Year-round shotgun metagenomes reveal stable microbial communities in agricultural soils and novel ammonia oxidizers responding to fertilization

Authors: ORELLANA, L - GEORGIA TECH; Chee Sanford, Joanne; SANFORD, R - UNIVERSITY OF ILLINOIS; LOEFFLER, F - UNIVERSITY OF TENNESSEE; KONSTANTINIDIS, K - GEORGIA TECH

Submitted to: Applied and Environmental Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/2/2017
Publication Date: 1/1/2018
Citation: Orellana, L.H., Chee-Sanford, J.C., Sanford, R.A., Loeffler, F.E., Konstantinidis, K.T. 2017. Year-round shotgun metagenomes reveal stable microbial communities in agricultural soils and novel ammonia oxidizers responding to fertilization. Applied and Environmental Microbiology. 84(2):e01646-17. doi:10.1128/AEM.01646-17.
DOI: https://doi.org/10.1128/AEM.01646-17

Interpretive Summary: Microbial population characteristics that underlie the seasonal dynamical changes observed in the native microbial communities of agricultural soils have yet to be clearly and comprehensively defined. Of particular interest is the period immediately following major activities such as nitrogen (N) fertilization, where microbial functional groups such as nitrifiers and denitrifiers that contribute largely to the fate of nitrogen compounds, respond to their environment and are accordingly active. ately, newer technology in sequencing whole microbial communities from natural environments (i.e. metagenomic analysis) and better-developed computational methods to accurately identify the genes that are indicated in the sequence pools obtained offer a more detailed understanding of population dynamics will have important implications for modeling efforts and predicting nutrient bioavailability and C- and N-cycling in soils. Here, we analyzed 20 metagenomes collected at 4 time points across 1 year from two depths (0-5 and 20-30 cm) in two Midwestern agricultural sites representing contrasting soil textures (sandy versus silty-loam), both with similar corn/soybean cropping histories. While there were spatial distinctions between the two locations and across soil depths, the taxonomical and functional community compositions were remarkably stable throughout the year. Genes related to light stress, DNA repair and nutrient uptake were abundant (> 2-fold) in the top layer whereas nitrogen-cycling genes and archaeal sequences were characteristic in the metagenomes from deeper soil layers. Ammonia-oxidizing archaea, in contrast to ammonia-oxidizing bacteria, along with unique Commanox nitrifier populations that can alone oxidize ammonia completely to nitrate, increased up to 5-fold in abundance upon the addition of nitrogen fertilizer at the sandy site, which represented among the largest abundance shifts observed. These results revealed that indigenous archaeal ammonia oxidizers may respond faster (r-strategists) to N-fertilization than previously thought. No single populations of denitrifiers were revealed but instead, the complete process of denitrification appeared to be carried out by a collective of different populations. Altogether, our study identified novel microbial populations and genes responding to seasonal and human-induced perturbations (e.g., fertilization practices) in agricultural soils. Microbial communities overall were fairly stable through the year, although key populations and genes responding to seasonal (e.g., fall biomass return) and human-induced perturbations (e.g., fertilization practices) were identified. These findings also demonstrate the potential significance in agricultural soils for the recently described Commamox organisms which contrast sharply to the traditional view that nitrification is a sequential process mediated first by ammonia oxizers followed by nitrite oxidizers. Furthermore, ammonia-oxidizing archaea appear to be a primary control in the immediate fate of nitrogen following fertilizer addition.

Technical Abstract: Insight to what underlies the seasonal dynamics of indigenous soil microbial communities in agricultural soils, especially after major activities such as nitrogen fertilization, remain elusive. More detailed understanding of population dynamics will have important implications for modeling efforts and predicting nutrient bioavailability and cycling in soils. Here, we analyzed 20 short-read metagenomes (Illumina) collected at 4 time points across 1 year from two depths (0-5 and 20-30 cm) in two Midwestern agricultural sites representing contrasting soil textures (sandy versus silty-loam), both with similar cropping histories. While there were spatial distinctions between the two locations and across soil depths, the taxonomical and functional community compositions were remarkably stable throughout the year. Among the 69 population genomes assembled from the sequences, 75% showed less than 2-fold change in abundance between any two sampling points. Genes related to light stress, DNA repair and nutrient uptake were abundant (> 2-fold) in the top layer whereas nitrogen-cycling genes and archaeal sequences were characteristic in the metagenomes from deeper soil layers. Interestingly, six deep branching Thaumarchaeota and three Comammox nitrifier Nitrospira increased up to 5-fold in abundance upon the addition of nitrogen fertilizer at the sandy site, which represented among the largest abundance shifts observed. These results revealed that indigenous archaeal ammonia oxidizers may respond faster (r-strategists) to N-fertilization than previously thought. None of 29 recovered potential denitrifier genomes encoded the complete denitrification pathway, suggesting that denitrification is carried out by a collective of different populations. Altogether, our study identified novel microbial populations and genes responding to seasonal and human-induced perturbations (e.g., fertilization practices) in agricultural soils.