scholarly journals Microbial river-to-sea continuum: gradients in benthic and planktonic diversity, osmoregulation and nutrient cycling

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Hwee Sze Tee ◽  
David Waite ◽  
Gavin Lear ◽  
Kim Marie Handley
Keyword(s):  
Salt Tolerance ◽  
Nutrient Cycling ◽  
Water Column ◽  
Nutrient Availability ◽  
Ammonia Oxidation ◽  
Sulfur Metabolism ◽  
Phosphate Limitation ◽  
Geochemical Data ◽  
Aquatic Communities ◽  
Local Conditions

Abstract Background Coastal aquatic ecosystems include chemically distinct, but highly interconnected environments. Across a freshwater-to-marine transect, aquatic communities are exposed to large variations in salinity and nutrient availability as tidal cycles create periodic fluctuations in local conditions. These factors are predicted to strongly influence the resident microbial community structure and functioning, and alter the structure of aquatic food webs and biogeochemical cycles. Nevertheless, little is known about the spatial distribution of metabolic properties across salinity gradients, and no study has simultaneously surveyed the sediment and water environments. Here, we determined patterns and drivers of benthic and planktonic prokaryotic and microeukaryotic community assembly across a river and tidal lagoon system by collecting sediments and planktonic biomass at nine shallow subtidal sites in the summer. Genomic and transcriptomic analyses, alongside a suite of complementary geochemical data, were used to determine patterns in the distribution of taxa, mechanisms of salt tolerance, and nutrient cycling. Results Taxonomic and metabolic profiles related to salt tolerance and nutrient cycling of the aquatic microbiome were found to decrease in similarity with increasing salinity, and distinct trends in diversity were observed between the water column and sediment. Non-saline and saline communities adopted divergent strategies for osmoregulation, with an increase in osmoregulation-related transcript expression as salinity increased in the water column due to lineage-specific adaptations to salt tolerance. Results indicated a transition from phosphate limitation in freshwater habitats to nutrient-rich conditions in the brackish zone, where distinct carbon, nitrogen and sulfur cycling processes dominated. Phosphorus acquisition-related activity was highest in the freshwater zone, along with dissimilatory nitrate reduction to ammonium in freshwater sediment. Activity associated with denitrification, sulfur metabolism and photosynthesis were instead highest in the brackish zone, where photosynthesis was dominated by distinct microeukaryotes in water (Cryptophyta) and sediment (diatoms). Despite microeukaryotes and archaea being rare relative to bacteria, results indicate that they contributed more to photosynthesis and ammonia oxidation, respectively. Conclusions Our study demonstrates clear freshwater–saline and sediment–water ecosystem boundaries in an interconnected coastal aquatic system and provides a framework for understanding the relative importance of salinity, planktonic-versus-benthic habitats and nutrient availability in shaping aquatic microbial metabolic processes, particularly in tidal lagoon systems.

scholarly journals Comprehensive transcriptome and metabolome profiling reveal metabolic mechanisms of Nitraria sibirica Pall. to salt stress

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Huanyong Li ◽  
Xiaoqian Tang ◽  
Xiuyan Yang ◽  
Huaxin Zhang
Keyword(s):  
Salt Stress ◽  
Amino Acid ◽  
Salt Tolerance ◽  
Metabolic Pathways ◽  
Amino Acid Metabolism ◽  
Acid Metabolism ◽  
Sulfur Metabolism ◽  
Enrichment Analysis ◽  
Extracellular Region ◽  
Nitraria Sibirica

