Reputational geographies and urban social cohesion

This article adds to recent literature in migration studies on the importance of place and space by drawing on extended interviews with residents in the Alum Rock area of East Birmingham. Our central theme is the exploration of reputational geographies; the symbolic and material boundaries drawn around places as indicators of social status, sites of memories and repositories of affect that can have profound socio-economic as well as emotional consequences for city residents. We argue that research and policy addressing urban social diversity must display a greater sensitivity to the deeply felt affiliations to, and memories of, local settings expressed by our respondents. We conclude that contemporary debates about multiculturalism and urban social cohesion require greater attention to the particularities of place and local identity.     

Geochemistry of Virus–Prokaryote Interactions in Freshwater and Acid Mine Drainage Environments,Ontario, Canada

An extensive water sample survey was conducted in southern Ontario, Canada across a variety of freshwater systems in order to further understand the role of viruses in aquatic environments. Backwards stepwise multiple regression analysis found that VLP (virus-like particle) abundance, phosphate, pH, sulfate, and magnesium are predictors of prokaryotic abundance with the model describing 90% of the variability in the data (R² = 0.90). Statistically significant (P < 0.05) predictors of VLP abundance were mineral saturation indices (SI) of goethite (R² = 0.78) although moderate Pearson component analysis correlations (r) were noted with ferrihydrite, jarosite, and pyrolusite. These relationships indicate that viral inactivation through mineral attachment may be a contributor to the moderate relationship between VLP and prokaryotic abundance (r_s = 0.45). In addition, VLP abundance is shown to have a stronger correlation with minerals SI values than prokaryotes indicating a stronger mineral influence with viruses.     

Phylogenetic beta diversity in bacterial assemblages across ecosystems: deterministic versus stochastic processes

Increasing evidence has emerged for non-random spatial distributions of microbes, but knowledge of the processes that cause variation in microbial assemblage among ecosystems is lacking. For instance, some studies showed that deterministic processes such as habitat specialization are important, while other studies hold that bacterial communities are assembled by stochastic forces. Here we examine the relative influence of deterministic and stochastic processes for bacterial communities from subsurface environments, stream biofilm, lake water, lake sediment and soil using pyrosequencing of the 16S ribosomal RNA gene. We show that there is a general pattern in phylogenetic signal in species ecological niches across recent evolutionary time for all studied habitats, enabling us to infer the influences of community assembly processes from patterns of phylogenetic turnover in community composition. The phylogenetic dissimilarities among-habitat types were significantly higher than within them, and the communities were clustered according to their original habitat types. For communities within-habitat types, the highest phylogenetic turnover rate through space was observed in subsurface environments, followed by stream biofilm on mountainsides, whereas the sediment assemblages across regional scales showed the lowest turnover rate. Quantifying phylogenetic turnover as the deviation from a null expectation suggested that measured environmental variables imposed strong selection on bacterial communities for nearly all sample groups. For three sample groups, spatial distance reflected unmeasured environmental variables that impose selection, as opposed to spatial isolation. Such characterization of spatial and environmental variables proved essential for proper interpretation of partial Mantel results based on observed beta diversity metrics. In summary, our results clearly indicate a dominant role of deterministic processes on bacterial assemblages and highlight that bacteria show strong habitat associations that have likely emerged through evolutionary adaptation.     

A decade of seasonal dynamics and co-occurrences within freshwater bacterioplankton communities from eutrophic Lake Mendota,WI, USA

With an unprecedented decade-long time series from a temperate eutrophic lake, we analyzed bacterial and environmental co-occurrence networks to gain insight into seasonal dynamics at the community level. We found that (1) bacterial co-occurrence networks were non-random, (2) season explained the network complexity and (3) co-occurrence network complexity was negatively correlated with the underlying community diversity across different seasons. Network complexity was not related to the variance of associated environmental factors. Temperature and productivity may drive changes in diversity across seasons in temperate aquatic systems, much as they control diversity across latitude. While the implications of bacterioplankton network structure on ecosystem function are still largely unknown, network analysis, in conjunction with traditional multivariate techniques, continues to increase our understanding of bacterioplankton temporal dynamics.     

