scholarly journals Metagenomic analysis exploring taxonomic and functional diversity of soil microbial communities in Chilean vineyards and surrounding native forests

2016 ◽  
Author(s):  
Luis E Castañeda ◽  
Olga Barbosa
Keyword(s):  
Functional Diversity ◽  
Soil Microbial Communities ◽  
Soil Conditions ◽  
Native Forest ◽  
Natural Habitats ◽  
Wine Production ◽  
Soil Biodiversity ◽  
Central Chile ◽  
Soil Microbial ◽  
Native Forests

Mediterranean biomes are biodiversity hotspots and also have been historically related to wine production. During the last decades, land occupied by vineyards has increased considerably threatening these Mediterranean ecosystems. Land use change and agricultural management affect soil biodiversity, changing physical and chemical properties of soil. These changes may have consequences on wine production, especially because soil is a key component of wine identity or terroir. Here, we characterized the taxonomic and functional diversity of bacterial and fungal communities present in soil from vineyards in Central Chile. To accomplish this goal we collected soil samples from organic vineyards from Central Chile and employed a shotgun metagenomic approach. Additionally, we also studied the surrounding native forest as a picture of the soil conditions prior to the establishment of the vineyard. Our metagenomic analyses revealed that both habitats shared most of the soil microbial species. In general, bacteria were more abundant than fungi in both types of habitats, including soil-living genera such as Candidatus Solibacter, Bradyrhizobium and Gibberella. Interestingly, we found presence of lactic bacteria and fermenting yeasts in soil, which are key during wine production. However, their abundances were extremely low, suggesting unlikeness of soil as a potential reservoir in Chilean vineyards. Regarding functional diversity, we found that genes for metabolism of amino acids, fatty acids, nucleotides and secondary metabolism were enriched in forest soils, whereas genes for metabolism of potassium, proteins and miscellaneous functions were more abundant in vineyard soils. Our results suggest that organic vineyards have similar soil community composition than forest habitats. Additionally, we suggest that native forests surrounding vineyards may be acting as microbial reservoir buffering the land conversion. We conclude that the implementation of environmentally friendly practices by the wine industry may help to maintain the microbial diversity and ecosystem functions related to natural habitats.

scholarly journals Metagenomic analysis exploring taxonomic and functional diversity of soil microbial communities in Chilean vineyards and surrounding native forests

2016 ◽  
Author(s):  
Luis E Castañeda ◽  
Olga Barbosa
Keyword(s):  
Functional Diversity ◽  
Soil Microbial Communities ◽  
Soil Conditions ◽  
Native Forest ◽  
Natural Habitats ◽  
Wine Production ◽  
Soil Biodiversity ◽  
Central Chile ◽  
Soil Microbial ◽  
Native Forests

Mediterranean biomes are biodiversity hotspots and also have been historically related to wine production. During the last decades, land occupied by vineyards has increased considerably threatening these Mediterranean ecosystems. Land use change and agricultural management affect soil biodiversity, changing physical and chemical properties of soil. These changes may have consequences on wine production, especially because soil is a key component of wine identity or terroir. Here, we characterized the taxonomic and functional diversity of bacterial and fungal communities present in soil from vineyards in Central Chile. To accomplish this goal we collected soil samples from organic vineyards from Central Chile and employed a shotgun metagenomic approach. Additionally, we also studied the surrounding native forest as a picture of the soil conditions prior to the establishment of the vineyard. Our metagenomic analyses revealed that both habitats shared most of the soil microbial species. In general, bacteria were more abundant than fungi in both types of habitats, including soil-living genera such as Candidatus Solibacter, Bradyrhizobium and Gibberella. Interestingly, we found presence of lactic bacteria and fermenting yeasts in soil, which are key during wine production. However, their abundances were extremely low, suggesting unlikeness of soil as a potential reservoir in Chilean vineyards. Regarding functional diversity, we found that genes for metabolism of amino acids, fatty acids, nucleotides and secondary metabolism were enriched in forest soils, whereas genes for metabolism of potassium, proteins and miscellaneous functions were more abundant in vineyard soils. Our results suggest that organic vineyards have similar soil community composition than forest habitats. Additionally, we suggest that native forests surrounding vineyards may be acting as microbial reservoir buffering the land conversion. We conclude that the implementation of environmentally friendly practices by the wine industry may help to maintain the microbial diversity and ecosystem functions related to natural habitats.

