Diversity and biogeography of bacterial community in the Ili River network varies locally and regionally.

Microorganisms in rivers indeed play a crucial role in nutrient cycling within aquatic ecosystems. Understanding the assembly mechanisms of bacterial communities in river networks is essential for predicting their special composition and functional characteristics in natural rivers. This study employed 16S rRNA gene amplicon sequence variation (ASVs) to scrutinize the bacterial community within the uniquely topographical Ili River network. The bacterial community composition varied across the three tributaries with distinct sources and the mainstream. The confluence of various sources diminished the diversity of the bacterial community and altered the functionality of within mainstream. We suggest that strong dispersal limitation predominantly shaped the community at the regional scale (46.6 %), underscoring the significant contribution of headwater sites to bacterial community composition. Contrary to expectation, the bacterial resources in the mainstream were not enriched by the higher diversity in three tributaries. Instead, confluence disturbance potentially increased the undominated processes (36.7 %) and alter the bacterial community composition at the local scale of the mainstream. The intricate coalescence at the confluence could potentially be an intriguing causative factor. Our research indicates that the composition of bacterial communities within intricate river networks exhibits biogeographic patterns, simultaneously influenced by river confluence and geographical features, necessitating multi-scale analysis.

Metagenomic binning and assembled genome analysis revealed the distinct composition of resistome and mobilome in the Ili River.

Rivers play an important role in receiving and transporting the resistome among different environmental compartments. However, the difference in resistome and mobilome between the water and sediment and their underlying mechanisms were still poorly understood. In this study, the Ili River, an important water source in the arid area of Central Asia, was selected as the studied target. The comprehensive profile of resistome and mobilome and their host in water and sediment were studied based on metagenomic binning and assembled genome (MAG) analysis. The relative abundance of resistome and mobilome in sediment were 28.0 - 67.8 × /Gb and 46.5 - 121.1 × /Gb, respectively, which were significantly higher than those in water (23.1 - 52.8 ×/Gb and 25.3 - 67.7 ×/Gb). Multidrug and macrolides-lincosamides-streptogramin (MLS) resistance genes were the main ARG types in both water and sediment from relative abundance. Transposases dominated the relative abundance of mobilome, followed by insert elements and integrases. Strong correlations were found between the relative abundance of resistome and mobilome (r > 0.6 and p < 0.01) in both water and sediment, indicating the mobilome played an important role in the propagation of resistome in the Ili River. The main hosts for multidrug resistance genes via MAG analysis differed in water (Alphaproteobacteria and Gammaproteobacteria) and sediment (Gammaproteobacteria). Distinct compositions of resistome and mobilome existed between water and sediment in the Ili River. Specificity-occupancy analysis of the differential resistome and mobilome showed that occurrence frequencies and habitat selections of the differential ARGs shaped the resistome of water and sediment. In contrast, habitat was the main driver that shaped the mobilome in the Ili River.

Heavy metal(loid)s shape the soil bacterial community and functional genes of desert grassland in a gold mining area in the semi-arid region.

Gold mining can create serious environmental problems, such as soil pollution by heavy metal (loid)s. In this study, we assessed the ecological risk of Hatu gold mining activities and synchronously investigated the bacterial community structure, distribution of soil nutrient-element cycling genes (CNPS) and heavy metal resistance genes (MRG) in adjacent desert grassland soil. The study area was above the moderate risk level, with the ecological risk index (RI) of each sampling site greater than 150. Arsenic, mercury and copper were the main pollutants. Proteobacteria, Actinobacteria and Firmicutes dominated the phyla of the bacterial communities. Species turnover rather than nestedness accounted for the significant differences in community structure among various regions in the mining area. In addition, the bioavailable heavy metal (loid)s (AHM) content had a strong correlation with beta diversity and species turnover of the bacterial community (p < 0.05). No clear difference was found in the total abundance of CNPS genes among various functional regions, but eight specific functional genes were identified from downwind grasslands with lower pollution levels. Among the MRGs, Hg MRG had the highest average total relative abundance, followed by Cu, Co/Zn/Cd and As. The mercury resistance gene subtype hgcAB was positively related to the diversity of the bacterial community, and the bacterial community of grassland soil showed congruency with the MRGs in the Hatu mining area. Total Hg (THg) showed the highest influence affecting the bacterial community, while NH4+-N had the greatest effect on CNPS genes and MRGs. These results highlighted the role of heavy metal (loid)s in shaping the bacterial community and functional genes in arid and semiarid desert grassland soil in gold mining regions.

Distinct soil bacterial patterns along narrow and broad elevational gradients in the grassland of Mt. Tianshan, China.

