Internal carbon recycling by heterotrophic prokaryotes compensates for mismatches between phytoplankton production and heterotrophic consumption.

Molecular observational tools are useful for characterizing the composition and genetic endowment of microbial communities but cannot measure fluxes, which are critical for the understanding of ecosystems. To overcome these limitations, we used a mechanistic inference approach to estimate dissolved organic carbon (DOC) production and consumption by phytoplankton operational taxonomic units and heterotrophic prokaryotic amplicon sequence variants and inferred carbon fluxes between members of this microbial community from Western English Channel time-series data. Our analyses focused on phytoplankton spring and summer blooms, as well as bacteria summer blooms. In spring blooms, phytoplankton DOC production exceeds heterotrophic prokaryotic consumption, but in bacterial summer blooms heterotrophic prokaryotes consume three times more DOC than produced by the phytoplankton. This mismatch is compensated by heterotrophic prokaryotic DOC release by death, presumably from viral lysis. In both types of summer blooms, large amounts of the DOC liberated by heterotrophic prokaryotes are reused through internal recycling, with fluxes between different heterotrophic prokaryotes being at the same level as those between phytoplankton and heterotrophic prokaryotes. In context, internal recycling accounts for approximately 75% and 30% of the estimated net primary production (0.16 vs 0.22 and 0.08 vs 0.29 µmol l-1 d-1) in bacteria and phytoplankton summer blooms, respectively, and thus represents a major component of the Western English Channel carbon cycle. We have concluded that internal recycling compensates for mismatches between phytoplankton DOC production and heterotrophic prokaryotic consumption, and we encourage future analyses on aquatic carbon cycles to investigate fluxes between heterotrophic prokaryotes, specifically internal recycling.

Identifying and protecting macroalgae detritus sinks toward climate change mitigation.

Harnessing natural solutions to mitigate climate change requires an understanding of carbon fixation, flux, and sequestration across ocean habitats. Recent studies have suggested that exported seaweed particulate organic carbon is stored within soft-sediment systems. However, very little is known about how seaweed detritus disperses from coastlines, or where it may enter seabed carbon stores, where it could become the target of conservation efforts. Here, focusing on regionally dominant seaweed species, we surveyed environmental DNA (eDNA) from natural coastal sediments, and studied their connectivity to seaweed habitats using a particle tracking model parameterized to reproduce seaweed detritus dispersal behavior based on laboratory observations of seaweed fragment degradation and sinking. Experiments showed that seaweed detritus density changed over time, differently across species. This, in turn, modified distances traveled by released fragments until they reached the seabed for the first time, during model simulations. Dispersal pathways connected detritus from the shore to the open ocean but, importantly, also to coastal sediments, and this was reflected by field eDNA evidence. Dispersion pathways were also affected by hydrodynamic conditions, varying in space and time. Both the properties and timing of released detritus, individual to each macroalgal population, and short-term near-seabed and medium-term water-column transport pathways, are thus seemingly important in determining the connectivity between seaweed habitats and potential sedimentary sinks. Studies such as this one, supported by further field verification of sedimentary carbon sequestration rates and source partitioning, are still needed to help quantify the role of seaweed in the ocean carbon cycle. Such studies will provide vital evidence to inform on the potential need to develop blue carbon conservation mechanisms, beyond wetlands.

Biogeochemical consequences of a changing Arctic shelf seafloor ecosystem.

Unprecedented and dramatic transformations are occurring in the Arctic in response to climate change, but academic, public, and political discourse has disproportionately focussed on the most visible and direct aspects of change, including sea ice melt, permafrost thaw, the fate of charismatic megafauna, and the expansion of fisheries. Such narratives disregard the importance of less visible and indirect processes and, in particular, miss the substantive contribution of the shelf seafloor in regulating nutrients and sequestering carbon. Here, we summarise the biogeochemical functioning of the Arctic shelf seafloor before considering how climate change and regional adjustments to human activities may alter its biogeochemical and ecological dynamics, including ecosystem function, carbon burial, or nutrient recycling. We highlight the importance of the Arctic benthic system in mitigating climatic and anthropogenic change and, with a focus on the Barents Sea, offer some observations and our perspectives on future management and policy.

