Abundance and co-occurrence patterns of core and satellite species of ground beetles on small lake islands

New insights into microbial community coalescence in the land-sea continuum

The land-sea continuum constitutes a mixing zone where soil microbial communities encounter, via runoff, those inhabiting marine coastal sediment resulting in community coalescence. Here, we propose an experimental approach, mimicking the land-sea continuum, to study the microbial community coalescence events in different situations, by 16S and 18S rRNA genes metabarcoding. The microbial community structure of sediment diverged with the soil inputs. For prokaryotes, phylogenetic enrichment and amplicon sequence variants (ASVs) replacements characterized the community changes in sediment receiving soil inputs. For fungi, despite phylogenetic enrichment was not observed, the fungal ASVs richness was maintained by soil inputs. Comparison of microbial communities revealed ASVs specific to sediment receiving soil inputs, and also ASVs shared with soil and/or runoff. Among these specific ASVs, four bacterial and one fungal ASVs were identified as indicators of coalescence. Our study provides evidences that coalescence involves the mixing of microorganisms and of the environment.

Macaronesia as a Fruitful Arena for Ecology, Evolution, and Conservation Biology

Research in Macaronesia has led to substantial advances in ecology, evolution and conservation biology. We review the scientific developments achieved in this region, and outline promising research avenues enhancing conservation. Some of these discoveries indicate that the Macaronesian flora and fauna are composed of rather young lineages, not Tertiary relicts, predominantly of European origin. Macaronesia also seems to be an important source region for back-colonisation of continental fringe regions on both sides of the Atlantic. This group of archipelagos (Azores, Madeira, Selvagens, Canary Islands, and Cabo Verde) has been crucial to learn about the particularities of macroecological patterns and interaction networks on islands, providing evidence for the development of the General Dynamic Model of oceanic island biogeography and subsequent updates. However, in addition to exceptionally high richness of endemic species, Macaronesia is also home to a growing number of threatened species, along with invasive alien plants and animals. Several innovative conservation and management actions are in place to protect its biodiversity from these and other drivers of global change. The Macaronesian Islands are a well-suited field of study for island ecology and evolution research, mostly due to its special geological layout with 40 islands grouped within five archipelagos differing in geological age, climate and isolation. A large amount of data is now available for several groups of organisms on and around many of these islands. However, continued efforts should be made toward compiling new information on their biodiversity, to pursue various fruitful research avenues and develop appropriate conservation management tools.

Small-Scale Variability in Bacterial Community Structure in Different Soil Types

Microbial spatial distribution has mostly been studied at field to global scales (i.e., ecosystem scales). However, the spatial organization at small scales (i.e., centimeter to millimeter scales), which can help improve our understanding of the impacts of spatial communities structure on microbial functioning, has received comparatively little attention. Previous work has shown that small-scale spatial structure exists in soil microbial communities, but these studies have not compared soils from geographically distant locations, nor have they utilized community ecology approaches, such as the core and satellite hypothesis and/or abundance-occupancy relationships, often used in macro-ecology, to improve the description of the spatial organization of communities. In the present work, we focused on bacterial diversity (i.e., 16S rRNA gene sequencing) occurring in micro-samples from a variety of locations with different pedo-climatic histories (i.e., from semi-arid, alpine, and temperate climates) and physicochemical properties. The forms of ecological spatial relationships in bacterial communities (i.e., occupancy-frequency and abundance-occupancy) and taxa distributions (i.e., habitat generalists and specialists) were investigated. The results showed that bacterial composition differed in the four soils at the small scale. Moreover, one soil presented a satellite mode distribution, whereas the three others presented bimodal distributions. Interestingly, numerous core taxa were present in the four soils among which 8 OTUs were common to the four sites. These results confirm that analyses of the small-scale spatial distribution are necessary to understand consequent functional processes taking place in soils, affecting thus ecosystem functioning.

Patterns in diversity and species composition in soft-sediment tidepool fishes across topographical types: Implications for conservation with spatial nuances

Fish communities inhabiting soft-sediment areas are representative conservation targets for coastal habitats, but how the ecological function of soft-sediment tidepools drives diversity is still unknown. To tackle this issue, the ecological functions of soft-sediment tidepools for fishes according to topographic types (open and closed habitats) on Okinawa-jima Island, located in subtropical Japan, were examined in diversity, species composition, and lifestyle (resident and transient species). Landward tidepools serve as permanent habitat for specialists, whereas seaward tidepools are more important for transient species as temporal habitats, which shaped the inverse trend in α- and β-diversity between topographic types, depending on the habitat heterogeneity and the biological characteristics of resident and transient species. We propose a strategy for the conservation and management of topographically distinct intertidal habitats, basically as a single set, while also considering the ecological functions with spatial nuances at smaller scales within coastal landscapes.

