Culturing captures members of the soil rare biosphere

The ecological significance of rare microorganisms within microbial communities remains an important, unanswered question. Microorganisms of extremely low abundance (the 'rare biosphere') are believed to be largely inaccessible and unknown. To understand the structure of complex environmental microbial communities, including the representation of rare and prevalent community members, we coupled traditional cultivation with pyrosequencing. We compared cultured and uncultured bacterial members of the same agricultural soil, including eight locations within one apple orchard and four time points. Our analysis revealed that soil bacteria captured by culturing were in very low abundance or absent in the culture-independent community, demonstrating unexpected accessibility of the rare biosphere by culturing.     

Amplification by PCR artificially reduces the proportion of the rare biosphere in microbial communities

The microbial world has been shown to hold an unimaginable diversity. The use of rRNA genes and PCR amplification to assess microbial community structure and diversity present biases that need to be analyzed in order to understand the risks involved in those estimates. Herein, we show that PCR amplification of specific sequence targets within a community depends on the fractions that those sequences represent to the total DNA template. Using quantitative, real-time, multiplex PCR and specific Taqman probes, the amplification of 16S rRNA genes from four bacterial species within a laboratory community were monitored. Results indicate that the relative amplification efficiency for each bacterial species is a nonlinear function of the fraction that each of those taxa represent within a community or multispecies DNA template. Consequently, the low-proportion taxa in a community are under-represented during PCR-based surveys and a large number of sequences might need to be processed to detect some of the bacterial taxa within the 'rare biosphere'. The structure of microbial communities from PCR-based surveys is clearly biased against low abundant taxa which are required to decipher the complete extent of microbial diversity in nature.     

Contrasted effects of diversity and immigration on ecological insurance in marine bacterioplankton communities

The ecological insurance hypothesis predicts a positive effect of species richness on ecosystem functioning in a variable environment. This effect stems from temporal and spatial complementarity among species within metacommunities coupled with optimal levels of dispersal. Despite its importance in the context of global change by human activities, empirical evidence for ecological insurance remains scarce and controversial. Here we use natural aquatic bacterial communities to explore some of the predictions of the spatial and temporal aspects of the ecological insurance hypothesis. Addressing ecological insurance with bacterioplankton is of strong relevance given their central role in fundamental ecosystem processes. Our experimental set up consisted of water and bacterioplankton communities from two contrasting coastal lagoons. In order to mimic environmental fluctuations, the bacterioplankton community from one lagoon was successively transferred between tanks containing water from each of the two lagoons. We manipulated initial bacterial diversity for experimental communities and immigration during the experiment. We found that the abundance and production of bacterioplankton communities was higher and more stable (lower temporal variance) for treatments with high initial bacterial diversity. Immigration was only marginally beneficial to bacterial communities, probably because microbial communities operate at different time scales compared to the frequency of perturbation selected in this study, and of their intrinsic high physiologic plasticity. Such local "physiological insurance" may have a strong significance for the maintenance of bacterial abundance and production in the face of environmental perturbations.     

Effects of small-scale disturbance on invasion success in marine communities

Introductions of non-indigenous species have resulted in many ecological problems including the reduction of biodiversity, decline of commercially important species and alteration of ecosystems. The link between disturbance and invasion potential has rarely been studied in the marine environment where dominance hierarchies, dynamics of larval supply, and resource acquisition may differ greatly from terrestrial systems. In this study, hard substrate marine communities in Long Island Sound, USA were used to assess the effect of disturbance on resident species and recent invaders, ascidian growth form (i.e. colonial and solitary growth form), and the dominant species-specific responses within the community. Community age was an additional factor considered through manipulation of 5-wk old assemblages and 1-yr old assemblages. Disturbance treatments, exposing primary substrate, were characterized by frequency (single, biweekly, monthly) and magnitude (20%, 48%, 80%) of disturbance. In communities of different ages, disturbance frequency had a significant positive effect on space occupation of recent invaders and a significant negative effect on resident species. In the 5-wk community, magnitude of disturbance also had a significant effect. Disturbance also had a significant effect on ascidian growth form; colonial species occupied more primary space than controls in response to increased disturbance frequency and magnitude. In contrast, solitary species occupied significantly less space than controls. Species-specific responses were similar regardless of community age. The non-native colonial ascidian Diplosoma listerianum responded positively to increased disturbance frequency and magnitude, and occupied more primary space in treatments than in controls. The resident solitary ascidian Molgula manhattensis responded negatively to increased disturbance frequency and magnitude, and occupied less primary space in treatments than in controls. Small-scale biological disturbances, by creating space, may facilitate the success of invasive species and colonial organisms in the development of subtidal hard substrate communities.     

