What role do biocontrol agents with Mg2+ play in the fate of antibiotic resistome and pathogenic bacteria in the phyllosphere?

The contamination of the plant phyllosphere with antibiotics and antibiotic resistance genes (ARGs), caused by application of antibiotics, is a significant environmental issue in agricultural management. Alternatively, biocontrol agents are environmentally friendly and have attracted a lot of interest. However, the influence of biocontrol agents on the phyllosphere resistome remains unknown. In this study, we applied biocontrol agents to control the wildfire disease in the Solanaceae crops and investigated their effects on the resistome and the pathogen in the phyllosphere by using metagenomics. A total of 250 ARGs were detected from 15 samples, which showed a variation in distribution across treatments of biocontrol agents (BA), BA with Mg2+ (T1), BA with Mn2+ (T2), and kasugamycin (T3) and nontreated (CK). The results showed that the abundance of ARGs under the treatment of BA-Mg2+ was lower than that in the CK group. The abundance of cphA3 (carbapenem resistance), PME-1 (carbapenem resistance), tcr3 (tetracycline antibiotic resistance), and AAC (3)-VIIIa (aminoglycoside antibiotic resistance) in BA-Mg2+ was significantly higher than that in BA-Mn2+ (P < 0.05). The abundance of cphA3, PME_1, and tcr3 was significantly negatively related to the abundance of the phyllosphere pathogen Pseudomonas syringae (P < 0.05). We also found that the upstream and downstream regions of cphA3 were relatively conserved, in which rpl, rpm, and rps gene families were identified in most sequences (92%). The Ka/Ks of cphA3 was 0 in all observed sequences, indicating that under the action of purifying selection, nonsynonymous substitutions are often gradually eliminated in the population. Overall, this study clarifies the effect of biocontrol agents with Mg2+ on the distribution of the phyllosphere resistome and provides evolutionary insights into the biocontrol process. IMPORTANCE: Our study applied metagenomics analysis to examine the impact of biocontrol agents (BAs) on the phyllosphere resistome and the pathogen. Irregular use of antibiotics has led to the escalating dissemination of antibiotic resistance genes (ARGs) in the environment. The majority of BA research has focused on the effect of monospecies on the plant disease control process, the role of the compound BA with nutrition elements in the phyllosphere disease, and the resistome is still unknown. We believe BAs are eco-friendly alternatives for antibiotics to combat the transfer of ARGs. Our results revealed that BA-Mg2+ had a lower relative abundance of ARGs compared to the CK group, and the phyllosphere pathogen Pseudomonas syringae was negatively related to three specific ARGs, cphA3, PME-1, and tcr3. These three genes also present different Ka/Ks. We believe that the identification of the distribution and evolution modes of ARGs further elucidates the ecological role and facilitates the development of BAs, which will attract general interest in this field.

Harnessing sulfate-reducing bacteria with plants growing to revitalize metal-tainted coal mine soils in Midwest China: metal sequestration performance, ecological networking interaction, and functional enzymatic prediction.

Heavy metal contamination from coal mining calls for advanced bioremediation, i.e., using sulfate-reducing bacteria (SRB) technology. Yet, the interaction of SRB with native soil microbiota during metal sequestration, especially in the presence of plants, remains ambiguous. In this study, we assessed the metal sequestration capabilities, ecological network interactions, and enzymatic functions in soils treated with a predominant SRB consortium, mainly Desulfovibrio (14 OTUs, 42.15%) and Desulfobulbus (7 OTUs, 42.27%), alongside Acacia dealbata (AD) and Pisum sativum (PS) plants. The SRB consortium notably enhanced the immobilization of metals such as Zn, Cu, As, and Pb in soil, with the conversion of metals to residual forms rising from 23.47 to 75.98%. Plant inclusion introduced variability, potentially due to changes in root exudates under metal stress. While AD flourished, PS demonstrated significant enhancement in conjunction with SRB, despite initial challenges. Comprehensive microbial analyses revealed the pivotal role of SRB in influencing microbial networking, underpinning critical ecological links. This interplay between plants and SRB not only enhanced microbial diversity but also enriched soil nutrients. Further, enzymatic assessments, highlighting enzymes like NADH:ubiquinone reductase and non-specific serine/threonine protein kinase, reinforced contribution of SRB to energy metabolism and environmental resilience of the entire soil microbial community. Overall, this research underscores the potential of SRB-driven bioremediation in revitalizing soils affected by coal mining.

