Rarefaction Analysis Research Articles

Increase in number of helminth species from Dutch red foxes over a 35-year period

BackgroundThe red fox (Vulpes vulpes) is host to a community of zoonotic and other helminth species. Tracking their community structure and dynamics over decades is one way to monitor the long term risk of parasitic infectious diseases relevant to public and veterinary health.MethodsWe identified 17 helminth species from 136 foxes by mucosal scraping, centrifugal sedimentation/flotation and the washing and sieving technique. We applied rarefaction analysis to our samples and compared the resulting curve to the helminth community reported in literature 35 years ago.ResultsFox helminth species significantly increased in number in the last 35 years (p-value <0.025). Toxascaris leonina, Mesocestoides litteratus, Trichuris vulpis and Angiostrongylus vasorum are four new veterinary-relevant species. The zoonotic fox tapeworm (E. multilocularis) was found outside the previously described endemic regions in the Netherlands.ConclusionsHelminth fauna in Dutch red foxes increased in biodiversity over the last three decades.

Genotyping of uncultured archaea in a polluted site of Suez Gulf, Egypt, based on 16S rRNA gene analyses

Culture-independent 16S rRNA gene analysis approach was used to explore and evaluate archaea in a polluted site, El-Zeitia, Suez Gulf, Egypt. Metagenomic DNA was extracted from a sediment sample. Archaeal 16S rRNA gene was PCR amplified using universal archaeal primers, followed by cloning and direct analyses by sequencing. Rarefaction analysis showed saturation, recording 21 archaeal 16S rRNA gene phylotypes, which represented the total composition of archaea in the studied sample. Phylogenetic analysis showed that all recorded phylotypes belonged to two archaeal phyla. Sixteen phylotypes were located in the branch of methanogenic Euryarchaeota and more closely related to species of the genera Methanosaeta and Methanomassiliicoccus. Five phylotypes were affiliated to the new archaeal phylum Thaumarchaeota, which represented by species Candidatus nitrosopumilus. The recorded phylotypes had unique sequences, characterizing them as new phylogenetic lineages. This work is the first investigation of uncultured archaea in the Suez Gulf, and implicated that the environmental characteristics shaped the diversity of archaeal 16S rRNA genes in the studied sample.

Benthic Macroinvertebrate Assemblage in Bulod River, Lanao del Norte, Philippines

Macroinvertebrates are biomonitor species in determining the water quality in freshwater bodies. Benthic macroinvertebrates were assessed in upstream, midstream and downstream of Bulod River, Tubod, Lanao del Norte, Philippines during the month of October-November 2013. The dip net method was used to collect the macroinvertebrates in each station. Identification of species was done using taxonomic keys. A total of 1198 individuals belonging to 24 families of aquatic insects, mollusks, flatworms and aquatic earthworms were identified. Aquatic insects (Class Hexapoda) mostly dominated the area which accounted 91% of the total abundance. Rarefaction analysis showed highest taxa richness in station 3. Family biotic index (FBI) indicates very good water quality in Station 1 (upstream) and Station 3 (downstream) which is evident by the presence of pollution-sensitive fauna, such as Ephemeroptera, Trichoptera and Plecoptera. The fairly poor water quality in Station 2 (midstream) indicates massive pollution due to various drastic disturbances due to agricultural and other anthropogenic activities.

Performance and bacterial communities of successive alkalinity-producing systems (SAPSs) in passive treatment processes treating mine drainages differing in acidity and metal levels

Successive alkalinity-producing systems (SAPSs) is a key unit process in the passive treatment of acidic mine drainage. Physico-chemistry and pyrosequencing-based bacterial communities of two passive treatment processes in Gapjung (GJ) and Seokbong (SB) were analyzed. The influent of SB harbored higher levels of acidity and metals than that of GJ. SAPS-SB demonstrated better performance of acidity neutralization and metal removal than SAPS-GJ, despite its shorter hydraulic retention time and higher acidity. System diagnosis revealed that the capacities of SAPSs were not well predicted in the design steps. Bacterial diversity indices and composition were compared at the same sequence read number for fair evaluation. Most of the bacterial sequences were affiliated with uncultured species. A notable difference was observed in the bacterial community compositions of the SAPSs in GJ and SB. Classes of putative sulfate-reducing bacteria, Clostridia (8.3 %) and Deltaproteobacteria (6.1 %), were detected in SAPS-GJ, and Clostridia (14.6 %) was detected in SAPS-SB. Bacilli, which is not a known sulfate-reducing bacterial group, was the second largest class (12.8 %) in SAPS-GJ and the largest class (51.1 %) in SAPS-SB, suggesting that Bacilli may have a prominent role in SAPS. One hundred ninety operational taxonomic units were shared, which occupied ~10 % of each number of total operational taxonomic units in SAPS-GJ and SAPS-SB, respectively. Bacilli and Clostridia were the major shared classes, and Bacillus, Lysinibacillus, and Ureibacillus were the major shared genera. Rarefaction analysis, richness estimates, diversity estimates, and abundance rank analysis show that the sediment bacterial community of SAPS-GJ was more diverse and more evenly distributed than that of SAPS-SB.

