Species co-occurrence: the case of congeneric species and a causal approach to patterns of species association

Aim To test whether congeneric species are significantly associated with one another in space, either positively or negatively. Also, to provide a framework for a causal investigation of co‐occurrence patterns by a parallel comparison of interactions in geographical and ecological data matrices. Location For the analysis of congeneric species’ co‐occurrences we used 30 matrices covering a wide range of taxa and geographical areas, while for the causal investigation we used the distribution of 50 terrestrial isopod species on 20 islands and 264 sampling stations in the central Aegean archipelago, as well as a number of ecological variables for each sampling station. Methods We developed a software program (cooc ) that incorporates the species‐by‐species approach to co‐occurrence analysis using EcoSim's output of prior null model analysis of co‐occurrence. We describe this program in detail, and use it to investigate one of the most common assembly rules, namely, the decreased levels of co‐occurrence among congeneric species pairs. For the causal analysis, we proceed likewise, cross‐checking the results from the geographical and the ecological matrices. There is only one possible combination of results that can support claims for direct competition among species. Results We do not get any strong evidence for widespread competition among congeneric species, while most communities investigated do not show significant patterns of species associations. The causal analysis suggests that the principal factors behind terrestrial isopod species associations are of historical nature. Some exceptional cases are also discussed. Main conclusions Presence/absence data for a variety of taxa do not support the assembly rule that congeneric species are under more intense competition compared to less related species. Also, these same data do not suggest strong interactions among species pairs, regardless of taxonomic status. When significant species associations can be seen in such matrices, they mainly reflect the effects of history or of habitat requirements.     

An improved method for the identification of areas of endemism using species co-occurrences

Aim To develop a simple method that (1) combines the notions of biotic elements (groups of taxa with ranges significantly more similar to each other than to the ranges of other taxa) and of areas of endemism (AoE, areas of non‐random distributional congruence among taxa), and (2) overcomes the constraints of a previously suggested null model‐based method that cannot deal with disjunctions and is strictly grid‐dependent. Location We used test data sets from southern Africa and Crete. Methods First, we used a null‐model approach to detect pairs of species that have a significant degree of co‐occurrence, in order to determine biotic elements. Subsequently, we used a parsimony analysis of endemicity to delineate candidate AoE, and multivariate analysis to define groups of biotic elements on the basis of species interactions (co‐occurrence, mutual exclusion, neutral) using only the species detected in the previous step. We applied this method to the well known data set for Sciobius in southern Africa, as well as to endemic invertebrates of Crete (Greece), in order to evaluate its performance. Results Our results are very similar to those of previous analyses, and produce meaningful delineation of AoE and biotic elements in both data sets. The method is flexible regarding null models and significance levels, and eliminates noise in the data. Main conclusions We offer a simple method that provides reasonable identification of both biotic elements and AoE, produces good‐fit statistics, reduces uninformative or junk output, and reduces computational time.     

Influence of sulfate reduction on the microbial dechlorination of pentachloroaniline in a mixed anaerobic culture

The reductive dechlorination of pentachloroaniline (PCA) was investigated in the absence and presence of sulfate in batch assays using a PCA-dechlorinating mixed anaerobic culture with methanol as the external electron donor at neutral pH and 22°C. PCA at an initial concentration of 7.8 μM was sequentially dechlorinated to dichlorinated anilines in the sulfate-free culture and the culture amended with 300 mg sulfate-S/L. At an initial concentration of 890 mg sulfate-S/L, a higher sulfate reduction rate was achieved, but PCA dechlorination was not observed until the sulfate concentration dropped to about 100 mg S/L. The transient inhibition of PCA is attributed to competition between sulfate reducing and dechlorinating species for electron donor, more likely for H₂ resulting from methanol fermentation. A long-term (118 days) PCA dechlorination assay with the sulfate-amended culture, which included five feeding cycles, resulted in accumulation of both sulfide (886 mg S/L) and acetate (1,900 mg COD/L). Under these conditions, the sulfate reducers were inhibited, while the rate and pathway of PCA dechlorination were not affected. The results of this study show that the rate of sulfate reduction rather than the sulfate concentration alone dictates the outcome of the competition between sulfate reducers and either dechlorinators or methanogens. The findings of the present study have significant implications relative to the fate and transport of PCA and its dechlorination products in sulfate-laden subsurface systems.     

