Assessing the nonlinear association of environmental factors with antibiotic resistance genes (ARGs) in the Yangtze River Mouth, China.

The emergence of antibacterial resistance (ABR) is an urgent and complex public health challenge worldwide. Antibiotic resistant genes (ARGs) are considered as a new pollutant by the WHO because of their wide distribution and emerging prevalence. The role of environmental factors in developing ARGs in bacterial populations is still poorly understood. Therefore, the relationship between environmental factors and bacteria should be explored to combat ABR and propose more tailored solutions in a specific region. Here, we collected and analyzed surface water samples from Yangtze Delta, China during 2021, and assessed the nonlinear association of environmental factors with ARGs through a sigmoid model. A high abundance of ARGs was detected. Amoxicillin, phosphorus (P), chromium (Cr), manganese (Mn), calcium (Ca), and strontium (Sr) were found to be strongly associated with ARGs and identified as potential key contributors to ARG detection. Our findings suggest that the suppression of ARGs may be achieved by decreasing the concentration of phosphorus in surface water. Additionally, Group 2A light metals (e.g., magnesium and calcium) may be candidates for the development of eco-friendly reagents for controlling antibiotic resistance in the future.

Stieleria tagensis sp. nov., a novel member of the phylum Planctomycetota isolated from Tagus River in Portugal.

A bacterial strain was isolated from a brackish water sample of Tagus river, Alcochete, Portugal and was designated TO1_6T. It forms light pink colonies on M13 medium supplemented with N-acetylglucosamine. Cells are pear-shaped to spherical, form rosettes and divide by budding. Strain TO1_6T presents a mesophilic and neutrophilic profile, with optimum growth at 20 to 25 °C and pH 7.0 to 7.5, and vitamin supplementation is not required to promote its growth. The genome of the novel isolate is 7.77 Mbp in size and has a DNA G + C content of 56.3%. Based on its 16S rRNA gene sequence, this strain is affiliated with the phylum Planctomycetota. Further taxonomic characterization using additional phylogenetic markers, namely rpoB gene sequence (encoding the ß-subunit of the DNA-dependent RNA polymerase), as well as Percentage of conserved proteins, average nucleotide identity and average amino acid identity, suggest the affiliation of strain TO1_6T to the genus Stieleria, a recently described taxon in the family Pirellulaceae, order Pirellulales and class Planctomycetia. Based on the genotypic, phylogenetic and physiological characterization, we here describe a new species represented by the type strain TO1_6T (= CECT 30432T, = LMG 32465T), for which the name Stieleria tagensis sp. nov. is proposed.

The longevity of fencing out livestock as a method of decreasing contaminant concentrations in a headwater stream.

Water quality can be improved by fencing off streams from livestock. However, the remedial effect of fencing can fail as livestock trample near stream areas. Water samples were taken every 3-4 wk, and flow was monitored over time in a headwater stream from 2003 to 2019. In November 2005, the stream edge and an area near the stream used for wallowing by farmed red deer was fenced off and planted in native trees, shrubs, and grasses. Contaminant (nitrogen and phosphorus species, sediment, and the fecal indicator bacteria Escherichia coli) concentrations decreased after fencing until at least 2013 (55-84%). However, nitrate concentrations more than doubled owing to the use of a portion of the catchment for a grazed winter forage crop in 2013. Most concentrations remained low after fencing, but sediment concentrations slowing increased (3% yr-1 ), which was attributed to animal tracking near the fence line. The presence of stock in the catchment enriched stormflow losses but prevented losses during baseflow. These data indicate that, when implemented well, fencing and planting could potentially sustain good water quality for decades in farmed red deer systems.

Plastic microbiome development in a freshwater ecosystem.

To understand biological interactions of plastic litter in freshwater ecosystems, as well the potential effects of plastics on ecosystem processes, studies of the activity and composition of plastic-associated microbial communities are needed. The physical properties and chemical composition of plastic polymers are key components of plastic product design, and may also select for distinct microbial biofilms colonizing plastic litter. We monitored growth and succession of biofilm communities on plastic substrates of common morphotypes (i.e., hard, soft, foam, and film) and a natural surface (i.e., an unglazed ceramic tile) incubated in an urban stream. We measured biofilm biomass, metabolism, extracellular enzyme activity, and bacterial, fungal and algal community composition over four weeks during primary succession. Results demonstrated a general increase in biofilm biomass and enzymatic activity corresponding to carbon, nitrogen and phosphorus metabolism during biofilm development for all substrate types. We observed higher respiration rates and negative net ecosystem productivity on foam and tile surfaces in comparison to hard, soft and film plastic surfaces. Biofilm bacterial, fungal and algal assemblages showed few significant differences in composition among substrates. However, all microbial communities changed significantly in composition over time. While substrate type was not the major factor driving biofilm composition and activity, these data show plastic litter in streams is well colonized by an active and dynamic biofilm community. As plastic litter is increasing across all types of aquatic ecosystems, it should be considered a medium for biologically active organisms that contribute to key ecosystem processes.

