Genetic Analysis and In Vitro Enzymatic Determination of Bacterial Community in Compost Teas from Different Sources

Abstract

Compost tea has been used throughout the world to control diseases and promote the growth of plants. The microbial community is the main factor involved both in the antagonistic effect against relevant phytopathogens and as a stimulator of plant growth. The objective of this research is to determine the bacterial diversity present in four types of compost as well as some of the mechanisms that may be involved in the positive effects of compost tea on crops. Aerated (ACT) and non-aerated (NCT) compost teas were obtained from four different composts: spent mushroom substrate compost (SMC), grape marc compost (GMC), greenhouse horticultural crop residues compost (CRC), and vermicompost (CRV). 16S rDNA-based DGGE profiles were obtained for each compost tea and their respective bacterial communities were analyzed. Of the 100 clones obtained, those typical for being dominant for all profiles were chosen. In total, 20 different clones were sequenced. The results showed that the bacterial communities of most compost teas had high richness, diversity, and evenness values, with relative abundance of species belonging to Bacteroidetes and Proteobacteria. The NCTs obtained from all the composts, especially CRC and CRV, showed high levels of siderophore production, while teas from GMC manifested high and consistent cellulase activity. The ACTs from all the composts, especially SMC, had high protease activity.     

Land use and climate change impacts on soil organic carbon stocks in semi-arid Spain

Purpose

The sensitivity of soil organic carbon to global change drivers, according to the depth profile, is receiving increasing attention because of its importance in the global carbon cycle and its potential feedback to climate change. A better knowledge of the vertical distribution of SOC and its controlling factors—the aim of this study—will help scientists predict the consequences of global change.

Materials and methods

The study area was the Murcia Province (S.E. Spain) under semiarid Mediterranean conditions. The database used consists of 312 soil profiles collected in a systematic grid, each 12 km² covering a total area of 11,004 km². Statistical analysis to study the relationships between SOC concentration and control factors in different soil use scenarios was conducted at fixed depths of 0–20, 20–40, 40–60, and 60–100 cm.

Results and discussion

SOC concentration in the top 40 cm ranged between 6.1 and 31.5 g?kg^?1, with significant differences according to land use, soil type and lithology, while below this depth, no differences were observed (SOC concentration 2.1–6.8 g?kg^?1). The ANOVA showed that land use was the most important factor controlling SOC concentration in the 0–40 cm depth. Significant differences were found in the relative importance of environmental and textural factors according to land use and soil depth. In forestland, mean annual precipitation and texture were the main predictors of SOC, while in cropland and shrubland, the main predictors were mean annual temperature and lithology. Total SOC stored in the top 1 m in the region was about 79 Tg with a low mean density of 7.18 kg?Cm^?3. The vertical distribution of SOC was shallower in forestland and deeper in cropland. A reduction in rainfall would lead to SOC decrease in forestland and shrubland, and an increase of mean annual temperature would adversely affect SOC in croplands and shrubland. With increasing depth, the relative importance of climatic factors decreases and texture becomes more important in controlling SOC in all land uses.

Conclusions

Due to climate change, impacts will be much greater in surface SOC, the strategies for C sequestration should be focused on subsoil sequestration, which was hindered in forestland due to bedrock limitations to soil depth. In these conditions, sequestration in cropland through appropriate management practices is recommended.     

Characterizing the variation in aggressiveness and sporulation of the NA1 and EU1 lineages of Phytophthora ramorum in Oregon

Phytophthora ramorum, the cause of sudden oak death, is an invasive pathogen present in parts of coastal California and south-western Oregon forests. The majority of these forest infestations have been caused by the NA1 clonal lineage. In 2015, the EU1 lineage of P. ramorum was isolated from a tanoak (Notholithocarpus densiflorus) tree located in a mixed-conifer forest of Curry County, Oregon. In order to evaluate the threat to Oregon forests of the EU1 lineage relative to the established NA1 lineage, a series of experiments was conducted comparing aggressiveness and sporulation of NA1 and EU1 isolates on logs and seedlings in the growth chamber and forest. There was no significant difference in lesion size on logs inoculated with NA1 and EU1 isolates for any of the tree species tested. Across all seedling experiments differences among isolates within lineage, in terms of both aggressiveness and sporulation, were more commonly observed than differences among lineages. Site to site variation in tanoak sporulation, as measured by rain bucket baiting, appears to be correlated with the number of P. ramorum-positive seedlings detected at each site.     

