Nitrogen Cycling In Sediments Research Articles

Riparian Forest Cover Modulates Phosphorus Storage and Nitrogen Cycling in Agricultural Stream Sediments.

Watershed land cover affects in-stream water quality and sediment nutrient dynamics. The presence of natural land cover in the riparian zone can reduce the negative effects of agricultural land use on water quality; however, literature evaluating the effects of natural riparian land cover on stream sediment nutrient dynamics is scarce. The objective of this study was to assess if stream sediment phosphorus retention and nitrogen removal varies with riparian forest cover in agricultural watersheds. Stream sediment nutrient dynamics from 28 sites with mixed land cover were sampled three times during the growing season. Phosphorus dynamics and nitrification rates did not change considerably throughout the study period. Sediment total phosphorus concentrations and nitrification rates decreased as riparian forest cover increased likely due to a decline in fine, organic material. Denitrification rates were strongly correlated to surface water nitrate concentrations. Denitrification rate and denitrification enzyme activity decreased with an increase in forest cover during the first sampling period only. The first sampling period coincided with the greatest connectivity between the watershed and in-stream processing, indicating that riparian forest cover indirectly decreased denitrification rates by reducing the concentrations of dissolved nutrients entering the stream. This reduction in load may allow the sediment to maintain greater nitrogen removal efficiency, because bacteria are not saturated with nitrogen. Riparian forest cover also appeared to lessen the effect of agriculture in the watershed by decreasing the amount of fine material in the stream, resulting in reduced phosphorus storage in the stream sediment.

Effects of drift algae accumulation and nitrate loading on nitrogen cycling in a eutrophic coastal sediment

The permeable (sandy) sediments that dominate the world's coastlines and continental shelves are highly exposed to nitrogen pollution, predominantly due to increased urbanisation and inefficient agricultural practices. This leads to eutrophication, accumulation of drift algae and changes in the reactions of nitrogen, including the potential to produce the greenhouse gas nitrous oxide (N2O). Nitrogen pollution in coastal systems has been identified as a global environmental issue, but it remains unclear how this nitrogen is stored and processed by permeable sediments. We investigated the interaction of drift algae biomass and nitrate (NO3−) exposure on nitrogen cycling in permeable sediments that were impacted by high nitrogen loading. We treated permeable sediments with increasing quantities of added macroalgal material and NO3− and measured denitrification, dissimilatory NO3− reduction to ammonium (DNRA), anammox, and nitrous oxide (N2O) production, alongside abundance of marker genes for nitrogen cycling and microbial community composition by metagenomics. We found that the presence of macroalgae dramatically increased DNRA and N2O production in sediments without NO3− treatment, concomitant with increased abundance of nitrate-ammonifying bacteria (e.g. Shewanella and Arcobacter). Following NO3− treatment, DNRA and N2O production dropped substantially while denitrification increased. This is explained by a shift in the relative abundance of nitrogen-cycling microorganisms under different NO3− exposure scenarios. Decreases in both DNRA and N2O production coincided with increases in the marker genes for each step of the denitrification pathway (narG, nirS, norB, nosZ) and a decrease in the DNRA marker gene nrfA. These shifts were accompanied by an increased abundance of facultative denitrifying lineages (e.g. Pseudomonas and Marinobacter) with NO3− treatment. These findings identify new feedbacks between eutrophication and greenhouse gas emissions, and in turn have potential to inform biogeochemical models and mitigation strategies for marine eutrophication.

Low denitrification rates and variable benthic nutrient fluxes characterize Long Island Sound sediments

Organic matter (OM) loading drives benthic metabolism and controls nitrogen (N), phosphorus (P), and carbon (C) cycling in coastal sediments. To better understand the influence of OM on benthic metabolism, we conducted sediment core incubations in Long Island Sound, NY (USA), an estuary heavily influenced by anthropogenic nutrient loading. Cores were collected during the summer and winter at five stations along a west to east transect representing a gradient of high to low nutrient inputs and subsequent OM deposition. Here we provide a comprehensive analysis of environmental drivers of benthic fluxes as well as the first directly measured rates of sediment denitrification and N-fixation, thus providing a missing piece of the N budget for Long Island Sound. Our findings show greatest sediment oxygen demand (SOD) in the western basin during the summer. Sediments were a source of dissolved inorganic N and P. Compared to historic SOD and ammonium fluxes, our measurements were about 50% lower, potentially reflecting larger scale perturbations (e.g., warming temperatures, decrease wind speed) or reduced N loading through improved management of wastewater treatment facilities. Sediments were a source of nitrous oxide (mean (± standard error): 8.63 ± 3.18 nmol m−2 h−1) and methane (23.80 ± 18.05 nmol m−2 h−1). Net sediment denitrification rates were low (10.34 ± 7.61 µmol N2–N m−2 h−1) and did not vary significantly across stations or seasons. These sediments have a N removal efficiency of ~ 30% with the potential to remove approximately 9% of the total land-based N load entering Long Island Sound.

