Nitrogen loss by anaerobic ammonium oxidation in a mangrove wetland of the Zhangjiang Estuary, China

Microbially-driven phosphorus cycling and its coupling mechanisms with nitrogen cycling in mangrove sediments

The phosphorus (P) cycle plays a crucial role in the biogeochemical cycling of mangrove sediments. However, the diversity of microbially-driven P-cycling and its coupling with nitrogen (N)-cycling remain poorly understood. In this study, we used metagenomic approaches to investigate microbial P-cycling and its potential interactions with N-cycling in mangrove sediments. Our results revealed that pH, total carbon, and total nitrogen were key environmental factors influencing the diversity of P-cycling microbial communities. Phosphorus metabolic pathways differed among mangrove sediment depths. In surface sediments (0-5 cm), microbial communities primarily acquired readily available inorganic phosphorus, whereas, in deeper sediments (>60 cm), they hydrolyzed more persistent triphosphates, reabsorbed nucleotides, and sourced free phosphate, reflecting a shift in phosphorus transport modes. We also identified glutamate metabolism as a potential pathway linking P-cycling with N-cycling, with these functions co-occurring in both contigs and genomes. Additionally, the diversity of microbial communities associated with the P-cycling increased with sediment depth, suggesting that microbially-driven P-cycling diversifies as depth increases. This study provides new insights into P-cycling and its potential coupling with N-cycling through glutamate metabolism, its coupling with N-cycling through glutamate metabolism.

Nitrogen oxides emissions from coastal wetland sediments: Experimental assessment of the influence of vegetation and nitrogen input

Nitrogen oxides (NOx = NO + NO2) have essential impacts on global climate and the environment, making it essential to study the contribution of wetland-generated NOx to environmental problems. With exogenous nitrogen input from anthropogenic activities, wetland sediments become active emission hotspots for NOx. In this study, we conducted field experiments in a typical salt marsh wetland to measure nitric oxide (NO, the primary component of NOx from sediments) exchange fluxes in both mudflat and vegetated sediments. We found that NO fluxes in vegetated sediments (0.40 ± 0.15 × 10-12 kg N m-2 s-1) were relatively higher than in mudflat sediments (-1.31 ± 1.39 × 10-12 kg N m-2 s-1), with this difference occurring only during the vegetation-dying season (autumn). Correlations between sediment NO fluxes and environmental parameters revealed that NO flux variation during the observation period was primarily influenced by sediment respiration, temperature, water content, and substrate availability. However, the influence of these factors on NO fluxes differed between mudflat and vegetated sediments. In-situ data analysis also suggested that tidal horizontal migration, which affects sediment substrate and salinity, may regulate sediment NO emissions. Furthermore, in-situ incubations with nitrogen addition (ammonia, nitrite, and nitrate) were conducted to study the response of sediment NO emissions to exogenous nitrogen. We observed that nitrogen addition caused a 259.7 % increase in NO emissions from vegetated sediments compared to the control during the effective period of nitrogen addition (days 1-3). However, although nitrogen addition markedly stimulated sediment NO emissions, the overall NO production capacity constrained the extent of this increase.

Nitrogen Removal Performance and Microbial Community Structure of IMTA Ponds (Apostistius japonicus-Penaeus japonicus-Ulva)

Denitrification and anaerobic ammonium oxidation (anammox) are key processes for nitrogen removal in aquaculture, reducing the accumulated nitrogen nutrients to nitrogen gas or nitrous oxide gas. Complete removal of nitrogen from aquaculture systems is an important measure to solve environmental pollution. In order to evaluate the nitrogen removal potential of marine aquaculture ponds, this study investigated the denitrification and anammox rates, the flux of nitrous oxide (N2O) at the water-air interface, the sediment microbial community structure, and the gene expression associated with the nitrogen removal process in integrated multi-trophic aquaculture (IMTA) ponds (Apostistius japonicus-Penaeus japonicus-Ulva) with different culture periods. The results showed that the denitrification and anammox rates in sediments increased with the increase of cultivation periods and depth, and there was no significant difference in nitrous oxide gas flux at the water-air interface between different cultivation periods (p > 0.05). At the genus and phylum levels, the abundance of microorganisms related to nitrogen removal reactions in sediments changed significantly with the increase of cultivation period and depth, and was most significantly affected by the concentration of particulate organic nitrogen (PON) in sediments. The expression of denitrification gene (narG, nirS, nosZ) in surface sediments was significantly higher than that in deep sediments (p < 0.05), and was negatively correlated with denitrification rate. All samples had a certain anammox capacity, but no known anammox bacteria were found in the microbial diversity detection, and the expression of gene (hzsB) related to the anammox process was extremely low, which may indicate the existence of an unknown anammox bacterium. The data of this study showed that the IMTA culture pond had a certain potential for nitrogen removal, and whether it could make a contribution to reducing the pollution of culture wastewater still needed additional practice and evaluation, and also provided a theoretical basis for the nitrogen removal research of coastal mariculture ponds.

