Combining analytical methodologies for the identification of Aspergillus section Flavi strains isolated from Brazilian agricultural commodities

The use of chemical analysis of microbial components, including proteins, became an important achievement in the 80’s of the last century to the microbial identification. This led a more objective microbial identification scheme, called chemotaxonomy, and the analytical tools used in the field are mainly 1D/2D gel electrophoresis, spectrophotometry, high-performance liquid chromatography, gas chromatography, and combined gas chromatography-mass spectrometry. The Edman degradation reaction was also applied to peptides sequence giving important insights to the microbial identification. The rapid development of these techniques, in association with knowledge generated by DNA sequencing and phylogeny based on rRNA gene and housekeeping genes sequences, boosted the microbial identification to an unparalleled scale. The recent results of mass spectrometry (MS), like Matrix-Assisted Laser Desorption/Ionisation Time-of-Flight (MALDI-TOF), for rapid and reliable microbial identification showed considerable promise. In addition, the technique is rapid, reliable and inexpensive in terms of labour and consumables when compared with other biological techniques. At present, MALDI-TOF MS adds an additional step for polyphasic identification which is essential when there is a paucity of characters or high DNA homologies for delimiting very close related species. The full impact of this approach is now being appreciated when more diverse species are studied in detail and successfully identified. However, even with the best polyphasic system, identification of some taxa remains time-consuming and determining what represents a species remains subjective. The possibilities opened with new and even more robust mass spectrometers combined with sound and reliable databases allow not only the microbial identification based on the proteome fingerprinting but also include de novo specific proteins sequencing as additional step. These approaches are pushing the boundaries in the microbial identification field.

Social wasps of two wetland ecosystems in brazilian Amazonia (Hymenoptera, Vespidae, Polistinae)

In Brazilian Amazonia, 20 genera and more than 200 species of polistine wasps are recorded. Local faunas with 70 to 80 species are usually found in non floodable forest environments. However, a variety of wetlands exist in the region, the most expressive in surface area being varzea systems. In this paper, information is presented on polistines from two areas of wetlands in the Brazilian states of Amazonas and Amapá. These are reciprocally compared and also with nearby terra firme locations. Collecting methods consisted of active search for nests, handnetting and automatic trapping of individuals. Forty-six species of 15 genera were collected in Mamirauá, AM, most being widespread common wasps. However, five species deserve special mention in virtue of rarity and/or restricted distribution: Metapolybia rufata, Chartergellus nigerrimus, Chartergellus punctatior, Clypearia duckei, and Clypearia weyrauchi. In Região dos Lagos, AP, 31 species of 9 genera were collected, nearly all being common species with the exception of some Polistes, like P. goeldi and P. occipitalis. Even though less rich than vespid faunas from terra firme habitats, the Mamirauá fauna proved to be quite expressive considering limitations imposed by the hydrological regime. In Região dos Lagos, however, the very low diversity found was below the worst expectations. The virtual absence of otherwise common species in environments like tidal varzea forests along Araguari River is truly remarkable. The causes of low diversity are probably related to isolation and relative immaturity of the region, allied to strong degradation of forested habitats.

Discrimination of Brazilian propolis according to the seasoning using chemometrics and machine learning based on UV-Vis scanning data

Propolis is a chemically complex biomass produced by honeybees (Apis mellifera) from plant resins added of salivary enzymes, beeswax, and pollen. The biological activities described for propolis were also identified for donor plants resin, but a big challenge for the standardization of the chemical composition and biological effects of propolis remains on a better understanding of the influence of seasonality on the chemical constituents of that raw material. Since propolis quality depends, among other variables, on the local flora which is strongly influenced by (a)biotic factors over the seasons, to unravel the harvest season effect on the propolis chemical profile is an issue of recognized importance. For that, fast, cheap, and robust analytical techniques seem to be the best choice for large scale quality control processes in the most demanding markets, e.g., human health applications. For that, UV-Visible (UV-Vis) scanning spectrophotometry of hydroalcoholic extracts (HE) of seventy-three propolis samples, collected over the seasons in 2014 (summer, spring, autumn, and winter) and 2015 (summer and autumn) in Southern Brazil was adopted. Further machine learning and chemometrics techniques were applied to the UV-Vis dataset aiming to gain insights as to the seasonality effect on the claimed chemical heterogeneity of propolis samples determined by changes in the flora of the geographic region under study. Descriptive and classification models were built following a chemometric approach, i.e. principal component analysis (PCA) and hierarchical clustering analysis (HCA) supported by scripts written in the R language. The UV-Vis profiles associated with chemometric analysis allowed identifying a typical pattern in propolis samples collected in the summer. Importantly, the discrimination based on PCA could be improved by using the dataset of the fingerprint region of phenolic compounds ( = 280-400m), suggesting that besides the biological activities of those secondary metabolites, they also play a relevant role for the discrimination and classification of that complex matrix through bioinformatics tools. Finally, a series of machine learning approaches, e.g., partial least square-discriminant analysis (PLS-DA), k-Nearest Neighbors (kNN), and Decision Trees showed to be complementary to PCA and HCA, allowing to obtain relevant information as to the sample discrimination.

