Bacterial community dynamics in full-scale activated sludge bioreactors: operational and ecological factors driving community assembly and performance

The assembling of bacterial communities in conventional activated sludge (CAS) bioreactors was thought, until recently, to be chaotic and mostly unpredictable. Studies done over the last decade have shown that specific, and often, predictable random and non-random factors could be responsible for that process. These studies have also motivated a "structure-function" paradigm that is yet to be resolved. Thus, elucidating the factors that affect community assembly in the bioreactors is necessary for predicting fluctuations in community structure and function. For this study activated sludge samples were collected during a one-year period from two geographically distant CAS bioreactors of different size. Combining community fingerprinting analysis and operational parameters data with a robust statistical analysis, we aimed to identify relevant links between system performance and bacterial community diversity and dynamics. In addition to revealing a significant β-diversity between the bioreactors' communities, results showed that the largest bioreactor had a less dynamic but more efficient and diverse bacterial community throughout the study. The statistical analysis also suggests that deterministic factors, as opposed to stochastic factors, may have a bigger impact on the community structure in the largest bioreactor. Furthermore, the community seems to rely mainly on mechanisms of resistance and functional redundancy to maintain functional stability. We suggest that the ecological theories behind the Island Biogeography model and the species-area relationship were appropriate to predict the assembly of bacterial communities in these CAS bioreactors. These results are of great importance for engineers and ecologists as they reveal critical aspects of CAS systems that could be applied towards improving bioreactor design and operation.     

Molecular phylogeny and ecological diversification in a clade of New World songbirds (genus Vireo)

We constructed a molecular phylogeny for a clade of eye-ringed vireos ( Vireo flavifrons and the V . solitarius complex) to examine existing hypotheses of speciation and ecological diversification. Complete sequences of the mtDNA cytochrome b gene were obtained from 47 individuals of this group plus four vireonid outgroups. Mean levels of sequence divergence in the clade varied from 0.29% to 5.7%. Differences were greatest between V . flavifrons and four taxa of ' V . solitarius '. The latter separated into three taxonomic, geographical and ecological groups: V . plumbeus plumbeus, V . cassinii cassinii , and V . solitarius solitarius plus V . solitarius alticola . These differed by an average of 2.6–3.2%. Populations within each group revealed low levels of sequence variation ( x- = 0.20%) and little geographical structuring. The mtDNA data generally corroborate results from allozymes. V. plumbeus shows a loss of yellow-green carotenoid pigmentation from the ancestral condition. The occupancy of relatively dry habitats by this species and V . cassinii represents a derived ecological shift from more-humid environments occupied by other species of vireonids. Ecological divergence in this clade occurred in allopatry and is associated with generic-level stability in morphometrics and foraging styles. Migratory behaviour and seasonal habitat shifts apparently evolved multiple times in vireos breeding in temperate environments. Present geographical and ecological distributions, and low levels of intrataxon genetic divergence, are hypothesized to be the result of postglacial regionalization of climate–plant associations and rapid northward expansion of breeding ranges.     

Complex life cycles drive community assembly through immigration and adaptive diversification

Most animals undergo ontogenetic niche shifts during their life. Yet, standard ecological theory builds on models that ignore this complexity. Here, we study how complex life cycles, where juvenile and adult individuals each feed on different sets of resources, affect community richness. Two different modes of community assembly are considered: gradual adaptive evolution and immigration of new species with randomly selected phenotypes. We find that under gradual evolution complex life cycles can lead to both higher and lower species richness when compared to a model of species with simple life cycles that lack an ontogenetic niche shift. Thus, complex life cycles do not per se increase the scope for gradual adaptive diversification. However, complex life cycles can lead to significantly higher species richness when communities are assembled trough immigration, as immigrants can occupy isolated peaks of the dynamic fitness landscape that are not accessible via gradual evolution.     

