Role of n-DAMO in Mitigating Methane Emissions from Intertidal Wetlands Is Regulated by Saltmarsh Vegetations.

Coastal wetlands are hotspots for methane (CH4) production, reducing their potential for global warming mitigation. Nitrite/nitrate-dependent anaerobic methane oxidation (n-DAMO) plays a crucial role in bridging carbon and nitrogen cycles, contributing significantly to CH4 consumption. However, the role of n-DAMO in reducing CH4 emissions in coastal wetlands is poorly understood. Here, the ecological functions of the n-DAMO process in different saltmarsh vegetation habitats as well as bare mudflats were quantified, and the underlying microbial mechanisms were explored. Results showed that n-DAMO rates were significantly higher in vegetated habitats (Scirpus mariqueter and Spartina alterniflora) than those in bare mudflats (P < 0.05), leading to an enhanced contribution to CH4 consumption. Compared with other habitats, the contribution of n-DAMO to the total anaerobic CH4 oxidation was significantly lower in the Phragmites australis wetland (15.0%), where the anaerobic CH4 oxidation was primarily driven by ferric iron (Fe3+). Genetic and statistical analyses suggested that the different roles of n-DAMO in various saltmarsh wetlands may be related to divergent n-DAMO microbial communities as well as environmental parameters such as sediment pH and total organic carbon. This study provides an important scientific basis for a more accurate estimation of the role of coastal wetlands in mitigating climate change.

Potential response of dark carbon fixation to global warming in estuarine and coastal waters.

Dark carbon fixation (DCF), through which chemoautotrophs convert inorganic carbon to organic carbon, is recognized as a vital process of global carbon biogeochemical cycle. However, little is known about the response of DCF processes in estuarine and coastal waters to global warming. Using radiocarbon labelling method, the effects of temperature on the activity of chemoautotrophs were investigated in benthic water of the Yangtze estuarine and coastal areas. A dome-shaped thermal response pattern was observed for DCF rates (i.e., reduced rates at lower or higher temperatures), with the optimum temperature (Topt ) varying from about 21.9 to 32.0°C. Offshore sites showed lower Topt values and were more vulnerable to global warming compared with nearshore sites. Based on temperature seasonality of the study area, it was estimated that warming would accelerate DCF rate in winter and spring but inhibit DCF activity in summer and fall. However, at an annual scale, warming showed an overall promoting effect on DCF rates. Metagenomic analysis revealed that the dominant chemoautotrophic carbon fixation pathways in the nearshore area were Calvin-Benson-Bassham (CBB) cycle, while the offshore sites were co-dominated by CBB and 3-hydroxypropionate/4-hydroxybutyrate cycles, which may explain the differential temperature response of DCF along the estuarine and coastal gradients. Our findings highlight the importance of incorporating DCF thermal response into biogeochemical models to accurately estimate the carbon sink potential of estuarine and coastal ecosystems in the context of global warming.

Effects of Aquatic Acidification on Microbially Mediated Nitrogen Removal in Estuarine and Coastal Environments.

Acidification of estuarine and coastal waters is anticipated to influence nitrogen (N) removal processes, which are critical pathways for eliminating excess N from these ecosystems. We found that denitrification rates decreased significantly under acidified conditions (P < 0.05), which reduced by 41-53% in estuarine and coastal sediments under an approximately 0.3 pH reduction of the overlying water. However, the N removal rates through the anaerobic ammonium oxidation (anammox) process were concomitantly promoted under the same acidification conditions (increased by 47-109%, P < 0.05), whereas the total rates of N loss were significantly inhibited by aquatic acidification (P < 0.05), as denitrification remained the dominant N removal pathway. More importantly, the emission of nitrous oxide (N2O) from estuarine and coastal sediments was greatly stimulated by aquatic acidification (P < 0.05). Molecular analyses further demonstrated that aquatic acidification also altered the functional microbial communities in estuarine and coastal sediments; and the abundance of denitrifiers was significantly reduced (P < 0.05), while the abundance of anammox bacteria remained relatively stable. Collectively, this study reveals the effects of acidification on N removal processes and the underlying mechanisms and suggests that the intensifying acidification in estuarine and coastal waters might reduce the N removal function of these ecosystems, exacerbate eutrophication, and accelerate global climate change.

