scholarly journals Soil microbial composition varies in response to coffee agroecosystem management

2020 ◽  
Vol 96 (9) ◽  
Author(s):  
Stephanie D Jurburg ◽  
Katherine L Shek ◽  
Krista McGuire
Keyword(s):  
Land Use ◽  
Bacterial Communities ◽  
Soil Chemistry ◽  
Soil Microbial Communities ◽  
Soil Microbiome ◽  
Stand Age ◽  
Microbial Composition ◽  
Coffee Plantations ◽  
Soil Microbial ◽  
Soil Microbial Composition

ABSTRACT Soil microbes are essential to the continued productivity of sustainably managed agroecosystems. In shade coffee plantations, the relationship between soil microbial composition, soil nutrient availability and coffee productivity have been demonstrated, but the effects of management on the composition of the soil microbial communities remains relatively unexplored. To further understand how management modulates the soil microbiome, the soil fungal and bacterial communities, soil chemistry, and canopy composition were surveyed in a Nicaraguan coffee cooperative, across 19 individual farms. Amplicon sequencing analyses showed that management (organic or conventional), stand age and previous land use affected the soil microbiome, albeit in different ways. Bacterial communities were most strongly associated with soil chemistry, while fungal communities were more strongly associated with the composition of the canopy and historical land use of the coffee plantation. Notably, both fungal and bacterial richness decreased with stand age. In addition to revealing the first in-depth characterization of the soil microbiome in coffee plantations in Nicaragua, these results highlight how fungal and bacterial communities are simultaneously modulated by long-term land use legacies (i.e. an agricultural plot's previous land use) and short-term press disturbance (i.e. farm age).

scholarly journals Soil microbial composition varies in response to coffee agroecosystem management

2020 ◽  
Author(s):  
Stephanie D. Jurburg ◽  
Katherine L. Shek ◽  
Krista McGuire
Keyword(s):  
Land Use ◽  
Bacterial Communities ◽  
Soil Chemistry ◽  
Soil Microbiome ◽  
Stand Age ◽  
Microbial Composition ◽  
Shade Coffee ◽  
Coffee Plantations ◽  
Soil Microbial ◽  
Soil Microbial Composition

ABSTRACTSoil microbes are essential to the continued productivity of sustainably-managed agroecosystems. In shade coffee plantations, the relationship between soil microbial composition, soil nutrient availability, and coffee productivity have been demonstrated, but the effect of management on the composition of the soil microbial communities remains relatively unexplored. To further understand how management modulates the soil microbiome, we surveyed the soil fungal and bacterial communities, as well as soil chemistry and canopy composition in a Nicaraguan coffee cooperative, across 19 individual farms. Using amplicon sequencing, we found that management (organic or conventional), stand age, and previous land use strongly affected the soil microbiome, albeit in different ways. Bacterial communities were most strongly associated with soil chemistry, while fungal communities were more strongly associated with the composition of the canopy and historical land use of the coffee plantation. Notably, both fungal and bacterial richness decreased with stand age. In addition to revealing the first in-depth characterization of the soil microbiome in coffee plantations in Nicaragua, our results highlight how fungal and bacterial communities are simultaneously modulated by long-term land use legacies (i.e., an agricultural plot’s previous land use) and short-term press disturbance (i.e., farm age).One-sentence-summaryThe composition of soil fungal and bacteria communities in shade coffee plantations depend on the combination of the farm’s management type, its previous land use, and the coffee plants’ stand age, but are differently influenced by each.

scholarly journals The impact of stand age and fertilization on the soil microbiome of Miscanthus × giganteus

2020 ◽  
Author(s):  
Lanying Ma ◽  
Fernando Igne Rocha ◽  
Jaejin Lee ◽  
Jinlyung Choi ◽  
Mauricio Tejera ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Community Structure ◽  
Soil Microbial Communities ◽  
N Fertilizer ◽  
Soil Microbiome ◽  
Stand Age ◽  
Soil Microbial ◽  
Miscanthus Giganteus

