Metagenomics reveals biogeochemical processes carried out by sediment microbial communities in a shallow eutrophic freshwater lake

Response of sulfate concentration to eutrophication on spatio-temporal scale in freshwater lakes

The dramatical increase of sulfur concentration in eutrophic lakes, especially sulfate (SO42-), has brought attention to the impact on the lake ecosystem; however, the mechanisms driving the intensification of eutrophication and the role of SO₄2- concentrations remain poorly understood. To assess the impact of eutrophication on SO42- dynamics in lakes, this study monitored SO42- concentrations in water and sediments across seven lakes with varying trophic statuses on a spatial scale, and in the eutrophic Lake Taihu over one year on a temporal scale, as well as a series of microcosms with different initial SO42- concentrations. Exogenous sulfur input is the primary driver of increased SO42- concentrations in lakes, the highest SO42- concentration in overlying water was 100 mg/L, as well as which reached 310.9 mg/L in sediment. The concurrent input of nutrients such as nitrogen and phosphorus exacerbated eutrophication, resulting in the destabilization of the sulfur cycle. Eutrophication promoted the SO42- concentration on the spatio-temporal scale, especially in sediment, and trophic lake index (TLI) showed a positive correlation with the SO42- in sediments (R2 = 0.99; 0.88). The SO42- concentration in water and TLI showed a nonlinear correlation on the temporal scale (R2 = 0.44), and showed a positive correlation on the spatial scale (R2 = 0.49). Microscopic experiments demonstrate that the anaerobic environment created by cyanobacteria decomposition induced sulfate reduction and significantly reduces SO42- concentrations. Concurrently, the anaerobic environment facilitates the coupling of iron reduction with sulfate reduction, leading to a substantial increase in Acid Volatile Sulfides (AVS) in the sediment. These findings reveal that eutrophication has a dual effect on the dynamic change of SO42- concentrations in overlying water, which is helpful to accurately evaluate and predict the change of SO42- concentrations in lakes.

Planting halophytes increases the rhizosphere ecosystem multifunctionality via reducing soil salinity

Soil salinization poses a significant global challenge, exerting adverse effects on both agriculture and ecosystems. Planting halophytes has the potential ability to improve saline-alkali land and enhance ecosystem multifunctionality (EMF). However, it remains unclear which halophytes are effective in improving saline-alkali land and what impact they have on the rhizosphere microbial communities and EMF. In this study, we evaluated the Na+ absorption capability of five halophytes (Grubovia dasyphylla, Halogeton glomeratus, Suaeda salsa, Bassia scoparia, and Reaumuria songarica) and assessed their rhizosphere microbial communities and EMF. The results showed that S. salsa possessed the highest shoot (3.13 mmol g-1) and root (0.92 mmol g-1) Na+ content, and its soil Na+ absorption, along with B. scoparia, was significantly higher than that of other plants. The soil pH, salinity, and Na+ content of the halophyte rhizospheres decreased by 6.21%, 23.49%, and 64.29%, respectively, when compared to the bulk soil. Extracellular enzymes in the halophyte rhizosphere soil, including α-glucosidase, β-glucosidase, β-1,4-N-acetyl-glucosaminidase, neutral phosphatase, and alkaline phosphatase, increased by 70.1%, 78.4%, 38.5%, 79.1%, and 64.9%, respectively. Furthermore, the halophyte rhizosphere exhibited higher network complexity of bacteria and fungi and EMF than bulk soil. The relative abundance of the dominant phyla Proteobacteria, Firmicutes, and Ascomycota in the halophyte rhizosphere soil increased by 9.4%, 8.3%, and 22.25%, respectively, and showed higher microbial network complexity compared to the bulk soil. Additionally, keystone taxa, including Muricauda, Nocardioides, and Pontibacter, were identified with notable effects on EMF. This study confirmed that euhalophytes are the best choice for saline-alkali land restoration. These findings provided a theoretical basis for the sustainable use of saline-alkali cultivated land.

