Bacterial, archaeal, and fungal community responses to acid mine drainage-laden pollution in a rice paddy soil ecosystem

Effects of acid mine drainage and sediment contamination on soil bacterial communities, interaction patterns, and functions in alkaline desert grassland

Acid mine drainage and sediments (AMD-Sed) contamination pose serious ecological and environmental problems. This study investigated the geochemical parameters and bacterial communities in the sediment layer (A) and buried soil layer (B) of desert grassland contaminated with AMD-Sed and compared them to an uncontaminated control soil layer (CK). The results showed that soil pH was significantly lower and iron, sulfur, and electroconductivity levels were significantly higher in the B layer compared to CK. A and B were dominated by Proteobacteria and Actinobacteriota, while CK was dominated by Firmicutes and Bacteroidota. The pH, Fe, S, and potentially toxic elements (PTEs) gradients were key influences on bacterial community variability, with AMD contamination characterization factors (pH, Fe, and S) explaining 48.6 % of bacterial community variation. A bacterial co-occurrence network analysis showed that AMD-Sed contamination significantly affected topological properties, reduced network complexity and stability, and increased the vulnerability of desert grassland soil ecosystems. In addition, AMD-Sed contamination reduced C/N-cycle functioning in B, but increased S-cycle functioning. The results highlight the effects of AMD-Sed contamination on soil bacterial communities and ecological functions in desert grassland and provide a reference basis for the management and restoration of desert grassland ecosystems in their later stages.

Amendments affect the community assembly and co-occurrence network of microorganisms in Cd and Pb tailings of the Eucalyptus camaldulensis rhizosphere

Mining tailings containing large amounts of Pb and Cd cause severe regional ecosystem pollution. Soil microorganisms play a regulatory role in the restoration of degraded ecosystems. The remediation of heavy metal-contaminated tailings with amendments and economically valuable Eucalyptus camaldulensis is a research hotspot due to its cost-effectiveness and sustainability. However, the succession and co-occurrence patterns of these microbial communities in this context remain unclear. Tailing samples of five kinds of Cd and Pb were collected in E. camaldulensis restoration models. Physicochemical properties, the proportions of different Cd and Pb forms, microbial community structure, and the co-occurrence network of rhizosphere tailings during different restoration process (organic bacterial manure, organic manure, inorganic fertilizer, bacterial agent) were considered. Organic and organic bacterial manures significantly increased pH, cation exchange capacity, and the proportion of residual Pb. Still, there was a significant decrease in the proportion of reducible Pb. The changes in microbial communities were related to physicochemical properties and the types of amendments. Organic and organic bacterium manures decreased the relative abundance of oligotrophic groups and increased the relative abundance of syntrophic groups. Inorganic fertilizers and bacterial agents decreased the relative abundance of saprophytic fungi. B. subtilis would play a better role in the environment improved by organic manure, increasing the relative abundance of beneficial microorganism and reducing the relative abundance of pathogenic microorganism. pH, cation exchange capacity, and the proportion of different forms of Pb were the main factors affecting the bacterial and fungi variation. All four amendments transformed the main critical groups of the microbial network structure from acidophilus and pathogenic microorganisms to beneficial microorganisms. Heavy metal-resistant microorganisms, stress-resistant microorganisms, beneficial microorganisms that promote nutrient cycling, and copiotrophic groups have become critical to building stable rhizosphere microbial communities. The topological properties and stability of the rhizosphere co-occurrence network were also enhanced. Adding organic and organic bacterium manures combined with E. camaldulensis to repair Cd and Pb tailings improved (1) pH and cation exchange capacity, (2) reduced the biological toxicity of Pb, (3) enhanced the stability of microbial networks, and (4) improved ecological network relationships. These positive changes are conducive to the restoration of the ecological functions of tailings.

Microbial dysbiosis in roots and rhizosphere of grapevines experiencing decline is associated with active metabolic functions

When grapevine decline, characterized by a premature decrease in vigor and yield and sometimes plant death, cannot be explained by pathological or physiological diseases, one may inquire whether the microbiological status of the soil is responsible. Previous studies have shown that the composition and structure of bacterial and fungal microbial communities in inter-row soil are affected in areas displaying vine decline, compared to areas with non-declining vines within the same plot. A more comprehensive analysis was conducted in one such plot. Although soil chemical parameters could not directly explain these differences, the declining vines presented lower vigor, yield, berry quality, and petiole mineral content than those in non-declining vines. The bacterial and fungal microbiome of the root endosphere, rhizosphere, and different horizons of the bulk soil were explored through enzymatic, metabolic diversity, and metabarcoding analysis in both areas. Despite the lower microbial diversity and richness in symptomatic roots and soil, higher microbial activity and enrichment of potentially both beneficial bacteria and pathogenic fungi were found in the declining area. Path modeling analysis linked the root microbial activity to berry quality, suggesting a determinant role of root microbiome in the berry mineral content. Furthermore, certain fungal and bacterial taxa were correlated with predicted metabolic pathways and metabolic processes assessed with Eco-Plates. These results unexpectedly revealed active microbial profiles in the belowground compartments associated with stressed vines, highlighting the interest of exploring the functional microbiota of plants, and more specifically roots and rhizosphere, under stressed conditions.

Unlocking water potential in drylands: Quicklime and fly ash enhance soil microbiome structure, ecological networks and function in acid mine drainage water-irrigated agriculture

In water-stressed regions, treated acid mine drainage (AMD) water for irrigated agriculture is a potential solution to address freshwater scarcity. However, a significant knowledge gap exists on the short and long-term effects of treated AMD water on soil health. This study used high-throughput Illumina sequencing and predictive metagenomic profiling to investigate the impact of untreated AMD (AMD), quicklime- (A1Q and A2Q) and quicklime and fly ash-treated AMD water (AFQ) irrigation on soil bacterial diversity, co-occurrence networks and function. Results showed that untreated AMD water significantly increased soil acidity, electrical conductivity (EC), sulfate (SO42-), and heavy metals (HM), including reduced microbial diversity, disrupted interaction networks, and functional capacity. pH, EC, Cu, and Pb were identified as key environmental factors shaping soil microbial diversity and structure. Predominantly, Pseudomonas, Ralstonia picketti, Methylotenera KB913035, Brevundimonas vesicularis, and Methylobacteriumoryzae, known for their adaptability to acidic conditions and metal resistance, were abundant in AMD soils. However, soils irrigated with treated AMD water exhibited significantly reduced acidity (pH > 6.5), HM and SO42- levels, with an enrichment of a balanced bacterial taxa associated with diverse functions related to soil health and agricultural productivity. These taxa included Sphingomonas, Pseudoxanthomonas, Achromobacter, Microbacterium, Rhodobacter, Clostridium, Massillia, Rhizobium, Paenibacillus, and Hyphomicrobium. Moreover, treated AMD water contributed to higher connectivity and balance within soil bacterial co-occurrence networks compared to untreated AMD water. These results show that quicklime/fly ash treatments can help lessen impacts of AMD water on soil microbiome and health, suggesting its potential for irrigated agriculture in water-scarce regions.

Deep groundwater irrigation altered microbial community and increased anammox and methane oxidation in paddy wetlands of Sanjiang Plain, China

The over-utilizing of nitrogen fertilizers in paddy wetlands potentially threatens to the surrounding waterbody, and a deep understanding of the community and function of microorganisms is crucial for paddy non-point source pollution control. In this study, top soil samples (0-15 cm) of paddy wetlands under groundwater's irrigation at different depths (H1: 6.8 m, H2: 13.7 m, H3: 14.8 m, H4: 15.6 m, H5: 17.0 m, and H6: 17.8 m) were collected to investigate microbial community and function differences and their interrelation with soil properties. Results suggested some soil factor differences for groundwater's irrigation at different depths. Deep-groundwater's irrigation (H2-H6) was beneficial to the accumulation of various electron acceptors. Nitrifying-bacteria Ellin6067 had high abundance under deep groundwater irrigation, which was consistent with its diverse metabolic capacity. Meanwhile, denitrifying bacteria had diverse distribution patterns. Iron-reducing bacteria Geobacter was abundant in H1, and Anaeromyxobacter was abundant under deep groundwater irrigation; both species could participate in Fe-anammox. Furthermore, Geobacter could perform dissimilatory nitrate reduction to ammonia using divalent iron and provide substrate supply for anammox. Intrasporangium and norank_f_Gemmatimonadacea had good chromium- and vanadium-reducting potentials and could promote the occurrence of anammox. Low abundances of methanotrophs Methylocystis and norank_f_Methyloligellaceae were associated with the relatively anoxic environment of paddy wetlands, and the presence of aerobic methane oxidation was favorable for in-situ methane abatement. Moisture, pH, and TP had crucial effects on microbial community under phylum- and genus-levels. Microorganisms under shallow groundwater irrigation were highly sensitive to environmental changes, and Fe-anammox, nitrification, and methane oxidation were favorable under deep groundwater irrigation. This study highlights the importance of comprehensively revealing the microbial community and function of paddy wetlands under groundwater's irrigation and reveals the underlying function of indigenous microorganisms in agricultural non-point pollution control and greenhouse gas abatement.

