Impacts of vegetation, tidal process, and depth on the activities, abundances, and community compositions of denitrifiers in mangrove sediment

Dynamics of nitrogen genes in intertidal sediments of Darwin Harbour and their connection to N-biogeochemistry

Microbial mediated nitrogen (N) transformation is subject to multiple controlling factors such as prevailing physical and chemical conditions, and little is known about these processes in sediments of wet-dry tropical macrotidal systems such as Darwin Harbour in North Australia. To understand key transformations, we assessed the association between the relative abundance of nitrogen cycling genes with trophic status, sediment partition and benthic nitrogen fluxes in Darwin Harbour. We analysed nitrogen cycling gene abundance using a functional gene microarray and quantitative PCRs targeting the denitrification gene (nosZ) and archaeal ammonia oxidation (AOA.1). We found a significant negative correlation between archaeal ammonia oxidation and silicate flux (P = 0.004), an indicator for diatom and benthic microalgal activity. It is suggested that the degradation of the diatomaceous organic matter generates localised anoxic conditions and inhibition of nitrification. Abundance of the nosZ gene was negatively correlated with nutrient load. The lowest nosZ gene levels were in hyper-eutrophic tidal creeks with anoxic conditions and increased levels of sulphide limiting the coupling of nitrification-denitrification (P = 0.016). Significantly higher levels of nosZ genes were measured in the surface (top 2 cm) compared to bulk sediment (top 10 cm) and there was a positive association with di-nitrogen flux (N2) in surface (P = 0.024) but not bulk sediment. This suggests that denitrifiers are most active in surficial sediment at the sediment-water interface. Elevated levels of nosZ genes also occurred in the sediments of tidal creek mouths and mudflats with these depositional zones combining the diffuse and seaward supply of nitrogen and carbon supporting denitrifiers. N-cycle molecular assays using surface sediments show promise as a rapid monitoring technique for impact assessment and measuring ecosystem function. This is particularly pertinent for tropical macrotidal systems where systematic monitoring is sparse and in many cases challenged by climatic extremes and remoteness.

Dynamics of benthic microeukaryotic communities in a mangrove wetland invaded by Spartina alterniflora: Effects of vegetation, seasonality, and sediment depth

Benthic microeukaryotes are crucial mediators of biogeochemical cycles in coastal wetland ecosystems, yet their spatial and temporal variability remains poorly understood. This study delineates the diversity patterns of benthic microeukaryotes in a Spartina alterniflora-invaded mangrove ecosystem in Fujian, China. Using high-throughput sequencing of 18S rRNA gene transcripts, we identified the influences of vegetation, seasonality, and sediment depth on microeukaryotic communities. We discovered that vegetation cover significantly affects community composition, primarily driven by nutrient concentrations and pH. The community structure of microeukaryotes varied seasonally and vertically, correlating with changes in sediment temperature, pH, salinity, and fucoxanthin concentration. Notably, invasive Spartina alterniflora habitats showed enhanced heterotrophic interactions, suggesting that invasive species can reshape benthic microeukaryotic co-occurrence patterns. Seasonal co-occurrence patterns revealed dominant Bacillariophyta assemblages exhibited distinct network modules enriched in the cold (spring) and warm (summer and fall) seasons, respectively, which indicated potential ecological niche differentiation. Our findings reveal the complex relationships between environmental factors and benthic microeukaryotic diversity, offering insights into microbial responses to natural and invasive vegetation influences.

Hypoxia and salinity constrain the sediment microbiota-mediated N removal potential in an estuary: A multi-trophic interrelationship perspective

