Denitrification prevails over anammox in tropical mangrove sediments (Goa, India)

Living in mangroves: a syntrophic scenario unveiling a resourceful microbiome

BACKGROUND

Mangroves are complex and dynamic coastal ecosystems under frequent fluctuations in physicochemical conditions related to the tidal regime. The frequent variation in organic matter concentration, nutrients, and oxygen availability, among other factors, drives the microbial community composition, favoring syntrophic populations harboring a rich and diverse, stress-driven metabolism. Mangroves are known for their carbon sequestration capability, and their complex and integrated metabolic activity is essential to global biogeochemical cycling. Here, we present a metabolic reconstruction based on the genomic functional capability and flux profile between sympatric MAGs co-assembled from a tropical restored mangrove.

RESULTS

Eleven MAGs were assigned to six Bacteria phyla, all distantly related to the available reference genomes. The metabolic reconstruction showed several potential coupling points and shortcuts between complementary routes and predicted syntrophic interactions. Two metabolic scenarios were drawn: a heterotrophic scenario with plenty of carbon sources and an autotrophic scenario with limited carbon sources or under inhibitory conditions. The sulfur cycle was dominant over methane and the major pathways identified were acetate oxidation coupled to sulfate reduction, heterotrophic acetogenesis coupled to carbohydrate catabolism, ethanol production and carbon fixation. Interestingly, several gene sets and metabolic routes similar to those described for wastewater and organic effluent treatment processes were identified.

CONCLUSION

The mangrove microbial community metabolic reconstruction reflected the flexibility required to survive in fluctuating environments as the microhabitats created by the tidal regime in mangrove sediments. The metabolic components related to wastewater and organic effluent treatment processes identified strongly suggest that mangrove microbial communities could represent a resourceful microbial model for biotechnological applications that occur naturally in the environment.

Microplastics strengthen nitrogen retention by intensifying nitrogen limitation in mangrove ecosystem sediments

Mangrove wetlands are hotspots of the global nitrogen (N) cycle and important sinks of microplastics (MPs) due to their ecotone location between terrestrial and marine ecosystems. However, the effects of MPs on N cycle processes in mangrove ecosystems are still poorly understood. Thus, the present study assessed the impacts by adding MPs to mangrove sediments in a microcosm incubation experiment. The results showed that MPs increased dissolved organic carbon and nitrate but reduced ammonium contents in the sediments. MPs increased C:N stoichiometric and N:C-acquiring enzymatic ratios, indicating an intensified N limitation in mangrove sediments following exposure of MPs. MPs decreased microbial community diversity and shifted sediment microbial communities from r- to K-strategists, consistent with the intensified N limitation. In response, dissimilatory nitrate reduction to ammonium (DNRA) rates increased while nitrous oxide (N2O) production reduced suggesting more efficient N utilization in MPs treatments. The MPs with heteroatoms such as PLA- and PVC-MPs, increased DNRA rates by 67.5-78.7%, exhibiting a stronger impact than PE-MPs. The variation partitioning analysis revealed that the variances of DNRA rates and N2O production could be attributed to synergistic effects of physicochemical properties, nutrient limitation, and microbial community in mangrove sediments. Overall, this study provides pertinent insights into the impacts of MPs as a new carbon source on nutrient limitation and N turnover in mangrove ecosystems.

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.

Estuarine benthic habitats provide an important ecosystem service regulating the nitrogen cycle

Globally, a key ecosystem service provided by sedimentary estuarine habitats is the regulation of nutrient cycles. The nitrogen (N) cycle is driven by complex biogeochemical transformations within these sediments-including nitrogen fixation, denitrification, assimilation and anaerobic ammonia oxidation-mediated by microorganisms. Evaluating ecosystem processes and their functional value is a knowledge gap for the wet-dry tropics and even more limited for macrotidal estuaries. The capacity of these important environments to withstand and assimilate increasing nitrogenous loads as a consequence of accelerating development pressures in tropical Australia is largely unknown. Because of the critical role nitrogen cycling plays in estuarine ecosystems, identifying important habitats that underpin N cycling, particularly denitrification known to mitigate anthropogenic N inputs, is important. Detailed benthic habitat mapping of the Darwin-Bynoe region of northern Australia has provided a rare opportunity to demarcate its key habitats, such as intertidal mudflats, seagrass, mangroves, reef and saltmarsh. Combined with new measurements of benthic nitrogen fluxes, it has been possible for the first time to map these processes and develop a simple integrated functional value for N cycling across key benthic habitats of a tropical macrotidal estuary. Maps generated in this process have provided broadscale identification of the functional importance of habitats with relevance to N removal processes. The role of intertidal sediments in denitrification has been highlighted. Furthermore, the study emphasises connectivity across benthic seascapes, where multiple services are likely to interact, in supporting overall function and ecosystem health. The distillation of composite processes in this mapping format allows resource managers and scientists to communicate outputs visually with a simple classification scheme which could be superimposed with additional data to support environmental assessment and management.

Benthic nitrate removal capacity in marine mangroves of Guadeloupe, Lesser Antilles

Mangrove sediments are known to be potentially active reducing zones for nitrogen removal. The goal of this work was to investigate the potential for nitrate reduction in marine mangrove sediments along a canal impacted by anthropogenic activity (Guadeloupe, Lesser Antilles). To this end, the effect of nitrate concentration, organic carbon load, and hydraulic retention time was assessed as factors affecting these nitrate reduction rates. Nitrate reduction potential was determined using flow-through reactors in marine mangrove sediments collected along "The Canal des Rotours" in Guadeloupe. Potential nitrate reduction rates, in the presence of indigenous organic carbon, generally increased upon increasing nitrate supply from around 120 nmol cm^-3 h^-1 (low nitrate) up to 378 nmol cm^-3 h^-1 (high nitrate). The potential for nitrate reduction increased significantly with the addition of mangrove leaves, whereas the addition of simple, easily degradable carbon (acetate) resulted in an almost fivefold increase in nitrate reduction rates (up to 748 nmol cm^-3  h^-1 ). The hydraulic retention time also had an impact on the nitrate reducing capacity due to an increased contact time between nitrate and the benthic microbial community. Marine mangrove sediments have a high potential to mitigate nitrogen pollution, mainly governed by the presence of large amounts of degradable carbon in the form of litter. The mangrove sediments from this Caribbean island, currently exposed to a small tidal effect, could increase their nitrate elimination capacities due to prolonged water retention via engineering.

