Sugarcane trash levels in soil affects the fungi but not bacteria in a short-term field experiment

Abstract The sugarcane in Brazil is passing through a management transition that is leading to the abolition of pre-harvest burning. Without burning, large amounts of sugarcane trash is generated, and there is a discussion regarding the utilization of this biomass in the industry versus keeping it in the field to improve soil quality. To study the effects of the trash removal on soil quality, we established an experimental sugarcane plantation with different levels of trash over the soil (0%, 50% and 100% of the original trash deposition) and analyzed the structure of the bacterial and fungal community as the bioindicators of impacts. The soil DNA was extracted, and the microbial community was screened by denaturing gradient gel electrophoresis in two different seasons. Our results suggest that there are no effects from the different levels of trash on the soil chemistry and soil bacterial community. However, the fungal community was significantly impacted, and after twelve months, the community presented different structures among the treatments.

Comparison of DNA extraction protocols for microbial communities from soil treated with biochar

Many studies have evaluated the effects of biochar application on soil structure and plant growth. However, there are very few studies describing the effect of biochar on native soil microbial communities. Microbial analysis of environmental samples requires accurate and reproducible methods for the extraction of DNA from samples. Because of the variety among microbial species and the strong adsorption of the phosphate backbone of the DNA molecule to biochar, extracting and purifying high quality microbial DNA from biochar-amended soil is not a trivial process and can be considerably more difficult than the extraction of DNA from other environmental samples. The aim of this study was to compare the relative efficacies of three commercial DNA extraction kits, the FastDNA® SPIN Kit for Soil (FD kit), the PowerSoil® DNA Isolation Kit (PS kit) and the ZR Soil Microbe DNA Kit MiniprepTM (ZR kit), for extracting microbial genomic DNA from sand treated with different types of biochar. The methods were evaluated by comparing the DNA yields and purity and by analysing the bacterial and fungal community profiles generated by PCR-DGGE. Our results showed that the PCR-DGGE profiles for bacterial and fungal communities were highly affected by the purity and yield of the different DNA extracts. Among the tested kits, the PS kit was the most efficient with respect to the amount and purity of recovered DNA and considering the complexity of the generated DGGE microbial fingerprint from the sand-biochar samples.

Tank bromeliad water: similar or distinct environments for research of bacterial bioactives?

The Atlantic Rainforest does not have a uniform physiognomy, its relief determines different environmental conditions that define the composition of its flora and fauna. Within this ecosystem, bromeliads that form tanks with their leaves hold water reservoirs throughout the year, maintaining complex food chains, based mainly on autotrophic and heterotrophic bacteria. Some works concluded that the water held by tank bromeliads concentrate the microbial diversity of their ecosystem. To investigate the bacterial diversity and the potential biotechnology of these ecosystems, tank bromeliads of the Neoregelia cruenta species from the Atlantic Rainforest in Brazil were used as models for this research. Bacteria isolated from these models were tested for production of bioactive compounds. DGGE of the water held by tank bromeliads was performed in different seasons, locations and sun exposure to verify whether these environmental factors affect bacterial communities. The DGGE bands profile showed no grouping of bacterial community by the environmental factors tested. Most of the isolates demonstrated promising activities in the tests performed. Collectively, these results suggest that tank bromeliads of the N. cruenta species provide important habitats for a diverse microbial community, suggesting that each tank forms a distinct micro-habitat. These tanks can be considered excellent sources for the search for new enzymes and/or new bioactive composites of microbial origin.

Diversity of the candidate phylum Poribacteria in the marine sponge Aplysina fulva

Poribacterial clone libraries constructed for Aplysina fulva sponge specimens were analysed with respect to diversity and phylogeny. Results imply the coexistence of several, prevalently "intraspecific" poribacterial genotypes in a single sponge host, and suggest quantitative analysis as a desirable approach in studies of the diversity and distribution of poribacterial cohorts in marine sponges

Comparison of different protocols for the extraction of microbial DNA from reef corals