Yield of the perennial grass Miscanthus × giganteus has shown an inconsistent and unpredictable response to nitrogen (N) fertilizer, yet fertilization underpins the crop’s environmental and economic sustainability. The interactions among soil microbial communities, N availability, and M. × giganteus and management may explain changes in plant productivity. In this study, soil samples from different stand ages of M. × giganteus in a replicated chronosequence field trial were used to investigate the effects of stand age and N fertilizer rates on microbial community structure. We hypothesized that there is a definable M. × giganteus soil microbiome and that this community varies significantly with stand age and fertilization. Our results showed that the main phyla in soil microbial communities, regardless of plant age, are similar but microbial community structures are significantly different. The variation in observed microbial communities generally decreases in older stand ages. The amount of N fertilizer applied also affected the microbial community structure associated with different aged M. × giganteus. Specifically, the relative abundance of Proteobacteria (Alphaproteobacteria and Gammaproteobacteria) and Acidobacteria (Subgroup Gp1) increased shortly after fertilization and were more associated with younger M. × giganteus. Further, our results show a significant relationship between bacterial alpha diversity and fertilization rates and that this response is also impacted by stand age. Overall, our results emphasize linkages between microbial community structure, plant age, and fertilization in M. × giganteus.

Diversity of Soil Microbial Communities under Different Soil Salinity Levels Analyzing by PLFA

2014 ◽  
Vol 955-959 ◽  
pp. 314-320 ◽  
Author(s):  
Xin Li ◽  
Yan Jiao ◽  
Ming De Yang
Keyword(s):  
Microbial Communities ◽  
Soil Salinity ◽  
Saline Soil ◽  
Phospholipid Fatty Acid ◽  
Soil Microbial Communities ◽  
Microbial Composition ◽  
Soil Microbial ◽  
Salinity Levels ◽  
Salinized Soil ◽  
Soil Microbial Composition

Under different soil salinity levels, diversity of soil microbial communities from Hetao irrigated land of Inner Mongolia was studied by phospholipid fatty acid (PLFA) analysis. The study found that PLFAs biomass in saline soil was significantly lower than those of strongly salinized soil and slight salinized soil. Microbes was bacteria-based from these soil. The bacterial PLFA loading in saline soil is significantly less than those of strongly salinized soil and slight salinized soil . Cluster analysis showed that changes had obviously taken place on soil microbial composition and quantity under different soil salinity levels.About 76.89% of variation in PLFA patterns explained by PC1(the first  principal components),and 17:1, 16:0, 18:1w9c, 18:1w9t, 18:2, 18:3w3c, 12:0 were strongly negatively correlated with PC1.However,soil salinity and pH were positively correlated with PC1.We conclude that soil salinity has  a profound affect on the microbial community structure.

scholarly journals Positive effects of crop diversity on productivity driven by changes in soil microbial composition

2020 ◽  
Author(s):  
Laura Stefan ◽  
Martin Hartmann ◽  
Nadine Engbersen ◽  
Johan Six ◽  
Christian Schöb
Keyword(s):  
Plant Growth ◽  
Microbial Diversity ◽  
Crop Yield ◽  
Soil Microbial Communities ◽  
Crop Diversity ◽  
Microbial Composition ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
Positive Effects ◽  
Soil Microbial Composition

SummaryIntensive agriculture has major negative impacts on ecosystem diversity and functioning, including that of soils. The associated reduction of soil biodiversity and essential soil functions, such as nutrient cycling, can restrict plant growth and crop yield. By increasing plant diversity in agricultural systems, intercropping could be a promising way to foster soil microbial diversity and functioning. However, plant–microbe interactions and the extent to which they influence crop yield under field conditions are still poorly understood. In this study, we performed an extensive intercropping experiment using eight crop species and 40 different crop mixtures to investigate how crop diversity affects soil microbial diversity and functions, and whether these changes subsequently affect crop yield. Experiments were carried out in mesocosms under natural conditions in Switzerland and in Spain, two countries with drastically different soils and climate, and our crop communities included either one, two or four species. We sampled and sequenced soil microbial DNA to assess soil microbial diversity, and measured soil basal respiration as a proxy for soil activity. Results indicate that in Switzerland, increasing crop diversity led to shifts in soil microbial community composition, and in particular to an increase of several plant-growth promoting microbes, such as members of the bacterial phylum Actinobacteria. These shifts in community composition subsequently led to a 15 and 35% increase in crop yield in 2 and 4-species mixtures, respectively. This suggests that the positive effects of crop diversity on crop productivity can partially be explained by changes in soil microbial composition. However, the effects of crop diversity on soil microbes were relatively small compared to the effects of abiotic factors such as fertilization (3 times larger) or soil moisture (3 times larger). Furthermore, these processes were context-dependent: in Spain, where soil resources were limited, soil microbial communities did not respond to crop diversity, and their effect on crop yield was less strong. This research highlights the potential beneficial role of soil microbial communities in intercropping systems, while also reflecting on the relative importance of crop diversity compared to abiotic drivers of microbiomes, thereby emphasizing the context-dependence of crop–microbe relationships.

