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

View Article: PubMed Central - PubMed

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.

No MeSH data available.


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.
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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.

Mentions: A large proportion of bacterial and fungal OTUs were not shared between culture dependent and independent techniques (Figure 4). For example, 135 OTUs detected were common in soil and SSMS datasets; only four OTUs were common in SSMS and artificial media and one OTU was present in the artificial media and soil datasets (Figure 4). In fact, there were more unique bacterial genera retrieved than shared between techniques. For instance, 824 bacterial OTUs were not retrieved from culture-dependent techniques. Overall, only 13 unique OTUs were obtained from artificial-cultivation. Surprisingly, 306 bacterial OTUs recovered from SSMS were also not detected in the other two approaches suggesting minor taxa are enriched for using the SSMS (Figure 4).


Microbial Diversity of Browning Peninsula, Eastern Antarctica Revealed Using Molecular and Cultivation Methods
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.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5383709&req=5

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.
Mentions: A large proportion of bacterial and fungal OTUs were not shared between culture dependent and independent techniques (Figure 4). For example, 135 OTUs detected were common in soil and SSMS datasets; only four OTUs were common in SSMS and artificial media and one OTU was present in the artificial media and soil datasets (Figure 4). In fact, there were more unique bacterial genera retrieved than shared between techniques. For instance, 824 bacterial OTUs were not retrieved from culture-dependent techniques. Overall, only 13 unique OTUs were obtained from artificial-cultivation. Surprisingly, 306 bacterial OTUs recovered from SSMS were also not detected in the other two approaches suggesting minor taxa are enriched for using the SSMS (Figure 4).

View Article: PubMed Central - PubMed

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.

No MeSH data available.