Bacterial community composition shifts in the gut of Periplaneta americana fed on different lignocellulosic materials

Cockroaches are insects that can accommodate diets of different composition, including lignocellulosic materials. Digestion of these compounds is achieved by the insect’s own enzymes and also by enzymes produced by gut symbionts. The presence of different and modular bacterial phyla on the cockroach gut tract suggests that this insect could be an interesting model to study the organization of gut bacterial communities associated with the digestion of different lignocellulosic diets. Thus, changes in the diversity of gut associated bacterial communities of insects exposed to such diets could give useful insights on how to improve hemicellulose and cellulose breakdown systems. In this work, through sequence analysis of 16S rRNA clone libraries, we compared the phylogenetic diversity and composition of gut associated bacteria in the cockroach Periplaneta americana collected in the wild-types or kept on two different diets: sugarcane bagasse and crystalline cellulose. These high fiber diets favor the predominance of some bacterial phyla, such as Firmicutes, when compared to wild-types cockroaches. Our data show a high bacterial diversity in P. americana gut, with communities composed mostly by the phyla Bacteroidetes, Firmicutes, Proteobacteria and Synergistetes. Our data show that the composition and diversity of gut bacterial communities could be modulated by diet composition. The increased presence of Firmicutes in sugarcane bagasse and crystalline cellulose-fed animals suggests that these bacteria are strongly involved in lignocellulose digestion in cockroach guts.BackgroundCockroaches are omnivorous animals that can incorporate in their diets food of different composition, including lignocellulosic materials. Digestion of these compounds is achieved by the insect’s own enzymes and also by enzymes produced by gut symbiont. However, the influence of diet with different fiber contents on gut bacterial communities and how this affects the digestion of cockroaches is still unclear. The presence of some bacterial phyla on gut tract suggests that cockroaches could be an interesting model to study the organization of gut bacterial communities during digestion of different lignocellulosic diets. Knowledge about the changes in diversity of gut associated bacterial communities of insects exposed to such diets could give interesting insights on how to improve hemicellulose and cellulose breakdown systems.Methodology/principal findingsWe compared the phylogenetic diversity and composition of gut associated bacteria in the cockroach P. americana caught on the wild or kept on two different diets: sugarcane bagasse and crystalline cellulose. For this purpose we constructed bacterial 16S rRNA gene libraries which showed that a diet rich in cellulose and sugarcane bagasse favors the predominance of some bacterial phyla, more remarkably Firmicutes, when compared to wild cockroaches. Rarefaction analysis, LIBSHUFF and UniFrac PCA comparisons showed that gene libraries of wild insects were the most diverse, followed by sugarcane bagasse fed and then cellulose fed animals. It is also noteworthy that cellulose and sugarcane bagasse gene libraries resemble each other.Conclusion/significanceOur data show a high bacterial diversity in P. americana gut, with communities composed mostly by the phyla Bacteroidetes, Firmicutes, Proteobacteria and Synergistetes. The composition and diversity of gut bacterial communities could be modulated by font of diet composition. The increased presence of Firmicutes in sugarcane bagasse and crystalline cellulose-fed animals suggests that these bacteria are strongly involved in lignocellulose digestion in cockroach guts.

