Microbial Diversity of Browning Peninsula, Eastern Antarctica Revealed Using Molecular and Cultivation Methods

Abstract

Browning Peninsula is an ice-free polar desert situated in the Windmill Islands, Eastern Antarctica. The entire site is described as a barren landscape, comprised of frost boils with soils dominated by microbial life. In this study, we explored the microbial diversity and edaphic drivers of community structure across this site using traditional cultivation methods, a novel approach the soil substrate membrane system (SSMS), and culture-independent 454-tag pyrosequencing. The measured soil environmental and microphysical factors of chlorine, phosphate, aspect and elevation were found to be significant drivers of the bacterial community, while none of the soil parameters analyzed were significantly correlated to the fungal community. Overall, Browning Peninsula soil harbored a distinctive microbial community in comparison to other Antarctic soils comprised of a unique bacterial diversity and extremely limited fungal diversity. Tag pyrosequencing data revealed the bacterial community to be dominated by Actinobacteria (36%), followed by Chloroflexi (18%), Cyanobacteria (14%), and Proteobacteria (10%). For fungi, Ascomycota (97%) dominated the soil microbiome, followed by Basidiomycota. As expected the diversity recovered from culture-based techniques was lower than that detected using tag sequencing. However, in the SSMS enrichments, that mimic the natural conditions for cultivating oligophilic "k-selected" bacteria, a larger proportion of rare bacterial taxa (15%), such as Blastococcus, Devosia, Herbaspirillum, Propionibacterium and Methylocella and fungal (11%) taxa, such as Nigrospora, Exophiala, Hortaea, and Penidiella were recovered at the genus level. At phylum level, a comparison of OTU's showed that the SSMS shared 21% of Acidobacteria, 11% of Actinobacteria and 10% of Proteobacteria OTU's with soil. For fungi, the shared OTUs was 4% (Basidiomycota) and <0.5% (Ascomycota). This was the first known attempt to culture microfungi using the SSMS which resulted in an increase in diversity from 14 to 57 microfungi OTUs compared to standard cultivation. Furthermore, the SSMS offers the opportunity to retrieve a greater diversity of bacterial and fungal taxa for future exploitation.

Keywords: antarctic soil; bacterial diversity; cultivation; frost boils; fungal diversity.

Figure 1

(A) Location of Browning Peninsula, Windmill Islands, Eastern Antarctica. (B) The spatially explicit design of sampling along three parallel transects, each 2 m apart. The sampling points were taken at 0, 2, 100, 102, 200, and 202 m distances along all three transects. (C) The photograph depicts a close up of Browning Peninsula.

Figure 2

Phylogenetic distribution of bacteria across (A) Browning Peninsula soil: data from metabarcoding and (B) SSMS soil enrichments: data from metabarcoding. (A) Actinobacteria and Chloroflexi were the most dominant bacterial phyla while, unclassified Gaiellaceae and unclassified Ellin6529 were most dominant at the genus level. (B) Most abundant bacterial phyla in SSMS enrichments were Proteobacteria followed by Actinobacteria and the dominant genera were Microbacterium and Sphingomonas. Others represent a sum of relative abundance of <2% phyla or genera present in all soils or SSMS enrichment used.

Figure 3

Phylogenetic distribution of fungi across (A) Browning Peninsula soil: data from metabarcoding and (B) SSMS soil enrichments: data from metabarcoding. (A) Dominant fungal phyla in Browning Peninsula soil were Ascomycota followed by Basidiomycota and at the genera level Devriesia and Buellia were most abundant. (B) Only Ascomycota and Basidiomycota were enriched in the SSMS, with Aureobasidium the most dominant fungal genera recovered. Others represent a sum of <2% relative abundance of other phyla or genera present in the soils or SSMS enrichments.

Figure 4

Venn diagram representing Browning Peninsula microbial diversity at the OTU level recovered from all three methods used in this study (A) bacteria (B) fungi. Orange circles indicate OTUs recovered from the soil datasets, blue represents the recovery of OTUs from artificial cultivation and brown represents OTUs recovered from the SSMS. The pink area represents common OTUs recovered from the soil, SSMS microcultivation and artificial cultivation.