A doubling of microphytobenthos biomass coincides with a tenfold increase in denitrifier and total bacterial abundances in intertidal sediments of a temperate estuary

The metabolites of light: Untargeted metabolomic approaches bring new clues to understand light-driven acclimation of intertidal mudflat biofilm

The microphytobenthos (MPB), a microbial community of primary producers, play a key role in coastal ecosystem functioning, particularly in intertidal mudflats. These mudflats experience challenging variations of irradiance, forcing the micro-organisms to develop photoprotective mechanisms to survive and thrive in this dynamic environment. Two major adaptations to light are well described in literature: the excess of light energy dissipation through non-photochemical quenching (NPQ), and the vertical migration in the sediment. These mechanisms trigger considerable scientific interest, but the biological processes and metabolic mechanisms involved in light-driven vertical migration remain largely unknown. To our knowledge, this study investigates for the first time metabolomic responses of a migrational mudflat biofilm exposed for 30 min to a light gradient of photosynthetically active radiation (PAR) from 50 to 1000 μmol photons m-2 s-1. The untargeted metabolomic analysis allowed to identify metabolites involved in two types of responses to light irradiance levels. On the one hand, the production of SFAs and MUFAs, primarily derived from bacteria, indicates a healthy photosynthetic state of MPB under low light (LL; 50 and 100 PAR) and medium light (ML; 250 PAR) conditions. Conversely, when exposed to high light (HL; 500, 750 and 1000 PAR), the MPB experienced light-induced stress, triggering the production of alka(e)nes and fatty alcohols. The physiological and ecological roles of these compounds are poorly described in literature. This study sheds new light on the topic, as it suggests that these compounds may play a crucial and previously unexplored role in light-induced stress acclimation of migrational MPB biofilms. Since alka(e)nes are produced from FAs decarboxylation, these results thus emphasize for the first time the importance of FAs pathways in microphytobenthic biofilms acclimation to light.

Shift of DNRA bacterial community composition in sediment cores of the Pearl River Estuary and the impact of environmental factors

Dissimilatory nitrate reduction to ammonia (DNRA) process, competing with denitrification and anaerobic ammonia oxidation (anammox) for nitrate, is an important nitrogen retention pathway in the environment. Previous studies on DNRA bacterial diversity and composition focused on the surface sediments in estuaries, but studies on the deep sediments are limited, and the linkage between DNRA community structure and complex estuarine environment remains unclear. In this study, through high-throughput sequencing of nrfA gene followed by high-resolution sample inference, we examined spatially and temporally the composition and diversity of DNRA bacteria along a salinity gradient in five sediment cores of the Pearl River Estuary (PRE). We found a higher diversity and richness of DNRA bacteria in sediments with lower organic carbon, where sea water intersects fresh water. Moreover, the DNRA bacterial communities had the specific spatially distribution coupling with their metabolic difference along the salinity gradient of the Pearl River Estuary, but no obvious difference along the sediment depth. The distribution of DNRA bacteria in the PRE was largely driven by various environmental factors, including salinity, Oxidation-Reduction Potential (ORP), ammonium, nitrate and C_org/NO₃^-. Furthermore, dominant DNRA bacteria were found to be the key populations of DNRA communities in the PRE sediments by network analysis. Collectively, our results showed that niche difference of DNRA bacteria indeed occurs in the Pearl River Estuary.

Nitrogen-cycling gene pool shrunk by species interactions among denser bacterial and archaeal community stimulated by excess organic matter and total nitrogen in a eutrophic bay

Microbial densities, functional genes, and their responses to environment factors have been studied for years, but still a lot remains unknown about their interactions with each other. In this study, the abundances of 7 nitrogen cycling genes in the sediments from Hangzhou Bay were analyzed along with bacterial and archaeal 16S rRNA abundances as the biomarkers of their densities. The amount of organic matter (OM) and total nitrogen (TN) strongly positively correlated with each other and microbial densities, while total phosphate (TP) and ammonia-nitrogen (NH₃-N) did not. Most studied genes were density suppressed, while nirS was density stable, and nosZ and hzo were density irrelevant. This suggests eutrophication could limit inorganic nitrogen cycle pathways and the removal of nitrogen in the sediment and emit more greenhouse gases. This study provides a new insight of microbial community structures, functions and their interactions in the sediments of eutrophic bays.

