Searching for branched glycerol dialkyl glycerol tetraether membrane lipid producing bacteria in soil

KEYWORDS:Branched GDGTs, proxy, pH, temperature, Acidobacteria, methylotrophy, high-throughput techniques

Bacteria present in soil and peat bog environments were previously found to produce branched glycerol dialkyl glycerol tetraether membrane lipids (GDGTs) that are used as a paleoenvironmental proxy to estimate historic soil temperature and pH. Based on the composition and abundance of branched GDGTs, two indices were previously defined, of which the degree of Cyclisation of Branched Tetraethers (CBT) is related to soil pH and the degree of Methylation of Branched Tetraethers (MBT) is related to both soil pH and mean annual air temperature (MAT) . It was hypothesized that bacteria produce branched GDGTs as a response to changes in pH and temperature. Members of the phylum Acidobacteria were proposed to produce branched GDGTs based on their abundance in peat environments, rich in GDGTs. Recently, it was shown that two representatives from subdivision 1 and 3, Edaphobacter aggregans Wbg-1^T and Acidobacteriaceae strain A2-4c, are able to produce these membrane lipids. However, environmental distribution of branched GDGTs is diverse indicating that members of additional subdivisions of Acidobacteria or yet other phyla might also be able to produce branched GDGTs.

TheAcidobacteria constitute a diverse and ubiquitous phylum and its members play an important role especially in terrestrial environments. Information about the Acidobacteria was collected, including their phylogeny and taxonomy, their role in nature, genomic traits and methods applied for their isolation.

Soil is a very dynamic and complex ecosystem and soil organisms are major components of the soil. They are crucial for both soil structure and soil processes. The biological activity in the soil mainly occurs in the topsoil, which contains soil organisms and plant roots. Soil microorganisms including bacteria, archaea and fungi are responsible for nutrient cycling and decomposition of organic residues. Microbial activities are strongly influenced by a range of abiotic and biotic factors and by the interaction between different microorganisms. To get insight into the influence of environmental parameters on the bacterial diversity in relation to production of branched GDGTs, soil samples containing variable amounts of these lipids were taken from different locations, namely from two different hot springs  (Surprise Valley, California, USA) and along the watershed of the Têt river (France). Bacterial community composition was characterized by using high-throughput cultivation independent techniques as well as selective cultivation. It was shown that both pH and temperature strongly affected microbial community composition. Data presented in this thesis furthermore suggest that besides Acidobacteria, members of additional phyla might also responsible for the observed production of branched GDGTs. Notably, occurrence and relative abundance of members of the Alpha- and Deltaproteobacteria and Bacteroidetes were related to the abundance of branched GDGTs. Furthermore, enrichment studies at different pH, temperature and with different substrates suggested that methanol might be a good carbon source to enrich for producers of branched GDGTs. Unfortunately, attempts towards the isolation of branched GDGTs producing bacteria were unsuccessful. However, a novel methylotrophic Azospirillum species, Azospirillum methanolicus, was isolated.In addition to that, novel methylotrophic candidate genera including Acidobacteria subdivision 1 and Pedobacter were identified from initial enrichment studies. 

In conclusion, data presented in this thesis showed that temperature and pH have a strong effect on the microbial community composition in all soil studied here. Although branched GDGTs producing bacteria were not isolated, the data described in this thesis may help to design new strategies to isolate and identify target bacteria in the future.