Impact of acyl-homoserine lactones on the response of nitrogen cycling in sediment to florfenicol stress

Antibiotic residuals disrupt environmental microbial metabolism and can alter the nitrogen cycle. Quorum sensing has both inter- and intra-species effects that are directly related to the population densities necessary for microbial nitrogen cycling. Here, we explored how acyl-homoserine lactones (AHLs) can change the response of nitrogen cycling to florfenicol in sediments. AHLs might promote microbial reproduction in sediment under florfenicol stress. The relative abundances of Proteobacteria and Euryarchaeota in the antibiotic and AHL treatment groups were higher than those in the control group. AHLs reduced the effects of antibiotics on the abundance of Nitrospira at sampling times of 3d, 10d, and 20d. In the annotation results, nitrate reductase showed the highest abundance, followed by nitrite reductase, nitrogenase, nitric oxide (NO) reductase, nitrous oxide reductase, and ammonia monooxygenase. The abundances of these genes have changed in response to pressure by florfenicol and the addition of AHLs. We also found significant associations between the nitrogen cycle-related functional genes and dominant genera. In particular, glutamate metabolic enzymes and nitrate/nitrite transporters were the primary participants in correlation. Florfenicol can rapidly alter microbial community structures in sediments, affect the functional diversity of microorganisms, and hinder the nitrogen cycle. The response of microorganisms to florfenicol was regulated by the addition of AHLs. This process might alter the use and production of nitrogenous substances in the environment by functional communities in sediments.

Diversity of microbial community and its metabolic potential for nitrogen and sulfur cycling in sediments of Phu Quoc island, Gulf of Thailand.

Although Phu Quoc island, Gulf of Thailand possesses diverse marine and coastal ecosystems, biodiversity and metabolic capability of microbial communities remain poorly investigated. The aim of our study was to evaluate the biodiversity and metabolic potential of sediment microbial communities in Phu Quoc island. The marine sediments were collected from three different areas and analyzed by using 16S rRNA gene-based amplicon approach. A total of 1,143,939 reads were clustered at a 97% sequence similarity into 8,331 unique operational taxonomic units, representing 52 phyla. Bacteria and archaea occupied averagely around 86% and 14%, respectively, of the total prokaryotic community. Proteobacteria, Planctomycetes, Chloroflexi, and Thaumarchaeota were the dominant phyla in all sediments, which were involved in nitrogen and sulfur metabolism. Sediments harboring of higher nitrogen sources were found to coincide with increased abundance of archaeal phylum Thaumarchaeota. Predictive functional analysis showed high abundance prokaryotic genes associated with nitrogen cycling including nifA-Z, amoABC, nirA, narBIJ, napA, nxrAB, nrfA-K, nirBD, nirS, nirK, norB-Z, nlnA, ald, and ureA-J, based on taxonomic groups detected by 16S rRNA sequencing. Although the key genes involved in sulfur cycling were found to be at low to undetectable levels, the other genes encoding for sulfur-related biological processes were present, suggesting that alternative pathways may be involved in sulfur cycling at our study site. In conclusion, our study for the first time shed light on diversity of microbial communities in Phu Quoc island.

Sediments nitrogen cycling influenced by submerged macrophytes growing in winter

Restoration of submerged macrophytes is one of the important measures for ecological treatment of eutrophic lakes. The changes in physical and chemical conditions caused by submerged macrophytes also affect the process of benthic nitrogen cycling. The growth period of Potamogeton crispus is mainly in winter. In order to understand the effect of submerged macrophytes growing in winter on nitrification rate and denitrification rate in the process of nitrogen cycling, experiments were carried out from winter to summer with vegetated and non-vegetated treatments. The results showed that the effect of submerged macrophytes on water temperature was not significant in winter. The nitrogen cycling was mainly affected by variables, which were inorganic nitrogen and dissolved oxygen. Submerged macrophytes had little effect on nitrification rate, but had a certain inhibition on denitrification rate by providing oxygen from photosynthesis. In total, submerged macrophytes growing in winter have little effect on nitrogen cycling in sediment. However, submerged macrophytes growing in winter can increase the attachment surface of microbes and inhibit resuspension of sediment, which play a complementary role to submerged macrophytes growing in summer for maintaining stability of eutrophic lakes.