Bacteria are essential regulators of soil biogeochemical cycles. While several studies of bacterial elevational patterns have been performed in recent years, the drivers of these patterns remain incompletely understood. To clarify bacterial distribution patterns and diversity across narrow- and broad-scale elevational gradients, we collected soil samples from 22 sites in the grasslands of Mt. Tianshan in China along three elevational transects and the overall elevation transect: (1) 6 sites at elevations of 1047-1587 m, (2) 8 sites at 876-3070 m, and (3) 8 sites at 1602-2110 m. The bacterial community diversity across the overall elevation transects exhibited a hump-like pattern, whereas consistent patterns were not observed in the separate elevational transects. The bacterial community composition at the phylum level differed across the transects and elevation sites. The Actinobacteria was the most abundant phylum overall (41.76%) but showed clear variations in the different transects. Furthermore, heatmap analyses revealed that both pH and mean annual temperature (MAT) were significantly (P < 0.05) correlated with bacterial community composition as well as the dominant bacterial phyla, classes, and genera. These findings provide an inclusive view of bacterial community structures in relation to the environmental factors of the different elevational patterns.

Distinct Composition and Assembly Processes of Bacterial Communities in a River from the Arid Area: Ecotypes or Habitat Types?

The composition, function, and assembly mechanism of the bacterial community are the focus of microbial ecology. Unsupervised machine learning may be a better way to understand the characteristics of bacterial metacommunities compared to the empirical habitat types. In this study, the composition, potential function, and assembly mechanism of the bacterial community in the arid river were analysed. The Dirichlet multinomial mixture method recognised four ecotypes across the three habitats (biofilm, water, and sediment). The bacterial communities in water are more sensitive to human activities. Bacterial diversity and richness in water decreased as the intensity of human activities increased from the region of water II to water I. Significant differences in the composition and potential function profile of bacterial communities between water ecotypes were also observed, such as higher relative abundance in the taxonomic composition of Firmicutes and potential function of plastic degradation in water I than those in water II. Habitat filtering may play a more critical role in the assembly of bacterial communities in the river biofilm, while stochastic processes dominate the assembly process of bacterial communities in water and sediment. In water I, salinity and mean annual precipitation were the main drivers shaping the biogeography of taxonomic structure, while mean annual temperature, total organic carbon, and ammonium nitrogen were the main environmental factors influencing the taxonomic structure in water II. These results would provide conceptual frameworks about choosing habitat types or ecotypes for the research of microbial communities among different niches in the aquatic environment.

Ecotoxicological Effects of Microplastics on Bird Embryo Development by Hatching without Eggshell.

Microplastics are an emerging global pollutant type that poses a great health threat to animals due to their uptake and translocation in animal tissues and organs. Ecotoxicological effects of microplastics on the development of bird embryos are not known. The bird egg is a complete development and nutrition system, and the entire embryo development occurs in the eggshell. Therefore, a direct record of bird embryo development under the stress of pollutants such as microplastics is highly limited by the opaque eggshell in traditional hatching. In this study, the effects of microplastics on quail embryo development were visually monitored by hatching without an eggshell. The main steps include the cleaning and disinfection of fertilized eggs, the incubation before exposure, the short-term incubation after exposure, and the sample extraction. The results show that compared with the control group, the wet weight and body length of the microplastics-exposed group displayed a statistical difference and the liver proportion of the whole exposed group significantly increased. Additionally, we evaluated external factors that affect the incubation: temperature, humidity, egg rotation angle, and other conditions. This experimental method provides valuable information on the ecotoxicology of microplastics and a novel way to study the adverse effects of pollutants on the development of embryos.

Effectively reducing antibiotic contamination and resistance in fishery by efficient gastrointestine-blood delivering dietary millispheres.

The overuse of antibiotics during the medication treatment is inevitable in the extensively-applied intensive and semi-intensive aquaculture mode; the accompanied antibiotic contamination and antimicrobial resistance pose threats to the ecosystems and cause great loss to the aquaculture industry. To solve the problem, this work introduced the antibiotic-laden dietary millispheres (DMSs) with internal porous structure for the high availability, attractiveness and digestibility to fish. Two types of antibiotics with distinct solubilities - tetracycline chloride (TCH) and sulfadiazine (SDZ) were made into the DMSs, individually, which were then directly adopted in the feeding of fish. Carassius auratus was chosen as the target fish in this work. The mesocosm study demonstrate that, compared with the regular way of oral administration (feeding the mixture of antibiotics and commercial feed pellets), the DMSs could use much less (i.e. one order of magnitude lower) antibiotic dose to reach the equivalent antibiotic concentration in gastrointestine and blood. As a robust alternative, either TCH- or SDZ-laden DMSs achieved efficient drug delivery in vivo, which importantly facilitated the source reduction of antibiotics, the alleviation of antibiotic contamination in fishery and the control of antibiotic resistance especially in sediments.

