Nonperennial streams dominate global river networks and are increasing in occurrence across space and time. When surface flow ceases or the surface water dries, flow or moisture can be retained in the subsurface sediments of the hyporheic zone, supporting aquatic communities and ecosystem processes. However, hydrological and ecological definitions of the hyporheic zone have been developed in perennial rivers and emphasize the mixing of water and organisms, respectively, from both the surface stream and groundwater. The adaptation of such definitions to include both humid and dry unsaturated conditions could promote characterization of how hydrological and biogeochemical variability shape ecological communities within nonperennial hyporheic zones, advancing our understanding of both ecosystem structure and function in these habitats. To conceptualize hyporheic zones for nonperennial streams, we review how water sources and surface and subsurface structure influence hydrological and physicochemical conditions. We consider the extent of this zone and how biogeochemistry and ecology might vary with surface states. We then link these components to the composition of nonperennial stream communities. Next, we examine literature to identify priorities for hydrological and ecological research exploring nonperennial hyporheic zones. Lastly, by integrating hydrology, biogeochemistry, and ecology, we recommend a multidisciplinary conceptualization of the nonperennial hyporheic zone as the porous subsurface streambed sediments that shift between lotic, lentic, humid, and dry conditions in space and time to support aquatic-terrestrial biodiversity. As river drying increases in extent because of global change, we call for holistic, interdisciplinary research across the terrestrial and aquatic sciences to apply this conceptualization to characterize hyporheic zone structure and function across the full spectrum of hydrological states.

Biochar had been widely used to improve the activity of photocatalysts, the biochar-based photocatalysts had more potential for environmental pollution remediation, but their effect on the sediment remained unknown. To understand these, the typical photocatalyst g-C3N4 was modified by biochar to develop g-C3N4/biochar with enhanced photocatalytic ability. Riverbed sediment was exposed to g-C3N4 and g-C3N4/biochar respectively for 30 days, and Illumina sequencing was utilized to examine the changes in the bacterial community in the sediment. The results showed that in riverbed sediment, g-C3N4 exposure had a concentration-dependent effect on the diversity of bacteria, while g-C3N4/biochar exposure had a slight influence on the bacterial diversity and the diversity almost maintained stable with different g-C3N4/biochar concentration. The application of g-C3N4 exhibited an inhibition influence on the growth of Acidobacteria, Gemmatimonadetes, and Rokubacteria in sediment, whose relative abundance increased when g-C3N4 was 25 mg/kg, and then decreased when g-C3N4 beyond this concentration. The presence of g-C3N4/biochar increased the relative abundance of Cyanobacteria in sediment and showed no obvious impact on other dominant phyla. Both g-C3N4 and g-C3N4/biochar could alter the levels of TP, NN, and AN in the sediment, but the magnitude of the changes of these physicochemical factors caused by g-C3N4/biochar was much smaller than those caused by g-C3N4. In addition, the complexity of the bacterial community network was reduced in a high concentration of g-C3N4, while it remained stable with different concentrations of g-C3N4/biochar treatments. Totally, this study demonstrated that, compared to g-C3N4, g-C3N4/biochar was able to maintain the relative stability of the bacterial community in riverbed sediment and mitigate the negative effects of photocatalysts to some extent, making biochar an ecological remediation agent with great potential for application.