Flow sorting of marine bacterioplankton after fluorescence in situ hybridization

We describe an approach to sort cells from coastal North Sea bacterioplankton by flow cytometry after in situ hybridization with rRNA-targeted horseradish peroxidase-labeled oligonucleotide probes and catalyzed fluorescent reporter deposition (CARD-FISH). In a sample from spring 2003 >90% of the cells were detected by CARD-FISH with a bacterial probe (EUB338). Approximately 30% of the microbial assemblage was affiliated with the Cytophaga-Flavobacterium lineage of the Bacteroidetes (CFB group) (probe CF319a), and almost 10% was targeted by a probe for the beta-proteobacteria (probe BET42a). A protocol was optimized to detach cells hybridized with EUB338, BET42a, and CF319a from membrane filters (recovery rate, 70%) and to sort the cells by flow cytometry. The purity of sorted cells was >95%. 16S rRNA gene clone libraries were constructed from hybridized and sorted cells (S-EUB, S-BET, and S-CF libraries) and from unhybridized and unsorted cells (UNHYB library). Sequences related to the CFB group were significantly more frequent in the S-CF library (66%) than in the UNHYB library (13%). No enrichment of beta-proteobacterial sequence types was found in the S-BET library, but novel sequences related to Nitrosospira were found exclusively in this library. These bacteria, together with members of marine clade OM43, represented >90% of the beta-proteobacteria in the water sample, as determined by CARD-FISH with specific probes. This illustrates that a combination of CARD-FISH and flow sorting might be a powerful approach to study the diversity and potentially the activity and the genomes of different bacterial populations in aquatic habitats.     

Comparison of different denaturing gradient gel electrophoresis primer sets for the study of marine bacterioplankton communities

An annual seasonal cycle of composition of a bacterioplankton community in an oligotrophic coastal system was studied by denaturing gradient gel electrophoresis (DGGE) using five different primer sets. Analysis of DGGE fingerprints showed that primer set 357fGC-907rM grouped samples according to seasons. Additionally, we used the set of 16S rRNA genes archived in the RDPII database to check the percentage of perfect matches of each primer for the most abundant bacterial groups inhabiting coastal plankton communities. Overall, primer set 357fGC-907rM was the most suitable for the routine use of PCR-DGGE analyses in this environment.     

The use of taxonomic distinctness to assess environmental disturbance of insect communities from running water

1. Taxonomic distinctness (or average taxonomic breadth) of a sample is a measure of diversity that has the great advantage of not being sensitive to variations in sampling effort, unlike measures of species richness. It can also be tested for departures from expectation and can thus be used to determine whether a site has suffered from a genuine loss of diversity. 2. Taxonomic distinctness or delta⁺ was measured using all insect species from three datasets obtained from running water habitats: reference or least disturbed sites from channel and bank habitats on rivers from the Australian state of Victoria; test sites distributed along a water quality gradient in Victoria and sites immediately below a series of dams in Victoria and New South Wales. The last two datasets comprised sites subject to a range of obvious disturbances. 3. At reference sites delta⁺ was generally within the range of expected values (95% confidence limits) for both habitats as would be anticipated for these essentially undisturbed sites. However, 13–14% of sites fell below the lower confidence limits. Sites in river basins with less cover of natural habitat had slightly but significantly lower delta⁺ values than those with more cover and these sites contributed to this anomaly. 4. Delta⁺ was inversely correlated with water quality (r = −0.54, P = 0.002) as measured by the first axis of a PCA of water quality variables. It was also inversely correlated with individual variables, such as turbidity and total phosphorous. 5. Delta⁺ was below expectation for 18 of the 19 dam sites and at 13 of these sites delta⁺ values were below the lower confidence limit. 6. Delta⁺ was a sensitive index of diversity that generally distinguished sites suffering from environmental disturbance. Only a few previous studies of river ecosystems have used delta⁺, which did not respond consistently to disturbance because either too few taxa at species or higher taxonomic levels were available or because longitudinal changes in species composition swamped the signal from delta⁺. Neither of these problems occurred with the current datasets. 7. Delta⁺ responded more readily to disturbance than number of species, perhaps because taxonomic distinctness reflects some of the multivariate nature of community samples, whereas number of species is blind to this aspect.     

