Species richness and taxonomic distinctness of lake macrophytes along environmental gradients in two continents

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天津近海自由生活线虫多样性分析

2007年4月在面临高度开发的天津近岸海域,对沉积物中自由生活的线虫样品进行了采集,并分析了其多样性,为生物多样性研究和环境监测提供科学数据.结果表明,该海域自由生活线虫有80余种,生物丰度以拉氏矛咽线虫Dorylaimopsis rabalais的优势最突出.调查海域的沉积物虽然受到了一定的污染,但其污染状况并不恶劣.垂直的层次分析表明一些多样性指数受采样深度影响,分析时应关注采样深度.     

Soil nematode biodiversity in terrestrial ecosystems

A review of the literature on nematode diversity (=number of species identified) of soil inhabiting nematodes was undertaken and analysed with regard to distance from the equator, vegetation type and sampling effort. After applying a correction factor for sampling effort the results indicated that species richness was greatest in temperate broadleaf forest (61.7 species per sample) followed by cultivated soil, grassland, tropical rainforest, temperate coniferous forests and polar vegetation. The maintenance of high biodiversity in cultivated soils is unexpected but may reflect the impact of dominance in calculating many indices. Species richness was greatest between latitudes 30–40° (93.9 species per sample) and least above 70°, the mean richness near the equator (i.e. 0–10°) was 80.6 species per sample. While these data would suggest that nematode diversity is not necessarily greatest at the equator, and evidence to support a 'humped back' theory of species richness is not conclusive, they contradict the suggestion that nematode diversity increases with increased latitude.     

A test of traditional diversity measures and taxonomic distinctness indices on benthic diatoms of soda pans in the Carpathian basin

Saline lakes are threatened all over the world and their conservation has been a key issue. Various diversity indices are available for ecological status assessments, however, with poorly explored relevance and applicability in saline, alkaline pans. Therefore, traditional diversity measures (species richness and Shannon diversity) and taxonomic distinctness indices (Average [AvTD] and Variance of Taxonomic Distinctness [VarTD]) were tested in more than 100 sampling sites of 39 soda pans in Central-Europe to find sufficient indicators of the ecological condition and simultaneously to facilitate their preservation according to the modern conservation practices. Results of the analyses showed that healthy soda pan ecosystems with high level of natural stress and reduced habitat heterogeneity are characterized by low diversity diatom assemblages. In soda pans where the stress can be extremely high from natural reasons, oligopoly of closely related species can develop: the average taxonomic distinctness appeared between genus and family level. The non-DNA-sequence based phylogenetic diversity measures (AvTD and VarTD), were generally sensitive to the trophic state of the lakes, in contrast to traditional diversity metrics, which were unequivocally indicative for the special physical and chemical parameters (e.g. conductivity, pH) of the soda pans. In some cases, when the response of the diversity measures for a given environmental variable (pH, temperature) overlapped, the AvTD was found to be a more precise indicator of the environmental changes (pH) than traditional ones. The decreasing tendency of the AvTD along the intensified natural impact may be explained by the long available time for the species to adapt to these special environments.     

Molecular profiling of nematode associates with Rhynchophorus ferrugineus in southern Italy

A survey of nematodes associated with the red palm weevil Rhynchophorus ferrugineus was conducted in southern Italy in 2015 and 2016 in order to create a species inventory and obtain data about nematode biodiversity. A total of 70 insect samples (pupae and adults) were collected from infested Phoenix canariensis, Phoenix dactylifera, and Chamaerops humilis palms in three Italian Regions: sampling took place at 11 locations in Apulia, 1 in Basilicata, and 1 in Sardinia regions. Individual insects were dissected to determine nematode presence, and different nematode species were also recovered from red palm weevil cocoons collected at the sites in Apulia. Individual nematodes were molecularly identified by sequencing the ITS, D2‐D3 expansion domains of the 28SrRNA gene and the mitochondrial COI and inferring the phylogenetic relationships. The insect‐associated nematofauna identified belonged to the families Rhabditidae, Cephalobidae, and Diplogastridae. Just two nematode species, Teratorhabditis synpapillata and Mononchoides macrospiculum, were always found in association with adult insects and cocoons taken from all sampling sites. This paper reports on the biodiversity of the nematodes associated with R. ferrugineus and on current knowledge of the specific habitat of specialized and divergent entomophilic nematodes.     