Reactive nitrogen (N) enrichment is a common environmental problem in estuarine ecosystems, while the microbial-mediated N removal process is complicated for other multi-environmental factors. Therefore, A systematic investigation is necessary to understand the multi-trophic microbiota-mediated N removal characteristics under various environmental factors in estuaries. Here, we studied how multiple factors affect the multi-trophic microbiota-mediated N removal potential (denitrification and anammox) and N2O emission along a river-estuary-bay continuum in southeastern China using the environmental DNA (eDNA) approach. Results suggested that hypoxia and salinity were the dominant environmental factors affecting multi-trophic microbiota-mediated N removal in the estuary. The synergistic effect of hypoxia and salinity contributed to the loss of taxonomic (MultiTaxa) and phylogenetic (MultiPhyl) diversity across multi-trophic microbiota and enhanced the interdependence among multi-trophic microbiota in the estuary. The N removal potential calculated as the activities of key N removal enzymes was also significantly constrained in the estuary (0.011), compared with the river (0.257) and bay (0.461). Structural equation modeling illustrated that metazoans were central to all sediment N removal potential regulatory pathways. The top-down forces (predation by metazoans) restrained the growth of heterotrophic bacteria, which may affect microbial N removal processes in the sediment. Furthermore, we found that the hypoxia and salinity exacerbated the N2O emission in the estuary. This study clarifies that hypoxia and salinity constrain estuarine multi-trophic microbiota-mediated N removal potential and highlights the important role of multi-trophic interactions in estuarine N removal, providing a new perspective on mitigating estuarine N accumulation.

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.

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.

Changes in Temporal Dynamics and Factors Influencing the Environment of the Bacterial Community in Mangrove Rhizosphere Sediments in Hainan

The structural characteristics of the rhizosphere soil’s microbial community is crucial to understanding the ecological function of mangroves. However, the mechanism influencing mangrove plants in soil microbial communities has yet to be determined. Here, the mangrove ecosystem of Xinying Mangrove National Wetland Park in Hainan Province was taken as the research object. The microbial communities, external regulatory factors, and the relationship between communities were analyzed using 16S rRNA high-throughput sequencing in the rhizosphere and non-rhizosphere sediments of mangrove forests under different spatiotemporal conditions. The results showed that there was no significant difference in the α-diversity of the bacterial community between the rhizosphere and non-rhizosphere sediments. However, β-diversity was significantly different. Redundancy analysis (RDA) showed that other environmental factors besides sulfide and Fe2+ affected the bacterial community structure in sediments. The co-occurrence pattern analysis of bacteria in the mangrove ecosystem indicates that the bacteria in rhizosphere sediments were more closely related than those in non-rhizosphere sediments. The results reveal significant differences between the rhizosphere and non-rhizosphere bacterial community diversity, structure, and their interaction in the mangrove ecosystem. Therefore, the ecological system of the mangrove wetland needs to be preserved and rehabilitated, which would have a tremendous impact on the sustainable development.

Study on the properties of denitrifying carbon sources from cellulose plants and their nitrogen removal mechanisms

Carbon sources of cellulose plants are promising materials that enhance the activities of denitrifying bacteria in the groundwater system. To further verify the denitrification performance of cellulose plants and the main factors of affecting the denitrifying system, six cellulose plants from agricultural wastes (wood chip, corn cob, rice husk, corn straw, wheat straw, and sugar cane) were selected for bioavailable organic matter leaching experiments, carbon denitrification experiments, functional bacteria identification, and analysis experiments. The results show that the extracts of cellulose plants contain a mixed carbon sources system including small molecular organic acids, sugars, nitrogen-containing organic components, and esters. The qPCR results showed that the denitrifying bacteria had obvious advantages compared to anaerobic ammonia-oxidizing bacteria during the stable period; the denitrification experiment showed that each of six cellulose plants removed more than 80% of nitrogen, and the denitrification rates reached 1.00-2.00 mg N cm^-3·d^-1. The supplement of cellulose plants promotes the metabolism rate of denitrifying bacteria, and the additional denitrifying bacteria have little effect on nitrate removal. In summary, the expected denitrification reaction occurred in the cellulose plant system, which is suitable as a carbon source material for water body nitrogen pollution remediation.

