Acidobacteria are ubiquitous and abundant members of soil bacterial communities. However, an ecological understanding of this important phylum has remained elusive because its members have been difficult to culture and few molecular investigations have focused exclusively on this group. We generated an unprecedented number of acidobacterial DNA sequence data using pyrosequencing and clone libraries (39 707 and 1787 sequences, respectively) to characterize the relative abundance, diversity and composition of acidobacterial communities across a range of soil types. To gain insight into the ecological characteristics of acidobacterial taxa, we investigated the largescale biogeographic patterns exhibited by acidobacterial communities, and related soil and site characteristics to acidobacterial community assemblage patterns. The 87 soils analyzed by pyrosequencing contained more than 8600 unique acidobacterial phylotypes (at the 97% sequence similarity level). One phylotype belonging to Acidobacteria subgroup 1, but not closely related to any cultured representatives, was particularly abundant, accounting for 7.4% of bacterial sequences and 17.6% of acidobacterial sequences, on average, across the soils. The abundance of Acidobacteria relative to other bacterial taxa was highly variable across the soils examined, but correlated strongly with soil pH (R ¼� 0.80, Po0.001). Soil pH was also the best predictor of acidobacterial community composition, regardless of how the communities were characterized, and the relative abundances of the dominant Acidobacteria subgroups were readily predictable. Acidobacterial communities were more phylogenetically clustered as soil pH departed from neutrality, suggesting that pH is an effective habitat filter, restricting community membership to progressively more narrowly defined lineages as pH deviates from neutrality.

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A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses

The organic geochemistry of glycerol dialkyl glycerol tetraether lipids: A review

Hydrogen-isotopic abundances of lipid biomarkers are emerging as important proxies in the study of ancient environments and ecosystems. A decade ago, pioneering studies made use of new analytical methods and demonstrated that the hydrogen-isotopic composition of individual lipids from aquatic and terrestrial organisms can be related to the composition of their growth (i.e., environmental) water. Subsequently, compound-specific deuterium/hydrogen (D/H) ratios of sedimentary biomarkers have been increasingly used as paleohydrological proxies over a range of geological timescales. Isotopic fractionation observed between hydrogen in environmental water and hydrogen in lipids, however, is sensitive to biochemical, physiological, and environmental influences on the composition of hydrogen available for biosynthesis in cells. Here we review the factors and processes that are known to influence the hydrogen-isotopic compositions of lipids-especially n-alkanes-from photosynthesizing organisms, and we provide a framework for interpreting their D/H ratios from ancient sediments and identify future research opportunities.

/pdf/molecular-paleohydrology-interpreting-the-hydrogen-isotopic-23nvag5di9.pdf

Molecular Paleohydrology: Interpreting the Hydrogen-Isotopic Composition of Lipid Biomarkers from Photosynthesizing Organisms

Summary The widespread occurrence and diversity of ammonia oxidizing Archaea suggests their contribution to the nitrogen cycle is of global significance. Their dis- tribution appeared limited to low- and moderate- temperature environments until the recent finding of a diagnostic membrane lipid, crenarchaeol, in terres- trial hot springs. We report here the cultivation of a thermophilic nitrifier ('Candidatus Nitrosocaldus yel- lowstonii'), an autotrophic crenarchaeote growing up to 74°C by aerobic ammonia oxidation. The major core lipid of this archaeon growing at 72°C is crenar- chaeol, providing the first direct evidence for its syn- thesis by a thermophile. These findings greatly extend the upper temperature limit of nitrification and document that the capacity for ammonia oxidation is broadly distributed among the Crenarchaeota.

/pdf/cultivation-of-a-thermophilic-ammonia-oxidizing-archaeon-4d0r6q1vdq.pdf

Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol.

New indices and calibrations derived from the distribution of crenarchaeal isoprenoid tetraether lipids: Implications for past sea surface temperature reconstructions

https://dspace.library.uu.nl/bitstream/handle/1874/21200/c9.pdf

Jurgen C. van den Donker

Papers

Environmental controls on bacterial tetraether membrane lipid distribution in soils