Diversity and Activity of Denitrifiers of Chilean Arid Soil Ecosystems

The Chilean sclerophyllous matorral is a Mediterranean semiarid ecosystem affected by erosion, with low soil fertility, and limited by nitrogen. However, limitation of resources is even more severe for desert soils such as from the Atacama Desert, one of the most extreme arid deserts on Earth. Topsoil organic matter, nitrogen and moisture content were significantly higher in the semiarid soil compared to the desert soil. Although the most significant loss of biologically preferred nitrogen from terrestrial ecosystems occurs via denitrification, virtually nothing is known on the activity and composition of denitrifier communities thriving in arid soils. In this study we explored denitrifier communities from two soils with profoundly distinct edaphic factors. While denitrification activity in the desert soil was below detection limit, the semiarid soil sustained denitrification activity. To elucidate the genetic potential of the soils to sustain denitrification processes we performed community analysis of denitrifiers based on nitrite reductase (nirK and nirS) genes as functional marker genes for this physiological group. Presence of nirK-type denitrifiers in both soils was demonstrated but failure to amplify nirS from the desert soil suggests very low abundance of nirS-type denitrifiers shedding light on the lack of denitrification activity. Phylogenetic analysis showed a very low diversity of nirK with only three distinct genotypes in the desert soil which conditions presumably exert a high selection pressure. While nirK diversity was also limited to only few, albeit distinct genotypes, the semiarid matorral soil showed a surprisingly broad genetic variability of the nirS gene. The Chilean matorral is a shrub land plant community which form vegetational patches stabilizing the soil and increasing its nitrogen and carbon content. These islands of fertility may sustain the development and activity of the overall microbial community and of denitrifiers in particular

Genetic diversity of terricolous Peltigera cyanolichen communities in different conservation states of native forest from southern Chile

Decreasing quality of forest habitats is among the major factors leading to a loss of epiphytic lichen diversity. However, there is little information about how this factor influences the diversity of terricolous lichens, which do not grow over living trees and could be less susceptible to such disturbances. In this work we describe the genetic diversity of Peltigera terricolous cyanolichens and their cyanobiont (Nostoc) from three habitats at the Karukinka Natural Park (Tierra del Fuego, southern Chile), which represent different conservation states: native mature-forest (low disturbance intensity), native youngforest (medium disturbance intensity) and grassland (high disturbance intensity). In both forest contexts, a higher diversity and a higher number of unique OTUs (operational taxonomic units) were found. In contrast, in the grassland, the diversity was lower and the Peltigera species were mostly cosmopolitan. The presence of unique OTUs and the higher diversity of lichens in native forest areas highlight the importance of their preservation, indicating that decreasing forest quality also has a negative impact on terricolous lichens diversity. [Int Microbiol 2013; 16(4):243-252]Keywords: Peltigera · Nostoc · lichens · genetic diversity · Karukinka Natural Park · southern Chil

Spore germination of Frankia strains isolated from Colletia hystrix and Retanilla ephedra (Rhamnaceae)

Two Frankia strains, Chl1 from Colletia hystrix and Re16 from Retanilla ephedra, were assayed to determine the germinability of their spores and the stages of the life cycle in different media. In BAP medium, both strains showed approximately 18% spore germination. However, in BAP medium lacking micronutrients and FeEDTA, strain Chl1 spores exhibited approximately 53% germination and strain Re16 spores about 42%. The survey also showed that the spores were not heat-resistant, the Rel6 spores being more sensitive than Chl1 spores. Both strains exhibited a small increase in their percentage of germination with a 15-pulse ultrasonic treatment

Nitrogen-Fixing Bacteria Associated with <i>Peltigera</i> Cyanolichens and <i>Cladonia</i> Chlorolichens

Lichens have been extensively studied and described; however, recent evidence suggests that members of the bacterial community associated with them could contribute new functions to the symbiotic interaction. In this work, we compare the nitrogen-fixing guild associated with bipartite terricolous lichens with different types of photobiont: Peltigera cyanolichens and Cladonia chlorolichens. Since cyanobacteria contribute nitrogen to the symbiosis, we propose that chlorolichens have more diverse bacteria with the ability to fix nitrogen compared to cyanolichens. In addition, since part of these bacteria could be recruited from the substrate where lichens grow, we propose that thalli and substrates share some bacteria in common. The structure of the nitrogen-fixing guild in the lichen and substrate bacterial communities of both lichens was determined by terminal restriction fragment length polymorphism (TRFLP) of the nifH gene. Multivariate analyses showed that the nitrogen-fixing bacteria associated with both types of lichen were distinguishable from those present in their substrates. Likewise, the structure of the nitrogen-fixing bacteria present in the cyanolichens was different from that of chlorolichens. Finally, the diversity of this bacterial guild calculated using the Shannon index confirms the hypothesis that chlorolichens have a higher diversity of nitrogen-fixing bacteria than cyanolichens

Phototrophic bacteria dominate consortia, potentially to remove CO2 and H2S from biogas under microaerophilic conditions

