@article {Vanreusel:2010tg,
	title = {The contribution of deep-sea macrohabitat heterogeneity to global nematode diversity},
	journal = {Marine Ecology-An Evolutionary Perspective},
	volume = {31},
	year = {2010},
	pages = {6-20},
	publisher = {WILEY-BLACKWELL PUBLISHING, INC},
	address = {COMMERCE PLACE, 350 MAIN ST, MALDEN 02148, MA USA},
	abstract = {The great variety of geological and hydrological conditions in the deep sea generates many different habitats. Some are only recently explored, although their true extent and geographical coverage are still not fully established. Both continental margins and mid-oceanic seafloors are much more complex ecologically, geologically, chemically and hydrodynamically than originally thought. As a result, fundamental patterns of species distribution first observed and explained in the context of relatively monotonous slopes and abyssal plains must now be re-evaluated in the light of this newly recognized habitat heterogeneity. Based on a global database of nematode genus composition, collected as part of the Census of Marine Life, we show that macrohabitat heterogeneity contributes significantly to total deep-sea nematode diversity on a global scale. Different deep-sea settings harbour specific nematode assemblages. Some of them, like coral rubble zones or nodule areas, are very diverse habitats. Factors such as increased substrate complexity in the case of nodules and corals seem to facilitate the co-existence of a large number of genera with different modes of life, ranging from sediment dwelling to epifaunal. Furthermore, strong biochemical gradients in the case of vents or seeps are responsible for the success of particular genera, which are not prominent in more typical soft sediments. Many nematode deep-sea genera are cosmopolitan, inhabiting a variety of deep-sea habitats and oceans, whereas only 21\% of all deep-sea genera recorded are restricted to a single habitat. In addition to habitat heterogeneity, regional differences are important in structuring nematode assemblages. For instance, seeps from different regions yield different genera that thrive on the sulphidic sediments. This study also shows that many areas and habitats remain highly under-sampled, affecting our ability to understand fully the contribution of habitat heterogeneity versus regional differences to global nematode diversity.},
	keywords = {Biodiversity, census of marine life, deep sea, habitat heterogeneity, meiofauna, nematode genera},
	doi = {DOI 10.1111/j.1439-0485.2009.00352.x},
	author = {Vanreusel, Ann and Fonseca, Gustavo and Danovaro, Roberto and da Silva, Maria Cristina and Esteves, Andre M. and Ferrero, Tim and Gad, Gunnar and Galtsova, Valentina and Gambi, Cristina and Genevois, Veronica da Fonseca and Ingels, Jeroen and Ingole, Baban and Lampadariou, Nikolaos and Merckx, Bea and Miljutin, Dmitry and Miljutina, Maria and Muthumbi, Agnes and Netto, Sergio and Portnova, Daria and Radziejewska, Teresa and Raes, Maarten and Tchesunov, Alexei and Vanaverbeke, Jan and Van Gaever, Saskia and Venekey, Virag and Bezerra, Tania Nara and Flint, Hannah and Copley, John and Pape, Ellen and Zeppilli, Daniela and Martinez, Pedro Arbizu and Galeron, Joelle}
}
@booklet {Gallucci:2008ph,
	title = {Effects of megafauna exclusion on nematode assemblages at a deep-sea site},
	volume = {55},
	year = {2008},
	note = {Deep-Sea Research Part I-Oceanographic Research Papers},
	pages = {332-349},
	publisher = {PERGAMON-ELSEVIER SCIENCE LTD},
	address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND},
	abstract = {Caging experiments were performed at the Arctic deep-sea long-term observatory HAUSGARTEN to investigate the effects of megafauna exclusion on nematode assemblages. Six experimental cages were deployed at 2500 m water depth and sampled after 4 years for meiofauna and a series of sediment parameters. With the exception of chlorophyll a and phaeopigments, which were significantly higher inside the cages, sediment parameters did not differ between inside and outside the cages. Yet multivariate analysis of the sedimentary environment showed a higher variability outside the cages, indicating higher environmental heterogeneity in the presence of megafauna. Nematode densities (aver. 1516 ind 10 cm(-2)) were significantly higher in sediments from inside the cages, whereas total number of species (aver. 70 sp.), Shannon-Wiener diversity (aver. 3.4) and Pielou evenness (aver. 0.8) did not differ between the two treatments. Also differences in faunal multivariate structure between cage and control samples were not significant. Nevertheless, Fisher{\textquoteright}s alpha diversity, the number of nematode genera and taxonomic distinctness showed significantly higher values outside the cages. Since univariate measures are often insensitive to changes in community structure.. and interpretation of the multivariate analysis was confounded by the large number of rare species, we further analysed our data