Association between host nitrogen absorption and root-associated microbial community in field-grown wheat

Plant roots and rhizosphere soils assemble diverse microbial communities, and these root-associated microbiomes profoundly influence host development. Modern wheat has given rise to numerous cultivars for its wide range of ecological adaptations and commercial uses. Variations in nitrogen uptake by different wheat cultivars are widely observed in production practices. However, little is known about the composition and structure of the root-associated microbiota in different wheat cultivars, and it is not sure whether root-associated microbial communities are relevant in host nitrogen absorption. Therefore, there is an urgent need for systematic assessment of root-associated microbial communities and their association with host nitrogen absorption in field-grown wheat. Here, we investigated the root-associated microbial community composition, structure, and keystone taxa in wheat cultivars with different nitrogen absorption characteristics at different stages and their relationships with edaphic variables and host nitrogen uptake. Our results indicated that cultivar nitrogen absorption characteristics strongly interacted with bacterial and archaeal communities in the roots and edaphic physicochemical factors. The impact of host cultivar identity, developmental stage, and spatial niche on bacterial and archaeal community structure and network complexity increased progressively from rhizosphere soils to roots. The root microbial community had a significant direct effect on plant nitrogen absorption, while plant nitrogen absorption and soil temperature also significantly influenced root microbial community structure. The cultivar with higher nitrogen absorption at the jointing stage tended to cooperate with root microbial community to facilitate their own nitrogen absorption. Our work provides important information for further wheat microbiome manipulation to influence host nitrogen absorption. KEY POINTS: • Wheat cultivar and developmental stage affected microbiome structure and network. • The root microbial community strongly interacted with plant nitrogen absorption. • High nitrogen absorption cultivar tended to cooperate with root microbiome.

Microbial community diversity and potential functionality in response to dam construction along the Three Gorge Reservoir, China

River and reservoir bacterial communities are the most basic part of river biomes and ecosystem structure, and play an important role in river biological processes. Yet, it remains unclear how highly regulated dam reservoirs affect both soil and sediment bacterial communities. A temporal distribution pattern of bacterial communities was investigated using Illumina MiSeq sequencing in a transition section of the Three Gorges Reservoir (TGR). In total, 106,682 features belong to the bacteria kingdom, encompassing 95 phyla, 228 classes, 514 orders, 871 families, 1959 genera, and 3,053 species. With water level regulation, Shannon diversity index, and observed species differed significantly, with no significant difference in Simpson evenness. Both in the high water level period (October) and the low water level period (June), Proteobacteria, Acidobacteri, and Chloroflexi were the most abundant phyla. Whereas, based on PCA plots and Circos plot, the microbial community structure has changed significantly. LEfSe method was used to identify the classified bacterial taxa with significant abundance differences between the low water level and high water level periods. KOs (KEGG Orthology) pathway enrichment analysis were conducted to investigate functional and related metabolic pathways in groups. To some extent, it can be inferred that water level regulation affects community growth by affecting the metabolism of the microbial community.

Remediation Agents Drive Bacterial Community in a Cd-Contaminated Soil

Soil remediation agents (SRAs) such as biochar and hydroxyapatite (HAP) have shown a promising prospect in in situ soil remediation programs and safe crop production. However, the effects of SRAs on soil microbial communities still remain unclear, particularly under field conditions. Here, a field case study was conducted to compare the effects of biochar and HAP on soil bacterial communities in a slightly Cd-contaminated farmland grown with sweet sorghum of different planting densities. We found that both biochar and HAP decreased the diversity and richness of soil bacteria, but they differently altered bacterial community structure. Biochar decreased Chao1 (-7.3%), Observed_species (-8.6%), and Shannon indexes (-1.3%), and HAP caused Shannon (-2.0%) and Simpson indexes (-0.1%) to decline. The relative abundance (RA) of some specific taxa and marker species was differently changed by biochar and HAP. Overall, sweet sorghum cultivation did not significantly alter soil bacterial diversity and richness but caused changes in the RA of some taxa. Some significant correlations were observed between soil properties and bacterial abundance. In conclusion, soil remediation with biochar and HAP caused alterations in soil bacterial communities. Our findings help to understand the ecological impacts of SRAs in soil remediation programs.

Risk assessment and microbial community structure in agricultural soils contaminated by vanadium from stone coal mining

High health risks of vanadium (V) released by the mining of vanadium titanomagnetite (VTM) have been widely recognized, but little is known about the risks and microbial community responses of V pollution as a consequence of the stone coal mining (SCM), another important resource for V mining. In this study, the topsoils and the profile soils were collected from the agricultural soils around a typical SCM in Hunan Province, China, with the investigation of ecological, health risks and microbial community structures. The results showed that ∼97.6% of sampling sites had levels of total V exceeding the Chinese National standard (i.e., 130 mg/kg), and up to 41.1% of V speciation in the topsoils was pentavalent vanadium (V(V)). Meanwhile, the proportions of HQ > 1 and 0.6-1 in the topsoils were ∼8.3% and ∼31.0% respectively, indicating that V might pose a non-carcinogenic risk to children. In addition, the microbial community varied between the topsoils and the profile soils. Both sulfur-oxidizing bacteria (e.g. Thiobacillus, MND1, Ignavibacterium) and sulfate-reducing bacteria (e.g. Desulfatiglans, GOUTB8, GOUTA6) might have been involved in V(V) reductive detoxification. This study helps better understand the pollution and associated risks of V in the soils of SCM and provides a potential strategy for bioremediation of the V-contaminated environment.

Massively parallel single-cell genomics of microbiomes in rice paddies

Plant growth-promoting microbes (PGPMs) have attracted increasing attention because they may be useful in increasing crop yield in a low-input and sustainable manner to ensure food security. Previous studies have attempted to understand the principles underlying the rhizosphere ecology and interactions between plants and PGPMs using ribosomal RNA sequencing, metagenomic sequencing, and genome-resolved metagenomics; however, these approaches do not provide comprehensive genomic information for individual species and do not facilitate detailed analyses of plant-microbe interactions. In the present study, we developed a pipeline to analyze the genomic diversity of the rice rhizosphere microbiome at single-cell resolution. We isolated microbial cells from paddy soil and determined their genomic sequences by using massively parallel whole-genome amplification in microfluidic-generated gel capsules. We successfully obtained 3,237 single-amplified genomes in a single experiment, and these genomic sequences provided insights into microbial functions in the paddy ecosystem. Our approach offers a promising platform for gaining novel insights into the roles of microbes in the rice rhizomicrobiome and to develop microbial technologies for improved and sustainable rice production.

Molecular Characterization of Distinct Fungal Communities in the Soil of a Rare Earth Mining Area

The exploitation of ion-absorbed rare earth elements (REEs) has caused serious ecological destruction and environmental pollution. Effects on soil fungal structure and diversity exerted by mining activities are usually ignored, although fungus is one of the most important components in soil ecosystems. In the present research, quantitative polymerase chain reaction (qPCR) and high-throughput Illumina MiSeq sequencing were conducted to characterize fungal community composition and structure in soil of a rare earth mining area after in situ leaching. Statistical analyses, network, and FUNGuild were used to conduct in-depth analyses. Ascomycota, Basidiomycota, and Glomeromycota were the most abundant phyla in the mining soils. Fungal community structures were stable after leaching practice, but nutrition contents (organic matter, TC, and TN) significantly and positively contributed to fungal abundances and diversities. Saprotrophs in phyla Ascomycota and Basidiomycota were the dominant fungal trophic mode, and they played critical roles in nutrient cycling, transformation processes, and reducing REE toxicity. Symbiotrophs of phyla Glomeromycota contributed to soil aggregation and slowing down nutrient losses after in situ leaching practice. In addition, fungi could regulate the interactions between species to resist the harsh environment of REE toxicity or ammonium caused by in situ leaching practice.

Heavy metal(loid)s shape the soil bacterial community and functional genes of desert grassland in a gold mining area in the semi-arid region

Gold mining can create serious environmental problems, such as soil pollution by heavy metal (loid)s. In this study, we assessed the ecological risk of Hatu gold mining activities and synchronously investigated the bacterial community structure, distribution of soil nutrient-element cycling genes (CNPS) and heavy metal resistance genes (MRG) in adjacent desert grassland soil. The study area was above the moderate risk level, with the ecological risk index (RI) of each sampling site greater than 150. Arsenic, mercury and copper were the main pollutants. Proteobacteria, Actinobacteria and Firmicutes dominated the phyla of the bacterial communities. Species turnover rather than nestedness accounted for the significant differences in community structure among various regions in the mining area. In addition, the bioavailable heavy metal (loid)s (AHM) content had a strong correlation with beta diversity and species turnover of the bacterial community (p < 0.05). No clear difference was found in the total abundance of CNPS genes among various functional regions, but eight specific functional genes were identified from downwind grasslands with lower pollution levels. Among the MRGs, Hg MRG had the highest average total relative abundance, followed by Cu, Co/Zn/Cd and As. The mercury resistance gene subtype hgcAB was positively related to the diversity of the bacterial community, and the bacterial community of grassland soil showed congruency with the MRGs in the Hatu mining area. Total Hg (THg) showed the highest influence affecting the bacterial community, while NH₄⁺-N had the greatest effect on CNPS genes and MRGs. These results highlighted the role of heavy metal (loid)s in shaping the bacterial community and functional genes in arid and semiarid desert grassland soil in gold mining regions.

Responsive change of crop-specific soil bacterial community to cadmium in farmlands surrounding mine area of Southeast China

In arable soils co-influenced by mining and farming, soil bacteria significantly affect metal (Cadmium, Cd) bioavailability and accumulation. To reveal the soil microecology response under this co-influence, three intersection areas (cornfield, vegetable field, and paddy field) were investigated. With a similar nutrient condition, the soils showed varied Cd levels (0.31-7.70 mg/kg), which was negatively related to the distance from mining water flow. Different soils showed varied microbial community structures, which were dominated by Chloroflexi (19.64-24.82%), Actinobacteria (15.49-31.96%), Acidobacteriota (9.46-20.31%), and Proteobacteria (11.88-14.57%) phyla. A strong correlation was observed between functional microbial taxon (e. g. Acidobacteriota), soil physicochemical properties, and Cd contents. The relative abundance of tolerant bacteria including Vicinamibacteraceae, Knoellia, Ardenticatenales, Lysobacter, etc. elevated with the increase of Cd, which contributed to the enrichment of heavy metal resistance genes (HRGs) and integration genes (intlI), thus enhancing the resistance to heavy metal pollution. Cd content rather than crop species was identified as the dominant factor that influenced the bacterial community. Nevertheless, the peculiar agrotype of the paddy field contributed to its higher HRGs and intlI abundance. These results provided fundamental information about the crop-specific physiochemical-bacterial interaction, which was helpful to evaluate agricultural environmental risk around the intersection of farmland and pollution sources.

