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

Isolation of Heavy Metal-Tolerant and Anti-Phytopathogenic Plant Growth-Promoting Bacteria from Soils

In this study, multifunctional soil bacteria, which can promote plant development, resist heavy metals, exhibit anti-phytopathogenic action against plant diseaes, and produce extracellular enzymes, were isolated to improve the effectiveness of phytoremediation techniques. In order to isolate multifunctional soil bacteria, a variety of soil samples with diverse characteristics were used as sources for isolation. To look into the diversity and structural traits of the bacterial communities, we conducted amplicon sequencing of the 16S rRNA gene on five types of soils and predicted functional genes using Tax4Fun2. The isolated bacteria were evaluated for their multifunctional capabilities, including heavy metal tolerance, plant growth promotion, anti-phytopathogenic activity, and extracellular enzyme activity. The genes related to plant growth promotion and anti-phytopathogenic activity were most abundant in forest and paddy soils. Burkholderia sp. FZ3 and FZ5 demonstrated excellent heavy metal resistance (≤ 1 mM Cd and ≤ 10 mM Zn), Pantoea sp. FC24 exhibited the highest protease activity (24.90 μmol tyrosine·g-DCW-1·h-1), and Enterobacter sp. PC20 showed superior plant growth promotion, especially in siderophore production. The multifunctional bacteria isolated using traditional methods included three strains (FC24, FZ3, and FZ5) from the forest and one strain (PC20) from paddy field soil. These results indicate that, for the isolation of beneficial soil microorganisms, utilizing target gene information obtained from isolation sources and subsequently exploring target microorganisms is a valuable strategy.

Plastic debris mediates bacterial community coalescence by breaking dispersal limitation in the sediments of a large river

Plastic debris has recently been proposed as a novel habitat for bacterial colonization, which can raise perturbations in bacterial ecology after burial in riverine sediments. However, community coalescence, as a prevalent process involving the interrelationships of multiple communities and their surrounding environments, has been rarely discussed to reveal the impact of the plastisphere on sedimentary bacterial community. This study analyzed the bacterial community in plastic debris and sediment along the Nujiang River, elucidating the role of the plastisphere in mediating community coalescence in sediments. Our results demonstrated that the plastisphere and sedimentary bacterial communities exhibited distinct biogeography along the river (r = 0.694, p < 0.01). Based on overlapped taxa and SourceTracker, the extent of coalescence between adjacent communities was in following orders: plastic-plastic (0.589) > plastic-sediment (0.561) > sediment-sediment (0.496), indicating the plastisphere promoted bacterial community coalescence along the river. Flow velocity and geographic distance were the major factors driving the plastisphere changes, suggesting that the plastisphere were vulnerable to dispersal. The null model and the neutral model provided additional support for the higher immigration ability of the plastisphere to overcome dispersal limitation, highlighting the potential importance of the plastisphere in community coalescence. Network analysis indicated the critical role of keystone species (Proteobacteria, Bacteroidetes, and Gemmatimonadetes) in mediating the coalescence between sedimentary bacterial community and the plastisphere. In summary, the plastisphere could mediate the coalescence of bacterial communities by overcoming dispersal limitation, which provides new perspectives on the plastisphere altering bacterial ecology in riverine sediments.

Submersed macrophytes Vallisneria natans and Vallisneria spinulosa improve water quality and affect microbial communities in sediment and water columns

Healthy aquatic ecosystems are essential for human beings. However, anthropogenic activities severely worsen water quality. In this study, using assembling mesocosms, we developed an efficient and easy-to-handle method to monitor the water quality by measuring the electrical conductivity (EC) of water. Our data demonstrate that the growth of two submersed macrophytes, Vallisnerianatans and Vallisneria spinulosa, improves water quality by decreasing EC. Furthermore, using high-throughput DNA sequencing, we analyzed the microbial community abundance and structure in sediment and water columns with or without plant growth. We generated 33,775 amplicon sequence variants from 69 samples of four sediment groups (BkM, CtM, VnR, and VsR) and three water column sample groups (CtW, VnW, and VsW). The results show that the relative abundance of bacteria was higher in the sediment than in the water column. Moreover, the diversity and composition of microbiomes were altered by Vallisneria spp. growth, and the α-diversity of the microbial communities decreased due to submersed macrophytes in both the sediment and water columns. The β-diversity of the microbial communities also varied significantly with or without Vallisneria spp. growth for both the sediment and water columns.

Impact of Anthropogenic Activities on Microbial Community Structure in Riverbed Sediments of East Kazakhstan

Heavy metal (HMe) pollution in regions with mining and metallurgy activities is known to be a serious environmental problem worldwide. Hydrological processes contribute to the dissemination of HMes (drainage, precipitation, flow rate). The aim of the present study is to investigate the microbial community structure in ten river sediments sampled in different regions of East Kazakhstan, which are contaminated with HMes. The overall degree of sediment contamination with HMes (Cr, Cu, Zn, Pb, and Cd) was assessed using the pollution index Zc, which ranged from 0.43 to 21.6, with the highest in Ridder City (Zc = 21.6) and Ust-Kamenogorsk City, 0.8 km below the dam of the hydroelectric power station (Zc = 19.6). The tested samples considerably differed in organic matter, total carbon, nitrogen, and phosphorus content, as well as in the abundance of HMe-related functional gene families and antibiotic resistance genes. Metagenomic analysis of benthic microorganisms showed the prevalence of Proteobacteria (88.84-97.61%) and Actinobacteria (1.21-5.98%) at the phylum level in all samples. At the class level, Actinobacteria (21.68-57.48%), Betaproteobacteria (19.38-41.17%), and Alphaproteobacteria (10.0-39.78%) were the most common among the classified reads. To the best of our knowledge, this is the first study on the metagenomic characteristics of benthic microbial communities exposed to chronic HMe pressure in different regions of East Kazakhstan.