Distinct fungal plastisphere across different river functional zones: A watershed scale study.

Fungi not only play important roles in biogeochemical processes but also can form biofilm on plastic debris. However, knowledge of structure composition and spatiotemporal pattern of fungal plastisphere on different kinds of plastic debris in river with specific usages, known as river functional zones, is still missing. In this study, we investigated the spatial distribution of the fungal plastisphere across a complete urban river with different functional zones (drinking, farm irrigation, aquaculture, and tail lake). Our research was performed based on both field residual plastic debris collection and a 30-day field in situ incubation experiments. Our study revealed that plastic debris enriched distinct fungal communities (including pathogenic fungi) significantly different from the surrounding water. Tracking the source of the fungi colonized on plastic debris suggested that the fungal taxa colonized on the different kinds of plastic debris were not from the surrounding water. Human activities had considerable effects on the fungal community structure on plastic debris, and the plastisphere fungal community structure strikingly varied across different river functional zones. Plastisphere may be used as an indicator for fungi biogeography and pathogenic fungi pollution in river with different functional zones. These findings are essential for ecological risk assessment and management decisions for pollution control of plastic debris and maintaining ecological health.

Increased inheritance of structure and function of bacterial communities and pathogen propagation in plastisphere along a river with increasing antibiotics pollution gradient.

Plastic debris provides a stable substrate and novel ecological niche for microorganisms in the aquatic environment, which was referred to as "Plastisphere". Little is known about distribution patterns and responses of ecological function and structure of microbial communities in the plastisphere along rivers which usually have antibiotics pollution gradient. In this study, the differences in the community structure between the plastisphere and the planktonic bacteria, and their spatial variation of the community structure and function along a river with increased antibiotics pollution gradient was investigated at the watershed scale. The diversity of bacteria colonized on most plastic debris was higher than in surrounding water. Plastic debris could accumulate a higher abundance of some potential pathogens than surrounding water even at high antibiotics concentrations. The source tracking results showed that downstream plastisphere inherited much higher proportions of bacterial taxa from upstream than planktonic bacteria. About 92.3-99.7% of bacteria communities in downstream water were not from upstream but from the input of downstream human activities. On the contrary, high proportions of bacterial taxa in downstream plastisphere were closely connected to upstream. The plastisphere possesses higher ecological functional diversity than the planktonic bacteria. Seventy nine functional groups across plastisphere were predicted using functional annotation of prokaryotic taxa and only 65 functional groups were found in the planktonic bacteria. Plastisphere also acts as hotspot for biogeochemical cycling of nutrients such as N and S. Intensive human activities of urban and downstream agriculture and aquaculture had great effects on microbial community structure and functional groups of the Urumqi River. Pastisphere communities are much more resistant to human disturbance than planktonic bacteria. Compared to surrounding water, plastisphere increased inheritance from upstream microbial structure and function and also increased survival and propagation of pathogens in the downstream water with high concentrations of antibiotics.

Selectively enrichment of antibiotics and ARGs by microplastics in river, estuary and marine waters.

The partition of antibiotics and antibiotic resistant genes (ARGs) between the microplastics (MPs) and the surrounding water with various salinity are still unclear. In this study, we hypothesized that adsorption of antibiotics on MPs might cause a significant change of the structure of microbial communities, diversity and abundance of ARGs on MPs and this might be further affected by change of salinity. In this study, we investigated adsorption of four common antibiotics (sulfamerazine, tetracycline, chloramphenicol and tylosin) to polyethylene (PE) MPs in river, estuary and marine waters, and the differences of antibiotic resistant genes (ARGs) and bacterial communities on MPs and in the three waters. The results showed that MPs can enrich antibiotics, ARGs and microbes from the surrounding water. Elevated salinity could reduce adsorption of antibiotics to MPs and the abundance of ARGs. For example, MPs can concentrate more antibiotics and ARGs in the fresh river water than in the estuary and the marine waters. In addition, ARGs and bacterial communities on MPs at various salinity were significantly different under the pressure of four antibiotics. On MPs, sul1, sulA/folP-01, tetA, tetC, tetX and ermE increased significantly but a few new ARGs such as sulA/folP-01 and tetA appeared. The structure of the bacterial communities on MPs was different from the surrounding water since some bacteria species found on MPs were barely detected in the surrounding water while some genera on MPs vanished after exposure to antibiotics. As the antibiotics adsorbed and the ARGs on MPs decreased with the water salinity, the structure of the communities on MPs thus varied with salinity change. These findings are important to understand the effects of MPs on the transport, fate and ecological risk of antibiotics and ARGs in different aquatic environments.