by dividing the species into three groups of frequency (frequent, intermediate and occasional) and into three groups of abundance (dominant, sub-dominant and scarce). Results from this analysis revealed that the higher nematode abundances inside the cages were mainly due to an increase in density of scarce species that were either frequent or intermediate in frequency. In contrast, occasional species were adversely affected. These results lead us to believe that it is mainly the frequent species occurring in low densities that take advantage of favourable conditions (i.e. lack of disturbance or increased phytodetritus) in the deep sea. The higher taxonomic distinctness, Fisher{\textquoteright}s diversity, and number of genera at the control sites, together with the fact that they were environmentally more heterogeneous, suggest that megafaunal organisms play an important role in creating microhabitats in the sediment and significantly influence deep-sea nematode assemblages. However, the lack of any changes in species richness inside the cages after 4 years suggests that they cannot fully account for the maintenance of the remarkable high levels of species coexistence in the deep sea. The key is more likely to be found in evolutionary history than actual ecology. (c) 2007 Elsevier Ltd. All rights reserved.},
	keywords = {Biodiversity, biological disturbance, caging experiment, sediment heterogeneity},
	doi = {DOI 10.1016/j.dsr.2007.12.001},
	author = {Gallucci, Fabiane and Fonseca, Gustavo and Soltwedel, Thomas}
}
@article {Widdicombe:2009qr,
	title = {Effects of CO2 induced seawater acidification on infaunal diversity and sediment nutrient fluxes},
	journal = {Marine Ecology-Progress Series},
	volume = {379},
	year = {2009},
	pages = {59-75},
	publisher = {INTER-RESEARCH},
	address = {NORDBUNTE 23, D-21385 OLDENDORF LUHE, GERMANY},
	abstract = {A mesocosm experiment was conducted to quantify the effects of short- (2 wk) and long-term (20 wk) exposure to acidified seawater on the structure and diversity of macrofaunal and nematode assemblages in 2 different sediment. types. The impact of acidified seawater on sediment nutrient fluxes was also determined. Using carbon dioxide (CO2) gas, seawater was acidified to pH 7.3 (mimicking ocean acidification), 6.5 or 5.6 (mimicking leakage from a sub-seabed CO2 store site). Control treatments were maintained in natural seawater [pH approximate to 8.0). Exposure to acidified seawater significantly altered community structure and reduced diversity for both macrofaunal and nematode assemblages, However, the impact on nematodes was less severe than that on macrofauna. While the communities in both sediment types were significantly affected by changes in seawater pH, impacts on sandy sediment fauna were greater than those on muddy sediment fauna. Sandy sediments also showed the greatest effects with respect to nutrient fluxes. In sand, the efflux of nitrite, nitrate and silicate decreased in response to increased acidification while the efflux of ammonium increased, In mud, acidification increased the efflux of ammonium but had no effect on the other nutrients. We conclude that both leakage from carbon storage and ocean acidification could cause significant changes in the structure and diversity of coastal sediment communities. Lowered seawater pH could also affect nutrient cycling directly by altering bacterial communities and indirectly through impacts on the abundance and activity of key bioturbators.},
	keywords = {Biodiversity, Carbon storage, Macrofauna, meiofauna, Nutrient flux, Ocean acidification},
	doi = {DOI 10.3354/meps07894},
	author = {Widdicombe, S. and Dashfield, S. L. and McNeill, C. L. and Needham, H. R. and Beesley, A. and McEvoy, A. and Oxnevad, S. and Clarke, K. R. and Berge, J. A.}
}
@article {Porazinska:2009yq,
	title = {Evaluating high-throughput sequencing as a method for metagenomic analysis of nematode diversity},
	journal = {Molecular Ecology Resources},
	volume = {9},
	year = {2009},
	pages = {1439-1450},
	publisher = {WILEY-BLACKWELL PUBLISHING, INC},
	address = {COMMERCE PLACE, 350 MAIN ST, MALDEN 02148, MA USA},
	abstract = {Nematodes play an important role in ecosystem processes, yet the relevance of nematode species diversity to ecology is unknown. Because nematode identification of all individuals at the species level using standard techniques is difficult and time-consuming, nematode communities are not resolved down to the species level, leaving ecological analysis ambiguous. We assessed the suitability of massively parallel sequencing for analysis of nematode diversity from metagenomic samples. We set up four artificial metagenomic samples involving 41 diverse reference nematodes in known abundances. Two samples came from pooling polymerase chain reaction products amplified from single nematode species. Two additional metagenomic samples consisted of amplified products of DNA extracted from pooled nematode species. Amplified products