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.

A multi-stable isotopic constraint on water column oxygen sinks in the Pearl River Estuary, South China

Bottom water oxygen depletion is a central concern in estuaries and coastal oceans worldwide. However, a mechanistic understanding and quantitative diagnosis of different oxygen-consuming processes are less clear. In this study, a multi-stable isotope approach is developed to delineate the role of oxygen respiration and nitrification contributing to total oxygen consumption in the Pearl River Estuary (PRE), a large eutrophic estuary in south China. The approach highly couples with analysis of the carbon isotope composition of dissolved inorganic carbon (δ¹³C-DIC) and with stable nitrogen isotope analysis in ammonium (δ¹⁵N-NH₄⁺) and nitrate (δ¹⁵N-NO₃^-). In all seasons, relatively low DO concentrations were observed in the upper reach and, to some extent, in the outer estuary during summer, while high concentrations of DO were found in the transition zone between the inner and outer estuary. On the basis of isotopic differentiation, our data reveal that much more depleted δ¹³C-DIC is coincident with DIC additions and low oxygen in the upper reach and inner estuary during most seasons. This is most likely a consequence of organic carbon (OC) degradation via aerobic respiration. Based on the carbon isotopic mass balance of DIC and the stoichiometry ratio of -ΔDO/ΔDIC, we found that the OC degradation dominates the total oxygen consumption in the upper reach, as well as in the inner estuary during summer (48.3%-93.5%). In addition, nitrification is another key process in contributing to total oxygen loss in the upper reach, as supported by the well-coupled variations of δ¹⁵N of NH₄⁺ and NO₃^- and apparent oxygen utilization (AOU). Using the formerly determined N isotopic fractionation and observed δ¹⁵N variation, we estimated that nitrification could account for 35.3%-44.1% and 28.5%-31.6% of the total oxygen consumption in the upper reach during winter and summer, respectively, while its contribution to total oxygen loss is minor in the inner and outer estuary. Overall, this study demonstrates the potential of the multi-stable isotopic approach to assess oxygen sink partitioning in large human-perturbed estuaries.

The role of coupled DNRA-Anammox during nitrate removal in a highly saline lake

Nitrate (NO₃^-) removal from aquatic ecosystems involves several microbially mediated processes, including denitrification, dissimilatory nitrate reduction to ammonium (DNRA), and anaerobic ammonium oxidation (anammox), controlled by slight changes in environmental gradients. In addition, some of these processes (i.e. denitrification) may involve the production of undesirable compounds such as nitrous oxide (N₂O), an important greenhouse gas. Saline lakes are prone to the accumulation of anthropogenic contaminants, making them highly vulnerable environments to NO₃^- pollution. The aim of this paper was to investigate the effect of light and oxygen on the different NO₃^- removal pathways under highly saline conditions. For this purpose, mesocosm experiments were performed using lacustrine, undisturbed, organic-rich sediments from the Pétrola Lake (Spain), a highly saline waterbody subject to anthropogenic NO₃^- pollution. The revised ¹⁵N-isotope pairing technique (¹⁵N-IPT) was used to determine NO₃^- sink processes. Our results demonstrate for the first time the coexistence of denitrification, DNRA, and anammox processes in a highly saline lake, and how their contribution was determined by environmental conditions (oxygen and light). DNRA, and especially denitrification to N₂O, were the dominant nitrogen (N) removal pathways when oxygen and/or light were present (up to 82%). In contrast, anoxia and darkness promoted NO₃^- reduction by DNRA (52%), combined with N loss by anammox (28%). Our results highlight the role of coupled DNRA-anammox, which has not yet been investigated in lacustrine sediments. We conclude that anoxia and darkness favored DNRA and anammox processes over denitrification and therefore to restrict N₂O emissions to the atmosphere.

Elucidation of dominant energy metabolic pathways of methane, sulphur and nitrogen in respect to mangrove-degradation for climate change mitigation

Mangroves play a key role in ecosystem balancing and climate change mitigation. It acts as a source and sink of methane (CH₄), a major greenhouse gas responsible for climate change. Energy metabolic pathways of methane production (methanogenesis) and oxidation (methanotrophy) are directly driven by sulphur (S) and nitrogen (N) metabolism and salinity in coastal wetlands. To investigate, how mangrove-degradations, affect the source-sink behaviour of CH₄; the pathways of CH₄, S and N were studied through whole-genome metagenomic approach. Soil samples were collected from degraded and undisturbed mangrove systems in Sundarban, India. Structural and functional microbial diversities (KEGG pathways) of CH₄, S and N metabolism were analysed and correlated with labile carbon pools and physico-chemical properties of soil. Overall, the acetoclastic pathway of methanogenesis was dominant. However, the relative proportion of conversion of CO₂ to CH₄ was more in degraded mangroves. Methane oxidation was higher in undisturbed mangroves and the serine pathway was dominant. After serine, the ribulose monophosphate pathway of CH₄ oxidation was dominant in degraded mangrove, while the xylulose monophosphate pathway was dominant in undisturbed site as it is more tolerant to salinity and higher pH. The assimilatory pathway (AMP) of S-metabolism was dominant in both systems. But in AMP pathway, adenosine triphosphate sulfurylase enzyme reads were higher in degraded mangrove, while NADPH-sulfite reductase abundance was higher in undisturbed mangrove due to higher salinity, and pH. In N-metabolism, the denitrification pathway was predominant in degraded sites, whereas the dissimilatory nitrate reduction pathway was dominant in undisturbed mangroves. The relative ratios of sulphur reducing bacteria (SRB): methanogens were higher in degraded mangrove; however, methanotrophs:methanogens was higher in undisturbed mangrove indicated lower source and greater sink capacity of CH₄ in the system. Microbial manipulation in mangrove-rhizosphere for regulating major energy metabolic pathways of methane could open-up a new window of climate change mitigation in coastal wetlands.