Filamentous fungi in free water and biofilms from Brazilian drinking water systems

In some regions of Brazil, especially where the water is scarce, drinking water is stored in water storage tanks. This practice gives the consumer the guarantee of available water. The water storage conditions such as the exposure to hot weather when the tanks are on rooftops allow the development of microorganisms and microbial biofilms which can deteriorate the water quality and increase the risk to human health [1,2]. This study describes the filamentous fungi (FF) detected in free water and biofilms in drinking water storage tanks in Recife - Pernambuco, Brazil. Five sampling times in triplicate were performed at two distinct points. Colony-forming units (CFU) of FF fungi were determined with 0.45 µm filtration membranes using peptone glucose rose Bengal agar (PGRBA). From the 30 samples analysed a total of 1136 CFU were obtained. The water biofilms were collected from samplers consisting of polyethylene coupons, previously installed in the reservoirs. These coupons were transferred to PGRBA plates and incubated using with the same conditions described for free FF. For the in situ detection of FF in biofilms the Calcofluor White staining technique was used. This procedure demonstrated FF forming biofilms on the surfaces of the coupons. Brazilian legislation does not define limits for FF in drinking water. However considering the potential risk of fungal contamination, the data obtained in this study will contribute to developing future quantitative and qualitative parameters for the presence of fungi in drinking water distribution systems in Brazil. [1] HageskaL, G, Lima, N, Skaar, I. The study of fungi in drinking water. Mycological Research, 113, 2009, 165-172. [2] Skaar I, Hageskal G. Fungi in Drinking Water. In.: Paterson RRM, Lima N. (Eds.) Molecular Biology of Food and Water Borne Mycotoxigenic and Mycotic Fungi. CRC Press, Taylor & Francis Group, Boca Raton, 2015, 597-606.

Perceptions of Amazonian deforestation in the British and Brazilian media

The Amazon rainforest stretches across more than six million square kilometers and nine countries. Of the original forest area it is thought that 18 per cent has been cleared, mainly for farming purposes. In Brazil, the main drivers of deforestation are beef ranching and soya production that together occupy more than 75 per cent of newly deforested land. The situation in the Amazon illustrates a fundamental dilemma facing environmentalists around the world: how to reconcile economic development with biodiversity conservation. In this paper the representation of this dilemma in the British and Brazilian news media is assessed. The results indicate that there were far more articles referring to deforestation in the Brazilian press (816 Brazilian to 29 UK) but that many of these make no mention of what factors are responsible for deforestation. The patterns of representation of the proximate (direct) causes of Amazonian deforestation were very similar in the two countries, with soya and beef cattle ranching commanding the most press attention. The ultimate (indirect) causes of deforestation, however, are treated very differently, with the Brazilian media seemingly far more aware of the role of economic development needs than the UK press. Interestingly, the role of international demand for soya, beef, and forest products in driving deforestation was highlighted primarily in the UK press. These findings are critically discussed in the context of media influence on public understandings of Amazonian deforestation.

A structured inventory of spiders (Arachnida, Araneae) in natural and artificial forest gaps at Porto Urucu, Western Brazilian Amazonia

A preliminary survey of the spider fauna in natural and artificial forest gap formations at “Porto Urucu”, a petroleum/natural gas production facility in the Urucu river basin, Coari, Amazonas, Brazil is presented. Sampling was conducted both occasionally and using a protocol composed of a suite of techniques: beating trays (32 samples), nocturnal manual samplings (48), sweeping nets (16), Winkler extractors (24), and pitfall traps (120). A total of 4201 spiders, belonging to 43 families and 393 morphospecies, were collected during the dry season, in July, 2003. Excluding the occasional samples, the observed richness was 357 species. In a performance test of seven species richness estimators, the Incidence Based Coverage Estimator (ICE) was the best fit estimator, with 639 estimated species. To evaluate differences in species richness associated with natural and artificial gaps, samples from between the center of the gaps up to 300 meters inside the adjacent forest matrix were compared through the inspection of the confidence intervals of individual-based rarefaction curves for each treatment. The observed species richness was significantly higher in natural gaps combined with adjacent forest than in the artificial gaps combined with adjacent forest. Moreover, a community similarity analysis between the fauna collected under both treatments demonstrated that there were considerable differences in species composition. The significantly higher abundance of Lycosidae in artificial gap forest is explained by the presence of herbaceous vegetation in the gaps themselves. Ctenidae was significantly more abundant in the natural gap forest, probable due to the increase of shelter availability provided by the fallen trees in the gaps themselves. Both families are identified as potential indicators of environmental change related to the establishment or recovery of artificial gaps in the study area.

