Abstract:
:The relationship between groundwater geochemistry and microbial community structure can be complex and difficult to assess. We applied nonlinear and generalized linear data analysis methods to relate microbial biomarkers (phospholipids fatty acids, PLFA) to groundwater geochemical characteristics at the Shiprock uranium mill tailings disposal site that is primarily contaminated by uranium, sulfate, and nitrate. First, predictive models were constructed using feedforward artificial neural networks (NN) to predict PLFA classes from geochemistry. To reduce the danger of overfitting, parsimonious NN architectures were selected based on pruning of hidden nodes and elimination of redundant predictor (geochemical) variables. The resulting NN models greatly outperformed the generalized linear models. Sensitivity analysis indicated that tritium, which was indicative of riverine influences, and uranium were important in predicting the distributions of the PLFA classes. In contrast, nitrate concentration and inorganic carbon were least important, and total ionic strength was of intermediate importance. Second, nonlinear principal components (NPC) were extracted from the PLFA data using a variant of the feedforward NN. The NPC grouped the samples according to similar geochemistry. PLFA indicators of Gram-negative bacteria and eukaryotes were associated with the groups of wells with lower levels of contamination. The more contaminated samples contained microbial communities that were predominated by terminally branched saturates and branched monounsaturates that are indicative of metal reducers, actinomycetes, and Gram-positive bacteria. These results indicate that the microbial community at the site is coupled to the geochemistry and knowledge of the geochemistry allows prediction of the community composition.
journal_name
Microb Ecoljournal_title
Microbial ecologyauthors
Schryver JC,Brandt CC,Pfiffner SM,Palumbo AV,Peacock AD,White DC,McKinley JP,Long PEdoi
10.1007/s00248-004-0137-0keywords:
subject
Has Abstractpub_date
2006-02-01 00:00:00pages
177-88issue
2eissn
0095-3628issn
1432-184Xjournal_volume
51pub_type
杂志文章abstract::Dialysis bags were used to examine the impact of predation and viral lysis on prokaryotic community composition (PCC) over a 5-day experiment in the oligomesotrophic Lake Pavin (France). The impact of the different predator communities (protists and metazoans) of prokaryotes was estimated by water fractionation (<5 mi...
journal_title:Microbial ecology
pub_type: 杂志文章
doi:10.1007/s00248-005-5030-y
更新日期:2005-11-01 00:00:00
abstract::The lower respiratory tract has been previously considered sterile in a healthy state, but advances in culture-independent techniques for microbial identification and characterization have revealed that the lung harbors a diverse microbiome. Although research on the lung microbiome is increasing and important question...
journal_title:Microbial ecology
pub_type: 杂志文章
doi:10.1007/s00248-017-1068-x
更新日期:2018-02-01 00:00:00
abstract::The predatory activity of bdellovibrios is affected by various environmental pollutants such as detergents, heavy metals, and pesticides. This was shown in a two-membered system ofBdellovibrio andPhotobacterium, in which the effect of the predator on the bioluminescence of the prey indicated the activity of the former...
journal_title:Microbial ecology
pub_type: 杂志文章
doi:10.1007/BF02032492
更新日期:1981-06-01 00:00:00
abstract::Actinobacteria are major producers of secondary metabolites; however, it is unclear how they are distributed in the environment. DNA was extracted from forest, pasture and cultivated soils, street sediments (dust and material in place), and sediments affected by animal activity (e.g. guano, vermicompost) and character...
journal_title:Microbial ecology
pub_type: 杂志文章
doi:10.1007/s00248-010-9752-0
更新日期:2011-02-01 00:00:00
abstract::Montmorillonitic clay influences the biological control ofEscherichia coli in aquatic systems, the magnitude of the effects being dependent on the state of the clay and the type of host-antagonist interaction. The interaction ofBdellovibrio andE. coli was partially inhibited by the presence of montmorillonite. Because...
journal_title:Microbial ecology
pub_type: 杂志文章
doi:10.1007/BF02013272
更新日期:1977-12-01 00:00:00
abstract::A temporal temperature gradient gel electrophoresis (TTGE) method was developed to determine the diversity of methanogen populations in the rumen. Tests with amplicons from genomic DNA from 12 cultured methanogens showed single bands for all strains, with only two showing apparently comigrating bands. Fingerprints of ...
journal_title:Microbial ecology
pub_type: 杂志文章
doi:10.1007/s00248-006-9182-1
更新日期:2007-07-01 00:00:00
abstract::To elucidate the degree of microdiversity within the genus Prochlorococcus, novel Prochlorococcus-specific polymerase chain reaction (PCR) primers were developed for the rpoC1 gene, which encodes the ribonucleic acid (RNA) polymerase core subunit. The size of the PCR fragment (925 bp) coupled with high sequence variat...
