The Arctic Ocean currently receives a large supply of global river discharge and terrestrial dissolved organic matter. Moreover, an increase in freshwater runoff and riverine transport of organic matter to the Arctic Ocean is a predicted consequence of thawing permafrost and increased precipitation. The fate of the terrestrial humic-rich organic material and its impact on the marine carbon cycle are largely unknown. Here, a metagenomic survey of the Canada Basin in the Western Arctic Ocean showed that pelagic Chloroflexi from the Arctic Ocean are replete with aromatic compound degradation genes, acquired in part by lateral transfer from terrestrial bacteria. Our results imply marine Chloroflexi have the capacity to use terrestrial organic matter and that their role in the carbon cycle may increase with the changing hydrological cycle.

The Arctic Ocean is relatively isolated from other oceans and consists of strongly stratified water masses with distinct histories, nutrient, temperature, and salinity characteristics, therefore providing an optimal environment to investigate local adaptation. The globally distributed SAR11 bacterial group consists of multiple ecotypes that are associated with particular marine environments, yet relatively little is known about Arctic SAR11 diversity. Here, we examined SAR11 diversity using ITS analysis and metagenome-assembled genomes (MAGs). Arctic SAR11 assemblages were comprised of the S1a, S1b, S2, and S3 clades, and structured by water mass and depth. The fresher surface layer was dominated by an ecotype (S3-derived P3.2) previously associated with Arctic and brackish water. In contrast, deeper waters of Pacific origin were dominated by the P2.3 ecotype of the S2 clade, within which we identified a novel subdivision (P2.3s1) that was rare outside the Arctic Ocean. Arctic S2-derived SAR11 MAGs were restricted to high latitudes and included MAGs related to the recently defined S2b subclade, a finding consistent with bi-polar ecotypes and Arctic endemism. These results place the stratified Arctic Ocean into the SAR11 global biogeography and have identified SAR11 lineages for future investigation of adaptive evolution in the Arctic Ocean.

Polyketides are an important group of secondary metabolites, many of which have important industrial applications in the food and pharmaceutical industries. Polyketides are synthesized from one of three classes of enzymes differentiated by their biochemical features and product structure: type I, type II or type III polyketide synthases (PKSs). Plant type III PKS enzymes, which will be the main focus of this review, are relatively small homodimeric proteins that catalyze iterative decarboxylative condensations of malonyl units with a CoA-linked starter molecule. This review will describe the plant type III polyketide synthetic pathway, including the synthesis of chalcones, stilbenes and curcuminoids, as well as recent work on the synthesis of these polyketides in heterologous organisms. The limitations and bottlenecks of heterologous expression as well as attempts at creating diversity through the synthesis of novel “unnatural” polyketides using type III PKSs will also be discussed. Although synthetic production of plant polyketides is still in its infancy, their potential as useful bioactive compounds makes them an extremely interesting area of study.

Here we harnessed the power of metaproteomics to assess the metabolic diversity and function of stratified aquatic microbial communities in the deep and expansive Lower St. Lawrence Estuary, located in eastern Canada. Vertical profiling of the microbial communities through the stratified water column revealed differences in metabolic lifestyles and in carbon and nitrogen processing pathways. In productive surface waters, we identified heterotrophic populations involved in the processing of high and low molecular weight organic matter from both terrestrial (e.g. cellulose and xylose) and marine (e.g. organic compatible osmolytes) sources. In the less productive deep waters, chemosynthetic production coupled to nitrification by MG-I Thaumarchaeota and Nitrospina appeared to be a dominant metabolic strategy. Similar to other studies of the coastal ocean, we identified methanol oxidation proteins originating from the common OM43 marine clade. However, we also identified a novel lineage of methanol-oxidizers specifically in the particle-rich bottom (i.e. nepheloid) layer. Membrane transport proteins assigned to the uncultivated MG-II Euryarchaeota were also specifically detected in the nepheloid layer. In total, these results revealed strong vertical structure of microbial taxa and metabolic activities, as well as the presence of specific "nepheloid" taxa that may contribute significantly to coastal ocean nutrient cycling.