Salt marsh sediment diversity: a test of the variability of the rare biosphere among environmental replicates

Much of the phylogenetic diversity in microbial systems arises from rare taxa that comprise the long tail of taxon rank distribution curves. This vast diversity presents a challenge to testing hypotheses about the effects of perturbations on microbial community composition because variability of rare taxa among environmental replicates may be sufficiently large that it would require a prohibitive degree of sequencing to discern differences between samples. In this study we used pyrosequencing of 16S rRNA tags to examine the diversity and within-site variability of salt marsh sediment bacteria. Our goal was to determine whether pyrosequencing could produce similar patterns in community composition among replicate environmental samples from the same location. We hypothesized that repeated sampling from the same location would produce different snapshots of the rare community due to incomplete sequencing of the taxonomically rich rare biosphere. We demonstrate that the salt marsh sediments we sampled contain a remarkably diverse array of bacterial taxa and, in contrast to our hypothesis, repeated sampling from within the same site produces reliably similar patterns in bacterial community composition, even among rare organisms. These results demonstrate that deep sequencing of 16s tags is well suited to distinguish site-specific similarities and differences among rare taxa and is a valuable tool for hypothesis testing in microbial ecology.     

Phylogenetic analysis of ribosomal RNA operons from uncultivated coastal marine bacterioplankton

Analyses of small subunit ribosomal RNA genes (SSU rDNAs) have significantly influenced our understanding of the composition of aquatic microbial assemblages. Unfortunately, SSU rDNA sequences often do not have sufficient resolving power to differentiate closely related species. To address this general problem for uncultivated bacterioplankton taxa, we analysed and compared sequences of polymerase chain reaction (PCR)-generated and bacterial artificial chromosome (BAC)-derived clones that contained most of the SSU rDNAs, the internal transcribed spacer (ITS) and the large subunit ribosomal RNA gene (LSU rDNA). The phylogenetic representation in the rRNA operon PCR library was similar to that reported previously in coastal bacterioplankton SSU rDNA libraries. We observed good concordance between the phylogenetic relationships among coastal bacterioplankton inferred from SSU or LSU rDNA sequences. ITS sequences confirmed the close intragroup relationships among members of the SAR11, SAR116 and SAR86 clades that were predicted by SSU and LSU rDNA sequence analyses. We also found strong support for homologous recombination between the ITS regions of operons from the SAR11 clade.     

Functional characteristics of culturable bacterioplankton from marine and estuarine environments.