Discharge of treated sewage effluent to rivers can degrade aquatic ecosystem quality, interacting with multiple stressors in the wider catchment. In predominantly rural catchments, the river reach influence of point source effluents is unknown relative to complex background pressures. We examined water column, sediment and biofilm biogeochemical water quality parameters along river transects (200 m upstream to 1 km downstream) during summer at five wastewater treatment works (WWTW) in Scotland. Treated sewage effluent (subset, n = 3) pollutant concentrations varied between sites. Downstream concentration profiles of water and sediment biogeochemical parameters showed complex spatial changes. A hypothesised point source signature of elevated concentrations of pollution immediately downstream of WWTW then a decaying pollution \'plume\' did not commonly occur. Instead, elevated soluble reactive phosphorus (SRP), ammonium and coliforms (maximum 0.23 mgP/l, 0.33 mgN/l and >2 × 106 MPN/100 ml) occurred immediately downstream of two WWTW, whereas some downstream pollutant concentrations decreased. Microbial substrate respiration responses only differed 1 km downstream. Significantly greater concentrations of sediment metal occurred >500 m downstream, likely due to the redeposition of historic contaminated sediments. Significantly lowered chlorophyll-a downstream of one WWTW coincided with elevated metals, despite water SRP and sediment P increases. Overall, stress caused to microbes and algae by effluent contaminants outweighed the subsidy effect of WWTW nutrients. We observed variable effluent flows to the rivers limited localised pollution downstream of WWTW and overall influence of arable land cover on river water quality. Together, this challenges views of consistently discharging point sources impacting low dilution sensitive rivers in summer contrasting with \'diffuse\' sources. Thus, river water column and benthic compartments are altered at varying scales by point source effluents in combination with rural catchment pollution sources, both discrete (e.g. farmyards and septic tanks) and diffuse.

Worldwide, the production of plastics is increasing, and plastic pollution in aquatic environments is a major global concern. Under natural conditions, plastic weathers to smaller pieces called microplastics (MP), which come in various shapes, with fibers often being the most common in freshwater sediments. The hyporheic zone, an ecotone between surface and groundwater, is important for the transport and fate of all MP particles. The main metabolic pathways in rivers take place in the hyporheic zone and are driven by a diverse microbial community. The objective of this study was to investigate in situ whether the presence of PET fibers in riverbed sediments affects patterns of colonization and the seasonal dynamics of microbial metabolic activities in the hyporheic zone. The effects of the presence of PET on microbial metabolism were evaluated in situ over a month (colonization study) and over a year (seasonal study) by measuring total protein content (TPC), and microbial respiration as respiratory electron transport system activity (ETSA) and by community-level physiological profiling (CLPP). Additionally, PET fibers were examined under a scanning electron microscope (SEM), and isotopic analysis (δ13C) of PET was performed after one year of exposure to field conditions. The findings demonstrated that during colonization and biofilm formation, and also over the seasons, the date had a large and significant impact on biofilm growth and activity, while PET presence slightly suppressed microbial biomass (TPC) and respiratory activity (ETSA). Overall microbial activity was repressed in the presence of PET fibers but there was a higher capacity for the utilization of complex synthetic polymer substrates (i.e., Tween 40) which have previously been linked to polluted environments. SEM micrographs showed diverse microbial communities adhering to PET fibers but little surface deterioration. Similarly, isotopic analysis suggested little deterioration of PET fibers after one year of in situ conditions. The study indicated that PET fibers present in riverbed sediments could have impacts on the metabolic functioning in rivers and thus affect their self-cleaning ability.

This study uncovered the prevalence, harboured species, and subtype diversity of Cryptosporidium species in river water and its sediment from the Apies River in South Africa. Cryptosporidium spp. concentrations in freshwater and its sediment were determined using Ziehl-Neelsen staining and quantitative Polymerase Chain Reaction (qPCR) techniques. Next-generation sequencing (NGS) targeting the 60 kDa glycoprotein (gp60) gene of Cryptosporidium spp. was performed to reveal the species, subtype families and subtypes harboured in freshwater and its sediment. Although the results revealed that water samples had a higher prevalence (30%) compared with sediment (28%), the number of observable Cryptosporidium spp. oocysts in sediment samples (ranging from 4.90 to 5.81 log10 oocysts per 1 Liter) was higher than that of river water samples (ranging from 4.60 to 5.58 log10 oocysts per 1 L) using Ziehl-Neelsen staining. The 18S ribosomal ribonucleic acid (rRNA) gene copy of Cryptosporidium in riverbed sediments ranged from 6.03 to 7.65 log10, whereas in river water, it was found to be between 4.20 and 6.79 log10. Subtyping results showed that in riverbed sediments, Cryptosporidium parvum accounted for 40.72% of sequences, followed by Cryptosporidium hominis with 23.64%, Cryptosporidium cuniculus with 7.10%, Cryptosporidium meleagridis with 4.44% and the least was Cryptosporidium wrairi with 2.59%. A considerable percentage of reads in riverbed sediment (21.25%) was not assigned to any subtype. River water samples had 45.63% of sequences assigned to C. parvum, followed by 30.32% to C. hominis, 17.99% to C. meleagridis and 5.88% to C. cuniculus. The data obtained are concerning, as Cryptosporidium spp. have intrinsic resistance to water treatment processes and low infectious doses, which can pose a risk to human health due to the various uses of water (for human consumption, leisure, and reuse).