The timing of diversification within the most divergent parrot clade

The Strigopidae are an ancient parrot (Psittaciformes) family consisting of three extant species placed in two genera (Nestor, Strigops) and restricted to New Zealand. Their evolutionary history is clouded because the timing of divergence events within this family has variously been attributed to Pleistocene climate change or much earlier earth‐historic events. Here we examine new psittaciform DNA sequence data, and combine them with previously published sequences, to shed light on the poorly understood timing of diversification within the Strigopidae. Using calibrations indirectly derived from both psittaciform and non‐psittaciform fossils, our data indicate a Late Pliocene or Early Pleistocene (ca 1.2–3.6 mya) differentiation between the two Nestor species (kea and kaka), possibly in response to shifts in habitat distribution associated with sea level fluctuations. The unique, monotypic, nocturnal and flightless genus Strigops (kakapo) is shown to have diverged from the Nestor lineage probably ca 28–29 mya, coinciding with the potential Oligocene submergence of Zealandia when much of its landmass may have been fragmented into smaller islands, providing a setting for allopatric diversification.     

Species interactions during diversification and community assembly in an island radiation of shrews

Background

Closely related, ecologically similar species often have adjacent distributions, suggesting competitive exclusion may contribute to the structure of some natural communities. In systems such as island archipelagos, where speciation is often tightly associated with dispersal over oceanic barriers, competitive exclusion may prevent population establishment following inter-island dispersal and subsequent cladogenesis.

Methodology/Principal Findings

Using a combination of tools, we test the hypothesis that the distributions of shrew (Crocidura) species in the Philippines are the result of competitive exclusion preventing secondary invasion of occupied islands. We first compare ecological niche models between two widespread, allopatric species and find statistical support for their ecological similarity, implying that competition for habitat between these species is possible. We then examine dispersion patterns among sympatric species and find some signal for overdispersion of body size, but not for phylogenetic branch length. Finally, we simulate the process of inter-island colonization under a stochastic model of dispersal lacking ecological forces. Results are dependent on the geographic scope and colonization probability employed. However, some combinations suggest that the number of inter-island dispersal events necessary to populate the archipelago may be much higher than the minimum number of colonization events necessary to explain current estimates of species richness and phylogenetic relationships. If our model is appropriate, these results imply that alternative factors, such as competitive exclusion, may have influenced the process of inter-island colonization and subsequent cladogenesis.

Conclusions/Significance

We interpret the combined results as providing tenuous evidence that similarity in body size may prevent co-occurrence in Philippine shrews and that competitive exclusion among ecologically similar species, rather than an inability to disperse among islands, may have limited diversification in this group, and, possibly other clades endemic to island archipelagos.     

Dynamics of clade diversification on the morphological hypercube

Understanding the relationship between taxonomic and morphological changes is important in identifying the reasons for accelerated morphological diversification early in the history of animal phyla. Here, a simple general model describing the joint dynamics of taxonomic diversity and morphological disparity is presented and applied to the data on the diversification of blastozoans. I show that the observed patterns of deceleration in clade diversification can be explicable in terms of the geometric structure of the morphospace and the effects of extinction and speciation on morphological disparity without invoking major declines in the size of morphological transitions or taxonomic turnover rates. The model allows testing of hypotheses about patterns of diversification and estimation of rates of morphological evolution. In the case of blastozoans, I find no evidence that major changes in evolutionary rates and mechanisms are responsible for the deceleration of morphological diversification seen during the period of this clade''s expansion. At the same time, there is evidence for a moderate decline in overall rates of morphological diversification concordant with a major change (from positive to negative values) in the clade''s growth rate.     

Traits reveal ecological strategies driving carrion insect community assembly

1. The succession of carrion-associated (necrophilous) insects on decomposing carrion is well documented. To exploit the changing nutritious and dynamic resources available throughout the carrion decomposition process, different species colonise and consume carrion in a predictable temporal sequence. The traits of these necrophilous insects should reflect their ecological strategies. Morphological traits of these insects, such as body size and wing size, however, have not previously been examined during active and advanced decomposition. 2. We used fourth-corner multivariate generalised linear models to identify insect community morphological trait patterns and to quantify their change through time on decomposing rabbit carcasses in grassland and woodland environments. 3. We found that larger-bodied species of flies and carrion-specialist beetles were associated with the early stages of decomposition. The morphological traits of ants, in contrast, showed no changes at carcasses through time and instead showed body size differences between grassland and woodland environments. 4. Our findings indicate that specialist flies and beetles that arrive early in the decomposition process possess traits that enable rapid discovery of carrion at a large scale. Generalist beetles and ants do not share this same trait and are instead adapted to locate and consume a wider variety of resources in their preferred habitat type at their local scale. 5. Our results provide insights into the morphological adaptations linked to the ecological strategies of distinct components of carrion insect communities. Further, our results offer insights into the community assembly dynamics that structure the communities of necrophilous insect species.     

