Similar Bacterial Communities Research Articles

Bacterial diversity of terra preta and pristine forest soil from the Western Amazon

The survey presented here describes the bacterial diversity and community structures of a pristine forest soil and an anthropogenic terra preta from the Western Amazon forest using molecular methods to identify the predominant phylogenetic groups. Bacterial community similarities and species diversity in the two soils were compared using oligonucleotide fingerprint grouping of 16S rRNA gene sequences for 1500 clones (OFRG) and by DNA sequencing. The results showed that both soils had similar bacterial community compositions over a range of phylogenetic distances, among which Acidobacteria were predominant, but that terra preta supported approximately 25% greater species richness. The survey provides the first detailed analysis of the composition and structure of bacterial communities from terra preta anthrosols using noncultured-based molecular methods.

Large-Scale Variation in Subsurface Stream Biofilms: A Cross-Regional Comparison of Metabolic Function and Community Similarity

We examined bacterial metabolic activity and community similarity in shallow subsurface stream sediments distributed across three regions of the eastern United States to assess whether there were parallel changes in functional and structural attributes at this large scale. Bacterial growth, oxygen consumption, and a suite of extracellular enzyme activities were assayed to describe functional variability. Community similarity was assessed using randomly amplified polymorphic DNA (RAPD) patterns. There were significant differences in streamwater chemistry, metabolic activity, and bacterial growth among regions with, for instance, twofold higher bacterial production in streams near Baltimore, MD, compared to Hubbard Brook, NH. Five of eight extracellular enzymes showed significant differences among regions. Cluster analyses of individual streams by metabolic variables showed clear groups with significant differences in representation of sites from different regions among groups. Clustering of sites based on randomly amplified polymorphic DNA banding resulted in groups with generally less internal similarity although there were still differences in distribution of regional sites. There was a marginally significant (p = 0.09) association between patterns based on functional and structural variables. There were statistically significant but weak (r2 approximately 30%) associations between landcover and measures of both structure and function. These patterns imply a large-scale organization of biofilm communities and this structure may be imposed by factor(s) such as landcover and covariates such as nutrient concentrations, which are known to also cause differences in macrobiota of stream ecosystems.

Impact of mariculture on microbial diversity in sediments near open ocean farming of Polydactylus sexfilis

Abstract A chemical and microbiological investigation was performed to determine ecological impact in sediments below a new offshore mariculture operation on the southwest coast of Oahu, Hawaii. Sediment samples collected directly below the fish enclosures were compared with sediment collected 300 m upcurrent. Total organic carbon was 25–37% higher in the control compared with cage samples and ammonia was 30–46% higher in cage samples. Sulfate reducing bacteria (SRB) counts were 36% higher in cage sample sediments. Genomic 16S rDNA was PCR amplified from total DNA extracted from sediments and analyzed by denaturing gradient gel electrophoresis (DGGE). Similar gradient profiles for control and cage samples were observed. Cloned 16S rDNA libraries for species sampling and determination indicate similar and diverse bacterial communities. Bacteria belonging to the γ- Proteobacteria class were frequently represented and atypical or pathogenic bacterial species were not detected. A mathematical model developed for prediction of organic material deposition suggests that while currents will reduce fecal loading and feed deposition beneath a cage, there is expected to be sufficient nutrient addition to impact those sediments. Time series or statistical information on the current field beneath the fish cages are needed to apply the model for predicting locations of high deposition. This would contribute to the development of a comprehensive monitoring program that would sample multiple locations over time to generate an accurate and comprehensive depiction of the environmental impacts of this new and expanding commercial endeavor.

Effect of Different Carbon Sources on Community Composition of Bacterial Enrichments from Soil