scholarly journals Metagenomic analysis exploring taxonomic and functional diversity of soil microbial communities in Chilean vineyards and surrounding native forests

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3098 ◽  
Author(s):  
Luis E. Castañeda ◽  
Olga Barbosa
Keyword(s):  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Soil Conditions ◽  
Native Forest ◽  
Natural Habitats ◽  
Wine Production ◽  
Soil Biodiversity ◽  
Soil Microbial ◽  
Native Forests ◽  
Vineyard Soils

Mediterranean biomes are biodiversity hotspots, and vineyards are important components of the Mediterranean landscape. Over the last few decades, the amount of land occupied by vineyards has augmented rapidly, thereby increasing threats to Mediterranean ecosystems. Land use change and agricultural management have important effects on soil biodiversity, because they change the physical and chemical properties of soil. These changes may also have consequences on wine production considering that soil is a key component ofterroir. Here, we describe the taxonomic diversity and metabolic functions of bacterial and fungal communities present in forest and vineyard soils in Chile. To accomplish this goal, we collected soil samples from organic vineyards in central Chile and employed a shotgun metagenomic approach to sequence the microbial DNA. Additionally, we studied the surrounding native forest to obtain a baseline of the soil conditions in the area prior to the establishment of the vineyard. Our metagenomic analyses revealed that both habitats shared most of the soil microbial species. The most abundant genera in the two habitats were the bacteriaCandidatus SolibacterandBradyrhizobiumand the fungusGibberella. Our results suggest that the soil microbial communities are similar in these forests and vineyards. Therefore, we hypothesize that native forests surrounding the vineyards may be acting as a microbial reservoir buffering the effects of the land conversion. Regarding the metabolic diversity, we found that genes pertaining to the metabolism of amino acids, fatty acids, and nucleotides as well as genes involved in secondary metabolism were enriched in forest soils. On the other hand, genes related to miscellaneous functions were more abundant in vineyard soils. These results suggest that the metabolic function of microbes found in these habitats differs, though differences are not related to taxonomy. Finally, we propose that the implementation of environmentally friendly practices by the wine industry may help to maintain the microbial diversity and ecosystem functions associated with natural habitats.

scholarly journals Comparative study on microbial community structure across orchard soil, cropland soil, and unused soil

2017 ◽  
Vol 12 (No. 4) ◽  
pp. 237-245 ◽  
Author(s):  
C. Cheng ◽  
D. Zhao ◽  
D. Lv ◽  
S. Li ◽  
G. Du
Keyword(s):  
Land Use ◽  
Microbial Communities ◽  
Functional Diversity ◽  
Soil Microbes ◽  
Soil Microbial Communities ◽  
Polymer Composition ◽  
Soil Conditions ◽  
Soil Layers ◽  
Soil Microbial ◽  
Orchard Soil

We examined the effects of three different soil conditions (orchard soil, cropland soil, unused soil) on the functional diversity of soil microbial communities. The results first showed that orchard and cropland land use significantly changed the distribution and diversity of soil microbes, particularly at surface soil layers. The richness index (S) and Shannon diversity index (H) of orchard soil microbes were significantly higher than the indices of the cropland and unused soil treatments in the 0–10 cm soil layer, while the S and H indices of cropland soil microbes were the highest in 10–20 cm soil layers. Additionally, the Simpson dominance index of cropland soil microbial communities was the highest across all soil layers. Next, we found that carbon source differences in soil layers under the three land use conditions can mainly be attributed to their carbohydrate and polymer composition, indicating that they are the primary cause of the functional differences in microbial communities under different land uses. In conclusion, orchard and cropland soil probably affected microbial distribution and functional diversity due to differences in vegetation cover, cultivation, and management measures.

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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