Ecogenomics reveals metals and land-use pressures on microbial communities in the waterways of a megacity

Exploring optical descriptors for rapid estimation of coastal sediment organic carbon and nearby land-use classifications via machine learning models

This study utilizes ultraviolet and fluorescence spectroscopic indices of dissolved organic matter (DOM) from sediments, combined with machine learning (ML) models, to develop an optimized predictive model for estimating sediment total organic carbon (TOC) and identifying adjacent land-use types in coastal sediments from the Yellow and Bohai Seas. Our results indicate that ML models surpass traditional regression techniques in estimating TOC and classifying land-use types. Penalized Least Squares Regression (PLR) and Cubist models show exceptional TOC estimation capabilities, with PLR exhibiting the lowest training error and Cubist achieving a correlation coefficient 0.79. In land-use classification, Support Vector Machines achieved 85.6 % accuracy in training and 92.2 % in testing. Maximum fluorescence intensity and ultraviolet absorbance at 254 nm were crucial factors influencing TOC variations in coastal sediments. This study underscores the efficacy of ML models utilizing DOM optical indices for near real-time estimation of marine sediment TOC and land-use classification.

Temperature and nutrients alter the relative importance of stochastic and deterministic processes in the coastal macroinvertebrates biodiversity assembly on long-time scales

Macroinvertebrates play a vital role in coastal ecosystems and are an important indicator of ecosystem quality. Both anthropogenic activity and environmental changes may lead to significant changes in the marine macroinvertebrate community. However, the assembly process of benthic biodiversity and its mechanism driven by environmental factors at large scales remains unclear. Here, using the benthic field survey data of 15 years at large spatial and temporal scales from the Yellow Sea Large Marine Ecosystem, we investigated the relative importance of environmental selection, dispersal processes, random-deterministic processes of macroinvertebrates community diversity assembly, and the responses of this relative importance driven by temperature and nutrients. Results showed that the macroinvertebrates community diversity is mainly affected by dispersal. Nitrogen and phosphorus are the most important negative factors among environmental variables, while geographical distance is the main limiting factor of β diversity. Within the range of 0.35-0.70 mg/L of nutrients, increasing nutrient concentration can significantly facilitate the contribution of the decay effect to β diversity. Within the temperature range studied (15.0-18.0°C), both warming and cooling can lead to a greater tendency for species diversity assembly processes to be dominated by deterministic processes. The analysis contributes to a better understanding of the assembly process of the diversity of coastal marine macroinvertebrates communities and how they adapt to global biogeochemical processes.

The role of agricultural drainage, storm-events, and natural filtration on the biogeochemical cycling capacity of aquatic and sediment environments in Lake Erie's drainage basin

Lake Erie is the most at risk of the Great Lakes for degraded water quality due to non-point source pollution caused by agricultural activities in the lake's watershed. The extent and temporal patterns of nutrient loading from these agricultural activities is influenced by the timing of agronomic events, precipitation events, and water flow through areas of natural filtration within the watershed. Downstream impacts of these nutrient loading events may be moderated by the co-loading of functionally relevant biogeochemical cycling microbial communities from agricultural soils. This study quantified loading patterns of these communities from tile drain sources, assessed whether functional communities from agricultural sources influenced downstream microbial functionality, and investigated how distance from agricultural sources, storm events, and areas of natural filtration altered nutrient cycling and nutrient fluxes in aquatic and sediment environments. Water and sediment samples were collected in the Wigle Creek watershed in Ontario, from tile drains through to Lake Erie, from May to November 2021, and microbial nitrogen (N) and phosphorous (P) cycling capacity (quantitative PCR), and nutrient levels were evaluated. Results showed that N and P functional groups were co-loaded with nutrients, with increased loading occurring during storm events and during agricultural activities including fertilization and harvest. Overall functional capacity in the aquatic environment decreased with distance from the agricultural sources and as water transited through natural filtration areas. In contrast, the sediment environment was more resilient to both agricultural disturbances and abiotic factors. This study expands our understanding of when and where different stages of N and P cycling occurs in agriculturally impacted watersheds, and identifies both seasons and regions to target with nutrient mitigation strategies.

Insights in Pharmaceutical Pollution: The Prospective Role of eDNA Metabarcoding

Environmental pollution is a growing threat to natural ecosystems and one of the world's most pressing concerns. The increasing worldwide use of pharmaceuticals has elevated their status as significant emerging contaminants. Pharmaceuticals enter aquatic environments through multiple pathways related to anthropogenic activity. Their high consumption, insufficient waste treatment, and the incapacity of organisms to completely metabolize them contribute to their accumulation in aquatic environments, posing a threat to all life forms. Various analytical methods have been used to quantify pharmaceuticals. Biotechnology advancements based on next-generation sequencing (NGS) techniques, like eDNA metabarcoding, have enabled the development of new methods for assessing and monitoring the ecotoxicological effects of pharmaceuticals. eDNA metabarcoding is a valuable biomonitoring tool for pharmaceutical pollution because it (a) provides an efficient method to assess and predict pollution status, (b) identifies pollution sources, (c) tracks changes in pharmaceutical pollution levels over time, (d) assesses the ecological impact of pharmaceutical pollution, (e) helps prioritize cleanup and mitigation efforts, and (f) offers insights into the diversity and composition of microbial and other bioindicator communities. This review highlights the issue of aquatic pharmaceutical pollution while emphasizing the importance of using modern NGS-based biomonitoring actions to assess its environmental effects more consistently and effectively.

Exploring the resilience of constructed wetlands to harmful algal blooms disturbances: A study on microbial response mechanisms

Constructed wetlands (CWs) have emerged as a promising environmentally sustainable technique for wastewater treatment. However, the susceptibility of CWs to disturbances caused by harmful algal blooms (HABs) raises concerns. This study aimed to investigate the impact of HABs on the pollutants' removal performance of CWs and the response of rhizosphere microbial community. Results revealed that CWs possessed an adaptive capacity that enabled them to recover caused by HABs. The rhizosphere was found to stimulate the occurrence of Acinetobacter, which played a critical role to help resist HABs disturbance. This study also observed an increased dissimilatory nitrate reduction metabolic pathway which promoted denitrification and enhanced the nitrogen removal efficiency of CWs. Additionally, the structural equation model further suggested that dissolved oxygen exerted a significant influence on the microbial activities and then affected the pollutants removal performance. Overall, our findings shed light on the mechanism for CW stability maintenance during HABs disturbance.

