DNA barcodes for soil animal taxonomy

Abstract

-The biodiversity of soil communities remains very poorly known and understood. Soil biological sciences are strongly affected by the taxonomic crisis, and most groups of animals in that biota suffer from a strong taxonomic impediment. The objective of this work was to investigate how DNA barcoding -a novel method using a microgenomic tag for species identifi cation and discrimination -permits better evaluation of the taxonomy of soil biota. A total of 1,152 barcode sequences were analyzed for two major groups of animals, collembolans and earthworms, which presented broad taxonomic and geographic sampling. Besides strongly refl ecting the taxonomic impediment for both groups, with a large number of species-level divergent lineages remaining unnamed so far, the results also highlight a high level (15%) of cryptic diversity within known species of both earthworms and collembolans. These results are supportive of recent local studies using a similar approach. Within an impeded taxonomic system for soil animals, DNA-assisted identifi cation tools can facilitate and improve biodiversity exploration and description. DNA-barcoding campaigns are rapidly developing in soil animals and the community of soil biologists is urged to embrace these methods.Index terms: Collembola, cryptic diversity, DNA barcoding, Oligochaeta, species identifi cation, taxonomic crisis, taxonomic impediment. Código de barras de DNA para a taxonomia de animais do soloResumo -A biodiversidade das comunidades do solo continua muito pouco conhecida e entendida. A biologia do solo é fortemente afetada pela crise taxonômica, e a maior parte dos grupos de animais dessa biota sofre forte impedimento taxonômico. O objetivo deste trabalho foi determinar como o código de barras de DNA -um método novo que usa uma etiqueta microgenômica para identifi cação e discriminação de espécies -permite uma melhor avaliação da taxonomia da biota edáfi ca. Foram analisadas 1.152 sequências de códigos de barras de dois grupos principais de animais, colêmbolos e minhocas, que apresentaram ampla amostragem taxonômica e geográfi ca. Além de refl etir fortemente o impedimento taxonômico de ambos os grupos, com um grande número de linhagens divergentes no nível da espécie que ainda não está descrita, os resultados também destacam um alto (15%) nível de diversidade críptica dentro de espécies conhecidas de minhocas e colêmbolos. Esses resultados apóiam estudos locais recentes que usaram métodos similares. Considerando as difi culdades taxonômicas enfrentadas para identifi car os animais de solo, ferramentas de identifi cação usando DNA podem facilitar e melhorar a exploração da biodiversidade e a sua descrição. As campanhas de código de barras de DNA estão se desenvolvendo rapidamente com animais do solo, e a comunidade de biólogos é incitada a adotar esses métodos.Termos para indexação: Collembola, diversidade críptica, código de barras de DNA, Oligochaeta, identifi cação de espécies, crise taxonômica, impedimento taxonômico.

Asian pheretimoid earthworms in North America north of Mexico: An illustrated key to the genera Amynthas, Metaphire, Pithemera, and Polypheretima (Clitellata: Megascolecidae)

“…As the three species all have manicate intestinal caeca and, due to parthenogenetic degradation, may bear two pairs or fewer spermathecal pores, species identification based entirely on morphology becomes impossible when male pores and genital markings are both absent. In this extreme case, DNA barcoding (Chang et al 2009b;Rougerie et al 2009) may become necessary. Fortunately, to our knowledge, this extreme situation has rarely been the case for US specimens, among which the majority of A. agrestis have three spermathecal pores on one or both sides of the body, and the majority of M. hilgendorfi have two pairs of spermathecal pores and distinct patches of pre-clitellar genital markings.…”

Variability of sexual organ possession rates and phylogenetic analyses of a parthenogenetic Japanese earthworm, Amynthas vittatus (Oligochaeta: Megascolecidae)

“…Recently, numerous molecular phylogenetic studies on earthworms have been conducted (Jamieson et al, 2002;Pop et al, 2003Pop et al, , 2007Heethoff et al, 2004;Pérez-Losada et al, 2005Chang et al, , 2007Chang et al, , 2008Chang et al, , 2009Admassu et al, 2006;Huang et al, 2007;King et al, 2008;Cameron et al, 2008;Minamiya et al, 2009;Richard et al, 2009;Novo et al, 2009Novo et al, , 2010Knott and Haimi, 2010). Many of these studies used the mitochondrial DNA (mtDNA) cytochrome oxidase subunit I (COI) gene (Pop et al, 2003(Pop et al, , 2007Pérez-Losada et al, 2005Admassu et al, 2006;Chang et al, 2007Chang et al, , 2008Chang et al, , 2009Huang et al, 2007;King et al, 2008;Cameron et al, 2008;Minamiya et al, 2009;Rougerie et al, 2009;Novo et al, 2009Novo et al, , 2010Knott and Haimi, 2010) because of the ease of primer design and the range of phylogenetic signals and rapid evolutionary rate of this gene (Hebert et al, 2003). To clarify the phylogenetic relationships of A. vittatus with different degree of degraded reproductive organs, we examined the morphological variations, such as the possession rate of both the male and spermathecal pores in A. vittatus found in various locations in Sendai city around Mt.…”

Interaction between Soil Physicochemical Parameters and Earthworm Communities in Irrigated Areas with Natural Water and Wastewaters

“…Taxonomic study was carried out on a total of 594 adult worms. The taxonomic key and nomenclature quoted by Rougerie et al [18] allowed classification of 7 species of Lumbricidae: Aporrectodea trapezoides (Dugés, 1828), Aporrectodea rosea (Savigny, 1826), Aporrectodea caliginosa (Savigny, 1826), Allolobophora molleri (Rosa, 1889), Octodrilus complanatus (Dugés, 1828), Eiseniella tetraedra tetraedra (Savigny, 1826), and Proctodrilus antipai antipai (Michaelsen, 1891).…”

“…This very varied biogeographic space in terms of climate, soil, and vegetation from the littoral to the desert could reveal a great diversity of earthworms with certainly species very adapted to the drought. Studies on this subject are difficult: on one hand, identification and classification of these organisms remain difficult due to lack of qualified taxonomists [18] and, on the other hand, study of earthworms is not obvious due to several constraints related to nature of soil and the complexity of these organisms [19].…”