Core and occasional species: A new way forward

Various methods have been used to divide communities into core species and occasional or satellite species. Some methods are somewhat arbitrary, and there is evidence that many communities are more multimodal than bimodal. They also tend to rely on having multiple years of data.A completely novel method is presented that not only has no requirement for long-term datasets but can divide communities into multiple groups. It is based on probability a species is present, calculated using Simpson's index and the sequential removal of species from the data.The sequential Simpson's index method was applied to species data from a grassland insect community. It was also applied to eleven other datasets that had been divided into core and occasional species in previously published studies.The new method was found not only to be consistent with previous core-occasional assessments but also able to identify multimodality in species abundance distributions.Although ideally used with a measure of persistence (frequency of occurrence) to rank species, community structure is consistently described even with only species abundance data.The method can be applied to short or long-term datasets and can help identify multimodality and provide valuable insight into how communities change in time or space.

Elements of fish metacommunity structure in Neotropical freshwater streams

The identification of the mechanisms underlying patterns of species co-occurrence is a way to identify which process(es) (niche, neutral, or both) structure metacommunities. The current paper had the goal of identifying patterns of co-occurrence in Neotropical stream fish and determining which processes structure the fish metacommunity, and identifying any gradients underlying this structure. Results indicated that the metacommunity formed by the species pool was structured by a pattern of nested co-occurrence (hyperdispersed species loss) and a mass-effect mechanism. However, a set of core species, displaying a Clementsian pattern, was structured by a species-sorting mechanism. Both, hyperdispersed species loss and the Clementsian patterns point to a discrete set of communities within the metacommunity. These communities could be isolated by the water physicochemical conditions or morphological characteristics of the stream channel.

Long-Term Changes of Species Composition and Functional Traits of Epiphytic Diatoms in the Szigetköz Region (Hungary) of the Danube River

Here we report the results of our decades-long study on epiphytic communities from two tributary systems of the Szigetköz section of the Danube River. The main goal of the investigation was to detect changes in the epiphytic communities at structural (core species, changes in the relative abundance of common species) and functional (trait changes) levels as a result of the most important anthropogenic effects on Szigetköz, i.e., hydro-morphological modifications. We also examined the impact of rehabilitation on the tributary systems in terms of ecological potential. We discovered that mainly motile diatom species characterized the epiphyton due to reduced water volume were introduced into the tributary system after the diversion of the Danube. The ecosystem stabilized in the rehabilitated section, while the non-rehabilitated section showed a worsening tendency, mainly in the parapotamic branches. Our long-term data sets may provide a good basis for comparisons of different aquatic ecosystems, to define changes in the abundance of core species and in the structure of community in response to different anthropogenic pressures. It is fundamental to determine adaptive traits in assessing the impact of global warming stressors on biodiversity.

Local and Landscape Drivers of Carabid Activity, Species Richness, and Traits in Urban Gardens in Coastal California

Urban ecosystems, as mosaics of residential, industrial, commercial, and agricultural land, present challenges for species survival due to impervious surface, degradation, fragmentation, and modification of natural habitat, pollution, and introduced species. Some urban habitats, such as community gardens, support biodiversity and promote ecosystem services. In gardens, local factors (e.g., vegetation, groundcover) and landscape surroundings (e.g., agriculture, built or impervious cover) may influence species abundance, richness, and functional traits that are present. We examined which local and landscape factors within 19 community gardens in the California central coast influence ground beetle (Carabidae) activity density, species richness, functional group richness, and functional traits—body size, wing morphology, and dispersal ability. Gardens with higher crop richness and that are surrounded by agricultural land had greater carabid activity density, while species and functional group richness did not respond to any local or landscape factor. Gardens with more leaf litter had lower carabid activity, and gardens with more leaf litter tended to have more larger carabids. Changes in local (floral abundance, ground cover) and landscape (urban land cover) factors also influenced the distribution of individuals with certain wing morphology and body size traits. Thus, both local and landscape factors influence the taxonomic and functional traits of carabid communities, with potential implications for pest control services that are provided by carabids.

Deciphering the Assembly Processes of the Key Ecological Assemblages of Microbial Communities in Thirteen Full-Scale Wastewater Treatment Plants

Limited information is currently available on the assembly processes (deterministic vs. stochastic) shaping the compositions of key microbial communities in activated sludge (AS). The relative importance of deterministic and stochastic processes for key bacterial and archaeal assemblages (i.e., core-satellite and habitat generalist-specialist) in AS from 13 wastewater treatment plants in China was investigated using 16S rDNA amplicon sequencing. The results obtained indicated 1,388 and 369 core operational taxonomic units (OTUs), 1,038 and 1,683 satellite OTUs, 255 and 48 habitat generalist OTUs, and 192 and 111 habitat specialist OTUs for Bacteria and Archaea, respectively. The proportions of shared OTUs between core and habitat specialist communities were similar to or higher than those between core and habitat generalist communities, suggesting a stronger inter-linkage between the former two groups. Deterministic processes, indicated by abundance-based β-null models, were responsible for shaping core communities, in which NH₄-N, OrgC/OrgN, Cr, and Ni were the main controlling factors. In contrast, satellite communities were predominantly influenced by stochastic processes. Moreover, we found that deterministic and stochastic processes were mainly responsible for shaping the assembly of habitat specialists and generalists, respectively. However, the influence of deterministic factors on habitat specialists remains unclear. The present study provides novel insights into the assembly mechanisms of AS microbial communities.

