Microbial diversity in marine biofilms along a water quality gradient on the Great Barrier Reef

Microbial communities are potential indicators for water quality as they respond rapidly to environmental changes. In the Whitsunday Islands, Australia, microbial biofilm communities from two offshore islands were compared to those from two inshore islands subjected to poor water quality. Biofilm community composition was characterized using three culture-independent molecular techniques. The clone libraries indicated high genetic diversity, with somewhat higher scores in the offshore sites (57%) compared to the inshore sites (41%). The majority of microbes in the biofilms were related to Alphaproteobacteria (39.8%), Gammaproteobacteria (14.1%), Bacteroidetes (13.2%), diatoms (8.3%) and Cyanobacteria (3.9%). Redundancy analysis (RDA) for the CARD-FISH data showed distinct microbial assemblages between offshore and inshore communities. Additionally, 5 out of 13 water quality parameters (DIN, Chla, POP, TSS and POC) explained a significant amount of variation in the microbial communities and high values of these were associated with inshore communities. Analysis of variance (ANOVA) indicated that Cyanobacteria (p = 0.01), Bacteroidetes (p = 0.04) and to some extent Alphaproteobacteria (p = 0.07), were significantly more abundant in the offshore biofilm communities. Principal Component Analysis (PCA) of DGGE data showed clear grouping of cyanobacterial communities into inshore and offshore communities. Reasons for community shifts in the bacterial lineages are currently not resolved. One possible causative factor may be that autotrophic primary producers are more dominant in offshore sites due to the higher light availability as well as the limitation by DIN. The trends found in this study are the bases for more detailed research on microbial indicator species for changes in water quality.     

Diversity and Abundance of Ammonia-Oxidizing Archaea and Bacteria in Diverse Chinese Paddy Soils

Ammonia-oxidizing archaea (AOA) and bacteria (AOB) in three types of paddy soils of China before and after rice plantation were investigated by using an integrated approach including geochemistry, 454 pyrosequencing, and quantitative polymerase chain reaction (PCR). The abundances of AOA amoA gene were 1～2 orders of magnitude higher than AOB amoA gene. The types of paddy soils had important impacts on the diversities of both AOA and AOB via clay mineralogy (smectite or illite-rich) and bioavailability of ammonium. The Nitrososphaera subcluster 5 and Nitrosopumilis cluster of AOA, and Nitrosomonas subcluster 5 and Nitrosospira subcluster 3 of AOB were well adapted to soils with high ammonium concentrations. AOA and AOB community structures were different before and after rice plantation, likely due to changes of pH and ammonium fertilization. The Nitrosospira subclusters 2 and 9 were well adapted to acidic paddy soils. However, the sensitivity of AOA and AOB community structures to these factors may be complicated by other geochemical conditions. The results of this study collectively demonstrated that multiple environmental factors, such as clay mineralogy, ammonium content and total organic carbon as well as soil pH, shaped AOA and AOB community structure and abundance.     

Limited genetic divergence among Australian alpine Poa tussock grasses coupled with regional structuring points to ongoing gene flow and taxonomic challenges

Background and Aims

While molecular approaches can often accurately reconstruct species relationships, taxa that are incompletely differentiated pose a challenge even with extensive data. Such taxa are functionally differentiated, but may be genetically differentiated only at small and/or patchy regions of the genome. This issue is considered here in Poa tussock grass species that dominate grassland and herbfields in the Australian alpine zone.

Methods

Previously reported tetraploidy was confirmed in all species by sequencing seven nuclear regions and five microsatellite markers. A Bayesian approach was used to co-estimate nuclear and chloroplast gene trees with an overall dated species tree. The resulting species tree was used to examine species structure and recent hybridization, and intertaxon fertility was tested by experimental crosses.

Key Results

Species tree estimation revealed Poa gunnii, a Tasmanian endemic species, as sister to the rest of the Australian alpine Poa. The taxa have radiated in the last 0·5–1·2 million years and the non-gunnii taxa are not supported as genetically distinct. Recent hybridization following past species divergence was also not supported. Ongoing gene flow is suggested, with some broad-scale geographic structure within the group.

Conclusions

The Australian alpine Poa species are not genetically distinct despite being distinguishable phenotypically, suggesting recent adaptive divergence with ongoing intertaxon gene flow. This highlights challenges in using conventional molecular taxonomy to infer species relationships in recent, rapid radiations.     

The analysis of microsatellites and compound microsatellites in 56 complete genomes of Herpesvirales

Simple sequence repeats (SSRs), or microsatellites, are special DNA/RNA sequences with repeated unit of 1–6 bp. The genomes of Herpesvirales have many repeating structures, which is an excellent system to study the evolution and roles of microsatellites and compound microsatellites in viruses. Therefore, 56 genomes of Herpesvirales were selected and the occurrence, composition and complexity of different repeats were investigated in the genomes. A total of 63,939 microsatellites and 5825 compound microsatellites were extracted from 56 genomes. It found that GC content has a significant strong correlation with both the counts of microsatellites (CM) and the counts of compound microsatellites (CCM). However, genome size has a moderate correlation only with CM and almost no correlation with CCM. The compound microsatellites occurring in genic regions are obviously more than that in intergenic regions. In general, the number of compound microsatellite decreases with the increase of complexity (C) (the count of individual microsatellites being part of a compound microsatellite) and the complexity hardly exceeds C = 4. The vast majority of compound microsatellites exist in intergenic regions, when C ≥ 10. The distributions of SSRs tend to be organism-specific rather than host-specific in herpesvirus genomes. The diversity of microsatellites and compound microsatellites may be helpful for a better understanding of the viral genetic diversity, genotyping, and evolutionary biology in herpesviruses genomes.     

