Microbiome of permeable sandy substrate in headwater river is shaped by water chemistry rather than grain size and heterogeneity

Internal transformation and damming regulate the longitudinal variation of DOM bioavailability in a large river

Understanding the spatial patterns of dissolved organic matter (DOM) and factors that influence them is crucial for maintaining river ecosystem functions and riverine health, considering the significant role of DOM in water quality and aquatic ecosystems. Nevertheless, there is limited knowledge regarding the spatial variation of DOM bioavailability and the factors driving them in large river systems. This study involved 39 sampling locations along the main stem of the Changjiang River, spanning its entire length (> 5000 km) during a dry season. Spatial patterns of DOM were assessed by measurements of DOC concentrations and eight fluorescence DOM indices, namely fluorescence index (FI-A and FI-B), Trytophan/Tyrosine, Humic A, Humic C, humification indices (HIX-A and HIX-B), and Freshness index (β/α). The results revealed that the water DOM in the main stem of the Changjiang River primarily originated from terrestrial sources. A decline in DOM bioavailability was observed from the upper to the lower basin, aligning with the carbon processing prediction rather than the river continuum concept (RCC). The pure effect of physicochemical factors (25.30%) was greater than that of geographic factors (9.40%). The internal transformation processes determined the significant longitudinal decreases of DOM bioavailability. While no significant difference in DOM bioavailability was observed between reaches before and after the dams, the construction of dams was found to improve DOM bioavailability at the subsection scale and reduce the spatial autocorrelation of DOM bioavailability across the entire basin.

Characteristics of bacterial community structure in the sediment of Chishui River (China) and the response to environmental factors

Sediment microorganisms performed an essential function in the biogeochemical cycle of aquatic ecosystems, and their structural composition was closely related to environmental carrying capacity and water quality. In this study, the Chishui River (Renhuai section) was selected as the research area, and the concentrations of environmental factors in the water and sediment were detected. High⁃throughput sequencing was adopted to reveal the characteristics of bacterial community structures in the sediment. In addition, the response of bacteria to environmental factors was explored statistically. Meanwhile, the functional characteristics of bacterial were also analyzed based on the KEGG database. The results showed that the concentration of environmental factors in the water and sediment displayed spatial differences, with the overall trend of midstream > downstream > upstream, which was related to the wastewater discharge from the Moutai town in the midstream directly. Proteobacteria was the most dominant phylum in the sediment, with the relative abundance ranged from 52.06% to 70.53%. The distribution of genus-level bacteria with different metabolic activities varied in the sediment. Upstream was dominated by Massilia, Acinetobacter, and Thermomonas. In the midstream, Acinetobacter, Cloacibacterium and Comamonas were the main genus. Nevertheless, the abundance of Lysobacter, Arenimonas and Thermomonas was higher in the downstream. Redundancy analysis (RDA) showed that total nitrogen (TN) and total phosphorus (TP) were the main environmental factors which affected the structure of bacterial communities in sediment, while total organic carbon (TOC) was the secondary. The bacterial community was primarily associated with six biological pathway categories such as metabolism. Carbohydrate metabolism and amino acid metabolism were the most active functions in the 31 subfunctions. This study could contribute to the understanding of the structural composition and driving forces of bacteria in the sediment, which might benefit for the ecological protection of Chishui River.

Impacts of substrate properties and aquatic nutrient concentrations on the relative abundance of nitrifying/denitrifying genes and the associated microbes in epilithic biofilms

Substrates like sand or gravels and aquatic nutrient concentrations of rivers are highly heterogeneous, influencing the abundance of functional genes in epilithic biofilms where nitrification-denitrification processes take place. To analyze how the relative abundance of nitrifying/denitrifying genes and the associated microbes changes with the physical properties of substrates and aquatic concentrations of nutrients, this paper utilized metagenomics to comprehensively characterize these functional genes (i.e., amoA, hao, and nxrB involved in nitrification, and napA, narG, nirS, norB, and nosZ associated with denitrification) from epilithic biofilms collected along the Shitingjiang River in Southwest China and further obtained the relative abundance of major nitrifiers and denitrifiers. The results show that substrate size most significantly affects the relative abundance of hao and norB by altering the hydrodynamic conditions. In sampling sites with high heterogeneity in substrate size distribution, the relative abundance of most denitrifying genes is also higher. The carbon-nitrogen ratio negatively correlates with the relative abundance of all the nitrifying genes, while ammonium, total inorganic carbon, and total organic carbon concentrations positively affect the relative abundance of amoA and nxrB. As to the relative abundance of nitrifiers and denitrifiers, mainly belonging to phyla Proteobacteria and Actinobacteria, substrate heterogeneity and the aquatic concentrations of nutrients have greater influences than substrate size. Also, the substrate heterogeneity exerted positive influence on functional species of Pseudogemmobacter bohemicus and Paracoccus zhejiangensis. Considering the genes' functions and the dominant species linked to denitrification, nitrous oxide is more likely to occur in rivers with higher heterogeneity and larger substrates.

