Microbiological and faunal soil attributes of coffee cultivation under different management systems in Brazil

Microbiological attributes as indicators of soil quality in coffee growing systems in Southwest Bahia, Brazil

Microorganisms are important indicators of soil quality due to their sensitivity to changes, reflecting the impacts caused by different land uses. The objective of this study was to evaluate the microbiological and physical-chemical attributes of the soil in areas cultivated with coffee under three different management systems (shaded coffee and full sun coffee with two spacings), as well as in adjacent areas under pasture and native forest, in Bahia, Brazil. The microbiological and physicochemical indicators evaluated were basal soil respiration (MBR), soil total organic carbon (TOC), microbial biomass carbon (MBC), metabolic quotient (qCO2), microbial quotient (qMic), enzyme activities (urease, acid phosphatase and fluorescein diacetate hydrolysis (FDA)). Physical and chemical indicators (particle size, texture, pH, P, K+, Ca2+, Mg2+, Al3+, and sum of bases) were also evaluated. Biological and chemical attributes were much more discriminative of study areas in the dry season. Microbial quotient (qMic) and metabolic quotient (qCO2) in the dry season showed that pasture is the most degraded land use. Conversely, nature forest and coffee with Grevillea were similar and were the best ones. In general, soil quality indicators were more sensitive to discriminate pasture and native forest from coffee systems, which, in turn, were not well discriminated among themselves.

Purple acid phosphatases in coffee-genome-wide identification and the transcriptional profile of selected members in roots upon Pi starvation

Phosphorus (P) availability is determinant for crop productivity and, despite the sufficient amount of this nutrient in arable land, most of it remains insoluble, leading to the need of high fertilizer input. To cope with P scarcity forecasts and also for cropping costs alleviation, genotypes better adapted to promote P solubilization and absorption are required, especially for perennial crops. Coffee is one of these important perennial crops cultivated in soils with low P availability, and thus we aimed to study adaptive strategies to coffee genotypes in acquire phosphorus. In this study, we focused on rhizosphere phosphatase activity, a major characteristic related to P solubilization from organic pools. To explore the genetic basis of this characteristic, we firstly identified 29 Purple Acid Phosphatases (PAP) genes in C. canephora genome and selected five candidates with higher potential to encode secreted PAPs. We found that C. arabica genotypes have diverse profiles of rhizosphere phosphatase activity, as well as microbial biomass carbon, which we measured to explore the impact of the plant on microbiota and also to discriminate the phosphatase activity origin (plant or microorganism-derived). We selected two C. arabica cultivars with contrasting phosphatase activity and found that one PAP gene has a correlated gene expression profile with this characteristic. This work explores coffee adaptative responses to P starvation conditions, and the information provided can further contribute to breeding programs aiming better adapted genotypes for sustainable agriculture in face of current challenges.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03399-6.

Contrasting Patterns of Functional Diversity in Coffee Root Fungal Communities Associated with Organic and Conventionally Managed Fields

The structure and function of fungal communities in the coffee rhizosphere are influenced by crop environment. Because coffee can be grown along a management continuum from conventional application of pesticides and fertilizers in full sun to organic management in a shaded understory, we used coffee fields to hold host constant while comparing rhizosphere fungal communities under markedly different environmental conditions with regard to shade and inputs. We characterized the shade and soil environment in 25 fields under conventional, organic, or transitional management in two regions of Costa Rica. We amplified the internal transcribed spacer 2 (ITS2) region of fungal DNA from coffee roots in these fields and characterized the rhizosphere fungal community via high-throughput sequencing. Sequences were assigned to guilds to determine differences in functional diversity and trophic structure among coffee field environments. Organic fields had more shade, a greater richness of shade tree species, and more leaf litter and were less acidic, with lower soil nitrate availability and higher soil copper, calcium, and magnesium availability than conventionally managed fields, although differences between organic and conventionally managed fields in shade and calcium and magnesium availability depended on region. Differences in richness and community composition of rhizosphere fungi between organic and conventionally managed fields were also correlated with shade, soil acidity, and nitrate and copper availability. Trophic structure differed with coffee field management. Saprotrophs, plant pathogens, and mycoparasites were more diverse, and plant pathogens were more abundant, in organic than in conventionally managed fields, while saprotroph-plant pathogens were more abundant in conventionally managed fields. These differences reflected environmental differences and depended on region.IMPORTANCE Rhizosphere fungi play key roles in ecosystems as nutrient cyclers, pathogens, and mutualists, yet little is currently known about which environmental factors and how agricultural management may influence rhizosphere fungal communities and their functional diversity. This field study of the coffee agroecosystem suggests that organic management not only fosters a greater overall diversity of fungi, but it also maintains a greater richness of saprotrophic, plant-pathogenic, and mycoparasitic fungi that has implications for the efficiency of nutrient cycling and regulation of plant pathogen populations in agricultural systems. As well as influencing community composition and richness of rhizosphere fungi, shade management and use of fungicides and synthetic fertilizers altered the trophic structure of the coffee agroecosystem.

Soil macrofauna in organic and conventional coffee plantations in Brazil

Abstract: Brazil has always been one of the most important coffee producing countries. Lately, there has equally been a renewed interest in alternative coffee production systems. The state of Espírito Santo is the second greatest coffee producer in Brazil; so, we used local coffee plantations to evaluate the relations between soil macrofauna and chemical and microbiological soil properties to identify which of these properties discriminate more effectively between the organic management system (OS) and the conventional management system (CS) of coffee plantations. For each of these two cultivation systems we chose three coffee farms who employed both cultivation systems and picked out the most similar fields from each property. At each site, first we sampled the litter at the soil surface. Afterwards, we sampled nine soil monoliths to evaluate the macrofauna, in summer and winter. We also collected nine supplemental soil samples, taken at a few centimeters from the soil monoliths, for chemical and microbiological analyses. Macrofauna density was evaluated by ANOVA and multivariate analysis. The chemical and microbiological properties are environmental variables, while the data on macrofauna are the explanatory variables. The total number of individuals recovered in this study was 3,354, and the climate, identified by the sampling season, was a great modulator of macrofauna, with higher numbers in winter. The principal components analysis showed that soil moisture, organic matter, nitrogen, phosphorus, boron, copper, pH, acid and alkaline phosphatases and microbial biomass carbon, were the most outstanding ones to discriminate both cultivation systems. We found no statistical significant differences in macrofauna density between OS and CS, probably due to a general great variability, since there was a tendency for much greater values in OS. We detected the interference of chemical and microbiological soil properties on the macrofauna community in both systems of coffee cultivation, and some results clearly correlated much better with climate data than with other factors. To our knowledge, this is the first time in which the data point to a clear separation between the more numerous and diversified soil macrofauna in coffee with organic cultivation from that with a conventional cultivation system.