Bacterial community rather than metals shaping metal resistance genes in water, sediment and biofilm in lakes from arid northwestern China.

Lakes in arid northwestern China are valuable freshwater resources that drive socioeconomic development. Environmental pollution can significantly influence the composition of microbial communities and the distribution of functional genes in lakes. This study investigated heavy metal pollution to identify possible correlations with metal resistance genes (MRGs) and bacterial community composition in water, sediment and biofilm samples from Bosten Lake and Ebi Lake in northwestern China. High levels of zinc were detected in all samples. However, the metals detected in the sediment samples of both lakes were determined to be at low risk levels according to an ecological index. The mercury resistance gene subtype merP had the greatest average abundance (4.61 × 10-3 copies per 16S rRNA) among all the samples, followed by merA and merC. The high abundance of merA in the pelagic zone rather than in benthic sediment suggests that the pelagic microbial community was important in mercury reduction. Proteobacteria were the main phylum found in the microbial communities in all samples. However, microbial communities in most of the water, sediment and biofilm samples had different compositions, indicating that the habitat niche plays an important role in shaping the bacterial communities in lakes. The microbial community, rather than the heavy metals, was the main driver of MRG distribution. The abundances of some bacterial genera involved in the decomposition of organic matter and the terrestrial nitrogen cycle were negatively correlated with heavy metals. This result suggests that metal pollution can adversely affect the biogeochemical processes that occur in lakes.

The kinetics, thermodynamics and mineral crystallography of CaCO3 precipitation by dissolved organic matter and salinity.

Calcium carbonate (CaCO3) precipitation is an important geochemical process. In the estuary zone and some arid shallow lakes, DOM (dissolved organic matter) and salinity are two frequent changing factors that may affect CaCO3 precipitation. The joint effect of DOM and salinity on CaCO3 precipitation kinetics and thermodynamics are still unclear. In this study, effects of DOM on CaCO3 precipitation process at 0.5‰ and 70‰ salinity were investigated by QCM (Quartz Crystal Microbalance) technique, real-time pH measurement and single-injection nanoliter ITC (isothermal titration calorimetry). The mineral crystallography was analyzed by SEM-EDS. Both DOM and salinity had inhibitory effect on CaCO3 precipitation. DOM had more pronounced inhibitory effect on CaCO3 precipitation at lower salinity. Regardless of DOM, 70‰ salinity inhibited CaCO3 precipitation >0.5‰ salinity. The CaCO3 precipitation kinetics followed the first-order kinetic model and the adhesion kinetics of the instantaneous nucleation and crystal growth stage could be well described by the exponential function. CaCO3 precipitation was an endothermic process and high salinity strongly hindered CaCO3 precipitation. The effect of DOM on the absorbed heat was significant at 0.5‰ salinity. At 70‰ salinity, regardless of the effect of DOM, CaCO3 precipitation rate was greatly slowed down because it needed much more heat. CaCO3 minerals were dominated by rhombohedral calcite while CaCO3 minerals were mainly shaped as spherical vaterite at 0.5‰ salinity and rhombohedral calcite at 70‰ salinity. The crystal phase changed during CaCO3 precipitation at 0.5‰ salinity. In conclusion, the presence of DOM had substantial impact on the micrograph of the CaCO3 minerals. The percentage of flawed crystals with rough surface increased significantly with increased DOM concentration.

Ca2+ complexation of dissolved organic matter in arid inland lakes is significantly affected by drastic seasonal change of salinity.

CaCO3 precipitation is one of the most common and important geochemical processes in the arid inland waters and it can be significantly affected by interaction of DOM with Ca2+. Effects of the drastic seasonal change of water salinity on interaction of DOM with Ca2+ in the arid inland waters were completely unknown. In the present study, complexation of DOM with Ca2+ in the freshwater (0.5‰ salinity) and hypersaline water (70‰ salinity) were comparatively examined by excitation-emission matrix (EEM) fluorescence quenching titration and isothermal titration calorimetry (ITC). The complexation of DOM with Ca2+ was significantly influenced by the drastic change of salinity. The ITC complexation is exothermic at 0.5‰ salinity but turns to an endothermic process at 70‰ salinity. More energy is needed for the complex reaction between DOM and Ca2+ under the hypersaline condition than in the fresh water. Fluorescence quenching titration indicates that DOM has stronger binding ability toward Ca2+ in the freshwater than in the saline water, and more fractions of DOM in the freshwater are accessible to Ca2+ than in the saline water. Ca2+ complexation in the DOM is dominated by the tryptophan-like components at both salinities and the complexation of Ca2+ with fulvic acid-like components is ignorable. The findings is important for understanding the aquatic geochemical processes in some lakes that seriously affected by irrigation water use in the arid zone.