Quantification of glycine betaine, choline and trimethylamine N-oxide in seawater particulates: Minimisation of seawater associated ion suppression

A liquid chromatography/mass spectrometry (LC/MS, electrospray ionisation) method has been developed for the quantification of nitrogenous osmolytes (N-osmolytes) in the particulate fraction of natural water samples. Full method validation demonstrates the validity of the method for measuring glycine betaine (GBT), choline and trimethylamine N-oxide (TMAO) in particulates from seawater. Limits of detection were calculated as 3.5, 1.2 and 5.9 pg injected onto column (equivalent to 1.5, 0.6 and 3.9 nmol per litre) for GBT, choline and TMAO respectively. Precision of the method was typically 3% for both GBT and choline and 6% for TMAO. Collection of the particulate fraction of natural samples was achieved via in-line filtration. Resulting chromatography and method sensitivity was assessed and compared for the use of both glass fibre and polycarbonate filters during sample collection. Ion suppression was shown to be a significant cause of reduced instrument response to N-osmolytes and was associated with the presence of seawater in the sample matri

Phytoplankton communities and acclimation in a cyclonic eddy in the southwest Indian Ocean

A study of phytoplankton in a cyclonic eddy was undertaken in the Mozambique Basin between Madagascar and southern Africa during austral winter. CHEMTAX analysis of pigment data indicated that the community comprised mainly haptophytes and diatoms, with Prochlorococcus, prasinophytes and pelagophytes also being prominent to the east and west of the eddy. There was little difference in community structure, chlorophyll-specific absorption [a*ph(440)] and pigment:TChla ratios between the surface and the sub-surface chlorophyll maximum (SCM), reflecting acclimation to fluctuating light conditions in a well mixed upper layer. Values for a*ph(440) were low for diatom dominance, high where prokaryote proportion was high, and intermediate for flagellate dominated communities. Chlorophyll c and fucoxanthin:TChla ratios were elevated over most of the eddy, while 19′-hexanoyloxyfucoxanthin ratios increased in the eastern and western sectors. In a community comprising mainly flagellates and Prochlorococcus to the west of the eddy, there was high a*ph(440) at the surface and elevated ratios for divinyl chlorophyll a, chlorophyll b and 19′-hexanoyloxyfucoxanthin at the SCM. An increase in diadinoxanthin:TChla ratios and a decline in the quantum efficiency of photochemistry in PSII under high light conditions, indicated some photoprotection and photoinhibition at the surface even in a well mixed environment. Diadinoxanthin was the main photoprotective carotenoid within the eddy, while zeaxanthin was the dominant photoprotective pigment outside the eddy. The results of this study will be useful inputs into appropriate remote sensing models for estimating primary production and the size class distribution of phytoplankton in eddies in the southwest Indian Ocean

Environmental influence on phytoplankton communities in the northern Benguela ecosystem

An investigation of surface phytoplankton communities was undertaken on the shelf of the northern Benguela upwelling ecosystem during austral autumn (May) and spring (September), along latitudinal transects at 20° S and 23° S, from 2 to 70 nautical miles offshore, as well as on a zigzag grid located between these transects. Microscopic identification of the phytoplankton and CHEMTAX analysis of pigment biomarkers were used to characterise the community composition. During May 2014, warmer, more-saline water with a shallower upper mixed layer corresponding to periods of less-intense offshore Ekman transport was encountered on the shelf. Satellite imagery indicated high phytoplankton biomass extending for a considerable distance from the coast, and CHEMTAX indicated diatoms as dominant at most of the stations (52–92%), although dinoflagellates were dominant at some inshore localities (57–74%). Species of Chaetoceros, Bacteriastrum and Cylindrotheca were the most abundant, with abundance of the Pseudo-nitzschia ‘seriata-group’ being particularly high at a number of stations. In September 2014, more-intense wind-forcing resulted in a deeper upper mixed layer and stronger upwelling of colder, less-saline water. Elevated phytoplankton biomass was confined close to the coast, where diatoms accounted for most of the population (54–87%), whereas small flagellates, such as prasinophytes, haptophytes and cryptophytes, as well as the cyanobacterium Synechococcus, dominated the communities (58–90%) farther from the coast. It is hypothesised that stronger upwelling and deeper vertical mixing in September of that year were not conducive for widespread diatom growth, and that small flagellates populated the water column by being entrained from offshore onto the shelf in the upwelled water that moved in towards the coast

Determination of picomolar dissolved free amino acids along a South Atlantic transect using reversed-phase high-performance liquid chromatography