Succession of Mite Assemblages (Acari, Mesostigmata) during Decomposition of Tree Leaves in Forest Stands Growing on Reclaimed Post-Mining Spoil Heap and Adjacent Forest Habitats

Mites significantly contribute, prevalently by vertical movement, to mixing of the organic layer with the mineral soil, thus they may be important in renewing soils. Our aim was to analyze the changes in abundance and species richness of mesostigmatid assemblages on decomposing leaves of Alnus glutinosa (L.) Gaertn., Betula pendula Roth, Pinus sylvestris L. and Quercus robur L. in pine and birch stands growing on a reclaimed spoil heap and adjacent forests. In December 2013, 1024 litterbags (mesh size = 1 mm) containing leaf litter of broadleaved and coniferous trees (mean initial dry weight per sample = 5.789 g) were laid out in the same number and kind in each of the two sites. Mites were extracted from litterbags which were collected every 3–6 months for 3 years. In total, 6466 mites were identified in 59 taxa. Total abundance was higher on forest habitats (5174 specimens) compared to the spoil (1292), and in birch compared to pine stands, both in forest (3345, 1829, respectively) and spoil habitats (981, 311). Throughout the experiment, mites were most abundant on oak litter samples (2063 specimens), while the remaining litter types had similar abundances (1455–1482). At the beginning of the experiment (3–6 months) mite abundance was very low, but was higher on forest habitats. The highest abundance was found after 9 months—144 specimens in pine stands on the spoil heap and 685 in birch stands on forest habitats. During the study, 49 taxa were found on forest and 29 on heap habitats. In birch stands, 37 and 22 taxa were found, whereas in pine 30 and 21, on forest and heap, respectively. The most frequent species on the heap were Amblyseius tubae Karg, Asca bicornis Canestrini et Fanzago, and Asca aphidioides Linneaeus, whereas in forest habitat—Zercon peltatus C.L. Koch, Veigaia nemorensis C.L. Koch, and Trachytes aegrota C.L. Koch. Habitat conditions, tree species and litter type significantly determined the mesostigmatid species composition, richness and abundance. By selection of dominant tree species during afforestation, it is possible to significantly affect the soil fauna composition, and thus indirectly the rate of decomposition.

Plant Rhizosphere Selection of Plasmodiophorid Lineages from Bulk Soil: The Importance of "Hidden" Diversity

Microbial communities closely associated with the rhizosphere can have strong positive and negative impacts on plant health and growth. We used a group-specific amplicon approach to investigate local scale drivers in the diversity and distribution of plasmodiophorids in rhizosphere/root and bulk soil samples from oilseed rape (OSR) and wheat agri-systems. Plasmodiophorids are plant- and stramenopile-associated protists including well known plant pathogens as well as symptomless endobiotic species. We detected 28 plasmodiophorid lineages (OTUs), many of them novel, and showed that plasmodiophorid communities were highly dissimilar and significantly divergent between wheat and OSR rhizospheres and between rhizosphere and bulk soil samples. Bulk soil communities were not significantly different between OSR and wheat systems. Wheat and OSR rhizospheres selected for different plasmodiophorid lineages. An OTU corresponding to Spongospora nasturtii was positively selected in the OSR rhizosphere, as were two genetically distinct OTUs. Two novel lineages related to Sorosphaerula veronicae were significantly associated with wheat rhizosphere samples, indicating unknown plant-protist relationships. We show that group-targeted eDNA approaches to microbial symbiont-host ecology reveal significant novel diversity and enable inference of differential activity and potential interactions between sequence types, as well as their presence.

