sp. nov. isolated from a fermentation system processing bovine manure.

Strain MS2379 was isolated from a pasteurized solution sample from a predominantly anaerobic fermentation system processing bovine manure in Pilot Point, Texas. Phylogenetic analyses based on both 16S rRNA gene and gene sequences showed that MS2379 was most closely related to (DSM 36) (DSM 13815) (DSM 8320) yet DNA-DNA relatedness through DNA-DNA hybridization revealed only 22.6, 32.

Identification of metolachlor mineralizing bacteria in aerobic and anaerobic soils using DNA-stable isotope probing.

The influence of soil environmental factors such as aeration on the ecology of microorganisms involved in the mineralization and degradation of the popular soil-applied pre-emergent herbicide, metolachlor is unknown. To address this knowledge gap, we utilized DNA-based stable isotope probing (SIP) where soil microcosms were incubated aerobically or anaerobically and received herbicide treatments with unlabeled metolachlor or C-metolachlor. Mineralization of metolachlor was confirmed as noted from the evolution of CO from C-metolachlor-treated microcosms and clearly demonstrated the efficient utilization of the herbicide as a carbon source.

Detection and Diversity of Fungal Nitric Oxide Reductase Genes (p450nor) in Agricultural Soils.

Unlabelled: Members of the Fungi convert nitrate (NO3 (-)) and nitrite (NO2 (-)) to gaseous nitrous oxide (N2O) (denitrification), but the fungal contributions to N loss from soil remain uncertain. Cultivation-based methodologies that include antibiotics to selectively assess fungal activities have limitations, and complementary molecular approaches to assign denitrification potential to fungi are desirable. Microcosms established with soils from two representative U.

Microbial functional diversity enhances predictive models linking environmental parameters to ecosystem properties.

Microorganisms drive biogeochemical processes, but linking these processes to real changes in microbial communities under field conditions is not trivial. Here, we present a model-based approach to estimate independent contributions of microbial community shifts to ecosystem properties. The approach was tested empirically, using denitrification potential as our model process, in a spatial survey of arable land encompassing a range of edaphic conditions and two agricultural production systems.

Effect of soil aeration and phosphate addition on the microbial bioavailability of carbon-14-glyphosate.

The adsorption, desorption, degradation, and mineralization of C-glyphosate [-(phosphonomethyl)glycine] were examined in Catlin (a fine-silty, mixed, superactive, mesic Oxyaquic Argiudoll), Flanagan (a fine, smectitic, mesic Aquic Argiudoll), and Drummer (a fine-silty, mixed, superactive, mesic Typic Endoaquoll) soils under oxic and anoxic soil conditions. With the exception of the Drummer soil, soil aeration did not significantly alter the adsorption pattern of C-glyphosate to soils. Herbicide desorption was generally enhanced with anaerobiosis in all the soil types.

Refined NrfA phylogeny improves PCR-based nrfA gene detection.

Dissimilatory nitrate reduction to ammonium (DNRA) and denitrification are contrasting microbial processes in the terrestrial nitrogen (N) cycle, in that the former promotes N retention and the latter leads to N loss (i.e., the formation of gaseous products).

Soil functional operating range linked to microbial biodiversity and community composition using denitrifiers as model guild.

Soil microorganisms are key players in biogeochemical cycles. Yet, there is no consistent view on the significance of microbial biodiversity for soil ecosystem functioning. According to the insurance hypothesis, declines in ecosystem functioning due to reduced biodiversity are more likely to occur under fluctuating, extreme or rapidly changing environmental conditions.

Candidatus "Thiodictyon syntrophicum", sp. nov., a new purple sulfur bacterium isolated from the chemocline of Lake Cadagno forming aggregates and specific associations with Desulfocapsa sp.

Strain Cad16(T) is a small-celled purple sulfur bacterium (PSB) isolated from the chemocline of crenogenic meromictic Lake Cadagno, Switzerland. Long term in situ observations showed that Cad16(T) regularly grows in very compact clumps of cells in association with bacteria belonging to the genus Desulfocapsa in a cell-to-cell three dimensional structure. Previously assigned to the genus Lamprocystis, Cad16(T), was here reclassified and assigned to the genus Thiodictyon.