Dissolved free amino acids (DFAA) in seawater are a form of nitrogen (N) available for marine microbes. In oligotrophic environments where N-containing nutrients are the limiting factor for microbial growth, N nutrition from DFAA could be crucial, but as yet it is poorly resolved. Measurements of individual DFAA are challenging as concentrations are typically in the low nmol L− 1 range. Here we report modifications to methodology using o-phthaldialdehyde (OPA) derivatization and reversed phase high performance liquid chromatography (HPLC) that provide a 30-fold improvement in sensitivity enabling the detection of 15 amino acids in seawater with a limit of detection as low as 10 pmol L− 1 with accuracy and precision of better than 10%. This analytical methodology is now suitable for the challenging quantitation of DFAA in oligotrophic seawaters. The method was successfully applied to a suite of seawater samples collected on a cruise crossing the South Atlantic Ocean, where concentrations of DFAAs were generally low (sub nmol L− 1), revealing basin-scale features in the oceanographic distributions of DFAA. This unique dataset implies that DFAAs are an important component of the N cycle in both near-coastal and open oceans. Further calculations suggest that the proportions of organic N originating from DFAA sources were significant, contributing between 0.2 and 200% that of NH4+ and up to 77% that of total inorganic nitrogen in the upper 400 m in some regions of the transect

Determining Atlantic Ocean province contrasts and variations

The Atlantic Meridional Transect (AMT) series of twenty-five cruises over the past twenty years has produced a rich depth-resolved biogeochemical in situ data resource consisting of a wealth of core variables. These multiple core datasets, key to the operation of AMT, such as temperature, salinity, oxygen and inorganic nutrients, are often only used as ancillary measurements for contextualising hypothesis-driven process studies. In this paper these core in situ variables, alongside data drawn from satellite Earth Observation (EO) and modelling, have been analysed to determine characteristic oceanic province variations encountered over the last twenty years on the AMT through the Atlantic Ocean. The EO and modelling analysis shows the variations of key environmental variables in each province, such as surface currents, the net heat flux and subsequent large scale biological responses, such as primary production. The in situ core dataset analysis allows the variation in features such as the tropical oxygen minimum zone to be quantified as well as showing clear contrasts between the provinces in nutrient stoichiometry. Such observations and relationships can be used within basin scale biogeochemical models to set realistic variation ranges

Benthic silicon cycling in the Arctic Barents Sea: a reaction–transport model study

Over recent decades the highest rates of water column warming and sea ice loss across the Arctic Ocean have been observed in the Barents Sea. These physical changes have resulted in rapid ecosystem adjustments, manifesting as a northward migration of temperate phytoplankton species at the expense of silica-based diatoms. These changes will potentially alter the composition of phytodetritus deposited at the seafloor, which acts as a biogeochemical reactor and is pivotal in the recycling of key nutrients, such as silicon (Si). To appreciate the sensitivity of the Barents Sea benthic system to the observed changes in surface primary production, there is a need to better understand this benthic–pelagic coupling. Stable Si isotopic compositions of sediment pore waters and the solid phase from three stations in the Barents Sea reveal a coupling of the iron (Fe) and Si cycles, the contemporaneous dissolution of lithogenic silicate minerals (LSi) alongside biogenic silica (BSi), and the potential for the reprecipitation of dissolved silicic acid (DSi) as authigenic clay minerals (AuSi). However, as reaction rates cannot be quantified from observational data alone, a mechanistic understanding of which factors control these processes is missing. Here, we employ reaction–transport modelling together with observational data to disentangle the reaction pathways controlling the cycling of Si within the seafloor. Processes such as the dissolution of BSi are active on multiple timescales, ranging from weeks to hundreds of years, which we are able to examine through steady state and transient model runs. Steady state simulations show that 60 % to 98 % of the sediment pore water DSi pool may be sourced from the dissolution of LSi, while the isotopic composition is also strongly influenced by the desorption of Si from metal oxides, most likely Fe (oxyhydr)oxides (FeSi), as they reductively dissolve. Further, our model simulations indicate that between 2.9 % and 37 % of the DSi released into sediment pore waters is subsequently removed by a process that has a fractionation factor of approximately −2 ‰, most likely representing reprecipitation as AuSi. These observations are significant as the dissolution of LSi represents a source of new Si to the ocean DSi pool and precipitation of AuSi an additional sink, which could address imbalances in the current regional ocean Si budget. Lastly, transient modelling suggests that at least one-third of the total annual benthic DSi flux could be sourced from the dissolution of more reactive, diatom-derived BSi deposited after the surface water bloom at the marginal ice zone. This benthic–pelagic coupling will be subject to change with the continued northward migration of Atlantic phytoplankton species, the northward retreat of the marginal ice zone and the observed decline in the DSi inventory of the subpolar North Atlantic Ocean over the last 3 decades

