Shell biofilm nitrification and gut denitrification contribute to emission of nitrous oxide by the invasive freshwater mussel Dreissena polymorpha (zebra mussel)

A systematic review of invasive non-native freshwater bivalves

The introduction of invasive species has become an increasing environmental problem in freshwater ecosystems due to the high economic and ecological impacts it has generated. This systematic review covers publications from 2010 to 2020, focusing on non-native invasive freshwater bivalves, a particularly relevant and widespread introduced taxonomic group in fresh waters. We collected information on the most studied species, the main objectives of the studies, their geographical location, study duration, and type of research. Furthermore, we focused on assessing the levels of ecological evidence presented, the type of interactions of non-native bivalves with other organisms and the classification of their impacts. A total of 397 publications were retrieved. The studies addressed a total of 17 species of non-native freshwater bivalves; however, most publications focused on the species Corbicula fluminea and Dreissena polymorpha, which are recognised for their widespread distribution and extensive negative impacts. Many other non-native invasive bivalve species have been poorly studied. A high geographical bias was also present, with a considerable lack of studies in developing countries. The most frequent studies had shorter temporal periods, smaller spatial extents, and more observational data, were field-based, and usually evaluated possible ecological impacts at the individual and population levels. There were 94 publications documenting discernible impacts according to the Environmental Impact Classification for Alien Taxa (EICAT). However, 41 of these publications did not provide sufficient data to determine an impact. The most common effects of invasive bivalves on ecosystems were structural alterations, and chemical and physical changes, which are anticipated due to their role as ecosystem engineers. Despite a considerable number of studies in the field and advances in our understanding of some species over the past decade, long-term data and large-scale studies are still needed to understand better the impacts, particularly at the community and ecosystem levels and in less-studied geographic regions. The widespread distribution of several non-native freshwater bivalves, their ongoing introductions, and high ecological and economic impacts demand continued research. Systematic reviews such as this are essential for identifying knowledge gaps and guiding future research to enable a more complete understanding of the ecological implications of invasive bivalves, and the development of effective management strategies.

Norfloxacin affects inorganic nitrogen compound transformation in tailwater containing Corbicula fluminea

The Asian clam, Corbicula fluminea, commonly used in engineered wetlands receiving tailwater, affects nitrogen compound transformation in water. This study investigates how a commonly observed antibiotic in tailwater, norfloxacin, impact nitrogen compound transformation in tailwater containing C. fluminea. The clam was exposed to artificial tailwater with norfloxacin (0, 0.2, 20, and 2000 μg/L) for 15 days. Water properties, C. fluminea ecotoxicity responses, microorganism composition and nitrification- or denitrification-related enzyme activities were measured. Results revealed norfloxacin-induced increases and reductions in tailwater NH4+ and NO2- concentrations, respectively, along with antioxidant system inhibition, organ histopathological damage and disruption of water filtering and digestion system. Microorganism composition, especially biodiversity indices, varied with medium (clam organs and exposure water) and norfloxacin concentrations. Norfloxacin reduced NO2- content by lowering the ratio between microbial nitrifying enzyme (decreased hydroxylamine oxidoreductase and nitrite oxidoreductase activity) and denitrifying enzyme (increased nitrate reductase and nitrite reductase activity) in tailwater. Elevated NH4+ content resulted from upregulated ammonification and inhibited nitrification of microorganisms in tailwater, as well as increased ammonia emission from C. fluminea due to organ damage and metabolic disruption of the digestion system. Overall, this study offers insights into using benthic organisms to treat tailwater with antibiotic residues, especially regarding nitrogen treatment.

Ecological Trait-Based Digital Categorization of Microbial Genomes for Denitrification Potential