Influence of short and long term processes on SAR11 communities in open ocean and coastal systems.

SAR11 bacteria dominate the surface ocean and are major players in converting fixed carbon back to atmospheric carbon dioxide. The SAR11 clade is comprised of niche-specialized ecotypes that display distinctive spatiotemporal transitions. We analyzed SAR11 ecotype seasonality in two long-term 16S rRNA amplicon time series representing different North Atlantic regimes: the Sargasso Sea (subtropical ocean-gyre; BATS) and the temperate coastal Western English Channel (WEC). Using phylogenetically resolved amplicon sequence variants (ASVs), we evaluated seasonal environmental constraints on SAR11 ecotype periodicity. Despite large differences in temperature and nutrient availability between the two sites, at both SAR11 succession was defined by summer and winter clusters of ASVs. The summer cluster was dominated by ecotype Ia.3 in both sites. Winter clusters were dominated by ecotypes Ib and IIa.A at BATS and Ia.1 and IIa.B at WEC. A 2-year weekly analysis within the WEC time series showed that the response of SAR11 communities to short-term environmental fluctuations was variable. In 2016, community shifts were abrupt and synchronized to environmental shifts. However, in 2015, changes were gradual and decoupled from environmental fluctuations, likely due to increased mixing from strong winds. We demonstrate that interannual weather variability disturb the pace of SAR11 seasonal progression.

Transformation of organic matter in a Barents Sea sediment profile: coupled geochemical and microbiological processes.

Process-based, mechanistic investigations of organic matter transformation and diagenesis directly beneath the sediment-water interface (SWI) in Arctic continental shelves are vital as these regions are at greatest risk of future change. This is in part due to disruptions in benthic-pelagic coupling associated with ocean current change and sea ice retreat. Here, we focus on a high-resolution, multi-disciplinary set of measurements that illustrate how microbial processes involved in the degradation of organic matter are directly coupled with inorganic and organic geochemical sediment properties (measured and modelled) as well as the extent/depth of bioturbation. We find direct links between aerobic processes, reactive organic carbon and highest abundances of bacteria and archaea in the uppermost layer (0-4.5 cm depth) followed by dominance of microbes involved in nitrate/nitrite and iron/manganese reduction across the oxic-anoxic redox boundary (approx. 4.5-10.5 cm depth). Sulfate reducers dominate in the deeper (approx. 10.5-33 cm) anoxic sediments which is consistent with the modelled reactive transport framework. Importantly, organic matter reactivity as tracked by organic geochemical parameters (n-alkanes, n-alkanoic acids, n-alkanols and sterols) changes most dramatically at and directly below the SWI together with sedimentology and biological activity but remained relatively unchanged across deeper changes in sedimentology. This article is part of the theme issue 'The changing Arctic Ocean: consequences for biological communities, biogeochemical processes and ecosystem functioning'.

Modulation of Polar Lipid Profiles in Chlorella sp. in Response to Nutrient Limitation.

We evaluate the effects of nutrient limitation on cellular composition of polar lipid classes/species in Chlorella sp. using modern polar lipidomic profiling methods (liquid chromatography⁻tandem mass spectrometry; LC-MS/MS). Total polar lipid concentration was highest in nutrient-replete (HN) cultures with a significant reduction in monogalactosyldiacylglycerol (MGDG), phosphatidylglycerol (PG), phosphatidylcholine (PC), and phosphatidylethanolamine (PE) class concentrations for nutrient-deplete (LN) cultures. Moreover, reductions in the abundance of MGDG relative to total polar lipids versus an increase in the relative abundance of digalactosyldiacylglycerol (DGDG) were recorded in LN cultures. In HN cultures, polar lipid species composition remained relatively constant throughout culture with high degrees of unsaturation associated with acyl moieties. Conversely, in LN cultures lipid species composition shifted towards greater saturation of acyl moieties. Multivariate analyses revealed that changes in the abundance of a number of species contributed to the dissimilarity between LN and HN cultures but with dominant effects from certain species, e.g., reduction in MGDG 34:7 (18:3/16:4). Results demonstrate that Chlorella sp. significantly alters its polar lipidome in response to nutrient limitation, and this is discussed in terms of physiological significance and polar lipids production for applied microalgal production systems.