Insights from quantitative metaproteomics and protein-stable isotope probing into microbial ecology

The recent development of metaproteomics has enabled the direct identification and quantification of expressed proteins from microbial communities in situ, without the need for microbial enrichment. This became possible by (1) significant increases in quality and quantity of metagenome data and by improvements of (2) accuracy and (3) sensitivity of modern mass spectrometers (MS). The identification of physiologically relevant enzymes can help to understand the role of specific species within a community or an ecological niche. Beside identification, relative and absolute quantitation is also crucial. We will review label-free and label-based methods of quantitation in MS-based proteome analysis and the contribution of quantitative proteome data to microbial ecology. Additionally, approaches of protein-based stable isotope probing (protein-SIP) for deciphering community structures are reviewed. Information on the species-specific metabolic activity can be obtained when substrates or nutrients are labeled with stable isotopes in a protein-SIP approach. The stable isotopes (¹³C, ¹⁵N, ³⁶S) are incorporated into proteins and the rate of incorporation can be used for assessing the metabolic activity of the corresponding species. We will focus on the relevance of the metabolic and phylogenetic information retrieved with protein-SIP studies and for detecting and quantifying the carbon flux within microbial consortia. Furthermore, the combination of protein-SIP with established tools in microbial ecology such as other stable isotope probing techniques are discussed.     

Community assembly after long-term fragmentation: a case study of tropical rainforest in Xishuangbanna,south-west China

Background: Tropical rainforests represent the most species-rich and at the same time the most fragmented terrestrial biome on Earth. Fragmentation of tropical rainforests is having wide-ranging consequences for the maintenance of local species diversity and community assembly patterns.

Aims: To examine floristic changes and changes in community phylogenetic structure in the forest fragment over the past five decades.

Methods: A new taxonomic diversity algorithm (within-family diversity) was developed to assess floristic changes in the forest fragment. Community phylogenetic structure was then compared before and after fragmentation.

Results: Taxonomic diversity changed greatly among families, with changes occurring randomly across the phylogeny. The forest fragment had higher phylogenetic diversity, higher mean pair-wise phylogenetic distance, but lower mean nearest-neighbour distance. The community phylogenetic structure has changed significantly from clustering to dispersion.

Conclusions: High species turnover occurred in the forest fragment. While shade-tolerant species have been lost, and ruderal and alien species have been added, overall phylogenetic diversity has increased with species being more phylogenetically distant. Competitive exclusion, which was related to the relatively drier conditions in the forest after fragmentation, led the plant community phylogenetic structure to be more dispersed.     

Specificity and localised distribution of mycorrhizal fungi in the soil may contribute to co-existence of orchid species

Co-occurring orchid species tend to occupy different areas and associate with different mycorrhizal fungi, suggesting that orchid mycorrhizal (OrM) fungi may be unevenly distributed within the soil and, therefore, impact the aboveground spatial distribution of orchids. To test this hypothesis, we investigated spatial variations in the community of potential OrM associates within the roots of three co-habitating orchid species (Anacamptis morio, Gymnadenia conopsea, and Orchis mascula) and the surrounding soil in an orchid-rich calcareous grassland in Southern Belgium using 454 amplicon pyrosequencing. Putative OrM fungi were broadly distributed in the soil, although variations in community composition were strongly related to the proximal host plant. The diversity and frequency of sequences corresponding to OrM fungi in the soil declined with increasing distance from orchid plants, suggesting that the clustered distribution of orchid species may to some extent be explained by the localised distribution of species-specific mycorrhizal associates.     

Environmental and spatial characterisation of an unknown fauna using DNA sequencing – an example with Himalayan Hydropsychidae (Insecta: Trichoptera)

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