Microorganisms in Aquatic Environments

The properties of intestinal bacteria/probiotics, such as cell surface hydrophobicity (CSH), auto-aggregation, and biofilm formation ability, play an important role in shaping the relationship between the bacteria and the host. The current study aimed to investigate the cell surface properties of fish intestinal bacteria and probiotics. Microbial adhesion to hydrocarbons was tested according to Kos and coauthors. The aggregation abilities of the investigated strains were studied as described by Collado and coauthors. The ability of bacterial isolates to form a biofilm was determined by performing a qualitative analysis using crystal violet staining based on the attachment of bacteria to polystyrene. These studies prove that bacterial cell surface hydrophobicity (CSH) is associated with the growth medium, and the effect of the growth medium on CSH is species-specific and likely also strain-specific. Isolates of intestinal lactobacilli from fish (Salmo ischchan) differed from isolates of non-fish/shrimp origin in the relationship between auto-aggregation and biofilm formation. Average CSH levels for fish lactobacilli and E. coli might were lower compared to those of non-fish origin, which may affect the efficiency of non-fish probiotics use in fisheries due to the peculiarities of the hosts’ aquatic lifestyles. Full article

Aquatic environments could be reservoirs of pathogenic yeasts with acquired antifungal resistance. The susceptibility to antifungal agents of yeasts present in the wastewater and natural waters of the city of Cali was evaluated. Samples were taken from two types of water: drinking water (Meléndez River, drinking water treatment plant “Puerto Mallarino” in the Cauca River) and wastewater (South Channel of the Cauca River, “Cañaveralejo-PTAR” wastewater treatment plant). Physico-chemical parameters, heavy metal concentration, and yeast levels were determined using standard procedures. Yeasts were identified using API 20 C AUX (BioMérieux) and sequence analysis of the ITS1-5.8S-ITS2 and D1/D2 regions of the large subunit of the ribosome. Susceptibility assays against fluconazole and amphotericin B using the minimum inhibitory concentration (MIC) test were determined using the microdilution method. The influence of physico-chemical parameters and heavy metals was established using principal component analysis (PCA). Yeast counts were higher at WWTP “PTAR” and lower at Melendez River, as expected. A total of 14 genera and 21 yeast species was identified, and the genus Candida was present at all locations. Susceptibility tests showed a 32.7% resistance profile to fluconazole in the order DWTP “Puerto Mallarino = WWTP “PTAR” > South Channel “Navarro”. There were significant differences (p < 0.05) in the physico-chemical parameters/concentration of heavy metals and yeast levels between the aquatic systems under study. A positive association was observed between yeast levels and total dissolved solids, nitrate levels, and Cr at the “PTAR” WWTP; conductivity, Zn, and Cu in the South Channel; and the presence of Pb in the “Puerto Mallarino” DWTP. Rhodotorula mucilaginosa, Candida albicans, and Candida sp. 1 were influenced by Cr and Cd, and Diutina catelunata was influenced by Fe (p < 0.05). The water systems explored in this study showed different yeast levels and susceptibility profiles, and, therefore, possible genetic differences among populations of the same species, and different physico-chemical and heavy metals concentrations, which were probably modulating the antifungal-resistant yeasts. All these aquatic systems discharge their content into the Cauca River. We highlight the importance to further investigate if these resistant communities continue to other locations in the second largest river of Colombia and to determine the risk posed to humans and animals. Full article

In this scientific work, the problem of studying the process of destruction of microorganisms in water by an Etro-03 device based on electric corona discharge is considered. In the research, a special Etro-03 ozonator device was developed for clearing water of biological pollutants. Testing of the installation was carried out in order to disinfect surface water in the Kapshagai reservoir. During the research, various harmful microorganisms were found in the composition of the primary water that did not meet the maximum permissible concentration (MPC). For example, coliphages, coli-indices, and the number of microbes in general came across in large numbers. During the technological process, various amounts of ozone (O3) were released into the water, the amount and effective economic indicators of which were determined. In the same way, the effective time of the decontamination process was determined. During the research process, an algorithm of theoretical calculations was developed, and a mathematical model was given to bring 1m³ of surface water as the indicator for which sanitary rules and norms are approved. Full article

Heterosigma akashiwo is a golden-brown unicellular phytoflagellate with a high potential to create harmful algal blooms (HABs) and kill fish in many coastal regions worldwide, resulting in significant economic losses. Climate change and global warming have been introduced as triggers that impact the frequency and severity of H. akashiwo and other bloom-forming species in the past decades. In this review paper, the author tried to briefly discuss the morphology and taxonomy of H. akashiwo and show how environmental parameters can influence the physiology and toxicity of this species. Although the toxin production and mechanisms are still a conundrum, the proposed fish-killing mechanisms will be reviewed in the next step. Full article

