DNA pyrosequencing evidence for large diversity differences between natural and managed coffee mycorrhizal fungal communities

Abstract

International audienceArabica coffee is a major agricultural commodity worldwide, representing 60 % of the world’s coffee production. Arabica coffee is cultivated in more than 36 countries and is a key cash crop for many developing countries. Despite the coffee’s huge economic importance, there is very limited knowledge on the association of arbuscular mycorrhizal fungi with coffee roots. Therefore, we assessed the mycorrhizal diversity and community composition in Arabica coffee (Coffea arabica L.), using 454 pyrosequencing, in its Ethiopian center of origin. We studied the five most common coffee management systems in Ethiopia. Using pyrosequencing, we retrieved 10,061 mycorrhizae sequences across 30 samples, generating 36 operational taxonomic units from the four mycorrhizae orders: Glomerales, Diversisporales, Archaeosporales, and Paraglomerales; and eight families. Our results show that mycorrhizal diversity strongly differed between natural forest coffee systems and the other management systems. Furthermore, 13 operational taxonomic units were uniquely found in natural forest coffee. Finally, the mycorrhizal community composition in shade coffee plantations was different from the community composition in the other managed systems and the natural forest coffee systems. This is the first in depth study of mycorrhizal communities in wild coffee in its Ethiopian region of origin. Furthermore, we show for the first time the major differences in mycorrhizal communities in coffee between natural coffee forest and more intensively managed coffee systems. We, therefore, provide evidence of the conservation value of natural coffee forest systems as they harbor a unique mycorrhizal diversity, with possible future applications in low input coffee agriculture

Unsustainability of recommended fertilization rates for coffee monoculture due to high N2O emissions

“…About 14 % of N and 38 % of P inputs were leached to rivers, which leads to water quality problems, such as eutrophication. As well, De Beenhouwer et al (2015) reported a strong reduction of soil microorganism diversity in intensively managed coffee systems, where chemical fertilizers and pesticides are abundantly used.…”

“…Coffee is the most intensively traded tropical agricultural commodity worldwide, cultivated in over 50 countries and covering more than 11 million ha (De Beenhouwer et al 2015). In Ecuador, coffee production has a great social, economic, and ecological importance because more than 4 % of the population directly relies on coffee production for their livelihoods; it is a primary source of foreign exchange for private producers and the State and it is part of the diverse agrosystems of the country.…”

Soil invertebrate diversity in coffee-pine agroforestry system at Sumedang, West Java

“…Among various crops, coffee is, along with cocoa, the most commonly cultivated crops in this system. This perennial and woody plant (Bagyaraj 2015) is originated from Ethiopia, where they found grows as a natural understorey shrub of rainforest (De Beenhouwer 2014). In Indonesia, at coffee production region, they are grown under shade of canopies of trees in agroforestry system (Verbist et al 2005;Hanisch et al 2011;Evizal et al 2016).…”

Evaluation of six primer pairs targeting the nuclear rRNA operon for characterization of arbuscular mycorrhizal fungal (AMF) communities using 454 pyrosequencing

“…Especially high throughput sequencing technologies such as 454 amplicon pyrosequencing (Margulies et al, 2005), enabling highly efficient characterization of microbial communities by sequencing medium-sized (200-600 bp) amplicons are currently often used (e.g. Öpik et al, 2009, 2013Lekberg et al, 2012;De Beenhouwer et al, 2014). For molecular identification of AMF, the nuclear ribosomal RNA (rRNA) operon is commonly used, mainly due to its high resolving power and alignment capability across broad taxonomic groups (Stockinger et al, 2010;Schoch et al, 2012).…”