Information on the structure of bacterioplankton communities is continuously increasing, while knowledge of their metabolic capabilities remains limited. In this study, the metabolic capacity of bacterioplankton was investigated, as such information is necessary to fully understand carbon cycling and other biogeochemical processes. The diversity of dominant culturable chemoorganotrophic bacteria from one estuarine and three marine environments was analyzed by random isolation of colony-forming units on solid media, taxonomical identification by partial 16S rRNA gene sequence analysis, and functional characterization of the isolates. A total of 76 16S rRNA gene sequences, representing 19 different genotypes, were obtained from the four sampling localities, including Bacillus, Pseudomonas, Pseudoalteromonas, Vibrio, and Erythrobacter as the most frequently isolated genera. The range of metabolic functions possessed by the cultured bacterial assemblages differed significantly between sites. Similarly, the percentage at each sampling station of bacteria capable of performing a specific function was significantly different for 18 of the 25 investigated metabolic functions. At two localities, the bacterial assemblages were dominated by a single genus (Pseudoalteromonas or Erythrobacter) and appeared to be functionally specialized. More than 95% of the isolates were capable of utilizing dissolved free amino acids and protein as their sole nitrogen sources, and all isolates of the specialized assemblages expressed beta-glucosidase. Furthermore, only some of the isolates were able to utilize NH4+, while up to two thirds of the isolates of the two marine sites were able to grow on NO3-.     

Propagule pressure and disturbance interact to overcome biotic resistance of marine invertebrate communities

Propagule pressure is fundamental to invasion success, yet our understanding of its role in the marine domain is limited. Few studies have manipulated or controlled for propagule supply in the field, and consequently there is little empirical data to test for non-linearities or interactions with other processes. Supply of non-indigenous propagules is most likely to be elevated in urban estuaries, where vessels congregate and bring exotic species on fouled hulls and in ballast water. These same environments are also typically subject to elevated levels of disturbance from human activities, creating the potential for propagule pressure and disturbance to interact. By applying a controlled dose of free-swimming larvae to replicate assemblages, we were able to quantify a dose–response relationship at much finer spatial and temporal scales than previously achieved in the marine environment. We experimentally crossed controlled levels of propagule pressure and disturbance in the field, and found that both were required for invasion to occur. Only recruits that had settled onto bare space survived beyond three months, precluding invader persistence in undisturbed communities. In disturbed communities initial survival on bare space appeared stochastic, such that a critical density was required before the probability of at least one colony surviving reached a sufficient level. Those that persisted showed 75% survival over the following three months, signifying a threshold past which invaders were resilient to chance mortality. Urban estuaries subject to anthropogenic disturbance are common throughout the world, and similar interactions may be integral to invasion dynamics in these ecosystems.     

Extinctions in a spatial model of fossil communities subject to correlated environmental disturbance

We present a spatial model to study the behaviour of species communities subjected to environmental stress in the form of coloured noise, focusing on long-time changes of time scales larger than 1 ka. The sensitivity to environmental change is introduced by assigning each species with an optimal value of a certain environmental variable like e.g., the temperature, and with a fitness function having the form of a Gaussian. Each species is represented by a point on a surface and competes with neighbours. Species can evolve to new species with a different optimal value, or they can migrate to regions with better environmental conditions. We find that coloured noise can prompt sudden extinctions in similarity with the fossil record. The model also reproduces the well-known fact that that eurytopic species (generalists) are favoured during environmental stresses, and shows that a strong environmental gradient may ameliorate the species performance.     

Parallel changes in the taxonomical structure of bacterial communities exposed to a similar environmental disturbance

Bacterial communities play a central role in ecosystems, by regulating biogeochemical fluxes. Therefore, understanding how multiple functional interactions between species face environmental perturbations is a major concern in conservation biology. Because bacteria can use several strategies, including horizontal gene transfers (HGT), to cope with rapidly changing environmental conditions, potential decoupling between function and taxonomy makes the use of a given species as a general bioindicator problematic. The present work is a first step to characterize the impact of a recent polymetallic gradient over the taxonomical networks of five lacustrine bacterial communities. Given that evolutionary convergence represents one of the best illustration of natural selection, we focused on a system composed of two pairs of impacted and clean lakes in order to test whether similar perturbation exerts a comparable impact on the taxonomical networks of independent bacterial communities. First, we showed that similar environmental stress drove parallel structural changes at the taxonomic level on two independent bacterial communities. Second, we showed that a long-term exposure to contaminant gradients drove significant taxonomic structure changes within three interconnected bacterial communities. Thus, this model lake system is relevant to characterize the strategies, namely acclimation and/or adaptation, of bacterial communities facing environmental perturbations, such as metal contamination.     

