Nitrogen Cycling Potential of a Grassland Litter Microbial Community

Abstract

bBecause microorganisms have different abilities to utilize nitrogen (N) through various assimilatory and dissimilatory pathways, microbial composition and diversity likely influence N cycling in an ecosystem. Terrestrial plant litter decomposition is often limited by N availability; however, little is known about the microorganisms involved in litter N cycling. In this study, we used metagenomics to characterize the potential N utilization of microbial communities in grassland plant litter. The frequencies of sequences associated with eight N cycling pathways differed by several orders of magnitude. Within a pathway, the distributions of these sequences among bacterial orders differed greatly. Many orders within the Actinobacteria and Proteobacteria appeared to be N cycling generalists, carrying genes from most (five or six) of the pathways. In contrast, orders from the Bacteroidetes were more specialized and carried genes for fewer (two or three) pathways. We also investigated how the abundance and composition of microbial N cycling genes differed over time and in response to two global change manipulations (drought and N addition). For many pathways, the abundance and composition of N cycling taxa differed over time, apparently reflecting precipitation patterns. In contrast to temporal variability, simulated global change had minor effects on N cycling potential. Overall, this study provides a blueprint for the genetic potential of N cycle processes in plant litter and a baseline for comparisons to other ecosystems. Microorganisms play a key role in the decomposition of terrestrial plant litter (1-3), a process that controls the balance of plant carbon (C) released into the atmosphere as CO 2 with that stored in the soil. Less often considered is the role that litter microorganisms play in nitrogen (N) cycling. The N available to microorganisms degrading plant litter comes from several sources. One source is organic N bound in plant tissues and microorganisms. Because the average C/N ratio is much higher in plant litter than in microbial decomposers, N availability is thought to limit litter decomposition (4-6). Fungal hyphae can further translocate N from the soil into plant litter (7). And in some ecosystems, atmospheric deposition of inorganic N from human-driven nitrogen oxide (NO x ) emissions can also be an important source (8-11).Microbes can rapidly alter the forms of N in plant litter through a variety of different N cycle pathways, and these changes in N availability can feed back to influence overall ecosystem functioning (12, 13). During decomposition, bacteria utilize N in both assimilatory and dissimilatory pathways. Assimilatory pathways require energy and lead to the conversion of inorganic N to organic N in microbes (e.g., utilizing N for protein, nucleic acid, and cellular component assembly). Dissimilatory pathways use N compounds to provide energy to microbes. Thus, the pathways by which microbes use N affect the fate of N in the ecosystem, specifically whether it is converted into microbi...

Global biogeography of microbial nitrogen-cycling traits in soil

“…The balance between DNRA and denitrification, which leads to the loss of N to the atmosphere, is thought to be key to soil N budgets. Our results confirm previous studies suggesting that this pathway may be more common than previously thought (45,46), but the taxa encoding the process in soil environments remain to be carefully characterized (47).…”

“…In each metagenomic library, we searched for sequences from eight N pathways, defined previously in ref. 46. These pathways included nitrification (number of genes targeted: n = 2), N fixation (n = 20), denitrification (n = 20), dissimilatory nitrate to nitrite reduction (n = 9), dissimilatory nitrite to ammonia reduction (n = 4), assimilatory nitrate to nitrite reduction (n = 2), assimilatory nitrite to ammonia reduction (n = 2), and ammonia assimilation (n = 10) (Fig.…”

Comparative Metagenomics Reveals Enhanced Nutrient Cycling Potential after 2 Years of Biochar Amendment in a Tropical Oxisol

“…Overall, all classes of Proteobacteria were more abundant in the biochar-amended samples, consistent with our previous study (22) in which we observed that biochar increased Proteobacteria abundance in the oxisol as early as 1 month and up to 1 year after the initial amendment. Notably, the orders Rhizobiales and Burkholderiales were most abundant and higher in biochar-amended samples and have been characterized as N fixers and more broadly as N-cycling generalists, carrying genes for the majority of the assimilatory and dissimilatory N pathways (45). Furthermore, some members of both bacterial orders have the ability to degrade recalcitrant compounds, including some naturally occurring aromatic compounds and organic contaminants such as those used as pesticides, herbicides, or fungicides.…”

High-resolution characterization of the human microbiome

“…Specifically, while large databases of protein-based HMMs exist, several specialized HMM databases have been recently introduced for metagenomic annotation. For example, FOAM 119 is a database designed to identify genes matching KEGG Orthology groups 116,120 that can aid in characterizing the metabolic potential of communities 121,122 . Resfams 108 , on the other hand, was developed to recognize the structure of antibiotic resistance genes and has been used to study the human gut resistomes of different cultures 123,124 .…”