Assessment of biological community in riparian zone contaminated by PAHs: Linking source apportionment to biodiversity

Riparian zone, an important land-water interface, plays an essential role in maintaining the ecological health of rivers, whereas the effects of Polycyclic aromatic hydrocarbons (PAHs) on the health of biological communities in riparian groundwater remain undetermined. To understand the responses of multiple communities to environmental variables, the distribution and ecosystem risk of 16 PAHs have been investigated in the Beiluo River, China. The distribution of multiple communities in riparian groundwater was investigated by environmental DNA metabarcoding, including 16S rRNA, 18S rRNA, and COI gene sequencing for bacteria, microbial eukaryotes (including algae, fungi, and protozoa), and metazoan, respectively, followed by correlation analysis between multiple communities and PAH contamination levels. The concentration of PAHs in the Beiluo River ranged largely from 35.32 to 728.59 ng/L. Here, the Shannon's diversity index of bacteria (Firmicutes) decreased possibly due to the occurrence of Pyrene, which mainly derives from coal and biomass combustion. Furthermore, the reduced richness of fungi (Ascomycota, Basidiomycota) and algae (Chlorophyta, Chrysophyceae) can be attributed to the presence of medium molecular weight (MMW) PAHs (Pyrene, Benz(a)anthracene, Chrysene), and low molecular weight (LMW) PAHs (Naphthalene, Fluorene, Phenanthrene). The richness and Shannon's diversity index of metazoan (Arthropoda) were promoted owing to MMW PAHs (Chrysene, Fluoranthene) generated from coal and biomass combustion and traffic emission. The ecological risk of PAHs in the groundwater environment of the Beiluo River was characterized as low to medium, where LMW and MMW PAHs posed higher risk than the high molecular weight (HMW) compounds. Overall, this study provides insights into the structures of riparian multi-biological communities altered by PAHs.

Spatiotemporal variation in nitrogen and phosphorus levels and microbial community in the upstream water transport channel to the Douhe Reservoir

The Douhe Reservoir is an important diversion water source and drinking water resource for Tianjin and the Tangshan cities. Panjiakou, Daheiting, Qiuzhuang, and the Douhe Reservoirs located from top to bottom in the LuanHe River region forming a group of cascade reservoirs. After over 30 years of aquaculture, the concentration of nitrogen (N) and phosphorus (P) have exceeded Class III of Environmental Quality Standard for Surface Water in China. We selected the Douhe Reservoir as the study site and choose sampling points in several upstream reservoirs and main reservoir area, and we collected a total of 18 water samples. Moreover, the distribution characteristics of N and P levels in flood season and dry season were studied in the Douhe Reservoir and upstream water channel, respectively. The results indicated that there were significant spatial differences between N and P distribution in the Douhe Reservoir and the upstream sites. We observed that the distribution of N and P had seasonal characteristics, and the contents of nitrate(NO3^--N), nitrogen(TN), total phosphorus(TP), and total dissolved phosphorus(TDP) in flood periods were higher than those in dry periods. The microbial community structure illustrated that the dominant phylum displayed seasonal differences between the upstream channel and the reservoir area. Among them, the abundance of some genera changed with the location of the channel, the microbial community structure, and the levels of N and P, especially in flood season. Particularly, NO₃^--N and TN had the most significant correlation. Hence, this study presented an important theoretical foundation for the risk prevention and the control of nutrient elements in the LuanHe River basin in the future, which would enhance the drinking water safety of Tianjin and Tangshan residents.

The relationship between land cover and microbial community composition in European lakes

Microbes are essential for element cycling and ecosystem functioning. However, many questions central to understanding the role of microbes in ecology are still open. Here, we analyze the relationship between lake microbiomes and the lakes' land cover. By applying machine learning methods, we quantify the covariance between land cover categories and the microbial community composition recorded in the largest amplicon sequencing dataset of European lakes available to date. Our results show that the aggregation of environmental features or microbial taxa before analysis can obscure ecologically relevant patterns. We observe a comparatively high covariation of the lakes' microbial community with herbaceous and open spaces surrounding the lake; nevertheless, the microbial covariation with land cover categories is generally lower than the covariation with physico-chemical parameters. Combining land cover and physico-chemical bioindicators identified from the same amplicon sequencing dataset, we develop analytical data structures that facilitate insights into the ecology of the lake microbiome. Among these, a list of the environmental parameters sorted by the number of microbial bioindicators we have identified for them points towards apparent environmental drivers of the lake microbial community composition, such as the altitude, conductivity, and area covered herbaceous vegetation surrounding the lake. Furthermore, the response map, a similarity matrix calculated from the Jaccard similarity of the environmental parameters' lists of bioindicators, allows us to study the ecosystem's structure from the standpoint of the microbiome. More specifically, we identify multiple clusters of highly similar and possibly functionally linked ecological parameters, including one that highlights the importance of the calcium-bicarbonate equilibrium for lake ecology. Taken together, we demonstrate the use of machine learning approaches in studying the interplay between microbial diversity and environmental factors and introduce novel approaches to integrate environmental molecular diversity into monitoring and water quality assessments.

Bacterial assemblages of urban microbiomes mobilized by runoff waters match land use typologies and harbor core species involved in pollutant degradation and opportunistic human infections

Cities are patchworks of urban catchments divided into functional units according to their commercial, residential and industrial activities, and socio-urbanistic patterns. The hypothesis of city surface microbiomes being structured by socio-urbanistic variables leading to an emergence of synurbic taxa was tested. According to the r/K microbial ecology theory, a gradient of well-adapted synurbic K-strategists and of opportunistic -r-strategists should occur over city surfaces. K-strategists would be core components while r-ones would be transiently detected. To resolve these patterns, sub-catchments (n = 21) of an area of high commercial and industrial activities were investigated over three time periods covering one year. The sub-catchments' land use patterns and associated human behaviors were converted into socio-urbanistic variables and groupings. Bacterial cells mobilized by runoffs per sub-catchment were recovered, and analyzed by classical approaches, microbial source tracking DNA assays and DNA meta-barcoding approaches. Relationships between these datasets, the runoff physico-chemical properties, and descriptors of the socio-urbanistic groupings were investigated. 16S rRNA meta-barcoding analyses showed evidence of the occurrence of K- and r-like strategists. Twenty-eight core genera were identified, and correlation networks revealed large bacterial modules organized around actinobacterial taxa involved in hydrocarbon degradation processes. Other bacterial networks were related to the occurrences of hygienic wastes, and involved bacteria originating from fecal contaminations. Several r-strategists like Sulfurospirillum were recorded and found associated to point source pollutions. The tpm-metabarcoding approach deciphered these r / K strategists at the species level among more than ten genera. Nine core K-like Pseudomomas species were identified. The P. aeruginosa human opportunistic pathogen and P. syringae phytopathogens were part of these K-strategists. Other tpm-harboring bacterial pathogens showed r-like opportunistic distribution patterns. Correlation network analyses indicated a strong incidence of hygienic wastes and hydrocarbon-pollutions on tpm-harboring bacteria. These analyses demonstrated the occurrence of core synurbic bacterial K-strategists over city surfaces.

