Ecological succession of fungal and bacterial communities in Antarctic mosses affected by a fairy ring disease

Extremophiles - We evaluated fungal and bacterial diversity in an established moss carpet on King George Island, Antarctica, affected by ‘fairy ring’ disease using metabarcoding. A...     

Abrupt induction of GDP-fucose: Asialo GM1 fucosyltransferase in the small intestine after conventionalization of germ-free mice

We studied the time-course of the induction of GDP-fucose: asialo GM1 fucosyltransferase and its product, i.e. fucosyl asialo GM1, of the small intestine after introduction of microorganisms to germ-free mice (conventionalization). We found that the fucosyltransferase activity was abruptly induced and asialo GM1 was converted into fucosyl asialo GM1 within a few days after conventionalization. However, two weeks after conventionalization this enzyme activity dropped to approximately 10^?2 level of the maximum value and asialo GM1 appeared again as one of the major glycolipids. These results showed that the microbial colonization in the gut evoked a drastic change of the glycolipid pattern at the intestinal epithelial cell-surface via the induction of a fucosyltransferase.     

Ecological succession in long-term experimentally evolved biofilms produces synergistic communities

Many biofilm populations are known for their exceptional biodiversity, but the relative contributions of the forces that could produce this diversity are poorly understood. This uncertainty grows in the old, well-established communities found on many natural surfaces and in long-term, chronic infections. If the prevailing interactions among species within biofilms are positive, productivity should increase with diversity, but if they tend towards competition or antagonism, productivity should decrease. Here, we describe the parallel evolution of synergistic communities derived from a clone of Burkholderia cenocepacia during ∼1500 generations of biofilm selection. This long-term evolution was enabled by a new experimental method that selects for daily cycles of colonization, biofilm assembly and dispersal. Each of the six replicate biofilm populations underwent a common pattern of adaptive morphological diversification, in which three ecologically distinct morphotypes arose in the same order of succession and persisted. In two focal populations, mixed communities were more productive than any monoculture and each variant benefited from the mixture. These gains in output resulted from asymmetrical cross-feeding between ecotypes and the expansion and partitioning of biofilm space that constructed new niches. Therefore, even in the absence of starting genetic variation, prolonged selection for surface colonization generates a dynamic of ecological succession that enhances productivity.     

Allogenic succession of marine bacterial communities in response to pharmaceutical waste

Vibrio spp. predominated in the culturable bacterial community of surface waters of the Puerto Rico Trench at the site of disposal for nearly ten years of pharmaceutical wastes. In this area and surrounding waters as far as 1000 km north of the dumpsite and south into the Caribbean Sea, Vibrio spp. comprised up to 100% of the culturable bacteria, with Acinetobacter spp. being the second most prevalent group. Pseudomonas spp., reported to be common in these waters a decade earlier, were virtually absent from all samples examined during a three year study involving 9 cruises. Staphylococcus spp. were also found in water samples collected within the dumpsite. Using cultures isolated from surface water samples collected at the dumpsite, laboratory experiments confirmed that pharmaceutical waste can enrich for Vibrio spp., in preference to Pseudomonas spp., with growth of the strains proportional to the amount of waste added.     

Allogenic succession of marine bacterial communities in response to pharmaceutical waste

Vibrio spp. predominated in the culturable bacterial community of surface waters of the Puerto Rico Trench at the site of disposal for nearly ten years of pharmaceutical wastes. In this area and surrounding waters as far as 1000 km north of the dumpsite and south into the Caribbean Sea, Vibrio spp. comprised up to 100% of the culturable bacteria, with Acinetobacter spp. being the second most prevalent group. Pseudomonas spp., reported to be common in these waters a decade earlier, were virtually absent from all samples examined during a three year study involving 9 cruises. Staphylococcus spp. were also found in water samples collected within the dumpsite. Using cultures isolated from surface water samples collected at the dumpsite, laboratory experiments confirmed that pharmaceutical waste can enrich for Vibrio spp., in preference to Pseudomonas spp., with growth of the strains proportional to the amount of waste added.     

Species associations during the succession of wood-inhabiting fungal communities

We studied fungal succession in decaying wood by compiling time-series data of fruit body observations. We tested the hypothesis that the presence of a primary species affects the probability of a succeeding species occurring later on the same log. Significant associations were detected for 15 species pairs; these were consistent with earlier findings on co-occurrence patterns in single time surveys. We used enrichment analysis to test if species with particular life-history attributes were more often associated with the occurrence of a succeeding species, or vice versa. White rot fungi and fungi abundant as mycelia were more often associated with the occurrence of succeeding species, compared to brown rot fungi and species with low mycelial abundance. Our results indicate that certain primary species cause priority effects and non-random co-occurrence patterns in the field. These successional patterns are likely to be connected both with substrate modification and species interactions.     