Exploring the Ecological Coherence between the Spatial and Temporal Patterns of Bacterioplankton in Boreal Lakes

One of the major contemporary challenges in microbial ecology has been to discriminate the reactive core from the random, unreactive components of bacterial communities. In previous work we used the spatial abundance distributions of bacterioplankton across boreal lakes of Québec to group taxa into four distinct categories that reflect either hydrology-mediated dispersal along the aquatic network or environmental selection mechanisms within lakes. Here, we test whether this categorization derived from the spatial distribution of taxa is maintained over time, by analyzing the temporal dynamics of the operational taxonomic units (OTUs) within those spatially derived categories along an annual cycle in the oligotrophic lake Croche (Québec, Canada), and assessing the coherence in the patterns of abundance, occurrence, and environmental range of these OTUs over space and time. We report that the temporal dynamics of most taxa within a single lake are largely coherent with those derived from their spatial distribution over large spatial scales, suggesting that these properties must be intrinsic of particular taxa. We also identified a set of rare taxa cataloged as having a random occupancy based on their spatial distribution, but which showed clear seasonality and abundance peaks along the year, yet these comprised a very small fraction of the total rare OTUs. We conclude that the presence of most rare bacterioplankton taxa in boreal lakes is random, since both their temporal and spatial dynamics suggest links to passive downstream transport and persistence in freshwater networks, rather than environmental selection.

Response of Core Microbial Consortia to Chronic Hydrocarbon Contaminations in Coastal Sediment Habitats

Traditionally, microbial surveys investigating the effect of chronic anthropogenic pressure such as polyaromatic hydrocarbons (PAHs) contaminations consider just the alpha and beta diversity and ignore the interactions among the different taxa forming the microbial community. Here, we investigated the ecological relationships between the three domains of life (i.e., Bacteria, Archaea, and Eukarya) using 454 pyrosequencing on the 16S rRNA and 18S rRNA genes from chronically impacted and pristine sediments, along the coasts of the Mediterranean Sea (Gulf of Lion, Vermillion coast, Corsica, Bizerte lagoon and Lebanon) and the French Atlantic Ocean (Bay of Biscay and English Channel). Our approach provided a robust ecological framework for the partition of the taxa abundance distribution into 859 core Operational taxonomic units (OTUs) and 6629 satellite OTUs. OTUs forming the core microbial community showed the highest sensitivity to changes in environmental and contaminant variations, with salinity, latitude, temperature, particle size distribution, total organic carbon (TOC) and PAH concentrations as main drivers of community assembly. The core communities were dominated by Gammaproteobacteria and Deltaproteobacteria for Bacteria, by Thaumarchaeota, Bathyarchaeota and Thermoplasmata for Archaea and Metazoa and Dinoflagellata for Eukarya. In order to find associations among microorganisms, we generated a co-occurrence network in which PAHs were found to impact significantly the potential predator – prey relationship in one microbial consortium composed of ciliates and Actinobacteria. Comparison of network topological properties between contaminated and non-contaminated samples showed substantial differences in the network structure and indicated a higher vulnerability to environmental perturbations in the contaminated sediments.

Bacterial Community Structure at the Microscale in Two Different Soils

The spatial distributions of bacteria in the soil matrix have a role in ecosystem function, for example, at the small scale, through gene transfer or xenobiotic degradation. Soil bacterial biogeography has been evidenced at the large scale, but data are scarce at the small scale. The objective of this work was to determine the spatial pattern of bacterial diversity, in spatially referenced microsamples, in order to define bacterial community spatial traits. Two soils with different physical structures, moderately aggregated (La Côte St André (LCSA)) or poorly aggregated (La Dombes (LD)), were studied. The spatial distribution of bacteria was studied in microsamples (diameter 3 mm) along 10- and 20-cm transects, with a taxonomic microarray. 16S rRNA gene sequencing was used to further study the spatial characteristics of the microbial communities in LD soil. The frequency-occupancy plot, in the LCSA and LD soils, using microarray and sequencing data, followed Hanski's core-satellite theory. The frequency-occupancy distribution plots obtained in two different soils showed bimodality and indicated that the microscale spatial distributions were different, particularly core taxa percentage. Core taxa are widespread and abundant, while satellite taxa are restricted in their distribution. The spread of satellite taxa was at a distance range larger than 5 cm, whereas the core taxa were distributed in a distance range less than 3 mm. Besides, there was a positive abundancy-occupancy relationship at this fine scale. It may be interesting to further evaluate the role of the different bacterial spatial distributions at the fine scale on soil function.

High-rate activated sludge communities have a distinctly different structure compared to low-rate sludge communities, and are less sensitive towards environmental and operational variables

High-rate activated sludge processes allow for the recovery of organics and energy from wastewaters. These systems are operated at a short sludge retention time and high sludge-specific loading rates, which results in a higher sludge yield and better digestibility than conventional, low-rate activated sludge. Little is known about the microbial ecology of high-rate systems. In this work, we address the need for a fundamental understanding of how high-rate microbial communities differ from low-rate communities. We investigated the high-rate and low-rate communities in a sewage treatment plant in relation to environmental and operational variables over a period of ten months. We demonstrated that (1) high-rate and low-rate communities are distinctly different in terms of richness, evenness and composition, (2) high-rate community dynamics are more variable and less shaped by deterministic factors compared to low-rate communities, (3) sub-communities of continuously core and transitional members are more shaped by deterministic factors than the continuously rare members, both in high-rate and low-rate communities, and (4) high-rate community members showed a co-occurrence pattern similar to that of low-rate community members, but were less likely to be correlated to environmental and operational variables. These findings provide a basis for further optimization of high-rate systems, in order to facilitate resource recovery from wastewater.

