Entire Bacterial Community Research Articles

Spatiotemporal changes in the structure and composition of a less-abundant bacterial phylum (Planctomycetes) in two perialpine lakes.

We used fingerprinting and cloning-sequencing to study the spatiotemporal dynamics and diversity of Planctomycetes in two perialpine lakes with contrasting environmental conditions. Planctomycetes, which are less-abundant bacteria in freshwater ecosystems, appeared to be structured in the same way as the entire bacterial community in these ecosystems. They were more diversified and displayed fewer temporal variations in the hypolimnia than in the epilimnia. Like the more-abundant bacterial groups in aquatic systems, Planctomycetes communities seem to be composed of a very small number of abundant and widespread operational taxonomic units (OTUs) and a large number of OTUs that are present at low abundance. This indicates that the concept of "abundant or core" and "rare" bacterial phylotypes could also be applied to less-abundant freshwater bacterial phyla. The richness and diversity of Planctomycetes were mainly driven by pH and were similar in both of the lakes studied, whereas the composition of the Planctomycetes community seemed to be determined by a combination of factors including temperature, pH, and nutrients. The relative abundances of the dominant OTUs varied over time and were differently associated with abiotic factors. Our findings demonstrate that less-abundant bacterial phyla, such as Planctomycetes, can display strong spatial and seasonal variations linked to environmental conditions and suggest that their functional role in the lakes studied might be attributable mainly to a small number of phylotypes and vary over space and time in the water column.

Temporal changes in Sphingomonas and Mycobacterium populations in mangrove sediments contaminated with different concentrations of polycyclic aromatic hydrocarbons (PAHs)

The change in community diversity and structure of the indigenous, dominant, polycyclic aromatic hydrocarbon (PAH)-degrading bacterial genera, Sphingomonas and Mycobacterium, due to contamination in the environment is not very well known. A combination of PCR-DGGE with specific primers and a cultivation-dependent microbiological method was used to detect different populations of Sphingomonas and Mycobacterium in mangrove sediments. The structure of the entire bacterial community (including Sphingomonas) did not show a shift due to environmental contamination, whereas the diversity of Mycobacterium populations in mangrove sediments with higher PAH contamination increased from exposure between Day 0 and Day 30. The isolated Mycobacterium strains migrated to the same position as the major bands of the bacterial communities in Mycobacterium-specific DGGE. A dioxygenase gene system, nidA, which is commonly found in PAH-degrading Mycobacterium strains, was also detected in the more highly contaminated sediment slurries. The present study revealed that Mycobacterium species were the dominant PAH-degraders and played an important role in degrading PAHs in contaminated mangrove sediments.

Concentration-dependent response of estrone-degrading bacterial community in activated sludge analyzed by microautoradiography-fluorescence in situ hybridization

Inefficient removal of estrone (E1) in wastewater treatment plants (WWTPs) causes feminizing effects in male aquatic creatures. As E1 is mainly removed by biodegradation, investigation of E1 degradation is important to determine better removal strategies. Using microautoradiography-fluorescence in situ hybridization (MAR-FISH), we demonstrated that the structures of [ 3H]E1-incorporating bacterial communities were different at different E1 concentrations applied to activated sludge. At 200 μg/L E1, almost all [ 3H]E1-incorporating cells were associated with either Betaproteobacteria or Gammaproteobacteria (60% and 40% of MAR (+) cells, respectively). The proportion of Betaproteobacteria and Gammaproteobacteria in the total number of [ 3H]E1-incorporating cells decreased as the concentration of E1 decreased. In contrast, the proportion of Alphaproteobacteria in the total number of [ 3H]E1-incorporating cells increased as the concentrations of E1 decreased. At the lowest applied concentration (540 ng/L), almost all the [ 3H]E1-incorporating cells were Alphaproteobacteria (96%). The results of MAR-FISH applied to sludge samples collected from various plant locations and activated sludge processes, and during different seasons also demonstrated the high contribution of Alphaproteobacteria to the entire E1-degrading bacterial community (50.4 ± 11% of the total number of [ 3H]E1-incorporating cells) at 1 μg/L E1. Since the E1 concentration in domestic wastewater is at sub-μg/L levels, the key E1 degraders in activated sludge of domestic WWTPs are probably be Alphaproteobacteria. All [ 3H]E1-incorporating Alphaproteobacteria were hybridized with probe ALF968. Few MAR (+) cells were Sphingomonadales. An E1-degrading bacterial community at low E1 concentration appeared to consist of diverse bacterial groups of Alphaproteobacteria. This study suggested that substrate concentration is an essential factor for revealing E1-degrading bacteria in complex communities.