Untangling microbial diversity and assembly patterns in rare earth element mine drainage in South China

Ion-adsorption rare earth element (REE) deposits are the main reservoirs of REEs worldwide, and are widely exploited in South China. Microbial diversity is essential for maintaining the performance and function of mining ecosystems. Investigating the ecological patterns underlying the REE mine microbiome is essential to understand ecosystem responses to environmental changes and to improve the bioremediation of mining areas. We applied 16S rRNA and ITS gene sequence analyses to investigate the composition characteristics of prokaryotic (bacteria, archaea) and fungal communities in a river impacted by REE acid mine drainage (REE-AMD). The river formed a unique micro-ecosystem, including the main prokaryotic taxa of Proteobacteria, Acidobacteria, Crenarchaeota, and Euryarchaeota, as well as the main fungal taxa of Ascomycota, Basidiomycota, and Chytridiomycota. Analysis of microbial diversity showed that, unlike prokaryotic communities that responded drastically to pollution disturbances, fungal communities were less affected by REE-AMD, but fluctuated significantly in different seasons. Ecological network analysis revealed that fungal communities have lower connectivity and centrality, and higher modularity than prokaryotic networks, indicating that fungal communities have more stable network structures. The introduction of REE-AMD mainly reduced the complexity of the community network and the number of keystone species, while the proportion of negative prokaryotic-fungal associations in the network increased. Ecological process analysis revealed that, compared to the importance of environmental selection for prokaryotes, stochastic processes might have contributed primarily to fungal communities in REE mining areas. These findings confirm that the different assembly mechanisms of prokaryotic and fungal communities are key to the differences in their responses to environmental perturbations. The findings also provide the first insights into microbiota assembly patterns in REE-AMD and important ecological knowledge for the formation and development of microbial communities in REE mining areas.

Spatial and temporal variations of metal fractions in paddy soil flooding with acid mine drainage

Environmental release of acid mine drainage (AMD) poses a potential threat to the environment and human health due to its high content of heavy metals. The impact of AMD flooding on unpolluted soil leads to serious pollution over time via a complex process, related to the geochemical behavior of toxic metals that so far has only been partially investigated. Here, a soil column study was conducted to investigate the migration of Cu and Cd fractions in unpolluted paddy soil following treatment with AMD collected from the Dabaoshan Mining area. Tessier's sequential extraction was performed to fractionate the metals at various depths over time. After 160 days of experimental flooding, the soil pH stabilized at 2.52 at a column depth of 5 cm. The fractions of Cu and Cd that were highly mobile increased significantly during AMD flooding. For Cd, the latter already occurred on day 67. At a depth of 20 cm, the total content of Cu maximally increased from initially 26.89 mg kg^-1 to 696.96 mg kg^-1 on day 160, while the content of Cd maximally increased from 0.22 mg kg^-1 to 391.30 mg kg^-1 on day 67. Reduced partition index analysis conformed that the mobility of both Cu and Cd significantly increased in contaminated soil during continuous AMD flooding. Scanning electron microscopy coupled with energy dispersive spectroscopy (SEM-EDS) identified a changed distribution of the elements in the soil, with Fe appearing to have aggregated. The correlation analysis between Cu and Cd in pore water and in different fractions in the soil's solid phase identified a dynamic distribution of these metals in certain geochemical components during their migration. The results of this study contribute to a scientific foundation to describe the geochemical behavior of heavy metals in soil subject to AMD flooding.

Antibiotics and microbial community-induced antibiotic-resistant genes distribution in soil and sediment in the eastern coastline of China

The health risk of antibiotic-resistant genes (ARGs) has been a global concern, while the report on occurrence and prevalence of ARGs in coastal zone is relatively scarce. This study investigated typical ARGs in soil and sediment in coastal line of eastern China and assessed its relationship with antibiotics and heavy metals as well as microbial community. Results showed that eight ARGs were all detected in the samples, and β-lactam resistance gene blaTEM reached the highest absolute abundance (6.28 × 10⁷ ~ 6.48 × 10⁸ copies/g) and relative abundance (2.3 × 10^-2 copies/16S rRNA) among samples. Amoxicillin and tetracycline were most frequently detected with the average concentration of 2.28 μg/kg and 3.48 μg/kg, respectively. Cr and Zn were found to be most abundant heavy metals with average value of 82.1 and 59.1 mg/kg, respectively. Proteobacteria, Campilobacterota, Bacteroidota, and Firmicutes were dominant phyla in most samples, while bacterial community varied significantly among samples. Redundancy analyses (RDA) showed that microbial community and antibiotics (amoxicillin and tetracycline) were driving factors of ARGs distribution, while heavy metals were not significantly correlated with ARGs. This study is helpful to understand the fate of ARGs in coastal zone.

Use of Metagenomic Whole Genome Shotgun Sequencing Data in Taxonomic Assignment of Dipterygium glaucum Rhizosphere and Surrounding Bulk Soil Microbiomes, and Their Response to Watering

The metagenomic whole genome shotgun sequencing (mWGS) approach was used to detect signatures of the rhizosphere microbiomes of Dipterygium glaucum and surrounding bulk soil microbiomes, and to detect differential microbial responses due to watering. Preliminary results reflect the reliability of the experiment and the rationality of grouping microbiomes. Based on the abundance of non-redundant genes, bacterial genomes showed the highest level, followed by Archaeal and Eukaryotic genomes, then, the least abundant viruses. Overall results indicate that most members of bacteria have a higher abundance/relative abundance (AB/RA) pattern in the rhizosphere towards plant growth promotion, while members of eukaryota have a higher pattern in bulk soil, most likely acting as pathogens. The results also indicate the contribution of mycorrhiza (genus Rhizophagus) in mediating complex mutualistic associations between soil microbes (either beneficial or harmful) and plant roots. Some of these symbiotic relationships involve microbes of different domains responding differentially to plant root exudates. Among these are included the bacterial genus Burkholderia and eukaryotic genus Trichoderma, which have antagonistic activities against the eukaryotic genus Fusarium. Another example involves Ochrobactrum phage POA1180, its bacterial host and plant roots. One of the major challenges in plant nutrition involves other microbes that manipulate nitrogen levels in the soil. Among these are the microbes that perform contraversal actions of nitrogen fixation (the methanogen Euryarchaeota) and ammonia oxidation (Crenarchaeota). The net nitrogen level in the soil is originally based on the AB/RA of these microbes and partially on the environmental condition. Watering seems to influence the AB/RA of a large number of soil microbes, where drought-sensitive microbes (members of phyla Acidobacteria and Gemmatimonadetes) showed an increased AB/RA pattern after watering, while others (Burkholderia and Trichoderma) seem to be among microbes assisting plants to withstand abiotic stresses. This study sheds light on the efficient use of mWGS in the taxonomic assignment of soil microbes and in their response to watering. It also provides new avenues for improving biotic and abiotic resistance in domestic plant germplasm via the manipulation of soil microbes.

Evaluating the remediation potential of MgFe2O4-montmorillonite and its co-application with biochar on heavy metal-contaminated soils

In this work, a novel and efficient magnesium ferrite-modified montmorillonite (MgFe2O4-MMT) compound was prepared. MgFe2O4-MMT and biochar were mixed at 0:10, 1:9, 3:7, 4:6, and 10:0 w/w combinations and were used for heavy metal immobilization in soil polluted with multiple heavy metals. MgFe2O4-MMT can significantly increase soil alkalinity, and it exhibited the most optimal effect in immobilization of heavy metals in soil. The amounts of Cd, Pb, Cu, and Zn that were extracted by the toxicity characteristic leaching procedure (TCLP) decreased by 58.4%, 50.3%, 42.9%, and 24.7%, respectively. MgFe2O4-MMT can immobilize heavy metals through electrostatic interactions and cation exchange processes. Although, the immobilization of potentially toxic elements by MgFe2O4-MMT and biochar was inferior to that by MgFe2O4-MMT. The combined application of MgFe2O4-MMT and biochar dramatically increased the diversity and richness of the soil bacterial community. The Chao1 index for M3B7 treatment group was 1.7 and 1.2 times higher than that for the control and MgFe2O4-MMT treatment groups, respectively. The combination of biochar and MgFe2O4-MMT might be a cost-effective and ecological remediation approach for mild Pb and Cd contamination.

Driving Factors of Microbial Community Abundance and Structure in Typical Forest Soils of Sanjiang Plain, Northeast China

Until recently, a comprehensive evaluation of the environmental drivers on the abundance and structure of the microbial community in typical forest soils has not been thoroughly conducted. In this study, the typical forest soils (Mongolian oak (Quercus mongolica) soil, MOS; white birch (Betula platyphylla) soil, WBS; and white poplar (Populus davidiana) soil, WPS) in the Sanjiang Plain were selected to ascertain the differences and the major environmental factors driving soil microbial community abundance and structure. Results indicated that differences existed in the abundance and structure of the bacterial, archaeal, and fungal community. Co-occurrence network analysis showed that the bacterial and fungal networks were more complex than those of archaeal networks. Unclassified Acidobacteria and unclassified Pyrinomonadaceae were the keystone taxa in the bacterial networks, while Pleotrichocladium and Leotia were the keystone taxa in the fungal networks. Among all environmental factors, pH, SOM, and total N exhibited dominant roles in affecting the abundance of bacteria, archaea, and fungi. The redundancy analysis (RDA) showed that pH was the vital environmental factor responsible for driving the structure of the bacterial, archaeal, and fungal community.

