Archaeal abundance in relation to root and fungal exudation rates

Abstract

Archaea are ubiquitous in forest soils, but little is known about the factors regulating their abundance and distribution. Low molecular weight organic compounds represent an important energy source for archaea in marine environments, and it is reasonable to suspect that archaeal abundance is dependent on such compounds in soils as well, represented by, for example, plant and fungal exudates. To test this hypothesis, we designed a microcosm experiment in which we grew ponderosa pine, sitka spruce, and western hemlock in forest soil. Root and mycorrhizal exudation rates were estimated in a 13C pulse-chase experiment, and the number of archaeal and bacterial 16S rRNA genes was determined by qPCR. Archaeal abundance differed among plant species, and the number of archaeal 16S rRNA genes was generally lower in soil receiving high concentration of exudates. The mycorrhizal fungi of ponderosa pine seemed to favor archaea, while no such effect was found for mycorrhized sitka spruce or western hemlock. The low abundance of archaea in the proximity of roots and mycorrhiza may be a result of slow growth rates and poor competitive ability of archaea vs. bacteria and does not necessarily reflect a lack of heterotrophic abilities of the archaeal community.

Archaeal Abundance across a pH Gradient in an Arable Soil and Its Relationship to Bacterial and Fungal Growth Rates

“…During the course of evolution, this might have led to niche differentiation. Accordingly, it has been suggested that archaea are adapted to chronic energy-deficiency stress, while bacteria are adapted to higher substrate concentrations and fast growth and might outcompete archaea when resources are plentiful (24,47). In support of this proposal, it has also been suggested that archaea are more abundant in the habitats with low occurrence of currently cultivable bacteria (45).…”

“…5). In contrast, another study (24) found a pH-independent decrease in archaeal abundance, as well as in the ratio between archaea and bacteria, in direct proximity to mycorrhizal roots and mycorrhizal hyphae in a forest soil with pH 5.5. Our observation of decreased archaeal abundance at high fungal growth rates is consistent with those findings.…”

“…If there is overlap in the use of resources by archaea and bacteria, we might expect to find low archaeal abundance where conditions promote high bacterial growth rates (24,47). This was not the case.…”

“…The abundance of bacterial 16S rRNA gene copies in the same DNA extracts has been previously reported in reference 38 and was assessed as detailed in that report, using forward primer Eub338 and reverse primer Eub518 (17). The primers were checked for specificity using the Ribosomal Database Project (http://rdp.cme.msu.edu/) and amplicon sequencing in independent soil samples (24), and both primer pairs were found to be domain specific. To estimate archaeal small-subunit rRNA gene abundances, standard curves were generated using a 10-fold serial dilution of Halobacterium salinarum DNA, while bacterial 16S rRNA gene abundance was quantified against a standard curve generated from a plasmid containing a full-length copy of the Escherichia coli 16S rRNA gene, again using a 10-fold serial dilution (as previously reported in reference 38).…”

Different Effects of Transgenic Maize and Nontransgenic Maize on Nitrogen-Transforming Archaea and Bacteria in Tropical Soils

“…Even considering that AOA are supposed to be chemolithotrophs, they may be selectable due to the release of specific C 1 compounds from the roots (44). Moreover, indirect selection can also take place, as root exudates, e.g., exudates containing particular organic acids, can modulate the local environmental conditions, such as pH (39).…”