Coupled effects of landscape structures and water chemistry on bacterioplankton communities at multi-spatial scales

Bacterioplankton communities in rivers are strongly influenced by the surrounding landscape, yet the relationships between land use and bacterioplankton communities at multi-spatial scales and the mechanisms that shape bacterioplankton communities remain unclear. Here, we collected surface water samples from 14 tributaries of the Yuan River, a secondary tributary of the Yangtze River, which has been heavily impacted by human activities. We characterized the bacterioplankton communities by high-throughput sequencing techniques, and managed to identify the mechanisms governing bacterioplankton community assembly. The results showed that, in general, both landscape compositions and landscape configurations had significant effects on bacterial communities, and the effects were greater at the buffer scale than at the sub-basin scale. Additionally, there was no distinct distance-decay pattern for the effects of landscape structures on bacterial communities from the near-distance (100 m) to the long-distance (1000 m) buffer zones, with the maximal effects occurring in the 1000 m circular buffer (wet season) and 500 m riparian buffer (dry season) zone, respectively. Land use influenced the bacterioplankton community both directly through exogenous inputs (mass effect) and indirectly by affecting water chemistry (species sorting). Variance partitioning analyses showed that the total explanations of bacterial community variations by water chemistry and the intersections of water chemistry and land use (56.2% in wet season and 50.4% in dry season) were higher than that of land use alone (6.1% in wet season and 25.4% in dry season). These suggest that mass effects and species sorting jointly shaped bacterial community assembly, but that the effects of species sorting outweighed those of mass effects. Nevertheless, more biotic and abiotic factors need to be considered to better understand the microbial assembly mechanisms in anthropogenically influenced riverine ecosystems.

Amsterdam urban canals contain novel niches for methane-cycling microorganisms

Urbanised environments have been identified as hotspots of anthropogenic methane emissions. Especially urban aquatic ecosystems are increasingly recognised as important sources of methane. However, the microbiology behind these emissions remains unexplored. Here, we applied microcosm incubations and molecular analyses to investigate the methane‐cycling community of the Amsterdam canal system in the Netherlands. The sediment methanogenic communities were dominated by Methanoregulaceae and Methanosaetaceae, with co‐occurring methanotrophic Methanoperedenaceae and Methylomirabilaceae indicating the potential for anaerobic methane oxidation. Methane was readily produced after substrate amendment, suggesting an active but substrate‐limited methanogenic community. Bacterial 16S rRNA gene amplicon sequencing of the sediment revealed a high relative abundance of Thermodesulfovibrionia. Canal wall biofilms showed the highest initial methanotrophic potential under oxic conditions compared to the sediment. During prolonged incubations the maximum methanotrophic rate increased to 8.08 mmol g_DW⁻¹ d⁻¹ that was concomitant with an enrichment of Methylomonadaceae bacteria. Metagenomic analysis of the canal wall biofilm lead to the recovery of a single methanotroph metagenome‐assembled genome. Taxonomic analysis showed that this methanotroph belongs to the genus Methyloglobulus. Our results underline the importance of previously unidentified and specialised environmental niches at the nexus of the natural and human‐impacted carbon cycle.

Ecological insights into the disturbances in bacterioplankton communities due to emerging organic pollutants from different anthropogenic activities along an urban river

Emerging organic pollutants (EOPs) in urban rivers have raised concerns regarding their eco-toxicological effects. However, the bacterioplankton community disturbances caused by EOPs in urban rivers and the associated ecological mechanisms remain unclear. This study provided profiles of the spatial distribution of a bacterioplankton community disturbed by human activity along an urban river. The results showed that EOP concentration and composition were differently distributed in residential and industrial areas, which significantly influenced bacterioplankton community structure. Based on redundancy analysis, parabens (methylparaben and propylparaben) were the major factors driving bacterioplankton community changes. Parabens inhibited gram-positive bacteria and promoted oxidative stress-tolerant bacteria in the river ecosystem. Parabens also disturbed ecological processes of bacterioplankton community assembly, shifting from a homogeneous selection (consistent selection pressure under similar environmental condition) to stochastic processes (random changes due to birth, death, immigration, and emigration) with changing in paraben concentrations. Heterogeneous selection was predicted to dominate microbial community assembly with paraben concentration changes exceeding 61.6 ng/L, which could deteriorate the river ecosystem. Furthermore, specific bacterial genera were identified as potential bioindicators to assess the condition of EOP contaminants in the river. Overall, this study highlights significant disturbances in bacterioplankton communities by EOPs at environmental concentrations, and our results could facilitate generation of appropriate management strategies aimed at EOPs in urban rivers.