[Identification of Bacterial Flora and Metabolic Function of Sediments in Different Channels of Duliujian River Basin, Tianjin].

Bacterial communities are highly sensitive to environmental changes, but their metabolic functions may be convergent under similar ecological conditions. In order to test this environmental attribute of the bacterial community and verify the feasibility in using the bacterial metabolic data to divide functional units at the river basin scale, the surface sediments in three continuous spatial units of the main stream (MS), left tributary (LT), and right tributary (RT) of the Duliujian River basin were selected as the research objects. Therefore, 16S rDNA high-throughput sequencing and the PICRUSt platform were used to analyze the bacterial diversity and metabolic function of sediments in different units. The results showed that there were no significant differences for the Shannon and Simpson indices between the different river channels (P>0.05); however, the bacterial diversity indices of Chao1, ACE, Observed_species, and PD_whole_tree of LT and RT were significantly higher than those of the MS (P<0.05). Moreover, the dominant bacterial phyla were not significantly different among the different river channels. In the present study, a total of 41 metabolic pathways were predicted based on the KEGG database, among which 34 metabolic pathways such as membrane transport, amino acid metabolism, and carbohydrate metabolism were significantly different. The functional metabolic abundance was higher in MS than that in RT and LT (P<0.05); however, there was no significant difference between those of RT and LT (P>0.05). Except for exchangeable phosphorus and nitrate nitrogen, there were no significant differences in other physicochemical properties among the different river channels (P>0.05). Furthermore, pH and iron/aluminum-phosphorus were found to significantly affect the bacterial structure, and SOM and TN were found to significantly affect the bacterial metabolic function. Overall, the sediments of MS and tributaries (LT and RT) of the river were clearly divided into level-1 and level-2 groups, indicating that the metabolic abundance of the bacterial community can be used as the key indicator in the division of functional units at the river basin scale. This study provided a theoretical basis and technical support for ecological functional division and management in coastal river basins.

Rahnella perminowiae sp. nov., Rahnella bonaserana sp. nov., Rahnella rivi sp. nov. and Rahnella ecdela sp. nov., isolated from diverse environmental sources, and emended description of the genus Rahnella.

Bacteria isolated from onion bulbs suffering from bacterial decay in the United States and Norway were previously shown to belong to the genus Rahnella based on partial housekeeping gene sequences and/or fatty acid analysis. However, many strains could not be assigned to any existing Rahnella species. Additionally, strains isolated from creek water and oak as well as a strain with bioremediation properties were assigned to Rahnella based on partial housekeeping gene sequences. The taxonomic status of these 21 strains was investigated using multilocus sequence analysis, whole genome analyses, phenotypic assays and fatty acid analysis. Phylogenetic and phylogenomic analyses separated the strains into five clusters, one of which corresponded to Rahnella aceris. The remaining four clusters could be differentiated both genotypically and phenotypically from each other and existing Rahnella species. Based on these results, we propose the description of four novel species: Rahnella perminowiae sp. nov. (type strain SL6T=LMG 32257T=DSM 112609T), Rahnella bonaserana sp. nov. (H11bT=LMG 32256T=DSM 112610T), Rahnella rivi sp. nov. (FC061912-KT=LMG 32259T=DSM 112611T) and Rahnella ecdela sp. nov. (FRB 231T=LMG 32255T=DSM 112612T).

Community structure of bacterioplankton and its relationship with environmental factors in the upper reaches of the Heihe River in Qinghai Plateau.

