Bioturbation determines the response of benthic ammonia-oxidizing microorganisms to ocean acidification

Ocean warming and acidification adjust inter- and intra-specific variability in the functional trait expression of polar invertebrates

Climate change is known to affect the distribution and composition of species, but concomitant alterations to functionally important aspects of behaviour and species-environment relations are poorly constrained. Here, we examine the ecosystem ramifications of changes in sediment-dwelling invertebrate bioturbation behaviour-a key process mediating nutrient cycling-associated with near-future environmental conditions (+ 1.5 °C, 550 ppm [pCO2]) for species from polar regions experiencing rapid rates of climate change. We find that responses to warming and acidification vary between species and lead to a reduction in intra-specific variability in behavioural trait expression that adjusts the magnitude and direction of nutrient concentrations. Our analyses also indicate that species behaviour is not predetermined, but can be dependent on local variations in environmental history that set population capacities for phenotypic plasticity. We provide evidence that certain, but subtle, aspects of inter- and intra-specific variation in behavioural trait expression, rather than the presence or proportional representation of species per se, is an important and under-appreciated determinant of benthic biogeochemical responses to climate change. Such changes in species behaviour may act as an early warning for impending ecological transitions associated with progressive climate forcing.

Structurally stable but functionally disrupted marine microbial communities under a future climate change scenario: Potential importance for nitrous oxide emissions

The blue mussel Mytilus edulis is a widespread and abundant bivalve species along the North Sea with high economic and ecological importance as an engineer species. The shell of mussels is intensively colonized by microbial organisms that can produce significant quantities of nitrous oxide (N2O), a potent greenhouse gas. To characterize the impacts of climate change on the composition, structure and functioning of microbial biofilms on the shell surface of M. edulis, we experimentally exposed them to orthogonal combinations of increased seawater temperature (20 vs. 23 °C) and decreased pH (8.0 vs. 7.7) for six weeks. We used amplicon sequencing of the 16S rRNA gene to characterize the alpha and beta diversity of microbial communities on the mussel shell. The functioning of microbial biofilms was assessed by measuring aerobic respiration and nitrogen emission rates. We did not report any significant impacts of climate change treatments on the diversity of mussel microbiomes nor on the structure of these communities. Lowered pH and increased temperature had antagonistic effects on the functioning of microbial communities with decreased aerobic respiration and N2O emission rates of microbial biofilms in acidified seawater compared to increased rates in warmer conditions. An overriding impact of acidification over warming was finally observed on N2O emissions when the two factors were combined. Although acidification and warming in combination significantly reduced N2O biofilm emissions, the promotion of aquaculture activities in coastal waters where shellfish do not normally occur at high biomass and density could nonetheless result in unwanted emissions of this greenhouse gas in a near future.

Nutrient exchanges at the sediment-water interface and the responses to environmental changes in the Yellow Sea and East China Sea

Release from the sediment is an important nutrient source to the water column of global oceans, especially for marginal seas with active biogeochemical processes. Benthic nutrient biogeochemistry and its responses to environmental changes were investigated in the eastern marginal seas of China using a two-layer diffusion-advection-reaction diagenetic model. Overall, the sediment represented the primary nutrient source with fluxes of ~-342 ± 197, -1.25 ± 0.50, and -114 ± 56 × 10⁸ mol/month for dissolved inorganic nitrogen (DIN), phosphate, and silicate, respectively. This could contribute up to ~42% of nutrients requested by primary production (PP), with a DIN/SiO₃^2-/PO₄^3- molar ratio of 273:91:1, which was higher than that in the overlying water (49:47:1). Future benthic nutrient fluxes were predicted under two environmental change scenarios (increasing and decreasing PP and biogenic silica). Our study may help rebuild nutrient budgets in the future and formulate environmental management policies in marginal seas.