Genetic Elucidation of Quorum Sensing and Cobamide Biosynthesis in Divergent Bacterial-Fungal Associations Across the Soil-Mangrove Root Interface

Plant roots in soil host a repertoire of bacteria and fungi, whose ecological interactions could improve their functions and plant performance. However, the potential microbial interactions and underlying mechanisms remain largely unknown across the soil-mangrove root interface. We herein analyzed microbial intra- and inter-domain network topologies, keystone taxa, and interaction-related genes across four compartments (non-rhizosphere, rhizosphere, episphere, and endosphere) from a soil-mangrove root continuum, using amplicon and metagenome sequencing technologies. We found that both intra- and inter-domain networks displayed notable differences in the structure and topology across four compartments. Compared to three peripheral compartments, the endosphere was a distinctive compartment harboring more dense co-occurrences with a higher average connectivity in bacterial-fungal network (2.986) than in bacterial (2.628) or fungal network (2.419), which could be related to three bacterial keystone taxa (Vibrio, Anaerolineae, and Desulfarculaceae) detected in the endosphere as they are known to intensify inter-domain associations with fungi and stimulate biofilm formation. In support of this finding, we also found that the genes involved in cell-cell communications by quorum sensing (rhlI, lasI, pqsH, and lasR) and aerobic cobamide biosynthesis (cobG, cobF, and cobA) were highly enriched in the endosphere, whereas anaerobic cobamide biosynthesis (encoded by cbiT and cbiE) was dominant in three peripheral compartments. Our results provide genetic evidence for the intensified bacterial-fungal associations of root endophytes, highlighting the critical role of the soil-root interface in structuring the microbial inter-domain associations.

Occurrence, distribution, and pollution indices of potentially toxic elements within the bed sediments of the riverine system in Pakistan

Potentially toxic elements (PTEs) are a major source of pollution due to their toxicity, persistence, and bio-accumulating nature in riverine bed sediments. The sediment, as the largest storage and source of PTEs, plays an important role in transformation of mercury (Hg), lead (Pb), nickel (Ni), chromium (Cr), copper (Cu), zinc (Zn), and other toxic PTEs. Several important industrial hubs that contain a large population along the banks of different rivers, such as Kabul, Sutlej, Ravi, Jhelum, and Chenab in Pakistan, are acting as major sources of PTEs. In this study, 150 bed sediment samples (n=30 from each river) were collected from different sites. Total (acid extracted) PTE (Hg, Cu, Cr, Ni, Zn, and Pb) concentrations in bed sediments were determined using inductively coupled plasma mass spectrometry (ICP-MS). Sediment pollution indices were calculated in the major rivers of Pakistan. The results demonstrated high levels of Hg and Ni concentrations which exceeded the guideline standards of river authorities in the world. The contamination factor (CF) and contamination degree (CD) indices for Hg, Ni, and Pb showed a moderate to high (CF≥6 and CD≥24) contamination level in all the selected rivers. The values of geo-accumulation index (I_geo) were also high (I_geo≥5) for Hg and Pb and heavily polluted for Ni, while Cr, Cu, and Zn showed low to unpolluted (I_geo) values. Similarly, the enrichment factor (EF) values were moderately severe (5≤EF≤10) for Hg, Pb, and Ni in Sutlej, Ravi, and Jhelum, and severe (10≤EF≤25) in Kabul and Jhelum. Moreover, Hg and Ni showed severe to very severe enrichment in all the sampling sites. The ecological risk index (ERI) values represented considerable, moderate, and low risks, respectively, for Hg (The ERI value should not be bold. Please unbold the  ERI in the whole paper. It should be same like RI, CD and EF. [Formula: see text]≥160), Pb and Ni (40≤[Formula: see text]≤80), and Cr, Cu, and Zn ([Formula: see text]≤40). Similarly, potential ecological risk index (PERI) values posed considerable (300≤RI≤600) risk in Ravi and moderate (150≤RI≤300) in Kabul and Jhelum, but low (RI≤150) risk in Ravi and Chenab. On the basis of the abovementioned results, it is concluded that bed sediment pollution can be dangerous for both ecological resources and human beings. Therefore, PTE contamination should be regularly monitored and a cost-effective and environmentally friendly wastewater treatment plant should be installed to ensure removal of PTEs before the discharge of effluents into the freshwater ecosystems.

