Quantitative proteomic comparison of salt stress in Chlamydomonas reinhardtii and the snow alga Chlamydomonas nivalis reveals mechanisms for salt-triggered fatty acid accumulation via reallocation of carbon resources.

BACKGROUND: Chlamydomonas reinhardtii is a model green alga strain for molecular studies; its fully sequenced genome has enabled omic-based analyses that have been applied to better understand its metabolic responses to stress. Here, we characterised physiological and proteomic changes between a low-starch C. reinhardtii strain and the snow alga Chlamydomonas nivalis, to reveal insights into their contrasting responses to salinity stress. RESULTS: Each strain was grown in conditions tailored to their growth requirements to encourage maximal fatty acid (as a proxy measure of lipid) production, with internal controls to allow comparison points. In 0.2 M NaCl, C. nivalis accumulates carbohydrates up to 10.4% DCW at 80 h, and fatty acids up to 52.0% dry cell weight (DCW) over 12 days, however, C. reinhardtii does not show fatty acid accumulation over time, and shows limited carbohydrate accumulation up to 5.5% DCW. Analysis of the C. nivalis fatty acid profiles showed that salt stress improved the biofuel qualities over time. Photosynthesis and respiration rates are reduced in C. reinhardtii relative to C. nivalis in response to 0.2 M NaCl. De novo sequencing and homology matching was used in conjunction with iTRAQ-based quantitative analysis to identify and relatively quantify proteomic alterations in cells exposed to salt stress. There were abundance differences in proteins associated with stress, photosynthesis, carbohydrate and lipid metabolism proteins. In terms of lipid synthesis, salt stress induced an increase in dihydrolipoyl dehydrogenase in C. nivalis (1.1-fold change), whilst levels in C. reinhardtii remained unaffected; this enzyme is involved in acetyl CoA production and has been linked to TAG accumulation in microalgae. In salt-stressed C. nivalis there were decreases in the abundance of UDP-sulfoquinovose (- 1.77-fold change), which is involved in sulfoquinovosyl diacylglycerol metabolism, and in citrate synthase (- 2.7-fold change), also involved in the TCA cycle. Decreases in these enzymes have been shown to lead to increased TAG production as fatty acid biosynthesis is favoured. Data are available via ProteomeXchange with identifier PXD018148. CONCLUSIONS: These differences in protein abundance have given greater understanding of the mechanism by which salt stress promotes fatty acid accumulation in the un-sequenced microalga C. nivalis as it switches to a non-growth state, whereas C. reinhardtii does not have this response.

Phosphate immobilisation dynamics and interaction with arsenic sorption at redox transition zones in floodplain aquifers: Insights from the Red River Delta, Vietnam.

Although phosphate (PO43-) may play a decisive role in enriching toxic arsenic (As) in the groundwater of many Asian deltas, knowledge gaps exist regarding its interactions with As. This study investigates the simultaneous immobilisation of PO43- and As in aquifer sediments at a redox transition zone in the Red River Delta of Vietnam. The majority of PO43- and As was found to be structurally bound in layers of Fe(III)-(oxyhydr)oxide precipitates, indicating that their formation represents a dominant immobilisation mechanism. This immobilisation was also closely linked to sorption. In the surface sorbed sediment pools, the molar ratios of total P to As were one order of magnitude higher than found in groundwater, reflecting a preferential sorption of PO43- over As. However, this competitive sorption was largely dependent on the presence of Fe(III)-(oxyhydr)oxides. Ongoing contact of the aquifer sediments with iron-reducing groundwater resulted in the reductive dissolution of weakly crystalline Fe(III)-(oxyhydr)oxides, which was accompanied by decreased competition for sorption sites between PO43- and As. Our results emphasise that, to be successful in the medium and long term, remediation approaches and management strategies need to consider competitive sorption between PO43- and As and dynamics of the biogeochemical Fe-cycle.

Arsenic behavior in groundwater in Hanoi (Vietnam) influenced by a complex biogeochemical network of iron, methane, and sulfur cycling.

The fate of arsenic (As) in groundwater is determined by multiple interrelated microbial and abiotic processes that contribute to As (im)mobilization. Most studies to date have investigated individual processes related to As (im)mobilization rather than the complex networks present in situ. In this study, we used RNA-based microbial community analysis in combination with groundwater hydrogeochemical measurements to elucidate the behavior of As along a 2 km transect near Hanoi, Vietnam. The transect stretches from the riverbank across a strongly reducing and As-contaminated Holocene aquifer, followed by a redox transition zone (RTZ) and a Pleistocene aquifer, at which As concentrations are low. Our analyses revealed fermentation and methanogenesis as important processes providing electron donors, fueling the microbially mediated reductive dissolution of As-bearing Fe(III) minerals and ultimately promoting As mobilization. As a consequence of high CH4 concentrations, methanotrophs thrive across the Holocene aquifer and the redox transition zone. Finally, our results underline the role of SO42--reducing and putative Fe(II)-/As(III)-oxidizing bacteria as a sink for As, particularly at the RTZ. Overall, our results suggest that a complex network of microbial and biogeochemical processes has to be considered to better understand the biogeochemical behavior of As in groundwater.