Phenotypic and genotypic heterogeneity among closely related soil-borne N2 - and N2 O-producing Bacillus isolates harboring the nosZ gene.

Little is known about the genetic and phenotypic diversity of Gram-positive denitrifying bacteria. We compared the production of gaseous denitrification products for 14 closely related Bacillus soil isolates at pH 6 and 7 during 48-h batch incubations using a robotic gas-sampling apparatus. Primers targeting the nosZ gene encoding the nitrous oxide reductase were designed to confirm the presence of this gene in the isolates.

Spatial distribution of ammonia-oxidizing bacteria and archaea across a 44-hectare farm related to ecosystem functioning.

Characterization of spatial patterns of functional microbial communities could facilitate the understanding of the relationships between the ecology of microbial communities, the biogeochemical processes they perform and the corresponding ecosystem functions. Because of the important role the ammonia-oxidizing bacteria (AOB) and archaea (AOA) have in nitrogen cycling and nitrate leaching, we explored the spatial distribution of their activity, abundance and community composition across a 44-ha large farm divided into an organic and an integrated farming system. The spatial patterns were mapped by geostatistical modeling and correlations to soil properties and ecosystem functioning in terms of nitrate leaching were determined.

Thiocystis chemoclinalis sp. nov. and Thiocystis cadagnonensis sp. nov., motile purple sulfur bacteria isolated from the chemocline of a meromictic lake.

Two isolates, designated CadH11(T) and Cad448(T), representing uncultured purple sulfur bacterial populations H and 448, respectively, in the chemocline of Lake Cadagno, a crenogenic meromictic lake in Switzerland, were obtained using enrichment and isolation conditions that resembled those used for cultured members of the genus Thiocystis. Phenotypic, genotypic and phylogenetic analyses of these isolates confirmed their assignment to the genus Thiocystis. However, 16S rRNA gene sequence similarities of 98.

Bacterial community diversity in paper mills processing recycled paper.

Paper mills processing recycled paper suffer from biofouling causing problems both in the mill and final product. The total bacterial community composition and identification of specific taxa in the process water and biofilms at the stock preparation and paper machine areas in a mill with recycled paper pulp was described by using a DNA-based approach. Process water in a similar mill was also analyzed to investigate if general trends can be found between mills and over time.

Diversity of Frankia populations in root nodules of geographically isolated Arizona alder trees in central Arizona (United States).

The diversity of uncultured Frankia populations in root nodules of Alnus oblongifolia trees geographically isolated on mountaintops of central Arizona was analyzed by comparative sequence analyses of nifH gene fragments. Sequences were retrieved from Frankia populations in nodules of four trees from each of three mountaintops (n = 162) and their levels of diversity compared using spatial genetic clustering methods and single-nucleotide or 1, 3, or 5% sequence divergence thresholds. With the single-nucleotide threshold level, 45 different sequences with significant differences between the mountaintops were retrieved, with the southern site partitioning in a separate population from the two other sites.

Diversity of frankiae in soils from five continents.

Clone libraries of nifH gene fragments specific for the nitrogen-fixing actinomycete Frankia were generated from six soils obtained from five continents using a nested PCR. Comparative sequence analyses of all libraries (n=247 clones) using 96 to 97% similarity thresholds revealed the presence of three and four clusters of frankiae representing the Elaeagnus and the Alnus host infection groups, respectively. Diversity of frankiae was represented by fewer clusters (i.

Growth of Frankia strains in leaf litter-amended soil and the rhizosphere of a nonactinorhizal plant.

The ability of Frankia strains to grow in the rhizosphere of a nonactinorhizal plant, Betula pendula, in surrounding bulk soil and in soil amended with leaf litter was analyzed 6 weeks after inoculation of pure cultures by in situ hybridization. Growth responses were related to taxonomic position as determined by comparative sequence analysis of nifH gene fragments and of an actinomycetes-specific insertion in Domain III of the 23S rRNA gene. Phylogenetic analyses confirmed the basic classification of Frankia strains by host infection groups, and allowed a further differentiation of Frankia clusters within the Alnus host infection group.