Influence of polycyclic aromatic hydrocarbon pollution on the diversity and function of bacterial communities in urban wetlands

Human disturbance has become the primary driving factor behind declining urban wetland ecological health due to rapid urbanization. Sediment microbial communities are critical for wetland ecosystem functioning but experience a range of natural and anthropogenic stressors due to rapid urbanization and land use changes, especially in developing countries. Polycyclic aromatic hydrocarbons (PAHs) released into the environment primarily come from anthropogenic sources like industrial activities and traffic emissions. Environmental PAH contamination is accelerating due to rapid urbanization, which also increases potential PAH-related dangers to human health. However, PAHs are widely distributed and not easy to centrally control. Microorganisms are the primary mediators of wetland purification, with most PAH-degrading microorganisms being bacteria. To better understand the influence of PAH contamination on urban wetland microbial communities, bacterial community compositions within sediments of urban wetlands in three land use types were investigated using high-throughput DNA sequencing and bioinformatics analyses. Statistical analyses revealed significant differences in overall microbial compositions among the three land use types, although γ-proteobacteria was the dominant phyla across all samples. Among the potential PAH-degrading bacterial taxa in sediments, Sphingomonas was the most prevalent. The distributions of PAH-degrading taxa were primarily affected by variance in organic compound abundances in addition to various physico-chemical variables, among which high-ring PAH content was a key parameter associated with bacterial distributions, except in the riverine wetlands. Functional inference via phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) indicated that 30 of the 43 genes related to PAH metabolism were predicted to be present within the genomes of bacteria among the three land use type. In particular, dioxygenase and dehydrogenase genes involved in PAH degradation were inferred to be prevalent, indicating that the host urban wetlands exhibited strong potential for organic pollutant degradation.

How sediment bacterial community shifts along the urban river located in mining city

Bacterial communities play critical roles in biogeochemical cycles and serve as sensitive indicators of environmental fluctuation. However, the influence of mineral resource exploitation on shaping the bacterial communities in the urban river is still ambiguous. In this study, high-throughput sequencing was used to determine the spatial distribution of the sediment bacterial communities along an urban river in the famous mining city Panzhihua of China. The results showed that mineral resource exploitation had a significant impact on the urban river bacterial community structure but not on the bacterial ecological functions. Distinct families of bacteria often associated with nutrients (i.e., Comamonadaceae and Sphingomonadaceae) and metal contaminants (i.e., Rhodobacteraceae) were more predominant in the residential and mining area, respectively. Relative to dispersal dynamics, environmentally induced species sorting may primarily influence bacterial community structure. Heavy metals and sediment physicochemical properties had both similar and significant influence on shaping bacterial community structure. Among heavy metals, essential metal elements explained more rates of bacterial variation than toxic metals at moderate contaminant levels. Moreover, the bacteria with multiple metal resistances identified in culture-dependent experiments were probably not suitable for indicating heavy metal contamination in field research. Thus, several sensitive bacterial genera such as Rhodobacter, Hylemonella, and Dechloromonas were identified as potential bioindicators to monitor metals (iron and titanium) and nutrients (phosphorus and organic carbon) in the river ecosystem of the Panzhihua region. Together, these results profiled the coupling effect of urbanization and mineral resource utilization on shaping sediment bacterial communities in urban rivers.

Changes in protist communities in drainages across the Pearl River Delta under anthropogenic influence

Drainages in the Pearl River Delta urban agglomeration (PRDUA) host vital aquatic ecosystems and face enormous pressures from human activities in one of the largest urban agglomerations in the world. Despite being crucial components of aquatic ecosystems, the interactions and assembly processes of the protistan community are rarely explored in areas with serious anthropogenic disturbance. To elucidate the mechanisms of these processes, we used environmental DNA sequencing of 18S rDNA to investigate the influence of environmental factors and species interactions on the protistan community and its assembly in drainages of the PRDUA during summer. The protistan community showed a high level of diversity and a marked spatial pattern in this region. Community assembly was driven primarily by stochastic processes based on the Sloan neutral community model, explaining 74.28%, 75.82%, 73.67%, 74.40% and 51.24% of community variations in the BJ (Beijiang), XJ (Xijiang), PRD (Pearl River Delta), PRE (Pearl River Estuary) areas and in total, respectively. Meanwhile, environmental variables including temperature, pH, dissolved oxygen, transparency, nutrients and land use were strongly correlated with the composition and assembly of the protistan community, explaining 40.40% of variation in the protistan community. Furthermore, the bacterial community was simultaneously analysed by the 16S rDNA sequencing. Co-occurrence network analysis revealed that species interactions within bacteria (81.41% positive) or protists (82.80% positive), and those between bacteria and protists (50% positive and 50% negative) impacted the protistan community assembly. In summary, stochastic processes dominated, whereas species interactions and environmental factors also played important roles in shaping the protistan communities in drainages across the PRDUA. This study provides insights into the ecological patterns, assembly processes and species interactions underlying protistan dynamics in urban aquatic ecosystems experiencing serious anthropogenic disturbance.

Assessments of Bacterial Community Shifts in Sediments along the Headwaters of São Francisco River, Brazil

Sustainable use of freshwater resources for human civilization needs requires the assessment and monitoring of freshwater health, and bacterial communities from riverbed sediments have been shown to be susceptible to chronic anthropogenic disturbances in freshwater ecosystems. Here, we took advantage of the occurrence of well-recognized adjacent sections from the Upper São Francisco River basin with well-recognized levels of anthropogenic activity intensity to test the applicability of sediment bacterial communities as bioindicators of impacts on freshwater ecosystems. We applied 16S amplicon sequencing to estimate the diversity and composition of bacterial communities from 12 sampling sites across the Upper São Francisco River basin, classified as being of no, low, or high intensity of anthropogenic activities, and used diversity metrics and LEfSe to compare the patterns of community structure. Our results revealed that accessed sediment environments associated with land areas with a high intensity of anthropogenic activities presented the lowest levels of community diversity, and the bacterial community compositions of these environments were significantly different from the other sampled areas. Our findings can be considered a source of evidence for the usefulness of bacterial community-based approaches as a tool for diagnosis and monitoring of ecosystem health in areas of vulnerable freshwater environments, and can even be incorporated into regular water quality programs.

