Posts Tagged 'archaea'

Potential impact of global climate change on benthic deep-sea microbes

Benthic deep-sea environments are the largest ecosystem on Earth, covering ∼65% of the Earth surface. Microbes inhabiting this huge biome at all water depths represent the most abundant biological components and a relevant portion of the biomass of the biosphere, and play a crucial role in global biogeochemical cycles. Increasing evidence suggests that global climate changes are affecting also deep-sea ecosystems, both directly (causing shifts in bottom-water temperature, oxygen concentration and pH) and indirectly (through changes in surface oceans’ productivity and in the consequent export of organic matter to the seafloor). However, the responses of the benthic deep-sea biota to such shifts remain largely unknown. This applies particularly to deep-sea microbes, which include bacteria, archaea, microeukaryotes and their viruses. Understanding the potential impacts of global change on the benthic deep-sea microbial assemblages and the consequences on the functioning of the ocean interior is a priority to better forecast the potential consequences at global scale. Here we explore the potential changes in the benthic deep-sea microbiology expected in the coming decades using case studies on specific systems used as test models.

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Microbiome dynamics in early life stages of the scleractinian coral Acropora gemmifera in response to elevated pCO2

Reef-building corals are complex holobionts, harbouring diverse microorganisms that play essential roles in maintaining coral health. However, microbiome development in early life stages of corals remains poorly understood. Here, microbiomes of Acropora gemmifera were analysed during spawning and early developmental stages, and also under different seawater partial pressure of CO2 (pCO2) conditions, using amplicon sequencing of 16S rRNA gene for bacteria and archaea and of ITS2 for Symbiodinium. No remarkable microbiome shift was observed in adults before and after spawning. Moreover, microbiomes in eggs were highly similar to those in spawned adults, possibly suggesting a vertical transmission from parents to offspring. However, significant stage-specific changes were found in coral microbiome during development, indicating that host development played a dominant role in shaping coral microbiome. Specifically, Cyanobacteria were particularly abundant in 6-day-old juveniles, but decreased largely in 31-day-old juveniles with a possible subclade shift in Symbiodinium dominance from C2r to D17. Larval microbiome showed changes in elevated pCO2, while juvenile microbiomes remained rather stable in response to higher pCO2. This study provides novel insights into the microbiome development during the critical life stages of coral.

Continue reading ‘Microbiome dynamics in early life stages of the scleractinian coral Acropora gemmifera in response to elevated pCO2’

Acidification enhances hybrid N2O production associated with aquatic ammonia-oxidizing microorganisms

Ammonia-oxidizing microorganisms are an important source of the greenhouse gas nitrous oxide (N2O) in aquatic environments. Identifying the impact of pH on N2O production by ammonia oxidizers is key to understanding how aquatic greenhouse gas fluxes will respond to naturally occurring pH changes, as well as acidification driven by anthropogenic CO2. We assessed N2O production rates and formation mechanisms by communities of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in a lake and a marine environment, using incubation-based nitrogen (N) stable isotope tracer methods with 15N-labeled ammonium (15NH+4) and nitrite (15NO−2), and also measurements of the natural abundance N and O isotopic composition of dissolved N2O. N2O production during incubations of water from the shallow hypolimnion of Lake Lugano (Switzerland) was significantly higher when the pH was reduced from 7.54 (untreated pH) to 7.20 (reduced pH), while ammonia oxidation rates were similar between treatments. In all incubations, added NH+4 was the source of most of the N incorporated into N2O, suggesting that the main N2O production pathway involved hydroxylamine (NH2OH) and/or NO−2 produced by ammonia oxidation during the incubation period. A small but significant amount of N derived from exogenous/added 15NO−2 was also incorporated into N2O, but only during the reduced-pH incubations. Mass spectra of this N2O revealed that NH+4 and 15NO−2 each contributed N equally to N2O by a “hybrid-N2O” mechanism consistent with a reaction between NH2OH and NO−2, or compounds derived from these two molecules. Nitrifier denitrification was not an important source of N2O. Isotopomeric N2O analyses in Lake Lugano were consistent with incubation results, as 15N enrichment of the internal N vs. external N atoms produced site preferences (25.0–34.4‰) consistent with NH2OH-dependent hybrid-N2O production. Hybrid-N2O formation was also observed during incubations of seawater from coastal Namibia with 15NH+4 and NO−2. However, the site preference of dissolved N2O here was low (4.9‰), indicating that another mechanism, not captured during the incubations, was important. Multiplex sequencing of 16S rRNA revealed distinct ammonia oxidizer communities: AOB dominated numerically in Lake Lugano, and AOA dominated in the seawater. Potential for hybrid N2O formation exists among both communities, and at least in AOB-dominated environments, acidification may accelerate this mechanism.