Antibiotic resistance is an alarming threat all over the world, and the biofilm formation efficacy of bacteria is making the situation worse. The antagonistic efficacy of Klebsiella pneumoniae against one of the known fish pathogens, Aeromonas sp., is examined in this study. Moreover, Aeromonas sp.’s biofilm formation ability and in vivo pathogenicity on Artemia salina are also justified here. Firstly, six selected bacterial strains were used to obtain antimicrobial compounds against this pathogenic strain. Among those, Klebsiella pneumoniae, another pathogenic bacterium, surprisingly demonstrated remarkable antagonistic activity against Aeromonas sp. in both in vitro and in vivo assays. The biofilm distrusting potentiality of Klebsiella pneumoniae’s cell-free supernatants (CFSs) was likewise found to be around 56%. Furthermore, the volatile compounds of Klebsiella pneumoniae were identified by GC-MS in order to explore compounds with antibacterial efficacy against Aeromonas sp. through an in silico study, where 5′-methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) (PDB: 5B7P) was chosen as a target protein for its unique characteristics and pathogenicity. Several volatile compounds, such as oxime- methoxy-phenyl-, fluoren-9-ol, 3,6-dimethoxy-9-(2-phenylethynyl)-, and 2H-indol-2-one, 1,3-dihydro- showed a strong binding affinity, with free energy of −6.7, −7.1, and −6.4 Kcal/mol, respectively, in complexes with the protein MTAN. Moreover, the root-mean-square deviation, solvent-accessible surface area, radius of gyration, root-mean-square fluctuations, and hydrogen bonds were used to ensure the binding stability of the docked complexes in the atomistic simulation. Thus, Klebsiella pneumoniae and its potential compounds can be employed as an alternative to antibiotics for aquaculture, demonstrating their effectiveness in suppressing Aeromonas sp. Full article

The host’s physiological history and environment determine the microbiome structure. In that sense, the strategy used for the salmon transfer to seawater after parr-smolt transformation may influence the Atlantic salmon’s intestinal microbiota. Therefore, this study aimed to explore the diversity and abundance of the Atlantic salmon intestinal microbiota and metagenome functional prediction during seawater transfer under three treatments. One group was exposed to gradual salinity change (GSC), the other to salinity shock (SS), and the third was fed with a functional diet (FD) before the seawater (SW) transfer. The microbial profile was assessed through full-16S rRNA gene sequencing using the Nanopore platform. In addition, metagenome functional prediction was performed using PICRUSt2. The results showed an influence of salinity changes on Atlantic salmon gut microbiota richness, diversity, and taxonomic composition. The findings reveal that GSC and the FD increased the Atlantic salmon smolt microbiota diversity, suggesting a positive association between the intestinal microbial community and fish health during seawater transfer. The reported knowledge can be applied to surveil the microbiome in smolt fish production, improving the performance of Atlantic salmon to seawater transfer. Full article

This study aimed to investigate the effects of thermal stratification and complete mixing conditions on the bacterial diversity of a deep alkaline lake. For this purpose, the water and sediment samples were collected during the winter turnover and stratification periods, and bacterial communities were assessed by metabarcoding. The results showed that temperature shaped the bacterial community patterns in the lake. While the bacterial communities of the water samples showed high similarity during the mixing period, communities had distinctive patterns in the epilimnion and hypolimnion during stratification. The diversity and evenness of the bacterial communities increased with depth, whereas the bacterial communities of sediments were more even and diverse than in water. Proteobacteria members dominated the sediment communities representing 41% to 62% of the total reads in the samples. Particularly, Gammaproteobacteria was the major class found in the sediment; higher abundances were recorded in the mixing period representing 33–51%. Additionally, Actinobacteria species were more abundant in the water samples representing 22–52% of all reads during the stratification period. Due to the complete mixing conditions in the lake, a homogenized bacterial community structure was observed in the lake with minor spatial changes, and a clear divergence was observed between epilimnion and hypolimnion. On the other hand, the sediment bacterial community showed a more stable profile. Full article