Spatio-Temporal Variation of Core and Satellite Arbuscular Mycorrhizal Fungus Communities in Miscanthus giganteus

Arbuscular mycorrhizal fungi (AMF) are a group of obligate plant symbionts which can promote plant nutrition. AMF communities are diverse, but the factors which control their assembly in space and time remain unclear. In this study, the contributions of geographical distance, environmental heterogeneity and time in shaping AMF communities associated with Miscanthus giganteus (a perennial grass originating from south-east Asia) were determined over a 13 months period. In particular, the community was partitioned into core (abundant and persistent taxa) and satellite (taxa with low abundance and persistence) constituents and the drivers of community assembly for each determined. β-diversity was exceptionally low across the 140 m line transects, and there was limited evidence of geographical scaling effects on the composition of the core, satellite or combined communities. However, AMF richness and community composition changed over time associated with fluctuation within both the core and satellite communities. The degree to which AMF community variation was explained by soil properties was consistently higher in the core community than the combined and satellite communities, suggesting that the satellite community had considerable stochasticity associated with it. We suggest that the partitioning of communities into their core and satellite constituents could be employed to enhance the variation explained within microbial community analyses.

Historical and contemporary factors generate unique butterfly communities on islands

The mechanisms shaping island biotas are not yet well understood mostly because of a lack of studies comparing eco-evolutionary fingerprints over entire taxonomic groups. Here, we linked community structure (richness, frequency and nestedness) and genetic differentiation (based on mitochondrial DNA) in order to compare insular butterfly communities occurring over a key intercontinental area in the Mediterranean (Italy-Sicily-Maghreb). We found that community characteristics and genetic structure were influenced by a combination of contemporary and historical factors, and among the latter, connection during the Pleistocene had an important impact. We showed that species can be divided into two groups with radically different properties: widespread taxa had high dispersal capacity, a nested pattern of occurrence, and displayed little genetic structure, while rare species were mainly characterized by low dispersal, high turnover and genetically differentiated populations. These results offer an unprecedented view of the distinctive butterfly communities and of the main processes determining them on each studied island and highlight the importance of assessing the phylogeographic value of populations for conservation.

Core-satellite populations and seasonality of water meter biofilms in a metropolitan drinking water distribution system

Drinking water distribution systems (DWDSs) harbor the microorganisms in biofilms and suspended communities, yet the diversity and spatiotemporal distribution have been studied mainly in the suspended communities. This study examined the diversity of biofilms in an urban DWDS, its relationship with suspended communities and its dynamics. The studied DWDS in Urbana, Illinois received conventionally treated and disinfected water sourced from the groundwater. Over a 2-year span, biomass were sampled from household water meters (n=213) and tap water (n=20) to represent biofilm and suspended communities, respectively. A positive correlation between operational taxonomic unit (OTU) abundance and occupancy was observed. Examined under a 'core-satellite' model, the biofilm community comprised 31 core populations that encompassed 76.7% of total 16 S rRNA gene pyrosequences. The biofilm communities shared with the suspended community highly abundant and prevalent OTUs, which related to methano-/methylotrophs (i.e., Methylophilaceae and Methylococcaceae) and aerobic heterotrophs (Sphingomonadaceae and Comamonadaceae), yet differed by specific core populations and lower diversity and evenness. Multivariate tests indicated seasonality as the main contributor to community structure variation. This pattern was resilient to annual change and correlated to the cyclic fluctuations of core populations. The findings of a distinctive biofilm community assemblage and methano-/methyltrophic primary production provide critical insights for developing more targeted water quality monitoring programs and treatment strategies for groundwater-sourced drinking water systems.

Reexamining Sample Size Requirements for Multivariate, Abundance-Based Community Research: When Resources are Limited, the Research Does Not Have to Be

Community ecologists commonly perform multivariate techniques (e.g., ordination, cluster analysis) to assess patterns and gradients of taxonomic variation. A critical requirement for a meaningful statistical analysis is accurate information on the taxa found within an ecological sample. However, oversampling (too many individuals counted per sample) also comes at a cost, particularly for ecological systems in which identification and quantification is substantially more resource consuming than the field expedition itself. In such systems, an increasingly larger sample size will eventually result in diminishing returns in improving any pattern or gradient revealed by the data, but will also lead to continually increasing costs. Here, we examine 396 datasets: 44 previously published and 352 created datasets. Using meta-analytic and simulation-based approaches, the research within the present paper seeks (1) to determine minimal sample sizes required to produce robust multivariate statistical results when conducting abundance-based, community ecology research. Furthermore, we seek (2) to determine the dataset parameters (i.e., evenness, number of taxa, number of samples) that require larger sample sizes, regardless of resource availability. We found that in the 44 previously published and the 220 created datasets with randomly chosen abundances, a conservative estimate of a sample size of 58 produced the same multivariate results as all larger sample sizes. However, this minimal number varies as a function of evenness, where increased evenness resulted in increased minimal sample sizes. Sample sizes as small as 58 individuals are sufficient for a broad range of multivariate abundance-based research. In cases when resource availability is the limiting factor for conducting a project (e.g., small university, time to conduct the research project), statistically viable results can still be obtained with less of an investment.

