Microbial community in a geothermal aquifer associated with the subsurface of the Great Artesian Basin, Australia

To investigate the biomass and phylogenetic diversity of the microbial community inhabiting the deep aquifer of the Great Artesian Basin (GAB), geothermal groundwater gushing out from the aquifer was sampled and analyzed. Microbial cells in the groundwater were stained with acridine orange and directly counted by epifluorescence microscopy. Microbial cells were present at a density of 10⁸–10⁹ cells per liter of groundwater. Archaeal and bacterial small-subunit rRNA genes (rDNAs) were amplified by PCR with Archaea- and Bacteria-specific primer sets, and clone libraries were constructed separately. A total of 59 clones were analyzed in archaeal and bacterial 16S rDNA libraries, respectively. The archaeal 16S rDNA clones were divided into nine operated taxonomic units (OTUs) by restriction fragment length polymorphism. These OTUs were closely related to the methanogenic genera Methanospirillum and Methanosaeta, the heterotrophic genus Thermoplasma, or miscellaneous crenarchaeota group. More than one-half of the archaeal clones (59% of total 59 clones) were placed beside phylogenetic clusters of methanogens. The majority of the methanogen-related clones (83%) was closely related to a group of hydrogenotrophic methanogens (genus Methanospirillum). The bacterial OTUs branched into seven phylogenetic clusters related to hydrogen-oxidizing thermophiles in the genera Hydrogenobacter and Hydrogenophilus, a sulfate-reducing thermophile in the genus Thermodesulfovibrio, chemoheterotropic bacteria in the genera Thermus and Aquaspirillum, or the candidate division OP10. Clones closely related to the thermophilic hydrogen-oxidizers in the genera Hydrogenobacter and Hydrogenophilus were dominant in the bacterial clone library (37% of a total of 59 clones). The dominancy of hydrogen-users strongly suggested that H₂ plays an important role as a primary substrate in the microbial ecosystem of this deep geothermal aquifer.     

Effect of biostimulants on 2,4,6-trinitrotoluene (TNT) degradation and bacterial community composition in contaminated aquifer sediment enrichments

2,4,6-Trinitrotoluene (TNT) is a toxic and persistent explosive compound occurring as a contaminant at numerous sites worldwide. Knowledge of the microbial dynamics driving TNT biodegradation is limited, particularly in native aquifer sediments where it poses a threat to water resources. The purpose of this study was to quantify the effect of organic amendments on anaerobic TNT biodegradation rate and pathway in an enrichment culture obtained from historically contaminated aquifer sediment and to compare the bacterial community dynamics. TNT readily biodegraded in all microcosms, with the highest biodegradation rate obtained under the lactate amended condition followed by ethanol amended and naturally occurring organic matter (extracted from site sediment) amended conditions. Although a reductive pathway of TNT degradation was observed across all conditions, denaturing gradient gel electrophoresis (DGGE) analysis revealed distinct bacterial community compositions. In all microcosms, Gram-negative γ- or β-Proteobacteria and Gram-positive Negativicutes or Clostridia were observed. A Pseudomonas sp. in particular was observed to be stimulated under all conditions. According to non-metric multidimensional scaling analysis of DGGE profiles, the microcosm communities were most similar to heavily TNT-contaminated field site sediment, relative to moderately and uncontaminated sediments, suggesting that TNT contamination itself is a major driver of microbial community structure. Overall these results provide a new line of evidence of the key bacteria driving TNT degradation in aquifer sediments and their dynamics in response to organic carbon amendment, supporting this approach as a promising technology for stimulating in situ TNT bioremediation in the subsurface.     

Stability of interstitial crustacean communities in an isolated alluvial aquifer

The temporal stability of interstitial crustacean communities was investigated in relation to environmental variability in a perched aquifer, characterized by limited connection with surface waters. The author hypothesized that strong physico-chemical stability would enhance persistence and affect dominance patterns for groundwater fauna. Fifteen wells were sampled four times over a two-year period in order to assess the global stability of ground waters and to evaluate temporal changes in species assemblages. For each station, environmental patterns displayed only minor changes, while between-site differences were much larger. At the scale of the aquifer, strong temporal stability was found for groundwater physical and chemical variables. Interstitial crustaceans displayed diverse assemblages dominated by cyclopoid taxa. High persistence characterized community composition and structure (species relative abundance patterns, species richness, Shannon's diversity index) over the study period. Most well faunas were dominated numerically by a single species, whether micro- or macrocrustacean assemblages were considered. Faunal persistence observed in the aquifer was greater than that reported in many surface waters and was probably related to the strong environmental stability.     