Warming, but Not Acidification, Restructures Epibacterial Communities of the Baltic Macroalga Fucus vesiculosus With Seasonal Variability

Due to ocean acidification and global warming, surface seawater of the western Baltic Sea is expected to reach an average of ∼1100 μatm pCO2 and an increase of ∼5°C by the year 2100. In four consecutive experiments (spanning 10-11 weeks each) in all seasons within 1 year, the abiotic factors temperature (+5°C above in situ) and pCO2 (adjusted to ∼1100 μatm) were tested for their single and combined effects on epibacterial communities of the brown macroalga Fucus vesiculosus and on bacteria present in the surrounding seawater. The experiments were set up in three biological replicates using the Kiel Outdoor Benthocosm facility (Kiel, Germany). Phylogenetic analyses of the respective microbiota were performed by bacterial 16S (V1-V2) rDNA Illumina MiSeq amplicon sequencing after 0, 4, 8, and 10/11 weeks per season. The results demonstrate (I) that the bacterial community composition varied in time and (II) that relationships between operational taxonomic units (OTUs) within an OTU association network were mainly governed by the habitat. (III) Neither single pCO2 nor pCO2:Temperature interaction effects were statistically significant. However, significant impact of ocean warming was detected varying among seasons. (IV) An indicator OTU (iOTU) analysis identified several iOTUs that were strongly influenced by temperature in spring, summer, and winter. In the warming treatments of these three seasons, we observed decreasing numbers of bacteria that are commonly associated with a healthy marine microbial community and-particularly during spring and summer-an increase in potentially pathogenic and bacteria related to intensified microfouling. This might lead to severe consequences for the F. vesiculosus holobiont finally affecting the marine ecosystem.

Benthic-based contributions to climate change mitigation and adaptation

Innovative solutions to improve the condition and resilience of ecosystems are needed to address societal challenges and pave the way towards a climate-resilient future. Nature-based solutions offer the potential to protect, sustainably manage and restore natural or modified ecosystems while providing multiple other benefits for health, the economy, society and the environment. However, the implementation of nature-based solutions stems from a discourse that is almost exclusively derived from a terrestrial and urban context and assumes that risk reduction is resolved locally. We argue that this position ignores the importance of complex ecological interactions across a range of temporal and spatial scales and misses the substantive contribution from marine ecosystems, which are notably absent from most climate mitigation and adaptation strategies that extend beyond coastal disaster management. Here, we consider the potential of sediment-dwelling fauna and flora to inform and support nature-based solutions, and how the ecology of benthic environments can enhance adaptation plans. We illustrate our thesis with examples of practice that are generating, or have the potential to deliver, transformative change and discuss where further innovation might be applied. Finally, we take a reflective look at the realized and potential capacity of benthic-based solutions to contribute to adaptation plans and offer our perspectives on the suitability and shortcomings of past achievements and the prospective rewards from sensible prioritization of future research. This article is part of the theme issue 'Climate change and ecosystems: threats, opportunities and solutions'.

Ocean acidification and hypoxia alter organic carbon fluxes in marine soft sediments

Anthropogenic stressors can alter the structure and functioning of infaunal communities, which are key drivers of the carbon cycle in marine soft sediments. Nonetheless, the compounded effects of anthropogenic stressors on carbon fluxes in soft benthic systems remain largely unknown. Here, we investigated the cumulative effects of ocean acidification (OA) and hypoxia on the organic carbon fate in marine sediments, through a mesocosm experiment. Isotopically labelled macroalgal detritus (¹³ C) was used as a tracer to assess carbon incorporation in faunal tissue and in sediments under different experimental conditions. In addition, labelled macroalgae (¹³ C), previously exposed to elevated CO₂ , were also used to assess the organic carbon uptake by fauna and sediments, when both sources and consumers were exposed to elevated CO₂ . At elevated CO₂ , infauna increased the uptake of carbon, likely as compensatory response to the higher energetic costs faced under adverse environmental conditions. By contrast, there was no increase in carbon uptake by fauna exposed to both stressors in combination, indicating that even a short-term hypoxic event may weaken the ability of marine invertebrates to withstand elevated CO₂ conditions. In addition, both hypoxia and elevated CO₂ increased organic carbon burial in the sediment, potentially affecting sediment biogeochemical processes. Since hypoxia and OA are predicted to increase in the face of climate change, our results suggest that local reduction of hypoxic events may mitigate the impacts of global climate change on marine soft-sediment systems.