Phylogenetic structure of angiosperm communities during tropical forest succession

The phylogenetic structure of ecological communities can shed light on assembly processes, but the focus of phylogenetic structure research thus far has been on mature ecosystems. Here, I present the first investigation of phylogenetic community structure during succession. In a replicated chronosequence of 30 sites in northeastern Costa Rica, I found strong phylogenetic overdispersion at multiple scales: species present at local sites were a non-random assemblage, more distantly related than chance would predict. Phylogenetic overdispersion was evident when comparing the species present at each site with the regional species pool, the species pool found in each age category to the regional pool or the species present at each site to the pool of species found in sites of that age category. Comparing stem size classes within each age category, I found that during early succession, phylogenetic overdispersion is strongest in small stems. Overdispersion strengthens and spreads into larger size classes as succession proceeds, corroborating an existing model of forest succession. This study is the first evidence that succession leaves a distinct signature in the phylogenetic structure of communities.     

Influence of conventionalization on small-intestinal mucosa of germ-free Wistar rats: quantitative light microscopic observations

Germ-free rats were inoculated with microbial flora from feces of conventionally reared rats and the mucosal structure was quantitatively observed at different time intervals after the inoculation and at different regions of the small intestine. In the ileum, desquamation figures were frequently seen on the villus tip, and several parameters of the mucosal elements, i.e., villus and crypt lengths, mitotic figures, goblet cells and thickness of lamina propria were significantly increased after the inoculation. On the other hand, in the duodenum and jejunum, such parameters except for the lamina propria showed no remarkable change during the course of the experiment, though the villus/crypt ratio increased temporarily at half a day after the inoculation. These regional differences of the mucosal response to the inoculation may be due to the different populations of microbial flora which settled in each region of the small intestine.     

Trait-based life-history strategies explain succession scenario for complex bacterial communities under varying disturbance

Trait-based approaches are increasingly gaining importance in community ecology, as a way of finding general rules for the mechanisms driving changes in community structure and function under the influence of perturbations. Frameworks for life-history strategies have been successfully applied to describe changes in plant and animal communities upon disturbance. To evaluate their applicability to complex bacterial communities, we operated replicated wastewater treatment bioreactors for 35 days and subjected them to eight different disturbance frequencies of a toxic pollutant (3-chloroaniline), starting with a mixed inoculum from a full-scale treatment plant. Relevant ecosystem functions were tracked and microbial communities assessed through metagenomics and 16S rRNA gene sequencing. Combining a series of ordination, statistical and network analysis methods, we associated different life-history strategies with microbial communities across the disturbance range. These strategies were evaluated using tradeoffs in community function and genotypic potential, and changes in bacterial genus composition. We further compared our findings with other ecological studies and adopted a semi-quantitative competitors, stress-tolerants, ruderals (CSR) classification. The framework reduces complex data sets of microbial traits, functions and taxa into ecologically meaningful components to help understand the system response to disturbance and hence represents a promising tool for managing microbial communities.     

Molecular analysis of bacterial community succession during prolonged compost curing

The compost environment consists of complex organic materials that form a habitat for a rich and diverse microbial community. The aim of this research was to study the dynamics of microbial communities during the compost-curing phase. Three different methods based on 16S rRNA gene sequence were applied to monitor changes in the microbial communities: (1) denaturing gradient gel electrophoresis of PCR-generated rRNA gene fragments; (2) partial rRNA gene clone libraries; and (3) a microarray of oligonucleotide probes targeting rRNA gene sequences. All three methods indicated distinctive community shifts during curing and the dominant species prevailing during the different curing stages were identified. We found a successional transition of different bacterial phylogenetic groups during compost curing. The Proteobacteria were the most abundant phylum in all cases. The Bacteroidetes and the Gammaproteobacteria were ubiquitous. During the midcuring stage, Actinobacteria were dominant. Different members of nitrifying bacteria and cellulose and macromolecule-degrading bacteria were found throughout the curing process. In contrast, pathogens were not detected. In the cured compost, bacterial population shifts were still observed after the compost organic matter and other biochemical properties had seemingly stabilized.     

rRNA‐based analysis to monitor succession of faecal bacterial communities in Holstein calves

Aims: To quantitatively analyse the faecal bacterial communities of Holstein calves and track their succession up to 12 weeks of age. Methods and Results: Faecal samples obtained from four female Holstein calves were analysed by the RNA‐based, sequence‐specific rRNA cleavage method. Twelve scissor probes covering major rumen bacterial groups were used, detecting c. 60–90% of the total 16S rRNAs. At 1 week of age, 16S rRNAs from members of the Bacteroides‐Prevotella group (40·0% of the total 16S rRNAs), Faecalibacterium (21·7%), the Clostridium coccoides–Eubacterium rectale group (16·7%) and the Atopobium cluster (10·9%) were detected at high levels. Throughout the 12‐week period, rRNAs of the Bacteroides‐Prevotella and the Cl. coccoides‐Eu. rectale groups constituted the major fraction of microbiota (c. 50–70% of the total). The relative abundances of the Atopobium cluster, Faecalibacterium, and some probiotic bacteria (such as those of the genera Lactobacillus and Bifidobacterium) decreased as the animal aged. Instead, an uncultivated rumen bacterial group, as well as Ruminococcus flavefaciens and Fibrobacter emerged at the detectable levels (1–2%) in the faeces sampled at a postweaning age. In addition, certain bacterial groups that were not covered by the probe suite increased as the animals aged. Conclusions: Young calves undergo dynamic changes in their intestinal bacterial community during the first 12 weeks of life. As young ruminants undergo metabolic and physiological development in their digestive tracts in the transition from a monogastric to a ruminant animal at an early age, the intestinal bacterial community may reflect such development. Significance and Impact of the Study: The succession of the bacterial communities in the faeces of calves was quantitatively monitored in the present study for the first time. The approach used here was demonstrated to be a useful means for determining the populations of predominant faecal bacterial groups in a variety of calf experiments in response to diet, stress and disease.     