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.

Diverse key nitrogen cycling genes nifH, nirS and nosZ associated with Pichavaram mangrove rhizospheres as revealed by culture-dependent and culture-independent analyses

Mangroves are highly productive unique ecosystems harboring diverse unexplored microbial communities that play crucial roles in nutrient cycling as well as in maintaining ecosystem services. The mangrove-associated microbial communities transform the dead vegetation into nutrient sources of nitrogen, phosphorus, potash, etc. To understand the genetic and functional diversity of the bacterial communities involved in nitrogen cycling of this ecosystem, this study explored the diversity and distribution of both the nitrogen fixers and denitrifiers associated with the rhizospheres of Avicennia marina, Rhizophora mucronata, Suaeda maritima, and Salicornia brachiata of the Pichavaram mangroves. A combination of both culturable and unculturable (PCR-DGGE) approaches was adopted to explore the bacterial communities involved in nitrogen fixation by targeting the nifH genes, and the denitrifiers were explored by targeting the nirS and nosZ genes. Across the rhizospheres, Gammaproteobacteria was found to be predominant representing both nitrogen fixers and denitrifiers as revealed by culturable and unculturable analyses. Sequence analysis of soil nifH, nirS and nosZ genes clustered to unculturable, with few groups clustering with culturable groups, viz., Pseudomonas sp. and Halomonas sp. A total of 16 different culturable genera were isolated and characterized in this study. Other phyla like Firmicutes and Actinobacteria were also observed. The PCR-DGGE analysis also revealed the presence of 29 novel nifH sequences that were not reported earlier. Thus, the mangrove ecosystems serve as potential source for identifying unexplored novel microbial communities that contribute to nutrient cycling.

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 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.

Introducing the Mangrove Microbiome Initiative: Identifying Microbial Research Priorities and Approaches To Better Understand, Protect, and Rehabilitate Mangrove Ecosystems

Mangrove ecosystems provide important ecological benefits and ecosystem services, including carbon storage and coastline stabilization, but they also suffer great anthropogenic pressures. Microorganisms associated with mangrove sediments and the rhizosphere play key roles in this ecosystem and make essential contributions to its productivity and carbon budget. Understanding this nexus and moving from descriptive studies of microbial taxonomy to hypothesis-driven field and lab studies will facilitate a mechanistic understanding of mangrove ecosystem interaction webs and open opportunities for microorganism-mediated approaches to mangrove protection and rehabilitation.

Mangrove ecosystems provide important ecological benefits and ecosystem services, including carbon storage and coastline stabilization, but they also suffer great anthropogenic pressures. Microorganisms associated with mangrove sediments and the rhizosphere play key roles in this ecosystem and make essential contributions to its productivity and carbon budget. Understanding this nexus and moving from descriptive studies of microbial taxonomy to hypothesis-driven field and lab studies will facilitate a mechanistic understanding of mangrove ecosystem interaction webs and open opportunities for microorganism-mediated approaches to mangrove protection and rehabilitation. Such an effort calls for a multidisciplinary and collaborative approach, involving chemists, ecologists, evolutionary biologists, microbiologists, oceanographers, plant scientists, conservation biologists, and stakeholders, and it requires standardized methods to support reproducible experiments. Here, we outline the Mangrove Microbiome Initiative, which is focused around three urgent priorities and three approaches for advancing mangrove microbiome research.

Denitrifier communities differ in mangrove wetlands across China

To explore the geographical variations in the nosZ-denitrifier community and the underlying influential factors, surface sediments were collected from six mangroves across China, including Yunxiao (YX), Futian (FT), Fangchenggang (FCG), Zhanjiang (ZJ), Dongzhaigang (DZG), and Dongfang (DF). The nosZ gene abundance in mangrove sediments were 1.60 × 10⁵-1.17 × 10⁶ copies g^-1 dry sediment, with a higher density in Avicennia marina forest than the mudflat. Denitrifier community richness and diversity increased with decreasing latitude based on the Chao1 richness and Shannon diversity index, with the highest diversity being observed in the DF mangrove. The denitrifier communities could be classified into three groups including south DF mangrove, middle FCG, ZJ and DZG mangroves, and north YX and FT mangroves based on HCA and PCoA analysis. The nosZ OTUs could be divided into seven distinct clusters with different proportionality characteristics among mangroves. Environmental factors (TN, TOC, and salinity) collectively shape denitrifier communities in mangrove sediments.

Biogeochemical Processes of C and N in the Soil of Mangrove Forest Ecosystems

The mangrove forest provides various ecosystem services in tropical and subtropical regions. Many of these services are driven by the biogeochemical cycles of C and N, and soil is the major reservoir for these chemical elements. These cycles may be influenced by the changing climate. The high plant biomass in mangrove forests makes these forests an important sink for blue C storage. However, anaerobic soil conditions may also turn mangrove forests into an environmentally detrimental producer of greenhouse gases (such as CH4 and N2O), especially as air temperatures increase. In addition, the changing environmental factors associated with climate change may also influence the N cycles and change the patterns of N2 fixation, dissimilatory nitrate reduction to ammonium, and denitrification processes. This review summarizes the biogeochemical processes of C and N cycles in mangrove forest soils based on recently published studies, and how these processes may respond to climate change, with the aim of predicting the impacts of climate change on the mangrove forest ecosystem.