Diversity of cutaneous bacteria with antifungal activity isolated from female four-toed salamanders

Among the microbiota of amphibian skin are bacteria that produce antifungal compounds. We isolated cutaneous bacteria from the skins of three populations of the nest-attending plethodontid salamander Hemidactylium scutatum and subsequently tested the bacterial isolates against two different fungi (related to Mariannaea elegans and Rhizomucor variabilis) that were obtained from dead salamander eggs. The culturable antifungal bacteria were phylogenetically characterized based on 16S rRNA phylogeny, and belonged to four phyla, comprising 14 bacterial families, 16 genera and 48 species. We found that about half of the antifungal bacterial genera and families were shared with a related salamander species, but there was virtually no overlap at the species level. The proportion of culturable antifungal bacterial taxa shared between two large populations of H. scutatum was the same as the proportion of taxa shared between H. scutatum and Plethodon cinereus, suggesting that populations within a species have unique antifungal bacterial species. Approximately 30% of individuals from both salamander species carried anti-M. elegans cutaneous bacteria and almost 90% of P. cinereus and 100% of H. scutatum salamanders carried anti-R. variabilis cutaneous bacteria. A culture independent method (PCR/DGGE) revealed a shared resident bacterial community of about 25% of the entire resident bacterial community within and among populations of H. scutatum. Thus, the culturable antifungal microbiota was far more variable on salamander skins than was the bacterial microbiota detected by PCR/DGGE. The resident cutaneous antifungal bacteria may play an important role in amphibians' innate defense against pathogens, including the lethal chytrid fungus Batrachochytrium dendrobatidis.

Microbial community dynamics in a humic lake: differential persistence of common freshwater phylotypes

In an effort to better understand the factors contributing to patterns in freshwater bacterioplankton community composition and diversity, we coupled automated ribosomal intergenic spacer analysis (ARISA) to analysis of 16S ribosomal RNA (rRNA) gene sequences to follow the persistence patterns of 46 individual phylotypes over 3 years in Crystal Bog Lake. Additionally, we sought to identify linkages between the observed phylotype variations and known chemical and biological drivers. Sequencing of 16S rRNA genes obtained from the water column indicated the presence of phylotypes associated with the Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, TM7 and Verrucomicrobia phyla, as well as phylotypes with unknown affiliation. Employment of the 16S rRNA gene/ARISA method revealed that specific phylotypes varied independently of the entire bacterial community dynamics. Actinobacteria, which were present on greater than 95% of sampling dates, did not share the large temporal variability of the other identified phyla. Examination of phylotype relative abundance patterns (inferred using ARISA fragment relative fluorescence) revealed a strong correlation between the dominant phytoplankton succession and the relative abundance patterns of the majority of individual phylotypes. Further analysis revealed covariation among unique phylotypes, which formed several distinct bacterial assemblages correlated with particular phytoplankton communities. These data indicate the existence of unique persistence patterns for different common freshwater phylotypes, which may be linked to the presence of dominant phytoplankton species.