Effects of temporal variability of disturbance on the succession in marine fouling communities in northern-central Chile

We investigated the effects of temporal variability in a disturbance regime on fouling communities at two study sites in a northern-central Chilean bay. Fouling assemblages grown on artificial settlement substrata were disturbed by mechanical removal of biomass at different time intervals. Using one single disturbance frequency (10 disturbance events over 5 months) we applied 7 different temporal disturbance treatments: a constant disturbance regime (identical intervals between disturbance events), and 6 variable treatments where both variableness and sequences of intervals between disturbance events were manipulated. Two levels of temporal variableness (low and high, i.e. disturbance events were either dispersed or highly clumped in time) in the disturbance regime were applied by modifying the time intervals between subsequent disturbance events. To investigate the temporal coupling between disturbance events and other ecological processes (e.g. larval supply and recruitment intensity), three different sequences of disturbance intervals were nested in each of the two levels of temporal variableness. Species richness, evenness, total abundance, and structure of communities that experienced the various disturbance regimes were compared at the end of the experiment (15 days after the last disturbance event). Disturbance strongly influenced the community structure and led to a decrease in evenness and total abundance but not species richness. In undisturbed reference communities, the dominant competitor Pyura chilensis (Tunicata) occupied most available space while this species was suppressed in all disturbed treatments. Surprisingly, neither temporal variableness in the disturbance regime nor the sequence of intervals between disturbance events had an effect on community structure. Temporal variability in high disturbance regimes may be of minor importance for fouling communities, because they are dominated by opportunistic species that are adapted to rapidly exploit available space.     

Lack of recovery from disturbance in high-arctic boulder communities

High-arctic boulder communities that are impacted by anthropogenic and natural influences can result in the removal or scouring of sessile organisms leaving either open space or damaged organisms. This project asks how sessile communities recover after disturbances by determining (1) timing of recolonization, (2) grazer effects on recolonization, and (3) vegetative regrowth rates for encrusting sponges and corallines. Cleared boulders were monitored over 7 years to determine recolonization timing and grazer impacts. Vegetative regrowth rates were determined by monitoring partial clearings for 4 years. This study found that recolonization was slow with less than 10 % of the boulder surfaces being colonized after 7 years. Recolonization was so slow that it was difficult to ascertain grazer impacts, although it appeared there were no impacts. Lastly, this study showed that vegetative regrowth of sponges and encrusting coralline algae was fast. Sponges averaged 100 % regrowth after 2 years and corallines averaged 40 % after 4 years. Coralline regrowth was slower when exposed to higher sedimentation. This study showed that community recovery from disturbances is very slow in the Beaufort Sea, especially if entire organisms are removed. However, if removal is partial, recovery can be quicker, particularly in low sediment areas. Complete community recovery in this system after a disturbance may take a decade or more.     

A comparison of DNA- and RNA-based clone libraries from the same marine bacterioplankton community

Clones from the same marine bacterioplankton community were sequenced, 100 clones based on DNA (16S rRNA genes) and 100 clones based on RNA (16S rRNA). This bacterioplankton community was dominated by alpha-Proteobacteria in terms of repetitive DNA clones (52%), but gamma-Proteobacteria dominated in terms of repetitive RNA clones (44%). The combined analysis led to a characterization of phylotypes otherwise uncharacterized if only the DNA or RNA libraries would have been analyzed alone. Of the DNA clones, 25.5% were found only in this library and no close relatives were detected in the RNA library. For clones from the RNA library, 21.5% of RNA clones did not indicate close relatives in the DNA library. Based on the comparisons between DNA and RNA libraries, our data indicate that the characterization of the bacterial community based on RNA has the potential to characterize distinct phylotypes from the marine environment, which remain undetected on the DNA level.     

Influence of salinity on bacterioplankton communities from the Brazilian rain forest to the coastal Atlantic Ocean

Background

Planktonic bacteria are recognized as important drivers of biogeochemical processes in all aquatic ecosystems, however, the taxa that make up these communities are poorly known. The aim of this study was to investigate bacterial communities in aquatic ecosystems at Ilha Grande, Rio de Janeiro, Brazil, a preserved insular environment of the Atlantic rain forest and how they correlate with a salinity gradient going from terrestrial aquatic habitats to the coastal Atlantic Ocean.