The use of microbial consortia to remove contaminants in industrial systems and in natural environments could be an alternative to the use of unique strains of microorganisms, since microbial consortia have greater robustness to environmental fluctuations. However, it is necessary to evaluate the relationship between the genetic structure and functionality of the consortia. In this work, the functional and structural stability over time of two bacterial consortia (C5 and C6) with the potential to remove CO2 and H2S from biogas was evaluated. Both consortia decreased the dissolved CO2 by over 30% at the end of the incubation period, but C5 presented shorter removal kinetics (3.9 days) than C6 (6.4 days). Additionally, a chemical oxidation of H2S could have occurred in the microcosms. Moreover, both consortia presented a stable genetic structure, measured by terminal restriction fragment length polymorphism profiles of the 16S rRNA gene, characterized by high homogeneity and prevalence of the genus Rhodopseudomonas throughout the incubation period, and an increasing abundance of Xanthobacter during the exponential phase of the growth curve in C5, which would account for the functionality of the consortia.FONDEF Project D07 I-100

Genetic diversity of Nostoc microsymbionts from Gunnera tinctoria revealed by PCR-STRR fingerprinting

The cyanobacteria belonging to the genus Nostoc fix atmospheric nitrogen, both as free-living organisms and in symbiotic associations with a wide range of hosts, including bryophytes, gymnosperms (cycads), the small water fern Azolla (Pteridophyte), the angiosperm genus Gunnera, and fungi (lichens). The Gunnera-Nostoc symbiosis is the only one that involves a flowering plant. In Chile, 12 species of Gunnera have been described with a broad distribution in the temperate region. We examined the genetic diversity of Nostoc symbionts from three populations of Gunnera tinctoria from Abtao, Chiloé Island, southern Chile, and microsymbionts from other two species of Gunnera from southern Chile, using PCR amplification of STRR (short tandemly repeated repetitive) sequences of the Nostoc infected tissue. To our knowledge, this is the first report of PCR fingerprinting obtained directly from symbiotic tissue of Gunnera. Genetic analyses revealed that Nostoc symbionts exhibit important genetic d

Environmental conditions shape soil bacterial community structure in a fragmented landscape

Several biogeographical hypotheses have been proposed to explain microbial distribution, but there is ongoing debate about the magnitude of the contribution of niche based processes and historical contingencies in determining patterns of microbial structure. In this context, currently fragmented relict forests of olivillo (Aextoxicon punctatum Ruiz et. Pay.), which belonged to a continuous community along the coast of Chile during the Pleistocene, and their surrounding scrublands are ideally suited for testing these hypotheses, since they remain as patches located at the northern tip of the distribution of the relicts. In each study site, edaphic and geographic variables were determined, and the bacterial structures were evaluated at the genetic and metabolic levels through fingerprint approaches along with multivariate analytical methods including redundancy (RDA) and variance partitioning (VPA) analyses. Forests possessed lower pH, and higher contents of moisture and organic matter. In addition, bacterial communities from both habitats differed, whereas the bacterial communities of the forests in different regions were very similar to each other. Our conclusion is that current abiotic soil factors, but not past events due to the historical connection of the forests, account for the variance in the structure of these soil bacterial communitiesNational Commission for Scientific and Technological Research (CONICYT) 22121214 projects PAIFAC FONDECYT (National Fund for Scientific and Technological Development) 1140527 VIU (Valorization of University Research) 11003

Seabird and pinniped shape soil bacterial communities of their settlements in Cape Shirreff, Antarctica.

Seabirds and pinnipeds play an important role in biogeochemical cycling by transferring nutrients from aquatic to terrestrial environments. Indeed, soils rich in animal depositions have generally high organic carbon, nitrogen and phosphorus contents. Several studies have assessed bacterial diversity in Antarctic soils influenced by marine animals; however most have been conducted in areas with significant human impact. Thus, we chose Cape Shirreff, Livingston Island, an Antarctic Specially Protected Area designated mainly to protect the diversity of marine vertebrate fauna, and selected sampling sites with different types of animals coexisting in a relatively small space, and where human presence and impact are negligible. Using 16S rRNA gene analyses through massive sequencing, we assessed the influence of animal concentrations, via their modification of edaphic characteristics, on soil bacterial diversity and composition. The nutrient composition of soils impacted by Antarctic fur seals and kelp gulls was more similar to that of control soils (i.e. soils without visible presence of plants or animals), which may be due to the more active behaviour of these marine animals compared to other species. Conversely, the soils from concentrations of southern elephant seals and penguins showed greater differences in soil nutrients compared to the control. In agreement with this, the bacterial communities of the soils associated with these animals were most different from those of the control soils, with the soils of penguin colonies also possessing the lowest bacterial diversity. However, all the soils influenced by the presence of marine animals were dominated by bacteria belonging to Gammaproteobacteria, particularly those of the genus Rhodanobacter. Therefore, we conclude that the modification of soil nutrient composition by marine vertebrates promotes specific groups of bacteria, which could play an important role in the recycling of nutrients in terrestrial Antarctic ecosystems

Carbon consumption patterns of microbial communities associated with Peltigera lichens from a Chilean temperate forest

© 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). Lichens are a symbiotic association between a fungus and a green alga or a cyanobacterium, or both. They can grow in practically any terrestrial environment and play crucial roles in ecosystems, such as assisting in soil formation and degrading soil organic matter. In their thalli, they can host a wide diversity of non-photoautotrophic microorganisms, including bacteria, which play important functions and are considered key components of the lichens. In this work, using the BioLog® EcoPlate system, we studied the consumption kinetics of different carbon-sources by microbial communities associated with the thallus and the substrate of Peltigera lichens growing in a Chilean temperate rain forest dominated by Nothofagus pumilio. Based on the similarity