Calcium carbonate alters the functional response of coastal sediments to eutrophication-induced acidification

Coastal ocean acidification research is dominated by laboratory-based studies that cannot necessarily predict real-world ecosystem response given its complexity. We enriched coastal sediments with increasing quantities of organic matter in the field to identify the effects of eutrophication-induced acidification on benthic structure and function, and assess whether biogenic calcium carbonate (CaCO₃) would alter the response. Along the eutrophication gradient we observed declines in macrofauna biodiversity and impaired benthic net primary productivity and sediment nutrient cycling. CaCO₃ addition did not alter the macrofauna community response, but significantly dampened negative effects on function (e.g. net autotrophy occurred at higher levels of organic matter enrichment in +CaCO₃ treatments than −CaCO₃ (1400 vs 950 g dw m⁻²)). By identifying the links between eutrophication, sediment biogeochemistry and benthic ecosystem structure and function in situ, our study represents a crucial step forward in understanding the ecological effects of coastal acidification and the role of biogenic CaCO₃ in moderating responses.

The absence of the pCO2 effect on dissolved 134Cs uptake in select marine organisms

Ocean acidification have been shown to not affect the capacity of bivalves to bioaccumulation ¹³⁴Cs in their tissue; but as this was studied on only one species to date. There is therefore a need to verify if this holds true for other bivalve species or other marine invertebrates. The present short communication confirms that in the scallop Mimachlamys varia and the prawn Penaeus japonicus, two species that supposedly have a record to preferentially concentrates this radionuclide, that bioconcentration of ¹³⁴Cs was shown not to be influenced by a decreasing pH (and thereby increasing seawater pCO₂). Although the dissolved ¹³⁴Cs was taken up in a similar manner under different pH values (8.1, 7.8, and 7.5) in both species, being described by a saturation state equilibrium model, the species displayed different bioconcentration capacities of ¹³⁴Cs: CF_ss in the prawns was approximately 10-fold higher than in scallops. Such results suggest that the Cs bioconcentration capacity are mainly dependent of the taxa and that uptake processes are independent the physiological ones involved in the biological responses of prawns and scallops to ocean acidification.

Independent and interactive effects of reduced seawater pH and oil contamination on subsurface sediment bacterial communities

Ocean acidification may exacerbate the environmental impact of oil hydrocarbon pollution by disrupting the core composition of the superficial (0-1 cm) benthic bacterial communities. However, at the subsurface sediments (approximately 5 cm below sea floor), the local biochemical characteristics and the superjacent sediment barrier may buffer these environmental changes. In this study, we used a microcosm experimental approach to access the independent and interactive effects of reduced seawater pH and oil contamination on the composition of subsurface benthic bacterial communities, at two time points, by 16S rRNA gene-based high-throughput sequencing. An in-depth taxa-specific variance analysis revealed that the independent effects of reduced seawater pH and oil contamination were significant predictors of changes in the relative abundance of some specific bacterial groups (e.g., Firmicutes, Rhizobiales, and Desulfobulbaceae). However, our results indicated that the overall microbial community structure was not affected by independent and interactive effects of reduced pH and oil contamination. This study provides evidence that bacterial communities inhabiting subsurface sediment may be less susceptible to the effects of oil contamination in a scenario of reduced seawater pH.

