Rodolfo Marsch

Molecular phylogeny and paclitaxel screening of fungal endophytes from Taxus globosa.

We studied the endophytic mycoflora associated with Taxus globosa, the Mexican yew. The study localities; Las Avispas (LA), San Gaspar (SG), and La Mina (LM) were three segments of cloud forest within the range of Sierra Gorda Biosphere Reserve, México. Overall, 245 endophytes were isolated and 105 representative Ascomycota (morphotaxons) were chosen for phylogenetic and genotypic characterization. Maximum likelihood analyses of large subunit of ribosomal RNA (LSU) rDNA showed well-supported clades of Dothideomycetes, Eurotiomycetes, Leotiomycetes, Pezizomycetes, and Sordariomycetes. Analyses of ITS rDNA groups showed 57 genotypes (95% sequence similarity), in general consistent with the phylogenetically delimitated taxa based on LSU rDNA sequences. The endophyte diversity measured by Fishers α, Shanonn, and Simpson indices was ca. three-fold and ca. two-fold greater in LM than in LA and SG respectively. A screening for paclitaxel using a competitive inhibition enzyme immunoassay showed 16 positive isolates producing between 65 and 250 ng l(-1). The isolates included Acremonium, Botryosphaeria, Fusarium, Gyromitra, Nigrospora, Penicillium, three novel Pleosporales, and Xylaria.

ATP-citrate lyase activity and carotenoid production in batch cultures of Phaffia rhodozyma under nitrogen-limited and nonlimited conditions

ATP-citrate lyase (ACL) is the key cytoplasmic enzyme which supplies acetyl-CoA for fatty acids in oleaginous yeast. Although it has been suggested that fatty acid and carotenoid biosynthesis may have a common source of acetyl-CoA in Phaffia rhodozyma, the source for carotenoids is currently unknown. The purpose of this work was to analyze the development of ACL activity during batch cultures of P. rhodozyma under ammonium-limited and nonammonium-limited conditions and study its possible relationship with carotenoid synthesis. Every experiment showed carotenoid accumulation linked to an increasing ACL activity. Moreover, the ACL activity increased with dissolved oxygen (DO), i.e., ACL responded to DO in a similar way as carotenoid synthesis. Additionally, in the ammonium-limited culture, ACL activity increased upon ammonium depletion. However, the contribution to carotenoid accumulation in that case was negligible. This suggests that P. rhodozyma has developed two components of ACL, each one responsive to a different environmental stimulus, i.e., DO and ammonium depletion. The role of each component is still unknown; however, considering that the former responds to DO and the known role of carotenoids as antioxidants, it may be a provider of acetyl-CoA for carotenoid synthesis.

Influence of Catclaw Mimosa Monancistra on the Dissipation of Soil PAHS

Phytoremediation is a cost-effective biotechnology for decontamination of polycyclic aromatic hydrocarbons (PAHs)-polluted soils. A greenhouse experiment was conducted to determine the growth of Mimosa monancistra, a N2-fixing leguminous plants, and its capacity to remove phenanthrene, anthracene, and benzo(a)pyrene (BaP) from soil. The PAHs decreased shoot and root dry biomass of M. monancistra 2.7- and 3.9-fold, respectively, compared to uncontaminated soil and inhibited nodule formation. The removal of phenanthrene and anthracene was similar in vegetated and unvegetated soil, but the dissipation of BaP was significantly faster in vegetated soil as compared to unvegetated soil after 14, 56, 70, and 90 d. After 90 d, dissipation of BaP was 96% in vegetated soil and 87% in unvegetated soil. Nitrification and ammonification were not affected by the addition of PAHs as concentrations of NH4 +, NO2 −, and NO3 − were similar in contaminated and uncontaminated vegetated soil. Growth of M. monancistra was inhibited by contamination with hydrocarbons, but removal of BaP was accelerated in the rhizosphere.

Bacterial Communities in Soil Under Moss and Lichen-Moss Crusts

Biological soil crusts are symbiotic microbial communities formed by green algae, mosses, fungi, lichens, cyanobacteria and bacteria in different proportions. Crusts contribute to soil fertility and favour water retention and infiltration. However, little is known about the bacterial community structure in soil under the crusts. Soil was sampled under a moss crust (considered the MOSS group), lichen plus moss (considered the LICHEN group) and bare soil (considered the BARE group) and the microbial communities determined using nearly full 16S rRNA gene libraries. Bacteria belonging to seven different phyla were found and the Acidobacteria and Alphaproteobacteria were the dominant in each group. The crusts affected negatively the abundance of the Burkholderiales. The phylogenetic diversity and bacterial community membership were different in the LICHEN group compared to the BARE and MOSS groups, but not species richness and community structure. The beta diversity analysis also revealed a different bacterial community structure beneath the LICHEN and MOSS crusts, suggesting species-specific influence. This is a first insight into the effect of a biological soil crust on the bacterial community structure in an organic matter rich soil of a high altitude mountain forest.