Planktonic microorganisms play a key role in the biogeochemical processes of the aquatic system, and they may be affected by many factors. High-throughput sequencing technology was used in this study to investigate and study the bacterioplankton community of water bodies in the upper reaches of the Heihe River Basin in Qinghai Plateau. Results showed that Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria are the predominant phyla in this river section, while the main genera are Thiomonas, Acidibacillus, Acidocella, Rhodanobacter, Acidithiobacter and Gallionella, which are autochthonous in the acid-mine drainage. Additionally, total nitrogen, total phosphorus, permanganate index and pH are significantly correlated with the bacterioplankton abundance and are the main limiting factors for the spatial distribution of the bacterioplankton. PICRUSt inferred that the mainstream microbial assemblages had a higher abundance of KOs belong to metabolism of terpenoids and polyketides, while the tributary had higher abundance of KOs belong to the immune system. The relationship between bacterioplankton community composition and environmental factors in the Heihe River basin was discussed for the first time in this study, which provides a theoretical basis for the healthy, orderly development of the water environment in the Heihe River Basin.

Antimicrobial resistance and ESBL genes in E. coli isolated in proximity to a sewage treatment plant.

This study was aimed to determine the prevalence of antibiotic-resistant Escherichia coli in the Szreniawa river with detailed aims of: (i) assessment of differences in the number of microbiological indicators of water quality in a diurnal cycle in a vicinity of the sewage treatment plant (STP); (ii) determination of prevalence of antimicrobial resistant E. coli isolated from three sites located at varying locations toward the STP; (iii) evaluation of the presence of extended-spectrum beta lactamase (ESBL)-determining genes in waterborne E. coli isolated from three sites of Szreniawa and (iv) genetic similarity assessment among the E. coli populations. Bacteriological contamination (coliforms, E. coli, E. faecalis) was assessed using membrane filtration. Fifty E. coli strains, the species of which was confirmed by MALDI-TOF analysis, were subjected to antimicrobial resistance tests using standard disk-diffusion method. Double disk synergy test was used to assess the ESBL production and PCR tests were conducted to detect the ESBL-conferring genes and evaluate the genetic diversity. A significant variation in the number of bacteriological indicators was observed both within and between the sampling sites, suggesting the effect of effluent from the STP, point discharge of household sewage and agricultural runoff on the water contamination. The resistance to amoxicillin/clavulanate (90%) and ampicillin (36%) was most prevalent. Multidrug resistance was observed in 40% of strains but no ESBL-producing strains were observed phenotypically. However, the presence of three ESBL-determining genes (TEM, OXA and CTX-M) was detected in 24, 10 and 8% of strains, respectively. A number of factors caused considerable pollution of the river and numerous multidrug resistant E. coli strains were isolated.

Spatial variation in bacterial biomass, community composition and driving factors across a eutrophic river.

Eutrophication is a global problem, and bacterial diversity and community composition are usually affected by eutrophication. However, limited information on the ecological significance of bacterial community during algae blooms of rivers has been given, more studies should be focused on the bacterial diversity and distribution characteristics in eutrophic rivers. In this study, we explored the spatial variations of bacterial biomass, community structure, and their relationship with environmental factors in the eutrophic Xiangxi River. The content of Chlorophyll (Chl) was about 16 mg/L in the midstream (S2, S3), which was in the range of light eutrophication. Significant spatial variation of bacterial community structure was found at different sites and depths (p < 0.05), and the driving environmental factor was found to be nitrogen, mainly detected as total nitrogen (TN), Kjeldahl nitrogen (KN), and ammonia nitrogen (NH4+) (p < 0.05). The midstream sites had some significantly different bacteria, including algicidal bacteria and dominant lineages during algal blooms. This result was consistent with the functional prediction, where significant higher abundance of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways was associated with algicidal substances in the midstream. At different water depths, some populations adapted to the surface layer, such as the class Flavobacteriia, and others preferred to inhabit in the bottom layer, such as Betaproteobacteria and Acidobacteria. The bacterial biomass was higher in the bottom layer than that in the surface and middle layer, and temperature and pH were found to be the major driving factors. The bacterial diversity increased with the increasing of depths in most sampling sites according to operational taxonomic units (OTUs), Chao1 and ACE indexes, and PO43- was demonstrated to be the most significant factor. In summary, this study offered the evidence for microbial distribution characteristics across different sites and depths in summer, and its relationship with environmental variables in a eutrophic river.

Eutrophication and Related Antibiotic Resistance of Enterococci in the Minjiang River, China.

