The composition and diversity of fungal communities associated with three endangered orchid species, Hadrolaelia jongheana, Hoffmannseggella caulescens, and Hoffmannseggella cinnabarina, found in ...different vegetation formations of the Atlantic Forest were determined by constructing clone libraries and by applying diversity and richness indices. Our results demonstrated the presence of Basidiomycetes. Sebacinales (81.61 %) and Cantharellales (12.10 %) were the dominant orders and are potential candidates for orchid mycorrhizal fungi. The Ascomycetes identified included the Helotiales (29.31 %), Capnodiales (18.10 %), and Sordariales (10.34 %), among others. These orders may represent potentially endophytic fungi. A Shannon–Wiener diversity index (H′) analysis showed a relatively high fungal community diversity associated with these tropical orchids. This diversity may offer greater flexibility in terms of the adaptation of the plants to changing environmental conditions and the potential facilitation of reintroduction programs. The Simpson diversity index values showed that all of the libraries included dominant species, and a LIBSHUFF analysis showed that the fungal communities were structurally different from each other, suggesting an influence of local factors on this diversity. This study offers important information for the development of conservation strategies for threatened and endemic species of Brazilian flora in an important and threatened hotspot.
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.
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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.
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.
Seasonal variation in the Canastra cheese mycobiota Martin, José Guilherme Prado; Silva, João Marcos Maia; César, Isabel Cristina da Rocha ...
Frontiers in microbiology,
02/2023, Volume:
13
Journal Article
Peer reviewed
Open access
Canastra cheese is the most well-known artisanal cheese produced in Brazil. Although its production includes a step to remove fungi from the cheese surface, in recent years some cheesemakers have ...preserved the autochthonous fungi grown during ripening due to an interest in the sensory characteristics attributed to these microorganisms. In this work, the mycobiota of artisanal cheeses produced in the Canastra region was characterized based on ITS marker gene analysis. A total of 96 artisanal cheeses from 16 different farms across 9 cities were collected during two different periods (dry and wet seasons). The Canastra cheese mycobiota was significantly impacted by the season, the city of production and the farm but altitude did not affect the fungal community of the cheeses analyzed.
was most abundant in the majority of samples across both seasons. During the wet season,
and
were the next most abundant species, followed by
and
These results highlight the importance of manufacturing practices and seasonality on the fungal composition of Canastra cheeses. These insights are particularly important in light of recent new regulation in Brazil, removing previous obstacles for surface fungi to persist on cheese. These new regulations will allow new approaches to cheese production, and ultimately, novel products.
The retreat of glaciers in Antarctica has increased in the last decades due to global climate change, influencing vegetation expansion, and soil physico-chemical and biological attributes. However, ...little is known about soil microbiology diversity in these periglacial landscapes. This study characterized and compared bacterial and fungal diversity using metabarcoding of soil samples from the Byers Peninsula, Maritime Antarctica. We identified bacterial and fungal communities by amplification of bacterial 16 S rRNA region V3-V4 and fungal internal transcribed spacer 1 (ITS1). We also applied
C dating on soil organic matter (SOM) from six profiles. Physico-chemical analyses and attributes associated with SOM were evaluated. A total of 14,048 bacterial ASVs were obtained, and almost all samples had 50% of their sequences assigned to Actinobacteriota and Proteobacteria. Regarding the fungal community, Mortierellomycota, Ascomycota and Basidiomycota were the main phyla from 1619 ASVs. We found that soil age was more relevant than the distance from the glacier, with the oldest soil profile (late Holocene soil profile) hosting the highest bacterial and fungal diversity. The microbial indices of the fungal community were correlated with nutrient availability, soil reactivity and SOM composition, whereas the bacterial community was not correlated with any soil attribute. The bacterial diversity, richness, and evenness varied according to presence of permafrost and moisture regime. The fungal community richness in the surface horizon was not related to altitude, permafrost, or moisture regime. The soil moisture regime was crucial for the structure, high diversity and richness of the microbial community, specially to the bacterial community. Further studies should examine the relationship between microbial communities and environmental factors to better predict changes in this terrestrial ecosystem.
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.
