Luiz Gustavo de Matos^a, Anderson Clayton da Silva Abreu^a, Vanessa Pereira Perez Alonso^e, Juliano Leonel Gonçalves^a, Maristela da Silva do Nascimento^b, Sérgio Bertelli Pflanzer Jr^b, Jonatã Henrique Rezende-de-Souza^b, Chiara Gini^c, Natália Faraj Murad^d, Marcelo Mendes Brandão^d, Nathália Cristina Cirone Silva^a

^aDepartment of Food Science and Nutrition, School of Food Engineering (FEA), Universidade Estadual de Campinas (UNICAMP), 13083-862, Campinas, Sao Paulo, Brazil
^bDepartment of Food Engineering and Technology, School of Food Engineering (FEA), Universidade Estadual de Campinas (UNICAMP), 13083-862, Campinas, Sao Paulo, Brazil
^cDepartment of Veterinary Medicine, Università degli Studi di Milano, Lodi, Lombardia, Italy
^dLaboratory of Systemic and Integrative Biology, Center of Molecular Biology and Genetic Engineering, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
^eIndependent researcher, Prague, Czechia

https://doi.org/10.1016/j.microb.2024.100035

The science behind dry-aged meat has increased during the last few years. Differently from wet-aging, where meat is vacuum packed, the dry-aging process happens without packaging or protection, which may change the bacterial diversity of the meat, and this change can alter the sensory characteristics of the meat. Different methods are used to identify the microbial of meat. The most used ones are traditional techniques and the Next Generation Sequencing (NGS), widely used to identify bacteria present in diverse types of food. The aim of this study was to evaluate the bacterial diversity of dry-aged and wet-aged beef by traditional microbiological tests and NGS to compare the bacterial diversity given by those different methodologies, as well as compare their specificity. Beef strip loins (n = 6) were collected directly from the slaughterhouse and transported to the laboratory. Samples were dry or wet-aged for 20 and 34 days. Before and after aging, samples were analyzed by Traditional microbiological analysis and NGS. It was observed, with traditional microbiology tests, a greater increase of total bacterial count in the wet-aged samples from 0 to 20 and 34 days, with psychotropic bacteria having the greatest increase. In the dry-aged samples there was a decrease in the total bacterial count, with only molds and yeast significant growth during aging. No E. coli growth was observed for any treatment. From metagenomics analysis, eleven main bacterial genera were detected in the meat microbiota, with a relative abundance higher than 2%, and the seven most abundant ones were Carnobacterium (47.9%), Pseudomonas (22.2%), Lactobacillus (5.4%), Romboutsia (2.8%), Leuconostoc (2.5%), Candidatus Nitrosotalea (2.4%) and Akkermansia (2.3%). Alpha diversity showed a higher richness on the non-aged samples, whereas wet-aged samples showed the smallest richness, the same for the samples aged for 34 days. In addition, beta diversity showed that the microorganisms are highly related when considering time, but different clustering when comparing aging types. Further, dry-aged beef showed a higher presence of Pseudomonas sp., which is a group of microorganisms with a large range of ideal bacterial growth conditions, whereas the wet-aged samples, due to their controlled anaerobic environment, a higher presence of Carnobacterium was observed. It was possible to observe that traditional microbiology is still an important tool in food safety, once it could clearly identify the main important groups of bacteria, once the microorganisms present in food are already very well described, allowing researchers and producers, depending on the methodology used, to check for them, while NGS show more groups, however, it is still an expensive tool, when considering the number of samples. Even showing different data between them, they were both efficient to differentiate the microbiota of the beef samples in their own specificity.

¹Rezende, G.S; ²Funnicelli, M.I.G;³Rocha, F.I ¹Malavazi, I; ^4,5Crauwels, S.; ⁶Brandao, M.M.; ¹Cunha, A.F.

1 Genetic and Evolution Department, Laboratory of Biochemistry and Applied Genetics (LBGA-UFSCar), SP, Brazil;
2 Laboratory of Bioinformatics, Department of Agricultural, Livestock and Environmental Biotechnology, São Paulo State University (UNESP), School of Agricultural and Veterinary Sciences, Jaboticabal, SP, Brazil
3 Mokichi Okada Research Center/ Korin Agriculture & Environment
4 Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Centre of Microbial and Plant Genetics (CMPG), Department of Microbial and Molecular Systems (M2S), KU Leuven, Leuven, Belgium
5 Leuven Institute for Beer Research (LIBR), KU Leuven, Leuven, Belgium
6 Universidade Estadual de Campinas. Centro de Biologia Molecular e Engenharia Genética - Laboratory of integrative and systemic biology (LaBIS- UNICAMP), SP, Brazil