A novel bacterial phylum that participates in carbon and osmolyte cycling in the Challenger Deep sediments

Large amounts of detrital organic matter and osmolytes accumulate in the sediments of hadal trenches (>6000 m depth) due to the funnelling effect. It is still unknown whether there are novel active microbes that depend on specific carbon sources in extreme and isolated environments. In this study, we present a novel active bacterial phylum, Candidatus Tianyabacteria in the FCB superphylum, which was enriched in sediments collected from the Challenger Deep. Genome binning resulted in high-quality Ca. Tianyabacteria genomes representing two Ca. Tianyabacteria lineages (L1 and L2) in sediments 0-21 cm below the surface (cmbsf); L1 tends to be abundant in the upper layers (0-9 cmbsf), and L2 seems to be more prevalent in the deeper layers (12-21 cmbsf). Gene annotation and transcriptomics results indicate that the two lineages might import and catalyse amino acids and myo-inositol into central carbon metabolism for a heterotrophic lifestyle. Probably due to differences in environmental oxygen levels, the L2 genomes harbour gene clusters responsible for denitrification and fermentation, while the L1 genomes encode octahaem cytochrome c and multicopper oxidase using unknown substrates. The Ca. Tianyabacteria are thus novel heterotrophic organisms that participate in processes of carbon, nitrogen and organic osmolyte cycling in hadal sediments.

Effects of submerged vegetation on sediment nitrogen-cycling bacterial communities in Honghu Lake (China)

Sediment nitrogen (N) cycling is an important biological removal process for N permanently and driven by N-cycling microbial community. There is a growing interest in interactions between submerged vegetation (SV) and sediment N-cycling bacterial community, because of the close link between rooted aquatic plants and the sediment microbes. However, the effects of SV on the sediment N-cycling bacterial community are still controversial. Furthermore, the discrimination of direct and indirect effects of SV on the N-cycling bacterial community remains unclear. Here, we investigated the biomass and species richness of SV and determined the corresponding environment factors (water quality and sediment properties) in Honghu Lake (China). We also used functional genes as markers to unveil the bacterial diversity and community composition and abundance in lake sediments. Our results showed that biomass and species richness of SV affected the composition, diversity and abundance of sediment N-cycling bacterial communities through improving lake water quality and sediment properties. With the increasing richness and abundance of SV, the diversity of most N-cycling bacterial assemblages including nitrifying, denitrifying and DNRA bacteria decreased, while the abundance increased. However, the anammox bacterial assemblage in sediments showed inverse trends. Sediment carbon vs. nitrogen (C:N) ratio negatively affected the abundance of amoA and nirS + nirK + nosZ bacterial assemblages. Additionally, due to the presence of SV, positive interactions among N-cycling bacterial assemblages were found, such as amoA and nrfA bacterial assemblages. Overall, our findings confirmed the significant effects of SV on the N-cycling bacterial community structure and abundance. Moreover, the direct effects of SV on the N-cycling bacterial community and the indirect effects through altering the sediment C were clarified in our study. Our results casted a new light on the negative effects of high C:N ratio. From the study, we made a conclusion that the better SV develops, the greater nitrogen removal occurs in lake sediments.

Sediment biogeochemistry along an oyster aquaculture chronosequence

Oyster aquaculture is expanding globally, and there has been a recent research surge examining how oyster farms alter coastal ecosystems. Yet, until now, the role of time in these studies has largely been missing. Here we used anin situchronosequence approach to determine how the presence of oyster aquaculture (Crassostrea virginica) altered sediment nitrogen (N), oxygen (O2), and phosphorus (P) cycling. Overall we found that the sum of nitrogen fluxes increased significantly following addition of aquaculture, and switched from net N consumption (i.e. net nitrogen fixation: -14.41 µmol N m-2h-1) to production (i.e. net denitrification: 553.57 µmol N m-2h-1). Ammonium (NH4+) fluxes did not differ between bare sediment and oyster aquaculture. Additionally, both the magnitude of N2and NH4+fluxes oscillated on an annual scale of aquaculture age, but not predictably so. We observed significantly more variance (σ2) in dinitrogen and NH4+fluxes in sediments beneath aquaculture, indicating increased non-linearity. O2fluxes increased from Years 4 to 6, before returning to baseline conditions. There were no differences in sediment P cycling. This study demonstrates that sediment biogeochemical processes can become non-linear under the pressure of oyster aquaculture, and this non-linearity likely has important implications for ecosystem function.