The response of the marine nitrogen cycle to ocean acidification

Ocean acidification (OA), arising from the influx of anthropogenically generated carbon, poses a massive threat to the ocean ecosystems. Our knowledge of the effects of elevated anthropogenic CO₂ in marine waters and its effect on the performance of single species, trophic interactions, and ecosystems is increasing rapidly. However, our understanding of the biogeochemical cycling of nutrients such as nitrogen is less advanced and lacks a comprehensive overview of how these processes may change under OA. We conducted a systematic review and meta-analysis of eight major nitrogen transformation processes incorporating 49 publications to synthesize current scientific understanding of the effect of OA on nitrogen cycling in the future ocean by 2100. The following points were identified by our meta-analysis: (a) Diazotrophic nitrogen fixation is likely enhanced by 29% ± 4% under OA; (b) species- and strain-specific responses of nitrogen fixers to OA were detectable, which may result in alterations in microbial community composition in the future ocean; (c) nitrification processes were reduced by a factor of 29% ± 10%; (d) declines in nitrification rates were not reflected by nitrifier abundance; and (e) contrasting results in unispecific culture experiments versus natural communities were apparent for nitrogen fixation and denitrification. The net effect of the nitrogen cycle process responses also suggests there may be a shift in the relative nitrogen pools, with excess ammonium originating from CO₂ -fertilized diazotrophs. This regenerated inorganic nitrogen may recycle in the upper water column increasing the relative importance of the ammonium-fueled regenerated production. However, several feedback mechanisms with other chemical cycles, such as oxygen, and interaction with other climate change stressors may counteract these findings. Finally, our review highlights the shortcomings and gaps in current understanding of the potential changes in nitrogen cycling under future climate and emphasizes the need for further ecosystem studies.

Organic Matter Regulates Ammonia-Oxidizing Bacterial and Archaeal Communities in the Surface Sediments of Ctenopharyngodon idellus Aquaculture Ponds

Ammonia-oxidizing bacteria (AOB) and archaea (AOA) play important roles in nitrogen removal in aquaculture ponds, but their distribution and the environmental factors that drive their distribution are largely unknown. In this study, we collected surface sediment samples from Ctenopharyngodon idellus ponds in three different areas in China that practice aquaculture. The community structure of AOB and AOA and physicochemical characteristics in the ponds were investigated. The results showed that AOA were more abundant than AOB in all sampling ponds except one, but sediment AOB and AOA numbers varied greatly between ponds. Correlation analyses indicated a significant correlation between the abundance of AOB and arylsulfatase, as well as the abundance of AOA and total nitrogen (TN) and arylsulfatase. In addition, AOB/AOA ratio was found to be significantly correlated with the microbial biomass carbon. AOB were grouped into seven clusters affiliated to Nitrosospira and Nitrosomonas, and AOA were grouped into six clusters affiliated to Nitrososphaera, Nitrososphaera sister group, and Nitrosopumilus. AOB/AOA diversity in the surface sediments of aquaculture ponds varied according to the levels of total organic carbon (TOC), and AOB and AOA diversity was significantly correlated with arylsulfatase and β-glucosidase, respectively. The compositions of the AOB communities were also found to be significantly influenced by sediment eutrophic status (TOC and TN levels), and pH. In addition, concentrations of acid phosphatase and arylsulfatase in surface sediments were significantly correlated with the prominent bacterial amoA genotypes, and concentrations of TOC and urease were found to be significantly correlated with the prominent archaeal amoA genotype compositions. Taken together, our results indicated that AOB and AOA communities in the surface sediments of Ctenopharyngodon idellus aquaculture ponds are regulated by organic matter and its availability to the microorganisms.