Antimicrobial resistance (AMR) in the aquatic environment has received increasing attention in recent years, and growing eutrophication problems may contribute to AMR in aquatic ecosystems. To evaluate whether and how eutrophication affects AMR, 40 surface water samples were collected from the Minjiang River, Fujian Province, China. Total nitrogen (TN), total phosphorus (TP), and chemical oxygen demand (CODMn) were measured as eutrophication factors. Additionally, enterococci species were isolated and their resistance to six common antibiotics was tested. Eutrophication generally showed a trend of increasing with the flow direction of the Minjiang River, with 25 sites (62.5%) having a TN/TP value over the Redfield value (16:1), which indicated that eutrophication in this region was of phosphorus limitation. High nutrition sites were in or near urban areas. Poor quality water was found in the middle and lower reaches of the Minjiang River system. The resistance frequency of 40 enterococci isolates to the six antibiotics tested was as follows: oxytetracycline > erythromycin > ciprofloxacin > chloramphenicol > ampicillin > vancomycin (70, 50, 17.5, 12.5, 2.5, 0%), and the multi-resistant rate reached 50% with eight resistance phenotypes. AMR also increased along the direction of water flow downstream, and most of the sites with the highest AMR were in or near urban areas, as was true for nutrition levels. Positive correlations between AMR and eutrophication factors (TN, TP, and CODMn) were identified using the Pearson's correlation coefficient, and TN/TP generally was negatively related to AMR. These results indicated that eutrophication may induce or selective for resistance of water-borne pathogens to antibiotics, with a high resistance level and a wide resistance spectrum.

Subsurface zones in intermittent streams are hotspots of microbial decomposition during the non-flow period.

The microbial decomposition of organic matter is a fundamental ecosystem process that transforms organic matter and fuels detritus-based food webs, influencing biogeochemical cycles such as C-cycling. The efficiency of this process can be compromised during the non-flow periods of intermittent and ephemeral streams (IRES). When water flow ceases, sediments represent the last wet habitat available to microorganisms and may play an important role in sustaining microbial decomposition. However, despite the increasing prevalence of IRES due to climate change and water abstraction, it is unclear to what degree the subsurface habitat can sustain microbial decomposition during non-flow periods. In order to gather information, we selected 20 streams across Catalonia (Spain) along a gradient of flow intermittency, where we measured microbial decomposition and fungal biomass by placing wood sticks in both the surface and subsurface zones (15 cm below the streambed) over the course of one hydrological year. Our results showed that microbial decomposition and fungal biomass were consistently greater in the subsurface zone than in the surface zone, when intermittency increased. Although flow intermittency was the main driver of both microbial decomposition and fungal biomass, phosphorus availability in the water, sediment C:N ratio and sediment grain size also played relevant roles in surface and subsurface organic matter processing. Thus, our findings demonstrate that although the OM processing in both zones decreases with increased intermittency, the subsurface zone made an important contribution during the non-flow periods in IRES. Therefore, subsurface activity during non-flow periods has the potential to affect and maintain ecosystem functioning.

Pseudomonas phragmitis sp. nov., isolated from petroleum polluted river sediment.

A Gram-stain-negative, rod-shaped bacterium, motile by means of a single polar flagellum, designated S-6-2T, was isolated from petroleum polluted river sediment in Huangdao, Shandong Province, PR China. The 16S rRNA gene sequence analysis revealed that S-6-2T represented a member of the genus Pseudomonas, sharing the highest sequence similarities with Pseudomonas parafulva (97.5 %) and Pseudomonas fulva (97.5 %). Phylogenetic analysis based on 16S rRNA gene, concatenated 16S rRNA, gyrB, rpoB and rpoD genes and genome core-genes indicated that S-6-2T was affiliated with the members of the Pseudomonas pertucinogena group. The average nucleotide identity (ANI) and genome-to-genome distance between the whole genome sequences of S-6-2T and closely related species of the genus Pseudomonas within the P. pertucinogena group were less than 77.94 % and 20.5 %, respectively. Differences in phenotypic characteristics were also found between S-6-2T and the closely related species. The major cellular fatty acids (>10 %) were summed feature 8 (C18 : 1ω7c/ C18  : 1ω6c), C16 : 0, C17 : 0cyclo and C12 : 0. The predominant respiratory quinone was ubiquinone 9. The major polar lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), one unidentified lipid (L1), two unidentified phospholipids (PL1 and PL2) and an aminophospholipid (APL). The DNA G+C content of the genome of S-6-2T was 60.1 mol%. On the basis of the evidence from the polyphasic taxonomic study, strain S-6-2T can be classified as representative of a novel species of the genus Pseudomonas, for which the name Pseudomonas phragmitis sp. nov. is proposed. The type strain is S-6-2T (=CGMCC 1.15798T=KCTC 52539T).