Mesozooplankton in the Southern Ocean: Spatial and temporal patterns from Discovery Investigations

Mesozooplankton samples taken during the Discovery Investigations in the Southern Ocean in the 1930s were analysed from a series of 5 transects along 80°W. The samples provide a unique level of depth-discrete resolution across large spatial scales, over most of the productive austral season. Stratified net hauls were taken between 0 and 1000m within the period December 1933 to November 1934. Within the epipelagic (0–100m), median zooplankton abundance (278ind. m−3) was ∼22 times greater than at 1000m. A 3–4-fold variability of abundance in the epipelagic contrasted with depths >250m where variability was <1-fold. Depth was the strongest factor separating samples (ANOSIM, R=0.66 p=0.1%), with a clear biological distinction between epipelagic and upper and lower mesopelagic horizons. Results from multi-dimensional scaling indicated that, when plankton abundance was integrated over all depth horizons, 3 different groups could be identified. These ‘communities’ were consistent with the spatial extents of Antarctic, Polar Frontal Zone, and sub-Antarctic water-mass regimes. Such groupings became less distinct when considering only deeper horizons (500–1000m) and excluding seasonal migrants. Seasonal signals across all data became less distinct with depth. Rarefaction analysis indicated that diversity increased with depth. Although depth alone was the most important influence on sample diversity, (r2=0.60), water mass regime and month improved the fit (r2=0.71). Overall plankton diversity was highest in the sub-Antarctic zone. Following atmospheric and ocean warming that has taken place close to the study area in the last 80years we hypothesise that species richness may increase in the Antarctic water masses as sub-Antarctic species increasingly encroach south.

Molecular diversity of the ammonia-oxidizing bacteria community in disused tin-mining ponds located within Kampar, Perak, Malaysia

Disused tin-mining ponds make up a significant amount of water bodies in Malaysia particularly at the Kinta Valley in the state of Perak where tin-mining activities were the most extensive, and these abundantly available water sources are widely used in the field of aquaculture and agriculture. However, the natural ecology and physicochemical conditions of these ponds, many of which have been altered due to secondary post-mining activities, remains to be explored. As ammonia-oxidizing bacteria (AOB) are directly related to the nutrient cycles of aquatic environments and are useful bioindicators of environmental variations, the focus of this study was to identify AOBs associated with disused tin-mining ponds that have a history of different secondary activities in comparison to ponds which were left untouched and remained as part of the landscape. The 16S rDNA gene was used to detect AOBs in the sediment and water sampled from the three types of disused mining ponds, namely ponds without secondary activity, ponds that were used for lotus cultivation and post-aquaculture ponds. When the varying pond types were compared with the sequence and phylogenetic analysis of the AOB clone libraries, both Nitrosomonas and Nitrosospira-like AOB were detected though Nitrosospira spp. was seen to be the most ubiquitous AOB as it was present in all ponds types. However, AOBs were not detected in the sediments of idle ponds. Based on rarefaction analysis and diversity indices, the disused mining pond with lotus culture indicated the highest richness of AOBs. Canonical correspondence analysis indicated that among the physicochemical properties of the pond sites, TAN and nitrite were shown to be the main factors that influenced the community structure of AOBs in these disused tin-mining ponds.

Changes in the Soil Bacterial Communities in a Cedar Plantation Invaded by Moso Bamboo

Moso bamboo is fast-growing and negatively allelopathic to neighboring plants. However, there is little information on the effects of its establishment and expansion to adjacent forest soil communities. To better understand the impacts of bamboo invasion on soil communities, the phylogenetic structure and diversity of the soil bacterial communities in moso bamboo forest, adjacent Japanese cedar plantation, and bamboo-invaded transition zone were examined using a combination of 16S rRNA gene clone libraries and bar-coded pyrosequencing techniques. Based on the number of operational taxonomic units (OTUs), Shannon diversity index, Chao1 estimator, and rarefaction analysis of both techniques, the bamboo soil bacterial community was the most diverse, followed by the transition zone, with the cedar plantation possessing the lowest diversity. The results from both techniques revealed that the Acidobacteria and Proteobacteria predominated in the three communities, though the relative abundance was different. The 250 most abundant OTUs represented about 70% of the total sequences found by pyrosequencing. Most of these OTUs were found in all three soil communities, demonstrating the overall similarity among the bacterial communities. Nonmetric multidimensional scaling analysis showed further that the bamboo and transition soil communities were more similar with each other than the cedar soils. These results suggest that bamboo invasion to the adjacent cedar plantation gradually increased the bacterial diversity and changed the soil community. In addition, while the 10 most abundant OTUs were distributed worldwide, related sequences were not abundant in soils from outside the forest studied here. This result may be an indication of the uniqueness of this region.