Ignored microbial-induced taste and odor in drinking water reservoirs: Novel insight into actinobacterial community structure, assembly, and odor-producing potential

The presence of actinobacteria in reservoirs can lead to taste and odor issues, posing potential risks to the safety of drinking water supply. However, the response of actinobacterial communities to environmental factors in drinking water reservoirs remains largely unexplored. To address this gap, this study investigated the community structure and metabolic characteristics of odor-producing actinobacteria in water reservoirs across northern and southern China. The findings revealed differences in the actinobacterial composition across the reservoirs, with Mycobacterium sp. and Candidatus Nanopelagicus being the most prevalent genera. Notably, water temperature, nutrient levels, and metal concentrations were associated with differences in actinobacterial communities, with stochastic processes playing a major role in shaping the community assembly. In addition, three strains of odor-producing actinobacteria were cultured in raw reservoir water, namely Streptomyces antibioticus LJH21, Streptomyces sp. ZEU13, and Streptomyces sp. PQK19, with peak ATP concentrations of 51 nmol/L, 66 nmol/L, and 70 nmol/L, respectively, indicating that odor-producing actinobacteria could remain metabolically active under poor nutrient pressure. Additionally, Streptomyces antibioticus LJH21 produced the highest concentration of geosmin at 24.4 ng/L. These findings enhance our understanding of regional variances and reproductive metabolic mechanisms of actinobacteria in drinking water reservoirs, providing a solid foundation for improving drinking water quality control, especially for taste and odor.

Eutrophication impacts the distribution and functional traits of viral communities in lakes

Viruses play a crucial role in aquatic ecosystems by regulating microbial composition and impacting biogeochemical cycling. While the response of viral diversity to the trophic status has been preliminarily explored in lake ecosystems, there is limited integrated exploration of the biogeography of viruses, host associations, and the auxiliary metabolic genes (AMGs), particularly for plateau lakes. Therefore, this research investigated the viral biogeography, virus-host association, and AMGs in the surface waters of 11 lakes varying in trophic levels (eutrophic and oligo-mesotrophic) in the Yunnan-Guizhou plateau region of China. A total of 73,105 viral operational taxonomic units were obtained from 11 samples, with 84.8 % remaining unannotated at the family level, indicating a predominance of novel viruses within these lakes. The most abundant viral family was Kyanoviridae (24.4 %), recognized as a common cyanophage. The vast majority of cyanobacteria and several eukaryotic algae were predicted as hosts for the viruses, with a lytic lifestyle predominating the life strategy of these cyanophages, implying the potential influence of the virus on algae. The viral community structure significantly correlated with both trophic status and the bacterial community. The structure equation model analysis revealed chlorophyll a was the primary factor affecting viral communities. Moreover, numerous AMGs linked to carbon metabolism, phosphorus metabolism, sulfur metabolism, and photosynthesis were found in these lakes, some of which showed virus preference for the trophic statuses, suggesting a vital role of the virus in driving biogeochemical cycling in the lake crossing different nutrient levels. In addition, a restricted presence of viruses was found to infect humans or harbor antibiotic resistance genes in the lakes, suggesting a subtle yet potential link to human health. Overall, these findings offer insights into the response of viral communities to eutrophication and their potential role in biogeochemical cycling and controlling algal propagation.

Multiple antibiotic resistance and herbicide catabolic profiles of bacteria isolated from Lake Villarrica surface sediments (Chile)

Antibiotics and herbicides are contaminants of emerging concern in aquatic environments. Lake Villarrica is a relevant freshwater body in Chile and was recently designated a 'saturated nutrient zone'. Here, we investigated the occurrence of multiple antibiotic resistance (MAR) and herbicide catabolic profiles among bacteria present in the surface sediments of Lake Villarrica. The occurrence of antibiotic-resistant genes (ARGs; blaTEM, catA and tetM) and herbicide-catabolic genes (HCGs; phnJ and atzA) was investigated by qPCR. Subsequently, the presence of culturable bacteria with multiple resistance to amoxicillin (AMX), chloramphenicol (CHL) and oxytetracycline (OXT) was studied. Forty-six culturable MAR (AMX + CHL + OXT) strains were isolated and characterized with respect to their resistance to 11 antibiotics by using a disc diffusion assay and testing their ability to use herbicides as a nutrient source. qPCR analyses revealed that ARGs and HCGs were present in all sediment samples (101 to 103 gene copies g-1), with significant (P ≤ 0.05) higher values in sites near Villarrica city and cattle pastures. The plate method was used to recover MAR isolates from sediment (103-106 CFU g-1), and most of the 46 isolates also showed resistance to oxacillin (100%), cefotaxime (83%), erythromycin (96%) and vancomycin (93%). Additionally, 54 and 57% of the MAR isolates were able to grow on agar supplemented (50 mg L-1) with atrazine and glyphosate as nutrient sources, respectively. Most of the MAR isolates were taxonomically close to Pseudomonas (76.1%) and Pantoea (17.4%), particularly those isolated from urbanized sites (Pucón city). This study shows the presence of MAR bacteria with herbicide catabolic activity in sediments, which is valuable for conservation strategies and risk assessments of Lake Villarrica. However, major integrative studies on sediments as reservoirs or on the fate of MAR strains and traces of antibiotics and herbicides as a result of anthropic pressure are still needed.