24The Arctic Ocean currently receives a large supply of global river discharge and terrestrial 25 dissolved organic matter. Moreover, an increase in freshwater runoff and riverine transport of 26 organic matter to the Arctic Ocean is a predicted consequence of thawing permafrost and 27 increased precipitation. The fate of the terrestrial humic-rich organic material and its impact on 28 the marine carbon cycle are largely unknown. Here, the first metagenomic survey of the Canada 29Basin in the Western Arctic Ocean showed that pelagic Chloroflexi from the Arctic Ocean are 30 replete with aromatic compound degradation genes, acquired in part by lateral transfer from 31 terrestrial bacteria. Our results imply marine Chloroflexi have the capacity to use terrestrial 32 organic matter and that their role in the carbon cycle may increase with the changing 33 hydrological cycle. 34 35 released to the Atlantic, at least in part by microbial processes 10 . As input of tDOM increases, 49 knowledge on its microbial transformation will be critical for understanding changes in Arctic 50 carbon cycling. 51The marine SAR202 is a diverse and uncultivated clade of Chloroflexi bacteria that 52 comprise roughly 10% of planktonic cells in the dark ocean [11][12][13][14][15] . SAR202 is also common in 53 marine sediments and deep lakes [16][17][18] . It has long been speculated that SAR202 may play a 54 role in the degradation of recalcitrant organic matter 12,15 , and the recent analysis of SAR202 55 single-cell amplified genomes (SAGs) lends support to this notion 19 . More generally, 56Chloroflexi, including those in the SAR202 clade, are also present in the upper layers of the 57 Arctic Ocean 20 , leading to the hypothesis that recalcitrant organic compounds present in high 58Arctic tDOM could be utilized by this group. 5960 Results 61In this study, we analyzed Chloroflexi metagenome assembled genomes (MAGs) 62 generated from samples collected from the vertically stratified waters of the Canada Basin in the 63 Western Arctic Ocean (Fig. 1a). A metagenomic co-assembly was generated from samples 64 originating from the surface layer (5 m to 7 m), the subsurface chlorophyll maximum (25 m to 79 65 m) and a layer corresponding to the terrestrially-derived DOM fluorescence (FDOM) maximum 66 previously described within the cold CB halocline comprised of Pacific-origin waters (177 m to 67 213 m) 21 . The Pacific-origin FDOM maximum is due to sea ice formation and interactions with 68 bottom sediments on the Beaufort and Chukchi shelves, which themselves are influenced by 69 coastal erosion and river runoff 21 . Binning based on tetranucleotide frequency and coverage 70 resulted in 360 MAGs from a diversity of marine microbes (Fig. 1b). Six near complete 71Chloroflexi MAGs were identified. Based on 16S rRNA gene phylogeny, these MAGs 72 represented 3 distinct SAR202 subclades (SAR202-II, -VI, -VII), the AncK29 clade and the TK10 73 Chloroflexi bacterium 5419 | Bioreactor (A0A1Q3SS95) Pseudomonas alcaligenes | Experimnetally validated (Q9S3...

BackgroundIdentifying the genetic basis of complex microbial phenotypes is currently a major barrier to our understanding of multigenic traits and our ability to rationally design biocatalysts with highly specific attributes for the biotechnology industry. Here, we demonstrate that strain evolution by meiotic recombination-based genome shuffling coupled with deep sequencing can be used to deconstruct complex phenotypes and explore the nature of multigenic traits, while providing concrete targets for strain development.ResultsWe determined genomic variations found within Saccharomyces cerevisiae previously evolved in our laboratory by genome shuffling for tolerance to spent sulphite liquor. The representation of these variations was backtracked through parental mutant pools and cross-referenced with RNA-seq gene expression analysis to elucidate the importance of single mutations and key biological processes that play a role in our trait of interest. Our findings pinpoint novel genes and biological determinants of lignocellulosic hydrolysate inhibitor tolerance in yeast. These include the following: protein homeostasis constituents, including Ubp7p and Art5p, related to ubiquitin-mediated proteolysis; stress response transcriptional repressor, Nrg1p; and NADPH-dependent glutamate dehydrogenase, Gdh1p. Reverse engineering a prominent mutation in ubiquitin-specific protease gene UBP7 in a laboratory S. cerevisiae strain effectively increased spent sulphite liquor tolerance.ConclusionsThis study advances understanding of yeast tolerance mechanisms to inhibitory substrates and biocatalyst design for a biomass-to-biofuel/biochemical industry, while providing insights into the process of mutation accumulation that occurs during genome shuffling.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-015-0241-z) contains supplementary material, which is available to authorized users.

Meta-omic technologies such as metagenomics, metatranscriptomics and metaproteomics can aid in the understanding of microbial community structure and metabolism. Although powerful, metagenomics alone can only elucidate functional potential. On the other hand, metaproteomics enables the description of the expressed in situ metabolism and function of a community. Here we describe a protocol for cell lysis, protein and DNA isolation, as well as peptide digestion and extraction from marine microbial cells collected on a cartridge filter unit (such as the Sterivex filter unit) and preserved in an RNA stabilization solution (like RNAlater). In mass spectrometry-based proteomics studies, the identification of peptides and proteins is performed by comparing peptide tandem mass spectra to a database of translated nucleotide sequences. Including the metagenome of a sample in the search database increases the number of peptides and proteins that can be identified from the mass spectra. Hence, in this protocol DNA is isolated from the same filter, which can be used subsequently for metagenomic analysis.

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