Abstract
We surveyed the functional gene composition and diversity of microbial biofilm communities in 18 New Zealand streams affected by different types of catchment land use, using a comprehensive functional gene array, GeoChip 3.0. A total of 5,371 nutrient cycling and energy metabolism genes within 65 gene families were detected among all samples (342 to 2,666 genes per stream). Carbon cycling genes were most common, followed by nitrogen cycling genes, with smaller proportions of sulphur, phosphorus cycling and energy metabolism genes. Samples from urban and native forest streams had the most similar functional gene composition, while samples from exotic forest and rural streams exhibited the most variation. There were significant differences between nitrogen and sulphur cycling genes detected in native forest and urban samples compared to exotic forest and rural samples, attributed to contrasting proportions of nitrogen fixation, denitrification, and sulphur reduction genes. Most genes were detected only in one or a few samples, with only a small minority occurring in all samples. Nonetheless, 42 of 65 gene families occurred in every sample and overall proportions of gene families were similar among samples from contrasting streams. This suggests the existence of functional gene redundancy among different stream biofilm communities despite contrasting taxonomic composition.
Highlights
The role of streams as landscape drainage systems makes these ecosystems susceptible to impacts of land use changes such as deforestation, agriculture, and urbanisation [1,2,3]
Triplicate results from three streams (Cascade, Opanuku, and Lucas) had very similar numbers and composition of genes (! 90% of detected genes shared between triplicate results; > 80% BrayCurtis similarity between triplicate results)
Triplicate results for each of the remaining three streams (Matakana, Hoteo, and Oakley) had consistent gene assemblages, except one triplicate result in each case had 20% to 40% fewer genes than the other two triplicate results, suggesting reduced GeoChip hybridization effectiveness in these cases
Summary
The role of streams as landscape drainage systems makes these ecosystems susceptible to impacts of land use changes such as deforestation, agriculture, and urbanisation [1,2,3]. While there is much interest in improving the health of degraded streams, our understanding of stream ecological processes is incomplete, limiting the effectiveness of management and restoration efforts. The links between microbial community composition, metabolic functions, and stream biogeochemistry are not well understood [4]. A majority of the diverse and abundant microorganisms found in streams occur in surfaceassociated biofilm communities, where they are thought to contribute significantly to in-stream. Functional Gene Composition of Microbial Stream Biofilms
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