Spatial variability in the abundance and composition of the free-living bacterioplankton community in the pelagic zone of Lake Bourget (France)

Spatial variations in the abundance and diversity of the free-living bacterioplankton community of a large Alpine lake, Lake Bourget (France), were investigated in the pelagic zone by means of two two-dimensional samplings taken in 2003. Lake-water samples were collected in winter during water mixing, and in early summer during stratification. The population abundance in each sample was determined by flow cytometry. Denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA gene fragments from organisms measuring less than 2 mum was used to assess eubacterioplankton community composition. In winter, no obvious differences were observed in either the abundance or the diversity of the bacterial community, on either the horizontal or the vertical scales. The only influence detected was that of river water input, but this was at a very minor scale relative to the surface area of the lake. In early summer, changes were found in the community composition on the vertical scale related to the thermal stratification of the water column. There were also marked differences on the horizontal scale at 15 m depth due to internal waves. The implications of these findings for sampling strategies are very important from the perspective of comparative studies of free-living bacterial community diversity and functioning in large and deep lakes.     

Successful phytoremediation of crude-oil contaminated soil at an oil exploration and production company by plants-bacterial synergism

Phytoremediation is a promising approach for the cleanup of soil contaminated with petroleum hydrocarbons. This study aimed to develop plant-bacterial synergism for the successful remediation of crude oil-contaminated soil. A consortia of three endophytic bacteria was augmented to two grasses, Leptochloa fusca and Brachiaria mutica, grown in oil-contaminated soil (46.8 g oil kg^?1 soil) in the vicinity of an oil exploration and production company. Endophytes augmentation improved plant growth, crude oil degradation, and soil health. Maximum oil degradation (80%) was achieved with B. mutica plants augmented with the endophytes and it was significantly (P < 0.05) higher than the use of plants or bacteria individually. Moreover, endophytes showed more persistence, the abundance and expression of alkB gene in the rhizosphere as well as in the endosphere of the tested plants than in unvegetated soil. A positive relationship (r = 0.70) observed between gene expression and crude oil reduction indicates that catabolic gene expression is important for hydrocarbon mineralization. This investigation showed that the use of endophytes with appropriate plant is an effective strategy for the cleanup of oil-contaminated soil under field conditions.     

Effect of gap size and age on climber abundance and diversity in Budongo Forest Reserve, Uganda

A study of the effects of gap size and age on climber abundance and diversity was carried out in Budongo Forest Reserve in Uganda. Data were collected from compartments N5, W21, B1 and B3. Stump records were used to locate and estimate the ages of 78 gaps. Sample plots 5 × 5 m were set up in the gaps to assess climber abundance and diversity.
Climbers were more abundant and diverse in gaps that were more than 400 m², 15 months old and had more than 25% canopy opening. Momordica foetida was the most abundant climber species occurring on stems, branches and crowns of seedlings and saplings. Therefore, in order to keep natural regeneration free from climber tangles and produce good quality timber, climber control should be a major activity in tropical high forest management.     

Effect of methionine and its related compounds on rumen bacterial activity

The effect of several methionine sources (L‐methionine = L‐MET; DL‐ methionine = DL‐MET, DL‐S‐methyl‐methionine‐sulphonium‐chloride = SMM; N‐hydroxymethyl‐DL‐methionine‐Ca = NHM; methionine‐hydroxy‐analog free acid=MHA; methionine‐sulphoxyde=MSO) on rumen bacterial growth was studied using a new methodical approach which utilises a methionine free assay medium (Bacto Methionine Assay Media, Difco) supplemented by increasing quantities of the methionine sources and inoculated with one drop of diluted rumen bacteria. The optical density was measured after 18 h incubation on 39 °C.

L‐ and DL‐MET promoted the highest growth response, while SMM and NHM exerted significantly (p < 0.05) lower optical densities. MHA and MSO showed no growth response.

The methodical approach and the possible bacterial strains, which might have contributed to the growth response have been discussed.     