The main land use/land cover changes (LULCC) have been associated with population growth and energy policies in the São Paulo State, Brazil, since 1970. The LULCC can alter the behavior of trace elements in different environmental systems, with the riverbed sediments being the main reservoirs or sinks for trace elements, and thus become a valuable environmental archive on temporal changes. Thus, the main purpose of the study was to apply a multi-tracer analysis to estimate the historical evolution of pollution in riverbed sediment of a subtropical watershed, the lower course of the Piracicaba River, São Paulo, Brazil. 210Pb measurements done on river sediment core samples allowed estimating a sedimentation rate of 9 mm yr-1 between 1971 and 2001. Zn was the most abundant trace element in the sediment core, followed by Cr, Cu, Ni, Pb, Sc and Cd. The total concentrations of Cd, Cr, Ni, Sc and Pb presented practically no variations in the sediment core, with a continuous excess of ca. 0.27 μg g-1 yr-1 of Cu and of ca. 0.54 μg g-1 yr-1 of Zn between 1971 and 2001. The excess of Cu and Zn was associated with labile fractions, in particular with carbonate bound to Zn and organic matter bound to Cu. The assessment of trace metal pollution indicated that most of the trace elements were of geogenic origin, except for Cu and Zn. According to the sediment quality guidelines used in Brazil, Pb showed no potential toxic effect, Cu, Cr and Zn were intermediate to Threshold Effect Level (TEL) and Probable Effect Level (PEL) and the Cd and Ni concentrations were above the PEL limits. The elemental and isotopic analysis of C and N and the C/N ratio indicated that the anthropogenic origin of POM found in the sediment core is related mainly to domestic sewage.

Selected pharmaceutical chemicals, steroids and xenoestrogens (PCSXs) consisting of 29 endocrine modulators, therapeutic drugs, pesticides, detergents, plastics, and active ingredients in household products were measured in water, riverbed sediments and fish collected in a tributary embayment of the Potomac River (Hunting Creek, Alexandria, VA, USA) in the vicinity of wastewater discharge. A total of 17 PCSXs were found in the Hunting Creek samples, with steroid hormones (e.g., progesterone and 17α-ethinylestradiol), triclosan, dextromethorphan and bisphenol A being the most prominent micropollutants detected.The geospatial distribution of the PCSXs in Hunting Creek indicated that the steroids correlated with wastewater treatment plant discharge in all matrices, but such an association is tentative in Hunting Creek given the complex nature of urban sources of PCSXs and hydrodynamics in an urban tidal river. The sediment PCSX concentrations correlated with sediment total organic carbon content at all sampling sites. For the most part, the PCSXs showed an enrichment in fish tissue relative to sediments when concentrations were normalized to lipids and sediment organic carbon contents, but the influence of endogenous steroids is also an important consideration for these chemicals.