Sediment nitrates reduction processes affected by non-native Sonneratia apetala plantation in South China

Numerous studies have highlighted the importance of nitrates (NOx-) reduction processes in estuarine and coastal ecosystems over the past decades. However, the biotic and abiotic factors sediment NOx- reduction processes in mangrove of varying ages are still not fully understood. Here, we investigated the dynamics of sediment NOx- reduction processes and associated gene abundances in mangroves of different ages (including 0-year unvegetated mudflats, 10 and 20-years Sonneratia apetala, as well as >40 years of mature native Kandelia obovate) on the Qi'ao Island using 15N stable-isotope pairing techniques and quantitative PCR. The denitrification (2.64-11.30 nmol g-1 h-1), anammox (0.06-0.83 nmol g-1 h-1), and dissimilatory nitrate reduction to ammonium (DNRA, 0.58-16.34 nmol g-1 h-1) rates varied spatially and seasonally, but their contributions to the total NOx- reduction (DEN%, ANA%, and DNRA%), associated gene abundance (nirS, anammox 16S rRNA, and nrfA), and organic matter only varied spatially. Organic matter and microbial abundances are the dominating factors controlling N loss and retention. Without considering confounding factors, mangroves conservation and restoration significantly increased DNRA rates, NIRI (DNRA/(denitrification + anammox)), organic matter content, and microbial abundances (p < 0.05 for all), but reduced N loss rates. Mangroves conservation and restoration are estimated to have increased sediment N retention (~931.81 t N yr-1) and reduced N loss (~481.32 t N yr-1) in coastal wetlands of China over the past 40 years (1980-2020). Overall, our results indicate that mangrove restoration and conservation can significantly increase sediment N retention due to the rapid biomass accumulation, and it can provide more nutrients for mangrove and microorganism growth, thus creating a virtuous cycle in these N-limited ecosystems.

Tidal effects on carbon dioxide emission dynamics in intertidal wetland sediments

Understanding the control mechanisms of carbon dioxide (CO2) emissions in intertidal wetland sediments is beneficial for the concern of global carbon biogeochemistry and climate change. Nevertheless, multiple controls on CO2 emissions from intertidal wetland sediments to the atmosphere still need to be clarified. This study investigated the effect of tidal action on CO2 emissions from salt marsh sediments covered by Spartina alterniflora in the Jiaozhou Bay wetland using the static chamber method combined with an infrared CO2 detector. The results showed that the CO2 emission fluxes from the sediment during ebb tides were higher than those during flood tides. The whole wetland sediment acted as a weak source of atmospheric CO2 (average flux: 24.44 ± 16.80 mg C m-2 h-1) compared to terrestrial soils and was affected by the cycle of seawater inundation and exposure. The tidal influence on vertical dissolved inorganic carbon (DIC) transport in the sediment was also quantitated using a two-end member mixing model. The surface sediment layer (5-15 cm) with maximum DIC concentration during ebb tides became the one with minimum DIC concentration during flood tides, indicating the DIC transport from the surface sediment to seawater. Furthermore, aerobic respiration by microorganisms was the primary process of CO2 production in the sediment according to 16 S rDNA sequencing analysis. This study revealed the strong impact of tidal action on CO2 emissions from the wetland sediment and provided insights into the source-sink pattern of CO2 and DIC at the land-ocean interface.

Driving force of tidal pulses on denitrifiers-dominated nitrogen oxide emissions from intertidal wetland sediments

Intertidal wetland sediments are an important source of atmospheric nitrogen oxides (NOx), but their contribution to the global NOx budget remains unclear. In this work, we conducted year-round and diurnal observations in the intertidal wetland of Jiaozhou Bay to explore their regional source-sink patterns and influence factors on NOx emissions (initially in the form of nitric oxide) and used a dynamic soil reactor to further extend the mechanisms underlying the tidal pulse of nitric oxide (NO) observed in our investigations. The annual fluxes of NOx in the vegetated wetland were significantly higher than those in the wetland without vegetation. Their annual variations could be attributed to changes in temperature and the amount of organic carbon in the sediment, which was derived from vegetated plants and promoted the carbon-nitrogen cycle. Anaerobic denitrifiers had advantages in the intertidal wetland sediment and accounted for the major NO production (63.8 %) but were still limited by nitrite and nitrate concentrations in the sediment. Moreover, the tidal pulse was likely a primary driver of NOx emissions from intertidal wetlands over short periods, which was not considered in previous investigations. The annual NO exchange flux considering the tide pulse contribution (8.93 ± 1.72 × 10-2 kg N ha-1 yr-1) was significantly higher than that of the non-pulse period (4.14 ± 1.13 × 10-2 kg N ha-1 yr-1) in our modeling result for the fluxes over the last decade. Therefore, the current measurement of NOx fluxes underestimated the actual gas emission without considering the tidal pulse.

Ecological interactions and the underlying mechanism of anammox and denitrification across the anammox enrichment with eutrophic lake sediments

BACKGROUND

Increasing attention has recently been devoted to the anaerobic ammonium oxidation (anammox) in eutrophic lakes due to its potential key functions in nitrogen (N) removal for eutrophication control. However, successful enrichment of anammox bacteria from lake sediments is still challenging, partly due to the ecological interactions between anammox and denitrifying bacteria across such enrichment with lake sediments remain unclear.