Biogeographic pattern of the nirS gene-targeted anammox bacterial community and composition in the northern South China Sea and a coastal Mai Po mangrove wetland

Functional genes, namely hzo/hao, nirS, hzs, and ccs gene, are efficient with high specificity for detecting anammox bacteria. Sc-nirS and An-nirS primer sets were proposed for targeting Scalindua/non-Scalindua anammox bacterial groups; previously, they have not been assessed for biogeographic study on marine-terrestrial transitional systems, specifically marine and terrestrial ecosystems. Here, we report phylogenetic distribution pattern of anammox bacteria in both northern South China Sea (nSCS) and Mai Po wetland (a coastal mangrove) using nirS gene-based primers. A well-delineated biogeographic distribution pattern from ocean to continental shelf was evident by combining both gene-based analyses as previously depicted using 16S rRNA as the biomarker. Furthermore, factors affecting the abundance and composition of An-nirS genes in Mai Po wetland were identified as substrate (NO₃^-/NO₂^- concentration) and anoxic/oxic condition in association to depth. An-nirS gene abundance was from 2.6 × 10³ to 1.2-1.4 × 10⁴ copies/g dry sediment in nSCS; and it was around 5 × 10³ and 1-2 × 10⁴ copies/g dry sediment in surface and subsurface sediments of Mai Po wetland, respectively. In addition, nirS gene abundance and distribution pattern of denitrifiers and anammox bacteria in the wetland indicates a competition relationship between them. Mangrove vegetation affected the community composition of An-nirS gene considerably, and a more homogeneous distribution pattern was observed in the mangrove forest than intertidal mudflats. Sc/An-nirS gene-based biogeographic insights on anammox bacteria have shed lights on the compositional and potential functional dynamics and emphasized the importance of molecular tools on refining the current microbial ecological patterns.

Nitrogen purification potential limited by nitrite reduction process in coastal eutrophic wetlands

Coastal wetlands accumulate enormous quantities of nitrogen due to their position at the interface between land and sea and high trapping capacity. Fortunately, they have high nitrogen (N) purifying (removal) capacity, which means that they likely play an important role in mitigating against coastal eutrophication. However studies that empirically measure the degree to which wetlands purify nitrogen and their removal pathways (e.g. denitrification, anammox, plant uptake, microbial immobilization, etc.) are rare. In this study, the N purification potential (denitrification and anammox) and enzyme activities related to denitrification in different subtropical wetlands types were conducted in nitrogen-enriched wetlands of Daya Bay, Southern China. We found the average N purification rate was 11.4 μmol N·kg^-1·h^-1, with denitrification accounting for 84.2%-100% of the total N₂ production in the wetlands of Daya Bay. The N purification potential in the wet season, subtidal areas and mangrove forests were generally observed to be higher than that in the dry season, high and low tidal areas, barren and estuary habitats, respectively. Correspondingly, these differences were mainly driven by the temperature, Eh and NH₄-N, respectively. Additionally, the nitrate reductase (Nar) and nitrite reductase (Nir) activities tended to be similar among different seasons and tidal areas, however, Nir activity in mangrove forest was 1.5-fold and 2-fold of the estuarine and barren areas, respectively. Meanwhile, Nir showed a positive correlation with denitrification rate. These results indicate that NO₂-N reduction, the key control mechanism for N purification, should be the rate-limiting step of the denitrification process in Daya Bay wetlands. Notably, mangroves could improve N removal rates by 48.0% compared to other wetlands. Therefore, protecting and restoring mangrove ecosystems could be an effective way to reduce the risk of coastal eutrophication.

Denitrification and anammox: Understanding nitrogen loss from Yangtze Estuary to the east China sea (ECS)

The Yangtze River, which is the largest in Euro-Asian, receives tremendous anthropogenic nitrogen input and is typically characterized by severe eutrophication and hypoxia. Two major processes, denitrification and anaerobic ammonium oxidation (anammox), play vital roles for removing nitrogen global in nitrogen cycling. In the current study, sediment samples were collected from both latitudinal and longitudinal transects along the coastal Yangtze River and the East China Sea (ECS). We investigated community composition and distributions of nosZ gene-encoded denitrifiers by high throughput sequencing, and also quantified the relative abundances of both denitrifying and anammox bacteria by q-PCR analysis. Denitrifying communities showed distinct spatial distribution patterns that were impacted by physical (water current and river runoffs) and chemical (nutrient availability and organic content) processes. Both denitrifying and anammox bacteria contributed to the nitrogen removal in Yangtze Estuary and the adjacent ECS, and these two processes shifted from coastal to open ocean with reverse trends: the abundance of nosZ gene decreased from coastal to open ocean while anammox exhibited an increasing trend based on quantifications of hzsB and 16S rRNA genes. Further correspondence correlation analysis revealed that salinity and nutrients were the main factors in structuring composition and distribution of denitrifying and anammox bacteria. This study improved our understanding of dynamic processes in nitrogen removal from estuarine to open ocean. We hypothesize that denitrification is the major nitrogen removal pathway in estuaries, but in open oceans, low nutrient and organic matter concentrations restrict denitrification, thus increasing the importance of anammox as a nitrogen removal process.