Free-living marine nematodes from San Julián Bay (Santa Cruz,Argentina)

The free-living marine nematodes of San Julián Bay dataset is based on sediment samples collected in January 2009 during the project PICT AGENCIA-FONCYT 2/33345-2005. A total of 36 samples have been taken at three locations in the San Julián Bay, Santa Cruz Province, Argentina on the coastal littoral at three tidal levels. This presents a unique and important collection for the nematode benthic biodiversity assessment as this area remains one of the least known regions in Patagonia. In total 10,030 specimens of free-living marine nematodes belonging to 2 classes, 9 orders, 35 families, 78 genera and 125 species were collected. The San Julián city site presented a very high species richness.     

Local scale processes drive long‐term change in biodiversity of sandy beach ecosystems

Evaluating impacts to biodiversity requires ecologically informed comparisons over sufficient time spans. The vulnerability of coastal ecosystems to anthropogenic and climate change‐related impacts makes them potentially valuable indicators of biodiversity change. To evaluate multidecadal change in biodiversity, we compared results from intertidal surveys of 13 sandy beaches conducted in the 1970s and 2009–11 along 500 km of coast (California, USA). Using a novel extrapolation approach to adjust species richness for sampling effort allowed us to address data gaps and has promise for application to other data‐limited biodiversity comparisons. Long‐term changes in species richness varied in direction and magnitude among beaches and with human impacts but showed no regional patterns. Observed long‐term changes in richness differed markedly among functional groups of intertidal invertebrates. At the majority (77%) of beaches, changes in richness were most evident for wrack‐associated invertebrates suggesting they have disproportionate vulnerability to impacts. Reduced diversity of this group was consistent with long‐term habitat loss from erosion and sea level rise at one beach. Wrack‐associated species richness declined over time at impacted beaches (beach fill and grooming), despite observed increases in overall intertidal richness. In contrast richness of these taxa increased at more than half (53%) of the beaches including two beaches recovering from decades of off‐road vehicle impacts. Over more than three decades, our results suggest that local scale processes exerted a stronger influence on intertidal biodiversity on beaches than regional processes and highlight the role of human impacts for local spatial scales. Our results illustrate how comparisons of overall biodiversity may mask ecologically important changes and stress the value of evaluating biodiversity change in the context of functional groups. The long‐term loss of wrack‐associated species, a key component of sandy beach ecosystems, documented here represents a significant threat to the biodiversity and function of coastal ecosystems.     

Sandy beaches at the brink

Sandy beaches line most of the world's oceans and are highly valued by society: more people use sandy beaches than any other type of shore. While the economic and social values of beaches are generally regarded as paramount, sandy shores also have special ecological features and contain a distinctive biodiversity that is generally not recognized. These unique ecosystems are facing escalating anthropogenic pressures, chiefly from rapacious coastal development, direct human uses — mainly associated with recreation — and rising sea levels. Beaches are increasingly becoming trapped in a 'coastal squeeze' between burgeoning human populations from the land and the effects of global climate change from the sea. Society's interventions (e.g. shoreline armouring, beach nourishment) to combat changes in beach environments, such as erosion and shoreline retreat, can result in severe ecological impacts and loss of biodiversity at local scales, but are predicted also to have cumulative large-scale consequences worldwide. Because of the scale of this problem, the continued existence of beaches as functional ecosystems is likely to depend on direct conservation efforts. Conservation, in turn, will have to increasingly draw on a consolidated body of ecological theory for these ecosystems. Although this body of theory has yet to be fully developed, we identify here a number of critical research directions that are required to progress coastal management and conservation of sandy beach ecosystems.     