Bacterial Communities Are More Sensitive to Water Addition Than Fungal Communities Due to Higher Soil K and Na in a Degraded Karst Ecosystem of Southwestern China

Precipitation is predicted to become more intense in Southern China in the context of climate change; however, the responses of microbial communities to variations in soil moisture have not been well documented for karst areas. The climate is typically in a subtropical monsoon category with two different seasons: a dry season (December-May) and a wet season (June-November). Based on a randomized complete block design (RCBD), a water addition experiment (0, +20, +40, and +60% relative to local precipitation) was established in April 2017, with five replicates, in a degraded grass-shrub community. Sampling was performed in May and at the end of August of 2017. Macroelements (C, H, N, P, K, Ca, Mg, and S), microelements (Mn, Fe, Zn, and Cu), and non-essential elements (Na, Al, and Si) were quantified in the soil. The total DNA of the soil samples was analyzed through 16S rRNA amplicon by Illumina Miseq. Subsequent to the addition of water during both the dry and wet seasons, the concentrations of non-metal elements (C, H, N, S, and P, except for Si) in the soil remained relatively stable; however, metal elements (K, Na, Fe, and Mg, along with Si) increased significantly, whereas Zn and Ca decreased. During the dry season, fungal and bacterial communities were significantly distinct from those during the wet season along the PC axis 1 (p < 0.001). Water addition did not alter the compositions of bacterial or fungal communities during the dry season. However, during the wet season, water addition altered the compositions of bacterial rather than fungal community based on principal component analysis. At the phylum level, the relative abundance of Actinobacteria increased with water addition and had a significantly positive correlation with K+ (r 2 = 0.70, p < 0.001) and Na+ (r 2 = 0.36, p < 0.01) contents, whereas that of Acidobacteria, Planctomycetes, and Verrucomicrobia decreased and showed negative correlation with soil K and Na content, and no changes were observed for the fungal phyla. This suggests that the karst bacterial communities can be influenced by the addition of water during the wet season likely linked to changes in soil K and Na contents. These findings implied that increased rainfall might alter the elemental compositions of karst soils, and bacterial communities are likely to be more sensitive to variations in soil moisture in contrast to their fungal counterparts.

Freshwater Sediment Microbial Communities Are Not Resilient to Disturbance From Agricultural Land Runoff

Microorganisms are critically important for the function of surface water ecosystems but are frequently subjected to anthropogenic disturbances at either acute (pulse) or long-term (press) scales. Response and recovery of microbial community composition and function following pulse disturbance is well-studied in controlled, laboratory scale experiments but is less well-understood in natural environments undergoing continual press disturbance. The objectives of this study were to determine the drivers of sediment microbial compositional and functional changes in freshwaters receiving continual press disturbance from agricultural land runoff and to evaluate the ability of the native microbial community to resist disturbance related changes as a proxy for freshwater ecosystem health. Freshwater sediments were collected seasonally over 1 year in Kewaunee County, Wisconsin, a region impacted by concentrated dairy cattle farming, manure fertilization, and associated agricultural runoff which together serve as a press disturbance. Using 16S rRNA gene amplicon sequencing, we found that sediments in locations strongly impacted by intensive agriculture contain significantly higher abundances (p < 0.01) of the genera Thiobacillus, Methylotenera, Crenotrhix, Nitrospira, and Rhodoferax compared to reference sediments, and functions including nitrate reduction, nitrite reduction, and nitrogen respiration are significantly higher (p < 0.05) at locations in close proximity to large farms. Nine species-level potential human pathogens were identified in riverine sediments including Acinetobacer lwoffi and Arcobacter skirrowii, two pathogens associated with the cattle microbiome. Microbial community composition at locations in close proximity to intensive agriculture was not resistant nor resilient to agricultural runoff disturbance within 5 months post-disturbance but did reach a new, stable microbial composition. From this data, we conclude that sediment microbial community composition is sensitive and shifts in response to chemical and microbial pollution from intensive agriculture, has a low capacity to resist infiltration by non-native, harmful bacteria and, overall, the natural buffering capacity of freshwater ecosystems is unable to fully resist the impacts from agricultural press disturbance.

Microbial community shift under exposure of dredged sediments from a eutrophic bay

Microbial communities occur in almost every habitat. To evaluate the homeostasis disruption of in situ microbiomes, dredged sediments from Guanabara Bay-Brazil (GB) were mixed with sediments from outside of the bay (D) in three different proportions (25%, 50%, and 75%) which we called GBD25, GBD50, and GBD75. Grain size, TOC, and metals-as indicators of complex contamination-dehydrogenase (DHA) and esterase enzymes (EST)-as indicators of microbial community availability-were determined. Microbial community composition was addressed by amplifying the 16S rRNA gene for DGGE analysis and sequencing using MiSeq platform (Illumina).We applied the quality ratio index (QR) to the GB, D, and every GBD mixture to integrate geochemical parameters with our microbiome data. QR indicated high environmental risk for GB and every GBD mixture, and low risk for D. The community shifted from aerobic to anaerobic profile, consistent with the characteristics of GB. Sample D was dominated by JTB255 marine benthic group, related to low impacted areas. Milano-WF1B-44 was the most representative of GB, often found in anaerobic and sulfur enriched environments. In GBD, the denitrifying sulfur-oxidizing bacteria, Sulfurovum, was the most representative, typically found in suboxic or anoxic niches. The canonical correspondence analysis was able to explain 60% of the community composition variation and exhibit the decrease of environmental quality as the contamination increases. Physiological and taxonomic shifts of the microbial assemblage in sediments were inferred by QR, which was suitable to determine sediment risk. The study produced sufficient information to improve the dredging plan and management.

Large-scale monitoring and ecological risk assessment of persistent toxic substances in riverine, estuarine, and coastal sediments of the Yellow and Bohai seas

The Yellow and Bohai seas comprise one of the most rapidly developing regions in the world, but efforts to assess coastal pollution by persistent toxic substances (PTSs) on wide spatial scale are lacking. The present study aimed to (1) measure the concentrations of PTSs, such as polycyclic aromatic hydrocarbons (PAHs), alkylphenols (APs), and styrene oligomers (SOs) via large-scale sediment monitoring (total of 125 locations), (2) assess potential ecological risk of PTSs in sediments to coastal ecosystems, (3) estimate various sources and fresh inputs of PTSs, (4) determine distribution patterns of PTSs by human activities and land-use type, and (5) address decadal (2008-2018) changes in distributions of PTSs. The high concentrations of PAHs [> 7000 ng g^-1 dry weight (dw)] in sediments were detected in Nantong in the Yellow Sea of China (YSC) and Huludao and Qinhuangdao in the Bohai Sea (BS), whereas lesser concentrations (< 200 ng g^-1 dw) were detected in the Yellow Sea of Korea (YSK). We found relatively high concentrations of sedimentary APs and SOs in Nantong, Huludao, and Qinhuangdao from the YSC and BS regions, but corresponding concentrations were generally below < 100 ng g^-1 dw in other locations. Concentrations of PAHs at 38 locations (30% of YSC and BS) posed a potential risk to aquatic ecosystems, whereas relatively low risk concentrations occurred in all locations of YSK. The main source of PAHs (concentrated in YSC and BS) were by-products of diesel and gasoline combustion (42% of total concentration), whereas biomass combustion (24%) dominated in YSK. Fresh inputs of PTSs indicated that the generation and use of PTSs continue across all regions and locations. Among PTSs, concentrations of PAHs were significantly associated with location (p < 0.05) relative to land-use within a given region, whereas concentrations of APs and SOs showed no significant relationships (p > 0.05) among or within regions. Over time, concentrations of PAHs have generally declined, but sediment contamination has increased at some locations in China, with sources shifting from a mixture of PAHs types to those linked to diesel and gasoline combustion. Additional studies are needed on the fate and potential ecological risk posed by certain PTSs in hotspots. This is one of the first efforts providing backgrounds on PTS pollution in the large marine ecosystem of the Yellow and Bohai seas.