RESULTS

This study thus designed to fill such knowledge gaps using bioreactors to enrich anammox bacteria with eutrophic lake sediments for more than 365 days. We continuously monitored the influent and effluent water, measured the anammox and denitrification efficiencies, quantified the anammox and denitrifying bacteria, as well as the related N cycling genes. We found that the maximum removal efficiencies of NH₄⁺ and NO₂^- reached up to 85.92% and 95.34%, respectively. Accordingly, the diversity of anammox and denitrifying bacteria decreased significantly across the enrichment, and the relative dominant anammox (e.g., Candidatus Jettenia) and denitrifying bacteria (e.g., Thauera, Afipia) shifted considerably. The ecological cooperation between anammox and denitrifying bacteria tended to increase the microbial community stability, indicating a potential coupling between anammox and denitrifying bacteria. Moreover, the nirS-type denitrifiers showed stronger coupling with anammox bacteria than that of nirK-type denitrifiers during the enrichment. Functional potentials as depicted by metagenome sequencing confirmed the ecological interactions between anammox and denitrification. Metagenome-assembled genomes-based ecological model indicated that the most dominant denitrifiers could provide various materials such as amino acid, cofactors, and vitamin for anammox bacteria. Cross-feeding in anammox and denitrifying bacteria highlights the importance of microbial interactions for increasing the anammox N removal in eutrophic lakes.

CONCLUSIONS

This study greatly expands our understanding of cooperation mechanisms among anammox and denitrifying bacteria during the anammox enrichment with eutrophic lake sediments, which sheds new insights into N removal for controlling lake eutrophication. Video Abstract.

Vertically stratified methane, nitrogen and sulphur cycling and coupling mechanisms in mangrove sediment microbiomes

BACKGROUND

Mangrove ecosystems are considered as hot spots of biogeochemical cycling, yet the diversity, function and coupling mechanism of microbially driven biogeochemical cycling along the sediment depth of mangrove wetlands remain elusive. Here we investigated the vertical profile of methane (CH₄), nitrogen (N) and sulphur (S) cycling genes/pathways and their potential coupling mechanisms using metagenome sequencing approaches.

RESULTS

Our results showed that the metabolic pathways involved in CH₄, N and S cycling were mainly shaped by pH and acid volatile sulphide (AVS) along a sediment depth, and AVS was a critical electron donor impacting mangrove sediment S oxidation and denitrification. Gene families involved in S oxidation and denitrification significantly (P < 0.05) decreased along the sediment depth and could be coupled by S-driven denitrifiers, such as Burkholderiaceae and Sulfurifustis in the surface sediment (0-15 cm). Interestingly, all S-driven denitrifier metagenome-assembled genomes (MAGs) appeared to be incomplete denitrifiers with nitrate/nitrite/nitric oxide reductases (Nar/Nir/Nor) but without nitrous oxide reductase (Nos), suggesting such sulphide-utilizing groups might be an important contributor to N₂O production in the surface mangrove sediment. Gene families involved in methanogenesis and S reduction significantly (P < 0.05) increased along the sediment depth. Based on both network and MAG analyses, sulphate-reducing bacteria (SRB) might develop syntrophic relationships with anaerobic CH₄ oxidizers (ANMEs) by direct electron transfer or zero-valent sulphur, which would pull forward the co-existence of methanogens and SRB in the middle and deep layer sediments.

CONCLUSIONS

In addition to offering a perspective on the vertical distribution of microbially driven CH₄, N and S cycling genes/pathways, this study emphasizes the important role of S-driven denitrifiers on N₂O emissions and various possible coupling mechanisms of ANMEs and SRB along the mangrove sediment depth. The exploration of potential coupling mechanisms provides novel insights into future synthetic microbial community construction and analysis. This study also has important implications for predicting ecosystem functions within the context of environmental and global change. Video Abstract.

Coupling effects of nitrate reduction and sulfur oxidation in a subtropical marine mangrove ecosystem with Spartina alterniflora invasion

The mangrove ecosystem has a high nitrate reduction capacity, which significantly alleviates severe nitrogen pollution. However, current research on nitrate reduction mechanisms in the mangrove ecosystem is limited. Furthermore, Spartina alterniflora invasion has disrupted the balance of the mangrove ecosystem and the effect of S. alterniflora on nitrate reduction has not yet been fully elucidated. Nitrate reduction was comprehensively investigated in a subtropical mangrove ecosystem in this study, which has been invaded by S. alterniflora for 40 years. Results showed that S. alterniflora significantly increased the relative and absolute abundance of nitrate reduction genes, especially nirS (nitrite reductase), in the mangrove ecosystem. Dissimilatory nitrate reduction to ammonium was the main pathway of nitrate reduction in the mangrove ecosystem. Nitrate reduction was mainly performed by Desulfobacterales and occurred in the shallow layers (0-10 cm) of mangrove sediments. A strong positive correlation was found between nitrate reduction and sulfur oxidation (especially sulfide oxidation), and the sulfide content was significantly positively correlated with the relative abundance of nitrate reduction genes. Moreover, 207 metagenomic assembled genomes (MAGs) were constructed, including 50 MAGs with high numbers (≥ 10) of nitrate reduction genes. This finding indicates that the dominant microbes had strong nitrate reduction potential in mangrove sediments. Our findings highlight the impact of S. alterniflora invasion on nitrate reduction in a subtropical marine mangrove ecosystem. This study provides new insights into our understanding of nitrogen pollution control and contributes to the exploration of new nitrogen-degrading microbes in mangrove ecosystems.