Integrating environmental and spatial processes in ecological community dynamics

The processes controlling the abundances of species across multiple sites form the cornerstone of modern ecology. In these metacommunities, the relative importance of local environmental and regional spatial processes is currently hotly debated, especially in terms of the validity of neutral model. I collected 158 published data sets with information on community structure, environmental and spatial variables. I showed that approximately 50% of the variation in community composition is explained by both environmental and spatial variables. The majority of the data sets were structured by species-sorting dynamics (SS), followed by a combination of SS and mass-effect dynamics. While neutral processes were the only structuring process in 8% of the collected natural communities, disregarding neutral dispersal processes would result in missing important patterns in 37% of the studied communities. Moreover, metacommunity characteristics such as dispersal type, habitat type and spatial scale predicted part of the detected variation in metacommunity structure.     

Advances, challenges and a developing synthesis of ecological community assembly theory

Ecological approaches to community assembly have emphasized the interplay between neutral processes, niche-based environmental filtering and niche-based species sorting in an interactive milieu. Recently, progress has been made in terms of aligning our vocabulary with conceptual advances, assessing how trait-based community functional parameters differ from neutral expectation and assessing how traits vary along environmental gradients. Experiments have confirmed the influence of these processes on assembly and have addressed the role of dispersal in shaping local assemblages. Community phylogenetics has forged common ground between ecologists and biogeographers, but it is not a proxy for trait-based approaches. Community assembly theory is in need of a comparative synthesis that addresses how the relative importance of niche and neutral processes varies among taxa, along environmental gradients, and across scales. Towards that goal, we suggest a set of traits that probably confer increasing community neutrality and regionality and review the influences of stress, disturbance and scale on the importance of niche assembly. We advocate increasing the complexity of experiments in order to assess the relative importance of multiple processes. As an example, we provide evidence that dispersal, niche processes and trait interdependencies have about equal influence on trait-based assembly in an experimental grassland.     

植物群落构建的生态过滤机制研究进展

生物多样性的形成和维持机制,即群落构建机制,一直以来都是群落生态学研究的核心问题。植物群落构建的确定性过程主要是生态过滤机制(包括环境过滤和生物过滤,其中生物过滤包括种间竞争和种内功能性状变异)作用的结果。学者们构建了大量的理论、方法、模型来解释和验证生态过滤机制对群落构建的影响,并取得了显著的成果。然而,关于生态过滤机制在不同尺度的作用、生态过滤机制的各要素分解和量化等方面的研究仍有诸多疑问。重点综述了环境过滤、种间竞争和种内功能性状变异的最新研究进展,并指出了现有研究的不足之处。在未来的研究中,应注重生态过滤机制的各要素分解和量化,加强研究手段的综合运用,关注时空动态变化对植物群落构建的影响,重视对不同植物群落构建机制的共性和个性特征的认识,同时强调与其他生态过程、群落构建机制的整合。通过这些尝试,有助于人们更好的理解植物群落构建过程中的生态过滤机制的作用。     

The role of pollinators in floral diversification in a clade of generalist flowers

Pollinator‐mediated evolutionary divergence has seldom been explored in generalist clades because it is assumed that pollinators in those clades exert weak and conflicting selection. We investigate whether pollinators shape floral diversification in a pollination generalist plant genus, Erysimum. Species from this genus have flowers that appeal to broad assemblages of pollinators. Nevertheless, we recently reported that it is possible to sort plant species into pollination niches varying in the quantitative composition of pollinators. We test here whether floral characters of Erysimum have evolved as a consequence of shifts among pollination niches. For this, we quantified the evolutionary lability of the floral traits and their phylogenetic association with pollination niches. As with pollination niches, Erysimum floral traits show weak phylogenetic signal. Moreover, floral shape and color are phylogenetically associated with pollination niche. In particular, plants belonging to a pollination niche dominated by long‐tongued large bees have lilac corollas with parallel petals. Further analyses suggest, however, that changes in color preceded changes in pollination niche. Pollinators seem to have driven the evolution of corolla shape, whereas the association between pollination niche and corolla color has probably arisen by lilac‐flowered Erysimum moving toward certain pollination niches for other adaptive reasons.     