After the collapse of Fundão Dam in Mariana‐MG, Brazil, the discharge of iron ore mining waste into the Doce River watershed negatively impacted the landscape. Monitoring the composition and species ...richness of soil microbiota may be useful bioindicators of ecosystem recovery. This study aimed to compare soil chemical properties, total fungal species, and arbuscular mycorrhizal fungi (AMF) in sites unaffected and affected by mining tailings in the first 3 years after the collapse of Fundão Dam. Soil and root samples were collected in dry and rainy seasons over 3 years in unaffected (adjacent forest and pasture) and affected areas (REC1, REC2, and PASTrec) by mine tailings. Changes in soil chemical properties over the sampling period were measured by routine chemical analyses. Total fungi in the soil was determined by high‐throughput sequencing. AMF community was evaluated using spore number, root colonization, and denaturing gradient gel electrophoresis. Affected sites had higher ranges of pH and lower soil organic matter than unaffected sites. Revegetation had a positive effect on soil fungal community. Increased similarity in AMF DGGE analysis was observed in the two sampling sites over time. A high similarity of total fungi and AMF was observed between REC and pasture areas, suggesting that revegetation strategy employed may be heading towards a pasture condition. Thus, post‐disturbance analysis of this study was important to evaluate of ecosystem recovery affected by the rupture of iron ore mining dam and demonstrated that the soil microbiota was a sensitive bioindicator in this long path of ecosystem recovery.
Ripening cycles of the coffee are important for planning the harvest and post-harvest processing of the fruit and influence the sensory quality of the coffee beverage. In the
Coffea arabica
, the ...number of these annual cycles depends on the edaphoclimatic conditions, soil microbiota, altitude, and genotype. In this study, we present in an unprecedented way how the microbial communities (bacteria and fungi) of the soil and fruits of the coffee tree and the quality of chemical and sensory of coffee fruits can change depending on the harvest season. We also evaluated whether there is a relationship between changes in microbial communities (soil and fruits) and chemical and sensory panels of the coffee in two seasons. Cherry coffee fruits sampling and soil were carried out in September and November which have different edaphoclimatic conditions. Profiles of the microbial community and chemical and sensory panels of the samples were performed using the DGGE technique, Mid-infrared spectroscopy, and Specialty Coffee Association protocols. Microbial communities (soils and fruits) profile was different between distinct sampling periods. Composition of the coffee varies with the harvest since the coffees harvested in September have higher concentrations of caffeine and chlorogenic acids and lower concentrations of proteins and lipids compared to the samples collected later. A correlation between infrared spectrum and microbial community was observed in the second harvest period which had a final sensory score higher than another harvest. These results show that edaphoclimatic factors and microbial communities can be associated with the final quality of the beverage.
The rupture of the Fundão dam in Brazil in November 2015 covered the soil with iron ore mining waste (IOMW) and removed vegetation. Arbuscular mycorrhizal fungi (AMF) can benefit vegetation growth ...and soil structure, assisting the rehabilitation of degraded areas. Therefore, the objective of the present work was to evaluate the AMF community structure and investigate the effect of the technosol physicochemical properties in these communities after revegetation programs were adopted in areas affected by IOMW. Soil samples were taken from an undisturbed atlantic forest (UND) and two regions influenced by IOMW, under natural recovery process (REC1) and under revegetation process introduced after the dam rupture (REC2) during the rainy season (February, E1) and dry season (September, E2) of 2017. AMF community structure in both seasons was assessed by PCR-DGGE, spore density, and glomalin-related soil protein (GRSP) content. Soil physical and chemical characteristics were also evaluated and related to the AMF community. In the summer, the AMF community profile was affected by the host plants used for revegetation, as REC2 showed 92% similarity with the natural forest against only 73% of REC1. In the winter, REC1 showed a higher similarity rate with REC2 and UND, as there was already vegetation cover in the area. The number of spores and the content of glomalin were not different between REC1 and REC2, but they were lower than UND. The number of spores in both areas was, on average, 12 (summer) and 8 times (winter) less than UND, and the total glomalin was 22 and 10 times less, respectively. The chemical characteristics of UND and soils under the recovery process (REC1 and REC2) were considerably different due to IOMW deposition. A small change in the soil chemical attributes has been observed after the revegetation in both REC areas, which was very slow toward the rehabilitation process, although the changes in the soil physicochemical characteristics were incipient till the period from 14 months (E1) to 21 months (E2). We concluded that the covering by plants of areas affected by IOMW improves AMF diversity since these fungi are biotrophic. Furthermore, the findings suggest that the short period (six months) can alter AMF communities. Therefore, revegetation processes adopted after dam collapse have promoted land reclamation, but this effect requires further monitoring.
•Iron ore mining waste altered soil biological and physicochemical characteristics.•Revegetation of degraded areas improved abundance and diversity of arbuscular mycorrhizal fungi community.•There is temporal variation in arbuscular mycorrhizal fungi community•Physicochemical changes of soil affect the arbuscular mycorrhizal fungi community.•Arbuscular mycorrhizal fungi are good biological indicators for soil quality monitoring.
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