Slight flow volume rises increase nitrogen loading to nitrogen-rich river, while dramatic flow volume rises promote nitrogen consumption

Concentrated rainfall and water transfer projects result in slight and dramatic increases in flow volume over short periods of time, causing nitrogen recontamination in the water-receiving areas of nitrogen-rich rivers. This study coupled hydrodynamic and biochemical reaction models to construct a model for quantifying diffusive transport and transformation fluxes of nitrogen across the water-sediment interface and analysed possible changes in the relative abundance of microbial functional genes using high-throughput sequencing techniques. In this study, the processes of ammonium (NH₄⁺-N) and nitrate (NO₃^--N) nitrogen release and sedimentation with resuspended particles, as well as mineralisation, nitrification, and denitrification processes were investigated at the water-sediment interface in the Fu River during slight and dramatic increases in flow volume caused by concentrated rainfall and water diversion projects. Specifically, a slight flow volume rise increased the release of NH₄⁺-N from the sediment, inhibited sedimentation of NO₃^--N, decreased the mineralisation rate, increased the nitrification rate, and had little effect on the denitrification process, ultimately increasing the nitrogen load to the river water. A dramatic increase in flow volume simultaneously increased NH₄⁺-N and NO₃^--N exchange fluxes, inhibited the mineralisation process, promoted nitrification-denitrification processes, and increased inorganic nitrogen consumption in the river. This study provides a solution for the re-pollution of rivers that occurs during the implementation of reservoir management and water diversion projects. Furthermore, these results indicate a potential global nitrogen sink that may have been overlooked.

Response mechanism of microbial community to seasonal hypoxia in marine ranching

Seasonal hypoxia, as an increasingly recognized environmental issue, frequently occurred in marine ranching from northern Yellow Sea, China. Although microorganisms play an important ecological role in marine ecosystems, but little is known on the response mechanism of microbial community to seasonal hypoxia in marine ranching. A total of 132 seawater samples and 47 sediment samples were collected from the marine ranching, both in the death disaster zone of sea cucumbers and the non-disaster zone, and in different months. 16S rRNA gene high-throughput sequencing was used to explore the microbial community and its influencing factors. The results showed that the stratification in community composition and dissolved oxygen content appeared in August. The Alpha diversity in seawater was higher in summer than in winter, and significant differences in Beta diversity appeared between the death disaster zone of sea cucumbers and the non-disaster zone in sediments. In addition, environmental effects explained more of the variation in bacterial community composition in seawater as compared with spatial effects did, whereas, sedimentary bacterial communities were more closely related to spatial effects. The present results could provide fundamental data for understanding the response mechanism of the microbial community to seasonal hypoxia in marine ranching and are of great significance for the management and protection of marine ranching.

Denitrification of Permeable Sand Sediment in a Headwater River Is Mainly Influenced by Water Chemistry, Rather Than Sediment Particle Size and Heterogeneity

Sediment particle size and heterogeneity play an important role in sediment denitrification through direct and indirect effects on, for example, the material exchange rate, environmental gradients, microbial biomass, and grazing pressure. However, these effects have mostly been observed in impermeable sediments. On the other hand, the material exchange of permeable sediments is dominated by advection instead of diffusion, with the exchange or transport rates exceeding those of diffusion by two orders of magnitude relative to impermeable sediments. The impact of permeable sediment particle size and heterogeneity on denitrification remains poorly understood, especially at the millimeter scale. Here, we conducted an in situ control experiment in which we sorted sand sediment into four homogeneous-particle-sizes treatments and four heterogeneous treatments. Each treatment was deployed, in replicate, within the riffle in three different river reaches with contrasting physicochemical characteristics. After incubating for three months, sediment denitrifier communities (nirS, nirK, nosZ), denitrification gene abundances (nirS, nirK, nosZ), and denitrification rates in all treatments were measured. We found that most of the denitrifying microbes in permeable sediments were unclassified denitrifying microbes, and particle size and heterogeneity were not significantly correlated with the functional gene abundances or denitrification rates. Water chemistry was the key controlling factor for the denitrification of permeable sediments. Water NO3--N directly regulated the denitrification rate of permeable sediments, instead of indirectly regulating the denitrification rate of sediments by affecting the chemical characteristics of the sediments. Our study fills a knowledge gap of denitrification in permeable sediment in a headwater river and highlights that particle size and heterogeneity are less important for permeable sediment denitrification.