scholarly journals Land-use intensification differentially affects bacterial, fungal and protist communities and decreases microbiome network complexity

2022 ◽  
Vol 17 (1) ◽  
Author(s):  
Sana Romdhane ◽  
Aymé Spor ◽  
Samiran Banerjee ◽  
Marie-Christine Breuil ◽  
David Bru ◽  
...  
Keyword(s):  
Land Use ◽  
Soil Microbial Communities ◽  
Fungal Communities ◽  
Soil Microbiome ◽  
Continuous Cropping ◽  
Land Use Intensity ◽  
Soil Microbial ◽  
Land Use Intensification ◽  
Perennial Grassland ◽  
Microbial Groups

Abstract Background Soil microbial communities are major drivers of cycling of soil nutrients that sustain plant growth and productivity. Yet, a holistic understanding of the impact of land-use intensification on the soil microbiome is still poorly understood. Here, we used a field experiment to investigate the long-term consequences of changes in land-use intensity based on cropping frequency (continuous cropping, alternating cropping with a temporary grassland, perennial grassland) on bacterial, protist and fungal communities as well as on their co-occurrence networks. Results We showed that land use has a major impact on the structure and composition of bacterial, protist and fungal communities. Grassland and arable cropping differed markedly with many taxa differentiating between both land use types. The smallest differences in the microbiome were observed between temporary grassland and continuous cropping, which suggests lasting effects of the cropping system preceding the temporary grasslands. Land-use intensity also affected the bacterial co-occurrence networks with increased complexity in the perennial grassland comparing to the other land-use systems. Similarly, co-occurrence networks within microbial groups showed a higher connectivity in the perennial grasslands. Protists, particularly Rhizaria, dominated in soil microbial associations, as they showed a higher number of connections than bacteria and fungi in all land uses. Conclusions Our findings provide evidence of legacy effects of prior land use on the composition of the soil microbiome. Whatever the land use, network analyses highlighted the importance of protists as a key element of the soil microbiome that should be considered in future work. Altogether, this work provides a holistic perspective of the differential responses of various microbial groups and of their associations to agricultural intensification.

scholarly journals Variations in soil nutrient dynamics and bacterial communities in long-term tea monoculture production systems

2021 ◽  
Author(s):  
Heng Gui ◽  
Lichao Fan ◽  
Donghui Wang ◽  
Peng Yan ◽  
Xin Li ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Nutrient Dynamics ◽  
Soil Microbial Communities ◽  
Soil Nutrient ◽  
Stand Age ◽  
Soil Microbial ◽  
Soil Bacterial Communities ◽  
Tea Plantations ◽  
Soil Bacterial

AbstractLong-term monoculture agriculture systems could lead to soil degradation and yield decline. The ways in which soil microbiotas interact with one another, particularly in response to long-term tea monoculture systems are currently unclear. In this study, through the comparison of three independent tea plantations across eastern China composed of varying stand ages (from 3 years to 90 years after conversion from forest), we found that long-term tea monoculture led to significant increases in soil total organic carbon (TOC) and microbial nitrogen (MBN). Additionally, the structure, function and co-occurrence network of soil microbial communities were investigated by pyrosequencing 16S rRNA genes. The pyrosequencing analysis revealed that structures and functions of soil bacterial communities were significantly affected by different stand ages of tea plantations, but sampling sites and land-use conversion (from forest to tea plantation) still outcompeted stand age to control the diversity and structure of soil bacterial communities. Further RDA analysis revealed that the C and N availability improvement in tea plantation soils led to variation of structure and function in soil microbial communities. Moreover, co-occurrence network analysis of soil bacterial communities also demonstrated that interactions among soil bacteria taxa were strengthened with the increasing stand age of respective tea stands. Overall, this study provides a comprehensive understanding of the impact of long-term monoculture stand age on soil nutrient dynamics and bacterial communities in tea production.

