microorganisms provide rapid and thorough measures unbiased by the need for cultivation. The requirement of timely extraction of high quality nucleic acids for molecular analysis is faced with specific challenges when used to study the influence of microorganisms on oil production. Production facilities are often ill equipped for nucleic acid extraction techniques, making the preservation and transportation of samples off-site a priority. As a potential solution, the possibility of extracting nucleic acids on-site using automated platforms was tested. The performance of two such platforms, the Fujifilm QuickGene-Mini80™ and Promega Maxwell®16 was compared to a widely used manual extraction kit, MOBIO PowerBiofilm™ DNA Isolation Kit, in terms of ease of operation, DNA quality, and microbial community composition. Three pipeline biofilm samples were chosen for these comparisons; two contained crude oil and corrosion products and the third transported seawater. Overall, the two more automated extraction platforms produced higher DNA yields than the manual approach. DNA quality was evaluated for amplification by quantitative PCR (qPCR) and end-point PCR to generate 454 pyrosequencing libraries for 16S rRNA microbial community analysis. Microbial community structure, as assessed by DGGE analysis and pyrosequencing, was comparable among the three extraction methods. Therefore, the use of automated extraction platforms should enhance the feasibility of rapidly evaluating microbial biofouling at remote locations or those with limited resources. PMID:23168231

Competitive resource allocation to metabolic pathways contributes to overflow metabolisms and emergent properties in cross-feeding microbial consortia.

PubMed

Carlson, Ross P; Beck, Ashley E; Phalak, Poonam; Fields, Matthew W; Gedeon, Tomas; Hanley, Luke; Harcombe, William R; Henson, Michael A; Heys, Jeffrey J

2018-04-17

Resource scarcity is a common stress in nature and has a major impact on microbial physiology. This review highlights microbial acclimations to resource scarcity, focusing on resource investment strategies for chemoheterotrophs from the molecular level to the pathway level. Competitive resource allocation strategies often lead to a phenotype known as overflow metabolism; the resulting overflow byproducts can stabilize cooperative interactions in microbial communities and can lead to cross-feeding consortia. These consortia can exhibit emergent properties such as enhanced resource usage and biomass productivity. The literature distilled here draws parallels between in silico and laboratory studies and ties them together with ecological theories to better understand microbial stress responses and mutualistic consortia functioning. © 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

Predicting taxonomic and functional structure of microbial communities in acid mine drainage

PubMed Central

Kuang, Jialiang; Huang, Linan; He, Zhili; Chen, Linxing; Hua, Zhengshuang; Jia, Pu; Li, Shengjin; Liu, Jun; Li, Jintian; Zhou, Jizhong; Shu, Wensheng

2016-01-01

Predicting the dynamics of community composition and functional attributes responding to environmental changes is an essential goal in community ecology but remains a major challenge, particularly in microbial ecology. Here, by targeting a model system with low species richness, we explore the spatial distribution of taxonomic and functional structure of 40 acid mine drainage (AMD) microbial communities across Southeast China profiled by 16S ribosomal RNA pyrosequencing and a comprehensive microarray (GeoChip). Similar environmentally dependent patterns of dominant microbial lineages and key functional genes were observed regardless of the large-scale geographical isolation. Functional and phylogenetic β-diversities were significantly correlated, whereas functional metabolic potentials were strongly influenced by environmental conditions and community taxonomic structure. Using advanced modeling approaches based on artificial neural networks, we successfully predicted the taxonomic and functional dynamics with significantly higher prediction accuracies of metabolic potentials (average Bray–Curtis similarity 87.8) as compared with relative microbial abundances (similarity 66.8), implying that natural AMD microbial assemblages may be better predicted at the functional genes level rather than at taxonomic level. Furthermore, relative metabolic potentials of genes involved in many key ecological functions (for example, nitrogen and phosphate utilization, metals resistance and stress response) were extrapolated to increase under more acidic and metal-rich conditions, indicating a critical strategy of stress adaptation in these extraordinary communities. Collectively, our findings indicate that natural selection rather than geographic distance has a more crucial role in shaping the taxonomic and functional patterns of AMD microbial community that readily predicted by modeling methods and suggest that the model-based approach is essential to better understand natural acidophilic microbial communities. PMID:26943622

Predicting taxonomic and functional structure of microbial communities in acid mine drainage.

PubMed

Kuang, Jialiang; Huang, Linan; He, Zhili; Chen, Linxing; Hua, Zhengshuang; Jia, Pu; Li, Shengjin; Liu, Jun; Li, Jintian; Zhou, Jizhong; Shu, Wensheng

2016-06-01

Predicting the dynamics of community composition and functional attributes responding to environmental changes is an essential goal in community ecology but remains a major challenge, particularly in microbial ecology. Here, by targeting a model system with low species richness, we explore the spatial distribution of taxonomic and functional structure of 40 acid mine drainage (AMD) microbial communities across Southeast China profiled by 16S ribosomal RNA pyrosequencing and a comprehensive microarray (GeoChip). Similar environmentally dependent patterns of dominant microbial lineages and key functional genes were observed regardless of the large-scale geographical isolation. Functional and phylogenetic β-diversities were significantly correlated, whereas functional metabolic potentials were strongly influenced by environmental conditions and community taxonomic structure. Using advanced modeling approaches based on artificial neural networks, we successfully predicted the taxonomic and functional dynamics with significantly higher prediction accuracies of metabolic potentials (average Bray-Curtis similarity 87.8) as compared with relative microbial abundances (similarity 66.8), implying that natural AMD microbial assemblages may be better predicted at the functional genes level rather than at taxonomic level. Furthermore, relative metabolic potentials of genes involved in many key ecological functions (for example, nitrogen and phosphate utilization, metals resistance and stress response) were extrapolated to increase under more acidic and metal-rich conditions, indicating a critical strategy of stress adaptation in these extraordinary communities. Collectively, our findings indicate that natural selection rather than geographic distance has a more crucial role in shaping the taxonomic and functional patterns of AMD microbial community that readily predicted by modeling methods and suggest that the model-based approach is essential to better understand natural acidophilic microbial communities.

Far and Wide - Microbial Bebop

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

Peter Larsen

2012-10-01

This musical composition was created from data of microbes (bacteria, algae and other microorganisms) sampled in the English Channel. Argonne National Laboratory biologist Peter Larsen created the songs as a unique way to present and comprehend large datasets. Microbial species of the Order Rickettsiales, such as the highly abundant, free-living planktonic species Pelagibacter ubique, are typical highly abundant taxa in L4 Station data. Its relative abundance in the microbial community at L4 Station follows a distinctive seasonal pattern. In this composition, there are two chords per measure, generated from photosynthetically active radiation measurements and temperature. The melody of each measuremore » is six notes that describe the relative abundance of the Order Rickettsiales. The first note of each measure is from the relative abundance at a time point. The next five notes of a measure follow one of the following patterns: a continuous rise in pitch, a continuous drop in pitch, a rise then drop in pitch, or a drop then rise in pitch. These patterns are matched to the relative abundance of Rickettsiales at the given time point, relative to the previous and subsequent time points. The pattern of notes in a measure is mapped to the relative abundance of Rickettsiales with fewer rests per measure indicating higher abundance. For time points at which Rickettsiales was the most abundant microbial taxa, the corresponding measure is highlighted with a cymbal crash. More information at http://www.anl.gov/articles/songs-key... Image: Diatoms under a microscope: These tiny phytoplankton are encased within a silicate cell wall. Credit: Prof. Gordon T. Taylor, Stony Brook University« less

Humic derivatives as promising hormone-like materials

NASA Astrophysics Data System (ADS)

Koroleva, R. P.; Khudaibergenova, E. M.; Kydralieva, K. A.; Jorobekova, Sh. J.

2009-04-01

The aim of this research is to prepare novel bio-inoculants derived from coal humic substances (HS) using bio-solubilization technique. This approach can be considered to some extent as model for supply plants with available nutrients throw the mineralisation of organic matter in soils by bacteria and fungi. Screening for the stable and active microorganisms' strains possessing ability to degrade humic substances was performed. The following subjects were examined using different isolation methods: natural microbial population from city soil, wood rot of Ulmis Pamila and biohumus of vermiculture of Eisenia foetida. Approaches for monitoring the humics-solubilizing fungi growth under liquid surface conditions in the presence of HS, proper conditions of bio-solubilization technique were elaborated. Coal humic acids (HA) from oxidized brown coal (Kyrgyz deposits) were isolated and added to a Czapek nutrient broth which was used either in full strength or without nitrogen source. The individual flasks were inoculated with natural microbial populations of corresponding cultivated soil, biohumus and wood rot samples for 12 months. Evaluation of phyto-hormonal activity of the produced HS and their derivatives in respect to higher plants with auxine and gibberellic tests was performed. To characterize structure of the biopreparations obtained, an experimental approach was undertaken that implies application of different complementary techniques for the structural analysis of biopreparations. As those were used: elemental and functional analysis, FTIR and 1H, 13C NMR spectroscopy and size-exclusion chromatography. According to the elemental composition of HS recovered from microbial cultures, a decrease in carbon and a significant increase of nitrogen in HS reisolated from the full strength broth inoculated with wood-decay microorganisms has been found. If biohumus microorganisms were used as inoculum, only minor changes were detected in the elemental composition of HS. A significant increase of H/C and O/C was also found in the HS. It can be attributed to formation new aliphatic and O-containing structures and decrease aromatic ones. Accumulation of fulvic acids was recorded in 6 months incubation. In 9 months, natural microbial populations from soil, biohumus, and wood rot had reduced the absorbance of HS media by 79, 75, and 62%, respectively. A relative reduction of the molecular weight was noticed after 3 months incubation, and accumulation of new low molecular weight fraction after 6 months incubation was recorded after chromatography on Toyopearl HW-50S. Reductions in amount were due to a random degradation of substances in all molecular size classes. A formation the high molecular weight fraction has been found, that can be caused by cross-linking of structural constituents of molecules due to radicals forming after biodestruction or by their interaction with metabolites. Data obtained by spectroscopic methods (UV/vis/FTIR) and element analysis indicated a decrease in particle size and a loss in aromaticity and aliphatic carbon in HS reisolated from microbial cultures. Simultaneously an increase in the N content of HS was observed, which probably from some constituents of microbial biomass such as proteins and aminosugars. The microbial degradation of HS strongly depended on the composition of the HS, the species selection of the microorganisms, and to a lesser extent on the culture conditions. A hormone-like activity has been showed by HS preparations which were characterized with low molecular weights (~5-15 kD). Each of these preparations was endowed with a single specific (auxin-like or gibberellin-like) activity. Biosolubilized HS with low molecular weight were displayed two kinds of activity. Acknowledgement. This research was supported by the ISTC grants of the projects KR-993.2.

Linking genes to microbial growth kinetics: an integrated biochemical systems engineering approach.

PubMed

Koutinas, Michalis; Kiparissides, Alexandros; Silva-Rocha, Rafael; Lam, Ming-Chi; Martins Dos Santos, Vitor A P; de Lorenzo, Victor; Pistikopoulos, Efstratios N; Mantalaris, Athanasios

2011-07-01

The majority of models describing the kinetic properties of a microorganism for a given substrate are unstructured and empirical. They are formulated in this manner so that the complex mechanism of cell growth is simplified. Herein, a novel approach for modelling microbial growth kinetics is proposed, linking biomass growth and substrate consumption rates to the gene regulatory programmes that control these processes. A dynamic model of the TOL (pWW0) plasmid of Pseudomonas putida mt-2 has been developed, describing the molecular interactions that lead to the transcription of the upper and meta operons, known to produce the enzymes for the oxidative catabolism of m-xylene. The genetic circuit model was combined with a growth kinetic model decoupling biomass growth and substrate consumption rates, which are expressed as independent functions of the rate-limiting enzymes produced by the operons. Estimation of model parameters and validation of the model's predictive capability were successfully performed in batch cultures of mt-2 fed with different concentrations of m-xylene, as confirmed by relative mRNA concentration measurements of the promoters encoded in TOL. The growth formation and substrate utilisation patterns could not be accurately described by traditional Monod-type models for a wide range of conditions, demonstrating the critical importance of gene regulation for the development of advanced models closely predicting complex bioprocesses. In contrast, the proposed strategy, which utilises quantitative information pertaining to upstream molecular events that control the production of rate-limiting enzymes, predicts the catabolism of a substrate and biomass formation and could be of central importance for the design of optimal bioprocesses. Copyright © 2011 Elsevier Inc. All rights reserved.

Optical control of antibacterial activity

NASA Astrophysics Data System (ADS)

Velema, Willem A.; van der Berg, Jan Pieter; Hansen, Mickel J.; Szymanski, Wiktor; Driessen, Arnold J. M.; Feringa, Ben L.

