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Unlike biologically available nitrogen and phosphorus, which are often at limiting concentrations in surface seawater, sulfur in the form of sulfate is plentiful and not considered to constrain marine microbial activity. Nonetheless, in a model system in which a marine bacterium obtains all of its carbon from co-cultured phytoplankton, bacterial gene expression suggests that at least seven dissolved organic sulfur (DOS) metabolites support bacterial heterotrophy. These labile exometabolites of marine dinoflagellates and diatoms include taurine, N-acetyltaurine, isethionate, choline-O-sulfate, cysteate, 2,3-dihydroxypropane-1-sulfonate (DHPS), and dimethylsulfoniopropionate (DMSP). Leveraging from the compounds identified in this model system, we assessed the role of sulfur metabolites in the ocean carbon cycle by mining the Tara Oceans dataset for diagnostic genes. In the 1.4 million bacterial genome equivalents surveyed, estimates of the frequency of genomes harboring the capability for DOS metabolite utilization ranged broadly, from only 1 out of every 190 genomes (for the C2 sulfonate isethionate) to 1 out of every 5 (for the sulfonium compound DMSP). Bacteria able to participate in DOS transformations are dominated by Alphaproteobacteria in the surface ocean, but by SAR324, Acidimicrobiia, and Gammaproteobacteria at mesopelagic depths, where the capability for utilization occurs in higher frequency than in surface bacteria for more than half the sulfur metabolites. The discovery of an abundant and diverse suite of marine bacteria with the genetic capacity for DOS transformation argues for an important role for sulfur metabolites in the pelagic ocean carbon cycle.

Background Impacts of biotic stressors, such as consumers, on coral microbiomes have gained attention as corals decline worldwide. Corallivore feeding can alter coral microbiomes in ways that contribute to dysbiosis, but feeding strategies are diverse – complicating generalizations about the nature of consumer impacts on coral microbiomes. Results In field experiments, feeding by Coralliophila violacea, a parasitic snail that suppresses coral growth, altered the microbiome of its host, Porites cylindrica, but these impacts were spatially constrained. Alterations in microbial community composition and variability were largely restricted to snail feeding scars; basal or distal areas ~ 1.5 cm or 6–8 cm away, respectively, were largely unaltered. Feeding scars were enriched in taxa common to stressed corals (e.g. Flavobacteriaceae, Rhodobacteraceae) and depauperate in putative beneficial symbionts (e.g. Endozoicomonadaceae) compared to locations that lacked feeding. Conclusions Previous studies that assessed consumer impacts on coral microbiomes suggested that feeding disrupts microbial communities, potentially leading to dysbiosis, but those studies involved mobile corallivores that move across and among numerous individual hosts. Sedentary parasites like C. violacea that spend long intervals with individual hosts and are dependent on hosts for food and shelter may minimize damage to host microbiomes to assure continued host health and thus exploitation. More mobile consumers that forage across numerous hosts should not experience these constraints. Thus, stability or disruption of microbiomes on attacked corals may vary based on the foraging strategy of coral consumers.

A number of tropical reefs have transitioned from coral to macroalgal dominance, but the role of macroalgal competition in coral decline is debated. There is a need to understand the relative roles of direct coral-algal effects versus indirect, microbially mediated effects shaping these interactions, as well as the relevant scales at which interactions operate under natural field, as opposed to laboratory, conditions. We conducted a manipulative field experiment investigating how direct contact versus close proximity (approx. 1.5 cm) with macroalgae ( Galaxaura rugosa , Sargassum polycystum ) impacted the growth, photosynthetic efficiency, and prokaryotic microbiome of the common Indo-Pacific coral Acropora millepora . Both coral growth and photosynthetic efficiency were suppressed when in direct contact with algae or their inert mimics––but not when in close proximity to corals without direct contact. Coral microbiomes were largely unaltered in composition, variability, or diversity regardless of treatment, although a few uncommon taxa differed in abundance among treatments. Negative impacts of macroalgae were contact dependent, accounted for by physical structure alone and had minimal effects on coral microbiomes. The spatial constraints of these interactions have important implications for understanding and predicting benthic community dynamics as reefs degrade.

