Ignacio H. Chapela

Transgenic DNA introgressed into traditional maize landraces in Oaxaca, Mexico

Concerns have been raised about the potential effects of transgenic introductions on the genetic diversity of crop landraces and wild relatives in areas of crop origin and diversification, as this diversity is considered essential for global food security. Direct effects on non-target species, and the possibility of unintentionally transferring traits of ecological relevance onto landraces and wild relatives have also been sources of concern. The degree of genetic connectivity between industrial crops and their progenitors in landraces and wild relatives is a principal determinant of the evolutionary history of crops and agroecosystems throughout the world. Recent introductions of transgenic DNA constructs into agricultural fields provide unique markers to measure such connectivity. For these reasons, the detection of transgenic DNA in crop landraces is of critical importance. Here we report the presence of introgressed transgenic DNA constructs in native maize landraces grown in remote mountains in Oaxaca, Mexico, part of the Mesoamerican centre of origin and diversification of this crop.

Ectomycorrhizal fungi introduced with exotic pine plantations induce soil carbon depletion

Abstract Exotic pine plantations are promoted for their presumed capacity to provide a net sink of atmospheric C. Millions of hectares worldwide will be subjected to conversion into plantations during the next decades. However, pine introductions are known to result in a marked depletion of soil C, a phenomenon which has remained unexplained. We studied plantations in paramo grasslands of Ecuador, where the effect of the exotic introduction of radiata pines ( Pinus radiata ) and their accompanying ectomycorrhizal fungi can be studied in isolation from other ecosystem disturbances. We suggest that ectomycorrhizal fungi can extract C previously accumulated by paramo grasslands based on (a) a drastic simplification of the ectomycorrhizal community shown by direct DNA identification, (b) a loss of up to 30% soil C within 2 levels.

Differential C Isotope Discrimination by Fungi during Decomposition of C3- and C4-Derived Sucrose

ABSTRACT Stable isotope analysis is a major tool used in ecosystem studies to establish pathways and rates of C exchange between various ecosystem components. Little is known about isotopic effects of many such components, especially microbes. Here we report on the discovery of an unexpected pattern of C isotopic discrimination by basidiomycete fungi with far-reaching consequences for our understanding of isotopic processing in ecosystems where these microbes mediate material transfers across trophic levels. We measured fractionation effects on three ecologically relevant basidiomycete species under controlled laboratory conditions. Sucrose derived from C3 and C4 plants is fractionated differentially by these microbes in a taxon-specific manner. The differentiation between mycorrhizal and saprotrophic fungi observed in the field by others is not explained by intrinsic discrimination patterns. Fractionation occurs during sugar uptake and is sensitive to the nonrandom distribution of stable isotopes in the sucrose molecule. The balance between respiratory physiology and fermentative physiology modulates the degree of fractionation. These discoveries disprove the assumption that fungal C processing does not significantly alter the distribution of stable C isotopes and provide the basis for a reevaluation of ecosystem models based on isotopic evidence that involve C transfer across microbial interfaces. We provide a mechanism to account for the observed differential discrimination effects.

Phylogeography and evolution in matsutake and close allies inferred by analyses of ITS sequences and AFLPs

Matsutake are commercially important ectomycorrhizal basidiomycetes in the genus Tricholoma. Despite their importance, the systematics of this species complex have remained elusive and little is known about their origin and biogeography. Using DNA analyses on a worldwide sample of matsutake, we present here the first comprehensive definition of natural groupings in this species complex. We infer patterns of migration and propose Eocene origins for the group in western North America by a transfer from an angiosperm-associated ancestor to an increasingly specialized conifer symbiont. From these origins, matsutake appear to have followed migratory routes parallel to those of coniferous hosts. Patterns of vicariance between eastern North America and eastern Asia are resolved and their origins are suggested to stem from migration through Beringia. Using an analysis of genetic dissimilarity and geographical distance, we reject both the possibility that migration into Europe and Asia occurred through Atlantic bridges and the connection between matsutake populations in the Mahgrebi Mountains and those from Europe. Instead, African and European matsutake appear to be the most recent ends of a westward expansion of the domain of these fungi from North America.

Biodiversity (Communications arising (reply)): Suspect evidence of transgenic contamination/Maize transgene results in Mexico are artefacts (see editorial footnote)

Our original publication contained two separate conclusions derived from two methodological approaches. First, using PCR, we detected the presence of three distinct transgenic DNA sequences in maize landraces in Oaxaca, Mexico. Second, we attempted to establish the genomic context of transgene insertion using i-PCR. The criticisms raised by Metz and Fütterer and by Kaplinsky et al. relate principally to our second statement.

