Only a Few Fungal Species Dominate Highly Diverse Mycofloras Associated with the Common Reed

Plants are naturally colonized by many fungal species that produce effects ranging from beneficial to pathogenic. However, how many of these fungi are linked with a single host plant has not been determined. Furthermore, the composition of plant-associated fungal communities has not been rigorously determined. We investigated these essential issues by employing the perennial wetland reed Phragmites australis as a model. DNA extracted from roots, rhizomes, stems, and leaves was used for amplification and cloning of internal transcribed spacer rRNA gene fragments originating from reed-associated fungi. A total of 1,991 clones from 15 clone libraries were differentiated by restriction fragment length polymorphism analyses into 345 operational taxonomical units (OTUs). Nonparametric estimators for total richness (Chao1 and ACE) and also a parametric log normal model predicted a total of about 750 OTUs if the libraries were infinite. Sixty-two percent of the OTUs sequenced were novel at a threshold of 3%. Several of these OTUs represented undocumented fungal species, which also included higher taxonomic levels. In spite of the high diversity of the OTUs, the mycofloras of vegetative organs were dominated by just a few typical fungi, which suggested that competition and niche differentiation influence the composition of plant-associated fungal communities. This suggestion was independently supported by the results of nested PCR assays specifically monitoring two OTUs over 3 years, which revealed significant preferences for host habitat and host organ.     

Only a few fungal species dominate highly diverse mycofloras associated with the common reed

Plants are naturally colonized by many fungal species that produce effects ranging from beneficial to pathogenic. However, how many of these fungi are linked with a single host plant has not been determined. Furthermore, the composition of plant-associated fungal communities has not been rigorously determined. We investigated these essential issues by employing the perennial wetland reed Phragmites australis as a model. DNA extracted from roots, rhizomes, stems, and leaves was used for amplification and cloning of internal transcribed spacer rRNA gene fragments originating from reed-associated fungi. A total of 1,991 clones from 15 clone libraries were differentiated by restriction fragment length polymorphism analyses into 345 operational taxonomical units (OTUs). Nonparametric estimators for total richness (Chao1 and ACE) and also a parametric log normal model predicted a total of about 750 OTUs if the libraries were infinite. Sixty-two percent of the OTUs sequenced were novel at a threshold of 3%. Several of these OTUs represented undocumented fungal species, which also included higher taxonomic levels. In spite of the high diversity of the OTUs, the mycofloras of vegetative organs were dominated by just a few typical fungi, which suggested that competition and niche differentiation influence the composition of plant-associated fungal communities. This suggestion was independently supported by the results of nested PCR assays specifically monitoring two OTUs over 3 years, which revealed significant preferences for host habitat and host organ.     

Patterns of composition and species richness of crustaceans and aquatic insects along environmental gradients in Mediterranean water bodies

Differences in the dynamics of ecological processes between Mediterranean and colder temperate aquatic systems could imply different patterns in faunal communities in terms of composition and biodiversity (i.e. species richness and rarity). In order to identify some of these patterns the crustacean and aquatic insect composition and biodiversity of four water body types, classified according to their salinity and water permanence, were compared. Moreover, the relationships between species richness and water, pond and landscape variables were analysed. A total number of 91 water bodies located throughout Catalunya (NE Iberian Peninsula) were sampled. Three species assemblages were observed: one for permanent freshwaters, another for temporary freshwaters, and a third one for saline waters (SW), since permanent and temporary saline water bodies had similar composition. Differences in salinity were associated with proportion of crustaceans versus insects and with singularity. Thus, saline ponds had a higher proportion of crustaceans, and lower values of singularity. Conductivity was significantly related to total (crustaceans plus insects) richness, and also related to insect richness. The main difference between the models obtained for crustacean species richness and insect species richness is the significance of landscape variables in the latter, and this fact could be related to the different dispersion types of these two faunal groups: active for insects versus passive for crustaceans. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Guest editors: R. Céréghino, J. Biggs, B. Oertli & S. Declerck The ecology of European ponds: defining the characteristics of a neglected freshwater habitat     