Microplastics promote methane emission in estuarine and coastal wetlands.

Increasing microplastic (MP) pollution poses significant threats to estuarine and coastal ecosystems. However, the effects of MPs on the emission of methane (CH4), a potent greenhouse gas, within these ecosystems and the underlying regulatory mechanisms have not been elucidated. Here, a combination of 13C stable isotope-based method and molecular techniques was applied to investigate how conventional petroleum-based MPs [polyethylene (PE) and polyvinyl chloride (PVC)] and biodegradable MPs [polylactic acid (PLA) and polyadipate/butylene terephthalate (PBAT)] regulate CH4 production and consumption and thus affect CH4 emission dynamics in estuarine and coastal wetlands. Results indicated that both conventional and biodegradable MPs enhanced the emission of CH4 (P < 0.05), with the promoting effect being more significant for biodegradable MPs. However, the mechanisms by which conventional and biodegradable MPs promote CH4 emissions were different. Specifically, conventional MPs stimulated the emission of CH4 by inhibiting the processes of CH4 consumption, but had no significant effect on CH4 production rate. Nevertheless, biodegradable MPs promoted CH4 emissions via accelerating the activities the methanogens while inhibiting the oxidation of CH4, thus resulting in a higher degree of promoting effect on CH4 emissions than conventional MPs. Consistently, quantitative PCR further revealed a significant increase in the abundance of methyl-coenzyme M reductase gene (mcrA) of methanogens under the exposure of biodegradable MPs (P < 0.05), but not conventional MPs. Furthermore, the relative abundance of most genes involved in CH4 oxidation exhibited varying degrees of reduction after exposure to all types of MPs, based on metagenomics data. This study reveals the effects of MPs on CH4 emissions in estuarine and coastal ecosystems and their underlying mechanisms, highlighting that the emerging biodegradable MPs exhibited a greater impact than conventional MPs on promoting CH4 emissions in these globally important ecosystems, thereby accelerating global climate change.

Active dark carbon fixation evidenced by 14C isotope assimilation and metagenomic data across the estuarine-coastal continuum.

Estuaries, as important land-ocean transitional zones across the Earth's surface, are hotspots of microbially driven dark carbon fixation (DCF), yet understanding of DCF process remains limited across the estuarine-coastal continuum. This study explored DCF activities and associated chemoautotrophs along the estuarine and coastal environmental gradients, using radiocarbon labelling and molecular techniques. Significantly higher DCF rates were observed at middle- and high-salinity regions (0.65-2.31 and 0.66-2.82 mmol C m-2 d-1, respectively), compared to low-salinity zone (0.07-0.19 mmol C m-2 d-1). Metagenomic analysis revealed relatively stable DCF pathways along the estuarine-coastal continuum, primarily dominated by Calvin-Benson-Bassham (CBB) cycle and Wood-Ljungdahl (WL) pathway. Nevertheless, chemoautotrophic communities driving DCF exhibited significant spatial variations. It is worth noting that although CBB cycle played an important role in DCF in estuarine sediments, WL pathway might play a more significant role, which has not been previously recognized. Overall, this study highlights that DCF activities coincide with the genetic potential of chemoautotrophy and the availability of reductive substrates across the estuarine-coastal continuum, and provides an important scientific basis for accurate quantitative assessment of global estuarine carbon sink.

Effects of periodic drying-wetting on microbial dynamics and activity of nitrite/nitrate-dependent anaerobic methane oxidizers in intertidal wetland sediments.