scholarly journals Positive Effects of Crop Diversity on Productivity Driven by Changes in Soil Microbial Composition

2021 ◽  
Vol 12 ◽  
Author(s):  
Laura Stefan ◽  
Martin Hartmann ◽  
Nadine Engbersen ◽  
Johan Six ◽  
Christian Schöb
Keyword(s):  
Plant Growth ◽  
Microbial Diversity ◽  
Crop Yield ◽  
Soil Microbial Communities ◽  
Crop Diversity ◽  
Microbial Composition ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
Positive Effects ◽  
Soil Microbial Composition

Intensive agriculture has major negative impacts on ecosystem diversity and functioning, including that of soils. The associated reduction of soil biodiversity and essential soil functions, such as nutrient cycling, can restrict plant growth and crop yield. By increasing plant diversity in agricultural systems, intercropping could be a promising way to foster soil microbial diversity and functioning. However, plant–microbe interactions and the extent to which they influence crop yield under field conditions are still poorly understood. In this study, we performed an extensive intercropping experiment using eight crop species and 40 different crop mixtures to investigate how crop diversity affects soil microbial diversity and activity, and whether these changes subsequently affect crop yield. Experiments were carried out in mesocosms under natural conditions in Switzerland and in Spain, two countries with drastically different soils and climate, and our crop communities included either one, two or four species. We sampled and sequenced soil microbial DNA to assess soil microbial diversity, and measured soil basal respiration as a proxy for soil activity. Results indicate that in Switzerland, increasing crop diversity led to shifts in soil microbial community composition, and in particular to an increase of several plant-growth promoting microbes, such as members of the bacterial phylum Actinobacteria. These shifts in community composition subsequently led to a 15 and 35% increase in crop yield in 2 and 4-species mixtures, respectively. This suggests that the positive effects of crop diversity on crop productivity can partially be explained by changes in soil microbial composition. However, the effects of crop diversity on soil microbes were relatively small compared to the effects of abiotic factors such as fertilization (three times larger) or soil moisture (three times larger). Furthermore, these processes were context-dependent: in Spain, where resources were limited, soil microbial communities did not respond to crop diversity, and their effect on crop yield was less strong. This research highlights the potential beneficial role of soil microbial communities in intercropping systems, while also reflecting on the relative importance of crop diversity compared to abiotic drivers of microbiomes and emphasizing the context-dependence of crop–microbe relationships.

scholarly journals Improvement of Soil Microbial Diversity through Sustainable Agricultural Practices and Its Evaluation by -Omics Approaches: A Perspective for the Environment, Food Quality and Human Safety

2021 ◽  
Vol 9 (7) ◽  
pp. 1400
Author(s):  
Marta Bertola ◽  
Andrea Ferrarini ◽  
Giovanna Visioli
Keyword(s):  
Microbial Diversity ◽  
Food Quality ◽  
Plant Biomass ◽  
Soil Microbial Communities ◽  
Well Being ◽  
Plant Health ◽  
Soil Microbiome ◽  
Soil Microbial Diversity ◽  
Soil Biodiversity ◽  
Soil Microbial

Soil is one of the key elements for supporting life on Earth. It delivers multiple ecosystem services, which are provided by soil processes and functions performed by soil biodiversity. In particular, soil microbiome is one of the fundamental components in the sustainment of plant biomass production and plant health. Both targeted and untargeted management of soil microbial communities appear to be promising in the sustainable improvement of food crop yield, its nutritional quality and safety. –Omics approaches, which allow the assessment of microbial phylogenetic diversity and functional information, have increasingly been used in recent years to study changes in soil microbial diversity caused by agronomic practices and environmental factors. The application of these high-throughput technologies to the study of soil microbial diversity, plant health and the quality of derived raw materials will help strengthen the link between soil well-being, food quality, food safety and human health.

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