Phylogenetics of Lophodermium from pine

Lophodermium comprises ascomycetous fungi that are both needle-cast pathogens and asymptomatic endophytes on a diversity of plant hosts. It is distinguished from other genera in the family Rhytismataceae by its filiform ascospores and ascocarps that open by a longitudinal slit. Nucleotide sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA were used to infer phylogenetic relationships within Lophodermium. Twenty-nine sequences from approximately 11 species of Lophodermium were analyzed together with eight sequences from isolates thought to represent six other genera of Rhytismataceae: Elytroderma, Lirula, Meloderma, Terriera, Tryblidiopsis and Colpoma. Two putative Meloderma desmazieresii isolates occurred within the Lophodermium clade but separate from one another, one grouped with L. indianum and the other with L. nitens. An isolate of Elytroderma deformans also occurred within the Lophodermium clade but on a solitary branch. The occurrence of these genera within the Lophodermium clade might be due to problems in generic concepts in Rhytismataceae, such as emphasis on spore morphology to delimit genera, to difficulty of isolating Rhytismataceae needle pathogens from material that also is colonized by Lophodermium or to a combination of both factors. We also evaluated the congruence of host distribution and several morphological characters on the ITS phylogeny. Lophodermium species from pine hosts formed a monophyletic sister group to Lophodermium species from more distant hosts from the southern hemisphere, but not to L. piceae from Picea. The ITS topology indicated that Lophodermium does not show strict cospeciation with pines at deeper branches, although several closely related isolates have closely related hosts. Pathogenic species occupy derived positions in the pine clade, suggesting that pathogenicity has evolved from endophytism. A new combination is proposed, Terriera minor (Tehon) P.R. Johnst.

Growth-Dependent Stable Carbon Isotope Fractionation by Basidiomycete Fungi: δ13C Pattern and Physiological Process

ABSTRACT We grew 11 basidiomycetes in axenic culture to characterize their physiological capacities to fractionate stable C isotopes. Generally, δ13C values of the fungal biomass were (i) enriched in 13C relative to the growth medium, (ii) variable among the isolates, and (iii) dependent on the growth rate and growth stage of the fungi. We found a multiphasic dynamic of fractionation for Cryptoporus volvatus and Marasmius androsaceus during various growth stages. The first phase, P1, corresponded to the exponential growth stage and was characterized by an increasing enrichment in 13C content of the fungal biomass relative to the growth medium ranging between 4.6 and 6.9‰. The second phase, P2, exhibited a continual depletion in 13C of the fungal biomass, with the δ13C values of the fungal biomass asymptotically returning to the δ13C value of the growth medium at inoculation. The expression of the various fractionation phases was dependent on the amount of low-concentration micronutrients and growth factors added to the growth medium. The onset of P2 occurred at reduced concentrations of these elements. All of the sugars in the growth medium (sucrose, maltose, and glucose) were utilized for growth, indicating that the observed fractionation was not an artifact derived from the preferential use of 13C-rich maltose, which was found at low concentrations in the growth medium. In this study, we establish a framework with which to explore the impact of physiological fractionations by fungal interfaces on natural distributions of stable C isotopes.

Teosinte in Europe – Searching for the Origin of a Novel Weed

A novel weed has recently emerged, causing serious agronomic damage in one of the most important maize-growing regions of Western Europe, the Northern Provinces of Spain. The weed has morphological similarities to a wild relative of maize and has generally been referred to as teosinte. However, the identity, origin or genetic composition of ‘Spanish teosinte’ was unknown. Here, we present a genome-wide analysis of single-nucleotide polymorphism (SNP) data for Spanish teosinte, sympatric populations of cultivated maize and samples of reference teosinte taxa. Our data are complemented with previously published SNP datasets of cultivated maize and two Mexican teosinte subspecies. Our analyses reveal that Spanish teosinte does not group with any of the currently recognized teosinte taxa. Based on Bayesian clustering analysis and hybridization simulations, we infer that Spanish teosinte is of admixed origin, most likely involving Zea mays ssp. mexicana as one parental taxon, and an unidentified cultivated maize variety as the other. Analyses of plants grown from seeds collected in Spanish maize fields and experimental crosses under controlled conditions reveal that hybridization does occur between Spanish teosinte and cultivated maize in Spain, and that current hybridization is asymmetric, favouring the introgression of Spanish teosinte into cultivated maize, rather than vice versa.

Loop-mediated isothermal amplification of single pollen grains

The polymerase chain reaction (PCR) has been a reliable and fruitful method for many applications in ecology. Nevertheless, unavoidable technical and instrumental requirements of PCR have limited its widespread application in field situations. The recent development of isothermal DNA amplification methods provides an alternative to PCR, which circumvents key limitations of PCR for direct amplification in the field. Being able to analyze DNA in the pollen cloud of an ecosystem would provide very useful ecological information, yet would require a field-enabled, high-throughput method for this potential to be realized. Here, we demonstrate the applicability of the loop-mediated DNA amplification method (LAMP), an isothermal DNA amplification technique, to be used in pollen analysis. We demonstrate that LAMP can provide a reliable method to identify species from the pollen cloud, and that it can amplify successfully with sensitivity down to single pollen grains, thus opening the possibility of field-based, high-throughput analysis.