Temperature drives the assembly of Bacillus community in mangrove ecosystem

Mangroves are located at the interface of terrestrial and marine environments, and experience fluctuating conditions, creating a need to better explore the relative role of the bacterial community. Bacillus has been reported to be the dominant group in the mangrove ecosystem and plays a key role in maintaining the biodiversity and function of the mangrove ecosystem. However, studies on bacterial and Bacillus community across four seasons in the mangrove ecosystem are scarce. Here, we employed seasonal large-scale sediment samples collected from the mangrove ecosystem in southeastern China and utilized 16S rRNA gene amplicon sequencing to reveal bacterial and Bacillus community structure changes across seasons. Compared with the whole bacterial community, we found that Bacillus community was greatly affected by season (temperature) rather than site. The key factors, NO₃-N and NH₄-N showed opposite interaction with superabundant taxa Bacillus taxa (SAT) and three rare Bacillus taxa including high rare taxa (HRT), moderate rare taxa (MRT) and low rare taxa (LRT). Network analysis suggested the co-occurrence of Bacillus community and Bacillus-bacteria, and revealed SAT had closer relationship compared with rare Bacillus taxa. HRT might act crucial response during the temperature decreasing process across seasons. This study fills a gap in addressing the assembly of Bacillus community and their role in maintaining microbial diversity and function in mangrove ecosystem.

Metagenomic insights into comparative study of nitrogen metabolic potential and microbial community between primitive and urban river sediments

As a result of anthropogenic pollution, the nitrogen nutrients load in urban rivers has increased, potentially raising the risk of river eutrophication. Here, we studied how anthropogenic impacts alter nitrogen metabolism in river sediments by comparing the metagenomic function of microbial communities between relatively primitive and human-disturbed sediments. The contents of organic matter (OM), total nitrogen (TN), NO₃^--N and NO₂^--N were higher in primitive site than in polluted sites, which might be due to vegetation density, sediment type, hydrology, etc. Whereas, NH₄⁺-N content was higher in midstream and downstream, indicating that nitrogen loading increased in the anthropogenic regions and subsequently leading higher NH₄⁺-N. Hierarchical cluster analyses revealed significant changes in the community structure and functional potential between the primitive and human-affected sites. Metagenomic analysis demonstrated that Demequina, Streptomyces, Rubrobacter and Dechloromonas were the predominant denitrifiers. Ardenticatena and Dechloromonas species were the most important contributors to dissimilatory nitrate reduction. Furthermore, anthropogenic pollution significantly increased their abundance, and resulting in a decrease in NO₃^-, NO₂^--N and an increase in NH₄⁺-N contents. Additionally, the SOX metabolism of Dechloromonas and Sulfuritalea may involve in the sulfur-dependent autotrophic denitrification process by coupling the conversion of thiosulfate to sulfate with the reduction of NO₃^--N to N₂. From pristine to anthropogenic pollution sediments, the major nitrifying bacteria harboring Hao transitioned from Nitrospira to Nitrosomonas. This study sheds light on the consequences of anthropogenic activities on nitrogen metabolism in river sediments, allowing for better management of nitrogen pollution and eutrophication in river.

Evaluation of PCR primers for detecting the distribution of nitrifiers in mangrove sediments

Ammonia-oxidizing archaea and ammonia-oxidizing bacteria (AOA and AOB), complete ammonia oxidizers (Comammox), and nitrite-oxidizing bacteria (NOB) play a crucial role in the nitrification process during the nitrogen cycle. However, their occurrence and diversity in mangrove ecosystems are still not fully understood. Here, a total of 11 pairs of PCR primers were evaluated to study the distribution and abundances of these nitrifiers in rhizosphere and non-rhizosphere sediments of a mangrove ecosystem. The amplification efficiency of these 11 pairs of primers was first evaluated and their performances were found to vary considerably. The CamoA-19F/CamoA-616R primer pair was suitable for the amplification of AOA in mangrove sediments, especially on the surface of rhizosphere sediments. Primer pair amoA1F/amoA2R was better for the characterization of novel AOB in the bacterial community of non-rhizosphere sediments of mangroves. In contrast, primer nxrB169F/nxrB638R showed a low abundance of NOB in mangrove sediments (except for R1). Comammox bacteria were abundant and diverse in mangrove sediments, as indicated by both the amoB gene for Comammox clade A and the amoA gene for Comammox Nitrospira clade B. However, the amoA gene for Comammox Nitrospira clade A was not successful in detecting them in the mangrove sediments. Furthermore, 568 operational taxonomic units (OTUs) were obtained by generating a clone library and a high abundance of OTUs was correlated with ammonium, pH, NO₂^-, and NO₃^-. Comammox and Comammox Nitrospira were identified by phylogenetic tree analysis, indicating that mangrove sediments harbor newly discovered nitrifiers. Additionally, many AOA and NOB were mainly distributed in the surface layer of the rhizosphere, whereas AOB and Comammox Nitrospira were in the subsurface of non-rhizosphere, as determined by qPCR analysis. Collectively, our findings highlight the limitations of some primers for the identification of specific nitrifying bacteria. Therefore, primers must be carefully selected to gain accurate insights into the ecological distribution of nitrifiers in mangroves. KEY POINTS: • Several sets of PCR primers perform well for the detection of nitrifiers in mangroves. • Mangroves are an important source of newly discovered nitrifiers. • Ammonium, pH, NO₂^-, and NO₃^- are important shapers of nitrifier communities in mangroves.

