Microbial co-occurrence network and its key microorganisms in soil with permanent application of composted tannery sludge

Response of sediment microbial communities to different levels of PAC contamination and exposure time

Coagulants such as polyaluminium chloride (PAC) are widely used for removing phosphorus from eutrophic water, but its application for water treatment can potentially harm the environment. In this study, a four-timepoint exposure experiment was performed at week 1, 3, 7 and 10 to investigate how microbial communities in lake sediments respond to different concentrations of PAC (RS (raw lake water with nothing added), Low, Medium and High). The results showed that, while PAC can efficiently decrease the amount of C, N and P in lake water, the presence of residual aluminum and aluminum precipitates can greatly affect the microbial communities in lake sediments. In particular, different concentrations of PAC and exposure time affected the microbial diversity and structure of lake sediments, with changes being especially obvious at high concentration of PAC after 10 weeks of exposure. Moreover, the use of PAC significantly increased the relative abundances of Gammaproteobacteria and Competibacter, while reducing those of Thermodesulfovibrionia, Vicinamibacterales, and BSV26 in time- and concentration-dependent manners. Network analysis further showed strong correlations between differential bacterial species of PAC in high concentration at 10 weeks, which further suggested that PAC treatment changed the complex structure of microbiota in lake sediment. Finally, correlation analysis indicated a close connection between water parameters and differential species induced by PAC treatment. Overall, PAC contamination changed the microbial communities at different taxonomy levels and influenced the functional pathways to potentiate the P removal, and the results offered interesting insights into the use of PAC in water treatment and its impact on biogeochemical cycling. These results indicated that more attention need to be paid to the potential impact of chemical phosphorus removing reagents on the environment, including eutrophic water.

Microbial communities in the rhizosphere of maize and cowpea respond differently to chromium contamination

Chromium (Cr) contamination can affect microorganisms in the soil, but the response of the microbial community in the rhizosphere of plants grown in Cr-contaminated soils is poorly understood. Therefore, this study assessed the microbial community, by amplicon sequencing, in the rhizosphere of maize and cowpea growing in uncontaminated (∼6.0 mg kg^-1 Cr) and Cr-contaminated soils (∼250 mg kg^-1 Cr). Comparing Cr-contaminated and uncontaminated soils, the microbial community in the maize rhizosphere clustered separately, while the microbial community in the cowpea rhizosphere did not present clear clustering. The microbial richness ranged from ∼5000 (rhizosphere in Cr-contaminated soil) to ∼8000 OTUs (in uncontaminated soil). In the comparison of specific bacterial groups in the rhizosphere of maize, Firmicutes were enriched in Cr-contaminated soil, including Bacilli, Bacillales, and Paenibacillus. Cowpea rhizosphere showed a higher abundance of six microbial groups in Cr-contaminated soil, highlighting Rhizobiales, Pedomicrobium, and Gemmatimonadetes. The microbial community in both rhizospheres presented a similar proportion of specialists comparing uncontaminated (2.2 and 3.4% in the rhizosphere of maize and cowpea, respectively) and Cr-contaminated soils (1.8 and 3.2% in the rhizosphere of maize and cowpea, respectively). This study showed that each plant species drove differently the microbial community in the rhizosphere, with an important effect of Cr-contamination on the microbial community assembly.

Bacterial community shifts in a di-(2-ethylhexyl) phthalate-degrading enriched consortium and the isolation and characterization of degraders predicted through network analyses