Seasonal variability in ecosystem functioning across estuarine gradients: The role of sediment communities and ecosystem processes

Functional trait approaches advance the understanding of biodiversity-ecosystem function (BDEF) relationships and its control by the environmental context. Application of these insights into management remains constrained due to lack of evidence from real-world ecosystems that capture the natural spatial and temporal gradients at which biodiversity and environmental conditions operate. In this study we measured macrofauna community traits, ecosystem processes and abiotic properties at 9 locations during 4 months, spanning a wide gradient in sedimentary habitats and salinity in the Scheldt estuary, and quantified the (a)biotic contribution to sediment community oxygen consumption, as a measure of ecosystem function. We found that functional attributes of the macrofauna community and its effect on bio-irrigation can predict ecosystem function, but especially during the colder period of the year. This result highlights that generalizations about BDEF relationships, and biodiversity loss on ecosystem functions, are limited whenever this temporal component is not acknowledged.

Host specificity in diatom-bacteria interactions alleviates antagonistic effects

While different microalgae tend to be associated with different bacteria, it remains unclear whether such specific associations are beneficial for the microalgae. We assessed the impact of bacterial isolates, derived from various marine benthic diatoms, on the growth of several strains belonging to the Cylindrotheca closterium diatom species complex. We first tested the effect of 35 different bacterial isolates on the growth of a single C. closterium strain, and then evaluated the impact of 8 of these isolates on the growth of 6 C. closterium strains and 1 Cylindrotheca fusiformis strain. Surprisingly, most interactions were neutral to antagonistic. The interactions were highly specific, with diatom growth in the presence of specific bacteria differing between Cylindrotheca strains and species, and closely related bacteria eliciting contrasting diatom growth responses. These differences could be related to the origin of the bacterial isolates, as only isolates from foreign diatom hosts significantly reduced diatom growth, implying coadaptation between different Cylindrotheca strains and their associated bacteria. Interestingly, the antagonistic effect of a Marinobacter strain was alleviated by the presence of a microbial inoculum that was native to the diatom host, suggesting that coadapted bacteria might also benefit their host indirectly by preventing the establishment of harmful bacteria.

Influences of nutritional conditions on degradation of dibutyl phthalate in coastal sediments with Cylindrotheca closterium

In this work, microphytobenthos Cylindrotheca closterium was planted on the surface of coastal sediments to investigate its influence on dibutyl phthalate (DBP) degradation in sediments under different nutritional conditions. The results indicated that C. closterium largely utilized nutrients from the overlying water. Addition of nitrogen, phosphorus or silicon increased algal biomass (as chlorophyll a) by 0.97-3.16, 1.75-2.36 and 1.61-3.09 times, respectively, meanwhile it changed bacterial community structure in sediments with C. closterium. Growth of C. closterium was more sensitive to nitrogen content in the overlying water. Inoculation of C. closterium increased the relative abundances of dominant aerobic bacteria by 10-67%. Compared with treatments without C. closterium, inoculation of C. closterium increased DBP degradation percentage in sediments (8.5-18.9% increment), which was positively correlated with chlorophyll a content. Thus, microphytobenthos showed the potential for improving the cleansing of polluted coastal sediments, which was obviously related to nutritional conditions in the overlying water.