HPLC and high-throughput sequencing revealed higher tea-leaves quality, soil fertility and microbial community diversity in ancient tea plantations: compared with modern tea plantations

BACKGROUND

Ancient tea plantations with an age over 100 years still reserved at Mengku Town in Lincang Region of Yunan Province, China. However, the characteristic of soil chemicophysical properties and microbial ecosystem in the ancient tea plantations and their correlation with tea-leaves chemical components remained unclear. Tea-leaves chemical components including free amino acids, phenolic compounds and purine alkaloids collected from modern and ancient tea plantations in five geographic sites (i.e. Bingdao, Baqishan, Banuo, Dongguo and Jiulong) were determined by high performance liquid chromatography (HPLC), while their soil microbial community structure was analyzed by high-throughput sequencing, respectively. Additionally, soil microbial quantity and chemicophysical properties including pH, cation exchange capacity (CEC), soil organic matter (SOM), soil organic carbon (SOC), total nitrogen (TN), total phosphorus (TP), total potassium (TK), alkali-hydrolyzable nitrogen (AN), available phosphorous (AP) and available potassium (AK) were determined in modern and ancient tea plantations.

RESULTS

Tea-leaves chemical components, soil chemicophysical properties and microbial community structures including bacterial and fungal community abundance and diversity evaluated by Chao 1 and Shannon varied with geographic location and tea plantation type. Ancient tea plantations were observed to possess significantly (P < 0.05) higher free amino acids, gallic acid, caffeine and epigallocatechin (EGC) in tea-leaves, as well as soil fertility. The bacterial community structure kept stable, while fungal community abundance and diversity significantly (P < 0.05) increased in ancient tea plantation because of higher soil fertility and lower pH. The long-term plantation in natural cultivation way might significantly (P < 0.05) improve the abundances of Nitrospirota, Methylomirabilota, Ascomycota and Mortierellomycota phyla.

CONCLUSIONS

Due to the natural cultivation way, the ancient tea plantations still maintained relatively higher soil fertility and soil microbial ecosystem, which contributed to the sustainable development of tea-leaves with higher quality.

The symbiotic system of sulfate-reducing bacteria and clay-sized fraction of purplish soil strengthens cadmium fixation through iron-bearing minerals

The microbe-clay mineral system is widely known to reduce the fluidity of heavy metals through biomineralization, thus mitigating soil pollution stemming from heavy metals. Here, we investigated the effect of mineral distinction on the solidification of cadmium (Cd) using sulfate-reducing bacteria (SRB) to construct symbiotic systems with purplish soil, clay-sized fraction of purple soil (Clay_-csp), clay particles of amorphous iron (Fe) oxide (Clay_-ox), clay particles removing crystalline Fe oxide (Clay_-CBD), and residues of Clay_-CBD treated by hydrochloric acid (Clay_-HCl). The difference in Cd morphology among purplish soil, Clay_-csp, and Clay_-ox indicated that the fixation of Cd in soil was largely determined by Fe oxides. The content of Cd in Clay_-csp decreased by 66.7% after the removal of amorphous Fe, confirming that clay easily adsorbed infinitive Fe oxides in purple soil. In the system of SRB and Clay_-ox, carbonate-bound Cd (F2) decreased by 14.85% and residual Cd (F5) increased by 14% from the retardation to late decline phase, eventually forming iron-sulfur (Fe-S) compounds. Based on the correlation analyses of Cd and Fe in amorphous-bound state and Fe-manganese (Mn) oxidation state in simulation experiments, it is demonstrated that Fe-Mn oxides control the behavior of Cd in soil clay, and SRB-mediated Fe-bearing minerals promote the transformation of Cd from activated to stable state.

Effect of rapeseed straw-derived biochar on soil bacterial community structure at tillering stage of Oryza Sativa

Numerous studies have reported the dynamics of microbes when biochar was applied, whereas the information on the alterations of bacterial community after application of rapeseed straw-derived biochar is limited. A pot experiment with two rapeseed straw-derived biochar application treatments (with biochar application at the rate of 200 g/pot, C1) and (without biochar application, 0 g/pot, C0) was conducted. No significant differences were observed in the number of operational taxonomic units, observed species, Shannon index, Simpson index, Chao1, ACE, and phylogenetic diversity whole tree between the C1 and C0 treatments. Taxonomic analysis at the genus level showed that the abundances of Gracilibacter, Lentimicrobium, unidentified Rikenellaceae, Hydrogenophaga, and Bacillus were higher in the C1 compared to the C0 treatment, while Candidatus Solibacter, Candidatus Koribacter, and Lutispora abundances were found to be higher abundant in the C0 compared to the C1 treatment. Obvious clusters were observed between the C1 and C0 in both principal component analysis and non-metric multidimensional scaling. These results indicate that soil bacterial community was altered after rapeseed straw-derived biochar was applied.

Effects of rare earth elements on bacteria in rhizosphere, root, phyllosphere and leaf of soil-rice ecosystem

The effects of rare earth mining on rice biomass, rare earth element (REE) content and bacterial community structure was studied through pot experiment. The research shows that the REE content in rice roots, shoots and grains was significantly positive correlated with that in soil, and the dry weight of rice roots, shoots and grains was highly correlated with soil physical and chemical properties, nutrient elements and REE contents; The exploitation of rare earth minerals inhibited a-diversity of endophytic bacteria in rhizosphere, root, phyllosphere and leaf of rice, significantly reduced the abundance index, OTU number, Chao, Ace index and also significantly reduced the diversity index-Shannon index, and also reduced uniformity index: Pielou's evenness index, which caused β-diversity of bacteria to be quite different. The exploitation of rare earth minerals reduces the diversity of bacteria, but forms dominant bacteria, such as Burkholderia, Bacillus, Buttiauxella, Acinetobacter, Bradyrhizobium, Candida koribacter, which can degrade the pollutants formed by exploitation of rare earth minerals, alleviate the compound pollution of rare earth and ammonia nitrogen, and also has the function of fixing nitrogen and resisting rare earth stress; The content of soil available phosphorus in no-mining area is lower, and the dominant bacteria of Pantoea formed in such soil, which has the function of improving soil phosphorus availability. Rare earth elements and physical and chemical properties of soil affect the community structure of bacteria in rhizosphere and phyllosphere of rice, promote the parallel movement of some bacteria in rhizosphere, root, phyllosphere and leaf of rice, promote the construction of community structure of bacteria in rhizosphere and phyllosphere of rice, give full play to the growth promoting function of Endophytes, and promote the growth of rice. The results showed that the exploitation of rare earth minerals has formed the dominant endophytic bacteria of rice and ensured the yield of rice in the mining area, however, the mining of mineral resources causes the compound pollution of rare earth and ammonia nitrogen, which makes REE content of rice in mining area significantly higher than that in non-mining area, and the excessive rare earth element may enter the human body through the food chain and affect human health, so the food security in the REE mining area deserves more attention.

The response of bacterial communities to V and Cr and novel reducing bacteria near a vanadium‑titanium magnetite refinery

Soil contamination with multiple heavy metals has always been a pressing issue, but little attention has been given to V and Cr and their chemical fractions' impacts on microorganisms because Cr₂O₃ usually occurs as an associated mineral in vanadium mines. To investigate this issue, samples (N1-N6) less affected by anthropogenic activities were selected for microbial analysis. The area near the refinery was heavily contaminated according to the PLI (pollution load index). Actinobacteriota, Proteobacteria, and Chloroflexi were the dominant phyla in the soil. The diversity of bacteria was positively influenced by V and Cr and negatively influenced by pH, while the abundance was positively correlated with soil nutrients. Interestingly, the influence of heavy metals in the residual fraction on the microbial community structure and functional metabolism was higher than that in the oxidizable fraction, which may be due to the relatively low heavy metal valence of the oxidizable fraction, suggesting that low valence binding forms of multivalence elements have little effect on microorganisms in the soil. Ultimately, two strains with great efficiency in reducing V and Cr were screened, and co-occurrence network characteristics with significant positive interactions suggested that Bacillus can coordinate community structure in the same niche. This research will help to explore the bioavailability of heavy metals and further achieve the bioremediation of heavy metal contamination in soil.

Addition of organic acids to acid mine drainage polluted wetland sediment leads to microbial community structure and functional changes and improved water quality

Acid mine drainage (AMD) is a serious environmental problem worldwide that requires efficient and sustainable remediation technologies including the use of biological mechanisms. A key challenge for AMD bioremediation is to provide optimal conditions for microbial-mediated immobilisation of trace metals. Although organic carbon and oxygen can enhance treatment efficiency, the effect on microbial communities is unclear. In this study, surface sediments from a natural wetland with proven efficiency for AMD bioremediation were artificially exposed to oxygen (by aeration) and/or organic carbon (in the form of mixed organic acids) and incubated under laboratory conditions. In addition to measuring changes in water chemistry, a metagenomics approach was used to determine changes in sediment bacterial, archaeal and fungal community structure, and functional gene abundance. The addition of organic carbon produced major changes in the abundance of microorganisms related to iron and sulfur metabolism (including Geobacter and Pelobacter) and increased levels of particulate metals via sulfate reduction. Aeration resulted in an increase in Sideroxydans abundance but no significant changes in metal chemistry were observed. The study concludes that the utilisation of organic carbon by microorganisms is more important for achieving efficient AMD treatment than the availability of oxygen, yet the combination of oxygen with organic carbon addition did not inhibit the improvements to water quality.