Coral reefs are degrading to algae-dominated reefs worldwide, with alterations of coral microbiomes commonly co-occurring with reef demise. The severe thermal anomaly during the 2016 El Nino event in the South Pacific killed many corals and stressed others. We examined the microbiome of turf algae and of the coral Porites sp. in contact with turf during this thermal event to investigate algal turf effects on the coral microbiome during a period of environmental stress. The microbial composition of turf did not differ between coral-contacted and non-contacted turfs. However, microbiomes of corals in direct contact with turf were similar to those of the turf microbiome, but differed significantly from coral portions 5 cm from the point of turf/coral contact and from portions of the coral that looked most healthy, regardless of location. Although the majority of significant differences occurred in coral samples at the point of contact, a small subset of microbial taxa was enriched in coral tissues taken 5 cm from turf contact compared to all other sample types, including samples from areas of the coral that appeared most healthy. These results suggest that the coral microbiome is susceptible to colonization by microbes from turf, but not vice versa. Results also suggest that algal contact elicits a subtle shift in the coral microbiome just beyond the contact site. The combination of turf microbiome stability and coral microbiome vulnerability at areas of contact may contribute to the continued decline in coral cover and increase in algal cover associated with coral–algae phase shifts.

In their role as primary producers, marine phytoplankton modulate heterotrophic bacterial activities through differences in the types and amounts of organic matter they release. This study investigates the transcriptional response of bacterium Ruegeria pomeroyi, a member of the Roseobacter clade known to affiliate with diverse phytoplankton groups in the ocean, during a shift in phytoplankton taxonomy. The bacterium was initially introduced into a culture of the dinoflagellate Alexandrium tamarense, and then experienced a change in phytoplankton community composition as the diatom Thalassiosira pseudonana gradually outcompeted the dinoflagellate. Samples were taken throughout the 30-day experiment to track shifts in bacterial gene expression informative of metabolic and ecological interactions. Transcriptome data indicate fundamental differences in the exometabolites released by the two phytoplankton. During growth with the dinoflagellate, gene expression patterns indicated that the main sources of carbon and energy for R. pomeroyi were dimethysulfoniopropionate (DMSP), taurine, methylated amines, and polyamines. During growth with the diatom, dihydroxypropanesulfonate (DHPS), xylose, ectoine, and glycolate instead appeared to fuel the bulk of bacterial metabolism. Expression patterns of genes for quorum sensing, gene transfer agent, and motility suggest that bacterial processes related to cell communication and signaling differed depending on which phytoplankton species dominated the co-culture. A remodeling of the R. pomeroyi transcriptome implicating more than a quarter of the genome occurred through the change in phytoplankton regime.

The fate of the sulfur moiety of dimethylsulfoniopropionate (DMSP) depends on the 'bacterial switch', a regulatory point between two metabolic pathways with different biogeochemical endpoints. Studies have focused on transcriptional patterns of known genes to determine physiological and environmental factors affecting this switch, but post-transcriptional regulation has been under-studied. Here we use a model bacterium containing both pathways to look for transcription of non-coding regulatory small RNAs (sRNAs) during DMSP metabolism. RNA-seq analysis of Ruegeria pomeroyi DSS-3 grown with DMSP, metabolic intermediates of DMSP degradation (MMPA or acetate), or methionine revealed 182 putative sRNAs, with 46 showing differential expression during growth on DMSP. A knockout mutant constructed for an upregulated sRNA had a phenotype that differed in its use of the two degradation pathways. Because transcription patterns of many differentially expressed sRNAs were not correlated with the transcription of their putative target gene, their effects on DMSP degradation would not be observable in the transcriptome. Overall, our results indicate that sRNAs are crucial but largely cryptic actors in regulating DMSP metabolism in this model marine bacterium and potentially other bacterial groups involved in the surface ocean sulfur cycle.