Spatial and vertical biogeography of coral reef sediment bacterial and diazotroph communities

Coral reefs are globally important marine ecosystems as sites of high biotic diversity. Reef flat sediments are reasonably homogeneous in composition. This substratum is subject to gradi- ents in water motion, grazing pressure and benthic productivity. This study used DNA fingerprinting techniques, automated rRNA intergenic spacer analysis (ARISA), and terminal restriction fragment length polymorphism (TRFLP) to examine patterns of bacterial assemblage composition within Heron Reef flat sediments, targeting the entire bacterial community (not including Archaea) and nitrogen- fixing bacteria. ARISA fingerprints contained between 51 and 148 operational taxonomic units (OTU) per surface sediment sample. The mean whole-community similarity between adjacent sites along a transect from Heron Island to the reef crest was 0.50 ± 0.03 (mean ± SE) Whittaker Index (comparison of relative abundances) and 0.46 ± 0.03 Jaccard Index (presence/absence only). Comparison of sedi- ment community fingerprints to a water column community fingerprint collected above the reef flat at high tide indicated that sediments contained different assemblages to the water column (mean similarity between sediments and water column assemblage = 0.15 ± 0.01 Jaccard Index); however, assemblage composition did not differ significantly from that expected by random association. Verti- cal sediment cores showed dissimilarity between surface (0 to 3 cm) and deep (3 to 5 cm) community fingerprints, which was probably related to redox state. Comparison of fingerprints of fecally-derived sediments from the sea cucumber Holothuria atra and surrounding sediments indicated that the impact of metazoan grazing could not be distinguished from ambient small spatial scale variability in sediment assemblage composition. The nifH-TRFLP fingerprints of sediment prokaryotic assem- blages (amplified from all samples, but only in sufficient quantities for analysis from 7 locations) indi- cated the presence of ubiquitous, potentially diverse diazotroph communities, with little assemblage similarity between locations. Our results suggested that while bacterial assemblages (including communities of nitrogen-fixing bacteria) in sediments of a coral reef are diverse, their assemblage composition is not related to grazing pressure but may be influenced by other biotic and abiotic environmental conditions such wave energy and sediment depth.

Associated bacterial communities of two deep-water sponges

A combination of approaches was used to examine the bacterial communities associated with 2 deep-water Scleritoderma spp. sponges. Denaturing gradient gel electrophoresis analysis of partial 16S rRNA genes extracted from sponge tissue was used to determine the structure of the sponge-associated bacterial community. Cultivation studies using a variety of marine-based media and medium additions were performed to characterize the cultivable aerobic heterotrophic bacterial community. DNA was extracted from recovered isolates, mixed, and PCR-denaturing gradient gel electrophoresis was performed to demonstrate the differences between the recoverable microorganisms and the entire bacterial community. Results indicated that, as expected, only a small fraction of the bacterial community could be cultivated and that the isolates appeared to be non-representative of sponge-associated communities for each specimen. Sequences recovered from the denaturing gel demonstrated the greatest similarity based on GenBank comparisons to uncultivated microbial associates of the lithistid sponge Theonella swinhoei and the verongid sponge Aplysina aerophoba, suggesting that the bacterial communities are similar between different host sponges from phylogenetically disparate orders.

Natural assemblages of marine proteobacteria and members of the Cytophaga-Flavobacter cluster consuming low- and high-molecular-weight dissolved organic matter.

We used a method that combines microautoradiography with hybridization of fluorescent rRNA-targeted oligonucleotide probes to whole cells (MICRO-FISH) to test the hypothesis that the relative contributions of various phylogenetic groups to the utilization of dissolved organic matter (DOM) depend solely on their relative abundance in the bacterial community. We found that utilization of even simple low-molecular-weight DOM components by bacteria differed across the major phylogenetic groups and often did not correlate with the relative abundance of these bacterial groups in estuarine and coastal environments. The Cytophaga-Flavobacter cluster was overrepresented in the portion of the assemblage consuming chitin, N-acetylglucosamine, and protein but was generally underrepresented in the assemblage consuming amino acids. The amino acid-consuming assemblage was usually dominated by the alpha subclass of the class Proteobacteria, although the representation of alpha-proteobacteria in the protein-consuming assemblages was about that expected from their relative abundance in the entire bacterial community. In our experiments, no phylogenetic group dominated the consumption of all DOM, suggesting that the participation of a diverse assemblage of bacteria is essential for the complete degradation of complex DOM in the oceans. These results also suggest that the role of aerobic heterotrophic bacteria in carbon cycling would be more accurately described by using three groups instead of the single bacterial compartment currently used in biogeochemical models.

