Gene abundance and expression for key indicator enzymes associated with glycolysis.

<p>Abundance (a) and expression (b) of the key enzyme in the Embden-Meyerhof (EMP) pathway, 6-phosphofructokinase, represented by COG205. Abundance (c) and expression (d) of the key enzyme in the pathway Entner-Doudoroff (ED) pathway, 2-keto-3-deoxy-6-phosphogluconate aldolase, represented by COG800.</p

Map of sample locations across the Columbia River coastal margin.

<p>Sampling sites are denoted by the black squares. The new plume, old plume, and coastal ocean samples were collected from the same location. Samples were collected aboard the R/V <i>Wecoma</i> between August 1^st and 8^th, 2010.</p

Abundance and expression of key genes involved in nitrogen, sulfur, and phosphorus transport and metabolism.

<p>The size of the bubble corresponds to the normalized abundance or expression of each gene. Black bubbles represent metagenomes, gray bubbles represent metatranscriptomes. Gene abbreviations are as follows: <i>napA</i> and <i>narG</i>, nitrate reductase; <i>nirK</i>, nitrite reductase; <i>norB</i>, nitric oxide reductase; <i>nosZ</i>, nitrous oxide reductase; <i>nrfA</i>, nitrite reductase to ammonia; <i>amoA/pmoA</i>, ammonia/methane monooxygenase; <i>dsr</i>, dissimilatory sulfite reductase; <i>apr</i>, adenosine-5′-phosphosulfate reductase; <i>pst</i>, high-affinity phosphate transporter; <i>phn</i>, phosphonate transport; <i>phoH</i>, phosphate starvation-inducible protein.</p

Sample environmental data and sequencing statistics.

<p>Environmental parameter abbreviations are as follows: DO, dissolved oxygen; TDP, total dissolved phosphorus; TDN, total dissolved nitrogen; POC, particulate organic carbon; PN, particulate nitrogen; DOC, dissolved organic carbon. The total number of annotated reads for each sample includes both paired and single reads.</p><p>* Cast data was unavailable, parameters used are from a CTD cast taken on a different day from a similar depth and location.</p><p>Sample environmental data and sequencing statistics.</p

Hierarchical clustering of samples across salinity.

<p>Dendrogram and heatmap of a) metagenomes and b) metatranscriptomes based on the normalized abundance of COG functions. Heatmaps depict the top twenty-five most abundant COGs.</p

Taxonomic changes across the salinity gradient.

<p>Bar charts represent the taxonomic changes seen in a) 16S sequences identified from metagenomes, b) COG annotated sequences from metagenomes, and c) COG annotated sequences from metatranscriptomes.</p

Bacterial photosynthesis and carbon fixation gene abundance and expression.

<p>Abundance (a) and expression (b) of oxygenic photosynthesis genes, represented by photosystem genes <i>psa</i> and <i>psb</i>. Abundance (c) and expression (d) of aerobic anoxygenic photosynthesis (AAP) genes, represented by <i>pufABLM</i>, and <i>puhA</i> genes. Abundance (e) and expression (f) of carbon fixation via the Calvin Benson Bassham cycle, represented by <i>rbcSL</i> and <i>prk</i> genes.</p

Table1.docx

<p>Routine monitoring of shellfish growing waters for bacteria indicative of human sewage pollution reveals little about the bacterial communities that co-occur with these indicators. This study investigated the bacterial community, potential pathogens, and fecal indicator bacteria in 40 water samples from a shellfish growing area in the Chesapeake Bay, USA. Bacterial community composition was quantified with deep sequencing of 16S rRNA gene amplicons, and absolute gene abundances were estimated with an internal standard (Thermus thermophilus genomes). Fecal coliforms were quantified by culture, and Vibrio vulnificus and V. parahaemolyticus with quantitative PCR. Fecal coliforms and V. vulnificus were detected in most samples, and a diverse assemblage of potential human pathogens were detected in all samples. These taxa followed two general patterns of abundance. Fecal coliforms and 16S rRNA genes for Enterobacteriaceae, Aeromonas, Arcobacter, Staphylococcus, and Bacteroides increased in abundance after a 1.3-inch rain event in May, and, for some taxa, after smaller rain events later in the season, suggesting that these are allochthonous organisms washed in from land. Clostridiaceae and Mycobacterium 16S rRNA gene abundances increased with day of the year and were not positively related to rainfall, suggesting that these are autochthonous organisms. Other groups followed both patterns, such as Legionella. Fecal coliform abundance did not correlate with most other taxa, but were extremely high following the large rainstorm in May when they co-occurred with a broad range of potential pathogen groups. V. vulnificus were absent during the large rainstorm, and did not correlate with 16S rRNA abundances of Vibrio spp. or most other taxa. These results highlight the complex nature of bacterial communities and the limited utility of using specific bacterial groups as indicators of pathogen presence.</p

Appendix A. Principal components analysis of DOM chemical composition at the beginning and end of experiments.

Principal components analysis of DOM chemical composition at the beginning and end of experiments

Table_1.DOCX

<p>Terrestrial plants benefit from many well-understood mutualistic relationships with root- and leaf-associated microbiomes, but relatively little is known about these relationships for seagrass and other aquatic plants. We used 16S rRNA gene amplicon sequencing and metatranscriptomics to assess potential mutualisms between microorganisms and the seagrasses Zostera marina and Zostera japonica collected from mixed beds in Netarts Bay, OR, United States. The phylogenetic composition of leaf-, root-, and water column-associated bacterial communities were strikingly different, but these communities were not significantly different between plant species. Many taxa present on leaves were related to organisms capable of consuming the common plant metabolic waste product methanol, and of producing agarases, which can limit the growth of epiphytic algae. Taxa present on roots were related to organisms capable of oxidizing toxic sulfur compounds and of fixing nitrogen. Metatranscriptomic sequencing identified expression of genes involved in all of these microbial metabolic processes at levels greater than typical water column bacterioplankton, and also identified expression of genes involved in denitrification and in bacterial synthesis of the plant growth hormone indole-3-acetate. These results provide the first evidence using metatranscriptomics that seagrass microbiomes carry out a broad range of functions that may benefit their hosts, and imply that microbe–plant mutualisms support the health and growth of aquatic plants.</p