Performance and mechanism of sulfamethoxazole removal in different bioelectrochemical technology-integrated constructed wetlands

Sulfamethoxazole (SMX) has a high concentration and detection frequency in aquatic environments due to the poor removal efficiency of traditional biological treatment processes. Bioelectrochemical technology-integrated constructed wetlands (CWs) have great potential for SMX removal; however, the process of SMX removal in different bioelectrochemical technology-integrated CWs (microbial fuel cell (MFC) and direct current (EC)) remains unclear. To address this, we examined the mechanism of SMX removal in MFCCW and ECCW. The results revealed that the SMX removal efficiency can reach 96.0 ± 2.4% in the ECCW and 97.2 ± 2.2% in the MFCCW. The enhancement of MFC for SMX removal in CW was slightly better than that in direct current (p > 0.05). It was found that the adsorption process of SMX in the substrate promoted by EC was more enhanced than that by MFC. Furthermore, bioelectrochemical technology improved plant activity, including root and enzymatic (superoxide dismutase, peroxidase, and catalase) activities, and fluorescence parameters (photochemical quenching coefficient, non-photochemical quenching coefficient, and quantum efficiency of PS II). Significant differences were found between CW and ECCW (p < 0.05), while no significant differences were found between CW and MFCCW (p > 0.05). The microbial activity and abundance in CW were improved by bioelectrochemical technology, and the microbial community structure was optimised to be simpler and more stable. However, EC tended to promote microbial and plant activity in CW, whereas MFC tended to optimise the microbial community and improve the tightness and stability of the module. The enhanced difference might also account for the changes in the SMX degradation pathway. 4-aminobenzenesulfonic acid (TP174), 3-amino-5-methylisoxazole (TP99) and 5-methylisoxazole (TP84) were all common products in the three reactors, whereas TP99 underwent further ring-opening in MFCCW and TP174 underwent further hydrolysis in ECCW. This study provided an important reference for the targeted regulation of plants and microorganisms in constructed wetlands via different bioelectrochemistry to enhance characteristic pollutants degradation.

Variation in archaeal and bacterial community profiles and their functional metabolic predictions under the influence of pure and mixed fertilizers in paddy soil

Impact of environmental perturbations i.e., nitrogen (N), phosphorus (P), potassium (K), and rice straw (Rs) on the dynamics of soil bacterial and archaeal communities are multifactor dependent and seeks a contemporary approach to study underlying mechanisms. The current study investigates the effect of pure and mixed fertilizers on soil physicochemical properties, the microbial community structure, and their functional metabolic predictions. It involved amendments with distinct combinations of N as C(H₂N)₂O, P and K as KH₂PO₄, K as KCl, and Rs in paddy soil microcosms with concentrations common in rice fields agriculture. Soil pH, electrical conductivity (EC), total carbon (TC), total nitrogen (TN), organic matter (OM), available K (AK), and total extractable P (TEP) were evaluated. To comprehend community variation and functional predictions, 16S rRNA-based high throughput sequencing (HTS) and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) were employed, respectively. Our findings showed enhanced community richness and diversity in all amendments compared to control. Proteobacteria, Actinobacteria, and Firmicutes were dominant bacterial phyla. Regarding relative abundance, Chloroflexi, Bacteroidetes, and Verrucomicrobia showed positive while Actinobacteria, Acidobacteria, and Gemmatimonadetes showed negative trends compared to controls. Thaumarchaeota and Euryarchaeota were dominant archaeal phyla and exhibited increasing and decreasing trends, respectively. The PICRUSt analysis indicated functional prediction more towards amino acid, carbohydrate, energy, and lipid metabolism while less towards others. Concerning energy metabolism, most and least responsive treatments were KP and controls, respectively. These outcomes enhanced our understanding regarding soil quality, fertilizer composition and application, and functional metabolomics of archaea and bacteria.

Safety and efficiency of sewage sludge and garden waste compost as a soil amendment based on the field application in woodland

Sewage sludge (SS) and garden waste (GW) compost can be used as soil amendments to improve the soil environment. Studies done till date have been focused on the changes of harmful substances during sludge composting, but the safety and efficacy of SS and GW composting on woodland soil environment are still unclear. In the study, a field experiment was performed using to investigate the safety and efficacy of SS and GW compost as a soil amendment on woodland soil. Soil nutrients (such as nitrogen, phosphorus and potassium), organic matter and electrical conductivity were significantly increased after the addition of the SS and GW compost, while there were no significant changes in soil heavy metals content and soil enzyme activities. From these soil properties, it was found that SS and GW compost was safe and efficacious in improving the soil environment. The application of SS and GW compost had no significant effect on microbial diversity. Co-occurrence network analysis revealed that SS and GW compost efficaciously enhanced the interaction between bacterial communities, which proved that it was safe and efficacious. Furthermore, SS and GW compost enhanced ABC transporters and carbohydrate metabolism of bacterial community, while reduced the pathotroph action (such as the plant pathogen) and wood saprotrophs. Overall, these results proved the safety and efficacy of SS and GW compost as soil amendments after being added to the soil. This study contributes to the use of harmless treatments and reutilization processes of SS and GW.

Microbial Community Diversity Dynamics in Acid Mine Drainage and Acid Mine Drainage-Polluted Soils: Implication on Mining Water Irrigation Agricultural Sustainability

Environmental degradation related to mining-generated acid mine drainage (AMD) is a major global concern, contaminating surface and groundwater sources, including agricultural land. In the last two decades, many developing countries are expanding agricultural productivity in mine-impacted soils to meet food demand for their rapidly growing population. Further, the practice of AMD water (treated or untreated) irrigated agriculture is on the increase, particularly in water-stressed nations around the world. For sustainable agricultural production systems, optimal microbial diversity, and functioning is critical for soil health and plant productivity. Thus, this review presents up-to-date knowledge on the microbial structure and functional dynamics of AMD habitats and AMD-impacted agricultural soils. The long-term effects of AMD water such as soil acidification, heavy metals (HM), iron and sulfate pollution, greatly reduces microbial biomass, richness, and diversity, impairing soil health plant growth and productivity, and impacts food safety negatively. Despite these drawbacks, AMD-impacted habitats are unique ecological niches for novel acidophilic, HM, and sulfate-adapted microbial phylotypes that might be beneficial to optimal plant growth and productivity and bioremediation of polluted agricultural soils. This review has also highlighted the impact active and passive treatment technologies on AMD microbial diversity, further extending the discussion on the interrelated microbial diversity, and beneficial functions such as metal bioremediation, acidity neutralization, symbiotic rhizomicrobiome assembly, and plant growth promotion, sulfates/iron reduction, and biogeochemical N and C recycling under AMD-impacted environment. The significance of sulfur-reducing bacteria (SRB), iron-oxidizing bacteria (FeOB), and plant growth promoting rhizobacteria (PGPRs) as key players in many passive and active systems dedicated to bioremediation and microbe-assisted phytoremediation is also elucidated and discussed. Finally, new perspectives on the need for future studies, integrating meta-omics and process engineering on AMD-impacted microbiomes, key to designing and optimizing of robust active and passive bioremediation of AMD-water before application to agricultural production is proposed.

Effects of Biogas Slurry Combined With Chemical Fertilizer on Soil Bacterial and Fungal Community Composition in a Paddy Field

The application of biogas slurry and chemical fertilizer in paddy fields can be a practical method to reduce the environmental risk and utilize the nutrients of biogas slurry. The responses of bacterial and fungal communities to the application of biogas slurry and chemical fertilizer are important reflections of the quality of the ecological environment. In this study, based on a 3-year field experiment with different ratios of biogas slurry and chemical fertilizer (applying the same pure nitrogen amount), the Illumina MiSeq platform was used to investigate the bacterial and fungal community diversity and composition in paddy soil. Our results revealed that compared with the observations under regular chemical fertilization, on the basis of stable paddy yield, the application of biogas slurry combined with chemical fertilizer significantly enhanced the soil nutrient availability and bacterial community diversity and reduced the fungal community diversity. Dissolved organic carbon (DOC), DOC/SOC (soil organic carbon), available nitrogen (AN) and available phosphorus (AP) were positively correlated with the bacterial community diversity, but no soil property was significantly associated with the fungal community. The bacterial community was primarily driven by the application of biogas slurry combined with chemical fertilizer (40.78%), while the fungal community was almost equally affected by the addition of pure biogas slurry, chemical fertilizer and biogas slurry combined with chemical fertilizer (25.65–28.72%). Biogas slurry combined with chemical fertilizer significantly enriched Proteobacteria, Acidobacteria, Planctomycetes, Rokubacteria, and Ascomycota and depleted Chloroflexi, Bacteroidetes, Crenarchaeota, Basidiomycota, and Glomeromycota. The observation of the alteration of some bacteria- and fungus-specific taxa provides insights for the proper application of biogas slurry combined with chemical fertilizer, which has the potential to promote crop growth and inhibit pathogens.