Mangrove Sediment Microbiome: Adaptive Microbial Assemblages and Their Routed Biogeochemical Processes in Yunxiao Mangrove National Nature Reserve, China

Microorganisms play important roles in mangrove ecosystems. However, we know little about the ecological implications of mangrove microbiomes for high productivity and the efficient circulation of elements in mangrove ecosystems. Here, we focused on mangrove sediments located at the Yunxiao National Mangrove Reserve in southeast China, uncovering the mangrove microbiome using the 16S rRNA gene and shotgun metagenome sequencing approaches. Physicochemical assays characterized the Yunxiao mangrove sediments as carbon (C)-rich, sulfur (S)-rich, and nitrogen (N)-limited environment. Then phylogenetic analysis profiling a distinctive microbiome with an unexpected high frequency of Chloroflexi and Nitrospirae appeared to be an adaptive characteristic of microbial structure in S-rich habitat. Metagenome sequencing analysis revealed that the metabolic pathways of N and S cycling at the community-level were routed through ammonification and dissimilatory nitrate reduction to ammonium for N conservation in this N-limited habitat, and dissimilatory sulfate reduction along with polysulfide formation for generating bioavailable S resource avoiding the biotoxicity of sulfide in mangrove sediments. In addition, methane metabolism acted as a bridge to connect C cycling to N and S cycling. Further identification of possible biogeochemical linkers suggested Syntrophobacter, Sulfurovum, Nitrospira, and Anaerolinea potentially drive the coupling of C, N, and S cycling. These results highlighting the adaptive routed metabolism flow, a previously undescribed property of mangrove sediment microbiome, appears to be a defining characteristic of this habitat and may significantly contribute to the high productivity of mangrove ecosystems, which could be used as indicators for the health and biodiversity of mangrove ecosystems.

Mangrove Facies Drives Resistance and Resilience of Sediment Microbes Exposed to Anthropic Disturbance

Mangrove forests are coastal ecosystems continuously affected by various environmental stresses and organized along constraint gradients perpendicular to the coastline. The aim of this study was to evaluate the resistance and resilience of sediment microbial communities in contrasted vegetation facies, during and after exposure to an anthropic disturbance. Our hypothesis was that microbial communities should be the most stable in the facies where the consequences of the anthropic disturbance are the most similar to those of natural disturbances. To test this, we focused on communities involved in N-cycle. We used an in situ experimental system set up in Mayotte Island where 2 zones dominated by different mangrove trees are daily exposed since 2008 to pretreated domestic wastewater (PW) discharges. These freshwater and nutrients inputs should increase microbial activities and hence the anoxia of sediments. We monitored during 1 year the long-term impact of this disturbance, its short-term impact and the resilience of microbial communities on plots where PW discharges were interrupted. Microorganism densities were estimated by qPCR, the nitrification (NEA) and denitrification (DEA) enzyme activities were evaluated by potential activity measurements and pigment analyses were performed to assess the composition of microbial photosynthetic communities. At long-term PW discharges significantly modified the structure of phototrophic communities and increased the total density of bacteria, the density of denitrifying bacteria and DEA. Similar effects were observed at short-term, notably in the facies dominated by Ceriops tagal. The results showed a partial resilience of microbial communities. This resilience was faster in the facies dominated by Rhizophora mucronata, which is more subjected to tides and sediment anoxia. The higher stability of microbial communities in this facies confirms our hypothesis. Such information should be taken into account in mangrove utilization and conservation policies.

Organic matter decomposition sustains sedimentary nitrogen loss in the Pearl River Estuary, China

The Pearl River Estuary (PRE) has long received tremendous amounts of anthropogenic nitrogen, and is facing severe environmental problems. Denitrification and anaerobic ammonium oxidation (anammox) are known to be two major nitrogen removal pathways in estuarine sediments. Through the use of slurry and intact sediment core incubations, we examined the nitrogen removal pathways and quantified the in situ denitrification and anammox with associated gaseous nitrogen production rates. Sedimentary nitrogen removal was predominated by denitrification (93-100%) relative to a minimal contribution (<7%) from anammox. Among the detected environmental factors, salinity, bottom water NO_x^- (nitrate and nitrite) concentration, sedimentary organic matter and dissolved oxygen consumption rates showed good correlations with denitrification and anammox rates. Sedimentary nitrogen loss was mainly supported by endogenic coupled nitrification-denitrification (6.0 ± 1.5 × 10⁶ mol N d^-1), with water-column-delivered NO_x^- (2.1 ± 0.6 × 10⁶ mol N d^-1) as the secondary source. Such results suggested that sedimentary nitrogen removal involved mainly particulate organic form (allochthonous or autochthonous) deposited onto sediments, rather than inorganic forms in overlying water. Meanwhile, total N₂O production from sediments was estimated to be 7.3 ± 2.1 × 10⁴ mol N d^-1, equivalent to ~35% of the daily N₂O emissions in the PRE.

Tropical land-sea couplings: Role of watershed deforestation, mangrove estuary processing, and marine inputs on N fluxes in coastal Pacific Panama

We review data from coastal Pacific Panama and other tropical coasts with two aims. First, we defined inputs and losses of nitrogen (N) mediating connectivity of watersheds, mangrove estuaries, and coastal sea. N entering watersheds-mainly via N fixation (79-86%)-was largely intercepted; N discharges to mangrove estuaries (3-6%), small compared to N inputs to watersheds, nonetheless significantly supplied N to mangrove estuaries. Inputs to mangrove estuaries (including watershed discharges, and marine inputs during flood tides) were matched by losses (mainly denitrification and export during ebb tides). Mangrove estuary subsidies of coastal marine food webs take place by export of forms of N [DON (62.5%), PN (9.1%), and litter N (12.9%)] that provide dissimilative and assimilative subsidies. N fixation, denitrification, and tidal exchanges were major processes, and DON was major form of N involved in connecting fluxes in and out of mangrove estuaries. Second, we assessed effects of watershed forest cover on connectivity. Decreased watershed forest cover lowered N inputs, interception, and discharge into receiving mangrove estuaries. These imprints of forest cover were erased during transit of N through estuaries, owing to internal N cycle transformations, and differences in relative area of watersheds and estuaries. Largest losses of N consisted of water transport of energy-rich compounds, particularly DON. N losses were similar in magnitude to N inputs from sea, calculated without considering contribution by intermittent coastal upwelling, and hence likely under-estimated. Pacific Panama mangrove estuaries are exposed to major inputs of N from land and sea, which emphasizes the high degree of bi-directional connectivity in these coupled ecosystems. Pacific Panama is still lightly affected by human or global changes. Increased deforestation can be expected, as well as changes in ENSO, which will surely raise watershed-derived loads of N, as well as significantly change marine N inputs affecting coastal coupled ecosystems.