Analysis of Metagenomic Data Containing High Biodiversity Levels

In this paper we have addressed the problem of analysing Next Generation Sequencing samples with an expected large biodiversity content. We analysed several well-known 16S rRNA datasets from experimental samples, including both large and short sequences, in numbers of tens of thousands, in addition to carefully crafted synthetic datasets containing more than 7000 OTUs. From this data analysis several patterns were identified and used to develop new guidelines for experimentation in conditions of high biodiversity. We analysed the suitability of different clustering packages for these type of situations, the problem of even sampling, the relative effectiveness of Chao1 and ACE estimators as well as their effect on sampling size for a variety of population distributions. As regards practical analysis procedures, we advocated an approach that retains as much high-quality experimental data as possible. By carefully applying selection rules combining the taxonomic assignment with clustering strategies, we derived a set of recommendations for ultra-sequencing data analysis at high biodiversity levels.     

Macrofaunal crustaceans in the benthic boundary layer from the shelf break to abyssal depths in the Ross Sea (Antarctica)

The New Zealand International Polar Year–Census of Antarctic Marine Life (NZ IPY-CAML) project added to previous benthic studies in the Ross Sea by extending sampling north from the continental shelf to previously unsampled areas of the shelf break, slope, abyssal plain and seamounts in the region. The aim of the current study is to give first insights into the deep-sea community structure of the Ross Sea focussing on a component of the benthic boundary layer that is macrofaunal crustaceans collected one metre above the seafloor. We assess changes in Ross Sea crustacean community composition from the shelf break (474 m) to the abyss (3,490 m) and compare the Ross Sea crustacean fauna to areas elsewhere in the Southern Ocean. Analyses reveal high relative abundances, suggesting an important role in the food web. Among the peracarid crustaceans, there was a decline in the proportion of amphipods with increasing depth. Three of 15 isopod families (Acanthaspidiidae, Nannoniscidae and Desmosomatidae) were identified to species level and about 72 % of the species were new to science. Isopod diversity in the Ross Sea abyss appears to be comparable to that in the highly speciose Weddell deep sea. Standardised sampling of these crustacean communities allows setting the biodiversity of the Ross Sea into a global context.     

福建洛阳河口潮间带大型底栖甲壳动物群落及其功能群研究

2013年8月、2013年10月、2014年1月和2014年4月分别在洛阳河口潮间带选取5种生境(红树林区Q1,Q2,Q3;光滩Q4,林缘光滩Q5)开展调查,以探讨不同生境间甲壳动物群落结构及功能群差异和影响因素。调查共获得甲壳动物18科35种,优势种和重要种有弧边招潮(Uca arcuata)、薄片蜾蠃蜚(Sinocorophium lamellatum)、宁波泥蟹(Ilyoplax ningpoensis)和秀丽长方蟹(Metaplax elegans),以穴居型植食者为主;不同生境间优势种存在明显变化,游泳型甲壳动物主要出现在生境Q1、Q2和Q3。洛阳江红树林生境Q1、Q2、Q3底栖甲壳动物物种多样性和功能群复杂性高于林缘光滩和光滩生境,而生物量和栖息密度则相反。通过对5种不同生境的物种数、生物量、密度、功能群、物种多样性指数进行生境-季节间双因素方差分析发现,不同生境间与季节间甲壳动物物种数、栖息密度、功能群、均匀度指数与多样性指数存在显著差异;生物量在生境间差异不显著,丰富度指数在季节间差异不显著;生境Q1、Q2和Q3差异不显著。而底栖甲壳动物群落相似性和非度量多维度标序(n MDS)分析表明林缘光滩Q5的甲壳动物群落结构与Q1、Q2、Q3的相似度高,与光滩生境相似度较低,这可能是因为红树林、林缘光滩、光滩三者生境的复杂程度、食物丰富程度和食物来源存在差异有关。综合分析表明生境复杂程度与季节是影响洛阳河口潮间带大型底栖甲壳动物分布的主要因素。     