Pelagic Bacteria-Particle Interactions and Community-Specific Growth Rates in Four Lakes along a Trophic Gradient.

Abstract The relationships between bacterial concentration, bacterial production, and cell-specific activity of both free and attached bacteria and environmental factors such as suspended solids, nutrients, and temperature were examined in four lakes, two in New Zealand and two in Switzerland. Estimates of cell-specific production were obtained by microautoradiographic counts of [3H]thymidine-labeled cells. Bacteria attached to particles accounted for only 1.3 to 11.6% of the total bacterial abundance, but showed overall 20-fold higher specific growth rates and were relatively more active than their free counterparts. On average, 80 to 100% of epibacteria were attached to organic particles. The abundance and production of free and attached bacteria were positively correlated; however, relationships between these fractions and some environmental variables differed. Cell-specific activities of active bacteria were not equivalent to mean cellular activities of the entire bacterial community and differed in their relationship to trophic state. [3H]Thymidine-positive bacteria were more tightly linked to chlorophyll a than were total bacteria. Our findings indicate that production by attached bacteria, fueled by phytoplankton carbon, supplies "new" free bacteria to the bacterial community. Our results support the idea that particulate organic matter acts as a source of dissolved nutrients to free bacteria. Bottom-up control of bacterial biomass, as shown by regressions of biomass vs production, appeared to be stronger in two ultraoligotrophic lakes than in two more eutrophic ones.

Distribution and life strategies of two bacterial populations in a eutrophic lake

Monoclonal antibodies and epifluorescence microscopy were used to determine the depth distribution of two indigenous bacterial populations in the stratified Lake Plusssee and characterize their life strategies. Populations of Comamonas acidovorans PX54 showed a depth distribution with maximum abundances in the oxic epilimnion, whereas Aeromonas hydrophila PU7718 showed a depth distribution with maximum abundances in the anoxic thermocline layer (metalimnion), i. e., in the water layer with the highest microbial activity. Resistance of PX54 to protist grazing and high metabolic versatility and growth rate of PU7718 were the most important life strategy traits for explaining the depth distribution of the two bacterial populations. Maximum abundance of PX54 was 16,000 cells per ml, and maximum abundance of PU7718 was 20,000 cells per ml. Determination of bacterial productivity in dilution cultures with different-size fractions of dissolved organic matter (DOM) from lake water indicates that low-molecular-weight (LMW) DOM is less bioreactive than total DOM (TDOM). The abundance and growth rate of PU7718 were highest in the TDOM fractions, whereas those of PX54 were highest in the LMW DOM fraction, demonstrating that PX54 can grow well on the less bioreactive DOM fraction. We estimated that 13 to 24% of the entire bacterial community and 14% of PU7718 were removed by viral lysis, whereas no significant effect of viral lysis on PX54 could be detected. Growth rates of PX54 (0.11 to 0.13 h-1) were higher than those of the entire bacterial community (0.04 to 0.08 h-1) but lower than those of PU7718 (0.26 to 0.31 h-1). In undiluted cultures, the growth rates were significantly lower, pointing to density effects such as resource limitation or antibiosis, and the effects were stronger for PU7718 and the entire bacterial community than for PX54. Life strategy characterizations based on data from literature and this study revealed that the fast-growing and metabolically versatile A. hydrophila PU7718 is an r-strategist or opportunistic population in Lake Plusssee, whereas the grazing-resistant C. acidovorans PX54 is rather a K-strategist or equilibrium population.