Impact of seasonality on the nutrient concentrations in Gautami-Godavari Estuarine Mangrove Complex, Andhra Pradesh, India

Spatiotemporal variations of dissolved nutrients were studied along Gautami-Godavari mangrove ecosystem to delineate their sources and fate. Average values of nitrate (NO₃^-), dissolved silica (DSi) and phosphate (PO₄^3-) is 2.09 mg/l, 12.7 mg/l and 0.16 mg/l in wet season and 0.47 mg/l, 6.96 mg/l and 0.29 mg/l in dry season respectively. In wet season river discharge has significant influence on NO₃^- and DSi. In dry season, NO₃^- and PO₄^3- are controlled by groundwater discharge, benthic exchange and various in situ processes owing to sediment redox condition. Mixing model shows net addition of phosphate in Coringa mangroves (95%) and Lower estuary (13%) and net removal of nitrate (24.79%) in Coringa mangrove and in estuary (58.9%). Thus present mangrove acts as net source for phosphate and net sink for nitrate and DSi. Nutrient ratio shows seasonal switching between potential Phosphorus and Nitrogen limitation in wet and dry season respectively.

The effect of bio-irrigation by the polychaete Lanice conchilega on active denitrifiers: Distribution, diversity and composition of nosZ gene

The presence of large densities of the piston-pumping polychaete Lanice conchilega can have important consequences for the functioning of marine sediments. It is considered both an allogenic and an autogenic ecosystem engineer, affecting spatial and temporal biogeochemical gradients (oxygen concentrations, oxygen penetration depth and nutrient concentrations) and physical properties (grain size) of marine sediments, which could affect functional properties of sediment-inhabiting microbial communities. Here we investigated whether density-dependent effects of L. conchilega affected horizontal (m-scale) and vertical (cm-scale) patterns in the distribution, diversity and composition of the typical nosZ gene in the active denitrifying organisms. This gene plays a major role in N2O reduction in coastal ecosystems as the last step completing the denitrification pathway. We showed that both vertical and horizontal composition and richness of nosZ gene were indeed significantly affected when large densities of the bio-irrigator were present. This could be directly related to allogenic ecosystem engineering effects on the environment, reflected in increased oxygen penetration depth and oxygen concentrations in the upper cm of the sediment in high densities of L. conchilega. A higher diversity (Shannon diversity and inverse Simpson) of nosZ observed in patches with high L. conchilega densities (3,185-3,440 ind. m-2) at deeper sediment layers could suggest a downward transport of NO3- to deeper layers resulting from bio-irrigation as well. Hence, our results show the effect of L. conchilega bio-irrigation activity on denitrifying organisms in L. conchilega reefs.

Sediment carbon and nutrient fluxes from cleared and intact temperate mangrove ecosystems and adjacent sandflats

The loss of mangrove ecosystems is associated with numerous impacts on coastal and estuarine function, including sediment carbon and nutrient cycling. In this study we compared in situ fluxes of carbon dioxide (CO₂) from the sediment to the atmosphere, and fluxes of dissolved inorganic nutrients and oxygen across the sediment-water interface, in intact and cleared mangrove and sandflat ecosystems in a temperate estuary. Measurements were made 20 and 25months after mangrove clearance, in summer and winter, respectively. Sediment CO₂ efflux was over two-fold higher from cleared than intact mangrove ecosystems at 20 and 25months after mangrove clearance. The higher CO₂ efflux from the cleared site was explained by an increase in respiration of dead root material along with sediment disturbance following mangrove clearance. In contrast, sediment CO₂ efflux from the sandflat site was negligible (≤9.13±1.18mmolm^-2d^-1), associated with lower sediment organic matter content. The fluxes of inorganic nutrients (NH₄⁺, NO_x and PO₄^3-) from intact and cleared mangrove sediments were low (≤20.37±18.66μmolm^-2h^-1). The highest NH₄⁺ fluxes were measured at the sandflat site (69.21±13.49μmolm^-2h^-1). Lower inorganic nutrient fluxes within the cleared and intact mangrove sites compared to the sandflat site were associated with lower abundance of larger burrowing macrofauna. Further, a higher fraction of organic matter, silt and clay content in mangrove sediments may have limited nutrient exchange.

Influence of polycyclic aromatic hydrocarbons on nitrate reduction capability in mangrove sediments

In the present study, we investigated the influence of phenanthrene (PHE), a three-ring polycyclic aromatic hydrocarbon (PAH) compound, on nitrate (NO₃^-) reduction processes in mangrove sediments using microcosms. After 10days, nitrate/nitrite reductase activity and abundance of narG and nirS significantly decreased in the bulk sediment at both 10/50mgPHEkg^-1 contamination groups. In the rhizosphere, abundance of narG, nirS and nirK markedly declined at PHE treated sediments, while the drop in reductase activity at 10mgkg^-1 PHE treatment was insignificant. After 50days, apart from 10mgPhekg^-1 treated bulk sediment, abundance of denitrifiers and reductase activity in all PHE spiked sediment samples significantly dropped. Therefore, the influence of PAHs on NO₃^- reduction capability in mangrove sediments is dependent on spiked concentration, temporal scale of exposure and interaction with roots. Generally, PAHs play an inhibitor role, slowing NO₃^- turnover rates, which warrant attention from coastal managers.