Field study on the soil bacterial associations to combined contamination with heavy metals and organic contaminants

The understanding of soil microbial associations to combined contamination would substantially benefit the restoration of damaged ecosystems, which is currently limited at the field scale. In this study, we investigated the soil bacterial associations to combined contamination with metals (Cd, Cu, Hg, Pb, and Zn), polyaromatic hydrocarbons (PAHs), and polybrominated diphenyl ethers (PBDEs). Samples were collected from field sites under five land-use patterns with electronic waste recycling. Results showed that the contents of Cd (0.22-12.86 mg/kg), Cu (17-14,136 mg/kg), Pb (4.6-77,014 mg/kg), Hg (0.28-22 mg/kg), Zn (26-42,495 mg/kg), PAHs (4.6-1753 μg/kg), and PBDEs (1.9-1079 μg/kg) varied significantly across sites. We observed positive correlations between catalase activity and heavy metals, indicative of a resistance response to the oxidative stress induced by metals. Furthermore, the bacterial community diversity was found to be determined primarily by PBDEs, whereas acenaphthylene, available phosphorus, and 2,2',3,3',4,5,6-heptabrominated diphenyl ether (BDE-183) were the three major drivers affecting community composition. The co-occurrence network constructed for bacterial communities exposed to combined contamination was non-random with scale-free, small-world and modularity features. We further proposed functional roles of the modules including stress resistance, hydrocarbon degradation, and nutrient cycling. Overall, the findings of redundancy analysis, variation partition analysis and the co-occurrence network indicated that soil bacterial community under combined contamination cooperated to survive. Members including Rhodoplanes and Nitrospira were capable of degrading PAHs and PBDEs in various pathways, while others, including Acinetobacter, Citrobacter, and Pseudomonas, reduced the metal toxicity to the community. Our findings provide new insights into the responses of soil bacteria, particularly in terms of inter-specific relationships, under combined contamination at the field scale.

Antibiotic resistance genes in surface water and groundwater from mining affected environments

Mining activities are known to generate a large amount of mine tailings and acid mine drainage which contain varieties of heavy metals. Heavy metals play an important role in co-selection for bacterial antibiotic resistance. However, the characteristics of antibiotic resistance genes (ARGs) in mining-affected water environments are still unclear. Here we investigated the pollution of metals, profiles of ARGs, mobile genetic elements (MGEs) and microbial community in mining-affected surface water and groundwater. The results showed that in the tested water samples, the concentrations of Zn and Mn were the highest, and Ni was the lowest. Higher abundances of ARGs with great proportion of sulfonamides, chloramphenicols and tetracyclines resistance genes were found in mining-affected water when compared with those without mining activities. Additionally, there were positive correlations between heavy metals (especially Ni, Zn and Mn) and these ARGs. Linear regression analysis suggested that MGEs were positively correlated with ARGs. In addition, total phosphorus was correlated with ARGs (p < 0.05). The microbial community was different between the mining-affected water and the reference (p < 0.05). Proteobacteria, Bacteroidetes and Actinobacteria were dominant phyla in the surface water and groundwater. Network analysis showed that many ARGs were significantly associated with these dominant bacteria, which suggested they might be potential hosts for these ARGs. These findings provide a clear evidence that the mining activities in the study area had a significant impact on surface water and groundwater to different degrees.

Soil Microbial Indicators within Rotations and Tillage Systems

Recent advancements in agricultural metagenomics allow for characterizing microbial indicators of soil health brought on by changes in management decisions, which ultimately affect the soil environment. Field-scale studies investigating the microbial taxa from agricultural experiments are sparse, with none investigating the long-term effect of crop rotation and tillage on microbial indicator species. Therefore, our goal was to determine the effect of rotations (continuous corn, CCC; continuous soybean, SSS; and each phase of a corn-soybean rotation, Cs and Sc) and tillage (no-till, NT; and chisel tillage, T) on the soil microbial community composition following 20 years of management. We found that crop rotation and tillage influence the soil environment by altering key soil properties, such as pH and soil organic matter (SOM). Monoculture corn lowered pH compared to SSS (5.9 vs. 6.9, respectively) but increased SOM (5.4% vs. 4.6%, respectively). Bacterial indicator microbes were categorized into two groups: SOM dependent and acidophile vs. N adverse and neutrophile. Fungi preferred the CCC rotation, characterized by low pH. Archaeal indicators were mainly ammonia oxidizers with species occupying niches at contrasting pHs. Numerous indicator microbes are involved with N cycling due to the fertilizer-rich environment, prone to aquatic or gaseous losses.

Identifying the Specific Root Microbiome of the Hyperaccumulator Noccaea brachypetala Growing in Non-metalliferous Soils

Noccaea brachypetala is a close relative of Noccaea caerulescens, a model plant species used in metal hyperaccumulation studies. In a previous survey in the Catalan Pyrenees, we found two occidental and two oriental N. brachypetala populations growing on non-metalliferous soils, with accumulated high concentrations of Cd and Zn. Our hypothesis was that the microbiome companion of the plant roots may influence the ability of these plants to absorb metals. We performed high-throughput sequencing of the bacterial and fungal communities in the rhizosphere soil and rhizoplane fractions. The rhizobiomes and shoot ionomes of N. brachypetala plants were analyzed along with those from other non-hyperaccumulator Brassicaceae species found at the same sampling locations. The analyses revealed that microbiome richness and relative abundance tended to increase in N. brachypetala plants compared to non-hyperaccumulator species, regardless of plant location. We confirmed that the root compartment is a key factor in describing the community composition linked to the cohabiting Brassicaceae species, and the rhizoplane fraction contained the specific and rare taxa associated with each species. N. brachypetala plants harbored a similar relative abundance of fungi compared to the other plant hosts, but there was a notable reduction in some specific taxa. Additionally, we observed an enrichment in the hyperaccumulator rhizoplane of previously described metal-tolerant bacteria and bacteria involved in nitrogen cycling. The bacteria involved in the nitrogen cycle could contribute indirectly to the hyperaccumulator phenotype by improving soil quality and fertility. Our results indicate that N. brachypetala captures a particular prokaryotic community from the soil. This particular prokaryotic community may benefit the extraction of metal ions and/or improve plant nutrition. Our research identified satellite groups associated with the root niche of a hyperaccumulator plant that may assist in improving biological strategies in heavy metal remediation.

Long-Term Fertilization History Alters Effects of Microplastics on Soil Properties, Microbial Communities, and Functions in Diverse Farmland Ecosystem

Microplastics (MPs) pollution has caused a threat to soil ecosystem diversity and functioning globally. Recently, an increasing number of studies have reported effects of MPs on soil ecosystems. However, these studies mainly focused on soil bacterial communities and a few limited functional genes, which is why MPs effects on soil ecosystems are still not fully understood. Fertilization treatment often coinsides with MPs exposure in practice. Here, we studied effects of an environmentally relevant concentration of polyethylene on soil properties, microbial communities, and functions under different soil types and fertilization history. Our results showed that 0.2% PE MPs exposure could affect soil pH, but this effect varied according to soil type and fertilization history. Long-term fertilization history could alter effects of MPs on soil bacterial and fungal communities in diverse farmland ecosystems (P < 0.05). Soil fungal communities are more sensitive to MPs than bacterial communities under 0.2% PE MPs exposure. MPs exposure has a greater impact on the soil ecosystem with a lower microbial diversity and functional genes abundance and increases the abundance of pathogenic microorganisms. These findings provided an integrated picture to aid our understanding of the impact of MPs on diverse farmland ecosystems with different fertilization histories.

Soil rehabilitation shaped different patterns of bacterial and archaeal community in AMD-irrigated paddy soil

Microorganisms are essential for soil rehabilitation and long-term sustainability of established plants. However, the recovery process of microorganisms in AMD-irrigated paddy soil is poorly understood at present. To verify this, we sampled AMD-irrigated paddy soils before at different rehabilitation stages by characterizing bacteria and archaea community from a chronosequence of AMD-irrigated rehabilitation to pre-disturbance levels from references sites. Next-generation sequencing is used to describe shifts in diversity and taxonomic composition of bacterial and archaeal. Co-occurrence networks are constructed to reveal potential microbial interaction patterns. The result showed bacterial community followed an observable taxonomic transition overtimes, with community structure becoming more similar to that of unmined reference sites. But the archaeal community only showed a seasonal change, which may hint that the archaeal community needs more time in rehabilitation. Both bacterial and archaeal community composition changes were apparent at high taxonomic levels, bacterial communities become dominated by Proteobacteria phylum, and archaeal community was dominated by Crenarchaeota, we proposed the possible reason is bacterial community were mainly derived by soil pH while the archaeal community was impacted by heavy metal. The bacterial co-occurrence networks increased in complexity during succession, improving the community's resistance to environmental disturbance, while the archaeal did not change monotonically with time. This study highlights the distinct recovery pattern of the bacterial and archaeal community during AMD-irrigated paddy soil rehabilitation, which provides a deep understanding of their role in paddy soil, and subsequent harnessing of their potential to pave the way in future rehabilitation strategies for mined sites.

Toxic trace element resistance genes and systems identified using the shotgun metagenomics approach in an Iranian mine soil

This study aimed to identify the microbial communities, resistance genes, and resistance systems in an Iranian mine soil polluted with toxic trace elements (TTE). The polluted soil samples were collected from a mining area and compared against non-polluted (control) collected soils from the vicinity of the mine. The soil total DNA was extracted and sequenced, and bioinformatic analysis of the assembled metagenomes was conducted to identify soil microbial biodiversity, TTE resistance genes, and resistance systems. The results of the employed shotgun approach indicated that the relative abundance of Proteobacteria, Firmicutes, Bacteroidetes, and Deinococcus-Thermus was significantly higher in the TTE-polluted soils compared with those in the control soils, while the relative abundance of Actinobacteria and Acidobacteria was significantly lower in the polluted soils. The high concentration of TTE increased the ratio of archaea to bacteria and decreased the alpha diversity in the polluted soils compared with the control soils. Canonical correspondence analysis (CCA) demonstrated that heavy metal pollution was the major driving factor in shaping microbial communities compared with any other soil characteristics. In the identified heavy metal resistome (HV-resistome) of TTE-polluted soils, major functional pathways were carbohydrates metabolism, stress response, amino acid and derivative metabolism, clustering-based subsystems, iron acquisition and metabolism, cell wall synthesis and capsulation, and membrane transportation. Ten TTE resistance systems were identified in the HV-resistome of TTE-polluted soils, dominated by "P-type ATPases," "cation diffusion facilitators," and "heavy metal efflux-resistance nodulation cell division (HME-RND)." Most of the resistance genes (69%) involved in resistance systems are affiliated to cell wall, outer membrane, periplasm, and cytoplasmic membrane. The finding of this study provides insight into the microbial community in Iranian TTE-polluted soils and their resistance genes and systems.