Effect of Aquaculture Reclamation on Sediment Nitrates Reduction Processes in Mangrove Wetland

Sediment denitrification, anaerobic ammonium oxidation (anammox), and nitrate dissimilation to ammonium (DNRA) play an important role in controlling the dynamics of nitrates (NOx−) and their fate in estuarine and coastal ecosystems. However, the effects of land-use change on NOx− reduction processes in mangrove sediments are still unclear. Here, we used a mud experiment method combined with a 15N stable isotope tracer method to study the mechanism and ecological environment of the change of land use pattern on the sediment NOx− reduction processes in mangrove wetlands. Our study showed that most physicochemical parameters, NOx− reduction rates, and their gene abundances varied considerably. The denitrification, anammox, and DNRA rates in mangrove sediment cores were in a range of 1.04–4.24 nmol g−1 h−1, 0.14–0.36 nmol g−1 h−1, and 0–2.72 nmol g−1 h−1, respectively. The denitrification, anammox, and DNRA rates in aquaculture sediment cores were in a range of 1.06–10.96 nmol g−1 h−1, 0.13–0.37 nmol g−1 h−1, and 0–1.96 nmol g−1 h−1, respectively. The highest values of denitrification, anammox, DNRA, the contribution of denitrification and DNRA to total NOx− reduction (DEN% and DNRA%), gene abundances (nirS, Amx 16S rRNA, and nrfA), total organic carbon (TOC), total nitrogen (TN), and TOC/TN in sediments were generally found in the top layer (0–5 cm) and then decreased with depth, while the contribution of anammox to total NOx− reduction (ANA%), Fe2+, and Fe2+/Fe3+ were generally increased with sediment depth in both mangrove and aquaculture ecosystems. When mangrove wetlands are transformed into pools, some properties (including TOC, TN, and Fe3+), DNRA rates, DRNA%, and nrfA gene abundances were decreased, while some properties (including NH4+, TOC/TN, Fe2+, and Fe2+/Fe3+), denitrification rates, DEN%, nirS, and ANAMMOX 16S gene abundances were increased. Sediment organic matter (TOC and TN) content and Fe2+ both affected NO3− reduction rates, with organic matter the most prominent factor. Thus, aquaculture reclamation enhances N loss while reducing N retention in sediments of mangrove wetlands, which plays an important role in regulating the source and fate of reactive N in mangrove ecosystems.

Effects of nitrogen on the longitudinal and vertical patterns of the composition and potential function of bacterial and archaeal communities in the tidal mudflats

Increasing attention has been focused on the diminishing health of coastal ecosystems. Understanding the effects of eutrophication on tidal flat ecosystems is beneficial for the restoration and management of coastal ecosystems. However, previous studies did not consider the effects of nitrogen on the structure and function of bacterial and archaeal communities in longitudinal and vertical profiles. Here, the diversity, composition, assembly mechanism, and potential metabolic function of the bacterial and archaeal communities were studied in two longitudinal tidal sections at different eutrophic levels. Nitrogen and salinity were the critical factors that influenced the bacterial and archaeal community composition using canonical correspondence and multivariate regression tree analyses. For the bacterial community, the higher nitrogen loading in tidal mudflats resulted in the convergence of diversity and structure in the longitudinal profile of bacteria, but divergence was detected in the vertical profile. For archaea, the diversity tended to be convergent in longitudinal and vertical profiles in the higher nitrogen area, but the change of structure was similar to that of bacteria. Besides the homogeneous processes influenced by salinity, the assembly process of the bacterial community was mainly influenced by heterogeneous selection (34.8%) and that of archaea by dispersal limitation (19.5%). However, the bacterial and archaeal communities in the higher nitrogen section presented more of an influence of heterogeneous selection (respectively, 39 and 5.6%) than that of the lower nitrogen section (respectively, 10 and 0.2%). Structural equation modeling indicated that nitrogen may have inhibited the effects of the bacterial community on nitrogen turnover in nitrogen-rich anoxic sediment environments, but may have strengthened the effect of the archaeal community on carbon metabolism compared to bacteria. This work deepens our understanding of the responses of bacterial and archaeal community structure and potential function to nitrogen pollution in tidal mudflats.

Ecological Role of Bacteria Involved in the Biogeochemical Cycles of Mangroves Based on Functional Genes Detected through GeoChip 5.0

Mangroves provide a variety of ecosystem services and contribute greatly to the global biogeochemical cycle. Microorganisms play important roles in biogeochemical cycles and maintain the dynamic balance of mangroves. However, the roles of bacteria in the biogeochemical cycles of mangroves and their ecological distribution and functions remain largely uncharacterized. This study thus sought to analyze and compare the ecological distributions and potential roles of bacteria in typical mangroves using 16S rRNA gene amplicon sequencing and GeoChip. Interestingly, the bacterial community compositions were largely similar in the studied mangroves, including Shenzhen, Yunxiao, Zhanjiang, Hainan, Hongkong, Fangchenggang, and Beihai mangroves. Moreover, gamma-proteobacterium_uncultured and Woeseia were the most abundant microorganisms in the mangroves. Furthermore, most of the bacterial communities were significantly correlated with phosphorus levels (P < 0.05; −0.93 < R < 0.93), suggesting that this nutrient is a vital driver of bacterial community composition. Additionally, GeoChip analysis indicated that the functional genes amyA, narG, dsrA, and ppx were highly abundant in the studied mangroves, suggesting that carbon degradation, denitrification, sulfite reduction, and polyphosphate degradation are crucial processes in typical mangroves. Moreover, several genera were found to synergistically participate in biogeochemical cycles in mangroves. For instance, Neisseria, Ruegeria, Rhodococcus, Desulfotomaculum, and Gordonia were synergistically involved in the carbon, nitrogen, and sulfur cycles, whereas Neisseria and Treponema were synergistically involved in the nitrogen cycle and the sulfur cycle. Taken together, our findings provide novel insights into the ecological roles of bacteria in the biogeochemical cycles of mangroves.