Changes in the seasonal rhythm of two forest communities during secondary succession

Changes in the seasonal rhythm of two plant phytocoenoses in a submountain beech forest during secondary succession were studied. Investigations were done on four monitoring plots with different stand density over the period of four successive years. The rhythm of the associations Dentario bulbiferae-Fagetum and Carici pilosae-Fagetum reflects the course of succession processes running six years after the human impact (cutting) in the ecosystem. Results of the phenological observations of the understorey species with the focus on the changes in flowering and colour spectrum allowed to make the comparisons between both associations in connection with different phyto-climatic conditions and in dependence on time. The most conspicuous changes in the seasonal rhythm and structure of the examined associations were found in conditions of the former clear-cut, currently in succession phase. A clear decrease (56%) in number of taxons with the dominance > 1% in one association towards the end of the 4-year study period was detected here. Simultaneously, a decrease in the number of flowering species was observed, while the relative rate of species being in the vegetative stage increased considerably (from 6 to 67%) over the growing season. The course of flowering of both of the associations missed discernible trends and peaks as well as colour spectra were partially changed during four monitored successive years on the formerly unstocked area.     

Evidence for community assembly constraints during succession in dune slack plant communities

Community assembly during succession can be constrained by both local and regional factors. Despite an increasing regional species pool size during succession, we found a limit on the number of species in 1 × 1 m plots in dune slacks. Three alternative hypotheses (habitat heterogeneity, dispersal limitation and niche limitation) explaining this community saturation were tested. A null model analysis showed that species richness in the plots had an unusually low variance suggesting that beta habitat diversity was not likely to explain the limitation on species richness. Because we did not find a correlation between the distribution of species over the slack and their dispersal capacity, we also excluded the dispersal limitation hypothesis. Finally, a guild proportionality analysis revealed that the abundances of forb, graminoid and ruderal species showed low an unusually low variance over all age classes involved. This provides evidence for nonrandom community assembly during succession, likely to be determined by competitive exclusion among species of the same guild.     

Changing assembly processes during a primary succession of plant communities on Mediterranean roadcuts

Aims Studying plant ecological succession provides insights into the spatiotemporal processes underlying community assembly and is of primary importance for restoration ecology. We investigate here colonization events and local community assembly over an original primary succession occurring on roadcuts after roadwork. For this, we addressed both the changes in species presence-absence (incidence data) to highlight pre-establishment filters and in species relative abundances to further assess the influence of local biotic processes.Methods We studied 43 limestone roadcuts in Mediterranean France, covering five age classes up to an age of 80 years, along with 13 natural cliffs as a reference, and we counted 14322 plant individuals on these sites. We applied a constrained nonsymmetric correspondence analysis of both the incidence (presence-absence) and abundance data to assess the variation of these data along the chronosequence.Important findings Along the first 30 years, the initially abundant short-lived species declined both in terms of incidence and abundance and were replaced by longer lived herbaceous and woody species. This first phase was characterized by species that are widespread in the surrounding scrublands and was comparable to an early secondary succession there. After 30 years, there were continuing changes in incidence data with age, but no more significant change in species' abundances. This second phase was marked by the late colonization of specialists that did not become dominant. Although colonization and establishment limitation was thereby apparent for specialist species, a slow convergence of community composition toward the situation of natural cliffs could be detected in the older stages of the chronosequence. These findings convey insights into the natural dynamics of man-made outcrop plant communities and may be useful for the ecological management and restoration of such contexts. It also illustrates the interest of comparing incidence and abundance data to investigate the relative influence of ecological determinants on the assembly of plant communities.     

Elevated success of multispecies bacterial invasions impacts community composition during ecological succession

Successful microbial invasions are determined by a species’ ability to occupy a niche in the new habitat whilst resisting competitive exclusion by the resident community. Despite the recognised importance of biotic factors in determining the invasiveness of microbial communities, the success and impact of multiple concurrent invaders on the resident community has not been examined. Simultaneous invasions might have synergistic effects, for example if resident species need to exhibit divergent phenotypes to compete with the invasive populations. We used three phylogenetically diverse bacterial species to invade two compositionally distinct communities in a controlled, naturalised in vitro system. By initiating the invader introductions at different stages of succession, we could disentangle the relative importance of resident community structure, invader diversity and time pre‐invasion. Our results indicate that multiple invaders increase overall invasion success, but do not alter the successional trajectory of the whole community.