Size-specific mortality of lake bacterioplankton by natural virus communities

AME Aquatic Microbial Ecology Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsSpecials AME 15:103-113 (1998) - doi:10.3354/ame015103 Size-specific mortality of lake bacterioplankton by natural virus communities Markus G. Weinbauer*, Manfred G. Höfle GBF-National Research Center of Biotechnology, AG Microbial Ecology, Mascheroder Weg 1, D-38124 Braunschweig, Germany *E-mail: mgw@gbf.de ABSTRACT: The potential effect that viral lysis has on the cell size distribution of bacterioplankton was investigated during late summer stratification in Lake Plußsee, Germany. Size-specific bacterial mortality due to viral lysis was estimated from in situ samples by a transmission electron microscopy based examination of visibly infected cells (VIC) and in an experiment with varying concentrations of the natural virus community. In all depth layers the highest percentage of cells was found in a cell length class that was smaller for the entire bacterial community (0.3-0.6 μm) than for VIC (0.6-0.9 μm). For cells <2.4 μm the highest frequency of VIC (FVIC) was detected in the size classes 0.6-0.9 and 0.9-1.2 μm, and the FVIC was high in the size classes 1.2-1.5 (all depth layers) and 1.5-1.8 μm (meta- and hypolimnion). The estimated mortality due to viral lysis in these size classes was significant with maxima of 29 to 55% in the epilimnion, 30 to 59% in the metalimnion and 56 to 107% in the hypolimnion. In all depth layers the FVIC of bacteria <0.3 μm in length was ca 30% of that averaged for the entire bacterial community, and in the experiment the percentage of cells <0.3 μm was highest in enclosures with high viral activity. In the experiment the average cell size was smaller in enclosures with high than in that with low viral activity. The data demonstrate that being small could be a strategy of cells to reduce mortality due to viral lysis probably by reducing the contact rates with viruses. Thus, viral lysis could be one of the mechanisms keeping the cell size small in aquatic ecosystems. In oxic water cells in the largest size class (>2.4 μm) were not infected with viruses, and in enclosures with epilimnetic lake water the percentage of cells >2.4 μm was highest in enclosures with highest viral abundance, suggesting that resistance against infection favored large cells. However, in the meta- and hypolimnion the FVIC was high for cells >2.4 μm and, since the burst size increased with bacterial cell size, lysis of large cells could contribute significantly to viral production. Also, a major portion of biomass was found in cells >2.4 μm. The finding that viral lysis is size-specific and can affect the cell size distribution of bacteria in lake water has important implications for our understanding of the mechanisms which regulate bacterial production and nutrient cycling in pelagic environments. KEY WORDS: Bacterioplankton size structure · Size-specific viral lysis · Lake Plußsee Full text in pdf format NextExport citation RSS - Facebook - Tweet - linkedIn Cited by Published in AME Vol. 15, No. 2. Publication date: July 02, 1998 Print ISSN: 0948-3055; Online ISSN: 1616-1564 Copyright © 1998 Inter-Research.

Total bacterial diversity in soil and sediment communities—A review

Advances in microbial methods have demonstrated that microorganisms globally are the dominating organisms both concerning biomass and diversity. Their functional and genetic potential may exceed that of higher organisms. Studies of bacterial diversity have been hampered by their dependence on phenotypic characterization of bacterial isolates. Molecular techniques have provided the tools for analyzing the entire bacterial community including those which we are not able to grow in the laboratory. Reassociation analysis of DNA isolated directly from the bacteria in pristine soil and marine sediment samples revealed that such environments contained in the order of 10 000 bacterial types. The diversity of the total bacterial community was approximately 170 times higher than the diversity of the collection of bacterial isolates from the same soil. The culturing conditions therefore select for a small and probably skewed fraction of the organisms present in the environment. Environmental stress and agricultural management reduce the bacterial diversity. With the reassociation technique it was demonstrated that in heavily polluted fish farm sediments the diversity was reduced by a factor of 200 as compared to pristine sediments. Here we discuss some molecular mechanisms and environmental factors controlling the bacterial diversity in soil and sediments.

