Microbial Community Profile and Water Quality in a Protected Area of the Caatinga Biome

Dynamics of Bacterioplankton Communities during Wet and Dry Seasons in the Danjiangkou Reservoir in Hubei, China

Water quality is directly linked to drinking water safety for millions of people receiving the water. The Danjiangkou Reservoir is the main water source for the Middle Route of the South-to-North Water Diversion Project (MR-SNWDP), located in the vicinity of Henan and Hubei provinces in China. Aquatic microorganisms are key indicators of biologically assessing and monitoring the water quality of the reservoir as they are sensitive to environmental and water quality changes. This study aimed to investigate the spatiotemporal variations in bacterioplankton communities during wet (April) and dry (October) seasons at eight monitoring points in Hanku reservoir and five monitoring points in Danku reservoir. Each time point had three replicates, labeled as wet season Hanku (WH), wet season Danku (WD), dry season Hanku (DH), and dry season Danku (DD) of Danjiangkou Reservoir in 2021. High-throughput sequencing (Illumina PE250) of the 16S rRNA gene was performed, and alpha (ACE and Shannon) and beta (PCoA and NDMS) diversity indices were analyzed. The results showed that the dry season (DH and DD) had more diverse bacterioplankton communities compared to the wet season (WH and WD). Proteobacteria, Actinobacteria, and Firmicutes were the most abundant phyla, and Acinetobacter, Exiguobacterium, and Planomicrobium were abundant in the wet season, while polynucleobacter was abundant in the dry season. The functional prediction of metabolic pathways revealed six major functions including carbohydrate metabolism, membrane transport, amino acid metabolism, signal transduction, and energy metabolism. Redundancy analysis showed that environmental parameters greatly affected bacterioplankton diversity during the dry season compared to the wet season. The findings suggest that seasonality has a significant impact on bacterioplankton communities, and the dry season has more diverse communities influenced by environmental parameters. Further, the relatively high abundance of certain bacteria such as Acinetobacter deteriorated the water quality during the wet season compared to the dry season. Our findings have significant implications for water resource management in China, and other countries facing similar challenges. However, further investigations are required to elucidate the role of environmental parameters in influencing bacterioplankton diversity in order to devise potential strategies for improving water quality management in the reservoir.

Spatiotemporal correlations between water quality and microbial community of typical inflow river into Taihu Lake, China

Changxing River, which is a typical inflow river into Taihu Lake and occurs severe algae invasion, is selected to study the effect of different pollution sources on the water quality and ecological system. Four types of pollution sources, including the estuary of Taihu Lake, discharge outlets of urban wastewater treatment plants, stormwater outlets, and nonpoint source agricultural drainage areas, were chosen, and next-generation sequencing and multivariate statistical analyses were used to characterize the microbial communities and reveal their relationship with water physicochemical properties. The results showed that ammonia nitrogen (NH₄⁺-N), total nitrogen (TN), and total phosphorus (TP) were the main pollutants in Changxing River, especially at stormwater outlets. At the same time, the diversity of microbial communities was the highest in the summer, and dominant microbes included Proteobacteria (40.9%), Bacteroidetes (21.0%), and Euryarchaeota (6.1%). The results of BIOENV analysis showed that the major seasonal differences in the diversity of microbial community of Changxing river were explained by the combination of water temperature (T), air pressure (P), TP, and COD_Mn. From the perspective of different pollution types, relative abundances of Microcystis and Nostocaceae at the estuary of Taihu Lake were correlated positively with dissolved oxygen (DO) and pH, and relative abundances of Pseudomonas and Arcobacter were correlated positively with concentrations of TN and nitrate nitrogen (NO₃^--N) at stormwater outlets. This study provided a reference for the impact of pollution types on river microbial ecosystem under complex hydrological conditions and guidance for the selection of restoration techniques for polluted rivers entering the important lake.