Microorganisms encode proteins that function in the transformations of useful and harmful nitrogenous compounds in the global nitrogen cycle. The major transformations in the nitrogen cycle are nitrogen fixation, nitrification, denitrification, anaerobic ammonium oxidation, and ammonification. The focus of this report is the complex biogeochemical process of denitrification, which, in the complete form, consists of a series of four enzyme-catalyzed reduction reactions that transforms nitrate to nitrogen gas. Denitrification is a microbial strain-level ecological trait (characteristic), and denitrification potential (functional performance) can be inferred from trait rules that rely on the presence or absence of genes for denitrifying enzymes in microbial genomes. Despite the global significance of denitrification and associated large-scale genomic and scholarly data sources, there is lack of datasets and interactive computational tools for investigating microbial genomes according to denitrification trait rules. Therefore, our goal is to categorize archaeal and bacterial genomes by denitrification potential based on denitrification traits defined by rules of enzyme involvement in the denitrification reduction steps. We report the integration of datasets on genome, taxonomic lineage, ecosystem, and denitrifying enzymes to provide data investigations context for the denitrification potential of microbial strains. We constructed an ecosystem and taxonomic annotated denitrification potential dataset of 62,624 microbial genomes (866 archaea and 61,758 bacteria) that encode at least one of the twelve denitrifying enzymes in the four-step canonical denitrification pathway. Our four-digit binary-coding scheme categorized the microbial genomes to one of sixteen denitrification traits including complete denitrification traits assigned to 3280 genomes from 260 bacteria genera. The bacterial strains with complete denitrification potential pattern included Arcobacteraceae strains isolated or detected in diverse ecosystems including aquatic, human, plant, and Mollusca (shellfish). The dataset on microbial denitrification potential and associated interactive data investigations tools can serve as research resources for understanding the biochemical, molecular, and physiological aspects of microbial denitrification, among others. The microbial denitrification data resources produced in our research can also be useful for identifying microbial strains for synthetic denitrifying communities.

Characterizing the Gut Microbial Communities of Native and Invasive Freshwater Bivalves after Long-Term Sample Preservation

Freshwater mussels are important indicators of the overall health of their environment but have suffered declines that have been attributed to factors such as habitat degradation, a loss of fish hosts, climate change, and excessive nutrient inputs. The loss of mussel biodiversity can negatively impact freshwater ecosystems such that understanding the mussel's gut microbiome has been identified as a priority topic for developing conservation strategies. In this study, we determine whether ethanol-stored specimens of freshwater mussels can yield representative information about their gut microbiomes such that changes in the microbiome through time could potentially be determined from museum mussel collections. A short-term preservation experiment using the invasive clam Corbicula fluminea was used to validate the use of ethanol as a method for storing the bivalve microbiome, and the gut microbiomes of nine native mussel species that had been preserved in ethanol for between 2 and 9 years were assessed. We show that ethanol preservation is a valid storage method for bivalve specimens in terms of maintaining an effective sequencing depth and the richness of their gut bacterial assemblages and provide further insight into the gut microbiomes of the invasive clam C. fluminea and nine species of native mussels. From this, we identify a "core" genus of bacteria (Romboutsia) that is potentially common to all freshwater bivalve species studied. These findings support the potential use of ethanol-preserved museum specimens to examine patterns in the gut microbiomes of freshwater mussels over long periods.

Shellfish as a bioremediation tool: A review and meta-analysis

Over the last century, human activities have increased the amount of nutrients inputs to terrestrial and aquatic ecosystems. These activities have altered nitrogen (N) and phosphorus (P) cycling, causing substantial changes in ecosystem function such as provision of clean air and water. Strategies that reduce and remove excess nutrients are urgently needed to remediate impacted systems. Reef-forming shellfish (oysters and mussels) can play a crucial role in nutrient cycling, particularly in N removal from aquatic systems by providing substrate for microbial colonisation and enhancing microbial denitrification in the surrounding sediments. However, the potential for shellfish to enhance nutrient cycling (and denitrification) will likely vary spatially and in response to several environmental factors. Here, we used 1) a qualitative analysis to review nutrient processes occurring on shellfish; and 2) a meta-analysis to evaluate the influence of shellfish on benthic metabolism and nutrient cycling in surrounding sediments, and how that is influenced by environmental factors such as grain size, seasonality, water body type, and tidal position. Overall, we found that shellfish increased oxygen consumption, with consequent release of ammonia (NH_4⁺) and phosphate (PO₄^3-) from shellfish and their surrounding sediments. These parameters did not depend on grain size, water body type and tidal height, but the release of PO₄^3- was variable between seasons, being highest during summer and autumn. Shellfish presence also enhanced denitrification measured as dinitrogen gas (N₂) efflux on both reefs and sediments. Denitrification was highest in lagoons; in sandy sediments; and during the warmest season (summer). Thus, our findings highlight that environmental context can mediate the effects of shellfish reefs on sediment function. This information is important for managers seeking to use these animals as an effective bioremediation tool.