Diatom-Bacteria Interactions Modulate the Composition and Productivity of Benthic Diatom Biofilms

Benthic diatoms are dominant primary producers in intertidal mudflats and constitute a major source of organic carbon to consumers and decomposers residing within these ecosystems. They typically form biofilms whose species richness, community composition and productivity can vary in response to environmental drivers and their interactions with other organisms (e.g., grazers). Here, we investigated whether bacteria can affect diatom community composition and vice versa, and how this could influence the biodiversity-productivity relation. Using axenic experimental communities with three common benthic diatoms (Cylindrotheca closterium, Navicula phyllepta, and Seminavis robusta), we observed an increase in algal biomass production in diatom co-cultures in comparison to monocultures. The presence of bacteria decreased the productivity of diatom monocultures while bacteria did not seem to affect the overall productivity of diatoms grown in co-cultures. The effect of bacteria on diatom growth, however, appeared to be species-specific, resulting in compositional shifts when different diatom species were grown together. The effect of the diatoms on the bacteria also proved to be species-specific as each diatom species developed a bacterial community that differed in its composition. Together, our results suggest that interactions between bacteria and diatoms residing in mudflats are a key factor in the structuring of the benthic microbial community composition and the overall functioning of that community.

Copper Affects Composition and Functioning of Microbial Communities in Marine Biofilms at Environmentally Relevant Concentrations

Copper (Cu) pollution in coastal areas is a worldwide threat for aquatic communities. This study aims to demonstrate the usefulness of the DNA metabarcoding analysis in order to describe the ecotoxicological effect of Cu at environmental concentrations on marine periphyton. Additionally, the study investigates if Cu-induced changes in community structure co-occurs with changes in community functioning (i.e., photosynthesis and community tolerance to Cu). Periphyton was exposed for 18 days to five Cu concentrations, between 0.01 and 10 μM, in a semi-static test. Diversity and community structure of prokaryotic and eukaryotic organisms were assessed by 16S and 18S amplicon sequencing, respectively. Community function was studied as impacts on algal biomass and photosynthetic activity. Additionally, we studied Pollution-Induced Community Tolerance (PICT) using photosynthesis as the endpoint. Sequencing results detected an average of 9,504 and 1,242 OTUs for 16S and 18S, respectively, reflecting the high biodiversity of marine periphytic biofilms. Eukaryotes represent the most Cu-sensitive kingdom, where effects were seen already at concentrations as low as 0.01 μM. The structure of the prokaryotic part of the community was impacted at slightly higher concentrations (0.06 μM), which is still in the range of the Cu concentrations observed in the area (0.08 μM). The current environmental quality standard for Cu of 0.07 μM therefore does not seem to be sufficiently protective for periphyton. Cu exposure resulted in a more Cu-tolerant community, which was accompanied by a reduced total algal biomass, increased relative abundance of diatoms and a reduction of photosynthetic activity. Cu exposure changed the network of associations between taxa in the communities. A total of 23 taxa, including taxa within Proteobacteria, Bacteroidetes, Stramenopiles, and Hacrobia, were identified as being particularly sensitive to Cu. DNA metabarcoding is presented as a sensitive tool for community-level ecotoxicological studies that allows to observe impacts simultaneously on a multitude of pro- and eukaryotic taxa, and therefore to identify particularly sensitive, non-cultivable taxa.

Nematodes stimulate biomass accumulation in a multispecies diatom biofilm

While the effects of abiotic parameters on microbial tidal biofilms are relatively well-documented, the effects of grazing and/or bioturbation by meiofauna are poorly understood. We investigated the impact of a natural nematode assemblage on the biomass and microbial community structure of a multispecies diatom biofilm. Nematodes stimulated diatom biomass accumulation of the biofilm and caused a shift in diatom community structure. Higher diatom biomass accumulation in the presence of nematodes could be the result of increased diatom biomass production through nutrient regeneration resulting from grazing or bioturbation, and/or through shifts in interspecific interactions between diatoms (e.g. competition) through selective grazing. Alternatively, lower biomass in the controls may be due to higher secretion of diatom production in the form of bound extracellular polymeric substances (EPS). Our observations underscore that meiobenthos, and especially nematodes, are important for the structure and production of tidal biofilms.