The removal of selenite and cadmium by immobilized biospheres: Efficiency, mechanisms and bacterial community

In this study, a complex bacterial consortium was enriched from a typical Pb-Zn mine area and immobilized by sodium alginate to form biospheres, which were used for treatment of selenite (Se(IV))- and cadmium (Cd(II))-containing wastewater without external carbon source. Batch experiments showed that the maximum Se(IV) removal efficiency was 92.36% under the optimal conditions of an initial pH of 5, dosage of 5 g/L, initial Se(IV) concentration of 7.9 mg/L and reaction time of 168 h. Subsequently, more than 99% of 11.2 mg/L Cd(II) was removed by the biospheres within 10 h. Physicochemical characterization showed that reduction and adsorption were the main mechanisms for Se(IV) and Cd(II) removal, respectively. During the removal process, selenium and CdSe nanoparticles were formed. Bacterial community analysis showed the dominant bacterial genera changed after treatment of Se(IV)- and Cd(II)-containing wastewater. Additionally, 16S rRNA gene function prediction results showed that amino acid transport, carbohydrate transport, ion transport and metabolism were the dominant gene functions. The present study provides a potential way for the biological treatment of Se(IV)- and Cd(II)-containing wastewater using immobilized biospheres without external carbon source in short-term.

Long-term effects of grazing on the biological, chemical, and physical soil properties of the Caatinga biome

Soil degradation is a global issue that affects both plant productivity and human life. Intensive grazing practices can accelerate this process, mainly due to rapid removal of biomass from the soil surface. However, the long-term effects of grazing on biological, chemical, and physical properties remain poorly understood, particularly in tropical drylands, such as the Caatinga biome. Our aim was to evaluate the soil properties and combine both culture-dependent and -independent analyses to assess metabolic activity and bacterial community structure. We collected samples (0-20 cm) of three different types of soil in the Caatinga biome: secondary Caatinga forest (NC), grazing exclusion (GE), and degraded areas by overgrazing (OG). We sought to investigate how grazing affects soil properties to determine the effectiveness of grazing exclusion in the restoration of soil fertility/functions. Redundancy analysis demonstrated NC were positively correlated with organic carbon (λ = 0.18, p = 0.0012) and total nitrogen (λ = 0.16, p = 0.0011), while OG was correlated with harmful soil parameters such as Na⁺ (λ = 0.08, p = 0.0400), electric conductivity (λ = 0.13, p = 0.0060) and exchangeable acidity (λ = 0.11, p = 0.0030). In addition, GE showed lower aluminum content and saturation, reducing these harmful parameters by 48 % and 34 %, respectively. Also, GE showed the highest values for the β-glucosidase (63.62 mg ρ-nitrophenol kg^-1 h^-1) and arylsulfatase (5.8 mg ρ-nitrophenol kg^-1 h^-1) activities. Changes in bacterial community structure were significant (p = 0.0096), with a higher difference comparing GE and OG (p = 0.0135). The GE area showed 20 % more phosphate solubilizers than OG, but there were no differences for siderophores production. All isolates were halotolerant and had at least 60 % nitrogen fixers. Our findings indicate that while soil recovery is slow, with grazing-exclusion areas presenting 18 years of implantation, it seems to improve in subsequent years. Finally, our results provide evidence that microbe-based technologies can mitigate soil degradation in the Caatinga biome.

Eukaryotic communities in coastal water from Shenzhen in South China

Eukaryotic microorganisms are ubiquitous in the marine environment, and have a wide variety of ecosystem functions. Shenzhen is one of the most developed cities in South China, but the eukaryotic communities in the water along its coastlines remain poorly understood. The study applied 18S rRNA gene ITS (internal transcribed spacer) sequencing to identify the eukaryotic community from twenty sites of Shenzhen coast water. The alpha-diversity of the samples between these sites were significantly different, and the seawater of eastern coast had higher alpha-diversity compared to that of the western coast. The abundance of Chlorophyta was notably higher in the seawater of western coast, but Picozoa was relatively depleted. Specifically, Cryptocaryon, Pseudovorticella, and Cyclotella were significantly higher in the water of western coast, while Guinardia, Minutocellus, and Amoebophrya were increased in eastern samples. The spatially variations of eukaryotic microorganism community in the seawater of Shenzhen coast were associated with the water quality. The results have important significance for the understanding of coastal eukaryotic community, their interaction network, and build a foundation for future management and protection of coastal water quality.