Dissecting the HGT network of carbon metabolic genes in soil-borne microbiota.

The microbiota inhabiting soil plays a significant role in essential life-supporting element cycles. Here, we investigated the occurrence of horizontal gene transfer (HGT) and established the HGT network of carbon metabolic genes in 764 soil-borne microbiota genomes. Our study sheds light on the crucial role of HGT components in microbiological diversification that could have far-reaching implications in understanding how these microbial communities adapt to changing environments, ultimately impacting agricultural practices. In the overall HGT network of carbon metabolic genes in soil-borne microbiota, a total of 6,770 nodes and 3,812 edges are present. Among these nodes, phyla Proteobacteria, Actinobacteriota, Bacteroidota, and Firmicutes are predominant. Regarding specific classes, Actinobacteria, Gammaproteobacteria, Alphaproteobacteria, Bacteroidia, Actinomycetia, Betaproteobacteria, and Clostridia are dominant. The Kyoto Encyclopedia of Genes and Genomes (KEGG) functional assignments of glycosyltransferase (18.5%), glycolysis/gluconeogenesis (8.8%), carbohydrate-related transporter (7.9%), fatty acid biosynthesis (6.5%), benzoate degradation (3.1%) and butanoate metabolism (3.0%) are primarily identified. Glycosyltransferase involved in cell wall biosynthesis, glycosylation, and primary/secondary metabolism (with 363 HGT entries), ranks first overwhelmingly in the list of most frequently identified carbon metabolic HGT enzymes, followed by pimeloyl-ACP methyl ester carboxylesterase, alcohol dehydrogenase, and 3-oxoacyl-ACP reductase. Such HGT events mainly occur in the peripheral functions of the carbon metabolic pathway instead of the core section. The inter-microbe HGT genetic traits in soil-borne microbiota genetic sequences that we recognized, as well as their involvement in the metabolism and regulation processes of carbon organic, suggest a pervasive and substantial effect of HGT on the evolution of microbes.

Optimizing SCND with carbon-rich hydrolysates from typical organic wastes: Material composition, augmentation performance, microbiome response, and life cycle impact.

The rapid growth of production and consumption has led to severe environmental pollution, creating a major challenge to achieving the United Nations' sustainable development goals (SDGs). To address it, recycling of organic wastes into value-added products is a possible solution. In this work, four typical organic wastes including sewage sludge (SS), chicken manure (CM), food waste (FW), and corn straw (CS) were employed to produce hydrolysates augmenting shortcut nitrification-denitrification (SCND) for nitrogen depletion in wastewater. The hydrolysates were carbon-rich, with total COD (TCOD), soluble COD (SCOD), and volatile fatty acids (VFA) concentrations ranging from 32.5 to 102.7, 5.7 to 48.4, and 2.0-16.5 mg/L, respectively. The most effective nitrogen depletion was obtained in units supplemented with CM and FW hydrolysates, which had reduced average NH3-N concentrations and near-zero TN removal failure rates under legal requirements. The microbial community analysis demonstrated that various functional bacteria from phylum to genus level were detected in all scenarios, which was corroborated by abundant genetic functions involved in nitrogen metabolism. Further, life cycle assessment revealed negative environmental impact on all categories, with an exception of eutrophication potential (EP) with negative values (∼-0.04 kg Phosphate eq.), allowing positive net environmental benefit (NEB). Operational cost analysis revealed that CM and FW are more effective but costlier than SS and CS. Together, these results indicate that, after hydrolysis, organic wastes can be efficient stimulant augmenting SCND performance for nitrogen depletion in wastewater, benefiting the overall environmental impact.

Decreasing lactate input for cost-effective sulfidogenic metal removal in sulfate-rich effluents: Mechanistic insights from (bio)chemical kinetics to microbiome response.