Spatial and temporal variation in the diet of the gentoo penguin (<Emphasis Type="Italic">Pygoscelis papua</Emphasis>) at Kerguelen Islands

Benthic divers are dependent on local resources and may therefore adopt different foraging strategies to cope with their energetic requirements in varying situations. We investigated the diet of gentoo penguins (Pygoscelis papua) at Kerguelen Islands, comparing its spatial and temporal variations with the general prey distribution. The study was conducted at four sites over 2 years. In total, 212 stomach contents were collected over the entire breeding season. The diet was composed mainly of neritic fish and crustaceans, with important spatial and seasonal variations. Fish dominated the diet at localities facing the open sea (from 38.0% to 94.6% by mass), whereas crustaceans dominated at the more protected site (84.3% by mass). Fish were more abundant in the winter diet and Euphausia vallentini, the major crustacean species, was more abundant in the summer diet. No inter-year variations were detected. These results are consistent with local prey availability, and highlight the large plasticity of the gentoo penguin diet and foraging behaviour.     

Coral—the world's most diverse symbiotic ecosystem

Zooxanthellate corals (i.e. those harbouring Symbiodinium) are the main builders of the world's shallow‐water marine coral reefs. They represent intimate diverse symbioses between coral animals, single‐celled photosynthetic dinoflagellates (Symbiodinium spp.), other microscopic eukaryotes, prokaryotes and viruses. Crabs and other crustaceans, worms, sponges, bivalves and hydrozoans, fishes, sea urchins, octopuses and sea stars are itinerant members of these ‘rainforests of the sea’. This review focuses on the biodiversity of scleractinian coral animals and their best studied microscopic epi‐ and endosymbionts. In relation to coral‐associated species diversity, Symbiodinium internal transcribed spacer region sequence types tally 10²–10³ or up to ~15 different operational taxonomic units (OTUs, or putative species at the 97% sequence identity level; this cut‐off was chosen based on intragenomic sequence diversity observed in monoclonal cultures) and prokaryotes (mostly bacterial) total 10²–10⁴ OTUs. We analysed all publically accessible 16S rRNA gene sequence data and found Gammaproteobacteria were extremely abundant, followed by Alphaproteobacteria. Notably, Archaea were poorly represented and ‘unassigned OTUs’ were abundant in data generated by high‐throughput DNA sequencing studies of corals. We outline and compare model systems that could be used in future studies of the coral holobiont. In our future directions, we recommend a global coral sampling effort including substantial attention being paid to method of coral tissue acquisition, which compartments (mucus, tissue, skeleton) to explore, broadening the holobiont members considered and linking biodiversity with functional investigations.     

Impact of hard-bottom substrata on the small-scale distribution of fish and decapods in shallow subtidal temperate waters

The micro-scale spatial distribution patterns of a demersal fish and decapod crustacean assemblage were assessed in a hard-bottom kelp environment in the southern North Sea. Using quadrats along line transects, we assessed the in situ fish and crustacean abundance in relation to substratum types (rock, cobbles and large pebbles) and the density of algae. Six fish and four crustacean species were abundant, with Ctenolabrus rupestris clearly dominating the fish community and Galathea squamifera dominating the crustacean community. Differences in the substratum types had an even stronger effect on the micro-scale distribution than the density of the dominating algae species. Kelp had a negative effect on the fish abundances, with significantly lower average densities in kelp beds compared with adjacent open areas. Averaged over all of the substrata, the most attractive substratum for the fish was large pebbles. In contrast, crustaceans did not show a specific substratum affinity. The results clearly indicate that, similar to other complex systems, significant micro-scale species–habitat associations occur in northern hard-bottom environments. However, because of the frequently harsh environmental conditions, these habitats are mainly sampled from ships with sampling gear, and the resulting data cannot be used to resolve small-scale species–habitat associations. A detailed substratum classification and community assessment, often only possible using SCUBA diving, is therefore important to reach a better understanding of the functional relationships between species and their environment in northern temperate waters, knowledge that is very important with respect to the increasing environmental pressure caused by global climate change.     