Influence of Macrofaunal Burrows on Extracellular Enzyme Activity and Microbial Abundance in Subtropical Mangrove Sediment

Bioturbation and bioirrigation induced by burrowing macrofauna are recognized as important processes in aquatic sediment since macrofaunal activities lead to the alteration of sediment characteristics. However, there is a lack of information on how macrofauna influence microbial abundance and extracellular enzyme activity in mangrove sediment. In this study, the environmental parameters, extracellular enzyme activities, and microbial abundance were determined and their relationships were explored. Sediment samples were taken from the surface (S) and lower layer (L) without burrow, as well as crab burrow wall (W) and bottom of crab burrow (B) located at the Mai Po Nature Reserve, Hong Kong. The results showed that the burrowing crabs could enhance the activities of oxidase and hydrolases. The highest activities of phenol oxidase and acid phosphatase were generally observed in B sediment, while the highest activity of N-acetyl-glucosaminidase was found in W sediment. The enzymatic stoichiometry indicated that the crab-affected sediment had similar microbial nitrogen (N) and phosphorous (P) availability relative to carbon (C), lower than S but higher than L sediment. Furthermore, it was found that the highest abundance of both bacteria and fungi was shown in S sediment, and B sediment presented the lowest abundance. Moreover, the concentrations of phosphorus and soluble phenolics in crab-affected sediment were almost higher than the non-affected sediment. The alterations of phenolics, C/P and N/P ratios as well as undetermined environmental factors by the activities of crabs might be the main reasons for the changes of enzyme activity and microbial abundance. Finally, due to the important role of phenol oxidase and hydrolases in sediment organic matter (SOM) decomposition, it is necessary to take macrofaunal activities into consideration when estimating the C budget in mangrove ecosystem in the future.

Effects of sub-seabed CO2 leakage: Short- and medium-term responses of benthic macrofaunal assemblages

The continued rise in atmospheric carbon dioxide (CO₂) levels is driving climate change and temperature shifts at a global scale. CO₂ Capture and Storage (CCS) technologies have been suggested as a feasible option for reducing CO₂ emissions and mitigating their effects. However, before CCS can be employed at an industrial scale, any environmental risks associated with this activity should be identified and quantified. Significant leakage of CO₂ from CCS reservoirs and pipelines is considered to be unlikely, however direct and/or indirect effects of CO₂ leakage on marine life and ecosystem functioning must be assessed, with particular consideration given to spatial (e.g. distance from the source) and temporal (e.g. duration) scales at which leakage impacts could occur. In the current mesocosm experiment we tested the potential effects of CO₂ leakage on macrobenthic assemblages by exposing infaunal sediment communities to different levels of CO₂ concentration (400, 1000, 2000, 10,000 and 20,000 ppm CO₂), simulating a gradient of distance from a hypothetic leakage, over short-term (a few weeks) and medium-term (several months). A significant impact on community structure, abundance and species richness of macrofauna was observed in the short-term exposure. Individual taxa showed idiosyncratic responses to acidification. We conclude that the main impact of CO₂ leakage on macrofaunal assemblages occurs almost exclusively at the higher CO₂ concentration and over short time periods, tending to fade and disappear at increasing distance and exposure time. Although under the cautious perspective required by the possible context-dependency of the present findings, this study contributes to the cost-benefit analysis (environmental risk versus the achievement of the intended objectives) of CCS strategies.

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.

Effects of CO2 enrichment on benthic primary production and inorganic nitrogen fluxes in two coastal sediments

Ocean acidification may alter the cycling of nitrogen in coastal sediment and so the sediment-seawater nitrogen flux, an important driver of pelagic productivity. To investigate how this perturbation affects the fluxes of NOX- (nitrite/nitrate), NH4+ and O2, we incubated estuarine sand and subtidal silt in recirculating seawater with a CO2-adjusted pH of 8.1 and 7.9. During a 41-day incubation, the seawater kept at pH 8.1 lost 97% of its NOX- content but the seawater kept at pH 7.9 lost only 18%. Excess CO2 increased benthic photosynthesis. In the silt, this was accompanied by a reversal of the initial NOX- efflux into influx. The estuarine sand sustained its initial NOX- influx but, by the end of the incubation, released more NH4+ at pH 7.9 than at pH 8.1. We hypothesise that these effects share a common cause; excess CO2 increased the growth of benthic microalgae and so nutrient competition with ammonia oxidising bacteria (AOB). In the silt, diatoms likely outcompeted AOB for NH4+ and photosynthesis increased the dark/light fluctuations in the pore water oxygenation inhibiting nitrification and coupled nitrification/denitrification. If this is correct, then excess CO2 may lead to retention of inorganic nitrogen adding to the pressures of increasing coastal eutrophication.