Niche partitioning of microbial communities in riverine floodplains.

Riverine floodplains exhibit high floral and faunal diversity as a consequence of their biophysical complexity. Extension of such niche partitioning processes to microbial communities is far less resolved or supported. Here, we evaluated the responses of aquatic biofilms diversity to environmental gradients across ten riverine floodplains with differing degrees of flow alteration and habitat diversity to assess whether complex floodplains support biofilm communities with greater biodiversity and species interactions. No significant evidence was found to support a central role for habitat diversity in promoting microbial diversity across 116 samples derived from 62 aquatic habitats, as neither α (H': 2.8-4.1) nor ß (Sørensen: 0.3-0.39) diversity were positively related to floodplain complexity across the ten floodplains. In contrast, our results documented the sensitivity of biofilm communities to regional templates manifested as gradients of carbon, nitrogen, and phosphorous availability. Large-scale conditions reflecting nitrogen limitation increased the relative abundance of N-fixing cyanobacteria (up to 0.34 as fraction of total reads), constrained the total number of interactions among bacterial taxa, and reinforced negative over positive interactions, generating unique microbial communities and networks that reflect large-scale species sorting in response to regional geochemical gradients.

Brevibacillus antibioticus sp. nov., with a broad range of antibacterial activity, isolated from soil in the Nakdong River.

A Gram-stain-positive, aerobic, motile, and rod-shaped bacterial strain designated TGS2-1T was isolated from sediment soil in the Nakdong River, Republic of Korea. The optimal growth of strain TGS2-1T was observed at 28°C and pH 7.0 without NaCl supplementation. Strain TGS2-1T revealed antibiosis against various bacteria, including Staphylococcus aureus KCCM 4051, CCARM 3089 (methicillin resistant strains), Enterococcus faecalis KCCM 11814, Escherichia coli KCTC 2443, Candida albicans KACC 7270, and Filobasidium neoformans KCTC 7902. Phylogenetic analyses based on the 16S rRNA gene sequences indicated that strain TGS2-1T belonged to the genus Brevibacillus and shared 93.8-99.7% sequence similarity with Brevibacillus species. Whole-genome sequencing of strain TGS2-1T revealed a genome size of 6.2 Mbp and DNA G + C content of 47.0 mol%. The TGS2-1T genome shared an average nucleotide identity and digital DNA-DNA hybridization of 74.6-93.3% and 18.6-67.1%, respectively, with six related Brevibacillus genomes. The major fatty acid constituents of strain TGS2-1T were anteiso-C15:0 (62.3%) and anteiso-C17:0 (10.8%). Cells of strain TGS2-1T contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, seven unidentified aminophospholipids, and five unidentified lipids. The isoprenoid quinone detected in the strain was menaquinone-7 (MK-7). Based on data obtained from this polyphasic taxonomic study, strain TGS2-1T represents a novel species belonging to genus Brevibacillus, for which the name B. antibioticus sp. nov. is proposed. The type strain is TGS2-1T (= KCCM 90326T = NBRC 113840T = FBCC-B2501).

Integrative study of microbial community dynamics and water quality along The Apatlaco River.

The increasing demand for clean water resources for human consumption, is raising concerning about the sustainable worldwide provisioning. In Mexico, rivers near to high-density urbanizations are subject to irrational exploitation where polluted water is a risk for human health. Therefore, the aims of this study are to analyze water quality parameters and bacterial community dynamics to understand the relation between them, in the Apatlaco river, which presents a clear environmental perturbance. Parameters such as total coliforms, chemical oxygen demand, harness, ammonium, nitrite, nitrate, total Kjeldahl nitrogen, dissolved oxygen, total phosphorus, total dissolved solids, and temperature were analyzed in 17 sampling points along the river. The high pollution level was registered in the sampling point 10 with 480 mg/L chemical oxygen demand, 7 mg/L nitrite, 34 mg/L nitrate, 2 mg/L dissolved oxygen, and 299 mg/L of total dissolved solids. From these sites, we selected four samples for DNA extraction and performed a metagenomic analysis using a whole metagenome shotgun approach, to compare the microbial communities between polluted and non-polluted sites. In general, Proteobacteria was the most representative phylum in all sites. However, the clean water reference point was enriched with microorganism from the Limnohabitans genus, a planktonic bacterium widespread in freshwater ecosystems. Nevertheless, in the polluted sampled sites, we found a high abundance of potential opportunistic pathogen genera such as Acinetobacter, Arcobacter, and Myroides, among others. This suggests that in addition to water contamination, an imminent human health risk due to pathogenic bacteria can potentially affect a population of ∼1.6 million people dwelling nearby. These results will contribute to the knowledge regarding anthropogenic pollution on the microbial population dynamic and how they affect human health and life quality.