Five egg-laying queens in a single colony of brazilian stingless bees (Melipona scutellaris Latreille

Polygyny, characterized by the presence of several egg-laying queens, is considered as a temporary colony status. In stingless bees it is rarely observed. This paper reports the first case of natural polygyny in Melipona scutellaris colony, with five egg-laying queens.

New record of a very specialized interaction: myrcidris epicharis Ward 1990 (Pseudomyrmecinae) and its myrmecophyte host Myrcia madida McVaugh (Myrtaceae) in Brazilian Meridional Amazon

In this study we present a new record of a plant-animal interaction: the mutualistic relationship between the specialist plant-ant Myrcidris epicharis Ward, 1990 (Pseudomyrmecinae) and its myrmecophyte host Myrcia madida McVaugh (Myrtaceae). We observed more than 50 individuals of M. madida occupied by M. epicharis in islands and margins of the Juruena River, in Cotriguaçu, Mato Grosso, Brazil (Meridional Amazon). We discuss a possible distribution of this symbiotic interaction throughout all the riparian forest of the Amazon River basin and its consequence to coevolution of the system.

Daldinia eschscholtzii (Ascomycota, Xylariaceae) isolated from the Brazilian Amazon: taxonomic features and mycelial growth conditions

The Amazon has a high diversity of fungi, including species of the genus Daldinia (Ascomycota, Xylariaceae), which produce secondary metabolites with recognized nematicidal and antimicrobial activity. The ecological role of Daldinia is important, as stromata serve as refuges to many insects and arthropodes, and the fungi contribute to the degradation of vegetable organic matter. The aim of this study was to analyze the taxonomic features and mycelial growth conditions in vitro of a Daldinia specimen collected in the Brazilian Amazon. Morphological and molecular studies of the fungus identified it as D. eschscholtzii. To evaluate mycelial growth, we cultivated the fungus at 20, 25, 30, 35, and 40 °C in malt extract-peptone agar (MEPA), malt extract-peptone (MEP), potato dextrose (PD), and minimum medium (MM). The best mycelial growth occurred at 35 °C, although the greatest amount of biomass was obtained at 25 °C and 30 °C. PD proved to be the best medium for biomass production.

Protected environments and substrates for production of genipap seedlings

Genipap (Genipa americana L., Rubiaceae ) is a native Brazilian species and can be used in the recovery of degraded forest areas or for food supply. In order for the species to reach its potential, production of high quality seedlings is essential. The objective of this study was to evaluate genipap seedlings in protected environments and different substrates. The environments tested were: (1) a greenhouse with polyethylene film in the top, with aluminized screen (Aliminet®) of 50%-shading under this film, and lateral sides covered with 50%-shading nylon net (Sombrite®), (2) a shaded hut, all sides covered with 50%-shading nylon net (Sombrite®), and (3) a nursery shelter, with all lateral sides uncovered and the roof covered with leaves of buriti (Mauritia flexuosa). In these environments the following substrates were tested: 50% cattle manure + 50% cassava foliage, 50% cattle manure + 50% Vida Verde®, 50% cattle manure + 50% vermiculite, and 25% cattle manure + 25% vermiculite + 25% of cassava foliage + 25% Vida Verde®. Because there was no repetition of the growth environment, the effect of environment was examined using statistical procedures for analysis of combined experiments. Within environments a completely randomized design was used with five replications. All substrates are suitable for the formation of genipap seedlings, where the recommended substrates are: 50% cattle manure + 50% cassava foliage and 50% cattle manure + 50% Vida Verde® for the greenhouse and the substrates composed of 50% cattle manure + 50% vermiculite and 25% cattle manure + 25% cassava foliage + 25% Vida Verde®+ 25% vermiculite for the shaded hut. The buriti shelter is not recommended for production of genipap seedlings.

Identification of duplicates of cassava accessions sampled on the North Region of Brazil using microsatellite markers

Duplicates are common in germplasm banks and their identification is needed to facilitate germplasm bank management and to reduce maintenance costs. The aim of this work was to identify duplicates of cassava from a germplasm bank in Eastern Amazon, which had been previously characterized both morphological and agronomically. In order to be genotyped with 15 microsatellite loci, 36 accessions were selected. These accessions were classified into 13 groups of similar morpho-agronomical characteristics. All loci were polymorphic, and 75 alleles were identified, with an average of five alleles per loci and H E = 0.66. There were determined 34 pairs of genotypes with identical multiloci profiles and the probability of genetic identity was 1.1x10-12 with probability of exclusion of 99.9999%. Among these duplicates, there are accessions sampled on different years and places, but with different names and accessions with the same name sampled in different places and years. The study identified genotypes that are grown in different places and that have been maintained over the years by local farmers.