2013-11-01

Bacterial resistance is a major problem in the modern world, stemming in part from the build-up of antibiotics in the environment. Novel molecular approaches that enable an externally triggered increase in antibiotic activity with high spatiotemporal resolution and auto-inactivation are highly desirable. Here we report a responsive, broad-spectrum, antibacterial agent that can be temporally activated with light, whereupon it auto-inactivates on the scale of hours. The use of such a ‘smart’ antibiotic might prevent the build-up of active antimicrobial material in the environment. Reversible optical control over active drug concentration enables us to obtain pharmacodynamic information. Precisely localized control of activity is achieved, allowing the growth of bacteria to be confined to defined patterns, which has potential for the development of treatments that avoid interference with the endogenous microbial population in other parts of the organism.

High-resolution (SIMS) versus bulk sulfur isotope patterns of pyrite in Proterozoic microbialites with diverse mat textures

NASA Astrophysics Data System (ADS)

Gomes, M. L.; Fike, D. A.; Bergmann, K.; Knoll, A. H.

2015-12-01

Sulfur (S) isotope signatures of sedimentary pyrite preserved in marine rocks provide a rich suite of information about changes in biogeochemical cycling associated with the evolution of microbial metabolisms and oxygenation of Earth surface environments. Conventionally, these S isotope records are based on bulk rock measurements. Yet, in modern microbial mat environments, S isotope compositions of sulfide can vary by up to 40‰ over a spatial range of ~ 1 mm. Similar ranges of S isotope variability have been found in Archean pyrite grains using both Secondary Ion Mass Spectrometry and other micro-analytical techniques. These micron-scale patterns have been linked to changes in rates of microbial sulfate reduction and/or sulfide oxidation, isotopic distillation of the sulfate reservoir due to microbial sulfate reduction, and post-depositional alteration. Fine-scale mapping of S isotope compositions of pyrite can thus be used to differentiate primary environmental signals from post-depositional overprinting - improving our understanding of both. Here, we examine micron-scale S isotope patterns of pyrite in microbialites from the Mesoproterozoic-Neoproterozoic Sukhaya Tunguska Formation and Neoproterozoic Draken Formation in order to explore S isotope variability associated with different mat textures and pyrite grain morphologies. A primary goal is to link modern observations of how sulfide spatial isotope distributions reflect active microbial communities present at given depths in the mats to ancient processes driving fine-sale pyrite variability in microbialites. We find large (up to 60‰) S isotope variability within a spatial range of less than 2.5cm. The micron-scale S isotope measurements converge around the S isotope composition of pyrite extracted from bulk samples of the same microbialites. These micron-scale pyrite S isotope patterns have the potential to reveal important information about ancient biogeochemical cycling in Proterozoic mat environments with implications for interpreting S isotope signatures from the geological record.

Strategies Influencing Spatial Heterogeneity of Microbial Life in a Soil Lysimeter

NASA Astrophysics Data System (ADS)

Sengupta, A.; Neilson, J. W.; Meira, A.; Wang, Y.; Meza, M.; Chorover, J.; Maier, R. M.; Troch, P. A. A.

2016-12-01

Soil microorganisms are critical drivers of biogeochemical processes. These microbes, in conjunction with their physical and chemical environment, contribute to ecosystem functioning and services of the landscape, have a profound impact on soil formation, and are of particular importance in oligotrophic environments; ecosystems that are characterized by low biotic diversity due to extremely low nutrient levels. Here, we present a study of microbial heterogeneity in a soil lysimeter under incipient conditions. The key questions asked were: 1) what is the spatial heterogeneity of microbes over a new and evolving landscape with inherent oligotrophic conditions, and 2) can patterns in diversity translate to patterns in microbe-mediated weathering processes and soil formation? We hypothesized that stratification of environmental conditions, brought about by varying water potential, flow paths, and redox conditions, will drive the heterogeneity of microbial life in a sub-meter scale. A suite of traditional and current microbiological tools were employed to study community characteristics. These included isolation on R2A media, quantitative polymerase chain reactions targeted at 16S rRNA bacterial and archaeal genes, and 18S fungal genes, and iTAG phylogenetic gene amplification. Illumina Mi-Seq platform generated sequences were analyzed using various bioinformatics pipelines to identify community patterns, classify microbial metabolic functions, and identify variables affecting the community dynamics. Numerous phyla (Verrucomicrobia, Actinobacteria, Planctomycetes, Proteobacteria, and Euryarchaeota) were identified. The surface layer had distinctly different distribution of communities compared to the other layers. Metabolically heterogeneous groups were found with respect to depth, with metabolic functions further confirmed by predictive functional profiling of the microbial communities. Therefore, despite being highly oligotrophic, the system was rich in species and functional diversity. Alongside physical and chemical data, the patterns observed in spatial and functional heterogeneity of microbes under incipient conditions is unique, and allows us to predict strategies undertaken by these microbes to survive in, and influence their oligotrophic environments.

Chlorine stress mediates microbial surface attachment in drinking water systems.

PubMed

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

2015-03-01

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

Cultivation and Characterization of Oil-Degrading Microbes and the Environmental Controls on Hydrocarbon Biodegradation Patterns

NASA Astrophysics Data System (ADS)

Redmond, M. C.

2016-02-01

The Deepwater Horizon oil spill highlighted the ability of microbes to degrade hydrocarbons in both cold, deep water and at the warm sea surface. However, the temperature and differing hydrocarbons in the deep ocean and sea surface led to different microbial communities and biodegradation patterns. In order to develop a better understanding of the factors that control microbial community composition and biodegradation patterns, we conducted laboratory microcosm studies with seawater samples from coastal South Carolina and hydrocarbon seeps in the Gulf of Mexico, incubated with different hydrocarbons, at different temperatures, and in static or shaking incubation conditions. We analyzed microbial community composition after three weeks and used successive transfers on liquid and then solid media to isolate cultures. More rapid growth was observed at 28 degrees than 4 degrees, with hexadecane compared to benzene, cyclohexane, or crude oil, and in shaking incubations compared to static. However, we were able to successfully culture microbes under all conditions. Physiological and genetic characterization of isolated strains is ongoing, and will be combined with assessment of hydrocarbon substrate preferences and kinetics under different environmental conditions.

[Molecular regulation of microbial secondary metabolites--a review].

PubMed

Wang, Linqi; Tan, Huarong

2009-04-01

Microbial secondary metabolites play an important role in the field of industry, agriculture, medicine and human health. The molecular regulation of secondary metabolites is gradually becoming noticeable and intriguing. In recent years, many researches have demonstrated that secondary metabolite biosynthesis is tightly linked to the physiological and developmental status in its producer. It is suggested that the biosynthesis of secondary metabolites involves in complex process concerning multi-level regulation. Here we reviewed the recent research progress on the molecular regulation of secondary metabolites in microorganisms. In known about ten thousand kinds of natural secondary metabolites, most of them (about 60%) were produced by Streptomycete. Therefore, the regulation of secondary metabolites in Streptomyces is chosen as the mainline in this review. Additionally, several well-studied antibiotics as the representative members were targeted. Finally, some suggestions, in response to the issues at present, have been presented in this paper.

Compositional Changes and Baking Performance of Rye Dough As Affected by Microbial Transglutaminase and Xylanase.

PubMed

Grossmann, Isabel; Döring, Clemens; Jekle, Mario; Becker, Thomas; Koehler, Peter

2016-07-20

Doughs supplemented with endoxylanase (XYL) and varying amounts of microbial transglutaminase (TG) were analyzed by sequential protein extraction, quantitation of protein fractions and protein types, and determination of water-extractable arabinoxylans. With increasing TG activity, the concentration of prolamins and glutelins decreased and increased, respectively, and the prolamin-to-glutelin ratio strongly declined. The overall amount of extractable protein decreased with increasing TG level showing that cross-linking by TG provided high-molecular-weight protein aggregates. The decrease of the high-molecular-weight arabinoxylan fraction and the concurrent increase of the medium-molecular-weight fraction confirmed the degradation of arabinoxylans by XYL. However, XYL addition did not lead to significant improved cross-linking of rye proteins by TG. Volume and crumb hardness measurements of bread showed increased protein connectivity induced by XYL and TG. Significant positive effects on the final bread quality were especially obtained by XYL addition.

Evidence of pathogenic microbes in the International Space Station drinking water: reason for concern?

NASA Technical Reports Server (NTRS)

La Duc, Myron T.; Sumner, Randall; Pierson, Duane; Venkat, Parth; Venkateswaran, Kasthuri

2004-01-01

Molecular analyses were carried out on four preflight and six postflight International Space Station (ISS)-associated potable water samples at various stages of purification, storage, and transport, to ascertain their associated microbial diversities and overall microbial burdens. Following DNA extraction, PCR amplification, and molecular cloning procedures, rDNA sequences closely related to pathogenic species of Acidovorax, Afipia, Brevundimonas, Propionibacterium, Serratia, and others were recovered in varying abundance. Retrieval of sequences arising from the iodine (biocide)-reducing Delftia acidovorans in postflight waters is also of concern. Total microbial burdens of ISS potable waters were derived from data generated by an ATP-based enumeration procedure, with results ranging from 0 to 4.9 x 10(4) cells/ml. Regardless of innate biases in sample collection and analysis, such circumstantial evidence for the presence of viable, intact pathogenic cells should not be taken lightly. Implementation of new cultivation approaches and/or viability-based assays are requisite to confirm such an occurrence.

Marine microbial biodiversity, bioinformatics and biotechnology (M2B3) data reporting and service standards

PubMed Central

2015-01-01

Contextual data collected concurrently with molecular samples are critical to the use of metagenomics in the fields of marine biodiversity, bioinformatics and biotechnology. We present here Marine Microbial Biodiversity, Bioinformatics and Biotechnology (M2B3) standards for “Reporting” and “Serving” data. The M2B3 Reporting Standard (1) describes minimal mandatory and recommended contextual information for a marine microbial sample obtained in the epipelagic zone, (2) includes meaningful information for researchers in the oceanographic, biodiversity and molecular disciplines, and (3) can easily be adopted by any marine laboratory with minimum sampling resources. The M2B3 Service Standard defines a software interface through which these data can be discovered and explored in data repositories. The M2B3 Standards were developed by the European project Micro B3, funded under 7th Framework Programme “Ocean of Tomorrow”, and were first used with the Ocean Sampling Day initiative. We believe that these standards have value in broader marine science. PMID:26203332

Microbial source tracking in highly vulnerable karst drinking water resources.

PubMed

Diston, D; Robbi, R; Baumgartner, A; Felleisen, R

2018-02-01

Water resources situated in areas with underlying karst geology are particularly vulnerable to fecal pollution. In such vulnerable systems, microbial source tracking (MST) methods are useful tools to elucidate the pathways of both animal and human fecal pollution, leading to more accurate water use risk assessments. Here, we describe the application of a MST toolbox using both culture-dependent bacteriophage and molecular-dependent 16S rRNA assays at spring and well sites in the karstic St Imier Valley, Switzerland. Culture-dependent and molecular-dependent marker performance varied significantly, with the 16S rRNA assays displaying greater sensitivity than their phage counterpart; HF183 was the best performing human wastewater-associated marker while Rum2Bac was the best performing ruminant marker. Differences were observed in pollution regimes between the well and spring sampling sites, with the spring water being more degraded than the well site. Our results inform the choice of marker selection for MST studies and highlight differences in microbial water quality between well and spring karst sites.

Molecular improvements in microbial α-amylases for enhanced stability and catalytic efficiency.

PubMed

Sindhu, Raveendran; Binod, Parameswaran; Madhavan, Aravind; Beevi, Ummalyma Sabeela; Mathew, Anil Kuruvilla; Abraham, Amith; Pandey, Ashok; Kumar, Vinod

2017-12-01

α-Amylases is one of the most important industrial enzyme which contributes to 25% of the industrial enzyme market. Though it is produced by plant, animals and microbial source, those from microbial source seems to have potential applications due to their stability and economic viability. However a large number of α-amylases from different sources have been detailed in the literature, only few numbers of them could withstand the harsh industrial conditions. Thermo-stability, pH tolerance, calcium independency and oxidant stability and starch hydrolyzing efficiency are the crucial qualities for α-amylase in starch based industries. Microbes can be genetically modified and fine tuning can be done for the production of enzymes with desired characteristics for specific applications. This review focuses on the native and recombinant α-amylases from microorganisms, their heterologous production and the recent molecular strategies which help to improve the properties of this industrial enzyme. Copyright © 2017 Elsevier Ltd. All rights reserved.