Soil is a highly heterogeneous matrix, which can contain thousands of different bacterial species per gram. Only a small component of this diversity (maybe <1%) is commonly captured using standard isolation techniques, although indications are that a larger proportion of the soil community is in fact culturable. Better isolation techniques yielding greater bacterial diversity would be of benefit for understanding the metabolic activity and capability of many soil microorganisms. We studied the response of soil bacterial communities to carbon source enrichment in small matrices by means of terminal restriction fragment length polymorphism (TRFLP) analysis. The community composition of replicate enrichments from soil displayed high variability, likely attributable to soil heterogeneity. An analysis of TRFLP data indicated that enrichment on structurally similar carbon sources selected for similar bacterial communities. The same analysis indicated that communities first enriched on glucose or benzoate and subsequently transferred into medium containing an alternate carbon source retained a distinct community signature induced by the carbon source used in the primary enrichment. Enrichment on leucine presented a selective challenge that was able to override the imprint left by primary enrichment on acetate. In a time series experiment community change was most rapid 18 hours after inoculation, corresponding to exponential growth. Community composition did not stabilize even 4 days after secondary enrichment. Four different soil types were enriched on four different carbon sources. TRFLP analysis indicated that in three out of four cases communities enriched on the same carbon source were more similar regardless of which soil type was used. Conversely, the garden soil samples yielded similar enrichment communities regardless of the enrichment carbon source. Our results indicate that in order to maximize the diversity of bacteria recovered from the environment, multiple enrichments should be performed using a chemically diverse set of carbon sources.

Environmental factors shape cloacal bacterial assemblages in great titParus majorand blue titP. caeruleusnestlings

Despite their potential ecological and evolutionary importance, factors shaping the composition of bacterial communities in wild vertebrate populations remain poorly understood. The goal of this study was to examine the relative contributions of environmental factors and genetic factors (e.g. species and common origin) to the variation of cloacal bacterial assemblages in wild bird nestlings. We conducted a partial cross‐fostering experiment with two passerine species, the great titParus majorand the blue titP. caeruleus,sharing similar habitats and breeding biology. Nestlings of the two species were exchanged four days after hatching and cloacal bacteria were sampled nine days later. The structure of cloacal bacterial communities was determined by Ribosomal Intergenic Spacer Analysis. Our results showed that each nestling displayed a unique bacterial community. Furthermore, nestlings raised in the same nest shared significantly similar bacterial communities. The similarity of bacterial community was higher among heterospecific siblings raised within the same nest than between biological siblings raised in separate nests. Effects of common origin between species could not be detected and, if present, were dominated by nest‐based short‐term environmental effects. Our results show that growth conditions within nests and individually based endogenous factors have significant effects on cloacal bacteria assemblages and could affect post‐fledging condition.

Polyphasic characterization of the bacterial community in an urban soil profile with in situ and culture-dependent methods

Bacterial communities of urban soils have not been thoroughly investigated up to now. Therefore, soil samples from the urban park Tiergarten in the centre of Berlin were taken from a profile in 15, 30 and 90 cm depth. The total number of bacteria (4′,6-diamidino-2-phenylindole (DAPI) counts) as well as biomass declined one order of magnitude from topsoil to subsoil. Soil texture changed comparably and water content and amount of organic matter dropped 3–10-fold. The number of culturable bacteria (colony forming units = CFU) also decreased with increasing soil depth. Amplified ribosomal DNA restriction analysis (ARDRA) revealed similar bacterial communities in the two upper soil layers in contrast to the deepest layer. The number of bacterial cells which were detected with probe EUB338 in relation to total cell counts differed between 43 and 35% in the three soil layers. With the probe active count method (PAC) this number could be increased up to 72% of total cell counts in topsoil whereas activation of cells declined with increasing depth. In relation to total cell counts (DAPI) α- Proteobacteria and β- Proteobacteria are equally distributed in all three depths, whereas γ- Proteobacteria declined within the soil profile. With the BIOLOG system we observed the general trend that the capability of utilizing diverse substrates decreased with soil depth whereas a few substrates, such as Tween 40 and Tween 80 could be utilised by the bacteria of all soil depths.

Weak coupling between community composition and functioning of aquatic bacteria

We performed a batch culture experiment with a factorial design in which sterile water from four lakes and bacterial assemblages (size‐fractionated lake water) from the same lakes were set up in all possible combinations. The functional performance (biomass yield, respiration, growth rates, and growth efficiency) of bacterial communities growing in the cultures depended primarily on the type of the medium and to a much lesser extent on the origin of the bacterial assemblage. Functional changes were only partly paralleled by changes in community composition, as indicated by terminal restriction fragment length polymorphism analysis. Similar bacterial communities developed in different cultures as a result of receiving either the same medium or the same inoculum, indicating that bacterial communities are comprised of populations of generalists that can grow under most conditions as well as populations with the life strategy of specialists. However, bacteria originating from a slightly acidic polyhumic lake failed to grow, grew unsteadily, or exhibited an extended lag phase when exposed to media originating from other lakes, indicating that the bacterial community in the polyhumic lake was not able to adapt rapidly to changes in environmental conditions.