Intrahabitat Differences in Bacterial Communities Associated with Corbicula fluminea in the Large Shallow Eutrophic Lake Taihu

The Asian clam Corbicula fluminea is a keystone zoobenthos in freshwater ecosystems. However, its associated microbiome is not well understood. We investigated the bacterial communities of this clam and its surrounding environment, including sediment and water simultaneously, in a large lake by means of 16S rRNA gene sequencing. Approximately two-thirds of the bacterial operational taxonomic units (OTUs) associated with clams were observed in the surrounding environment and mostly from particle-associated samples. The associated bacterial communities were site specific and more similar to environmental bacteria from the same site than those at other sites, suggesting a local environmental influence on host bacteria. However, the significant differences in bacterial diversities and compositions between the clam and the environment also indicated strong host selection pressure on bacteria from the surrounding environment. Bacteria affiliated with Firmicutes, Spirochaetes, Tenericutes, Bacteroidetes, Epsilonbacteraeota, Patescibacteria, and Fusobacteria were found to be significantly enriched in the clams in comparison to their local environment. Oligotyping analyses of the core-associated bacterial OTUs also demonstrated that most of the core OTUs had lower relative abundances and occurrence frequencies in environmental samples. The core bacterial OTUs were found to play an important role in maintaining the stability of the bacterial community network. These core bacteria included the two most abundant taxa Romboutsia and Paraclostridium with the potential function of fermenting polysaccharides for assisting host clams in food digestion. Overall, we demonstrate that clam-associated bacteria were spatially dynamic and site specific, which were mainly structured both by local environments and host selection. IMPORTANCE The Asian clam Corbicula fluminea is an important benthic clam in freshwater ecosystems due to its high population densities and high filtering efficiency for particulate organic matter. While the associated microbiota is believed to be vital for host living, our knowledge about the compositions, sources, and potential functions is still lacking. We found that C. fluminea offers a unique ecological niche for specific lake bacteria. We also observed high intrahabitat variation in the associated bacterial communities. Such variations were driven mainly by local environments, followed by host selection pressure. While the local microbes served as a source of the clam-associated bacteria, host selection resulted in enrichments of bacterial taxa with the potential for assisting the host in organic matter digestion. These results significantly advance our current understanding of the origins and ecological roles of the microbiota associated with a keynote clam in freshwater ecosystems.

Zebra Mussel Holobionts Fix and Recycle Nitrogen in Lagoon Sediments

Bivalves are ubiquitous filter-feeders able to alter ecosystems functions. Their impact on nitrogen (N) cycling is commonly related to their filter-feeding activity, biodeposition, and excretion. A so far understudied impact is linked to the metabolism of the associated microbiome that together with the host constitute the mussel's holobiont. Here we investigated how colonies of the invasive zebra mussel (Dreissena polymorpha) alter benthic N cycling in the shallow water sediment of the largest European lagoon (the Curonian Lagoon). A set of incubations was conducted to quantify the holobiont's impact and to quantitatively compare it with the indirect influence of the mussel on sedimentary N transformations. Zebra mussels primarily enhanced the recycling of N to the water column by releasing mineralized algal biomass in the form of ammonium and by stimulating dissimilatory nitrate reduction to ammonium (DNRA). Notably, however, not only denitrification and DNRA, but also dinitrogen (N2) fixation was measured in association with the holobiont. The diazotrophic community of the holobiont diverged substantially from that of the water column, suggesting a unique niche for N2 fixation associated with the mussels. At the densities reported in the lagoon, mussel-associated N2 fixation may account for a substantial (and so far, overlooked) source of bioavailable N. Our findings contribute to improve our understanding on the ecosystem-level impact of zebra mussel, and potentially, of its ability to adapt to and colonize oligotrophic environments.

Potential nitrous oxide production by marine shellfish in response to warming and nutrient enrichment

Bivalves facilitate microbial nitrogen cycling, which can produce nitrous oxide (N2O), a potent greenhouse gas. Potential N₂O production by three marine bivalves (Mytilus edulis, Mercenaria mercenaria and Crassostrea virginica) was measured in the laboratory including responses to nitrogen (N) loading and/or warming over short-terms (up to 14 or 28 days). N additions (targeting 100 μM-N ammonium nitrate) or warming (22 °C) individually and in combination were applied with experimental controls (20 μM-N, 19 °C). N₂O production rates were higher with N additions for all species, but warming lacked significant direct effects. Ammonium and nitrate concentrations varied but were consistent with nitrification as a potential N₂O source for all bivalves. Highest N₂O emissions (7.5 nmol N₂O g^-1 h^-1) were from M. edulis under hypoxic conditions coincident with a drop in pH. Macro-epifauna on M. edulis did not significantly alter N₂O production. Thus, under short-term hypoxic conditions, micro-organisms in M. edulis guts may be a particularly significant source of N₂O.