Cyanobacteria constitute a pioneer colonizer of specific environments for whom settlement in new biotopes precedes the establishment of composite microbial consortia. Some heterotrophic bacteria constitute cyanobacterial partners that are considered as their cyanosphere, being potentially involved in mutualistic relationships through the exchange and recycling of key nutrients and the sharing of common goods. Several non-axenic cyanobacterial strains have been recently isolated, along with their associated cyanospheres, from the thermal mud of Balaruc-les-Bains (France) and the biofilms of the retention basin where they develop. The community structure and relationships among the members of the isolated cyanobacterial strains were characterized using a metagenomic approach combined with taxonomic and microscopic descriptions of the microbial consortia. The results provided insights into the potential role and metabolic capabilities of the microorganisms of thermal mud-associated cyanobacterial biofilms. Thus, the physical proximity, host-specificity, and genetic potential functions advocate for their complementarity between cyanobacteria and their associated microbiota. Besides these findings, our results also highlighted the great influence of the reference protein database chosen for performing functional annotation of the metagenomes from organisms of the cyanosphere and the difficulty of selecting one unique database that appropriately covers both autotroph and heterotroph metabolic specificities. Full article

The Taiyangshan Wetland, a valuable wetland resource in the arid zone of central Ningxia, is critical for flood storage and drought resistance, climate regulation, and biodiversity protection. Nevertheless, the community structure and diversity of bacterioplankton in the Taiyangshan Wetland remains unclear. High-throughput sequencing was used to analyze the differences in bacterioplankton structure and major determinants in the Taiyangshan Wetland from April to October 2020. The composition and diversity of the bacterioplankton community varied significantly in different sampling periods but showed negligible differences across lake regions. Meanwhile, the relative abundances of bacterioplankton Bacteroidetes, Actinobacteria, Firmicutes, Chloroflexi, Tenericutes, Epsilonbacteraeota, and Patescibacteria were significantly different in different sampling periods, while the relative abundances of Cyanobacteria in different lake regions were quite different. Network analysis revealed that the topological attributes of co-occurrence pattern networks of bacterioplankton were high, and bacterioplankton community compositions were complicated in the month of July. A mantel test revealed that the bacterioplankton community in the entire wetland was affected by water temperature, electrical conductivity, dissolved oxygen, salinity, total nitrogen, ammonia nitrogen, chemical oxygen demand, fluoride, and sulfate. The bacterioplankton community structure was affected by ten environmental parameters (e.g., water temperature, dissolved oxygen, salinity, and permanganate index) in April, while the bacterioplankton community was only related to 1~2 environmental parameters in July and October. The bacterioplankton community structure in Lake Region IV was related to seven environmental parameters, including dissolved oxygen, pH, total nitrogen, and chemical oxygen demand, whereas the bacterioplankton community structures in the other three lake regions were related to two environmental parameters. This study facilitates the understanding of the bacterioplankton community in wetlands in arid areas and provides references to the evaluation of aquatic ecological management of the Taiyangshan Wetland. Full article

Recirculating aquaculture systems (RAS) are important for water quality management in aquaculture facilities, and can help resume water consumption. However, information about the community structure of the micro-ecosystem existing in biofilters, especially the participation of the known nitrifying groups (i.e., AOA, AOB, NOB, and comammox Nitrospira), remains to be fully clarified. In this research, we compared the community structures in three RAS systems operated at different temperatures in a marine aquarium, through both amoA-targeted qPCR assay and 16S rRNA-targeted next-generation sequencing. As result, AOA was the primary nitrifier in the biofilters and was typically abundant and diverse in high-temperature samples (ca. 25 °C). NOB’s relative abundance patterns were numerically similar to that of AOA, suggesting a cooperation relationship between AOA and NOB in the marine RAS system. AOB was at a comparable level with AOA in medium-temperature samples (ca. 19 °C), while their abundance sharply decreased in high-temperature samples. The number of observed OTUs of AOA in high-temperature samples was 1.9 and 1.5 times as much as that detected in low (ca. 10 °C) and medium temperature samples respectively, suggesting a much more diverse and predominant occurrence of AOA at high temperatures. Comammox Nitrospira was only detected at a low level in the biofilter samples, suggesting a negligible contribution to the nitrification process in such ammonia-limited, saline biofilms. Although comammox Nitrospira cannot be detected by 16S rRNA-based analysis, the high diversity and abundance of NOB that were detected in high-temperature samples indicated the prospective possibility of the occurrence of complete ammonia oxidation at high temperatures. Full article