454 Pyrosequencing to Describe Microbial Eukaryotic Community Composition, Diversity and Relative Abundance: A Test for Marine Haptophytes

Next generation sequencing of ribosomal DNA is increasingly used to assess the diversity and structure of microbial communities. Here we test the ability of 454 pyrosequencing to detect the number of species present, and assess the relative abundance in terms of cell numbers and biomass of protists in the phylum Haptophyta. We used a mock community consisting of equal number of cells of 11 haptophyte species and compared targeting DNA and RNA/cDNA, and two different V4 SSU rDNA haptophyte-biased primer pairs. Further, we tested four different bioinformatic filtering methods to reduce errors in the resulting sequence dataset. With sequencing depth of 11000–20000 reads and targeting cDNA with Haptophyta specific primers Hap454 we detected all 11 species. A rarefaction analysis of expected number of species recovered as a function of sampling depth suggested that minimum 1400 reads were required here to recover all species in the mock community. Relative read abundance did not correlate to relative cell numbers. Although the species represented with the largest biomass was also proportionally most abundant among the reads, there was generally a weak correlation between proportional read abundance and proportional biomass of the different species, both with DNA and cDNA as template. The 454 sequencing generated considerable spurious diversity, and more with cDNA than DNA as template. With initial filtering based only on match with barcode and primer we observed 100-fold more operational taxonomic units (OTUs) at 99% similarity than the number of species present in the mock community. Filtering based on quality scores, or denoising with PyroNoise resulted in ten times more OTU99% than the number of species. Denoising with AmpliconNoise reduced the number of OTU99% to match the number of species present in the mock community. Based on our analyses, we propose a strategy to more accurately depict haptophyte diversity using 454 pyrosequencing.

Effects of Urbanization on Tree Species Functional Diversity in Eastern North America

Urban forests provide ecosystem services for millions of people. Numerous introductions have elevated tree species richness in cities, which may enhance functional diversity. However, few studies have examined changes in tree community composition or functional diversity with urbanization, even though functional diversity, and not species number per se, is directly linked with ecosystem function and associated services. We combined tree abundance data from both urban and extra-urban forest inventory plots for seven metropolitan areas in eastern North America to analyze changes in species composition, Shannon’s diversity, and functional diversity with urbanization. As expected, urban tree diversity was reduced at local scales, and the effect varied with land use. Rarefaction analysis indicated that at large scales, urban tree species pools were equal with respect to species or functional diversity compared to extra-urban forests, but in urban areas at small scales this diversity is not realized because of low tree density. Ordination revealed that with urbanization, introduced species increased in importance, and regional variation in species composition became more homogenous. Increasing tree density and/or tree cover through changes in management practices and urban design could facilitate local scale urban tree diversity using existing species pools, which are functionally diverse. Monitoring of forests at large spatial scales that include urban areas, and the use of methods that account for abundance and functional trait variation can provide insights into the effects of urbanization on tree diversity at multiple scales.

Variations in dung beetles assemblages (Coleoptera: Scarabaeidae) within two rain forest habitats in French Guiana

The structure of dung beetle communities inhabiting tropical forests are known to be sensitive to many kinds of environmental changes such as microclimate related to vegetation structure. I examined Scarabaeinae assemblages in two sites of undisturbed high forest and two sites of low forest forming a transitional zone with the open habitat of an inselberg in French Guiana. Sampling was made with pitfall and flight interception traps during 2003 and 2004. The driest and warmest conditions characterized the low forest sites. Across two years we obtained 2 927 individuals from 61 species with pitfall traps and 1 431 individuals from 85 species with flight interception traps. Greater species richness and abundance characterized all sites sampled with pitfall traps during 2003 more than 2004. In 2003 no differences were detected among sites by rarefaction analyses. In 2004 the species richest high forest site was significantly different from one of the low forest sites. For both years Clench model asymptotes for species richness were greater in high forest than in low forest sites. For both years, mean per-trap species richness, abundance and biomass among high forest sites were similar and higher than in low forest sites, especially where the lowest humidity and the highest temperature were recorded. Within the two low forest sites, species richness and abundance recorded during the second year, decreased with distance to edge. Different dominant roller species characterized the pitfall samples in one site of low forest and in other sites. Small variations in microclimatic conditions correlated to canopy height and openness likely affected dung beetle assemblages but soil depth and the presence of large mammals providing dung resource may also play a significant role.