Effects of multiple antibiotics exposure on denitrification process in the Yangtze Estuary sediments

Denitrification is a dominant reactive nitrogen removal pathway in most estuarine and coastal ecosystems, and plays a significant role in regulating N₂O release. Although multiple antibiotics residues are widely detected in aquatic environment, combined effects of antibiotics on denitrification remain indistinct. In this work, 5 classes of antibiotics (sulfonamides, chloramphenicols, tetracyclines, macrolides, and fluoroquinolones) were selected to conduct orthogonal experiments in order to explore their combined effects on denitrification. ¹⁵N-based denitrification and N₂O release rates were determined in the orthogonal experiments, while denitrifying functional genes were examined to illustrate the microbial mechanism of the combined antibiotics effect. Denitrification rates were inhibited by antibiotics treatments, and synergistic inhibition effect was observed for multiple antibiotics exposure. Different classes of antibiotics had different influence on N₂O release rates, but multiple antibiotics exposure mostly led to stimulatory effect. Abundances of denitrifying functional genes were inhibited by multiple antibiotics exposure due to the antimicrobial properties, and different inhibition on denitrifiers may be the major mechanism for the variations of N₂O release rates. Combined effects of antibiotics on denitrification may lead to nitrate retention and N₂O release in estuarine and coastal ecosystems, and consequently cause cascading environmental problems, such as greenhouse effects and hyper-eutrophication.

Substrates specialization in lipid compounds and hydrocarbons of Marinobacter genus

The impact of petroleum contamination and of burrowing macrofauna on abundances of Marinobacter and denitrifiers was tested in marine sediment mesocoms after 3 months incubation. Quantification of this genus by qPCR with a new primer set showed that the main factor favoring Marinobacter abundance was hydrocarbon amendment followed by macrofauna presence. In parallel, proportion of nosZ-harboring bacteria increased in the presence of marcrofauna. Quantitative finding were explained by physiological data from a set of 34 strains and by genomic analysis of 16 genomes spanning 15 different Marinobacter-validated species (Marinobacter hydrocarbonoclasticus, Marinobacter daeopensis, Marinobacter santoriniensis, Marinobacter pelagius, Marinobacter flavimaris, Marinobacter adhaerens, Marinobacter xestospongiae, Marinobacter algicola, Marinobacter vinifirmus, Marinobacter maritimus, Marinobacter psychrophilus, Marinobacter lipoliticus, Marinobacter manganoxydans, Marinobacter excellens, Marinobacter nanhaiticus) and 4 potential novel ones. Among the 105 organic electron donors tested in physiological analysis, Marinobacter pattern appeared narrow for almost all kinds of organic compounds except lipid ones. Strains of this set could oxidize a very large spectrum of lipids belonging to glycerolipids, branched, fatty acyls, and aromatic hydrocarbon classes. Physiological data were comforted by genomic analysis, and genes of alkane 1-monooxygenase, haloalkane dehalogenase, and flavin-binding monooxygenase were detected in most genomes. Denitrification was assessed for several strains belonging to M. hydrocarbonoclasticus, M. vinifirmus, Marinobacter maritinus, and M. pelagius species indicating the possibility to use nitrate as alternative electron acceptor. Higher occurrence of Marinobacter in the presence of petroleum appeared to be the result of a broader physiological trait allowing this genus to use lipids including hydrocarbon as principal electron donors.

Bacterial diversity in relatively pristine and anthropogenically-influenced mangrove ecosystems (Goa, India)

To appreciate differences in benthic bacterial community composition at the relatively pristine Tuvem and the anthropogenically-influenced Divar mangrove ecosystems in Goa, India, parallel tag sequencing of the V6 region of 16S rDNA was carried out. We hypothesize that availability of extraneously-derived anthropogenic substrates could act as a stimulatant but not a deterrent to promote higher bacterial diversity at Divar. Our observations revealed that the phylum Proteobacteria was dominant at both locations comprising 43–46% of total tags. The Tuvem ecosystem was characterized by an abundance of members belonging to the class Deltaproteobacteria (21%), ~ 2100 phylotypes and 1561 operational taxonomic units (OTUs) sharing > 97% similarity. At Divar, the Gammaproteobacteria were ~ 2× higher (17%) than at Tuvem. A more diverse bacterial community with > 3300 phylotypes and > 2000 OTUs mostly belonging to Gammaproteobacteria and a significantly higher DNT (n = 9, p < 0.001, df = 1) were recorded at Divar. These findings suggest that the quantity and quality of pollutants at Divar are perhaps still at a level to maintain high diversity. Using this technique we could show higher diversity at Divar with the possibility of Gammaproteobacteria contributing to modulating excess nitrate.

Nitrate ammonification in mangrove soils: a hidden source of nitrite?