Studies on the survival of bacterial enteric pathogens in riverbed sediments have mostly focused on individual organisms. Reports on the competitive survival of these pathogens in riverbed sediments under the same experimental setup are limited. We investigated the survival of Escherichia coli, Salmonella enterica ser. Typhimurium, Vibrio cholerae and Shigella dysenteriae in riverbed sediments of the Apies River. Experiments were performed in flow chambers containing three sediment types and connected to aquarium pumps immersed in river water to maintain continuous water circulation. Each chamber was inoculated with ~107 CFU/mL (final concentration) of each microorganism and kept at 4, 20 and 30 °C. Chambers were sampled on days 0, 1, 2, 7, 14 and 28. At 4 °C, only E. coli and S. typhimurium survived throughout the 28 experimental days. V. cholerae had the shortest survival time at this temperature and was not detected in any of the sediment chambers 24 h after inoculation. S. dysenteriae only survived until day 7. At an increased temperature of 20 °C, only S. dysenteriae was not detected on day 28 of the experiment. At 30 °C, V. cholerae and Salmonella survived longer (28 days) than E. coli (14 days) and S. dysenteriae (4 days). Vibrio cholerae was shown to have the highest T 90 values (32 days) in all sediment types at 20 and 30 °C. We conclude that the sediments of the Apies River present a favourable environment for the survival of indicator and pathogenic bacteria depending on the prevailing temperature.

In most developing countries, especially in Southern Africa, little is known about the presence of diarrhoeagenic Escherichia coli (DEC) pathotypes in riverbed sediments. The present study sought to investigate the presence of DEC virulence genes in riverbed sediments of the Apies River, a river used by many communities in Gauteng, South Africa. Water and sediment samples were collected from the river between July and August 2013 (dry season) and also between January and February 2014 (wet season) following standard procedures. Isolation of E. coli was done using the Colilert®-18 Quanti-Tray® 2000 system. DNA was extracted from E. coli isolates using the InstaGene™ matrix from Bio-Rad and used as template DNA for real-time PCR. Water pH, temperature, dissolved oxygen, electrical conductivity and turbidity were measured in situ. Over 59 % of 180 samples analysed were positive for at least one of the seven DEC virulence genes investigated. The eaeA gene was the most isolated gene (29.44 %) while the ipaH gene the least isolated (8.33 %). The ipaH gene (p = 0.012) and the ST gene (stIa, p = 0.0001, and stIb, p = 0.019) were positively correlated with temperature. The detection of diarrhoeagenic E. coli virulence genes in the sediments of the Apies River shows that the sediments of this river might not only be a reservoir of faecal indicator bacteria like E. coli but also pathogenic strains of this bacterium. These organisms could represent a public health risk for poor communities relying on this water source for various purposes such as drinking and recreational use. There is therefore an urgent need to monitor these DEC pathotypes especially in areas without adequate water supplies.

Many South Africans living in resource-poor settings with little or no access to pipe-borne water still rely on rivers as alternative water sources for drinking and other purposes. The poor microbial quality of such water bodies calls for appropriate monitoring. However, routine monitoring only takes into consideration the microbial quality of the water column, and does not include monitoring of the riverbed sediments for microbial pollution. This study sought to investigate the microbial quality of riverbed sediments in the Apies River, Gauteng Province, South Africa, using Escherichia coli as a faecal indicator organism and to investigate the impact of seasonal variation on its abundance. Weekly samples were collected at 10 sampling sites on the Apies River between May and August 2013 (dry season) and between January and February 2014 (wet season). E. coli was enumerated using the Colilert®-18 Quanti-Tray® 2000 system. All sites tested positive for E. coli. Wastewater treatment work effluents had the highest negative impact on the river water quality. Seasonal variations had an impact on the concentration of E. coli both in water and sediments with concentrations increasing during the wet season. A strong positive correlation was observed between temperature and the E. coli concentrations. We therefore conclude that the sediments of the Apies River are heavily polluted with faecal indicator bacteria and could also harbour other microorganisms including pathogens. The release of such pathogens into the water column as a result of the resuspension of sediments due to extreme events like floods or human activities could increase the health risk of the populations using the untreated river water for recreation and other household purposes. There is therefore an urgent need to reconsider and review the current South African guidelines for water quality monitoring to include sediments, so as to protect human health and other aquatic lives.