Earthworm gut: An overlooked niche for anaerobic ammonium oxidation in agricultural soil

Soil fauna takes an active part in accelerating turnover of nutrients in terrestrial ecosystems. Anaerobic ammonium oxidation (anammox) has been widely characterized, however, whether anammox is active in earthworm gut and the effect of earthworm on anammox in soil remain unknown. In this study, the activity, abundance and community of anammox bacteria in earthworm guts and soils from microcosms were determined using a ¹⁵N-tracing technique, quantitative PCR, and anammox bacterial 16S rRNA gene amplicon sequencing. Results showed that anammox rates in guts ranged between 5.81 and 14.19 nmol N g^-1 dw gut content h^-1, which were significantly (P < 0.01) higher than that in their surrounding soils during 30 day incubation. On the contrary, abundances of hzsB genes encoding subunit B hydrazine synthase in guts were significantly (P < 0.05) lower than those in their surrounding soils. Anammox rates, denitrification N₂ production rates and hzsB genes in soils with earthworms were significantly (P < 0.05) lower than those in control soils. Anammox bacterial compositions differed significantly (P < 0.05) between gut and soil, and earthworm altered anammox bacterial communities in soils. Brocadia, Kuenenia and abundant unclassified anammox bacteria were detected in collected soils and gut contents, in which Brocadia was only detected in guts. These results suggested that microbes in earthworm gut increase, but present of earthworm reduces anammox and denitrification associated N loss by altering the anammox bacterial community compositions in soils.

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.

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.

Effects of water level and vegetation on nitrate dynamics at varying sediment depths in laboratory-scale wetland mesocosms

Recent increases in the frequency of extreme floods and droughts associated with climate change can affect fluctuating groundwater or wetland water levels and wetland plant growth, and consequently cause redox condition changes in nitrogen dynamics in wetland sediments. Here, we studied the fate of nitrate (NO₃^-), dissolved organic carbon (DOC), and the microbial characteristics at different sediment depths in response to water levels (i.e., 5 or 2.5 cm) above the sediment surface and in the presence or absence of plants (Phragmites communis Trin) for four months in three wetland mesocosms. Results showed that mesocosm A (MA) with a high water level (5 cm above the surface) and plants had significantly higher DOC concentrations (17.57 ± 8.22 mg/L) in sediment that were actively consumed by microorganisms than other mesocosms with low water level (MB) and without plant (MC) (8.77 ± 2.38 mg/L and 7.87 ± 2.72 mg/L in MB and MC, respectively). Consequently, the most of influent NO₃^- (20 mg-N/L) dramatically reduced in the vicinity of plant roots (-20 to -15 cm sediment depth) where active denitrification was expected in MA. Moreover, the functional genes involved in denitrification such as narG (2.4 × 10⁸ -3.5 × 10⁸ copies·g^-1) and nirS (5.6 × 10⁶-1.1 × 10⁷ copies·g^-1) were more abundant in this mesocosm. The profile of the microbial community structure at the class level revealed that Alphaproteocbacteria (MA: 14.19 ± 1.19%; MB: 14.01 ± 0.51%; MC: 15.21 ± 2.76%) and Actinobacteria (MA: 8.21 ± 1.91%; MB: 13.91 ± 2.13%; MC: 11.75 ± 3.43%) were predominant in all three mesocosms. Interestingly, the clustered heatmap supported the obvious difference in microbial composition of MA from other mesocosms showing relatively more abundant Clostridia (6.71 ± 1.54%) and Deltaproteobacteria (7.05 ± 0.68%). These results can provide an insight to understand the biogeochemical nitrogen cycle associated with climate change in wetland systems.