Correlations of functional genes involved in methane, nitrogen and sulfur cycling in river sediments

Microorganisms in sediments play an important role in carbon (C)- , nitrogen (N)- and sulfur (S)-cycles by regulating forms and contents of these elements. The coupled system or synergistic reaction between these elemental cycles could effectively alleviate the pollution of C, N, and S in sediments. However, little is known about the indicators indicating the coupled system in surface sediments. We hypothesized that the correlations of functional genes could be used as a reference index speculating the coupled systems of C-N-S in this study. Here, 135 sediment samples from Huaihe River Basin in Northern Anhui Province were collected. To test this hypothesis, we investigated the relationships of C, N, S-functional genes, the co-occurrence analysis of microbial functional groups and the contributions of functional genes to nutrients. The findings revealed that the synergetic relationships between raw or predicted genes could speculate the coupled systems. The network analysis of microbial co-occurrence patterns also implied the occurrence of coupled processes. Moreover, the results shed light on the important role of Desulfobacterium and Methanosaeta. This hypothesis was further underpinned by the dominant prediction of the C- and S-functional genes on the nitrogen nutrition. Taken together, we could concluded that that the sulfate-reducing gene (aprA) and the methanogenic gene (mcrA) played a major role in the coupled processes in the elemental biogeochemical cycle. This study provided a valuable reference for predicting the coupled metabolism of river sediments.

The effects of crude oil on microbial nitrogen cycling in coastal sediments

Crude oil could affect certain critical microbial processes of nitrogen cycling (N-cycling) in coastal sediments, and disturb the nitrogen balance. However, the understanding of the effects of crude oil on coastal sediments N-cycling under human disturbance was still limited. In this study, two sediments (named SY and HB with heavy and slight pollution, respectively) were sampled from Hangzhou Bay, China. After an incubation with exposure to different amounts of crude oil in above two sediments for 30 days, we found that crude oil affected microbial N-cycling in multiple levels. Potential rate measurements revealed that crude oil stimulated potential denitrification and N2O emissions in both sediments, which showed a higher influence on denitrification rates in higher concentration of oil. Quantitative PCR revealed that crude oil greatly increased abundances of bacterial and archaeal 16S rRNA genes and N-cycling genes (nirS, nosZ, nrfA, part of AOA and AOB amoA). On the other hand, only a few genes (16S rRNA and nrfA) showed higher transcriptional activities in oil-addition treatments. Results about relative changes of N-cycling genes revealed that the variations of N-cycling genes in oil-addition treatments were related to sediment types but not crude oil concentrations, and the genes in HB were more sensitive to crude oil than SY. Network analysis of N-cycling genes found that crude oil decreased the complexity of N-cycling gene networks in SY, while increased complexity in HB, and led to more competition among N-cycling microbes. Our findings help to look into the effects of crude oil on key N-cycling processes, and improve the understanding of the interactions among N-cycling under crude oil contamination.

Seasonal patterns of benthic-pelagic coupling in oyster habitats

Oysters enhance benthic-pelagic coupling in coastal systems by moving large quantities of suspended particulates to the sediments, stimulating biogeochemical processes. Recent research efforts have focused on quantifying the impact of oysters on coastal biogeochemical cycling, yet there is little consensus on how oysters influence processes across systems. A potential driver of this variance is availability of organic material suspended in the water column and subsequent loading to sediment by oysters. Here, we measured fluxes of sediment di-nitrogen (N2-N), ammonium (NH4+), combined nitrate-nitrite (NOx), and phosphate (PO43-) in spring, summer, and fall at 2 oyster reefs and 1 farm in a temperate estuary (Narragansett Bay, Rhode Island). We then linked these fluxes with patterns of water column primary production. Nitrogen removal from the system was highest in spring, when we detected net sediment denitrification (48.8 µmol N2-N m-2 h-1) following a winter-spring diatom bloom. In contrast, we measured sediment N2 fixation in fall (-44.8 µmol N2-N m-2 h-1) at rates nearly equivalent to spring denitrification. In the summer, we measured a nearly net zero sediment N2-N flux (-2.7 µmol N2-N m-2 h-1). Recycling of nitrogen to the water column was consistent across seasons, composed almost exclusively of NH4+. These results demonstrate that sediment nitrogen cycling in oyster habitats is dynamic and can change rapidly based on seasonal patterns of productivity. At carrying capacity, the impact of oysters on nitrogen cycling is large and should be considered during efforts to increase oyster populations through aquaculture or reef restoration.