Effect of bacterial lypopolysaccharide on penicillin-induced seizure activity in rats

In experiments on Wistar rats, we found that, within an early period (2 to 4 h) after injection of bacterial lypopolysaccharide, LPS (0.1 mg/kg, i.p.), the latency of generalized seizures induced by injection of benzylpenicillin (sodium salt; 3.0 million IU/kg, i.p.) became significantly shorter, while the severity of seizure manifestations was higher than in the control group. Within this period, the power of oscillations of the delta and alpha-frequency ranges increased in the frontal cortex and hippocampal structures; fast ECoG components (beta and gamma rhythms) were suppressed, and the power of the theta activity decreased. In the hippocampal structures, these changes were more clearly pronounced, as compared with the neocortex. Within a later period of the action of LPS (12 to 18 h from the moment of injection), the latency of penicillin-induced seizures significantly exceeded the control value, and the severity of such seizures was lower. Under such conditions, we observed a smaller power of the synchronized activity of delta and alpha frequencies combined with intensification of the theta activity (most clearly pronounced in the hippocampal structures), and also an increase in the power of “desynchronized” rhythms (beta and gamma oscillations) in the cortex and hippocampus. Neirofiziologiya/Neurophysiology, Vol. 40, No. 3, pp. 236–241, May–June, 2008.     

Diversity of 16S rRNA and dioxygenase genes detected in coal‐tar‐contaminated site undergoing active bioremediation

Aims: In order to develop effective bioremediation strategies for polyaromatic hydrocarbons (PAHs) degradation, the composition and metabolic potential of microbial communities need to be better understood, especially in highly PAH contaminated sites in which little information on the cultivation‐independent communities is available. Methods and Results: Coal‐tar‐contaminated soil was collected, which consisted of 122·5 mg g^?1 total extractable PAH compounds. Biodegradation studies with this soil indicated the presence of microbial community that is capable of degrading the model PAH compounds viz naphthalene, phenanthrene and pyrene at 50 ppm each. PCR clone libraries were established from the DNA of the coal‐tar‐contaminated soil, targeting the 16S rRNA to characterize (i) the microbial communities, (ii) partial gene fragment encoding the Rieske iron sulfur center (α‐subunit) common to all PAH dioxygenase enzymes and (iii) β‐subunit of dioxygenase. Phylotypes related to Proteobacteria (Alpha‐, Epsilon‐ and Gammaproteobacteria), Acidobacteria, Actinobacteria, Firmicutes, Gemmatimonadetes and Deinococci were detected in 16S rRNA derived clone libraries. Many of the gene fragment sequences of α‐subunit and β‐subunit of dioxygenase obtained from the respective clone libraries fell into clades that are distinct from the reference dioxygenase gene sequences. Presence of consensus sequence of the Rieske type [2Fe‐2S] cluster binding site suggested that these gene fragments encode for α‐subunit of dioxygenase gene. Conclusions: Sequencing of the cloned libraries representing α‐subunit gene fragments (Rf1) and β‐subunit of dioxygenase showed the presence of hitherto unidentified dioxygenase in coal‐tar‐contaminated soil. Significance and Impact of the Study: The combination of the Rieske primers and bacterial community profiling represents a powerful tool for both assessing bioremediation potential and the exploration of novel dioxygenase genes in a contaminated environment.     

The influence of plant cover on surfperch abundance at an offshore temperate reef

Synopsis At an offshore reef near Santa Barbara, southern California, young-of-year (young) of five surfperch species (Embiotocidae: Embiotoca jacksoni, E. lateralis, Hypsurus caryi, Rhacochilus toxotes, Damalichthys vacca) once thrived in a dense kelp understory of Pterygophora californica and Laminaria farlowii, but disappeared after a severe storm in February, 1980 deforested their habitat. Measurements of fish density and kelp cover made before deforestation indicated that the young surfperch appeared in the spring and disappeared in the fall as cover increased and declined. Adult surfperch and large kelp bass (Paralabrax clathratus), which can eat young but not adult surfperch, remained all year. We tested to see if kelp cover was an essential refuge for the young by pruning back (thinning) kelp blades from one of two transects. The thinning caused a significant redistribution of young which clearly avoided open spaces, but not of adults which are less vulnerable to predation. Measurements of fish density made after the storm-induced deforestation showed that adult surfperch and kelp bass still remained abundant even after the young surfperch were gone. Only after an abrupt reforestation in 1983, more than a year after the present study was terminated, were young once again seen on the reef. Although young surfperch may seek tiny prey living on kelp blades, most lines of evidence indicated that the distribution of the young is more a response to risk of predation. Hence the extent of kelp understory was probably the main determinant of the survival of young surfperch on the reef.     