Latitudinal variability and adaptation of phytoplankton in the Atlantic Ocean

This study assessed the variability of a range of phytoplankton groups between repeat cruises over the mid�Atlantic Ocean (50◦N-50◦S), and demonstrated the important contribution of the pico-phytoplankton to the microalgal biomass in the oligotrophic tropical and sub-tropical regions. Pigment data from two meridional transects were analysed by quantitative chemotaxonomic analysis (CHEMTAX) to yield information concerning the composition of phytoplankton communities along the transects. Total chlorophyll a (TChla) in Octo�ber–November 2012 (AMT22) and 2013 (AMT23) varied from 0.03 mg m− 3 in the southern Sub-Tropical Gyre to 1.13 and 1.92 mg m− 3 at 40o S and 42o S respectively. Synechococcus accounted for 35–50% and Prochlorococcus 30–35% of the TChla in oligotrophic surface waters on AMT22, while haptophytes dominated the temperate regions. Prochlorococcus was dominant (30–60%) on AMT23, with Synechococcus contributing 20–40% and haptophytes 10–20%, and it was noted that the dominance of Prochlorococcus occurred in water masses where the inorganic nitrate concentrations were extremely low (≤0.02 mmol m− 3 ). Prochlorococcus and haptophytes dominated the deep chlorophyll maximum (DCM) on AMT22, with the Synechococcus proportion being low, while Prochlorococcus was generally dominant on AMT23, although Synechococcus and haptophytes were also prominent. Photo-pigment indices indicated that chlorophyll b was mainly associated with Prochlorococcus but also related to prasinophytes. Chlorophyll c and photosynthetic carotenoids increased with an increase in the proportion of haptophytes and to a lesser extent with the proportion of diatoms and pelagophytes. Pro�chlorococcus and Synechococcus were the main contributors to the photoprotective carotenoids and relationships indicated that Synechococcus accounted for more of this pool in 2012, but the Prochlorococcus contribution was greater in 2013. Temperature, stratification, nutrients and light appeared to be the main hydrographic variables influencing phytoplankton composition along the transects

Low-cost molecular methods to characterise gastrointestinal nematode co-infections of goats in Africa

AVAILABILITY OF DATA AND MATERIALS : Raw diagnostic, DNA extraction, and PCR data are shown in Additional file 1: Table S1. All other original results including tabulated data, PCR results, and other materials are available on request where not included in the manuscript.SUPPLEMENTARY INFORMATION : ADDITIONAL FILE 1. TABLE S1. Raw baseline data on DNA extraction, quality, quantity and yield. ADDITIONAL FILE 2. TABLE S2. Primers and cycling conditions used for each PCR technique. ADDITIONAL FILE 3. TABLE S3. Nemabiome raw read results from Eurofins 2nd PCR amplicon sequencing. ADDITIONAL FILE 4. TABLE S4. DNA extraction costs. ADDITIONAL FILE 5. TABLE S5. HRMC peak temperatures and Singleplex PCR relative species abundance. ADDITIONAL FILE 6. TABLE S6. Proportional read differences between Mothur and DADA2 nemabiome pipelines. ADDITIONAL FILE 7. FILE S1. 72-well gel electrophoresis comb design. ADDITIONAL FILE 8. FIGURES S1–S5. FIGURE S1: Assessing quality of DNA extraction methods. FIGURE S2: Assessing GIN species detection likelihoods by DNA extraction method and infection intensity. FIGURE S3: High-resolution melt curves with pan-nematode ITS-2 primers. FIGURE S4: Nemabiome ITS-2 amplicon with the DADA2 IDTAXA pipeline. FIGURE S5: Cross-validation of PCR methods with nemabiome using the DADA2 IDTAXA pipeline.BACKGROUND : Veterinary diagnostics aid intervention strategies, track zoonoses, and direct selective breeding programs in livestock. In ruminants, gastrointestinal nematode (GIN) parasites are a major cause of production losses, but morphologically similar species limit our understanding of how specific GIN co-infections impact health in resource-limited settings. To estimate the presence and relative abundance of GINs and other helminths at the species level, we sought to develop a low-cost and low-resource molecular toolkit applied to goats from rural Malawi smallholdings. METHODS : Goats were subjected to health scoring and faecal sampling on smallholdings in Lilongwe district, Malawi. Infection intensities were estimated by faecal nematode egg counts with a faecal subsample desiccated for DNA analysis. Two DNA extraction methods were tested (low-resource magbead kit vs high-resource spin-column kit), with resulting DNA screened by endpoint polymerase chain reaction (PCR), semi-quantitative PCR, quantitative PCR (qPCR), high-resolution melt curve analysis (HRMC), and ‘nemabiome’ internal transcribed spacer 2 (ITS-2) amplicon sequencing. RESULTS : Both DNA isolation methods yielded comparable results despite poorer DNA purity and faecal contaminant carryover from the low-resource magbead method. GINs were detected in 100% of samples regardless of infection intensity. Co-infections with GINs and coccidia (Eimeria spp.) were present in most goats, with GIN populations dominated by Haemonchus contortus, Trichostrongylus colubriformis, Trichostrongylus axei, and Oesophagostomum columbianum. Both multiplex PCR and qPCR were highly predictive of GIN species proportions obtained using nemabiome amplicon sequencing; however, HRMC was less reliable than PCR in predicting the presence of particular species. CONCLUSIONS : These data represent the first ‘nemabiome’ sequencing of GINs from naturally infected smallholder goats in Africa and show the variable nature of GIN co-infections between individual animals. A similar level of granularity was detected by semi-quantitative PCR methods, which provided an accurate summary of species composition. Assessing GIN co-infections is therefore possible using cost-efficient low-resource DNA extraction and PCR approaches that can increase the capacity of molecular resources in areas where sequencing platforms are not available; and also open the door to affordable molecular GIN diagnostics. Given the diverse nature of infections in livestock and wildlife, these approaches have potential for disease surveillance in other areas.The Biotechnology and Biological Sciences Research Council.https://parasitesandvectors.biomedcentral.com/am2024Veterinary Tropical DiseasesSDG-02:Zero HungerSDG-03:Good heatlh and well-bein