journal_title:Microbial ecology
pub_type: 杂志文章
doi:10.1007/s00248-007-9259-5
更新日期:2008-01-01 00:00:00
abstract::The bacterial flora in the intestinal tract of goldfish (Carassius auratus) was investigated at different stages of fish development. The floras of the diets and the water and sediment of a culture pond were also analyzed. The total counts in the intestine ranged from 2.2 × 10(6)-2.1 × 10(8) cells g(-1) wet weight.Aer...
journal_title:Microbial ecology
pub_type: 杂志文章
doi:10.1007/BF02012646
更新日期:1988-05-01 00:00:00
abstract::Metagenomics and the development of high throughput next generation sequencing capabilities have forced significant development in the field of phylogenetics: the study of the evolutionary relatedness of the planet's inhabitants. Herein, I review the major tree-building strategies, challenges and opportunities which e...
journal_title:Microbial ecology
pub_type: 杂志文章,评审
doi:10.1007/s00248-013-0236-x
更新日期:2013-07-01 00:00:00
abstract::Plant community characteristics impact rhizosphere Streptomyces nutrient competition and antagonistic capacities. However, the effects of Streptomyces on, and their responses to, coexisting microorganisms as a function of plant host or plant species richness have received little attention. In this work, we characteriz...
journal_title:Microbial ecology
pub_type: 杂志文章
doi:10.1007/s00248-016-0907-5
更新日期:2017-07-01 00:00:00
abstract::The marine chrysophyteMonochrysis lutheri was grown in phosphorus-limited continuous cultures at temperatures of 15°, 18.8° and 23°C. The effect of temperature on the maximum growth rate was well-defined by the Arrhenius equation, but the Q10 for this alga (1.7) was somewhat lower than has been determined previously f...
journal_title:Microbial ecology
pub_type: 杂志文章
doi:10.1007/BF02013523
更新日期:1979-09-01 00:00:00
abstract::The abundance, distribution, and phylogenetic diversity of members of the Fe(III)-reducing family Geobacteraceae were studied along a gradient of metal contaminants in Lake Coeur d'Alene, Idaho. Partial 16S rRNA gene fragments were amplified by PCR using primers directed toward conserved regions of the gene within the...
journal_title:Microbial ecology
pub_type: 杂志文章
doi:10.1007/s00248-005-8002-3
更新日期:2003-08-01 00:00:00
abstract::Several Mesorhizobium species are able to induce effective nodules in chickpea, one of the most important legumes worldwide. Our aims were to examine the biogeography of chickpea rhizobia, to search for a predominant species, and to identify the most efficient microsymbiont, considering Portugal as a case study. One h...
journal_title:Microbial ecology
pub_type: 杂志文章
doi:10.1007/s00248-009-9536-6
更新日期:2009-11-01 00:00:00
abstract::Interactions between mushrooms, yeasts, and parasitic fungi are probably common in nature, but are rarely described. Bolete fruiting bodies are associated with a broad spectrum of microorganisms including yeasts, and they are commonly infected with filamentous mycoparasites of the genus Sepedonium (teleomorph Hypomyce...
journal_title:Microbial ecology
pub_type: 杂志文章
doi:10.1007/s00248-011-9923-7
更新日期:2012-02-01 00:00:00
abstract::Sediment input to the Illinois River has drastically decreased river depth and reduced habitats for aquatic organisms. Dredging is being used to remove sediment from the Illinois River, and the dredged sediment is being applied to the surface of a brownfield site in Chicago with the goal of revegetating the site. In o...
journal_title:Microbial ecology
pub_type: 杂志文章
doi:10.1007/s00248-008-9410-y
更新日期:2009-01-01 00:00:00
abstract::It is suspected that phagotrophic marine protozoa might possess feeding receptors that enable them to discern the nutritional quality of individual prey items (during prey-handling) on the basis of their cell-surface biochemistry. This article reviews advances in our understanding of the molecular mechanisms that medi...
journal_title:Microbial ecology
pub_type: 杂志文章,评审
doi:10.1007/s00248-008-9421-8
更新日期:2009-05-01 00:00:00
abstract::Biological soil crust is composed of lichens, cyanobacteria, green algae, mosses, and fungi. Although crusts are a dominant source of nitrogen (N) in arid ecosystems, this study is among the first to demonstrate their contribution to N availability in xeric temperate habitats. The study site is located in Lucas County...
journal_title:Microbial ecology
pub_type: 杂志文章
doi:10.1007/s00248-005-0121-3
更新日期:2006-02-01 00:00:00
abstract::Staphylococcus aureus, an opportunistic pathogen member of the nasal and skin microbiota, can also be found in human oral samples and has been linked to infectious diseases of the oral cavity. As the nasal and oral cavities are anatomically connected, it is currently unclear whether S. aureus can colonize the oral cav...
journal_title:Microbial ecology
pub_type: 杂志文章
doi:10.1007/s00248-018-1291-0
更新日期:2019-08-01 00:00:00
abstract::Ribosomal RNA (rRNA) is one of the most important macromolecules in the cell. It is well established that high-temperature environmental conditions destabilize rRNA, leading to a selection for G+C-rich stabilizing structures. Our knowledge about the nucleotide composition effect of other environmental conditions, howe...