Hypoxically Induced Nitric Oxide: Potential Role as a Vasodilator in Mytilus edulis Gills

Intertidal Mytilus edulis experience rapid transgression to hypoxia when they close their valves during low tide. This induces a physiological stress response aiming to stabilize tissue perfusion against declining oxygen partial pressure in shell water. We hypothesized that nitric oxide (NO) accumulation supports blood vessel opening in hypoxia and used live imaging techniques to measure NO and superoxide anion (O2∙-) formation in hypoxia-exposed gill filaments. Thirty minutes of moderate (7 kPa pO₂) and severe hypoxia (1 kPa pO₂) caused 1.6- and 2.4-fold increase, respectively, of NO accumulation in the endothelial muscle cells of the hemolymphatic vessels of the gill filaments. This led to a dilatation of blood vessel diameter by 43% (7 kPa) and 56% (1 kPa), which facilitates blood flow. Experiments in which we applied the chemical NO-donor Spermine NONOate (concentrations ranging from 1 to 6 mM) under normoxic conditions corroborate the dilatational effect of NO on the blood vessel. The formation of O2∙- within the filament epithelial cells increased 1.5 (7 kPa) and 2-fold (1 kPa) upon treatment. Biochemical analysis of mitochondrial electron transport complexes in hypoxia-exposed gill tissue indicates decreased activity of complexes I and III in both hypoxic conditions; whereas complex IV (cytochrome-c oxidase) activity increased at 7 kPa and decreased at 1 kPa compared to normoxic exposure conditions. This corresponds to the pattern of pO₂-dependent gill respiration rates recorded in ex-vivo experiments. Severe hypoxia (1 kPa) appears to have a stabilizing effect on NO accumulation in gill cells, since less O₂ is available for NO oxidation to nitrite/nitrate. Hypoxia thus supports the NO dependent inhibition of complex IV activity, a mechanism that could fine tune mitochondrial respiration to the local O₂ availability in a tissue. Our study highlights a basal function of NO in improving perfusion of hypoxic invertebrate tissues, which could be a key mechanism of tolerance toward environmental O₂ variations.

Intensified nutrients removal in constructed wetlands by integrated Tubifex tubifex and mussels: Performance and mechanisms

The synergy of Tubifex tubifex (T. tubifex) and mussels on SFCWs (named SFCW-MT) performance was well studied in laboratory throughout a year. The SFCW-MT were steady operated with high TN and TP treatment, with the removal efficiencies of 37.85 ± 5.22% and 39.26 ± 5.20% even in winter. The mussels had excellent NH₄-N removal efficiency, and avoid the shortage of NH₄-N removal with T. tubifex in winter. Simultaneously, the SFCW-MT improved the NO₃-N treatment by 51% than that in control group. The plant growth was improved in SFCW-MT, which reflected in the improvement of total chlorophyll contents and plant heights. The N and P absorbed by wetland plants and adsorbed by substrate were both increased with mussels. Microbial analysis results revealed that, the mussels could keep the abundance of nitrifiers despite the negative effect of T. tubifex. On that basis, the improved proportions of denitrifiers (Firmicutes) have a significantly recognized role in NO₃-N transformation in SFCW-MT. The gut and membrane sections of mussels, as well as T. tubifex, also has proportions of denitrifiers and part of nitrifiers, and thus changed the microbial community in substrate. This evidence indicated that the co-existence of T. tubifex and mussels have potential application for simultaneous removal of NH₄-N and NO₃-N in CWs.

