Impacts of Organic and Conventional Crop Management on Diversity and Activity of Free-Living Nitrogen Fixing Bacteria and Total Bacteria Are Subsidiary to Temporal Effects

Abstract

A three year field study (2007–2009) of the diversity and numbers of the total and metabolically active free-living diazotophic bacteria and total bacterial communities in organic and conventionally managed agricultural soil was conducted using the Nafferton Factorial Systems Comparison (NFSC) study, in northeast England. Fertility management appeared to have little impact on both diazotrophic and total bacterial communities. However, copy numbers of the nifH gene did appear to be negatively impacted by conventional crop protection measures across all years suggesting diazotrophs may be particularly sensitive to pesticides. Impacts of crop management were greatly overshadowed by the influence of temporal effects with diazotrophic communities changing on a year by year basis and from season to season. Quantitative analyses using qPCR of each community indicated that metabolically active diazotrophs were highest in year 1 but the population significantly declined in year 2 before recovering somewhat in the final year. The total bacterial population in contrast increased significantly each year. It appeared that the dominant drivers of qualitative and quantitative changes in both communities were annual and seasonal effects. Moreover, regression analyses showed activity of both communities was significantly affected by soil temperature and climatic conditions.

Long term effects of nutrient management regimes on abundance of bacterial genes and soil biochemical processes for fertility sustainability in a semi-arid tropical Alfisol

“…Further, soil respiration is considered to reflect the soil carbon availability for the microbiome. In the present study, soil respiration rates increased with organic nutrient management, while IC and control had significantly lower respiration are in accordance with previous works reported in different soil ecosystems (Enwall et al, 2007;Liu et al, 2010;Masto et al, 2006;Orr et al, 2012;van Diepeningen et al, 2006). The metabolic quotient, the ratio between respiration rate and MBC, reflects metabolically active fraction of soil microbiome.…”

“…In the present study, 16S rRNA gene abundance in OM was significantly higher than in IC in 2009 and comparable in 2010, and implies that changes in bacterial community structure and abundance are often subtle (Chinnadurai et al, 2014;Drenovsky et al, 2004) and seasonal and plant growth effects often have a greater influence than those due to nutrient management processes (Moreno et al, 2009;Orr et al, 2011). Similar to our finding, He et al (2007) and Orr et al (2012) reported insignificant difference in 16S rRNA gene density between organic and inorganic nutrient management enforced soils. However, when compare to unfertilized control soil, both OM and IC having significantly higher 16S rRNA gene abundance clearly explained that the fertility source (either organic or inorganic) is the dominant factor driving the bacterial community structure (Esperschutz et al, 2007;Widmer et al, 2006) and 16S RNA gene density (Orr et al, 2011).…”

“…Hayden et al (2010) claimed that nifH abundance in Australian agricultural soil was affected due to localized effects of soil chemistry and microbiology rather than land-use. In contrast to this, Orr et al (2012) reported that qualitative and quantitative changes in the nitrogenfixing bacterial community were due to annual and climatic effects, especially soil temperature, not due to the long term effects of nutrient managements (organic or conventional). In their earlier report (Orr et al, 2011), comparing the long term organic and conventional nutrient managements and crop protection strategies on the diversity and abundance of diazotrophic bacteria suggest that the crop rotation rather than soil properties drive the community composition and abundance of free-living nitrogen fixing bacteria.…”

“…The values of 16S RNA gene copy numbers cannot be accurately compared to cell number, as the copy number of 16S rRNA gene per genome is variable (Fogel et al, 1999). However, the relative abundance of 16S rRNA gene among the soils is comparable (Kandeler et al, 2006;Orr et al, 2011Orr et al, , 2012. In the present study, 16S rRNA gene abundance in OM was significantly higher than in IC in 2009 and comparable in 2010, and implies that changes in bacterial community structure and abundance are often subtle (Chinnadurai et al, 2014;Drenovsky et al, 2004) and seasonal and plant growth effects often have a greater influence than those due to nutrient management processes (Moreno et al, 2009;Orr et al, 2011).…”

A rapid flow cytometry method to assess bacterial abundance in agricultural soil

“…It is often hypothesized that organic agriculture promotes bacterial abundance and diversity in soil when compared with conventional systems (as observed by Lee and Yun, 2011;Liu et al, 2007;Van Diepeningen et al, 2006, for example). However, other studies found no distinguishable difference between crop management systems (Berthrong et al, 2013;Orr et al, 2012;Williams and Hedlund, 2013;Xue et al, 2013). Surprisingly, here there was no significant difference in FCM counts between organic and conventional systems, most likely because of important standard deviations.…”