Crustacean biodiversity as an important factor for mosquito larval control

Newly established ponds, which are highly dynamic systems with changing levels of biological interactions among species, are common larval mosquito habitats. We investigated the impact of crustacean abundance and taxa diversity on mosquito oviposition and larval development. The effects of the biological larvicide Bacillus thuringiensis israelensis (Bti) on mosquito larvae were monitored according to fluctuations in crustacean communities. Populations of the mosquito Culex pipiens colonized artificial ponds that contained crustacean communities at different time points of colonization by crustaceans: 1) ‘no colonization’ (no crustaceans), 2) ‘simultaneous colonization’ by crustaceans and mosquitoes, and 3) ‘head‐start colonization’ by crustaceans (preceding colonization by mosquitoes). All types of ponds were treated with three concentrations of Bti (10, 100, or 1,000 µg/liter). Colonization of all ponds by Cx. pipiens (in terms of oviposition, larval abundance, and larval development) decreased significantly with increasing diversity of crustacean taxa. The total abundance of crustaceans had a minor effect on colonization by Cx. pipiens. The presence of crustaceans increased the sensitivity of Cx. pipiens larvae to Bti treatment by a factor of 10 and delayed the time of recolonization. This effect of Bti was relevant in the short term. In the long term, the presence of Cx. pipiens was determined by crustacean biodiversity.     

Microbial diversity of an anoxic zone of a hydroelectric power station reservoir in Brazilian Amazonia

Microbial diversity was evaluated in an anoxic zone of Tucuruí Hydroelectric Power Station reservoir in Brazilian Amazonia using a culture-independent approach by amplifying and sequencing fragments of the 16S rRNA gene using metagenomic DNA as a template. Samples obtained from the photic, aphotic (40 m) and sediment (60 m) layers were used to construct six 16S rDNA libraries containing a total of 1,152 clones. The sediment, aphotic and photic layers presented 64, 33 and 35 unique archaeal operational taxonomic units (OTUs). The estimated richness of these layers was evaluated to be 153, 106 and 79 archaeal OTUs, respectively, using the abundance-based coverage estimator (ACE) and 114, 83 and 77 OTUs using the Chao1 estimator. For bacterial sequences, 114, 69 and 57 OTUs were found in the sediment, aphotic and photic layers, which presented estimated richnesses of 1,414, 522 and 197 OTUs (ACE) and 1,059, 1,014 and 148 OTUs (Chao1), respectively. Phylogenetic analyses of the sequences obtained revealed a high richness of microorganisms which participate in the carbon cycle, namely, methanogenic archaea and methanotrophic proteobacteria. Most sequences obtained belong to non-culturable prokaryotes. The present study offers the first glimpse of the huge microbial diversity of an anoxic area of a man-made lacustrine environment in the tropics.     

Estimating species richness using environmental DNA

The foundation for any ecological study and for the effective management of biodiversity in natural systems requires knowing what species are present in an ecosystem. We assessed fish communities in a stream using two methods, depletion‐based electrofishing and environmental DNA metabarcoding (eDNA) from water samples, to test the hypothesis that eDNA provides an alternative means of determining species richness and species identities for a natural ecosystem. In a northern Indiana stream, electrofishing yielded a direct estimate of 12 species and a mean estimated richness (Chao II estimator) of 16.6 species with a 95% confidence interval from 12.8 to 42.2. eDNA sampling detected an additional four species, congruent with the mean Chao II estimate from electrofishing. This increased detection rate for fish species between methods suggests that eDNA sampling can enhance estimation of fish fauna in flowing waters while having minimal sampling impacts on fish and their habitat. Modern genetic approaches therefore have the potential to transform our ability to build a more complete list of species for ecological investigations and inform management of aquatic ecosystems.     