Feed input leads to a large amount of nitrogen-containing sediment accumulating in the substrate in the pond culture process, threatening the safety of aquaculture production. Planting lotus roots (Nelumbo nucifera Gaertn.) in ponds can accelerate the removal of bottom nitrogen, while the role of nitrogen cycle-related microorganisms in the removal is still unclear. In this study, eight yellow catfish (Pelteobagrus fulvidraco) culture ponds with the same basic situation were divided into fishponds with planted lotus roots and ponds with only fish farming. Sediment samples were taken from the fishponds with planted lotus roots and the ponds with only fish farming before and after fish farming, marked as FPB, FPA, FOB, and FOA, respectively, and subjected to physicochemical and metagenomic sequencing analyses. The results show that the contents of NH₄⁺, NO₂⁻, TN, TP, and OM were significantly lower (p < 0.05) in FPA than in FOA. The abundance of metabolic pathways for inorganic nitrogen transformation and ammonia assimilation increased considerably after culture compared to the sediments before culture. A total of eight ammonia production pathways and two ammonia utilization pathways were annotated in the sediments of the experimental ponds, with a very high abundance of ammonia assimilation. Acinetobacter and Pseudomonas (34.67%, 18.02%) were the dominant bacteria in the pond sediments before culture, which changed to Thiobacillus (12.16%) after culture. The FPA had significantly higher relative abundances of Thiobacillus denitrificans and Sulfuricella denitrificans, and the FOA had significantly a higher abundance of Microcystis aeruginosa compared to other samples. The massive growth of Microcystis aeruginosa provided two new inorganic nitrogen metabolic pathways and one organic nitrogen metabolic pathway for FOA. The relative abundances of these three microorganisms were negatively correlated with NH₄⁺ content (p < 0.01) and significantly positively correlated with AP, OM content, and pH value. Compared with ponds with only fish farming, lotus root–fish co-culture can significantly reduce the nitrogen content in sediment, increase the abundance of denitrifying bacteria, and inhibit algae growth. Still, it has little effect on the abundance of nitrogen cycle-related enzymes and genes. In summary, it is shown that, although lotus roots promote the growth of denitrifying microorganisms in the sediment, nitrogen removal relies mainly on nutrient uptake by lotus roots. Full article

Titanium dioxide nanoparticle (TiO₂ NP) toxicity to the growth of organisms has been gradually clarified; however, its effects on microorganism-mediated phosphorus turnover are poorly understood. To evaluate the influences of TiO₂ NPs on phosphorus fractionation and the bacterial community, aquatic microorganisms were exposed to different concentrations of TiO₂ NPs with different exposure times (i.e., 0, 10, and 30 days). We observed the adhesion of TiO₂ NPs to the cell surfaces of planktonic microbes by using SEM, EDS, and XRD techniques. The addition of TiO₂ NPs resulted in a decrease in the total phosphorus of water and an increase in the total phosphorus of sediments. Additionally, elevated TiO₂ NPs enhanced the sediment activities of reductases (i.e., dehydrogenase [0.19–2.25 μg/d/g] and catalase [1.06–2.92 μmol/d/g]), and significantly decreased the absolute abundances of phosphorus-cycling-related genes (i.e., gcd [1.78 × 10⁴–9.55 × 10⁵ copies/g], phoD [5.50 × 10³–5.49 × 10⁷ copies/g], pstS [4.17 × 10²–1.58 × 10⁶ copies/g]), and sediment bacterial diversity. TiO₂ NPs could noticeably affect the bacterial community, showing dramatic divergences in relative abundances (e.g., Actinobacteria, Acidobacteria, and Firmicutes), coexistence patterns, and functional redundancies (e.g., translation and transcription). Our results emphasized that the TiO₂ NP amount—rather than the exposure time—showed significant effects on phosphorus fractions, enzyme activity, phosphorus-cycling-related gene abundance, and bacterial diversity, whereas the exposure time exhibited a greater influence on the composition and function of the sediment bacterial community than the TiO₂ NP amount. Our findings clarify the responses of phosphorus fractions and the bacterial community to TiO₂ NP exposure in the water–sediment ecosystem and highlight potential environmental risks of the migration of untreated TiO₂ NPs to aquatic ecosystems. Full article

In the large and morphologically diverse phylum of Chlorophyta, new taxa are discovered every year and their phylogenetic relationships are reconstructed by the incorporation of molecular phylogenetic methods into traditional taxonomy. Herein, we aim to contribute to the photosynthetic microorganisms’ diversity knowledge in the Mediterranean area, a relatively unexplored ecoregion with high diversity. Based on a polyphasic approach, 18 Chlorophyta isolates were investigated and characterized. Morphological characteristics and ultrastructure, the phylogeny based on 18S rRNA gene (small subunit ribosomal RNA), 18S–28S internal transcribed spacer (ITS region), and the ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit region (rbcL gene), support establishing four new genera (Nomia, Ava, Akraea, Lilaea) and five new species (Spongiosarcinopsis limneus, N. picochloropsia, Av. limnothalassea, Ak. chliaropsychia, and L. pamvotia) belonging to orders Sphaeropleales, Chlorellales, and Chlamydomonadales. For some of them, this is the first report of their occurrence in specific aquatic environments. Full article