involved two rapidly evolving similar to 400-bp sections coding for the small and large subunit of rRNA. The total number of reads ranged from 4159 to 14771 per metagenomic sample. Of these, 82\% were > 199 bp in length. Among the reads > 199 bp, 86\% matched the referenced species with less than three nucleotide differences from a reference sequence. Although neither rDNA section recovered all nematode species, the use of both loci improved the detection level of nematode species from 90 to 97\%. Overall, results support the suitability of massively parallel sequencing for identification of nematodes. In contrast, the frequency of reads representing individual species did not correlate with the number of individuals in the metagenomic samples, suggesting that further methodological work is necessary before it will be justified for inferring the relative abundances of species within a nematode community.},
	keywords = {454 genome sequencer FLX, Biodiversity, DNA barcoding, high-throughput sequencing, metagenomic, nematode},
	doi = {DOI 10.1111/j.1755-0998.2009.02611.x},
	author = {Porazinska, Dorota L. and Giblin-Davis, Robin M. and Faller, Lina and Farmerie, William and Kanzaki, Natsumi and Morris, Krystalynne and Powers, Thomas O. and Tucker, Abraham E. and Sung, Way and Thomas, W. Kelley}
}
@article {Schander:2005tm,
	title = {What can biological barcoding do for marine biology?},
	journal = {Marine Biology Research},
	volume = {1},
	year = {2005},
	pages = {79-83},
	publisher = {TAYLOR \& FRANCIS AS},
	address = {PO BOX 12 POSTHUSET, NO-0051 OSLO, NORWAY},
	abstract = {The idea of using nucleotide sequences as barcodes for species identification has stirred up debates in the community of taxonomists and systematists. We argue that barcodes are potentially extremely useful tools for taxonomy for several reasons. Barcodes may, for example, help to identify cryptic and polymorphic species and give means to associate life history stages of unknown identity. Barcode systems would thus be particularly helpful in cases when morphology is ambiguous or uninformative and would provide tools for higher taxonomic resolution of disparate life forms. Comparative analysis of short DNA sequences may also represent heuristic access cards to a deeper understanding of evolutionary relationships between organisms. However, barcodes are the "essence{\textquoteright}{\textquoteright} of species identities no more than taxonomic holotypes are "the species{\textquoteright}{\textquoteright}. It makes no sense to think that morphology and other biological information about organisms can be made obsolete by barcode systems. The biological significance of matching or diverging nucleotide sequences will still have to be the subject of taxonomic decisions that must be open for scrutiny. It is imperative, therefore, that barcodes are associated with specimen vouchers.},
	keywords = {Biodiversity, diagnostics, DNA barcodes, identification, taxonomy},
	doi = {DOI 10.1080/17451000510018962},
	author = {Schander, C and Willassen, E}
}
@article {Abebe:2008xy,
	title = {Global diversity of nematodes (Nematoda) in freshwater},
	journal = {Hydrobiologia},
	volume = {595},
	year = {2008},
	pages = {67-78},
	publisher = {SPRINGER},
	address = {VAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDS},
	abstract = {Despite free-living nematodes being present in all types of limnetic habitats including unfavorable conditions that exclude many other meiobenthic invertebrates, they received less attention than marine and terrestrial forms. Two-fifths of the nematode families, one-fifth of the nearly 1800 genera and only 7\% of the about 27,000 nominal species are recorded from freshwater habitats. The Dorylaimia are the most successful in freshwater habitats with nearly two-thirds of all known freshwater nematodes belonging to this subclass. Members of the subclass Enoplia are principally marine though include some exclusively freshwater taxa with extreme endemism. The subclass Chromadoria includes half of the freshwater nematode families and members of the Monhysterida and Plectida are among the most widely reported freshwater nematodes. Studies on freshwater nematodes show extreme regional bias; those from the southern hemisphere are extremely underrepresented, especially compared to European freshwater bodies. The majority of records are from a single biogeographic region. Discussion on nematode endemism is largely premature since apart from Lake Baikal, the nematofauna of ancient lakes as centers of speciation is limited and recent discoveries show high nematode abundance and diversity in cryptic freshwater bodies, underground calcrete formations and stromatolite pools potentially with a high number of new taxa.},
	keywords = {Biodiversity, distribution, free-living nematodes, freshwater nematodes, Global estimate, nematode biogeography},
	doi = {DOI 10.1007/s10750-007-9005-5},
	author = {Abebe, Eyualem and Decraemer, Wilfrida and De Ley, Paul}
}