This study aimed to test different protocols for the extraction of microbial DNA from the coral Mussismilia harttii. Four different commercial kits were tested, three of them based on methods for DNA extraction from soil (FastDNA SPIN Kit for soil, MP Bio, PowerSoil DNA Isolation Kit, MoBio, and ZR Soil Microbe DNA Kit, Zymo Research) and one kit for DNA extraction from plants (UltraClean Plant DNA Isolation Kit, MoBio). Five polyps of the same colony of M. harttii were macerated and aliquots were submitted to DNA extraction by the different kits. After extraction, the DNA was quantified and PCR-DGGE was used to study the molecular fingerprint of Bacteria and Eukarya. Among the four kits tested, the ZR Soil Microbe DNA Kit was the most efficient with respect to the amount of DNA extracted, yielding about three times more DNA than the other kits. Also, we observed a higher number and intensities of DGGE bands for both Bacteria and Eukarya with the same kit. Considering these results, we suggested that the ZR Soil Microbe DNA Kit is the best adapted for the study of the microbial communities of corals.

Comparison of different protocols for the extraction of microbial DNA from reef corals

This study aimed to test different protocols for the extraction of microbial DNA from the coral Mussismilia harttii. Four different commercial kits were tested, three of them based on methods for DNA extraction from soil (FastDNA SPIN Kit for soil, MP Bio, PowerSoil DNA Isolation Kit, MoBio, and ZR Soil Microbe DNA Kit, Zymo Research) and one kit for DNA extraction from plants (UltraClean Plant DNA Isolation Kit, MoBio). Five polyps of the same colony of M. harttii were macerated and aliquots were submitted to DNA extraction by the different kits. After extraction, the DNA was quantified and PCR-DGGE was used to study the molecular fingerprint of Bacteria and Eukarya. Among the four kits tested, the ZR Soil Microbe DNA Kit was the most efficient with respect to the amount of DNA extracted, yielding about three times more DNA than the other kits. Also, we observed a higher number and intensities of DGGE bands for both Bacteria and Eukarya with the same kit. Considering these results, we suggested that the ZR Soil Microbe DNA Kit is the best adapted for the study of the microbial communities of corals.

Zooplankton in littoral waters of a tropical lake: a revisited biodiversity / Zooplâncton da região litorânea de um lago tropical: a biodiversidade revisitada

The present study was carried out in Lake Dom Helvécio, in the state of Minas Gerais, with two main objectives: to demonstrate the contribution of the littoral zone, in order to better characterize zooplankton fauna; and to assess the distribution of zooplankton species in different habitats, i.e., the littoral zone with and without aquatic vegetation. The samples were collected in February and July 2006, throughout the littoral zone of the lake, in areas with and without aquatic vegetation. We identified a total of 188 species, of which 130 are new records for Lake Dom Helvécio. One hundred and eighty-four species were identified in the littoral zone with aquatic vegetation, and 117 in the zone with no vegetation. The higher zooplankton richness in areas of the littoral zone with aquatic vegetation can be related to the greater environmental heterogeneity. Compared to previous studies on the littoral zones of lakes along the middle River Doce, the present study expended greater sampling effort, and identified many more species. In relation to biological conservation, this study demonstrated the importance of the littoral zone for better characterization and conservation of the zooplankton fauna, especially when it is colonized by aquatic vegetation. Underestimating the richness of species may provide inaccurate data on the biota, as well as on the ecological conditions in an environment.

O presente estudo foi realizado no lago Dom Helvécio (MG) tendo como principais objetivos: demonstrar a contribuição da região litorânea para uma melhor caracterização da fauna zooplanctônica, avaliar a distribuição destas espécies em diferentes habitats (região litorânea com e sem vegetação aquática). As amostras foram coletadas nos meses de fevereiro e julho de 2006, ao longo da região litorânea, em pontos amostrais com e sem vegetação aquática. Um total de 188 espécies foi identificado. Desses organismos, 130 representaram novos registros para o lago Dom Helvécio. Foram identificadas 184 espécies na região litorânea com vegetação aquática e 117 na região litorânea sem vegetação. A maior riqueza em espécies zooplanctônicas na região litorânea com vegetação aquática está relacionada com a maior heterogeneidade ambiental. Quando comparado aos estudos realizados anteriormente na região litorânea de lagos do médio rio Doce, este estudo destaca-se pelo maior esforço amostral e número de espécies identificadas. No tocante à conservação biológica, o presente estudo mostrou a importância da região litorânea, especialmente quando colonizada por vegetação aquática para uma melhor caracterização e conservação da fauna zooplanctônica. A riqueza em espécies subestimada pode fornecer dados irreais sobre a biota, bem como das condições ecológicas de um ambiente.