Silver nanoparticles and Fe(III) co-regulate microbial community and N2O emission in river sediments

The effects of environmental concentration silver nanoparticles (ecAgNPs) on microbial communities and the nitrogen cycling in river sediments remain largely uncharacterized. As a fundamental component of sediments, Fe(III) can interact with AgNPs and participate in nitrogen transformation processes. N2O is an important intermediate in nitrogen transformation processes and can be a potent greenhouse gas with significant environmental effects. However, the impacts of the co-existence of AgNPs and Fe(III) on microbial communities and N2O emission in river sediments are still unclear. In the present study, mesocosm experiments were conducted to assess the changes of microbial communities and N2O emission in response to the co-existence of AgNPs and environmental concentration Fe(III). Our results revealed that the microbial community diversity and N2O emission in river sediments responded differently to ecAgNPs (0.05 mg/kg) and high-polluting concentration AgNPs (hcAgNPs, 5 mg/kg), which was further regulated by the environmental concentration Fe(III) (1 mg/g and 10 mg/g). After ecAgNPs treatments, a marked increase was observed in microbial diversity compared to hcAgNPs treatments, regardless of the Fe(III) concentration in the sediment. The β-NTI index indicated that AgNPs had stronger impacts on phylogenetic distance of bacterial communities in sediments containing 1 mg/g Fe(III) than that containing 10 mg/g Fe(III). In sediments containing 1 mg/g Fe(III), ecAgNPs did not affect N2O emission, but hcAgNPs significantly inhibited the emission of N2O. However, in sediments containing 10 mg/g Fe(III), N2O emission was significantly stimulated upon exposure to ecAgNPs, but the inhibition effect of hcAgNPs was barely observed. Functional prediction and real-time PCR analyses indicated that AgNPs and Fe(III) predominantly affected N2O emissions by affecting the abundance of the nirK gene. Our results provide new insights into the ecological impacts of the co-existence of environmental concentration AgNPs and Fe(III) in altering microbial communities and nitrogen transformation functions in river sediments.

Metagenomics coupled with biogeochemical rates measurements provide evidence that nitrate addition stimulates respiration in salt marsh sediments

AbstractHigh‐throughput sequencing has enabled robust shotgun metagenomic sequencing that informs our understanding of the genetic basis of important biogeochemical processes. Slower to develop, however, are the application of these tools in a controlled experimental framework that pushes the field beyond exploratory analysis toward hypothesis‐driven research. We performed flow‐through reactor experiments to examine how salt marsh sediments from varying depths respond to nitrate addition and linked biogeochemical processes to this underlying genetic foundation. Understanding the mechanistic basis of carbon and nitrogen cycling in salt marsh sediments is critical for predicting how important ecosystem services provided by marshes, including carbon storage and nutrient removal, will respond to global change. Prior to the addition of nitrate, we used metagenomics to examine the functional potential of the sediment microbial community that occurred along a depth gradient, where organic matter reactivity changes due to decomposition. Metagenomic data indicated that genes encoding enzymes involved in respiration, including denitrification, were higher in shallow sediments, and genes indicative of resource limitation were greatest at depth. After 92 d of nitrate enrichment, we measured cumulative increases in dissolved inorganic carbon production, denitrification, and dissimilatory nitrate reduction to ammonium; these rates correlated strongly with genes that encode essential enzymes in these important pathways. Our results highlight the importance of controlled experiments in linking biogeochemical rates to underlying genetic pathways. Furthermore, they indicate the importance of nitrate as an electron acceptor in fueling microbial respiration, which has consequences for carbon and nitrogen cycling and fate in coastal marine systems.