Nitrate reduction is considered to be a minor microbial pathway in the oxidation of mangrove-derived organic matter due to a limited supply of nitrate in mangrove soils. At a limited availability of this electron acceptor compared to the supply of degradable carbon, nitrate ammonification is thought to be the preferential pathway of nitrate reduction. Mangrove forest mutually differ in their productivity, which may lead to different available carbon to nitrate ratios in their soil. Hence, nitrate ammonification is expected to be of more importance in high- compared to low-productive forests. The hypothesis was tested in flow-through reactors that contain undisturbed mangrove soils from high-productive Avicennia germinans and Rhizophora mangle forests in Florida and low-productive Avicennia marina forests in Saudi Arabia. Nitrate was undetectable in the soils from both regions. It was assumed that a legacy of nitrate ammonification would be reflected by a higher ammonium production from these soils upon the addition of nitrate. Unexpectedly, the soils from the low-productive forests in Saudi Arabia produced considerably more ammonium than the soils from the high-productive forests in Florida. Hence, other environmental factors than productivity must govern the selection of nitrate ammonification or denitrification. A rather intriguing observation was the 1:1 production of nitrite and ammonium during the consumption of nitrate, more or less independent from sampling region, location, sampling depth, mangrove species and from the absence or presence of additional degradable carbon. This 1:1 ratio points to a coupled production of ammonium and nitrite by one group of nitrate-reducing microorganisms. Such a production of nitrite will be hidden by the presence of active nitrite-reducing microorganisms under the nitrate-limited conditions of most mangrove forest soils.

Depositional record of trace metals and degree of contamination in core sediments from the Mandovi estuarine mangrove ecosystem, west coast of India

The concentrations of seven trace metals (Fe, Mn, Cu, Cr, Co, Pb and Zn) in three sediment cores were analysed to assess the depositional trends of metals and their contamination level in the Mandovi estuary, west coast of India. All sediment cores showed enrichment of trace metals in the upper part of core sediments and decrease in concentration with depth, suggesting excess of anthropogenic loading (including mining activities) occurred during the recent past. Scanning electron microscope (SEM) images distinguished the shape, size and structure of particles derived from lithogenic and anthropogenic sources in core sediments. The geo-accumulation index (I(geo)) values indicate that Mandovi estuary is 'moderately polluted' with Pb, whereas 'unpolluted to moderately polluted' with Fe, Mn, Cu, Cr, Co and Zn. The comparative analysis of trace metals revealed that Fe and Mn were highly enriched in the Mandovi estuary compared to all other Indian estuaries.

Effects of sulfamethazine on denitrification and the associated N2O release in estuarine and coastal sediments

Denitrification is an important pathway of nitrogen removal and nitrous oxide (N2O) production in estuarine and coastal ecosystems, and plays a significant role in counteracting aquatic eutrophication induced by excessive nitrogen loads. Estuarine and coastal environments also suffer from increasing antibiotic contamination because of the growing production and usage of antibiotics. In this study, sediment slurry incubation experiments were conducted to determine the influence of sulfamethazine (SMT, a sulphonamide antibiotic) on denitrification and the associated N2O production. Genes important for denitrification and antibiotic resistance were quantified to investigate the microbial physiological mechanisms underlying SMT's effects on denitrification. SMT was observed to significantly inhibit denitrification rates, but increasing concentrations of SMT enhanced N2O release rates. The negative exponential relationships between denitrifying gene abundances and SMT concentrations showed that SMT reduced denitrification rates by restricting the growth of denitrifying bacteria, although the presence of the antibiotic resistance gene was detected during the incubation period. These results imply that the wide occurrence of residual antibiotics in estuarine and coastal ecosystems may influence eutrophication control, greenhouse effects, and atmospheric ozone depletion by inhibiting denitrification and stimulating the release of N2O.

Compositional profile of α / β-hydrolase fold proteins in mangrove soil metagenomes: prevalence of epoxide hydrolases and haloalkane dehalogenases in oil-contaminated sites

The occurrence of genes encoding biotechnologically relevant α/β-hydrolases in mangrove soil microbial communities was assessed using data obtained by whole-metagenome sequencing of four mangroves areas, denoted BrMgv01 to BrMgv04, in São Paulo, Brazil. The sequences (215 Mb in total) were filtered based on local amino acid alignments against the Lipase Engineering Database. In total, 5923 unassembled sequences were affiliated with 30 different α/β-hydrolase fold superfamilies. The most abundant predicted proteins encompassed cytosolic hydrolases (abH08; ∼ 23%), microsomal hydrolases (abH09; ∼ 12%) and Moraxella lipase-like proteins (abH04 and abH01; < 5%). Detailed analysis of the genes predicted to encode proteins of the abH08 superfamily revealed a high proportion related to epoxide hydrolases and haloalkane dehalogenases in polluted mangroves BrMgv01-02-03. This suggested selection and putative involvement in local degradation/detoxification of the pollutants. Seven sequences that were annotated as genes for putative epoxide hydrolases and five for putative haloalkane dehalogenases were found in a fosmid library generated from BrMgv02 DNA. The latter enzymes were predicted to belong to Actinobacteria, Deinococcus-Thermus, Planctomycetes and Proteobacteria. Our integrated approach thus identified 12 genes (complete and/or partial) that may encode hitherto undescribed enzymes. The low amino acid identity (< 60%) with already-described genes opens perspectives for both production in an expression host and genetic screening of metagenomes.

Nitrogen-limited mangrove ecosystems conserve N through dissimilatory nitrate reduction to ammonium

Earlier observations in mangrove sediments of Goa, India have shown denitrification to be a major pathway for N loss1. However, percentage of total nitrate transformed through complete denitrification accounted for <0–72% of the pore water nitrate reduced. Here, we show that up to 99% of nitrate removal in mangrove sediments is routed through dissimilatory nitrate reduction to ammonium (DNRA). The DNRA process was 2x higher at the relatively pristine site Tuvem compared to the anthropogenically-influenced Divar mangrove ecosystem. In systems receiving low extraneous nutrient inputs, this mechanism effectively conserves and re-circulates N minimizing nutrient loss that would otherwise occur through denitrification. In a global context, the occurrence of DNRA in mangroves has important implications for maintaining N levels and sustaining ecosystem productivity. For the first time, this study also highlights the significance of DNRA in buffering the climate by modulating the production of the greenhouse gas nitrous oxide.