Denitrification by sulfur-oxidizing bacteria is an effective nitrate removal strategy in engineered aquatic systems. However, the community taxonomic and metabolic diversity of sulfur-driven denitrification (SDN) systems, as well as the relationship between nitrate removal and SDN community structure, remains underexplored. This is particularly true for SDN reactors applied to marine aquaria, despite the increasing use of this technology to supplement filtration. We applied 16S rRNA gene, metagenomic, and metatranscriptomic analyses to explore the microbial basis of SDN reactors operating on Georgia Aquarium9s Ocean Voyager, the largest indoor closed-system seawater exhibit in the United States. The exhibit9s two SDN systems vary in water retention time and nitrate removal efficiency. The systems also support significantly different microbial communities. These communities contain canonical SDN bacteria, including a strain related to Thiobacillus thioparus that dominates the system with the higher water retention time and nitrate removal but is effectively absent from the other system. Both systems contain a wide diversity of other microbes whose metagenome-assembled genomes contain genes of SDN metabolism. These include hundreds of strains of the epsilonproteobacterium Sulfurimonas, as well as gammaproteobacterial sulfur oxidizers of the Thiotrichales and Chromatiales, and a relative of Sedimenticolathiotaurini with complete denitrification potential. The SDN genes are transcribed and the taxonomic richness of the transcript pool varies markedly among the enzymatic steps, with some steps dominated by transcripts from noncanonical SDN taxa. These results indicate complex and variable SDN communities that may involve chemical dependencies among taxa as well as the potential for altering community structure to optimize nitrate removal. IMPORTANCE Engineered aquatic systems such as aquaria and aquaculture facilities have large societal value. Ensuring the health of animals in these systems requires understanding how microorganisms contribute to chemical cycling and waste removal. Focusing on the largest seawater aquarium in the United States, we explore the microbial communities in specialized reactors designed to remove excess nitrogen through the metabolic activity of sulfur-consuming microbes. We show that the diversity of microbes in these reactors is both high and highly variable, with distinct community types associated with significant differences in nitrogen removal rate. We also show that the genes encoding the metabolic steps of nitrogen removal are distributed broadly throughout community members, suggesting that the chemical transformations in this system are likely a result of microbes relying on other microbes. These results provide a framework for future studies exploring the contributions of different community members, both in waste removal and in structuring microbial biodiversity.

Summary Bacteria of the SAR11 clade constitute up to one half of all microbial cells in the oxygen-rich surface ocean. DNA sequences from SAR11 are also abundant in oxygen minimum zones (OMZs) where oxygen falls below detection and anaerobic microbes play important roles in converting bioavailable nitrogen to N2 gas. Evidence for anaerobic metabolism in SAR11 has not yet been observed, and the question of how these bacteria contribute to OMZ biogeochemical cycling is unanswered. Here, we identify the metabolic basis for SAR11 activity in anoxic ocean waters. Genomic analysis of single cells from the world’s largest OMZ revealed diverse and previously uncharacterized SAR11 lineages that peak in abundance at anoxic depths, but are largely undetectable in oxygen-rich ocean regions. OMZ SAR11 contain adaptations to low oxygen, including genes for respiratory nitrate reductases (Nar). SAR11 nar genes were experimentally verified to encode proteins catalyzing the nitrite-producing first step of denitrification and constituted ~40% of all OMZ nar transcripts, with transcription peaking in the zone of maximum nitrate reduction rates. These results redefine the ecological niche of Earth’s most abundant organismal group and suggest an important contribution of SAR11 to nitrite production in OMZs, and thus to pathways of ocean nitrogen loss.

In oligotrophic ocean waters where bacteria are often subjected to chronic nutrient limitation, community transcriptome sequencing has pointed to the presence of highly abundant small RNAs (sRNAs). The role of sRNAs in regulating response to nutrient stress was investigated in a model heterotrophic marine bacterium Ruegeria pomeroyi grown in continuous culture under carbon (C) and nitrogen (N) limitation. RNAseq analysis identified 99 putative sRNAs. Sixty-nine were cis-encoded and located antisense to a presumed target gene. Thirty were trans-encoded and initial target prediction was performed computationally. The most prevalent functional roles of genes anti-sense to the cis-sRNAs were transport, cell-cell interactions, signal transduction, and transcriptional regulation. Most sRNAs were transcribed equally under both C and N limitation, and may be involved in a general stress response. However, 14 were regulated differentially between the C and N treatments and may respond to specific nutrient limitations. A network analysis of the predicted target genes of the R. pomeroyi cis-sRNAs indicated that they average fewer connections than typical protein-encoding genes, and appear to be more important in peripheral or niche-defining functions encoded in the pan genome.