Study of microbial community structures in UASB sludge treating municipal wastewater by denaturing gradient gel electrophoresis of 16S rDNA

The structures of microbial communities in lab-scale upflow anaerobic sludge blanket (UASB) reactors for treating municipal wastewater with different ratios of COD soluble/COD total were studied using denaturing gradient gel electrophoresis (DGGE) of 16S rRNA genes. The microbial structure of the inoculum sludge obtained from a full-scale UASB reactor of treating potato processing wastewater was compared with the structures of sludges collected from three lab-scale UASB reactors after eight months feeding with raw municipal wastewater, with CEPS (chemically enhanced primary sedimentation) pretreated municipal wastewater, and with a synthetic municipal sewage, respectively. Computer-aided numerical analysis of the DGGE fingerprints showed that the bacterial community underwent major changes. The sludges for treating raw and CEPS pretreated wastewater had very similar bacterial and archaeal communities (82% and 96% similarity) but were different from that for treating the synthetic sewage. Hence, despite similar % COD in the particulate form in the synthetic and the real wastewater, the two wastewaters were selected for different microbial communities. Prominent DGGE bands of Bacteria and Archaea were purified and sequenced. The 16S rRNA gene sequences of the dominant archaeal bands found in the inoculum, and UASB sludge fed with raw sewage, CEPS pretreated wastewater, and synthetic sewage were closely associated with Methanosaeta concilii. In the UASB sludge fed with synthetic sewage, another dominant band associated with an uncultured archaeon 39-2 was found together with M. concilii.

Similarity of bacterial communities in sawdust- and straw-amended cow manure composts

We analyzed bacterial communities in two cow manure composts derived from the same feed manure and composted in the same location, but composted with different carbon amendments, and in peat-based potting mixes amended with these composts. Bacterial communities were characterized by PCR-denaturing gradient gel electrophoresis (DGGE) analysis of extracted DNAs, and population fingerprints generated for each sample were compared. Sequence analyses of dominant DGGE bands revealed that members of the phylum Bacteroidetes were the most dominant bacteria detected in this study (19 of 31 clones). These analyses demonstrate that bacterial community profiles of individual composts were highly similar, as were profiles of compost-amended potting mixes. However, potting mix profiles differed substantially from the original compost profiles and from that of the peat base. These data indicate that highly similar bacterial populations were active in the two composts, and suggest that the effects of the initial carbon amendment on the mature compost bacterial communities were minor, while factors such as the feed manure and composting location may have been more influential.

Within- and between-lake variability in the composition of bacterioplankton communities: investigations using multiple spatial scales.

This study examined the similarity of epilimnetic bacterial community composition (BCC) across several within- and among-lake spatial scales, and the environmental factors giving rise to similar bacterial communities in different lakes were also explored. Samples were collected from 13 northern and southern Wisconsin lakes representing gradients in lake size, productivity, dissolved organic carbon and humic acid contents, and pH. Hypotheses regarding patchy distribution of bacterial communities in lakes were tested by comparing samples collected from nearby (tens of meters) and distant (hundreds of meters) sampling sites in the same lake. BCC was characterized by using a molecular fingerprinting technique, automated ribosomal intergenic spacer analysis (ARISA). Overall, samples collected at the 10-m, 100-m, and between-lake scales differed by 13, 17, and 75%, respectively. Variation at these last two scales was significant. The development of within-lake variation in BCC appeared to depend on the isolation of water by lake shoreline features such as bays or narrow constrictions. ARISA profiles from northern lakes had fewer peaks and were less similar to each other than were those of the southern lakes, suggesting that regional features do not necessarily lead to the development of similar bacterial communities. Lakes at similar positions on productivity and dissolved organic carbon concentration gradients had similar bacterial communities, and bacterial diversity was positively correlated with lake productivity and water temperature. Factorial studies taking into account these gradients, as well as regional spatial scales, should provide much insight into the nature of aquatic bacterial biogeography.

Development of the intestinal bacterial composition in hospitalized preterm infants in comparison with breast-fed, full-term infants.