Summer depth selection in crustacean zooplankton in nutrient‐poor boreal lakes is affected by recent residential development

1. Strong vertical gradients in light, water temperature, oxygen, algal concentration and predator encounters during summer in stratified lakes may influence patterns of depth selection in crustacean zooplankton, especially Daphnia species. 2. To test how crustacean depth selection varies among lakes along a gradient of catchment disturbance by recent residential development and land use change, we calculated the weighted mean depth distribution of the biomass of crustaceans by day and night in eight nutrient‐poor boreal lakes. 3. Generally, the greatest biomass of crustaceans was located at the metalimnion or at the lower boundary of the euphotic zone during thermal stratification in July. The crustacean zooplankton avoided warm surface layers and tended to stay in colder deep waters by both day and night. They also remained at greater depths in lakes with a more extensive euphotic zone. 4. There was some evidence of upward nocturnal migrations of large Daphnia and copepods in some lakes, and one case of downward migration in a lake inhabited by chaoborid larvae. 5. Multivariate regression trees (MRT) were used to cluster crustaceans and Daphnia species in homogeneous groups based on lake natural and disturbance factors. For crustaceans, the depth of the euphotic zone, the sampling depth (epilimnion, metalimnion and hypolimnion), time (day or night) of sampling and the biomass of chlorophyll a were the main driving factors. For Daphnia species, the drainage area, the sampling depth, the cleared land surface area within the catchment and the concentration of total dissolved phosphorus were the main factors.     

The net result: evaluating species richness extrapolation techniques for littoral pond invertebrates

1. Total species richness for an assemblage or site is a valuable measure in conservation monitoring and assessment, but protocols for sampling and species richness determination in wetland habitats such as ponds, bogs or mires remain largely unrefined. 2. Techniques for estimation of total richness of an assemblage based upon replicated sampling offer the opportunity to derive useful estimates of total richness based upon small numbers of samples, and limit sampling‐derived disturbance which can be particularly problematic in small aquatic habitats. 3. We quantified the performance of eight of the most commonly encountered estimators of species richness for a variety of littoral zone macrofauna from ponds, comparing estimated richness to maximum richness derived from sampling. 4. Estimates using non‐parametric techniques based on species incidence provided the most accurate and precise estimates. The estimators Chao 2 and incidence‐based coverage estimator (ICE) from this category were reliable and consistent slight over‐estimators; the abundance‐based estimator Chao1 also performed well. 5. Species inventory based on relatively small numbers of samples might be significantly improved by use of non‐parametric estimators for quantification of species richness. 6. Use of non‐parametric estimators of species richness can assist biodiversity inventory by preventing erroneous rankings of habitat richness based upon observed species numbers from limited sampling.     

Biodiversity of brachyuran crabs (Crustacea: Decapoda) from non-consolidated sublittoral bottom on the northern coast of São Paulo State, Brazil

The brachyuran community of the coast of São Paulo State is represented by about 188 species of crabs inhabiting different kinds of coastal marine environments. The biodiversity of brachyurans found on non-consolidated sublittoral bottom was investigated. The Ubatuba region (Ubatumirim, Ubatuba and Mar Virado bays, Couves and Mar Virado Islands, offshore region) was sampled for 3 years (1998–2000), at depths of 2–40 m. All sampling was performed using a fishing boat equipped with two double-rig nets. We collected 79 brachyuran species representing 9 superfamilies (4 Dromioidea, 1 Homoloidea, 2 Calappoidea, 5 Leucosioidea, 20 Majoidea, 7 Parthenopoidea, 17 Portunoidea, 18 Xanthoidea, and 5 Pinnotheroidea) and 41 genera. Ubatuba bay showed the greatest species richness with 50 species, followed by Ubatumirim with 45 and Mar Virado with 29. The number of species collected represents about 57% of the known species of crabs already reported for the shore of São Paulo State. It is worth noticing that this percentage is restricted only to non-consolidated sublittoral bottom. This fact indicates a great biodiversity of the habitat in this studied region, probably one to the diversity of habitat types present in the bays.     

The Diversity of Coral Reefs: What Are We Missing?