Small-scale variation of ammonia oxidisers within intertidal sediments dominated by ammonia-oxidising bacteria Nitrosomonas sp. amoA genes and transcripts

While numerous studies have investigated the abundance of ammonia oxidising bacteria and archaea (AOB/AOA) via the ammonia monooxygenase gene amoA, less is known about their small-scale variation and if amoA gene abundance equates to activity. Here we present a spatial and temporal study of ammonia oxidation in two small intertidal bays, Rusheen and Clew bay, Ireland. Potential Nitrification Rate (PNR) was ten-fold higher in Rusheen bay (Clew: 0.27 ± SD 0.55; Rusheen: 2.46 ± SD 3.4 NO2- µg-1 g-1 day-1, P < 0.001) than in Clew bay but amoA gene abundances were similar between bays, and comparable to those in other coastal ecosystems. Within bays AOB genes increased towards the muddy sediments and were positively correlated with PNR and pH. Less spatial variation was observed in AOA abundances which nevertheless positively correlated with pH and temperature and negatively with salinity and ammonia. Transcriptionally active AOB and AOA were quantified from all sites in Rusheen bay, February 2014, following the general trends observed at DNA level. AOB phylotypes predominantly from the known Nitrosomonas group were distributed across the bay, while Nitrosomonas group B phylotypes were absent from low salinity sites. AOA genes and transcripts were primarily affiliated with Thaumarchaeota group I.1a.

Faunal Burrows Alter the Diversity, Abundance, and Structure of AOA, AOB, Anammox and n-Damo Communities in Coastal Mangrove Sediments

In the present work, the diversity, community structures, and abundances of aerobic ammonia-oxidizing archaea (AOA) and bacteria (AOB), anaerobic ammonium-oxidizing (anammox) bacteria, and denitrifying anaerobic methane oxidization (n-damo) bacteria were unraveled in the bioturbated areas of the coastal Mai Po mangrove sediments. Results indicated that the bioturbation by burrowing in mangrove sediments was associated with higher concentration of NH₄⁺ but lower concentrations of both NO₂^- and NO₃^-, and increase in diversity and richness of both AOA and AOB, but relatively lower diversity and richness of n-damo bacteria. The phylotypes of anammox bacterial community were significantly increased while their phylogenetic lineages observed in the less bioturbated areas were also maintained. Infauna also showed a great impact on the composition of n-damo bacterial phylotypes and burrowing activity altered the n-damo community structure profoundly in the sampled areas. The communities of n-damo bacteria in the surrounding bulk sediments showed similar structures to marine n-damo communities, but those on the burrow wall and in the ambient surface layer had a freshwater pattern, which was different from previous findings in Mai Po wetland. On the other hand, the abundances of AOA, AOB, and n-damo bacteria were greatly stimulated on burrow walls while the abundance of anammox bacteria remained unchanged. Infaunal burrows and mangrove roots affected the relative abundance of AOA and AOB. The benthic infauna stimulated the abundances of AOA, AOB, anammox, and n-damo bacteria. Furthermore, NH₄⁺ and NO₂^- were important environmental factors changing the structure of each group. The communities of anammox and n-damo bacteria in bioturbated areas showed a competitive relationship.