Flood pulse and spatial dynamics of mercury in sediments in Puruzinho lake, Brazilian Amazon

The study was conducted in Puruzinho lake (Humaitá, AM) considering seasonal periods of rainy and dry in way to elucidate the flood pulse importance in the deposition, remobilization and distributions of mercury and organic matter in bottom sediments in the Madeira River Basin (Brazilian Amazon). Bottom sediments and soils samples were analyzed for total mercury and organic matter. Mercury concentrations obtained in bottom sediment were 32.20-146.40 ng g-1 and organic matter values were 3.5 - 18.0%. The main region for accumulation of mercury and organic matter was in the central and deepest lake area In the rainy season there was a greater distribution of Hg and organic matter, mainly controlled by means of income of the Madeira river water during flooding, while the predominant process in the dry season was the remobilization of total Hg due to the resuspension of bottom sediments.

The influence of the conservation status and changes in the rainfall regime on forest-savanna mosaic dynamics in Northern Brazilian Amazonia

Coupled carbon/climate models are predicting changes in Amazon carbon and water cycles for the near future, with conversion of forest into savanna-like vegetation. However, empirical data to support these models are still scarce for Amazon. Facing this scenario, we investigated whether conservation status and changes in rainfall regime have influenced the forest-savanna mosaic over 20 years, from 1986 to 2006, in a transitional area in Northern Amazonia. By applying a spectral linear mixture model to a Landsat-5-TM time series, we identified protected savanna enclaves within a strictly protected nature reserve (Maracá Ecological Station - MES) and non-protected forest islands at its outskirts and compared their areas among 1986/1994/2006. The protected savanna enclaves decreased 26% in the 20-years period at an average rate of 0.131 ha year-1, with a greater reduction rate observed during times of higher precipitation, whereas the non-protected forest islands remained stable throughout the period of study, balancing the encroachment of forests into the savanna during humid periods and savannization during reduced rainfall periods. Thus, keeping favorable climate conditions, the MES conservation status would continue to favor the forest encroachment upon savanna, while the non-protected outskirt areas would remain resilient to disturbance regimes. However, if the increases in the frequency of dry periods predicted by climate models for this region are confirmed, future changes in extension and directions of forest limits will be affected, disrupting ecological services as carbon storage and the maintenance of local biodiversity.

Leaf anatomical features of three Theobroma species (Malvaceae s.l.) native to the Brazilian Amazon

Theobroma species have economic importance due to their use in the cosmetic and food industries, mainly in the production of chocolate. However, the anatomy of their vegetative structures remains poorly studied. The goal of this study was to describe the anatomical features of Theobroma grandiflorum, T. speciosum and T. subincanum to contribute to the biological knowledge of these species, as well as provide support to the biotechnological studies of native fruit plants of the Amazon. Leaves at different developmental stages were collected and analyzed under light microscopy and scanning electron microscopy. Sessile and stalked stellate trichomes and digitiform glandular trichomes were observed in the expanded leaves of T. grandiflorum and T. subincanum. These species were also similar in the morphology of the midrib, the organization of the mesophyll and the presence of starch grains in the midrib pith cells. Claviform glandular trichomes and mucilage cells in the epidermis occurred only in the expanded leaves of T. speciosum. The presence of mucilage secretory trichomes in shoot apices (colleters) of all species is a new finding for the genus Theobroma.

Data supporting the role of enzymes and polysaccharides during cassava postharvest physiological deterioration

This data article is referred to the research article entitled The role of ascorbate peroxidase, guaiacol peroxidase, and polysaccharides in cassava (Manihot esculenta Crantz) roots under postharvest physiological deterioration by Uarrota et al. (2015). Food Chemistry 197, Part A, 737746. The stress duo to PPD of cassava roots leads to the formation of ROS which are extremely harmful and accelerates cassava spoiling. To prevent or alleviate injuries from ROS, plants have evolved antioxidant systems that include non-enzymatic and enzymatic defence systems such as ascorbate peroxidase, guaiacol peroxidase and polysaccharides. In this data article can be found a dataset called newdata, in RData format, with 60 observations and 06 variables. The first 02 variables (Samples and Cultivars) and the last 04, spectrophotometric data of ascorbate peroxidase, guaiacol peroxidase, tocopherol, total proteins and arcsined data of cassava PPD scoring. For further interpretation and analysis in R software, a report is also provided. Means of all variables and standard deviations are also provided in the Supplementary tables (data.long3.RData, data.long4.RData and meansEnzymes.RData), raw data of PPD scoring without transformation (PPDmeans.RData) and days of storage (days.RData) are also provided for data analysis reproducibility in R software.