High-throughput sequencing reveals the spatial distribution variability of microbial community in coastal waters in Shenzhen

Seashore habitats are located between terrestrial and marine ecosystems, which are a hotspot for anthropogenic impacts. Shenzhen is one of the most developed cities in south China, but the microbial functions of its coastal ecosystems remain poorly understood. The study applied 16S rRNA gene sequencing methods to identify the bacterial community from twenty sites of Shenzhen inshore waters. The microbial structure of the samples between eastern Shenzhen and western Shenzhen seashores is notably different, suggesting the spatial variability. Proteobacteria, Cyanobacteria, Actinobacteria, and Bacteroidetes were dominant phyla in the community, and the relative abundance of Bacteroidetes was significantly higher in eastern seashores. Specifically, samples from western Shenzhen contained much more Prochlorococcus, while Synechococcus was more abundant in eastern samples. Moreover, the metabolism of terpenoids and polyketides, and transport and catabolism were significantly more abundant in eastern samples, while antibiotic-resistant pathways were enriched in western samples. The results have important significance to understand bacterial ecosystem of coastal water and promote water quality management and protection activity in Shenzhen. This study can also help developing an optimal strategy for the green economy development and the policy planning of Guangdong-Hong Kong-Macao Greater Bay Area.

Adverse effects of levofloxacin and oxytetracycline on aquatic microbial communities

The widespread use of levofloxacin (LEV) and oxytetracycline (OTC) in hospitals and farms inevitably contributes to water pollution through waste disposal processes, municipal wastewater treatment, and manure application to farmlands, which adversely affects aquatic microorganisms. Here, we evaluated the toxicity of LEV and OTC to cyanobacteria and eukaryotic algae monocultures and freshwater microcosms. Three test cyanobacteria were inhibited by both LEV and OTC at all examined concentrations. The growth of the eukaryotic organisms C. vulgaris and Monoraphidium sp. was only inhibited by high concentrations of OTC ranging from 1000 to 10,000 μg/L; however, they were less sensitive to LEV and OTC than cyanobacteria. In the aquatic microcosms, 5 μg/L of LEV and OTC did not affect the alpha diversity of prokaryotic and eukaryotic communities or the composition of the eukaryotic microbial communities after 14 d of exposure. However, this concentration of LEV and OTC significantly changed the prokaryotic microbial community structure at the genus level, and different antibiotics affected the prokaryotic microbial community differently, suggesting that different antibiotics affect prokaryotes through different molecular mechanisms, thereby leading to differences in prokaryotic microbial growth patterns. Moreover, the changes in the prokaryotic microbial community composition suggested that low antibiotic concentrations in water could disturb prokaryotic microbial communities and cause ecological risks.

Stochastic determination of the spatial variation of potentially pathogenic bacteria communities in a large subtropical river

Understanding the composition and assembly mechanism of waterborne pathogen is essential for preventing the pathogenic infection and protecting the human health. Here, based on 16S rRNA sequencing, we investigated the composition and spatial variation of potentially pathogenic bacteria from different sections of the Pearl River, the most important source of water for human in Southern China. The results showed that the potential pathogen communities consisted of 6 phyla and 64 genera, covering 11 categories of potential pathogens mainly involving animal parasites or symbionts (AniP), human pathogens all (HumPA), and intracellular parasites (IntCelP). Proteobacteria (75.87%) and Chlamydiae (20.56%) were dominant at the phylum level, and Acinetobacter (35.01%) and Roseomonas (8.24%) were dominant at the genus level. Multivariate analysis showed that the potential pathogenic bacterial community was significantly different among the four sections in the Pearl River. Both physicochemical factors (e.g., NO₃-N, and suspended solids) and land use (e.g., urban land and forest) significantly shaped the pathogen community structure. However, spatial effects contributed more to the variation of pathogen community based on variation partitioning and path analysis. Null model based normalized stochasticity ratio analysis further indicated that the stochastic process rather than deterministic process dominated the assembly mechanisms by controlling the spatial patterns of potential pathogens. In conclusion, high-throughput sequencing shows great potential for monitoring the potential pathogens, and provided more comprehensive information on the potentially pathogenic community. Our study highlighted the importance of considering the influences of dispersal-related processes in future risk assessments for the prevention and control of pathogenic bacteria.