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Multi-taxon activity profiling reveals differential microbial response to reduced seawater pH and oil pollution

There is growing concern that predicted changes to global ocean chemistry will interact with anthropogenic pollution to significantly alter marine microbial composition and function. However, knowledge of the compounding effects of climate change stressors and anthropogenic pollution is limited. Here, we used 16S and 18S rRNA (cDNA) based activity profiling to investigate the differential responses of selected microbial taxa to ocean acidification and oil hydrocarbon contamination under controlled laboratory conditions. Our results revealed that a lower relative abundance of sulphate-reducing bacteria (Desulfosarcina/Desulfococcus clade) due to an adverse effect of seawater acidification and oil hydrocarbon contamination (reduced pH-oil treatment) may be coupled to changes in sediment archaeal communities. In particular, we observed a pronounced compositional shift and marked reduction in the prevalence of otherwise abundant operational taxonomic units (OTUs) belonging to the archaeal Marine Benthic Group B (MBGB) and Marine Hydrothermal Vent Group (MHVG) in the reduced pH-oil treatment. Conversely, the abundance of several putative hydrocarbonoclastic fungal OTUs was higher in the reduced pH-oil treatment. Sediment hydrocarbon profiling, furthermore, revealed higher concentrations of several alkanes in the reduced pH-oil treatment, corroborating the functional implications of the structural changes to microbial community composition. Collectively, our results advance the understanding of the response of a complex microbial community to the interaction between reduced pH and anthropogenic pollution. In future acidified marine environments, oil hydrocarbon contamination may alter the typical mixotrophic and k-/r-strategist composition of surface sediment microbiomes towards a more heterotrophic state with lower doubling rates, thereby impairing the ability of the ecosystem to recover from acute oil contamination events.

Continue reading ‘Multi-taxon activity profiling reveals differential microbial response to reduced seawater pH and oil pollution’

Increasing CO2 changes community composition of pico- and nano-sized protists and prokaryotes at a coastal Antarctic site

Ocean acidification is a globally recognised phenomenon, but little is known of its impacts on Antarctic marine microbes. Here we report on the community response of pico- and nanophytoplankton, heterotrophic nanoflagellates (HNF) and prokaryotes (Archaea and Bacteria) to elevated CO2 during 3 minicosm experiments over the 2008/2009 summer at Davis Station, Antarctica. Coastal seawater was incubated in 650 l minicosms (n = 6) for ≤12 d at CO2 concentrations ranging from preindustrial levels to those predicted for 2100 and beyond. The abundance of pico- and nano-sized protists and prokaryotes were determined by flow cytometry, using chlorophyll autofluorescence to discriminate the phytoplankton, SYBR-Green to stain the prokaryotes and LysoTracker Green stain to discriminate the HNF. While the effects on nanophytoplankton abundance were inconclusive, our results show that increasing CO2 can alter the composition of the microbial community in Antarctic coastal waters. Our 3 experiments consistently showed lower concentrations of HNF and higher abundances of picophytoplankton and prokaryotes in treatments exposed to elevated CO2. While the mechanism remains to be confirmed, our study suggests that CO2 may reduce the mortality of picoplankton by HNF grazing. Our results indicate that changes in the composition of Antarctic microbial communities may occur within the concentration range of 750 to 1118 ppm CO2, potentially impacting the Antarctic food web through reduced food availability.