This study reports changes in coal-mine drainage constituent concentrations through an anaerobic SO4-reducing bioreactor monitored over a 3-a period. The purpose of the study was to identify and monitor over time the biogeochemical mechanisms that control the attenuation of toxic compounds in the mine drainage. This information is needed to investigate bioreactor performance and longevity. The water treated at the case example site, the Tab-Simco Mine, was highly acidic with an average pH of 2.9, a net acidity of 1674 mg/L CaCO3 equivalent-CCE, and high levels of dissolved SO 4 2 - , Al, Fe and Mn. The results of this study indicated that the treatment system increased the pH of the acid mine drainage (AMD) to 6.2 and decreased the median acidity to 22.7 mg/L CCE, SO 4 2 - from 2981 to 1750 mg/L, Fe from 450.6 to 1.76 mg/L, Al from 113 to 0.42 mg/L, and Mn from 36.4 to 23.3 mg/L. Geochemical modeling indicates that the bioreactor discharge is saturated with respect to the minerals alunite, gibbsite, siderite, rhodochrosite, jarosite, and Fe hydroxide precipitates. The observed trends also include seasonal variations in SO 4 2 - reduction and a general decline in the amount of alkalinity produced. The average δ34S value of the SO 4 2 - in the untreated AMD was +7.3‰. In the bioreactor, δ34S value of SO 4 2 - increased from an average of +6.9‰ to +9.2‰, suggesting the presence of bacterial SO4 reduction processes. Preliminary results of a bacterial community analysis show that DNA sequences corresponding to bacteria capable of SO4 reduction were present in the bioreactor outflow sample. However, these sequences were outnumbered by sequences similar to bacteria capable of reoxdizing reduced sulfur species. This study illustrates the dynamic nature of metal removal in SO4-reducing bioreactor-based treatment systems.

© 2015 International Society for Microbial Ecology. The 'bacterial switch' is a proposed regulatory point in the global sulfur cycle that routes dimethylsulfoniopropionate (DMSP) to two fundamentally different fates in seawater through genes encoding either the cleavage or demethylation pathway, and affects the flux of volatile sulfur from ocean surface waters to the atmosphere. Yet which ecological or physiological factors might control the bacterial switch remains a topic of considerable debate. Here we report the first field observations of dynamic changes in expression of DMSP pathway genes by a single marine bacterial species in its natural environment. Detection of taxon-specific gene expression in Roseobacter species HTCC2255 during a month-long deployment of an autonomous ocean sensor in Monterey Bay, CA captured in situ regulation of the first gene in each DMSP pathway (dddP and dmdA) that corresponded with shifts in the taxonomy of the phytoplankton community. Expression of the cleavage pathway was relatively greater during a high-DMSP-producing dinoflagellate bloom, and expression of the demethylation pathway was greater in the presence of a mixed diatom and dinoflagellate community. These field data fit the prevailing hypothesis for bacterial DMSP gene regulation based on bacterial sulfur demand, but also suggest a modification involving oxidative stress response, evidenced as upregulation of catalase via katG, when DMSP is demethylated.