High material cost is the biggest barrier for the industrial use of low-molecular-weight organics (i.e. lactate) as external carbon and electron source for sulfidogenic metal removal in sulfate-rich effluents. This study aims to provide mechanistic evidence from kinetics to microbiome analysis by batch modeling to support the possibility of decreasing the lactate input to achieve cost-effective application. The results showed that gradient COD/SO42- ratios at a low level had promising treatment performance, reaching neutralized pH with nearly total elimination of COD (91%-99%), SO42- (85%-99%), metals (80%-99%) including Cu, Zn, and Mn. First-order kinetics exhibited the best fit (R2 = 0.81-0.98) to (bio)chemical reactions, and the simulation results revealed that higher COD/SO42- accelerated the reaction rate of SO42- and COD but not suitable to that of metals. On the other hand, we found that the decreasing COD/SO42- ratio increased average path distance but decreased clustering coefficient and heterogeneity in microbial interaction network. Genetic prediction found that the sulfate-reduction-related functions were significantly correlated with the reaction kinetics changed with COD/SO42- ratios. Our study, combining reaction kinetics with microbiome analysis, demonstrates that the use of lactate as a carbon source under low COD/SO42- ratios entails significant efficiency of metal removal in sulfate-rich effluent using SRB-based technology. However, further studies should be carried out, including parameter-driven optimization and life cycle assessments are necessary, for its practical application.

Viruses Regulate Microbial Community Assembly Together with Environmental Factors in Acid Mine Drainage.

Viruses are widespread in various ecosystems, and they play important roles in regulating the microbial community via host-virus interactions. Recently, metagenomic studies showed that there are extremely diverse viruses in different environments from the ocean to the human gut, but the influences of viral communities on microbial communities are poorly understood, especially in extreme environments. Here, we used metagenomics to characterize microbial communities and viral communities in acid mine drainage (AMD) and evaluated how viruses shape microbial community constrained by the harsh environments. Our results showed that AMD viral communities are significantly associated with the microbial communities, and viral diversity has positive correlations with microbial diversity. Viral community explained more variations of microbial community composition than environmental factors in AMD of a polymetallic mine. Moreover, we found that viruses harboring adaptive genes regulate a relative abundance of hosts under the modulation of environmental factors, such as pH. We also observed that viral diversity has significant correlations with the global properties of microbial cooccurrence networks, such as modularity. In addition, the results of null modeling analyses revealed that viruses significantly affect microbial community phylogeny and play important roles in regulating ecological processes of community assembly, such as dispersal limitation and homogenous dispersal. Together, these results revealed that AMD viruses are critical forces driving microbial network and community assembly via host-virus interactions. IMPORTANCE Viruses as mobile genetic elements play critical roles in the adaptive evolution of their hosts in extreme environments. However, how viruses further influence microbial community structure and assembly is still unclear. A recent metagenomic study observed diverse viruses unexplored in acid mine drainage, revealing the associations between the viral community and environmental factors. Here, we showed that viruses together with environmental factors can constrain the relative abundance of host and microbial community assembly in AMD of copper mines and polymetallic mines. Our results highlight the importance of viruses in shaping the microbial community from the individual host level to the community level.

Life cycle assessment and cost analysis for copper hydrometallurgy industry in China.

Understanding the environmental and economic impacts of copper hydrometallurgy throughout the whole life cycle is necessary for sustainable development of the copper industry. In this study, the environmental impacts and economic costs throughout the two major copper hydrometallurgical routes in China, including heap leaching and heap-agitation leaching, are analyzed and compared using the life cycle assessment (LCA) and life cycle cost (LCC) technique. The life cycle inventory compiled from the annual statistics of the Muliashi Copper Mine, and the data regarding energy and materials process are based on the GaBi databases. The environmental impacts are quantified into 12 indicators. The results show that compared with heap leaching route, heap-agitation leaching route reduces 36.8% of abiotic depletion potential (ADP elements), but increases over half of cumulative energy demand (CED), marine aquatic ecotoxicity potential (MAETP) and human toxicity potential (HTP). Furthermore, the stage of electrowinning and agitation leaching contributes the largest environmental impact to heap leaching and heap-agitation leaching route, respectively. This is mainly due to huge consumption of electricity and sulfuric acid. The analysis of economic cost reveals that heap leaching route needs internal cost of $3225/t Cu and external cost of $426/t Cu. Compared with heap leaching route, heap-agitation leaching route increased the internal and external cost by 18.9% and 54.2%, respectively. But the economic return from heap-agitation leaching is double that from heap leaching. Together, these results indicate heap-agitation leaching has a larger environmental impact and higher economic benefit than heap leaching, which is helpful for the government to design ecological compensation policies in the balance between ecological environment and economic development.