Tropical reefs shelter one quarter to one third of all marine species but one third of the coral species that construct reefs are now at risk of extinction. Because traditional methods for assessing reef diversity are extremely time consuming, taxonomic expertise for many groups is lacking, and marine organisms are thought to be less vulnerable to extinction, most discussions of reef conservation focus on maintenance of ecosystem services rather than biodiversity loss. In this study involving the three major oceans with reef growth, we provide new biodiversity estimates based on quantitative sampling and DNA barcoding. We focus on crustaceans, which are the second most diverse group of marine metazoans. We show exceptionally high numbers of crustacean species associated with coral reefs relative to sampling effort (525 species from a combined, globally distributed sample area of 6.3 m(2)). The high prevalence of rare species (38% encountered only once), the low level of spatial overlap (81% found in only one locality) and the biogeographic patterns of diversity detected (Indo-West Pacific>Central Pacific>Caribbean) are consistent with results from traditional survey methods, making this approach a reliable and efficient method for assessing and monitoring biodiversity. The finding of such large numbers of species in a small total area suggests that coral reef diversity is seriously under-detected using traditional survey methods, and by implication, underestimated.     

Six new non-native ants (Formicidae) in the Canary Islands and their possible impacts

Biological invasions are one of the main causes of biodiversity loss, especially on oceanic islands. Ants are among the most damaging pests in the world. After systematic sampling of more than 1,000 localities in the Canary Islands, six new exotic ant species are reported for the first time: Pheidole bilimeki (Myrmicinae), Pheidole navigans (Myrmicinae), Strumigenys membranifera (Myrmicinae), Brachymyrmex cordemoyi (Formicinae), Tapinoma darioi (Dolichoderinae) and Technomyrmex pallipes (Dolichoderinae). Moreover, another two recently reported species have been genetically confirmed. Morphological and genetic data were analysed to confirm the identity of the new records. For each species, information regarding identification, distribution, global invasive records and possible impacts is given. The arrival of these species may endanger local biodiversity.     

Bellwether of the Canaries: anthropogenic effects on the land snail fauna of the Canary Islands

Natural areas near human-modified landscapes experience factors that may affect local biodiversity at levels commensurate with natural environmental factors. The land snails of the Canary Islands provide excellent opportunities to evaluate the importance of anthropogenic agents in mediating the diversity and distribution of species. Land snails are particularly sensitive to disturbance and are an integral part of terrestrial ecosystems. This study analyzed the distributions and abundances of terrestrial macrosnail shell assemblages at 60 localities throughout the coastal scrub biome of the Canary Islands. This was accomplished using data on natural and anthropogenic variables to assess their relative importance in governing land snail diversity. A total of 34,801 dead shells represented a diverse malacofauna with highly localized endemism. Due to uncertain species identifications, samples from the 18 sites from the two easternmost islands are described, but excluded from statistical analyses. Regression tree analysis indicated that proximity to agricultural sites was the most important predictor of species diversity. Sites with no or very little agricultural area (≤ 0.167 km²) within a 1 km radius had significantly higher richness and diversity. These results have implications for Canary Islands conservation. Protected areas that are patchworks of natural and agricultural landscapes are still subject to native biodiversity loss because of anthropogenic impacts even when the footprint of agriculture is small.     

The relationship between percentage of singletons and sampling effort: A new approach to reduce the bias of richness estimates

Estimate the richness of a community with accuracy despite differences in sampling effort is a key aspect to monitoring high diverse ecosystems. We compiled a worldwide multitaxa database, comprising 185 communities, in order to study the relationship between the percentage of species represented by one individual (singletons) and the intensity of sampling (number of individuals divided by the number of species sampled). The database was used to empirically adjust a correction factor to improve the performance of non-parametrical estimators under conditions of low sampling effort. The correction factor was tested on seven estimators (Chao1, Chao2, Jack1, Jack2, ACE, ICE and Bootstrap). The correction factor was able to reduce the bias of all estimators tested under conditions of undersampling, while converging to the original uncorrected values at higher intensities. Our findings led us to recommend the threshold of 20 individuals/species, or less than 21% of singletons, as a minimum sampling effort to produce reliable richness estimates of high diverse ecosystems using corrected non-parametric estimators. This threshold rise for 50 individuals/species if non-corrected estimators are used which implies in an economy of 60% of sampling effort if the correction factor is used.