Janne Soininen

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 quantitative analysis of temporal turnover in aquatic species assemblages across ecosystems

Recent meta-analyses have shown that beta diversity through space is jointly driven by species traits, geographical gradients, and ecosystem properties. Spatial variation is, however, only one aspect of beta diversity. The other component is variation in species assemblages through time, that is, temporal turnover. We examined the decrease of assemblage similarity in time in aquatic ecosystems in relation to several ecological, physical, and geographical factors using an extensive data set derived from the literature. The data set was first divided into intra-annual and interannual studies depending on the temporal extent of the studies. Sampling duration was one the most significant variables affecting the degree of temporal turnover, and we found that turnover was faster in studies with shorter temporal extent. Our results further suggested that the rate of temporal turnover increased with increasing ecosystem size, thus contradicting the general species-time-area relationship. Temporal turnover also varied among the ecosystem types: lake assemblages showed faster turnover than stream or marine assemblages in the interannual data set. We found that temporal turnover exhibited large-scale geographical variation, as there was a latitudinal gradient in turnover. Turnover was faster in the tropics in the intra-annual data set, but the pattern was reversed in the interannual data set, where turnover was faster at high latitudes. Finally, we found that the degree of temporal turnover was related to organism characteristics, as larger organisms with active mobility showed slower temporal turnover than smaller organisms. Our results suggest that the degree of species turnover in time is jointly driven by several ecological, physical, and geographical factors in aquatic ecosystems and that the turnover is not uniform across taxonomic groups. Our findings have important consequences for understanding how different biotic assemblages track temporal changes in the environment and how resilient assemblages are toward such changes.

ENVIRONMENTAL AND SPATIAL CONTROL OF FRESHWATER DIATOMS—A REVIEW

The examination of correlates of diatom community structure has long been centred on local environmental factors instead of broad-scale biogeographical factors largely because diatom distribution has been considered cosmopolitan. However, a number of recent publications have stressed the role of regional constraints such as historical factors, evolution and variability in modern day dispersal ability in determining the diatom community structure. This study aims to review the literature examining freshwater diatom community structure in relation to environmental and spatial gradients, and to consider the results in a wider ecological context. Diatom literature stresses the importance of ion concentration and trophic status as major environmental drivers of diatom distribution in lakes and streams, while physical factors typically have a lesser effect on community structure. Moreover, studies where spatial configuration accounted for a significant proportion of the community variance clearly outnumbered the studies suggesting strict local environmental control. Freshwater diatom communities seem also to be strongly spatially structured. According to studies from both lakes and streams, pure spatial factors account for about 20–30% of the total explainable community variation, and thereby suggest that diatoms lack strict ubiquitous dispersal. For the studies conducted in lakes, a meta-analysis showed that the proportion of variance explained by local environmental factors decreased, though non-significantly, as study extent increased. Although the pattern was relatively weak, this may imply that the role of spatial factors increased with increasing study area. These results suggest that bioassessment programs utilising diatoms should consider spatial factors explicitly using, for example, regional stratification as diatom communities are strongly spatially structured.

Making more out of sparse data: hierarchical modeling of species communities

Community ecologists and conservation biologists often work with data that are too sparse for achieving reliable inference with species-specific approaches. Here we explore the idea of combining species-specific models into a single hierarchical model. The community component of the model seeks for shared patterns in how the species respond to environmental covariates. We illustrate the modeling framework in the context of logistic regression and presence-absence data, but a similar hierarchical structure could also be used in many other types of applications. We first use simulated data to illustrate that the community component can improve parameterization of species-specific models especially for rare species, for which the data would be too sparse to be informative alone. We then apply the community model to real data on 500 diatom species to show that it has much greater predictive power than a collection of independent species-specific models. We use the modeling approach to show that roughly one-third of distance decay in community similarity can be explained by two variables characterizing water quality, rare species typically preferring nutrient-poor waters with high pH, and common species showing a more general pattern of resource use.

Phylogenetic clustering increases with elevation for microbes

Although phylogenetic approaches are useful for providing insights into the processes underlying biodiversity patterns, the studies of microbial phylogenetic relatedness are rare, especially for elevational gradients. Using high-throughput pyrosequencing, we examined the biodiversity patterns for biofilm bacterial communities that were scraped from stream stones along an elevational gradient from 1820 to 4050 m in China. The patterns of bacterial species richness and phylogenetic diversity were hollow towards higher elevations. The bacterial communities consisted of closer relatives than expected and displayed increasing terminal phylogenetic clustering towards mountain top. The increasing phylogenetic clustering with elevation contrasts reports for macroorganisms that revealed phylogenetic overdispersion at low or intermediate elevations. Because water temperature showed the strongest correlation with phylogenetic relatedness (r(2)  = 0.516), the elevational pattern in the bacterial phylogenetic structure indicated that environmental filtering possibly due to lower temperature or more frequent temperature fluctuations increased towards higher elevations. Evidence supporting the environmental filtering on bacteria was also reflected by the orderly succession in the relative abundance of different bacterial phyla along the elevational gradient and in the high evenness of bacterial taxa at higher elevations. Overall, our results indicated that ecological processes possibly related to temperature may play a dominant role in structuring bacterial biodiversity along the elevational gradient.

Species Turnover along Abiotic and Biotic Gradients: Patterns in Space Equal Patterns in Time?