Vulnerability of macronutrients to the concurrent effects of enhanced temperature and atmospheric pCO2 in representative shelf sea sediment habitats

Fundamental changes in seawater carbonate chemistry and sea surface temperatures associated with the ocean uptake of anthropogenic CO2 are accelerating, but investigations of the susceptibility of biogeochemical processes to the simultaneous occurrence of multiple components of climate change are uncommon. Here, we quantify how concurrent changes in enhanced temperature and atmospheric pCO2, coupled with an associated shift in macrofaunal community structure and behavior (sediment particle reworking and bioirrigation), modify net carbon and nutrient concentrations (NH4-N, NOx-N, PO4-P) in representative shelf sea sediment habitats (mud, sandy-mud, muddy-sand and sand) of the Celtic Sea. We show that net concentrations of organic carbon, nitrogen and phosphate are, irrespective of sediment type, largely unaffected by a simultaneous increase in temperature and atmospheric pCO2. However, our analyses also reveal that a reduction in macrofaunal species richness and total abundance occurs under future environmental conditions, varies across a gradient of cohesive to non-cohesive sediments, and negatively moderates biogeochemical processes, in particular nitrification. Our findings indicate that future environmental conditions are unlikely to have strong direct effects on biogeochemical processes but, particularly in muddy sands, the abundance, activity, composition and functional role of invertebrate communities are likely to be altered in ways that will be sufficient to regulate the function of the microbial community and the availability of nutrients in shelf sea waters.

Quantification of the effects of ocean acidification on sediment microbial communities in the environment: the importance of ecosystem approaches

To understand how ocean acidification (OA) influences sediment microbial communities, naturally CO2-rich sites are increasingly being used as OA analogues. However, the characterization of these naturally CO2-rich sites is often limited to OA-related variables, neglecting additional environmental variables that may confound OA effects. Here, we used an extensive array of sediment and bottom water parameters to evaluate pH effects on sediment microbial communities at hydrothermal CO2 seeps in Papua New Guinea. The geochemical composition of the sediment pore water showed variations in the hydrothermal signature at seep sites with comparable pH, allowing the identification of sites that may better represent future OA scenarios. At these sites, we detected a 60% shift in the microbial community composition compared with reference sites, mostly related to increases in Chloroflexi sequences. pH was among the factors significantly, yet not mainly, explaining changes in microbial community composition. pH variation may therefore often not be the primary cause of microbial changes when sampling is done along complex environmental gradients. Thus, we recommend an ecosystem approach when assessing OA effects on sediment microbial communities under natural conditions. This will enable a more reliable quantification of OA effects via a reduction of potential confounding effects.

Impact of CO2 leakage from sub-seabed carbon dioxide capture and storage (CCS) reservoirs on benthic virus-prokaryote interactions and functions

Atmospheric CO₂ emissions are a global concern due to their predicted impact on biodiversity, ecosystems functioning, and human life. Among the proposed mitigation strategies, CO₂ capture and storage, primarily the injection of CO₂ into marine deep geological formations has been suggested as a technically practical option for reducing emissions. However, concerns have been raised that possible leakage from such storage sites, and the associated elevated levels of pCO₂ could locally impact the biodiversity and biogeochemical processes in the sediments above these reservoirs. Whilst a number of impact assessment studies have been conducted, no information is available on the specific responses of viruses and virus–host interactions. In the present study, we tested the impact of a simulated CO₂ leakage on the benthic microbial assemblages, with specific focus on microbial activity and virus-induced prokaryotic mortality (VIPM). We found that exposure to levels of CO₂ in the overlying seawater from 1,000 to 20,000 ppm for a period up to 140 days, resulted in a marked decrease in heterotrophic carbon production and organic matter degradation rates in the sediments, associated with lower rates of VIPM, and a progressive accumulation of sedimentary organic matter with increasing CO₂ concentrations. These results suggest that the increase in seawater pCO₂ levels that may result from CO₂ leakage, can severely reduce the rates of microbial-mediated recycling of the sedimentary organic matter and viral infections, with major consequences on C cycling and nutrient regeneration, and hence on the functioning of benthic ecosystems.