Bacterial indicator taxa in soils under different long-term agricultural management.

In this study, the species indicator test was used to identify key bacterial taxa affected by changes in the soil environment as a result of conservation agriculture or conventional practices.

The Archaeal Diversity and Population in a Drained Alkaline Saline Soil of the Former Lake Texcoco (Mexico)

Draining soil of the former Lake Texcoco, Mexico with pH > 10.0 and electrolytic conductivity (EC) > 100 dS m−1 for 17 years has reduced pH to 7.8 and EC to 0.68 dS m−1. Metagenomic DNA from the archaeal community was extracted directly from this soil and used as template to amplify the 16S ribosomal genes by PCR to construct gene libraries. Most of the cloned Archaea were related to mesophilic crenarchaeota and were not-yet-cultured. Sequence and phylogenetic analyses of these clones identified a group of Archaea with close affiliation to the ammonia-oxidizing Archaea. The cloned sequences from the drained soil diverged clearly from Haloarchaea found in the undrained soil from the lake.

Haloarchaeal assimilatory nitrate-reducing communities from a saline alkaline soil

Assimilatory nitrate reduction (ANR) is a pathway wherein NO(3)(-) is reduced to NH(4)(+), an N species that can be incorporated into the biomass. There is little information about the ANR genes in Archaea and most of the known information has been obtained from cultivable species. In this study, the diversity of the haloarchaeal assimilatory nitrate-reducing community was studied in an extreme saline alkaline soil of the former lake Texcoco (Mexico). Genes coding for the assimilatory nitrate reductase (narB) and the assimilatory nitrite reductase (nirA) were used as functional markers. Primers to amplify and detect partial narB and nirA were designed. The analysis of these amplicons by cloning and sequencing showed that the deduced protein fragments shared >45% identity with other NarB and NirA proteins from Euryarchaeota and <38% identity with other nitrate reductases from Bacteria and Crenarchaeota. Furthermore, these clone sequences were clustered within the class Halobacteria with strong support values in both constructed dendrograms, confirming that desired PCR products were obtained. The metabolic capacity to assimilate nitrate by these haloarchaea seems to be important given that at pH 10 and higher, NH(4)(+) is mostly converted to toxic and volatile NH(3), and NO(3)(-) becomes the preferable N source.

Isolation and phylogenic identification of soil haloalkaliphilic strains in the former Texcoco Lake

A wide diversity of organisms exists in soil. Well-adapted groups can be found in extreme environments. A great economic and metabolic potential for extremozymes produced by organisms living at extreme environments has been reported. Extreme characteristics such as high salt content and high pH level make the soil of the former Texcoco Lake a unique place which has not been exploited. Therefore, in this study, 66 strains from soil of the former Texcoco Lake were isolated and phylogenetically analyzed using universal oligonucleotide primers. Different genera such as Kocuria, Micrococcus, Nesterenkonia, Halomonas, Salinicoccus, Kurthia, Gracilibacillus, and Bacillus were found. However, only 22 from all isolated strains were identified at specie level.

Enhanced dissipation of polycyclic aromatic hydrocarbons in the rhizosphere of the Athel tamarisk (Tamarix aphylla L. Karst.) grown in saline-alkaline soils of the former lake Texcoco.

Remediation of polycyclic aromatic hydrocarbons (PAHs) contaminated alkaline saline soil with phreatophyte or “water loving plants” was investigated by spiking soil from the former lake Texcoco with 100 mg phenanthrene (Phen) kg−1 soil, 120 mg anthracene (Ant) kg−1 soil and 45 mg benzo(a)pyrene (BaP) kg−1 soil and vegetating it with Athel tamarisk (Tamarix aphylla L. Karst.). The growth of the Athel tamarisk was not affected by the PAHs. In soil cultivated with Athel tamarisk, the leaching of PAHs to the 32–34 cm layer decreased 2-fold compared to the uncultivated soil. The BaP concentration decreased to 39% of the initial concentration at a distance smaller than 3 cm from the roots and to 45% at a distance larger than 3cm, but 59% remained in unvegetated soil after 240 days. Dissipation of Ant and Phen decreased with depth, but not BaP. The biodegradation of PAHs was affected by their chemical properties and increased in the presence of T. aphylla, but decreased with depth.