The freshwater green microalgae, Dictyosphaerium chlorelloides (CCALA 330), has the ability to produce extracellular polysaccharides (EPS). Conditions for optimum growth and EPS overproduction were determined in laboratory-scale tubular photobioreactors (PBR) with a working volume of 300 mL. Multiple limitations in nutrient supply were proven to be an effective method for EPS overproduction. Salinity stress was also applied to the culture, but no significant increase in EPS production was observed. The effects of different nitrogen sources were examined and the microalgae exhibited the fastest growth and EPS production in medium containing ammonium nitrate. Under determined optimal conditions, EPS concentration reached 10 g/L (71% of the total biomass) and a total biomass of 14 g/L at the end of 17 days cultivation. Pilot-scale cultivation was also carried out in a column type airlift photobioreactor (PBR) with a working volume of 60 L. A new and efficient methodology was developed for separating cells from the EPS-containing culture broth. Due to the strong attachment between cells and EPS, high-pressure homogenization was carried out before a centrifugation process. The EPS in the supernatant was subsequently purified using ultrafiltration. The green microalgae Dictyosphaerium chlorelloides may therefore be appropriate for the commercial production of EPS. Full article

Irradiation with ultraviolet light (UV) at 254 nm is effective in inactivating a wide range of human pathogens. In Sweden, a UV dose of 400 J/m² is often used for the treatment of drinking water. To investigate its effect on virus inactivation, enteric viruses with different genomic organizations were irradiated with three UV doses (400, 600, and 1000 J/m²), after which their viability on cell cultures was examined. Adenovirus type 2 (double-stranded DNA), simian rotavirus 11 (double-stranded RNA), and echovirus 30 (single-stranded RNA) were suspended in tap water and pumped into a laboratory-scale Aquada 1 UV reactor. Echovirus 30 was reduced by 3.6-log₁₀ by a UV dose of 400 J/m². Simian rotavirus 11 and adenovirus type 2 were more UV resistant with only 1-log₁₀ reduction at 400 J/m² and needed 600 J/m² for 2.9-log₁₀ and 3.1-log₁₀ reductions, respectively. There was no significant increase in the reduction of viral viability at higher UV doses, which may indicate the presence of UV-resistant viruses. These results show that higher UV doses than those usually used in Swedish drinking water treatment plants should be considered in combination with other barriers to disinfect the water when there is a risk of fecal contamination of the water. Full article

Water microorganisms contribute to the key components of ecosystems in dryland waters, which are extremely important for wildlife. However, the distribution patterns of water microbes across different basal water sources are still largely unknown. This study was conducted to compare microorganisms in the water bodies of different types of water sources in the Kalamaili Mountain Ungulate Nature Reserve in China. Bioinformatic analysis revealed that the undirected microbial co-existence network consisted of 15 main modules referring to different water sources, which indicated specific molecular co-existence relationships. It was found that the most dominant phyla (namely Proteobacteria, Patescibacteria, Firmicutes, Bacteroidota, and Actinobacteriota) of the molecular ecological network shared the same structures as the microbial community, which justified the construction of the network via a random network formation. Principal coordinate analysis (PCoA) based on Bray–Curtis distances revealed that there were still considerable variations among different habitats, showing separate sample clusters. Additionally, the different topological roles of subnetworks trimmed to a uniform size indicated different co-existence patterns in the microbiome. The artificially recharged water from concrete pond substrate (ARC) subnetworks had a relatively discrete co-occurrence, while the natural water sources (NRE) and artificially recharged water from earthen pond substrate (ARE) groups were more compact with giant modules. The NRE and ARE groups were also richer in microbial composition and had a higher number of species with low abundance. Consequently, concrete substrates may contribute to dysfunction in water microbiomes. Moreover, the functional diversity of the NRE and ARE groups is due to more intra-module connections and more inter-module connections, indirectly leading to a stable function resilient to external environmental influences. In conclusion, the microecology of the NRE was more stable than that of the concrete substrate, and artificial transportation had less effect on the microbial community. Full article