Spatial Variation in Bacterioplankton Communities in the Pearl River, South China: Impacts of Land Use and Physicochemical Factors

River ecosystems are critical for human and environmental health, with bacterioplankton playing a vital role in biogeochemical cycles. Unveiling the spatial patterns of bacterioplankton communities in relation to environmental factors is important for understanding the processes of microbial variation and functional maintenance. However, our understanding of the correlations among bacterioplankton communities, physicochemical factors, and land use, especially in large rivers affected by intensive anthropogenic activities, remains relatively poor. Here, we investigated the bacterioplankton communities in July 2018 in three main tributaries of the Pearl River, i.e., Beijiang, Xijiang, and Pearl River Delta, based on 16S rRNA high-throughput sequencing. Results showed that the most dominant phyla, Proteobacteria, Actinobacteria, Cyanobacteria, and Planctomycetes accounted for 33.75%, 22.15%, 11.65%, and 10.48% of the total abundance, respectively. The bacterioplankton communities showed remarkable differences among the three tributaries in terms of composition, structure, diversity, and predictive functional profiles. Mantel and partial Mantel tests revealed that the bacterioplankton communities were affected by physicochemical variables (p < 0.01) and land use (p < 0.01). Redundancy analysis identified specific conductivity, dissolved oxygen, agricultural land, ammonium, urban land, and water transparency as the dominant environmental factors influencing the bacterioplankton communities in the Pearl River. Variation partitioning analysis indicated that both physicochemical factors and land use had direct effects on the bacterioplankton community, and that land use may also shape bacterioplankton communities through indirect effects of physicochemical factors on riverine ecosystems. This study provides fundamental information on the diversity, spatial patterns, and influencing factors of bacterioplankton communities in the Pearl River, which should enhance our understanding of how such communities change in response to environmental gradients and anthropogenic activities.

Remote sensing, isotopic composition and metagenomics analyses revealed Doce River ore plume reached the southern Abrolhos Bank Reefs

On November 5th, 2015, the Fundão dam rupture released >50 million m³ of ore tailings into the Doce River, Minas Gerais State, Brazil. The huge volume of mud spread along the river and reached the sea, 17 days after the disaster, in Regência, Espírito Santo State (ES). In 2018, after three years of the disaster, the impacts of the ore tailings in the marine environment are still unclear. This study aims to investigate possible short-term impacts in marine biodiversity caused by the ore tailings' mud over the reef ecosystems that are closest to the disaster area: i.e. recently discovered reefs in the southern Abrolhos Bank. A remote sensing surveillance including winds, sea surface temperature, total suspended material and watercolor (MODIS Aqua data) indicated that the iron tailings plume reached the southern portion of Abrolhos Bank on June 16th, 2016. Subsequently, to obtain further evidence of the presence of the tailings in the coral reefs, water samples were collected in a gradient spanning from the river estuary to the reefs in southern Abrolhos Bank, we also analyzed the isotopic and microbial composition of the samples, as well as the reef benthic composition. Despite no clues of negative impact on benthic (coral) communities, isotopic analysis confirmed the presence of the plume over the reefs area. This study serves as a baseline for future long-term impact assessments of the health of coral reefs in the Abrolhos Bank.

Metagenomic analysis of drinking water samples collected from treatment plants of Hyderabad City and Mehran University Employees Cooperative Housing Society