The organosulfur compound dimethylsulfoniopropionate (DMSP) is produced by phytoplankton and is ubiquitous in the surface ocean. Once released from phytoplankton, marine bacteria degrade DMSP by either the cleavage pathway to form the volatile gas dimethylsulfide (DMS) or the demethylation pathway, yielding methanethiol (MeSH), which is readily assimilated or oxidized. The enzyme DmdB, a methylmercaptopropionate (MMPA)-coenzyme A (CoA) ligase, catalyzes the second step in the demethylation pathway and is a major regulatory point. The two forms of DmdB present in the marine roseobacter Ruegeria pomeroyi DSS-3, RPO_DmdB1 and RPO_DmdB2, and the single form in the SAR11 clade bacterium “ Candidatus Pelagibacter ubique” HTCC1062, PU_DmdB1, were characterized in detail. DmdB enzymes were also examined from Ruegeria lacuscaerulensis ITI-1157, Pseudomonas aeruginosa PAO1, and Burkholderia thailandensis E264. The DmdB enzymes separated into two phylogenetic clades. All enzymes had activity with MMPA and were sensitive to inhibition by salts, but there was no correlation between the clades and substrate specificity or salt sensitivity. All Ruegeria species enzymes were inhibited by physiological concentrations (70 mM) of DMSP. However, ADP reversed the inhibition of RPO_DmdB1, suggesting that this enzyme was responsive to cellular energy charge. MMPA reversed the inhibition of RPO_DmdB2 as well as both R. lacuscaerulensis ITI-1157 DmdB enzymes, suggesting that a complex regulatory system exists in marine bacteria. In contrast, the DmdBs of the non-DMSP-metabolizing P. aeruginosa PAO1 and B. thailandensis E264 were not inhibited by DMSP, suggesting that DMSP inhibition is a specific adaptation of DmdBs from marine bacteria.

Summary Introduction Reoperative pyeloplasty for recurrent ureteropelvic junction obstruction (UPJO) can be technically challenging and is associated with greater morbidity and lower success rates than an initial repair. Robotic-assisted laparoscopic pyeloplasty (RALP) previously has been demonstrated to be a safe and effective approach for management of recurrent UPJO; however, the length of follow-up has been limited. The objective of this study was to confirm the safety and efficacy of RALP for UPJO in children following failed previous pyeloplasty and provide clinical benchmarks for intermediate length follow-up in this patient population. Methods An IRB approved retrospective chart review was performed for all patients undergoing reoperative RALP from June 2006 to December 2014. All cases were performed by surgeons from two institutions for persistent UPJO following failed initial pyeloplasty. Information including demographic information, radiographic studies, and operative interventions performed between the initial repair and reoperative surgery, reoperative RALP intraoperative data, postoperative clinical course and imaging studies, and subsequent interventions following reoperative RALP were extracted. Results Twenty-three children underwent reoperative RALP. Eleven patients had right- and 12 left-sided repairs. Median age at reoperative RALP was 4.0 years and median interval between surgeries was 1.3 years. Indications for repeat repair included pain, infection, and/or radiographic evidence of worsening obstruction and/or deteriorating renal function. Mean operative time was 198 min from incision to port closure. Mean length of stay was 2.3 days. Six complications occurred in five patients within 30 days postoperatively, including ileus, pneumonia, and urinary tract infection. Median length of follow-up was 26 months (range 4–45 months) for all patients and 31 months (range 16–45 months) in 18 patients with >12 months of follow-up. More than 80% of patients presenting with flank pain prior to reoperative RALP had resolution of this symptom. To date, 78% of patients with >12 months of follow-up have not required further operative intervention. Excellent results have been achieved in 14 of 18 patients (78%) with sufficient postoperative follow-up in terms of length of follow-up (>12 months), symptom resolution, and/or improved imaging results. Conclusions RALP following previous pyeloplasty is technically feasible with acceptable operative times, lengths of stay, and complication rates. Reoperative RALP is our preferred modality for repair of recurrent UPJO with the vast majority of patients having successful outcomes based on imaging, resolution of symptoms, and the rare need for further intervention across an intermediate length follow-up period. Table . Summary of reoperative pyeloplasty experience in 23 patients. Median age (years) at Redo Surgery (Range) 4.0 (14 months-19 years) Median time (years) between Primary and Redo Surgery (Range) 1.3 (4 months–17 years) Reconstructive technique utilized Anderson-Hynes Dismembered 20 Y–V plasty 1 Lower-to-upper pole moiety pyeloureterostomy 2 Retrograde ureteral stent placement/exchange a 13 Antegrade ureteral stent placement 10 (1 nephroureteral stent utilized) Conversion to open technique 0 Mean length of stay 2.3 days (1.1–4.4 days) Outcome b Median length of follow up: 26 months (range 4–45 months) Improved (%) 19 (83%) Stable (%) 3 (13%) Worse (%) 1 (4%) Outcome b in patients with > 12 months follow-up (N = 18) Median length of follow up: 31 months (range 16–45 months) Improved (%) 14 (78%) Stable (%) 3 (17%) Worse (%) 1 (5%) See text for further details. a 1 patient had nephrostomy tube placed at presentation (pyelonephritis) and a retrograde stent placed at the time of surgery. b Criteria: Resolution of symptoms and/or improvement on imaging.