journal_title:Microbial ecology
pub_type: 杂志文章
doi:10.1007/s00248-008-9446-z
更新日期:2009-04-01 00:00:00
abstract::We have generated new sensors for the specific detection and studies of bioavailability of metals by engineering Pseudomonas fluorescens with reporter gene systems. One broad host range mercury (pTPT11) and two arsenite (pTPT21 and pTPT31) sensor plasmids that express metal presence by luminescence phenotype were cons...
journal_title:Microbial ecology
pub_type: 杂志文章
doi:10.1007/s002480000095
更新日期:2001-02-01 00:00:00
abstract::Peatland testate amoebae (TA) are well-established bioindicators for depth to water table (DWT), but effects of hydrological changes on TA communities have never been tested experimentally. We tested this in a field experiment by placing Sphagnum carpets (15 cm diameter) collected in hummock, lawn and pool microsites ...
journal_title:Microbial ecology
pub_type: 杂志文章
doi:10.1007/s00248-014-0367-8
更新日期:2014-05-01 00:00:00
abstract::We studied the relationship between testate amoebae (Protozoa) communities and the depth to the water table (DWT), pH, conductivity, and microhabitat type in Sphagnum dominated peatlands of north-western Poland and built predictive (transfer function) models for inferring DWT and pH based on the testate amoebae commun...
journal_title:Microbial ecology
pub_type: 杂志文章
doi:10.1007/s00248-004-0105-8
更新日期:2005-07-01 00:00:00
abstract::Nasal swabs of 100 healthy dogs were obtained in 2011 in Tunisia and tested for Staphylococcus pseudintermedius recovery. Antimicrobial resistance profile and virulence gene content were determined. Multilocus-sequence-typing (MLST) and SmaI-pulsed-field gel electrophoresis (PFGE) were investigated. S. pseudintermediu...
journal_title:Microbial ecology
pub_type: 杂志文章
doi:10.1007/s00248-013-0243-y
更新日期:2013-08-01 00:00:00
abstract::Eucalyptus plantations offer a cost-effective and renewable source of raw material. There is substantial interest in improving forestry production, especially through sustainable strategies such as the use of plant growth-promoting bacteria. However, little is known about Eucalyptus microbiology. In this study, the en...
journal_title:Microbial ecology
pub_type: 杂志文章
doi:10.1007/s00248-017-1014-y
更新日期:2018-01-01 00:00:00
abstract::Muscodor spp. are proficient producers of bioactive volatile organic compounds (VOCs) with many potential applications. However, all members of this genus produce varying amounts and types of VOCs which suggests the involvement of epigenetics as a possible explanation. The members of this genus are poorly explored for...
journal_title:Microbial ecology
pub_type: 杂志文章
doi:10.1007/s00248-016-0901-y
更新日期:2017-05-01 00:00:00
abstract::Sediment samples were collected monthly from Acton Lake, a eutrophic reservoir located in an agricultural region of southwestern Ohio, from three stations (River, Middle, and Dam) during the period May 1995 through January 1997. Sedimentary microbial biomass and community structures from these stations were studied us...
journal_title:Microbial ecology
pub_type: 杂志文章
doi:10.1007/s002480000102
更新日期:2001-10-01 00:00:00
abstract::The yeast-like fungus Coniochaeta pulveracea was studied with regard to its novel lignocellulolytic activities and the possible effect thereof on yeasts from the woody phylloplane. An enrichment procedure was used to isolate C. pulveracea from a decaying Acacia tree, and the identity of the isolate was confirmed using...
journal_title:Microbial ecology
pub_type: 杂志文章
doi:10.1007/s00248-011-9869-9
更新日期:2011-10-01 00:00:00
abstract::The main current methods for controlling American Foulbrood (AFB) in honeybees, caused by the bacterial pathogen Paenibacillus larvae, are enforced incineration or prophylactic antibiotic treatment, neither of which is fully satisfactory. This has led to an increased interest in the natural relationships between the p...
journal_title:Microbial ecology
pub_type: 杂志文章
doi:10.1007/s00248-019-01434-3
更新日期:2020-04-01 00:00:00
abstract::Analysis of continuous culture methodology suggests that this potentially powerful tool for kinetic analysis can be improved by minimizing several inherent shortcomings. Medium background substrates - organic carbon, phosphate, and manganese - were shown to dominate kinetic observations at concentrations below chemica...
journal_title:Microbial ecology
pub_type: 杂志文章
doi:10.1007/BF02011647
更新日期:1975-12-01 00:00:00
abstract::The occurrence of hypolithic cyanobacteria colonizing translucent stones was quantified along the aridity gradient in the Atacama Desert in Chile, from less arid areas to the hyperarid core where photosynthetic life and thus primary production reach their limits. As mean rainfall declines from 21 to journal_title:Microbial ecology pub_type: 杂志文章 doi:10.1007/s00248-006-9055-7 更新日期:2006-10-01 00:00:00