Marine Microbial Gene Abundance and Community Composition in Response to Ocean Acidification and Elevated Temperature in Two Contrasting Coastal Marine Sediments.

Marine ecosystems are exposed to a range of human-induced climate stressors, in particular changing carbonate chemistry and elevated sea surface temperatures as a consequence of climate change. More research effort is needed to reduce uncertainties about the effects of global-scale warming and acidification for benthic microbial communities, which drive sedimentary biogeochemical cycles. In this research, mesocosm experiments were set up using muddy and sandy coastal sediments to investigate the independent and interactive effects of elevated carbon dioxide concentrations (750 ppm CO2) and elevated temperature (ambient +4°C) on the abundance of taxonomic and functional microbial genes. Specific quantitative PCR primers were used to target archaeal, bacterial, and cyanobacterial/chloroplast 16S rRNA in both sediment types. Nitrogen cycling genes archaeal and bacterial ammonia monooxygenase (amoA) and bacterial nitrite reductase (nirS) were specifically targeted to identify changes in microbial gene abundance and potential impacts on nitrogen cycling. In muddy sediment, microbial gene abundance, including amoA and nirS genes, increased under elevated temperature and reduced under elevated CO2 after 28 days, accompanied by shifts in community composition. In contrast, the combined stressor treatment showed a non-additive effect with lower microbial gene abundance throughout the experiment. The response of microbial communities in the sandy sediment was less pronounced, with the most noticeable response seen in the archaeal gene abundances in response to environmental stressors over time. 16S rRNA genes (amoA and nirS) were lower in abundance in the combined stressor treatments in sandy sediments. Our results indicated that marine benthic microorganisms, especially in muddy sediments, are susceptible to changes in ocean carbonate chemistry and seawater temperature, which ultimately may have an impact upon key benthic biogeochemical cycles.

Sponge-Inspired Dibromohemibastadin Prevents and Disrupts Bacterial Biofilms without Toxicity.

Since the banning of several families of compounds in antifouling (AF) coatings, the search for environmentally friendly AF compounds has intensified. Natural sources of AF compounds have been identified in marine organisms and can be used to create analogues in laboratory. In a previous study, we identified that dibromohemibastadin-1 (DBHB) is a promising AF molecule, leading to the inhibition of the activity of phenoloxidase, an enzyme involved in the attachment of mussels to surfaces. This paper describes the activity of the DBHB on biofilm formation and its detachment and on bacterial adhesion and communication: quorum sensing. DBHB has an anti-biofilm activity without affecting adhesion of marine and terrestrial bacteria at a dose of 10 µM. Moreover, DBHB activity on quorum sensing (QS) is demonstrated at doses of 8 and 16 µM. The activity of DBHB on QS is compared to kojic acid, a quorum sensing inhibitor already described. This compound is a promising environmentally friendly molecule potentially useful for the inhibition of microfouling.

Mediation of nitrogen by post-disturbance shelf communities experiencing organic matter enrichment.

Microbes and benthic macro-invertebrates interact in sediments to play a major role in the biogeochemical cycling of organic matter, but the extent to which their contributions are modified following natural and anthropogenic changes has received little attention. Here, we investigate how nitrogen transformations, ascertained from changes in archaeal and bacterial N-cycling microbes and water macronutrient concentrations ([NH4-N], [NO2-N], [NO3-N]), in sand and sandy mud sediments differ when macrofaunal communities that have previously experienced contrasting levels of chronic fishing disturbance are exposed to organic matter enrichment. We find that differences in macrofaunal community structure related to differences in fishing activity affect the capacity of the macrofauna to mediate microbial nitrogen cycling in sand, but not in sandy mud environments. Whilst we found no evidence for a change in ammonia oxidiser community structure, we did find an increase in archaeal and bacterial denitrifier (AnirKa, nirS) and anammox (hzo) transcripts in macrofaunal communities characterized by higher ratios of suspension to deposit feeders, and a lower density but higher biomass of sediment-reworking fauna. Our findings suggest that nitrogen transformation in shelf sandy sediments is dependent on the stimulation of specific nitrogen cycling pathways that are associated with differences in the composition and context-dependent expression of the functional traits that belong to the resident bioturbating macrofauna community.