Spatial and temporal evolution of groundwater arsenic contamination in the Red River delta, Vietnam: Interplay of mobilisation and retardation processes.

Geogenic arsenic (As) contamination of groundwater poses a major threat to global health, particularly in Asia. To mitigate this exposure, groundwater is increasingly extracted from low-As Pleistocene aquifers. This, however, disturbs groundwater flow and potentially draws high-As groundwater into low-As aquifers. Here we report a detailed characterisation of the Van Phuc aquifer in the Red River Delta region, Vietnam, where high-As groundwater from a Holocene aquifer is being drawn into a low-As Pleistocene aquifer. This study includes data from eight years (2010-2017) of groundwater observations to develop an understanding of the spatial and temporal evolution of the redox status and groundwater hydrochemistry. Arsenic concentrations were highly variable (0.5-510 µg/L) over spatial scales of <200 m. Five hydro(geo)chemical zones (indicated as A to E) were identified in the aquifer, each associated with specific As mobilisation and retardation processes. At the riverbank (zone A), As is mobilised from freshly deposited sediments where Fe(III)-reducing conditions occur. Arsenic is then transported across the Holocene aquifer (zone B), where the vertical intrusion of evaporative water, likely enriched in dissolved organic matter, promotes methanogenic conditions and further release of As (zone C). In the redox transition zone at the boundary of the two aquifers (zone D), groundwater arsenic concentrations decrease by sorption and incorporations onto Fe(II) carbonates and Fe(II)/Fe(III) (oxyhydr)oxides under reducing conditions. The sorption/incorporation of As onto Fe(III) minerals at the redox transition and in the Mn(IV)-reducing Pleistocene aquifer (zone E) has consistently kept As concentrations below 10 µg/L for the studied period of 2010-2017, and the location of the redox transition zone does not appear to have propagated significantly. Yet, the largest temporal hydrochemical changes were found in the Pleistocene aquifer caused by groundwater advection from the Holocene aquifer. This is critical and calls for detailed investigations.

Characterisation and pure culture of putative health-associated oral bacterium BU063 (Tannerella sp. HOT-286) reveals presence of a potentially novel glycosylated S-layer.

Tannerella HOT-286 (phylotype BU063) is a recently identified novel filamentous Gram-negative anaerobic oral bacterium cultured for the first time recently in co-culture with Propionibacterium acnes. In contrast to the related periodontal disease-associated pathobiont Tannerella forsythia, it is considered a putative health-associated bacterium. In this paper, we identified that this organism could be grown in pure culture if N-acetyl muramic acid (NAM) was provided in the media, although surprisingly the genetic basis of this phenomenon is not likely to be due to a lack of NAM synthesis genes. During further microbiological investigations, we showed for the first time that T. HOT-286 possesses a prominent extracellular S-layer with a novel morphology putatively made up of two proteins modified with an unknown glycan. These data further our knowledge of this poorly understood organism and genus that is an important part of the oral and human microbiome.

Insights into arsenic retention dynamics of Pleistocene aquifer sediments by in situ sorption experiments.

The migration of arsenic (As) enriched groundwater into Pleistocene aquifers as a consequence of extensive groundwater abstraction represents an increasing threat to the precious water resources in Asian delta regions. Pleistocene aquifer sediments are typically rich in FeIII-(hydr)oxides and are capable to adsorb high amounts of As. This results in a pronounced accumulation of As in Pleistocene aquifers, where high As groundwater infiltrates from adjacent Holocene aquifers. However, As retention by Pleistocene aquifers over long-term time scales remains largely unknown. We studied As sorption in situ by placing natural Pleistocene sediments and pure mineral phases directly inside groundwater monitoring wells at a study site near Hanoi (Vietnam). This in situ exposure allows for constant flushing of the samples with unaltered groundwater and the establishment of undisturbed sorption equilibria similar to those in local aquifer sediments, which is not readily attainable in traditional laboratory sorption experiments. The groundwaters in our experimental wells were characterized by different As concentrations (0.01-6.63 µmol/L) and redox states, reaching from suboxic to anoxic conditions (Eh of +159 to -4 mV). Results show that adsorption is the dominant As retention mechanism, independent from the respective groundwater chemistry (i.e. concentrations of dissolved P, HCO3- and Si). Whilst most of the As sorbed within the first week, sorption further increased slowly but consistently by 6-189%, respectively, within six months. Hence, the As sorption behavior of Pleistocene aquifer sediments should be determined over longer periods to avoid an underestimation of the As sorption capacity. Accompanying desorption experiments revealed that about 51% of the sorbed As was remobilized within six months when exposed to low As groundwater. We therefore conclude that a considerable proportion of the As accumulated in the aquifer sediments is prone to remobilization once the As concentrations in migrating groundwater decline. Remobilization of As should be considered in local water management plans to avoid contamination of precious groundwater resources with this As legacy.