The quality assessment of water, supplied to the end user, is an essential part to assess the physical, chemical, and biological status of water, which impacts on human health. For the quality assessment of drinking water treatment plants and distribution systems of Hyderabad City and Mehran University of Engineering and Technology, Jamshoro, Pakistan, 13 surface drinking water samples were collected from three treatment plants, two of Hyderabad City, including WASA treatment plant and its distribution system (n = 5), Hala Nakka treatment plant and its distribution system (n = 6), and Mehran University Employees Cooperative Housing Society (MUECHS) treatment plant and its distribution system (n = 2). Physicochemical parameters of all drinking water samples were in the range compared to EPA and WHO guidelines, except in L-12 sample. Notably, no free-chlorine was detected in all samples. In metagenomics analysis, targeting V3-V4 hypervariable region of 16S rRNA gene, in QIIME2 environment, high bacterial prevalence was observed in all samples. On average, 348 OTUs were observed per sample. Among all samples, treated water sample from the Hala Nakka Treatment Plant (HNTR) was the most diverse sample in bacterial composition (Shannon 7.51 and Simpsons reciprocal indices 0.98). Overall, Proteobacteria, Bacteroidetes, Cyanobacteria, Verrucomicrobia, and Actinobacteria were the five most abundant phyla (relative abundances of 43.6, 37.9, 8.5, 2.5, and 2.4 percent, respectively). Notably, Cyanobacteria are well-known toxin producers which effect the human, and animal health. At genus level, Flavobacterium (4.86%) and Aquirestis (3.77%) were the most abundant genera. Functional predictions, based on 16S rRNA gene by PICRUSt, predicted 6909 KEGG orthologies, relating to 245 KEGG pathways. Among the predicted pathways of KEGG orthologies, pathways to human infections were also found. In conclusion, this study gave a deep insight into bacterial contamination in drinking water samples of Hyderabad City and MUECHS treatment plants and water quality status in Hyderabad and Mehran University of Engineering and Technology.

Streptophyta and Acetic Acid Bacteria Succession Promoted by Brass in Slow Sand Filter System Schmutzdeckes

Macro- and microorganism activities are important for the effectiveness of the slow sand filtration (SSF), where native microorganisms remove contaminants mainly by substrate competition, predation, and antagonism. The aim of the present study was to evaluate the addition of the oligodynamic metals iron, copper, and brass, inserted separately into SSF to enhance pollutant removal in water samples. Four laboratory-scale SSFs were built and tested: control, iron, copper, and brass. Water analysis included physicochemical evaluation, total and fecal coliform quantification. An analysis on microbial communities in the SSFs schmutzdecke was achieved by using 16S rRNA amplification, the Illumina MiSeq platform, and the QIIME bioinformatics software. The results demonstrated that inorganic and organic contaminants such as coliforms were removed up to 90%. The addition of metals had no significant effect (p > 0.05) on the other parameters. The microbial community analysis demonstrated different compositions of the SSF with brass-influent, where the eukaryote Streptophyta was predominant (31.4%), followed by the acetic acid bacteria Gluconobacter (24.6%), and Acetobacteraceae (7.7%), these genera were absent in the other SSF treatments. In conclusion, the use of a SSF system can be a low cost alternative to reduce microbial contamination in water and thus reduce gastrointestinal diseases in rural areas.

Insights on the freshwater microbiomes metabolic changes associated with the world's largest mining disaster

To evaluate the impacts of the Fundão tailings dam failure (Minas Gerais, Brazil) on water quality of the Doce River, we analyzed metagenomics and physicochemical parameters during the month of the disaster and again 6 and 10 months after the disaster. To compare dam conditions before and after the failure, we performed a meta-analysis of physicochemical data from a public database. Immediately after the failure, suspended particulate matter (SPM) in the Doce River was 225-1877 mg L^-1. Turbidity and dissolved aluminum and iron concentrations were extremely high, whereas dissolved oxygen was below Brazilian legislation norm (<5 mg L^-1) in several locations. Six months later, physicochemical values were below thresholds set by Brazilian guidelines (e.g., SPM = 8-166 mg L^-1). Short-term impacts on microbial communities included an increase in Actinobacteria and Bacteroidetes and gene sequences related to microbial virulence, motility, respiration, membrane transport, iron and nitrogen metabolism, suggesting changes in microbial metabolic profiles. The 11 recovered partial genomes from metagenomes (MAGs) had genes related to Fe cycle and metal resistance.

