In recent years, several studies have been developed to understand the impact of fermentation on the final quality of coffee and have indicated that postharvest processing could be a determinant of ...quality. However, a trend has appeared as a scientific counterpoint, indicating that the interactions between soil, fruit, altitude, and slope exposures with respect to the Sun are important to understand the behavior of the microbiome in coffee. Studies on the microbiota of coffee have addressed its role during the fermentation process, however the knowledge of indigenous microorganisms harbored in fruits and soil of coffee trees growing in fields are essential, as they can contribute to fermentation. Therefore, the aim of this work was to evaluate the influence of topographic and edaphic factors on the bacterial and fungal communities present in the soil and in the fruits of Coffea arabica trees. Samples of fruits and soil were collected from different growing areas at different altitudes and soil conditions. The microbial DNA was extracted and sequenced. The results showed the contribution of environmental factors in the structure of bacterial and fungal communities. The richness, evenness and diversity of the mycobiome and bacteriome were higher in the soil than in the fruits, independent of altitude. In addition, coffee trees at higher altitudes tended to have more bacteria shared between the soil and fruits. The co-occurrence/co-exclusion network showed that bacteria-bacteria connections were greater in higher altitudes. On another hand, fungi-fungi and fungi-bacteria connections were higher in low altitudes. This was the first study that evaluates in deep the influence of environmental factors in the microbiota habiting fruits and soil coffee trees, which may affect the coffee beverage quality.
Agroecology aims to maintain ecosystem services by minimizing the impact of agriculture and promoting the use of biological potential. Arbuscular mycorrhizal fungi (AMF) are elements which are key to ...improving crop productivity and soil quality. It is pertinent to understand how agricultural management in the tropics affects the AMF spatio-temporal community composition, especially in crops of global importance, such as coffee (Coffea arabica L.). Soil and root samples were collected from three localities under three management systems (agroecological, conventional and forest fragment), during the phenological stages of coffee (flowering, grain filling, harvesting). Spores were extracted for morphological identification and molecular community analysis by PCR-DGGE. Dendrograms were prepared and the bands were sequenced and analyzed by bioinformatics. No differences were observed in the richness of morphospecies between management systems, localities and period, but little is known about tropical species. Molecular analysis showed that the agroecological management system was similar to natural forest and with a higher diversity indices than conventional management. Locality and period of sample affect AMF community composition. It is necessary to associate classical taxonomic evaluations with molecular biological techniques because different approaches can lead to different outcomes. This study contributes to the understanding of the impact of agriculture management systems on AMF and provides evidence that agroecology is a management system applicable to sustainable coffee production.
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Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Growing concerns regarding the impact of the accumulation of plastic waste over several decades on the environmental have led to the development of biodegradable plastic. These plastics can be ...degraded by microorganisms and absorbed by the environment and are therefore gaining public support as a possible alternative to petroleum-derived plastics. Among the developed biodegradable plastics, oxo-biodegradable polymers have been used to produce plastic bags. Exposure of this waste plastic to ultraviolet light (UV) or heat can lead to breakage of the polymer chains in the plastic, and the resulting compounds are easily degraded by microorganisms. However, few studies have characterized the microbial degradation of oxo-biodegradable plastics. In this study, we tested the capability of Pleurotus ostreatus to degrade oxo-biodegradable (D2W) plastic without prior physical treatment, such as exposure to UV or thermal heating. After 45 d of incubation in substrate-containing plastic bags, the oxo-biodegradable plastic, which is commonly used in supermarkets, developed cracks and small holes in the plastic surface as a result of the formation of hydroxyl groups and carbon-oxygen bonds. These alterations may be due to laccase activity. Furthermore, we observed the degradation of the dye found in these bags as well as mushroom formation. Thus, P. ostreatus degrades oxo-biodegradable plastics and produces mushrooms using this plastic as substrate.
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Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Edaphoclimatic conditions, planting altitudes, soil, the microbiome of plants and fruits, genotypes, and postharvest processing are variables that contribute to the chemical and sensory quality of ...the coffee. Thus, the objective of this study was to evaluate the impacts of planting altitude and fermentation of fruits on the chemical and sensory quality of the coffee using Nuclear Magnetic Resonance (NMR) and Linear Discriminant Analysis (LDA). Cherry coffees were harvested in eight points of altitudes between 826 and 1078.08 m. A completely randomized design with e planting altitudes, five fermentation processes, and five repetitions was performed. Lipids, trigonelline, citrate, and malate were the compounds that most contribute to the chemical discrimination of coffee in the altitudes below 969 m. While, in the high altitudes (> 1000 m), this discrimination was due to the HMF, quinic acid, caffeine, and formic acid, and the global notes of coffee beverages were higher than 80 points. In fermented coffee, the LDA of the chemical data indicates the formation of five clusters, showing how the compounds can suffer changes depending on the form of processing used in coffee. The best score of beverage was observed in samples of 1078.08 m under dry fermentation and only in samples of 969 m was observed a significant difference in the sensory score between spontaneous fermentation and induced fermentation. Thus, coffee sensory scores were dependent on planting and fermentation methods and NMR and LDA techniques proved important in chemical and sensory discrimination of coffees.