Paralichthys olivaceus (olive flounder) is widely cultivated in Korea. However, data on the antibiotic susceptibility of bacterial pathogens that infect olive flounders in Korea are limited. The susceptibility of 84 strains of 3 pathogenic bacteria (Streptococcus spp., Vibrio spp., and Edwardsiella piscicida) to 18 antibiotics was tested using the minimum inhibitory concentration (MIC) panels, and the distribution of the MIC values for each species was confirmed. Among the panel antibiotics, nine commonly used antibiotics were selected, and the multiple antibiotic resistance (MAR) index and antibiotic resistance pattern were indicated using the disk diffusion method. It was confirmed that most of the isolates had a MAR index greater than 0.2, indicating a high-risk source. The distribution patterns of the MIC values and resistance pattern between gram-positive and gram-negative bacteria showed slightly different results. Ampicillin, erythromycin, and clindamycin were more effective against gram-positive bacteria than gram-negative bacteria. However, the MIC values of flumequine for gram-positive bacteria were higher than those of gram-negative bacteria. Through the distribution patterns of the MIC values and resistance patterns presented in this study, the need for monitoring the multidrug-resistant bacteria in aquaculture is emphasised. Full article

Nanobubble technology has promising development and application prospects in the fields of sewage treatment, soil and groundwater remediation, animal and plant growth, and biomedicine. However, few studies have investigated its effect on shrimp aquaculture. In this study, we investigated the effect of nano-aerators on microbial communities of the water, sediment, and shrimp gut in a Litopenaeus vannamei aquaculture pond using 16S rRNA high-throughput sequencing. The results indicated that the nano-aerator significantly increased the microbial community diversity and species abundance in the pond, and the microbial community diversity of the pond sediment increased under short-term aeration conditions. Compared to that with ordinary aerators, nano-aerators increased the proportion of beneficial bacteria, such as Exiguobacterium and Acinetobacter, in the water and sediment microbial communities. Moreover, the proportions of beneficial bacteria in the gut, including Rhodobacter, Oscillospira, and Faecalibacterium, were all increased by using the nano-aerator. Therefore, our findings suggest that nano-aerators could promote the activity of beneficial bacteria in aquaculture ecosystems, thereby regulating water quality, reducing disease incidence, and improving aquaculture efficiency and benefits. Our findings provide new insights into the effects of nano-aerators on microbes in crustacean culture ponds. Full article

The city of Zhangye (Gansu Region, China) has been subjected to several changes related to the development of new profitable human activities. Unfortunately, this growth has led to a general decrease in water quality due to the release of several toxic wastes and pollutants (e.g., heavy metals) into the Heihe River. In order to assess the environmental exposure and the potential threat to human health, microbiological diversity for the monitoring of water pollution by biotic and abiotic impact factors was investigated. In particular, we analysed samples collected on different sites using 454 pyrotag sequencing of the 16S ribosomal genes. Then, we focused on alpha-diversity indices to test the hypothesis that communities featuring lower diversity show higher resistance to the disturbance events. The findings report that a wide range of environmental factors such as pH, nutrients and chemicals (heavy metals (HMs)), affected microbial diversity by stimulating mutualistic relationships among bacteria. Furthermore, a selection in bacterial taxa related to the different concentrations of polluting compounds was highlighted. Supporting the hypothesis, our investigation highlights the importance of microbial communities as sentinels for ecological status diagnosis. Full article

Due to its ability to collect and remove aquaculture waste, an in-pond raceway system (IPRS) has been used to decrease the uncontrolled waste discharge in the traditional cage aquaculture method in large water bodies. However, when applied to large water bodies, its environmental performance is still lacking. This study focused on analyzing the microbial characteristics and the interaction between largemouth bass (gill and gut) microbiota and the environment (water and sediment) microbiota of an IPRS. Further, it revealed the primary relationship from the perspective of microbiota in the IPRS. The results show that (1) the alpha diversity of microbiota in the water is significantly lower than that of fish and sediment. The relationship between water microbiota and fish microbiota is limited. (2) The water microbiota inside and outside the tank showed high similarity and were not significantly affected by environmental factors. (3) The SourceTrack analysis showed that fish microbiota is one of the primary sources of sediment microbiota, and more than 15% of the sediment microbiota come from fish. Microbes such as Faecalibacterium, Escherichia-Shigella, and Bacteroides can significantly enrich the sediment. Our study revealed the characteristics and preliminary interaction of fish and environmental microbiota in the IPRS. It provided a reference for evaluating microbial health status in the application of IPRS in large water bodies’ aquaculture. Full article