Metabolically active, non-nitrogen fixing, Trichodesmium in UK coastal waters during winter.

Trichodesmium, a colonial cyanobacterium typically associated with tropical waters, was observed between January and April 2014 in the western English Channel. Sequencing of the heterocyst differentiation (hetR) and 16S rRNA genes placed this community within the Clade IV Trichodesmium, an understudied clade previously found only in low numbers in warmer waters. Nitrogen fixation was not detected although measurable rates of nitrate uptake and carbon fixation were observed. Trichodesmium RuBisCO transcript abundance relative to gene abundance suggests the potential for viable and potentially active Trichodesmium carbon fixation. Observations of Trichodesmium when coupled with a numerical advection model indicate that Trichodesmium communities can remain viable for >3.5 months at temperatures lower than previously expected. The results suggest that Clade IV Trichodesmium occupies a different niche to other Trichodesmium species, and is a cold- or low-light-adapted variant.

Elevated CO2 induces a bloom of microphytobenthos within a shell gravel mesocosm.

The geological storage of carbon dioxide (CO2) is expected to be an important component of future global carbon emission mitigation, but there is a need to understand the impacts of a CO2 leak on the marine environment and to develop monitoring protocols for leakage detection. In the present study, sediment cores were exposed to CO2-acidified seawater at one of five pH levels (8.0, 7.5, 7.0, 6.5 and 6.0) for 10 weeks. A bloom of Spirulina sp. and diatoms appeared on sediment surface exposed to pH 7.0 and 7.5 seawater. Quantitative PCR measurements of the abundance of 16S rRNA also indicated an increase within the pH 7.0 and 7.5 treatments after 10 weeks incubation. More detailed analysis of the microbial communities from the pH 7.0, 7.5 and 8.0 treatments confirmed an increase in the relative abundance of Spirulina sp. and Navicula sp. sequences, with changes in the relative abundance of major archaeal and bacterial groups also detected within the pH 7.0 treatment. A decreased flux of silicate from the sediment at this pH was also detected. Monitoring blooms of microphytobenthos may prove useful as an indicator of CO2 leakage within coastal areas.

Geothermal Gases--Community Experiences, Perceptions, and Exposures in Northern California.

Lake County, California, is in a high geothermal-activity area. Over the past 30 years, the city of Clearlake has reported health effects and building evacuations related to geothermal venting. Previous investigations in Clearlake revealed hydrogen sulfide at levels known to cause health effects and methane at levels that can cause explosion risks. The authors conducted an investigation in multiple cities and towns in Lake County to understand better the risk of geothermal venting to the community. They conducted household surveys and outdoor air sampling of hydrogen sulfide and methane and found community members were aware of geothermal venting and some expressed concerns. The authors did not, however, find hydrogen sulfide above the California Environmental Protection Agency air quality standard of 30 parts per billion over one hour or methane above explosive thresholds. The authors recommend improving risk communication, continuing to monitor geothermal gas effects on the community, and using community reports and complaints to monitor and document geothermal venting incidents.

Type 1 diabetes mellitus and gluten induced disorders.

Over the last five decades the association between coeliac disease and other autoimmune disorders such as autoimmune thyroid disease or diabetes mellitus type 1 has been well established through many studies and to this day is subject to on-going clinical and scientific investigation worldwide. While no link has been established between celiac disease and type-2 diabetes mellitus, coeliac disease is common in patients with type 1 diabetes. The improvement of symptoms in patients with both conditions through dietary intervention, in the form of a gluten free diet, has been widely described within the literature. Our objectives were to review and synthesise the current knowledge on the nutritional treatment for patients with both conditions.

Disturbance to conserved bacterial communities in the cold-water gorgonian coral Eunicella verrucosa.