Metataxonomic and metagenomic analysis of mangrove microbiomes reveals community patterns driven by salinity and pH gradients in Paranaguá Bay, Brazil

While environmental drivers regulate the structure of mangrove microbial communities, their exact nature and the extent of their influence require further elucidation. By means of 16S rRNA gene-based sequencing, we determined the microbial taxonomic profiles of mangroves in the subtropical Paranaguá Bay, Brazil, considering as potential drivers: salinity, as represented by two sectors in the extremes of a salinity gradient (<5 PSU and >30 PSU); proximity to/absence of the prevailing plants, Avicennia schaueriana, Laguncularia racemosa, Rhizophora mangle, and Spartina alterniflora; and the chemical composition of the sediments. Salinity levels within the estuary had the strongest influence on microbial structure, and pH was important to separate two communities within the high salinity environment. About one fourth of the total variation in community structure resulted from covariation of salinity and the overall chemical composition, which might indicate that the chemical profile was also related to salinity. The most prevalent bacterial phyla associated with the mangrove soils analyzed included Proteobacteria, Actinobacteria, Chloroflexi, Bacteroidetes, Acidobacteria, and Cyanobacteria. Taxonomic and functional comparisons of our results for whole-genome sequencing with available data from other biomes showed that the studied microbiomes cluster first according to biome type, then to matrix type and salinity status. Metabolic functions were more conserved than organisms within mangroves and across all biomes, indicating that core functions are preserved in any of the given conditions regardless of the specific organisms harboring them.

Changes in nitrogen functional genes in soil profiles of grassland under long-term grazing prohibition in a semiarid area

Grazing prohibition has been used to restore degraded grassland ecosystems in semiarid areas; however, the impact of this measure on soil nitrogen (N) cycling is poorly understood. Furthermore, recent studies have tended to focus on the topsoil and ignored a steep gradient of nutrient accumulation with soil depth. Here, we investigated changes in N functional genes (NFGs) involved in organic N decomposition (chiA), archaeal and bacterial ammonia oxidation (amoA-AOA and amoA-AOB), respectively, denitrification (nirK and nirS), and N fixation (nifH) in soil profiles from a chronosequence of grazing prohibition (0, 10, 15, 25, and 35 years) in the semiarid grasslands of the Loess Plateau, China. The abundance of all the investigated NFGs in grassland soils after 35 years' grazing prohibition was higher than in grazed grassland. This result suggests that microbial N turnover potential is facilitated by grazing prohibition, probably through enhanced biomass production via increases in nutrient input into the soil. The higher ratio of (chiA + nifH)/(amoA-AOA + amoA-AOB) and values of (nirK + nirS) in grazing-prohibited grasslands than in grazed grassland suggest that prohibition of grazing not only improved microbial N storage potential but also increased N gas emission potential. The abundances of NFGs varied along the soil profiles and responded differently to environmental factors. The chiA and nifH abundances decreased with soil depth and were associated with variation in aboveground biomass, NH₄⁺-N, and organic carbon, while amoA-AOA, nirK, and nirS genes increased with depth and were more affected by soil organic carbon, moisture, and bulk density. Multivariate regression tree analysis demonstrated that aboveground biomass was the best explanatory variable for the changes in NFGs in grazed grassland, while soil organic carbon was the best in the grazing-prohibited grasslands. Our results provide new insight into the soil N cycling potential of degraded and restored semiarid grassland ecosystems.

Microbial community structure of soils in Bamenwan mangrove wetland

Microbial community diversity and composition are important for the maintenance of mangrove ecosystem. Bacterial and archaeal community composition of the Bamenwan Mangrove Wetland soil in Hainan, China, was determined using pyrosequencing technique. Bacterial community composition presented differences among the five soil samples. Rhizobiales with higher abundance were observed in inner mangrove forest samples, while Desulfobacterales were in the seaward edge samples, and Frankiales, Gaiellales and Rhodospirillales in the landedge sample. For archaea, Crenarchaeota and Euryarchaeota dominated in five samples, but the proportion in each samples were different. Dominant archaeal community composition at the order level was similar in the seaward edge samples. The dominant archaeal clusters in the two inner mangrove forest samples were different, with Soil Crenarchaeotic Group (SCG) and Halobacteriales in sample inside of Bruguiera sexangula forest and SCG, Methanosarcinales and Marine Benthic Group B (MBGB) in sample inside of Xylocarpus mekongensis forest. The dominant archaeal clusters in land sample were unique, with Terrestrial Group and South African Gold Mine Group 1. The metabolic pathways including metabolism, genetic information processing, environmental information processing, cellular processes, organismal systems and human diseases were all detected for bacterial and archaeal functional profiles, but metabolic potentials among five samples were different.