Continue reading ‘Increasing CO2 changes community composition of pico- and nano-sized protists and prokaryotes at a coastal Antarctic site’

Effect of simulated ocean acidification on the composition of microbial assemblages in New Zealand’s coastal sediment and their potential for ammonia oxidation

The ocean’s pH has decreased by 0.1 units in the last two centuries due to anthropogenic CO2 emissions and it is predicted will continue to decrease by 0.3 units during the next century. One key ecosystem process that may be altered by such a decrease is the microbial oxidation of ammonia, the first step of nitrification. At low pH, the equilibrium concentration shifts towards ammonium rather than ammonia and therefore ammonia oxidation by microorganisms can be inhibited. Previous studies have demonstrated an inhibitory effect of a low seawater pH on ammonia oxidation in the seawater column. Such effect on ammonia oxidation in coastal sediment, however, is not well understood. The relevance of studying the potential effect of acidified seawater on the oxidation of ammonia in coastal sediment is that nitrate, the end product of nitrification, is the second most preferred electron acceptor used by microorganisms to decompose organic matter. Nitrate is also an essential source of nitrogen for primary producers. I established a facility of recirculating seawater to study the effect of an experimental pH decrease of 0.3 units on the oxidation of ammonia in two contrasting types of coastal sediment, sandy and muddy sediment. My objectives were to investigate (1) the assemblage structure of ammonia-oxidising archaea and bacteria; and (2) the gene expression of amoA, the gene for the enzyme that catalyses ammonia oxidation. I also investigated the effect of the seawater pH decrease on the pH of the muddy sediment pore water. Overall, my study was inconclusive. I was able, however, to demonstrate that the seawater pH decrease altered the pore water pH in muddy sediment. I found enhanced pore water pH diel variations at the upper oxic zone, which were attributed to intensified respiration and photosynthesis of diatoms stimulated by the supply of CO2. This suggested that the diatom’s CO2-growth stimulation might play an important role in the effect of the future acidified ocean on the sediment’s biogeochemistry. I also demonstrated a shift in the pore water pH at the suboxic zone towards lower pH, suggesting that the seawater pH decrease exceeded the buffering capacity of the sediment. In terms of sandy coastal sediment, I was able to determine that the experimentally lowered seawater pH did not have a significant effect on the structure of the overall microbial assemblage (not only ammonia-oxidising microorganisms, which were scarce). The reason for this study to be inconclusive was low statistical power. Such low statistical power resulted mainly from the excessive depth of sediment sampled for analyses, the low amounts of nucleic acids extracted from the sediments and the presence of inhibitors in these extractions, which prevented the nucleic acids from being amplified or detected by the technique used. Informing the sampling with a preliminary pore water pH profile, improving the nucleic acids extraction technique and trying alternative methods to overcome inhibition would improve the outcome of future studies.

Continue reading ‘Effect of simulated ocean acidification on the composition of microbial assemblages in New Zealand’s coastal sediment and their potential for ammonia oxidation’

Response of marine bacterioplankton pH homeostasis gene expression to elevated CO2

Human-induced ocean acidification impacts marine life. Marine bacteria are major drivers of biogeochemical nutrient cycles and energy fluxes1; hence, understanding their performance under projected climate change scenarios is crucial for assessing ecosystem functioning. Whereas genetic and physiological responses of phytoplankton to ocean acidification are being disentangled2, 3, 4, corresponding functional responses of bacterioplankton to pH reduction from elevated CO2 are essentially unknown. Here we show, from metatranscriptome analyses of a phytoplankton bloom mesocosm experiment, that marine bacteria responded to lowered pH by enhancing the expression of genes encoding proton pumps, such as respiration complexes, proteorhodopsin and membrane transporters. Moreover, taxonomic transcript analysis showed that distinct bacterial groups expressed different pH homeostasis genes in response to elevated CO2. These responses were substantial for numerous pH homeostasis genes under low-chlorophyll conditions (chlorophyll a <2.5 μg l−1); however, the changes in gene expression under high-chlorophyll conditions (chlorophyll a >20 μg l−1) were low. Given that proton expulsion through pH homeostasis mechanisms is energetically costly, these findings suggest that bacterioplankton adaptation to ocean acidification could have long-term effects on the economy of ocean ecosystems.