Empirical evidence reveals seasonally dependent reduction in nitrification in coastal sediments subjected to near future ocean acidification

Research so far has provided little evidence that benthic biogeochemical cycling is affected by ocean acidification under realistic climate change scenarios. We measured nutrient exchange and sediment community oxygen consumption (SCOC) rates to estimate nitrification in natural coastal permeable and fine sandy sediments under pre-phytoplankton bloom and bloom conditions. Ocean acidification, as mimicked in the laboratory by a realistic pH decrease of 0.3, significantly reduced SCOC on average by 60% and benthic nitrification rates on average by 94% in both sediment types in February (pre-bloom period), but not in April (bloom period). No changes in macrofauna functional community (density, structural and functional diversity) were observed between ambient and acidified conditions, suggesting that changes in benthic biogeochemical cycling were predominantly mediated by changes in the activity of the microbial community during the short-term incubations (14 days), rather than by changes in engineering effects of bioturbating and bio-irrigating macrofauna. As benthic nitrification makes up the gross of ocean nitrification, a slowdown of this nitrogen cycling pathway in both permeable and fine sediments in winter, could therefore have global impacts on coupled nitrification-denitrification and hence eventually on pelagic nutrient availability.

Long-term effects of warming and ocean acidification are modified by seasonal variation in species responses and environmental conditions

Warming of sea surface temperatures and alteration of ocean chemistry associated with anthropogenic increases in atmospheric carbon dioxide will have profound consequences for a broad range of species, but the potential for seasonal variation to modify species and ecosystem responses to these stressors has received little attention. Here, using the longest experiment to date (542 days), we investigate how the interactive effects of warming and ocean acidification affect the growth, behaviour and associated levels of ecosystem functioning (nutrient release) for a functionally important non-calcifying intertidal polychaete (Alitta virens) under seasonally changing conditions. We find that the effects of warming, ocean acidification and their interactions are not detectable in the short term, but manifest over time through changes in growth, bioturbation and bioirrigation behaviour that, in turn, affect nutrient generation. These changes are intimately linked to species responses to seasonal variations in environmental conditions (temperature and photoperiod) that, depending upon timing, can either exacerbate or buffer the long-term directional effects of climatic forcing. Taken together, our observations caution against over emphasizing the conclusions from short-term experiments and highlight the necessity to consider the temporal expression of complex system dynamics established over appropriate timescales when forecasting the likely ecological consequences of climatic forcing.

Bioturbation determines the response of benthic ammonia-oxidizing microorganisms to ocean acidification

Ocean acidification (OA), caused by the dissolution of increasing concentrations of atmospheric carbon dioxide (CO2) in seawater, is projected to cause significant changes to marine ecology and biogeochemistry. Potential impacts on the microbially driven cycling of nitrogen are of particular concern. Specifically, under seawater pH levels approximating future OA scenarios, rates of ammonia oxidation (the rate-limiting first step of the nitrification pathway) have been shown to dramatically decrease in seawater, but not in underlying sediments. However, no prior study has considered the interactive effects of microbial ammonia oxidation and macrofaunal bioturbation activity, which can enhance nitrogen transformation rates. Using experimental mesocosms, we investigated the responses to OA of ammonia oxidizing microorganisms inhabiting surface sediments and sediments within burrow walls of the mud shrimp Upogebia deltaura. Seawater was acidified to one of four target pH values (pHT 7.90, 7.70, 7.35 and 6.80) in comparison with a control (pHT 8.10). At pHT 8.10, ammonia oxidation rates in burrow wall sediments were, on average, fivefold greater than in surface sediments. However, at all acidified pH values (pH ≤ 7.90), ammonia oxidation rates in burrow sediments were significantly inhibited (by 79-97%; p < 0.01), whereas rates in surface sediments were unaffected. Both bacterial and archaeal abundances increased significantly as pHT declined; by contrast, relative abundances of bacterial and archaeal ammonia oxidation (amoA) genes did not vary. This research suggests that OA could cause substantial reductions in total benthic ammonia oxidation rates in coastal bioturbated sediments, leading to corresponding changes in coupled nitrogen cycling between the benthic and pelagic realms.