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.

Denitrifier communities impacted by heavy metal contamination in freshwater sediment

Heavy metals are widely detected in natural environments, however their impacts on denitrifier community in freshwater ecosystem remain unclear. The present study investigated the changes of denitrifier communities (based on nosZ (nitrous oxide reductase) gene) in a freshwater reservoir contaminated by a severe accidental spill of heavy metals. The abundance of nosZ-denitrifiers drastically decreased, and their community richness, diversity and structure also showed considerable variations. The mainly detected denitrifying bacteria included Pseudogulbenkiania, Pseudomonas and two unknown groups. These major nosZ-denitrifier groups responded in different ways to heavy metal pollution. Metal contamination could exert a profound influence on denitrifier community in freshwater sediment. This work could provide some new insights to the impact of metal pollution on nitrogen cycling.

Salinity is a key factor driving the nitrogen cycling in the mangrove sediment

Coastal ecosystems are hotspots for nitrogen cycling, and specifically for nitrogen removal from water and sediment through the coupled nitrification-denitrification process. Salinity is globally important in structuring bacterial and archaeal communities, but the association between salinity and microbially-mediated nitrification and denitrification remains unclear. The denitrification activity and composition and structure of microbial nitrifiers and denitrifiers were characterized across a gradient of manipulated salinity (0, 10, 20 and 30ppt) in a mangrove sediment. Salinity negatively correlated with both denitrifying activity and the abundance of nirK and nosZ denitrifying genes. Ammonia-oxidizing bacteria (AOB), which dominated nitrification, had significantly greater abundance at intermediate salinity (10 and 20ppt). However, a positive correlation between ammonia concentration and salinity suggested that nitrifying activity might also be inhibited at higher salinity. The community structure of ammonia-oxidizing archaea (AOA) and bacteria (AOB), as well as nirK, nirS and nosZ denitrifying communities, were all significantly correlated with salinity. These changes were also associated with structural shifts in phylogeny. These findings provide a strong evidence that salinity is a key factor that influences the nitrogen transformations in coastal wetlands, indicating that salinity intrusion caused by climate change might have a broader impact on the coastal biospheres.

How do Elevated CO2 and Nitrogen Addition Affect Functional Microbial Community Involved in Greenhouse Gas Flux in Salt Marsh System

Salt marshes are unique ecosystem of which a microbial community is expected to be affected by global climate change. In this study, by using T-RFLP analysis, quantitative PCR, and pyrosequencing, we comprehensively analyzed the microbial community structure responding to elevated CO₂ (eCO₂) and N addition in a salt marsh ecosystem subjected to CO₂ manipulation and N addition for about 3 years. We focused on the genes of microbes relevant to N-cycling (denitrification and nitrification), CH₄-flux (methanogens and methanotrophs), and S-cycling (sulfate reduction) considering that they are key functional groups involved in the nutrient cycle of salt marsh system. Overall, this study suggests that (1) eCO₂ and N addition affect functional microbial community involved in greenhouse gas flux in salt marsh system. Specifically, the denitrification process may be facilitated, while the methanogenesis may be impeded due to the outcompeting of sulfate reduction by eCO₂ and N. This implies that future global change may cause a probable change in GHGs flux and positive feedback to global climate change in salt marsh; (2) the effect of eCO₂ and N on functional group seems specific and to contrast with each other, but the effect of single factor would not be compromised but complemented by combination of two factors. (3) The response of functional groups to eCO₂ and/or N may be directly or indirectly related to the plant community and its response to eCO₂ and/or N. This study provides new insights into our understanding of functional microbial community responses to eCO₂ and/or N addition in a C3/C4 plant mixed salt marsh system.