Variation in Frankia populations of the Elaeagnus host infection group in nodules of six host plant species after inoculation with soil.

The potential role of host plant species in the selection of symbiotic, nitrogen-fixing Frankia strains belonging to the Elaeagnus host infection group was assessed in bioassays with two Morella, three Elaeagnus, and one Shepherdia species as capture plants, inoculated with soil slurries made with soil collected from a mixed pine/grassland area in central Wisconsin, USA. Comparative sequence analysis of nifH gene fragments amplified from homogenates of at least 20 individual lobes of root nodules harvested from capture plants of each species confirmed the more promiscuous character of Morella cerifera and Morella pensylvanica that formed nodules with frankiae of the Alnus and the Elaeagnus host infection groups, while frankiae in nodules formed on Elaeagnus umbellata, Elaeagnus angustifolia, Elaeagnus commutata, and Shepherdia argentea generally belonged to the Elaeagnus host infection group. Diversity of frankiae of the Elaeagnus host infection groups was larger in nodules on both Morella species than in nodules formed on the other plant species.

Diversity of frankiae in root nodules of Morella pensylvanica grown in soils from five continents.

Bioassays with Morella pensylvanica as capture plant and comparative sequence analyses of nifH gene fragments of Frankia populations in nodules formed were used to investigate the diversity of Frankia in soils over a broad geographic range, i.e., from sites in five continents (Africa, Europe, Asia, North America, and South America).

Characterization of bacteria in mixed biofilm communities using denaturing gradient gel electrophoresis (DGGE).

Most microorganisms in nature, including those within biofilms, live in mixed populations. PCR-based molecular genetic techniques are very useful in studying microbial diversity since unculturable as well as culturable organisms can be investigated. One such technique is denaturing gradient gel electrophoresis (DGGE), which separates PCR-amplified community 16S rRNA (and other gene) sequences on the basis of G+C content.

Analysis of nitrogen-fixing members of the epsilon subclass of Proteobacteria in salt marsh sediments.

Based on phylogenetic analysis of clones retrieved from two nifH gene clone libraries that were created using cDNA from suboxic sediment samples obtained from areas densely vegetated with the high-salt marsh plant Spartina patens, a primer set was designed to target nitrogen-fixing bacteria with sequence similarities to members of the epsilon subclass of Proteobacteria. Nested PCR, denaturing gel electrophoresis, and subsequent sequence analysis of reamplified fragments confirmed the specificity of the primer set by retrieving nifH sequences of only putative members of the epsilon subclass of Proteobacteria, all of which were characterized by a highly divergent 27- or 36-bp insertion in both DNA and cDNA.

Saprophytic growth of inoculated Frankia sp. in soil microcosms.

The potential of two Frankia strains to grow saprophytically was studied in nonsterile soil microcosms with ground leaf litter of Alnus glutinosa as the sole carbon and nitrogen sources. Strains Ag45/Mut15 and ArI3, which represent two taxonomic subgroups within the Alnus host infection group were inoculated alone, or together to investigate potential competition. Their growth was analyzed by in situ and dot-blot hybridization.

Rheinheimera texasensis sp. nov., a halointolerant freshwater oligotroph.

A Gram-negative, rod-shaped, motile, non-spore-forming bacterium, designated strain A62-14B(T), was isolated from a constant-temperature, spring-fed, freshwater lake. On the basis of the complete 16S rRNA gene sequence, strain A62-14B(T) was shown to belong to the class Gammaproteobacteria, being most closely related to Rheinheimera sp. HTB082 (96.

Microbial survival in space shuttle crash.

A slow growing, heat resistant bacterium, identified by 16S rRNA gene sequencing as Microbispora sp., was recovered from the wreckage of the ill-fated space shuttle Columbia (STS-107). As this organism survived disintegration of the space craft, heat of reentry, and impact, it supports the possibility of a natural mechanism for the interplanetary spread of life by meteorites.