Temperature Driven Changes in Benthic Bacterial Diversity Influences Biogeochemical Cycling in Coastal Sediments

Marine sediments are important sites for global biogeochemical cycling, mediated by macrofauna and microalgae. However, it is the microorganisms that drive these key processes. There is strong evidence that coastal benthic habitats will be affected by changing environmental variables (rising temperature, elevated CO2), and research has generally focused on the impact on macrofaunal biodiversity and ecosystem services. Despite their importance, there is less understanding of how microbial community assemblages will respond to environmental changes. In this study, a manipulative mesocosm experiment was employed, using next-generation sequencing to assess changes in microbial communities under future environmental change scenarios. Illumina sequencing generated over 11 million 16S rRNA gene sequences (using a primer set biased toward bacteria) and revealed Bacteroidetes and Proteobacteria dominated the total bacterial community of sediment samples. In this study, the sequencing coverage and depth revealed clear changes in species abundance within some phyla. Bacterial community composition was correlated with simulated environmental conditions, and species level community composition was significantly influenced by the mean temperature of the environmental regime (p = 0.002), but not by variation in CO2 or diurnal temperature variation. Species level changes with increasing mean temperature corresponded with changes in NH4 concentration, suggesting there is no functional redundancy in microbial communities for nitrogen cycling. Marine coastal biogeochemical cycling under future environmental conditions is likely to be driven by changes in nutrient availability as a direct result of microbial activity.

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

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

Deep nirS amplicon sequencing of San Francisco Bay sediments enables prediction of geography and environmental conditions from denitrifying community composition

Denitrification is a dominant nitrogen loss process in the sediments of San Francisco Bay. In this study, we sought to understand the ecology of denitrifying bacteria by using next-generation sequencing (NGS) to survey the diversity of a denitrification functional gene, nirS (encoding cytchrome-cd₁ nitrite reductase), along the salinity gradient of San Francisco Bay over the course of a year. We compared our dataset to a library of nirS sequences obtained previously from the same samples by standard PCR cloning and Sanger sequencing, and showed that both methods similarly demonstrated geography, salinity and, to a lesser extent, nitrogen, to be strong determinants of community composition. Furthermore, the depth afforded by NGS enabled novel techniques for measuring the association between environment and community composition. We used Random Forests modelling to demonstrate that the site and salinity of a sample could be predicted from its nirS sequences, and to identify indicator taxa associated with those environmental characteristics. This work contributes significantly to our understanding of the distribution and dynamics of denitrifying communities in San Francisco Bay, and provides valuable tools for the further study of this key N-cycling guild in all estuarine systems.

Dissimilatory nitrogen reduction in intertidal sediments of a temperate estuary: small scale heterogeneity and novel nitrate-to-ammonium reducers

The estuarine nitrogen cycle can be substantially altered due to anthropogenic activities resulting in increased amounts of inorganic nitrogen (mainly nitrate). In the past, denitrification was considered to be the main ecosystem process removing reactive nitrogen from the estuarine ecosystem. However, recent reports on the contribution of dissimilatory nitrate reduction to ammonium (DNRA) to nitrogen removal in these systems indicated a similar or higher importance, although the ratio between both processes remains ambiguous. Compared to denitrification, DNRA has been underexplored for the last decades and the key organisms carrying out the process in marine environments are largely unknown. Hence, as a first step to better understand the interplay between denitrification, DNRA and reduction of nitrate to nitrite in estuarine sediments, nitrogen reduction potentials were determined in sediments of the Paulina polder mudflat (Westerschelde estuary). We observed high variability in dominant nitrogen removing processes over a short distance (1.6 m), with nitrous oxide, ammonium and nitrite production rates differing significantly between all sampling sites. Denitrification occurred at all sites, DNRA was either the dominant process (two out of five sites) or absent, while nitrate reduction to nitrite was observed in most sites but never dominant. In addition, novel nitrate-to-ammonium reducers assigned to Thalassospira, Celeribacter, and Halomonas, for which DNRA was thus far unreported, were isolated, with DNRA phenotype reconfirmed through nrfA gene amplification. This study demonstrates high small scale heterogeneity among dissimilatory nitrate reduction processes in estuarine sediments and provides novel marine DNRA organisms that represent valuable alternatives to the current model organisms.