Grapes are globally popular with wine production being one of the most well-known uses of grapes globally. Brazil has a growing wine industry, and the Serra Gaúcha region is a significant contributor to the country's wine production, while other states are also increasing the production. Environmental factors heavily influence grape quality, shaping the crucial "terroir" for wines. Here, the soil quality was assessed through nutrient analysis and microbial diversity, which could significantly impact grape health and final wine attributes. Soil samples from São Paulo's vineyards, focusing on Syrah, Malbec, and Cabernet Sauvignon, underwent physicochemical and microbial analysis via 16S rRNA metabarcoding and highlighted significant differences in soil composition between vineyards. Statistical analyses like PCA and CAP showcased region-based separation and intricate associations between microbiota, region, and grape variety. Correlation analyses pinpointed microbial genera linked to specific soil nutrients. Random Forest analysis identified abundant bacterial genera per grape variety and the Network analyses revealed varied co-occurrence patterns, notably Cabernet Sauvignon exhibiting complex microbial interactions. This study unveils complex relationships between soil microbiota, nutrients, and diverse grape varieties in distinct vineyard regions. Understanding these specific microorganisms associated with grapes holds promise for enhancing vineyard management, grape quality, and wine production, potentially optimizing soil health and bolstering grapevine resilience against pests and diseases, contributing to the unique character of wines known as terroir.

Keywords: Grape; Microbiota; Nutrients, Vineyards; Soil diversity.

Supplementary material:

Rezende, Graziela Silva; Funnicelli, Michelli Inácio Gonçalves; Rocha, Fernando Igne; Malavazi, Iran; Crauwels, Sam; Brandão, Marcelo Mendes; Cunha, Anderson Ferreira da, 2023, "Supporting material referenced on the manuscript metabarcoding analysis reveals an interaction among distinct groups of bacteria associated with three different varietals of grapes used for wine production in Brazil", https://doi.org/10.25824/redu/XCR8XR

Pedro G. Ribeiro^1,2,3, Darli Massardo⁴, Renato Rogner Ramos⁵, Marília B. Lion⁶, Márcio Zikán Cardoso^6,7, Marcus R. Kronforst⁴, André V. L. Freitas⁵, Marcelo Mendes Brandão¹, Karina L. Silva-Brandão^1,8 

¹Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas 13083-875, SP, Brazil;
²Institute of Entomology, Biology Centre of the Czech Academy of Sciences, České Budějovice 37005, South Bohemia, Czech Republic;
³Faculty of Science, University of South Bohemia, České Budějovice 37005, South Bohemia, Czech Republic;
⁴Department of Ecology & Evolution, The University of Chicago, Chicago 60637, IL, USA;
⁵Departamento de Biologia Animal and Museu de Zoologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas 13083-862, SP, Brazil;
⁶Departamento de Ecologia, Universidade Federal do Rio Grande do Norte, Natal 59072-970, RN, Brazil;
⁷Departamento de Ecologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil;
⁸Leibniz Institute for the Analysis of Biodiversity Change, Museum of Natur – Zoology, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany.

Amazonian white sand ecosystems (WSEs) are isolated patches of scleromorphic vegetation above white sandy soils that occur exclusively in the Amazon Forest. Due to unique soil characteristics, harsh irradiation, and temperature conditions, these ecosystems present low diversity and high floral and faunal endemism. Nevertheless, they are underrepresented in geological and biological studies, especially regarding the genetic structure and diversity of the species inhabiting them. Here, we investigated the genetic differentiation among populations of Heliconius hermathena Hewitson, 1854 (Lepidoptera, Nymphalidae), a specialized butterfly on the Amazonian white sand ecosystems, as well as their associated Wolbachia endosymbionts. Using the mitochondrial genome, we inferred high levels of genetic differentiation among individuals from six different subspecies of H. hermathena occurring in eight different localities. We also found high levels of structure among H. hermathena populations and postulated that isolation of WSEs and genetic drift must have played an important role in generating and maintaining the species’ current patterns of genetic differentiation. The infection by Wolbachia reached 97% of the specimens, and although isolated both genetically and geographically, the populations investigated share similar Wolbachia contigs. We discuss the importance of habitat isolation for population structure in Amazonia and, therefore, its contribution to the outstanding biodiversity in the region and to the comprehension of the diversification of its endemic species. We also discuss the role of this emblematic species as a model to understand butterfly diversity in isolated environments.

Key words: Amazonia, campinas, mitochondrial genome, Nymphalidae, Wolbachia.