Nitrite/nitrate-dependent anaerobic methane oxidation (n-DAMO) plays an important role in methane (CH4) consumption in intertidal wetlands. However, little is known about the responses of n-DAMO in intertidal wetlands to periodic drying-wetting caused by tidal cycling. Here, comparative experiments (waterlogged, desiccated, reflooded) with the Yangtze estuarine intertidal sediments were performed to examine the effects of periodic tidal changes on n-DAMO microbial communities, abundances, and potential activities. Functional gene sequencing indicated the coexistence of n-DAMO bacteria and archaea in the tide-fluctuating environments and generally higher biodiversity under reflooded conditions than consecutive inundation or emersion. The n-DAMO microbial abundance and associated activity varied significantly during alternative exposure and inundation, with higher abundance and activity under the waterlogged than desiccated conditions. Reflooding of intertidal wetlands might intensify n-DAMO activities, indicating the resilience of n-DAMO microbial metabolisms to the wetting-drying events. Structural equation modeling and correlation analysis showed that n-DAMO activity was highly related to n-DAMO microbial abundance and substrate availability under inundation, whereas salt accumulation in sediment was the primary factor restraining n-DAMO activity under the desiccation. Overall, this study reveals tidal-induced shifts of n-DAMO activity and associated contribution to mitigating CH4, which may help accurately project CH4 emission from intertidal wetlands under different tidal scenarios.

Tidal dynamics regulates potential coupling of carbon­nitrogen­sulfur cycling microbes in intertidal flats.

Tide-driven hydrodynamic process causes significant geochemical gradients that influence biogeochemical cycling and ecological functioning of estuarine and coastal ecosystems. However, the effects of tidal dynamics on microbial communities, particularly at the functional gene level, remain unclear even though microorganisms play critical roles in biogeochemical carbon (C), nitrogen (N) and sulfur (S) cycling. Here, we used 16S rRNA gene amplicon sequencing and microarray-based approach to reveal the stratification of microorganisms related to C, N and S cycles along vertical redox gradients in intertidal wetlands. Alpha-diversity of bacteria and archaea was generally higher at the deep groundwater-sediment interface. Microbial compositions were markedly altered along the sediment profile, and these shifts were largely due to changes in nutrient availability and redox potential. Furthermore, functional genes exhibited redox partitioning between interfaces and transition layer, with abundant genes involved in C decomposition, methanogenesis, heterotrophic denitrification, sulfite reduction and sulfide oxidation existed in the middle anoxic zone. The influence of tidal dynamics on sediment function was highly associated with redox state, sediment texture, and substrates availability, leading to distinct distribution pattern of metabolic coupling of microbes involved in energy flux and elemental cycling in intertidal wetlands. These results indicate that tidal cycles are critical in determining microbial community and functional structure, and they provide new insights into sediment microbe-mediated biogeochemical cycling in intertidal habitats.

Effects of acidification on nitrification and associated nitrous oxide emission in estuarine and coastal waters.

In the context of an increasing atmospheric carbon dioxide (CO2) level, acidification of estuarine and coastal waters is greatly exacerbated by land-derived nutrient inputs, coastal upwelling, and complex biogeochemical processes. A deeper understanding of how nitrifiers respond to intensifying acidification is thus crucial to predict the response of estuarine and coastal ecosystems and their contribution to global climate change. Here, we show that acidification can significantly decrease nitrification rate but stimulate generation of byproduct nitrous oxide (N2O) in estuarine and coastal waters. By varying CO2 concentration and pH independently, an expected beneficial effect of elevated CO2 on activity of nitrifiers ("CO2-fertilization" effect) is excluded under acidification. Metatranscriptome data further demonstrate that nitrifiers could significantly up-regulate gene expressions associated with intracellular pH homeostasis to cope with acidification stress. This study highlights the molecular underpinnings of acidification effects on nitrification and associated greenhouse gas N2O emission, and helps predict the response and evolution of estuarine and coastal ecosystems under climate change and human activities.