Network analysis reveals ecological links between N-fixing bacteria and wood-decaying fungi

Nitrogen availability in dead wood is highly restricted and associations with N-fixing bacteria are thought to enable wood-decaying fungi to meet their nitrogen requirements for vegetative and generative growth. We assessed the diversity of nifH (dinitrogenase reductase) genes in dead wood of the common temperate tree species Fagus sylvatica and Picea abies from differently managed forest plots in Germany using molecular tools. By incorporating these genes into a large compilation of published nifH sequences and subsequent phylogenetic analyses of deduced proteins we verified the presence of diverse pools corresponding to functional nifH, almost all of which are new to science. The distribution of nifH genes strongly correlated with tree species and decay class, but not with forest management, while higher fungal fructification was correlated with decreasing nitrogen content of the dead wood and positively correlated with nifH diversity, especially during the intermediate stage of wood decay. Network analyses based on non-random species co-occurrence patterns revealed interactions among fungi and N-fixing bacteria in the dead wood and strongly indicate the occurrence of at least commensal relationships between these taxa.

Life history affects how species experience succession in pen shell metacommunities

In nature, very few species are common and broadly distributed. Most species are rare and occupy few sites; this pattern is ubiquitous across habitats and taxa. In spatially structured communities (metacommunities), regional distribution and local abundance may change as the relative effects of within-habitat processes (e.g., species interactions) and among-habitat processes (e.g., dispersal) may vary through succession. A field experiment with the marine benthic inhabitants of pen shells (Atrina rigida) tested how common and rare species respond to succession and metacommunity size. I followed community development through time and partitioned species into sessile and motile based on their natural history. Rare species drive diversity patterns and are influenced by metacommunity size: there are strong abundance-distribution differences between common and rare species in large metacommunities, but motile species show lower rates of change than sessile species. In small metacommunities both common and rare species have similar changes through time; the dichotomous distinction of common and rare species is not present. Edge effects in metacommunities affect species' changes in distribution and abundance. In large metacommunities diversity is higher in edge habitats relative to small metacommunities during early succession. However, edge effects benefit motile species over time in small metacommunities showing a rapid increase in diversity. Individual mobility is sensitive to regional community size and allows individuals to sort among different communities. In contrast, sessile species do not show this edge effect. Metacommunity theory is a useful framework for understanding spatially structured communities, but the natural history of coexisting species cannot be ignored.

Reducing bias in bacterial community analysis of lower respiratory infections

High-throughput pyrosequencing and quantitative PCR (Q-PCR) analysis offer greatly improved accuracy and depth of characterisation of lower respiratory infections. However, such approaches suffer from an inability to distinguish between DNA derived from viable and non-viable bacteria. This discrimination represents an important step in characterising microbial communities, particularly in contexts with poor clearance of material or high antimicrobial stress, as non-viable bacteria and extracellular DNA can contribute significantly to analyses. Pre-treatment of samples with propidium monoazide (PMA) is an effective approach to non-viable cell exclusion (NVCE). However, the impact of NVCE on microbial community characteristics (abundance, diversity, composition and structure) is not known. Here, adult cystic fibrosis (CF) sputum samples were used as a paradigm. The effects of PMA treatment on CF sputum bacterial community characteristics, as analysed by pyrosequencing and enumeration by species-specific (Pseudomonas aeruginosa) and total bacterial Q-PCR, were assessed. At the local community level, abundances of both total bacteria and of P. aeruginosa were significantly lower in PMA-treated sample portions. Meta-analysis indicated no overall significant differences in diversity; however, PMA treatment resulted in a significant alteration in local community membership in all cases. In contrast, at the metacommunity level, PMA treatment resulted in an increase in community evenness, driven by an increase in diversity, predominately representing rare community members. Importantly, PMA treatment facilitated the detection of both recognised and emerging CF pathogens, significantly influencing 'core' and 'satellite' taxa group membership. Our findings suggest failure to implement NVCE may result in skewed bacterial community analyses.