Brazilian coffee production relies on the cultivation of Coffea arabica and Coffea canephora. Climate change has been responsible for the decreasing yield of the crops in the country yet the ...associated microbial community can mitigate these effects by improving plant growth and defense. Although some studies have tried to describe the microorganisms associated with these Coffea species, a study that compares the microbiome on a wider spatial scale is needed for a better understanding of the terroir of each coffee planting region. Therefore, our aim was to evaluate the microbial communities harbored in soils and fruits of these Coffea species in four Brazilian floristic domains (Amazon, Atlantic Forest Caatinga, and Cerrado). One hundred and eight samples (90 of soil and 90 of fruits) were used in the extraction and sequencing of the fungal and bacterial DNA. We detected more than 1000 and 500 bacterial and fungal genera, respectively. Some soil microbial taxa were more closely related to one coffee species than the other species. Bacillus bataviensis tends to occur more in arid soils from the Caatinga, while the fungus Saitozyma sp. was more related to soils cultivated with C. arabica. Thus, the species and the planting region (floristic domain) of coffee affect the microbial composition associated with this crop. This study is the first to report microbial communities associated with coffee produced in four floristic domains that include sites in eight Brazilian states. Data generated by DNA sequencing provides new insights into microbial roles and their potential for the developing more sustainable coffee management, such as the production of biofertilizers and starter culture for fermentation of coffee cherries.
Eucalypt cultivation is an important economic activity worldwide. In Portugal, Eucalyptus globulus plantations account for one-third of the total forested area. The nutritional requirements of this ...crop have been well studied, and nitrogen (N) is one of the most important elements required for vegetal growth. N dynamics in soils are influenced by microorganisms, such as diazotrophic bacteria (DB) that are responsible for biological nitrogen fixation (BNF), so the aim of this study was to evaluate and identity the main groups of DB in E. globulus plantations. Samples of soil and root systems were collected in winter and summer from three different Portuguese regions (Penafiel, Gavião and Odemira). We observed that DB communities were affected by season, N fertilization and moisture. Furthermore Bradyrhizobium and Burkholderia were the most prevalent genera in these three regions. This is the first study describing the dynamic of these bacteria in E. globulus plantations, and these data will likely contribute to a better understanding of the nutritional requirements of eucalypt cultivation and associated organic matter turnover.
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Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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•Microbial richness increases depending on the condition of the fermentation.•Microorganisms actions could be correlated with sensory attributes.•Fermentation conditions promote ...sensory and chemical changes in coffee.
In view of the possibility of diversifying metabolic routes promoted by fermentation, this study proposed a new processing method for coffee, which consists of adapting a technique already consolidated in winemaking, carbonic maceration. The assay occurred under anaerobic conditions with different time and temperature fermentation. The aim of this study was to determine the differences in coffee characteristics (sensorial, chemical, and microbial) after carbonic maceration and fermentation. Specialty Coffee Association protocol, nuclear magnetic resonance, and denaturing gradient gel electrophoresis were used in these analyzes. A significant functional relationship between global score and temperature (38 °C), for the fermentation time of 96 h was observed. Bacterial diversity and sensory characteristics had a positive correlation. Furthermore, trigonelline, formic acid, hydroxymethylfurfural, lipids, and γ-butyrolactone also contributed to score and sensory quality of coffee beverage. Thus, our data show consistent factors to infer on the microbiological action on the sensory quality of coffee beverage.