Between-island compositional dissimilarity of avian communities

Compositional dissimilarity patterns of biotic communities can vary among different types of insular systems and among taxa with different dispersal abilities. In this work we examined compositional dissimilarity patterns of four avian groups, namely birds of prey, waterbirds, seabirds and landbirds, in various insular systems around the world. Compositional dissimilarity of avian communities was calculated for 25 presence-absence matrices compiled from the literature. We used generalized linear mixed-effects models to check for differences in between-island compositional dissimilarity among the aforementioned avian groups that differ in their dispersal abilities, as well as between two different types of insular systems, oceanic and continental shelf. In agreement with our original hypothesis, landbirds which have relatively poorer dispersal abilities than birds of prey and waterbirds, exhibit higher between-island compositional dissimilarity compared to these two avian groups. On the contrary, seabirds present a deviation from the expected pattern, since they show higher between-island compositional dissimilarity compared to landbirds, even though they also have better dispersal abilities than landbirds, which can be explained by the relatively irregular occurrence of proper breeding habitats among islands for this avian group. Island type (oceanic or continental shelf) does not appear to affect between-island compositional dissimilarity of avian communities. Distance, area and elevation differences among islands are positively related to compositional dissimilarity. In conclusion, compositional dissimilarity of avian communities differs between avian groups but cannot always be associated with differences in the dispersal ability among these groups.     

A comprehensive model of simultaneous denitrification and methanogenic fermentation processes

The denitrification process was incorporated into the IWA Anaerobic Digestion Model No. 1 (ADM1) in order to account for the effect of denitrification on the methanogenic fermentation process. The model was calibrated and optimized using previously published experimental data and kinetic parameter values obtained with a mixed, mesophilic (35°C) methanogenic culture. Model simulations were used to predict the effect of nitrate reduction on the methanogenic fermentation process in batch, semi‐continuous, and continuous flow reactors experiencing operational changes and/or system disturbances. The extended model clearly revealed the importance of substrate competition between denitrifiers and non‐denitrifiers as well as the impact of N‐oxide inhibition on process interactions between fermentation, methanogenesis, and denitrification. Biotechnol. Bioeng. 2010;105: 98–108. © 2009 Wiley Periodicals, Inc.     

Microbial community adaptation to quaternary ammonium biocides as revealed by metagenomics

Quaternary ammonium compounds (QACs) represent widely used cationic biocides that persist in natural environments. Although microbial degradation, sensitivity and resistance to QACs have been extensively documented, a quantitative understanding of how whole communities adapt to QAC exposure remain elusive. To gain insights into these issues, we exposed a microbial community from a contaminated river sediment to varied levels of benzalkonium chlorides (BACs, a family of QACs) for 3 years. Comparative metagenomic analysis showed that the BAC‐fed communities were dramatically decreased in phylogenetic diversity compared with the control (no BAC exposure), resulting presumably from BAC toxicity, and dominated by Pseudomonas species (> 50% of the total). Time‐course metagenomics revealed that community adaptation occurred primarily via selective enrichment of BAC‐degrading Pseudomonas populations, particularly P. nitroreducens, and secondarily via amino acid substitutions and horizontal transfer of a few selected genes in the Pseudomonas populations, including a gene encoding a PAS/PAC sensor protein and ring‐hydroxylating dioxygenase genes. P. nitroreducens isolates were reproducibly recoverable from communities after prolonged periods of no‐BAC exposure, suggesting that they are robust BAC‐degraders. Our study provides new insights into the mechanisms and tempo of microbial community adaptation to QAC exposure and has implications for treating QACs in biological engineered systems.     

Hotspots of endemic terrestrial invertebrates in southern Greece

In the present paper we identify biodiversity hotspots of endemic terrestrial invertebrates in southern Greece, using four different criteria and five taxonomic groups. The hotspots identification procedure was facilitated by the use of the MapInfoPro G.I.S. software. We mapped the known distribution of 424 endemic species on a digital map of southern Greece in 548 10 × 10 km² grids. The total number of registrations (records per grid) is 3826 in 465 grids. Registrations are unevenly distributed in the five sub-regions of the study area, a fact that results from both the unequal collecting effort applied in each sub-region and their different levels of endemism. We first identified the hotspots for each individual taxonomic group, and then for the total species pool. Finally, we analyzed the species saturation pattern in order to find the minimum number of grids needed for the inclusion of 85% of the total number of species. The most important hotspots are mostly at the higher mountains of the study area, especially on Taygetos and Idi Mts. We also give a brief evaluation of the performance of the four criteria used in the case of endemic species analyses.