Detection of a Reproducible, Single-Member Shift in Soil Bacterial Communities Exposed to Low Levels of Hydrogen

Abstract

Soil is exposed to hydrogen when symbiotic rhizobia in legume root nodules cannot recycle the hydrogen that is generated during nitrogen fixation. The hydrogen emitted is most likely taken up by free-living soil bacteria that use hydrogen as an energy source, though the bacteria that do this in situ remain unclear. In this study, we investigated the effect of hydrogen exposure on the bacteria of two different soils in a microcosm setup designed to simulate hydrogen-emitting root nodules. Although the size and overall composition of the soil bacterial community did not significantly alter after hydrogen exposure, one ribotype increased in relative abundance within each soil. This single-ribotype shift was identified by generating multiple terminal restriction fragment length polymorphism (T-RFLP) profiles of 16S rRNA genes from each soil sample, with gene sequence confirmation to identify terminal restriction fragments. The increased abundance of a single ribotype after hydrogen exposure, within an otherwise similar community, was found in replicate samples taken from each microcosm and was reproducible across replicate experiments. Similarly, only one member of the soil bacterial community increased in abundance in response to hydrogen exposure in soil surrounding the root nodules of field-grown soybean (Glycine max). The ribotypes that increased after hydrogen exposure in each soil system tested were all from known hydrogen-oxidizing lineages within the order Actinomycetales. We suggest that soil actinomycetes are important utilizers of hydrogen at relevant concentrations in soil and could be key contributors to soil's function as a sink in the global hydrogen cycle.

Evaluation of different crop sequences for wheat and maize in sandy soil

“…This result is supported by the findings of Espinoza et al, (2015). The inclusion of legumes in a cropping sequence can also improve soil quality, porosity, and structure (McCallum et al, 2004) and influence specific microorganism populations in the rhizosphere (Osborne et al, 2010) for the benefit of following crops.…”

Atmospheric Hydrogen Scavenging: from Enzymes to Ecosystems

“…Exposure of agricultural soil microcosms to high pH 2 stimulated CO 2 fixation and enriched for H 2 -oxidizing Beta-and Gammaproteobacteria (60). In contrast, exposure of soils to a moderate pH 2 produced a shift in the soil bacterial community that was reproducible in both microcosms and the field; the relative abundance of ribotypes corresponding to soil actinomycetes, specifically Pseudonocardia, Mycobacterium, and Streptomyces species, increased (61). Hence, moderate pH 2 might select for the high-affinity group 5 and group 2a [NiFe]-hydrogenases encoded by these genera over the low-affinity proteobacterial group 1 [NiFe]-hydrogenases (16,23,62).…”

“…Several studies have demonstrated that exposure of soils to different partial pressures of H 2 can influence microbial community structure (15,60,61). Exposure of agricultural soil microcosms to high pH 2 stimulated CO 2 fixation and enriched for H 2 -oxidizing Beta-and Gammaproteobacteria (60).…”

Effect of Growth Media and Incubation Time on the Culturability of Soil Bacteria

“…Like the Soil extract agar as used by [2] and [5]. Newly developed media in contrast resulted in high viable counts and in the isolation of members of rarely isolated group regardless of the inoculums size [8]. Increased incubation time of up to 3 months allowed the development of visible colonies of members of rarely isolated groups which took longer time to form visible colonies than that of members of commonly isolated groups.…”