Culture-independent molecular approaches reveal a mostly unknown high diversity of active nitrogen-fixing bacteria associated with Pennisetum purpureum—a bioenergy crop

Aims Previous studieshaveshownthatelephantgrassis colonized by nitrogen-fixing bacterial species; however, these results were based on culture-dependent methods, an approach that introduces bias due to an incomplete assessment of the microbial community. In this study, we used culture-independent methods to survey the diversity of endophytes and plant-associated bacterial communities in five elephant grass genotypes used in bioenergy production. Methods The plants of five genotypes of elephant grass were harvested from the experimental area of Embrapa Agrobiologia and divided into stem and root tissues. Total DNA and RNAwere extracted from plant tissues and the bacterial communities were analyzed by DGGE and clone library of the 16S rRNA and nifH genes at both the cDNA and DNA levels. Results Overall, the patterns based on DNA- and RNAderivedDGGE-profilesdiffered,especiallywithintissue samples. DNA-based DGGE indicated that both total bacterial and diazotrophic communities associated with roots (rhizoplane+endophytes) differed clearly from those obtained from stems (endophytes). These results were confirmed by the phylogenetic analyses of RNAderived sequences of 16S rRNA (total bacteria; 586 sequences), but not for nifH (186). In fact, rarefaction analyses showed a higher diversity of diazotrophic organisms associated with stems than roots. Based on 16S rRNA sequences, the clone libraries were dominated by sequences affiliated to members of Leptotrix (12.8 %) followed by Burkholderia (9 %) and Bradyrhizobium (6.5 %), while most of the nifH clones were closely related to the genus Bradyrhizobium (26 %). Conclusions Our results revealed an unexpectedly large diversity of metabolically active bacteria, providing new insights into the bacterial species predominantly found in

Comparative metagenomics: natural populations of induced prophages demonstrate highly unique, lower diversity viral sequences

To understand the similarities and differences between a free living viral population and its co-occurring temperate population, metagenomes of each type were prepared from the same seawater sample from Tampa Bay, FL. Libraries were prepared from extracted DNA of the ambient viruses and induced prophages from the co-occurring, viral-reduced microbial assemblage. Duplicate libraries were also prepared using the same DNA amplified by multiple displacement amplification. A non-viral-reduced, induced, amplified viral dataset from the same site in 2005 was reanalysed for temporal comparison. The induced viral metagenome was higher in identifiable virus sequences and differed from the other three datasets based on principal component, rarefaction, trinucleotide composition and contig spectrum analyses. This study indicated that induced prophages are unique and have lower overall community diversity than ambient viral populations from the same site. Both of the amplified contemporary metagenomes were enriched in single-stranded DNA (ssDNA) viral sequences. Six and 16 complete, circular ssDNA viral genomes were assembled from the amplified induced and ambient libraries, respectively, mostly similar to circoviruses. The amplified ambient metagenome contained genomes similar to an RNA-DNA hybrid virus recently identified in a hot spring and to an ssDNA virus infecting the diatom Chaetoceros.

Resampling-Based Approaches to Study Variation in Morphological Modularity

Modularity has been suggested to be connected to evolvability because a higher degree of independence among parts allows them to evolve as separate units. Recently, the Escoufier RV coefficient has been proposed as a measure of the degree of integration between modules in multivariate morphometric datasets. However, it has been shown, using randomly simulated datasets, that the value of the RV coefficient depends on sample size. Also, so far there is no statistical test for the difference in the RV coefficient between a priori defined groups of observations. Here, we (1), using a rarefaction analysis, show that the value of the RV coefficient depends on sample size also in real geometric morphometric datasets; (2) propose a permutation procedure to test for the difference in the RV coefficient between a priori defined groups of observations; (3) show, through simulations, that such a permutation procedure has an appropriate Type I error; (4) suggest that a rarefaction procedure could be used to obtain sample-size-corrected values of the RV coefficient; and (5) propose a nearest-neighbor procedure that could be used when studying the variation of modularity in geographic space. The approaches outlined here, readily extendable to non-morphometric datasets, allow study of the variation in the degree of integration between a priori defined modules. A Java application – that will allow performance of the proposed test using a software with graphical user interface – has also been developed and is available at the Morphometrics at Stony Brook Web page (http://life.bio.sunysb.edu/morph/).