Assembly processes of bacterial and fungal communities in metal(loid)s smelter soil

There are few studies on concurrent bacterial and fungal community assembly processes that govern the metal(loid)s biogeochemical cycles at smelters. Here, a systematic investigation combined geochemical characterization, co-occurrence patterns, and assembly mechanisms of bacterial and fungal communities inhabiting soils around an abandoned arsenic smelter. Acidobacteriota, Actinobacteriota, Chloroflexi, and Pseudomonadota were dominant in bacterial communities, whereas Ascomycota and Basidiomycota dominated fungal communities. The random forest model indicated the bioavailable fractions of Fe (9.58%) were the main positive factor driving the beta diversity of bacterial communities, and the total N (8.09%) was the main negative factor for fungal communities. Microbe-contaminant interactions demonstrate the positive impact of the bioavailable fractions of certain metal(loid)s on bacteria (Comamonadaceae and Rhodocyclaceae) and fungi (Meruliaceae and Pleosporaceae). The fungal co-occurrence networks exhibited more connectivity and complexity than the bacterial networks. The keystone taxa were identified in bacterial (including Diplorickettsiaceae, norank_o_Candidatus_Woesebacteria, norank_o_norank_c_AT-s3-28, norank_o_norank_c_bacteriap25, and Phycisphaeraceae) and fungal (including Biatriosporaceae, Ganodermataceae, Peniophoraceae, Phaeosphaeriaceae, Polyporaceae, Teichosporaceae, Trichomeriaceae, Wrightoporiaceae, and Xylariaceae) communities. Meanwhile, community assembly analysis revealed that deterministic processes dominated the microbial community assemblies, which were highly impacted by pH, total N, and total and bioavailable metal(loid) content. This study provides helpful information to develop bioremediation strategies for the mitigation of metal(loid)s-polluted soils.

Nitrogen removal and microbial mechanisms in a novel tubular bioreactor-enhanced floating treatment wetland for the treatment of high nitrate river water

A novel tubular bioreactor-enhanced floating treatment wetland (TB-EFTW) was developed for the in situ treatment of high nitrate river water. When compared with the enhanced floating treatment wetland (EFTW), the TB-EFTW system achieved 30% higher total nitrogen removal efficiency. Further, the average TN level of the TB-EFTW effluent was below the Grade IV requirement (1.5 mg/L) specified in Chinese standard (GB3838-2002). Microbial analysis revealed that both aerobic and anoxic denitrifying bacteria coexisted in the new system. The relative abundance of aerobic and anoxic denitrifiers were 42.69% and 22% at the middle and end of the tubular bioreactor (TB), respectively. It is reasonable to assume that effective nitrogen removal can mainly be attributed to the addition of solid carbon source and the spatial difference in DO distribution (oxic-anoxic areas in sequence) inside the TB. The initial investment cost and operating costs associated with the TB-EFTW system are approximately 14,000 and 3500 yuan per 1000 m3 river water, respectively. Considering its low cost, minimal maintenance requirements, and effective nitrogen removal, this newly developed system can be regarded as a promising technology for treating high nitrate river water. PRACTITIONER POINTS: A novel TB-EFTW system was developed to upgrade traditional in situ treatment techniques. The TB-EFTW could achieve 30% higher nitrogen removal efficiency than EFTWs. Both aerobic and anoxic denitrifying bacteria coexisted in the system. The system shows better technical and economic performance compared with routine techniques.

Application of Polyaluminium Chloride Coagulant in Urban River Water Treatment Influenced the Microbial Community in River Sediment

Polyaluminium chloride (PAC) has been widely used as a chemical coagulant in water treatment. However, little is known about the impact of PAC performance on the microbial community in sediments. In this study, the archaeal, bacterial, and fungal communities in urban river sediments with and without PAC treatment were investigated. Prokaryotic diversity decreased at the PAC addition site (A2) and increased along with the river flow (from A3 to A4), while eukaryotic diversity was the opposite. The abundance of core microbiota showed a similar trend. For example, the dominant Proteobacteria presented the highest relative abundance in A1 (26.8%) and the lowest in A2 (15.3%), followed by A3 (17.5%) and A4 (23.0%). In contrast, Rozellomycota was more dominant in A2 (56.6%) and A3 (58.1%) than in A1 (6.2%) and A4 (16.3%). Salinity, total dissolved solids, and metal contents were identified as the key physicochemical factors affecting the assembly of core microorganisms. The predicted functions of archaea and fungi were mainly divided into methane cycling and saprotrophic nutrition, respectively, while bacterial function was more diversified. The above findings are helpful to enhance our understanding of microorganism response to PAC and have significance for water treatment within the framework of microecology.