Microbial abundance and activity of nitrite/nitrate-dependent anaerobic methane oxidizers in estuarine and intertidal wetlands: Heterogeneity and driving factors.

Nitrite/nitrate-dependent anaerobic methane oxidation (n-DAMO) is a crucial link between carbon and nitrogen cycles in estuarine and coastal ecosystems. However, the factors that affect the heterogeneous variability in n-DAMO microbial abundance and activity across estuarine and intertidal wetlands remain unclear. This study examined the spatiotemporal variations in n-DAMO microbial abundance and associated activity in different estuarine and intertidal habitats via quantitative PCR and 13C stable isotope experiments. The results showed that Candidatus 'Methylomirabilis oxyfera' (M. oxyfera)-like DAMO bacteria and Candidatus 'Methanoperedens nitroreducens' (M. nitroreducens)-like DAMO archaea cooccurred in estuarine and intertidal wetlands, with a relatively higher abundance of the M. oxyfera-like bacterial pmoA gene (4.0 × 106-7.6 × 107 copies g-1 dry sediment) than the M. nitroreducens-like archaeal mcrA gene (4.5 × 105-9.4 × 107 copies g-1 dry sediment). The abundance of the M. oxyfera-like bacterial pmoA gene was closely associated with sediment pH and ammonium (P<0.05), while no significant relationship was detected between M. nitroreducens-like archaeal mcrA gene abundance and the measured environmental parameters (P>0.05). High n-DAMO microbial activity was observed, which varied between 0.2 and 84.3 nmol 13CO2 g-1 dry sediment day-1 for nitrite-DAMO bacteria and between 0.4 and 32.6 nmol 13CO2 g-1 dry sediment day-1 for nitrate-DAMO archaea. The total n-DAMO potential tended to be higher in the warm season and in the upstream freshwater and low-salinity estuarine habitats and was significantly related to sediment pH, total organic carbon, Fe(II), and Fe(III) contents (P<0.05). In addition to acting as an important methane (CH4) sink, n-DAMO microbes had the potential to consume a substantial amount of reactive N in estuarine and intertidal environments, with estimated nitrogen elimination rates of 0.5-224.7 nmol N g-1 dry sediment day-1. Overall, our investigation reveals the distribution pattern and controlling factors of n-DAMO bioprocesses in estuarine and intertidal marshes and gains a better understanding of the coupling mechanisms between carbon and nitrogen cycles.

Crab bioturbation alters nitrogen cycling and promotes nitrous oxide emission in intertidal wetlands: Influence and microbial mechanism.

Intertidal wetlands provide important ecosystem functions by acting as nitrogen (N) cycling hotspots, which can reduce anthropogenic N loading from land to coastal waters. Benthic bioturbations are thought to play an important role in mediating N cycling in intertidal marshes. However, how the burrowing activity of benthos and their microbial symbionts affect N transformation and greenhouse gas nitrous oxide (N2O) emission remains unclear in these environments. Here, we show that bioturbation of crabs reshaped the structure of intertidal microbial communities and their N cycling function. Molecular analyses suggested that the microbially-driven N cycling might be accelerated by crab bioturbation, as the abundances of most of the N related functional genes were higher on the burrow wall than those in the surrounding bulk sediments, except for genes involved in N fixation, dissimilatory nitrate reduction to ammonium (DNRA), and N2O reduction, which were further confirmed by isotope-tracing experiments. Especially, the potential rates of the main N2O production pathways, nitrification and denitrification, were 2-3 times higher in the burrow wall sediments. However, even higher N2O emission rates (approximately 6 times higher) were observed in this unique microhabitat, which was due to a disproportionate increase in N2O production over N2O consumption driven by burrowing activity. In addition, the sources of N2O were also significantly affected by crab bioturbation, which increased the contribution of hydroxylamine oxidation pathway. This study reveals the mechanism through which benthic bioturbations mediate N cycling and highlights the importance of considering burrowing activity when evaluating the ecological function of intertidal wetlands.