Postdoctoral Fellow | Center for Cancer Research

Cancer.gov

The Khare lab in the Laboratory of Molecular Biology, NCI Center for Cancer Research, NIH, is looking to recruit highly motivated researchers interested in a postdoctoral fellowship to study the molecular and genetic basis of complex microbial behaviors. Our lab is focused on multiple research avenues including interspecies interactions, antibiotic persistence, and adaptation

Molecular Diversity of Bacteroidales in Fecal and Environmental Samples and Swine-Associated Subpopulations

EPA Science Inventory

Several swine-specific microbial source tracking methods are based on PCR assays targeting Bacteroidales 16S rRNA gene sequences. The limited application of these assays can be explained by the poor understanding of their molecular diversity in fecal sources and environmental wat...

Exploring the immune signalling pathway-related genes of the cattle tick Rhipicephalus microplus: From molecular characterization to transcriptional profile upon microbial challenge.

PubMed

Rosa, Rafael D; Capelli-Peixoto, Janaína; Mesquita, Rafael D; Kalil, Sandra P; Pohl, Paula C; Braz, Glória R; Fogaça, Andrea C; Daffre, Sirlei

2016-06-01

In dipteran insects, invading pathogens are selectively recognized by four major pathways, namely Toll, IMD, JNK, and JAK/STAT, and trigger the activation of several immune effectors. Although substantial advances have been made in understanding the immunity of model insects such as Drosophila melanogaster, knowledge on the activation of immune responses in other arthropods such as ticks remains limited. Herein, we have deepened our understanding of the intracellular signalling pathways likely to be involved in tick immunity by combining a large-scale in silico approach with high-throughput gene expression analysis. Data from in silico analysis revealed that although both the Toll and JAK/STAT signalling pathways are evolutionarily conserved across arthropods, ticks lack central components of the D. melanogaster IMD pathway. Moreover, we show that tick immune signalling-associated genes are constitutively transcribed in BME26 cells (a cell lineage derived from embryos of the cattle tick Rhipicephalus microplus) and exhibit different transcriptional patterns in response to microbial challenge. Interestingly, Anaplasma marginale, a pathogen that is naturally transmitted by R. microplus, causes downregulation of immune-related genes, suggesting that this pathogen may manipulate the tick immune system, favouring its survival and vector colonization. Copyright © 2015 Elsevier Ltd. All rights reserved.

Deciphering the distance to antibiotic resistance for the pneumococcus using genome sequencing data

PubMed Central

Mobegi, Fredrick M.; Cremers, Amelieke J. H.; de Jonge, Marien I.; Bentley, Stephen D.; van Hijum, Sacha A. F. T.; Zomer, Aldert

2017-01-01

Advances in genome sequencing technologies and genome-wide association studies (GWAS) have provided unprecedented insights into the molecular basis of microbial phenotypes and enabled the identification of the underlying genetic variants in real populations. However, utilization of genome sequencing in clinical phenotyping of bacteria is challenging due to the lack of reliable and accurate approaches. Here, we report a method for predicting microbial resistance patterns using genome sequencing data. We analyzed whole genome sequences of 1,680 Streptococcus pneumoniae isolates from four independent populations using GWAS and identified probable hotspots of genetic variation which correlate with phenotypes of resistance to essential classes of antibiotics. With the premise that accumulation of putative resistance-conferring SNPs, potentially in combination with specific resistance genes, precedes full resistance, we retrogressively surveyed the hotspot loci and quantified the number of SNPs and/or genes, which if accumulated would confer full resistance to an otherwise susceptible strain. We name this approach the ‘distance to resistance’. It can be used to identify the creep towards complete antibiotics resistance in bacteria using genome sequencing. This approach serves as a basis for the development of future sequencing-based methods for predicting resistance profiles of bacterial strains in hospital microbiology and public health settings. PMID:28205635

Molecular analysis of microbial diversity in advanced caries.

PubMed

Chhour, Kim-Ly; Nadkarni, Mangala A; Byun, Roy; Martin, F Elizabeth; Jacques, Nicholas A; Hunter, Neil

2005-02-01

Real-time PCR analysis of the total bacterial load in advanced carious lesions has shown that the total load exceeds the number of cultivable bacteria. This suggests that an unresolved complexity exists in bacteria associated with advanced caries. In this report, the profile of the microflora of carious dentine was explored by using DNA extracted from 10 lesions selected on the basis of comparable total microbial load and on the relative abundance of Prevotella spp. Using universal primers for the 16S rRNA gene, PCR amplicons were cloned, and approximately 100 transformants were processed for each lesion. Phylogenetic analysis of 942 edited sequences demonstrated the presence of 75 species or phylotypes in the 10 carious lesions. Up to 31 taxa were represented in each sample. A diverse array of lactobacilli were found to comprise 50% of the species, with prevotellae also abundant, comprising 15% of the species. Other taxa present in a number of lesions or occurring with high abundance included Selenomonas spp., Dialister spp., Fusobacterium nucleatum, Eubacterium spp., members of the Lachnospiraceae family, Olsenella spp., Bifidobacterium spp., Propionibacterium sp., and Pseudoramibacter alactolyticus. The mechanisms by which such diverse patterns of bacteria extend carious lesions, including the aspect of infection of the vital dental pulp, remain unclear.

Microbial alcohol-conferred hemolysis is a late response to alcohol stress.

PubMed

Shuster, Amir; Korem, Moshe; Jacob-Hirsch, Jasmine; Amariglio, Ninette; Rechavi, Gideon; Rosenberg, Mel

2011-06-01

We have reported previously that growth on alcohol vapors confers hemolytic properties on certain yeast species and strains ['microbial alcohol-conferred hemolysis' (MACH)]. In a recent study, we analyzed the genetic basis of MACH in Saccharomyces cerevisiae using the EUROSCARF mutant collection. The data suggested that intact mitochondrial and respiratory chain functions are critical for the observed alcohol-mediated hemolysis. We proposed that the uncontrolled cellular uptake of alcohol results in yeast 'hyper-respiration', leading to elaboration of hemolytic molecules such as hydrogen peroxide and lytic lipids. In the current study, we have further analyzed the molecular mechanisms involved in the MACH phenomenon in S. cerevisiae, using DNA microarrays. The patterns of regulation were confirmed by quantitative reverse transcriptase PCR. The results presented here lend further support to this hypothesis, based on upregulation of the genes responsible for coping with vast amounts of hydrogen peroxide produced as a byproduct of excessive oxidation of alcohol. These results, taken together, show that alcohol-mediated hemolysis in yeast appears to be related to the overproduction of hemolytic byproducts, particularly hydrogen peroxide, which accumulates during long-term exposure of S. cerevisiae to both ethanol and n-butanol. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Molecular Analysis of Bacterial Communities in Biofilms of a Drinking Water Clearwell

PubMed Central

Zhang, Minglu; Liu, Wenjun; Nie, Xuebiao; Li, Cuiping; Gu, Junnong; Zhang, Can

2012-01-01

Microbial community structures in biofilms of a clearwell in a drinking water supply system in Beijing, China were examined by clone library, terminal restriction fragment length polymorphism (T-RFLP) and 454 pyrosequencing of the amplified 16S rRNA gene. Six biofilm samples (designated R1–R6) collected from six locations (upper and lower sites of the inlet, middle and outlet) of the clearwell revealed similar bacterial patterns by T-RFLP analysis. With respect to the dominant groups, the phylotypes detected by clone library and T-RFLP generally matched each other. A total of 9,543 reads were obtained from samples located at the lower inlet and the lower outlet sites by pyrosequencing. The bacterial diversity of the two samples was compared at phylum and genus levels. Alphaproteobacteria dominated the communities in both samples and the genus of Sphingomonas constituted 75.1%–99.6% of this phylum. A high level of Sphingomonas sp. was first observed in the drinking water biofilms with 0.6–1.0 mg L−1 of chlorine residual. Disinfectant-resistant microorganisms deserve special attention in drinking water management. This study provides novel insights into the microbial populations in drinking water systems and highlights the important role of Sphingomonas species in biofilm formation. PMID:23059725

Grassland to woodland transitions: Dynamic response of microbial community structure and carbon use patterns

NASA Astrophysics Data System (ADS)

Creamer, Courtney A.; Filley, Timothy R.; Boutton, Thomas W.; Rowe, Helen I.

2016-06-01

Woodland encroachment into grasslands is a globally pervasive phenomenon attributed to land use change, fire suppression, and climate change. This vegetation shift impacts ecosystem services such as ground water allocation, carbon (C) and nutrient status of soils, aboveground and belowground biodiversity, and soil structure. We hypothesized that woodland encroachment would alter microbial community structure and function and would be related to patterns in soil C accumulation. To address this hypothesis, we measured the composition and δ13C values of soil microbial phospholipids (PLFAs) along successional chronosequences from C4-dominated grasslands to C3-dominated woodlands (small discrete clusters and larger groves) spanning up to 134 years. Woodland development increased microbial biomass, soil C and nitrogen (N) concentrations, and altered microbial community composition. The relative abundance of gram-negative bacteria (cy19:0) increased linearly with stand age, consistent with decreases in soil pH and/or greater rhizosphere development and corresponding increases in C inputs. δ13C values of all PLFAs decreased with time following woody encroachment, indicating assimilation of woodland C sources. Among the microbial groups, fungi and actinobacteria in woodland soils selectively assimilated grassland C to a greater extent than its contribution to bulk soil. Between the two woodland types, microbes in the groves incorporated relatively more of the relict C4-C than those in the clusters, potentially due to differences in below ground plant C allocation and organo-mineral association. Changes in plant productivity and C accessibility (rather than C chemistry) dictated microbial C utilization in this system in response to shrub encroachment.

Host gene-microbiome interactions: molecular mechanisms in inflammatory bowel disease.

PubMed

Chu, Hiutung

2017-07-24

Recent studies have identified links between host genetic variants and microbial recognition of the microbiome. Defects in host-microbiome interactions in individuals harboring inflammatory bowel disease risk alleles may result in imbalances of the microbial community, impaired pathogen clearance, and failure to sense beneficial commensal microbes. These findings highlight the importance of maintaining bi-directional communication at the mucosal interface during intestinal homeostasis.

Understanding Caries From the Oral Microbiome Perspective.

PubMed

Tanner, Anne C R; Kressirer, Christine A; Faller, Lina L

2016-07-01

Dental caries is a major disease of the oral cavity with profound clinical significance. Caries results from a transition of a healthy oral microbiome into an acidogenic community of decreased microbial diversity in response to excessive dietary sugar intake. Microbiological cultivation, molecular identification, gene expression and metabolomic analyses show the importance of the entire microbial community in understanding the role of the microbiome in the pathology of caries.

Induced Genome-Wide Binding of Three Arabidopsis WRKY Transcription Factors during Early MAMP-Triggered Immunity.

PubMed

Birkenbihl, Rainer P; Kracher, Barbara; Somssich, Imre E

2017-01-01

During microbial-associated molecular pattern-triggered immunity (MTI), molecules derived from microbes are perceived by cell surface receptors and upon signaling to the nucleus initiate a massive transcriptional reprogramming critical to mount an appropriate host defense response. WRKY transcription factors play an important role in regulating these transcriptional processes. Here, we determined on a genome-wide scale the flg22-induced in vivo DNA binding dynamics of three of the most prominent WRKY factors, WRKY18, WRKY40, and WRKY33. The three WRKY factors each bound to more than 1000 gene loci predominantly at W-box elements, the known WRKY binding motif. Binding occurred mainly in the 500-bp promoter regions of these genes. Many of the targeted genes are involved in signal perception and transduction not only during MTI but also upon damage-associated molecular pattern-triggered immunity, providing a mechanistic link between these functionally interconnected basal defense pathways. Among the additional targets were genes involved in the production of indolic secondary metabolites and in modulating distinct plant hormone pathways. Importantly, among the targeted genes were numerous transcription factors, encoding predominantly ethylene response factors, active during early MTI, and WRKY factors, supporting the previously hypothesized existence of a WRKY subregulatory network. Transcriptional analysis revealed that WRKY18 and WRKY40 function redundantly as negative regulators of flg22-induced genes often to prevent exaggerated defense responses. © 2016 American Society of Plant Biologists. All rights reserved.

Convergent Evolution of Pathogen Effectors toward Reactive Oxygen Species Signaling Networks in Plants.

PubMed

Jwa, Nam-Soo; Hwang, Byung Kook

2017-01-01

Microbial pathogens have evolved protein effectors to promote virulence and cause disease in host plants. Pathogen effectors delivered into plant cells suppress plant immune responses and modulate host metabolism to support the infection processes of pathogens. Reactive oxygen species (ROS) act as cellular signaling molecules to trigger plant immune responses, such as pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) and effector-triggered immunity. In this review, we discuss recent insights into the molecular functions of pathogen effectors that target multiple steps in the ROS signaling pathway in plants. The perception of PAMPs by pattern recognition receptors leads to the rapid and strong production of ROS through activation of NADPH oxidase Respiratory Burst Oxidase Homologs (RBOHs) as well as peroxidases. Specific pathogen effectors directly or indirectly interact with plant nucleotide-binding leucine-rich repeat receptors to induce ROS production and the hypersensitive response in plant cells. By contrast, virulent pathogens possess effectors capable of suppressing plant ROS bursts in different ways during infection. PAMP-triggered ROS bursts are suppressed by pathogen effectors that target mitogen-activated protein kinase cascades. Moreover, pathogen effectors target vesicle trafficking or metabolic priming, leading to the suppression of ROS production. Secreted pathogen effectors block the metabolic coenzyme NADP-malic enzyme, inhibiting the transfer of electrons to the NADPH oxidases (RBOHs) responsible for ROS generation. Collectively, pathogen effectors may have evolved to converge on a common host protein network to suppress the common plant immune system, including the ROS burst and cell death response in plants.