The bacterial communities associated with healthy and diseased colonies of the cold-water gorgonian coral Eunicella verrucosa at three sites off the south-west coast of England were compared using denaturing gradient gel electrophoresis (DGGE) and clone libraries. Significant differences in community structure between healthy and diseased samples were discovered, as were differences in the level of disturbance to these communities at each site; this correlated with depth and sediment load. The majority of cloned sequences from healthy coral tissue affiliated with the Gammaproteobacteria. The stability of the bacterial community and dominance of specific genera found across visibly healthy colonies suggest the presence of a specific microbial community. Affiliations included a high proportion of Endozoicomonas sequences, which were most similar to sequences found in tropical corals. This genus has been found in a number of invertebrates and is suggested to have a role in coral health and in the metabolisation of dimethylsulfoniopropionate (DMSP) produced by zooxanthellae. However, screening of colonies for the presence of zooxanthellae produced a negative result. Diseased colonies showed a decrease in affiliated clones and an increase in clones related to potentially harmful/transient microorganisms but no increase in a particular pathogen. This study demonstrates that a better understanding of these bacterial communities, the factors that affect them and their role in coral health and disease will be of critical importance in predicting future threats to temperate gorgonian communities.

Diverse profiles of N-acyl-homoserine lactone molecules found in cnidarians.

Many marine habitats, such as the surface and tissues of marine invertebrates, including corals, harbour diverse populations of microorganisms, which are thought to play a role in the health of their hosts and influence mutualistic and competitive interactions. Investigating the presence and stability of quorum sensing (QS) in these ecosystems may shed light on the roles and control of these bacterial communities. Samples of 13 cnidarian species were screened for the presence and diversity of N-acyl-homoserine lactones (AHLs; a prevalent type of QS molecule) using thin-layer chromatography and an Agrobacterium tumefaciens NTL4 biosensor. Ten of 13 were found to harbour species-specific, conserved AHL profiles. AHLs were confirmed in Anemonia viridis using liquid chromatography tandem mass spectrometry. To assess temporal role and stability, AHLs were investigated in A. viridis from intertidal pools over 16 h. Patterns of AHLs showed conserved profiles except for two mid-chain length AHLs, which increased significantly over the day, peaking at 20:00, but had no correlation with pool chemistry. Denaturing gel electrophoresis of RT-PCR-amplified bacterial 16S rRNA showed the presence of an active bacterial community that changed in composition alongside AHL profiles and contained a number of bands that affiliate with known AHL-producing bacteria. Investigations into the quorum sensing-controlled, species-specific roles of these bacterial communities and how these regulatory circuits are influenced by the coral host and members of the bacterial community are imperative to expand our knowledge of these interactions with respect to the maintenance of coral health.

Exogenous Reelin modifies the migratory behavior of neurons depending on cortical location.

Malformations of cortical development can arise when projection neurons generated in the germinal zones fail to migrate properly into the cortical plate. This process is critically dependent on the Reelin glycoprotein, which when absent leads to an inversion of cortical layers and blurring of borders. Reelin has other functions including supporting neuron migration and maintaining their trajectories; however, the precise role on glial fiber-dependent or -independent migration of neurons remains controversial. In this study, we wish to test the hypothesis that migrating cortical neurons at different levels of the cortical wall have differential responses to Reelin. We exposed neurons migrating across the cortical wall to exogenous Reelin and monitored their migratory behavior using time-lapse imaging. Our results show that, in the germinal zones, exogenous Reelin retarded neuron migration and altered their trajectories. This behavior is in contrast to the response of neurons located in the intermediate zone (IZ), possibly because Reelin receptors are not expressed in this zone. In the reeler cortex, Reelin receptors are expressed in the IZ and exposure to exogenous Reelin was able to rescue the migratory defect. These studies demonstrate that migrating neurons have nonequivalent responses to Reelin depending on their location within the cortical wall.

Interference with the germination and growth of Ulva zoospores by quorum-sensing molecules from Ulva-associated epiphytic bacteria.