AbstractNitraria sibirica Pall., a typical halophyte that can survive under extreme drought conditions and in saline-alkali environments, exhibits strong salt tolerance and environmental adaptability. Understanding the mechanism of molecular and physiological metabolic response to salt stress of plant will better promote the cultivation and use of halophytes. To explore the mechanism of molecular and physiological metabolic of N. sibirica response to salt stress, two-month-old seedlings were treated with 0, 100, and 400 mM NaCl. The results showed that the differentially expressed genes between 100 and 400 mmol L−1 NaCl and unsalted treatment showed significant enrichment in GO terms such as binding, cell wall, extemal encapsulating structure, extracellular region and nucleotide binding. KEGG enrichment analysis found that NaCl treatment had a significant effect on the metabolic pathways in N. sibirica leaves, which mainly including plant-pathogen interaction, amino acid metabolism of the beta alanine, arginine, proline and glycine metabolism, carbon metabolism of glycolysis, gluconeogenesis, galactose, starch and sucrose metabolism, plant hormone signal transduction and spliceosome. Metabolomics analysis found that the differential metabolites between the unsalted treatment and the NaCl treatment are mainly amino acids (proline, aspartic acid, methionine, etc.), organic acids (oxaloacetic acid, fumaric acid, nicotinic acid, etc.) and polyhydric alcohols (inositol, ribitol, etc.), etc. KEGG annotation and enrichment analysis showed that 100 mmol L−1 NaCl treatment had a greater effect on the sulfur metabolism, cysteine and methionine metabolism in N. sibirica leaves, while various amino acid metabolism, TCA cycle, photosynthetic carbon fixation and sulfur metabolism and other metabolic pathways have been significantly affected by 400 mmol L−1 NaCl treatment. Correlation analysis of differential genes in transcriptome and differential metabolites in metabolome have found that the genes of AMY2, BAM1, GPAT3, ASP1, CML38 and RPL4 and the metabolites of L-cysteine, proline, 4-aminobutyric acid and oxaloacetate played an important role in N. sibirica salt tolerance control. This is a further improvement of the salt tolerance mechanism of N. sibirica, and it will provide a theoretical basis and technical support for treatment of saline-alkali soil and the cultivation of halophytes.

scholarly journals An experimental assessment of the distribution of environmental DNA along the water column

2020 ◽  
Author(s):  
André O. Agostinis ◽  
Giorgi Dal Pont ◽  
Alexandre Borio ◽  
Aline Horodesky ◽  
Ana Paula da Silva Bertão ◽  
...  
Keyword(s):  
Water Column ◽  
Environmental Dna ◽  
Aquatic Communities ◽  
Natural Conditions ◽  
Sampling Protocol ◽  
Experimental Assessment ◽  
Qpcr Analysis ◽  
Time Period ◽  
Sampling Protocols ◽  
Different Depths

AbstractThe study of environmental DNA (eDNA) is increasingly becoming a valuable tool to survey and monitor aquatic communities. However, there are important gaps in our understanding of the dynamics governing the distribution of eDNA under natural conditions. In this report we carry out controlled experiments to assess the extent and timing of eDNA distribution along the water column. A sample of known eDNA concentration was placed at the bottom of a 5-m high tube (20 cm in diameter and total volume of 160 L), and water samples were obtained at different depths over an 8 h-period. The presence of the target eDNA was assessed by qPCR analysis. This sampling protocol allowed for assessing the timescale for the diffusion of eDNA while minimizing the influence of turbulence. We demonstrate that, after a time-period of as little as 30 min, the eDNA had spread across the entire container. The implications of these results for eDNA sampling protocols in the field are discussed.

scholarly journals Effects of temperature and organic pollution on nutrient cycling in marine sediments

2015 ◽  
Vol 12 (15) ◽  
pp. 4565-4575 ◽  
Author(s):  
C. Sanz-Lázaro ◽  
T. Valdemarsen ◽  
M. Holmer
Keyword(s):  
Climate Change ◽  
Organic Matter ◽  
Nutrient Cycling ◽  
Water Column ◽  
Temperature Rise ◽  
Nutrient Release ◽  
Organic Pollution ◽  
Coastal Sediments ◽  
Effect Of Temperature ◽  
Climate Change Scenarios

Abstract. Increasing ocean temperature due to climate change is an important anthropogenic driver of ecological change in coastal systems. In these systems sediments play a major role in nutrient cycling. Our ability to predict ecological consequences of climate change is enhanced by simulating real scenarios. Based on predicted climate change scenarios, we tested the effect of temperature and organic pollution on nutrient release from coastal sediments to the water column in a mesocosm experiment. PO43− release rates from sediments followed the same trends as organic matter mineralization rates, increased linearly with temperature and were significantly higher under organic pollution than under nonpolluted conditions. NH4+ release only increased significantly when the temperature rise was above 6 °C, and it was significantly higher in organic polluted compared to nonpolluted sediments. Nutrient release to the water column was only a fraction from the mineralized organic matter, suggesting PO43− retention and NH4+ oxidation in the sediment. Bioturbation and bioirrigation appeared to be key processes responsible for this behavior. Considering that the primary production of most marine basins is N-limited, the excess release of NH4+ at a temperature rise > 6 °C could enhance water column primary productivity, which may lead to the deterioration of the environmental quality. Climate change effects are expected to be accelerated in areas affected by organic pollution.