Interactive effects of seasonal drought and elevated atmospheric carbon dioxide concentration on prokaryotic rhizosphere communities.

PubMed

Drigo, Barbara; Nielsen, Uffe N; Jeffries, Thomas C; Curlevski, Nathalie J A; Singh, Brajesh K; Duursma, Remko A; Anderson, Ian C

2017-08-01

Global change models indicate that rainfall patterns are likely to shift towards more extreme events concurrent with increasing atmospheric carbon dioxide concentration ([CO 2 ]). Both changes in [CO 2 ] and rainfall regime are known to impact above- and belowground communities, but the interactive effects of these global change drivers have not been well explored, particularly belowground. In this experimental study, we examined the effects of elevated [CO 2 ] (ambient + 240 ppm; [eCO 2 ]) and changes in rainfall patterns (seasonal drought) on soil microbial communities associated with forest ecosystems. Our results show that bacterial and archaeal communities are highly resistant to seasonal drought under ambient [CO 2 ]. However, substantial taxa specific responses to seasonal drought were observed at [eCO 2 ], suggesting that [eCO 2 ] compromise the resistance of microbial communities to extreme events. Within the microbial community we were able to identify three types of taxa specific responses to drought: tolerance, resilience and sensitivity that contributed to this pattern. All taxa were tolerant to seasonal drought at [aCO 2 ], whereas resilience and sensitivity to seasonal drought were much greater in [eCO 2 ]. These results provide strong evidence that [eCO 2 ] moderates soil microbial community responses to drought in forests, with potential implications for their long-term persistence and ecosystem functioning. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Etiology and microbial patterns of pulmonary infiltrates in patients with orthotopic liver transplantation.

PubMed

Torres, A; Ewig, S; Insausti, J; Guergué, J M; Xaubet, A; Mas, A; Salmeron, J M

2000-02-01

To evaluate the etiology and microbial patterns of pulmonary infiltrates in liver transplant patients using a bronchoscopic diagnostic approach and the impact of diagnostic results on antimicrobial treatment decisions. A prospective cohort study. A 1,000-bed tertiary-care university hospital. Fifty consecutive liver transplant patients with 60 episodes of pulmonary infiltrates (33 episodes during mechanical ventilation) were studied using flexible bronchoscopy with protected specimen brush (PSB) and BAL. A definite infectious etiology was confirmed in 29 episodes (48%). Eighteen episodes corresponded to probable pneumonia (30%), 10 episodes had noninfectious etiologies (17%), and 3 remained undetermined (5%). Opportunistic infections were the most frequent etiology (16/29, 55%, including 1 mixed etiology). Bacterial infections (mainly Gram-negative) accounted for 14 of 29 episodes (48%), including 1 of mixed etiology. The majority of bacterial pneumonia episodes (n = 10, 71%) occurred in period 1 (1 to 28 days posttransplant) during mechanical ventilation, whereas opportunistic episodes were predominant in periods 2 and 3 (29 to 180 days and > 180 days posttransplant, respectively; n = 14, 82%). Microbial treatment was changed according to diagnostic results in 21 episodes (35%). Microbial patterns in liver transplant patients with pulmonary infiltrates corresponded to nosocomial, mainly Gram-negative bacterial pneumonia in period 1, and to opportunistic infections in period 2 and, to a lesser extent, period 3. A comprehensive diagnostic evaluation including PSB and BAL fluid examination frequently guided specific antimicrobial therapy.

A Peptide-Based Method for 13C Metabolic Flux Analysis in Microbial Communities

PubMed Central

Ghosh, Amit; Nilmeier, Jerome; Weaver, Daniel; Adams, Paul D.; Keasling, Jay D.; Mukhopadhyay, Aindrila; Petzold, Christopher J.; Martín, Héctor García

2014-01-01

The study of intracellular metabolic fluxes and inter-species metabolite exchange for microbial communities is of crucial importance to understand and predict their behaviour. The most authoritative method of measuring intracellular fluxes, 13C Metabolic Flux Analysis (13C MFA), uses the labeling pattern obtained from metabolites (typically amino acids) during 13C labeling experiments to derive intracellular fluxes. However, these metabolite labeling patterns cannot easily be obtained for each of the members of the community. Here we propose a new type of 13C MFA that infers fluxes based on peptide labeling, instead of amino acid labeling. The advantage of this method resides in the fact that the peptide sequence can be used to identify the microbial species it originates from and, simultaneously, the peptide labeling can be used to infer intracellular metabolic fluxes. Peptide identity and labeling patterns can be obtained in a high-throughput manner from modern proteomics techniques. We show that, using this method, it is theoretically possible to recover intracellular metabolic fluxes in the same way as through the standard amino acid based 13C MFA, and quantify the amount of information lost as a consequence of using peptides instead of amino acids. We show that by using a relatively small number of peptides we can counter this information loss. We computationally tested this method with a well-characterized simple microbial community consisting of two species. PMID:25188426

The Vineyard Yeast Microbiome, a Mixed Model Microbial Map

PubMed Central

Setati, Mathabatha Evodia; Jacobson, Daniel; Andong, Ursula-Claire; Bauer, Florian

2012-01-01

Vineyards harbour a wide variety of microorganisms that play a pivotal role in pre- and post-harvest grape quality and will contribute significantly to the final aromatic properties of wine. The aim of the current study was to investigate the spatial distribution of microbial communities within and between individual vineyard management units. For the first time in such a study, we applied the Theory of Sampling (TOS) to sample gapes from adjacent and well established commercial vineyards within the same terroir unit and from several sampling points within each individual vineyard. Cultivation-based and molecular data sets were generated to capture the spatial heterogeneity in microbial populations within and between vineyards and analysed with novel mixed-model networks, which combine sample correlations and microbial community distribution probabilities. The data demonstrate that farming systems have a significant impact on fungal diversity but more importantly that there is significant species heterogeneity between samples in the same vineyard. Cultivation-based methods confirmed that while the same oxidative yeast species dominated in all vineyards, the least treated vineyard displayed significantly higher species richness, including many yeasts with biocontrol potential. The cultivatable yeast population was not fully representative of the more complex populations seen with molecular methods, and only the molecular data allowed discrimination amongst farming practices with multivariate and network analysis methods. Importantly, yeast species distribution is subject to significant intra-vineyard spatial fluctuations and the frequently reported heterogeneity of tank samples of grapes harvested from single vineyards at the same stage of ripeness might therefore, at least in part, be due to the differing microbiota in different sections of the vineyard. PMID:23300721

Modified Alternan: A Novel Microbial Gum with Potential as a Low-Viscosity Bulking Agent

USDA-ARS?s Scientific Manuscript database

Alternan is a microbial gum produced by rare strains of the GRAS lactic acid bacterium, Leuconostoc mesenteroides. The unique alternating alpha-(1,6) and alpha-(1,3) linkage pattern of this glucan imparts high solubility and resistance to most digestive enzymes. Previously, we invented a bioconver...

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

PubMed

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

2017-08-01

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

Associations among Wine Grape Microbiome, Metabolome, and Fermentation Behavior Suggest Microbial Contribution to Regional Wine Characteristics

PubMed Central

Bokulich, Nicholas A.; Collins, Thomas S.; Masarweh, Chad; Allen, Greg; Heymann, Hildegarde; Ebeler, Susan E.

2016-01-01

ABSTRACT Regionally distinct wine characteristics (terroir) are an important aspect of wine production and consumer appreciation. Microbial activity is an integral part of wine production, and grape and wine microbiota present regionally defined patterns associated with vineyard and climatic conditions, but the degree to which these microbial patterns associate with the chemical composition of wine is unclear. Through a longitudinal survey of over 200 commercial wine fermentations, we demonstrate that both grape microbiota and wine metabolite profiles distinguish viticultural area designations and individual vineyards within Napa and Sonoma Counties, California. Associations among wine microbiota and fermentation characteristics suggest new links between microbiota, fermentation performance, and wine properties. The bacterial and fungal consortia of wine fermentations, composed from vineyard and winery sources, correlate with the chemical composition of the finished wines and predict metabolite abundances in finished wines using machine learning models. The use of postharvest microbiota as an early predictor of wine chemical composition is unprecedented and potentially poses a new paradigm for quality control of agricultural products. These findings add further evidence that microbial activity is associated with wine terroir. PMID:27302757

NEMiD: a web-based curated microbial diversity database with geo-based plotting.

PubMed

Bhattacharjee, Kaushik; Joshi, Santa Ram

2014-01-01

The majority of the Earth's microbes remain unknown, and that their potential utility cannot be exploited until they are discovered and characterized. They provide wide scope for the development of new strains as well as biotechnological uses. The documentation and bioprospection of microorganisms carry enormous significance considering their relevance to human welfare. This calls for an urgent need to develop a database with emphasis on the microbial diversity of the largest untapped reservoirs in the biosphere. The data annotated in the North-East India Microbial database (NEMiD) were obtained by the isolation and characterization of microbes from different parts of the Eastern Himalayan region. The database was constructed as a relational database management system (RDBMS) for data storage in MySQL in the back-end on a Linux server and implemented in an Apache/PHP environment. This database provides a base for understanding the soil microbial diversity pattern in this megabiodiversity hotspot and indicates the distribution patterns of various organisms along with identification. The NEMiD database is freely available at www.mblabnehu.info/nemid/.

Anaerobic microbial communities in Lake Pavin, a unique meromictic lake in France.

PubMed

Lehours, Anne-C; Bardot, Corinne; Thenot, Aurelie; Debroas, Didier; Fonty, Gerard

2005-11-01

The Bacteria and Archaea from the meromictic Lake Pavin were analyzed in samples collected along a vertical profile in the anoxic monimolimnion and were compared to those in samples from the oxic mixolimnion. Nine targeted 16S rRNA oligonucleotide probes were used to assess the distribution of Bacteria and Archaea and to investigate the in situ occurrence of sulfate-reducing bacteria and methane-producing Archaea involved in the terminal steps of the anaerobic degradation of organic material. The diversity of the complex microbial communities was assessed from the 16S rRNA polymorphisms present in terminal restriction fragment (TRF) depth patterns. The densities of the microbial community increased in the anoxic layer, and Archaea detected with probe ARCH915 represented the largest microbial group in the water column, with a mean Archaea/Eubacteria ratio of 1.5. Terminal restriction fragment length polymorphism (TRFLP) analysis revealed an elevated archaeal and bacterial phylotype richness in anoxic bottom-water samples. The structure of the Archaea community remained rather homogeneous, while TRFLP patterns for the eubacterial community revealed a heterogeneous distribution of eubacterial TRFs.

NEMiD: A Web-Based Curated Microbial Diversity Database with Geo-Based Plotting

PubMed Central

Bhattacharjee, Kaushik; Joshi, Santa Ram

2014-01-01

The majority of the Earth's microbes remain unknown, and that their potential utility cannot be exploited until they are discovered and characterized. They provide wide scope for the development of new strains as well as biotechnological uses. The documentation and bioprospection of microorganisms carry enormous significance considering their relevance to human welfare. This calls for an urgent need to develop a database with emphasis on the microbial diversity of the largest untapped reservoirs in the biosphere. The data annotated in the North-East India Microbial database (NEMiD) were obtained by the isolation and characterization of microbes from different parts of the Eastern Himalayan region. The database was constructed as a relational database management system (RDBMS) for data storage in MySQL in the back-end on a Linux server and implemented in an Apache/PHP environment. This database provides a base for understanding the soil microbial diversity pattern in this megabiodiversity hotspot and indicates the distribution patterns of various organisms along with identification. The NEMiD database is freely available at www.mblabnehu.info/nemid/. PMID:24714636

Molecular Analysis of Microbial Community Structures in Pristine and Contaminated Aquifers: Field and Laboratory Microcosm Experiments

PubMed Central

Shi, Y.; Zwolinski, M. D.; Schreiber, M. E.; Bahr, J. M.; Sewell, G. W.; Hickey, W. J.

