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Core functional traits of bacterial communities in the Upper Mississippi River show limited variation in response to land cover.

ABSTRACT: Taxonomic characterization of environmental microbial communities via high-throughput DNA sequencing has revealed that patterns in microbial biogeography affect community structure. However, shifts in functional diversity related to variation in taxonomic composition are poorly understood. To overcome limitations due to the prohibitive cost of high-depth metagenomic sequencing, tools to infer functional diversity based on phylogenetic distributions of functional traits have been developed. In this study we characterized functional microbial diversity at 11 sites along the Mississippi River in Minnesota using both metagenomic sequencing and functional-inference-based (PICRUSt) approaches. This allowed us to determine how distance and variation in land cover throughout the river influenced the distribution of functional traits, as well as to validate PICRUSt inferences. The distribution and abundance of functional traits, by metagenomic analysis, were similar among sites, with a median standard deviation of 0.0002% among tier 3 functions in KEGG. Overall inferred functional variation was significantly different (P ? 0.035) between two water basins surrounded by agricultural vs. developed land cover, and abundances of bacterial orders that correlated with functional traits by metagenomic analysis were greater where abundances of the trait were inferred to be higher. PICRUSt inferences were significantly correlated (r = 0.147, P = 1.80 × 10(-30)) with metagenomic annotations. Discrepancies between metagenomic and PICRUSt taxonomic-functional relationships, however, suggested potential functional redundancy among abundant and rare taxa that impeded the ability to accurately assess unique functional traits among rare taxa at this sequencing depth. Results of this study suggest that a suite of "core functional traits" is conserved throughout the river and distributions of functional traits, rather than specific taxa, may shift in response to environmental heterogeneity.

SUBMITTER: Staley C

PROVIDER: S-EPMC4126211 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Core functional traits of bacterial communities in the Upper Mississippi River show limited variation in response to land cover.

Staley Christopher C Gould Trevor J TJ Wang Ping P Phillips Jane J Cotner James B JB Sadowsky Michael J MJ

Frontiers in microbiology 20140808

Taxonomic characterization of environmental microbial communities via high-throughput DNA sequencing has revealed that patterns in microbial biogeography affect community structure. However, shifts in functional diversity related to variation in taxonomic composition are poorly understood. To overcome limitations due to the prohibitive cost of high-depth metagenomic sequencing, tools to infer functional diversity based on phylogenetic distributions of functional traits have been developed. In th ...[more]

PMID: 25152748

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Project description:Aquatic systems worldwide can exist in multiple ecosystem states (i.e., a recurring collection of biological and chemical attributes), and effectively characterizing multidimensionality will aid protection of desirable states and guide rehabilitation. The Upper Mississippi River System is composed of a large floodplain river system spanning 2200 km and multiple federal, state, tribal and local governmental units. Multiple ecosystem states may occur within the system, and characterization of the variables that define these ecosystem states could guide river rehabilitation. We coupled a long-term (30-year) highly dimensional water quality monitoring dataset with multiple topological data analysis (TDA) techniques to classify ecosystem states, identify state variables, and detect state transitions over 30 years in the river to guide conservation. Across the entire system, TDA identified five ecosystem states. State 1 was characterized by exceptionally clear, clean, and cold-water conditions typical of winter (i.e., a clear-water state); State 2 had the greatest range of environmental conditions and contained most the data (i.e., a status-quo state); and States 3, 4, and 5 had extremely high concentrations of suspended solids (i.e., turbid states, with State 5 as the most turbid). The TDA mapped clear patterns of the ecosystem states across several riverine navigation reaches and seasons that furthered ecological understanding. State variables were identified as suspended solids, chlorophyll a, and total phosphorus, which are also state variables of shallow lakes worldwide. The TDA change detection function showed short-term state transitions based on seasonality and episodic events, and provided evidence of gradual, long-term changes due to water quality improvements over three decades. These results can inform decision making and guide actions for regulatory and restoration agencies by assessing the status and trends of this important river and provide quantitative targets for state variables. The TDA change detection function may serve as a new tool for predicting the vulnerability to undesirable state transitions in this system and other ecosystems with sufficient data. Coupling ecosystem state concepts and TDA tools can be transferred to any ecosystem with large data to help classify states and understand their vulnerability to state transitions.

Dataset Information

Core functional traits of bacterial communities in the Upper Mississippi River show limited variation in response to land cover.

Publications

Core functional traits of bacterial communities in the Upper Mississippi River show limited variation in response to land cover.

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