Ulva zoospores preferentially settle on N-acylhomoserine lactone (AHL) producing marine bacterial biofilms. To investigate whether AHL signal molecules also affect the success and rate of zoospore germination in addition to zoospore attraction, the epiphytic bacteria associated with mature Ulva linza were characterized and bacterial isolates representative of this community tested for the ability to produce AHLs. Two of these AHL-producing isolates, Sulfitobacter spp. 376 and Shewanella spp. 79, were transformed with plasmids expressing the Bacillus spp. AHL lactonase gene aiiA to generate AHL-deficient variants. The germination and growth of U. linza zoospores was studied in the presence of these AHL-deficient strains and their AHL-producing counterparts. This revealed that the AHLs produced by Sulfitobacter spp. and Shewanella spp. or the bacterial products they regulate have a negative impact on both zoospore germination and the early growth of the Ulva germling. Further experiments with Escherichia coli biofilms expressing recombinant AHL synthases and synthetic AHLs provide data to demonstrate that zoospores germinated and grown in the absence of AHLs were significantly longer than those germinated in the presence of AHLs. These results reveal an additional role for AHLs per se in the interactive relationships between marine bacteria and Ulva zoospores.

Minor impact of ocean acidification to the composition of the active microbial community in an Arctic sediment.

Effects of ocean acidification on the composition of the active bacterial and archaeal community within Arctic surface sediment was analysed in detail using 16S rRNA 454 pyrosequencing. Intact sediment cores were collected and exposed to one of five different pCO(2) concentrations [380 (present day), 540, 750, 1120 and 3000 µatm] and RNA extracted after a period of 14 days exposure. Measurements of diversity and multivariate similarity indicated very little difference between pCO(2) treatments. Only when the highest and lowest pCO(2) treatments were compared were significant differences evident, namely increases in the abundance of operational taxonomic units most closely related to the Halobacteria and differences to the presence/absence structure of the Planctomycetes. The relative abundance of members of the classes Planctomycetacia and Nitrospira increased with increasing pCO(2) concentration, indicating that these groups may be able to take advantage of changing pH or pCO(2) conditions. The modest response of the active microbial communities associated with these sediments may be due to the low and fluctuating pore-water pH already experienced by sediment microbes, a result of the pH buffering capacity of marine sediments, or due to currently unknown factors. Further research is required to fully understand the impact of elevated CO(2) on sediment physicochemical parameters, biogeochemistry and microbial community dynamics.

Ocean acidification and rising temperatures may increase biofilm primary productivity but decrease grazer consumption.

Climate change may cause ecosystems to become trophically restructured as a result of primary producers and consumers responding differently to increasing CO2 and temperature. This study used an integrative approach using a controlled microcosm experiment to investigate the combined effects of CO2 and temperature on key components of the intertidal system in the UK, biofilms and their consumers (Littorina littorea). In addition, to identify whether pre-exposure to experimental conditions can alter experimental outcomes we explicitly tested for differential effects on L. littorea pre-exposed to experimental conditions for two weeks and five months. In contrast to predictions based on metabolic theory, the combination of elevated temperature and CO2 over a five-week period caused a decrease in the amount of primary productivity consumed by grazers, while the abundance of biofilms increased. However, long-term pre-exposure to experimental conditions (five months) altered this effect, with grazing rates in these animals being greater than in animals exposed only for two weeks. We suggest that the structure of future ecosystems may not be predictable using short-term laboratory experiments alone owing to potentially confounding effects of exposure time and effects of being held in an artificial environment over prolonged time periods. A combination of laboratory (physiology responses) and large, long-term experiments (ecosystem responses) may therefore be necessary to adequately predict the complex and interactive effects of climate change as organisms may acclimate to conditions over the longer term.

Rickettsia spp. 364D causing a cluster of eschar-associated illness, California.

We describe the clinical course of the first 3 pediatric cases infected with Rickettsia spp. 364D. Although the pathogen was identified in California ticks decades ago, only recently have human cases been documented. Clinical features are generally mild, characterized by eschar, fever, headache, malaise and lymphadenopathy. Antigenic similarity among rickettsiae leads to cross-reactive antibody responses; definitive diagnosis requires molecular methods.