IMPORTANCE Bacteria have important functions in biogeochemical cycles, but studies on their function in an important ecosystem, mangroves, are still limited. Here, we investigated the ecological role of bacteria involved in biogeochemical cycles in seven representative mangroves of southern China. Furthermore, various functional genes from bacteria involved in biogeochemical cycles were identified by GeoChip 5.0. The functional genes associated with the carbon cycle (particularly carbon degradation) were the most abundant, suggesting that carbon degradation is the most active process in mangroves. Additionally, some high-abundance bacterial populations were found to synergistically mediate key biogeochemical cycles in the mangroves, including Neisseria, Pseudomonas, Treponema, Desulfotomaculum, and Nitrosospira. In a word, our study gives novel insights into the function of bacteria in biogeochemical cycles in mangroves.

Restoration impacts on rates of denitrification and greenhouse gas fluxes from tropical coastal wetlands

Forested coastal wetlands are globally important systems sequestering carbon and intercepting nitrogen pollution from nutrient-rich river systems. Coastal wetlands that have suffered extensive disturbance are the target of comprehensive restoration efforts. Accurate assessment of restoration success requires detailed mechanistic understanding of wetland soil biogeochemical functioning across restoration chrono-sequences, which remains poorly understood for these sparsely investigated systems. This study investigated denitrification and greenhouse gas fluxes in mangrove and Melaleuca forest soils of Vietnam, using the ¹⁵N-Gas flux method. Denitrification-derived N₂O was significantly higher from Melaleuca than mangrove forest soils, despite higher potential rates of total denitrification in the mangrove forest soils (8.1 ng N g^-1 h^-1) than the Melaleuca soils (6.8 ng N g^-1 h^-1). Potential N₂O and CO₂ emissions were significantly higher from the Melaleuca soils than from the mangrove soils. Disturbance and subsequent recovery had no significant effect on N biogeochemistry except with respect to the denitrification product ratio in the mangrove sites, which was highest from the youngest mangrove site. Potential CO₂ and CH₄ fluxes were significantly affected by restoration in the mangrove soils. The lowest potential CO₂ emissions were observed in the mid-age plantation and potential CH₄ fluxes decreased in the older forests. The mangrove system, therefore, may remove excess N and improve water quality with low greenhouse gas emissions, whereas in Melaleucas, increased N₂O and CO₂ emissions also occur. These emissions are likely balanced by higher carbon stocks observed in the Melaleuca soils. These mechanistic insights highlight the importance of ecosystem restoration for pollution attenuation and reduction of greenhouse gas emissions from coastal wetlands. Restoration efforts should continue to focus on increasing wetland area and function, which will benefit local communities with improved water quality and potential for income generation under future carbon trading.

Salinity-driven nitrogen removal and its quantitative molecular mechanisms in artificial tidal wetlands

The present study investigated the performance in nitrogen removal and associated nitrogen transformation processes in seven mesocosms fed with saline water (0‰ to 30‰) to simulate tidal flow constructed wetlands (TF CWs). The highly effective and steady removal of NH₄⁺-N (84.74% averagely) was obtained at various salinities, while the rates varied from 6.34% to 89.19% and 22.54% to 87.48% for NO₃^--N and total nitrogen (TN), respectively. Overall, nitrogen removal efficiencies were greater at lower salinities. Molecular biological analyses verified the co-occurrence of dissimilatory nitrate reduction to ammonium (DNRA), denitrification, anaerobic ammonium oxidation (anammox) and nitrification in the mesocosms, reportedly contributing to nitrogen removal in TF CWs. The absolute copy numbers of nitrogen functional genes and total bacterial 16S rRNA were 2.54 × 10³-7.35 × 10⁷ and 3.21 × 10⁷-7.82 × 10⁹ copies g^-1 dg (dry gravel), respectively, with the dominant phyla, i.e., Chloroflexi, Proteobacteria, Actinobacteriota, Cyanobacteria, and Firmicutes, accounting for over 80% of the sequences. The relative abundances of the genera related to nitrification and dissimilatory nitrate reduction processes, i.e., denitrification, anammox and DNRA, varied from 0.16% to 0.89% and from 3.66% to 11.59%, respectively, while quantitative relationships confirmed NH₄⁺-N transformation rate was jointly controlled by amoA, hzsB, nxrA and nrfA, and NO₃^--N removal rate by nirS, nosZ, narG, qnorB and nxrA. These findings may shed light on quantitative molecular mechanisms for nitrogen removal in TF CWs for the saline water treatment, providing a sustainable solution to nitrogen pollution problem in the estuary ecosystem.