The establishment and succession of bacterial communities in hospitalized preterm infants has not been extensively studied. Because earlier studies depended on classical cultural techniques, their results were limited. This study monitored the establishment and succession of the neonatal microbiota in the first weeks of life by analyzing the 16S rDNA variety in fecal samples applying PCR-denaturing gradient gel electrophoresis (PCR-DGGE). Fecal samples from 29 preterm infants hospitalized in a neonatal intensive care unit, including samples from antibiotic-treated infants and one with neonatal necrotizing enterocolitis, were subjected to PCR-DGGE analysis. Daily DGGE profiles from all preterm infants during the first 4 wk were obtained and analyzed. In addition, feces of 15 breast-fed, full-term infants and a variety of clinical bacterial isolates were examined and compared with the PCR-DGGE profiles of the preterm infants. During the first days of life, the DGGE profiles were rather simple but increased in their complexity over time. It became obvious that not only the intraindividual band-pattern similarity increased over time, but also the interindividual. During the observation period, similarity values (Cs) increased in each preterm infant from 0 to 80%, whereas interindividual Cs increased from 18.1 to 57.4%, revealing the acquisition of a highly similar bacterial community in these infants. In contrast, Cs-values obtained for breast-fed, full-term infants were rather low (11.2%). Escherichia coli, Enterococcus sp., and Klebsiella pneumoniae were the bacteria most commonly found in all preterm infants. The interindividual bacterial composition in hospitalized preterm infants is more similar in comparison with breast-fed, full-term infants and is not necessarily influenced by birth weight, diet, or antibiotic treatment.

Arbuscular mycorrhizal infection changes the bacterial 16 S rDNA community composition in the rhizosphere of maize

Mycorrhizal and non-mycorrhizal (NM) maize plants were grown for 4 or 7weeks in an autoclaved quartz sand-soil mix. Half of the NM plants were supplied with soluble P (NM-HP) while the other half (NM-LP), like the mycorrhizal plants, received poorly soluble Fe and Al phosphate. The mycorrhizal plants were inoculated with Glomus mosseae or G. intraradices. Soil bacteria and those associated with the mycorrhizal inoculum were reintroduced by adding a filtrate of a low P soil and of the inocula. At 4 and 7weeks, plants were harvested and root samples were taken from the root tip (0-1cm), the subapical zone (1-2cm) and the mature root zone at the site of lateral root emergence. DNA was extracted from the roots with adhering soil. At both harvests, the NM-HP plants had higher shoot dry weight than the plants grown on poorly soluble P. Mycorrhizal infection of both fungi ranged between 78% and 93% and had no effect on shoot growth or shoot P content. Eubacterial community compositions were examined by polymerase chain reaction-denaturing gradient gel electrophoresis of 16S rDNA, digitisation of the band patterns and multivariate analysis. The community composition changed with time and was root zone specific. The differences in bacterial community composition in the rhizosphere between the NM plants and the mycorrhizal plants were greater at 7 than at 4weeks. The two fungi had similar bacterial communities after 4weeks, but these differed after 7weeks. The observed differences are probably due to changes in substrate composition and amount in the rhizosphere.

Similarity of particle-associated and free-living bacterial communities in northern San Francisco Bay, California