Accumulation and ecological risk assessment of diazinon in surface sediments of Baiyangdian lake and its potential impact on probiotics and pathogens

Diazinon is an organophosphorus pesticide widely used in agriculture and household pest control, and its use also poses several environmental and health hazards. In this study, we investigated the spatial and temporal distribution of diazinon in Baiyangdian, evaluated its potential ecological risk and toxicity to aquatic organisms based on RQ (Risk quotient) and TU (Toxic unit) analysis, and assessed the potential effects of diazinon accumulation on probiotics and pathogens based on statistical analysis of high-throughput sequencing data. The results showed that diazinon in Baiyangdian posed a low to moderate chronic risk to sediment-dwelling organisms and a low toxicity effect on aquatic invertebrates, which was mainly concentrated in October and human-intensive areas. Meanwhile, increases in sediment electrical conductivity (EC), amorphous iron oxides content and phenol oxidase activity favored diazinon accumulation in sediments, whereas the opposite was the case for sediment organic carbon, β-1,4-glucosidase, phosphatase, catalase and pH, suggesting that environmental indicators play a key role in the behavior and distribution of diazinon. In addition, diazinon in heavily contaminated areas seem to inhibit the rare probiotics (Bifidobacterium adolescentis and Serratia sp.), while promoted dominant pathogens (e.g., Burkholderia cenocepacia), which can lead to increased disease risk to humans and ecosystems, disruption of ecological balance and potential health problems. However, probiotic Streptomyces xiamenensis resist to diazinon would be a potential degrader for diazinon remove. In conclusion, this study unveiled the effects of diazinon pollution on wetland ecosystems, emphasizing ecological impacts and potential health concerns. In addition, the discovery of diazinon resistant probiotics provided new insights into wetland ecological restoration.

Intermittent electrostimulation-modified direct interspecies electron transfer for enhanced methanogenesis in anaerobic digestion of sulfate-rich wastewater

Methane recovery and organics removal in sulfate (SO42-)-rich wastewater anaerobic digestion are hindered by electron competition between methanogenesis and sulfidogenesis. Here, intermittently electrostimulated bioelectrodes were developed to facilitate direct interspecies electron transfer (DIET)-driven syntrophic methanogenesis, increasing substrate competition among methanogenic archaea (MA). By optimising the electrochemical environment, MA was able to employ electron transfer more efficiently than sulfate-reducing bacteria (SRB), resulting in significant methane accumulation (58.1 ± 1.0 mL-CH4/m3reactor) and COD removal (90.5 ± 0.5 %) at lower COD/SO42- ratio. Intermittent electrostimulation improved the metabolic pathway for electroactive bacteria to utilize acetate and direct electrons to electrotrophic MA, decreasing SRB abundance and affecting the sulfate reduction pathway. Intermittently electrostimulated biofilms significantly increased gene levels of key enzymes in electron transport for cytochrome and e-pili biosynthesis, crucial for DIET, demonstrating enhanced DIET-driven syntrophic methanogenesis. This study provides a strategic approach to optimize methanogenesis in sulfate-rich wastewater anaerobic digestion.

Microbial community and extracellular polymeric substance dynamics in arid-zone temporary pan ecosystems

