Transcriptional Response of Nitrifying Communities to Wetting of Dry Soil

Abstract

The first rainfall following a severe dry period provides an abrupt water potential change that is both an acute physiological stress and a defined stimulus for the reawakening of soil microbial communities. We followed the responses of indigenous communities of ammonia-oxidizing bacteria, ammonia-oxidizing archaea, and nitrite-oxidizing bacteria to the addition of water to laboratory incubations of soils taken from two California annual grasslands following a typically dry Mediterranean summer. By quantifying transcripts for a subunit of bacterial and archaeal ammonia monooxygenases (amoA) and a bacterial nitrite oxidoreductase (nxrA) in soil from 15 min to 72 h after water addition, we identified transcriptional response patterns for each of these three groups of nitrifiers. An increase in quantity of bacterial amoA transcripts was detectable within 1 h of wet-up and continued until the size of the ammonium pool began to decrease, reflecting a possible role of transcription in upregulation of nitrification after drought-induced stasis. In one soil, the pulse of amoA transcription lasted for less than 24 h, demonstrating the transience of transcriptional pools and the tight coupling of transcription to the local soil environment. Analysis of 16S rRNA using a high-density microarray suggested that nitrite-oxidizing Nitrobacter spp. respond in tandem with ammonia-oxidizing bacteria while nitrite-oxidizing Nitrospina spp. and Nitrospira bacteria may not. Archaeal ammonia oxidizers may respond slightly later than bacterial ammonia oxidizers but may maintain elevated transcription longer. Despite months of desiccation-induced inactivation, we found rapid transcriptional response by all three groups of soil nitrifiers.

Multiple Factors Affect Diversity and Abundance of Ammonia-Oxidizing Microorganisms in Iron Mine Soil

“…Meanwhile, this result suggests that AOA is more adaptable to drought or a low-nitrogen environment than AOB. Some studies have confirmed this conclusion (Placella and Firestone 2013;Verhamme et al 2011), and the extensive adaptability of AOA may explain why AOA had much greater numbers than AOB and occupied the main ecological niche of ammonia oxidizing process in the desert area. AOA and AOB abundance had a close relationship with PAO (r = 0.642, P \ 0.01 and r = 0.551 P \ 0.05 [ Table 2]) indicating that both AOA and AOB play dominant roles in ammoxidation in the whole region.…”

“…Furthermore, many researchers found that soil physical and chemical properties, such as pH, temperature, moisture, substrate concentration, soil types, and land-use types, played important roles in niche separation between AOA and AOB (Gubry-Rangin et al 2011;O'Sullivan et al 2013;Placella and Firestone 2013;Verhamme et al 2011;Yao et al 2013). In addition to the influence of soil properties, heavy metal, which has turned out to be a key factor in regulating microbial nitrogen cycle (Morel and Price 2003), could exert effects on ammonia oxidizers.…”

Nitrite-Oxidizing Bacterium Nitrobacter winogradskyi Produces N -Acyl-Homoserine Lactone Autoinducers

“…Our results add to a large body of work suggesting that induction of many acyl-HSL QS systems is both cell density and growth phase dependent (13). Although NOB are generally found at low cell densities in soils (10 5 to 5 ϫ 10 5 nxrA copies g Ϫ1 ) (56,57), heterogeneous spatial distribution and restricted diffusion under unsaturated soil conditions could, in fact, permit autoinducers to reach effective localized concentrations (11). Indeed, our experiments confirmed that the QS system of N. winogradskyi was induced at a cell density of approximately 3.2 ϫ10 6 cells ml Ϫ1 during batch culture (Fig.…”

Drying and rewetting events change the response pattern of nitrifiers but not of denitrifiers to the application of manure containing antibiotic in soil

“…It is difficult to draw conclusions about the role of moisture in AOA /AOB niche differentiation due to dissimilarities in experimental design. Nevertheless, it is well possible that AOB and AOA develop different strategies to react to changes in soil moisture, e.g., via the regulation of amoA gene transcription (Placella and Firestone, 2013).…”