scholarly journals Development of a Submerged Aquatic Vegetation Growth Model in a Coupled Wave-Current-Sediment-Transport Modeling System (COAWST v3.4)

2019 ◽  
Author(s):  
Tarandeep S. Kalra ◽  
Neil K. Ganju ◽  
Jeremy M. Testa
Keyword(s):  
Sediment Transport ◽  
Nutrient Cycling ◽  
Water Column ◽  
Submerged Aquatic Vegetation ◽  
Aquatic Vegetation ◽  
Dissolved Inorganic Carbon ◽  
Sediment Dynamics ◽  
Velocity Sedimentation ◽  
Ecosystem Change ◽  
Deterministic Modelling

Abstract. The coupled biophysical interactions between submerged aquatic vegetation (SAV), hydrodynamics (currents and waves), sediment dynamics, and nutrient cycling have long been of interest in estuarine environments. Recent observational studies have addressed feedbacks between SAV meadows, current velocity, sedimentation, and nutrient cycling and suggest SAV are ecosystem engineers whose growth can be self-reinforcing. To represent these dynamic processes in a numerical model, the presence of SAV and its effect on hydrodynamics (currents and waves) and sediment dynamics was incorporated into the open source model COAWST. In this study, we extend the COAWST modelling framework to account for dynamic changes of SAV and associated epiphyte biomass. Modelled SAV biomass is represented as a function of temperature, light, and nutrient availability and exchanges nutrients, detritus, dissolved inorganic carbon, and dissolved oxygen with the water-column biogeochemistry model. The dynamic simulation of SAV biomass allows the plants to both respond to and cause changes in water column and sediment bed properties, hydrodynamics, and sediment transport (i.e., a two-way feedback). We demonstrate the behavior of these modelled processes through application to an idealized domain, then apply the model to a eutrophic harbour where SAV dieback is a result of anthropogenic nitrate loading and eutrophication. These cases demonstrate an advance in the deterministic modelling of coupled bio-physical processes and will further our understanding of future ecosystem change.

scholarly journals The Effect of Charophyte Communities on Phosphorus Flow in Lake Shinji, Japan

2017 ◽  
Vol 5 (1) ◽  
pp. 13 ◽  
Author(s):  
Takashi Komuro ◽  
Hiroshi Kamiya ◽  
Masumi Yamamuro ◽  
Yasushi Seike
Keyword(s):  
Nutrient Cycling ◽  
Water Column ◽  
Vascular Plants ◽  
Aerial Photographs ◽  
Effective Measure ◽  
Dissolved Phosphorus ◽  
Water Lake ◽  
Phosphorus Accumulation ◽  
Lake Shinji ◽  
Phosphorus Flow

Charophytes are a group of aquatic algae similar to vascular plants; they play an important role in the nutrient cycling of lakes. Specifically, under eutrophication, charophytes have a greater capacity for phosphorus accumulation than vascular plants. During their development, charophytes accumulate calcium within their structures, along with dissolved phosphorus from the water column. The calcified structures are deposited onto the lakebed after the death of the plant, with phosphorus co-precipitating with calcium, limiting its return to the water. Lake Shinji is one of many lakes in Japan where the charophyte population is in decline or extinct. Using aerial photographs acquired 70 years ago, we estimate the extent of the historical charophyte community in Lake Shinji, and quantitatively evaluate and examine the extent to which charophytes accumulated phosphorus in the lake sediment. The amount of phosphorus accumulated by the charophyte community in Lake Shinji is estimated to be 0.56-25.5 t P y-1. Charophytes are not found in Lake Shinji today, and although various species of vascular plants have recolonised the lake, no significant improvement in water transparency has been observed. This study concludes that charophytes are likely to be a more effective measure in combating eutrophication than vascular plants.

scholarly journals Nitrite consumption and associated isotope changes during a river flood event