The assembly and disassembly of ecological networks

Global change has created a severe biodiversity crisis. Species are driven extinct at an increasing rate, and this has the potential to cause further coextinction cascades. The rate and shape of these coextinction cascades depend very much on the structure of the networks of interactions across species. Understanding network structure and how it relates to network disassembly, therefore, is a priority for system-level conservation biology. This process of network collapse may indeed be related to the process of network build-up, although very little is known about both processes and even less about their relationship. Here we review recent work that provides some preliminary answers to these questions. First, we focus on network assembly by emphasizing temporal processes at the species level, as well as the structural building blocks of complex ecological networks. Second, we focus on network disassembly as a consequence of species extinctions or habitat loss. We conclude by emphasizing some general rules of thumb that can help in building a comprehensive framework to understand the responses of ecological networks to global change.     

Trait evolution, community assembly, and the phylogenetic structure of ecological communities

Taxa co-occurring in communities often represent a nonrandom sample, in phenotypic or phylogenetic terms, of the regional species pool. While heuristic arguments have identified processes that create community phylogenetic patterns, further progress hinges on a more comprehensive understanding of the interactions between underlying ecological and evolutionary processes. We created a simulation framework to model trait evolution, assemble communities (via competition, habitat filtering, or neutral assembly), and test the phylogenetic pattern of the resulting communities. We found that phylogenetic community structure is greatest when traits are highly conserved and when multiple traits influence species membership in communities. Habitat filtering produces stronger phylogenetic structure when taxa with derived (as opposed to ancestral) traits are favored in the community. Nearest-relative tests have greater power to detect patterns due to competition, while total community relatedness tests perform better with habitat filtering. The size of the local community relative to the regional pool strongly influences statistical power; in general, power increases with larger pool sizes for communities created by filtering but decreases for communities created by competition. Our results deepen our understanding of processes that contribute to phylogenetic community structure and provide guidance for the design and interpretation of empirical research.     

Patterns of ecological diversification in thelodonts

Here we explore the spatial, temporal and phylogenetic patterns of ecological diversification for the entire clade of thelodonts, one of the earliest groups of vertebrates and longest lasting of the Palaeozoic agnathans in the fossil record. Parsimony and maximum‐likelihood methods are used to reconstruct ancestral states of their geographical distributions, habitats and lifestyles. Our results support the concept that thelodonts originated during the Middle?–Late Ordovician probably in marine open waters of Laurasia, with a demersal lifestyle on hard substrates being the ancestral condition for the whole clade. Later, thelodonts underwent a complex ecological diversification and palaeobiogeographical history, comparable in many aspects to those of some major groups of living fishes. Different modes of life evolved repeatedly and a wide range of habitats were colonized by distinct groups, including deep waters and brackish marine and/or freshwater environments. Diadromous strategies presumably appeared on nine different occasions. The palaeobiogeographical history of thelodonts reveals significant differences in the dispersal potential of some major groups. Dispersal of thelodontiforms entailed displacements over long distances and the crossing of deep‐water biogeographical barriers, whereas those of furcacaudiforms were always limited to areas interconnected by shallow platforms. We propose that the evolution of pelagic larval stages in thelodontiforms might explain this biogeographical pattern and could satisfactorily account for the greater evolutionary success of this group.     

