Fungal Diversity in Permafrost and Tallgrass Prairie Soils under Experimental Warming Conditions

Abstract

Soil fungi play a major role in terrestrial ecosystem functioning through interactions with soil structure, plants, micro-and mesofauna, and nutrient cycling through predation, pathogenesis, mutualistic, and saprotrophic roles. The diversity of soil fungi was assessed by sequencing their 28S rRNA gene in Alaskan permafrost and Oklahoma tallgrass prairie soils at experimental sites where the effect of climate warming is under investigation. A total of 226,695 reads were classified into 1,063 genera, covering 62% of the reference data set. Using the Bayesian Classifier offered by the Ribosomal Database Project (RDP) with 50% bootstrapping classification confidence, approximately 70% of sequences were returned as "unclassified" at the genus level, although the majority (ϳ65%) were classified at the class level, which provided insight into these lesser-known fungal lineages. Those unclassified at the genus level were subjected to BLAST analysis against the ARB-SILVA database, where ϳ50% most closely matched nonfungal taxa. Compared to the more abundant sequences, a higher proportion of rare operational taxonomic units (OTU) were successfully classified to genera at 50% bootstrap confidence, indicating that the fungal rare biosphere in these sites is not composed of sequencing artifacts. There was no significant effect after 1 year of warming on the fungal community structure at both sites, except perhaps for a few minor members, but there was a significant effect of sample depth in the permafrost soils. Despite overall significant community structure differences driven by variations in OTU dominance, the prairie and permafrost soils shared 90% and 63% of all fungal sequences, respectively, indicating a fungal "seed bank" common between both sites.

Compositional Stability of the Bacterial Community in a Climate-Sensitive Sub-Arctic Peatland

“…On the other hand, the lack of detectable effect of experimental warming on bacterial community composition agrees with results from previous studies of soil microbes in grasslands (Penton et al, 2013), and temperate upland soils (Kuffner et al, 2012). In a somewhat different context, Cruz-Martinez et al (2009) also found community resistance to precipitation manipulation—despite considerable treatment effects on overlying vegetation.…”

Fungal Communities Respond to Long-Term CO 2 Elevation by Community Reassembly

“…The grassland soil ecosystem in the BioCON experimental site in Minnesota was dominated by Ascomycota (81% at aCO 2 and 77% at eCO 2 ) and Basidiomycota (11% at aCO 2 and 14% at eCO 2 ). Compared to the reports by previous studies (31,(58)(59)(60)(61), fungal community composition in soil varied greatly across different types of soil ecosystems. Such variations in fungal community composition between different studies might be caused by different coverage of different primer sets or phylogenetic markers (such as ITS versus 28S) (62), but more likely caused by plant species, soil, and/or climate differences (58).…”

“…Glomeromycota is the phylum that most arbuscular mycorrhizal fungi belong to and was previously reported to be dominant in grasslands (63) and widespread among different global ecosystems (64). Since a previous study using the same primer set identified at least 15% Glomeromycota in an Oklahoma tallgrass prairie soil, the low relative abundance of Glomeromycota identified here did not arise from the primer set used for PCR amplification, which was also verified by the NCBI primer tool (60). Since arbuscular mycorrhizal fungi form symbioses with many herbaceous land plants, the low relative abundance of Glomeromycota may result from different plant species composition in these ecosystems because fine roots were not removed prior to DNA extraction and rhizosphere soil and bulk soil were not specifically distinguished during sampling process in either study.…”

Experimental warming alters potential function of the fungal community in boreal forest

“…Specifically, yeasts possess more genes encoding stress tolerance traits than do free‐living filamentous fungi (Treseder & Lennon, ). Others have noted increases in taxonomic groups dominated by free‐living filamentous fungi (Deslippe et al ., ; Xiong et al ., ; Semenova et al ., ) and ectomycorrhizal fungi (Clemmensen et al ., ; Allison & Treseder, ; Deslippe et al ., ; Penton et al ., ) in warming manipulations. Warming may have alleviated cold stress for free‐living filamentous fungi, allowing them to proliferate.…”

“…In particular, fungi are responsible for most of the breakdown of organic C compounds in high latitudes, especially those in more recalcitrant forms (Dighton, ; Ponge, ; van der Heijden et al ., ). Previous field studies have reported shifts in fungal community composition under experimental warming (Clemmensen et al ., ; Allison & Treseder, ; Allison et al ., ; Deslippe et al ., , ; Penton et al ., ; Xiong et al ., ). Fungal responses to increases in soil temperature could have important consequences for global climate.…”