Exploring the use of cytochrome oxidase c subunit 1 (COI) for DNA barcoding of free-living marine nematodes

Background

The identification of free-living marine nematodes is difficult because of the paucity of easily scorable diagnostic morphological characters. Consequently, molecular identification tools could solve this problem. Unfortunately, hitherto most of these tools relied on 18S rDNA and 28S rDNA sequences, which often lack sufficient resolution at the species level. In contrast, only a few mitochondrial COI data are available for free-living marine nematodes. Therefore, we investigate the amplification and sequencing success of two partitions of the COI gene, the M1-M6 barcoding region and the I3-M11 partition.

Methodology

Both partitions were analysed in 41 nematode species from a wide phylogenetic range. The taxon specific primers for the I3-M11 partition outperformed the universal M1-M6 primers in terms of amplification success (87.8% vs. 65.8%, respectively) and produced a higher number of bidirectional COI sequences (65.8% vs 39.0%, respectively). A threshold value of 5% K2P genetic divergence marked a clear DNA barcoding gap separating intra- and interspecific distances: 99.3% of all interspecific comparisons were >0.05, while 99.5% of all intraspecific comparisons were <0.05 K2P distance.

Conclusion

The I3-M11 partition reliably identifies a wide range of marine nematodes, and our data show the need for a strict scrutiny of the obtained sequences, since contamination, nuclear pseudogenes and endosymbionts may confuse nematode species identification by COI sequences.     

Genetic variability and differentiation of three Russian populations of potato cyst nematode <Emphasis Type="Italic">Globodera rostochiensis</Emphasis> as revealed by nuclear markers

Genetic variability of yellow potato cyst nematode G. rostochiensis from three Russian populations (Karelia, Vladimir oblast, and Moscow oblast) was investigated using two types of nuclear markers. Using RAPD markers identified with the help of six random primers (P-29, OPA-10, OPT-14, OPA-11, OPB-11, and OPH-20), it was possible to distinguish Karelian population from the group consisting of the populations from two adjacent regions (Moscow oblast and Vladimir oblast). Based on the combined matrix, containing 294 RAPD fragments, dendrogram of genetic differences was constructed, and the indices of genetic divergence and partition (P, H, and G _st), as well as the gene flow indices N _m between the nematode samples examined, were calculated. The dendrogram structure, genetic diversity indices, and variations of genetic distances between single individuals in each population from Karelia and Central Russia pointed to genetic isolation and higher genetic diversity of the nematodes from Karelia.Based on polymorphism of rDNA first intergenic spacer ITS1, attribution of all populations examined to the species G. rostochiensis was proved. Small variations of the ITS1 sequence in different geographic populations of nematodes from different regions of the species world range did not allow isolation of separate groups within the species. Possible factors (including interregional transportations of seed potato) affecting nematode population structure in Russia are discussed.     

The fungal matrices of <Emphasis Type="Italic">Ophiostoma ips</Emphasis> hinder movement of the biocontrol nematode agent, <Emphasis Type="Italic">Deladenus siricidicola</Emphasis>, disrupting management of the woodwasp, <Emphasis Type="Italic">Sirex noctilio</Emphasis>

