Do we need to understand microbial communities to predict ecosystem function? A comparison of statistical models of nitrogen cycling processes

Graham, Emily B.; Wieder, William R.; Leff, Jonathan W.; Weintraub, Samantha R.; Townsend, Alan R.; Cleveland, Cory C.; Philippot, Laurent; Nemergut, Diana R.

doi:10.1016/j.soilbio.2013.08.023

Cited by 156 publications

(115 citation statements)

References 25 publications

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“…Of course, there are a number of caveats to interpreting metagenomic data (51). Most importantly, for many pathways, gene abundance in a community has not been found to correlate consistently with environmental process rates, which limits our ability to draw conclusions about activity (52)(53)(54). Still, a powerful feature of metagenomics data is the ability to make comparisons across many functional pathways and taxa at the same time.…”

Section: Discussionmentioning

confidence: 99%

Nitrogen Cycling Potential of a Grassland Litter Microbial Community

Nelson

Berlemont

Martiny

et al. 2015

Appl Environ Microbiol

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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...

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Section: Discussionmentioning

confidence: 99%

Nitrogen Cycling Potential of a Grassland Litter Microbial Community

Nelson

Berlemont

Martiny

et al. 2015

Appl Environ Microbiol

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“…Monitoring gene abundance itself may be useful for determining the variability of that particular organism, but that may not explain fluctuations in the corresponding process. Therefore, studies whose main objective is to examine a particular biogeochemical process may not require, or even be hindered by inclusion gene abundance for determining and predicting process (Graham et al, 2014). However, state-of-the-art technologies, like metagenomic assessment of proteinencoding genes, may more accurately reflect process, as they capture more gene diversity (Tyson et al, 2004;Mackelprang et al, 2011).…”

Section: Does Gene Abundance Infer Process?mentioning

confidence: 99%

Relationships between protein-encoding gene abundance and corresponding process are commonly assumed yet rarely observed

et al. 2014

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For any enzyme-catalyzed reaction to occur, the corresponding protein-encoding genes and transcripts are necessary prerequisites. Thus, a positive relationship between the abundance of gene or transcripts and corresponding process rates is often assumed. To test this assumption, we conducted a meta-analysis of the relationships between gene and/or transcript abundances and corresponding process rates. We identified 415 studies that quantified the abundance of genes or transcripts for enzymes involved in carbon or nitrogen cycling. However, in only 59 of these manuscripts did the authors report both gene or transcript abundance and rates of the appropriate process. We found that within studies there was a significant but weak positive relationship between gene abundance and the corresponding process. Correlations were not strengthened by accounting for habitat type, differences among genes or reaction products versus reactants, suggesting that other ecological and methodological factors may affect the strength of this relationship. Our findings highlight the need for fundamental research on the factors that control transcription, translation and enzyme function in natural systems to better link genomic and transcriptomic data to ecosystem processes.

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“…affect the composition and biogeochemical activity of a given soil microbial community [Graham et al, 2014]. When the strength of the relationship between edaphic factors and microbial activity is strong, the microbial community data might be less valuable.…”

Section: Relationship Between Bacterial Abundance Bacterial Communitmentioning

confidence: 99%

Nitrogen cycling processes and microbial community composition in bed sediments in the Yukon River at Pilot Station

et al. 2014

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Information on the contribution of nitrogen (N)-cycling processes in bed sediments to river nutrient fluxes in large northern latitude river systems is limited. This study examined the relationship between N-cycling processes in bed sediments and N speciation and loading in the Yukon River near its mouth at the Bering Sea. We conducted laboratory bioassays to measure N-cycling processes in sediment samples collected over distinct water cycle seasons. In conjunction, the microbial community composition in the bed sediments using genes involved in N-cycling (narG, napA, nosZ, and amoA) and 16S rRNA gene pyrosequences was examined. Temporal variation was observed in net N mineralization, nitrate uptake, and denitrification rate potentials and correlated strongly with sediment carbon (C) and extractable N content and microbial community composition rather than with river water nutrient concentrations. The C content of the bed sediment was notably impacted by the spring flood, ranging from 1.1% in the midst of an ice-jam to 0.1% immediately after ice-out, suggesting a buildup of organic material (OM) prior to scouring of the bed sediments during ice break up. The dominant members of the microbial community that explained differences in N-processing rates belonged to the genera Crenothrix, Flavobacterium, and the family of Comamonadaceae. Our results suggest that biogeochemical processing rates in the bed sediments appear to be more coupled to hydrology, nutrient availability in the sediments, and microbial community composition rather than river nutrient concentrations at Pilot Station.

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Do we need to understand microbial communities to predict ecosystem function? A comparison of statistical models of nitrogen cycling processes

Cited by 156 publications

References 25 publications

Nitrogen Cycling Potential of a Grassland Litter Microbial Community

Nitrogen Cycling Potential of a Grassland Litter Microbial Community

Relationships between protein-encoding gene abundance and corresponding process are commonly assumed yet rarely observed

Nitrogen cycling processes and microbial community composition in bed sediments in the Yukon River at Pilot Station

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