Methane fluxes from coastal sediments are enhanced by macrofauna

Methane and nitrous oxide are potent greenhouse gases (GHGs) that contribute to climate change. Coastal sediments are important GHG producers, but the contribution of macrofauna (benthic invertebrates larger than 1 mm) inhabiting them is currently unknown. Through a combination of trace gas, isotope, and molecular analyses, we studied the direct and indirect contribution of two macrofaunal groups, polychaetes and bivalves, to methane and nitrous oxide fluxes from coastal sediments. Our results indicate that macrofauna increases benthic methane efflux by a factor of up to eight, potentially accounting for an estimated 9.5% of total emissions from the Baltic Sea. Polychaetes indirectly enhance methane efflux through bioturbation, while bivalves have a direct effect on methane release. Bivalves host archaeal methanogenic symbionts carrying out preferentially hydrogenotrophic methanogenesis, as suggested by analysis of methane isotopes. Low temperatures (8 °C) also stimulate production of nitrous oxide, which is consumed by benthic denitrifying bacteria before it reaches the water column. We show that macrofauna contributes to GHG production and that the extent is dependent on lineage. Thus, macrofauna may play an important, but overlooked role in regulating GHG production and exchange in coastal sediment ecosystems.

Denitrification potential of the eastern oyster microbiome using a 16S rRNA gene based metabolic inference approach

The eastern oyster (Crassostrea virginica) is a foundation species providing significant ecosystem services. However, the roles of oyster microbiomes have not been integrated into any of the services, particularly nitrogen removal through denitrification. We investigated the composition and denitrification potential of oyster microbiomes with an approach that combined 16S rRNA gene analysis, metabolic inference, qPCR of the nitrous oxide reductase gene (nosZ), and N₂ flux measurements. Microbiomes of the oyster digestive gland, the oyster shell, and sediments adjacent to the oyster reef were examined based on next generation sequencing (NGS) of 16S rRNA gene amplicons. Denitrification potentials of the microbiomes were determined by metabolic inferences using a customized denitrification gene and genome database with the paprica (PAthway PRediction by phylogenetIC plAcement) bioinformatics pipeline. Denitrification genes examined included nitrite reductase (nirS and nirK) and nitrous oxide reductase (nosZ), which was further subdivided by genotype into clade I (nosZI) or clade II (nosZII). Continuous flow through experiments measuring N₂ fluxes were conducted with the oysters, shells, and sediments to compare denitrification activities. Paprica properly classified the composition of microbiomes, showing similar classification results from Silva, Greengenes and RDP databases. Microbiomes of the oyster digestive glands and shells were quite different from each other and from the sediments. The relative abundance of denitrifying bacteria inferred by paprica was higher in oysters and shells than in sediments suggesting that oysters act as hotspots for denitrification in the marine environment. Similarly, the inferred nosZI gene abundances were also higher in the oyster and shell microbiomes than in the sediment microbiome. Gene abundances for nosZI were verified with qPCR of nosZI genes, which showed a significant positive correlation (F_1,7 = 14.7, p = 6.0x10^-3, R² = 0.68). N₂ flux rates were significantly higher in the oyster (364.4 ± 23.5 μmol N-N₂ m^-2 h^-1) and oyster shell (355.3 ± 6.4 μmol N-N₂ m^-2 h^-1) compared to the sediment (270.5 ± 20.1 μmol N-N₂ m^-2 h^-1). Thus, bacteria carrying nosZI genes were found to be an important denitrifier, facilitating nitrogen removal in oyster reefs. In addition, this is the first study to validate the use of 16S gene based metabolic inference as a method for determining microbiome function, such as denitrification, by comparing inference results with qPCR gene quantification and rate measurements.

The filter feeder Dreissena polymorpha affects nutrient, silicon, and metal(loid) mobilization from freshwater sediments

Organic sediments in aquatic ecosystems are well known sinks for nutrients, silicon, and metal(loid)s. Organic matter-consuming organisms like invertebrate shredders, grazers, and bioturbators significantly affect element fixation or remobilization by changing redox conditions or binding properties of organic sediments. Little is known about the effect of filter feeders, like the zebra mussel Dreissena polymorpha, an invasive organism in North American and European freshwater ecosystems. A laboratory batch experiment exposing D. polymorpha (∼1200 organisms per m²) to organic sediment from a site contaminated with arsenic, copper, lead, and uranium revealed a significant uptake and accumulation of arsenic, copper, iron, and especially uranium both into the soft body tissues and the seashell. This is in line with previous observations of metal(loid) accumulation from biomonitoring studies. Regarding its environmental impact, D. polymorpha significantly contributed to mobilization of silicon, iron, phosphorus, arsenic, and copper and to immobilization of uranium (p < 0.001), probably driven by redox conditions, microbial activity within the gut system, or active control of element homeostasis. No net mobilization or immobilization was observed for zinc and lead, because of their low mobility at the prevailing pH of 7.5-8.5. The present results suggest that D. polymorpha can both ameliorate (nutrient mobilization, immobilization of toxicants mobile under oxic conditions) or aggravate negative effects (mobilization of toxicants mobile under reducing conditions) in ecosystems. Relating the results of the present study to observed population densities in natural freshwater ecosystems suggests a significant influence of D. polymorpha on element cycling and needs to be considered in future studies.