Deladenus (=?Beddingia) siricidicola (Tylenchida: Neotylenchidae) is the most effective biocontrol agent used against the invasive wood wasp, Sirex noctilio (Fabricius) (Hymenoptera: Siricidae). The nematodes feed and reproduce on the wood-inhabiting fungus, Amylostereum areolatum (Chaillet ex Fr.) Boidin (Russulales: Amylostereaceae) and parasitise larvae of S. noctilio. In the nematode biocontrol program, the nematodes are inoculated into herbicide-weakened ‘trap trees’. Recent declines in nematode parasitism of S. noctilio in Australia have coincided with an increased incidence of an exotic bark beetle, Ips grandicollis (Eichhoff) (Coleoptera: Curculionidae), attacking trap trees and vectoring a wood-inhabiting fungus, Ophiostoma ips (Rumbold) Nannfelt (Ophiostomatales: Ophiostomataceae), which may inhibit migration of the nematode within the tree to the detriment of S. noctilio biocontrol. Several in vitro and in vivo experiments were conducted to investigate the effect of fungal interactions on the ability of D. siricidicola to locate and reproduce on A. areolatum. Deladenus siricidicola showed preference to A. areolatum in the presence and absence of O. ips, but the presence of O. ips negatively affected the choice response and the number of eggs laid by the nematodes. Deladenus siricidicola was unable to survive and reproduce on O. ips. Results give a clearer understanding of the choice response of D. siricidicola in I. grandicollis infested trees, explaining the disruptive impact of bark beetles on biocontrol of S. noctilio, an effect that could extend from Australia to other important pine growing countries.     

Role of Nematodes in Soil Health and Their Use as Indicators

The composition of nematode communities (plant-parasitic and free-living) may be used as bioindicators of soil health or condition because composition correlates well with nitrogen cycling and decomposition, two critical ecological processes in soil. Maturity and trophic diversity indices withstand statistical rigor better than do abundances, proportions, or ratios of trophic groups. Maturity indices respond to a variety of land-management practices, based largely on inferred life history characteristics of families. Similarity indices may be more useful than diversity indices because they reflect taxon composition. Improving existing indices or developing alternative indices refined by a greater understanding of the biology of key taxa may enhance the utility of nematodes as bioindicators.     

Highly diverse community structure in a remote central Tibetan geothermal spring does not display monotonic variation to thermal stress

We report an assessment of whole-community diversity for an extremely isolated geothermal location with considerable phylogenetic and phylogeographic novelty. We further demonstrate, using multiple statistical analyses of sequence data, that the response of community diversity is not monotonic to thermal stress along a gradient of 52-83 degrees C. A combination of domain- and division-specific PCR was used to obtain a broad spectrum of community phylotypes, which were resolved by denaturing gradient gel electrophoresis. Among 58 sequences obtained from microbial mats and streamers, some 95% suggest novel archaeal and bacterial diversity at the species level or higher. Moreover, new phylogeographic and thermally defined lineages among the Cyanobacteria, Chloroflexi, Eubacterium and Thermus are identified. Shannon-Wiener diversity estimates suggest that mats at 63 degrees C supported highest diversity, but when alternate models were applied [Average Taxonomic Distinctness (AvTD) and Variation in Taxonomic Distinctness (VarTD)] that also take into account the phylogenetic relationships between phylotypes, it is evident that greatest taxonomic diversity (AvTD) occurred in streamers at 65-70 degrees C, whereas greatest phylogenetic distance between taxa (VarTD) occurred in streamers of 83 degrees C. All models demonstrated that diversity is not related to thermal stress in a linear fashion.     

Crustaceans as ecological indicators of metropolitan sandy beaches health

We have investigated how indices of beach health perform in predicting the abundances of the crustaceans Emerita brasiliensis and Atlantorchestoidea brasiliensis from 22 metropolitan beaches in the cities of Rio de Janeiro and Niterói. Urbanization, Recreation and Conservation indices were used to assess sandy beaches health. Grain size and beach slope were used as morphodynamics indicators. Diagram from the principal component analysis clearly separated beaches with different urbanization and conservation levels. Generalized additive models (GAM's) were adjusted for species abundance using the indices and morphodynamic parameters as explanatory variables. Lower abundances were predicted for beaches with high levels of urbanization, whereas predictions of higher abundances occurred on beaches with high conservation levels. Using theoretic inference we showed that the urbanization index was the most important predictor for abundance of A. brasiliensis and the conservation index was the most important predictor for E. brasiliensis, reflecting different responses by upper tidal and intertidal species. A. brasiliensis occupies the intermediate and upper beach zones and E. brasiliensis is a swash zone filter-feeder that is more abundant in pristine beaches. Both species are highly subject to the impact of bathers and coastal modification. Unexpected, the recreation index did not show a negative effect on abundance predictions. Urbanization and conservation indices can be suitable metrics to measure anthropogenic effects on macrobenthic species. Moreover, mole crabs and sandhoppers species can be easily monitored. Coastal urbanization is a global phenomenon and we used the diagram of urbanization and conservation levels to expose possible directions for management strategies of metropolitan sandy beaches.     