Di-(2-ethylhexyl) phthalate (DEHP) is an extensively used and toxic phthalate plasticizer that is widely reported in marine environments. Degradation of DEHP by bacteria from several environments have been studied, but little is known about marine sediment bacteria that can degrade DEHP and other phthalate plasticizers. Therefore, in this study, we enriched a bacterial consortium C10 that can degrade four phthalate plasticizers of varying alkyl chain lengths (DEHP, dibutyl phthalate, diethyl phthalate, and dimethyl phthalate) from marine sediment. The major bacterial genera in C10 during degradation of the phthalate plasticizers were Glutamicibacter, Ochrobactrum, Pseudomonas, Bacillus, Stenotrophomonas, and Methylophaga. Growth of C10 on DEHP intermediates (mono-ethylhexyl phthalate, 2-ethylhexanol, phthalic acid, and protocatechuic acid) was studied and these intermediates enhanced the Brevibacterium, Ochrobactrum, Achromobacter, Bacillus, Sporosarcina, and Microbacterium populations. Using a network-based approach, we predicted that Bacillus, Stenotrophomonas, and Microbacterium interacted cooperatively and were the main degraders of phthalate plasticizers. Through selective isolation techniques, we obtained twenty isolates belonging to Bacillus, Microbacterium, Sporosarcina, Micrococcus, Ochrobactrum, Stenotrophomonas, Alcaligenes, and Cytobacillus. The best DEHP-degraders were Stenotrophomonas acidaminiphila OR13, Microbacterium esteraromaticum OR16, Sporosarcina sp. OR19, and Cytobacillus firmus OR20 (83.68%, 59.1%, 43.4%, and 40.6% degradation of 100 mg/L DEHP in 8 d), which agrees with the prediction of key degraders. This is the first report of DEHP degradation by all four bacteria and, thus, our findings reveal as yet unknown PAE-degradation capabilities of marine sediment bacteria. This study provides insights into how bacterial communities adapt to degrade or resist the toxicities of different PAEs and demonstrates a simple approach for the prediction and isolation of potential pollutant degraders from complex and dynamic bacterial communities.

Role of coke media strategy in an adsorption-biological coupling technology for wastewater treatment performance, microbial community, and metabolic pathways features

With the increase of wastewater discharge, the requirement of wastewater treatment technology is gradually increased. How to treat wastewater economically, while making the treatment process short, easy to manage and low running cost, is the focus of attention. Adsorption-biological coupling technology could make adsorption and biodegradation complement each other, which has coupled accumulation effect. In this study, with coke as the adsorbent, the efficiency of the adsorption-biological coupling reactor on the treatment of total phosphorus (TP), chemical oxygen demand (COD), and ammonia nitrogen (NH₃-N) in domestic wastewater under different influent modes was investigated. Meanwhile, microbial community and metabolic pathways analysis of the reactor were carried out. Results showed that when the influent modes of the coupling reactor was once a day and the daily sewage treatment capacity was 2 L, the treatment efficiency of TP, COD, and NH₃-N was the best. The removal rate of TP and NH₃-N was 87.96% and 96.14%, respectively. The dominant phylum was Proteobacteria (39.84-44.49%), and the dominant genus was Sphingomonas (4.27-7.16%), and Gemmatimonas (1.27-3.58%). According to the metagenomic analysis, carbon metabolism process was evenly distributed in U (upper), M (middle), and L (lower) layers of the coupling reactor. Phosphate metabolism was mainly in the U layer at first, then in the M and L layers gradually. Carbon metabolism and phosphate metabolism provided sufficient energy for microbial degradation of pollutants. Nitrogen removal in the reactor mainly happened in the S and Z layers by nitrification (M00528) and denitrification (M00529), respectively.

Applications of Cr-rich composted tannery sludge in the soil decrease microbial biomass and select specific bacterial groups

The tannery industries generate a solid waste known as tannery sludge, which is composed of organic and inorganic compounds, mainly chromium (Cr). When Cr is not removed from the tannery sludge, this solid waste is metal-rich and its application could affect the soil microorganisms. Alternatively, the composting of the tannery sludge can contribute to decreasing the concentration of Cr in the composted tannery sludge (CTS). However, in some cases, the concentration of Cr remains high in the CTS. During the last 10 years, the Cr-rich CTS has been successively applied in the soil, and its effect on soil microbial properties was verified. Here, we discuss the effect of successive applications of Cr-rich CTS on soil microbes. Interestingly, the findings have shown that successive applications of Cr-rich CTS selected specific soil microbial groups with potential functions. In addition, the studies added a new focus to further research evaluating the potential effect of successive applications of Cr-rich CTS on the rare microbial community.