A Review and Perspective of eDNA Application to Eutrophication and HAB Control in Freshwater and Marine Ecosystems

Changing ecological communities in response to anthropogenic activities and climate change has become a worldwide problem. The eutrophication of waterbodies in freshwater and seawater caused by the effects of human activities and nutrient inputs could result in harmful algae blooms (HABs), decreases water quality, reductions in biodiversity and threats to human health. Rapid and accurate monitoring and assessment of aquatic ecosystems are imperative. Environmental DNA (eDNA) analysis using high-throughput sequencing has been demonstrated to be an effective and sensitive assay for detecting and monitoring single or multiple species in different samples. In this study, we review the potential applications of eDNA approaches in controlling and mitigating eutrophication and HABs in freshwater and marine ecosystems. We use recent studies to highlight how eDNA methods have been shown to be a useful tool for providing comprehensive data in studies of eutrophic freshwater and marine environments. We also provide perspectives on using eDNA techniques to reveal molecular mechanisms in biological processes and mitigate eutrophication and HABs in aquatic ecosystems. Finally, we discuss the feasible applications of eDNA for monitoring biodiversity, surveying species communities and providing instructions for the conservation and management of the environment by integration with traditional methods and other advanced techniques.

Response of chemical properties, microbial community structure and functional genes abundance to seasonal variations and human disturbance in Nanfei River sediments

The Nanfei River, located in Hefei City, Anhui Province, subjected to increased nutrient loads from point and/or non-point source. Little is known about the indicators indicating heterogeneity of surface sediments. We aimed to identify the suitable indicators that can reflect the sediment heterogeneity by analyzing the sensitivity of sediment physicochemical properties group, microbial communities and diversity indices group and C, N, S-functional genes group to seasonal and regional changes. River sediments from different areas (urban area, urban-rural fringe and rural area) were collected in the level, dry and wet seasons, respectively. The chemical parameters had most significant regional heterogeneity, but no seasonal differences. Seasons had a greater impact on the overall microbial community structure than the areas. Specifically, the relative abundance of Firmicutes and Bacteroidetes were more sensitive to seasonal changes. Overall, seasonal changes showed the greatest impact on the functional genes group, with the S-functional genes (dsrB and aprA) group providing the clearest seasonal variation. Considering the seasonal distribution of functional genes and their sensitivity to environmental factors, we speculated that the sulfate-reducing gene (dsrB), the methanogenic gene (mcrA) and the anammox gene (hzo) could be identified as sensitive indicators to indicate the seasonal heterogeneity of surface sediments in different river sections of the same river in the short term. We also concluded that environmental variables were more conducive to indicating the regional heterogeneity of sediments. This study provided a valuable reference for assessing the heterogeneity or ecological stress of river sediments.

The spatial and seasonal variations of bacterial community structure and influencing factors in river sediments

Studying the composition and structure of bacterial communities in sediments helps to understand the contribution of bacteria to environmental changes and the role of feedback in response to disturbances. However, seasonal changes in bacterial communities of river sediments with different pollution levels and sources have not been clear yet. In this study, we collected sediment samples during the dry season, wet season and level season from 40 sites with various pollution sources in three inflow rivers (Fengle-Hangbu River, Nanfei River and Zhegao River) of Chaohu Lake. Bacterial community compositions were determined based on high-throughput sequencing. The 'Bioenv' in the R package 'Vegan' and redundancy analysis was used to explore the influence of environmental factors on the bacterial community in the river sediments. Results showed that a significant deviation in bacterial communities was found among seasons and rivers. In addition, seasonal dynamics had a greater impact on shaping bacterial communities than rivers with different pollution sources. A higher diversity was found in the wet season as compared to the other seasons. The bacterial diversity was negatively correlated with nutrients (OM, TN, NH₄⁺, IP, OP and TP) and metals (Cu and Zn). Bacterial communities were more sensitive to heavy metals pressure than nutrients. We also concluded that heavy metals (Cu and Cd) were the key contributing factors in explaining variations in bacterial communities. This study provided a valuable reference for assessing ecological stress.

Microbial community activity in response to multiple contaminant exposure: a feasible tool for sediment quality assessment

Sediments represent complex mixtures and the impacts of their physical and chemical processes on biota are important for assessing potential health risks. We aimed to rank sediment samples from Guanabara Bay by developing an algorithm (quality ratio-QR), focusing on key sediment parameters (fine grain size, total organic carbon (TOC), metal concentrations) and enzymatic activities (dehydrogenase (DHA-energy production into cell) and esterases (EST-hydrolase organic matter outside the cell membrane)) of in situ microbial communities. Our QR is supported by quantitative information and significant correlations between geochemical and microbial processes. The QR is a function of the dependent term DHA/EST and the geochemical term (TOC×∑CF)/fine-grained sediment, where ∑CF is the sum of contamination factors (ratio between actual and background metal concentrations). We could rank our sampling sites into three risk classes based on QR: low, medium, and high. Our findings suggest altered homeostasis due to the development of contamination resistance. We applied a sensitivity analysis, using Brazilian law for sediment quality assessment, to calibrate our risk index. Our QR is suitable for measuring the potential health risk of any sediment, especially in developing countries with serious technical limitations, since its evaluated parameters are cheap, fast, and easy to obtain.