Metagenomic analysis of soil and freshwater from zoo agricultural area with organic fertilization

Microbial communities drive biogeochemical cycles in agricultural areas by decomposing organic materials and converting essential nutrients. Organic amendments improve soil quality by increasing the load of essential nutrients and enhancing the productivity. Additionally, fresh water used for irrigation can affect soil quality of agricultural soils, mainly due to the presence of microbial contaminants and pathogens. In this study, we investigated how microbial communities in irrigation water might contribute to the microbial diversity and function of soil. Whole-metagenomic sequencing approaches were used to investigate the taxonomic and the functional profiles of microbial communities present in fresh water used for irrigation, and in soil from a vegetable crop, which received fertilization with organic compost made from animal carcasses. The taxonomic analysis revealed that the most abundant genera were Polynucleobacter (~8% relative abundance) and Bacillus (~10%) in fresh water and soil from the vegetable crop, respectively. Low abundance (0.38%) of cyanobacterial groups were identified. Based on functional gene prediction, denitrification appears to be an important process in the soil community analysed here. Conversely, genes for nitrogen fixation were abundant in freshwater, indicating that the N-fixation plays a crucial role in this particular ecosystem. Moreover, pathogenicity islands, antibiotic resistance and potential virulence related genes were identified in both samples, but no toxigenic genes were detected. This study provides a better understanding of the community structure of an area under strong agricultural activity with regular irrigation and fertilization with an organic compost made from animal carcasses. Additionally, the use of a metagenomic approach to investigate fresh water quality proved to be a relevant method to evaluate its use in an agricultural ecosystem.

Ecogenomics and Taxonomy of Cyanobacteria Phylum

Cyanobacteria are major contributors to global biogeochemical cycles. The genetic diversity among Cyanobacteria enables them to thrive across many habitats, although only a few studies have analyzed the association of phylogenomic clades to specific environmental niches. In this study, we adopted an ecogenomics strategy with the aim to delineate ecological niche preferences of Cyanobacteria and integrate them to the genomic taxonomy of these bacteria. First, an appropriate phylogenomic framework was established using a set of genomic taxonomy signatures (including a tree based on conserved gene sequences, genome-to-genome distance, and average amino acid identity) to analyse ninety-nine publicly available cyanobacterial genomes. Next, the relative abundances of these genomes were determined throughout diverse global marine and freshwater ecosystems, using metagenomic data sets. The whole-genome-based taxonomy of the ninety-nine genomes allowed us to identify 57 (of which 28 are new genera) and 87 (of which 32 are new species) different cyanobacterial genera and species, respectively. The ecogenomic analysis allowed the distinction of three major ecological groups of Cyanobacteria (named as i. Low Temperature; ii. Low Temperature Copiotroph; and iii. High Temperature Oligotroph) that were coherently linked to the genomic taxonomy. This work establishes a new taxonomic framework for Cyanobacteria in the light of genomic taxonomy and ecogenomic approaches.

Diversity of Microbial Carbohydrate-Active enZYmes (CAZYmes) Associated with Freshwater and Soil Samples from Caatinga Biome

Semi-arid and arid areas occupy about 33% of terrestrial ecosystems. However, little information is available about microbial diversity in the semi-arid Caatinga, which represents a unique biome that extends to about 11% of the Brazilian territory and is home to extraordinary diversity and high endemism level of species. In this study, we characterized the diversity of microbial genes associated with biomass conversion (carbohydrate-active enzymes, or so-called CAZYmes) in soil and freshwater of the Caatinga. Our results showed distinct CAZYme profiles in the soil and freshwater samples. Glycoside hydrolases and glycosyltransferases were the most abundant CAZYme families, with glycoside hydrolases more dominant in soil (∼44%) and glycosyltransferases more abundant in freshwater (∼50%). The abundances of individual glycoside hydrolase, glycosyltransferase, and carbohydrate-binding module subfamilies varied widely between soil and water samples. A predominance of glycoside hydrolases was observed in soil, and a higher contribution of enzymes involved in carbohydrate biosynthesis was observed in freshwater. The main taxa associated with the CAZYme sequences were Planctomycetia (relative abundance in soil, 29%) and Alphaproteobacteria (relative abundance in freshwater, 27%). Approximately 5-7% of CAZYme sequences showed low similarity with sequences deposited in non-redundant databases, suggesting putative homologues. Our findings represent a first attempt to describe specific microbial CAZYme profiles for environmental samples. Characterizing these enzyme groups associated with the conversion of carbohydrates in nature will improve our understanding of the significant roles of enzymes in the carbon cycle. We identified a CAZYme signature that can be used to discriminate between soil and freshwater samples, and this signature may be related to the microbial species adapted to the habitat. The data show the potential ecological roles of the CAZYme repertoire and associated biotechnological applications.