On-Site Blackwater Treatment Fosters Microbial Groups and Functions to Efficiently and Robustly Recover Carbon and Nutrients

Wastewater is considered a renewable resource water and energy. An advantage of decentralized sanitation systems is the separation of the blackwater (BW) stream, contaminated with human pathogens, from the remaining household water. However, the composition and functions of the microbial community in BW are not known. In this study, we used shotgun metagenomics to assess the dynamics of microbial community structure and function throughout a new BW anaerobic digestion system installed at The Netherlands Institute of Ecology. Samples from the influent (BW), primary effluent (anaerobic digested BW), sludge and final effluent of the pilot upflow anaerobic sludge blanket (UASB) reactor and microalgae pilot tubular photobioreactor (PBR) were analyzed. Our results showed a decrease in microbial richness and diversity followed by a decrease in functional complexity and co-occurrence along the different modules of the bioreactor. The microbial diversity and function decrease were reflected both changes in substrate composition and wash conditions. Our wastewater treatment system also decreased microbial functions related to pathogenesis. In summary, the new sanitation system studied here fosters microbial groups and functions that allow the system to efficiently and robustly recover carbon and nutrients while reducing pathogenic groups, ultimately generating a final effluent safe for discharge and reuse.

Bacterial diversity on an abandoned, industrial wasteland contaminated by polychlorinated biphenyls, dioxins, furans and trace metals

Most former industrial sites are contaminated by mixtures of trace elements and organic pollutants. Levels of pollutants do not provide information regarding their biological impact, bioavailability and possible interactions between substances. There is genuine interest in combining chemical analyses with biological investigations. We studied a brownfield where several industrial activities were carried out starting in the 1970s, (incineration of pyralene transformers, recovery of copper by burning cables in the open air). Four representative plots showing different levels of polychlorobiphenyls were selected. Organic and trace metal levels were measured together with soil pedological characteristics. The bacterial community structure and functional diversity were assessed by 16S metagenomics with deep sequencing and community-level physiological profiling. Additionally, a vegetation survey was performed. Polychlorobiphenyls (8 mg.kg^-1 to 1500 mg.kg^-1) were from 2.4 × 10³-fold to 6 × 10⁵-fold higher than the European background level of 2.5 μg.kg^-1. Polychlorinated dibenzo-p-dioxins and dibenzofurans ranged from 0.5 to 8.0 μg.kg^-1. The soil was also contaminated with trace metals, i.e., Cu > 187, Zn > 217 and Pb > 372 mg.kg^-1. Location within the study area, trace metal content and soil humidity were stronger determinants than organic pollutants of bacterial community structures and activities. Thus, the highest biological activity and the greatest bacteriological richness were observed in the plot that was less contaminated with trace metals, despite the high level of organic pollutants in the plot. Moreover, trace element pollution was associated with a relatively low presence of Actinobacteria and Rhizobia. The plot with the highest metal contamination was rich in metal-resistant bacteria such as Sphingomonadales, Geodermatophilaceae and KD4-96 (Chloroflexi phylum). Acidobacteria and Sphingomonadales, capable of resisting trace metals and degrading persistent organic pollutants, were dominant in the plots that had accumulated metal and organic contamination, but bacterial activity was lower in these plots than in the other plots.

Methanobacterium Capable of Direct Interspecies Electron Transfer

Direct interspecies electron transfer (DIET) from bacteria to methanogens is a revolutionary concept for syntrophic metabolism in methanogenic soils/sediments and anaerobic digestion. Previous studies have indicated that the potential for DIET is limited to methanogens in the Methanosarcinales, leading to the assumption that an abundance of other types of methanogens, such as Methanobacterium species, indicates a lack of DIET. We report here on a strain of Methanobacterium, designated strain YSL, that grows via DIET in defined cocultures with Geobacter metallireducens. The cocultures formed aggregates, in which cells of strain YSL and G. metallireducens were uniformly dispersed throughout. This close association of the two species is the likely explanation for the ability of a strain of G. metallireducens that could not express electrically conductive pili to grow in coculture with strain YSL. Granular activated carbon promoted the initial formation of the DIET-based cocultures. The discovery of DIET in Methanobacterium, the genus of methanogens that has been the exemplar for interspecies electron transfer via H₂, suggests that the capacity for DIET is much more broadly distributed among methanogens than previously considered. More innovative approaches to microbial isolation and characterization are needed in order to better understand how methanogenic communities function.

Deciphering the rhizosphere microbiome of a bamboo plant in response to different chromium contamination levels

Bamboo has been considered a potential plant species for phytoremediation due to its high biomass and heavy metal (HM) resistance. However, little is known about the interactions between bamboo and soil microbial activities in HM-contaminated soils. Here, we investigated the characteristics of microbial communities in the rhizosphere soil of Lei bamboo (Phyllostachys praecox) along a chromium (Cr) gradient. We found that the soil Cr content was positively correlated with the total organic carbon (TOC) and HCl-extractable Cr but negatively correlated with the pH and bacterial and fungal Shannon indices. Proteobacteria and Ascomycota predominated in the bamboo rhizosphere under Cr pollution. A co-occurrence network showed that two of the most Cr-sensitive bacterial genera and keystone taxa were from the Acidobacteria, indicating that this phylum can be as an indicator for the studied Cr-polluted soils. Redundancy analysis revealed that both the soil bacterial and fungal community compositions were significantly correlated (p < 0.05) with Cr, pH, TOC, alkali-hydrolysable N (AN), and available phosphorus (AP). The increase in TOC as the Cr content increased can be ascribed to an adverse Cr effect on the soil microflora, probably because the microbial biomass was less effective in mineralizing soil C under Cr-polluted conditions.

Responsiveness change of biochemistry and micro-ecology in alkaline soil under PAHs contamination with or without heavy metal interaction

Co-presence of organic pollutants and heavy metals in soil is causing increasing concerns, but the lack of knowledge of relation between soil ecology and pollutant fate is limiting the developing of specific control strategy. This study investigated soil change under pyrene stress and its interaction with cadmium (Cd). Soil physicochemical properties were not seriously influenced. However, pollutants' presence easily varied soil microbial activity, quantity, and diversity. Under high-level pyrene, Cd presence contributed to soil indigenous microorganisms' adaption and soil microbial community structure stability. Soils with both pyrene and Cd presented 7.11-12.0% higher pyrene degradation compared with single pyrene treatment. High-throughput sequencing analysis indicated the proportion of Mycobacterium sp., a commonly known PAHs degrader, increased to 25.2-48.5% in treatments from 0.52% in control. This phenomenon was consistent with the increase of PAHs probable degraders (the ratio increased to 2.86-6.57% from 0.24% in control). Higher Cd bioavailability was also observed in soils with both pollutants than that with Cd alone. And Cd existence caused the elevation of Cd resistant bacterium Limnobacter sp. (increased to 12.2% in CdCK from 2.06% in control). Functional gene prediction also indicated that abundance of genes related to nutrient metabolism decreased dramatically with pollutants, while the abundances of energy metabolism, lipid metabolism, secondary metabolites biosynthesis-related genes increased (especially for aromatic compound degradation related genes). These results indicated the mutual effect and internal-interaction existed between pollutants and soils resulted in pollutants' fate and soil microbial changes, providing further information regarding pollutants dissipation and transformation under soil microbial response.

Soil Bacterial Community Structure in Turfy Swamp and Its Response to Highway Disturbance

In recent years, the construction and development of highways in turfy swamp areas has been very common. When highways pass through turfy swamps, they can change the local soil, vegetation and hydrological environment, but the impact on soil microorganisms is unclear. We studied the impact of highways on soil microbial communities and diversity in three turfy swamps. Soil samples were collected in the affected area (distance from the expressway 10 m) and control area (distance from the expressway 500–1000 m), and the soil properties, heavy metal content and microbial composition were measured. Subsequent statistical analysis showed that soil organic carbon (SOC), total nitrogen (TN), Cd, Cr, Zn, Cu, density and especially water table (WT) are the main driving forces affecting the composition of microorganisms. The WT and density can also be used to predict the change trend of the ratio of proteobacteria to acid bacteria, reflecting the soil nutrient status. In general, the composition of soil microorganisms in turfy swamp is mainly affected by road drainage and heavy metal emissions. This research provides new insights into the impact of highways on turfy swamps from the perspective of bacterial diversity and community composition, and it also provides a basis for the restoration of the wetland ecological environment.

Alkaline amendments improve the health of soils degraded by metal contamination and acidification: Crop performance and soil bacterial community responses

Soil degradation due to heavy metal contamination and acidification has negative effects on soil health and crop growth. Many previous studies have tried to improve the growth of crops and decrease their metal uptake. The recovery of soil health, however, has rarely been focused in soil remediation. In this study, a pot trial was conducted with lettuce (Lactuca sativa L.) growing in heavy metal contaminated and acidic soils, to examine the effects of alkaline amendments (limestone, LS; calcium magnesium phosphate fertilizer, Pcm) and organic amendments (cow manure compost, CMC; biochar, BC) on the growth of lettuce and on the availability of heavy metals, enzyme activities, and bacterial community structures in the soils. The results showed that, in comparison with the CMC and BC treatments, LS and Pcm were more effective at improving lettuce growth and reducing metal concentrations in shoots. Urease and catalase activities in LS and Pcm amended soils were consistently higher than in those with CMC and BC. Additionally, the alkaline amendments dramatically improved the bacterial diversity and shaped more favorable bacterial community structures. Proteobacteria and Gemmatimonadetes were predominant in soils amended with alkaline treatments. The beneficial bacterial genera Gemmatimonas and f_Gemmatimonadaceae, which are vital for phosphate dissolution, microbial nitrogen metabolism, and soil respiration, were also enriched. The results suggest that alkaline amendments were superior to organic amendments, and thus may be useful for the future recovery of soil functions and health under heavy metal contamination and low pH.