Coupled effects of land use pattern and hydrological regime on composition and diversity of riverine eukaryotic community in a coastal watershed of Southeast China

The coupled effects of land use pattern and hydrological regime on composition and diversity of riverine eukaryotic community are needed for understanding riverine ecosystem health and algal blooming mechanism. In-situ monitoring and 18S rRNA gene sequencing were used to investigate spatiotemporal variations of eukaryotic community in three types of watershed with different dominant land use type (i.e. urban, forest, and natural) during three seasons (i.e. dry, transition, and wet seasons) in a coastal watershed of Southeast China. Results showed that agricultural and urban watersheds had significantly higher diversity in dry and transition seasons, and higher richness in transition and wet seasons than those in forest watershed. The non-metric multidimensional scaling analysis further verified great spatiotemporal variations of eukaryotic community. Stramenopiles, Alveolata, Animalia, and Eukaryota, dominated the sequences reads for all sampling sites in three seasons. Agricultural watershed had the highest relative abundant of Animalia, whereas Eukaryota was the most abundant in urban watershed and forest watershed had the highest relative abundance of Stramenopiles and Alveolata. The RDA ordination showed that Builtup and streamflow were two most important factors for moderate taxa and abundant taxa, respectively. Variation partitioning revealed that land use pattern and hydrological regime together explained 54.4%, 61% and 67.2% variances of the composition of eukaryotic community. Among three sampling seasons, the relative contribution of land use pattern was higher than that of hydrological regime. The results of this investigation demonstrated how land use pattern and hydrological regime affected the composition and diversity of riverine eukaryotic community. The findings can provide a useful insight into the riverine eukaryotic communities and their underlying ecological mechanisms in coastal China watersheds.

Insights Into Limnothrix sp. Metabolism Based on Comparative Genomics

Currently only four genome sequences for Limnothrix spp. are publicly available, and information on the genetic properties of cyanobacteria belonging to this genus is limited. In this study, we report the draft genome of Limnothrix sp. CACIAM 69d, isolated from the reservoir of a hydroelectric dam located in the Amazon ecosystem, from where cyanobacterial genomic data are still scarce. Comparative genomic analysis of Limnothrix revealed the presence of key enzymes in the cyanobacterial central carbon metabolism and how it is well equipped for environmental sulfur and nitrogen acquisition. Additionally, this work covered the analysis of Limnothrix CRISPR-Cas systems, pathways related to biosynthesis of secondary metabolites and assembly of extracellular polymeric substances and their exportation. A trans-AT PKS gene cluster was identified in two strains, possibly related to the novel toxin Limnothrixin biosynthesis. Overall, the draft genome of Limnothrix sp. CACIAM 69d adds new data to the small Limnothrix genome library and contributes to a growing representativeness of cyanobacterial genomes from the Amazon region. The comparative genomic analysis of Limnothrix made it possible to highlight unique genes for each strain and understand the overall features of their metabolism.

In situ microbiota distinguished primary anthropogenic stressor in freshwater sediments

Conventional assessment and evaluation of sediment quality are based on laboratory-based ecotoxicological and chemical measurements with lack of concern for ecological relevance. Microbiotas in sediment are responsive to pollutants and can be used as alternative ecological indicators of sediment pollutants; however, the linkage between the microbial ecology and ecotoxicological endpoints in response to sediment contamination has been poorly evaluated. Here, in situ microbiotas from the Three Gorges Reservoir (TGR) area of the Yangtze River were characterized by DNA metabarcoding approaches, and then, changes of in situ microbiotas were compared with the ecotoxicological endpoint, aryl hydrocarbon receptor (AhR) mediated activity, and level of polycyclic aromatic hydrocarbons (PAHs) in sediments. PAHs and organic pollutant mixtures mediating AhR activity had different effects on the structures of microbiotas. Specifically, Shannon indices of protistan communities were negatively correlated with the levels of AhR mediated activity and PAHs. The sediment AhR activity was positively correlated with the relative abundance of prokaryotic Acetobacteraceae, but had a negative correlation with protistan Oxytrichidae. Furthermore, a quantitative classification model was built to predict the level of AhR activity based on the relative abundances of Acetobacteraceae and Oxytrichidae. These results suggested that in situ Protista communities could provide a useful tool for monitoring and assessing ecological stressors. The observed responses of microbial community provided supplementary evidence to support that the AhR-active pollutants, such as PAHs, were the primary stressors of the aquatic community in TGR area.

Metagenomics Reveals the Influence of Land Use and Rain on the Benthic Microbial Communities in a Tropical Urban Waterway

Unravelling the microbial metagenomes of urban waterway sediments suggest that well-managed urban waterways have the potential to support diverse sedimentary microbial communities, similar to those of undisturbed natural freshwaters. Despite the fact that these urban waterways are well managed, our study shows that environmental pressures from land use and rain perturbations play a role in shaping the structure and functions of microbial communities in these waterways. We propose that although pulsed disturbances, such as rain perturbations, influence microbial communities, press disturbances, including land usage history, have a long-term and stronger influence on microbial communities. Our study found that the functions of microbial communities were less affected by environmental factors than the structure of microbial communities was, indicating that core microbial functions largely remain conserved in challenging environments.

Growing demands for potable water have led to extensive reliance on waterways in tropical megacities. Attempts to manage these waterways in an environmentally sustainable way generally lack an understanding of microbial processes and how they are influenced by urban factors, such as land use and rain. Here, we describe the composition and functional potential of benthic microbial communities from an urban waterway network and analyze the effects of land use and rain perturbations on these communities. With a sequence depth of 3 billion reads from 48 samples, these metagenomes represent nearly full coverage of microbial communities. The predominant taxa in these waterways were Nitrospira and Coleofasciculus, indicating the presence of nitrogen and carbon fixation in this system. Gene functions from carbohydrate, protein, and nucleic acid metabolism suggest the presence of primary and secondary productivity in such nutrient-deficient systems. Comparison of microbial communities by land use type and rain showed that while there are significant differences in microbial communities in land use, differences due to rain perturbations were rain event specific. The more diverse microbial communities in the residential areas featured a higher abundance of reads assigned to genes related to community competition. However, the less diverse communities from industrial areas showed a higher abundance of reads assigned to specialized functions such as organic remediation. Finally, our study demonstrates that microbially diverse populations in well-managed waterways, where contaminant levels are within defined limits, are comparable to those in other relatively undisturbed freshwater systems.