Multi-scale factors affecting composition, diversity, and abundance of sediment denitrifying microorganisms in Yangtze lakes

Sediment denitrification is the dominant nitrogen removal pathway in many aquatic habitats and can be regulated by local-, landscape-, and regional-scale factors. However, the mechanisms for how these multiple scale factors and their interactions affect the sediment denitrifying communities remain poorly understood. In this study, we investigated the community composition, diversity, and abundance of nitrite reductase genes (nirK and nirS)-encoding denitrifiers in 74 sediment samples from 22 Yangtze lakes using clone library and quantitative PCR techniques. Information of location, climate, catchment land use, water quality, sediment properties, and plant communities at each sampling site was analyzed to elucidate the effects of regional, landscape, and local factors on the characteristics of sediment denitrifying communities. Results of canonical correspondence analysis indicated that local factors were the key determinants of denitrifying community composition, accounting for over 20% of the total variation. Additionally, certain regional and landscape factors, including elevation and catchment built-up land, were also significantly related to the composition of denitrifying communities. Variance partitioning analyses revealed that diversity and abundance in the nirK denitrifier community were largely influenced by local factors, while those in the nirS community were controlled by both local and regional factors. Our findings highlight the importance of using different scale factors to explain adequately the composition and structure of denitrifying communities in aquatic environments.

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.

Changes in land use driven by urbanization impact nitrogen cycling and the microbial community composition in soils

Transition of populations from rural to urban living causes landscape changes and alters the functionality of soil ecosystems. It is unclear how this urbanization disturbs the microbial ecology of soils and how the disruption influences nitrogen cycling. In this study, microbial communities in turfgrass-grown soils from urban and suburban areas around Xiamen City were compared to microbial communities in the soils from rural farmlands. The potential N₂O emissions, potential denitrification activity, and abundances of denitrifiers were higher in the rural farmland soils compared with the turfgrass soils. Ammonia oxidizing archaea (AOA) were more abundant than ammonia oxidizing bacteria (AOB) in turfgrass soils. Within turfgrass soils, the potential nitrification activities and AOA abundances were higher in the urban than in the suburban soils. These results indicate a more pivotal role of AOA in nitrification, especially in urban soils. Microbial community composition was distinctly grouped along urbanization categories (urban, suburban, and rural) classified according to the population density, which can in part be attributed to the differences in soil properties. These observed changes could potentially have a broader impact on soil nutrient availability and greenhouse gas emissions.

Responses of bacterial and archaeal communities to nitrate stimulation after oil pollution in mangrove sediment revealed by Illumina sequencing

This study aimed to investigate microbial responses to nitrate stimulation in oiled mangrove mesocosm. Both supplementary oil and nitrate changed the water and sediment chemical properties contributing to the shift of microbial communities. Denitrifying genes nirS and nirK were increased several times by the interaction of oil spiking and nitrate addition. Bacterial chao1 was reduced by oil spiking and further by nitrate stimulation, whereas archaeal chao1 was only inhibited by oil pollution on early time. Sampling depth explained most of variation and significantly impacted bacterial and archaeal communities, while oil pollution only significantly impacted bacterial communities (p<0.05). Despite explaining less variation, nitrate addition coupled with oil spiking enhanced the growth of hydrocarbon degraders in mangrove. The findings demonstrate the impacts of environmental factors and their interactions in shaping microbial communities during nitrate stimulation. Our study suggests introducing genera Desulfotignum and Marinobacter into oiled mangrove for bioaugmentation.

Temporal and spatial variations of greenhouse gas fluxes from a tidal mangrove wetland in Southeast China