Cystic fibrosis therapy: a community ecology perspective

Current therapy for cystic fibrosis (CF) focuses on minimizing the microbial community and the host's immune response through the aggressive use of airway clearance techniques, broad-spectrum antibiotics, and treatments that break down the pervasive endobronchial biofilm. Antibiotic selection is typically based on the susceptibility of individual microbial strains to specific antibiotics in vitro. Often this approach cannot accurately predict medical outcomes because of factors both technical and biological. Recent culture-independent assessments of the airway microbial and viral communities demonstrated that the CF airway infection is considerably more complex and dynamic than previously appreciated. Understanding the ecological and evolutionary pressures that shape these communities is critically important for the optimal use of current therapies (in both the choice of therapy and timing of administration) and the development of newer strategies. The climax-attack model (CAM) presented here, grounded in basic ecological principles, postulates the existence of two major functional communities. The attack community consists of transient viral and microbial populations that induce strong innate immune responses. The resultant intense immune response creates microenvironments that facilitate the establishment of a climax community that is slower-growing and inherently resistant to antibiotic therapy. Newer methodologies, including sequence-based metagenomic analysis, can track not only the taxonomic composition but also the metabolic capabilities of these changing viral and microbial communities over time. Collecting this information for CF airways will enable the mathematical modeling of microbial community dynamics during disease progression. The resultant understanding of airway communities and their effects on lung physiology will facilitate the optimization of CF therapies.

Biological diversity of fish communities: pattern and process

For over 150 years, ecologists have been striving to explain fundamental patterns of biological diversity, such as the observation that communities invariably consist of common and rare species, and to unravel the processes that underpin these patterns. This task is increasingly urgent given the accelerating loss of biological diversity. Although fishes are the most diverse vertebrate taxon and fish communities occur in a wide range of habitats, they have been relatively little studied in the quest to elucidate the processes that shape patterns of biological diversity. Here, some of the topics that investigations of fish assemblages can illuminate are highlighted. These include the characteristics of ecological communities and the role that dispersal limitation plays in structuring them, the distinction between core and occasional species, the insights that evaluating abundance in different currencies can bring and the assessment of community capacity. Questions are identified that future investigations of fish communities might tackle and a case study of a biodiverse ecoregion (Thailand and Peninsula Malaysia) is used to illustrate the need for better links between these ecological questions and effective conservation practice.

The macroecology of rapid evolutionary radiation

A long-standing debate in ecology addresses whether community composition is the result of stochastic factors or assembly rules. Non-random, over-dispersed patterns of species co-occurrence have commonly been attributed to competition--a particularly important force in adaptive radiation. We thus examined the macroecology of the recently radiated cichlid rock-fish assemblage in Lake Malawi, Africa at a spectrum of increasingly fine spatial scales (entire lake to depth within rock-reef sites). Along this range of spatial scales, we observed a signal of community structure (decreased co-occurrence of species) at the largest and smallest scales, but not in between. Evidence suggests that the lakewide signature of structure is driven by extreme endemism and micro-allopatric speciation, while patterns of reduced co-occurrence with depth are indicative of species interactions. We identified a 'core' set of rock-reef species, found in combination throughout the lake, whose depth profiles exhibited replicated positive and negative correlation. Our results provide insight into how ecological communities may be structured differently at distinct spatial scales, re-emphasize the importance of local species interactions in community assembly, and further elucidate the processes shaping speciation in this model adaptive radiation.

Partitioning core and satellite taxa from within cystic fibrosis lung bacterial communities

Cystic fibrosis (CF) patients suffer from chronic bacterial lung infections that lead to death in the majority of cases. The need to maintain lung function in these patients means that characterising these infections is vital. Increasingly, culture-independent analyses are expanding the number of bacterial species associated with CF respiratory samples; however, the potential significance of these species is not known. Here, we applied ecological statistical tools to such culture-independent data, in a novel manner, to partition taxa within the metacommunity into core and satellite species. Sputa and clinical data were obtained from 14 clinically stable adult CF patients. Fourteen rRNA gene libraries were constructed with 35 genera and 82 taxa, identified in 2139 bacterial clones. Shannon–Wiener and taxa-richness analyses confirmed no undersampling of bacterial diversity. By decomposing the distribution using the ratio of variance to the mean taxon abundance, we partitioned objectively the species abundance distribution into core and satellite species. The satellite group comprised 67 bacterial taxa from 33 genera and the core group, 15 taxa from 7 genera (including Pseudomonas (1 taxon), Streptococcus (2), Neisseria (2), Catonella (1), Porphyromonas (1), Prevotella (5) and Veillonella (3)], the last four being anaerobes). The core group was dominated by Pseudomonas aeruginosa. Other recognised CF pathogens were rare. Mantel and partial Mantel tests assessed which clinical factors influenced the composition observed. CF transmembrane conductance regulator genotype and antibiotic treatment correlated with all core taxa. Lung function correlated with richness. The clinical significance of these core and satellite species findings in the CF lung is discussed.