Molecular analysis of microbial nitrogen transformation and removal potential in mangrove wetlands under anthropogenic nitrogen input

Mangrove ecosystems are natural nitrogen removal systems that are primarily mediated by nitrogen cycle microorganisms, but their relative contributions to nitrogen transformation and removal in mangrove sediments under anthropogenic nitrogen input needs further resolution and characterization. Here, we investigated the responses and the relative contributions of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), anaerobic ammonium oxidizing (anammox) bacteria and denitrifying bacteria after spiking urea into mangrove sediments incubated in a laboratory microcosm experiment for four weeks. During incubation, the diversity, abundances and transcription levels of the hzo genes for anammox bacteria, amoA genes for AOA and AOB, and nirS genes for denitrifying bacteria were monitored using targeted gene clone library analyses and quantitative PCR assays at the DNA and RNA levels. The results showed that mangrove sediments harbour habitat-specific anammox bacteria which related to Candidatus Scalindua and Candidatus Kuenenia clades. Mangrove specific AOA related to deep branched clades within Candidatus Nitrososphaera and Candidatus Nitrosotalea, and AOB related to Nitrosomonas and Nitrosospira were also detected in the collected sediment samples. Growth and activity of AOA were detected at all levels of amendment of nitrogen input, whereas AOB growth was detectable only at the high-level nitrogen input (1.5 mg urea per gram of dry sediment) with no amoA transcripts and lower abundance than AOA. The abundance and transcription levels of the nirS gene were higher (~1000 times) than those of the hzo gene in all groups. Pearson correlation analysis demonstrated that the abundance of both AOA and AOB amoA genes had a significant positive correlation with the nirS gene (p < 0.01). These results indicated that nitrification (primarily mediated by the AOA)-denitrification process played the most important role in nitrogen removal from the amendment of nitrogen short-term input in the mangrove sediments.

Nitrogen removal through collaborative microbial pathways in tidal flow constructed wetlands

Constructed wetlands are efficient in removing nitrogen from water; however, little is known about nitrogen-cycling pathways for nitrogen loss from tidal flow constructed wetlands. This study conducted molecular and stable isotopic analyses to investigate potential dissimilatory nitrate reduction to ammonium (DNRA), denitrification, nitrification, anaerobic ammonium oxidation (anammox), and their contributions to nitrogen removal by two tidal wetland mesocosms, PA (planted with Phragmites australis) and NP (unplanted), designated to treat Yangtze River Estuary water. Our results show the mesocosms removed ~22.6% of TN from nitrate-dominated river water (1.19 mg·L^-1), with better performance obtained in PA than that in NP, which was consistent with the molecular and stable isotopic data. The potential activities of DNRA, anammox, denitrification and nitrification varied between 0.6 and 1.6, 4.6-37.3, 36.4-305.7, and 463.7-945.9 nmol N₂ g^-1 dry soil d^-1, respectively, with higher values obtained in PA than NP. Nitrification accounted for 94.3-99.4% of NH₄⁺ oxidation, with the rest through anammox. Denitrification contributed to 77.9-90.3% of NO_x^- reduction, compared to 9.2-21.6% and 0.5-1.5% via anammox and DNRA, respectively; 78.4-90.9% of N₂ was produced through denitrification, with the rest via anammox. Pearson correlation analyses suggest NH₄⁺ was the major factor regulating nitrification, while NO₃^- played an important role in the competition between denitrification and DNRA, and NO₂^- was a key restrictive factor for anammox. Overall, this study reveals the importance of nitrification, denitrification, anammox and DNRA in nitrogen removal, providing new insight into the nitrogen-cycling mechanisms in natural/artificial tidal wetlands.

Nitrogen Cycling and Mass Balance in the World’s Mangrove Forests

Nitrogen (N) cycling in mangroves is complex, with rapid turnover of low dissolved N concentrations, but slow turnover of particulate N. Most N is stored in soils. The largest sources of N are nearly equal amounts of mangrove and benthic microalgal primary production. Dissolved N fluxes between the forests and tidal waters show net uptake, indicating N conservation. N2-fixation is underestimated as rapid rates measured on tree stems, aboveground roots and cyanobacterial mats cannot currently be accounted for at the whole-forest scale due to their extreme patchiness and the inability to extrapolate beyond a localized area. Net immobilization of NH4+ is the largest ecosystem flux, indicating N retention. Denitrification is the largest loss of N, equating to 35% of total N input. Burial equates to about 29% of total inputs and is the second largest loss of N. Total inputs slightly exceed total outputs, currently suggesting net N balance in mangroves. Mangrove PON export equates to ≈95% of PON export from the world’s tropical rivers, but only 1.5% of the entire world’s river discharge. Mangrove N2O emissions, denitrification, and burial contribute 0.4%, 0.5–2.0% and 6%, respectively, to the global coastal ocean, which are disproportionate to their small worldwide area.

Riverine microplastic pollution matters: A case study in the Zhangjiang River of Southeastern China

Microplastics have pulled the alarm for its far-reaching impacts in the environment and potential risks to human health. Here, we first investigated the microplastic pollution in the Zhangjiang River of southeastern China. Water samples were collected across a river catchment using bulk sampling method. The abundance, distribution, and characteristics of microplastics were analyzed using stereomicroscopy and micro-Raman spectroscopy. The results indicated that microplastic abundance ranged from 50 to 725 items m^-3 with an average of 246 items m^-3. PP and PE were the major polymers and accounted for ~75%. The dominant shape, color, and size of microplastics are fragment, white, and 0.5-1 mm, respectively. The findings established the baseline information on the microplastic pollution in the Zhangjiang River, which may improve the knowledge of sources of microplastic debris to the local watershed and future evaluation on the role of river catchments in transporting microplastics to the estuary and beyond into the ocean.