1999-01-01

This study used phylogenetic probes in hybridization analysis to (i) determine in situ microbial community structures in regions of a shallow sand aquifer that were oxygen depleted and fuel contaminated (FC) or aerobic and noncontaminated (NC) and (ii) examine alterations in microbial community structures resulting from exposure to toluene and/or electron acceptor supplementation (nitrate). The latter objective was addressed by using the NC and FC aquifer materials for anaerobic microcosm studies in which phylogenetic probe analysis was complemented by microbial activity assays. Domain probe analysis of the aquifer samples showed that the communities were predominantly Bacteria; Eucarya and Archaea were not detectable. At the phylum and subclass levels, the FC and NC aquifer material had similar relative abundance distributions of 43 to 65% β- and γ-Proteobacteria (B+G), 31 to 35% α-Proteobacteria (ALF), 15 to 18% sulfate-reducing bacteria, and 5 to 10% high G+C gram positive bacteria. Compared to that of the NC region, the community structure of the FC material differed mainly in an increased abundance of B+G relative to that of ALF. The microcosm communities were like those of the field samples in that they were predominantly Bacteria (83 to 101%) and lacked detectable Archaea but differed in that a small fraction (2 to 8%) of Eucarya was detected regardless of the treatment applied. The latter result was hypothesized to reflect enrichment of anaerobic protozoa. Addition of nitrate and/or toluene stimulated microbial activity in the microcosms, but only supplementation of toluene alone significantly altered community structures. For the NC material, the dominant subclass shifted from B+G to ALF, while in the FC microcosms 55 to 65% of the Bacteria community was no longer identifiable by the phylum or subclass probes used. The latter result suggested that toluene exposure fostered the proliferation of phylotype(s) that were otherwise minor constituents of the FC aquifer community. These studies demonstrated that alterations in aquifer microbial communities resulting from specific anthropogenic perturbances can be inferred from microcosm studies integrating chemical and phylogenetic probe analysis and in the case of hydrocarbon contamination may facilitate the identification of organisms important for in situ biodegradation processes. Further work integrating and coordinating microcosm and field experiments is needed to explore how differences in scale, substrate complexity, and other hydrogeological conditions may affect patterns observed in these systems. PMID:10224013

Selective sweeps in growing microbial colonies

NASA Astrophysics Data System (ADS)

Korolev, Kirill S.; Müller, Melanie J. I.; Karahan, Nilay; Murray, Andrew W.; Hallatschek, Oskar; Nelson, David R.

2012-04-01

Evolutionary experiments with microbes are a powerful tool to study mutations and natural selection. These experiments, however, are often limited to the well-mixed environments of a test tube or a chemostat. Since spatial organization can significantly affect evolutionary dynamics, the need is growing for evolutionary experiments in spatially structured environments. The surface of a Petri dish provides such an environment, but a more detailed understanding of microbial growth on Petri dishes is necessary to interpret such experiments. We formulate a simple deterministic reaction-diffusion model, which successfully predicts the spatial patterns created by two competing species during colony expansion. We also derive the shape of these patterns analytically without relying on microscopic details of the model. In particular, we find that the relative fitness of two microbial strains can be estimated from the logarithmic spirals created by selective sweeps. The theory is tested with strains of the budding yeast Saccharomyces cerevisiae for spatial competitions with different initial conditions and for a range of relative fitnesses. The reaction-diffusion model also connects the microscopic parameters like growth rates and diffusion constants with macroscopic spatial patterns and predicts the relationship between fitness in liquid cultures and on Petri dishes, which we confirmed experimentally. Spatial sector patterns therefore provide an alternative fitness assay to the commonly used liquid culture fitness assays.

Amino acids as a source of organic nitrogen in Antarctic endolithic microbial communities

NASA Technical Reports Server (NTRS)

McDonald, G.; Sun, H.

2002-01-01

In the Antarctic Dry Valleys, cryptoendolithic microbial communities occur within porous sandstone rocks. Current understanding of the mechanisms of physiological adaptation of these communities to the harsh Antarctic environment is limited, because traditional methods of studying microbial physiology are very difficult to apply to organisms with extremely low levels of metabolic activity. In order to fully understand carbon and nitrogen cycling and nutrient uptake in cryptoendolithic communities, and the metabolic costs that the organisms incur in order to survive, it is necessary to employ molecular geochemical techniques such as amino acid analysis in addition to physiological methods.

High-Resolution Microbial Community Succession of Microbially Induced Concrete Corrosion in Working Sanitary Manholes

PubMed Central

Ling, Alison L.; Robertson, Charles E.; Harris, J. Kirk; Frank, Daniel N.; Kotter, Cassandra V.; Stevens, Mark J.; Pace, Norman R.; Hernandez, Mark T.

2015-01-01

Microbially-induced concrete corrosion in headspaces threatens wastewater infrastructure worldwide. Models for predicting corrosion rates in sewer pipe networks rely largely on information from culture-based investigations. In this study, the succession of microbes associated with corroding concrete was characterized over a one-year monitoring campaign using rRNA sequence-based phylogenetic methods. New concrete specimens were exposed in two highly corrosive manholes (high concentrations of hydrogen sulfide and carbon dioxide gas) on the Colorado Front Range for up to a year. Community succession on corroding surfaces was assessed using Illumina MiSeq sequencing of 16S bacterial rRNA amplicons and Sanger sequencing of 16S universal rRNA clones. Microbial communities associated with corrosion fronts presented distinct succession patterns which converged to markedly low α-diversity levels (< 10 taxa) in conjunction with decreasing pH. The microbial community succession pattern observed in this study agreed with culture-based models that implicate acidophilic sulfur-oxidizer Acidithiobacillus spp. in advanced communities, with two notable exceptions. Early communities exposed to alkaline surface pH presented relatively high α-diversity, including heterotrophic, nitrogen-fixing, and sulfur-oxidizing genera, and one community exposed to neutral surface pH presented a diverse transition community comprised of less than 20% sulfur-oxidizers. PMID:25748024

High-resolution microbial community succession of microbially induced concrete corrosion in working sanitary manholes.

PubMed

Ling, Alison L; Robertson, Charles E; Harris, J Kirk; Frank, Daniel N; Kotter, Cassandra V; Stevens, Mark J; Pace, Norman R; Hernandez, Mark T

2015-01-01

Microbially-induced concrete corrosion in headspaces threatens wastewater infrastructure worldwide. Models for predicting corrosion rates in sewer pipe networks rely largely on information from culture-based investigations. In this study, the succession of microbes associated with corroding concrete was characterized over a one-year monitoring campaign using rRNA sequence-based phylogenetic methods. New concrete specimens were exposed in two highly corrosive manholes (high concentrations of hydrogen sulfide and carbon dioxide gas) on the Colorado Front Range for up to a year. Community succession on corroding surfaces was assessed using Illumina MiSeq sequencing of 16S bacterial rRNA amplicons and Sanger sequencing of 16S universal rRNA clones. Microbial communities associated with corrosion fronts presented distinct succession patterns which converged to markedly low α-diversity levels (< 10 taxa) in conjunction with decreasing pH. The microbial community succession pattern observed in this study agreed with culture-based models that implicate acidophilic sulfur-oxidizer Acidithiobacillus spp. in advanced communities, with two notable exceptions. Early communities exposed to alkaline surface pH presented relatively high α-diversity, including heterotrophic, nitrogen-fixing, and sulfur-oxidizing genera, and one community exposed to neutral surface pH presented a diverse transition community comprised of less than 20% sulfur-oxidizers.

Changes in microbial communities along redox gradients in polygonized Arctic wet tundra soils

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

Lipson, David A.; Raab, Theodore K.; Parker, Melanie

2015-07-21

This study investigated how microbial community structure and diversity varied with depth and topography in ice wedge polygons of wet tundra of the Arctic Coastal Plain in northern Alaska, and what soil variables explain these patterns. We observed strong changes in community structure and diversity with depth, and more subtle changes between areas of high and low topography, with the largest differences apparent near the soil surface. These patterns are most strongly correlated with redox gradients (measured using the ratio of reduced Fe to total Fe in acid extracts as a proxy): conditions grew more reducing with depth and weremore » most oxidized in shallow regions of polygon rims. Organic matter and pH also changed with depth and topography, but were less effective predictors of the microbial community structure and relative abundance of specific taxa. Of all other measured variables, lactic acid concentration was the best, in combination with redox, for describing the microbial community. We conclude that redox conditions are the dominant force in shaping microbial communities in this landscape. Oxygen and other electron acceptors allowed for the greatest diversity of microbes: at depth the community was reduced to a simpler core of anaerobes, dominated by fermenters ( Bacteroidetes and Firmicutes).« less

Changes in microbial communities along redox gradients in polygonized Arctic wet tundra soils.

PubMed

Lipson, David A; Raab, Theodore K; Parker, Melanie; Kelley, Scott T; Brislawn, Colin J; Jansson, Janet

2015-08-01

This study investigated how microbial community structure and diversity varied with depth and topography in ice wedge polygons of wet tundra of the Arctic Coastal Plain in northern Alaska and what soil variables explain these patterns. We observed strong changes in community structure and diversity with depth, and more subtle changes between areas of high and low topography, with the largest differences apparent near the soil surface. These patterns are most strongly correlated with redox gradients (measured using the ratio of reduced Fe to total Fe in acid extracts as a proxy): conditions grew more reducing with depth and were most oxidized in shallow regions of polygon rims. Organic matter and pH also changed with depth and topography but were less effective predictors of the microbial community structure and relative abundance of specific taxa. Of all other measured variables, lactic acid concentration was the best, in combination with redox, for describing the microbial community. We conclude that redox conditions are the dominant force in shaping microbial communities in this landscape. Oxygen and other electron acceptors allowed for the greatest diversity of microbes: at depth the community was reduced to a simpler core of anaerobes, dominated by fermenters (Bacteroidetes and Firmicutes). © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Microbial cross-contamination by airborne dispersion and contagion during defeathering of poultry.

PubMed

Allen, V M; Hinton, M H; Tinker, D B; Gibson, C; Mead, G C; Wathes, C M

2003-09-01

1. A readily identifiable strain of Escherichia coli K12 was used as a 'marker' organism to determine the sources, routes and patterns of microbial cross-contamination during mechanical defeathering of broiler chicken carcases. 2. Inoculation of scald water with the marker organism led to a relatively even pattern of carcase contamination during subsequent defeathering. Microbial cross-contamination was greater by this route of inoculation than by either surface inoculation of a 'seeder' carcase or oral inoculation of a live bird one day before slaughter. 3. Dispersal of the marker organism was strongly influenced by the mechanical action of the defeathering machines. Forward transmission of the marker occurred by aerosol or large airborne droplets and particulates such as feathers. Moving carcases through the defeathering machines when these were non-operational clearly reduced backward transmission of the marker. 4. Although microbial dispersal was unaffected by increasing the spacing between individual carcases or installing a water curtain at the entry and exit of the defeathering machines, shielding of carcases with aluminium baffles reduced counts of the marker organism from contaminated carcases by > 90%. 5. The results imply that microbial cross-contamination of broiler chicken carcases during defeathering occurs mainly via the airborne route, which could be contained by physical means.

Microbial secondary succession in soil microcosms of a desert oasis in the Cuatro Cienegas Basin, Mexico

PubMed Central

López-Lozano, Nguyen E.; Heidelberg, Karla B.; Nelson, William C.; García-Oliva, Felipe; Eguiarte, Luis E.

2013-01-01

Ecological succession is one of the most important concepts in ecology. However for microbial community succession, there is a lack of a solid theoretical framework regarding succession in microorganisms. This is in part due to microbial community complexity and plasticity but also because little is known about temporal patterns of microbial community shifts in different kinds of ecosystems, including arid soils. The Cuatro Cienegas Basin (CCB) in Coahuila, Mexico, is an arid zone with high diversity and endemisms that has recently been threatened by aquifer overexploitation. The gypsum-based soil system of the CCB is one of the most oligotrophic places in the world. We undertook a comparative 16S rRNA 454 pyrosequencing study to evaluate microbial community succession and recovery over a year after disturbance at two sites. Results were related to concurrent measurements of humidity, organic matter and total C and N content. While each site differed in both biogeochemistry and biodiversity, both present similar pattern of change at the beginning of the succession that diverged in later stages. After one year, experimentally disturbed soil was not similar to established and undisturbed adjacent soil communities indicating recovery and succession in disturbed soils is a long process. PMID:23638384

Molecular and Microscopic Insights into the Formation of Soil Organic Matter in a Red Pine Rhizosphere

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

Dohnalkova, Alice C.; Tfaily, Malak M.; Smith, A. Peyton

Microbially-derived carbon inputs to soils play an important role in forming soil organic matter (SOM), but detailed knowledge of basic mechanisms of carbon (C) cycling, such as stabilization of organic C compounds originating from rhizodeposition, is scarce. This study aimed to investigate the stability of rhizosphere-produced carbon components in a model laboratory mesocosm of Pinus resinosa grown in a designed mineral soil mix with limited nutrients. We utilized a suite of advanced imaging and molecular techniques to obtain a molecular-level identification of newly-formed SOM compounds, and considered implications regarding their degree of long-term persistence. The microbes in this controlled, nutrient-limitedmore » system, without pre-existing organic matter, produced extracellular polymeric substances that formed associations with nutrient-bearing minerals and contributed to the microbial mineral weathering process. Electron microscopy revealed unique ultrastructural residual signatures of biogenic C compounds, and the increased presence of an amorphous organic phase associated with the mineral phase was evidenced by X-ray diffraction. Here, these findings provide insight into the formation of SOM products in ecosystems, and show that the plant- and microbially-derived material associated with mineral matrices may be important components in current soil carbon models.« less

Molecular and Microscopic Insights into the Formation of Soil Organic Matter in a Red Pine Rhizosphere

DOE PAGES

Dohnalkova, Alice C.; Tfaily, Malak M.; Smith, A. Peyton; ...