A meta-analysis of the publicly available bacterial and archaeal sequence diversity in saline soils

An integrated view of bacterial and archaeal diversity in saline soil habitats is essential for understanding the biological and ecological processes and exploiting potential of microbial resources from such environments. This study examined the collective bacterial and archaeal diversity in saline soils using a meta-analysis approach. All available 16S rDNA sequences recovered from saline soils were retrieved from publicly available databases and subjected to phylogenetic and statistical analyses. A total of 9,043 bacterial and 1,039 archaeal sequences, each longer than 250bp, were examined. The bacterial sequences were assigned into 5,784 operational taxonomic units (OTUs, based on ≥97% sequence identity), representing 24 known bacterial phyla, with Proteobacteria (44.9%), Actinobacteria (12.3%), Firmicutes (10.4%), Acidobacteria (9.0%), Bacteroidetes (6.8%), and Chloroflexi (5.9%) being predominant. Lysobacter (12.8%) was the dominant bacterial genus in saline soils, followed by Sphingomonas (4.5%), Halomonas (2.5%), and Gemmatimonas (2.5%). Archaeal sequences were assigned to 602 OTUs, primarily from the phyla Euryarchaeota (88.7%) and Crenarchaeota (11.3%). Halorubrum and Thermofilum were the dominant archaeal genera in saline soils. Rarefaction analysis indicated that less than 25% of bacterial diversity, and approximately 50% of archaeal diversity, in saline soil habitats has been sampled. This analysis of the global bacterial and archaeal diversity in saline soil habitats can guide future studies to further examine the microbial diversity of saline soils.

Increased culturability of soil bacteria from Marcellus shale temperate forest in Pennsylvania

Soil bacteria comprise a largely untapped resource with only 1-10% of bacterial species predicted to live in soil being culturable in the laboratory. Establishing culture-dependent protocols that identify unique operational taxonomic units (OTUs) is an important research topic in soil bacterial ecology. The culturability of soil bacteria may be improved by employing different culture media due to inherent preferences of growth substrate utilization. Soil-extract agar, R-2A agar, and 1% nutrient agar were used in this study to isolate bacteria obtained from soil samples collected in winter months to increase the understanding of bacterial diversity in Abernathy Field Station, a Marcellus shale temperate forest in Washington, Pennsylvania. Changes in bacterial diversity can be used to assess the early impact of anthropological factors, such as hydraulic fracturing in the Marcellus shale region, which may lead to severe environmental problems. For the purpose of long term ecological monitoring, data obtained from this year’s sample collection were analyzed in conjunction with previous years’ assessments. Bacterial isolates were analyzed taxonomically and phylogenetically. Unique OTUs were identified through comparative analysis of 16S rDNA. The Shannon-Weaver and Simpson’s diversity indices ranked isolates on soil-extract agar highest for species richness, and rarefaction analysis suggests that sampling saturation of OTUs identified on soil-extract agar has not yet been reached. Each culture medium studied supported isolates of four common phyla: Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. Soil-extract agar supported the greatest proportion of pigmented colonies including a Cyanobacterium which exhibited intra-16S rDNA polymorphism. Each culture medium supported the growth of unique OTUs and genera with Bacillus, Flavobacterium, Pseudomonas, Rhizobium, and Streptomyces found on each. This study suggests that utilizing different culture media can increase the culturability of soil bacteria.

Effects of forest management on the diversity of deadwood-inhabiting fungi in Central European forests

Land use and land use change affect deadwood amount, quality and associated biodiversity in forest ecosystems. Old growth or virgin forests, which are exceptionally rare in temperate Europe harbor more deadwood and associated fungal species than managed forests. Whether and how more recent abandonment of management, to reestablish more natural forests, affects deadwood amount and fungal diversity on deadwood is unknown. Our main aim was to compare deadwood amount, characteristics and deadwood inhabiting fungi in differently managed forest types typical for large areas of Central Europe. We sampled deadwood inhabiting fungi on 27 forest plots of 400m2 each in three geographically distant regions in Germany. Three forest management types, namely managed coniferous, managed deciduous and unmanaged deciduous forests, were represented by nine plots each. In autumn 2008 we collected all fungal fruiting bodies on deadwood >7cm of diameter. We found deadwood amounts and fungal species numbers in unmanaged forests to be lower than in managed forests, which we attributed to the lack of natural tree death during the short time since management abandonment of usually 10–30years. However, rarefaction analysis among deadwood items in forest plots indicated a slightly higher species density in unmanaged forests, which may be the first signal of a positive effect on fungal species richness on deadwood after management was abandoned. Although the three study regions span a large geographical gradient, we did not detect differences in the fungal species composition or in deadwood amounts and patterns, which reflects the wide distribution of this group of organisms and points to consistent management procedures among study regions. A very clear composition difference however occurred between deciduous and coniferous wood showing species substrate specialization. We conclude that the amount of deadwood is the main driver of deadwood fungal species richness, and substrate diversity in terms of various decay degrees, deadwood tree species and deadwood size are also important. Thus, to promote species richness of deadwood fungi it is vital to enhance deadwood amounts and diversity.