Living oysters and their shells as sites of nitrification and denitrification

Oysters provide a critical habitat, are a food resource for higher trophic levels and support important commercial fisheries throughout the world. Oyster reefs can improve water quality by removing phytoplankton. While sediment denitrification may be enhanced adjacent to oyster reefs, little is known about nitrification and denitrification associated with living oysters and their shells. We measured nitrification and denitrification in living oysters (Crassostrea virginica and Crassostrea gigas) and empty oyster shells. Nitrification was similar between live oysters and empty oyster shells, however, denitrification was enhanced significantly on living oysters compared to shells. This is the first demonstration of nitrification and denitrification associated with living oysters and their shells. Our data suggest that loss of historic oyster reefs has likely affected the resilience of estuaries to eutrophication. The additional benefit of oyster mediated denitrification should be considered in restoration of oyster reefs as a tool for managing eutrophication.

Optimization of hard clams, polychaetes, physical disturbance and denitrifying bacteria of removing nutrients in marine sediment

Marine organisms are known to play important roles in transforming nutrients in sediments, however, guidelines to optimize sediment restoration are not available. We conducted a laboratory mesocosm experiment to investigate the role of hard clams, polychaetes, the degree of physical disturbance and denitrifying bacterial concentrations in removing total nitrogen (TN), total phosphorus (TP), and total organic carbon (TOC) in marine sediments. Response surface methodology was employed to analyze the results of initial experiments and in a subsequent experiment identified optimal combinations of parameters. Balancing the TN, TP, TOC removal efficiency, our model predicted 39% TN removal, 33% TP removal, and 42% TOC removal for a 14-day laboratory bioremediation trial using hard clams biomass of 1.2kgm(-2), physical disturbance depth of 16.4cm, bacterial density of 0.18Lm(-2), and polychaetes biomass of 0.16kgm(-2), respectively. These results emphasize the value of combining different species in field-based bioremediation.

Direct Nitrous Oxide Emission from the Aquacultured Pacific White Shrimp (Litopenaeus vannamei)

The Pacific white shrimp (Litopenaeus vannamei) is widely used in aquaculture, where it is reared at high stocking densities, temperatures, and nutrient concentrations. Here we report that adult L. vannamei shrimp emit the greenhouse gas nitrous oxide (N2O) at an average rate of 4.3 nmol N2O/individual × h, which is 1 to 2 orders of magnitude higher than previously measured N2O emission rates for free-living aquatic invertebrates. Dissection, incubation, and inhibitor experiments with specimens from a shrimp farm in Germany indicated that N2O is mainly produced in the animal's gut by microbial denitrification. Microsensor measurements demonstrated that the gut interior is anoxic and nearly neutral and thus is favorable for denitrification by ingested bacteria. Dinitrogen (N2) and N2O accounted for 64% and 36%, respectively, of the nitrogen gas flux from the gut, suggesting that the gut passage is too fast for complete denitrification to be fully established. Indeed, shifting the rearing water bacterial community, a diet component of shrimp, from oxic to anoxic conditions induced N2O accumulation that outlasted the gut passage time. Shrimp-associated N2O production was estimated to account for 6.5% of total N2O production in the shrimp farm studied here and to contribute to the very high N2O supersaturation measured in the rearing tanks (2,099%). Microbial N2O production directly associated with aquacultured animals should be implemented into life cycle assessments of seafood production.

IMPORTANCE

The most widely used shrimp species in global aquaculture, Litopenaeus vannamei, is shown to emit the potent greenhouse gas nitrous oxide (N2O) at a particularly high rate. Detailed experiments reveal that N2O is produced in the oxygen-depleted gut of the animal by bacteria that are part of the shrimp diet. Upon ingestion, these bacteria experience a shift from oxic to anoxic conditions and therefore switch their metabolism to the anaerobic denitrification process, which produces N2O as an intermediate and dinitrogen (N2) gas as an end product. The N2O/N2 production ratio is unusually high in the shrimp gut, because denitrification cannot be fully established during the short gut passage time of food-associated bacteria. Nitrous oxide emission directly mediated by L. vannamei contributes significantly to the overall N2O emission from aquaculture facilities.