2017-08-26

Microbially-derived carbon inputs to soils play an important role in forming soil organic matter (SOM), but detailed knowledge of basic mechanisms of carbon (C) cycling, such as stabilization of organic C compounds originating from rhizodeposition, is scarce. This study aimed to investigate the stability of rhizosphere-produced carbon components in a model laboratory mesocosm of Pinus resinosa grown in a designed mineral soil mix with limited nutrients. We utilized a suite of advanced imaging and molecular techniques to obtain a molecular-level identification of newly-formed SOM compounds, and considered implications regarding their degree of long-term persistence. The microbes in this controlled, nutrient-limitedmore » system, without pre-existing organic matter, produced extracellular polymeric substances that formed associations with nutrient-bearing minerals and contributed to the microbial mineral weathering process. Electron microscopy revealed unique ultrastructural residual signatures of biogenic C compounds, and the increased presence of an amorphous organic phase associated with the mineral phase was evidenced by X-ray diffraction. Here, these findings provide insight into the formation of SOM products in ecosystems, and show that the plant- and microbially-derived material associated with mineral matrices may be important components in current soil carbon models.« less

Low-molecular-weight hydroxyacids in marine atmospheric aerosol: evidence of a marine microbial origin

NASA Astrophysics Data System (ADS)

Miyazaki, Y.; Sawano, M.; Kawamura, K.

2014-04-01

Lactic acid (LA) and glycolic acid (GA), which are low-molecular-weight hydroxyacids, were identified in the particle and gas phases within the marine atmospheric boundary layer over the western subarctic North Pacific. Major portion of LA (81%) and GA (57%) were present in the particulate phase, which is consistent with the presence of a hydroxyl group in these molecules leading to the low volatility of the compounds. The average concentration of LA in more biologically influenced marine aerosols (average 33 ± 58 ng m-3) was substantially higher than that in less biologically influenced aerosols (average 11 ± 12 ng m-3). Over the oceacnic region of phytoplankton blooms, the concentration of aerosol LA was comparable to that of oxalic acid, which was the most abundant diacid during the study period. A positive correlation was found between the LA concentrations in more biologically influenced aerosols and chlorophyll a in seawater (r2 = 0.56), suggesting an important production of aerosol LA possibly associated with microbial (e.g., lactobacillus) activity in seawater and/or aerosols. Our finding provides a new insight into the poorly quantified microbial sources of marine organic aerosols (OA) because such low-molecular-weight hydroxyacids are key intermediates for OA formation.

Low-molecular-weight hydroxyacids in marine atmospheric aerosol: evidence of a marine microbial origin

NASA Astrophysics Data System (ADS)

Miyazaki, Y.; Sawano, M.; Kawamura, K.

2014-08-01

Lactic acid (LA) and glycolic acid (GA), which are low-molecular-weight hydroxyacids, were identified in the particle and gas phases within the marine atmospheric boundary layer over the western subarctic North Pacific. A major portion of LA (81%) and GA (57%) was present in the particulate phase, which is consistent with the presence of a hydroxyl group in these molecules leading to the low volatility of the compounds. The average concentration (±SD) of LA in more biologically influenced marine aerosols (33 ± 58 ng m-3) was substantially higher than that in less biologically influenced aerosols (11 ± 12 ng m-3). Over the oceanic region of phytoplankton blooms, the concentration of aerosol LA was comparable to that of oxalic acid, which was the most abundant diacid during the study period. A positive correlation was found between the LA concentrations in more biologically influenced aerosols and chlorophyll a in seawater (r2 = 0.56), suggesting an important production of aerosol LA possibly associated with microbial (e.g., lactobacillus) activity in seawater and/or aerosols. Our finding provides a new insight into the poorly quantified microbial sources of marine organic aerosols (OAs) because such low-molecular-weight hydroxyacids are key intermediates for OA formation.

The alternative Medicago truncatula defense proteome of ROS—defective transgenic roots during early microbial infection

PubMed Central

Kiirika, Leonard M.; Schmitz, Udo; Colditz, Frank

2014-01-01

ROP-type GTPases of plants function as molecular switches within elementary signal transduction pathways such as the regulation of ROS synthesis via activation of NADPH oxidases (RBOH-respiratory burst oxidase homolog in plants). Previously, we reported that silencing of the Medicago truncatula GTPase MtROP9 led to reduced ROS production and suppressed induction of ROS-related enzymes in transgenic roots (MtROP9i) infected with pathogenic (Aphanomyces euteiches) and symbiotic microorganisms (Glomus intraradices, Sinorhizobium meliloti). While fungal infections were enhanced, S. meliloti infection was drastically impaired. In this study, we investigate the temporal proteome response of M. truncatula MtROP9i transgenic roots during the same microbial interactions under conditions of deprived potential to synthesize ROS. In comparison with control roots (Mtvector), we present a comprehensive proteomic analysis using sensitive MS protein identification. For four early infection time-points (1, 3, 5, 24 hpi), 733 spots were found to be different in abundance: 213 spots comprising 984 proteins (607 unique) were identified after S. meliloti infection, 230 spots comprising 796 proteins (580 unique) after G. intraradices infection, and 290 spots comprising 1240 proteins (828 unique) after A. euteiches infection. Data evaluation by GelMap in combination with a heatmap tool allowed recognition of key proteome changes during microbial interactions under conditions of hampered ROS synthesis. Overall, the number of induced proteins in MtROP9i was low as compared with controls, indicating a dual function of ROS in defense signaling as well as alternative response patterns activated during microbial infection. Qualitative analysis of induced proteins showed that enzymes linked to ROS production and scavenging were highly induced in control roots, while in MtROP9i the majority of proteins were involved in alternative defense pathways such as cell wall and protein degradation. PMID:25101099

Bacterial communities in full-scale wastewater treatment systems.

PubMed

Cydzik-Kwiatkowska, Agnieszka; Zielińska, Magdalena

2016-04-01

Bacterial metabolism determines the effectiveness of biological treatment of wastewater. Therefore, it is important to define the relations between the species structure and the performance of full-scale installations. Although there is much laboratory data on microbial consortia, our understanding of dependencies between the microbial structure and operational parameters of full-scale wastewater treatment plants (WWTP) is limited. This mini-review presents the types of microbial consortia in WWTP. Information is given on extracellular polymeric substances production as factor that is key for formation of spatial structures of microorganisms. Additionally, we discuss data on microbial groups including nitrifiers, denitrifiers, Anammox bacteria, and phosphate- and glycogen-accumulating bacteria in full-scale aerobic systems that was obtained with the use of molecular techniques, including high-throughput sequencing, to shed light on dependencies between the microbial ecology of biomass and the overall efficiency and functional stability of wastewater treatment systems. Sludge bulking in WWTPs is addressed, as well as the microbial composition of consortia involved in antibiotic and micropollutant removal.

Culture-independent phylogenetic analysis of the microbial community in industrial sugarcane bagasse feedstock piles.

PubMed

Rattanachomsri, Ukrit; Kanokratana, Pattanop; Eurwilaichitr, Lily; Igarashi, Yasuo; Champreda, Verawat

2011-01-01

Sugarcane bagasse is an important lignocellulosic by-product with potential for conversion to biofuels and chemicals in biorefinery. As a step towards an understanding of microbial diversity and the processes existing in bagasse collection sites, the microbial community in industrial bagasse feedstock piles was investigated. Molecular biodiversity analysis of 16S rDNA sequences revealed the presence of a complex bacterial community. A diverse group of mainly aerobic and facultative anaerobic bacteria was identified reflecting the aerobic and high temperature microenvironmental conditions under the pile surface. The major bacterial taxa present were identified as Firmicutes, Alpha- and Gammaproteobacteria, Acidobacteria, Bacteroidetes, and Actinobacteria. Analysis of the eukaryotic microbial assemblage based on an internal transcribed spacer revealed the predominance of diverse cellulolytic and hemicellulolytic ascomycota. A microbial interaction model is proposed, focusing on lignocellulose degradation and methane metabolism. The insights into the microbial community in this study provide a basis for efficient utilization of bagasse in lignocellulosic biomass-based industries.

[Effects of applying inorganic P and wheat straw on the microbial biomass P and microbial P concentration in a calcareous soil with low concentration available P].

PubMed

Zhao, Xiao-Rong; Zhou, Ran; Li, Gui-Tong; Lin, Qi-Mei

2009-02-01

In an incubation test, a calcareous soil with low concentration of available P was amended with KH2PO4 (0, 25, 50, and 100 mg P x kg(-1)) and ground wheat straw (5 g C x kg(-1)), and incubated at 25 degrees C for 90 days. The aim was to investigate the change patterns of soil microbial biomass P and microbial P concentration as well as their relationships with soil available P. The results showed that both soil microbial biomass P and microbial P concentration increased with increasing inorganic P addition, with the maximum being 71.37 and 105.34 mg x kg(-1), respectively. The combined application of inorganic P (except 100 mg P x kg(-1)) and wheat straw decreased the soil microbial biomass P and microbial P concentration, being most obvious at early incubation period. Soil microbial biomass P and microbial P concentration had significant positive correlations (P < 0.05) with soil available P (R2 = 0.26 and 0.40, n = 49, respectively). The applied P could rapidly transform into microbial biomass P. The maximum apparent contribution rate of applied P to microbial biomass P was 71%. The added wheat straw could further improve the apparent contribution rate.

Linking Spatial Structure and Community-Level Biotic Interactions through Cooccurrence and Time Series Modeling of the Human Intestinal Microbiota.

PubMed

de Muinck, Eric J; Lundin, Knut E A; Trosvik, Pål

2017-01-01

The gastrointestinal (GI) microbiome is a densely populated ecosystem where dynamics are determined by interactions between microbial community members, as well as host factors. The spatial organization of this system is thought to be important in human health, yet this aspect of our resident microbiome is still poorly understood. In this study, we report significant spatial structure of the GI microbiota, and we identify general categories of spatial patterning in the distribution of microbial taxa along a healthy human GI tract. We further estimate the biotic interaction structure in the GI microbiota, both through time series and cooccurrence modeling of microbial community data derived from a large number of sequentially collected fecal samples. Comparison of these two approaches showed that species pairs involved in significant negative interactions had strong positive contemporaneous correlations and vice versa, while for species pairs without significant interactions, contemporaneous correlations were distributed around zero. We observed similar patterns when comparing these models to the spatial correlations between taxa identified in the adherent microbiota. This suggests that colocalization of microbial taxon pairs, and thus the spatial organization of the GI microbiota, is driven, at least in part, by direct or indirect biotic interactions. Thus, our study can provide a basis for an ecological interpretation of the biogeography of the human gut. IMPORTANCE The human gut microbiome is the subject of intense study due to its importance in health and disease. The majority of these studies have been based on the analysis of feces. However, little is known about how the microbial composition in fecal samples relates to the spatial distribution of microbial taxa along the gastrointestinal tract. By characterizing the microbial content both in intestinal tissue samples and in fecal samples obtained daily, we provide a conceptual framework for how the spatial structure relates to biotic interactions on the community level. We further describe general categories of spatial distribution patterns and identify taxa conforming to these categories. To our knowledge, this is the first study combining spatial and temporal analyses of the human gut microbiome. This type of analysis can be used for identifying candidate probiotics and designing strategies for clinical intervention.

Microbial biogeography of San Francisco Bay sediments

NASA Astrophysics Data System (ADS)

Lee, J. A.; Francis, C. A.