Denitrification responses to increasing cadmium exposure in Baltic Sea sediments

Benthic ecosystems have come under intense pressure, due to eutrophication-driven oxygen decline and industrial metal contamination. One of the most toxic metals is Cadmium (Cd), which is lethal to many aquatic organisms already at low concentrations. Denitrification by facultative anaerobic microorganisms is an essential process to transform, but also to remove, excess nitrate in eutrophied systems. Cd has been shown to decrease denitrification and sequester free sulfide, which is available when oxygen is scarce and generally inhibits complete denitrification (i.e. N2O to N2). In polluted sediments, an interaction between oxygen and Cd may influence denitrification and this relationship has not been studied. For example, in the Baltic Sea some sediments are double exposed to both Cd and hypoxia. In this study, we examined how the double exposure of Cd and fluctuations in oxygen affects denitrification in Baltic Sea sediment. Results show that oxygen largely regulated N2O and N2 production after 21 days of exposure to Cd (ranging from 0 to 500 μg/L, 5 different treatments, measured by the isotope pairing technique (IPT)). In the high Cd treatment (500 μg/L) the variation in N2 production increased compared to the other treatments. Increases in N2 production are suggested to be an effect of 1) enhanced nitrification that increases NO3− availability thus stimulating denitrification, and 2) Cd successfully sequestrating sulfide (yielding CdS), which allows for full denitrification to N2. The in situ field sediment contained initially high Cd concentrations in the pore water (∼10 μg/L) and microbial communities might already have been adapted to metal stress, making the effect of low Cd levels negligible. Here we show that high levels of cadmium pollution might increase N2 production and influence nitrogen cycling in marine sediments.

Source of organic detritus and bivalve biomass influences nitrogen cycling and extracellular enzyme activity in estuary sediments

In aquatic ecosystems, natural processes that remove nitrogen from the biologically available pool (e.g. denitrification) have been intensively studied as an ecosystem function that reduces eutrophication. The quantity of sediment organic matter is a key driver of denitrification with percent organic content positively related to rates of nitrogen removal; however, few studies have investigated the influence of the quality of organic matter on nitrogen cycling in estuarine sediments despite shifts in primary producers with eutrophication. This laboratory study using intact benthic communities investigates the influence of various organic detritus sources, which vary in their C:N ratio, on nitrogen gas (N2) and solute fluxes and extracellular enzyme activity in estuarine sediments. A custom-built tank with a removable front plate was used with a planar optode film to image sediment oxygenation. Mangrove leaf detritus significantly increased the net N2 production in sediments, while the deposition of other detrital sources and control sediments produced net N2 consumption. Sulfatase activity was significantly reduced in the mangrove leaves and seagrass treatments, suggesting alteration of heterotrophic microbial activity with reducing oxygen conditions. Leucine aminopeptidase activity, indicating nitrogen cycling, was reduced in all treatments, suggesting the organic detritus provided a nitrogen supplement or reduced the activity of extracellular enzymes producing microbes. Bivalve biomass increased net nitrogen gas fluxes in some treatments. Our results indicate different detrital sources may have varying impacts on the removal of bioavailable nitrogen through denitrification and show that feedbacks in biogeochemical cycles may occur with changes in organic detrital source pools.

The Effect of Chironomid Larvae on Nitrogen Cycling and Microbial Communities in Soft Sediments

The combination of biogeochemical methods and molecular techniques has the potential to uncover the black-box of the nitrogen (N) cycle in bioturbated sediments. Advanced biogeochemical methods allow the quantification of the process rates of different microbial processes, whereas molecular tools allow the analysis of microbial diversity (16S rRNA metabarcoding) and activity (marker genes and transcripts) in biogeochemical hot-spots such as the burrow wall or macrofauna guts. By combining biogeochemical and molecular techniques, we analyzed the role of tube-dwelling Chironomus plumosus (Insecta, Diptera) larvae on nitrification and nitrate reduction processes in a laboratory experiment with reconstructed sediments. We hypothesized that chironomid larvae stimulate these processes and host bacteria actively involved in N-cycling. Our results suggest that chironomid larvae significantly enhance the recycling of ammonium (80.5 ± 48.7 µmol m−2 h−1) and the production of dinitrogen (420.2 ± 21.4 µmol m−2 h−1) via coupled nitrification–denitrification and the consumption of water column nitrates. Besides creating oxygen microniches in ammonium-rich subsurface sediments via burrow digging and ventilation, chironomid larvae serve as hot-spots of microbial communities involved in N-cycling. The quantification of functional genes showed a significantly higher potential for microbial denitrification and nitrate ammonification in larvae as compared to surrounding sediments. Future studies may further scrutinize N transformation rates associated with intimate macrofaunal–bacteria associations.