Widespread detection of Candidatus Accumulibacter phosphatis, a polyphosphate-accumulating organism, in sediments of the Columbia River estuary.

Enhanced biological phosphorus removal (EBPR) exploits the metabolism of polyphosphate-accumulating organisms (PAOs) to remove excess phosphorus (P) from wastewater treatment. Candidatus Accumulibacter phosphatis (Accumulibacter) is the most abundant and well-studied PAO in EBPR systems. In a previous study, we detected polyphosphates throughout peripheral bay sediments, and hypothesized that an estuary is an ideal setting to evaluate PAOs in a natural system, given that estuaries are characterized by dynamic dissolved oxygen fluctuations that potentially favour PAO metabolism. We detected nucleotide sequences attributable to Accumulibacter (16S rRNA, ppk1) in sediments within three peripheral bays of the Columbia River estuary at abundances rivalling those observed in conventional wastewater treatment plants (0.01%-2.6%). Most of the sequences attributable to Accumulibacter were Type I rather than Type II, despite the fact that the estuary does not have particularly high nutrient concentrations. The highest diversity of Accumulibacter was observed in oligohaline peripheral bays, while the greatest abundances were observed at the mouth of the estuary in mesohaline sediments in the spring and summer. In addition, an approximately 70% increase in polyphosphate concentrations observed at one of the sites between dawn and dusk suggests that PAOs may play an important role in P cycling in estuary sediments.

Impacts of microbial assemblage and environmental conditions on the distribution of anatoxin-a producing cyanobacteria within a river network.

Blooms of planktonic cyanobacteria have long been of concern in lakes, but more recently, harmful impacts of riverine benthic cyanobacterial mats been recognized. As yet, we know little about how various benthic cyanobacteria are distributed in river networks, or how environmental conditions or other associated microbes in their consortia affect their biosynthetic capacities. We performed metagenomic sequencing for 22 Oscillatoriales-dominated (Cyanobacteria) microbial mats collected across the Eel River network in Northern California and investigated factors associated with anatoxin-a producing cyanobacteria. All microbial communities were dominated by one or two cyanobacterial species, so the key mat metabolisms involve oxygenic photosynthesis and carbon oxidation. Only a few metabolisms fueled the growth of the mat communities, with little evidence for anaerobic metabolic pathways. We genomically defined four cyanobacterial species, all which shared <96% average nucleotide identity with reference Oscillatoriales genomes and are potentially novel species in the genus Microcoleus. One of the Microcoleus species contained the anatoxin-a biosynthesis genes, and we describe the first anatoxin-a gene cluster from the Microcoleus clade within Oscillatoriales. Occurrence of these four Microcoleus species in the watershed was correlated with total dissolved nitrogen and phosphorus concentrations, and the species that contains the anatoxin-a gene cluster was found in sites with higher nitrogen concentrations. Microbial assemblages in mat samples with the anatoxin-a gene cluster consistently had a lower abundance of Burkholderiales (Betaproteobacteria) species than did mats without the anatoxin-producing genes. The associations of water nutrient concentrations and certain co-occurring microbes with anatoxin-a producing Microcoleus motivate further exploration for their roles as potential controls on the distributions of toxigenic benthic cyanobacteria in river networks.

Bioremediation of contaminated urban river sediment with methanol stimulation: Metabolic processes accompanied with microbial community changes.