Evaluation of seven housekeeping genes for multilocus sequence analysis of the genus Mesorhizobium: Resolving the taxonomic affiliation of the Cicer canariense rhizobia

Cicer canariense is a wild chickpea that can be nodulated by Mesorhizobium strains belonging to nine different genomic groups or genospecies. In this study, multilocus sequence analysis (MLSA) of seven protein-coding genes, recA, glnII, dnaK, rpoB, gyrB, truA and thrA, was used to resolve the phylogenetic relationships and taxonomic affiliation of 27 representative strains from all the genotypes. Individual phylogenies were mostly congruent, although there were a few discrepancies. Some genes were more discriminative than others, but concatenation of the seven genes produced a robust phylogeny of the genus Mesorhizobium. MLSA gave good support for the taxonomic affiliations of most of the genomic groups to previously recognized species and delineated several potential new species. Five genospecies found in C. canariense nodules showed average nucleotide identity values for seven genes (ANIg7) of >96% and they could be assigned to previously described Mesorhizobium species. Two large closely related genomic groups had M. caraganae as the closest species and they shared ANIg7 values in the 94–95% range, suggesting that they could be different subspecies or sister species. The predominant genospecies represented a novel monophyletic lineage that was well resolved from all currently recognized species of Mesorhizobium, with the highest ANIg7 below 92%. Other single strains represented potential new species.     

广东石门台亚热带典型常绿阔叶林和亚热带山顶矮林群落特征

为了研究亚热带典型常绿阔叶林和亚热带山顶矮林的物种组成和群落结构,在广东石门台国家自然保护区内分别建立了1 hm2亚热带典型常绿阔叶林样地和1 hm2亚热带山顶矮林样地,以样地内所有胸径（DBH）≥1 cm的乔木、灌木和藤本为研究对象,分析两种森林类型的物种组成、密度、径级和株高结构。结果显示：（1）两种森林的Srensen物种相似性指数为0.41,优势种不同,但优势科却较相似;其中,茶科和杜鹃花科在两种森林中所占比例较高;（2）亚热带典型常绿阔叶林的幼苗（1 cm≤DBH〈2.5 cm）和幼树（2.5 cm≤DBH〈12.5 cm）密度都显著小于亚热带山顶矮林,但两种森林的小树（12.5 cm≤DBH〈25 cm）和大树（DBH≥25 cm）密度均无显著差异;亚热带典型常绿阔叶林幼苗和大树的平均胸径都显著大于亚热带山顶矮林,而幼树的平均胸径则显著小于亚热带山顶矮林,小树的平均胸径无显著差异;亚热带典型常绿阔叶林中小树和大树的平均高度都显著大于亚热带山顶矮林,而幼苗的平均高度显著小于亚热带山顶矮林,幼树的平均高度无显著差异。综合分析表明,亚热带典型常绿阔叶林和亚热带山顶矮林的物种组成、密度、胸径和高度结构差异较大,亚热带典型常绿阔叶林群落稳定性强于亚热带山顶矮林。     

Where the bears roam in Majella National Park,Italy

The Brown bear (Ursus arctos Linnaeus, 1758) occupies contiguous areas in Eastern and Northern Europe. In Western Europe, the largest remnant populations occur in Cantabria, Spain and the Apennines, Italy. Under Italian law the bear and its occupied range are protected. The occupied range of the Apennine brown bear includes Majella National Park. However, information on the distribution within Majella NP is extrapolated and inconsistent, thus precluding evidence-based protected area and species management. To address this lack of information, bear presence records (1996–2010) were collated and corrected for observational bias. Multiple Species Distribution Models (SDMs) were created at 800 m resolution to predict year-round and seasonal bear distribution. A hierarchical, stepwise maxent SDM approach was applied using climatic, terrain, vegetation, and anthropogenic predictors of bear distribution. Occupied ranges were identified by point density analysis of bear presence. Our climate-only SDMs predicted bear presence in areas with relatively low snowfall and temperate temperatures. Year-round bear distribution was also accurately predicted by using temperate-montane elevations and mesic, mesotrophic vegetation substrates, irrespective of vegetation. Ski-resorts were negative predictors of year-round bear occurrence. Bears were predicted in autumn and winter by beech forest, in spring by meadows and in summer by a variety of vegetation categories. The regional and our local models predicted bear throughout the south. However, our predicted and occupied range in the north includes the Orta valley and exclude alpine heights, contrary to the regional models. Only our summer bear range is similar to a regional SDM. We demonstrated that multiple maxent SDMs using a modest number of observations and a comprehensive set of environmental variables may generate essential distributional information for protected area and species management where full wildlife and food source censuses are lacking.