Molecular approach to describing a seed‐based food web: the post‐dispersal granivore community of an invasive plant

Communities of post-dispersal granivores can shape the density and dispersion of exotic plants and invasive weeds, yet plant ecologists have a limited perception of the relative trophic linkages between a seed species and members of its granivore community. Dandelion seeds marked with Rabbit IgG were disseminated into replicated plots in the recipient habitat (South Dakota) and the native range (Czech Republic). Arthropods were collected in pitfall traps, and their guts were searched for the protein marker using enzyme-linked immunosorbent assay (ELISA). Seed dishes were placed in each plot, and dandelion seed removal rates were measured. The entire experiment was repeated five times over the dandelion flowering period. Gut analysis revealed that approximately 22% of specimens tested positive for the seed marker. A more diverse granivore community had trophic linkages to seeds than has been previously realized under field conditions. This community included taxa such as isopods, millipedes, weevils, rove beetles, and caterpillars, in addition to the traditionally recognized ants, crickets, and carabid beetles. Rarefaction and Chao analysis estimated approximately 16 and 27 species in the granivore communities of the Czech Republic and South Dakota, respectively. Synthesis: Generalist granivore communities are diverse and polyphagous, and are clearly important as a form of biotic resistance to invasive and weedy plants. These granivore communities can be managed to limit population growth of these pests.

Assessing bacterial diversity in a seawater‐processing wastewater treatment plant by 454‐pyrosequencing of the 16S rRNA and amoA genes

SummaryThe bacterial community composition of activated sludge from a wastewater treatment plant (Almería, Spain) with the particularity of using seawater was investigated by applying 454-pyrosequencing. The results showed that Deinococcus-Thermus, Proteobacteria, Chloroflexi and Bacteroidetes were the most abundant retrieved sequences, while other groups, such as Actinobacteria, Chlorobi, Deferribacteres, Firmicutes, Planctomycetes, Spirochaetes and Verrumicrobia were reported at lower proportions. Rarefaction analysis showed that very likely the diversity is higher than what could be described despite most of the unknown microorganisms probably correspond to rare diversity. Furthermore, the majority of taxa could not be classified at the genus level and likely represent novel members of these groups. Additionally, the nitrifiers in the sludge were characterized by pyrosequencing the amoA gene. In contrast, the nitrifying bacterial community, dominated by the genera Nitrosomonas, showed a low diversity and rarefaction curves exhibited saturation. These results suggest that only a few populations of low abundant but specialized bacteria are responsible for removal of ammonia in these saline wastewater systems.

The impacts of biologically induced micro-environments on biodiversity in a dry Mediterranean grassland

Background: Many dryland plant communities are characterised by scattered shrubby vegetation. In such dry ecosystems, individual shrubs modify the local micro-environment and affect the surrounding plant community. Aims: The present study was conducted in a dry Mediterranean grassland community, with scattered shrubs, to determine the impacts of biologically induced micro-environments on the surrounding plant community. Methods: The plant community was sampled at four distances in four micro-environments, defined by cardinal compass directions (north, south, east and west) to assess vegetation composition near individual shrubs and at increasing distances from them. To quantify the impact of shrubs on surrounding species composition, we used a rarefaction approach in addition to alpha and beta diversity and cover parameters. Also, the productivity–diversity relationship was investigated. Results: We found significant micro-environment differences in non-shrub communities in terms of vegetation, bare ground and litter cover, above-ground biomass, species richness and Shannon diversity index. The diversity–productivity relationship was best fit by unimodal and linear models. Rarefaction analysis accumulated more species in the west aspect than in the other aspects. Beta diversity values for consecutive distances were significantly higher than the farthest distances. Conclusions: These findings suggest that shrubs create micro-environments and influence plant community characteristics according to distance and aspect, and therefore add to the complexity and biodiversity of the system; by creating diverse microhabitats they contribute to enhanced plant diversity.