The functional role and diversity of soil nematodes are stronger at high elevation in the lesser Himalayan Mountain ranges

Soil nematodes are a foremost component of terrestrial biodiversity; they display a whole gamut of trophic guilds and life strategies, and by their activity, affect major ecosystem process, such as organic matter degradation and carbon cycling. Based on nematodes'' functional types, nematode community indices have been developed, and can be used to link variation in nematodes community composition and ecosystem processes. Yet, the use of these indices has been mainly restricted to anthropogenic stresses. In this study, we propose to expand the use of nematodes'' derived ecological indices to link soil and climate properties with soil food webs, and ecosystem processes that all vary along steep elevation gradients. For this purpose, we explored how elevation affects the trophic and functional diversity of nematode communities sampled every 300 m, from about 1,000 m to 3,700 m above sea level, across four transects in the lesser Himalayan range of Jammu and Kashmir. We found that (a) the trophic and functional diversity of nematodes increases with elevation; (b) differences in nematodes communities generate habitat‐specific functional diversity; (c) the maturity index (ΣMI) increases with elevation, while the enrichment index decreases, indicating less mature and less productive ecosystems, enhanced fungal‐based energy flow, and a predominant role of nematodes in generating carbon influxes at high‐elevation sites. We thus confirm that the functional contribution of soil nematodes to belowground ecosystem processes, including carbon and energy flow, is stronger at high elevation. Overall, this study highlights the central importance of nematodes in sustaining soil ecosystems and brings insights into their functional role, particularly in alpine and arctic soils.     

Development of a polymerase chain reaction-based denaturing gradient gel electrophoresis technique to study nematode species biodiversity using the 18s rDNA gene

A polymerase chain reaction (PCR)-based denaturing gradient gel electrophoresis (DGGE) technique was developed to evaluate nematode biodiversity. Amplified fragments (approximately 630 bp) of nematode 18S rDNA could be separated by DGGE at 60 °C for 5.5 h using a gradient of 30–55% denaturant. No DNA from the nematodes’ food source was observed on the gels. The sensitivity of the system was tested using DNA from six species of Steinernema. The system clearly separated PCR fragments from all species except S. tami and S. carpocapsae, which had similar melting behaviour despite being widely separated on the phylogenetic tree.     

Reproducibility of read numbers in high-throughput sequencing analysis of nematode community composition and structure

Although nematodes are the most abundant metazoan animals on Earth, their diversity is largely unknown. To overcome limitations of traditional approaches (labour, time, and cost) for assessing biodiversity of nematode species in environmental samples, we have previously examined the suitability of high-throughput sequencing for assessing species level diversity with a set of control experiments employing a mixture of nematodes of known number and with known sequences for target diagnostic loci. Those initial experiments clearly demonstrated the suitability of the approach for identification of nematode taxa but lacked the replicate experiments necessary to evaluate reproducibility of the approach. Here, we analyze reads generated from three different PCR amplifications and three different sequencing reactions to examine the differential PCR amplification, the possibility of emulsion PCR artefacts, and differences between sequencing reactions. Our results suggest that both qualitative and quantitative data are consistent and highly reproducible. Variation associated with in-house PCR amplification or emPCR and sequencing are present but the representation of each nematode is very consistent from experiment to experiment and supports the use of read counts to estimate relative abundance of taxa in a metagenetic sample.     