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The inhibition of N2O production by ocean acidification in cold temperate and polar waters

The effects of ocean acidification (OA) on nitrous oxide (N2O) production and on the community composition of ammonium oxidising archaea (AOA) were examined in the northern and southern sub-polar and polar Atlantic Ocean. Two research cruises were performed during June 2012 between the North Sea and Arctic Greenland and Barent Seas, and in January-February 2013 to the Antarctic Scotia Sea. Seven stations were occupied in all during which shipboard experimental manipulations of the carbonate chemistry were performed through additions of NaHCO3-+HCl in order to examine the impact of short- term (48 hour for N2O and between 96 and 168 hour for AOA) exposure to control and elevated conditions of OA. During each experiment, triplicate incubations were performed at ambient conditions and at 3 lowered levels of pH which varied between 0.06 and 0.4 units according to the total scale and which were targeted at CO2 partial pressures of ~500, 750 and 1000 µatm. The AOA assemblage in both Arctic and Antarctic regions was dominated by two major archetypes that represent the marine AOA clades most often detected in seawater. There were no significant changes in AOA assemblage composition between the beginning and end of the incubation experiments. N2O production was sensitive to decreasing pHT at all stations and decreased by between 2.4 and 44% with reduced pHT values of between 0.06 and 0.4. The reduction in N2O yield from nitrification was directly related to a decrease of between 28 and 67% in available NH3 as a result of the pH driven shift in the NH3:NH4+ equilibrium. The maximum reduction in N2O production at conditions projected for the end of the 21st century was estimated to be 0.82 Tg N y−1.

Continue reading ‘The inhibition of N2O production by ocean acidification in cold temperate and polar waters’

Influence of temperature, pH, and salinity on membrane lipid composition and TEX86 of marine planktonic thaumarchaeal isolates

Marine ammonia-oxidizing archaea of the phylum Thaumarchaeota are a cosmopolitan group of microorganisms representing a major fraction of the picoplankton in the ocean. The cytoplasmic membranes of Thaumarchaeota consist predominantly of intact polar isoprenoid glycerol dibiphytanyl glycerol tetraether (GDGT) lipids, which may be used as biomarkers for living Thaumarchaeota. Fossil thaumarchaeal GDGT core lipids accumulate in marine sediments and serve as the basis for geochemical proxies such as the TEX86 paleothermometer. Here, we demonstrate that the responses of membrane lipid compositions and resulting TEX86 values to growth temperature strongly diverge in three closely related thaumarchaeal pure cultures, i.e., Nitrosopumilus maritimus and two novel strains isolated from South Atlantic surface water, although the inventories of intact polar lipids and core lipids were overall similar in the three strains. N. maritimus and its closely related strain NAOA6 showed linear relationships of TEX86 and growth temperature but no correlation of TEX86 and temperature was observed in the more distantly related strain NAOA2. In contrast, the weighted average number of cyclopentane moieties (ring index) was linearly correlated with growth temperature in all strains. This disparate relationship of TEX86 to growth temperature among closely related Thaumarchaeota suggests that the ring index but not the TEX86 ratio represents a universal response to growth temperature in marine planktonic Thaumarchaeota. Furthermore, the distinct TEX86-temperature relationships in the cultivated strains indicate that environmental GDGT signals may include an ecological component, which has important implications for ocean temperature reconstructions using the TEX86 proxy. In contrast, different growth medium salinities in the range 27 to 51‰ tested for N. maritimus showed no systematic effect on intact polar GDGT composition and TEX86. Similarly, N. maritimus showed only small changes in intact polar GDGT composition and TEX86 when grown at different medium pH in the range 7.3 to 7.9. Overall, our pure culture studies suggest that the TEX86 paleotemperature proxy is not solely dependent on growth temperature, but may amalgamate physiological, environmental, and ecological factors.

Continue reading ‘Influence of temperature, pH, and salinity on membrane lipid composition and TEX86 of marine planktonic thaumarchaeal isolates’

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 to the abundance of microbial 16S rRNA 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 to 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 for blooms of microphytobenthos may prove useful as an indicator of CO2 leakage within coastal areas.

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Ocean acidification in the IPCC AR5 WG II

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