Connecting the dots: linking nitrogen cycle gene expression to nitrogen fluxes in marine sediment mesocosms

Abstract

Connecting molecular information directly to microbial transformation rates remains a challenge, despite the availability of molecular methods to investigate microbial biogeochemistry. By combining information on gene abundance and expression for key genes with quantitative modeling of nitrogen fluxes, we can begin to understand the scales on which genetic signals vary and how they relate to key functions. We used quantitative PCR of DNA and cDNA, along with biogeochemical modeling to assess how the abundance and expression of microbes responsible for two steps in the nitrogen cycle changed over time in estuarine sediment mesocosms. Sediments and water were collected from coastal Massachusetts and maintained in replicated 20 L mesocosms for 45 days. Concentrations of all major inorganic nitrogen species were measured daily and used to derive rates of nitrification and denitrification from a Monte Carlo-based non-negative least-squares analysis of finite difference equations. The mesocosms followed a classic regeneration sequence in which ammonium released from the decomposition of organic matter was subsequently oxidized to nitrite and then further to nitrate, some portion of which was ultimately denitrified. Normalized abundances of ammonia oxidizing archaeal ammonia monoxoygenase (amoA) transcripts closely tracked rates of ammonia oxidation throughout the experiment. No such relationship, however, was evident between denitrification rates and the normalized abundance of nitrite reductase (nirS and nirK) transcripts. These findings underscore the complexity of directly linking the structure of the microbial community to rates of biogeochemical processes.

Ammonia oxidizer populations vary with nitrogen cycling across a tropical montane mean annual temperature gradient

“…) and aquatic (Bowen et al. ) environments, and several studies point to AOA as the dominant ammonia oxidizers in most natural environments (Leininger et al. , Nicol and Schleper ).…”

“…, Bowen et al. ), and may influence ecosystem C cycling as abiotic conditions change (Litton and Giardina ). Despite evidence that specific microbial functional groups are key regulators of N cycling rates (Webster et al.…”

“…, Bowen et al. ). Despite the insights these approaches have provided (Torsvik and Øvreås , Fuhrman , Schimel ), the unique roles of environmental drivers in gene‐flux linkages under natural conditions remain unclear.…”

“…Community composition and relative gene expression (i.e. quantity of RNA transcripts produced per DNA gene copy) of these groups can modulate N cycling dynamics (Wilmes and Bond 2006, Blazewicz et al 2013, Bowen et al 2014, and may influence ecosystem C cycling as abiotic conditions change (Litton and Giardina 2008). Despite evidence that specific microbial functional groups are key regulators of N cycling rates (Webster et al 2005, Baldrian et al 2012, Taylor et al 2012, Litchman et al 2015) no research to date has generated a mechanistic understanding of how functional groups and related N fluxes respond to environmental change in situ (Bissett et al 2013, Sundqvist et al 2013.…”

“…Natural covariation of ecophysiological drivers (e.g. moisture; precipitation; temperature; pH) across gradients has caused researchers to rely on laboratory and field manipulations to study variables in isolation (Melillo et al 2002, Horz et al 2004, Bowen et al 2014. Despite the insights these approaches have provided (Torsvik and Øvre as 2002, Fuhrman 2009, Schimel 2016 (Vitousek et al 1988, Raich et al 1997, Knoepp and Swank 1998, Schuur and Matson 2001, Salinas et al 2011, Girardin et al 2013, but the influence of mean annual temperature (MAT) has been difficult to parse from its covariates, such as precipitation, plant diversity, and soil age (Austin and Sala 2002, Litton et al 2011, Sundqvist et al 2013, McCalley et al 2014).…”