Methodology/Principal Findings

We analyzed chemical and microbiological parameters of water samples and constructed 16S rRNA gene libraries of free living bacteria obtained at three marine (two coastal and one offshore) and three freshwater (water spring, river, and mangrove) environments. A total of 836 sequences were analyzed by MOTHUR, yielding 269 freshwater and 219 marine operational taxonomic units (OTUs) grouped at 97% stringency. Richness and diversity indexes indicated that freshwater environments were the most diverse, especially the water spring. The main bacterial group in freshwater environments was Betaproteobacteria (43.5%), whereas Cyanobacteria (30.5%), Alphaproteobacteria (25.5%), and Gammaproteobacteria (26.3%) dominated the marine ones. Venn diagram showed no overlap between marine and freshwater OTUs at 97% stringency. LIBSHUFF statistics and PCA analysis revealed marked differences between the freshwater and marine libraries suggesting the importance of salinity as a driver of community composition in this habitat. The phylogenetic analysis of marine and freshwater libraries showed that the differences in community composition are consistent.

Conclusions/Significance

Our data supports the notion that a divergent evolutionary scenario is driving community composition in the studied habitats. This work also improves the comprehension of microbial community dynamics in tropical waters and how they are structured in relation to physicochemical parameters. Furthermore, this paper reveals for the first time the pristine bacterioplankton communities in a tropical island at the South Atlantic Ocean.     

Temporal variability in the diversity and composition of stream bacterioplankton communities

Bacterioplankton in freshwater streams play a critical role in stream nutrient cycling. Despite their ecological importance, the temporal variability in the structure of stream bacterioplankton communities remains understudied. We investigated the composition and temporal variability of stream bacterial communities and the influence of physicochemical parameters on these communities. We used barcoded pyrosequencing to survey bacterial communities in 107 streamwater samples collected from four locations in the Colorado Rocky Mountains from September 2008 to November 2009. The four sampled locations harboured distinct communities yet, at each sampling location, there was pronounced temporal variability in both community composition and alpha diversity levels. These temporal shifts in bacterioplankton community structure were not seasonal; rather, their diversity and composition appeared to be driven by intermittent changes in various streamwater biogeochemical conditions. Bacterial communities varied independently of time, as indicated by the observation that communities in samples collected close together in time were no more similar than those collected months apart. The temporal turnover in community composition was higher than observed in most previously studied microbial, plant or animal communities, highlighting the importance of stochastic processes and disturbance events in structuring these communities over time. Detailed temporal sampling is important if the objective is to monitor microbial community dynamics in pulsed ecosystems like streams.     

Optimization of terminal-restriction fragment length polymorphism analysis for complex marine bacterioplankton communities and comparison with denaturing gradient gel electrophoresis.

The potential of terminal-restriction fragment length polymorphism (T-RFLP) and the detection of operational taxonomic units (OTUs) by capillary electrophoresis (CE) to characterize marine bacterioplankton communities was compared with that of denaturing gradient gel electrophoresis (DGGE). A protocol has been developed to optimize the separation and detection of OTUs between 20 and 1, 632 bp by using CE and laser-induced fluorescence detection. Additionally, we compared T-RFLP fingerprinting to DGGE optimized for detection of less abundant OTUs. Similar results were obtained with both fingerprinting techniques, although the T-RFLP approach and CE detection of OTUs was more sensitive, as indicated by the higher number of OTUs detected. We tested the T-RFLP fingerprinting technique on complex marine bacterial communities by using the 16S rRNA gene and 16S rRNA as templates for PCR. Samples from the Northern and Middle Adriatic Sea and from the South and North Aegean Sea were compared. Distinct clusters were identifiable for different sampling sites. Thus, this technique is useful for rapid evaluation of the biogeographical distribution and relationships of bacterioplankton communities.