Biogeochemical phosphorus cycling in groundwater ecosystems - Insights from South and Southeast Asian floodplain and delta aquifers.

The biogeochemical cycling of phosphorus (P) in South and Southeast Asian floodplain and delta aquifers has received insufficient attention in research studies, even though dissolved orthophosphate (PO43-) in this region is closely linked with the widespread contamination of groundwater with toxic arsenic (As). The overarching aim of this study was to characterize the enrichment of P in anoxic groundwater and to provide insight into the biogeochemical mechanisms underlying its mobilization, subsurface transport, and microbial cycling. Detailed groundwater analyses and in situ experiments were conducted that focused on three representative field sites located in the Red River Delta (RRD) of Vietnam and the Bengal Delta Plain (BDP) in West Bengal, India. The results showed that the total concentrations of dissolved P (TDP) ranged from 0.03 to 1.50 mg L-1 in groundwater, with PO43- being the dominant P species. The highest concentrations occurred in anoxic sandy Holocene aquifers where PO43- was released into groundwater through the microbial degradation of organic carbon and the concomitant reductive dissolution of Fe(III)-(hydr)oxides. The mobilization of PO43- may still constitute an active process within shallow Holocene sediments. Furthermore, a sudden supply of organic carbon may rapidly decrease the redox potential, which causes an increase in TDP concentrations in groundwater, as demonstrated by a field experiment. Considering the subsurface transport of PO43-, Pleistocene aquifer sediments represented effective sinks; however, the enduring contact between oxic Pleistocene sediments and anoxic groundwater also changed the sediments PO43--sorption capacity over time. A stable isotope analysis of PO43--bound oxygen indicated the influences of intracellular microbial cycling as well as a specific PO43- source with a distinct isotopically heavy signal. Consequently, porous aquifers in Asian floodplain and delta regions proved to be ideal natural laboratories to study the biogeochemical cycling of P and its behavior in groundwater environments.

Change of carbon source causes dramatic effects in the phospho-proteome of the archaeon Sulfolobus solfataricus.

Protein phosphorylation is known to occur in Archaea. However, knowledge of phosphorylation in the third domain of life is rather scarce. Homology-based searches of archaeal genome sequences reveals the absence of two-component systems in crenarchaeal genomes but the presence of eukaryotic-like protein kinases and protein phosphatases. Here, the influence of the offered carbon source (glucose versus tryptone) on the phospho-proteome of Sulfolobus solfataricus P2 was studied by precursor acquisition independent from ion count (PAcIFIC). In comparison to previous phospho-proteome studies, a high number of phosphorylation sites (1318) located on 690 phospho-peptides from 540 unique phospho-proteins were detected, thus increasing the number of currently known archaeal phospho-proteins from 80 to 621. Furthermore, a 25.8/20.6/53.6 Ser/Thr/Tyr percentage ratio with an unexpectedly high predominance of tyrosine phosphorylation was detected. Phospho-proteins in most functional classes (21 out of 26 arCOGs) were identified, suggesting an important regulatory role in S. solfataricus. Focusing on the central carbohydrate metabolism in response to the offered carbon source, significant changes were observed. The observed complex phosphorylation pattern hints at an important physiological function of protein phosphorylation in control of the central carbohydrate metabolism, which might particularly operate in channeling carbon flux into the respective metabolic pathways.

Evaluation of dioxin-like activities in settled house dust from Vietnamese E-waste recycling sites: relevance of polychlorinated/brominated dibenzo-p-dioxin/furans and dioxin-like PCBs.

Few studies have investigated the human exposure to the ensemble of dioxin-related compounds (DRCs) released from uncontrolled e-waste recycling, especially from a toxic effect standpoint. This study evaluated the TCDD toxic equivalents (TEQs) in persistent extracts of settled house dust from two Vietnamese e-waste recycling sites (EWRSs) using the Dioxin-Responsive Chemically Activated LUciferase gene eXpression assay (DR-CALUX), combined with chemical analysis of PCDD/Fs, DL-PCBs, PBDD/Fs, and monobromo PCDD/Fs to determine their TEQ contribution. The CALUX-TEQ levels in house dust ranged from 370 to 1000 pg g(-1) in the EWRSs, approximately 3.5-fold higher than in the urban control site. In EWRS house dust, the concentrations of the unregulated PBDFs were 7.7-63 ng g(-1), an order of magnitude higher than those of regulated DRCs (PCDD/Fs and DL-PCBs), and PBDFs were also principal CALUX-TEQ contributors (4.2-22%), comparable to PCDD/Fs (8.1-29%). The CALUX-TEQ contribution of DRCs varied, possibly depending on thermal processing activities (higher PCDD/F-TEQs) and PBDE content in the waste (higher PBDF-TEQs). However, the percentage of unknown dioxin-like activities was high in all dust samples, indicating large contribution from unidentified DRCs and/or synergy among contaminants. Estimates of TEQ intake from dust ingestion suggest that children in the EWRSs may be adversely affected by DRCs from dust.