Biological characterization of citrus tristeza virus isolates by in vitro tissue cultures

Stem segments from Mexican lime, sweet orange, grapefruit, Citrus excelsa and alemow, infected with five citrus tristeza virus (CTV) isolates, were cultured in vitro . Regeneration of roots and shoots were modified as a result of infection. The effect of CTV on the morphogenesis of stem segments cultured in vitro depended on the CTV isolate and the plant host, and showed a correlation with the in vivo effects observed in biological indexing. Evaluation of the morphogenic response of stem segments of Mexican lime and grapefruit can be used as an additional tool for the biological characterization of CTV isolates. The symptoms on sweet orange plants obtained from regenerated shoots indicated that CTV is unevenly distributed in the host plant cells and that the regeneration process may be utilized as a tool to separate strains from complex field isolates.     

Land cover changes and fragmentation in mountain neotropical ecosystems of Oaxaca,Mexico under community forest management

Changes in land cover have a direct impact on forest ecosystem goods and services. In this study, changes in land cover in Sierra de Juarez–Oaxaca ecosystems were estimated using a consistent processing of Landsat images and OBIA methodology. Additionally, landscape analyses using FRAGSTAT were conducted. In 2014, Sierra de Juarez–Oaxaca was covered by approximately 84% of forests, mainly pine-oak and cloud forests. After extensive deforestation until 2001, this trend was reversed and the forest cover surface area in 2014 was slightly higher than in 1979. The comparison of the landscape structure of the forested and agricultural lands suggests an increase in habitat heterogeneity. However, interspersion and juxtaposition indices, showing the patch shape by patch area and perimeter, were similar throughout the study period(1979–2014). Social and economic drivers can explain this situation: namely, community organization, forest enterprises, payment for ecosystem services programs, and changes of agricultural activity. Communities in the Sierra of Oaxaca have reforested degraded lands, created community forest enterprises, and preserved the forest under conservation schemes like those proposed by the Mexican payment for ecosystem services programs. However, their sustainable management faces internal challenges and has become highly dependent on political and institutional decisions beyond their control.     

Evaluation of IFA, MAT, ELISAs and immunoblotting for the detection of anti-Toxoplasma gondii antibodies in paired serum and aqueous humour samples from experimentally infected pigs

The study evaluated the efficiency of diagnostic laboratory methods to detect anti-Toxoplasma gondii antibodies in paired serum and aqueous humour samples from experimentally infected pigs. 18-mixed breed pigs were used during the experiment; these were divided into two groups, G1 (infected group, n=10) and G2 (uninfected group, n=8). Infection was performed with 4 x 10(4) VEG strain oocysts at day 0 by the oral route in G1 animals. All pigs were euthanized at day 60, when retina, aqueous humour, and blood samples were collected. Anti-T. gondii antibody levels were assessed in serum (s) and aqueous humour (ah) by indirect immunofluorescence assay (IFA), modified agglutination test (MAT), m-ELISA (using crude membranes from T. gondii tachyzoites as antigen) and r-ELISA (using rhoptries from T. gondii tachyzoites as antigen). Polymerase chain reactions (PCR) of samples from the retina were performed by using Tox4 and Tox5 primers. Antibody titers of G1 animals ranged from 128 to 1024 and from 16 to 256 in serum and aqueous humour, respectively. There were differences in the correlation coefficients between IFA(s) x IFA (ah) (r=0.62, P=0.05), MAT(s) x MAT (ah) (r=0.97, P<0.0001); however, there was no significant difference between r-ELISA(s) x r-ELISA (ah) (r= 0.14, P=0.7). Antibodies present in serum and aqueous humour recognized similar antigens. Samples of retina were positive by PCR in 30% (3/10) of infected pigs. G2 animals remained without antibody levels and were PCR negative throughout the experiment. These results suggest that the use of a combination of tests and immunoblotting for paired aqueous humour and serum samples could improve the sensitivity and specificity for the diagnosis of ocular toxoplasmosis.     

Assessing conservation priorities of endemic freshwater fishes in the Tropical Andes region

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