Co-occurrence network analysis reveals loss of microbial interactions in anaerobic digester subjected to repeated organic load shocks

Fluctuations in the anaerobic digestion (AD) organic loading rate (OLR) cause shocks to the AD microbiome, which lead to unstable methane productivity. Managing these fluctuations requires a larger digester, which is impractical for community-scale applications, limiting the potential of AD in advancing a circular economy. To allow operation of small-scale AD while managing OLR fluctuations, we need to tackle the issue through elucidation of the microbial community dynamics via 16S rRNA gene sequencing. This study elucidated the interrelation of the AD performance and the dynamics of the microbial interactions within its microbiome in response to repeated high OLR shocks at different frequencies. The OLR shocks were equivalent to 4 times the baseline OLR of 2 g VS/L/d. We found that less frequent organic load shocks result to deterioration of methane productivity. Co-occurrence network analysis shows that this coincides with the breakdown of the microbiome network structure. This suggests loss of microbial interactions necessary in maintaining stable AD. Identification of species influencing the network structure revealed that a species under the genus Anaerovorax has the greatest influence, while orders Spirochaetales and Synergistales represent the greatest number of the influential species. We inferred that the impact imposed by the OLR shocks shifted the microbiome activity towards biochemical pathways that are not contributing to methane production. Establishing a small-scale AD system that permits OLR fluctuations would require developing an AD microbiome resilient to infrequent organic loading shocks.

Biogeography, assembly processes and species coexistence patterns of microbial communities in metalloids-laden soils around mining and smelting sites

Microbes are important component in terrestrial ecosystem, which are believed to play vital roles in biogeochemical cycles of metalloids in mining and smelting surroundings. Many studies on microbial diversity and structures have been investigated around mining and smelting sites, whereas the ecological processes and co-occurrence patterns that influence the biogeographic distributions of microbial communities is yet poorly understood. Herein, microbial biogeography, assembly mechanism and co-occurrence pattern around mining and smelting zone were systematically unraveled using 16S rRNA gene sequencing. The 66 microbial phyla co-occurring across all the samples were dominated by Proteobacteria, Chloroflexi, Acidobacteria and Crenarchaeota. Obvious distance-decay (r = 0.3448, p < 0.001) of microbial community was observed across geographic distances. Differences in microbial communities were driven by the joint impacts of soil factors, spatial and metalloids levels. Dispersal limitation dominated the microbial assemblies in whole, SC and GX sites while homogeneous selection governed that in YN site. The changes in pH and Sb level significantly influenced the deterministic and stochastic processes of microbial communities. Network analysis suggested a typical module distribution, which had apparent ecological links among taxa in modules. This study provides first insight of the mechanism to maintain microbial diversity in metalloids-laden biospheres.

Soil Microbial Resource Limitations and Community Assembly Along a Camellia oleifera Plantation Chronosequence

Understanding soil microbial element limitation and its relation with the microbial community can help in elucidating the soil fertility status and improving nutrient management of planted forest ecosystems. The stand age of a planted forest determines the aboveground forest biomass and structure and underground microbial function and diversity. In this study, we investigated 30 plantations of Camellia oleifera distributed across the subtropical region of China that we classified into four stand ages (planted <9 years, 9–20 years, 21–60 years, and >60 years age). Enzymatic stoichiometry analysis showed that microbial metabolism in the forests was mainly limited by C and P. P limitation significantly decreased and C limitation slightly increased along the stand age gradient. The alpha diversity of the soil microbiota remained steady along stand age, while microbial communities gradually converged from scattered to clustered, which was accompanied by a decrease in network complexity. The soil bacterial community assembly shifted from stochastic to deterministic processes, which probably contributed to a decrease in soil pH along stand age. Our findings emphasize that the stand age regulated the soil microbial metabolism limitation and community assembly, which provides new insight into the improvement of C and P management in subtropical planted forest.

Engineering Multigenerational Host-Modulated Microbiota against Soilborne Pathogens in Response to Global Climate Change

Crop migration caused by climatic events has favored the emergence of new soilborne diseases, resulting in the colonization of new niches (emerging infectious diseases, EIDs). Soilborne pathogens are extremely persistent in the environment. This is in large part due to their ability to reside in the soil for a long time, even without a host plant, using survival several strategies. In this regard, disease-suppressive soils, characterized by a low disease incidence due to the presence of antagonist microorganisms, can be an excellent opportunity for the study mechanisms of soil-induced immunity, which can be applied in the development of a new generation of bioinoculants. Therefore, here we review the main effects of climate change on crops and pathogens, as well as the potential use of soil-suppressive microbiota as a natural source of biocontrol agents. Based on results of previous studies, we also propose a strategy for the optimization of microbiota assemblages, selected using a host-mediated approach. This process involves an increase in and prevalence of specific taxa during the transition from a conducive to a suppressive soil. This strategy could be used as a model to engineer microbiota assemblages for pathogen suppression, as well as for the reduction of abiotic stresses created due to global climate change.