Diatoms constitute an important part of the phytoplankton community in lakes and reservoirs and play a significant role in regulating ecological balance. Danjiangkou Reservoir is the water source area of the middle route of China’s South-to-North Water Diversion project. In order to explore the spatial and temporal distribution and know the governing factors of the diatom community, 18srRNA sequencing was carried out from seven sampling sites of the reservoir. At the same time, the concentration of nutrients present in the collected sample water was also determined. The results showed that a total of 51 genera and 96 species were thriving the community of diatoms in Danjiangkou Reservoir. Discostella was dominant in summer and autumn, accounting for 98.84% and 62.71% of the diatom abundance, respectively. Aulacoseira was dominant in spring and winter, accounting for 60.62% and 60.90%, respectively. Discostella and Aulacoseira showed significant differences in seasonal variation (p < 0.05). The colinear network of diatoms changed significantly with the seasons, mainly consisting of Aulacoseira, Discostella, and Stephanodiscus. RDA redundancy analysis showed that water temperature (WT), total nitrogen (TN), NH₄⁺-N, pH, and electrical conductivity (Cond) were the main environmental factors driving the changes in diatom community structure. Full article

Nutrient limitation of phytoplankton is common but by no means universal in large temperate rivers. Previous field studies in the Columbia River, USA, are suggestive of nutrient limitations of phytoplankton, especially during summer, but this has never been tested experimentally. We therefore undertook monthly 5-day nutrient amendment incubation experiments from May–September 2018 using Columbia River water collected at Vancouver, Washington, USA. We compared replicate treatment bottles containing natural microplankton assemblages and amended nutrients (NO₃, PO₄ and SiO₄ in combination) with replicate control bottles containing natural microplankton assemblages and ambient nutrients. Phytoplankton abundance and biomass were compared between treatments and controls on each day of each experiment, and microplankton assemblage structure was evaluated using Permutational Multivariate Analysis of Variance and Non-Metric Multi-Dimensional Scaling ordination on Day 0 (ambient) and Day 5 of each experiment. Nutrient amendment significantly affected phytoplankton abundance and biomass, particularly in June–August, although this varied between taxa (e.g., cyanobacteria, dinoflagellates, flagellates and ciliates showed more frequent positive responses than chlorophytes and diatoms did). Abundance-based microplankton assemblage structure was significantly correlated with PO₄, SiO₄ and NO₃ concentrations, and BIOENV procedure in R revealed that the best subset of explanatory variables included SiO₄ and NO₃ concentrations. Biomass-based assemblage structure was significantly correlated with SiO₄ and NO₃, although BIOENV explanatory variables included only SiO₄. These results are suggestive of summertime nutrient control of phytoplankton abundance and biomass, as well as microplankton composition, in the lower Columbia River, at least during some months. Since eutrophication is increasing in the watershed, this could have important implications for higher level consumers (e.g., zooplankton and out-migrating juvenile salmon). Full article

Carbapenems are antibiotics of pivotal importance in human medicine, the efficacy of which is threatened by the increasing prevalence of carbapenem-resistant Enterobacterales (CRE). Urban ponds may be reservoirs of CRE, although this hypothesis has been poorly explored. We assessed the proportion of CRE in urban ponds over a one-year period and retrieved 23 isolates. These were submitted to BOX-PCR, PFGE, 16S rDNA sequencing, antibiotic susceptibility tests, detection of carbapenemase-encoding genes, and conjugation assays. Isolates were affiliated with Klebsiella (n = 1), Raoultella (n = 11), Citrobacter (n = 8), and Enterobacter (n = 3). Carbapenemase-encoding genes were detected in 21 isolates: bla_KPC (n = 20), bla_GES-5 (n = 6), and bla_VIM (n = 1), with 7 isolates carrying two carbapenemase genes. Clonal isolates were collected from different ponds and in different campaigns. Citrobacter F6, Raoultella N9, and Enterobacter N10 were predicted as pathogens from whole-genome sequence analysis, which also revealed the presence of several resistance genes and mobile genetic elements. We found that bla_KPC-3 was located on Tn4401b (Citrobacter F6 and Enterobacter N10) or Tn4401d (Raoultella N9). The former was part of an IncFIA-FII pBK30683-like plasmid. In addition, bla_GES-5 was in a class 3 integron, either chromosomal (Raoultella N9) or plasmidic (Enterobacter N10). Our findings confirmed the role of urban ponds as reservoirs and dispersal sites for CRE. Full article