The intense pollution of urban river sediments with rapid urbanization has attracted considerable attention. Complex contaminated sediments urgently need to be remediated to conserve the ecological functions of impacted rivers. This study investigated the effect of using methanol as a co-substrate on the stimulation of the indigenous microbial consortium to enhance the bioremediation of petroleum hydrocarbons (PHs) and polycyclic aromatic hydrocarbons (PAHs) in an urban river sediment. After 65 days of treatment, the PAHs degradation efficiencies in the sediment adding methanol were 4.87%-40.3% higher than the control. The removal rate constant of C31 was 0.0749 d-1 with 100 mM of supplied methanol, while the corresponding rate was 0.0399 d-1 in the control. Four-ring PAHs were effectively removed at a degradation efficiency of 65%-69.8%, increased by 43.3% compared with the control. Sulfate reduction and methanogenesis activity were detected, and methane-producing archaea (such as Methanomethylovorans, with a relative abundance of 25.87%-58.53%) and the sulfate-reducing bacteria (SRB, such as Desulfobulbus and Desulfobacca) were enriched. In addition, the chemolithoautotrophic sulfur-oxidizing bacteria (SOB, such as Sulfuricurvum, with a relative abundance of 34%-39.2%) were predominant after the depletion of total organic carbon (TOC), and markedly positively correlated with the PHs and PAHs degradation efficiencies (P < 0.01). The SRB and SOB populations participated in the sulfur cycle, which was associated with PHs and PAHs degradation. Other potential functional bacteria (such as Dechloromonas) were also obviously enriched and significantly positively correlated with the TOC concentration after methanol injection (P < 0.001). This study provides a new insight into the succession of the indigenous microbial community with methanol as a co-substrate for the enhanced bioremediation of complexly contaminated urban river sediments.

Microbial Organic Matter Utilization in High-Arctic Streams: Key Enzymatic Controls.

In the Arctic, climate changes contribute to enhanced mobilization of organic matter in streams. Microbial extracellular enzymes are important mediators of stream organic matter processing, but limited information is available on enzyme processes in this remote area. Here, we studied the variability of microbial extracellular enzyme activity in high-Arctic fluvial biofilms. We evaluated 12 stream reaches in Northeast Greenland draining areas exhibiting different geomorphological features with contrasting contents of soil organic matter to cover a wide range of environmental conditions. We determined stream nitrogen, phosphorus, and dissolved organic carbon concentrations, quantified algal biomass and bacterial density, and characterized the extracellular enzyme activities involved in catalyzing the cleavage of a range of organic matter compounds (e.g., ß-glucosidase, phosphatase, ß-xylosidase, cellobiohydrolase, and phenol oxidase). We found significant differences in microbial organic matter utilization among the study streams draining contrasting geomorphological features, indicating a strong coupling between terrestrial and stream ecosystems. Phosphatase and phenol oxidase activities were higher in solifluction areas than in alluvial areas. Besides dissolved organic carbon, nitrogen availability was the main driver controlling enzyme activities in the high-Arctic, which suggests enhanced organic matter mineralization at increased nutrient availability. Overall, our study provides novel information on the controls of organic matter usage by high-Arctic stream biofilms, which is of high relevance due to the predicted increase of nutrient availability in high-Arctic streams in global climate change scenarios.

Comparison among the microbial communities in the lake, lake wetland, and estuary sediments of a plain river network.

Sediment microbial communities from plain river networks exert different effects on pollutant transformation and migration in lake basins. In this study, we examined millions of Illumina reads (16S rRNA gene amplicons) to compare lake, lake wetland, and estuary bacterial communities through a technically consistent approach. Results showed that bacterial communities in the sampled lake sediments had the highest alpha-diversity (Group B), than in sampled lake wetland sediments and estuary sediments. Proteobacteria was the most abundant (more than 30%) phyla in all the sediments. The lake sediments had more Nitrospirae (1.63%-11.75%) and Acidobacteria (3.46%-10.21%) than the lake wetland and estuary sediments, and estuary sediments had a greater abundance of the phylum Firmicutes (mean of 22.30%). Statistical analysis (LEfSe) revealed that lake wetland sediments contained greater abundances of the class Anaerolineaceae, orders Xanthomonadales, Pseudomonadales, and genera Flavobacterium, Acinetobacter. The lake sediments had a distinct community of diverse primary producers, such as phylum Acidobacteria, order Ignavibacteriales, and families Nitrospiraceae, Hydrogenophilaceae. Total phosphorus and organic matter were the main factors influencing the bacterial communities in sediments from several parts of the lake wetland and river estuary (p < .05). The novel insights into basin pollution control in plain river networks may be obtained from microbial distribution in sediments from different basin regions.