The dynamics of diversification in evolving Pseudomonas populations

Determining the mechanisms that promote the evolution of diversity is a central problem in evolutionary biology. Previous studies have demonstrated that diversification occurs in complex environments and that genotypes specialized on alternative resources can be maintained over short time scales. Here, we describe a selection experiment that has tracked the dynamics of adaptive diversification within selection lines of the asexual bacteria Pseudomonas fluorescens over about 900 generations. We cultured experimental populations from the same two isogenic ancestral strains in simple, single-substrate environments or in complex, four-substrate environments. Following selection we assayed the growth of genotypes from each population on each substrate individually. We estimated mutational heritability, Vm/VE, as 1 x 10(-3) per generation in simple environments and 3 x 10(-3) per generation in complex environments. These values are roughly consistent with estimates reported in other systems. Populations selected in complex environments evolved into genetically diverse communities. Genotypes exhibited greater metabolic differentiation from other genotypes in their own population than to genotypes evolving in other populations, presumably as a result of resource competition. In populations selected in simple environments, little genetic diversity evolved, and genotypes shared very similar phenotypes. Our findings suggest that ecological opportunity provided by environmental complexity plays a major role in the evolution and maintenance of diversity.     

Application of ecological and evolutionary theory to microbiome community dynamics across systems

A fundamental aim of microbiome research is to understand the factors that influence the assembly and stability of host-associated microbiomes, and their impact on host phenotype, ecology and evolution. However, ecological and evolutionary theories applied to predict microbiome community dynamics are largely based on macroorganisms and lack microbiome-centric hypotheses that account for unique features of the microbiome. This special feature sets out to drive advancements in the application of eco-evolutionary theory to microbiome community dynamics through the development of microbiome-specific theoretical and conceptual frameworks across plant, human and non-human animal systems. The feature comprises 11 research and review articles that address: (i) the effects of the microbiome on host phenotype, ecology and evolution; (ii) the application and development of ecological and evolutionary theories to investigate microbiome assembly, diversity and stability across broad taxonomic scales; and (iii) general principles that underlie microbiome diversity and dynamics. This cross-disciplinary synthesis of theoretical, conceptual, methodological and analytical approaches to characterizing host–microbiome ecology and evolution across systems addresses key research gaps in the field of microbiome research and highlights future research priorities.     

Ecosystem size-induced environmental fluctuations affect the temporal dynamics of community assembly mechanisms

Understanding processes that determine community membership and abundance is important for many fields from theoretical community ecology to conservation. However, spatial community studies are often conducted only at a single timepoint despite the known influence of temporal variability on community assembly processes. Here we used a spatiotemporal study to determine how environmental fluctuation differences induced by mesocosm volumes (larger volumes were more stable) influence assembly processes of aquatic bacterial metacommunities along a press disturbance gradient. By combining path analysis and network approaches, we found mesocosm size categories had distinct relative influences of assembly process and environmental factors that determined spatiotemporal bacterial community composition, including dispersal and species sorting by conductivity. These processes depended on, but were not affected proportionately by, mesocosm size. Low fluctuation, large mesocosms primarily developed through the interplay of species sorting that became more important over time and transient priority effects as evidenced by more time-delayed associations. High fluctuation, small mesocosms had regular disruptions to species sorting and greater importance of ecological drift and dispersal limitation indicated by lower richness and higher taxa replacement. Together, these results emphasize that environmental fluctuations influence ecosystems over time and its impacts are modified by biotic properties intrinsic to ecosystem size.Subject terms: Microbial ecology, Microbial ecology, Freshwater ecology     

Dealing with incomplete taxon sampling and diversification of a large clade of mushroom-forming fungi

The absence of an adequate fossil record can hinder understanding the process of diversification that underlies the evolutionary history of a given group. In such cases, investigators have used ultrametric trees derived from molecular data from extant taxa to gain insights into processes of speciation and extinction over time. Inadequate taxon sampling, however, impairs such inferences. In this study, we use simulations to investigate the effect of incomplete taxon sampling on the accumulation of lineages through time for a clade of mushroom-forming fungi, the Hebelomateae. To achieve complete taxon sampling, we use a new Bayesian approach that incorporates substitute lineages to estimate diversification rates. Unlike many studies of animals and plants, we find no evidence of a slowdown in speciation. This indicates the Hebelomateae has not undergone an adaptive radiation. Rather, these fungi have evolved under a relatively constant rate of diversification since their most recent common ancestor, which we date back to the Eocene. The estimated net diversification rate (0.08-0.19 spp./lineage/Ma) is comparable with that of many plants and animals. We suggest that continuous diversification in the Hebelomateae has been facilitated by climatic and vegetation changes throughout the Cenozoic. We also caution against modeling multiple genes as a single partition when performing phylogenetic dating analyses.