Opportunistic premise plumbing pathogens (OPPP) are microorganisms that are native to the plumbing environment and that present an emerging infectious disease problem. They share characteristics, such as disinfectant resistance, thermal tolerance, and biofilm formation. The colonisation of domestic water systems presents an elevated health risk for immune-compromised individuals who receive healthcare at home. The literature that has identified the previously described OPPPs (Aeromonas spp., Acinetobacter spp., Helicobacter spp., Legionella spp., Methylobacterium spp., Mycobacteria spp., Pseudomonas spp., and Stenotrophomonas spp.) in residential drinking water systems were systematically reviewed. By applying the Preferred reporting items for systematic reviews and meta-analyses guidelines, 214 studies were identified from the Scopus and Web of Science databases, which included 30 clinical case investigations. Tap components and showerheads were the most frequently identified sources of OPPPs. Sixty-four of these studies detected additional clinically relevant pathogens that are not classified as OPPPs in these reservoirs. There was considerable variation in the detection methods, which included traditional culturing and molecular approaches. These identified studies demonstrate that the current drinking water treatment methods are ineffective against many waterborne pathogens. It is critical that, as at-home healthcare services continue to be promoted, we understand the emergent risks that are posed by OPPPs in residential drinking water. Future research is needed in order to provide consistent data on the prevalence of OPPPs in residential water, and on the incidence of waterborne homecare-associated infections. This will enable the identification of the contributing risk factors, and the development of effective controls. Full article

Enterobacteria that commonly inhabit marine environments have a great impact on human health. In this study, enterobacteria isolated from seawater in the Upper Gulf of Thailand were identified and characterized. Seawater from nine sampling sites along the Upper Gulf of Thailand contained presumptive enterobacteria that ranged from 0.22 ± 0.44 to 17.00 ± 3.97 CFU/mL. The 101 strains belonged to seven species in which Klebsiella pneumoniae was the majority (47.5% of strains). The highest prevalence was resistant to ampicillin (76.2%) and ticarcillin (72.3%), respectively, whereas none was resistant to imipenem. Forty-five antibiotic resistance patterns were observed and 33.7% exhibited multidrug resistance, emphasizing the concern about public health. Three β-lactamase genes, including ampC, blaSHV, and blaTEM, were detected at the frequencies of 47.5%, 21.8%, and 11.9%, respectively. Six virulence genes, including csgD, uge, kfu, eaeA, magA, and LTI, were detected at the frequencies of 37.6%, 31.7%, 19.8%, 16.8%, 12.9%, and 5.9%, respectively. The condition of 4% NaCl downregulated the expression of the kfu and uge genes. The 67.3% and 63.4% of strains synthesized silver nanoparticles ranging between 3.04 ± 0.64 and 20.64 ± 0.95 μg/mL and gold nanoparticles ranging between 7.77 ± 0.45 and 57.57 ± 8.00 μg/mL, respectively. Full article

The mechanism of bacterial community assembly has been the hot spot in the field of microbial ecology and it is difficult to quantitatively estimate the influences of different ecological processes. Here, a total of 23 pairs of planktonic and sedimentary samples were collected from five lakes in Wuhan, China. significant higher α-diversity (p < 0.001) and β-diversity (p < 0.001) of bacterial communities were observed in sediment than those in water. Some phylum had linear relationships with the comprehensive TSI (TSIc) by regression analysis. Non-metric multidimensional scaling (NMDS) and redundancy analysis (RDA) revealed that the depth of water, NO₃⁻-N, NH₄⁺-N, PO4³⁻, and COD_cr were the key environmental variables in planktonic bacterial communities, whereas in sediment they were the depth, NO₃⁻-N, and NH₄⁺-N. Furthermore, variation partitioning analysis (VPA) showed that spatial and environmental factors could only explain 40.2% and 27.9% of the variation in planktonic and sedimentary bacterial communities, respectively. More importantly, null model analysis suggested that different assembly mechanisms were found between in water and in sediment with the fact that planktonic bacterial community assembly was mainly driven by dispersal limitation process whereas variable selection process played a vital role in that of sediment. Full article

The gut microbiota (GM) compositions of aquatic animals are influenced by microorganisms in ambient water and sediment. However, the extent to which environmental microorganisms can affect shrimp GM composition is unknown. We analyzed the impact of water and sediment microorganisms on the GM of Macrobrachium rosenbergii at different growth stages. We collected water, sediment, and M. rosenbergii gut samples at the early, middle, and late stages of an M. rosenbergii culture and analyzed the microbiota composition. The shrimps’ body weight differed significantly between sampling stages. The shrimp GM composition differed significantly from that of the ambient water and sediment, and these differences were remarkably stronger than those between the shrimp GM at different sampling times and in different ponds. The proportion of sediment bacteria in the shrimp GM was approximately three times higher than that of water bacteria, which changed among ponds and over sampling time. These results provide important reference information for a deeper understanding of the impact of environmental microorganisms on the composition of shrimp GM. Moreover, the results also provide reference information for increasing the production of shrimp culture as well as ensuring a good health status of the culture. Full article