2014-12-01

The largest estuary on the west coast of North America, San Francisco Bay is an ecosystem of enormous biodiversity, and also enormous human impact. The benthos has experienced dredging, occupation by invasive species, and over a century of sediment input as a result of hydraulic mining. Although the Bay's great cultural and ecological importance has inspired numerous surveys of the benthic macrofauna, to date there has been almost no investigation of the microbial communities on the Bay floor. An understanding of those microbial communities would contribute significantly to our understanding of both the biogeochemical processes (which are driven by the microbiota) and the physical processes (which contribute to microbial distributions) in the Bay. Here, we present the first broad survey of bacterial and archaeal taxa in the sediments of the San Francisco Bay. We conducted 16S rRNA community sequencing of bacteria and archaea in sediment samples taken bimonthly for one year, from five sites spanning the salinity gradient between Suisun and Central Bay, in order to capture the effect of both spatial and temporal environmental variation on microbial diversity. From the same samples we also conducted deep sequencing of a nitrogen-cycling functional gene, nirS, allowing an assessment of evolutionary diversity at a much finer taxonomic scale within an important and widespread functional group of bacteria. We paired these sequencing projects with extensive geochemical metadata as well as information about macrofaunal distribution. Our data reveal a diversity of distinct biogeographical patterns among different taxa: clades ubiquitous across sites; clades that respond to measurable environmental drivers; and clades that show geographical site-specificity. These community datasets allow us to test the hypothesis that salinity is a major driver of both overall microbial community structure and community structure of the denitrifying bacteria specifically; and to assess whether patterns of diversity observed at the broadest of taxonomic scales also apply to patterns observed within a single extremely diverse gene (nirS). In sum, this project provides a first look at the forces driving the migration and selection of microbial communities in San Francisco Bay.

Effects of plastic film residues on occurrence of phthalates and microbial activity in soils.

PubMed

Wang, Jun; Lv, Shenghong; Zhang, Manyun; Chen, Gangcai; Zhu, Tongbin; Zhang, Shen; Teng, Ying; Christie, Peter; Luo, Yongming

2016-05-01

Plastic film mulching has played an important role in Chinese agriculture, especially in vegetable production, but large amounts of film residues can accumulate in the soil. The present study investigated the effects of plastic film residues on the occurrence of soil PAEs and microbial activities using a batch pot experiment. PAE concentrations increased with increasing plastic film residues but the soil microbial carbon and nitrogen, enzyme activities and microbial diversity decreased significantly. At the end of the experiment the PAE concentrations were 0-2.02 mg kg(-1) in the different treatments. Soil microbial C and N, enzyme activities, AWCD value, and Shannon-Weaver and Simpson indices declined by about 28.9-76.2%, 14.9-59.0%, 4.9-22.7%, 23.0-42.0% and 1.8-18.7%, respectively. Soil microbial activity was positively correlated with soil PAE concentration, and soil PAE concentrations were impacted by plastic color and residue volume. Correlations among, and molecular mechanisms of, plastic film residues, PAE occurrence and microbial activity require further study. Copyright © 2016 Elsevier Ltd. All rights reserved.

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.

Geochemical drivers of organic matter decomposition in Arctic tundra soils

DOE PAGES

Herndon, Elizabeth M.; Yang, Ziming; Graham, David E.; ...

2015-12-07

Climate change is warming tundra ecosystems in the Arctic, resulting in the decomposition of previously-frozen soil organic matter (SOM) and release of carbon (C) to the atmosphere; however, the processes that control SOM decomposition and C emissions remain highly uncertain. In this study, we evaluate geochemical factors that influence anaerobic production of carbon dioxide (CO 2) and methane (CH 4) in the active layers of four ice-wedge polygons. Surface and soil pore waters were collected during the annual thaw season over a two-year period in an area containing waterlogged, low-centered polygons and well-drained, high-centered polygons. We report spatial and seasonalmore » patterns of dissolved gases in relation to the geochemical properties of Fe and organic C as determined using spectroscopic and chromatographic techniques. Iron was present as Fe(II) in soil solution near the permafrost boundary but enriched as Fe(III) in the middle of the active layer, similar to dissolved aromatic-C and organic acids. Dissolved CH 4 increased relative to dissolved CO 2 with depth and varied with soil moisture in the middle of the active layer in patterns that were positively correlated with the proportion of dissolved Fe(III) in transitional and low-centered polygon soils but negatively correlated in the drier flat- and high-centered polygons. These results suggest that microbial-mediated Fe oxidation and reduction influence respiration/fermentation of SOM and production of substrates (e.g., low-molecular-weight organic acids) for methanogenesis. As a result, we infer that geochemical differences induced by water saturation dictate microbial products of SOM decomposition, and Fe geochemistry is an important factor regulating methanogenesis in anoxic tundra soils.« less

Strong inter-population cooperation leads to partner intermixing in microbial communities

DOE PAGES

Momeni, Babak; Brileya, Kristen A.; Fields, Matthew W.; ...

2013-01-22

Patterns of spatial positioning of individuals within microbial communities are often critical to community function. However, understanding patterning in natural communities is hampered by the multitude of cell–cell and cell–environment interactions as well as environmental variability. Here, through simulations and experiments on communities in defined environments, we examined how ecological interactions between two distinct partners impacted community patterning. We found that in strong cooperation with spatially localized large fitness benefits to both partners, a unique pattern is generated: partners spatially intermixed by appearing successively on top of each other, insensitive to initial conditions and interaction dynamics. Intermixing was experimentally observedmore » in two obligatory cooperative systems: an engineered yeast community cooperating through metabolite-exchanges and a methane-producing community cooperating through redox-coupling. Even in simulated communities consisting of several species, most of the strongly-cooperating pairs appeared intermixed. Thus, when ecological interactions are the major patterning force, strong cooperation leads to partner intermixing.« less

Effect of Macondo Prospect 252 Oil on Microbiota Associated with Pelagic Sargassum in the Northern Gulf of Mexico.

PubMed

Torralba, Manolito G; Franks, James S; Gomez, Andres; Yooseph, Shibu; Nelson, Karen E; Grimes, D Jay

2017-01-01

The environmental impact of major oil spills on marine microorganisms has yet to be thoroughly investigated using molecular biology techniques. The Deepwater Horizon (DWH) drilling rig explosion of 2010 affected an approximately 176,000 km 2 surface area of the Gulf of Mexico (GOM) when an estimated 210 million gallons of oil from the Macondo Prospect spilled into the environment. Pelagic Sargassum, a complex of two surface drifting species (Sargassum natans and Sargassum fluitans) of marine brown macroalgae and a critically important habitat in the GOM ecosystem, was suffused by Macondo Prospect 252 oil released during the DWH event. Using 16S rRNA PCR and Roche 454 pyrosequencing, the effect of the oil on the bacterial population associated with pelagic Sargassum and contiguous waters was examined by comparing sequence data generated from samples collected from oiled and non-oiled locations in the northern GOM. Sequence data showed similar microbial composition in Sargassum regardless of exposure to oil primarily dominated by five phyla; Proteobacteria, Bacteroidetes, Actinobacteria, Verrucomicrobia, and unclassified bacteria. The microbial composition in water samples was significantly less diverse than for Sargassum and consisted primarily of Proteobacteria, Firmicutes, and Bacteroidetes. Due to the evenly distributed abundance of microbial species on oiled and non-oiled pelagic Sargassum, study findings indicate that DWH spilled oil had minimal effect on the composition and diversity of the microbial community associated with Sargassum and contiguous waters. However, higher abundances of Sulfitobacter and one species of Psychrobacter were found in oiled water samples when compared to non-oiled water samples indicating some effect of DHW oil in the microbial composition of seawater. Though there are a number of marine studies using molecular biology approaches, this is the first molecular examination of the impact of the DWH oil spill on bacterial communities associated with pelagic Sargassum and contiguous waters from the GOM.

Microbial Ecology of Soil Aggregation in Agroecosystems

NASA Astrophysics Data System (ADS)

Hofmockel, K. S.; Bell, S.; Tfailly, M.; Thompson, A.; Callister, S.

2017-12-01

Crop selection and soil texture influence the physicochemical attributes of the soil, which structures microbial communities and influences soil C cycling storage. At the molecular scale, microbial metabolites and necromass alter the soil environment, which creates feedbacks that influence ecosystem functions, including soil C accumulation. By integrating lab to field studies we aim to identify the molecules, organisms and metabolic pathways that control carbon cycling and stabilization in bioenergy soils. We investigated the relative influence of plants, microbes, and minerals on soil aggregate ecology at the Great Lakes Bioenergy Research experiment. Sites in WI and MI, USA have been in corn and switchgrass cropping systems for a decade. By comparing soil aggregate ecology across sites and cropping systems we are able to test the relative importance of plant, microbe, mineral influences on soil aggregate dynamics. Soil microbial communities (16S) differ in diversity and phylogeny among sites and cropping systems. FT-ICR MS revealed differences in the molecular composition of water-soluble fraction of soil organic matter for cropping systems and soil origin for both relative abundance of assigned formulas and biogeochemical classes of compounds. We found the degree of aggregation, measured by mean weighted diameter of aggregate fractions, is influenced by plant-soil interactions. Similarly, the proportion of soil aggregate fractions varied by both soil and plant factors. Differences in aggregation were reflected in differences in bacterial, but not fungal community composition across aggregate fractions, within each soil. Scanning electron microscopy revealed stark differences in mineral-organic interactions that influence the microbial niche and the accessibility of substrates within the soil. The clay soils show greater surface heterogeneity, enabling interactions with organic fraction of the soil. This is consistent with molecular data that reveal differences in the abundance of chemical classes in clay loams compared to sandy loams. Together our data demonstrate that the potential for aggregation and C storage is strongly influenced by soil mineralogy with important implications for plant-microbe interactions that mediate C biogeochemistry.

Molecular evidence for a microbial role in ooid formation and preservation of molecular biosignatures in ancient oolite

NASA Astrophysics Data System (ADS)

Mariotti, G.; O'Reilly, S. S.; Winter, A.; Newman, S. A.; Pruss, S. B.; Bosak, T.; Klepac-Ceraj, V.; McDermott, F. P.; Summons, R. E.

2015-12-01

Ooids are concentrically laminated carbonate grains, occurring in a limited number of modern shallow marine and lacustrine settings. Oolitic sedimentary rocks (oolite) are common in the geological record, particularly in the Precambrian, and subsequent to some mass extinction events. Despite their significance, controversy remains about processes that form and shape ooids. Abiotic models typically favour carbonate precipitation in suspension in supersaturated, agitated water while biotic models emphasise microbial benthic contribution to ooid carbonate precipitation in relatively low turbulence waters. While various interpretations of ooids in the geological record have been made, the ongoing formation debate, together with post-depositional diagenesis, hinders our ability to interpret and utilize ooids to reconstruct Earth's past environments and biodiversity. Recently, Neoproterozoic oolitic carbonates have been shown to preserve C-isotopic records of environmental change and carbon cycle anomalies. This prompts the question whether molecular organic biosignatures can be found in well-preserved oolite. Here, lipid biomarker analysis and Illumina sequencing of modern ooids at Pigeon Cay, the Bahamas, revealed colonization of ooids by biofim-producing α-proteobacteria and diatoms, sulfate-reducing bacteria, anoxygenic phototrophs, as well as some cyanobacteria, in calm waters adjacent to the surf zone. These were comparable to communities associated with microbially-cemented grapestones. Relict lipids bound within ooid carbonate were also dominated by bacterial fatty acids, hydroxy acids and hopanoids. This indicates that a common, bacteria-dominated, microbial community is directly involved in carbonate precipitation of ooids and grapestones, likely by autotrophic metabolism and organomineralization of biofilms. Analysis of oolites as old as Jurassic in age revealed the preservation of hydrocarbons, as well as appreciable amounts of fatty acids, and emphasises the potential utility of oolites to preserve organic biosignatures. Further comparison of biomarkers from ooids from different environmental conditions and preservation state will provide insight into syngenetic molecular signals of environmental conditions and biological diversity in ancient oolite.

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

[Fermentation production of microbial catalase and its application in textile industry].

PubMed

Zhang, Dongxu; Du, Guocheng; Chen, Jian

2010-11-01

Microbial catalase is an important industrial enzyme that catalyzes the decomposition of hydrogen peroxide to water and oxygen. This enzyme has great potential of application in food, textile and pharmaceutical industries. The production of microbial catalase has been significantly improved thanks to advances in bioprocess engineering and genetic engineering. In this paper, we review the progresses in fermentation production of microbial catalase and its application in textile industry. Among these progresses, we will highlight strain isolation, substrate and environment optimization, enzyme induction, construction of engineering strains and application process optimization. Meanwhile, we also address future research trends for microbial catalase production and its application in textile industry. Molecular modification (site-directed mutagenesis and directed revolution) will endue catalase with high pH and temperature stabilities. Improvement of catalase production, based on the understanding of induction mechanism and the process control of recombinant stain fermentation, will further accelerate the application of catalase in textile industry.

Microbial bebop: creating music from complex dynamics in microbial ecology.