2016 ◽  
Vol 13 (19) ◽  
pp. 5649-5659 ◽  
Author(s):  
Juliane Jacob ◽  
Tina Sanders ◽  
Kirstin Dähnke
Keyword(s):  
Water Column ◽  
Isotope Effect ◽  
Ammonia Oxidation ◽  
Isotope Effects ◽  
Flood Event ◽  
Natural Environments ◽  
Elbe River ◽  
Natural Systems ◽  
Nitrate Consumption ◽  
The Elbe River

Abstract. In oceans, estuaries, and rivers, nitrification is an important nitrate source, and stable isotopes of nitrate are often used to investigate recycling processes (e.g. remineralisation, nitrification) in the water column. Nitrification is a two-step process, where ammonia is oxidised via nitrite to nitrate. Nitrite usually does not accumulate in natural environments, which makes it difficult to study the single isotope effect of ammonia oxidation or nitrite oxidation in natural systems. However, during an exceptional flood in the Elbe River in June 2013, we found a unique co-occurrence of ammonium, nitrite, and nitrate in the water column, returning towards normal summer conditions within 1 week. Over the course of the flood, we analysed the evolution of δ15N–NH4+ and δ15N–NO2− in the Elbe River. In concert with changes in suspended particulate matter (SPM) and δ15N SPM, as well as nitrate concentration, δ15N–NO3− and δ18O–NO3−, we calculated apparent isotope effects during net nitrite and nitrate consumption. During the flood event, > 97 % of total reactive nitrogen was nitrate, which was leached from the catchment area and appeared to be subject to assimilation. Ammonium and nitrite concentrations increased to 3.4 and 4.4 µmol L−1, respectively, likely due to remineralisation, nitrification, and denitrification in the water column. δ15N–NH4+ values increased up to 12 ‰, and δ15N–NO2− ranged from −8.0 to −14.2 ‰. Based on this, we calculated an apparent isotope effect 15ε of −10.0 ± 0.1 ‰ during net nitrite consumption, as well as an isotope effect 15ε of −4.0 ± 0.1 ‰ and 18ε of −5.3 ± 0.1 ‰ during net nitrate consumption. On the basis of the observed nitrite isotope changes, we evaluated different nitrite uptake processes in a simple box model. We found that a regime of combined riparian denitrification and 22 to 36 % nitrification fits best with measured data for the nitrite concentration decrease and isotope increase.

scholarly journals Influence of ammonia oxidation rate on thaumarchaeal lipid composition and the TEX86 temperature proxy

2016 ◽  
Vol 113 (28) ◽  
pp. 7762-7767 ◽  
Author(s):  
Sarah J. Hurley ◽  
Felix J. Elling ◽  
Martin Könneke ◽  
Carolyn Buchwald ◽  
Scott D. Wankel ◽  
...  
Keyword(s):  
Water Column ◽  
Oxidation Rate ◽  
Nutrient Dynamics ◽  
Ammonia Oxidation ◽  
Membrane Lipids ◽  
Reducing Power ◽  
Archaeal Community ◽  
Surface Mixed Layer ◽  
Culture Methods ◽  
Ammonia Oxidation Rate

Archaeal membrane lipids known as glycerol dibiphytanyl glycerol tetraethers (GDGTs) are the basis of the TEX86 paleotemperature proxy. Because GDGTs preserved in marine sediments are thought to originate mainly from planktonic, ammonia-oxidizing Thaumarchaeota, the basis of the correlation between TEX86 and sea surface temperature (SST) remains unresolved: How does TEX86 predict surface temperatures, when maximum thaumarchaeal activity occurs below the surface mixed layer and TEX86 does not covary with in situ growth temperatures? Here we used isothermal studies of the model thaumarchaeon Nitrosopumilus maritimus SCM1 to investigate how GDGT composition changes in response to ammonia oxidation rate. We used continuous culture methods to avoid potential confounding variables that can be associated with experiments in batch cultures. The results show that the ring index scales inversely (R2 = 0.82) with ammonia oxidation rate (ϕ), indicating that GDGT cyclization depends on available reducing power. Correspondingly, the TEX86 ratio decreases by an equivalent of 5.4 °C of calculated temperature over a 5.5 fmol·cell−1·d−1 increase in ϕ. This finding reconciles other recent experiments that have identified growth stage and oxygen availability as variables affecting TEX86. Depth profiles from the marine water column show minimum TEX86 values at the depth of maximum nitrification rates, consistent with our chemostat results. Our findings suggest that the TEX86 signal exported from the water column is influenced by the dynamics of ammonia oxidation. Thus, the global TEX86–SST calibration potentially represents a composite of regional correlations based on nutrient dynamics and global correlations based on archaeal community composition and temperature.