Seasonal measurements of the nitrogenous osmolyte glycine betaine in marine temperate coastal waters

Glycine betaine (GBT) is a nitrogenous osmolyte ubiquitous throughout the marine environ�ment. Despite its widespread occurrence and sig�nifcance in microbial cycling, knowledge of the seasonality of this compound is lacking. Here, we present a seasonal dataset of GBT concentrations in marine suspended particulate material. Analysing coastal waters in the Western English Channel, GBT peaked in summer and autumn but did not follow the observed maxima in total phytoplankton biomass orchlorophyll a. Instead, we found evidence that GBT concentrations were associated with specifc phyto�plankton groups or species, particularly in the sum�mer when GBT correlated with dinofagellate bio�mass. In contrast, autumn maxima corresponded with a period of rapidly changing salinity and nutrient availability, with potential contributions from some phytoplankton species and Harpacticoid copepods. This suggests distinct environmental drivers for dif�ferent periods of the GBT seasonality. Building on evidence that GBT and dinofagellate biomass peak in summer, concomitantly with low nutrients, we propose that GBT positively afects dinofagellate ftness, allowing them to outcompete other plank�ton when inorganic nutrients are depleted. By using this assumption, we improved the performance of a marine ecosystem model to reproduce the observed increase in dinofagellates biomass in the transition from spring to summer. This work sheds light on the interplay between phytoplankton succession, compet�itive advantage and changing environmental factors relevant to climate change. It paves the way for future multidisciplinary research aiming to understand the importance of dinofagellates in key coastal ecosys�tems and their potential signifcance for methylamine production, compounds relevant for particle growth in atmospheric chemistry

Simultaneous Detection of Alkylamines in the Surface Ocean and Atmosphere of the Antarctic Sympagic Environment

Measurements of alkylamines from seawater and atmospheric samples collected simultaneously across the Antarctic Peninsula, South Orkney and South Georgia Islands are reported. Concentrations of mono-, di-, and trimethylamine (MMA, DMA, and TMA, respectively), and their precursors, the quarternary amines glycine betaine and choline, were enhanced in sympagic seawater samples relative to ice-devoid pelagic ones, suggesting the microbiota of sea ice and sea ice-influenced ocean is a major source of these compounds. Primary sea-spray aerosol particles artificially generated by bubbling seawater samples were investigated by aerosol time-of-flight mass spectrometry (ATOFMS) of single particles; their mixing state indicated that alkylamines were aerosolized with sea spray from dissolved and particulate organic nitrogen pools. Despite this unequivocal sea spray-associated source of alkylamines, ATOFMS analyses of ambient aerosols in the sympagic region indicated that the majority (75–89%) of aerosol alkylamines were of secondary origin, that is, incorporated into the aerosol after gaseous air–sea exchange. These findings show that sympagic seawater properties are a source of alkylamines influencing the biogenic aerosol fluxed from the ocean into the boundary layer; these organic nitrogen compounds should be considered when assessing secondary aerosol formation processes in Antarctica