Prokaryotes play crucial roles in the rehabilitation process to restore the ecological integrity of disturbed areas. This work reports on the profiles of N‐fixing microorganisms and Actinobacteria, ...from DGGE, the prokaryotic composition from next‐generation sequencing (NGS) and physicochemical soil characteristics. We compared a deactivated mining site where mining ended about 10 years ago, when the revegetation process was begun (RV), and a reference site, with natural vegetation (NT), both located at Retiro das Almas Mine, in the Quadrilátero Ferrífero region, Minas Gerais, Brazil. In both sites, the most abundant archaeal and bacterial groups included Euryarchaeota, Thaumarchaeota, Proteobacteria, Actinobacteria, Acidobacteria, and Verrucomicrobia and revealed differences in their ecological metrics and distribution. Proteobacteria and Actinobacteria were most abundant in RV sites, while Acidobacteria and Verrucomicrobia were most abundant in NT sites. Less abundant phyla, such as Bathyarchaeota (Archaea) and GAL 15 (Bacteria) were found only in NT, while Gracilibacteria, Ignavibacteriae BJ‐169, and BRC1 were only found in RV. The majority of identified bacterial genera were shared by RV and NT. Soil P, pH, and particle density were most significant (p < 0.05) in RV, while Fe, Ca, organic matter, potential acidity and dispersed clays, were most significant (p < 0.05) in NT, showing differences in soil characteristics, which led the prokaryotic composition in these sites. DGGE profiles of N‐fixing microorganisms revealed N‐fixing predominance in both sites, although after 10 years prokaryotes diversity increased in RV site. Our results revealed that prokaryotic structure and composition are indicative of RV soil resilience.
Microbial diversity associated with coffee quality.
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•Coffee production requires complex procedures that affect both production and quality.•Microorganisms influence coffee growth and ...chemical profile.•Bioprospecting of coffee-associated microorganisms and metabolites can enhance sensory profiles.•Microorganisms can generate new sensory profiles through targeted fermentations.
Coffee stands as one of the world's most popular beverages, and its quality undergoes the influence of numerous pre- and post-harvest procedures. These encompass genetic variety, cultivation environment, management practices, harvesting methods, and post-harvest processing. Notably, microbial communities active during fermentation hold substantial sway over the ultimate quality and sensory characteristics of the final product. The interaction between plants and microorganisms assumes critical significance, with specific microbes assuming pivotal roles in coffee plant growth, fruit development, and, subsequently, the fruit's quality. Microbial activities can synthesize or degrade compounds that influence the sensory profile of the beverage. However, studies on the metabolic products generated by various coffee-related microorganisms and their chemical functionality, especially in building sensory profiles, remain scarce. The primary aim of this study was to conduct a literature review, based on a narrative methodology, on the current understanding of the plant-microorganism interaction in coffee production. Additionally, it aimed to explore the impacts of microorganisms on plant growth, fruit production, and the fermentation processes, directly influencing the ultimate quality of the coffee beverage. Articles were sourced from ScienceDirect, Scopus, Web of Science, and Google Scholar using specific search terms such as “coffee microorganisms”, “microorganisms-coffee interactions”, “coffee fermentation”, “coffee quality”, and ‘coffee post-harvest processing”. The articles used were published in English between 2000 and 2023. Selection criteria involved thoroughly examining articles to ensure their inclusion was based on results about the contribution of microorganisms to both the production and quality of the coffee beverage. The exploration of microorganisms associated with the coffee plant and its fruit presents opportunities for bioprospecting, potentially leading to targeted fermentations via starter cultures, consequently generating new profiles. This study synthesizes existing data on the current understanding of the coffee-associated microbiome, its functionalities within ecosystems, the metabolic products generated by microorganisms, and their impacts on fermentation processes and grain and beverage quality. It highlights the importance of plant-microorganism interactions in the coffee production chain.
A drug that is widely used in the treatment of psychiatric disorder is lithium (Li) salts. The people who make therapeutic use of this drug develop a series of side effects. Through metataxonomic ...data, this study assessed the impacts of lithium, as Li carbonate or Li-enriched mushrooms, on the microbial composition of the ileum, colon, and feces of piglets. Employing Bray–Curtis metric, no differences were observed among the treatments evaluated. Nevertheless, the alpha diversity indices showed differences in the Simpson, Shannon, and Chao-1 indices in the colon and Chao-1 in the feces in the diets with Li compared with the diets without Li. The taxa with the highest relative abundance varied among the ileum, colon, and feces, with a predominance of the phyla Firmicutes, Bacteroidota, and Proteobacteria in diets with Li. Many groups of microorganisms that are important for the health of the host (e.g.,
Lactobacillus
, Ruminococcaceae,
Enterorhabdus
, Muribaculaceae, and
Coprococcus
) had their relative abundance increased in animals that received diets with the recommended dose of lithium. Furthermore, there was an increase in the abundance of
Prevotellaceae
and
Bacteroidales
(in the diet with Li-enriched mushroom) and
Clostridia
,
Ruminococcus, Burkholderia,
and
Bacteroidales
(diets with Li carbonate) at the recommended dosages. This is the first study to show the effects of Li carbonate and Li-enriched mushrooms on the intestinal microbiota of piglets. Thus, the effects of lithium on the body may be related to its ability to change the composition of the intestinal microbiota.
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