scholarly journals Effects of global climate change and organic pollution on nutrient cycling in marine sediments

2015 ◽  
Vol 12 (1) ◽  
pp. 21-49
Author(s):  
C. Sanz-Lázaro ◽  
T. Valdemarsen ◽  
M. Holmer
Keyword(s):  
Climate Change ◽  
Organic Matter ◽  
Nutrient Cycling ◽  
Water Column ◽  
Temperature Rise ◽  
Nutrient Release ◽  
Organic Pollution ◽  
Coastal Sediments ◽  
Effect Of Temperature ◽  
Climate Change Scenarios

Abstract. Increasing ocean temperature due to climate change is an important anthropogenic driver of ecological change in coastal systems, where sediments play a major role in nutrient cycling. Our ability to predict ecological consequences of climate change is enhanced by simulating real scenarios especially when the interactions among drivers may not be just additive. Based on predicted climate change scenarios, we tested the effect of temperature and organic pollution on nutrient release from coastal sediments to the water column in a mesocosm experiment. PO43− release rates from sediments followed the same trends as organic matter mineralization rates, and increased linearly with temperature and were significantly higher under organic pollution than under non-polluted conditions. NH4+ release only increased significantly when the temperature rise was above 6 °C, and was significantly higher in organic polluted compared to non-polluted sediments. Nutrient release to the water column was only a fraction from the mineralized organic matter, suggesting PO43− retention and NH4+ oxidation in the sediment. Bioturbation and bioirrigation appeared to be key processes responsible of this behaviour. Considering that the primary production of most marine basins is N-limited, the excess release of NH4+ at temperature rise >6 ° could enhance water column primary productivity, which may lead to the deterioration of the environmental quality. Climate change effects are expected to be accelerated in areas affected by organic pollution.

scholarly journals Resuspension and estuarine nutrient cycling: insights from the Neuse River Estuary

2010 ◽  
Vol 7 (2) ◽  
pp. 2767-2798 ◽  
Author(s):  
D. R. Corbett
Keyword(s):  
Water Quality ◽  
Nutrient Cycling ◽  
Water Column ◽  
Bottom Water ◽  
River Estuary ◽  
Neuse River Estuary ◽  
Nutrient Concentrations ◽  
Neuse River ◽  
Advective Flux ◽  
The Past

Abstract. For at least the past several decades, North Carolina's Neuse River Estuary (NRE) has been subject to water quality problems relating to increased eutrophication. Research studies initiated in the past several years have addressed the complex nutrient cycles in this system. Most of this research, however, is concerned with the nutrient processes of the water column and the passive diffusion processes of the benthic sedimentary environment. Resuspension of bottom sediments, by bioturbation, tides, or wind-generated waves, may have a significant effect on the flux of nutrients in an estuarine system These processes can result in the advective transport of sediment porewater, rich with nitrogen, phosphorus and carbon, into the water column. Thus, estimates of nutrient and carbon inputs from the sediments may be too low. This study focused on the potential change in porewater and bottom water nutrient concentrations associated with measured resuspension events. Previous research used short-lived radionuclides and meteorological data to characterize the sediment dynamics of the benthic system of the estuary. These techniques in conjunction with the presented porewater inventories allowed evaluation of the depth to which sediments have been disturbed and the advective flux of nutrients to the water column. The largest removal episode occurred in the lower NRE as the result of a wind event and was estimated that the top 2.2 cm of sediment and corresponding porewater were removed. NH4+ advective flux (resuspended) was 2 to 6 times greater than simply diffusion. Phosphate fluxes were estimated to be 15 times greater than the benthic diffusive flux. Bottom water conditions with elevated NH4+ and PO43− indicate that nutrients stored in the sediments continue to play an important role in overall water quality and this study suggests that the advective flux of nutrients to the water column is critical to understand estuarine nutrient cycling.

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