Soil free-living nematodes as indicators of both industrial pollution and livestock activity in Central Asia

The effect of industrial pollution on soil free-living nematode communities, trophic groups, and taxon composition was investigated along an 18-km transect that included the Angren power plant, a gold-refinery plant, farm areas, and recreation areas. Soil samples were collected in May 2005 and October 2006 from the upper (0–10 and 10–20 cm) soil layers in downwind directions from the industrial complex emission sources of the Angren industrial sites.Direct and indirect (through soil property changes), separate and integrated effects of industrial pollution and livestock activity on the soil nematode community were found. The total number of nematodes was found to be negatively correlated with the amounts of chemical elements in soil and positively correlated with the calcium concentration in soil. The nematode communities, trophic diversity, and taxon composition were found to be affected by the variety and concentration of chemical elements.The widely used ecological indices applied in the present research were sensitive to environmental disturbances caused by industrial pollution as well as livestock activity. The Wasilewska index, nematode channel ratio, and maturity index were mostly affected by trace metal concentration, while the diversity indices and species richness were mostly affected by soil property changes. The nematode channel ratio indicated that the bacterial-based decomposition process was dominant in soils exposed to both strong industrial pollution and livestock activity. The diversity indices indicated the disappearance of rare species in the industrial area and an increase of the contribution of common nematodes with increasing depth and distance from the unfavorable area. The current study confirmed that the grazing in accompaniment to industrial pollution, intensify a negative effect on soil nematode communities.     

Response of soil nematode community structure and diversity to long-term land use in the black soil region in China

Soil nematodes are sensitive to environmental changes and are used widely as indicators of soil conditions. The community structure and diversity of soil nematodes were studied in different long-term land use regimes in the black soil area in Northeast China. The land use regimes were maintained for 22?years, and included crop land (CL), grass land (GL) and bare land (BL). Soil samples were taken throughout the growing season, and nematodes were extracted and identified. A total of 39 nematode genera with relative abundance over 0.1?% were identified. Heterodera was the dominant genus in CL; Boleodorus was the dominant genus in GL, and Boleodorus, Eucephalobus and Filenchus were the dominant genera in BL. Land use had a significant effect on abundance of all soil nematode tropic groups and ecological indices. Sampling time had an effect on soil nematode abundance, but only on three of the eight nematode ecological indices MI (maturity index of free-living nematode), CI (channel index) and EI (enrichment index). SR (species richness index) was highest in GL where plant species diversity was also high. The CI was the highest in BL among three land uses, which means the soil food web dominated, with fungal decomposition channels in BL. Soil nematode community structure and diversity was shown to be an effective and informative tool for analyzing ecological aspects of land use in black soil regions. The data are inconclusive as to whether the effect of land use on soil nematode parameters is direct, or indirect via inducing changes in soil physicochemical properties.     

Response of the wheat rhizosphere soil nematode community in wheat/walnut intercropping system in Xinjiang,Northwest China

Intercropping Persian walnut (Juglans regia L.) and wheat (Triticum aestivum L.) have been widely applied in the Xinjiang Uygur Autonomous Region in Northwest China as a means of reducing soil and water losses and improving both land-use efficiency and economic returns. To understand how changes in soil conditions and nematode community structure can contribute to the evaluation of wheat–walnut intercropping systems from the view of soil fauna, we studied the soil nematode community in wheat rhizosphere soil under both monoculture and intercropping systems for 2 years. The results showed that the pH and total nitrogen and organic matter contents in intercropping systems with walnut trees were decreased compared with those of system with wheat alone. The nematode communities differed significantly between intercropping and monoculture plots, e.g., Rhabditis and Dorylaimus were dominant only in monocultures, whereas Tylenchus was dominant only in intercropping systems. Moreover, intercropping systems resulted in decreased nematode abundance, increased proportions of plant-feeding nematodes, and decreased omnivores/predators, particularly in the second year (2012). The decrease in diversity indices (H′) and ecological indices (WI, EI, and SI) of the nematode communities indicated high disturbance and low soil fertility in intercropping systems. Overall, wheat intercropping with walnut had a significant negative effect on wheat rhizosphere soil conditions.