AME Aquatic Microbial Ecology Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsSpecials AME 21:103-114 (2000) - doi:10.3354/ame021103 Similarity of particle-associated and free-living bacterial communities in northern San Francisco Bay, California James T. Hollibaugh1,*, Patricia S. Wong1, Michael C. Murrell2,** 1Department of Marine Sciences, University of Georgia, Athens, Georgia 30602-3636, USA2Institute of Marine Science, University of California, Santa Cruz, California 95064, USA *E-mail: aquadoc@uga.edu **Present address: Gulf Ecology Division, USEPA, 1 Sabine Island Drive, Gulf Breeze, Florida 32561, USA ABSTRACT: We used denaturing gradient gel electrophoresis (DGGE) of 16S rDNA PCR amplicons to analyze the composition of Bacteria communities in samples collected during the summer, low flow season from northern San Francisco Bay, California. There were clear compositional differences in communities sampled at different locations in the Bay and at different times of the year. Particle-associated (attached) and free-living (free) bacteria in a given sample were generally more similar than communities in different samples. At times, the attached and free communities in a sample appeared identical, suggesting a fairly rapid exchange between them. The free-living community tended to be richer (more operational taxonomic units [OTU] per sample) than the attached community; however, the difference was not statistically significant. Richness declined through the summer. The richest samples were collected on the June cruise (51 OTU sample-1) while the least rich samples were collected on the September cruise (21 OTU sample-1). The number of distinct OTUs encountered in all samples from a cruise ranged from 61 (April) to 45 (October). The greatest number of unique OTUs (26) was found in April samples while the fewest (3) was found in September. There was no consistent hierarchy of richness between samples. Sample groups representing location and size fractions contained from 55 to 61 different OTUs and from 8 to 18 unique (found only once) OTUs. An average of 23% of the OTUs from a given station and size fraction were unique while an average of 5.5% were found on all cruises. Ubiquitous OTUs (found at all stations) ranged from 34% (free-living, June) to 7% (free-living, August) of the distinct OTUs encountered on a given cruise. Our results suggest little difference in the biogeochemical role played by attached versus free bacteria in San Francisco Bay, particularly in the estuarine turbidity maximum. These results are generally consistent with our analyses of the metabolic potential of these communities. KEY WORDS: Particles · Estuary · Bacteria · Community · San Francisco Bay · Diversity · Richness · DGGE Full text in pdf format NextExport citation RSS - Facebook - Tweet - linkedIn Cited by Published in AME Vol. 21, No. 2. Publication date: March 31, 2000 Print ISSN: 0948-3055; Online ISSN: 1616-1564 Copyright © 2000 Inter-Research.

Patterns of Rhizosphere Microbial Community Structure Associated with Co-Occurring Plant Species

1 Rhizosphere populations of free-living bacteria and fungi associated with particular co-occurring plants were characterized to examine patterns of microbial community structure in natural plant communities. Soil was collected from three co-occurring perennial plant pairs in an undisturbed field at Smoot Hill Biological Reserve, Pullman, Washington, USA, and from three different perennial plant pairs in an old-field community in Durham, North Carolina, USA. 2 Bacteria and fungi isolated from these rhizosphere soils were tested for their ability to utilize various carbon substrates, their tolerance of antibiotics, and their sensitivity to osmotic and metal stresses. Multivariate analysis of physiological characteristics showed that rhizosphere microbial populations associated with particular plant pairs were significantly different from one another. Plots of the first and second linear discriminative functions from a canonical analysis showed clustering of bacterial and fungal physiological characteristics according to plant pair. 3 Replicates of particular plant pairs were planted into both greenhouse and field experiments to test whether bacterial community structure was influenced by different plant pairs. Repeated profile analyses showed that initially similar rhizosphere bacterial communities differentiated in both the greenhouse and field experiments and that these differences were associated with plant pairs. 4 The data suggest structure in rhizosphere populations of free-living bacteria and fungi can be influenced by plants. They provide a first step in understanding the link between the structure and function of natural plant and microbial communities.

97/02341 Environmental impact of mining and smelting industries in Poland

The emergence of resistance genes is a global phenomenon that poses a significant threat to both animals and humans. Lakes are important reservoirs of genes that confer resistant to antibiotics and metals. In this study, we investigated the distribution and diversity of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) in the sediment of Daihai Lake using high-throughput sequencing and metagenomic analysis. The results indicated that all sampling sites had similar bacterial community structures, with Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes being the most abundant. A total of 16 ARG types containing 111 ARG subtypes were deposited in the sediment. Among the resistance genes to bacitracin, multidrug, macrolide-lincosamide-streptogramin (MLS), tetracycline, beta-lactam, and sulfonamide were the dominant ARG types, accounting for 89.9–94.3% of the total ARGs. Additionally, 15 MRG types consisting of 146 MRG subtypes were identified. In all samples, MRGs of the same type presented resistance to Pb, Ni, Hg, W, Zn, Ag, Cr, Fe, As, Cu, and multimetals. Overall, the distribution and diversity of antibiotic and metal resistance genes showed no significant differences in the samples. Plasmids (91.03–91.82%) were the most dominant mobile genetic elements in the sediments of Daihai Lake. Network analysis indicated that the target ARGs and MRGs were significantly positively correlated with the microorganisms. Potential hosts for various ARGs and MRGs include Proteobacteria, Euryarchaeota, Actinobacteria, Chloroflexi, and Bacteroidetes.