IMPORTANCE Unravelling the microbial metagenomes of urban waterway sediments suggest that well-managed urban waterways have the potential to support diverse sedimentary microbial communities, similar to those of undisturbed natural freshwaters. Despite the fact that these urban waterways are well managed, our study shows that environmental pressures from land use and rain perturbations play a role in shaping the structure and functions of microbial communities in these waterways. We propose that although pulsed disturbances, such as rain perturbations, influence microbial communities, press disturbances, including land usage history, have a long-term and stronger influence on microbial communities. Our study found that the functions of microbial communities were less affected by environmental factors than the structure of microbial communities was, indicating that core microbial functions largely remain conserved in challenging environments.

Ecogenomic responses of benthic communities under multiple stressors along the marine and adjacent riverine areas of northern Bohai Sea, China

Benthic communities in the aquatic ecosystem are influenced by both natural and anthropogenic stressors. To understand the ecogenomic responses of sediment communities to the multiple stressors of polluted environments, the bacteria, protistan and metazoan communities in sediments from marine and adjacent riverine areas of North Bohai Sea were characterized by environmental DNA meta-systematics, and their associations with environmental variables were assessed by multiple statistical approaches. The bacterial communities were dominated by Firmicutes (mean 22.4%), Proteobacteria (mean 21.6%) and Actinobacteria (mean 21.5%). The protistan communities were dominated by Ochrophyta (33.7%), Cercozoa (18.9%) and Ciliophora (17.9%). Arthropoda (71.1%) dominated the metazoan communities in sediments. The structures of communities in sediments were shaped by both natural variables (spatial variability and/or salinity (presented as Na and Ca)) and anthropogenic contaminants, including DDTs, PAHs or metals (Cu, Al, Co, Cr, Cu, Fe, K, Mg, Mn, Ni and Zn). Particularly, the correlation network of multiple communities was modulated by the concentrations of Na and DDTs at the family level. Overall, environmental DNA meta-systematics can provide a powerful tool for biomonitoring, sediment quality assessment, and key stressors identification.

Environmental DNA metabarcoding reveals primary chemical contaminants in freshwater sediments from different land-use types

Land-use intensification threatens freshwater biodiversity. Freshwater eukaryotic communities are affected by multiple chemical contaminants with a land-use specific manner. However, biodiversities of eukaryotes and their associations with multiple chemical contaminants are largely unknown. This study characterized in situ eukaryotic communities in sediments exposed to mixtures of chemical contaminants and assessed relationships between various environmental variables and eukaryotic communities in sediments from the Nanfei River. Eukaryotic communities in the sediment samples were dominated by Annelida, Arthropoda, Rotifera, Ochrophyta, Chlorophyta and Ciliophora. Alpha-diversities (Shannon entropy) and structures of eukaryotic communities were significantly different between land-use types. According to the results of multiple statistical tests (PCoA, distLM, Mantel and network analysis), dissimilarity of eukaryotic community structures revealed the key effects of pyrethroid insecticides, manganese, zinc, lead, chromium and polycyclic aromatic hydrocarbons (PAHs) on eukaryotic communities in the sediment samples from the Nanfei River. Furthermore, taxa associated with land-use types were identified and several sensitive eukaryotic taxa to some of the primary contaminants were identified as potential indicators to monitor effects of the primary chemical contaminants. Overall, environmental DNA metabarcoding on in situ eukaryotic communities provided a powerful tool for biomonitoring and identifying primary contaminants and their complex effects on benthic eukaryotic communities in freshwater sediments.

The Relationship between pH and Bacterial Communities in a Single Karst Ecosystem and Its Implication for Soil Acidification

Enhanced monsoon duration and soil acidification from acid rain are expected to impact the distribution of microbial communities in surface and subsurface environments, although these impacts are poorly understood for most systems. In central China, soluble carbonate bedrock forms extensive karst landscapes. Current predictions are that the amount of monsoonal precipitation and acid rainfall in central China will increase, which is expected to lead to changes in the pH balance of karst ecosystems. To evaluate the role of pH, total organic carbon, and other geochemical parameters (e.g., Ca²⁺, Mg²⁺, NH₄⁺, NO_x, SO₄^2-) in shaping bacterial communities within a single karst system in central China, samples were collected from the thin surface soils overlying Heshang Cave, cave sediments, and weathered cave passage rocks from the entrance, twilight, and dark zones, as well as from epikarstic drip waters inside the cave. Illumina sequencing of 16S rRNA genes and multivariate statistical analyses revealed that each tested community was distinct and the community variability was significantly correlated with pH, total organic carbon, and potassium concentrations. Specifically, surface soils were dominated by Acidobacteria, Verrucomicrobia and Planctomycetes, and diversity significantly decreased with acidic pH values. Nitrospirae, Gemmatimonadetes, Firmicutes, and Chloroflexi were unique to cave sediments, while Actinobacteria and Proteobacteria dominated weathered rocks and drip waters, respectively. The results reveal important implications regarding the effects of acidification on bacterial communities in karst areas, and on the control of pH in shaping bacterial communities throughout a karst system. Increased water flux into and through karst habitats due to monsoonal precipitation may result in deeper penetration of acidic solutions into karst and shift the bacterial communities inside the cave in the future.

Using in situ bacterial communities to monitor contaminants in river sediments

Bacterial communities in sediments of human-impacted rivers are exposed to multiple anthropogenic contaminants and eventually lead to biodiversity lost and ecological functions disable. Nanfei River of Anhui province has been contaminated by pollutants from industrial and/or agricultural sources. This study was conducted to investigate the structure of in situ sediment bacterial communities in Nanfei River and to examine the correlation between the different taxonomic components and contaminant concentrations. The bacterial communities were dominated by Proteobacteria, Bacteroidetes and Chloroflexi. Both the profiles of environmental predictors and the composition of microbial communities differed among agriculture, industrial and confluence regions. There were significant associations between bacterial community phylogenies and the measured contaminants in the sediments. Nutrients (TN and TP) and two metals (Cd and Zn) were negatively correlated with the essential "core" of the bacterial interaction network (Betaproteobacteria and Deltaproteobacteria). Metals (Fe, Ni and Zn) and nutrients (TN and TP) had higher impact on bacterial community compositions than PAHs, OPs and PRTs according to the correlation and network analyses. Furthermore, several sensitive candidate genera were identified as potential bioindicators to monitor key contaminants by species contaminant correlation analysis. Overall, in situ bacterial communities could provide a useful tool for monitoring and assessing ecological stressors in freshwater sediments.