Soil anammox and denitrification processes connected with N cycling genes co-supporting or contrasting under different water conditions

The anaerobic ammonium oxidizing bacteria (anammox) are the hidden culprit behind the excessive nitrogen loss under a favorable environment, since their detection and abundance get disturbed by several unknown factors. This study intends to find the gap between actual anammox working capacity under different water conditions and fertilizers in the laboratory. The ¹⁵N-isotopic tracer technique was used to measure anammox and denitrification rate, and anammox community structure was analyzed through high-throughput sequencing with cytochrome cd-1 nitrite reductase functional gene (an_nirS gene, initially found in Candidatus Scalindua). The experiment consisted of four treatments, i.e., (I) CK_ Control, (II) UR_Urea, (III) PM_Pig Manure, and (IV) SRF_ Slow release fertilizer, under two water conditions, i.e., (a) Continuous flooding_ CF, (b) Alternate wetting and drying_ AWD. Results showed that anammox under CF decreased over time by -40.24%, and denitrification increased up to 39.25%. However, anammox activity under AWD increased up to 10.62% with the availability of NO₂^-, and surprisingly accompanied by the reduction in denitrification loss (-31.97%), being the most critical factor. We found that soil nifH and AOB genes were strongly favorable for anammox activity, while we observed the presence of anammox and AOB genes co-existing at the same time in paddy soil. The high-throughput sequencing with an_nirS functional gene showed a much higher diversity of anammox genera ever reported, mostly uncultured and unidentified. We concluded that water management is more prominent than fertilizer for anammox, and the most critical factor is the duration of AWD cycle, because of short term air supply could boost anammox activity and gene abundance, and could reduce denitrifier activity as well as nirK gene abundance.

Revealing structure and assembly for rhizophyte-endophyte diazotrophic community in mangrove ecosystem after introduced Sonneratia apetala and Laguncularia racemosa

Biological nitrogen fixation (BNF) mediated by diazotrophic communities is a major source of bioavailable nitrogen in mangrove wetlands, which plays important roles in maintaining the health and stability of mangrove ecosystems. Recent large-scale mangrove afforestation activities have drawn great attention due to introduced mangrove species and their potential impacts on bio-functionalities of local ecosystems. However, the effects of introduced mangrove species on diazotrophic communities remain unclear. Here, we analyzed rhizosphere and endosphere diazotrophic communities between native mangrove species (Avicennia marina) and introduced mangrove species (Sonneratia apetala and Laguncularia racemose) by sequencing nifH gene amplicons. Our results showed that S. apetala and L. racemose introduction significantly (P < 0.05) increased nutrition components (e.g., total carbon and total nitrogen) in rhizosphere, as well as the diazotrophs richness in rhizosphere and endosphere. The relative abundance of clusters III diazotrophs in the rhizosphere and Rhizobium in the endosphere were significantly increased with L. racemosa or S. apetala introduction. Fe and pH were the main environmental factors driving the divergence of endophyte-rhizophyte diazotrophs between native and introduced mangroves. The correlation-based network analyses indicated that the interaction among rhizophyte-endophyte diazotrophs is more harmonious in native mangrove, while there exist more competition in introduced mangroves. These findings expand our current understanding of BNF in mangrove afforestation, and providing new perspectives to sustainable management of mangrove ecosystem.

Depth-specific distribution and significance of nitrite-dependent anaerobic methane oxidation process in tidal flow constructed wetlands used for treating river water

Tidal flow constructed wetlands (TF CWs) have been considered an effective approach to treat contaminated river water, as well as a significant role in global matter cycles, especially for carbon and nitrogen. Notably, it has been thought that methane oxidation was completely catalyzed by the aerobic process, ignoring the anaerobic methane oxidation, such as the nitrite-dependent anaerobic methane oxidation (n-damo) process. In our current work, therefore, we used molecular and stable isotopes to investigate the biodiversity, quantity and potential rate of n-damo bacteria in the TF CWs located in the Xisha Wetland Park in the Yangtze River estuary, China. The results revealed that n-damo process was active in the collected soil cores, with a decreasing trend along water depths and rates ranging from 8.48 to 23.45 nmol CO₂ g^-1 dry soil d^-1. The n-damo bacterial contributions to CH₄ oxidation and N₂ production in TF CWs reached 9.49-26.26% and 20.73-47.11%, respectively, suggesting that n-damo bacteria was an important nitrogen and methane sink in the TF CWs, but had been previously overlooked. The copy numbers of total bacterial 16S rRNA and pmoA genes were 1.84-11.21 × 10⁹ and 0.59-2.72 × 10⁶ copies g^-1 ds, respectively, as the higher abundance was found in the soil at lower water levels during tidal submergence. Diverse n-damo bacterial 16S rRNA gene sequences belonged to group B, C and D were measured, and it was found that group B and C were the most frequently measured n-damo clusters in the TF CWs. In addition, nitrite was the key factor regulating the n-damo bacterial distribution in the TF CWs. This study would broaden our horizons and help us better understand the nitrogen and methane cycles in tidal ecosystems.