Responses of soil microeukaryotic communities to short-term fumigation-incubation revealed by MiSeq amplicon sequencing

Abstract

In soil microbiology, there is a “paradox” of soil organic carbon (SOC) mineralization, which is that even though chloroform fumigation destroys majority of the soil microbial biomass, SOC mineralization continues at the same rate as in the non-fumigated soil during the incubation period. Soil microeukaryotes as important SOC decomposers, however, their community-level responses to chloroform fumigation are not well understood. Using the 18S rRNA gene amplicon sequencing, we analyzed the composition, diversity, and C-metabolic functions of a grassland soil and an arable soil microeukaryotic community in response to fumigation followed by a 30-day incubation. The grassland and arable soil microeukaryotic communities were dominated by the fungal Ascomycota (80.5–93.1% of the fungal sequences), followed by the protistan Cercozoa and Apicomplexa. In the arable soil fungal community, the predominance of the class Sordariomycetes was replaced by the class Eurotiomycetes after fumigation at days 7 and 30 of the incubation. Fumigation changed the microeukaryotic α-diversity in the grassland soil at days 0 and 7, and β-diversity in the arable soil at days 7 and 30. Network analysis indicated that after fumigation fungi were important groups closely related to other taxa. Most phylotypes (especially Sordariomycetes, Dothideomycetes, Coccidia, and uncultured Chytridiomycota) were inhibited, and only a few were positively stimulated by fumigation. Despite the inhibited Sordariomycetes, the fumigated communities mainly consisted of Eurotiomycetes and Sordariomycetes (21.9 and 36.5% relative frequency, respectively), which are able to produce hydrolytic enzymes associated with SOC mineralization. Our study suggests that fumigation not only decreases biomass size, but modulates the composition and diversity of the soil microeukaryotic communities, which are capable of driving SOC mineralization by release of hydrolytic enzymes during short-term fumigation-incubation.

Metagenomics Study of the Microbes in Constructed Wetland System Treating Sewage

“…Eurotiomycetes was positively stimulated by fumigation. Many researchers concluded that Eurotiomycetes is capable of surviving in extreme conditions and produce extracellular and hydrolytic enzymes [30]. [31].…”

Through the Eye of the Needle — The Story of the Soil Microbial Biomass

“…Most of the fungal population was eliminated and remained low for many weeks. Other work, using modern molecular methods (Dominguez-Mendoza et al, 2014;Chen et al, 2015), also showed that there are distinctly different microbial community structures in fumigated and non-fumigated soils.…”

“…It is theoretically possible that the community structure of the small recolonising microbial population is the same as that in the intact non-fumigated soil. However, Chen et al (2015) showed that the much diminished soil microbial biomass in the fumigated soil has a much smaller diversity (survivors mainly belong to the classes Bacilli, Eurotiomycetes and Sordariomycetes). Others have also shown vast differences in the community structure of pre-and post-fumigation populations (Reber, 1967;Dominguez-Mendoza et al, 2014).…”

Stable isotope informed genome-resolved metagenomics uncovers potential trophic interactions in rhizosphere soil

“…While there has been a surge of interest in viral diversity and ecology, there have been relatively few studies documenting bacterial-phage interactions in soil (12)(13)(14). Also present in soil are fungi, protists and larger organisms that have been documented via 18S rRNA gene sequencing (15,16) and more classical methods (17,18). While some studies have documented bipartite interactions, such as fungi-bacteria (19,20), bacteria-phage (12,21), plant-fungi (22,23), detailing complex multi-trophic interactions in soil remains a huge challenge.…”