Ecological Effects of Heavy Metal Pollution on Soil Microbial Community Structure and Diversity on Both Sides of a River around a Mining Area

The objectives of this study were to understand the characteristics of heavy metal pollution caused by mining activities on the two sides of the Shun'an river and the response of soil microorganisms to the habitats by different contamination levels and vegetation. This paper selected soil samples from the banks of the Shun'an River near the Shizishan mining area, which is at the left of the river, in Tongling, Anhui Province, China. Using Illumina MiSeq 2500 technology, we analyzed the relationship between environmental factors and microbial communities. As the distance from the mining area increased, the heavy metal comprehensive pollution and potential risk value decreased. Additionally, the pollution severity and risk value of the left bank, where the mining area lies, were generally higher than those of the right bank. Because the symmetric sampling points on both banks of the river had similar planting types, their environmental factors and microbial community structure were similar and clustered. However, under different vegetation, the paddy soils tended to have a higher nutrient content and community richness and diversity than the vegetable fields or the abandoned land. It was found that soil microbial communities in this area were mostly affected by pH and Nemerow pollution index (P_N). The pH significantly affected the abundance and structure of most microorganisms. In addition, Proteobacteria, Acidobacteria, and Bacteroidetes had significant tolerance to Zn, Pb, and Cd. By exploring the potential use of these tolerant microorganisms, we seek to provide strains and the theoretical basis for the bioremediation of areas contaminated by heavy metal.

Assessment of the tolerance to Fe, Cu and Zn of a sulfidogenic sludge generated from hydrothermal vents sediments as a basis for its application on metals precipitation

A paramour factor limiting metal-microorganism interaction is the metal ion concentration, and the metal precipitation efficiency driven by microorganisms is sensitive to metal ion concentration. The aim of the work was to determine the tolerance of the sulfidogenic sludge generated from hydrothermal vent sediments at microcosms level to different concentrations of Fe, Cu and Zn and the effect on the microbial community. In this study the chemical oxygen demand (COD) removal, sulfate-reducing activity (SRA) determination, inhibition effect through the determination of IC₅₀, and the characterization of the bacterial community´s diversity were conducted. The IC₅₀ on SRA was 34 and 81 mg/L for Zn and Cu, respectively. The highest sulfide concentration (H₂S mg/L) and % of sulfate reduction obtained were: 511.30 ± 0.75 and 35.34 ± 0.51 for 50 mg/L of Fe, 482.48 ± 6.40 and 33.35 ± 0.44 for 10 mg/L of Cu, 442.26 ± 17.1 and 30.57 ± 1.18 for 10 mg/L of Zn, respectively. The COD removal rates were of 71.81 ± 7.6, 53.92 ± 1.07 and 57.68 ± 10.2 mg COD/ L d for Fe (50 mg/L), Cu (40 mg/L) and Zn (20 mg/L), respectively. Proteobacteria, Firmicutes, Chloroflexi and Actinobacteria were common phyla to four microcosms (stabilized sulfidogenic and added with Fe, Cu or Zn). The dsrA genes of Desulfotomaculum acetoxidans, Desulfotomaculum gibsoniae and Desulfovibrio desulfuricans were expressed in the microcosms supporting the SRA results. The consortia could be explored for ex-situ bioremediation purposes in the presence of the metals tested in this work.

Current situation and forecast of environmental risks of a typical lead-zinc sulfide tailings impoundment based on its geochemical characteristics

The potential environmental implications of a Pb (Lead)-Zn (Zinc) sulfide tailing impoundment were found to be dependent on its geochemical characteristics. One typical lead-zinc sulfide tailing impoundment was studied. Ten boreholes were set with the grid method and 36 tailings were sampled and tested. According to the results of metal content analysis, the tailing samples contained considerably high contents of heavy metals, ranging from 6.99 to 89.0 mg/kg for Cd, 75.3 to 602 mg/kg for Cu, 0.53% to 2.63% for Pb and 0.30% to 2.54% for Zn. Most of the heavy metals in the sample matrix showed a uniform concentration distribution, except Cd. Cd, Pb, Zn, and Mn were associated with each other, and were considered to be the dominant contributors based on hierarchical cluster analysis. XRD, SEM and XPS were employed for evaluation of the tailing weathering characteristics, confirming that the tailings had undergone intensive weathering. The maximum potential acidity of the tailings reached 244 kg H₂SO₄/ton; furthermore, the bioavailability of heavy metals like Pb, Cd, Cr, Cu, and Zn was 37.8%, 12.9%, 12.2%, 5.95%, and 5.46% respectively. These metals would be potentially released into drainage by the weathering process. Analysis of a gastrointestinal model showed that Pb, Cr, Ni and Cu contained in the tailings were high-risk metals. Thus, control of the heavy metals' migration and their environmental risks should be planned from the perspective of geochemistry.

Sustainable resolutions for environmental threat of the acid mine drainage

Acid Mine Drainage (AMD) caused by abandoned mines is an enormous source of negative impact on the environment and the species that inhabit it. The low levels of pH and high concentration of metals and metalloids (copper, gadolinium, lithium, etc.) in mining pits with standing water lead to changing the balance of surrounding organisms and ecosystems. The scale of the issue and the quantity of AMD sites throughout the globe are factors that make AMD a critical environmental threat. Many AMD treatments have been implemented to reduce the negative impact of AMD, with many solutions being very costly and only suited for particular project situations. Policymakers have strong leverage in correcting AMD problems by developing regulations and laws. This study proposes three more sustainable solutions for reducing and eventually eliminating the impact of AMD with less capital investment while also resolving the landfill problem as well. Also, some governmental strategies are suggested for forming collaborative relationships between industry professionals from different perspectives with the goal to resolve the AMD issue through innovative ideas. Implementation of previous strategies and suggested ones, as well as the further involvement of more communities, can enhance the sustainability of life exposed to AMD.

16S rRNA Gene Amplicon Based Metagenomic Signatures of Rhizobiome Community in Rice Field During Various Growth Stages

Rice is a major staple food across the globe. Its growth and productivity is highly dependent on the rhizobiome where crosstalk takes place between plant and the microbial community. Such interactions lead to selective enrichment of plant beneficial microbes which ultimately defines the crop health and productivity. In this study, rhizobiome modulation is documented throughout the development of rice plant. Based on 16S rRNA gene affiliation at genus level, abundance, and diversity of plant growth promoting bacteria increased during the growth stages. The observed α diversity and rhizobiome complexity increased significantly (p < 0.05) during plantation. PCoA indicates that different geographical locations shared similar rhizobiome diversity but exerted differential enrichment (p < 0.001). Diversity of enriched genera represented a sigmoid curve and subsequently declined after harvest. A major proportion of dominant enriched genera (p < 0.05, abundance > 0.1%), based on 16S rRNA gene, were plant growth promoting bacteria that produces siderophore, indole-3-acetic acid, aminocyclopropane-1-carboxylic acid, and antimicrobials. Hydrogenotrophic methanogens dominated throughout cultivation. Type I methanotrophs (n = 12) had higher diversity than type II methanotrophs (n = 6). However, the later had significantly higher abundance (p = 0.003). Strong enrichment pattern was also observed in type I methanotrophs being enriched during water logged stages. Ammonia oxidizing Archaea were several folds more abundant than ammonia oxidizing bacteria. K-strategists Nitrosospira and Nitrospira dominated ammonia and nitrite oxidizing bacteria, respectively. The study clarifies the modulation of rhizobiome according to the rice developmental stages, thereby opening up the possibilities of bio-fertilizer treatment based on each cultivation stages.

Distinct responses of planktonic and sedimentary bacterial communities to anthropogenic activities: Case study of a tributary of the Three Gorges Reservoir, China

Anthropogenic activities can cause serious negative effects on ecosystems. Despite the ecological significance of bacterial communities, the integrated biogeography of planktonic and sedimentary bacterial communities in response to anthropogenic activities is not adequately understood. Here, we examined environmental parameters and the composition of planktonic and sedimentary bacteria in the Yulin River, a tributary of Three Gorges Reservoir, in response to changes in land use and dam construction. The results revealed that human-induced land use changes enhanced the nutrient concentrations in surface water and dam construction reduced the content of carbon and nitrogen in immediately downstream sediments. Intensified human-dominated land use showed a slight impact on sedimentary bacterial communities but largely reduced the diversity of planktonic bacterial communities. Moreover, human-induced land use changes increased the abundance of genes associated with denitrification, nitrification, and anammox in planktonic bacterial communities by 19.04%, 32.40% and 30.45%, respectively. In dam construction regions, the diversity and nutrient-related metabolic activity of sedimentary bacterial communities immediately downstream of the dam were decreased, whereas these changes were not observed in planktonic bacterial communities. Additionally, bacterial community composition was significantly related to nutrient concentrations variability and followed a distance-decay pattern. Furthermore, environmental effects explained more of the variation in planktonic bacterial community composition as compared with spatial effects did, whereas, sedimentary bacterial communities were more closely related to spatial effects. Our results demonstrated the distinct responses of planktonic and sedimentary bacterial communities to anthropogenic activities, and offered new insight for understanding their potential ecological influence on rivers.