The effectiveness of a passive flow sulfate-reducing bioreactor processing acid mine drainage (AMD) generated from an abandoned coal mine in Southern Illinois was evaluated using geochemical and microbial community analysis 10 months post bioreactor construction. The results indicated that the treatment system was successful in both raising the pH of the AMD from 3.09 to 6.56 and in lowering the total iron level by 95.9%. While sulfate levels did decrease by 67.4%, the level post treatment (1153 mg/l) remained above recommended drinking water levels. Stimulation of biological sulfate reduction was indicated by a +2.60‰ increase in δ(34)S content of the remaining sulfate in the water post-treatment. Bacterial community analysis targeting 16S rRNA and dsrAB genes indicated that the pre-treated samples were dominated by bacteria related to iron-oxidizing Betaproteobacteria, while the post-treated water directly from the reactor outflow was dominated by sequences related to sulfur-oxidizing Epsilonproteobacteria and complex carbon degrading Bacteroidetes and Firmicutes phylums. Analysis of the post-treated water, prior to environmental release, revealed that the community shifted back to predominantly iron-oxidizing Betaproteobacteria. DsrA analysis implied limited diversity in the sulfate-reducing population present in both the bioreactor outflow and oxidation pond samples. These results support the use of passive flow bioreactors to lower the acidity, metal, and sulfate levels present in the AMD at the Tab-Simco mine, but suggest modifications of the system are necessary to both stimulate sulfate-reducing bacteria and inhibit sulfur-oxidizing bacteria.

Desulfovibrio vulgaris is an anaerobic sulfate-reducing bacterium capable of facilitating the removal of toxic metals such as uranium from contaminated sites via reduction. As such, it is essential to understand the intricate regulatory cascades involved in how D. vulgaris and its relatives respond to stressors in such sites. One approach is the identification and analysis of small non-coding RNAs (sRNAs); molecules ranging in size from 20-200 nucleotides that predominantly affect gene regulation by binding to complementary mRNA in an anti-sense fashion and therefore provide an immediate regulatory response. To identify sRNAs in D. vulgaris, a bacterium that does not possess an annotated hfq gene, RNA was pooled from stationary and exponential phases, nitrate exposure, and biofilm conditions. The subsequent RNA was size fractionated, modified, and converted to cDNA for high throughput transcriptomic deep sequencing. A computational approach to identify sRNAs via the alignment of seven separate Desulfovibrio genomes was also performed. From the deep sequencing analysis, 2,296 reads between 20 and 250 nt were identified with expression above genome background. Analysis of those reads limited the number of candidates to ~;;87 intergenic, while ~;;140 appeared to be antisense to annotated open reading frames (ORFs). Further BLAST analysis of the intergenicmore » candidates and other Desulfovibrio genomes indicated that eight candidates were likely portions of ORFs not previously annotated in the D. vulgaris genome. Comparison of the intergenic and antisense data sets to the bioinformatical predicted candidates, resulted in ~;;54 common candidates. Current approaches using Northern analysis and qRT-PCR are being used toverify expression of the candidates and to further develop the role these sRNAs play in D. vulgaris regulation.« less

A wording error in a sentence in the abstract misrepresented a main finding of the research. The sentence should read: Expression of the demethylation pathway was relatively greater during a high-DMSP-producing dinoflagellate bloom, and expression of the cleavage pathway was greater in the presence of a mixed diatom and dinoflagellate community. The sentence has now been corrected. The supplementary file published with the paper was missing figure legends. The correct file is now provided.