Frequency, size and distribution of bacteriophages in different marine bacterial morphotypes

The frequencies of cells containing mature phages, the burst sizes, the phage head sizes and the distribution of phages inside cells of different bacterial morphotypes were investigated in the northern Adriatic Sea. Coccoid bacteria more frequently (2 .5%) contained mature phages than rodshaped bacteria (1.2%) and spirillae (1.4 %). Including an estimation of non-v~sible infection we found that up to 27 % of rods were infected with viruses, up to 79% of cocci and up to 100% of spirillae. The highest overall infection frequency of the entire bacterial community was 30 %. The percentage of rods with mature phages was significantly correlated to increasing rod densities. It is suggested that a threshold density of about 2 X 10' rods ml-' exists that is necessary for infection with phages. No threshold densities could be determined for cocci and spirillae. Burst sizes varied strongly between different host morphotypes. The burst sizes of rods increased significantly with the frequency of rods containing mature phages, probably as a result of superinfection of bacteria with phages. The volume of the host cells seemed to influence the number of phages produced per cell. Most of the phages within rods and all phages within spirillae were smaller than 60 nm, whereas the majority of phages within cocci were larger than 60 nm. Analyses of the distribution of phages inside the cells showed that phages were frequently concentrated in 2 defined areas at the 2 opposite ends of both rods and spirillae. Our results from an in situ study suggest that the production of bacteriophages is strongly influenced by the structure of the bacterial community, i.e. by the relative abundances of the various morphotypes.

Size-selective grazing of coastal bacterioplankton by natural assemblages of pigmented flagellates, colorless flagellates, and ciliates

Fluorescently-labelled bacteria (FLB) were used to study the feeding strategies of a natural assemblage of estuarine protozoans and to examine whether the protozoan grazing could account for the in situ size structure of the bacterioplankton. The FLB, DTAF-stained enterococci, ranging in volume from 0.01 to 0.30 × 10(-1) µm(3), were added to a natural planktonic assemblage at a density of 5.5% of the natural bacterioplankton. Initial densities (individuals ml(-1)) were as follows: total natural bacteria, 2.2 × 10(6); FLB, 1.2 × 10(5); pigmented flagellates, 300; colorless flagellates, 250; and ciliates, 30. FLB consumption rates were determined by examining the contents of protozoan food vacuoles, and the long-term effect of grazing (over a period of 100 hours) was determined by monitoring the decline in the FLB density in experimental vessels. The average consumption rates of FLB by pigmented flagellates were similar to those by flagellates that lacked chloroplasts (0.9 and 0.6 FLB protozoan(-1) hour(-1), respectively). The ciliates consumed bacteria at an average rate that was 17-fold higher (per cell) than flagellates, and they displayed a greater preference for larger bacteria than did the flagellates. FLB of the mid-size classes (0.025-0.100 µm(3)) were heavily grazed by the entire protozoan assemblage; the smallest (<0.025 µm(3)) and the largest (>0.100 µm(3)) FLB escaped protozoan grazing. This had a profound effect on the resulting size distribution of FLB. At the end of a 100-hour incubation, the percentage of mid-size FLB (0.025 to 0.100 µm(3)) decreased 2.0-2.2-fold, while the percentage of the smallest and the largest FLB increased 2.0-2.5-fold. Resultant densities of FLB were consistent with initial clearance rates determined for the protozoan groups. The grazing rates of protozoans on FLB were species-specific; whereas some species consumed FLB, others did not demonstrate bacterivory. The results suggest that protozoan grazing has a major effect on the size distribution of coastal bacterioplankton. By selectively feeding on a particular size-class of bacteria, planktonic ciliates may consume 15-90% day(-1) of the standing stock of largest size classes of bacterioplankton. Thus, ciliates, which were present in low abundance in the field, could not balance the production of the entire bacterial community, but they may strongly influence the portion of the bacterial community represented by the largest bacterial class. The direct effect of flagellates (e.g., grazing) was limited to smaller bacteria.