title: Functional gene composition, diversity and redundancy in microbial stream biofilm communities.
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.
authors: School of Biological Sciences, University of Auckland, Auckland, New Zealand.
authors: Andrew
authors: A
authors: Dopheide
authors: School of Biological Sciences, University of Auckland, Auckland, New Zealand.
authors: Gavin
authors: G
authors: Lear
authors: Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States of America.
authors: Zhili
authors: Z
authors: He
authors: Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States of America.
authors: Jizhong
authors: J
authors: Zhou
authors: School of Biological Sciences, University of Auckland, Auckland, New Zealand.
authors: Gillian D
authors: GD
authors: Lewis
mesh_terms: D001419:Bacteria / Q000145:classification / Q000235:genetics*; D018441:Biofilms; D057486:Carbon Cycle / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D017753:Ecosystem; D005798:Genes, Bacterial / Q000235:genetics*; D014644:Genetic Variation; D064307:Microbiota / Q000235:genetics*; D005810:Multigene Family; D009520:New Zealand; D058458:Nitrogen Cycle / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D010758:Phosphorus / Q000378:metabolism; D012988:Soil Microbiology; D013455:Sulfur / Q000378:metabolism
chemical_list: D004269:DNA, Bacterial; D010758:Phosphorus; D013455:Sulfur