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Functional redundancy of marine bacteria in biogeochemical cycles

Final Report Summary - FUNDIVERSITY (Functional redundancy of marine bacteria in biogeochemical cycles)

Little is known about the linkages between microbial diversity and ecosystem functions despite the recognition that the extremely diverse microorganisms inhabiting the Earth are the major drivers of biogeochemical cycles. Traditional studies with cultured microorganisms have limited applicability because they usually represent a minor percentage (<1%) of the existing diversity. Recent advances in sequencing technologies have drastically improved our ability to study the diversity of uncultured microorganisms and their participation in biogeochemical processes through the analysis of their genes. The project FUNDIVERSITY made use of such approaches to address the functional redundancy of coastal marine bacteria. This central question in microbial ecology, how unique or redundant bacteria are for ecosystem functioning, was addressed through a time-series study of 3.5 years on the southern Bay of Biscay continental shelf. The project had 3 objectives that were successfully achieved as detailed below.
Objective 1: Analyse changes in bacterial community composition at the level of the 16S rRNA gene and a set of functional genes along 3 years at the marine coastal station E2 offshore Gijón/Xixón, in order to explore their redundancy at the seasonal scale. A detailed picture of the diversity, community structure and seasonal dynamics of bacterial taxa was obtained by 454 pyrosequencing of 39 monthly DNA samples (Jul’09-Dec’12), obtaining ca. 500000 total sequence reads, allowing us to obtaining the first multi-year high-throughput analysis of bacterial diversity at a high taxonomic resolution. Ca. 80 bacterial taxa with persistent re-ocurrent seasonal patterns were found. These results suggest that a large fraction of bacterial taxa are highly predictable from environmental conditions and show low levels of redundancy in this coastal ecosystem.
Objective 2: Explore the relationship between changes in phylogenetic and functional genetic diversity and changes in ocreanographic physical, chemical and biological parameters, in order to explore their predictability in the system. A large number of bacterial taxa were positively correlated with temperature, nutrient concentrations or the strength of water column mixing, providing hints on their ecological niches. Bacterioplankton functional performance was also approached for 1.5 years using BIOLOG Eco plates , which offer an array of substrates potentially usable by natural bacterial communities thus providing an estimate of their functional capabilities. No direct relationship was found between phylogenetic and functional diversity, likely due to the fact that only a few species are able to grow on BIOLOG plates. However, strong seasonal patterns in the number of substrates used were identified at the deepest station E3, while lack of seasonality at the shallowest station E1 was probably linked to sustained input of organic matter favouring generalist bacterial assemblages.
Objective 3: Analyze the expression of a set of selected functional genes of interest at different times of the year in order verify whether some ecosystem processes are a common metabolic strategy among different bacterial phylotypes
Rather than the original plan of combining metagenomics and qPCR gene expression analysis, a more ambitious, amplification-free analysis of bacterial communities functioning was finally performed by studying functional gene transcripts (i.e. metatranscriptomics) of samples collected over 2 complete seasonal cycles from spring 2011 through winter 2012. A total of 8 metatranscriptomes were successfully isolated, generating over 3.5 million mRNA transcripts using Illumina Miseq technology. Although the change in methodology has been challenging, bioinformatics analyses are virtually completed. Deciphering to what extent specific functional genes are expressed by distinct bacterial taxa over the seasons will provide important insights into the overall functional redundancy of bacterial communities at this coastal site.
FUNDIVERSITY has been one of the few multiyear studies on marine bacterioplankton diversity to date. Besides advancing the rarely addressed topic of functional redundancy, its results will be highly relevant for predicting marine ecosystems response to global warming. For more information, please contact Dr. Laura Alonso-Sáez (laura.alonsosaez@gmail.com) or Dr. Xosé Anxelu G. Morán (xelu.moran@gi.ieo.es).