Degradation of forchlorfenuron by nitrification and denitrification reactions in the gut and shell biofilm of Limnoperna fortunei

The capacity and mechanism of Limnoperna fortunei to reduce the concentration of forchlorfenuron [or 1-(2-chloropyridin-4-yl)-3-phenylurea (CPPU)] in water has been studied under laboratory conditions. Firstly, the evasive response of mussels to CPPU (10, 20, 40 and 60 mg L(-1)) was evaluated, and a toxicity test was carried out at these concentrations. Secondly, the effect of two different sizes of mussels on CPPU concentrations was investigated in a 24-day experiment. Thirdly, the role of intact mussels and valvae only were respectively evaluated in another 24-day experiment. The CPPU concentration decreased by about 40 % in the presence of large mussels and about 20 % in the presence of valvae only. Finally, nucleic acid extracts from the gut and biofilm microbial communities of L. fortunei were analyzed, and the number of copies of the bacterial genes amoA, nirK and nirS were determined. Based on these results, we propose possible mechanisms for CPPU degradation involving bacteria-associated nitrification and denitrification reactions. In summary, we found that the CPPU half-life depended on the presence of mussels, their size and their associated microorganisms.

Ecological roles and biotechnological applications of marine and intertidal microbial biofilms

This review is a retrospective of ecological effects of bioactivities produced by biofilms of surface-dwelling marine/intertidal microbes as well as of the industrial and environmental biotechnologies developed exploiting the knowledge of biofilm formation. Some examples of significant interest pertaining to the ecological aspects of biofilm-forming species belonging to the Roseobacter clade include autochthonous bacteria from turbot larvae-rearing units with potential application as a probiotic as well as production of tropodithietic acid and indigoidine. Species of the Pseudoalteromonas genus are important examples of successful surface colonizers through elaboration of the AlpP protein and antimicrobial agents possessing broad-spectrum antagonistic activity against medical and environmental isolates. Further examples of significance comprise antiprotozoan activity of Pseudoalteromonas tunicata elicited by violacein, inhibition of fungal colonization, antifouling activities, inhibition of algal spore germination, and 2-n-pentyl-4-quinolinol production. Nitrous oxide, an important greenhouse gas, emanates from surface-attached microbial activity of marine animals. Marine and intertidal biofilms have been applied in the biotechnological production of violacein, phenylnannolones, and exopolysaccharides from marine and tropical intertidal environments. More examples of importance encompass production of protease, cellulase, and xylanase, melanin, and riboflavin. Antifouling activity of Bacillus sp. and application of anammox bacterial biofilms in bioremediation are described. Marine biofilms have been used as anodes and cathodes in microbial fuel cells. Some of the reaction vessels for biofilm cultivation reviewed are roller bottle, rotating disc bioreactor, polymethylmethacrylate conico-cylindrical flask, fixed bed reactor, artificial microbial mats, packed-bed bioreactors, and the Tanaka photobioreactor.

Chironomus plumosus larvae increase fluxes of denitrification products and diversity of nitrate-reducing bacteria in freshwater sediment

Benthic invertebrates affect microbial processes and communities in freshwater sediment by enhancing sediment-water solute fluxes and by grazing on bacteria. Using microcosms, the effects of larvae of the widespread midge Chironomus plumosus on the efflux of denitrification products (N2O and N2+N2O) and the diversity and abundance of nitrate- and nitrous-oxide-reducing bacteria were investigated. Additionally, the diversity of actively nitrate- and nitrous-oxide-reducing bacteria was analyzed in the larval gut. The presence of larvae increased the total effluxes of N2O and N2+N2O up to 8.6- and 4.2-fold, respectively, which was mostly due to stimulation of sedimentary denitrification; incomplete denitrification in the guts accounted for up to 20% of the N2O efflux. Phylotype richness of the nitrate reductase gene narG was significantly higher in sediment with than without larvae. In the gut, 47 narG phylotypes were found expressed, which may contribute to higher phylotype richness in colonized sediment. In contrast, phylotype richness of the nitrous oxide reductase gene nosZ was unaffected by the presence of larvae and very few nosZ phylotypes were expressed in the gut. Gene abundance of neither narG, nor nosZ was different in sediments with and without larvae. Hence, C. plumosus increases activity and diversity, but not overall abundance of nitrate-reducing bacteria, probably by providing additional ecological niches in its burrow and gut.