Tidal mangrove wetlands are a source of methane (CH4) and nitrous oxide (N2O); but considering the high productivity of mangroves, they represent a significant sink for carbon dioxide (CO2). An exotic plant Spartina alterniflora has invaded east China over the last few decades, threatening these coastal mangrove ecosystems. However, the atmospheric gas fluxes in mangroves are poorly characterized and the impact of biological invasion on greenhouse gas (GHG) fluxes in the wetland remains unclear. In this study, the temporal and spatial dynamics of key GHG fluxes (CO2, CH4, and N2O) at an unvegetated mudflat, cordgrass (S. alterniflora), and mangrove (Kandelia obovata) sites along an estuary of the Jiulong River in Southeast China were investigated over a 2-year period. The CO2 and CH4 fluxes demonstrated a seasonal and vegetation-dependent variation while N2O fluxes showed no such dependent pattern. Air temperature was the main factor influencing CO2 and CH4 fluxes. Cumulative global warming potential (GWP) ranked in the order of mangrove > cordgrass > mudflat and summer > spring > autumn > winter. Moreover, CH4 accounted for the largest proportion (68%) of GWP, indicating its dominant contribution to the warming potential in mangroves. Notwithstanding the lack of information on plant coverage, cordgrass invasion exhibited a minor influence on GHG emissions. These findings support the notion that mangrove forests are net accumulation sites for GHGs. As vegetation showed considerable effects on fluxes, more information about the significance of vegetation type with a special emphasis on the effects of invasive plants is crucial.

The activity and community structure of total bacteria and denitrifying bacteria across soil depths and biological gradients in estuary ecosystem

The distribution of soil microorganisms often shows variations along soil depth, and even in the same soil layer, each microbial group has a specific niche. In particular, the estuary soil is intermittently flooded, and the characteristics of the surface soil layer are different from those of other terrestrial soils. We investigated the microbial community structure and activity across soil depths and biological gradients composed of invasive and native plants in the shallow surface layer of an estuary ecosystem by using molecular approaches. Our results showed that the total and denitrifying bacterial community structures of the estuarine wetland soil differed according to the short depth gradient. In growing season, gene copy number of 16S rRNA were 1.52(±0.23) × 10(11), 1.10(±0.06) × 10(11), and 4.33(±0.16) × 10(10) g(-1) soil; nirS were 5.41(±1.25) × 10(8), 4.93(±0.94) × 10(8), and 2.61(±0.28) × 10(8) g(-1) soil; and nirK were 9.67(±2.37) × 10(6), 3.42(±0.55) × 10(6), and 2.12(±0.19) × 10(6) g(-1) soil in 0 cm, 5 cm, and 10 cm depth layer, respectively. The depth-based difference was distinct in the vegetated sample and in the growing season, evidencing the important role of plants in structuring the microbial community. In comparison with other studies, we observed differences in the microbial community and functions even across very short depth gradients. In conclusion, our results suggested that (i) in the estuary ecosystem, the denitrifying bacterial community could maintain its abundance and function within shallow surface soil layers through facultative anaerobiosis, while the total bacterial community would be both quantitatively and qualitatively affected by the soil depth, (ii) the nirS gene community, rather than the nirK one, should be the first candidate used as an indicator of the microbial denitrification process in the estuary system, and (iii) as the microbial community is distributed and plays a certain niche role according to biogeochemical factors, the study of the microbial community even in surface soil should be performed in detail by considering the soil depth.

Genetic associations as indices of nitrogen cycling rates in an aerobic denitrification biofilter used for groundwater remediation

An aerobic denitrification biofilter (ADB) for groundwater remediation was developed with high removal efficiencies (total nitrogen (TN): 82.3-95.8%; NO3(-)-N: 93.2-98.2%). Nitrate (NO3(-)-N) transformation rates stabilized between 21.0 and 23.4 g/(m(3) h), whereas nitrite (NO2(-)-N) and ammonium (NH4(+)-N) transformation rates remained less than 6.0 g/(m(3) h) as the dissolved oxygen (DO) level increased from 1.0 mg/L to 6.0 mg/L. Nitric oxide (NO) and nitrous oxide (N2O) accumulated with great fluctuations (NO: 0-1.6×10(-3) g/(m(3) h); N2O: 0.1-1.1g/(m(3)h)) throughout the experiment. This study suggested that gene associations reflect quantitative relationships with aerobic denitrification rates and can provide useful information regarding aerobic denitrification processes in groundwater. Especially, the qnorB/nosZ ratio acts as the main driver for NO3(-)-N and NH4(+)-N transformation, while the qnorB/nosZ ratio followed by the (nirS+nirK)/nosZ ratio serve a dominant role in the accumulation of N2O and NO.