Nitrifier abundance and diversity peak at deep redox transition zones

More than half of the global ocean floor is draped by nutrient-starved sediments characterized by deep oxygen penetration and a prevalence of oxidized nitrogen. Despite low energy availability, this habitat hosts a vast microbial population, and geochemical characteristics suggest that nitrogen compounds are an energy source critical to sustaining this biomass. However, metabolic rates of nitrogen transformation and their link to microbial survival in this global-scale ecosystem remain virtually unknown. Here we provide quantitative constraints on microbial nitrogen cycling in open ocean oligotrophic sediments from seafloor to basement, spanning approximately 8 million years. We find active microbial nitrogen transformation throughout the sediment column but at very low rates. Local peaks in diversity and abundance of nitrifiers and denitrifiers occur at redox transition zones deep within the sediments, strongly indicating that these microbes are revived from their maintenance state and start growing again after millions of years of attrition.

Polychaete mucopolysaccharide alters sediment microbial diversity and stimulates ammonia-oxidising functional groups.

Sediment nitrogen cycling is a network of microbially mediated biogeochemical processes that are vital in regulating ecosystem functioning. Mucopolysaccharides (mucus) are produced by many invertebrates and have the potential to be an important source of organic carbon and nitrogen to sediment microorganisms. At present, we have limited understanding of how mucopolysaccharide moderates total sediment microbial communities and specific microbial functional groups that drive nitrogen cycling processes. To start addressing this knowledge gap, sediment slurries were incubated with and without Hediste diversicolor mucus. Changes in dissolved inorganic nitrogen (ammonia, nitrite and nitrate) concentrations and bacterial and archaeal community diversity were assessed. Our results showed that mucopolysaccharide addition supported a more abundant and distinct microbial community. Moreover, mucus stimulated the growth of bacterial and archaeal ammonia oxidisers, with a concomitant increase in nitrite and nitrate. Hediste diversicolor mucopolysaccharide appears to enhance sediment nitrification rates by stimulating and fuelling nitrifying microbial groups. We propose that invertebrate mucopolysaccharide secretion should be considered as a distinct functional trait when assessing invertebrate contributions to sediment ecosystem function. By including this additional trait, we can improve our mechanistic understanding of invertebrate-microbe interactions in nitrogen transformation processes and provide opportunity to generate more accurate models of global nitrogen cycling.

Spatial and temporal heterogeneity in the structure and function of sediment bacterial communities of a tropical mangrove forest.

Bacterial communities of mangrove sediments are well appreciated for their role in nutrient cycling. However, spatiotemporal variability in these communities over large geographical scale remains understudied. We investigated sediment bacterial communities and their metabolic potential in an intertidal mangrove forest of India, Bhitarkanika, using high-throughput sequencing of 16S rRNA genes and community-level physiological profiling. Bulk surface sediments from five different locations representing riverine and bay sites were collected over three seasons. Seasonality largely explained the variation in the structural and metabolic patterns of the sediment bacterial communities. Freshwater Actinobacteria were more abundant in monsoon, whereas γ-Proteobacteria demonstrated higher abundance in summer. Distinct differences in the bacterial community composition were noted between riverine and bay sites. For example, salt-loving marine bacteria affiliated to Oceanospirillales were more prominent in the bay sites than the riverine sites. L-asparagine, N-acetyl-D-glucosamine, and D-mannitol were the preferentially utilized carbon sources by bacterial communities. Bacterial community composition was largely governed by salinity and organic carbon content of the sediments. Modeling analysis revealed that the abundance of δ-Proteobacteria increased with salinity, whereas β-Proteobacteria displayed an opposite trend. Metabolic mapping of taxonomic data predicted biogeochemical functions such as xylan and chitin degradation, ammonia oxidation, nitrite reduction, and sulfate reduction in the bacterial communities suggesting their role in carbon, nitrogen, and sulfur cycling in mangrove sediments. This study has provided valuable clues about spatiotemporal heterogeneity in the structural and metabolic patterns of bacterial communities and their environmental determinants in a tropical mangrove forest.