PubMed

Larsen, Peter; Gilbert, Jack

2013-01-01

In order for society to make effective policy decisions on complex and far-reaching subjects, such as appropriate responses to global climate change, scientists must effectively communicate complex results to the non-scientifically specialized public. However, there are few ways however to transform highly complicated scientific data into formats that are engaging to the general community. Taking inspiration from patterns observed in nature and from some of the principles of jazz bebop improvisation, we have generated Microbial Bebop, a method by which microbial environmental data are transformed into music. Microbial Bebop uses meter, pitch, duration, and harmony to highlight the relationships between multiple data types in complex biological datasets. We use a comprehensive microbial ecology, time course dataset collected at the L4 marine monitoring station in the Western English Channel as an example of microbial ecological data that can be transformed into music. Four compositions were generated (www.bio.anl.gov/MicrobialBebop.htm.) from L4 Station data using Microbial Bebop. Each composition, though deriving from the same dataset, is created to highlight different relationships between environmental conditions and microbial community structure. The approach presented here can be applied to a wide variety of complex biological datasets.

Organic molecules as chemical fossils - The molecular fossil record

NASA Technical Reports Server (NTRS)

Eglinton, G.

1983-01-01

The study of biochemical clues to the early earth and the origin of life is discussed. The methods used in such investigation are described, including the extraction, fractionation, and analysis of geolipids and the analysis of kerogen. The occurrence of molecular fossils in the geological record is examined, discussing proposed precursor-product relationships and the molecular assessment of deep sea sediments, ancient sediments, and crude petroleums. Alterations in the molecular record due to diagenesis and catagenesis are considered, and the use of microbial lipids as molecular fossils is discussed. The results of searches for molecular fossils in Precambrian sediments are assessed.

Evidence of Microbial Regulation of Biogeochemical Cycles from a Study on Methane Flux and Land Use Change

PubMed Central

Nazaries, Loïc; Pan, Yao; Bodrossy, Levente; Baggs, Elizabeth M.; Millard, Peter; Murrell, J. Colin

2013-01-01

Microbes play an essential role in ecosystem functions, including carrying out biogeochemical cycles, but are currently considered a black box in predictive models and all global biodiversity debates. This is due to (i) perceived temporal and spatial variations in microbial communities and (ii) lack of ecological theory explaining how microbes regulate ecosystem functions. Providing evidence of the microbial regulation of biogeochemical cycles is key for predicting ecosystem functions, including greenhouse gas fluxes, under current and future climate scenarios. Using functional measures, stable-isotope probing, and molecular methods, we show that microbial (community diversity and function) response to land use change is stable over time. We investigated the change in net methane flux and associated microbial communities due to afforestation of bog, grassland, and moorland. Afforestation resulted in the stable and consistent enhancement in sink of atmospheric methane at all sites. This change in function was linked to a niche-specific separation of microbial communities (methanotrophs). The results suggest that ecological theories developed for macroecology may explain the microbial regulation of the methane cycle. Our findings provide support for the explicit consideration of microbial data in ecosystem/climate models to improve predictions of biogeochemical cycles. PMID:23624469

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.

Large-scale distribution of microbial and viral populations in the South Atlantic Ocean.

PubMed

De Corte, Daniele; Sintes, Eva; Yokokawa, Taichi; Lekunberri, Itziar; Herndl, Gerhard J

2016-04-01

Viruses are abundant, diverse and dynamic components of the marine environments and play a significant role in the ocean biogeochemical cycles. To assess potential variations in the relation between viruses and microbes in different geographic regions and depths, viral and microbial abundance and production were determined throughout the water column along a latitudinal transect in the South Atlantic Ocean. Path analysis was used to examine the relationships between several abiotic and biotic parameters and the different microbial and viral populations distinguished by flow cytometry. The depth-integrated contribution of microbial and viral abundance to the total microbial and viral biomass differed significantly among the different provinces. Additionally, the virus-to-microbe ratio increased with depth and decreased laterally towards the more productive regions. Our data revealed that the abundance of phytoplankton and microbes is the main controlling factor of the viral populations in the euphotic and mesopelagic layers, whereas in the bathypelagic realm, viral abundance was only weakly related to the biotic and abiotic variables. The relative contribution of the three viral populations distinguished by flow cytometry showed a clear geographical pattern throughout the water column, suggesting that these populations are composed of distinct taxa able to infect specific hosts. Overall, our data indicate the presence of distinct microbial patterns along the latitudinal transect. This variability is not limited to the euphotic layer but also detectable in the meso- and bathypelagic layers. © 2016 The Authors. Environmental Microbiology Reports published by Society for Applied Microbiology and John Wiley & Sons Ltd.

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

The role of microbial low-molecular-weight autoregulatory factors (alkylhydroxybenzenes) in resistance of microorganisms to radiation

NASA Astrophysics Data System (ADS)

El-Registan, G. I.; Mulyukin, A. L.; Nikolaev, Yu. A.; Stepanenko, I. Yu.; Shanenko, E. A.; Strakhovskaya, M. G.; Revina, A. A.

Low-molecular-weight cell-to-cell communication factors are produced by various pro- and eukaryotes and involved in autoregulation of the growth and development of microbial cultures. As for some bacterial and yeast species, these factors were identified as isomers and homologs of alkylhydroxybenzenes (AHBs). Depending on the concentration, they participate in controlling the transition to stationary phase, entering the resting state, and stress resistance of vegetative cells to gamma-irradiation, photooxidation (singlet oxygen), heat shock. Chemical analogs of microbial AHBs protected microbial cultures from stressful situations and prolonged starvation and exerted (1) the stabilizing activity toward biomacromolecules and supermolecular structures (cell membranes) and (2) the ability to scavenge active oxygen species. The stabilizing effect of AHBs as chemical chaperones resulted from their complex formation with protected macromolecules due to intermolecular hydrogen bonds, hydrophobic and electrostatic interactions and was demonstrated on models of individual enzymes (trypsin, amylase, etc.). The action of AHBs as active oxygen species scavengers was related to their oxidative conversion to water-insoluble polymeric products. Particularly, AHBs protected the yeast from the action of (a) active oxygen species formed during gamma-irradiation (50 krad, 196 rad/sec) or (b) singlet oxygen generated in cells photosensitized by chlorin e6 (10 mkg/L). It is important that microbial AHBs were not species-specific and defended cultured animal cells (ras-transformed fibroblasts) from the action of organic toxicants. The use of AHBs as protectants and adaptogens will be discussed as well as perspectives of further investigations.

Microbial regulation of terrestrial nitrous oxide formation: understanding the biological pathways for prediction of emission rates.

PubMed

Hu, Hang-Wei; Chen, Deli; He, Ji-Zheng

2015-09-01

The continuous increase of the greenhouse gas nitrous oxide (N2O) in the atmosphere due to increasing anthropogenic nitrogen input in agriculture has become a global concern. In recent years, identification of the microbial assemblages responsible for soil N2O production has substantially advanced with the development of molecular technologies and the discoveries of novel functional guilds and new types of metabolism. However, few practical tools are available to effectively reduce in situ soil N2O flux. Combating the negative impacts of increasing N2O fluxes poses considerable challenges and will be ineffective without successfully incorporating microbially regulated N2O processes into ecosystem modeling and mitigation strategies. Here, we synthesize the latest knowledge of (i) the key microbial pathways regulating N2O production and consumption processes in terrestrial ecosystems and the critical environmental factors influencing their occurrence, and (ii) the relative contributions of major biological pathways to soil N2O emissions by analyzing available natural isotopic signatures of N2O and by using stable isotope enrichment and inhibition techniques. We argue that it is urgently necessary to incorporate microbial traits into biogeochemical ecosystem modeling in order to increase the estimation reliability of N2O emissions. We further propose a molecular methodology oriented framework from gene to ecosystem scales for more robust prediction and mitigation of future N2O emissions. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Use of molecular approaches in hydrogeological studies: the case of carbonate aquifers in southern Italy

NASA Astrophysics Data System (ADS)

Bucci, Antonio; Petrella, Emma; Celico, Fulvio; Naclerio, Gino

2017-06-01

Waterborne pathogens represent a significant health risk in both developed and developing countries with sensitive sub-populations including children, the elderly, neonates, and immune-compromised people, who are particularly susceptible to enteric infections. Annually, approximately 1.8 billion people utilize a faecally contaminated water source, and waterborne diseases are resulting in up to 2.1 million human mortalities globally. Although groundwater has traditionally been considered less susceptible to contamination by enteric pathogens than surface water due to natural attenuation by overlying strata, the degree of microbial removal attributable to soils and aquifers can vary significantly depending on several factors. Thus, accurate assessment of the variable presence and concentration of microbial contaminants, and the relative importance of potentially causative factors affecting contaminant ingress, is critical in order to develop effective source (well) and resource (aquifer) protection strategies. "Traditional" and molecular microbiological study designs, when coupled with hydrogeological, hydrochemical, isotopic, and geophysical methods, have proven useful for analysis of numerous aspects of subsurface microbial dynamics. Accordingly, this overview paper presents the principal microbial techniques currently being employed (1) to predict and identify sources of faecal contamination in groundwater, (2) to elucidate the dynamics of contaminant migration, and (3) to refine knowledge about the hydrogeological characteristics and behaviours of aquifer systems affected by microbial contamination with an emphasis on carbonate aquifers, which represent an important global water supply. Previous investigations carried out in carbonate aquifers in southern Italy are discussed.

Microbial Enzymatic Degradation of Biodegradable Plastics.

PubMed

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

2017-01-01

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

Standing variation in spatially growing populations

NASA Astrophysics Data System (ADS)

Fusco, Diana; Gralka, Matti; Kayser, Jona; Hallatschek, Oskar

Patterns of genetic diversity not only reflect the evolutionary history of a species but they can also determine the evolutionary response to environmental change. For instance, the standing genetic diversity of a microbial population can be key to rescue in the face of an antibiotic attack. While genetic diversity is in general shaped by both demography and evolution, very little is understood when both factors matter, as e.g. for biofilms with pronounced spatial organization. Here, we quantitatively explore patterns of genetic diversity by using microbial colonies and well-mixed test tube populations as antipodal model systems with extreme and very little spatial structure, respectively. We find that Eden model simulations and KPZ theory can remarkably reproduce the genetic diversity in microbial colonies obtained via population sequencing. The excellent agreement allows to draw conclusions on the resilience of spatially-organized populations and to uncover new strategies to contain antibiotic resistance.

Macrophage genetic reprogramming during chronic peritonitis is augmented by LPS pretreatment.

PubMed

Kanaan, Ziad; Gardner, Sarah; Carruba, Christopher; Mattingly, Jameson; Druen, Devin; Cheadle, William G

2012-06-15

Persistent and tertiary chronic peritonitis is a clinically challenging problem especially in those who are critically ill. This could be attributed to a state of immune-paralysis, known as microbial tolerance. Microbial tolerance is the diminished pro-inflammatory protein response following repeated stimulation by numerous pathogen-associated molecular patterns (PAMPs) of varying origins, which we have shown in this novel model of chronic peritonitis. We aimed in this study to investigate the molecular mechanisms behind microbial tolerance and the early innate immune response resolution in this model. C57BL/6 mice were pretreated intra-peritoneally (IP) with saline or endotoxin LPS 10 mg/kg (LPS 10). Following pretreatment, peritonitis was induced 24 h later injecting 10(3)Klebsiella pneumonia CFU IP. Gentamicin was administered 4 h prior to infection and BID thereafter. Peritoneal exudate cells (PEC) were obtained through peritoneal lavage and RNA was isolated (n = 3) at 4, 24, and 48 h following infection. SA Biosciences© RT2-Profiler PCR array mouse Toll-like receptor signaling pathway (PAMM_018A) data were further analyzed by Ingenuity Pathway Inc. analysis (IPA). Of the 89 genes studied, 26 were significantly up-regulated (fold change > 1.2 and P value < 0.05) in the saline pretreated group at 4, 24, and 48 h after infection. There were no down-regulated genes. In the LPS-pretreated group, 35 genes were significantly up-regulated; of these genes, 13 were not increased in the saline pretreated infected mice. This left 22 up-regulated genes in both infected groups. At 4 h, 6 of these 22 genes (CHUK, HMGB1, HSPD1, IRAK2, LY96, and TLR4) were further 2-fold increased in the LPS pretreatment group compared with the saline pretreatment group. Only IRAK2 was 2-fold increased at 24 h. By 48 h, no LPS effect was seen. When applying IPA analysis, six main canonical pathways were constantly dysregulated in the same significance order in both the saline and LPS group at 4, 24, and 48 h. These were: Toll-like receptor and NF-κB signaling, hepatic cholestasis, interleukin-6, and LPS-mediated MAPK signaling pathways, and pattern recognition receptors of bacterial pathway. Peritonitis increased PEC gene expression associated with sepsis and a pro-inflammatory response, which was further augmented by LPS pretreatment over 24 h only. Prior exposure to LPS did not induce PEC gene tolerance to subsequent infection with Klebsiella at the mRNA level. Post-transcriptional modification as microRNA down-regulation of inflammatory cytokines could possibly explain such phenomena. Published by Elsevier Inc.