Recent decades have seen a remarkable increase in the number of studies examining biodiversity in nature. Beta diversity—the turnover of community composition in space and time—has received particular attention. Here, I discuss recent findings in spatial and temporal turnover along abiotic and biotic gradients at two different extents. Turnover in space and time seem to exhibit similar scale dependency along latitudinal gradients; turnover is faster in the tropics at narrow study extents, but the pattern is reversed at broad extents as turnover accelerates nearer to the poles. Moreover, organisms at high trophic positions have higher turnover rates in space at broad study extents than do organisms at low trophic positions, but trophic position does not affect temporal turnover rates. Future studies that simultaneously examine variation in community composition in space, time, and along environmental gradients would shed more light on the mechanistic basis of community organization.

Neutrality, niches, and determinants of plankton metacommunity structure across boreal wetland ponds

ABSTRACT We examined the determinants of zooplankton and phytoplankton metacommunity structure across 25 boreal wetland ponds. Our objective was to determine whether plankton metacommunities exhibit spatial structuring, thus suggesting neutrality, or are merely structured by local environmental features, suggesting that they are under niche-based control. According to Redundancy Analysis (RDA), zooplankton community structure was primarily controlled by concentration of major ions and geographical location of the pond, while phytoplankton community structure was primarily controlled by major ion concentration, nitrogen concentration, and geographical location. According to variance partitioning in RDA, zooplankton community structure was attributed more to pure spatial position of the pond (16.7% of variance) than to pure environmental factors (4.7% of variance). For phytoplankton, community composition was controlled by both spatial and environmental factors, although the effect of pure spatial position (11.1% of variance) on phytoplankton community structure was somewhat weaker than for zooplankton. For zooplankton, community similarity was negatively (P < 0.01) related to both geographical and environmental distance. For phytoplankton, community similarity was negatively (P < 0.05) related only to geographical distance. Finally, cluster analyses showed that zooplankton and phytoplankton communities formed highly dissimilar groupings, thus implying low community concordance. Our results suggest that both zooplankton and phytoplankton comply with both neutral and niche-based models. Our results further imply that even across small spatial scales and even for small organisms such as plankton, communities might be strongly spatially structured. The finding that spatial configuration was even more important than local environmental factors in controlling zooplankton community composition suggests that zooplankton may be dispersal-limited within relatively small spatial scales or that zooplankton metacommunities might be related to mass effects.

Ecological status of some Finnish rivers evaluated using benthic diatom communities

The applicability of some diatom methods to quality assessment of differenttypes of Finnish rivers was compared using dominant taxa of diatomcommunities and nutrient level estimations using Trophic Diatom Index(TDI) and a new Phosphorus Diatom Equation (PDE) [Tot. Pcalc (μg l-1) = 39 – 0.278 ol-% – 0.117 olme-% – 0.346me-% – 0.006 meeu-% + 1.193 eu-%; n = 97; r2 = 0.742;SE = 17.4]. The overall quality estimations were done by Index ofPollution Sensitivity (IPS) and by Generic Diatom Index (GDI); limit valuesfor quality classes are proposed.

Macroecology of unicellular organisms - patterns and processes.

Macroecology examines the relationship between organisms and their environment at large spatial (and temporal) scales. Typically, macroecologists explain the large-scale patterns of abundance, distribution and diversity. Despite the difficulties in sampling and characterizing microbial diversity, macroecologists have recently also been interested in unicellular organisms. Here, I review the current advances made in microbial macroecology, as well as discuss related ecosystem functions. Overall, it seems that microorganisms suit surprisingly well to known species abundance distributions and show positive relationship between distribution and adundance. Microbial species-area and distance-decay relationships tend to be weaker than for macroorganisms, but nonetheless significant. Few findings on altitudinal gradients in unicellular taxa seem to differ greatly from corresponding findings for larger taxa, whereas latitudinal gradients among microorganisms have either been clearly evident or absent depending on the context. Literature also strongly emphasizes the role of spatial scale for the patterns of diversity and suggests that patterns are affected by species traits as well as ecosystem characteristics. Finally, I discuss the large role of local biotic and abiotic variables driving the community assembly in unicellular taxa and eventually dictating how multiple ecosystem processes are performed. Present review highlights the fact that most microorganisms may not differ fundamentally from larger taxa in their large-scale distribution patterns. Yet, review also shows that many aspects of microbial macroecology are still relatively poorly understood and specific patterns depend on focal taxa and ecosystem concerned.

Seasonal persistence and stability of diatom communities in rivers: are there habitat specific differences?

Epilithic, epiphytic and epipelic diatoms were sampled at four sampling stations monthly from June to October in three boreal rivers in South Finland to examine the seasonal community persistence and stability of diatom communities in three habitats. The variation of successive samples in ordination space using Non-Metric Multidimensional Scaling was substantial and without an evident pattern; there were no clear differences between community stability on three different substrata. At two stations, Multi Response Permutation Procedures showed significant among-group differences indicating that diatom communities were distinctly different among the three substrata. According to Indicator Species Analysis, we found several species showing significant (p < 0.05) specificity for, and fidelity to, certain substrata at two stations. The stability between sampling months in the rank abundance of diatom taxa was lowest among epiphytic communities. At each station, Spearman rank correlation decreased substantially until August indicating a distinct change in rank abundances. Communities tended to revert to their pre-disturbance state toward autumn after a major spate in the end of August. Using linear regression, we found that changes in total P were significantly (p < 0.05) related to community stability in the epilithon. Species turnover seemed to be highest among epiphyton and lowest among epipelic communities. Although these differences could partly result from lower diversity in epiphyton, they probably reflect lower persistence among epiphytic communities in these boreal rivers.