The empirical Bayes approach as a tool to identify non-random species associations

A statistical challenge in community ecology is to identify segregated and aggregated pairs of species from a binary presence-absence matrix, which often contains hundreds or thousands of such potential pairs. A similar challenge is found in genomics and proteomics, where the expression of thousands of genes in microarrays must be statistically analyzed. Here we adapt the empirical Bayes method to identify statistically significant species pairs in a binary presence-absence matrix. We evaluated the performance of a simple confidence interval, a sequential Bonferroni test, and two tests based on the mean and the confidence interval of an empirical Bayes method. Observed patterns were compared to patterns generated from null model randomizations that preserved matrix row and column totals. We evaluated these four methods with random matrices and also with random matrices that had been seeded with an additional segregated or aggregated species pair. The Bayes methods and Bonferroni corrections reduced the frequency of false-positive tests (type I error) in random matrices, but did not always correctly identify the non-random pair in a seeded matrix (type II error). All of the methods were vulnerable to identifying spurious secondary associations in the seeded matrices. When applied to a set of 272 published presence-absence matrices, even the most conservative tests indicated a fourfold increase in the frequency of perfectly segregated "checkerboard" species pairs compared to the null expectation, and a greater predominance of segregated versus aggregated species pairs. The tests did not reveal a large number of significant species pairs in the Vanuatu bird matrix, but in the much smaller Galapagos bird matrix they correctly identified a concentration of segregated species pairs in the genus Geospiza. The Bayesian methods provide for increased selectivity in identifying non-random species pairs, but the analyses will be most powerful if investigators can use a priori biological criteria to identify potential sets of interacting species.

Comments about some species abundance patterns: classic, neutral, and niche partitioning models

The literature on species abundance models is extensive and a great deal of new and important contributions have been published in the last three decades. Broadly speaking, one can recognize five families of species abundance models: i) purely statistical or classic models (Broken-stick, Log-normal, Logarithmic and Geometric series); ii) branching process (Zipf-Mandelbrot and Fractal branching models); iii) population dynamics (Neutral models included); iv) spatial distribution of individuals (Multifractal and HEAP models) and v) niche partitioning (Sugihara's breakage and Tokeshi models). Among these the neutral, the classic and the niche partitioning models have been the most applied to natural communities, the former having been more extensively discussed than the others in the last years. The objective of this paper is to comment some aspects of the classic, neutral and niche partitioning models in a way that the proposed distributions may contribute to the analysis of the empirical patterns of species abundance. In spite of the variety of models, the distributions in general vary between the log-normal and the logarithmic series. From these models the Power-Fraction, together with independent niche dimensions measures, are amenable to experimental tests and may offer answers on which resources are important in the structuring of biological communities.

Island Colonization of Carabidae: Neutrality or Habitat Choice?

Carabidae of 15 island and two forested mainland sites from the largest archipelago in Poland, the Mazurian Lake Mamry, were sampled to infer whether island colonization can be linked to habitat heterogeneity and island isolation or whether a previously applied neutral model explains observed spatial distributions best. Kruskall-Wallis rank tests and regression analysis did not point to wing development (a proxy for dispersal ability), island isolation, and heterogeneity as significant factors that influence occupancy. Subsequent analysis of species co-occurrences and nestedness pointed to random pairwise species associations. Co-occurrence analysis of all species pairs found many fewer significantly non-random species pairs (at the 5% error benchmark) than expected by chance. These results do not point to habitat selection by ground beetles but rather favor the view that island colonization is a random process that is best modeled from a neutral perspective.

Characterization of the complex bacterial communities colonizing biliary stents reveals a host-dependent diversity

This study provides a comprehensive survey of the spatial and temporal bacterial composition of biliary stent biofilms. The bacterial diversity, distribution and dynamics of 59 biliary and 4 pancreatic stent communities from 40 patients being treated at two different hospitals, which implant stents either simultaneously or consecutively, were characterized by single-strand conformation polymorphism (SSCP) analysis. Fifty-one phylotypes belonging to 5 bacterial phyla and 24 bacterial families were detected across 63 stents. This is a much broader diversity than previously detected through culture-dependent methods, particularly in regard to the diversity of obligate anaerobes. Stent bacterial diversity was patient-dependent and more similar when stents were implanted simultaneously rather than consecutively. Stent bacterial community composition differed between hospitals specifically because of the difference in abundance of Bifidobacteria. Co-colonization of Veillonella sp., Streptococcus anginosus and organisms closely related to Fusobacterium nucleatum revealed a potentially important attachment and survival strategy that has yet to be reported in biliary stents. This work reveals a more complete survey of the identities of bacterial species that form biofilms in biliary stents, their co-colonization patterns and the natural variation in species composition between different patients, hospitals and locations along the stent. Consideration of the community composition from individual patients will allow tailoring of prophylactic antibiotic treatments and thus will make the management of stent biofilms more effective.