Suplementary Material

André Ricardo Oliveira Conson¹, Natália Faraj Murad¹, Rogerio Martins Gonçalves¹, Karina Lucas Silva-Brand?o², Fernando Luis Cônsoli³, Celso Omoto³, Marcelo Mendes Brandão¹

1 Center of Molecular Biology and Genetic Engineering, University of Campinas, Campinas, Brazil
2 Federal university of ABC, Centre for Natural Sciences and Humanities, Santo André, Brazil
3 Department of Entomology and Acarology, College of Agriculture “Luiz de Queiroz”, University of são Paulo, Piracicaba, Brazil

One of the most important lepidopteran pests worldwide is the noctuid Helicoverpa armigera. The generalist feeding habit of the species is of great interest for agriculture since the cultivation of different annual crops may provide ideal conditions for survival and set of new populations. Since its introduction in South America, H. armigera has infested a wide range of hosts whereas knowledge about enzymes responsible for the digestive and detoxification processes are still scarce, specially under natural conditions. Thus, to develop efficient controlling methods of this pest, it is mandatory first to determine which genes are involved in its plant interactions and their expression levels. In the present study, H. armigera larvae from natural populations were sampled in order to investigate its transcriptome pattern toward different host plants. Larvae were sampled from soybean (Glycine max (L.) Merr), cotton (Gossypium hirsutum L.), bean (Phaseolus vulgaris (L.)), pearl millet (Pennisetum glaucum (L.)), maize (Zea mays L.) and grain sorghum (Sorghum bicolor (L) Moench). A transcriptome de novo assembly resulted in 132,378 transcripts, and 65,947 were successfully annotated. Host conditions in H. armigera revealed 43 differentially expressed transcripts. The largest number was obtained in comparison between soybean and bean, resulting in 27 down-regulated and seven up-regulated transcripts in soybean. A set of differentially expressed transcripts specifically associated with cotton and bean were identified. Functional analysis showed that genes involved in electron transport chain are implicated in host responses. We also visualized expression patterns in important gene families, including serine proteases and intracellular lipid-binding proteins. This study of H. armigera transcriptome provided a set of candidate transcripts that demonstrates host-insect interactions on natural conditions.

Key-words: Noctuidae, polyphagous, RNA-seq, digestive enzymes, gene expression

This manuscript is under production, and, no supplementary material is currently available.

Catherine Béliveau, Patrick Gagné, Sandrine Picq, Oksana Vernygora, Christopher I. Keeling, Kristine Pinkney, Daniel Doucet, Fayuan Wen, J. Spencer Johnston, Halim Maaroufi, Brian Boyle, Jérôme Laroche, Ken Dewar, Nikoleta Juretic, Gwylim Blackburn, Audrey Nisole, Bryan Brunet, Marcelo Brandao, Lisa Lumley, Jun Duan, Guoxing Quan, Christopher J. Lucarotti, Amanda D. Roe, Felix A.H. Sperling, Roger C. Levesque, Michel Cusson

Genome Biology and Evolution, evac087
https://doi.org/10.1093/gbe/evac087

Insects have developed various adaptations to survive harsh winter conditions. Among freeze-intolerant species, some produce “antifreeze proteins” (AFPs) that bind to nascent ice crystals and inhibit further ice growth. Such is the case of the spruce budworm, Choristoneura fumiferana (Lepidoptera: Tortricidae), a destructive North American conifer pest that can withstand temperatures below -30°C. Despite the potential importance of AFPs in the adaptive diversification of Choristoneura, genomic tools to explore their origins have until now been limited. Here we present a chromosome-scale genome assembly for C. fumiferana, which we used to conduct comparative genomic analyses aimed at reconstructing the evolutionary history of tortricid AFPs. The budworm genome features 16 genes homologous to previously reported C. fumiferana AFPs (CfAFPs), 15 of which map to a single region on chromosome 18. Fourteen of these were also detected in five congeneric species, indicating Choristoneura AFP diversification occurred before the speciation event that led to C. fumiferana. Although budworm AFPs were previously considered unique to the genus Choristoneura, a search for homologs targeting recently sequenced tortricid genomes identified seven CfAFP-like genes in the distantly related Notocelia uddmanniana. High structural similarity between Notocelia and Choristoneura AFPs suggests a common origin, despite the absence of homologs in three related tortricids. Interestingly, one Notocelia AFP formed the C-terminus of a “zonadhesin-like” protein, possibly representing the ancestral condition from which tortricid AFPs evolved. Future work should clarify the evolutionary path of AFPs between Notocelia and Choristoneura and assess the role of the “zonadhesin-like” protein as precursor of tortricid AFPs.