Effect of drying and rewetting on bacterial growth rates in soil

The effect of soil moisture on bacterial growth was investigated, and the effects of rewetting were compared with glucose addition because both treatments increase substrate availability. Bacterial growth was estimated as thymidine and leucine incorporation, and was compared with respiration. Low growth rates were found in air-dried soil, increasing rapidly to high stable values in moist soils. Respiration and bacterial growth at different soil moisture contents were correlated. Rewetting air-dried soil resulted in a linear increase in bacterial growth with time, reaching the levels in moist soil (10 times higher) after about 7 h. Respiration rates increased within 1 h to a level >10 times higher than that in moist soil. After the initial flush, there was a gradual decrease in respiration rate, while bacterial growth increased to levels twice that of moist soil 24 h after rewetting, and decreased to levels similar to those in moist soil after 2 days. Adding glucose resulted in no positive effect on bacterial growth during the first 9 h, despite resulting in more than five times higher respiration. This indicated that the initial increase in bacterial growth after rewetting was not due to increased substrate availability.     

Leaf microbiota in an agroecosystem: spatiotemporal variation in bacterial community composition on field-grown lettuce

The presence, size and importance of bacterial communities on plant leaf surfaces are widely appreciated. However, information is scarce regarding their composition and how it changes along geographical and seasonal scales. We collected 106 samples of field-grown Romaine lettuce from commercial production regions in California and Arizona during the 2009–2010 crop cycle. Total bacterial populations averaged between 10⁵ and 10⁶ per gram of tissue, whereas counts of culturable bacteria were on average one (summer season) or two (winter season) orders of magnitude lower. Pyrosequencing of 16S rRNA gene amplicons from 88 samples revealed that Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria were the most abundantly represented phyla. At the genus level, Pseudomonas, Bacillus, Massilia, Arthrobacter and Pantoea were the most consistently found across samples, suggesting that they form the bacterial ‘core'' phyllosphere microbiota on lettuce. The foliar presence of Xanthomonas campestris pv. vitians, which is the causal agent of bacterial leaf spot of lettuce, correlated positively with the relative representation of bacteria from the genus Alkanindiges, but negatively with Bacillus, Erwinia and Pantoea. Summer samples showed an overrepresentation of Enterobacteriaceae sequences and culturable coliforms compared with winter samples. The distance between fields or the timing of a dust storm, but not Romaine cultivar, explained differences in bacterial community composition between several of the fields sampled. As one of the largest surveys of leaf surface microbiology, this study offers new insights into the extent and underlying causes of variability in bacterial community composition on plant leaves as a function of time, space and environment.     

Effect of antibiotics on the bacterial population of the rabbit caecum

The effect feeding antibiotics has on the bacterial population of the rabbit caecum was investigated. No changes in total volatile fatty acid production or total bacterial counts were observed compared with nonantibiotic treated controls. However, treatment with chlortetracycline resulted in an increase of propionate at the apparent cost of butyrate (P<0.05). Denaturing gradient gel electrophoresis analysis indicated that the two antibiotics that inhibit protein synthesis (chlortetracycline and tiamulin) exerted the most similar changes on the bacterial population structure, decreasing the diversity of the profiles. Sequence analysis of DNA from excised denaturing gradient gel electrophoresis bands was carried out. The majority of the sequences observed were most similar to bacterial sequences previously described in other gut environments, with 11% being most similar to those previously reported from the rabbit, and 95% of the sequences having 95% or greater identity to sequences already in GenBank.     

Dynamics of an oligotrophic bacterial aquifer community during contact with a groundwater plume contaminated with benzene, toluene, ethylbenzene, and xylenes: an in situ mesocosm study

An in situ mesocosm system was designed to monitor the in situ dynamics of the microbial community in polluted aquifers. The mesocosm system consists of a permeable membrane pocket filled with aquifer material and placed within a polypropylene holder, which is inserted below groundwater level in a monitoring well. After a specific time period, the microcosm is recovered from the well and its bacterial community is analyzed. Using this system, we examined the effect of benzene, toluene, ethylbenzene, and xylene (BTEX) contamination on the response of an aquifer bacterial community by denaturing gradient gel electrophoresis analysis of PCR-amplified 16S rRNA genes and PCR detection of BTEX degradation genes. Mesocosms were filled with nonsterile or sterile aquifer material derived from an uncontaminated area and positioned in a well located in either the uncontaminated area or a nearby contaminated area. In the contaminated area, the bacterial community in the microcosms rapidly evolved into a stable community identical to that in the adjacent aquifer but different from that in the uncontaminated area. At the contaminated location, bacteria with tmoA- and xylM/xylE1-like BTEX catabolic genotypes colonized the aquifer, while at the uncontaminated location only tmoA-like genotypes were detected. The communities in the mesocosms and in the aquifer adjacent to the wells in the contaminated area consisted mainly of Proteobacteria. At the uncontaminated location, Actinobacteria and Proteobacteria were found. Our results indicate that communities with long-term stability in their structures follow the contamination plume and rapidly colonize downstream areas upon contamination.