Microbial extracellular polymeric substances (EPS) are an important component in sediment ecology. However, most research is highly skewed towards the northern hemisphere and in more permanent systems. This paper investigates EPS (i.e., carbohydrates and proteins) dynamics in arid Austral zone temporary pans sediments. Colorimetric methods and sequence-based metagenomics techniques were employed in a series of small temporary pan ecosystems characterised by alternating wet and dry hydroperiods. Microbial community patterns of distribution were evaluated between seasons (hot-wet and cool-dry) and across depths (and inferred inundation period) based on estimated elevation. Carbohydrates generally occurred in relatively higher proportions than proteins; the carbohydrate:protein ratio was 2.8:1 and 1.6:1 for the dry and wet season respectively, suggesting that EPS found in these systems was largely diatom produced. The wet- hydroperiods (Carbohydrate mean 102 μg g-1; Protein mean 65 μg g-1) supported more EPS production as compared to the dry- hydroperiods (Carbohydrate mean 73 μg g-1; Protein mean 26 μg g-1). A total of 15,042 Unique Amplicon Sequence Variants (ASVs) were allocated to 51 bacterial phyla and 1127 genera. The most abundant genera had commonality in high temperature tolerance, with Firmicutes, Actinobacteria and Proteobacteria in high abundances. Microbial communities were more distinct between seasons compared to within seasons which further suggested that the observed metagenome functions could be seasonally driven. This study's findings implied that there were high levels of denitrification by mostly nitric oxide reductase and nitrite reductase enzymes. EPS production was high in the hot-wet season as compared to relatively lower rates of nitrification in the cool-dry season by ammonia monooxygenases. Both EPS quantities and metagenome functions were highly associated with availability of water, with high rates being mainly associated with wet- hydroperiods compared to dry- hydroperiods. These data suggest that extended dry periods threaten microbially mediated processes in temporary wetlands, with implications to loss of biodiversity by desiccation.

Pathogen profile of Baiyangdian Lake sediments using metagenomic analysis and their correlation with environmental factors

Increasing concerns about public health and safety after covid-19 have raised pathogen studies, especially in aquatic environments. However, the extent to how different location and human activities affect geographic occurrence and distribution of pathogens in response to agricultural pollution, boat tourism disturbances and municipal wastewater inflow in a degraded lake remains unclear. Since the surrounding residents depend on the lake for their livelihood, understanding the pathogens reserved in lake sediment and the regulation possibility by environmental factors are challenges with far-reaching significance. Results showed that 187 pathogens were concurrently shared by the nine sediment samples, with Salmonella enterica and Pseudomonas aeruginosa being the most abundant. The similar composition of the pathogens suggests that lake sediment may act as reservoirs of generalist pathogens which may pose infection risk to a wide range of host species. Of the four virulence factors (VFs) types analyzed, offensive VFs were dominant (>46 % on average) in all samples, with dominant subtypes including adherence, secretion systems and toxins. Notably, the lake sediments under the impact of agricultural use (g1) showed significantly higher diversity and abundance of pathogen species and VFs than those under the impact of boat tourism (g2) and/or municipal wastewater inflow with reed marshes filtration (g3). From the co-occurrence networks, pathogens and pesticides, aggregate fractions, EC, pH, phosphatase have strong correlations. Strong positive correlations between pathogens and diazinon in g1 and ppDDT in g2 and g3 suggest higher pesticide-pathogen co-exposure risk. These findings highlight the need to explore pathogen - environmental factor interaction mechanisms in the human-impacted water environments where the control of pathogen invasion by environmental factors may accessible.

Distribution of organophosphorus pesticides and its potential connection with probiotics in sediments of a shallow freshwater lake

Despite the serious health threats due to wide use of organophosphorus pesticides (OPPs) have been experimentally claimed to be remediated by probiotic microorganisms in various food and organism models, the interactions between OPPs and probiotics in the natural wetland ecosystem was rarely investigated. This study delves into the spatial and temporal distribution, contamination levels of OPPs in the Baiyangdian region, the diversity of probiotic communities in varying environmental contexts, and the potential connection with OPPs on these probiotics. In typical shallow lake wetland ecosystem-Baiyangdian lake in north China, eight OPPs were identified in the lake sediments, even though their detection rates were generally low. Malathion exhibited the highest average content among these pesticides (9.51 ng/g), followed by fenitrothion (6.70 ng/g). Conversely, chlorpyrifos had the lowest detection rate at only 2.14%. The region near Nanliu Zhuang (F10), significantly influenced by human activities, displayed the highest concentration of total OPPs (136.82 ng/g). A total of 145 probiotic species spanning 78 genera were identified in Baiyangdian sediments. Our analysis underscores the relations of environmental factors such as phosphatase activity, pH, and electrical conductivity (EC) with probiotic community. Notably, several high-abundance probiotics including Pseudomonas chlororaphis, Clostridium sp., Lactobacillus fermentum, and Pseudomonas putida, etc., which were reported to exhibit significant potential for the degradation of OPPs, showed strongly correlations with OPPs in the Baiyangdian lake sediments. The outcomes of this research offer valuable insights into the spatiotemporal dynamics of OPPs in natural large lake wetland and the probability of their in-situ residue bioremediation through the phosphatase pathway mediated by probiotic such as Lactic acid bacteria in soils/sediments contaminated with OPPs.